dataesr/scientific-paragraphs-categorization huggingface dataset:
Study Selection and Methodological Quality Figure  1  shows the articles that were selected for evaluation. The electronic database searches identified 1,235 articles: 746 from PubMed, 223 from Embase, 30 from PEDRO, 98 from Cochrane and 138 from WEB of science. Checks for duplicates excluded 171 papers and the remaining 958 were screened based on titles and abstracts. We assessed the methodology of the remaining 106 papers. Ninety articles were excluded because they did not meet the inclusion criteria. The remaining 16 articles were analyzed. They reported on 10 independent studies. Six additional publications  (24) (25) (26) (27) (28) (29)  correspond to supplementary analyses of four of the 10 selected  (30) (31) (32) (33). Consequently, these six publications are not reported here because they used the same cohorts and protocols as studies that were already included.
In general, an early start of the tummy time intervention had a larger effect on motor development than a late start. The strengths of this protocol included the 12 months' duration of the intervention and the follow up with the BSID as well as the simplicity of the protocol for parents, resulting in high compliance. Regarding the sample of tummy time exercises, the authors made parents aware of the risks of over stimulating spinal hyperextension and used adaptations to preserve spinal curvature, for example, by using towels under the arms to avoid neck hyperextension in the prone position. Regarding limitations, no data were collected relating to the infants' medical histories or relating to potential physical therapy engaged in by the infants. Further, a blinded assessor was not used and tummy time data for the control group were not collected.
Analysis of Pupil Size We processed the data using Pupil Player software. During data processing, we eliminated blinks and data exceeding typical ranges. In other words, we eliminated data indicating pupil size beyond the interval of 2-4 mm, referring to the typical pupil diameter in bright light, this to exclude 12% of the data. We then calculated the average pupil size (in mm) during each condition, namely, the average pupil size during retrograde Brain Sci. 2022, 12, 115 6 of 9 retrieval, anterograde retrieval, construction of next week events, construction of next month events, and construction of the next year events. Figure  2  illustrates pupil size in each condition. Because data involved many measures (i. e. , each condition involved pupil size measured across hundreds of frames), we were able to conduct statistical analysis for pupil size, as depicted below.
Analysis of Pupil Size We processed the data using Pupil Player software. During data processing, we eliminated blinks and data exceeding typical ranges. In other words, we eliminated data indicating pupil size beyond the interval of 2-4 mm, referring to the typical pupil diameter in bright light, this to exclude 12% of the data. We then calculated the average pupil size (in mm) during each condition, namely, the average pupil size during retrograde retrieval, anterograde retrieval, construction of next week events, construction of next month events, and construction of the next year events. Figure  2  illustrates pupil size in each condition. Because data involved many measures (i. e. , each condition involved pupil size measured across hundreds of frames), we were able to conduct statistical analysis for pupil size, as depicted below.
Amplicons were then sent for Sanger sequencing, on a 3730xl DNA Analyzer (Applied Biosystems), at the McGill University and Genome Quebec Innovation Center. Sequence trace files in ABI format, as well as reference sequences in FASTA format, were loaded into the novoSNP 3. 0. 1 program for Windows users  (Weckx et al. , 2005 ). Variation at each location was determined by following the procedures outlined in  Weckx et al. (2005). A subset of male subjects were used for genotyping (Supplementary Table  4 ).
Targeted bisulfite sequencing Genomic DNA was extracted using the QIAmp DNA Mini Kit (Qiagen) and quantified using a NanoDrop2000 spectrophotometer. Four of the seventy three subjects used in our initial expression based analysis were removed as a result of low DNA concentrations. DNA was bisulfite converted using the EpiTect Fast 96 Bisulfite Kit (Qiagen). We next used a PCR-based library preparation procedure, described by  Chen et al. (2017). Briefly, a first round of PCR amplification was performed on bisulfite-converted DNA (BS-DNA) using the Kapa HiFi HotStart Uracil+ master mix (Kappa Biosystems). Primers were designed using the MethylPrimer Express software v1. 0 (ThermoFisher) against the OXTR gene on the negative strand (GRCh37/hg19) (see Supplementary Table  5 ). BS-DNA was PCR amplified on a ProFlex thermocycler (Thermofisher): 95 • C, 3 min then 45 cycles of 98 • C for 20 s, 60 • C for 15 s, 72 • C for 15 s, and finished with 72 • C for 1 min.
