dataesr/scientific-paragraphs-categorization huggingface dataset:
Cells were washed directly before performing fluorescence imaging. Measurement of the ratio of 450 nm (blue)/ 535 nm (green) fluorescence allowed determining whether the bacteria established a phagosome-cytosol communication. Reading was performed by a fluorescence microscope with AutoPlay (Nikon) for the automatic acquisition of at least 50 cells per well and image analyses were performed using a dedicated algorithm using METAMORPH software  [47]. The experiment was repeated twice with similar results.
Statistical analyses Fisher's exact test and the Student's t-test were used for all comparisons (GraphPad PRISM version 6. 0d; GraphPad Software, Inc). A p-value less than 0. 05 was considered significant (n. s. ¼ non-significant, *p , 0. 05; **p , 0. 01; ***p , 0. 001; ****p , 0. 0001).
A. -L. R. , A. V. , A. B. , R. S. , A. B. , L. L. , T. D. , L. M. , M. R. and F. G. -M. carried out the microbiology, bacterial-cells interaction, confocal microscopy, electronic microscopy (A. V. with C. d. C. ). J. -L. H. , L. K. , C. d. C. , I. V. , R. B. , L. M. and J. -L. G. participated in the design of the study and drafted the manuscript; A. -L. R. , A. B. , R. S. , L. M. , I. V. , R. B. and J. -L. H. carried out the statistical analyses; J. -L. H. , L. K. , R. B. , C. d. C. and I. V. conceived the study, designed the study, coordinated the study and drafted the manuscript. All authors gave final approval for publication. European Community FP7 Marie Curie Career Integration Grant Europe (autophagtuberculosis 293416), University of Toulouse and Vaincre la Mucoviscidose. A. V. would like to thank Infectiopole Sud for financial support.
Acknowledgements. We greatly acknowledge  Dr S. Canaan  for critical reading of the manuscript and help in formatting the TIFF files of EM figures and  V. Dubois  for formatting the figures. We wish to acknowledge  TRI-Genotoul Imaging facility (Toulouse, France ). The authors wish to thank  Jean Paul Chauvin , head of this EM facility, for expert technical assistance with the electron microscopes and the digital camera.
Functional maps of BOLD signal were computed using Statistical Parametric Mapping (SPM8, Wellcome Trust Centre for Neuroimaging, University College London, UK) run in MATLAB R2012a (MathWorks, Natick, MA). For first-level single-subject analysis, functional images were preprocessed for slice timing and motion corrections, and smoothed with a 6×6×6 3D Gaussian kernel  [25]. For second-level group analysis, anatomical and functional volumes were co-registered, spatially normalized into the Montreal Neurological Institute (MNI) template, and the preprocessed functional images were smoothed with an 8×8×8 3D Gaussian kernel. Voxel-wise analysis of BOLD signal consisted of modeling the activation and baseline conditions with a boxcar function convolved with the canonical hemodynamic response function using a general linear model  [26]  with motion parameters as covariates and applying a 128 Hz high-pass filter  [27].
Cortical Terminations of WM Fascicles Image datasets were co-registered (mutual information algorithm) using iPlan Stereotaxy 3. 0 software. The FA, color-coded direction, and BOLD-cluster maps were co-registered with T1-weighted MR images (anatomical reference). Accuracy of registration was carefully reviewed (visual analysis of merged images and test-retests) using the following landmarks: putamen, pallidum, corpus callosum (whole body and major and minor forceps), anterior and posterior limbs of the internal capsule, cerebellar contour, tentorium of the posterior fossa, sylvian region, upper brainstem contour, ventricular system (frontal horns and trigone), interhemispheric fissure and main cerebral gyrations. For each individual, we generated 3D surface renderings of the brain from T1-weighted MR images used to determine the cortical terminations of WM fascicles within the frontal, parietal, temporal and occipital lobes of the right and left hemispheres.
Connections between WM Fascicles and BOLD Clusters Structure-function relationships were investigated by analyzing WM fascicle-BOLD cluster connections at individual level (each subject being its own anatomical reference) within cortical territories known as essential language areas in order to figure out which WM fascicles are related to language processing. A connection was determined when fibers went through a cluster, regardless of number of fibers involved (Fig  3 ). Since fMRI clusters were located within the gray matter and fascicles terminated in the subcortical WM, each cluster was enlarged by 4 mm in the depth direction using a "scaling object" tool (iPlan Stereotaxy 3. 0) to encompass the gray-white matter interface.
