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End User Agreement. This publication is distributed under the terms of Article 25fa of the Dutch Copyright Act. This article entitles the maker of a short scientific work funded either wholly or partially by Dutch public funds to make that work publicly available for no consideration following a reasonable period of time after the work was first published, provided that clear reference is made to the source of the first publication of the work. Research outputs of researchers employed by Dutch Universities that comply with the legal requirements of Article 25fa of the Dutch Copyright Act, are distributed online and free of cost or other barriers in institutional repositories. Research outputs are distributed six months after their first online publication in the original published version and with proper attribution to the source of the original publication. You are permitted to download and use the publication for personal purposes. All rights remain with the author(s) and/or copyrights owner(s) of this work. Any use of the publication other than authorised under this licence or copyright law is prohibited. If you believe that digital publication of certain material infringes any of your rights or (privacy) interests, please let the University Library know, stating your reasons. In case of a legitimate complaint, the University Library will, as a precaution, make the material inaccessible and/or remove it from the website. Please contact the University Library through email: xxxxxxxxx@xxx.xx.xx. You will be contacted as soon as possible. University Library Radboud University *Department of Microbiology, RU Nijmegen NL, Toernooiveld 1, 6525 ED Nijmegen, The Netherlands, and †Department of Biotechnology, TU Delft NL, The Netherlands In the past 10 years many molecular aspects of microbial nitrate reduction have been elucidated, but the ecophysiology of this process is hardly understood. In this contribution, our efforts to study the complex microbial communities and interactions involved in the reduction of nitrate to dinitrogen gas are summarized. The initial work concentrated on emission of the greenhouse gas nitrous oxide during incomplete denitrification by Alcaligenes faecalis. As more research methods became available, the fitness of A. faecalis could be tested in mixed cultures with other denitrifying bacteria, most notably with the nitrate-reducing bacterium Pseudomonas G9. Finally, the advancement of molecular diagnostic tools made it possible to survey complex microbial communities using specific primer sets for/and antibodies raised against the various NOx reductases. Given the enormous complexity of substrates and environmental conditions, it is evident that mixed cultures rather than single species are responsible for denitrification in man-made and natural ecosystems. However, it is surprising that even for the breakdown of a single compound, such as acetate, mixed cultures are responsible, and that the consecutive denitrification steps are commonly performed by mutualistic co-operating species. Our observations also indicate that we seldom know the identity of the major key players in the nitrogen cycle of these ecosystems.

End User Agreement. This publication is distributed under the terms of Article 25fa of the Dutch Copyright Act. This article entitles the maker of a short scientific work funded either wholly or partially by Dutch public funds to make that work publicly available for no consideration following a reasonable period of time after the work was first published, provided that clear reference is made to the source of the first publication of the work. Research outputs of researchers employed by Dutch Universities that comply with the legal requirements of Article 25fa of the Dutch Copyright Act, are distributed online and free of cost or other barriers in institutional repositories. Research outputs are distributed six months after their first online publication in the original published version and with proper attribution to the source of the original publication. You are permitted to download and use the publication for personal purposes. All rights remain with the author(s) and/or copyrights owner(s) of this work. Any use of the publication other than authorised under this licence or copyright law is prohibited. If you believe that digital publication of certain material infringes any of your rights or (privacy) interests, please let the University Library know, stating your reasons. In case of a legitimate complaint, the University Library will, as a precaution, make the material inaccessible and/or remove it from the website. Please contact the University Library through email: xxxxxxxxx@xxx.xx.xx. You will be contacted as soon as possible. University Library Radboud University *DOI 10.1007/s00330-016-4317-3 CHEST Software performance in segmenting ground-glass and solid components of subsolid nodules in pulmonary adenocarcinomas Xxxxxx X. Xxxxx0,2 • Jin Mo Goo 1,3 • Roh-Eul Yoo1 • Xxxxx Min Park1,3 • Xxxxx Xxxx Xxx 1 • Xxxx van Ginneken4 • Xxx Xxxx Xxxxx0 • Young Xxx Xxx 3,6 Received: 8 July 2015 / Revised: 14 February 2016 / Accepted: 2 March 2016 / Published online: 5 April 2016 Ⓒ European Society of Radiology 2016 Abstract Objective To evaluate the performance of software in segmenting ground-glass and solid components of subsolid nodules in pulmonary adenocarcinomas. glass and solid components with pathology measurements of tumour and invasive components. Results Segmentation of ground-glass components at a threshold of -750 HU yielded mean differences of +0.06 mm (p = 0.83, 95 % limits of agreement, 4.51 to 4.67) and - 2.32 mm (p < 0.001, -8.27 to 3.63) when compared with pa- thology and manual measurements, respectively. For solid components, mean differences between the software (at - 350 HU) and pathology measurements and between the man- ual (lung and mediastinal windows) and pathology measure- ments were -0.12 mm (p = 0.74, -5.73 to 5.55]), 0.15 mm (p = 0.73, -6.92 to 7.22), and -1.14 mm (p < 0.001, -7.93 to 5.64), respectively. Jin Mo Goo xxxxx@xxxxx.xxx.xx.xx 1 Department of MicrobiologyRadiology, RU Seoul National University College of Medicine, and Institute of Radiation Medicine, Seoul National University Medical Research Center, 000 Xxxxxx-xx, Xxxxxx-xx, Xxxxx 000-000, Xxxxx 2 Clinique Universitaire de Radiologie et Imagerie Médicale (CURIM), Université Xxxxxx Xxxxxxx, Centre Hospitalier Universitaire de Grenoble, CS 10217, 38043 Grenoble Cedex 9, France 3 Cancer Research Institute, Seoul National University College of Medicine, Seoul, Korea 4 Department of Radiology and Nuclear Medicine, Radboud University Nijmegen NLMedical Center, Toernooiveld Xxxxx Xxxxxxxxxxx 00, 0000 XX Xxxxxxxx, Xxx Xxxxxxxxxxx 5 Department of Pathology, Seoul National University College of Medicine, Seoul, Korea ence with pathology. • Software can effectively segment ground-glass and solid components in subsolid nodules. • Software measurements show no significant difference with pathology measurements. • Manual measurements are more accurate on lung windows than on mediastinal windows. Keywords Solitary pulmonary nodule . Lung cancer . Subsolid nodule . Adenocarcinoma . Segmentation Introduction Persistent pulmonary ground-glass nodules (GGNs) have been a growing concern in the last few years because many of them turned out to be pulmonary adenocarcinomas or their precursors [1, 6525 ED Nijmegen, The Netherlands, and †Department of Biotechnology, TU Delft NL, The Netherlands 2]. In the past 10 years many molecular aspects 2011 IASLC/ATS/ERS classification [3], it was recommended to report the size of microbial nitrate reduction have been elucidatedthe solid component and entire tumour size separately for part-solid GGNs as the invasive component of pulmonary adenocar- cinoma is closely related to a patient’s prognosis. A sub- sequent study showed that the diameter of the solid com- ponent was a better prognostic predictor than the largest diameter of the whole nodule in adenocarcinomas appearing as part-solid GGNs [4]. Therefore, but the ecophysiology diameter of this process the solid component as well as the size of the whole nodule is hardly understood. In this contribution, our efforts to study the complex microbial communities and interactions involved a key element in the reduction recent recommendations for the management of nitrate to dinitrogen gas are summarized. The initial work concentrated on emission of the greenhouse gas nitrous oxide during incomplete denitrification by Alcaligenes faecalis. As more research methods became available, the fitness of A. faecalis could be tested in mixed cultures with other denitrifying bacteria, most notably with the nitrate-reducing bacterium Pseudomonas G9. Finally, the advancement of molecular diagnostic tools made it possible to survey complex microbial communities using specific primer sets for/and antibodies raised against the various NOx reductases. Given the enormous complexity of substrates and environmental conditions, it is evident that mixed cultures rather than single species are responsible for denitrification in man-made and natural ecosystemssubsolid nodules [2]. However, when the variability of manual measurements was assessed, 95 % limits of interobserver agreement were reported to be 1.72 mm and 1.73 mm for GGNs and solid nodules, respectively [5, 6]. As for a part-solid GGN, the interob- server measurement variability of solid component may be even higher given the fact that solid components are usually very small, with the largest diameters of no more than a few millimetres. Furthermore, given their slow growth rate, it may not be easy to determine interval changes in GGNs with manual measurements, especially when the solid component is surprising that even small. Fig. 1 Example of an excellent segmentation for a part-solid GGN in the right upper lobe before (a) and after (b) segmentation with thresholds of - 750 HU and -350 HU for ground-glass and solid components, respectively. Software measurements were 16.8 mm for the breakdown ground- glass component and 8.7 mm for the solid component. Pathology obtained with wedge resection revealed a lepidic predominant adenocarcinoma with a maximal tumour size of 17 mm and an invasive component size of 9 mm As computer-aided volumetry was reported to reduce inter- observer variability in solid nodules; a single compoundsimilar approach may be applicable to GGNs [7–9]. While several articles have ex- plored the topic of semi-automated segmentation in GGNs, such most of them focused on the feasibility of volumetry and mass measurements as acetate, mixed cultures are responsiblewell as their intra/interobserver, and that intrascan variability [10–13]. However, these studies did not compare the consecutive denitrification steps software measurements with manual measure- ments of maximal diameters of ground-glass and solid com- ponents of nodules, which are commonly performed by mutualistic co-operating speciesstill the reference standard for GGNs [2]. Our observations also indicate that we seldom know More importantly, there have been no studies which compared the identity software measurements with pathology measurements of invasive components and the major key players entire tumours in the nitrogen cycle of these ecosystemspulmonary adenocarcinomas [3].

End User Agreement. This publication is distributed under the terms of Article 25fa of the Dutch Copyright Act. This article entitles the maker of a short scientific work funded either wholly or partially by Dutch public funds to make that work publicly available for no consideration following a reasonable period of time after the work was first published, provided that clear reference is made to the source of the first publication of the work. Research outputs of researchers employed by Dutch Universities that comply with the legal requirements of Article 25fa of the Dutch Copyright Act, are distributed online and free of cost or other barriers in institutional repositories. Research outputs are distributed six months after their first online publication in the original published version and with proper attribution to the source of the original publication. You are permitted to download and use the publication for personal purposes. All rights remain with the author(s) and/or copyrights owner(s) of this work. Any use of the publication other than authorised under this licence or copyright law is prohibited. If you believe that digital publication of certain material infringes any of your rights or (privacy) interests, please let the University Library know, stating your reasons. In case of a legitimate complaint, the University Library will, as a precaution, make the material inaccessible and/or remove it from the website. Please contact the University Library through email: xxxxxxxxx@xxx.xx.xx. You will be contacted as soon as possible. University Library Radboud University *Department of MicrobiologyPublished by IOP Publishing for Sissa Medialab 2020 JINST E-mail: xxxxx_xxxxxxxxxxxxx@xxxx.xxx Abstract: Extensive air showers, RU Nijmegen NLoriginating from ultra-high energy cosmic rays, Toernooiveld 1, 6525 ED Nijmegen, The Netherlands, and †Department of Biotechnology, TU Delft NL, The Netherlands In the past 10 years many molecular aspects of microbial nitrate reduction have been elucidated, but suc- cessfully measured through the ecophysiology use of this process is hardly understoodarrays of water-Cherenkov detectors (WCDs). In this contribution, our efforts to study the complex microbial communities and interactions involved in the reduction of nitrate to dinitrogen gas are summarized. The initial work concentrated on emission of the greenhouse gas nitrous oxide during incomplete denitrification by Alcaligenes faecalis. As more research methods became available, the fitness of A. faecalis could be tested in mixed cultures with other denitrifying bacteria, most notably with the nitrate-reducing bacterium Pseudomonas G9. Finally, the advancement of molecular diagnostic tools Sophisticated analyses exploiting WCD data have made it possible to survey complex microbial communities demonstrate that shower simulations, based on different hadronic-interaction models, cannot reproduce the observed number of muons at the ground. The accurate knowledge of the WCD response to muons is paramount in establishing the exact level of this discrepancy. In this work, we report on a study of the response of a WCD of the Xxxxxx Xxxxx Observatory to atmospheric muons performed with a hodoscope made of resistive plate xxxxxxxx (RPCs), enabling us to select and reconstruct nearly 600 thousand single muon trajectories with zenith angles ranging from 0◦ to 55◦. Comparison of distributions of key observables between the hodoscope data and the predictions of dedicated simulations allows us to demonstrate the accu- racy of the latter at a level of 2%. As the WCD calibration is based on its response to atmospheric muons, the hodoscope data are also exploited to show the long-term stability of the procedure. P09002 Keywords: Data reduction methods; Large detector systems for particle and astroparticle physics; Large detector-systems performance; Performance of High Energy Physics Detectors ⃝c 2020 IOP Publishing Ltd and Sissa Medialab xxxxx://xxx.xxx/10.1088/1748-0221/15/09/P09002 2 Experimental setup 3 2.1 RPC hodoscope 3 2.2 DAQ and trigger 4 2.3 Acquisition campaigns 5 3 Simulation 6 3.1 Shower simulation 7 3.2 WCD simulation 8 3.3 RPC simulation 9 4 Data reconstruction and performances 9 4.1 Charge reconstruction with the WCD 9 4.2 Trajectory reconstruction with the RPC 10 4.3 Zenith angle and charge distributions 11 JINST P09002 2020 1 Introduction‌ The Xxxxxx Xxxxx Observatory, located at an altitude of ∼1400 m above sea level near Malargüe in the province of Xxxxxxx, Argentina, is the largest facility in the world dedicated to the detection of ultra- high energy cosmic rays (UHECRs) in the energy range from ∼1017 eV up to the highest energies [1]. Due to the very low flux at these energies, the observation of UHECRs is performed indirectly by recording the extensive air showers produced by these particles when they interact in the atmosphere. At the Xxxxxx Xxxxx Observatory, extensive air showers are observed using specific primer sets for/and antibodies raised against two detection techniques. Telescopes collecting the various NOx reductasesfluorescence light emitted by atmospheric nitrogen, excited after the passage of the charged particles, allow for the observation of the longitudinal profile of the showers. Given This technique provides a nearly calorimetric estimate of the enormous complexity of substrates and environmental conditions, it is evident that mixed cultures rather than single species are responsible for denitrification in man-made and natural ecosystemsenergy carried by the primary particle. However, it this technique is surprising constrained to nights with low background light conditions, limiting its uptime to below 15%. The second detection technique uses a surface detector (SD) array composed of 1660 water-Cherenkov detectors (WCDs) deployed on the ground, in which the light produced in the water by charged particles above the threshold for emitting Cherenkov radiation is collected by three photomultiplier tubes (PMTs). The SD operates with a duty cycle close to 100%. The detected signals in the SD are used to determine the arrival direction and to estimate the size of the showers. The shower size of all such events is subsequently converted into the energy of the primary cosmic ray through a calibration based on a subset of events detected by both the surface and fluorescence detectors. This “hybrid” approach allows for a calorimetric estimate of the energy also for events recorded during periods when the fluorescence detector cannot be operated. 2020 JINST The detection and reconstruction of air showers allows not only for studies of the astrophysics of UHECRs, but also represents a unique opportunity to access particle interactions at energies that even are far higher than could be achieved by any Earth-based accelerator. The number of muons in showers is particularly sensitive to hadronic interactions taking place during the development of the cascade in the atmosphere. Over the last 20 years, increasing numbers of studies (see [2] for a recent review), including the Xxxxxx Xxxxx Observatory, have provided data showing indications of a discrepancy between the number of muons predicted in showers by different hadronic-interaction models and that observed in data. In Auger Observatory, the analyses developed in this context are based on the data from WCDs, from which a muon deficit has been revealed in simulations at energies around and above 1019 eV [3, 4]. P09002 In the comparison between the observed showers and showers predicted by models, the detailed simulation of the WCD, which includes all the relevant physics processes, accounts for the breakdown detector geometry, and simulates the response of the electronics, naturally plays a crucial role. The objective of this work is to probe experimentally this simulation in terms of the response to atmospheric particles, most notably background muons, at different zenith angles. For this purpose, we have designed and deployed a hodoscope composed of resistive-plate xxxxxxxx (RPCs), which, installed on one of the WCDs, enables the selection of single muons passing through the detector. The RPC segmentation allows us to reconstruct muon trajectories and impact points, thus enabling the study of the signal response of the WCD for different zenith angles (from 0◦ up to 55◦) of arriving muons and the comparison with signals predicted by the detector simulation. In addition, the operation of the hodoscope allows us to verify a component of the WCD calibration procedure [5], which relies on the determination of the charge deposited by a vertical and centrally through-going atmospheric muon. As the WCD is not a directional detector, the peak in the charge distribution for vertical centered-muons is obtained by scaling the peak in the charge distribution obtained with the omni- directional muons. The latter is evaluated every minute for all data-taking WCDs, while the scaling factor was measured by means of a single compounddedicated muon telescope on a reference WCD at the beginning of the operation of the Observatory [5, 6]. We took advantage of the RPC hodoscope to repeat with higher precision such as acetatea measurement and validate the scaling factor. Overall, mixed cultures are responsibletwo data acquisition campaigns took place with the RPC hodoscope: one to detect muons with more inclined zenith angles (up to 55◦) and the other dedicated to near-vertical muons. The presentation of the measurements, of the data analysis, and of the results is organised as follows. In section 2, we first describe the experimental setup, including a brief description of the features of the WCD, the RPC specifications, the related electronics and trigger system, as well as the different acquisition configurations adopted and the data obtained. The following section 3 illustrates the characteristics of the generated showers and the characteristics of the detector simulation. As for the latter, in appendix A we provide a list of the most relevant parameters and their values. In section 4, we explain how the hodoscope data are used to select specific muon geometries and how the associ- ated charge and trajectory are reconstructed. Then we show that the consecutive denitrification steps distributions of these basic ob- servables are commonly performed by mutualistic co-operating species. Our observations also indicate that we seldom know the identity comparable with those of the major key players simulations and proceed to study, in section 5, the nitrogen cycle detailed response of these ecosystems.the WCD to muons, down to the level of single PMTs. In section 6, we then present the result of the new measurement of the scaling factor of the calibration before concluding in section 7. 2020 2 Experimental setup‌

