dataesr/scientific-paragraphs-categorization huggingface dataset:
Xerencia de Xestion Integrada de Vigo-SERGAS ,  Instituto de Salud Carlos III, Spain ; Grant  10CSA012E ,  Consellería de Industria Programa Sectorial de Investigación Aplicada, PEME I + D e I + D Suma del Plan Gallego de Investigación, Desarrollo e Innovación Tecnológica de la Consellería de Industria de la Xunta de Galicia, Spain ; Grant  EC11-192. Fomento de la Investigación Clínica Independiente ,  Ministerio de Sanidad, Servicios Sociales e Igualdad, Spain ; and Grant  FEDER-Innterconecta. Ministerio de Economia y Competitividad, Xunta de Galicia, Spain. The BSUCH study was supported by the  Dietmar-Hopp Foundation , the  Helmholtz Society  and the  German Cancer Research Center (DKFZ). The CAMA study was funded by  Consejo Nacional de Ciencia y Tecnología (CONACyT)  ( SALUD-2002-C01-7462 ).
Sample collection and processing was funded in part by grants from the  National Cancer Institute  ( NCI R01CA120120  and  K24CA169004 ). CBCS is funded by the  Canadian Cancer Society  (grant #  313 , 404 ) and the  Canadian Institutes of Health Research. CCGP is supported by funding from the  University of Crete. The CECILE study was supported by  Fondation de France ,  Institut National du Cancer (INCa) ,  Ligue Nationale contre le Cancer ,  Agence Nationale de Sécurité Sanitaire, de l' Alimentation, de l'Environnement et du Travail (ANSES) ,  Agence Nationale de la Recherche (ANR). The CGPS was supported by the  Chief Physician Johan Boserup and Lise Boserup Fund , the  Danish Medical Research Council , and Herlev and Gentofte.
Differential expression analysis Most bioinformatics analyses were performed by the MBB platform in Montpellier (http://mbb. univ-montp2. fr/). For each condition (CNT, CCI and CES) 3 biological replicates were sequenced to provide a mean of 50 million paired-end reads per sample. Pre-processing of the raw RNA-seq data to remove contaminants, adapters, low-quality sequences and unpaired reads was performed with TrimGalore (https://github. com/FelixKrueger/ TrimGalore) with standard parameters (quality 30 and length 50 bp). The New Tuxedo protocol  [95]  was used for the assembly of transcripts and the quantification of gene expression levels before analyzing differential expression with DESeq2. First, reads from each sample were mapped to the mouse reference genome (GRCm38) with HISAT2-2. 1.
0  [96]  with default parameters and -dta to provide alignments tailored for transcript assemblers. To assemble transcripts following this protocol, StringTie-1. 3. 3b was provided with Mus_musculus. GRCm38. 90. gtf as a reference annotation gene model file downloaded from ensembl web site (ftp://ftp. ensembl. org/pub/release-75/ gtf/mus_musculus/). This guided assembly was provided a parameter to limit the processing of read alignments to only the assembled transcripts matching the reference transcripts. The StringTie's acompagning script (http:// www. ccb. jhu. edu/software/stringtie/dl/prepDE. py) was then used. The dendrogram representing the result of the clustering of all pairwise dissimilarities between the transcript expressions was obtained with the help of the Trinity tool (https://github.
A second search with the same search terms and same procedures was performed on April 6th, 2022, with the date limit January first, 2022 to April 6th, 2022. This search retrieved 75 and 54 articles for screening. Duplicates were removed resulting in 54 studies for screening of which 29 were retrieved and 14 were included. Furthermore, data of our study was included. 39 Fig. 2  presents the flow diagram combined for both searches. Data collection process: data was collected by one researcher (IE) and checked by two other researchers (KP and NG). Data collected was on differentially expressed miRNAs between COVID-19 patients and controls or different severity grades of COVID-19 patients. Furthermore, pre-analytical data, data on experimental procedures, normalization and statistical analysis was collected.
This change has implications for the dynamics of subduction immediately preceding collision, as buoyancy contrasts and the weak coupling of magma-poor rifted margins favour the exhumation of UHP rocks in collisional orogens, thus allowing the exhumation of UHP rocks in the Neoproterozoic orogens of Gondwana. Acknowledgements. This research was supported by the Serrapilheira Institute (Serra-1709-21887). Methods Thermomechanical modelling. The 3-D geodynamic simulations were carried out using LaMEM  [62]  (https://bitbucket. org/bkaus/lamem). LaMEM is an open-source code using a finite difference staggered grid discretization combined with a particle-in-cell method to solve the energy, momentum and mass conservation equations. Rock rheologies are assumed to be visco-elasto-platic and the total deviatoric strain rate is given by: 𝜖˙! " = 𝜖˙! " #!$ + 𝜖˙! " %& + 𝜖˙! " '& = ( )* !"" 𝜏 !" + ( )+ ,-#$ ,.