TRIPOD (Transparent Reporting of a multivariable prediction model for Individual Prognosis or Diagnosis) methodology was used for the development, the Quality Assurance and the description of the experimental procedures. Conclusion: In an internationally approved quality assurance framework, ML seems promising in predicting the outcome of patients that would benefit or not of the PII. Once confirmed in larger and/or multi-centric databases, ML could support the physician in tailoring the treatment and in deciding if deliver or not the PII. www. impactjournals.
Research Paper of the PII, but all the patients receiving it are exposed to the potential risk of its acute and late toxicity. Moreover, a study by Crowley et al. supports the use, for selected cases of ACC, of smaller than standard radiation fields, avoiding PII, in order to reduce acute and late toxicity  [6] , an attitude of particular interest in patients presenting an intrinsic higher risk of toxicity (e. g. HIV+ patients, elderly patients…)  [7, 8]. Unfortunately, none of the available classical statistical techniques or predictive models allow the identification of patients presenting a higher risk of inguinal microscopic invasion (for example, higher than 5%). Predictive models based on the Machine Learning (ML) and Artificial Intelligence (AI) techniques are being more and more adopted in the medical and bio-molecular field, as these methods have many attractive theoretic properties, specifically, the ability of analysing very large datasets and to detect non predefined relations such as nonlinear effects and/or interactions  [9, 10].
Importance of the considered features By applying the Information gain technique (see Methods section) to the considered dataset of patients, we found that 8 of the considered features carried a significant amount of information for the correct classification of the patients' outcome: PS, T and N stage, uTNM, Stage of the tumor, cTNM stage, tumor site, no symptoms or pain or tenesmus at diagnosis, histology and method used for the histologic definition, the presence of positive inguinal nodes, the administration of neoadjuvant CT, the treatment of an anal canal cancer relapsing after an initial surgery. In order to validate such results, we generate new predictive models using the same ML techniques, based only on the features selected by the Information gain technique. The mean accuracy was not worsened (data not shown).
Literature sources and search In August 2015 we searched MEDLINE, PEDro, OSTMED. DR, and the Cochrane Library databases and as well as Google Scholar, the Journal of American Osteopathy Association (JAOA) and the International Journal of Osteopathic Medicine (IJOM) websites. The search strategy was as follows: • for reliability studies, we started with the combination of keywords ["reliability" OR "agreement" OR "reproducibility"] AND ["cranial" OR "craniosacral" OR "cranium" OR "primary respiratory mechanism"]. When the number of references exceeded 100 hits with the above equation, we added ["osteopathy" OR "osteopathic"]. • for efficacy studies, we used the combination of keywords ["cranial manipulation" OR "osteopathy in the cranial field" OR "cranial osteopathy" OR "craniosacral technique"] AND ["medicine" OR "treatment" OR "therapy" OR "technique" OR "manipulation" OR "osteopathy" OR "osteopathic"].
Study selection For inclusion in our review, studies had to meet the aforementioned eligibility criteria. For study selection, we considered all techniques claimed by the authors to belong to the field of cranial osteopathy or mentioned in the classical osteopathic literature. If in doubt, we considered the technique to be inside the field. Studies that described the use of techniques or diagnostic/therapeutic strategies from cranial osteopathy together with other diagnostic/ therapeutic modes but without performing subgroup analysis were excluded. The systematic selection process was composed of 3 steps. Firstly we made a selection by title. Duplications due to overlap in the coverage of the databases and off-topic studies were excluded. Secondly, the abstracts of each study were analyzed.
The second study rated as having low risk of bias, by Haller et al. [44]  aimed at investigating craniosacral therapy (CST) compared to sham treatment in patients with chronic non-specific neck pain. The primary outcome was pain intensity assessed with visual analog scale and 16 secondary outcomes were investigated. Data (between CST and sham groups) were compared immediately and three months after the intervention. The results showed statistical and clinically relevant differences in favor of CST for the primary outcome and seven of the secondary outcomes immediately after treatment. At three months the results remained statistically and clinically relevant for the primary outcome and statistical differences still existed for five of the secondary outcomes. While this study is methodologically relatively strong, it nevertheless has some limitations.
| DISCUSSION This study addresses the prevalence of self-reported TBI in a population of female prisoners in a French prison. Secondary aims included studying covariables known to be associated with TBI. The main findings were that the rate of self-reported history of TBI was high, with an overall prevalence of 21%, and violence was the most frequent causes of TBI among women. The majority of reported TBIs were moderate or severe (57%). Furthermore, the rate of epilepsy was high (6%). Among women who reported a TBI, perceived health was worse e 30% of missing data for juvenile females and >23% for adult females. and alcohol and psychotropic drugs use was more frequent than among those who did not report a TBI. This study is the first to report on the prevalence of TBI among females prisoners in France.
