dataesr/scientific-paragraphs-categorization huggingface dataset:
Small animal MRI Eight WT (n = 8, five females, three males, mean age = 101 days, SD = 39. 7) and eight homozygous mutant (n = 8, five females, three males, mean age = 95. 2 days, SD = 34. 8) for a total of 16 animals were employed for high resolution, pre-clinical MR imaging experiments. Data from one WT animal were excluded as part of a pilot study. For in vivo structural MRI, mice were anesthetized with isoflurane, placed in a plastic bed and restrained with gauze pads to minimize the possible influence of motion artifacts. For the duration of each MRI scan, mice were maintained under isoflurane gas anesthesia at approximately 37°C using a warm air blower and respiration was monitored using a pressure pad. Imaging was performed using the 7 Hz. The repetition time (TR) and the number of acquired slices were varied for two pairs of WT/KO mice in order to achieve greater slice coverage along the rostro-caudal axis (TR: 4000 ms to 4750 ms, number of slices: 40 to 50).
Cohort Study Our cohort consists of 15 individuals with biallelic DENND5A variants coming from 14 families with 21 unique variants. Females make up 60% of the cohort and the average age at the time of the last clinic visit from which answers to questionnaires were based upon was 9 years (SD = Supplementary table 1 provides comprehensive phenotypic data for each member of the cohort resulting from clinical evaluations by their physicians. "0" indicates a phenotype was not reported, "1" indicates a phenotype was documented to be present, and a cell left blank means its presence is unknown. The results of the study revealed the most frequently reported phenotypes observed in individuals with biallelic DENND5A variants are global developmental delay (93%), seizures (87%), ventriculomegaly (71%), hypotonia (67%), corpus callosum volume loss (64%), and microcephaly (60%; Fig.
4B ). K205X is predicted to undergo nonsense-mediated mRNA decay, but our DENND5A antibody recognizes a region of the protein more C-terminal to the stop codon. mRNA levels were thus measured, but RT-qPCR data revealed that all cells derived from cohort members express DENND5A mRNA near control levels (Supplementary Fig. 3A ). Lymphoblasts from a healthy donor as well as from two homozygous cohort members were collected and immortalized with Epstein-Barr virus to establish lymphoblastoid cell lines. DENND5A protein expression was significantly reduced in both patient-derived cell lines compared to control cells (Fig. 4C ), whereas in overexpression experiments these mutations expressed near WT levels (Fig. 4A ). A downward shift was observed in the DENND5A band corresponding to D541G for an unknown reason, potentially implying a posttranslational modification or splice variant.
35  However, no genetic data is available regarding the known pseudo-TORCH patients to our knowledge, and it is unknown if DENND5A variants are behind any of these cases. Physicians encountering infants and children with global developmental delay accompanied by hallmark features identified in this report such as seizures, ventriculomegaly, hypotonia, reduced corpus callosum volume, and/or microcephaly should consider screening for DENND5A variants and referring the families to genetic counseling. We also support the gene-disease assertion for DENND5A variants to be updated to "strong", thus allowing compelling variants in this gene to be classified as "Likely Pathogenic" according to ClinGen guidelines. The identification of additional DENND5A EE cases will prove valuable for future clinical and biological studies and thus improved treatment options and prognostic information for health care providers and families alike.
Acknowledgements We would like to acknowledge all cohort members in this study, their families, and treating clinicians for their participation. The views expressed are those of the author(s) and do not reflect the official policy of the  Department of the Army , the  Department of Defense or the U. S. Government. Participant 10 was recruited as part of the  German-Jordanian Autosomal Recessive Intellectual Disability project  ( GeJo-ARID ) funded by the  German Academic Exchange Service (DAAD)  as part of the  German-Arab Transformation Program Line4  (Project -ID 57166498 ). The content is solely the responsibility of the authors and does not necessarily represent the official views of the National Institutes of Health. Scott ,  Judy Schaechter ,  Timothy Schedl ,  Kelly Schoch ,  Daryl A.
