dataesr/scientific-paragraphs-categorization huggingface dataset:
Conclusions In this study, we demonstrated the contributions of multitemporal and multimodal imagery and the use of deep learning models allowing the extraction of spatio-spectral and spatio-temporal features for a better extraction and semantic segmentation of UF. Furthermore, the results, which demonstrate better F1 Score for the 10 classes ConvLSTM+Inception-S1S2 method, showed that it is better to segment and diversify an over-represented class composed of spectrally and texturally distinct objects. This method has also greater metrics scores thanks to the addition of a spatio-spectral feature extractor. The current scores for UF are encouraging and show that combining and extracting different types of features and balancing the initial dataset provides better results by reducing confusion between the classes studied (Figures 9, 10 and A3).
Individual clones were handpicked and plated into 96 well plates. DNA was extracted using Quick Extract DNA extraction solution (Epicentre#QE09050) and nested PCR was performed using Forward (CATGGAACATCCTTGTGGGGA) and Reverse (CTGAGATTCAGCTTGTTGAAGTTA) primers for exon 45 region and Forward (AGTTTGTCCTGAAAGGTGGGT) and Reverse (CCTCCCAAGCTCCAGTTTAGC) primers for exon 54 region. The PCR products were purified using EXO-SAP enzyme (ThermoFisher) and sent for Sanger sequencing analysis (through Genewiz). Clones harboring the correct DMD mutation were amplified and sent for G-band karyotyping (outsourced to Diagnostic Cytogenetics Inc. , Seattle, WA, USA. Data not shown). The collected sequencing data confirmed the presence of a dystrophin-null phenotype in our engineered DMD line (Figure  S1B ).
Measurement of EMT contraction EMT contraction was elicited via broad-field electrical stimulation. A purpose-built plate lid supporting graphite electrodes that was compatible with the Mantarray hardware was used in conjunction with a C-Pace EP in-culture stimulator (IonOptix, Westwood, MA, USA). EMT cultures were subjected to electrical pulses of 10 V for 5 ms at a rate of 1 Hz for analysis of twitch contractions and 10 to 30 Hz to analyze tetanic responses. Post-deflection was measured by tracking the deformation of the magnetic field caused by movement of the magnet embedded in the flexible post using the dedicated Mantarray software suite. As the described system is noninvasive, individual EMTs could be monitored for changes in function over time. For the purposes of these studies, contractile properties of cultured EMTs were measured every 3 to 4 days between days 7 and 14 post tissue formation.
Images were taken at the University of Washington's Garvey Imaging Core using a Nikon A1 Confocal System on a Ti-E inverted microscope platform. 12-bit 1024x1024 pixel images were acquired with Nikon NIS Elements 3. 1 software. Antibodies used in this study were as follows: rabbit anti-desmin (1 in 200, Abcam), mouse anti-myosin heavy chain (1 in 500, Sigma-Aldrich), rabbit anti-m-line titin (1 in 300, Myomedix), mouse anti-MF20 (1 in 200, Developmental Studies Hybridoma Bank, Iowa City, Iowa, USA), rabbit polyclonal anti-dystrophin (1 in 1000, Abcam), Alexafluor-594 conjugated goat-anti-rabbit secondary antibody (1 in 200, ThermoFisher Scientific), Alexafluor-568 conjugated donkey-anti-rabbit secondary antibody (1 in 500, ThermoFisher Scientific), Alexafluor-488 conjugated donkey-anti-mouse secondary antibody (1 in 500, ThermoFisher Scientific), and Alexafluor-488 conjugated goat-anti-mouse secondary antibody (1 in 200, ThermoFisher Scientific).
Statistical analysis All experiments were performed with technical duplicates or triplicates, and repeated using at least 3 independently-differentiated iPSC skeletal muscle populations. Significant differences between groups were evaluated using either unpaired, two-tailed t-tests or Mann Whiney-U tests depending on whether the data was normally distributed. One-way analysis of variance (ANOVA), or ANOVA on ranks depending on data normality, with post hoc tests for multiple comparisons was used to compare data sets with more than two experimental groups. All drug studies were performed across at least 5 doses and the data was then used to plot dose response curves for calculation of EC50 values from each metric analyzed. Dose response curves were fit to the collected data by running a nonlinear regression (log(agonist/antagonist) versus normalized response) with a least-squares fit in GraphPad Prism.
