dataesr/scientific-paragraphs-categorization huggingface dataset:
Results We have collected full XFEL diffraction data sets from two soluble proteins as model systems: the small, 14. 3 kDa, chicken egg-white lysozyme and the relatively large, heterohexameric, 120 kDa, phycocyanin disk-like complex involved in light harvesting in photosynthesis as part of a phycobilisome in cyanobacteria. The proteins were first crystallized in their corresponding crystallization buffers, after which the slurries of microcrystals were concentrated by centrifugation to the desired concentration and mixed with appropriate LCP host lipids (Figs. 1a  and 1b ) using a lipid syringe mixer as described previously  (Liu et al. , 2014). Mechanical mixing allows the fast and efficient formation of LCP; however, the shear forces can damage or dissolve the crystals if mixing is too vigorous.
Lysozyme structure The structure of lysozyme was solved at 1. 9 A ˚resolution using 54 544 indexed single-crystal diffraction snapshots. The resulting overall structure is very similar to the previously published lysozyme structure determined by SFX using a GDVN injector  (Boutet et al. , 2012). Since the software has substantially advanced over the last two years, we have also reprocessed the data from  Boutet et al. (2012)  using more recent versions of  Cheetah (v. 2013. 3) and CrystFEL (v. 0. 5. 3a), resulting in considerably improved data statistics. Both data sets were processed in the same way using the same versions of the software to avoid bias (Table  1 ). We compared the structures of lysozyme obtained using both LCP and GDVN injectors to ensure the validity of our procedure. The structures aligned very closely, with an r.
m. s. d. of only 0. 5 A ˚. The B-factor distributions are very similar, with a slightly higher average B factor in the case of the LCP structure. The quality of the maps is also very similar, with no structural differences observable in difference maps (Figs. 2a  and 2b ). Small differences were only detected around the side chains of solvent-exposed bulky amino-acid residues. These minor differences can be expected given the variations in the crystal-preparation protocols, crystal size and crystal-delivery methods. We can therefore conclude that using LCP as a carrier medium for SFX data collection results in a similar quality structure compared with the previously used GDVN injector, while offering the important advantage of consuming considerably less crystallized protein (0. 1 mg using the LCP injector versus 15 mg using the GDVN injector).
Phycocyanin structure As the second test protein, microcrystals of phycocyanin (PC), a photosynthetic pigment protein from the thermophilic cyanobacterium T. elongatus, were used. SFX data were collected using the LCP injector and compared with the structure of PC obtained previously using the GDVN injector. Both structures were of very similar resolution and quality. During the LCP-SFX experiment, data were collected from less than 7 ml of LCP sample (containing 3 ml crystal suspension), which yielded 18 794 hits, from which 6629 patterns were indexed at 1. 75 A ˚resolution (Table  2 ). The quality of the structural model can be assessed from the details presented for one of the chromophores of PC shown in Fig. 3. The simulated-annealing composite OMIT 2mF o À DF c electrondensity map at a contour level of 1.
In the case of lysozyme, the precipitant was compatible with 7. 9 MAG, 9. 7 MAG and 9. 9 MAG/7. 9 MAG mixture lipids, while the PC precipitant was not compatible with 9. 7 MAG but worked well with a 1:1 9. 9 MAG:7. 9 MAG mixture. Data collected by SFX contain many randomly changing parameters, such as the exact crystal orientation, the crystal size and mosaicity and the XFEL pulse intensity and energy. Data processing relies on averaging of all these fluctuations, in the simplest case by Monte Carlo integration over many observations of the same reflection, and this requires a high multiplicity of data for convergence. Therefore, for efficient SFX data collection it is important to attain a high density of microcrystals, ensuring a high crystal hit rate. A clear advantage of working with crystals of soluble proteins, compared with membrane-protein crystals grown in LCP, is the ability to concentrate the crystal slurry to the desired concentration simply by centrifugation.
