dataesr/scientific-paragraphs-categorization huggingface dataset:
Patient selection Patients with primary diagnosed glioblastoma consecutively treated in our Comprehensive Cancer Center between April 2006 and March 2010 were identified through the electronically records database. Inclusion criteria were: a histopathologically proved glioblastoma, treated by surgical total or subtotal resection (thus excluding patients with a "biopsy-only") and full course of radiation, with immediate (<48 h) post-operative magnetic resonance image (MRI) to assess tumor resection and with documented radiological follow-up for at least 6 months after surgery. Patient data, including demographics, imaging data, treatment and clinical outcomes were retrospectively collected. The cut-off date for the analysis was September 2014. This study was approved by our Institutional Review Board and our local ethics committee.
Imaging data Pre-operative imaging data (T1-weighted MRI pre-and post-contrast and FLAIR sequence) were assessed to define the tumor volume and the tumor localization with regard to the SVZ. Given the difficulty to differentiate between non-tumoral vasogenic-edema versus tumorinfiltrative area within the non-enhancing FLAIR hyperintensity lesion in T2-weighted sequences, contacting tumors were defined as tumors having a distance of 0 mm between the contrast enhancing tumor edge and the SVZ, as performed in most previous studies  [26] [27] [28] [29] [30]. Post-operative post-contrast T1-weighted imaging was used to distinguish : patients with gross total resection (GTR) in case of no residual enhancement or near total resection (NTR) in case of only rim enhancement of the resection cavity, from patients with subtotal resection (STR), namely with residual nodular enhancement  [44].
SVZ delineation and dosimetry data collection According to Barani's delineation suggestions  [47] , ipsilateral (iSVZ), contralateral (cSVZ), and bilateral (bSVZ) SVZs were retrospectively segmented by a single physician as a 5-mm lateral margin of the lateral ventricles based on the patient's original treatment planning CT scan. In a neural stem cells sparing attempt, two delineation methods were assessed: with (TH+)  [34, 36, 38, 39]  and without (TH-)  [37]  temporal horn (Fig. 1 ). Dosevolume histograms were retrospectively generated on the original plans, and dose-volume parameters to each SVZ volume were extracted: mean dose and volume of SVZ (%) receiving more than x Gy (VxGy).
For SVZ dosimetric data analysis, several dose-volume parameters were used as variables. Patients were also dichotomized using published mean dose to SVZ volumes cut-off of 40 Gy  [38]  and 43 Gy  [34] , as well as using optimal cut-off searched with the minimal p-value approach (1000 bootstrap internal validation). Multivariate analysis was assessed using the Cox proportional hazards model including significant covariates in univariate analysis. All reported p-values were two-sided. For all statistical tests, differences were considered significant at the 5% level. All statistical analyses were conducted using STATA 13. 0 software.
An additional and/or alternative one would be that some of patients who received a higher bSVZ irradiation experienced an "artificial" increase in TTP via a more durable transition through a migratory phenotype, before engaging towards a proliferative one. Then a strategy to encompass such a mechanism of radioresistance would be to associate prophylactic irradiation of bSVZ with intensity modulated radiotherapy (and hippocampal sparing) ensuring a V20Gy >84%, and inhibitors of migration which could target integrinmediated signalling pathway. This strategy has never been assessed but could provide promising results. Meanwhile, some more robust data should soon come from three ongoing or recently concluded clinical trials regarding the impact of SVZ irradiation in GBM (NCT01478854 exploring a deliberate sparing of neurogenesis niches, contrary to NCT02039778 and NCT02177578, exploring a deliberate SVZ irradiation).
Acknowledgements The authors would like to thank  Chantal Franco ,  Murielle Mounier  and  Patricia Garnier  for assistance with collecting clinical data, and  Grégory Hangard ,  Stéphanie Ochoa ,  Fabienne Carillo ,  Christelle Lanaspèze ,  Thierry Lacaze ,  Nathalie Defour  and  Laure Vieillevigne  for assistance with restoring treatment plan data.
