dataesr/scientific-paragraphs-categorization huggingface dataset:
Conclusions The most ancient specimens of Bison schoetensacki in the fossil record date back to the beginning of the Middle Pleistocene (i. e. some 750,000 years ago), but the continuing presence of this species up to the Upper Pleistocene has been a matter of controversy. Our studies of a Siréjol bone fragment provide strong support to the notion that this species existed for a long period of time, extending to the Upper Pleistocene. Moreover, comparison of our mitochondrial and nuclear genome data with those of recent studies suggest that 15,000 to > 50,000-year-old Bison schoetensacki remains are present in a number of Eurasian sites. The DNA data   S6. Specimen name and country of origin are indicated for ancient and historical samples. The tree was rooted using the sequence of Bubalus bubalis.
Refer to text for explanation about clade 1 and clade 2 show that Bison schoetensacki positions in a bison clade referred to as CladeX  [28]  or Bb1  [39]  which should be renamed accordingly. Scenarios of bison evolution considered that Bison bonasus evolved either from Bison priscus or from Bison schoetensacki lineages. The genetic data clearly support the latter rather than the former hypothesis. The divergence date between Bison bonasus and Bison schoetensacki is nevertheless still unclear since it has been estimated around 120 (152-92) kya and around 246 (283-212) kya in the two studies with different datasets  [28, 39]. Opposite conclusions have also been reached regarding the evolution of Bison bonasus as due either to incomplete lineage sorting  [39]  or to hybridization between Bison priscus and ancestors of Bos primigenius  [28].
Acknowledgements All necessary permits were obtained for the described study, which complied with all relevant regulations. We thank the  Direction Régionale des Affaires Culturelles Midi-Pyrénées ,  Service Régional de l'Archéologie  ( 32 ,  rue de la Dalbade ,  BP811 ,  31080 Toulouse Cedex 6 ,  France ) for permitting us to collect the cave hyena coprolite from the Grotte-aux-Ours cave and perform its analysis, and the  Musée des Confluences  ( 86, quai Perrache, 69002 Lyon, France ) for permitting us to analyze the Bison schoetensacki bone fragment from the Siréjol cave. We thank the  Plateau Technique du MNHN, site du Musée de l'Homme (Plateforme Paléogénomique et Génétique Moléculaire, Musée de l'Homme, Paris)  and the  Service de Systématique Moléculaire  ( UMS 2700 OMSI CNRS-MNHN ) for their contribution to this work.
Availability of data and materials The datasets supporting the conclusions of this article are available in the EBI and GenBank repositories. More specifically, the Illumina reads of this study have been deposited at EBI (http://www. ebi. ac. uk) under the accession number ERP015025. The assembled Bison schoetensacki and Crocuta crocuta mitochondrial genome sequences have been deposited in the GenBank database (http://www. ncbi. nlm. nih. gov/genbank) under the accession numbers KU886087 and KU937361, respectively.
Only results of those students were mentioned who consented to be a part of the study. The same students were inducted for all 3 modules. Module-I consist of cell biology and genetics. The second module consists of Musculoskeletal/ blood and lymphoid tissue. While the third module consist of Cardiovascular and Respiratory system. One hundred and forty items (in module papers) comprising with four options and one correct without any negative marking are selected from these modular exams. These items are constructed to assess various levels of knowledge according to bloom's taxonomy. 8 hese 140 items are selected from the existing MCQ bank after a pre-validation by the MCQ review committee of the department. All the modular examinations are in pencil and paper format. 9 Test results were assessed by Optical Machine Reader with a are computed using custom software program.
RESULTS For the samples in the training set, data pretreatment was started with 16 quality control (QC) samples. After screening ion peak areas on the basis of the acquired data from the QC samples, (shown in Supplementary Information 1), 230 peaks corresponding to compounds in the serum were obtained. Peaks in the test (noncontrol) samples were identified qualitatively according to the peaks characterized in the QC samples and then quantified by integration of their areas. The recorded peak area represents the relative concentration of the corresponding compound in the serum. A data set for test samples containing peak area information for all 230 defined peaks was established and analyzed in the following discriminatory analyses. An assessment by principal component analysis (PCA) for all QC samples was performed (Supplementary Figure  1 ).
