dataesr/scientific-paragraphs-categorization huggingface dataset:
CAZy predictions were completed in diamond (version 0. 8. 22. 84)  [50] , for MAGs and contigs (31 July 2018, database update) from dbcan2  [51]. DESeq2 R package (version 1. 18. 1) was used to obtain differential statistics on taxonomic composition and functional annotations from predicted ORFs from contigs using COG, CAZy, and KO annotation abundances  [52]. The contig ORF counts' abundances within DESeq2 followed a paired analysis, which blocked by sampling plot pre-/postfertilization, then normalized with variance stabilizing normalization. We pooled contigs from pre-/post-fertilization, then used the differential read abundances across all samples to obtain MAGs. Contigs were binned using Concoct  [53] , Maxbin2  [54] , and Metabat2  [55] , including the refinement program within metawrap  [56].
Metawrap was used for refinement of MAGs, blobiology prediction, and quantification of bin (MAG) abundance via quant_bin module  [56]. CheckM was used to evaluate completeness, contamination, redundancy, and genome properties of the MAGs  [57]. All MAG qualities were reported according to the MIMAG standards  [8]. We tested a variety of methods to resolve the taxonomy of the MAGs, including metawrap's classifier, classify genomes (https://github. com/AlessioMilanese/classify-genomes, (accessed on 15 April 2023)), which uses the metagenomic operational taxonomic units (mOTU) v2 taxonomy, JSpeciesWS Tetra Correlation Search  [58] , GTDB-Tk  [59] , and blastp of ribosomal protein S9 gene (obtained from Prokka annotation). Only GTDB-Tk provided the taxonomic identifications that were supported by ribosomal protein S9 gene blastp results.
Read-Based mOTU Picking and Statistical Analysis mOTUs analysis of the quality-filtered and decontaminated reads (not contigs) used in the de novo metagenomic assembly were used as input mOTUs v2  [45] , then parsed and further analyzed with the phyloseq (version 1. 22. 3) R package  [60]. Alpha diversity measurements with statistical testing for mOTUs (including t-test, Wilcox, Kruskal, and ANOVA) were completed in the phyloseq (version 1. 22. 3) R package. Beta-diversity metrics were obtained for mOTUs using the UniFrac (weighted/unweighted) and Brays-Curtis distances in phyloseq (version 1. 22. 3) R package. DESeq2 R package (version 1. 18. 1) was used within phyloseq (version 1. 22. 3) R package for mOTU differential statistics using negative binomial distribution corrected with variance-stabilizing normalization.
Data and Analysis Code Availability Raw sequence data, assembled contigs, and supplemental data are all available on NCBI Bioproject/BioSample/SRA as PRJNA954399-Lux Arbor Metagenome, and are also available at Open Science Framework, with code, at https://osf. io/mzrvj/ (accessed on 15 April 2023). All code for this study is available on www. github. com/friesenlab/MMPRNT_ panicum_metagenome_mags/ (accessed on 15 April 2023).
21 Gbp assembly size and an average N50 value of 1982 bp (Table  1 ). Across all samples, we obtained 190,172 contigs > 5 kbp, with an average of 23,771 contigs of 5 kbp per sample on a 1. 19 Gbp assembly size with an average N50 value of 9254 bp (Table  1 ). Of those 190,172 > 5 kbp contigs, 44,171 of them were >10 kbp in length, and 237 were >100 Kbps. Max contig length was 697,599 across all samples. We pooled all contigs, then used concoct, maxbin2, and metabat2, including the refinement program within metawrap. Concoct yielded no usable bins. When comparing metabat2 to maxbin2, metabat2 produced more raw MAGs than maxbin2 (435 vs. 319), the completeness was lower for metabat2 (39. 7% vs. 48. 0%), and higher contamination was present amongst the metabat2 bins (28. 0% vs. 16. 4%) (Figure  S2 ).
e. , moleculo) have yielded similar results to our Lux Arbor short read assembly. To compare on average, a single sample from Lux Arbor had 23,771 contigs > 5 kbp, while a Kansas native prairie soil with a similar amount of data had 4683 (100 bp paired-end) and 8532 (250 bp paired-end)  [10]. A single moleculo sequence library from a pooled Kansas prairie sample yielded 10,198 contigs > 10 kbp in length, and our Lux Arbor sample yielded 44,171 contigs > 10 kbp in length using only short reads. The maximum contig length obtained from a hybrid assembly of Kansas prairie was <63 kbp, whereas Lux Arbor had 237 contigs > 100 kbp in length, with a max contig of 697,599 bp  [10]. Recently, a closed bacterial genome has been obtained from the Saccharibacteria, formerly candidate phyla TM7, from stable isotope-labeled rhizosphere metagenome, suggesting that binning complete genomes directly from soil is possible  [16].