Acknowledgements This work was supported by  NIH/NIGMS  grant  R01 GM108635  (VC), the  Center for Applied Structural Discovery (CASD)  at the  Biodesign Institute at ASU  (RF, WL, SB, SR UW, JCHS and PF),  NSF Science and Technology Center  grant  1231306  (JCHS, PF, UW and VC), the  Helmholtz Association , the  German Research Foundation (DFG) Cluster of Excellence 'Center for Ultrafast Imaging'  and the  German Federal Ministry of Education and Research (BMBF)  project  FKZ 05K12CH1  (AB, TAW and MM). MM acknowledges support from the  Marie Curie Initial Training Network NanoMem  (grant  317079 ). Use of the Linac Coherent Light Source (LCLS),  SLAC National Accelerator Laboratory  is supported by the  US Department of Energy, Office of Science, Office of Basic Energy Sciences  under Contract No.
Acknowledgments. The project BIOCLOUDS has been financed by the  French INSU/LEFE  and the  German DFG. One of the authors (AF) acknowledges with gratitude the support provided. The authors want to thank  Drs. M. Joly ,  M. Monier , and  C. Schaupp  for helpful discussions. The calculations for this study have been done on computer facilities of the  Institut du Développement des ressources en Informatique Scientifique (IDRIS) ,  CNRS at Orsay  and the  Centre Informatique National de l'Enseignement Supérieur (CINES)  at Montpellier under Project  940180. The authors acknowledge with gratitude the hours of computer time and the support provided.
Determination of T M We calculated the duration of mitosis (T M ) by extrapolating the proportion of mitotic cells within each actively cycling population to the total duration of their cell cycle. For this purpose, we used data from 19 ferret samples from the first 24 hours of the cumulative labeling experiment, because the progenitor type and cycling cell proportions did not change significantly after 24 hours of cumulative EdU labeling (data not shown). We counted the average number of cells undergoing mitosis, based on PH3 and 4 0 -6-diamidino-2-phenylindole (DAPI) staining (VZ: 5. 6 6 2. 2; ISVZ: 9. 6 6 3. 8; OSVZ: 5. 8 6 2. 8 [mean 6 SD mitotic cells per 250 lm of ventricular surface, n 5 19]), as well as the number of cycling cells in each area (VZ: 294. 2 6 56. 3; ISVZ: 538. 1 6 116.
Cycling cell subpopulations in the germinal zones of P1 ferret neocortex Next, we determined the cycling cells in each subpopulation in the germinal zones of newborn ferret kits at P1, a late neurogenic stage  (Noctor et al. , 1997). For this purpose, we performed triple immunofluorescence for Pax6, Tbr2, and the cycling cell marker Ki67 (Fig. 2A, B ). When expressed as proportion of cycling cell subpopulation per germinal zone (Fig. 2D ), and consistent with the data shown in Figure  1 , Pax61 & Tbr22 progenitors constituted the largest subpopulation of cycling cells in the VZ, followed by Pax61 & Tbr21 progenitors (Fig. 2D ). Conversely, in the ISVZ, Pax61 & Tbr21 progenitors constituted the largest cycling cell subpopulation, followed by Pax61 & Tbr22 progenitors. In the OSVZ, cycling Pax61 & Tbr22 and Pax61 & Tbr21 progenitors were approximately equally abundant and together constituted the vast majority of cycling cells, as was the case for the VZ and ISVZ (Fig.
Cell cycle of ferret cortical progenitors The Journal of Comparative Neurology | Research in Systems Neuroscience bars) were comparable to those calculated from the cumulative EdU labeling data (Figs. 6D, arrows, 5B, Table  1 ). Depicting the duration of each cell cycle phase as a proportion of the total cell cycle (Fig. 5B , Table  1 ) rather than as absolute time (Fig. 5A ) revealed three distinct cell cycle parameter profiles. The first one is shared by APs, Pax61 & Tbr21 progenitors in the VZ, and bRG in the OSVZ, which spend approximately onethird of their cell cycle in S-phase (32. 4%, 35. 1%, and 32. 9%, respectively) and close to 60% in G1 (61. 2%, 61. 0%, and 61. 8%, respectively). The second one is characteristic of Pax61 & Tbr21 progenitors in both the ISVZ and OSVZ and of bRG in the ISVZ, which spend around 20% of the cell cycle in S-phase (21.