Bioinformatic analyses As described previously by  Chen et al. (2017) , universal primers sequences were trimmed and sequencing reads with a Phred quality score less than 20 were discarded. Bismark v0. 14. 4 was used to align the remaining reads to the GRCh37/hg19 genome. Bismark was run using Bowtie 2 (version 2. 1. 0). The extraction of the number of unconverted and converted CpGs for each cytosine was done with the script bis-mark_methylation_extractor provided with Bismark with the following parameters: -p -no_overlap -cytosine_report -counts -s -bedGraph. DNA methylation percentage was calculated for each cytosine as the unconverted (cytosine) read counts divided by total read counts (cytosine and thymine). Only negative strand methylation was examined. All fifty nine CpG dinucleotides covered by our three amplicons met our criteria of having an average coverage of ≥ 10x.
Statistical analyses Statistical analyses were carried out by the IBM SPSS package v27. Group differences in age, PMI, pH, and RIN, were assessed via a univariate one-way ANOVA. Chi squared tests were used to investigate the distribution of categorical variables between groups. Though some group differences did emerge, variables were only controlled for if found to be a significant predictor of gene expression or methylation. Outliers in expression data were identified by having a z score of ≥ 2. 5. As opposed to discarding these values, a 90% Winsorization of the data was used to minimize their effects. Possible contributions of covariates were assessed using a backward stepwise linear regression, with a removal value of p ≥ 0. 1, to select the most parsimonious set of factors that influenced expression.
The input factor list included, age, post-mortem interval, pH, alcohol/drug abuse, sex and presence of antidepressants or other psychotropic substances at death. The effect of group on OXTR expression was then assessed using a one-way ANCOVA while controlling for the effects of RIN, alcohol/drug abuse, and presence of other psychotropic substances at death. The normality assumption for the unstandardized residuals of this model was assessed via the Lilliefors-corrected Kolmogorov-Smirnov test, while equality of variance was assessed via Levine's test. Bonferroni corrected post-hoc comparisons were used to investigate differences in OXTR expression between groups. The same steps were then taken to study the effect of rs53576 genotype on expression. In this case expression data were log transformed to meet the normality assumption and the effect of alcohol/drug use was controlled for.
Funding and disclosure GT holds a Canada Research Chair (Tier 1) and is supported by grants from the  Canadian Institute of Health Research (CIHR)  ( FDN148374  and  ENP161427 ). DA is a  Vanier Scholar  funded by the  Canadian Institute of Health Research (CIHR). The  Douglas-Bell Canada Brain Bank  is supported in part by funding from the  Canada First Research Excellence Fund , awarded to  McGill University  for the  Healthy Brains for Healthy Lives initiative , and from the  Fonds de recherche du Québec -Santé (FRQS)  through the  Quebec Network on Suicide ,  Mood Disorders  and Related Disorders. The authors declare no conflict of interest.
Statistical Analysis All statistical tests (eg, linear mixed-effects models, χ 2 , Wilcoxon signed rank test, t tests, nonparametric permutation, and bootstrap tests) were conducted using the Statistics and Machine Learning Toolbox (MATLAB version 2015a; MathWorks), and the Mediation Toolbox. 39, 40 Computational modeling was implemented using the using the VBA toolbox. 41, 42 Two-sided P values were statistically significant at less than. 05.
Study design This was a multicentric, open, parallel-group, randomised controlled trial including individuals who underwent ACLR between December 2016 and January 2020. This study conformed to standards from the latest revision of the Declaration of Helsinki and was approved by the Committee for the Protection of Persons (CPP Sud-est I, no. : 2016-34). The University Hospital of Saint-E ´tienne (France) was the sponsor of this study (ClinicalTrials. gov: NCT02929004).