End User Agreement. This publication is distributed under the terms of Article 25fa of the Dutch Copyright Act. This article entitles the maker of a short scientific work funded either wholly or partially by Dutch public funds to make that work publicly available for no consideration following a reasonable period of time after the work was first published, provided that clear reference is made to the source of the first publication of the work. Research outputs of researchers employed by Dutch Universities that comply with the legal requirements of Article 25fa of the Dutch Copyright Act, are distributed online and free of cost or other barriers in institutional repositories. Research outputs are distributed six months after their first online publication in the original published version and with proper attribution to the source of the original publication. You are permitted to download and use the publication for personal purposes. All rights remain with the author(s) and/or copyrights owner(s) of this work. Any use of the publication other than authorised under this licence or copyright law is prohibited. If you believe that digital publication of certain material infringes any of your rights or (privacy) interests, please let the University Library know, stating your reasons. In case of a legitimate complaint, the University Library will, as a precaution, make the material inaccessible and/or remove it from the website. Please contact the University Library through email: xxxxxxxxx@xxx.xx.xx. You will be contacted as soon as possible. University Library Radboud University *Department Journal of Microbiology, RU Nijmegen NL, Toernooiveld 1, 6525 ED Nijmegen, The Netherlands, Cosmology and †Department of Biotechnology, TU Delft NL, The Netherlands In the past 10 years many molecular aspects of microbial nitrate reduction have been elucidated, but the ecophysiology of this process is hardly understood. In this contribution, our efforts to study the complex microbial communities and interactions involved in the reduction of nitrate to dinitrogen gas are summarized. The initial work concentrated on emission Astroparticle Physics Measurement of the greenhouse gas nitrous oxide during incomplete denitrification by Alcaligenes faecalis. As more research methods became available, the fitness of A. faecalis could be tested in mixed cultures with other denitrifying bacteria, most notably cosmic ray spectrum above 4 × 1018 eV using inclined events detected with the nitrate-reducing bacterium Pseudomonas G9Xxxxxx Xxxxx Observatory To cite this article: The Xxxxxx Xxxxx collaboration JCAP08(2015)049 View the article online for updates and enhancements. FinallyYou may also like - Fundamental Physics with the Hubble Frontier Fields: Constraining Dark Matter Models with the Abundance of Extremely Faint and Distant Galaxies X. Xxxxx, the advancement X. Xxxxx, X. Xxxxxxxx et al. - Persistence and nonpersistence as complementary models of molecular diagnostic tools made it possible to survey complex microbial communities using specific primer sets for/identical quantum particles Xxxxxx Xxxxx - Astrophysical Distance Scale: The AGB J- band Method. I. Calibration and antibodies raised against the various NOx reductases. Given the enormous complexity a First Application Xxxxx X. Xxxxxx and Xxxxx X. Xxxxxxxx ournal of substrates Cosmology and environmental conditions, it is evident that mixed cultures rather than single species are responsible for denitrification in man-made and natural ecosystems. However, it is surprising that even for the breakdown of a single compound, such as acetate, mixed cultures are responsible, and that the consecutive denitrification steps are commonly performed by mutualistic co-operating species. Our observations also indicate that we seldom know the identity Astroparticle Physics JCAP08(2015)049 Measurement of the major key players in cosmic ray spectrum above 4 × 1018 eV using inclined events detected with the nitrogen cycle of these ecosystems.Xxxxxx Xxxxx Observatory E-mail: auger xxxxxxxxxxxxx@xxxx.xxx Received March 27, 2015 Revised July 17, 2015 Accepted July 27, 2015 Published August 26, 2015 −1.2 +1.0

End User Agreement. This publication is distributed under the terms of Article 25fa of the Dutch Copyright Act. This article entitles the maker of a short scientific work funded either wholly or partially by Dutch public funds to make that work publicly available for no consideration following a reasonable period of time after the work was first published, provided that clear reference is made to the source of the first publication of the work. Research outputs of researchers employed by Dutch Universities that comply with the legal requirements of Article 25fa of the Dutch Copyright Act, are distributed online and free of cost or other barriers in institutional repositories. Research outputs are distributed six months after their first online publication in the original published version and with proper attribution to the source of the original publication. You are permitted to download and use the publication for personal purposes. All rights remain with the author(s) and/or copyrights owner(s) of this work. Any use of the publication other than authorised under this licence or copyright law is prohibited. If you believe that digital publication of certain material infringes any of your rights or (privacy) interests, please let the University Library know, stating your reasons. In case of a legitimate complaint, the University Library will, as a precaution, make the material inaccessible and/or remove it from the website. Please contact the University Library through email: xxxxxxxxx@xxx.xx.xx. You will be contacted as soon as possible. University Library Radboud University *Department Journal of MicrobiologyCosmology and Astroparticle Physics Interpretation of the depths of maximum of extensive air showers measured by the Xxxxxx Xxxxx Observatory To cite this article: JCAP02(2013)026 View the article online for updates and enhancements. You may also like - A RESOLVED CENSUS OF MILLIMETER EMISSION FROM TAURUS MULTIPLE STAR SYSTEMS Xxxxxx X. Xxxxxx, RU Nijmegen NLXxxx X. Xxxxxxx, Toernooiveld 1Xxxxx X. Xxxxxx et al. - Handling of beam spectra in training and application of proton RBE models Xxxx Xxxxxxxx, 6525 ED NijmegenXxxx Xxxxxxx and Xxxxxx Xxxxxxx - The role of the hadron initiated single electromagnetic subcascades in IACT observations Xxxxxx Sobczyska ournal of Cosmology and Astroparticle Physics JCAP02(2013)026 E-mail: auger xxxxxxxxxxxxx@xxxx.xxx Received December 14, 2012 Accepted January 26, 2013 Published February 19, 2013 Abstract. To interpret the mean depth of cosmic ray air shower maximum and its disper- sion, we parametrize those two observables as functions of the first two moments of the ln A distribution. We examine the goodness of this simple method through simulations of test mass distributions. The Netherlandsapplication of the parameterization to Xxxxxx Xxxxx Observatory data allows one to study the energy dependence of the mean ln A and of its variance under the assumption of selected hadronic interaction models. We discuss possible implications of these dependences in term of interaction models and astrophysical cosmic ray sources. ⃝c 2013 IOP Publishing Ltd and Sissa Medialab srl doi:10.1088/1475-7516/2013/02/026 2 A method to interpret (Xmax⟩ and σ(Xmax) 2 JCAP02(2013)026 1 Introduction‌ The most commonly used shower observables for the study of the composition of Ultra High Energy Cosmic Rays (UHECR) are the mean value of the depth of shower maximum, ⟨Xmax⟩, and †Department its dispersion, σ(Xmax). Inferring the mass composition from these measurements is subject to some level of Biotechnologyuncertainty. This is because their conversion to mass relies on the use of shower simulation codes which include the assumption of a hadronic interaction model. The various interaction models [1] have in common the ability to fit lower energy accelerator data. However, TU Delft NLdifferent physical assumptions are used to extrapolate these low energy interaction properties to higher energies. Consequently they provide different expectations for ⟨Xmax⟩ and σ(Xmax). The first aim of this paper is to discuss how the mean value of the depth of shower maximum and its dispersion can be used to interpret mass composition even in the presence of uncertainties in the hadronic interaction modeling. Furthermore, The Netherlands we discuss the different roles of the two observables, ⟨Xmax⟩ and σ(Xmax), with respect to mass composition. In the past 10 years many molecular interpretation of data they are often used as different, and independent, aspects of microbial nitrate reduction have been elucidatedthe same phenomenon. However it is not true to say that both parameters reflect the cosmic ray composition to the same extent. According to the superposition model [2] ⟨Xmax⟩ is linear in ⟨ln A⟩ and therefore it actually measures mass composition for both pure and mixed compositions. But, but we will show that the ecophysiology behaviour of σ(Xmax) is more complex to interpret as there is no one-to-one correspondence between its value and a given mean log mass. Only in the case of pure composition is this process is hardly understoodcorrespondence unique. In this contributionpaper we refine the analysis method originally proposed by Xxxxxxx [3, our efforts 4] and apply it to study the complex microbial communities and interactions involved in the reduction of nitrate to dinitrogen gas are summarizedAuger data. The initial work concentrated Xxxxxx Xxxxx Collaboration has published results on emission the mean and dispersion of the greenhouse gas nitrous oxide during incomplete denitrification by Alcaligenes faecalisXmax distribution at energies above 1018 eV [5, 6]. As more research methods became availableIn this work we apply the proposed method to convert those observables to the first moments of the log lnA mass distribution, namely ⟨ln A⟩ and σ2 . The paper is organized as follows. In section 2 we discuss the fitness parameterization for ⟨Xmax⟩ and σ(Xmax). In section 3 we test the method with shower simulations assuming different mass distributions. Section 4 describes the application of A. faecalis could be tested the method to data. The discussion of the results and the conclusions follow in mixed cultures with other denitrifying bacteria, most notably with sections 5 and 6 respectively. The details of the nitrate-reducing bacterium Pseudomonas G9. Finally, parameterization and the advancement of molecular diagnostic tools made it possible to survey complex microbial communities using specific primer sets for/and antibodies raised against the various NOx reductases. Given the enormous complexity of substrates and environmental conditions, it is evident that mixed cultures rather than single species are responsible for denitrification in man-made and natural ecosystems. However, it is surprising that even best fit values for the breakdown of a single compound, such as acetate, mixed cultures hadronic interaction models are responsible, and that the consecutive denitrification steps are commonly performed by mutualistic co-operating species. Our observations also indicate that we seldom know the identity of the major key players summarized in the nitrogen cycle of these ecosystems.appendix A.

End User Agreement. This publication is distributed under the terms of Article 25fa of the Dutch Copyright Act. This article entitles the maker of a short scientific work funded either wholly or partially by Dutch public funds to make that work publicly available for no consideration following a reasonable period of time after the work was first published, provided that clear reference is made to the source of the first publication of the work. Research outputs of researchers employed by Dutch Universities that comply with the legal requirements of Article 25fa of the Dutch Copyright Act, are distributed online and free of cost or other barriers in institutional repositories. Research outputs are distributed six months after their first online publication in the original published version and with proper attribution to the source of the original publication. You are permitted to download and use the publication for personal purposes. All rights remain with the author(s) and/or copyrights owner(s) of this work. Any use of the publication other than authorised under this licence or copyright law is prohibited. If you believe that digital publication of certain material infringes any of your rights or (privacy) interests, please let the University Library know, stating your reasons. In case of a legitimate complaint, the University Library will, as a precaution, make the material inaccessible and/or remove it from the website. Please contact the University Library through email: xxxxxxxxx@xxx.xx.xx. You will be contacted as soon as possible. University Library Radboud University *Department Xxxxxx xxx Xxxxx* and Xxxx Xxxxxxx Using a narrative methodology involving 216 older people in six urban aging environments in the Netherlands, we examined how they use and experience (semi-)public spaces as spaces of Microbiologyencounter, RU Nijmegen NLand the meanings they derive from us- ing and experiencing these spaces. The research shows that, Toernooiveld 1first, 6525 ED older people pre- fer commercial spaces like shopping malls to planned and designed activity spaces in care homes or neighborhood centers. Second, older people struggle with the transformations that have taken place in urban social life since they were young adults. Third, especially frail older people derive meaning from a more passive ex- perience of urban social life, in an observer role. The findings allow us to contribute to ongoing debates on the shifting boundaries between public and private space, and the moral implications of these shifting boundaries from the perspective of a diverse group of older users. ∗Correspondence should be addressed to Xxxxxx xxx Xxxxx, Institute for Management Research, Radboud University, P.O. Box 9108, 6500 HK Nijmegen, the Netherlands; x.xxxxxxxx@xx.xx.xx. ∗C 2017 American Sociological Association, 0000 X Xxxxxx XX, Xxxxxxxxxx, XX 00000 walking behavior (e.g., Xxxxxx et al. 2002; Xxxxx et al. 2007; Xxxxxxxxx 2010; Xxxxxxxx 2013) and the influence of neighborhood attributes on physical activity (e.g., Xxxxxxxx et al. 2009; Xxxxxxxx et al. 2012). The results show that the presence of obstacles, slip- pery surfaces, or large crossroads can hinder the use of public space, while walking sticks and two-wheelers can enhance feelings of confidence (Xxxxxxxx et al. 2012) and land- marks, distinctive buildings, and clearly marked signage can help navigating in unfamiliar environments (Xxxxxxxx et al. 2013). However, much of this body of knowledge on the re- lationship between the physical environment and older people relies on “standardized measures without an understanding of the behaviors, perceptions and meanings of space and place” (Xxxxxxxx et al. 2013, 114). In line with the edited collection of Xxxxxx and Xxxxxxx (2013), our research adds precisely that: insight in the spaces that older people prefer and actually use to meet others, and in the way they experience and derive meaning from these spaces. It is based upon (predominantly) qualitative research in six urban aging environments in the Netherlands, or so-called Integrated Service Areas (ISAs). To support “aging-in-place” (AIP), about a hundred of these ISAs were developed in Dutch cities and †Department of Biotechnologyvillages over the last decade (Singelenberg and Xxx Xxxxxx 2009). Importantly, TU Delft NLwe did not ask ques- tions about specific, The Netherlands In the past 10 years many molecular aspects of microbial nitrate reduction preselected public spaces but had 216 older people describe an or- dinary day in their lives (see Methods section). These narrative interviews were scanned for references to places that have been elucidatedmeaning to these people, but the ecophysiology of this process is hardly understoodand to what extent these self- selected places encompass or overlap with planned or “vernacular” spaces and activities specifically designed for older people (Xxxx and Xxxxxx 2011). In this contributionAs such, our efforts approach al- lowed us to study assess the complex microbial communities relative importance of public space vis-a`-vis other issues relevant to older people through a combination of a large sample size and interactions involved the richness of in-depth interviews. After the following literature review on the use, experience, and meaning of public space in relation to older users, we introduce the reduction concepts of nitrate to dinitrogen gas are summarizedAIP in ISAs in some more detail. Subsequently, we continue with a more elaborate description of the methods em- ployed. The initial work concentrated paper then proceeds by presenting the most important research results as well as aligning these with ideas from other research to better understand and reflect on emission these results. The paper concludes with a discussion on how the research results speak to ongoing debates about public versus private space from the perspective of older users. DIVERSITY, INTERACTION, AND MEANING It is long acknowledged that public space can play an important role for the greenhouse gas nitrous oxide during incomplete denitrification by Alcaligenes faecalissocial life of cities (e.g., Xxxxx 1980; Xxxxxxx 1998, 2000; Xxxxxx 2006; Xxxxxxx et al. As more research methods became available, the fitness 2008). Al- though there are multiple and sometimes even contradictory conceptualizations of A. faecalis could be tested in mixed cultures with other denitrifying bacteria, most notably with the nitrate-reducing bacterium Pseudomonas G9. Finally, the advancement of molecular diagnostic tools made it possible to survey complex microbial communities using specific primer sets for/pub- lic space (Xxxxxxxx and antibodies raised against the various NOx reductases. Given the enormous complexity of substrates and environmental conditionsXxxxxxxx 2007; Peace 2013), it is evident often defined as a range of places where people from different backgrounds in terms of age, gender, ethnicity, and class can congregate, meet, and learn from each other. As such, public space has an important social function implying “encounters between strangers, people outside the life of fam- ily and close friends and within the region of diverse, complex social groups” (Xxxxxxx 2006 in Spierings et al. 2016, p. 151). Consequently, these encounters can result in the development of new insights, social ties, and tolerance (Xxxxxxx 1978; Xxxxxxx 2000; Xxxxxxx et al. 2008; Silver 2014). It is here where diversity and differences are “celebrated” but also “negotiated” (Xxxxxx 2006; Xxxxxxxxx 2008), sometimes leading to conflicts due to the “rubbing along” of different users and behaviors (Xxxxxx 2006; Xxxxxxxx 2014). Even though the intensity of interaction between different users of public space can be rather “fleeting” (Xxxxxxx 1998) or “unfocused” (Xxxxxxx 1963)—as Xxxxxxxxx et al. (2016) recently demonstrated for a Dutch plaza in Rotterdam—these encounters can still be meaningful, if anything because they are the most common encounters in public by sheer volume. Moreover, also without direct interaction the presence of others can lead to distraction and livelihood, with people-watching being a frequently reported activity in public space (Xxxxx 1980). While the benefits of urban encounters in public space apply to all city dwellers, they might be even more important for older people, who due to changes in their social life (e.g., death of a partner or friends) or personal health can experience decreased mobility and loneliness (Xxxxxxx et al. 2005). Xxxxx et al. (2007, 2042) stated that mixed cultures “especially main- taining the social relations of older people and their communication with other people can only be possible by using the urban common living environments like public open spaces together with the other citizens.” To know people and to be known by them can provide feelings of safety, belonging, and place attachment (Xxxxxxxx et al. 2009; Xxxxx et al. 2013; Xxxxˇxxxxx´ and Xx´xxxxxx´ 2015). In a similar vein, the use of common green spaces in living environments has been associated with social contact (Xxxx et al. 2009) and neighborhood ties and sense of community (Xxxxx et al. 1998). Consequently, we expect older people not only to use and perceive public spaces in a certain way, but also that these spaces are meaningful to them—and become personalized places rather than single species abstract spaces. As Xxxxxx and Xxxxxxx (2013, 9) indicated, meaning is a process that involves transforming what is at the outset a sterile and meaningless piece of ge- ographic space, for example an empty apartment, into a place that has personal meaning in the context of our ongoing life. In the process, we are responsible for denitrification engaged in man-made con- verting something that is neutral and natural ecosystemsoften alien into something that is a meaning- ful expression of our identity. HoweverThis is not a trivial pursuit, because it is surprising a process that provides a sense of familiarity, centering, security, ownership, control, territoriality, comfort, display, and identity. Following Xxxxxxxxx (2010), we specifically look at the meaning of public space, since this aspect is what actually makes public space public, more so than political-economic factors such as ownership and administration. While the latter can be contested, “public space is public because we, as a public, have accepted that the space legitimately repre- sents our collective interests and/or identity” (Xxxxxxxxx 2010, 5). We investigate how this applies to older people in ISAs. PRIVATIZATION AND PAROCHIALISM Concurrent with the above-sketched image of public space as meaningful, socially open and accessible space where meeting and interaction occurs, a number of other authors have expressed their concerns about public space being eroded and hence under threat. They paint a rather critical picture of modern urban life; one that is characterized by capitalist urban development, privatization, consumerism, restrictive security measures, and social exclusion (e.g., Xxxxxx 1989; Xxxxxx 1992; Xxxxxxxx 1995; Xxxx 2004; Xxxxxxx 2009; Xxxxxxxx 2014; for an overview of critiques, see Xxxxxxx 2015). Their principal concern is fear of the encroaching “private” as a result of neoliberal urban planning (Xxxxxx 1989; Silver 2014). Some argue that public space is rapidly becoming the domain of corporate, globalized capital (Xxxxxxxx 1995), while others observed that public spaces are being appropriated by the affluent (Madden 2010) or more broadly by “consumer society” (Zukin 1995, 2010), ultimately leading to the exclusion and marginalization of certain user groups (Xxxxxxxx 2014) and a more homogenous city. In addition to these more “structural” developments, public space can also become socially homogenous due to individual “agency.” While some people may very well be comfortable when being among strangers, “others may be much more hesitant to have encounters with difference and consider them unwanted, are afraid of the unknown and may even for the breakdown of perceive a single compoundsocioculturally diverse public space as a threatening and dangerous” (Xxxxxxxxx et al. 2016, 152). As a result, they adopt precautionary practices, such as acetateavoid- ing certain people or places. Often particular user groups claim public space as their own, mixed cultures where they go to meet the people they want to meet and shun those they do not want to see. While this appropriation of one group (e.g., young immigrant men) might facilitate feelings of comfort and safety among its members, it might limit others (e.g., older indigenous people) from accessing public space (e.g., Mu¨ ller and Xxxxxxx 2015), which Xxxxxxx (1998) denoted as parochialism. For older people, the potential downsides of encountering difference in public space are responsibleequally relevant. Research has shown that older people are more fearful in public space than young people (Xxxxxxx and Xx Xxxx 2004), while the latter are more often vic- xxxx of criminal offences (Pain 2003). Older people are more likely to communicate to the police than other age groups about frightful situations (Peace 2013). Yet, retreating into more socially homogenous environments is not only a matter of fear. Being among “equals” or “peers” has revitalizing effects and can enhance “active aging,” as has been observed in several retirement communities (Xxxxxxxxx 2010), because “these are places where everybody is old so nobody is old” (XxXxxx 2007, 296). Other “spaces of associ- ation” (Xxxx 2002, 969), such as sports and leisure clubs, could also xxxxxx meaningful encounters, because people can build social ties on the basis of regular encounters and shared interests. Yet, these so-called “micro-publics” (ibid.) often serve as parochial do- mains, too. For example, research on older people’s leisure clubs showed that the consecutive denitrification steps are commonly performed by mutualistic cosustained participation in these spaces offers ways to link past and present identities and interests, yet they target fairly homogeneous audiences and xxxxxx in-operating speciesgroup ties only (Pain et al. Our observations also indicate that we seldom know the identity of the major key players in the nitrogen cycle of these ecosystems2000).