Cell cycle length of ferret neocortical progenitors Our cell cycle analyses complement a pioneering study that analyzed T C and T S in the different proliferative areas of the ferret neocortex at P0 and P6  (Reillo and Borrell, 2012). If we analyze our data in an analogous way, considering the entire cycling population in each proliferative area, we obtain values with similar trends: longer total cell cycle in VZ and OSVZ, and longer S-phase in the VZ than in either SVZ area (VZ: T C 5 49. 4 hours, T S 5 13. 3 hours; ISVZ: T C 5 43. 0 hours; T S 5 7. 0 hours; OSVZ: T C 5 48. 7 hours; T S 5 6. 7 hours). However, cycling cells at P1 display different values, with an overall longer T C and shorter T S than at P0  (Reillo and Borrell, 2012) ; this could reflect either methodological differences (because our study used a greater number of biological replicates) or an underlying biological significance, whereby great changes in the dynamics of the cell cycle of neural progenitors would occur in the first postnatal days, perhaps as a consequence of the change of environment elicited by birth.
ACKNOWLEDGMENTS M. T. G. was enrolled in the Dresden International PhD Program, as a member of the  International Max Planck Research School for Cell, Developmental , and  Systems Biology  and the  Dresden International Graduate School for Biomedicine and Bioengineering. We thank  Jan Peychl  and the  Light Microscopy Facility , as well as  Jussi Helppi  and the staff of the  BioMedical Services at the MPI-CBG  for technical assistance,  Dr. Barbara Langen  and the rest of the staff at  BioCrea (GmbH, Radebeul)  for ferret housing and care, and  Drs. Eric Lewitus  and  Josh Currie  for their comments on the manuscript.
Methods This was an observational study conducted by the ESICM Trials Group (17-23 April 2013 or 23-29 May 2013) and registered on ClinicalTrials. Gov (NCT01787071). ICUs were able to enter the study in one of the 2 weeks. The possibility to choose between 2 weeks was chosen in order to compensate for differences in national holidays in different countries and therefore to maximize the recruitment of study units. IRB approval was obtained in each country and the local investigators were responsible to ensure that with local and national requirements were fulfilled. In most participating countries informed consent from the patient was waived owing to the observational study design. National coordinators and local investigators are listed in the electronic supplementary material (ESM). We included all consecutive adult (18 years old and above) patients, up to a maximum of 20 per participating unit, in whom an FC was performed during a 1-week period.
FC was defined as administration of any bolus of fluid (crystalloid or colloid) in less than 2 h. Administration of red blood cells or fresh frozen plasma was not considered as an FC. The exclusion criteria were previous inclusion in the study, overt bleeding, and time of an FC exceeding 120 min. Only one FC, ideally the first, was considered for each patient. Only one FC per patient was recorded. We collected data on patient demographics, indications for the FC, the type, amount, and rate of fluids administered, available hemodynamic variables, and judgment on the efficacy and safety of the FC. The case report form (CRF) is available in the ESM. Anonymous CRF data were uploaded by local investigators using a Web-based electronic CRF (Clinfile, Sevres, France). The data were stored securely in a server located in Brussels.
ESM). A total of 2213 patients were analyzed. Data on demographic factors and concomitant treatment are presented in Table  1. The main diagnostic groups were sepsis (n = 595, 27. 0 % [CI 25. 2-28. 9 %]), cardiac (n = 454, 20. 6 % [CI 18. 9-22. 3 %]), and respiratory failure (n = 238, 10. 8 % [CI 9. 5-12. 1 %]). The median amount of fluid given during an FC was 500 ml [500-1000]. The median time was 24 min [40-60 min], and the median rate of fluid administration was 1000 [500-1333] ml/h. Crystalloids were the most used (in 74. 0 % [CI 72. 2-75. 8 %] of the cases) including normal saline in 45. 9 % [CI 25. 2-28. 9 %], and balanced solutions were used in 53. 5 % [CI 51. 4-55. 6 %] of FCs (Table  2 ). The main indication for fluid administration was hypotension in 1211 (58. 7 % [CI 56. 7-60. 1 %]) of FCs.
First, we recorded only when FCs were given and not when FCs were not given. Thus, in practice we may have underestimated the times when variables used to predict fluid responsiveness were used. Second, we encouraged investigators to record data on the first fluid challenge, which may have several implications. At early stages, a positive response to fluids is more likely and patients are often less invasively monitored. Studying patients at later stages may have yielded different results. Third, we allowed a wide range of options (volume, type of fluid, first or subsequent FC) to be recorded during an FC. It is possible that some investigators considered an FC what would be normally defined a more sustained volume expansion. We conclude that the current practice and evaluation of FC in critically ill patients seems to be arbitrary.