For instance, minimising quadriceps strength loss during the first months post-ACLR can predict improved running biomechanics  [39]. Yet, we found no functional changes when considering TUG and 6MWT performance, but these tests are not sensitive in the context of ACLR (i. e. , no changes were observed in the control group). Our study involved a relatively small sample size, lower than the initial sample size reported in ClinicalTrials. gov. Although we report a between-group effect size of 1. 33 for PRE-POST changes in quadriceps strength of the injured leg, reaching an a posteriori power of 0. 86, this may have prevented some results to be significant (e. g. , LSI Strength ). Including more participants would have better revealed surgery-induced alterations in RFD as well as the potential effects of LVT.
Results EM (score at free recall test) and FI (score at fluid intelligence test) performances of the general population are presented in Table  2. Statistical analyses were carried out using STATISTICA software (version 13). First, in order to identify the effects of age and physical exercise, treated as continuous variables, and their interaction either on EM or on FI performances, we performed a General Linear Model ANCOVA-based analysis (GLM) with age and physical exercise entered as independent variables, and EM or FI as dependent variables. More precisely, these analyses were conducted with gender, educational level, general knowledge index, and leisure activity index partialled out (entered as covariables in ANCOVA) to better examine the independent effects of age and physical exercise.
Data analyses The data were analyzed using SPSS 23. 0 software. We carried out hierarchical multiple regression analyses to determine the contribution of psychological resources and vulnerabilities to violations, errors, and prosocial driving behaviors, while controlling for the driver's gender and age. A cluster analysis was also performed to identify specific patterns of psychological resources, vulnerabilities, and driving behaviors. The IRI fantasy scale was excluded from analyses because it measures an individual's ability to project him/herself onto the feelings and emotions of imaginary characters, which does not apply to the driving activity. The correlation between the short-FTEQ and the IRI's empathic concern was high (0. 70), to avoid collinearity only the short-FTEQ was used as a measure of emotional empathy.
The present study analyzes the largest dataset of psychiatric disorders, trauma and suicidal behavior conducted to date in the Afghan general population to address three aims: rst, we examine the burden of suicidal ideation and attempt, and demographic correlates including gender and age, in the Afghan general population; second, we examine the association with experiences of trauma and stressful experiences; third, we examine associations with psychiatric and substance disorders including mood and anxiety disorders, psychotic experiences, and tobacco and other drug use.
MRI acquisition MRI images were acquired using a Philips Achieva dStream 3. 0-T MRI scanner equipped with a 32-channel head coil. Rs-fMRI: echo-planar imaging (EPI) sequence. Time repetition (TR)/time echo (TE) = 3000/40 ms, flip angle (FA) = 90°, field of view (FOV) = 240 mm, matrix = 80 × 80, voxel size = 3. 0 × 3. 0 × 3. 0 mm, 46 axial slices. Each scan session was 600 s long and included 200 volumes. Resting-state data were acquired while each subject was asked to stay awake, eyes opened, and not thinking about anything in particular.
MRI processing Rs-fMRI images were preprocessed using the Conn software including the following steps: realignment and unwarp, slice timing correction, and outlier detection using strict settings: 97th percentiles in the normative sample, global signal z-value threshold 5, subject motion mm threshold 0. 9, direct segmentation and normalization (also applied to T1 images for each subject), smoothing with an 8-mm kernel. BOLD time series were denoised using the aCompCor method  [31] [32] [33]  of the CONN toolbox (www. nitrc. org/ proje cts/ conn;  [34] ), which consisted in regressing out from the functional time-series the first two principal components of the time-series extracted from white matter and CSF. The.