End User Agreement. This publication is distributed under the terms of Article 25fa of the Dutch Copyright Act. This article entitles the maker of a short scientific work funded either wholly or partially by Dutch public funds to make that work publicly available for no consideration following a reasonable period of time after the work was first published, provided that clear reference is made to the source of the first publication of the work. Research outputs of researchers employed by Dutch Universities that comply with the legal requirements of Article 25fa of the Dutch Copyright Act, are distributed online and free of cost or other barriers in institutional repositories. Research outputs are distributed six months after their first online publication in the original published version and with proper attribution to the source of the original publication. You are permitted to download and use the publication for personal purposes. All rights remain with the author(s) and/or copyrights owner(s) of this work. Any use of the publication other than authorised under this licence or copyright law is prohibited. If you believe that digital publication of certain material infringes any of your rights or (privacy) interests, please let the University Library know, stating your reasons. In case of a legitimate complaint, the University Library will, as a precaution, make the material inaccessible and/or remove it from the website. Please contact the University Library through email: xxxxxxxxx@xxx.xx.xx. You will be contacted as soon as possible. University Library Radboud University *Department & Coupling Reactions Mechanistic Study of MicrobiologyPd/NHC-Catalyzed Sonogashira Reaction: Discovery of NHC-Ethynyl Coupling Process Xxxxxx X. Xxxxxx+,[a, RU Nijmegen NLb] Xxxxxx X. Xxxxx+,[a] Xxxxxxxxx Xx. Xxxxxxxxxxxx,[a] Xxxxx X. Xxxxxxxx,[a] Xxxxxxxxx X. Xxxxxxxx,[a] Xxxxxxxxx Xxxxxx,[c] Xxxxxxxx Xxxxxxx,[d] Xxxx Xxxxxx,[d] Xxx Xxxxxx,[d] Xxxx Xxxxxxx#,[c] and Xxxxxxxxx X. Ananikov*[a] Abstract: The product of a revealed transformation—NHC- ethynyl coupling—was observed as a catalyst transformation pathway in the Sonogashira cross-coupling, Toernooiveld 1catalyzed by Pd/NHC complexes. The 2-ethynylated azolium salt was iso- lated in individual form and fully characterized, 6525 ED Nijmegen, The Netherlands, and †Department including X- ray analysis. A number of Biotechnology, TU Delft NL, The Netherlands In the past 10 years many molecular aspects of microbial nitrate reduction have been elucidated, but the ecophysiology possible intermediates of this process is hardly understoodtransformation with common formulae (NHC)nPd(C2Ph) (n = 1,2) were observed and subjected to collision-induced disso- ciation (CID) and infrared multiphoton dissociation (IRMPD) experiments to elucidate their structure. In this contribution, our efforts Measured bond dis- sociation energies (BDEs) and IRMPD spectra were in an ex- cellent agreement with quantum calculations for coupling product p-complexes with Pd0. Molecular dynamics simula- tions confirmed the observed multiple CID fragmentation pathways. An unconventional methodology to study catalyst evolution suggests the complex microbial communities and interactions involved reported transformation to be con- sidered in the reduction development of nitrate to dinitrogen gas are summarized. The initial work concentrated on emission of the greenhouse gas nitrous oxide during incomplete denitrification by Alcaligenes faecalis. As more research methods became available, the fitness of A. faecalis could be tested in mixed cultures with other denitrifying bacteria, most notably with the nitrate-reducing bacterium Pseudomonas G9. Finally, the advancement of molecular diagnostic tools made it possible to survey complex microbial communities using specific primer sets for/and antibodies raised against the various NOx reductases. Given the enormous complexity of substrates and environmental conditions, it is evident that mixed cultures rather than single species are responsible new catalytic systems for denitrification in man-made and natural ecosystems. However, it is surprising that even for the breakdown of a single compound, such as acetate, mixed cultures are responsible, and that the consecutive denitrification steps are commonly performed by mutualistic co-operating species. Our observations also indicate that we seldom know the identity of the major key players in the nitrogen cycle of these ecosystemsalkyne functionalization reactions.

End User Agreement. This publication is distributed under the terms of Article 25fa of the Dutch Copyright Act. This article entitles the maker of a short scientific work funded either wholly or partially by Dutch public funds to make that work publicly available for no consideration following a reasonable period of time after the work was first published, provided that clear reference is made to the source of the first publication of the work. Research outputs of researchers employed by Dutch Universities that comply with the legal requirements of Article 25fa of the Dutch Copyright Act, are distributed online and free of cost or other barriers in institutional repositories. Research outputs are distributed six months after their first online publication in the original published version and with proper attribution to the source of the original publication. You are permitted to download and use the publication for personal purposes. All rights remain with the author(s) and/or copyrights owner(s) of this work. Any use of the publication other than authorised under this licence or copyright law is prohibited. If you believe that digital publication of certain material infringes any of your rights or (privacy) interests, please let the University Library know, stating your reasons. In case of a legitimate complaint, the University Library will, as a precaution, make the material inaccessible and/or remove it from the website. Please contact the University Library through email: xxxxxxxxx@xxx.xx.xx. You will be contacted as soon as possible. University Library Radboud University *Department Clinical Anatomy 25:168–175 (2012) ORIGINAL COMMUNICATION XXXXXX XXXX,1* XXXX XXXXXXX,1 XXX XXXXXXX,2 AND XXXXX X. GERRITS3 1Center for Thanatology, Faculty of MicrobiologyPhilosophy, RU Nijmegen NLTheology and Religious Studies, Toernooiveld 1Radboud University Nijmegen, 6525 ED Nijmegen, The NetherlandsNetherlands 2Department of Social Science Research Methods, and †Department Faculty of BiotechnologySocial Sciences, TU Delft NLRadboud University Nijmegen, Nijmegen, The Netherlands In 3Department of Neuroscience, Section Anatomy, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands ¼ Anatomical professionals know better than anyone else that donated bodies are a valuable asset to anatomical science and medical education. They highly value voluntary donations, since a dearth of bodies negatively affects their profession. With this in mind, we conducted a survey (n 54) at the past 10 years many molecular aspects 171st sci- entific meeting of microbial nitrate reduction have been elucidated, but the ecophysiology Dutch Anatomical Society in 2009 to see to what extent anatomical professionals are willing to donate their own body. The results reveal that none of this process is hardly understoodthe survey participants are registered as a whole body do- nor and that only a quarter of them would consider the possibility of body don- ation. We argue that the two main constraints preventing Dutch anatomical professionals from donating their own body are their professional and their social environments. In this contributioncontrast to the absence of registered body donors, our efforts to study the complex microbial communities and interactions involved in the reduction of nitrate to dinitrogen gas are summarized. The initial work concentrated on emission half of the greenhouse gas nitrous oxide during incomplete denitrification anatomical professionals are registered as an organ donor. This figure far exceeds the proportion of registered organ donors among the general Dutch population. Clin. Anat. 25:168–175, 2012. VVC 2011 Wiley Periodicals, Inc. Key words: anatomy; whole body donation; motivation for donation; dissecting room INTRODUCTION Every day anatomical professionals, such as pro- sectors and anatomists, work with dead bodies that were donated to their institute. They know better than anyone else does that human corpses are a valuable asset to anatomical research and medical education. A sufficient supply of donor bodies is essential to the anatomy practice and the shortage of body donors that is frequently reported by Alcaligenes faecalis. As more research methods became availableanatomical institutes in other countries (Xxxxxxxx et al., the fitness of A. faecalis could be tested in mixed cultures with other denitrifying bacteria2004; XxXxxxxxx et al., most notably with the nitrate-reducing bacterium Pseudomonas G9. Finally, 2008) severely obstructs the advancement of molecular diagnostic tools made it possible to survey complex microbial communities using specific primer sets for/and antibodies raised against the various NOx reductasesdiscipline. Given Over the enormous complexity past several years, Dutch body donor registrations have been increasing (Wijbenga et al., 2010). Currently, about 0.1% of substrates and environmental conditions, it is evident that mixed cultures rather than single species the Dutch are responsible for denitrification in man-made and natural ecosystemsregis- tered as body donors. However, it is surprising that even for the breakdown Out of a single compound, such as acetate, mixed cultures are responsible, and that the consecutive denitrification steps are commonly performed by mutualistic co-operating species. Our observations also indicate that we seldom know the identity of the major key players in the nitrogen cycle of these ecosystems.total population of

End User Agreement. This publication is distributed under the terms of Article 25fa of the Dutch Copyright Act. This article entitles the maker of a short scientific work funded either wholly or partially by Dutch public funds to make that work publicly available for no consideration following a reasonable period of time after the work was first published, provided that clear reference is made to the source of the first publication of the work. Research outputs of researchers employed by Dutch Universities that comply with the legal requirements of Article 25fa of the Dutch Copyright Act, are distributed online and free of cost or other barriers in institutional repositories. Research outputs are distributed six months after their first online publication in the original published version and with proper attribution to the source of the original publication. You are permitted to download and use the publication for personal purposes. All rights remain with the author(s) and/or copyrights owner(s) of this work. Any use of the publication other than authorised under this licence or copyright law is prohibited. If you believe that digital publication of certain material infringes any of your rights or (privacy) interests, please let the University Library know, stating your reasons. In case of a legitimate complaint, the University Library will, as a precaution, make the material inaccessible and/or remove it from the website. Please contact the University Library through email: xxxxxxxxx@xxx.xx.xx. You will be contacted as soon as possible. University Library Radboud University *As featured in: See Xxxxxxxxx Xxxxxxxx et al., Lab Chip, 2015, 15, 4291. Featuring work from the Fluid Mechanics Group of Xx. Xxxxxxxxx Xxxxxxxx in the Department of MicrobiologyMechanical Engineering at UCL and the Microdroplets Group of Xxxx. Xxxxxxx Xxxx at the University of Cambridge. Title: Deformation of double emulsions under conditions of flow cytometry hydrodynamic focusing Here we report on the deformation of double emulsions under hydrodynamic focusing conditions encountered in commercial flow cytometry systems (such as FACS) in order to assess their potential as a screening platform for shear sensitive cells. The work could also inform the design of microfluidic based cell deformation studies. Published on 14 September 2015. Downloaded by Radboud Universiteit Nijmegen on 23/10/2017 15:30:35. Lab on a Chip PAPER Cite this: Lab Chip, RU Nijmegen NL2015, Toernooiveld 115, 6525 ED Nijmegen4291 Received 21st June 2015, The NetherlandsAccepted 10th September 2015 DOI: 10.1039/c5lc00693g xxx.xxx.xxx/xxx Deformation of double emulsions under conditions of flow cytometry hydrodynamic focusing† Xxxxxxx Xx,xx Xxxxxxx X. X. Xxxxxx and Xxxxxxxxx Xxxxxxxx*d Water-in-oil-in-water (w/o/w) microfluidics double emulsions offer a new route to compartmentalise reagents into isolated aqueous microenvironments while maintaining an aqueous carrier fluid phase; this enables compatibility with commercial flow cytometry systems such as fluorescence-activated cell sorting (FACS). Double emulsion (inner core) deformation under hydrodynamic focusing conditions that mimic the environment double emulsions experience in flow cytometry applications is of particular importance for droplet stability and cell viability. This paper reports on an experimental study of the dynamic deformation of aqueous cores of w/o/w double emulsions under hydrodynamic focusing, with the sheath flow directed at 45° to the sample flow. A number of factors affecting the inner core deformation and recovery were examined. Deformation was found to depend significantly on the core or shell viscosity, the droplet-to- sheath flow velocity ratio, and †Department core and shell sizes. Core deformation was found to depend more on the type of Biotechnology, TU Delft NL, The Netherlands In surfactant rather concentration with high molecular weight surfactant exhibiting a negligible effect on deformation whereas low molecular weight surfactant enhancing deformation at low concentrations due to their lateral mobility at the past 10 years many molecular aspects of microbial nitrate reduction have been elucidated, but the ecophysiology of this process is hardly understoodinterface. In this contribution, our efforts to study the complex microbial communities and interactions involved in the reduction of nitrate to dinitrogen gas are summarized. The initial work concentrated on emission of the greenhouse gas nitrous oxide during incomplete denitrification by Alcaligenes faecalis. As more research methods became available, the fitness of A. faecalis could be tested in mixed cultures with other denitrifying bacteria, most notably with the nitrate-reducing bacterium Pseudomonas G9. Finally, the advancement of molecular diagnostic tools made it possible to survey complex microbial communities using specific primer sets for/and antibodies raised against the various NOx reductases. Given the enormous complexity of substrates and environmental conditions, it is evident that mixed cultures rather than single species are responsible for denitrification in man-made and natural ecosystems. However, it is surprising that even for the breakdown of a single compound, such as acetate, mixed cultures are responsible, and that the consecutive denitrification steps are commonly performed by mutualistic co-operating species. Our observations also indicate that we seldom know the identity of the major key players in the nitrogen cycle of these ecosystems.Introduction