Attributable fractions Fractions of CVD and depression attributable to psychosocial work exposures in Europe were provided in one of our previous publications  12  and covered job strain, effort-reward imbalance (ERI), job insecurity, long working hours and workplace bullying. Attributable fraction (AF) estimates were based on the prevalences of exposure to these factors obtained from the 2015 European Working Conditions survey data of the European Foundation for the improvement of living and working conditions (EUROFOUND). Relative risk (RR) estimates were obtained from the literature. 1, 12 e used the same AFs to estimate the number of morbidity and mortality cases attributable to each psychosocial work exposure. RRs used to compute AFs derived from meta-analyses based on prospective studies.
Burden of diseases In line with the Global Burden of Diseases study,  19  we used as health outcome indicators prevalent cases, deaths, Years of Life Lost (YLL), Years of Life Lost due to Disability (YLD) and Disability-Adjusted Life Years (DALY). These indicators were extracted from the Global Health Data Exchange (GHDx) database for the year 2015. The GHDx database provided data for all 28 EU countries, for the working-age population (15-64 years), for men and women together and for men and women separately and for CVD and depression. 20, 21 n the GHDx database, YLLs were computed using standard life expectancy at each age, which is based on the lowest observed death rates for each 5-year age group in populations larger than 5 million. 20, 21 The same standard life expectancy was used for all EU countries.
This method avoids ethical issues related to gaps in average life expectancy between European countries, which would attribute a greater burden to deaths occurring in countries where the life expectancy is longer. YLDs were provided by the GHDx database with the 2013 calculation of disability weights. 21, 22 ll data were available for CVD in the GHDx database. For depression, data were not available for deaths, YLLs and consequently DALYs. As suggested in the literature, 53. 7% of suicide cases were found to be related to depression. 23 Thus, we extracted data related to suicide and multiplied these indicators by 53. 7%, which provided an estimate of mortality related to depression. This estimation method for mortality related to depression was used previously. 4 o estimate the burden of disease attributable to each exposure and all studied exposures, the health outcome indicators were multiplied by the previously mentioned AFs.
Burden per 100 000 workers To take into account differences in population sizes between countries, we calculated the prevalence rate R P , the mortality rate R M and the DALY rate R D for each health outcome attributable to each exposure per 100 000 workers as follows: R Data for the employed population were extracted from the Eurostat database (Labour Force Survey 2015). We tested the differences between countries and between genders using the Wald test. 24 ll results were provided for each country and the whole 28 EU, and for men and women together and separately. Statistical analyses were performed using SAS software and maps were designed using Microsoft Excel.
The burden per 100 000 workers was also provided for each exposureoutcome pair, which allowed comparisons between 28 EU countries of the burden borne by workers, taking into account the size of the employed population. Therefore, this study provided detailed estimates on the burden due to psychosocial work factors, something which is very rare on this topic. This study has also several limitations. Although we used the most recent available data (2015), we were unable to provide information that may be relevant for the burden of diseases during the coronavirus disease 2019 pandemic. There were differences in the definition of the outcomes between RR estimates used to compute AF estimates and health outcomes data from GHDx. For instance, GHDx database provided data on the prevalence of atrial fibrillation and flutter, whereas RR estimates were available for atrial fibrillation only, which may have overestimated our results on the burden of this health outcome.
In addition, the RR estimates were from reviews/meta-analyses that were themselves based on a number of primary studies that may have been heterogeneous in the measurement of the outcome. Furthermore, for a given outcome, the definition may have been different from a review/meta-analysis to another. 1, 12 The results for the five health outcomes included in the study should not be added together since there may be comorbidities. We used health outcome data for each disease, multiplied by the employment rate among the population aged 15-64 in each country to provide relevant estimates for the working population. This method was based on the hypothesis that cases are equally distributed in the working and non-working population, which may not be the case. Because the healthy worker effect leads to select healthier people at the workplace, there may be a bias towards overestimation.