Baseline characteristics of patients Eighty-five samples from 46 patients fulfilling the inclusion criteria were included in the study. Among the samples, 38 were included in the training set while the remaining 47 were included in the validation set. Design of the current study is depicted in Figure  1. The samples were grouped by sampling time (BT: before RFA therapy; AT: 2 months after RFA therapy) and recurrence status (NR: non-recurrent patients; R: recurrent patients). Baseline information for all included patients is shown in Table  1. On the basis of the statistical data in the table, no significant variation (p > 0. 05) from the clinical assessments was found between the recurrent group and the non-recurrent group, both in the training set and validation set samples.
Free fatty acids It is notable that comprehensive turnover of free fatty acids in the recurrent patients was observed both before and after RFA treatment according to HCC recurrence status. Even-carbon chain fatty acids including long-chain and medium-chain saturated fatty acids (SFAs) and monounsaturated fatty acids (MUFAs) were increased in the NR AT vs. R AT comparison. Interestingly, short-chain and medium-chain fatty acids were determined to be increased in R BT compared to NR BT. However, arachidonic acid (ARA, 20:4) and docosahexaenoic acid (DHA 22:6), which are long-chain polyunsaturated acids (PUFAs), were decreased in R AT and R BT , respectively (Shown in Figures  3, 4A ). These data are consistent with existing data on cancer recurrence. For example, the actions of PUFAs on immune function, such as anti-inflammatory properties, are well known  [24].
Only HCV-related HCC patients with active viral replication were selected based on these criteria and were included in the present analyses. HCC was diagnosed according to the Barcelona criteria: histological evidence or convergent demonstration of a focal lesion more than 2 cm in size and with arterial hyper-vascularization by two different imaging techniques, or the combination of one imaging technique showing this morphological aspect with an AFP level superior to 400 ng/mL. The decision to treat patients with RFA was made by a multidisciplinary team according to international recommendations  [42]. All RFAs were percutaneously performed by the same operator under ultrasound guidance and general anaesthesia. Clinical, biological, and radiological data of patients were recorded on the day of the first blood collection which was considered as the inclusion date.
Data processing Pretreatments such as deconvolution, peak matching, and retention time alignment of the spectra were performed with the help of Leco ChromaTOF software (St. Joseph MI, version 3. 25) and XCMS (xcmsonline. scripps. edu). The assignment of the ion peaks was achieved by matching to a library (NIST, Mainlib, Replib, Wiley and Feihn). The assignment of peaks was based on m/z and the calculated RI which was associated with the retention time. The qualification for most of the principal discriminators was confirmed by analyzing the correspondent reference substance. For cases in which several peaks corresponded to a single metabolite, we retained the one with the lowest RSD. The recording of the area of each identified ion peak was regarded as the relative quantification for its corresponding metabolite.
A data set recording the area for the ion peaks was generated. Peaks were screened by the same method performed in one of our previous studies  [43]. PCA and PLS-DA were done using SIMCA-P software (version 11, Umetrics, Umeå, Sweden). Heat maps were displayed by the MultiExperiment Viewer (Mev, version 4. 9. 0, Dana-Farber Cancer Institute, MA, USA). Other statistical analyses were performed using SPSS (version 19, IBM, Chicago, USA). The acquisition of spectra for some available reference substances served to confirm the qualification of most of the discriminators. To investigate the predictive ability of the defined candidate biomarkers of HCC recurrence, the validation of defined principal metabolites was performed by feature selection of RF. The calculation was performed according to an algorithm written in the C++ language.
ACKNOWLEDGMENTS We first thank  Xin Huang  for his programming and technical assistance on the random forest analysis, and  Corentine Goossense ,  Xianping Lin , and  Alexandre Baillard  for their help with sample preparation. We also express our thanks to  Dr. Yang Liu ,  Dr. Yanni Zhao , and  Dr. Jieyu Zhao  for their inspiring suggestions. We acknowledge the contribution of a medical writer,  Sandy Field, PhD , for editing of the manuscript.
Statistical analysis Characteristics of the HIV and primary care groups were compared using chi-squared tests or t-tests as appropriate for quantitative variables. All analyses were then stratified by group and by sex. We performed a Kaplan-Meier analysis to describe the time between arrival in France and first HIV test, and used a discrete-time logistic regression to analyze factors associated with the probability of HIV testingfor each year included, taking into account both fixed and timedependent variables. Data were weighted according to each individual's probability of inclusion in the survey. Analyses were conducted using STATA 13. 1 (Stata Corp. , College Station, Texas, USA). Data are available in S1 Dataset.