Our data suggest that Lux Arbor soils have lower microbial community complexity than Kansas prairie soil, based on the quality of metagenomic de novo assembly obtained. This nominates Lux Arbor and, possibly, other marginal soils to provide a testbed for soil and rhizosphere metagenomics. Obtaining metagenomic bins to resolve individual microbial genomes within the soil and rhizosphere has remained problematic, as the common assumption is that the higher the microbial complexity, the harder it is to resolve genomes directly from a sample. Low-complexity permafrost soil has had great success in resolving genomes, with over 1500 individual MAGs resolved with expressed metabolisms using transcriptomics and proteomics  [64] , but we have yet to obtain this order of magnitude with ease in nonpermafrost soil.
The first genome-centric view of a soil ecosystem was in the Kansas native prairie, where 129 MAGs were obtained, but, on average, the genome completeness was quite low at ~40%  [10]. The second grassland soil resolved 372 total genomic bins, with 181 that were partial to near-complete  [11]. A recent study of Amazon soil (using MIMAG guidelines) had 29 MAGs that were medium quality in representing over ten phyla, including members of the Candidate phyla radiation  [12]. A Mediterranean grassland soil MAG study obtained 793 MAGs that were near-complete  [65]. We compared concoct, maxbin2, and metabat2 within metawrap, and found that, on average, maxbin2 provided higher quality and lower contamination MAGs than metabat2, resulting in the 29 MAGs that we described (Figure  S2 ). In this study, we resolved genomes in the Lux Arbor switchgrass rhizosphere that represented uncultivated phyla, including the Acidobacteria group (rare subgroup 23), Candidate phyla UBA10199, Candidatus Eisenbacteria, and Dormibacterota (AD3).
Dormibacterota may lose autotrophy under more stressful environmental conditions. We resolved only the third representative from the elusive candidate phyla Eisenbacteria. Our MAG is the first to be found amongst soil or rhizosphere ecosystems. The previous two were found via genome resolved metagenomics in the Atlantic Ocean deep vent sample (BioSample: SAMN09287800), named Candidatus Eisenbacteria bacterium SZUA-252, and Rifle, Colorado, USA background sediment (BioSample: SAMN04313721), named Candidatus Eisenbacteria bacterium RBG_16_71_46  [73]. This phyla appears to be extremely rare, as 8000 MAG studies did not find any representatives across thousands of samples  [68]. Here, we add another representative of this rare phyla for further comparative genome analysis. In contrast to previous studies, the metagenomes we report nominate the betaproteobacterium Janthinobacterium as a candidate organism for association nitrogen fixation in the switchgrass rhizosphere.
Our Nitrospira MAGs lack the genes required for comammox, including the amo gene. The Nitrospira of Lux Arbor have the metabolic potential for urease, and the urease inhibitor N-(n-butyl) thiophosphoric triamide (NBPT) did not alter the ure gene copy number present pre-versus post-fertilization. However, it is unknown from our data whether urease enzyme function was altered in the post-fertilized plots, but NBPT is the most successful urease inhibitor on the market, reducing ammonium volatilization loss by 53%  [81]. Further analysis of urease gene expression and urease enzyme function is needed to validate that NBPT inhibition occurs on the expression or functional level. Carbon substrate metabolism, predicted using CAZy in the switchgrass roots of Lux Arbor, appears to be limited in terms of both the bulk metabolic potential and the individual genome level.
Numerical results and discussion The proposed model has been tested through numerical simulations in some illustrative cases. In particular, we consider a rectangular sample made of trabecular bone tissue. In the first test, we analyze a cantilever plate under a uniform distribution of a shear force density (t) on the side opposite the clamp (see Fig. 2 ). The second test, instead, is a three-point flexural one, where we employ the symmetry of the system to examine only half of the specimen (see Fig. 10 ). Since our formulation is variational, the numerical implementation of the tests has been conducted with the finite element method using the principle of virtual work (5) directly inside the commercial software COMSOL Multiphysics. We perform simulations in Comsol for testing the proposed approach because of its high flexibility and ease of use.
Genotyping and single nucleotide polymorphism filtering Genomic DNA of the 54 genotypes was extracted from the leaves using a mixed alkyltrimethylammonium bromide buffer and the kit NucleoMag Plant (Macherey-Nagel, Germany). DNA samples were quantified using ThermoFisher Scientific fluorometry Qubit, and fragment length was assessed with the Agilent Tapestation system. Illumina Tru-SEQ DNA PCR free and TruSeq Nano DNA Preparation Kit have been applied to generate sequencing libraries. Paired high-throughput sequencing (2 × 150 bp) was performed on an Illumina NovaSeq 6000 instrument on the GeT-PlaGe platform (Toulouse, France). The quality of the whole genome sequencing (WGS) raw reads were first checked using the FastQC package version 0. 11. 7,  23 trimmed by removing adaptor sequences and low-quality sequences using Trimmomatic version 0.
