dataesr/scientific-paragraphs-categorization huggingface dataset:
Microscopic analysis and quantification of gliosis and amyloid plaques Quantification of gliosis and amyloid plaques were performed on 30 μm thick brain coronal sections costained with either GFAP and 6E10 or IBA1 and 6E10 antibodies, at the frontal cortex, hippocampal and sensory cortex levels. Images were acquired using an inverted Axio Observer microscope (Zeiss, Jena, Germany) equipped with DAPI, FITC and TRITC epifluorescence filters. Images of large brain sections were obtained using the mosaic mode of the Axiovision software (Zeiss). For 6E10, GFAP and IBA1 staining quantifications, ImageJ software was used. The pictures were binarized to 16 bit black and white images and a fixed intensity threshold was applied for all images. Percentage of covered area by the fluorescent staining was calculated.
Microarray assay RNA samples from three animals in each group were pooled for microarray hybridization. Sample amplification, labeling, and hybridization were performed in line with the Agilent one-color microarray-base analysis (low input quick amp labeling) protocol (Agilent Technologies). Briefly, total RNA was reverse-transcribed into cDNA using the T7 promoter primer. The reaction intending to synthesize cyanine-3-labeled cRNA from cDNA was performed in a solution containing dNTP mix, T7 RNA polymerase and cyanine 3-dCTP and then incubated at 40 °C for 2 h. Labeled cRNA was purified and fragmented before hybridization on Agilent 8x60k Mouse Gene Expression Arrays (Agilent Technologies), containing 62,975 oligonucleotide probes, at 65 °C for 17 h. Raw microarray signals were scanned and extracted using Agilent Feature Extraction Software (Agilent Technologies).
Microarray data analysis Biological interpretation of the data was performed using two different programs. The NIH DAVID tool was used to obtain functional annotation clusters related to the datasets of interest. Ingenuity Pathway Analysis (IPA, Ingenuity Systems) was also used to identify biological functions and upstream regulators relevant to the lists of DEGs analyzed. The main criterion to validate a differentially expressed gene was a fold change over 1. 5 or under -1. 5 when considering expression values in the group supplemented with vitamin D3 relative to the control diet group, whether considering wild type or transgenic animals. Upregulated and downregulated genes were analyzed in the same datasets to obtain the biologically relevant function categories. Right-tailed Fisher's exact test was used to calculate a p-value determining the top statistically significant biological functions assigned to the data set.
Statistical analysis Significant differences between groups were determined using the Kaleida Graph software. We used one-way ANOVA followed by a post-hoc Bonferroni test for multiple comparisons. Kruskal-Wallis test was used to compare two experimental groups. Values represent the mean ± SEM of the indicated number of independent experiments/animals, and the level of significance was set for p < 0. 05 * or p < 0,01**.
Acknowledgments  Aurélia Cès  for her help with the behavioral experiments and  Philippe Benech  for his input in analyzing the transcriptomic data. This work was supported by public [ Aix-Marseille Université (AMU) ,  Centre National de la Recherche Scientifique (CNRS) ] and private grants [ Fondation de l'Avenir, Demain Debout, Combattre la Paralysie ]. KB was granted a research associate fellowship by the  French "Fondation Plan Alzheimer " and  A*MIDEX  (Management of talents).
Imaging analyses Grey matter density was assessed in our patient from his first T1 MRI sequence (Fig. 1a ), and compared to the grey matter density of a group of 30 age-matched healthy controls (age = 44. 9 ± 3. 8) from the online database OASIS (http://www. oasis-brains. org/), using a whole brain z-score map. The 18 F-FDG-PET scan from our patient (Fig. 1c ) was also compared to another group of 23 age-matched healthy controls (age = 44. 3 ± 9. 4) using z-scores map (for details on the control population and imaging processing procedures, see Additional file 1). All z-scores below -2 or above 2 were considered as significant. The patient showed global bilateral decrease of grey matter density affecting all cortical regions as well as subcortical structures and cerebellum (Fig. 1b  and Additional file 2).