Data Collection This is a descriptive cross-sectional study undertaken on a non-probabilistic sample of 7221 participants from 14 countries, as follows: Brazil (n = 322), Croatia (n = 686), Greece (n = 636), Latvia (n = 300), Lebanon (n = 357), Lithuania (n = 510), Mexico (n = 1139), Poland (n = 520), Portugal (n = 527), Romania (n = 492), Serbia (n = 344), Slovenia (n = 517), Spain (n = 575), and Turkey (n = 296). All ethical principles were strictly followed when designing the questionnaire and collecting data, especially those of the Declaration of Helsinki. The Ethics Committee of the Polytechnic Institute of Viseu approved this questionnaire survey with reference 45/SUB/2021. Data were collected between July and November 2021, using a computer/web-based methodology. The questionnaire was delivered through the electronic platform Google Forms, under the restrictions caused by the COVID-19 pandemic.
Statistical Analysis The software used for the statistical analysis was SPSS Version 28 from IBM, Inc. (Armonk, NY, USA). Basic descriptive statistics were used and statistical tests were used to test differences between groups of variables. Parametric tests were used because they are stronger and more powerful than their non-parametric counterparts. In the present case, the high number of cases allowed obtaining data that presented a normal distribution (according to the Kolmogorov-Smirnov test), thus making it possible to use parametric tests. The tests used were the t-test for independent samples and Analysis of Variance-ANOVA, with a post hoc test of Tukey to identify the differences. In all tests, a significance level of 5% was considered (p < 0. 05).
3%) or rural areas (19. 1%). Income was also a variable in the study, with a question that related income to the average salary in each of the countries. For the participants in the study, when compared to the average income, 5. 9% had a much lower income, 15. 9% had a lower income, 38. 1% had an equal income, 32. 5% had a higher income, and 7. 6% had a much higher income, in each of the countries. Because the level of education is also relevant in this type of study, this question was also formulated, in a general way, to be representative across the different countries. The data showed that approximately one third of the participants were undergraduates, completed secondary or elementary school (35. 8%), approximately a third (32. 3%) had completed a university degree, and another third (31.
Acknowledgments: This work was supported by the  FCT-Foundation for Science and Technology, I. P. Furthermore , we would like to thank the  CERNAS, CIDEI , and  UCISA:E Research Centers  and the  Polytechnic Institute of Viseu  for their support. This research was developed in the ambit of project " EISuFood-Edible Insects as Sustainable Food ", with Reference CERNAS-IPV/ 2020/003.
| Fish sampling An institutional database  (Er} os et al. , 2020)  provided data on fish assemblages and environmental variables for 429 stream and river sites (Figure  1 ). The database was created from the data collected during country-wide fish and habitat surveys between 2013 and 2018. Fish were generally collected during the summer or early autumn base flow period  (Er} os et al. , 2020). Two types of electrofishing methods were used  (Er} os et al. , 2017) , which were consistent with widely used electrofishing protocols  (Oberdorff et al. , 2001; Pont et al. , 2006). For streams (drainage basin area <1,000 km 2 ), a battery-powered electrofishing device was used (Hans-Grassl IG 200/2B device, PDC). The crew sampled a 150 m long reach, slowly walking upstream and with single-pass fishing of the whole stream width.
| Habitat degradation index LUI ¼ %pasture þ 2 Â %arable land þ 4 Â %urban area. The percentages of land use categories in each site (i. e. its corresponding catchment) were determined by GIS imagery using the Corine Land Cover database. To characterize chemical degradation (ii), conductivity, dissolved oxygen content and pH were measured with an OAKTON Waterproof PCD 650 portable handheld meter, and the content of nitrogen forms (i. e. nitrite, nitrate, ammonium) and phosphate were measured using field kits (Visocolor ECO, Macherey-Nagel 158 GmbH & Co. KG. , Germany). These parameters were transformed if necessary (using square-root, double square-root or log-transformation), and analysed in a standardized principal component analysis. The first principal component (explaining about 50% of the total variability and related to nitrogen forms and phosphate; (see Figure  S2 ) was used as an index of chemical degradation.
Distribution of the sampling sites in the Pannon Biogeographical region, Hungary, and the degree of degradation at each site. (b) Frequency distribution of sites along the habitat degradation gradient local relative abundance (hereafter called local rarity), the geographical range size (geographical restrictedness) and the habitat breadth (habitat specificity). Local rarity was quantified using the mean relative abundance of each species across all sites. Values of species geographical restrictedness were extracted from the global database of geographical distribution of freshwater fishes built by Carvajal-Quintero et al. (2019), providing the geographical range size of species in km 2. Habitat specificity was calculated using the outlying T A B L E 1 Species list, fish code abbreviations and the total number of individuals for each species.