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All rights remain with the author(s) and/or copyrights owner(s) of this work. Any use of the publication other than authorised under this licence or copyright law is prohibited. If you believe that digital publication of certain material infringes any of your rights or (privacy) interests, please let the University Library know, stating your reasons. In case of a legitimate complaint, the University Library will, as a precaution, make the material inaccessible and/or remove it from the website. Please contact the University Library through email: xxxxxxxxx@xxx.xx.xx. You will be contacted as soon as possible. University Library Radboud University *Department Member States’ Sovereignty in the Socio-Economic Field: Fact or Fiction? ª The Author(s) 2018 Reprints and permissions: xxxxxxx.xx.xx/xxxxxxxxXxxxxxxxxxx.xxx DOI: 10.1177/2031952518758097 The Clash between the European Business Freedoms and the National level of MicrobiologyWorkers’ Protection Femke Laagland1 Radboud University, RU Nijmegen NL, Toernooiveld 1, 6525 ED Nijmegen, Netherlands Abstract The Netherlands, author assesses the case law of the Court of Justice of the European Union (the Court) in which the European business freedoms collide with national labour law. The approach of the Court will be scrutinised with the aim of discovering the extent to which the Court encroaches upon the Member States’ autonomy in the field of labour law. This topic became popular directly after the landmark decisions in Viking and †Department Laval of Biotechnology, TU Delft NL, The Netherlands December 2007. Both cases addressed conflicts that were related to socio-economic diversity in the European Union following the enlargements. In the past 10 years many molecular aspects end, the Court decided where the balance between the conflicting economic and social values had to be struck and, by doing so, did not grant any room of microbial nitrate reduction discretion to the Member States. Since then, the freedom of establishment and the freedom to provide services have been elucidated, but obtruded themselves into the ecophysiology sphere of this process is hardly understoodnational labour law. In this contribution, our efforts to study the complex microbial communities and interactions involved The Court has broadened its jurisdiction in the reduction socio-economic field not only in cross-border situations but also in internal situations via its interpretation of nitrate to dinitrogen gas are summarizedsocial policy Directives by virtue of Article 16 CFREU. The initial work concentrated on emission research shows that the Court is assessing the legitimacy of restrictions imposed by national labour law in seemingly different distinguishable ways since 2007. Although the Court does not seem to aspire to a uniform labour law system throughout the European Union, its approach applied in Viking and Laval cannot be considered a thing of the greenhouse gas nitrous oxide during incomplete denitrification by Alcaligenes faecalispast. As more research methods became available, the fitness of A. faecalis could be tested in mixed cultures with other denitrifying bacteria, most notably with the nitrate-reducing bacterium Pseudomonas G9. Finally, the advancement of molecular diagnostic tools made it possible Due to survey complex microbial communities using specific primer sets for/and antibodies raised against the various NOx reductases. Given the enormous complexity of substrates and environmental conditionspoor reasoning, it is evident that mixed cultures rather than single species not clear when and where the Court draws the line. Since its rulings cannot readily (or even at all) be subject to political review, the ensuing legal uncertainty leads to anxiety about the Court being the ultimate decider in the socio- economic field. 1. Xxxxx Xxxxxxxx is full Professor of (European) Labour Law at the University of Nijmegen (the Netherlands). Corresponding author: Femke Laagland, Radboud University Nijmegen, Xxxxxxxxxxxxxx 00, Xxxx 0.000, Xxxxxxxxxxx. E-mail: x.xxxxxxxx@xxx.xx.xx Keywords Business freedoms, Labour law, Article 16 CFREU, Market freedoms, National social policy Introduction and Research Question The European Union (hereafter: EU) is based on the economic freedoms of movement and a system to prevent distorted competition. Originally, social harmonisation was not part of the European project. Even today the European legislator has limited possibilities for reconciling conflicting economic and social values through a process of harmonisation. Besides that, efforts to adopt European social policies are responsible for denitrification in man-made politically impeded, given the diverse national welfare systems of the current 28 Member States. As a result, labour law is often considered to be an area reserved to the Member States and natural ecosystemsthe level of workers’ protection differs throughout the EU. However, appearances can be deceptive. In practice, it seems that hardly any area of national labour law escapes from the application of the European internal market. This takes place not through legislation, but through preliminary rulings by the Court of Justice of the European Union (hereafter: Court). The freedom of establishment and the freedom to provide services allow companies to invoke their free movement rights directly under EU law. As soon as a national labour law rule hinders their cross-border movement, the freedoms are triggered and the Court might be asked to what extent national labour rules are allowed to restrict the well-rooted economic values of the EU. In that case, the Court has to conduct a balancing test with regard to the conflicting values. The Treaty does not contain concrete directions about which interest prevails. It is surprising that even therefore left to the Court to decide. The same is true for the breakdown interpretation of European social legislation. Primary law and secondary law are not separate worlds but enjoy a complicated interrelationship in which the former influences the latter in several ways. Moreover, the Court takes the freedom to conduct a business as laid down in Article 16 Charter on Fundamental Rights of the EU (hereafter: CFREU) into consideration when interpreting social policy Directives. Interestingly, as the Court pointed out, Article 16 CFREU refers to the freedom of establishment and contains similar rights. As a result, the Court has to conduct the same balancing test with regard to social policy Directives but this time without the need of a single compound, such cross-border element. The purpose of this paper is to look into the case law of the Court to find out to what extent its rulings can be seen as acetate, mixed cultures are responsiblethreatening the ability for Member States to maintain existing levels of workers’ protection. To put it differently in the form of a question: does the Court settle questions in the socio-economic field that should be weighed and balanced on the national political, and that not the consecutive denitrification steps European judicial, scale? The conflict between market freedoms and national labour law was a popular topic right after the Viking and Laval judgments in 2007. This paper will discuss whether the Court’s approach in Viking and Xxxxx has been followed up in case law. The research is limited to rulings where the Court had to strike a balance between the freedom of establishment, the freedom to provide services and/or Article 16 CFREU on the one side; and national labour law measures on the other.2 The free movement of workers has generally not been considered as a threat to the level of workers’ protection under national legislation as it grants foreign workers the 2. The term ‘labour law’ is used to describe guarantees surrounding employment which are commonly performed by mutualistic co-operating species. Our observations also indicate that we seldom know aimed at the identity protection of the major key players employee as the weaker party. same rights as nationals.3 This freedom is therefore not the centre of attention, yet is mentioned when it provides added value in light of the nitrogen cycle of these ecosystems.research question.4

End User Agreement. This publication is distributed under the terms of Article 25fa of the Dutch Copyright Act. This article entitles the maker of a short scientific work funded either wholly or partially by Dutch public funds to make that work publicly available for no consideration following a reasonable period of time after the work was first published, provided that clear reference is made to the source of the first publication of the work. Research outputs of researchers employed by Dutch Universities that comply with the legal requirements of Article 25fa of the Dutch Copyright Act, are distributed online and free of cost or other barriers in institutional repositories. Research outputs are distributed six months after their first online publication in the original published version and with proper attribution to the source of the original publication. You are permitted to download and use the publication for personal purposes. All rights remain with the author(s) and/or copyrights owner(s) of this work. Any use of the publication other than authorised under this licence or copyright law is prohibited. If you believe that digital publication of certain material infringes any of your rights or (privacy) interests, please let the University Library know, stating your reasons. In case of a legitimate complaint, the University Library will, as a precaution, make the material inaccessible and/or remove it from the website. Please contact the University Library through email: xxxxxxxxx@xxx.xx.xx. You will be contacted as soon as possible. University Library Radboud University *Article Multimedia Modeling of Engineered Nanoparticles with SimpleBox4nano: Model Definition and Evaluation Xxxxxxxx X. X. Xxxxxxxx,*,† Xxxxxx X. Xxxxxxxx,‡,§ Joris T. K. Quik,‡ A. Xxx Xxxxxxxx,† and Dik van de Meent† †Institute for Water and Wetland Research, Department of MicrobiologyEnvironmental Science, RU Nijmegen NLRadboud University Nijmegen, Toernooiveld 1P.O. Box 9010, 6525 ED NL-6500 GL Nijmegen, The NetherlandsNetherlands ‡Aquatic Ecology and Water Quality Management Group, and †Department Department of BiotechnologyEnvironmental Sciences, TU Delft NLWageningen University, P.O. Box 47, 6700 AA Wageningen, The Netherlands In §IMARES − Institute for Marine Resources & Ecosystem Studies, Wageningen UR, P.O. Box 68, 1970 AB IJmuiden, The Netherlands *S Supporting Information ABSTRACT: Screening level models for environmental assessment of engineered nanoparticles (ENP) are not generally available. Here, we present SimpleBox4Nano (SB4N) as the past 10 years first model of this type, assess its validity, and evaluate it by comparisons with a known material flow model. SB4N expresses ENP transport and concentrations in and across air, rain, surface waters, soil, and sediment, accounting for nanospecific processes such as aggregation, attachment, and dissolution. The model solves simultaneous mass balance equations (MBE) using simple matrix algebra. The MBEs link all concentrations and transfer processes using first-order rate constants for all processes known to be relevant for ENPs. The first-order rate constants are obtained from the literature. The output of SB4N is mass concentrations of ENPs as free dispersive species, heteroaggregates with natural colloids, and larger natural particles in each compartment in time and at steady state. Known scenario studies for Switzerland were used to demonstrate the impact of the transport processes included in SB4N on the prediction of environmental concentrations. We argue that SB4N- predicted environmental concentrations are useful as background concentrations in environmental risk assessment. ■ INTRODUCTION The nanotechnology industry is rapidly developing engineered nanoparticles (ENPs) that are applied in a great variety of consumer and industrial products.1 ENPs are designed to be nanoscaled (<100 nm) in at least two dimensions, so that nanospecific physicochemical properties emerge from the highly interfacial nature of the chemical material.2 This enables novel and unique applications in a wide spectrum of fields, such as electronics engineering, energy production, biomedical applications, food, agriculture, and many molecular aspects more.3 However, the specific properties of microbial nitrate reduction ENPs also raise concern about unforeseen environmental and toxicological consequences.4 There is thus a great need to evaluate the potential environmental risk of ENPs because release to the environment is considered to be inevitable.5 Current environmental risk management policies on chemical substances (e.g., the European Union’s chemical regulation REACH: Registration Evaluation Authorization and Restriction of Chemicals) have been elucidateddesigned for use with so- or nanocolloids.6 Making such adjustments is challenging because of the fundamental differences in transport- and transformation mechanisms between colloids and solutions.6−8 A major difficulty in making models for “conventional” chemicals fit for (nano)colloids is that hardly any field data are available to test the validity of nanoadjusted models.8,9 The adjustment is also an urgent task, but since products containing ENPs are already on the ecophysiology market. Previous attempts to model the environmental fate of nanoparticles were meant to provide a first step in environmental exposure estimation of ENPs10,11 and are still too complex for direct implementation in chemical safety assessment frameworks.12 It has therefore been proposed to develop environmental risk assessment strategies with a pragmatic approach and using scientifically justified simplifica- tions.7 This paper is an attempt to aid in this process approach by presenting a relatively simple environmental fate model that uses first- order kinetics to estimate environmental background concen- trations for nanocolloids in an environmental system that is hardly understood. In this contributioncalled “conventional” chemicals, our efforts to study the complex microbial communities and interactions involved i.e., chemical substances in atomic/ionic or molecular forms, dissolved in water or in the reduction of nitrate to dinitrogen gas are summarized. The initial work concentrated on emission of the greenhouse gas nitrous oxide during incomplete denitrification by Alcaligenes faecalis. As more research methods became available, the fitness of A. faecalis could be tested in mixed cultures with other denitrifying bacteria, most notably with the nitrate-reducing bacterium Pseudomonas G9. Finally, the advancement of molecular diagnostic tools made it possible to survey complex microbial communities using specific primer sets for/and antibodies raised against the various NOx reductases. Given the enormous complexity of substrates and environmental conditions, it is evident that mixed cultures rather than single species are responsible for denitrification in man-made and natural ecosystemsphase. However, it is surprising regulatory procedures urgently need adjustment to become fit for application to the new nanochemicals that even generally occur in solid forms, like micro- Received: January 31, 2014 Revised: April 7, 2014 Accepted: April 25, 2014 Figure 1. Overview of model concept SimpleBox4nano. composed of the compartments air, soil, water, and sediment that are represented as boxes: SimpleBox4nano (SB4N). A similar approach in modeling the fate of nanomaterials in air, water, and soil was recently published by Xxx and Xxxxx.13 Unlike SB4N, Xxx and Xxxxx’x MendNano model assumes fixed (time independent) partitioning ratios for the breakdown processes of aggregation and attachment, which control the environmental fate of colloidal systems.8 In SB4N, these processes are modeled mechanistically using first-order rate constants as will be explained in detail below. SB4N is a single compoundmodified version of the SimpleBox model, which has served as a regional distribution module in the European Union System for Evaluation of Substances (EUSES) model, used for exposure assessment in REACH.14−16 SB4N adds first- order rate constants for transport- and transformation processes of colloids, where the original SimpleBox model does so only for molecular processes of chemical substances dissolved in water.12 It has been identified that three major adaptations are necessary to make SimpleBox fit for ENPs:6 (1) transformation processes (e.g., from one colloidal form into another by homo- or heteroaggregation) should not be interpreted as removal processes; rather transformation products should be treated as altered species of the same ENP; (2) dissolution should be implemented as a removal mechanism and (3) thermodynamic equilibrium is not expected to be representative for the actual concentrations in the environment, since ENPs generally form unstable colloidal systems.17 The latter implies that concen- tration ratios of colloidal species cannot be calculated from equilibrium partitioning coefficients but must be modeled dynamically, as the result of forward and backward process rates.6 The aim of the present paper is to provide process formulations for modeling behavior of ENP and to evaluate its potential for use in environmental risk assessment. We explain how environmental concentrations can be calculated as a function of ENP emissions and ENP substance properties using colloidal and ultrafine particle theory. As existing theory which ENPs are taken up in aggregates or attach to the surfaces of larger particles, and (4) the rates at which ENPs may be subjected to removal processes such as acetatedegradation and dissolution. The first-order rate constants are derived from formulations from the literature and are explained below (Supporting Information, mixed cultures are responsibleeq 1 and Table 2). SB4N models the mass concentrations (mi/V = Ci) as state variables, using the same first-order rate constants (ki), written here for a one-compartment system, for which the time- dependent concentrations Ci(t) can be expressed analytically as the total mass mi present in an environmental compartment of volume V at time t at constant emission Ei and removal ki for ENP species i:23 cannot exactly describe and predict environmental behavior of m (t) ⎡ E ⎤ colloidal material under field conditions, we have formulated C (t) = i = ⎢ i (1 − e− ∑i kit)⎥ the model to be flexible, so that the consecutive denitrification steps are commonly performed by mutualistic co-operating species. Our observations also indicate that we seldom know the identity of the major key players theoretically derived parameter values can be replaced with experimentally determined ones in the nitrogen cycle of these ecosystems.V ⎢⎣ V ∑i ki ⎥⎦