Molecular genetics SNCA gene (encoding the alpha-synuclein) mutations were investigated using bidirectional Sanger sequencing on an ABI 3730 automated sequencer (Applied Biosystem) and SeqScape v2. 6 software (Applied Biosystems), and multiplex ligation-dependent probe amplification (MLPA, MRC-Holland). PRNP gene (encoding the prion protein) mutations were investigated using a previously described protocol  [5]. Neither missense mutations nor  18 F-FDG uptake. Patient's cortical atrophy below -2 standard deviations is displayed with a white to dark red scale. Patient's hypometabolism below -2 standard deviations is displayed with a light green to dark blue scale while hypermetabolism is displayed with an orange to yellow scale. R = Right side multiplications were found in the SNCA gene (alpha-synuclein), and no mutation was identified in the PRNP gene (prion protein) either.
Methods and Findings The hazard ratios of various common infections were assessed in 275,072 adults prescribed glucocorticoids orally for 15 d (women: 57. 8%, median age: 63 [interquartile range 48-73] y) in comparison to those not prescribed glucocorticoids. For each infection, incidence rate ratios were calculated for five durations of exposure (ranging from 15-30 d to >12 mo), and risk factors were assessed. Data were extracted from The Health Improvement Network (THIN) primary care database. When compared to those with the same underlying disease but not exposed to glucocorticoids, the adjusted hazard ratios for infections with significantly higher risk in the glucocorticoid-exposed population ranged from 2. 01 (95% CI 1. 83-2. 19; p < 0. 001) for cutaneous cellulitis to 5. 84 (95% CI 5.
Data Source: The Health Improvement Network Approximately 98% of the population in the UK is registered with a general practitioner. THIN is a database of anonymized electronic medical records from UK general practices. Participating general practitioners systematically and prospectively retrieve and enter clinical information on patients, including demographics data, diagnoses, and prescriptions, so that the database provides a longitudinal medical record for each patient. THIN is representative of the UK population, and comparisons to external statistics and other independent studies have shown that both the clinical diagnostic and prescribing information is well recorded and accurate  [11, 12]. The data are entered in routine general practice and therefore reflect "real life" clinical care.
Prescribing is well recorded in terms of general practitioner prescriptions since the computerized entry made by the doctor is also used to issue a prescription to the patient. To date, THIN includes data from almost 600 general practices and more than 12 million individuals. For this study, we used data from 1 January 2000 to 31 December 2012 from all general practices that contributed to the database during this period. The data used for this study were obtained from a license to THIN. For further information on access to the database, please contact IMS Health (contact details can be found at http://www. csdmruk. imshealth. com/index. html).
Identification of Infectious Events All diagnoses and symptoms are recorded in THIN using the Read classification system  [14]. This classification was used to create medical lists that enabled us to identify cases of three bacterial (i. e. , septicemia, lower respiratory tract infection [LRTI], cutaneous cellulitis), two viral (i. e. , herpes zoster, varicella), one parasitic (i. e. , scabies), and two fungal (i. e. , local candidiasis, dermatophytosis) infections recorded in the database (code lists available in S1 Table ). These infections were chosen because they cover a set of bacterial/viral/fungal/parasitic and local/systemic infections frequently diagnosed in primary care. We initially planned to include infectious colitis based on previous work suggesting an association between infectious colitis and glucocorticoid exposure, but exploratory work indicated that this infection was poorly recorded in primary care.
Biological Data We searched the medical file of all glucocorticoid-exposed patients included in the study in order to extract data regarding lymphocyte count and albumin level measured before record of the infectious event (or before a randomly defined date during exposure for those who did not have any of the infections of interest recorded). After exploratory work, we chose to include in the analyses biological data recorded within the period ranging from 3 mo to 1 d before these dates. In cases of several available lymphocyte counts and albumin levels during the period of interest, means were calculated and used in the analyses.
What Did the Researchers Do and Find? Using The Health Improvement Network (THIN) primary care database, the researchers identified 275,072 adults prescribed oral glucocorticoids in the UK between 2000 and 2012, a random sample of people not prescribed glucocorticoids but with a diagnosis of the same underlying disease as the exposed individuals, and cases of infection in both cohorts. Compared to the unexposed group, the glucocorticoid-exposed group had an increased risk of three bacterial infections (septicemia, lower respiratory tract infection [LRTI], and cutaneous cellulitis), one viral infection (herpes zoster), and one fungal infection (local candidiasis) but no increased risk of varicella virus infection, dermatophytosis (a fungal infection), or scabies (a parasitic infection). The increased risk was highest for LRTI-the risk of LRTI was nearly six-fold higher in the glucocorticoid-exposed group than in the unexposed group.