One would however generally expect that several of the flavour-violating entries could be non-vanishing, especially if the flavour structure is generated by some mechanism at a higher scale. Consequently, a comprehensive study of the most general NMFV configuration of the MSSM, where all flavour-violating Lagrangian terms are taken into account and confronted to current data and theoretical constraints, is in order. A first step in this direction is achieved with this work. We consider the most general mixings between second and third generation squarks. Any non-CKM induced mixing with the first generation is ignored as a result of constraints imposed by kaon data  [27]. Choosing a phenomenological approach, we model the flavourviolating effects under investigation by a set of 19 free parameters defined at the TeV scale and identify, by means of a Markov Chain Monte Carlo parameter scanning technique, the regions of the parameter space that are favoured in light of current data.
The associated predictions are calculated with the SuperIso package  [42, 43]. In addition, we compute the neutral B-meson mass difference ∆M Bs , the branching ratio associated with the B s → µ + µ -, K 0 → π 0 νν and K + → π + νν decays and the kaon parameter K with the SPheno code  [30, 31]. We furthermore employ SPheno for the estimation of the supersymmetric contributions to the anomalous magnetic moment of the muon a µ 1  and for a calculation of the lightest Higgs boson mass m h. The data transfer between SPheno and SuperIso is achieved through the Flavour Les Houches Accord standard  [44] , and the Wilson coefficients for all hadronic observables are calculated in SPheno (at the scale Q = 160 GeV) and SuperIso (at a scale Q = m W ) from the values of the running coupling constants and the supersymmetric masses and parameters that have been evaluated with SPheno.
Conclusion We have studied non-minimal flavour-violation in the MSSM by allowing for flavour mixing between the second and third generation squarks. We have used a Markov Chain Monte Carlo scanning technique to explore the underlying parameter space and imposed a set of experimental constraints arising from B-meson and kaon physics. We have additionally enforced the model to accommodate a light Higgs boson with a mass of 125 GeV. In view of the recently started second LHC run, we have used our MCMC scan results to propose four benchmark scenarios allowed by current data that exhibit distinct features and that are suitable for future analyses of NMFV effects in the MSSM. In most proposed scenarios, several squarks have masses close to 1 TeV so that they should be reachable within the next few years.
While the CMS and ATLAS data were obtained at central rapidities, LHCb performed measurements at forward rapidities, 2 < y < 4. 5. Actually, only few measurements were able to explore the small-p T range down to p T,min 0, namely those by CDF  [6]  and the two by LHCb  [14, 15]. In all other data, the cut p T,min > 5 GeV was imposed. A unified theoretical description of these data, which covers both the very small and the large p T range, requires special efforts, which we shall undertake in this paper. On the theoretical side, it is generally accepted that for the treatment of B-meson production at small p T values, as well as for the calculation of the integrated cross section including the small-p T range, i. e. , with p T of order O(m b ) and below, where m b is the b-quark mass, one should use the so-called massive scheme or fixed-flavor-number scheme (FFNS)  [16,17,18,19,?] , in which the number of active quark flavors in the initial state is limited to n f = 4, and the b quark appears with explicit mass dependence only in the final state.
This study entitled "effects of exopolysaccharide-producing starter cultures on physicochemical, rheological and sensory properties of fermented camel's milk"  (Ibrahim et al. , 2015)  contributes to the technical innovation in the camel milk sector which is one of main objective of the project. The health aspect is not forgotten and in the paper "effects of two anthelmintics on gastrointestinal infestation by parasitic worms in camels"  (Seddik et al. , 2015) , the authors follow the kinetics of parasitic eggs elimination after two anthelmintic treatments: sub-cutaneous injection of Ivermectine and Albendazole by oral route. These 10 papers are just a small part of the data already published by the partners of PROCAMED project in different national and international papers or in national and international conferences, but by gathering these papers in one special issue, they participate to show the wide diversity of the studies and of the approaches.