Funding This work was funded by a  Foundation Grant  from the  Canadian Institutes of Health Research to PSM , and a grant from the  Alain and Sandra Bouchard Foundation for Intellectual Disabilities  to PSM and TMD. This work was also supported by the  King Salman Center for Disability Research  through Research Group no  RG-2022-010  (FSA). This work was also performed under the  Care4Rare Canada Consortium  funded by  Genome Canada  and the  Ontario Genomics Institute  ( OGI-147 ), the  Canadian Institutes of Health Research, Ontario Research Fund ,  Genome Alberta ,  Genome British Columbia ,  Genome Quebec , and  Children's Hospital of Eastern Ontario Foundation  (DC, ESYG, MO). Research reported in this manuscript was also supported by the  NIH Common Fund , through the  Office of Strategic Coordination/Office of the NIH Director  under Award Number(s) [ U01HG007672 ,  U01HG007943 ] (HC).
While each ventricle was segmented separately, the volumes of both lateral ventricles were pooled together for all statistical analyses to account for the presence of fused lateral ventricles in several of the mutant mice. Q-Q plots and Levene's tests for both datasets indicate the data are normally distributed and variances are homogenous. Statistical analyses were performed by another independent researcher using R version 4. 1. 2 with Companion to Applied Regression package version 3. 0, SPSS, and Tidyverse version 1. 3. 1 software.
4. 8 ) 8. Seven individuals are homozygous for DENND5A variants and, for the first time, we report eight individuals with compound heterozygous DENND5A variants exhibiting phenotypic overlap. Six members of the cohort were reported to have at least one additional variant flagged as potentially pathogenic, but the only gene with a variant of uncertain significance or potential pathogenicity that all individuals had in common was DENND5A. Table1summarizes each person in the cohort, including their DENND5A variant(s) and allele frequencies obtained from the gnomAD v2. 1. 1 dataset (https://gnomad. broadinstitute. org), and the presence (+) or absence (-) of the six most commonly reported phenotypes. None of the DENND5A variants present in the cohort were found in the homozygous state among 140,000 individuals on gnomAD, a database that removes individuals affected by severe pediatric disease, indicating that biallelic pathogenic variants are incompatible with normal development.
89 and. 96 and between. 82 and. 92, respectively. Individual demographic characteristics. We assessed gender, age, marital status, socio-economical status, education level, and population size of the town/city of the participants (see Table  1  for the classification of said variables). Additionally, we asked the participants about the number of days they were obliged to stay at home and the number of people they are living in the same household with. Country-level variables. Countries were classified based on the severity of the national COVID-19 health crisis during our data collection period. Severity level 1 represents the lowest level (less than 100 infected per million inhabitants), 2 a medium level (between 100 and 2000) and 3 the highest severity level (more than 2000 infected) of the pandemic (see Table  1 ).
Data analytic strategy We used Mplus (Muth en & Muth en, 2016) for the factor analyses and SPSS (Version 24). Prior to the analyses, data were tested for normality and missing values. Data was removed for those participants who failed to complete one or more full questionnaires or showed straight lining behavior. Missing data in the formal questionnaires was less than 0. 1%, (missing completely at random) and was replaced with the expectation maximization algorithm. Missing data on demographic variables was less than 0. 2% and was not replaced. To validate MCCS, exploratory factor analysis (EFA) using principal component analysis with oblimin rotation was conducted on the first randomly selected half of the Spanish sample (n = 316). Then, confirmatory factor analyses (CFAs) were performed on the second half of the Spanish sample (n = 328) and on all samples from each country.
The collected insects were transported to the laboratory, where M. V. K. identified and counted the individuals of common species and pinned all individuals of rare species and of species of uncertain identities. These pinned specimens, identified primarily by †J. Jalava (samples of 1992-2003) and by J. Kullberg (samples of 2004 Kullberg (samples of -2006)) , were deposited in the Zoological Museum, University of Helsinki (MZH). As in studies based on the light-   S2. Insert: the position of the study area in Northern Europe. trap catches  (Hunter et al. , 2014; Keret et al. , 2020) , our data reflect the relative abundances of collected species rather than their population densities in the strict sense.