Additional Information This list of resources contains links that can be accessed when viewing the PDF on a device or via the online version of the article at http://dx. doi. org/10. 1371/journal. pmed. 1002024. • This study is further discussed in a PLOS Medicine Perspective by Lionel Rostaing and Paolo Malvezzi • The UK National Health Service Choices website provides information about corticosteroids (glucocorticoids are a specific type of corticosteroids) • The Mayo Clinic has an article about the benefits and risks of corticosteroids • Wikipedia has information on autoimmune disease, inflammatory disorders, and glucocorticoids (note that Wikipedia is a free online encyclopedia that anyone can edit; available in several languages) • MedlinePlus provides links to further information about autoimmune diseases and about corticosteroids • More information about The Health Improvement Network database of anonymized electronic medical records is available.
Statistical Analysis In view of the relative small number of cardiac anesthesiologists in France, we decided to attempt to survey all of them; hence, a sample size calculation was unnecessary. After all completed questionnaires had been received, they were analyzed using MedCalc software (version 12. 5. 0, MedCalc Software bvba, Ostend, Belgium). All descriptive data are presented as the number (percentage of survey respondees) [95% confidence interval].
Similar guidelines are available for noncardiac surgery,  20, 21  and so national datasets might improve the clarity and uniformity of patient management and help to avoid costly reassessments. 20 r the postoperative period, our survey results prompted similar findings. A recent study demonstrated that a standardized protocol increased the likelihood of early extubation and was not associated with elevated reintubation rates. 22 Fast-track cardiac care for adult cardiac surgery patients appeared to be safe, and decreased the time to extubation and the length of stay in the ICU. 23, 24 he present study had several limitations. First, the survey was declarative, and 198 (43%) of the invited anesthesiologists participated in the study. Among the answered questionnaires, 95. 6% [95% CI: 92. 7-98.
ACKNOWLEDGMENTS We thank  Prof. Chia-Fu Chou  ( Institute of Physics, Academia Sinica, Taipei, Taiwan ) for providing the microfabricated devices for studying the cell cytoskeleton under spatial confinement. The microscopy was done at the  Bordeaux Imaging Center , a service unit of the  CNRS-INSERM and Universite de Bordeaux , part of the national infrastructure  France BioImaging. The help of  Patrice Mascalchi  is acknowledged. We also thank the animal facilities of the  Universitede Bordeaux. The help of  Thierry Dakhli ,  Raphael Pineau , and  Laetitia Medan  is acknowledged. We also thank  Ray Cooke  for copyediting the.
manuscript. This work was funded by  INSERM, ANR (Agence Nationale pour la Recherche)   VASCULOSOMES  ( ANR BLANC 2010 1237 01 ),  Fondation de France  (grant  00056836 ), and  Ligue Nationale Francaise contre le Cancer (Comitedes Pyrenees Atlantiques ). P. S. was supported by a grant from  La Ligue Nationale Francaise contre le Cancer  and T. D. by a fellowship from the  Association pour la Recherche Contre le Cancer. F. A. received financial support from the  French State  in the framework of the Investments for the future,  Program IdEx Bordeaux  ( ANR-10-IDEX-03-02 ). B. P. and E. M. are supported by the  Deutsche Forschungsgemeinschaft (DFG)   MO2562/1-1.
Small angle X-ray scattering (SAXS) experiments SAXS samples were prepared in 5 mM phosphate/citrate, 150 mM NaCl pH 7 or pH 4. The initial protein concentration of the samples was 10 mg/ml. Prior to data collection, these samples were injected on the online HPLC system of the SWING Beamline at Synchrotron SOLEIL (Gif-sur-Yvette) to eliminate aggregates. Synchrotron radiation X-ray scattering data were collected at 17°C following standard procedures of the SWING Beamline and were processed with FOXTROT (from SWING beamline) and PRIMUS (Primary analysis and Manipulation with Small Angle Scattering DATA) from the ATSAS package (http://www. embl-hamburg. de/ biosaxs/software. html). The scattering curves were corrected from scattering due to the buffer and Guinier plots corresponding to each curve were generated (S2 Fig).