Density phase diagrams. The investigation of mineral phase equilibria transformation and density variation were modelled using the Gibbs free energy minimization program package Theriak-Domino  [64]  utilizing the internally consistent thermodynamic dataset ds-62  [65]. The following mineral activity-composition models were used: clinopyroxene and clinoamphibole  [66]  ; garnet, orthopyroxene, biotite, chlorite, and muscovite  [67]  ; clinozoizitezoizite and olivine  [68]  ; plagioclase  [69]  ; spinel  [70]  ; and ilmenite  [71]. Quartz, coesite, Al2SiO5 polymorphs, rutile, titanite, talc, lawsonite and albite were considered as pure phases. The thermodynamic models were calculated under fluid-saturated conditions (aH2O = 1), except for the dry peridotite, with the metamorphic phase transitions restricted to the subsolidus field.
Valdivia Bank (VB) is a Late Cretaceous oceanic plateau formed by volcanism from the Tristan-Gough hotspot at the Mid-Atlantic Ridge (MAR). To better understand its origin and evolution, magnetic data were used to generate a magnetic anomaly grid, which was inverted to determine crustal magnetization. The magnetization model reveals quasi-linear polarity zones crossing the plateau and following expected MAR paleo-locations, implying formation by seafloor spreading over ∼4 Myr during the formation of anomalies C34n-C33r. Paleomagnetism and biostratigraphy data from International Ocean Discovery Program Expedition 391 confirm the magnetic interpretation. Anomaly C33r is split into two negative bands, likely by a westward ridge jump. One of these negative anomalies coincides with deep rift valleys, indicating their age and mechanism of formation.
Thompson during cruises TN373 and TN374 (2019-2020) collecting ∼10,730 km of new data (Figure  2 ). Combining the new data set with previously available data, we constructed a magnetic anomaly map and performed inverse modeling to determine the crustal magnetization. Paleomagnetic and biostratigraphic data from International Ocean Discovery Program (IODP) Expedition 391 drill sites verify the magnetic model. The results indicate that VB becomes younger from east to west, consistent with formation at the MAR.
Magnetic Anomaly Map Magnetic measurements from a total of 28 cruises spanning 56 years  were compiled for a magnetic anomaly grid encompassing VB (Figure  2 ; Table  S1  in Supporting Information S1). The combined data set amounts to ∼37,610 km of track length. Twenty-six of these surveys were acquired from the National Center for Environmental Information (NCEI) database, while the remaining two surveys (TN-373, TN-374) were recently collected. These latter two cruises collected >10 6 data points in a pattern of 25 transects (∼10,731 km) across VB and nearby Walvis Ridge (Figure  2 ). To obtain magnetic anomalies caused by the crustal field, the Earth's main core field was subtracted from the total field using the 13th generation International Geomagnetic Reference Field (IGRF-13;  Alken et al.
, 2021). The resulting anomalies were processed to remove noise, such as spikes or offsets caused by technical issues or disturbances from external factors (e. g. , magnetic storms). After noise removal, the data were checked for systematic errors such as drift or offset by analyzing crossover errors (COE), which are data misfits at track crossings. When merging data spanning several decades, the observed data from different surveys often do not agree at track intersections for reasons such as navigation errors, resulting in large COE. Correcting COE improves grid accuracy and can significantly reduce artificial noise and data artifacts. COE analysis was done using the x2sys package of GMT 6 software  (Wessel et al. , 2019)  following a procedure similar to that outlined in  Huang et al. (2021).
The magnetic anomaly map implies that similar ridge-centered volcanism formed VB. Based on the magnetization inversion results, VB contains four polarity bands: wider positive and negative magnetization zones on the east and west flanks, respectively, surrounding narrow positive and negative bands near the center (Figure  2 ). IODP Expedition 391 core data agree with the identification of two of these polarity bands: C33r on the west flank and C34n on the east flank. In their synthesis of South Atlantic magnetic anomalies,  Cande et al. (1988)  did not identify C34n near VB. In a prior study, we identified C34n as the positive anomaly at the western edge of the curved C33r  (Thoram et al. , 2019). Here we follow the drilling results and identify C34n as the strong positive anomaly on the distal east flank of VB.