MeThOds study participants Participant data were acquired from the Natural History Project database of the Dystonia Coalition (https://www. rarediseasesnetwork. org/ cms/ dystonia), a multi-centre, cross-sectional study of subjects diagnosed with isolated, idiopathic dystonia. Subjects 18 years of age or older with isolated dystonia affecting any body region and presence of symptoms for no more than 5 years were enrolled across 28 clinical sites in the USA, Canada, Germany, France and Italy (see online supplementary appendix 1 for list of additional dystonia coalition investigators that contributed subjects included in our analysis). We excluded comorbidities that would confound diagnosis or evaluation other than dystonia or tremor, including medical or neurological disorders that would preclude completing the neurological examination protocol and questionnaires.
dystonia phenotype Subjects were categorised according to their initial site of dystonia, which included five regions: cervical (neck and shoulder), laryngeal (larynx), limb (upper arm, hand, upper leg and foot), lower cranial (lower face, tongue and jaw) and upper cranial (upper face). Subject data were excluded from analyses if onset site was the trunk or pelvis, not reported, or if more than one body region was reported as being initial sites of dystonia.
The relationship of pain and dystonia severity to the severity of neuropsychiatric symptoms across AOFD phenotypes was further investigated using regression type methods and analysis of covariance, correcting for pain severity and dystonia severity (as measured by the GDRS), for continuous outcomes followed by pairwise comparisons among the dystonia onset site groups. SAS software V. 9. 4 was used for all data analyses. Significance level was defined as a p<0. 05.
Participants Data from a total of 493 AOFD subjects enrolled in the Natural History Project met our initial search criteria, but 15 subjects were excluded due to having more than one region of initial dystonia onset reported, leaving 478 subjects for analyses (table  1 ). Subjects reporting onset of dystonia in a limb were predominantly affected in their upper limbs (52 of 60 subjects). Data for BDI, HADS-D, HADS-A, LSAS and SF-36 (Pain) rating scales were available for 93% of the subjects, in part, due to exclusion of data from one centre that used an older version of the BDI. There were more women than men in all onset site groups, but no significant difference across the groups (χ 2 =0. 92, p=0. 922). Age at onset differed across the groups (F 4,123 =5. 74, p<0. 001), with pairwise comparisons showing upper cranial had an older age of onset than cervical (p=0.
Thus, it may be that speech difficulties (eg, reduced intelligibility) in particular lead to secondary stigma and social anxiety. This is further supported by a study comparing patients with laryngeal dystonia to patients with vocal fold paralysis that found no significant difference in social phobia between the two groups. 27 lthough our study leveraged an international, multicentred database repository and is the largest of its kind, it is nevertheless limited by smaller sample sizes within some of the dystonia groups. Our study also may be weighted towards subjects who were evaluated at specialty tertiary centres and possibly have more severe forms of dystonia or more severe non-motor symptoms associated with their dystonia, potentially limiting the generalisability of our results. In our study, we also restricted our analysis to those with recent onset of dystonia to capture neuropsychiatric symptoms as it relates to the initial body region affected and at a relatively early stage of disease.
This study was supported by a grant from the  National Institutes  of health (Dystonia coalition  U54 Ns065701 ). We would like to thank  Laura J Wright ,  Ma , for her assistance with accessing the Dystonia coalition database and ami  R Rosen, Ms , for providing organisational support for the Dystonia coalition. Contributors BDB: project conception, design, organisation and execution; recruitment and clinical assessment of subjects; statistical analysis design and oversight; manuscript drafting and revision. JJ: project conception, design and organisation; manuscript review and critique.
Study population and data collection We retrospectively analyzed data from all patients who underwent a PD for benign or malignant tumors of the head of the pancreas or peri-ampullary area at two tertiary centers between March 2012 and April 2015. The recorded data included the patient demographics, co-morbidities, ASA score, need for pre-operative biliary drainage, administration of a neoadjuvant treatment, intra-operative blood loss, blood transfusions, operative time, intra-operative MPD diameter and pancreatic gland texture, need for vascular resection, type of pancreatic anastomosis, pylorus preservation, modality of drainage of the pancreatic anastomosis and/or the MPD, amylase levels on operatively placed drains, use of somatostatin analogs, type and severity of post-operative complications, length of hospital stay and histopathological data.