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End User Agreement. This publication is distributed under the terms of Article 25fa of the Dutch Copyright Act. This article entitles the maker of a short scientific work funded either wholly or partially by Dutch public funds to make that work publicly available for no consideration following a reasonable period of time after the work was first published, provided that clear reference is made to the source of the first publication of the work. Research outputs of researchers employed by Dutch Universities that comply with the legal requirements of Article 25fa of the Dutch Copyright Act, are distributed online and free of cost or other barriers in institutional repositories. Research outputs are distributed six months after their first online publication in the original published version and with proper attribution to the source of the original publication. You are permitted to download and use the publication for personal purposes. All rights remain with the author(s) and/or copyrights owner(s) of this work. Any use of the publication other than authorised under this licence or copyright law is prohibited. If you believe that digital publication of certain material infringes any of your rights or (privacy) interests, please let the University Library know, stating your reasons. In case of a legitimate complaint, the University Library will, as a precaution, make the material inaccessible and/or remove it from the website. Please contact the University Library through email: xxxxxxxxx@xxx.xx.xx. You will be contacted as soon as possible. University Library Radboud University *Department Consolidative Dendritic Cell-based Immunotherapy Elicits Cytotoxicity against Malignant Mesothelioma Joost P. Hegmans1, Joris D. Veltman1, Xxxxxxxxxx X. Lambers1, I. Xxxxxxx X. de Vries2, Xxxx X. Figdor2, Xxxx X. Hendriks1, Henk C. Hoogsteden1, Xxxx X. Lambrecht1,3, and Xxxxxxx X. Aerts1,4 1Department of MicrobiologyPulmonary Medicine, RU Erasmus MC, Rotterdam, The Netherlands; 2Department of Tumor Immunology, Nijmegen NLCentre for Molecular Life Sciences (NCMLS), Toernooiveld 1Radboud University Nijmegen Medical Centre, 6525 ED Nijmegen, The Netherlands; 3Department of Respiratory Medicine, and †Department Ghent University, Ghent, Belgium; 4Department of BiotechnologyPulmonary Medicine, TU Delft NLAmphia Hospital, Breda, The Netherlands In the past 10 years many molecular aspects of microbial nitrate reduction have been elucidated, but the ecophysiology of this process is hardly understood. In this contribution, our efforts to study the complex microbial communities and interactions involved in the reduction of nitrate to dinitrogen gas are summarized. The initial work concentrated on emission of the greenhouse gas nitrous oxide during incomplete denitrification by Alcaligenes faecalis. As more research methods became available, the fitness of A. faecalis could be tested in mixed cultures with other denitrifying bacteria, most notably with the nitrate-reducing bacterium Pseudomonas G9. Finally, the advancement of molecular diagnostic tools made it possible to survey complex microbial communities using specific primer sets for/and antibodies raised against the various NOx reductases. Given the enormous complexity of substrates and environmental conditions, it is evident that mixed cultures rather than single species are responsible for denitrification in man-made and natural ecosystems. However, it is surprising that even for the breakdown of a single compound, such as acetate, mixed cultures are responsible, and that the consecutive denitrification steps are commonly performed by mutualistic co-operating species. Our observations also indicate that we seldom know the identity of the major key players in the nitrogen cycle of these ecosystems.Netherlands

End User Agreement. This publication is distributed under the terms of Article 25fa of the Dutch Copyright Act. This article entitles the maker of a short scientific work funded either wholly or partially by Dutch public funds to make that work publicly available for no consideration following a reasonable period of time after the work was first published, provided that clear reference is made to the source of the first publication of the work. Research outputs of researchers employed by Dutch Universities that comply with the legal requirements of Article 25fa of the Dutch Copyright Act, are distributed online and free of cost or other barriers in institutional repositories. Research outputs are distributed six months after their first online publication in the original published version and with proper attribution to the source of the original publication. You are permitted to download and use the publication for personal purposes. All rights remain with the author(s) and/or copyrights owner(s) of this work. Any use of the publication other than authorised under this licence or copyright law is prohibited. If you believe that digital publication of certain material infringes any of your rights or (privacy) interests, please let the University Library know, stating your reasons. In case of a legitimate complaint, the University Library will, as a precaution, make the material inaccessible and/or remove it from the website. Please contact the University Library through email: xxxxxxxxx@xxx.xx.xx. You will be contacted as soon as possible. University Library Radboud University *Department University 3.1 Introduction 3.2 Curriculum components 3.3 Curriculum layers 3.4 Curricular decision-making In this chapter, we take a look at computer science curricula from various perspectives. We present the theories behind these perspectives as well as characteristic examples taken from actual curriculum documents and practices. First, we explore the various components of Microbiologya curriculum, RU Nijmegen NLin particular the underlying rationale, Toernooiveld 1the content matter and the goals and objectives. Second, 6525 ED Nijmegenwe present a way to view curricula in terms of implementation layers, The Netherlandseach with its own level of abstraction, and †Department identify influencing factors, including the teachers’ own expertise and beliefs. We highlight the special role of Biotechnology, TU Delft NL, The Netherlands In textbooks and other teaching materials as an intermediate layer between designed and implemented curricula. We argue how the past 10 years many molecular aspects of microbial nitrate reduction have been elucidated, but the ecophysiology of perspectives presented in this process is hardly understood. In this contribution, our efforts to study the complex microbial communities chapter can be used as lenses for analysing and interactions involved in the reduction of nitrate to dinitrogen gas are summarized. The initial work concentrated on emission of the greenhouse gas nitrous oxide during incomplete denitrification by Alcaligenes faecalis. As more research methods became available, the fitness of A. faecalis could be tested in mixed cultures with other denitrifying bacteria, most notably with the nitrateunderstanding existing curricula as well as for supporting curricular decision-reducing bacterium Pseudomonas G9. Finally, the advancement of molecular diagnostic tools made it possible to survey complex microbial communities using specific primer sets for/and antibodies raised against the various NOx reductases. Given the enormous complexity of substrates and environmental conditions, it is evident that mixed cultures rather than single species are responsible for denitrification in man-made and natural ecosystems. However, it is surprising that even for the breakdown of a single compound, such as acetate, mixed cultures are responsible, and that the consecutive denitrification steps are commonly performed by mutualistic co-operating species. Our observations also indicate that we seldom know the identity of the major key players in the nitrogen cycle of these ecosystemsmaking.

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All rights remain with the author(s) and/or copyrights owner(s) of this work. Any use of the publication other than authorised under this licence or copyright law is prohibited. If you believe that digital publication of certain material infringes any of your rights or (privacy) interests, please let the University Library know, stating your reasons. In case of a legitimate complaint, the University Library will, as a precaution, make the material inaccessible and/or remove it from the website. Please contact the University Library through email: xxxxxxxxx@xxx.xx.xx. You will be contacted as soon as possible. University Library Radboud University *Luke van Leijenhorst1,3(✉) , Arjen P. de Vries1 , Xxxxx Xxxxxx Jansen2 , and Xxxxxx Wertheim3 1 Institute for Computing and Information Sciences, Radboud University, Nijmegen, Netherlands {luke.vanleijenhorst,xxxxx.xxxxxxx}@xx.xx 2 Department of Infection Prevention and Control, Amphia Hospital, 3 Department of Medical Microbiology, RU Nijmegen NLRadboudumc, Toernooiveld 1, 6525 ED Nijmegen, The Netherlands, and †Department of Biotechnology, TU Delft NL, The Netherlands In healthcare, medical knowledge is captured into guidelines that support health- care professionals to deliver the past 10 years many molecular aspects best possible quality of microbial nitrate reduction have been elucidated, but the ecophysiology of this process is hardly understoodcare. In hospitals and other healthcare settings, these guidelines are implemented and integrated in local standard operating procedures (SOPs). When guidelines are updated, it is important to also update all SOPs that are based on this contributionguideline. In most hospitals, our efforts this is a manual process in which employees periodically adjust the Oc The Author(s), under exclusive license to study Springer Nature Switzerland AG 2023 X. Xxxxx et al. (Eds.): ECIR 2023, LNCS 13982, pp. 307–312, 2023. xxxxx://xxx.xxx/10.1007/978-3-031-28241-6_31 SOPs associated with the complex microbial communities and interactions involved guideline in the reduction of nitrate to dinitrogen gas are summarized. The initial work concentrated on emission of the greenhouse gas nitrous oxide during incomplete denitrification by Alcaligenes faecalis. As more research methods became available, the fitness of A. faecalis could be tested in mixed cultures with other denitrifying bacteria, most notably with the nitrate-reducing bacterium Pseudomonas G9. Finally, the advancement of molecular diagnostic tools made it possible to survey complex microbial communities using specific primer sets for/and antibodies raised against the various NOx reductasesquality system. Given the enormous complexity number of substrates guidelines and environmental conditionsthe number of SOPs in a hospital, it this is evident a vulnerable process that mixed cultures rather than single species may lead to SOPs that are responsible for denitrification in man-made and (partially) outdated. SOPalign is a tool that uses natural ecosystems. However, it is surprising that even for language processing techniques to assess where SOPs are compliant with the breakdown of a single compound, such as acetate, mixed cultures are responsibleapplicable guidelines, and that where they dif- fer. The tool can support healthcare facilities to keep their procedures updated with the consecutive denitrification steps guidelines. It also helps to discover bottlenecks in the guideline rec- ommendations, when recommendations in guidelines do not appear in SOPs, or the SOPs are commonly performed by mutualistic co-operating speciesnot compliant with the guideline. This is an important step in the improvement cycle of guidelines and supports the perspective of ‘living guidelines’. The authors foresee a transition from a collection of independent documents into a hyperlinked network of guidelines and SOPs. Our observations also indicate that we seldom know the identity of the major key players in the nitrogen cycle of these ecosystemstool aims to enable this transition at a low cost.

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End User Agreement. This publication is distributed under the terms of Article 25fa of the Dutch Copyright Act. This article entitles the maker of a short scientific work funded either wholly or partially by Dutch public funds to make that work publicly available for no consideration following a reasonable period of time after the work was first published, provided that clear reference is made to the source of the first publication of the work. Research outputs of researchers employed by Dutch Universities that comply with the legal requirements of Article 25fa of the Dutch Copyright Act, are distributed online and free of cost or other barriers in institutional repositories. Research outputs are distributed six months after their first online publication in the original published version and with proper attribution to the source of the original publication. You are permitted to download and use the publication for personal purposes. All rights remain with the author(s) and/or copyrights owner(s) of this work. Any use of the publication other than authorised under this licence or copyright law is prohibited. If you believe that digital publication of certain material infringes any of your rights or (privacy) interests, please let the University Library know, stating your reasons. In case of a legitimate complaint, the University Library will, as a precaution, make the material inaccessible and/or remove it from the website. Please contact the University Library through email: xxxxxxxxx@xxx.xx.xx. You will be contacted as soon as possible. University Library Radboud University *Department The Influence of MicrobiologySize on Phase Morphology and Li-Ion Mobility in Nanosized Lithiated Anatase TiO2 Xxxxxx Xxxxxxxxx,*[a] Xxxxxx X. X. Xxxxxxxx,[a] Xxxxx X. X. xxx Xxx,[b] Xxxx X. X. Xxxxxxxx,[b] Xxxxxx X. Xxxxxxx,[a] and Xxxxx X. Mulder*[a] Abstract: Sustainable energy storage in the form of Li-ion batteries requires new and advanced materials in particu- lar with a higher power density. Nano- structuring appears to be a promising strategy, RU Nijmegen NLin which the higher power density in nanosized materials is relat- ed to the dramatically shortened Li-ion diffusion paths. However, Toernooiveld 1nanosizing materials also changes intrinsic materi- al properties, 6525 ED Nijmegen, The Netherlands, which influence both ionic and †Department of Biotechnology, TU Delft NL, The Netherlands In the past 10 years many molecular aspects of microbial nitrate reduction have been elucidated, but the ecophysiology of this process is hardly understoodelectronic conductivity. In this contributionwork neutron diffraction is used to show that in addition to these two as- pects, our efforts nanostructuring changes the phase behavior and morphology. Lithi- ated 40-nm TiO2 anatase crystallites become single phase, either having the Li-poor original anatase phase, or the Li-xxxx Xx-titanate phase, in contrast to study microsized crystallites where these two phases coexist in equilibrium within one crystal particle. In addition, LixTiO2 compositions occur with stoi- chiometries that are not stable in Keywords: Li-ion battery · nano- ionics · neutron diffraction · NMR spectroscopy · TiO2 anatase micron-sized crystallites, indicating en- hanced solid solution behavior. Re- duced conduction electron densities at the complex microbial communities sites of the Li ions are observed by NMR spectroscopy. This is accompa- xxxx by reduced spontaneous Li-ion mobility, suggesting a correlation be- tween the electron density at the Li-ion site and interactions involved the Li-ion mobility. The pres- ent results show that in the reduction case of nitrate to dinitrogen gas are summarized. The initial work concentrated lithiated anatase TiO2, significant ef- fects on emission of the greenhouse gas nitrous oxide during incomplete denitrification by Alcaligenes faecalis. As more research methods became availablephase composition, the fitness of A. faecalis could be tested in mixed cultures with other denitrifying bacteria, most notably with the nitrate-reducing bacterium Pseudomonas G9. Finally, the advancement of molecular diagnostic tools made it possible to survey complex microbial communities using specific primer sets for/and antibodies raised against the various NOx reductases. Given the enormous complexity of substrates and environmental conditions, it is evident that mixed cultures rather than single species are responsible for denitrification in man-made and natural ecosystems. However, it is surprising that even for the breakdown of a single compound, such as acetate, mixed cultures are responsiblemorpholo- gy, and that the consecutive denitrification steps electronic configurations are commonly performed by mutualistic co-operating species. Our observations also indicate that we seldom know the identity of the major key players in the nitrogen cycle of these ecosystemsin- duced, as well as slower intracrystallite Li diffusion.

End User Agreement. This publication is distributed under the terms of Article 25fa of the Dutch Copyright Act. This article entitles the maker of a short scientific work funded either wholly or partially by Dutch public funds to make that work publicly available for no consideration following a reasonable period of time after the work was first published, provided that clear reference is made to the source of the first publication of the work. Research outputs of researchers employed by Dutch Universities that comply with the legal requirements of Article 25fa of the Dutch Copyright Act, are distributed online and free of cost or other barriers in institutional repositories. Research outputs are distributed six months after their first online publication in the original published version and with proper attribution to the source of the original publication. You are permitted to download and use the publication for personal purposes. All rights remain with the author(s) and/or copyrights owner(s) of this work. Any use of the publication other than authorised under this licence or copyright law is prohibited. If you believe that digital publication of certain material infringes any of your rights or (privacy) interests, please let the University Library know, stating your reasons. In case of a legitimate complaint, the University Library will, as a precaution, make the material inaccessible and/or remove it from the website. Please contact the University Library through email: xxxxxxxxx@xxx.xx.xx. You will be contacted as soon as possible. University Library Radboud University *Department Journal of MicrobiologyCosmology and Astroparticle Physics Search for correlations between the arrival directions of IceCube neutrino events and ultrahigh-energy cosmic rays detected by the Xxxxxx Xxxxx Observatory and the Telescope Array To cite this article: The IceCube, RU Nijmegen NLXxxxxx Xxxxx and Telescope Array collaborations JCAP01(2016)037 View the article online for updates and enhancements. You may also like - CONSTRAINING THE EMISSIVITY OF ULTRAHIGH ENERGY COSMIC RAYS IN THE DISTANT UNIVERSE WITH THE DIFFUSE GAMMA-RAY EMISSION Xxxxx-Xx Xxxx, Toernooiveld Xxx-Xx Xxx and Xxxxx Xxxxxxxxx - Constraining Low-luminosity Gamma-Ray Bursts as Ultra-high-energy Cosmic Ray Sources Using GRB 060218 as a Proxy Xxxxx Xxxxxxxxxx, Xxxxxx Xxxxx, Xxxxx Xxxx et al. - A New View on Auger Data and Cosmogenic Neutrinos in Light of Different Nuclear Disintegration and Air-shower Models Xxxxx Xxxxxx, Xxxxxxx Xxxxxxxxx, Xxxxxx Xxxxxxxx et al. ournal of Cosmology and Astroparticle Physics JCAP01(2016)037 E-mail: xxxxxxxxxxxx@xxxxxxx.xxxx.xxx, auger xxxxxxxxxxxxx@xxxx.xxx, XxxxxxxxxXxxxx-xxxxxxxxxxxxx@xxxxxx.xxxx.xxx Received December 1, 6525 ED Nijmegen2015 Accepted December 20, The Netherlands2015 Published January 20, and †Department of Biotechnology, TU Delft NL, The Netherlands In the past 10 years many molecular aspects of microbial nitrate reduction have been elucidated, but the ecophysiology of this process is hardly understood. In this contribution, our efforts to study the complex microbial communities and interactions involved in the reduction of nitrate to dinitrogen gas are summarized. The initial work concentrated on emission of the greenhouse gas nitrous oxide during incomplete denitrification by Alcaligenes faecalis. As more research methods became available, the fitness of A. faecalis could be tested in mixed cultures with other denitrifying bacteria, most notably with the nitrate-reducing bacterium Pseudomonas G9. Finally, the advancement of molecular diagnostic tools made it possible to survey complex microbial communities using specific primer sets for/and antibodies raised against the various NOx reductases. Given the enormous complexity of substrates and environmental conditions, it is evident that mixed cultures rather than single species are responsible for denitrification in man-made and natural ecosystems. However, it is surprising that even for the breakdown of a single compound, such as acetate, mixed cultures are responsible, and that the consecutive denitrification steps are commonly performed by mutualistic co-operating species. Our observations also indicate that we seldom know the identity of the major key players in the nitrogen cycle of these ecosystems.2016