Life history traits We restricted our analyses of the association between spatial patterns in the abundance of individual Lepidoptera species with their life history traits to the 96 most abundant species, for which we collected at least 25 individuals in 15 sites during  1993 , 1994 , 1996 and 1997 (Data S2) (Data S2). We classified these 96 species based on overwintering stage (egg, larva, pupa or imago), larval food (live vascular plants or any other substances, e. g. live mosses or decaying wood), feeding strategy (internal feeders, whose larvae develop inside live plant tissues, or external feeders) and feeding guild (internal feeders: leaf miners, stem borers and larvae feeding inside flowers or seeds; external feeders: defoliators and leaf-rollers, whose larvae feed inside a shelter constructed from plant leaves).
Data analysis A sample, in terms of our study, consisted of all individuals of moths and butterflies collected from one site during two person-hours. Abundance was quantified by the number of individuals in a sample. Diversity was measured by the Shannon H index and was based on the numbers of individuals of each species in a sample. We also used individual rarefaction (PAST program:  Hammer et al. , 2001)  to generate the numbers of species expected in a sample of 100 individuals for each of the study sites and in a sample of 1000 individuals for proximate and distant sites during the periods with high and low pollution. These rarefaction-based estimates were used to avoid obvious effects of sample size on actual species richness; they were considered significantly different if their 95% confidence intervals (CI 95 ) did not overlap.
We used the log 10 -transformed distance from the smelter as a measure of the pollution-induced environmental disturbance  (Kozlov et al. , 2009). We explored the spatial and temporal variation in the abundance (square-root transformed to normalise the distribution of the residuals) and diversity (Shannon index) of the Lepidoptera in individual samples using linear mixed models (SAS GLIMMIX procedure; SAS Institute, 2009) with a Gaussian error distribution. In these models, the distance from the polluter, year and their interaction, as well as collector, wind speed and temperature, were considered fixed effects, whereas the study site was treated as a random effect. We adjusted the standard errors and denominator degrees of freedom following  Kenward and Roger (2009) , and we evaluated the significance of a random effect by testing the likelihood ratio against the χ 2 distribution  (Littell et al.
Data overview We obtained 581 samples of moths and butterflies from 15 study sites (Data S1). These samples, which were collected by ten persons (including the authors) during 1992-2006, contained 25,628 individuals, 25,606 of which were identified to the species level. Within 345 identified species (Data S2), Argyresthia pygmaeella (Argyresthiidae, 2390 individuals) and Ancylis myrtillana (Tortricidae, 2353 individuals) were most abundant. Half of the collected species (172 of 345) were represented by one to six individuals, and their overall contribution to our catches was 1. 5%. Of these 172 species, 50 were collected from industrial barrens only. Surprisingly, the fauna of the severely polluted habitats included critically endangered Eucosma saussureana and vulnerable Argyroploce concretana, Cydia cornucopiae and Erebia disa.
This feeding habit can also protect these Fig. 3. Abundance (a), diversity (b) and species richness (c) of moths and butterflies in relation to the distance from the Monchegorsk copper-nickel smelter during the high-emission period  (1993, 1994, 1996 and 1997). Values are least-square means (±SE) from the SAS GLIMMIX procedure (a, b) and the estimated means (±SE) from rarefaction analysis (c); the values of abundance are backtransformed. Correlations refer to log 10 -transformed distance; the correlation with abundance is based on the square-root transformed values. insects from desiccation  (Tooker and Giron, 2020) , which poses a greater risk in the industrial barrens than in forests due to the increased wind speed and higher temperatures in the barrens during the sunny days  (Kozlov and Zvereva, 2007).
Acknowledgements We thank  E. Haukioja  and  †K. Mikkola  for methodological advices and for supporting the first phase of the project;  A. Blashkevich ,  A. L. Lvovsky ,  E. Melnikov ,  A. V. Selikhovkin ,  I. A. Selikhovkin ,  A. Vassiliev  and  †I. Vishnyakov  for participation in data collection;  M. Mutanen  and  T. Muus  for information on life histories of several moth species; and  V. Barcan  for providing meteorological and emission data. We are deeply indebted to †J. Jalava,  J. Kullberg  and  L. Kaila  for identification of problematic specimens and to five anonymous reviewers for their inspiring comments to an earlier version of the manuscript. The study was supported by the  Academy of Finland  (projects  122133 ,  211662 ,  213969 ,  214824 ,  316182 , and researcher posts of M.