| Limitations Our study is cross-sectional and as data were collected by means of an interview (self-report), the results should be interpreted with caution. As, however, the reliability of prisoners' responses is frequently challenged, it is interesting that a recent study involving 200 Australian prisoners highlighted the fact that inmates' responses to questionnaires corresponded closely to the reality  (Schofield et al. , 2011). These findings run counter to the conventional wisdom that responses by the criminal population are dishonest and therefore unusable. One could also argue a recall bias, which is an error caused by differences in the accuracy or completeness of the recollections retrieved by participants regarding past events or experiences. Even if cases and controls were not of the same mean age (35 for cases, 29 among controls), findings about differences can be considered sound enough to be discussed because it is difficult to believe that anyone would not remember having sustained a TBI.
ACKNOWLEDGMENTS The authors wish to express their gratitude to  Prof. H Williams  for his contribution to the creation of the questionnaire. We would like to thank  Dr R. Katz  and  Mr. James Moore  for having scrutinized the manuscript and  Mme G. Bard  for collecting the data, collating references, and formatting the text. We would also like to thank the physicians and nurses from the Fleury-Mérogis medical team who participated in the administration of the questionnaire. We also thank the anonymous reviewers for their thoughtful comments on the first version of the manuscript, which enabled us to improve it. The results of this work have already been presented at the SOFMER conference (Montpellier 2015).
FUNDING INFORMATION This study was funded by the  "Fondation des Gueules Cassées " and has been supported by the  "Centre Ressources du Traumatisme Crânien Ile de France " and  Sorbonne Univ Paris 06 ,  UMR 7371 ,  UMR S 1146 ,  Laboratoire d'Imagerie Biomédicale, F-75005, Paris, France.
Spectral imaging GL261 murine glioma cells expressing DsRed2 (plasmid: pDsRed2-N1, Clontech,Mountain View, USA) were cultured as previously described  [11, 16]  on glass-bottom Petri dishes. Five microliters of a QD655 solution (QTracker 655, Molecular Probes; 8µl in 50 μl of PBS qsp) were added and images were acquired successively under an 800nm NLO excitation and a 1050nm OPO excitation with the same laser power. Fluorescence signals were collected from 411 to 696nm on a descanned 32-channel spectral detector with a λ-space of 8. 9nm. Spectral deconvolution was performed under the Zeiss Zen 2012 software.
Importantly, our results on the excitation of QD655 and EYFP outline that the 2P excitation spectrum cannot be simply predicted from the monophoton excitation spectrum of the fluorophores. Several similar examples for QD, proteins and organic dyes can be found in online spectra database (http://www. spectra. arizona. edu/). Finally, because commercial solutions already offer the possibility to deliver the fundamental pump wavelength simultaneously with the tuned OPO wavelength, at powers compatible with in depth imaging, we show that 5) multicolor imaging of fluorescent transgenic mice enter a new era. This should greatly facilitate the investigation of many questions related to the pathophysiology of various diseases and to assess the effects of pharmacological treatments directly in the living animal.
Acknowledgments The authors would like to acknowledge  Celine Caravagna  for contributing to surgical procedures and  Gwenaelle Tardif  for genotyping and cell culture. This work was supported by grants from  Fondation de la Recherche Médicale  ( ING20140129149 ) and from  Agence Nationale de la Recherche  ( ANR15-CE16-0009-01 ) to FD, from  Site de Recherche Intégré en Cancérologie  ( INCA-DGOS-INSERM 6038 ) and ARSEP Fondation to GR as well as a CIFRE PhD fellowship by  Carl Zeiss France  to AJ.
Immunohistochemistry For Six1 immunostaining, SOL and gastrocnemius plantaris (GP) muscles were embedded in cryomatrix and quickly frozen in isopentane cooled with liquid nitrogen. Cryostat sections (10 μm) were fixed in 4 % PFA and washed in 1× PBS. The sections were treated with Antigen Unmasking Solution (H-3300, Vector Laboratories) at 95 °C for 10 min and washed in 1× PBS for three times. Sections were treated with 1 % H 2 O 2 solution for 20 min. After three washes in 1× PBS, they were permeabilized with 0. 1 % Triton X-100 for 20 min and left for 1 h in blocking solution (1× PBS, 1. 5 % goat serum, 0. 1 % Triton X-100). Rabbit polyclonal antibodies directed against Six1 (HPA001893, Sigma) (1/100 dilution), and dystrophin (NCL-DYS2, Leica Biosystems) (1/50 dilution) were applied overnight at 4 °C to the treated sections.