Body composition and indirect calorimetry The whole-body composition was measured using EchoMRI. Comprehensive Laboratory Animal Monitoring System (CLAMS; Columbus Instruments, Columbus, OH, USA) was used to measure oxygen consumption (VO 2 ), carbon dioxide production (VCO 2 ), food intake and water intake. The respiratory exchange ratio (RER) was calculated with VCO 2 /VO 2. Energy expenditure (EE) was estimated using VO 2 and VCO 2 values from indirect calorimetry, using the following equation EE (in kcalÁh À1 ) = (3. 815 9 VO 2 ) + (1. 232 9 VCO 2 ). For the data obtained from HFD-fed mice, the regression comparing VO 2 or EE and body weight was analysed and plotted with CalR  [30].
CDK7 adipose-specific knockout mice have decreased fat mass A first indication of the participation of CDK7 in WAT physiology came from the transcriptome data that we generated from perigonadal white adipose tissue (pgWAT) in CDK7 fat-specific knockout mice (GSE149128)  [29]. Pathway analysis showed that a significant proportion of the 190 downregulated genes (P < 0. 05, log FC 0. 5) that were found in the WAT of the Cdk7 aKO mice are involved in lipid metabolism (lipid synthesis, uptake and lipolysis) (Fig. 1A ), such as Fasn, Dgat2 and Lipe (Table  2 ). While the first characterization of the Cdk7 aKO mice indicated no difference in body weight compared with Cdk7 fl/fl mice (Fig. S1A ), a more detailed analysis of body composition by EchoMRI analysis showed that Cdk7 aKO mice had significantly lower fat mass and.
Acknowledgements The authors acknowledge all the members of the  Fajas laboratory  for support and discussions. The authors thank Fr ed eric Preitner,  Gilles Willemin  and  Guy Nie -derh€ auser from  Mouse Metabolic Facility of CIG (University of Lausanne, Switzerland ) for experimental assistance. We thank  M. Barbacid  and  D. Santamaria  ( CNIO, Spain ) for providing the Cdk7 flox mice.
Funding Yizhe Chen  and  Honglei Ji  were supported by scholarship (No. 201706300109  and No. 201406300121) from  China Scholarship Council. IC Lopez-Mejia was supported by an  SNSF   Ambizione Grant  ( PZ00P3_168077 ). This research from  Prof. Fajas  laboratory is funded by the  Swiss National Foundation , grant number  179271.
Patient cohort A cohort of 13 NS patients from 10 kindreds with a median age of 32 years and 19 age-and sex-matched healthy controls (HCs) (median age, 30 years) was recruited. NS was confirmed by the identification of deleterious mutations in SPINK5 and negative LEKTI immunostaining for the 13 NS patients including 9 NS-ILC and 4 NS-SE patients. Demographic information of patients is provided in Table  I. Treatments included emollients on a daily basis and topical corticosteroids during acute flare-ups. Skin and blood were collected by biopsy before any biotherapy and at least 48 hours from the application of a corticosteroid. The protocol was approved by the international review board of Necker Hospital (NCT02081313), and the study was conducted in accordance with the principles of the Declaration of Helsinki.
RNA sequencing library of NS skin Total RNA was isolated from a 5 mm skin biopsy sample. After a DNase treatment with HL-dsDNase (ArcticZymes Technologies, Tromsø, Norway), complementary DNA was prepared using the NuGEN Ovation RNA-Seq System (NuGEN, San Juan, Puerto Rico) from 100 ng of total RNA. RNA-Seq libraries were sequenced on an Illumina HiSeq device (Illumina, San Diego, Calif). Further details are provided in the Online Repository at www. jacionline. org. The transcriptomic data were deposited at the Gene Expression Omnibus (GEO) data repository under accession number GSE164285.
Proteomic analysis of NS skin Proteins were extracted from frozen skin samples using RapiGest containing buffer followed by reduction and alkylation. Proteins were digested by first incubating with LysC, then incubating with trypsin. Data were acquired with a Q-Exactive Plus (Thermo Fisher Scientific, Waltham, Mass) mass spectrometer. Further details are provided in the Online Repository. Mass spectrometry data as well as data analysis results have been deposited to ProteomeXchange via MassIVE (ID: PXD023658).