20 o assess the potential shedding of the parental Schwarz vaccine strain and MV1-F4 vaccine candidate, excretions and body fluids of monkeys immunized with these vaccine strains were tested for the presence of MV viral sequences by RT-qPCR assay. Of the 8 time points at which shedding analysis was performed, MV viral RNA was only detected at day 11, the expected peak of viremia, in some biological fluids samples from few immunized monkeys. However, none of these samples contained infectious virus, indicating that no shedding of infectious virus particles was observed for either of the 2 vaccines. 20 The introduction of HIV F4 fusion protein did not alter the tropism of the parental strain or its shedding capacity. No data are available regarding the biodistribution and shedding of MV-CHIK.
However, no alteration in tropism is expected for the same vector containing the genes coding for structural proteins from chikungunya virus. With regards to the 2 recombinant oncolytic MV vectors described before, the following data are available: MV-CEA and MV-NIS: In order to maximize viral infection of the tumor cells, MV-CEA and MV-NIS were administrated by intraperitoneal route to patients with recurrent ovarian cancer. 21, 27, 28. In pre-clinical studies performed in measles na€ ıve IFNAR KO CD46 Ge mice, there was no evidence of viral replication outside the peritoneal cavity (i. e. , the brain, heart and skeletal muscle). 122 In phase I clinical studies, 21 women were administered and low levels of MV-CEA genomes were found by RT-qPCR in peripheral blood mononuclear cells (PBMCs) of 4 asymptomatic patients.
The intent of this document is to establish a strategy which may be used to conduct and document read-across predictions for data gap filling. As such, it provides guiding principles for developing read-across predictions for discrete organic compounds. Where possible, emphasis has been placed on undertaking and describing the read-across prediction in the best manner to facilitate regulatory acceptance. This document represents, in part, discussions in and progress made in the European Commission and Cosmetics Europe funded SEURAT-1 Cluster (www. seurat-1. eu). As such, the primary focus of this document is directed towards read-across predictions for chronic toxicity, or improving the possibility to read-across from repeat dose toxicity tests. However, in order to achieve this aim, the document draws upon current expertise and knowledge from other toxicological endpoints and the information, templates and work plans contained herein are generally applicable to all read-across scenarios and endpoints.
More recently, the OECD has provided reporting formats for analogue and chemical category approaches  (OECD, 2014a). The documentation of read-across predictions, which are largely based on process of using the OECD QSAR Toolbox, includes a number of steps: 1) Formulate the problem (i. e. , understanding assessment strategy and identify the critical data needs). 2) Curate chemical structure of the target compound(s) and other category members. 3) Profile the target compound(s) and other category members. 4) Develop the similarity rationale for the read-across prediction. 5) Establish the category selection criteria and search for potential source analogues or category members. 6) Gather data for the category members and construction of data matrix. 7) Assessing the adequacy and uncertainty associated with the read-across.
Acknowledgements TWS was funded by a consultancy agreement with Cosmetics Europe, the Personal Care Association. MTDC acknowledges funding from the COSMOS Project which is funded by the  Wu, S. , Fisher, J. , Naciff, J. , Laufersweiler, M. , Lester, C. , Daston, G. , Blackburn, K. , 2013. Framework for identifying chemicals with structural features associated with the potential to act as developmental or reproductive toxicants. Chem. Res. Toxicol. 26, 1840 -1861. Yang, L. , Neagu, D. , Cronin, M. T. D. , Hewitt, M. , Enoch, S. J. , Madden, J. C. , Przybylak, K. , 2013. Towards a fuzzy expert system on toxicological data quality assessment. Mol. Inf. 32, [65] [66] [67] [68] [69] [70] [71] [72] [73] [74] [75] [76] [77] [78]  Table  1. Criteria for Category Membership 1) A description of structural and chemical property similarities and differences among the category analogues and how these similarities and differences are linked to the read-across hypothesis.
Research materials and methods As described above, research on landscape perception was carried out during the work for Urban Planning. With an explicit focus on new settlements areas, a discussion of some of the empirical and phenomenal data collected during the study will help to understand the perceived landscape as an expression of the ways of life in a contemporary, peri-urban mountain town, and how new settlements and new buildings reify this expression. The research took on the conception of the landscape as the symbolic and material expression of the relationship between societies and territories (among the others:  Turri, 1979 Turri, and 2008 Turri, (1974)) ;  Cosgrove, 1984)  that emerges through landscape features as well as the representation of these features as the outcome of an act of cultural reflection  (Farinelli, 1991).