Comparison of the behavioral task between groups For the procedural perceptual-motor memory assessment, we performed a repeated measures ANOVA on reaction times between B1 and B4 (general learning), B4 and B5 (specific learning), and B5 and B6 (retention), with the group as the intersubject factor and the blocks as intrasubject factors. The normality of data was assessed by the Shapiro-Wilk test, the homogeneity of variance with Levene's test, and the sphericity with Mauchly's test. As the variable "number of errors" for each block was not normally distributed, we used a non-parametric Friedman test on each group with the blocks as intrasubject factors for general learning and a paired sample t test for specific learning and retention. To compare the performance on motor skills in the two groups, we used the Mann-Whitney U test, because the distribution of variables assessed by the Shapiro-Wilk test was not normal.
B t p Step 1 Gender -0. To make our results comparable with those of previous studies, we repeated the statistical analysis using a categorical definition of overweight/obesity (coded as 1 = non-overweight, 2 = overweight) based on the WHO growth reference data for children and adolescents. The role of temperament was assessed by conducting a MANOVA with the three scales of the JTCI (NS, HA, and RD) as dependent variables. The omnibus test was significant (Wilks' Lambda = 0. 91, F = 2. 98, df = 3, 96, p = 0. 03). Compared to non-overweight subjects, overweight/obesity subjects scored higher on the RD (F = 4. 46, p = 0. 04) and lower on the NS scale (F = 4. 88, p = 0. 03). The role of behavioral problems was assessed by conducting a MANOVA with the three broad-band scales of the CBCL, internalizing, externalizing, and total problems, as depen-dent variables.
Methods: We used discharge reports from the French national hospital database called Programme de médicalisation des systèmes d'information (PMSI) to gather longitudinal data that describe psychiatric hospitalizations for people found NCRMD between 2011 and 2020, the age, sex, and principal diagnoses of these patients, the length of their hospitalization, and the trajectories of their psychiatric care before and after their NCRMD psychiatric hospitalization. Results: We identified 3,020 patients who were hospitalized for psychiatric care after having been found NCRMD between 2011 and 2020. The number of admissions on these grounds has remained stable over this period, ranging from 263 in 2011 to 227 in 2021. They were mostly young men diagnosed with a psychotic disorder (62%). The majority (87%) were hospitalized in general psychiatric hospitals, and only 13% were admitted to maximum-security units (Unités pour malades difficiles, UMD).
Of note, deinstitutionalization has been associated with an increase in the number of people found NCRMD as well as a rise in forensic beds in several countries  (10) (11) (12) (13). Despite the significant implications from a public health perspective  (14) , the sociodemographic and clinical characteristics of these persons remain completely unknown in France, as does the average duration of the hospitalizations. Similarly, the psychiatric care trajectories before and after NCRMD psychiatric hospitalization have never been investigated, nor has the impact of a stay in a maximum-security psychiatric unit (UMD), which is a major issue for this population  (15). The present study used discharge reports from the French national hospital database called Programme de médicalisation des systèmes d'information (PMSI) for the period from 2011 to 2020 to describe longitudinal retrospective administrative data of psychiatric hospitalizations for people found NCRMD.
Data Source The PMSI database, which contains standardized discharge reports for all inpatient stays in psychiatric hospitals in France, was used in this study. A unique national identification number for each patient allows the data from all hospital stays for the same patient to be linked. The database includes individuallevel data on the dates of admission and discharge, hospital code number, sector code, and outcome (i. e. , discharge, hospital transfer, death). Sociodemographic data from these records include sex, age, and place of residence. The principal diagnosis, defined as the main reason for admission, and the associated diagnoses related to comorbidities, are also collected and coded according to the French version of the International Statistical Classification of Diseases and Related Health Problems, 10th Revision (ICD10).
Statistical Analysis For each year, we present the number of ongoing psychiatric hospitalizations of people found NCRMD, as well as the number of admissions to and discharges from NCRMD psychiatric hospitalization. Age on admission, sex, principal diagnosis on admission, duration of hospitalization, and death before discharge are described for each patient. As no data were available before 2011, we divided the study population into two groups to study the trajectories before NCRMD admission and after NCRMD hospitalization discharge: Group 1 consisted of patients found NCRMD who were admitted in or after 2016, allowing us to study their psychiatric care trajectory over the 5 years before their NCRMD admission. For Group 1, we examined whether patients with prior hospitalizations had the same distribution of principal diagnoses as those without prior hospitalizations.