5 mL with the complete set of GdnHCl solutions. Samples were incubated overnight before fluorescence measurements on a Jasco FP-750 spectrofluorimeter. Excitation wavelength was 295 nm with a bandwidth of 5 nm for both excitation and emission beams. The emission spectra were recorded from 310 to 370 nm at a scan rate of 125 nm/min. Fluorescence intensity ratio at 360 nm over 320 nm (rFI 360/320 ) were determined. These wavelengths are related to tryptophan fluorescence intensities in apolar (320 nm) and solvated (360 nm) environments, respectively, and the values of rFI 360/320 are therefore very sensitive to weak polarity changes in the tryptophan surroundings. Each data point represents the average of three values obtained from emission spectra that were corrected for blank measurements.
Single channel conductance measurements showed that LC blocks the ion channel formed in the membrane by H N for BoNT/A and BoNT/E during translocation  [45]. Reconciliation of this model with our observations would imply that the channel made by H N would be closed by the passage of LC between the lipids of the bilayer and one of the faces of H N embedded in the membrane. de la Recherche (ANR-10-LABX-33). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.
Acknowledgments We thank  Nicolas Durafourc  and  Maïté Paternostre  for help with LUV preparation. For help with protein production and purification we thank  Cassandra Porebski. For help with AUC experiments we thank  Bertrand Raynal. AA was supported by  DGA  and  CEA. This work was funded by the  joint ministerial program  of R&D against CBRNE threats. SIMOPRO is a member of the  Laboratory of Excellence LERMIT  supported by a grant from the  Agence Nationale.
For the purposes of this study, four sources of information were consulted. First, to compare the TB burdens in the various provinces, data from the national TB prevalence survey undertaken in 1990 were used. 8 s the data from subsequent surveys did not provide province-specific data, they could not be used for this purpose. Second, to compare trends during the period of FI-DELIS implementation, the annual number of new smear-positive TB cases notified and the calculated case notification rates (CNRs) within the province Objective: To determine whether the FIDELIS projects contributed to the increased case detection rate for new smear-positive pulmonary tuberculosis (PTB) in China. Methods: We compared the case notification rates (CNRs) in the intervention year with those of the previous year in the FIDELIS areas, then compared the difference between the CNRs of the intervention year and the previous year in the FIDELIS areas with those in the non-FI-DELIS areas within the province.
Conclusion: The FIDELIS projects may have contributed to the increase in case detection of new smear-positive PTB in China, but the level of evidence is low. were considered separately for the FIDELIS and the non-FIDELIS provinces. The CNR was obtained from the total number of new smear-positive cases notified within the given year for the whole province, divided by the province population. Data providing the total number of new smear-positive cases notified within the given year were obtained from the National TB Control Centre of the Chinese Center for Disease Control and Prevention, Beijing, China. Data describing the population of the whole province were available publicly. Notification numbers and rates were compared for the entire province, and not only for the areas specific to the projects.
Third, all routinely reported data from the FIDELIS monthly reports were double-entered, checked and verified in an electronic database without personal identifiers. To compare the FIDELIS CNRS with those of the previous year, the numbers of cases notified in the report forms were used. Finally, for comparison of the FIDELIS and non-FIDELIS areas within a specific province where FIDELIS was implemented in part of the province, the numbers of cases detected in the year of the project and the previous year for both the FIDELIS and non-FIDELIS areas within the province were obtained from the IRAG reports. STATA v. 12. 0 (StataCorp, College Station, TX, USA) was used for statistical analysis. First, the median prevalence of TB in 1990 in FIDELIS provinces was compared with that of non-FIDELIS provinces using the Kruskal-Wallis test.
CONCLUSIONS Our analysis of the FIDELIS project data in China provides limited evidence that the project might have had a role in contributing to the increase in rates of detection of new sputum smear-positive cases of TB in certain project areas in China. In future these types of projects should perhaps be designed in such a way that evaluation of the projects' impact would be simpler and more reliable, for example, by using a step-wedge design. Objectif : Déterminer si les projets de la « Fund for Innovative DOTS Objetivo: Determinar si los proyectos de la iniciativa FIDELIS contribuían a aumentar la detección de casos nuevos de tuberculosis pulmonar (TBP) con baciloscopia positiva en la China. Métodos: Se comparó la tasa de notificación de casos (CNR) durante el año de la intervención, con la tasa del año anterior en las zonas vinculadas con el proyecto FIDELIS, y se examinó además la diferencia de la CNR durante el año de la intervención y el año anterior en zonas de la provincia que no participaron en el proyecto.