To fill this gap, we used publicly available IgG repertoire data of 9 human donors from a recent ultradeep repertoire profiling study of immunoglobulin heavychains (IGH)  [47]. The data was downloaded from Sequence Read Archive and processed as in  [49]. Repertoires were obtained from the sequencing of IGH mRNA molecules to which unique molecular identifiers (UMI) FIG. 4 : Comparison to repertoire data. A. Clonotype abundance distribution of IgG repertoires of healthy donors from  [47]. B. Estimated mutatibility σv in units of the rescaled cross-reactivity r * , defined as the antigenic distance at which clonotypes stop growing. σv is obtained as a function of d by inverting the linear relationship estimated in the inset of Fig. 3E , assuming q = 2 and Γ = 1. 4 (estimated from  [18] ). were appended.
For each IGH nucleotide clonotype found in the dataset, we counted the number of distinct UMI attached to it, as a proxy for the overall abundance of that clonotype in the expressed repertoire. The distributions of these abundances are shown for all 9 donors in Fig. 4A. In agreement with the theory, they display a clear power-law decay p(n ) ∼ n -1-β , with β = 1. 2-2. 4. Since the experimental distribution is derived from small subsamples of the blood repertoire, the absolute abundances cannot be directly compared to those of the model. In particular, subsampling means that the experimental distribution focuses on the very largest clonotypes. Thus, comparisons between model and data should be restricted to the tail behavior of the distribution, namely on its power-law exponent β. The bulk repertoire is a mixture of antigen-specific sub-repertoires, each predicted to be a power law with a potentially different exponent.
Acknowledgements The study was supported by the  European Research Council   COG 724208  and  ANR-19-CE45-0018  " RESP-REP " from the  Agence Nationale de la Recherche  and  DFG  grant  CRC 1310  " Predictability in Evolution ". The authors thank  Natanael Spisak  for pre-processing the raw data from [47], and for useful discussions and suggestions.
, who evaluated E-selectin levels in 37 SCD patients with retinopathy and 34 without retinopathy, did not find any correlation between E-selectin levels and retinopathy. However, only 14/36 SCD patients had proliferative retinopathy in their study. 47 gh levels of soluble endothelial adhesion molecules, especially E-selectin, were reported in diabetic patients with proliferative retinopathy. 37, 48, 49 3] The elevation of E-selectin levels in sickle cell retinopathy and its possible pathophysiological implications need to be confirmed by larger studies and might prompt us to evaluate this new molecule in the treatment of SCD retinopathy. In our study, CEC and PEC counts were detected at very low levels. In contrast, previous preliminary data reported significantly higher CEC counts in SCD patients at steady state compared to controls.
The classification is referred to as the FAO agricultural problem land approach  28  , associated with the FAO/UNESCO Digital Soil Map of the World  29  , and now integrated into and superseded by the Harmonized World Soils Database (HWSD)  30  and into FAO's Global Agro-Ecological Zones (GAEZ)  31. For abandoned agricultural land, another key type of marginal land, extensive research has proposed different definitions and mapping approaches  [32] [33] [34]. Agricultural land abandonment has been considered to be mainly driven by biophysical constraints, but also by reasons pertaining to farm structure, agricultural viability, as well as to changing population, political regimes, nature conservation and other regional contexts  33, 35. These approaches generically consist of comparing satellite data corresponding to two different periods, and interpreting the temporal land cover differences.
Several studies attempted to quantify and map marginal land use across spatial (global, national, regional and local data) and temporal (historic to current data) resolutions  36. At the global scale, it has been quantified by mapping current land cover and land suitability indices  37. However, it has not always been possible to identify the relative importance of agricultural (i. e. abandoned) and non-agricultural land types on the identification of marginal land, because of a combination of factors: analyses based exclusively on (bio)economic drivers, quality of underlying datasets and scales, and lack of detail on current land covers' spatial (i. e. granularity) and temporal resolutions  18. Beyond the challenge of defining and identifying marginal lands, the design of SOC sequestration pathways involving biomass requires the correct pairing of suitable plant species with specific target areas, based on the compatibility of plant species with the target areas' biophysical characteristics.