Second, we had access only to health data from the PMSI, and no information about the severity of the offenses or the patients' criminal history was therefore available in this database. It was not possible to study offenses (and incarcerations) prior to patients' admission to and after their discharge from their NCRMD psychiatric hospitalization. Third, for the same reason, we presented the number of hospital admissions for people found NCRMD each year, but it was not possible to calculate the ratio of people found NCRMD to the total number of convictions each year in France. Fourth, the description of the patients was limited to their age, sex and diagnosis, making it impossible to investigate the clinical characteristics associated with the longest lengths of stay or hospitalizations in maximum-security units.
Datasets The main dataset consisted of 1039 healthy volunteers (483 males, 556 females), aged 22-37 years (mean = 28. 74, SD = 3. 69), from the Human Connectome Project (HCP)  (Glasser et al. 2013). The image acquisition, image preprocessing, fMRI analysis and parcellation of the HCP dataset have been described previously  (Glasser et al. 2016 (Glasser et al. , 2013) )  and see Supplementary Materials for details. Informed consent was obtained and the study was approved by the Institutional Review Board of Washington University at St. Louis. Since the HCP language tasks were auditorily presented, we reanalyzed another dataset of 31 healthy adults collected at the University of York, UK, to examine the extent to which each parcel responded to visual language and maths inputs  (Wang et al. 2021).
Task paradigms In the current study, we analyzed data from the auditory language and math tasks in the HCP dataset. The following task details are adapted from  Barch et al. (2013). We also analyzed data from visually presented semantic, math, and spatial working memory tasks from a dataset collected at the University of York, and provide details about these tasks adapted from  Fedorenko et al. (2011)  and  Wang et al. (2021). The York datasets help to confirm whether parcels showing an association between distance to sensorymotor cortex and activation are heteromodal or unimodal in their response, since we expect larger distances to be associated with greater activation for heteromodal regions, and smaller distances to be associated with greater activation for unimodal regions.
Language task from the HCP dataset The task from  Binder et al. (2011)  consisted of two runs that each interleaved 4 blocks of a story task and 4 blocks of a math task. Each block was introduced with an auditory cue word, "story" or "math," presented 3 s prior to the beginning of the block. A response period of 2 s was provided after each story or math question. The lengths of the blocks varied (average of approximately 30 s), but the task was designed so that the math task blocks matched the length of the story task blocks, with some additional math trials at the end of the task to complete the 3. 8-minute run as needed. In story blocks, participants were presented with brief auditory stories (5-9 sentences) adapted from Aesop's fables, followed by a 2-alternative forced-choice question about the topic of the story.
Math task from the HCP dataset The math task was designed to provide a comparison with the story task that was attentionally demanding, similar in auditory and phonological input, and unlikely to generate activation of regions involved in semantic processing, though likely to engage number-related processing in the parietal cortex. The math task also presented trials auditorily and required participants to complete addition and subtraction problems. The trials were arithmetic operations (e. g. "fourteen plus twelve"), followed by "equals" and then two choices (e. g. "twenty-nine or twenty-six"). The participants pressed a button to select either the first or the second answer. The materials were generated using the same text-tospeech method used for the story task stimuli, with matched word and phoneme rate, speaking style, and prosodic features.
Visually-presented semantic task from the York dataset Participants read sentences and lists of pronounceable nonwords, followed by a probe recognition test (present/absent judgment about a single word or nonword). Sentences contrasted with nonwords reliably activate high-level semantic and language regions  (Fedorenko et al. 2011). Each trial started with a 100-ms blank screen. Stimuli were presented at the center of the screen, one item at a time, at the rate of 450 ms per item. The sequence was followed by a probe word/nonword; participants had 2 s to decide whether this item had been presented in the sequence, giving a total trial duration of 7. 5 s. Each run included 16 experimental blocks with 3 trials per block and 5 fixation blocks lasting for 14 s. Each run lasted a total of 430 s.