Statistical analysis All analyses were performed using Stata software (version 13; StataCorp, College Station, TX) and were performed for a two-sided type I error of α = 5%. Baseline characteristics were presented as the mean ± standard deviation for continuous data (Shapiro-Wilk test was used to assess normality), and as the number of patients and associated percentages for categorical parameters. Comparisons of the patient's characteristics between groups were carried out using the chi-squared test for categorical variables, and Student's t-test or the Mann-Whitney test when assumptions of the t-test were not met (normality and homoscedasticity studied using Fisher-Snedecor test) for quantitative variables. Next, a generalized linear regression model (logistic for dichotomous dependent outcome) was considered to study the effect of predictive factors in multivariate analysis by backward and forward stepwise regression of the factors considered significant in univariate analysis and according to clinically relevant parameters.
Data pre-processing All data processing of the Raman spectra was performed using MatLab 7. 2 and established protocols  [44]. Data pre-processing included smoothing, baseline correction, vector normalization and substrate removal. All spectra, including substrate backgrounds, were vector normalized and smoothed using a Savitzky-Golay smoothing method (order 5, 13 point window). A rubber band correction for baseline removal for all the spectra was carried out and the substrate spectra were subtracted from each spectrum.
Data analysis The Raman spectral data have been analysed by comparing the mean spectra of each patient, including control/healthy persons as well as HCV patients. The assignments of the Raman spectral features used in interpretation of the results were taken from the literature  [24, 35, [45] [46]  and are described in Table  2. In order to further elucidate the biochemical basis of the development of HCV as compared to the healthy/control samples, PCA was performed. PCA is a mathematical procedure involving the transformation of possibly correlated variables into a smaller number of uncorrelated variables, known as principal components (PC), basically to reduce the dimensionality of the data whilst maintaining their variability. The first principal component accounts for the dominant source of variability in the data, and each succeeding principal component accounts for the next highest source of the remaining variability.
The loadings of the PC can be understood as the orthogonal dimensions of biochemical differences which facilitate separation of different groups of spectra of Raman data along their variability as each spectrum scores along these dimensions. To improve the diagnostic potential, PCA-LDA was then performed on the whole dataset to produce confusion matrices using the scores  [47]. Specifically, the algorithm was performed using a stratified 10-fold cross validation, splitting the data into calibrations and test sets. For each virus load tested, 90% of the Raman spectra were used for calibration while the remaining 10% constituted the test sets. Ultimately, the confusion matrix built results from the 10 iterations and gives the overall classification from the 10 test sets. The classification which resulted in the maximum accuracy while keeping the number of latent variables to a minimum was chosen for all successive models.
This work has been supported by the Research grant of worth 10,000 US $ (Grant number: O/Ref: I. C. P. S. R/ 3. 8. 2. 1. 1/11, by Islamic Educational, Scientific and Cultural Organisation (ISESCO), Morocco awarded to the Corresponding author for this Project for the period May, 2015-May, 2017. The corresponding author (PI of this project/research grant) is very much thankful to the donor funding agency and highly acknowledge here in this manuscript.
Research Grant: This work has been supported by the Research grant of worth 10,000 US $ (Grant number: O/Ref: I. C. P. S. R/ 3. 8. 2. 1. 1/11, by Islamic Educational, Scientific and Cultural Organisation (ISESCO), Morocco awarded to the Corresponding author for this Project for the period May, 2015-May, 2017. The corresponding author (PI of this project/research grant) is very much thankful to the donor funding agency and highly acknowledge here in this manuscript.