SDH/GPDH staining Fresh-frozen sections were incubated in 0. 2 M phosphate buffer (pH 7. 6) containing sodium succinate and nitroblue tetrazolium, NBT (N6876, Sigma Aldrich) for 30 min at 37 °C. Sections were then washed with water and mounted in glycerine gelatin medium. GPDH staining was performed by incubation of unfrozen muscle sections with α-glycerol phosphate as described  [37]. For quantification of SDH and GPDH staining, the color images were converted to thresholded images at hue (121-208) and brightness (0-140) by a threshold tool of ImageJ software. The area of thresholded images was measured by ImageJ and normalized by the whole soleus muscle area.
ChIP experiments GP and tibialis anterior (TA) muscles of 2 months old female mice were minced with scissors immediately after harvesting and fixed in 1 % formaldehyde for 10 min. Formaldehyde was quenched by addition of 0. 125 M glycine, and muscles were washed twice in PBS. Muscles were then incubated on ice in lysis buffer (10 mM Tris-HCl pH 7. 9, 85 mM KCl, 0. 5 % NP40, protease inhibitors (Complete, Roche)) for 10 min and homogenized with a mortar and subsequently with a dounce homogenizer. Nuclei were obtained by centrifugation, incubated in SDS lysis buffer (50 mM Tris-HCl pH 8, 10 mM EDTA, 1 % SDS, protease inhibitors) for 10 min, and sonicated in a bioruptor apparatus (Diagenode). The debris was removed by centrifugation. Sonicated DNA was incubated with 1 μg of Six1 antibodies (HPA001893, Sigma) under rotation at 4 °C overnight.
Western blot Cell or tissue lysates of GP and SOL from cSix1KO and control mice (20-40 μg) were denatured in Laemmli buffer, separated by SDS-polyacrylamide gel electrophoresis and transferred to nitrocellulose membrane. Membranes were blocked in 50 mM Tris-HCl pH 7. 6, 137 mM NaCl and 0. 1 % (v/v) Tween-20 containing 10 % (w/v) skimmed milk or 5 % (w/v) BSA for 1 h at room temperature and incubated overnight at 4 °C with the indicated primary antibodies (Complex I, NADH dehydrogenase, ab14713, Abcam (Cambridge, UK); Complex II, succinate dehydrogenase, ab109865, Abcam (Cambridge, UK); cytochrome bc1 complex, ab110252, Abcam (Cambridge, UK); Complex IV, cytochrome C oxidase, ab14744, Abcam (Cambridge, UK); Complex V, ATP synthase, ab14748, Abcam (Cambridge, UK); hexokinase II, Sc-6521 (Santa Cruz Biotechnology); glycogen synthase 1, CST #3893, Cell Signaling Technology; AS160, 07-741, Millipore; GLUT4, kind donation from Geoffrey Holman, University of Bath); lamin B, sc-6216 (Santa Cruz Biotechnology); β-tubulin, 05-661 (Millipore); Six1, HPA001893 (Sigma).
Acknowledgements We thank  V. Moncollin  at  ENS Lyon  for help with the adult muscle ChIP experiments, the imaging facility at  Institute Cochin  for technical assistance, the sequencing and genomic platform at  Institute Cochin  for microarray experiments and  F. Dumont  and  S. Jacques  for advice. We Thank  Dr. Daniel Metzger  for the gift of the HSA-CRE ert2 mouse line. We thank  Dr. Sophie Gautron  and  Dr. Stefano Schiaffino  for critical reading of the manuscript and  Dr Pascale Bossard  for helpful discussions. I. S. is supported by  ANR ,  The Uehara Memorial Foundation  and  JSPS Postdoctoral Fellowships for Research Abroad. Financial support was provided by the  Institut National de la Santé et la Recherche Médicale (INSERM) , the  "Association Française contre les Myopathies" (AFM) , the  Centre National de la Recherche Scientifique (CNRS) , and the  Agence Nationale pour la Recherche  ( ANR RPV09108KKA ).