Statistical analyses Statistical analyses were performed by GraphPad Prism v8. 4. 3 (GraphPad Software, La Jolla, Calif) and R v3. 5. 0 (R Foundation for Statistical Computing, Vienna, Austria; https://www. r-project. org/). Further details are provided in the Online Repository. Differences were considered significant at P <. 05. Experimental procedures of immunostaining, immunophenotyping of PBMCs, Western blot analysis, and serum cytokine profiling by Luminex (Austin, Tex) are described in the Online Repository.
Complement activation is more pronounced in NS-ILC skin Proteomic data showed increased expression of complement C1S as well as IgG and IgM heavy chains. Enhanced expression of classical complement components was confirmed at the transcript level by RNA-Seq data. In particular, C1QB and C1QC presented significantly increased transcript levels in nonlesion and lesion skin compared to healthy controls (Fig  4, A ). C1R was also significantly increased in lesion NS-ILC skin compared to healthy controls. Because these components initiate the classical cascade, cleavage of complement C3 was assessed by Western blot analysis of NS skin (Fig 4  , B ). Complement C3 could be detected in NS skin lysates but not in healthy controls. Complement C3a full length (115 kDa) and fragments iC3b (68 kDa) and C3dg (40 kDa) were observed.
The first 3 authors contributed equally as co-first authors. Authors 4 and 5 contributed equally as co-second authors. This project was funded by the  French National Research Agency   ANR-17-CE14-0025   Tfh Atopy (A. H. ),  ANR-19-CE17-0017  Target-NS (A. H. ), the  Imagine Institute with Cross-Lab program , and  Association Ichtyose France  (A. H. ). A. H. and O. S. were supported by the  European Union 's  Horizon 2020 research and innovation program  under the  ERA-NET Cofund action 643578  ( KLKIN  project); J. E. G. and L. C. T. are supported by  NIH   P30-AR075043  and  AI130025. or in this article's Online Repository at www. jacionline. org. We deposited RNA-Seq data on the Gene Expression Omnibus (GEO; accession no. GSE164285 ) and proteomic.
Still, the internal organization of the hyperdirect pathway in the human brain remains unexplored. In this study, we seek to reconstruct hyperdirect pathways fibers projecting from the primary motor cortex using multi-fiber deterministic tractography and to investigate the internal organization of hyperdirect fascicles projecting from the trunk, arm, hand, face, and tongue area. We used MRI datasets from the Human Connectome Project as they offer the highest quality diffusion MRI data currently available to investigate brain connectivity. To the best of our knowledge, this is the first study of the somatotopy of the hyperdirect pathway in the human brain.
MRI Data Acquisition We used high-resolution structural and diffusion MRI data from five healthy subjects (100307, 100408, 101915, 103414, 106016) of the Washington University, University of Minnesota, and Oxford University Human Connectome Project (WU-Minn HCP) consortium  (39). The WU-Minn HCP scans were acquired on young healthy subjects (age  [21] [22] [23] [24] [25] [26] [27] [28] [29] [30] [31] [32] [33] [34] [35]  and represent the best neuroimaging data available for investigating the topography of the white matter in the human brain. The subjects were scanned on a customized Siemens 3. 0 Tesla Skyra scanner using a 32channel head coil and a customized gradient. The structural MRI data included T1-weighted and T2-weighted volumes acquired with the following parameters: T1-weighted: TE = 2.
Segmentation of the Regions of Interest We defined three sets of anatomical regions of interest (ROIs) in the primary motor cortex (M1), internal capsule (IC) and subthalamic nucleus (STN) using the 3D Slicer open-source platform for medical research  (45). In the first set of ROIs, we outlined the precentral gyrus in a volume-rendered image of the T1-weighted scan. In the second set of ROIs, we generated a fractional anisotropy (FA) map and a diffusion-encoded color (DEC) map from the diffusion-weighted images using the SlicerDMRI extension of 3D Slicer  (46, 47). We manually segmented the posterior limb of the IC in axial cross-sections of the FA map overlaid on the DEC map using the Segment Editor module of 3D Slicer. In the third set of ROIs, as the contours of the STN were not directly visible in the T1-weighted images, we used the automated atlas-based segmentation approach of the pyDBS software implemented in 3D Slicer  (48).