Inversion Procedure Details Direct application of Eq. (  31 ) is first presented in figures, just after the original sample, and one can see edge artifacts due to horizontal and vertical translations of the sample and the different scale rates between voxels located at the edge of a single reconstruction and those located at the center. First, the obvious solution presented is to normalize scales following the z-axis direction, where we can still see these edge artifacts, and conclude that problem is not only about scaling. In the last solution presented, we removed these voxels located at edges, where we can appreciate an encouraging 3-D reconstruction of the sample. A cosine window function was used in the Fourier domain of projections to control high frequencies. Data not recorded in the hole area were filled by a numerical solution of a heat diffusion problem from values of energies captured at the hole edge.
Search methods for identification of studies Electronic searches. We searched separately for interventional and cohort studies in PubMed, EMBASE, Google Scholar and the Cochrane Database of Systematic Reviews (search strategy and search results in S1 Appendix). Searching other resources. We looked for cross references in the included studies, and reports; online and offline. We communicated with relevant experts in the fields for any article/research study (ongoing or recently completed) on this topic. A grey literature search included ISI Web of Science with conference proceedings, ClinicalTrials. gov, national and international trials registers, the World Health Organization (WHO) International Clinical Trials Registry Platform (ICTRP) search portal (apps. who. int/trialsearch/), metaRegister of Controlled Trials (mRCT) (controlledtrials.
Data collection and analysis Selection of studies. We removed duplicates and imported the bibliography to Rayyan for initial screening of title and abstracts. Rayyan is an open access web application (https:// rayyan. qcri. org/). Once the bibliography was uploaded, it facilitated independent screening of bibliographic records (with blinding) followed by a providing a summary of screening (number of records included or excluded with consensus and number with no consensus). [35]  During full text screen, the study was included for data extraction only if it fulfilled all the criteria (study type, participant, intervention/exposure with comparator, and outcome). If the study did not meet any one of the above criteria, it was excluded. Screening was done by two investigators (KJ and PM) independently.
The investigators resolved any disagreements by mutual consent; with recourse to a third investigator (ANS for title/abstract screen; HDS for full text screen), if required. Data extraction and management. Two investigators (KJ and PM) independently extracted study data from full text of the included studies into a data extraction form. (S2 Appendix) Any disagreement was resolved by discussion with a third investigator (HDS). If primary data were unavailable in the supplementary file and/or no effect measures (adjusted/unadjusted) were reported, we requested the same form the authors. We sent three email reminders, fortnightly and awaited response for a maximum period of 1 month after writing the first mail to them. Assessment of risk of bias in included studies. For interventional study, we planned to rate each included trial as being at high, low or unclear risk of bias under the following domains: sequence generation, allocation concealment, blinding of participants, personnel and outcome assessors, incomplete outcome data, selective outcome reporting and other Table  1.
Results We found 2326 articles after database search. After removal of duplicates, 2054 underwent a title and abstract screen and 56 were assessed for eligibility (full text screen). Nine studies were included for qualitative assessment (data extraction). Considering high methodological and clinical heterogeneity, we decided to report the results qualitatively. (Fig  1 ) Reasons for exclusion of studies during full text screen have been reported in Table  2. Characteristics of included studies are presented in S1 Annex. Of the nine studies included in the review, all were cohort studies: eight dealt with glycemic control and its effect on TB treatment outcomes (Table  3 )  [40] [41] [42] [43] [44] [45] [46] [47]  and two dealt with type of DM treatment and TB treatment outcomes. (Table  4 )  [47, 48]  All studies included both sexes and adults, with children being included in one.
[43]  It was unclear whether children were included in the other two studies. [40, 46]  Four studies included patients with and without HIV,  [40, 42, 44, 47]  three studies excluded patients with HIV  [41, 45, 46]  and in the remaining two information on HIV status was not available  [43, 48]. None of the authors responded with primary data or unreported outcomes. Hence, we did not perform any primary data analysis for adjusted effect measures. We derived unadjusted RRs from the data extracted from narrative texts/tables. As sufficient number of studies under each primary objective was less than 10, we did not plot the funnel plot to detect publication bias.