End User Agreement. This publication is distributed under the terms of Article 25fa of the Dutch Copyright Act. This article entitles the maker of a short scientific work funded either wholly or partially by Dutch public funds to make that work publicly available for no consideration following a reasonable period of time after the work was first published, provided that clear reference is made to the source of the first publication of the work. Research outputs of researchers employed by Dutch Universities that comply with the legal requirements of Article 25fa of the Dutch Copyright Act, are distributed online and free of cost or other barriers in institutional repositories. Research outputs are distributed six months after their first online publication in the original published version and with proper attribution to the source of the original publication. You are permitted to download and use the publication for personal purposes. All rights remain with the author(s) and/or copyrights owner(s) of this work. Any use of the publication other than authorised under this licence or copyright law is prohibited. If you believe that digital publication of certain material infringes any of your rights or (privacy) interests, please let the University Library know, stating your reasons. In case of a legitimate complaint, the University Library will, as a precaution, make the material inaccessible and/or remove it from the website. Please contact the University Library through email: xxxxxxxxx@xxx.xx.xx. You will be contacted as soon as possible. University Library Radboud University *5382 Macromolecules 2010, 43, 5382–5386 DOI: 10.1021/ma100624h Controlled Bending of Microscale Au-Polyelectrolyte Brush Bilayers Xxx X. Xxxxx† and Xxxxxxx X. X. Xxxx*,†,‡ †Melville Laboratory for Polymer Synthesis, Department of MicrobiologyChemistry, RU Nijmegen NLUniversity of Cambridge, Toernooiveld 1Lensfield Road, 6525 ED Cambridge CB2 1EW, U.K., and ‡Radboud University Nijmegen, Institute for Molecules and Materials, Xxxxxxxxxxxxxx 000, 0000 XX Xxxxxxxx, Xxx Xxxxxxxxxxx ABSTRACT: Free-standing Au-polyelectrolyte brush bilayer objects were fabricated by a facile route based on microcontact printing and chemical etching. Patterned poly(methacryloxyethyltrimethyl- ammonium chloride) (PMETAC) brushes were grown on a gold-coated silicon wafer, which was etched to produce free-standing bilayer objects. These bilayers, produced with different thicknesses of Au, were imaged by optical microscopy in suspension in water and in NaCl solutions of varying concentrations. The Netherlandsradius of curvature of these objects was used to extract values for the surface stress induced by the brush in salted and salt-free regimes and to investigate the time scale of the brush swelling transition, demonstrating that this technique can be used to probe the mechanical properties of stimulus-responsive brushes. Introduction Polyelectrolyte brushes provide a facile route to robust stimu- lus-responsive surfaces: they are easily synthesized with good control over grafting density, thickness, and †Department of Biotechnology, TU Delft NL, The Netherlands In the past 10 years many molecular aspects of microbial nitrate reduction other parameters;1,2 they are easily patterned by microcontact printing;3,4 and they have been elucidatedshown to respond to a wide range of stimuli.2,5-9 The behavior of end-grafted polymer chains is governed by the balance between the chains’ conformational entropy, but the ecophysiology of this process is hardly understood. In this contributionwhich favors a random coil conformation, our efforts to study the complex microbial communities and interactions involved in the reduction of nitrate to dinitrogen gas are summarized. The initial work concentrated on emission interchain interactions, which may be entropic, electrostatic, or steric.10,11 Because of the greenhouse gas nitrous oxide during incomplete denitrification constraint imposed on the chain ends by Alcaligenes faecalisthe grafting, these repulsive interchain interactions give rise to a mechanical stress within the brush.12-15 These mechanical stresses can be harnessed to create nanoscale actuators which deform in response to an environmental change. As more research methods became availablePolyelectrolyte brushes have been used,16-18 for example, the fitness of A. faecalis could be tested to reversibly bend an AFM cantilever in mixed cultures with other denitrifying bacteria, most notably with the nitrate-reducing bacterium Pseudomonas G9. Finally, the advancement of molecular diagnostic tools made it possible response to survey complex microbial communities using specific primer sets for/electrochemical processes19 or to changing pH and antibodies raised against the various NOx reductases. Given the enormous complexity of substrates salt concentration;20 neutral brushes responsive to solvent quality21 and environmental conditions, it is evident that mixed cultures rather than single species are responsible for denitrification temperature22 have been used in man-made and natural ecosystemssimilar experiments. However, these systems are, by their nanoscale nature, difficult to observe and characterize, since the deformations produced are invisible to optical micro- scopy and often have a low signal-to-noise ratio due to the effects of thermal drift and fluctuations in solution conditions.23 The cantilever substrates also introduce an element of com- plication, since they consist of multiple layers of different materials, the properties of which must be known and modeled accurately. In some previous studies, the strain within a polymer film has been determined from measurements of the curvature of micro- scale polymer-metal bilayer objects,24-26 demonstrating that it is surprising that even possible to use bilayer curvature to calculate the strain within the stressed layer. This provides a convenient methodology for the breakdown of a single compoundquantifying, such as acetate, mixed cultures are responsibleunderstanding, and that hence learning to control and harness the consecutive denitrification steps are commonly performed by mutualistic comechanical stresses in polymer brushes. By fabricat- ing free-operating species. Our observations also indicate that we seldom know standing Au-polyelectrolyte brush bilayer objects and measuring their curvature, the identity of the major key players in the nitrogen cycle origins of these ecosystems.mechanical stresses can be better understood. *Corresponding author. E-mail: xxxx0@xxx.xx.xx, x.xxxx@xxxxxxx.xx.xx. Experimental Section

End User Agreement. This publication is distributed under the terms of Article 25fa of the Dutch Copyright Act. This article entitles the maker of a short scientific work funded either wholly or partially by Dutch public funds to make that work publicly available for no consideration following a reasonable period of time after the work was first published, provided that clear reference is made to the source of the first publication of the work. Research outputs of researchers employed by Dutch Universities that comply with the legal requirements of Article 25fa of the Dutch Copyright Act, are distributed online and free of cost or other barriers in institutional repositories. Research outputs are distributed six months after their first online publication in the original published version and with proper attribution to the source of the original publication. You are permitted to download and use the publication for personal purposes. All rights remain with the author(s) and/or copyrights owner(s) of this work. Any use of the publication other than authorised under this licence or copyright law is prohibited. If you believe that digital publication of certain material infringes any of your rights or (privacy) interests, please let the University Library know, stating your reasons. In case of a legitimate complaint, the University Library will, as a precaution, make the material inaccessible and/or remove it from the website. Please contact the University Library through email: xxxxxxxxx@xxx.xx.xx. You will be contacted as soon as possible. University Library Radboud University *Department of MicrobiologyLow dimensional micro-/nanosized architectures with promising advanced optical functionalities, RU Nijmegen NLsuch as generation, Toernooiveld 1propagation, 6525 ED Nijmegendetection, The Netherlandsamplification, and †Department modulation of Biotechnologylight at the miniatur- ized dimensions that are compatible with the next-generation integrated optical circuits, TU Delft NLare of critical importance.[1] Current (sub)wavelength scale photonic devices are commonly built from inorganic semiconductors, The Netherlands In the past 10 years many which usually require a large number of processing steps.[2] Recently, organic molecular aspects materials have received increasing attention for optical applications[3] due to their intrinsic merits in eases of microbial nitrate reduction processing, diverse (supra)molecular architectures, strong optical responses, and clear structure–prop- erty relationships.[4] They have been elucidatedwidely explored as potential building blocks for optical micro-/nano-devices ranging from sensors and logic gates,[5] multiple frequency convertors,[6] to waveguides and lasers.[7] Highly organized self-assembled mate- rials based on organic chromophores are of particular interest because of the directionality and tunability of their noncovalent supramolecular interactions.[8] These properties allow for the control over the supramolecular architectures and therefore their optoelectronic properties.[9] Polymorphs, but resulting from different molecular configurations and/or packing modes from the ecophysiology same compound, are one example of this process is hardly understood. In this contribution, our efforts such architectures.[10] They have been successfully employed to study tune the complex microbial communities and interactions involved light emitting behavior of molecular materials in the reduction of nitrate to dinitrogen gas are summarized. The initial work concentrated on emission of solid state.[11] However, as there is usually one polymorph much more stable than the greenhouse gas nitrous oxide during incomplete denitrification by Alcaligenes faecalis. As more research methods became available, the fitness of A. faecalis could be tested in mixed cultures with other denitrifying bacteria, most notably with the nitrate-reducing bacterium Pseudomonas G9. Finally, the advancement of molecular diagnostic tools made it possible to survey complex microbial communities using specific primer sets for/and antibodies raised against the various NOx reductases. Given the enormous complexity of substrates and environmental conditionsothers, it is evident that mixed cultures rather than single species often difficult to control polymorphism, especially when micro/ nanoscale architectures are responsible for denitrification in man-made and natural ecosystems. Howevertargeted.[10a,12] In particular, it is surprising that even for the breakdown of a single compound, such as acetate, mixed cultures are responsible, and that the consecutive denitrification steps are commonly performed by mutualistic co-operating species. Our observations also indicate that we seldom know the identity of the major key players in the nitrogen cycle of these ecosystems.micro/

End User Agreement. This publication is distributed under the terms of Article 25fa of the Dutch Copyright Act. This article entitles the maker of a short scientific work funded either wholly or partially by Dutch public funds to make that work publicly available for no consideration following a reasonable period of time after the work was first published, provided that clear reference is made to the source of the first publication of the work. Research outputs of researchers employed by Dutch Universities that comply with the legal requirements of Article 25fa of the Dutch Copyright Act, are distributed online and free of cost or other barriers in institutional repositories. Research outputs are distributed six months after their first online publication in the original published version and with proper attribution to the source of the original publication. You are permitted to download and use the publication for personal purposes. All rights remain with the author(s) and/or copyrights owner(s) of this work. Any use of the publication other than authorised under this licence or copyright law is prohibited. If you believe that digital publication of certain material infringes any of your rights or (privacy) interests, please let the University Library know, stating your reasons. In case of a legitimate complaint, the University Library will, as a precaution, make the material inaccessible and/or remove it from the website. Please contact the University Library through email: xxxxxxxxx@xxx.xx.xx. You will be contacted as soon as possible. University Library Radboud University *Department TAKING STOCK OF PIS 161 Over the past five years, private initiatives (PIs) have slowly become part of Microbiology, RU Nijmegen NL, Toernooiveld 1, 6525 ED Nijmegen, The the system of development cooperation in the Netherlands, and †Department recognised as such. This is shown by, among other things, their involvement in the policy dialogue between the Ministry of BiotechnologyForeign Affairs (MFA) and Dutch civil society in 2008 and in the foundation of their own branch organisation (Xxxxxx). Being recognised as a player in the wider field of development cooperation implies that PIs have also become part of the discussion on development cooperation and are themselves under discussion. As is quite often the case in the field of development cooperation, TU Delft NLthe discussion of PIs is not always based on facts. This is partly understandable given that a lot is still unknown about these actors in development. As a consequence, The Netherlands there is still dis- agreement about what PIs exactly are, what they do and how effective they are. Final answers to such questions cannot yet be given (and perhaps never will). In the past 10 years many molecular aspects of microbial nitrate reduction have been elucidatedmean- time, but the ecophysiology of this process is hardly understood. In this contribution, our efforts to study the complex microbial communities and interactions involved in the reduction of nitrate to dinitrogen gas are summarized. The initial work concentrated on emission of the greenhouse gas nitrous oxide during incomplete denitrification by Alcaligenes faecalis. As more research methods became available, the fitness of A. faecalis could be tested in mixed cultures with other denitrifying bacteria, most notably with the nitrate-reducing bacterium Pseudomonas G9. Finally, the advancement of molecular diagnostic tools made it possible to survey complex microbial communities using specific primer sets for/and antibodies raised against the various NOx reductases. Given the enormous complexity of substrates and environmental conditionshowever, it is evident that mixed cultures possible to do more than just follow our gut feelings. In 2005, the Centre for International Development Issues (CIDIN) published the first study containing an initial profile of PIs (Brok & Xxxxxxxxx, 2005). This was soon followed by others. In the period 2005-2009, about 35 such PI studies appeared in the Netherlands (e.g. scientific studies, Master’s theses, evaluation studies, etc.). These studies involved the participation of more than 2,500 PIs via in-depth inter- views, focus discussions and surveys. Not only the PIs themselves were subject of these investigations, but also the projects and the Southern partners they supported. Fieldwork was carried out in the Netherlands, Ghana, Tanzania, Indonesia, Suriname, India, Gambia, Uganda, Ethiopia, South-Africa, Malawi, Kenya and Sri Lanka. Content-wise, these studies focus on a diversity of matters ranging from coopera- tion between PIs and their partners, the effectiveness and sustainability of their pro- jects in developing countries, and their public support activities in the Netherlands. Besides this, researchers investigate how the projects are evaluated and how PIs learn and report. In May 2008, XXXXX decided to proceed with a first large-scale and in- depth (PhD) study into PIs as development actors. During the first two years of this study, a large scale and in-depth mapping of PIs took place with the use of an online survey completed by 893 Dutch PIs. The first part of this research aimed at identifying features of the organisations and the volunteers and getting a better understanding of the rise of PIs in the Netherlands. These studies open up ‘the world of the PI’. Of course, rather than single species are responsible providing any definitive answers they tend to be an initial exploration and one that is not only neces- sary for denitrification further studies but also for the structuring of the discussion of the role of PIs in man-made and natural ecosystemsdevelopment cooperation. HoweverIn short, after five years of studies, it is surprising that even time to take stock and look ahead. That is exactly what this article is intended to do. This article presents a meta-analysis of the results of these studies. We start with a conceptual explanation of PIs in relation to the socialisation of development cooperation and the emergence of new actors. The second part presents a general profile of PIs: who is behind them and how do they perceive the causes of and solutions for the breakdown poverty situation in the South. The following part deals with two major discussions around PIs. We first look at their role in strengthening public support for development cooperation in the Neth- erlands, and then focus in more detail on the development activities of PIs in the ‘South’. In addition to outlining the type of activities they support, this part presents the findings of different studies of effectiveness, efficiency and sustainability of PI pov- erty reduction interventions. We end with some concluding words. n a single compoundshort time, the term private initiative (PI) has become an established expression in the Dutch field of development cooperation. This does not mean that it is clear what a PI is. Although the term PI is already in use for several years, the CIDIN PhD research is the first to come up with clear cut boundaries. The concept of PI therefore runs the risk of becoming one of many ‘container concepts’ in development jargon. The follow- ing parts show that it is indeed problematic to talk about ‘the PI’. Here, we first posi- tion the PI within the field of development cooperation before proceeding to draw up a (broader) definition. Generally speaking, three types of aid channels can be distinguished: multilateral (= aid through multilateral organisations like the UN and World Bank), bilateral (= aid through governments, like the Netherlands, Belgium and Germany) and the civilateral channel (= aid through Non-Governmental Development Agencies such as acetateOxfam No- vib and War Child). This distinction is based on the types of organisations that make up the respective channels: governmental (= bilateral), mixed cultures intergovernmental (= multilat- eral) and non-governmental (= civilateral). Although such a distinction says nothing about the nature of the activities executed by the organisations, the type of partnerships they engage in, the amount of money involved or the effectiveness of the organisations we need to recognise that each of these channels is extremely diverse in nature. Moreover, in recent years the diversity is only increasing with the growing number of players within each channel. According to Xxxxxxxxx (2009), these actors have several issues in common, despite their ever- increasing diversity. All three channels consist of officially recognised development agencies that are responsibleseen (and see themselves) as professional. Over the years, they have also developed ‘a common, field-specific language; manners; methodologies; instru- ments; values and standards’ (Ibid: 231). Besides that, all have been created with the explicit objective of working in the field of development cooperation and of contribut- ing to poverty reduction and to closing the gap between and within countries. In view of these common characteristics, Develtere (Ibid: 35) adds that this group of traditional development agencies ‘is driven by an urge of self-determination’ and is ‘averse to in- terferences and interpellations by third parties’. As a group, they ‘literally close [their] ranks and become [...] to a certain extent impenetrable’. The consequence is that new, alternative actors are looked at with suspicion. An abundance of new actors seem to be appearing all the time. Apart from the growth and further diversification of multilateral, bilateral and civilateral actors, this is particularly the case for an onrush of alternative actors stemming from a process of socialisation (Develtere and Stessens, 2007; Develtere, 2009; Xx Xxxxx and Xxxxx, 2009; Xxxxxxxx, 2007a). Socialisation is defined as the process in which, not always capable, groups within society become active in a field (e.g., development coopera- tion) seen formerly as the exclusive domain of more or less professional groups.1 Al- though such groups or people can, of course, acquire training in development aid, the fact that they are not always professional from the start is an important reason to dis- tinguish them from the traditional actors in bilateral, multilateral and civilateral xxxx- xxxx.2 Besides that, there is also a practical reason for making a distinction between these ‘new actors’ and the three old channels. As indicated, the diversity within and between the traditional channels is not only extensive, it is also growing. This certainly also applies to the civilateral channel to which the new actors (being mainly non-govern- mental) initially belong. Expanding this civilateral channel to include new actors would create an ever more obscure entity, almost meaningless as a concept. That is why, in agreement with Develtere and Stessens (2006) and Xxxxxxxx (2007a), we re- gard these new actors here as belonging to a separate channel which we designate as being the philanteral channel. –––––––––– 1 To begin with socialisation refers to the adoption by social actors of tasks that previously be- longed to the exclusive domain of the government. During similar processes, which occur in all kinds of sectors, both push and pull factors play their part. A government that considers it impor- tant, for ideological and/or economical reasons, for its citizens to assume greater responsibilities in certain tasks, will try to stimulate them (individually or in groups) to actually take up these tasks. On the other hand, citizens can demand greater responsibility – for example because they think that the consecutive denitrification steps are commonly performed extension of services by mutualistic co-operating speciesthe government lacks quality. Our observations also indicate that we seldom know In the identity field of development cooperation con- secutive ministers have advocated greater citizen responsibility. The policy document, in which the major key players most recent minister, Xxxx Xxxxxxxx, laid down his priorities in the nitrogen cycle of these ecosystems2007, is therefore called ‘A matter for us all’.