Acknowledgments The authors would like to thank all the persons who participated in the study, the  RAAC-Sida , COMEDE, FORIM and SOS hepatitis associations for their support in preparing and conducting the survey,  G Vivier ,  E Lelièvre  (INED) and  A Gervais  ( AP-HP ) for their support in preparing the questionnaire,  H. Panjo  for statistical support,  A Guillaume  for communication tools, the  ClinSearch and Ipsos societies  for data collection,  Laetitia Haroutunian  for the literature search and staff at all participating centers. Finally, our thanks to  Jude Sweeney  for the English revision and editing of this manuscript.
Characterization techniques The shape and size of the particles was examined by transmission electron microscopy (TEM, Philips 200CM). Particle size distributions were obtained from the micrographs by counting several hundreds of particles, using the free software ImageJ. Additional information on the size and colloidal stability of the particles in aqueous suspension (0. 5 mg•mL -1 of solid) was obtained from Dynamic Light Scattering (DLS) measurements. The experiments were carried out using a Malvern Zetasizer Nano-ZS90 equipment, which was used as well to measure the Zeta potential of the suspensions. The crystalline structure of the prepared particles was assessed by X-ray diffraction (XRD) using a Panalytical, X´ Pert Pro diffractometer (CuKα) with an X-Celerator detector over an angular range of 10º < 2θ < 120º, 2θ step width of 0.
02º, and 10 s counting time. Silicon was used as internal standard. The TOPAS software (TOPAS version 4. 2, Bruker AXS, 2009) was used to calculate the unit cell volume of the barium-lutetium structure using the Rietveld method. 19 Refined parameters were background coefficients, scale factor, zero, unit cell parameters, displacement parameters of Ba 2+ and Lu 3+ and profile parameters. The isomorphic substitution of Nd 3+ by Lu 3+ in the barium-lutetium fluoride crystal structure was proved as well by determination and comparison of unit cell parameters of the undoped and Nd 3+ -doped nanoparticles. The quantitative composition of the samples was analyzed by inductively coupled plasma atomic emission spectroscopy (ICP-AES, Horiba Jobin Yvon, Ultima 2). The powder samples were previously dissolved in hydrochloride acid.
The signal was recorded and averaged using a Tektronix DPO4104B-L digital oscilloscope. Micro-CT (eXplore CT120; GE HealthCare) examinations were performed using the following parameters: acquisition consisted of 720 views acquired, with a 20 ms exposure time per view (Gain: 25 and Offset: 20). X-ray tube voltage and current were set at 100 kV and 50 mA. CT images were reconstructed using a binning mode of 1x1x1 and a voxel size of 50x50x50 µm3. Images were analyzed using MicroView analysis+ software (version 2. 2, GE Healthcare).
This change is likely due to the different ionic radii of Ba 2+ and Lu 3+ (1. 42 Å and 0. 977 Å, respectively, in VIII coordination), as well as to the extra fluoride anions present in the structure to balance the excess positive charge due to the heterovalent substitution. We have carried out a LeBail refinement of the structure with the TOPAS software using as starting parameters those of BaF 2 in space group Fm-3m. A unit cell volume of 184. 66(6) Å 3 was obtained for our sample. The unit cell volumes reported in the literature for several Lu-containing BaF 2 compositions (10, 16. 5, 18, and 25 mol% Lu)  24  as well as the one reported for pure BaF 2 (PDF 00-004-0452, ICDD 2015) were plotted in Figure  2c  versus the corresponding Lu content. All the reported data points were successfully fitted to a straight line, which extrapolated exactly to our value for the 70 mol % Lu, thus indicating that the solid solubility of Lu 3+ in BaF 2 stands up to, at least, 70% in the experimental conditions of our reaction.
Wild-type (WT) and variants of Jo and In were purified independently and mixed in different combinations (Fig. 3c ). The covalent complex His-Jo-His-In was formed only when both WT forms of Jo and In were mixed, while each point mutation totally impaired the complex assembly (Fig. 3c ). The rather slow kinetics of the Jo-In complex formation might originate from an alteration of the structure of the protein fragments when isolated from the parent RrgA protein. In this case, one might expect the His-Jo-In complex to display a structure slightly different from the D2 domain of RrgA. To test this possibility, we have solved and refined the crystal structure of the His-Jo-In complex (PDB: 5MKC) at 2. 04 Å (Table  2 ). The structure of the complex shows that the Jo and In moieties grasp into an 11-β -stranded sandwich (Fig.