However, people without DM were the reference. We extracted numbers for treatment outcomes among the subgroups of glycemic control in people with TB-DM. Culture non-conversion, but not end treatment outcomes, was associated with glycemic control when compared to poor control at baseline (unadjusted RR (0. 95 CI):0. 23 (0. 05-0. 94)). [41] (Table  3 , S1 Annex) Data extracted from the study by Park SW et al from South Korea revealed no association between sputum conversion at 2 months and glycemic control (HbA1c<7) at baseline. [45]  Though Tabarsi P et al did not exactly address our research question(s), we could extract the data that we required. HbA1c was measured at baseline and 3 months of ATT and was categorized as elevated if HbA1c was !6. 5%. Those with 'Elevated-normal' and 'elevated-elevated' at baseline and 3 months respectively were included in our analysis to represent good control and poor control respectively.
Acknowledgments The review was conducted as a part of the training course aimed to build capacity on undertaking Systematic Reviews within India, especially in the context of tuberculosis. The training project was conceived and implemented by the South East Asia office of The International Union against Tuberculosis and  Lung Diseases  ( The Union ) in collaboration with  Central TB Division, Ministry of Health and Family Welfare, Government of India  and The  Cochrane South Asia. The training was generously supported by  U. S. Agency for International Development (USAID). We would like to acknowledge the support of  Hannah Stowe McMurry  while drafting the initial version of the systematic review protocol. We thank all the authors who responded to our mails and provided necessary information.
Patients and Methods This study was carried out in liver transplant patients at Henri Mondor Hospital in the suburbs of Paris, France. Between January 2013 and May 2016, all patients admitted consecutively to our Intensive Care Unit (ICU) following LT were enrolled in the study. Demographic and clinical characteristics, investigations for mycological and bacterial infections, and antimicrobial therapies were all recorded prospectively. The patients were studied during their hospitalization in and after the ICU. Our Institutional Review Board approved the study (2012-12) and the database was declared to the French Data Protection Authority (Commission Nationale Informatique et Liberté) (No. 1699340).
Statistical Analysis Continuous data were presented as medians and ranges. Fisher's exact test (categorical variables) and the Mann-Whitney test (continuous variables) were used to compare demographic data based on the patient's IC status. Kaplan-Meier curves were generated, and a log-rank test was utilized to compare patients with and without IFI. The following parameters for diagnostic performance, and their 95% confidence intervals, were calculated: sensitivity, specificity, positive predictive value (PPV), and negative predictive value (NPV). To identify the ability of BG to diagnose invasive candidiasis, receiver operating characteristic (ROC) curves were constructed. All statistical analyses were performed using SPSS (version 18; SPPS, Inc, IBM, Chicago, IL, USA). The areas under the curves (AUCs) reflected the discriminative ability of BG.
Vascular assessment The vascular ultrasound study was performed in the context of care in a temperature-controlled room after a 15-min rest (Vivid 7, General Electric, Horten, Norway). All subjects had fasted for at least 12 h before vascular evaluation. A single blinded investigator (BE) conducted vascular measurements in the controls and SLE patients. All data were analysed offline (EchoPAC™, General Electric Ultrasound). The internal carotid artery was imaged in a longitudinal and cross-sectional view. The maximal thickness was measured as the internal carotid wall thickness at the carotid bulb level at end diastole, as gated on electrocardiography (ECG). Carotid plaques were defined as a thickness greater than 1. 5 mm according to current recommendation  [14]. Intima media thickness (IMT) was measured offline from B-mode diastolic images, as gated on ECG by semiautomatic detection with dedicated software (General Electric).
Before introduction in the model, interactions between explanatory variable were explored. The Akaike information criterion was used in a stepwise procedure to retain the best model. We checked the linearity for each continuous predictor using the residuals versus fitted values plot, and we used likelihood ratio test with models using non-linear transformations. Statistical analyses were performed with GraphPad Prism 5. 01 software and R statistical software version 3. 2 (R Foundation for statistical Computing, Vienna, Austria). All tests were two-sided and p values <0. 05 were considered statistically significant.