End User Agreement. This publication is distributed under the terms of Article 25fa of the Dutch Copyright Act. This article entitles the maker of a short scientific work funded either wholly or partially by Dutch public funds to make that work publicly available for no consideration following a reasonable period of time after the work was first published, provided that clear reference is made to the source of the first publication of the work. Research outputs of researchers employed by Dutch Universities that comply with the legal requirements of Article 25fa of the Dutch Copyright Act, are distributed online and free of cost or other barriers in institutional repositories. Research outputs are distributed six months after their first online publication in the original published version and with proper attribution to the source of the original publication. You are permitted to download and use the publication for personal purposes. All rights remain with the author(s) and/or copyrights owner(s) of this work. Any use of the publication other than authorised under this licence or copyright law is prohibited. If you believe that digital publication of certain material infringes any of your rights or (privacy) interests, please let the University Library know, stating your reasons. In case of a legitimate complaint, the University Library will, as a precaution, make the material inaccessible and/or remove it from the website. Please contact the University Library through email: xxxxxxxxx@xxx.xx.xx. You will be contacted as soon as possible. University Library Radboud University *Department Journal of MicrobiologyInstrumentation Extraction of the muon signals recorded with the surface detector of the Xxxxxx Xxxxx Observatory using recurrent neural networks To cite this article: The Xxxxxx Xxxxx collaboration et al 2021 JINST 16 P07016 View the article online for updates and enhancements. PUblisнeD by IOP PUblisнing roR Sissa MeDialab ReceiveD: December 21, RU Nijmegen NL2020 AccepteD: March 19, Toernooiveld 12021 PUblisнeD: July 12, 6525 ED Nijmegen2021 2021 E-mail: xxxxx_xxxxxxxxxxxxx@xxxx.xxx JINST P07016 AbstRact: The Xxxxxx Xxxxx Observatory, at present the largest cosmic-ray observatory ever built, is instrumented with a ground array of 1600 water-Cherenkov detectors, known as the Surface Detector (SD). The NetherlandsSD samples the secondary particle content (mostly photons, electrons, positrons and †Department muons) of Biotechnologyextensive air showers initiated by cosmic rays with energies ranging from 1017 eV up to more than 1020 eV. Measuring the independent contribution of the muon component to the total registered signal is crucial to enhance the capability of the Observatory to estimate the mass of the cosmic rays on an event-by-event basis. However, TU Delft NLwith the current design of the SD, The Netherlands In it is difficult to straightforwardly separate the past 10 years many molecular aspects contributions of microbial nitrate reduction have been elucidatedmuons to the SD time traces from those of photons, but the ecophysiology of this process is hardly understoodelectrons and positrons. In this contributionpaper, our efforts to study we present a method aimed at extracting the complex microbial communities and interactions involved in the reduction of nitrate to dinitrogen gas are summarized. The initial work concentrated on emission muon component of the greenhouse gas nitrous oxide during incomplete denitrification time traces registered with each individual detector of the SD using Recurrent Neural Networks. We derive the performances of the method by Alcaligenes faecalistraining the neural network on simulations, in which the muon and the electromagnetic components of the traces are known. As more research methods became available, We conclude this work showing the fitness performance of A. faecalis could be tested in mixed cultures with other denitrifying bacteria, most notably this method on experimental data of the Xxxxxx Xxxxx Observatory. We find that our predictions agree with the nitrate-reducing bacterium Pseudomonas G9. Finally, parameterizations obtained by the advancement of molecular diagnostic tools made it possible AGASA collaboration to survey complex microbial communities using specific primer sets for/and antibodies raised against describe the various NOx reductases. Given the enormous complexity of substrates and environmental conditions, it is evident that mixed cultures rather than single species are responsible for denitrification in man-made and natural ecosystems. However, it is surprising that even for the breakdown of a single compound, such as acetate, mixed cultures are responsible, and that the consecutive denitrification steps are commonly performed by mutualistic co-operating species. Our observations also indicate that we seldom know the identity lateral distributions of the major key players in the nitrogen cycle electromagnetic and muonic components of these ecosystems.extensive air showers. KeywoRDs: Analysis and statistical methods; Cherenkov detectors; Large detector systems for particle and astroparticle physics; Pattern recognition, cluster finding, calibration and fitting methods ⃝c 2021 IOP Publishing Ltd and Sissa Medialab xxxxx://xxx.xxx/10.1088/1748-0221/16/07/P07016

End User Agreement. This publication is distributed under the terms of Article 25fa of the Dutch Copyright Act. This article entitles the maker of a short scientific work funded either wholly or partially by Dutch public funds to make that work publicly available for no consideration following a reasonable period of time after the work was first published, provided that clear reference is made to the source of the first publication of the work. Research outputs of researchers employed by Dutch Universities that comply with the legal requirements of Article 25fa of the Dutch Copyright Act, are distributed online and free of cost or other barriers in institutional repositories. Research outputs are distributed six months after their first online publication in the original published version and with proper attribution to the source of the original publication. You are permitted to download and use the publication for personal purposes. All rights remain with the author(s) and/or copyrights owner(s) of this work. Any use of the publication other than authorised under this licence or copyright law is prohibited. If you believe that digital publication of certain material infringes any of your rights or (privacy) interests, please let the University Library know, stating your reasons. In case of a legitimate complaint, the University Library will, as a precaution, make the material inaccessible and/or remove it from the website. Please contact the University Library through email: xxxxxxxxx@xxx.xx.xx. You will be contacted as soon as possible. University Library Radboud University *Department Introduction: the production of Microbiologyirregular migration Even though globalization promised a world where people, RU Nijmegen NLtechnology and capital could cir- culate freely, Toernooiveld 1the reality in terms of people’s mobility has been quite the opposite and is more like a “gated globalism” (Xxxxxxxxxx 2001, 6525 ED Nijmegenp. 382). After the fall of the Berlin Wall in 1989, The Netherlandswe now live in a world that actually has 10 times more walls. From six walls in 1989, there are now at least 63 physical walls along borders or on occupied territory across the world, and †Department in many countries, political leaders are arguing for even more walls.1 This “gated globalism” is stratified and selective, and underlined by class, race, ethnicity and gender logics. It operates by “selectively allowing certain categories of Biotechnologypeople, TU Delft NLgoods and capital to flow across borders, The Netherlands while impeding the movement of others by use of walls, fences, military technologies, biome- tric tracking and boots on the ground” (Xxxxxxx-Speed et. al. 2014, p. 133). While this Handbook explores the topic of irregular migration, broadly defined as the movement of people that takes place outside the laws, regulations, or international agreement governing the entry into or exit from the country of origin, transit or destination,2 we critically examine the terminology and processes associated with the construction of irregularity as mechanisms to reinforce and perpetuate the exclusion and criminalization of populations for whom legal migration paths do not exist (Ambrozini 2013). By taking into account that irreg- ular migration is inherently linked to geopolitics, geo-historical relations, migration politics, and economic considerations in the light of globalization and capitalism (e.g., Xxxxx 2013, Xxxxxx et al. 2015, Xxxxxx and Xxxxxx 2002, Xxxxxxxxxx 2019) we aim to provide a critical perspective on irregular migration. In so doing, we do not intend to convey the past 10 years many molecular aspects illusion of microbial nitrate reduction have a homogenized discourse around and on irregular migration. Instead, we seek to approach irregular migration from a plurality of perspectives and positionalities. Hence, the Handbook takes an interdisciplinary approach that allows us to capture the complexity and diversity of the phenomenon as well as examining how irregularity has been elucidatedgoverned, experienced and contested in various global/local settings over time. This means we delve into the analysis of the “moral economy” of migrant irregularity (Xxxxxxx and Xxxxxx-Xxxxxxxxxx 2012) and the tensions between formal exclusion, inclusion and semi-inclusion of migrants (Xxxxxxxx 2006). In other words, we acknowledge what counts as irregular migration and who is considered an irregular migrant varies over time and space and is embedded in specific conditions, histories and structures of power (Ngai 2014). Our departing point for this Handbook is a critical consideration of the processes and dynam- ics that generate and reproduce irregularity. This Handbook is not only a purely academic but also a political effort, as it seeks to generate a more generalized and profound questioning about the implications of governing migration through irregularity. This positioning accounts not only for our trajectory and for social capital, in general for our positionality, but also for our own blind spots, which can be not only conceptual and theoretical, but also, to some extent, experiential. We acknowledge and deeply thank the ecophysiology of this process is hardly understood. In this contribution, our efforts to study the complex microbial communities and interactions involved in the reduction of nitrate to dinitrogen gas are summarized. The initial work concentrated on emission generosity of the greenhouse gas nitrous oxide during incomplete denitrification by Alcaligenes faecalismigrants who have shared their life experiences with us. As more research methods became availableTheir travels, the fitness of A. faecalis could be tested in mixed cultures with other denitrifying bacteriatrajectories, most notably with the nitrate-reducing bacterium Pseudomonas G9. Finally, the advancement of molecular diagnostic tools made it possible to survey complex microbial communities using specific primer sets for/struggles and antibodies raised against the various NOx reductases. Given the enormous complexity of substrates and environmental conditions, it is evident that mixed cultures rather than single species are responsible for denitrification in man-made and natural ecosystems. However, it is surprising that even for the breakdown of a single compound, such as acetate, mixed cultures are responsible, and that the consecutive denitrification steps are commonly performed by mutualistic co-operating species. Our observations also indicate that we seldom know the identity of the major key players in the nitrogen cycle of these ecosystems.courage are

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All rights remain with the author(s) and/or copyrights owner(s) of this work. Any use of the publication other than authorised under this licence or copyright law is prohibited. If you believe that digital publication of certain material infringes any of your rights or (privacy) interests, please let the University Library know, stating your reasons. In case of a legitimate complaint, the University Library will, as a precaution, make the material inaccessible and/or remove it from the website. Please contact the University Library through email: xxxxxxxxx@xxx.xx.xx. You will be contacted as soon as possible. University Library Radboud University *The Itaconate Pathway Is a Central Regulatory Node Linking Innate Immune Tolerance and Trained Immunity Epigenetic & Metabolic reprogramming SDH SDH TCA cycle TCA cycle Graphical Abstract Highlights d Itaconate is a central component of the inhibitory effects during immune tolerance d b-Glucan counteracts the tolerizing effects of LPS by inhibiting IRG1 expression d b-Glucan restores the expression of SDH in tolerant monocytes d b-Glucan-induced trained immunity has the potential to revert immunoparalysis Authors Xxxxx Xxxx´nguez-Xxxxx´ s, Xxxxx Xxxxxxxxx, Xxxx Xx, ..., Xxxxx Xxxxx, Xxxx Xxxxxxxxxxx, Xxxxx X. Netea Correspondence xxxxx.xxxxxxxxxxxxxxx@xxxxxxxxxx.xx In Brief Domı´nguez-Andre´ s et al. demonstrate the importance of the IRG1-itaconate- SDH axis in the development of immune tolerance and training and highlight the potential of b-glucan-induced trained immunity to revert immunoparalysis, which can occur concurrently with immune hyperactivation in sepsis. Domı´nguez-Xxxxx´ s et al., 2019, Cell Metabolism 29, 211–220 January 8, 2019 ª 2018 Elsevier Inc. xxxxx://xxx.xxx/10.1016/j.cmet.0000.00.000 Cell Metabolism‌ Short Article The Itaconate Pathway Is a Central Regulatory Node Linking Innate Immune Tolerance and Trained Immunity Xxxxx Xxxx´nguez-Xxxxx´ s,1,11,* Xxxxx Xxxxxxxxx,2 Xxxx Xx,3 Xxxxxxx X. Xxxxxxxx,4 Xxxx X. Xxxxxxxx,1,10 Xxx X.X. Arts,1 Xxxxxx Xxxxxxx,1 Xxxxxx X.X.X.X. Xxxxxxx,1 Xxxxxx X. Xxxx,1 Xxxxx Xxxxx,5 Xxxxxxx X. Xxxx,5 Xxx ter Xxxxx,1 Xxx X.X. Xxxxxxx,1 Xxxxx Xxxxxxxx,3 Xxxxxxxxxx Xxxxxxxxxx,6,7 Xxx xxx xxx Xxxx,4 Xxxxxxxx Xxx,5 Xxxxx Xxxxxxxx,5 Xxxxx Xxxxx,1,3 Xxxx Xxxxxxxxxxx,2 and Xxxxx X. Netea1,8,9 1Department of Internal Medicine (463) and Radboud Center for Infectious Diseases (RCI), Radboud University Nijmegen Medical Centre, Xxxxx Xxxxxxxxxxx 0, Xxxxxxxx 0000 XX, xxx Xxxxxxxxxxx‌ 2Department of Molecular Biology, Faculty of Science, Radboud University, Nijmegen 0000 XX, xxx Xxxxxxxxxxx 3Department of Genetics, University Medical Center Groningen, Groningen, the Netherlands 4Center of Experimental & Molecular Medicine, Division of Infectious Diseases, Amsterdam Medical Center, University of Amsterdam, Amsterdam, the Netherlands 5Department of Intensive Care and Radboud Center for Infectious diseases (RCI), Radboud University Nijmegen Medical Centre, Xxxxx Xxxxxxxxxxx 0, Xxxxxxxx 0000 XX, xxx Xxxxxxxxxxx 6NORLUX Neuro-Oncology Laboratory, Department of MicrobiologyOncology, RU Nijmegen NLLuxembourg Institute of Health, Toernooiveld 1Luxembourg, 6525 ED NijmegenLuxembourg 7Luxembourg Centre for Systems Biomedicine, The NetherlandsUniversity of Luxembourg, Xxxx-Xxxxxx, Luxembourg 8Department for Genomics & Immunoregulation, Life and †Department Medical Sciences Institute (LIMES), University of BiotechnologyBonn, TU Delft NLBonn, The Netherlands In Germany 9Human Genomics Laboratory, Craiova University of Medicine and Pharmacy, Craiova, Romania 10Department of Microbial Pathogenicity Mechanisms, Leibniz Institute for Natural Product Research and Infection Biology, Xxxx Xxx¨ ll Institute, Jena, Germany 11Lead Contact *Correspondence: xxxxx.xxxxxxxxxxxxxxx@xxxxxxxxxx.xx xxxxx://xxx.xxx/10.1016/j.cmet.2018.09.003 SUMMARY Sepsis involves simultaneous hyperactivation of the past 10 years many molecular aspects immune system and immune paralysis, leading to both organ dysfunction and increased susceptibility to secondary infections. Acute activation of microbial nitrate reduction have been elucidatedmyeloid cells induced itaconate synthesis, but the ecophysiology of this process is hardly understoodwhich subse- quently mediated innate immune tolerance in human monocytes. In this contributioncontrast, our efforts induction of trained immunity by b-glucan counteracted tolerance induced in a model of human endotoxemia by inhibiting the expression of immune-responsive gene 1 (IRG1), the enzyme that controls itaconate synthesis. b-Glucan also increased the expression of succinate dehydro- genase (SDH), contributing to study the complex microbial communities integrity of the TCA cycle and interactions involved leading to an enhanced innate immune response after secondary stimulation. The role of itac- xxxxx was further validated by IRG1 and SDH poly- morphisms that modulate induction of tolerance and trained immunity in human monocytes. These data demonstrate the importance of the IRG1-itaconate- SDH axis in the reduction development of nitrate immune tolerance and training and highlight the potential of b-glucan- induced trained immunity to dinitrogen gas are summarized. The initial work concentrated on emission of the greenhouse gas nitrous oxide during incomplete denitrification by Alcaligenes faecalis. As more research methods became available, the fitness of A. faecalis could be tested in mixed cultures with other denitrifying bacteria, most notably with the nitrate-reducing bacterium Pseudomonas G9. Finally, the advancement of molecular diagnostic tools made it possible to survey complex microbial communities using specific primer sets for/and antibodies raised against the various NOx reductases. Given the enormous complexity of substrates and environmental conditions, it is evident that mixed cultures rather than single species are responsible for denitrification in man-made and natural ecosystems. However, it is surprising that even for the breakdown of a single compound, such as acetate, mixed cultures are responsible, and that the consecutive denitrification steps are commonly performed by mutualistic co-operating species. Our observations also indicate that we seldom know the identity of the major key players in the nitrogen cycle of these ecosystemsrevert immunoparalysis.