Covalent complex reconstitution in vitro. The individual Jo and In fusions, as well as the Jo-In complex were separated by SDS-PAGE using 12. 5% or 15% polyacrylamide gels. Gels were stained with Coomassie blue and band intensities were quantified using a GelChemiDoc imager (BioRad) and Image J software. To detect the formation of the covalent complex in the crude bacterial extracts, cells from 1-L culture were resuspended in 50 ml of 50 mM Tris pH 8. 0, 200 mM NaCl (plus 20 mM imidazole when the protocol includes a Ni-affinity chromatography purification step) and a protease inhibitor cocktail (Complete EDTA free, Sigma-Aldrich). Cells were lyzed by sonication for 2 min (2 sec ON and 8 sec OFF). The lysate was clarified by centrifugation (20 min at 39,191 × g at 4 °C). Samples of 5 μ l were loaded onto polyacrylamide gels to separate the individual Jo and In from the covalent complex.
Bacterial cultures producing separately Jo and In were mixed before cell lysis and purification of the Jo-In complex. To visualize the formation of the complex in vitro, 10 μ M of purified wild-type or mutant Jo and In proteins were mixed and incubated at 20 °C for 30 min in 50 mM Tris pH 8. 0, 200 mM NaCl. To stop the reaction, samples were heated in SDS loading buffer for 5 min at 100 °C. The kinetics of the reaction was determined by incubating 10 μ M of Jo and In in 50 mM Tris pH 8. 0, 200 mM NaCl at 20 °C. Samples were harvested at different times and frozen to stop the reaction before analysis by SDS-PAGE and Coomassie blue staining. A complex-reconstitution experiment was also performed during 60 min in different buffers to test the influence of the pH. The intensities of the Coomassie blue stained bands corresponding to Jo, In and the complex His-Jo-His-In were quantified using the Image J software.
Structure determination and refinement. Statistics on data collection and refinement are summarized in Table  2. Experimental set up of the beamline and data quality of the collected images were monitored with MxCuBE  25, 26  and ADXV  27. Data was indexed and scaled with XDS program suite  28. XDSGUI  29  was used to perform data quality and resolution cutoff check-up  [30] [31] [32] [33] [34]. The reduced reflections information data was imported in to the CCP4 program suite  35. The structure was solved by Molecular Replacement method (MR) with PHASER  36  , using as a search model the partial structure of RrgA (PDB: 2WW8), residues 186-627. The MR solution structure was rebuilt de-novo, in order to remove bias from the model, as implemented in ARP/wARP  37. The structure was completed (29-630) by cycles of manual model building with COOT  38.
Water molecules were added to the residual electron density map as implemented in ARP/wARP  37. Cycles of restrained refinement employing NCS and TLS  39, 40  were performed with REFMAC  41  as implemented in the CCP4 program suite. Several cycles of manual model building and refinement were performed until R work and R free converged  42. Stereochemical verification was performed with MolProbity 43 and PROCHECK  44. The secondary structure assignment was verified with DSSP  45. Figures were generated with PyMol (http://www. pymol. org). Final refined model coordinates were deposited at the Protein Data Bank (PDB, http://www. rcsb. org)  46 , ID code: 5MKC.
Cells were grown at 37 °C in TH to an OD 600nm of 0. 3, transferred to microscope slides, and observed at 37 °C on an Olympus IX81 microscope equipped with a Yokogawa CSU-X1 confocal spinning disk unit. Image acquisition was performed using a UAPON 100× (N. A. 1. 49) oil immersion objective and Andor TM iXon Ultra Electron Multiplying Charge Coupled Device (EMCCD) camera. Epifluorescence confocal of GFP signal (488 nm excitation and 520/28 nm emission) and Differential Interference Contrast (DIC) transmission imaging were collected using IQ software (Andor TM ), and further analyzed using Volocity (Perkin Elmer TM ). In addition to the specific GFP channel, images were acquired in the red emission channel (561 nm excitation and 617/73 nm emission) to estimate the background autofluorescence signal.