Lymph node metastases Negative EUS-FNA of regional lymph nodes and negative staging laparotomy/ hand-assisted-laparoscopy with biopsy of regional lymph nodes Abbreviations: CA 19-9; carbohydrate antigen 19-9, EUS-FNA; Endoscopic ultrasonography-fine needle aspiration. doi:10. 1371/journal. pone. 0156127. t001 was extracted from the ELTR database containing all patients that were transplanted between 1990 and 2010 for hCCA. There were 249 patients from 57 European centers. Twenty-seven centers transplanted 2 patients. The list provided only basic variables, insufficient for indepth analyses. Therefore, all centers were contacted with a request to participate in the study. Centers were preferably addressed in their own language (English, Italian, French, Swedish, Dutch). Each center was asked to upload additional information regarding patient and tumor.
Statistics Statistical analyses were carried out using IBM SPSS Statistics, (IBM, Armonk, New York, USA). The results are expressed as the means ±SD. Comparison of means was performed with the Student t-test for independent samples. Comparison of categorical variables was performed with the Chi-Square test and Fisher's exact probability test. Five-year survival rates were calculated using the Kaplan-Meier method and the differences between groups were calculated using the log rank test. Univariate analyses were conducted for patient survival by Kaplan-Meier estimates of survival probabilities and the log-rank test for comparisons. A Cox proportional hazard regression model was used to analyze associations with patient survival in multivariable analysis. P values were two-sided and values of less than 0.
Results and Discussion Twenty-one centers uploaded data of 173 patients in the electronic database, resulting in a response rate of 69%. All patients were transplanted between 1990 and 2010. Twenty-six patients were excluded from the database, 12 because they were erroneously coded in the ELTR (the indication for transplantation was not hilar cholangiocarcinoma) and 14 because hCCA was incidentally found after liver transplantation. A study group of 147 patients remained. Eighty-two patients were transplanted in the first decade between 1990 and 2000 and 65 patients were transplanted between 2000 and 2010. The status of the distal bile duct margin was established in 137 patients and was tumor free (R0 resection) in 125 patients (91. 2%). Mean follow-up was 4. 1 years (± 5. 0).
Acknowledgments Professor René Adam is custodian of the European Liver Transplant Registry (ELTR). Dr. William F. Bennet is an ELTR Board member. We are much obliged to the following collaborators of this study: • Dr. Frank Lehner and Professor Jurgen Klempnauer from the department of Visceral and Transplant Surgery, Hannover Medical School, Hannover, Germany. • Professor Bo-Göran Ericzon from the department of Transplantation Surgery, Center for Surgical Sciences, Karolinska Institute, Karolinska University Hospital Huddinge, Stockholm, Sweden. • Professor Roland Croner from the department of Surgery, University Hospital Erlangen, Erlangen, Germany. • Professor Johann Pratschke and Dr. Robert Sucher from the Department of Visceral, Transplant and Thoracic Surgery, Innsbruck Medical University, Innsbruck, Austria • Dr.
Then, libraries were constructed and captured by using SureSelect Human All Exon v5 kit (Agilent), following the manufacturer's protocol. Paired-end (2 × 151 bases) sequencing was performed on a NextSeq500 device (Illumina). Obtained sequences were aligned and annotated with the human Hg19 genome based on the SureSelect Human All Exon v5 manifest by using Burrows-Wheeler Aligne (BWA) and Genome Analysis toolkit (GATK) algorithms. Only sequences with a read depth of 10 × and a mutation allele frequency superior to 5% were conserved for the analysis. The analysis is fostered on 137 clinically relevant genes related to biological pathways linked to cancer predisposition or available targeted therapies (Supplementary Table  1 ). Copy number variations were studied by using Control-FREEC software as described  [5, 6].
It was interesting to see that among the 8 altered genes (Table  1 ), we observed a SMAD4 stop mutation, which is frequently found in CRC. An activating mutation of AKT1 was observed (Q79K). It could be targetable by protein kinase B (AKT)/mTor inhibitors. Surprisingly, we observed a constitutive Chek2 mutation (R117G), a gene involved in the homologous repair process. This mutation is cited in the public database for conferring a predisposition to cancer. Moreover, the analysis of copy number variation showed a loss of heterozygosity in chromosome 22 (from 29091114 to 29130709) (Figure  1A ). This analysis suggested a complete deletion of Check2 function in tumor cells. After discussion of the case at the molecular tumor board, the patient was proposed to receive off-label PARP inhibitor olaparib which previously showed efficiency in patients with Chek2 mutation in metastatic prostate cancer  [7].