Data Availability Statement All the magnetic data used in this study, including data from cruises TN-373 and TN-374 are archived on the Zenodo database (https://doi. org/10. 5281/zenodo. 7662198). The new magnetic data will eventually be added to the NCEI marine geophysics database. The 1-min resolution VB magnetic anomaly grid and magnetization grid generated in this study are also archived on the Zenodo database (https://doi. org/10. 5281/zenodo. 7662198).
[8] [9] [10] [11] [12] [13]  Machol et al. described a cohort of 15 individuals with variable clinical manifestations resembling CSS and NCBRS. 8  The Online Mendelian Inheritance in Man (OMIM) database now classifies the SMARCC2-associated phenotype as Coffin-Siris syndrome 8 (MIM #601734). The described phenotype included neurodevelopmental delay (DD), mild to severe intellectual disability (ID), profound speech delay, behavioral abnormalities, muscular hypotonia, and feeding disorders in infancy. Recurrent dysmorphic facial features were thick eyebrows, long eyelashes, anteverted nares, and thin upper and thick lower lip vermilion. SMARCC2 contains 4 well-described and highly conserved functional domains, namely, the SWIRM (named after the chromosomal proteins SWI3, RSC8, and MOIRA in which it was discovered) domain, the SANT (named after the initials of the proteins Swi3, Ada2, N-CoR, and TFIIIB) domain, and 2 domains in a coiled-coil region, termed dimerization (DR), and core assembly region (CAR) (see Figure  1A ).
Constitutional abolition of Smarcc2 during postnatal and adult hippocampal neurogenesis in mice increased astrogenesis, resulting in an abnormal spatial distribution of radial glial-like cells, ultimately linked to behavioral and learning impairments. 14  Additionally, intact Smarcc2 expression determines cerebral cortex volume, thickness, forebrain, and cortex development. 14, 15  To date, reports of SMARCC2 variants have been mostly part of individual case reports or large NDD studies with limited clinical information. [9] [10] [11] [12] [13] 16  In an attempt to better characterize the clinical and molecular spectrum of SMARCC2-associated NDD, a large cohort of 65 affected individuals was collected, including 41 novel individuals with de novo or inherited variants, whose clinical and molecular findings were systematically described, and 24 previously published individuals, whose data were thoroughly curated.
Variant annotation and scoring Variants were standardized to the SMARCC2 reference transcript NM_003075. 5 (GRCh37/hg19) using Mutalyzer 3  19  and annotated using the Ensembl Variant Effect Predictor. 20  All SMARCC2 variants were subsequently reclassified based on the recommendations of the American College of Medical Genetics and Genomics (ACMG)  21  and subsequent updates. An a priori and a posteriori classification system was used based on either prior evidence or our findings, such as new mutational hotspots, clustering in functional domains, recurrence, and functional results supporting pathogenicity. Compare File S2 sheets "clinical_ table" and "ACMG criteria. ".
Clinical information Clinical manifestations were systematically described and standardized according to the Human Phenotype Ontology terminology (File S2 sheet "clinical_table" and File S1 "Clinical reports"). 22  Information on clinical abnormalities and facial dysmorphic features, which were available for 58 SMARCC2 subjects including all novel ones, were summarized and compared (Tables  1, 2 , and S1). When available, cranial magnetic resonance imaging (cMRI) data were evaluated by an experienced pediatric neuroradiologist. The composite facial gestalt of missense/in-frame and LGD variant individuals shown in Figure  2  was generated by applying the Face2Gene research application (FDNA Inc) to a single 2D frontal facial photograph. A total of 24 images of novel and previously published SMARCC2 individuals (10 with missense/in-frame and 14 with LGD variants) were analyzed.
Protein model analysis of missense variants We used the published structures PDBDEV_00000056  23  (PDB-Dev) and 6LTH  24  (protein data bank; PDB) to map pathogenic variants of BAF complex subunits. We utilized the published crystal structure of the SMARCC1 N terminus (6YXO  25  ) to generate a homology model (File S4) of the paralogous SMARCC2 region with PHYRE2 26 (One-to-One threading option), which we used to investigate pathogenic variants in this region. We used previously studied missense variants in this N-terminal region extracted from tumor samples in the cBioPortal/ COSMIC databases to compare the effects and localization of variants identified in our cohort. 25  Structures were visualized with the Pymol software (OpenSource Version 2. 5. 0; Schrodinger, LLC). Missense variants in other BAF base complex subunits (File S2 sheet "missense_other_BAF") were reviewed from published literature reports (Table  S2 ), standardized to fit the model transcript and used to analyze spatial proximity in the BAF complex model.