(c) The covalent complex is observed in the presence of the wild-type (WT) proteins and is impaired by Lys 191 Ala, Asn 695 Ala and Asp 600 Ala mutations. For clarity reason, the one-letter amino acid code is figured. Wild-type and mutant forms of purified His-Jo and His-In were incubated for 30 min at 20 °C. The samples were analyzed by Coomassie blue-stained gels. (d) Ribbon representation of the His-Jo-In complex (left panel). Jo is colored in cyan and In in blue. Red asterisks indicates the position of Lys 191 in Jo and Asn 695 in In proteins. Right panel: close-up view of the key residues for the amide bond formation (represented in sticks), the electron density is also shown. (e) Crystal structure of the Jo-In complex (cyan and blue, respectively) superimposed on the D2 domain (grey) in the context of the full-length RrgA protein (PDB ID: 1WW8).
Acknowledgements We acknowledge the platforms of the Grenoble Instruct center (ISBG;  UMS 3518 CNRS-CEA-UGA-EMBL ) supported by the  French Infrastructure for Integrated Structural Biology Initiative FRISBI  ( ANR-10-INSB-05-02 ) and by the  Grenoble Alliance for Integrated Structural Cell Biology GRAL  ( ANR-10-LABX-49-01 ) within the  Grenoble Partnership for Structural Biology  (PSB). Support for this work comes in part from the  Agence Nationale de la Recherche  (grants  ANR-11-BSV8-005-01   PILIPATH ,  ANR-12-BSV3-0003-01 PVL-Suscept ), the  Commissariat à l'Energie Atomique (Fonds de  soutien technologique à la valorisation des recherches de DSV, 2011) and the  University of Grenoble Alpes. B. J. was funded by a  Ph. D. grant from the  Grenoble Alpes University. We are grateful to  T.
The compromised disc morphogenesis seen with mutant RPGR would mislocalise rhodopsin to the inner segment, resulting in cell stress and degeneration cryoprotected, embedded and sectioned in a similar fashion. hTERT-RPE cells grown on slides were fixed in 4% paraformaldehyde for 30 min at RT. Sections/cells were blocked/permeabilised with 2% NDS (Sigma), 2% BSA (Sigma) and 0. 5% Triton X100 (Fisher) for 1 h at RT, washed with PBS, incubated with primary antibodies overnight at 4 o C, washed in PBS, incubated with secondary antibodies for 60 min at RT, washed in PBS, incubated in Phalloidin for 30 min at RT, washed in PBS, incubated in Hoechst for 5 min at RT and mounted with coverslips using Fluoromount-G (Southern Biotech). Images were taken on a Leica SPE confocal microscope and analysed using the ImageJ and ImagePro software.
Acknowledgements We would like to acknowledge  Dr Xinhua Shu  ( Glasgow Caledonian University ) for kindly housing the Rpgr KO mice. We would also like to thank  CB, HB, MB and KR  for their generous tissue donation to generate the iPSCs. This work was supported by grants from the  Wellcome Trust  (R. M. , H. A. by Grant Number  100470/Z/12/Z ; C. f. -C. by an  Investigator Award ),  Retinitis Pigmentosa Fighting Blindness  (R. M. , H. A. , A. F. W. ; Grant Number  GR583 ), the  Academy of Medical Sciences  (R. M. , M. J. ; Grant Number  SGL014 \1011 ), a  Medical Research Council Programme Grant  (A. F. W. ), an  ERC  Fellowship (C. M. , M. L. ), a  DFG Grant  (C. G. , W. W. ; Grant Number  SPP1464 ) and the  NIH  (W. Z. , H. K. ; Grant Number  EY022372 ).
Background: It is estimated that the standard, passive case finding (PCF) strategy for detecting cases of tuberculosis (TB) in Myanmar has not been successful: 26% of cases are missing. Therefore, alternative strategies, such as active case finding (ACF) by community volunteers, have been initiated since 2011. This study aimed to assess the contribution of a Community Based TB Care Programme (CBTC) by local non-government organizations (NGOs) to TB case finding in Myanmar over 4 years. Methods: This was a descriptive study using routine, monitoring data. Original data from the NGOs were sent to a central registry within the National TB Programme and data for this study were extracted from that database. Data from all 84 project townships in five regions and three states in Myanmar were used.
Data variables, data collection and sources of data Data variables included: (i) the number of presumptive TB cases referred and of these (ii) the number of treated TB cases each year, that were identified by local NGOs, and (iii) the number of total TB registered cases in each township. Data were sourced from the local CBTC NGOs' monthly reports and the NTP's annual reports. Local NGOs used standardized recording and reporting forms which were endorsed by the NTP. Original data from the NGOs were sent to a central registry within the NTP and data for this study were extracted from that database. Data were collected between July 2011 and December 2014.