A simulation time horizon over 2020-2100 was selected in line with IPCC future climate scenarios throughout the twenty-first century for comparison purposes. A R code combined with the data treatment strategy depicted in Fig. 4 , constitutes the proposed generalizable framework. The framework is able to produce estimations showing whether more SOC would be sequestered, in the long-term, than it would be lost to rain-driven erosion, if the matching plant species were systematically grown on the identified target areas. To our knowledge, no previous global study on SOC sequestration considered such careful identification of marginal land (i. e. integrating pedoclimatic constraints, plant species tolerances, and land conservation), while balancing both SOC stock changes and SOC losses to erosion.
Preselection criteria and approach used are detailed in Supplementary Results, Table  S2 , including SOC sequestration potentials in Table  S1  and Fig. S10. In total, 432 plant species were associated to the 50 preselected biopumps based on FAO's ECOCROP database  42. Datasets on the plant environmental requirements (i. e. climatic and edaphic conditions) were retrieved from the database to further assess the suitability of plant species on target areas. All datasets on plant species tolerance are available from a data repository  43. The eventual introduction of invasive species in the receiving ecosystems was not considered beyond the exclusion of world protected areas. The matching exercise resulted in 561 viable combinations (out of 50 112 theoretically possible matches) of target areas (116 GEZ × world regions) × biopumps (432 plant species), where 27 biopumps (associated to 56 plant species) were compatible with 12 world regions and 12 GEZ.
Discussion The framework design is generic enough to be implemented in other settings, regarding target area definition, plant species of interest, scopes (e. g. geographic boundaries), as well as temporal and spatial resolutions. The provided R script in Ref. 43  is usable in different situations as long as the required input data is organised in the prescribed way. Moreover, the framework is flexible to accommodate different SOC sequestration and erosion models (e. g. by wind), depending on the required outputs and data availability. For our example, we selected the monthly time-stepped RothC model (detailed in "Methods" section), being an appropriate SOC model due to its: (i) demonstrated performance to replicate observed SOC changes in validation experiments, as compared with other models (described in Supplementary Methods), (ii) applicability to a wide range of world climates and regions in combination with GIS products  4, 38  ; (iii) recognition, being recommended as a standard spatialized SOC model at a 30 arcsec resolution by the FAO  44.
7 Mha year -1 ) and 269 Mha (0. 9 Mha year -1 ) based on the datasets HYDEv3. 0  48 and SAGE  49  respectively. A recent study  35  quantified the world's current extend of land use change and developed a model called HILDA+ to provide annual harmonised global land use data with national inventories at near-present. Cropland use changes were identified at 1029 Mha over the period 1960-2015 (about 0. 19 Mha year -1 ) with HYDEv3. 2  50 and 1035 Mha over the period 1960-2011 (about 0. 20 Mha year -1 ) with SAGE  49. A comparison of the former and the later with HILDA+ over the same periods showed higher results by 31% and 24%, respectively. The annualised values are comparable among different studies with different temporal resolutions; however, it generates uncertainty in the interannual variability as well as in scope and definition of abandoned agricultural land vs.
selecting plant species or groups of species (in our example: promising biopumps) and determining their environmental requirements/tolerances, and 4. matching target area × biopumps as determined by the compatibility of plant species to target areas' biophysical characteristics, and modelling soil C flows of the resulting target areas-biopump pairs. The full list of exploited data and sources of georeferenced data is presented in the dataset  43  and Supplementary Methods, Table  S1.
5) map  61  for the year 2017, and retaining SOCdeficient areas featuring up to 50 Mg ha -1. In step 1. 4, we filtered out areas corresponding to geographically defined protected areas, particularly important for biodiversity and ecosystem services, covered in the World Database on Protected Areas (WDPA v1. 6) map, a georeferenced product of the UN Environment Programme World Conservation Monitoring Centre (UNEP-WCMC)  62. In step 1. 5, we identified the biophysical constraints associated with the lands satisfying the previous two conditions, in order to discard areas featuring (sub-)severe soil and terrain restrictions that would exceed the tolerances of potential plant species. These constraints correspond to those associated with degraded lands in the georeferenced FAO Dominant Type of Problem Lands product for a generic perspective, complemented by the Harmonized World Soil Database (HWSD v1.