2678A>G p. (Glu893Gly)). De novo non-truncating variants in this domain were classified as likely pathogenic according to the PM1_Moderate criterion if computational predictions (CADD PHRED v1. 6 score ≥28. 1) indicated they were pathogenic. Variants in the DR and SWIRM domains are rare and lack molecular/functional evidence, thus classified as variants of uncertain significance (VUS). N-terminal missense variants included 1 previously BAF core module. 25  Circles above the protein model indicate novel heterozygous variants, whereas squares below the model indicate previously described variants (beige: inframe; orange: missense; berry: splice; black: truncating). The size of the lollipop represents the number of affected families with the variant, the number inside shows the number of individuals.
Nevertheless, considering that computational analysis indicated high conservation and constraint of amino acid substitutions for both regions (Figure  S1 ), future studies addressing non-truncating changes in these domains could help identify additional clusters. All LOF changes were (likely) pathogenic. We focused on the pathogenicity of the c. 3129del p. (Gly1044Aspfs*17) because this variant was the only one listed in public databases, and exceeded the allele frequency cutoff (2 in gno-mAD). RNA expression analysis in 1 affected individual with this alteration in heterozygous state showed the expected NMD, although it was incomplete. A suspected milder impact of this alteration due to residual expression requires protein analysis, but no further material from this individual or others with LGD variants was available to compare expression levels.
Moreover, such limited resemblance makes it hard for clinicians and geneticists to clinically suspect this BAFopathy without genetic testing. The large number of pathogenic variants identified in this study allowed the identification of 2 clinical patterns associated with truncating and non-truncating variants, respectively. Affected individuals carrying missense/in-frame variants had a more severe phenotype, especially in neurodevelopment (Table  1 ), growth parameters (Table  2 ), and facial dysmorphisms (Figure  2A  and B ). The de novo occurrence of the vast majority of non-truncating variants in this cohort corroborates their severe effect. On the contrary, the impact of LGD variants was milder, explaining their frequent inheritance from a phenotypically healthy parent and their possible presence in public databases (compare p-MvT and OR-MvT in Tables  1  and 2 ).
Acknowledgments The authors thank the individuals and their families for participating in this study. Furthermore, we are indebted to GeneDX for establishing contact with the clinicians. The authors I. M. , A. R. , D. W. , V. C. , O. K. , G. W. E. S. , A. R. , and G. V. are members of the European Reference Network on Rare Congenital Malformations and Rare Intellectual Disability ERN-ITHACA [ EU Framework Partnership  Agreement ID:  3HP-HP-FPA ERN-01-2016/739516 ]. The authors acknowledge  ERN-ITHACA  for posting a call for a collaborative project, which led to the recruitment of SMARCC2 individuals. Also, we acknowledge  TUDP  for performing exome sequencing of Fam-21 with the Telethon project  GSP15001. Funding B. P. is supported by the  Deutsche Forschungsgemeinschaft (DFG)  through grant  PO2366/2-1.
Genomic approaches in biodiversity research High-throughput genomic sequencing technologies have lately evolved from mainly generating short (50-300 bp) to much longer (>10 000 bp) DNA sequencing reads. Genetic and genomic approaches commonly used in biodiversity research include DNA barcoding/metabarcoding, reduced representation DNA techniques, transcriptome sequencing (RNA-Seq), and wholegenome (re-)sequencing (Figure  1 ). Successful execution of these approaches depends on the quantity and quality of the available biological material, laboratory and bioinformatic skills, feasibility and costs, and on the quality and completeness of the available reference genome database. We review these common approaches, including their specific merits and limitations (Table  1 ). Since the quality of the starting biological material is a major consideration in applying genomic approaches, we also review approaches that use noninvasive sampling.
Acknowledgments We thank  Cecilia Helmerson ,  Antonio Rivas ,  Nelson Lauzon , and  Sally Leys , for the pictures of the Atlantic cod, the Iberian lynx, the European beech, and the freshwater sponge, respectively. We also thank  Fabien Condamine ,  Love Dalén ,  Richard Durbin ,  Bruno Fosso ,  Roderic Guigó ,  Marc Hanikenne ,  Alberto Pallavicini ,  Olga Vinnere Pettersson ,  Xavier Turon , and  Detlef Weigel  for their contributions to the manuscript, as well as the whole ERGA community for making this possible.