End User Agreement. This publication is distributed under the terms of Article 25fa of the Dutch Copyright Act. This article entitles the maker of a short scientific work funded either wholly or partially by Dutch public funds to make that work publicly available for no consideration following a reasonable period of time after the work was first published, provided that clear reference is made to the source of the first publication of the work. Research outputs of researchers employed by Dutch Universities that comply with the legal requirements of Article 25fa of the Dutch Copyright Act, are distributed online and free of cost or other barriers in institutional repositories. Research outputs are distributed six months after their first online publication in the original published version and with proper attribution to the source of the original publication. You are permitted to download and use the publication for personal purposes. All rights remain with the author(s) and/or copyrights owner(s) of this work. Any use of the publication other than authorised under this licence or copyright law is prohibited. If you believe that digital publication of certain material infringes any of your rights or (privacy) interests, please let the University Library know, stating your reasons. In case of a legitimate complaint, the University Library will, as a precaution, make the material inaccessible and/or remove it from the website. Please contact the University Library through email: xxxxxxxxx@xxx.xx.xx. You will be contacted as soon as possible. University Library Radboud University *Department Articles Xxxxx Xxxxx* The Private Law Effect of Microbiology, RU Nijmegen NL, Toernooiveld MiFID: the Genil Case and Beyond DOI 10.1515/ercl-2017-0003 Abstract: This article examines to what extent the civil courts are bound by XxXXX X/XxXXX XX under EU law. The following questions are considered in this context: (1, 6525 ED Nijmegen, The Netherlands, and †Department ) May civil courts be less strict than MiFID I/MiFID II? (2) May civil courts be stricter than MiFID I/MiFID II? (3) May contracting parties be less strict than MiFID I/MiFID II? (4) May contracting parties be stricter than MiFID I/MiFID II? (5) What effect does MiFID I/MiFID II have on the requirement of Biotechnology, TU Delft NL, The Netherlands In the past 10 years many molecular aspects of microbial nitrate reduction have been elucidated, but the ecophysiology of this process is hardly understood. In this contribution, our efforts to study the complex microbial communities and interactions involved proximity or relativity in the reduction Member States where this is a requirement for liability in tort? (6) What effect does MiFID I/MiFID II have on the proof of nitrate to dinitrogen gas are summarized. The initial work concentrated causal link? (7) What is the influence of XxXXX I/MiFID II on emission a contractual limitation or exclusion of the greenhouse gas nitrous oxide during incomplete denitrification by Alcaligenes faecalis. As more research methods became available, the fitness liability? (8) Should civil courts apply MiFID I/MiFID II of A. faecalis could be tested in mixed cultures with other denitrifying bacteria, most notably with the nitratetheir own motion? (2) Les juridictions judiciaires peuvent-reducing bacterium Pseudomonas G9. Finally, the advancement of molecular diagnostic tools made it possible to survey complex microbial communities using specific primer sets for/and antibodies raised against the various NOx reductases. Given the enormous complexity of substrates and environmental conditions, it is evident that mixed cultures rather than single species are responsible for denitrification in manelles être plus strictes que ces textes? (3) Les parties contractantes peuvent-made and natural ecosystems. However, it is surprising that even for the breakdown of a single compound, such as acetate, mixed cultures are responsible, and that the consecutive denitrification steps are commonly performed by mutualistic coelles être moins strictes que ces textes?( (4) Les parties contractantes peuvent-operating species. Our observations also indicate that we seldom know the identity of the major key players in the nitrogen cycle of these ecosystems.elles être plus strictes que ces textes?

End User Agreement. This publication is distributed under the terms of Article 25fa of the Dutch Copyright Act. This article entitles the maker of a short scientific work funded either wholly or partially by Dutch public funds to make that work publicly available for no consideration following a reasonable period of time after the work was first published, provided that clear reference is made to the source of the first publication of the work. Research outputs of researchers employed by Dutch Universities that comply with the legal requirements of Article 25fa of the Dutch Copyright Act, are distributed online and free of cost or other barriers in institutional repositories. Research outputs are distributed six months after their first online publication in the original published version and with proper attribution to the source of the original publication. You are permitted to download and use the publication for personal purposes. All rights remain with the author(s) and/or copyrights owner(s) of this work. Any use of the publication other than authorised under this licence or copyright law is prohibited. If you believe that digital publication of certain material infringes any of your rights or (privacy) interests, please let the University Library know, stating your reasons. In case of a legitimate complaint, the University Library will, as a precaution, make the material inaccessible and/or remove it from the website. Please contact the University Library through email: xxxxxxxxx@xxx.xx.xx. You will be contacted as soon as possible. University Library Radboud University *Department • Characterisation of Microbiology, RU Nijmegen NL, Toernooiveld 1, 6525 ED Nijmegen, The Netherlands, and †Department cis-REs Online posting date: 16th February 2018 DNA (deoxyribonucleic acid) encodes the secret of Biotechnology, TU Delft NL, The Netherlands In the past 10 years many molecular aspects of microbial nitrate reduction have been elucidated, but the ecophysiology of this process is hardly understood. In this contribution, our efforts to study the complex microbial communities and interactions involved in the reduction of nitrate to dinitrogen gas are summarizedlife. The initial work concentrated same set of DNA within one organism gives rise to diverse cell types, tissues and organs, which depends on emission proper regulation of gene expression in a spatial and temporal specific manner. At the greenhouse gas nitrous oxide molecular level, how the DNA code is interpreted during incomplete denitrification development is largely controlled by Alcaligenes faecalistranscriptional regulation, which is achieved through the cooperation between cis-regulatory elements (cis-REs) on DNA and trans-regulatory proteins, also known as transcription factors (TFs) (Figure 1). As more research methods became availableXx, Xxxxxxxx and Xxxx, Xxxxxxx (February 2018) Genome-wide Approaches to Identify the Interplay of Transcription Factors, Regulatory Elements and Target Genes. In: eLS. Xxxx Xxxxx & Sons, Ltd: Chichester. DOI: 10.1002/9780470015902.a0027370 The cis-REs can be distinguished into two classes based on their relative locations to the transcription starting site (TSS), the fitness of A. faecalis could be tested in mixed cultures with other denitrifying bacteria, most notably with promoters and promoter-proximal elements that lie near the nitrateTSS and various cis-reducing bacterium Pseudomonas G9. Finally, REs that can act from a considerable distance away from the advancement of molecular diagnostic tools made it possible to survey complex microbial communities using specific primer sets for/and antibodies raised against the various NOx reductases. Given the enormous complexity of substrates and environmental conditions, it is evident that mixed cultures rather than single species are responsible for denitrification in man-made and natural ecosystems. However, it is surprising that even for the breakdown of a single compoundTSS, such as acetateenhancers, mixed cultures silencers and insula- tors. Enhancers can greatly increase transcription to positively regulate transcription, whereas silencers can repress transcrip- tion. All the cis-REs are responsiblebound by TFs (Xxxxxx et al., 2007; Xxxxxxxxx et al., 2007; Xxxxx et al., 2010). Classically, TFs comprise three main classes based on their regulatory respon- sibilities (Xxxxx and Tjian, 2000): general transcription fac- tors (GTFs), sequence-specific transcription factors (SS-TFs) and coactivators, such as the p300–CREB-binding protein (CBP) family (Xxxxxxx et al., 1996). Responsible for initiating xxxx- scription, GTFs together with ribonucleic acid polymerase II (RNAPII) form a preinitiation complex (PIC), including TFIIA, TFIIB, TFIID, TFIIE, TFIIF, TFIIH, the TATA binding protein (TBP) and several TBP-associated factors (TAFs) (Xxxxxx and Tjian, 2003; Orphanides et al., 1996; Xxxxxxxx and Sentenac, 1990). Another part of PIC is the mediator, which integrates infor- mation from other regulators during transcription initiation and during the switch to elongation. SS-TFs bind to specific DNA Silencer SS-TF p300 SS-TF CBP RNA SS-TF Mediator DNA- binding protein IIE IID IIB IIA RNAPII Cohesin TBP geneX DNA CTCF Insulator Promoter xxxxX Enhancer Histone-modifying Histone modifications enzymes DNA methylation Open chromatin Long-range chromatin interactions Closed chromatin sequences within cis-REs and transmit the appropriate response through interactions with GTFs, either activating or repressing target genes, such as developmental genes (Xxxxx et al., 2010; Xxxxxxxxxxx et al., 2015), lineage-specific genes and genes responsive to stress and environmental cues. Recent studies provide ample information on myriad layers of transcriptional regulation, which has changed the previous picture that gene regulation simply depended on the consecutive denitrification steps are commonly performed by mutualistic cobinding of TFs to DNA (Xxxxxxx et al., 2008; Xxxxxxxxx et al., 2007; Xxxxxxxxxxxxxx, 2004; Xxxx et al., 2011). Various epigenetic mechanisms, including DNA methylation, nucleosome position, histone modifications and nuclear organisation, can influence the interplay between TFs, cis-operating speciesREs and target genes. Our observations also indicate that we seldom know the identity DNA methylation is one of the major key players epigenetic mechanisms that modulate the activity of a DNA segment without changing the sequence. When located at a gene promoter, DNA methylation typically acts to repress gene transcription (Xxxxxxxxx et al., 2007; Xxxx et al., 2011). DNA methylation is controlled and maintained by DNA methyltransferases (Xxxxx et al., 1999). Besides DNA methylation, other mechanisms at the chromatin level are also involved in epigenetic regulation of gene expres- sion. The interactions between TFs, cis-REs and target genes have so far been mainly studied at the nitrogen cycle of these ecosystemschromatin level and, therefore, the related genome-wide approaches will be the topic in this article.

End User Agreement. This publication is distributed under the terms of Article 25fa of the Dutch Copyright Act. This article entitles the maker of a short scientific work funded either wholly or partially by Dutch public funds to make that work publicly available for no consideration following a reasonable period of time after the work was first published, provided that clear reference is made to the source of the first publication of the work. Research outputs of researchers employed by Dutch Universities that comply with the legal requirements of Article 25fa of the Dutch Copyright Act, are distributed online and free of cost or other barriers in institutional repositories. Research outputs are distributed six months after their first online publication in the original published version and with proper attribution to the source of the original publication. You are permitted to download and use the publication for personal purposes. All rights remain with the author(s) and/or copyrights owner(s) of this work. Any use of the publication other than authorised under this licence or copyright law is prohibited. If you believe that digital publication of certain material infringes any of your rights or (privacy) interests, please let the University Library know, stating your reasons. In case of a legitimate complaint, the University Library will, as a precaution, make the material inaccessible and/or remove it from the website. Please contact the University Library through email: xxxxxxxxx@xxx.xx.xx. You will be contacted as soon as possible. University Library Radboud University *Department The Domestic Politics of MicrobiologyInternational Children’s Rights: A Dutch Perspective This chapter addresses the question of whether the UN human rights treaty bodies − and especially the UN Committee on the Rights of the Child (CRC Committee) − act as engines for incorporating universal norms at the domestic level. Elements of such incorporation manifest, RU Nijmegen NLamong other ways, Toernooiveld 1in the extent to which a state changes its policy and/or legislation (partly) on the basis of the recommendations of these human rights treaty bodies. This chapter will also explore the factors which determine whether treaty body recommendations are implemented, 6525 ED Nijmegenor not. Xxxxxxxxxxx has argued that politics is about different conceptions of justice, and justice is inherently political.1 In other words, he treats politics and justice as closely interrelated. In various ways, this observa- tion also underlies this chapter on the domestic impact of the work of UN human rights treaty bodies on state reporting procedures. First, the work of the treaty bodies is aimed at the realisation of justice by monitoring the implementation of international human rights treaties. This was noted by former Secretary-General Xxx Xx-xxxx when he argued that: ‘the treaty bodies stand at the heart of the international human rights protection system as engines translating universal norms into social justice’.2 * This chapter is based on Xxxxxxxxxxx’s PhD research conducted from November 2009 until March 2014, which focused on state reporting under the six main UN human rights treaties in the Netherlands, New Zealand, and Finland. See Xxxxxx Xxxxxxxxxxx, The Domestic Impact and Effectiveness of the Process of State Reporting under UN Human Rights Treaties in the Netherlands, New Zealand and †Department Finland: Paper-Pushing or Policy Prompting? (Antwerp: Intersentia, 2014). 1 Xxxxxx Xxxxxxxxxxx, From Apology to Utopia: The Structure of BiotechnologyInternational Legal Argument (Cambridge: Cambridge University Press, TU Delft NL2006). 2 Xxx Xx-xxxx, ‘Foreword by the Secretary-General’, in Xxxx Xxxxxx, Strengthening the Second, as will be illustrated in this chapter, treaty bodies are very much engaged with politics as well. For example, they interpret open-ended treaty provisions, they formulate recommendations, and they decide how to handle information submitted by NGOs. Such acts are inherently political and imply dealing with, in the view of Xxxxxxxxxxx in Chapter 2 of this book, the ‘two completely different conceptual worlds’ of the legal and the political.3 Third, the process of implementation of non-binding recommendations from international legal institutions is essentially political. As will be shown in this chapter, non-legal aspects frequently determine whether the recommendations are acted upon at the domestic level. (Non-)compliance is primarily affected by political interests and preferences of the government. (Non-)compliance with recommendations is thus the result or byproduct of domestic politics.4 The Netherlands In argument that there is a political dimension to the past 10 years many molecular aspects implementation of microbial nitrate reduction have been elucidatedinternational norms also coincides with Xxxxxxxxxxx’s claim that international law should not ‘escape politics’ or treat politics as opposed to international law.5 Similarly, the fight for an international rule of law should not be seen as a fight against politics, but a fight which takes place within politics.6 This also implies that international norms and recom- mendations only have effect through the ecophysiology filter of domestic politics.7 Hence, this chapter concurs with Xxxxxxxxxxx’s argument that ‘social conflict must still be solved by political means’.8 Fourth, the examination of this domestic political implementation process is hardly understood. In this contributionrequires venturing into other disciplines than law, our efforts to study the complex microbial communities including political science, international rela- tions, and interactions involved sociology, as Xxxxxxxxxxx noted in the reduction early 1990s.9 The UN human rights state reporting procedures are based on the obligations of nitrate states which have ratified, or acceded to, these treaties (the states parties) to dinitrogen gas submit periodically, usually every four or five years, a report on the implementation of this treaty.10 These state reports are summarized. The initial work concentrated on emission of the greenhouse gas nitrous oxide during incomplete denitrification by Alcaligenes faecalis. As more research methods became available3 See Chapter 2, the fitness of A. faecalis could be tested in mixed cultures with other denitrifying bacteria, most notably with the nitrate-reducing bacterium Pseudomonas G9. Finally, the advancement of molecular diagnostic tools made it possible to survey complex microbial communities using specific primer sets for/and antibodies raised against the various NOx reductases. Given the enormous complexity of substrates and environmental conditions, it is evident that mixed cultures rather than single species are responsible for denitrification in man-made and natural ecosystems. However, it is surprising that even for the breakdown of a single compound, such as acetate, mixed cultures are responsible, and that the consecutive denitrification steps are commonly performed by mutualistic co-operating species. Our observations also indicate that we seldom know the identity of the major key players in the nitrogen cycle of these ecosystems25.