Calves were separated from their dams immediately after birth, so that no suckling occurred. If a calf was suspected to have suckled, the dam data was removed from the final analysis. Cows were milked within the first 2 h post-calving. All information on calves at birth (date and time of birth, sex, weight, health status, presentation and calving difficulties) were recorded but not used here. For the pluriparous cows (n = 63), data included parity, previous lactation performances, that is milk yield and composition, length of lactation and length of preceding dry period. Under routine herd management, cows were dried at either 2 to 2. 5 months before expected day of parturition if they still produced 15 to 25 kg milk per day, or at around 3 months before expected day of parturition if they produced <15 kg milk/day.
Colostral IgG1 concentration was determined via a semi-automated single radial immunodiffusion technique  (Mancini et al. , 1965; Levieux and Ollier, 1999)  using commercial kits (ID Ring BOV IgG; ID Biotech, Issoire, France). Sample dilution was adjusted to meet the manufacturer's recommendations (1000 times). Between-and within-assay repeatability was 5% and 9%, respectively, according to ID Biotech, and 10% and 15%, respectively, according to our own in-lab tests run before performing the analyses. Furthermore, in order to gauge colostrum quality, the colostrum density of each sample was also determined in-lab under standard temperature and humidity conditions by analyzing weight-to-volume ratios five times per sample. Statistical analysis R Software was used for all analyses  (Venables and Smith, 2010).
Distributions of continuous variables were examined and, if necessary, log-transformed (SCC to somatic cell score (SCS), but only SCC data are reported and discussed). To study IgG1 concentration and its average variation between quarters, ANOVA model was used including the effect of quarter and cow. In this approach, type-I error rate was controlled, and once the effect of the quarter on IgG1 levels was proven, a Student-Newman-Keuls test was used to compare all pairs of quarters to inform the interpretation. A similar approach was used to compare left v. right quarters and hind v. front quarters. For the study on factors influencing colostral IgG1 levels, the model tested BW, calving date, parity, dry period length, fat, protein and urea levels in the colostrum, SCS, and all information on previous lactation (duration, milk yield, fat and protein concentration).
Acknowledgments The authors thank the technical staff at the  Dairy Research Station at Méjusseaume ,  Le Rheu  for taking care of the animals and running the colostrum and serum samplings. They also thank  C. Doré  for running the laboratory analysis,  M. Kloareg  for running the statistical analysis and A-T-T Scientific Editing Services ( Clermont-Ferrand, France ) for proofreading the manuscript.
ACKNOWLEDGMENTS The authors are supported by the  French Ligue contre le Cancer  (équipe labellisée);  Agence National de la Recherche (ANR) -Projets blancs ;  ANR  under the frame of E-Rare-2, the  ERA-Net for Research on Rare Diseases; Association pour la recherche sur le cancer (ARC) ;  Cancéropôle Ile-de-France ;  Institut National du Cancer (INCa) ;  Institut Universitaire de France ;  Fondation pour la Recherche Médicale (FRM) ; the  European Commission (ArtForce) ; the  European Research Council (ERC) ; the  LeDucq Foundation ; the  LabEx Immuno-Oncology ; the  SIRIC Stratified Oncology Cell DNA Repair and Tumor Immune Elimination (SOCRATE) ; the  SIRIC Cancer Research and Personalized Medicine (CARPEM) ; and the  Paris Alliance of Cancer Research Institutes (PACRI).
Background: Most estimates of postpartum hemorrhage (PPH) are calculated from studies that use administrative or medical birth databases, and only a few from prospective observational studies. Our principal objective was to estimate the incidence of PPH according to their severity (mild or severe) in vaginal deliveries (>500 mL, ≥1000 mL) and cesareans (>1000 mL and ≥1500 mL). The secondary objectives were to describe the incidence of PPH according to maternity unit characteristics, causes, and types of PPH management. Methods: This prospective observational study took place in French maternity wards. Women who gave birth at a term ≥ 22 weeks were eligible for the study. 182 maternity units participated in a study with prospective data collection from 1 February, 2011, to 31 July, 2011. The main outcome measure was PPH incidence.