S3 ), compared with those exerted on Kv1. 1 currents, indicating that NFA does not modulate the gating of Kv1. 1 channels by acting on Ca 2+ -activated chloride channels 16/anoctamin-1 (ANO1; TMEM16A), which are endogenously expressed by oocytes. To validate the oocyte data in another expression system, we performed whole-cell patch-clamp recordings from HEK293 cells transfected with Kv1. 1 channels before and after NFA application. Consistent with the findings in oocytes, we recorded a significant NFA-mediated increase in Kv1. 1 currents at negative potentials, associated with a shift in the voltage dependence toward more hyperpolarized potentials, and slower deactivation kinetics (SI Appendix, Fig. S4 A-D ). To further validate our findings using a neuronal cell system, we tested the effects of NFA using Neuro-2a cells (N2a).
Materials and Methods TEVC recordings from Xenopus laevis oocytes were performed 1 to 5 d after Kv1. 1 and Kv1. 2 RNA injection using a GeneClamp 500 amplifier (Axon Instruments) as previously described  (35, 85). For gating current measurements, we expressed in oocytes the Shaker N-terminal Δ6-46 deletion mutant channel that lacks fast inactivation and carries the W434F mutation that abolishes ion conduction (GenBank accession #M17211). The oocytes were voltage-clamped using the cut-open oocyte technique  (33, 34). HEK293 cells were cultured in Dulbecco's modified Eagle's medium (DMEM, Gibco) at 37 °C with 5% CO 2. Human Kv1. 1 and Kv1. 2 cDNAs were subcloned into the mammalian expression vector pCDNA 3 and transiently transfected with the pEGFP-N vector using Lipofectamine 2000 (Invitrogen), according to the manufacturer's instructions.
ACKNOWLEDGMENTS The authors thank the  University of Lille , the  Pasteur Institute , the  "Centre National de la Recherche Scientifique (CNRS) " and the  "Institut National pour la Santé et la Recherche Médicale " for their constant support. Philippe Lefebvre  and  Tony Lefebvre  were supported by the CPER CTRL 18 FEDER (acronym:  Chol-O-Rev ) cofounded by the  EU  under the  European Regional Development Fund  and the  Hauts-de-France Regional Council , the MEL (contract No. 2017-ESR_14 ) and the  French State  (contract No. 2018-R3-CTRL-phase 2 ).
We first fitted consecutive models for the whole species distribution with these four variables under current environmental conditions (see Materials and Methods), before projecting them over past conditions. Models with combinations of two variables had the lowest AIC values generally, however, only the model using prec_March-June and tmin_Nov-Feb showed Area under the Curve (AUC) values and predictive ability better than null models (p-value < 0. 05) and was consequently chosen as our final model (see Fig. S5b  for the distribution of these variables across genetic clades). Based on this model and using paleoclimatic datasets, we projected the potential wholespecies distribution in Europe, North Africa, and the Middle East since the Last Glacial Maximum (ca. 22 kya), as well as for the five genetic clades (Fig.
Population genetic structure and demographic history The genetic structure of the samples was estimated by using principal component analysis and admixture analysis. To obtain independent SNPs, they were filtered for minor allele frequency > 0. 05 and linkage disequilibrium < 0. 4 using the function snpgdsLDpruning of the R package SNPRelate  (Zheng et al. 2012 ). The principal components were calculated using the resulting 15,960 independent SNPs and the function snpgdsPCA of SNPRelate. On the same dataset, ancestry coefficients were estimated using the function sNMF of the R package LEA  (Frichot and François 2015). Results for 2-10 K values for 20 replicates per K were retained, and the optimal K value was determined by calculating ΔΚ as described by  (Evanno et al. 2005 ). The hierarchical cluster analysis was eventually performed using a set of 75,000 random SNPs with the R package pvclust version 2.
We therefore kept only one haplotype per individual. We used the Relate package  (Speidel et al. 2019)  to infer genome-wide genealogies and coalescence rates across all individuals. To take into account local variation in recombination rates, we used a recombination map for B. distachyon obtained from  Huo et al. (2011). To obtain demographic estimates of times and population sizes, we used a mutation rate of 7x10 -9 substitutions/generation  (Lynch et al. 2016 ) and a generation time of one year as B. distachyon is annual. We set the prior for the effective haploid population size to 75,000 individuals based on previous estimates  (Stritt et al. 2022 ). We subsequently fitted a time-varying population size history and inferred genomewide topologies using the EstimatePopulationSize. sh script provided with the Relate package.