39  24  with the following parameters: SLIDINGWINDOW,   A consolidated variant call format (VCF) file for all genotypes was produced by VCFtools version 0. 1. 16,  28 containing about 17 million SNPs. All InDel-like variants were eliminated. Then, the VCF file was filtered using the following parameters: --max-missing 0. 2 -minQ 30 --minDP 8 --maf 0. 05 -allele 2. With filters applied to reduce the quantity and eliminate bad-quality SNPs, there were 1. 9 million SNPs left. The SNP density was estimated using the "CMplot" package  29  in R4. 0. 23. 30.
Population structure, principal component analysis, linkage disequilibrium, and SNP annotation A python centralized package named "RESEQ2" has been designed internally in our research group, which gathers several next-generation sequencing data analysis packages (such as PLINK 1. 07, 31 ADMIXTURE 1. 23,  32  VCFtools 0. 1. 16, 28 GATK 4. 1. 6. 0, ANNOVAR 2. 4  33  ). The phylogenetic relationships among the accessions were measured based on the genetic distance using the neighbor-joining method (with 1000 bootstrap replicates) in PLINK 1. 07. 31 The resulting phylogenetic tree was visualized in MEGA-11. The population structure (K from 1-10; 100 runs per K) was assessed with ADMIXTURE 1. 23,  32  and the accessions with the membership coefficients (> 60%) were assigned to a specific Cluster.
Genome-wide association studies Genome-wide association studies (GWAS) were performed with all 1. 9 M SNPs using the statistical model Fixed and random model circulating probability unification (FarmCPU), and Mixed Linear Model implemented in the GAPIT3 package  35  under R4. 0. 23  30   algorithm allows an improvement in the statistical power, an increase in the calculation efficiency, and a reduction of false associations in the GWAS approach. 36 The FarmCPU formula is : Where Y is the phenotype, Si is the testing marker, S is the pseudo-QTN, K is the kinship matrix, and e is residual. The kinship and first principal components are fitted as covariate variables in the FarmCPU to reduce the false positives. To eliminate the ambiguity of determining associated markers that are in LD with a testing marker, the model eliminates the confounding from kinship by using only the kinship derived from the associated markers.
The Manhattan plots were also generated in R4. 0. 23. 30 SNPs having a significant association with traits were determined by the adjusted p-value. The threshold of P< 10 -8 (0. 05/n, with n = number of SNPs) was set to report a significant association. The quantile-quantile plots were generated by plotting the negative logarithms (-log10) P-values relative to their expected p-values to fit model relevance GWAS with the null hypothesis of no association and to determine to what extent the models considered the structure of the population. The effect of alleles at significant SNPs was assessed by comparing phenotyping data for allelic groups.
Validation of the significantly associated SNPs for tuber FC in an external panel We obtained a phenotypic dataset on tuber FC of 30 D. alata accessions maintained and phenotyped in Vietnam. These accessions were planted at An Khánh District of Hoai Duc (Hanoï city) during the growing season 2016-2017. At harvest, FC of three mature tubers per accession was visually noted as explained above (1: white, 2: cream, or 3: purple). 22 The accessions were In silico comparative analysis of QTLs from previous studies on tuber FC and OB in D. alata Quantitative trait loci (QTL) results from three previously published studies concerning QTLs related to tuber FC and OB in D. alata were extracted. 1, 22, 34 Marker sequences for each reported QTL was retrieved, and local blast (Blastn) was used to identify corresponding physical positions in the reference genome V.
In the diecious species Pistachio, only 44 accessions were used to successfully detect sex loci. 46 In our initial analyses, simulation on different panel sizes to estimate the power for detecting true SNPtrait associations showed that when the variance explained by the locus was superior to 7%, all panels equally performed (data not shown). Hence, with a small panel, the only risk seems to not detect true SNP-trait associations for small effect loci. This is not problematic because small effect loci are not useful in marker-assisted breeding. Moreover, with a smaller panel, statistical power   Based on the high-quality resequencing data, we observed a rapid LD-decay in D. alata. This is expected in dioecious species due to a high degree of recombination. 47 Our results suggest that a high SNP density is required for association analyses.
10970010, ja, Downloaded from https://onlinelibrary. wiley. com/doi/10. 1002/jsfa. 12721 by CIRAD -DGDRS -DIST, Wiley Online Library on [30/05/2023]. See the Terms and Conditions (https://onlinelibrary. wiley. com/terms-and-conditions) on Wiley Online Library for rules of use; OA articles are governed by the applicable Creative Commons Licensegenotyped (by WGS) as explained above, and a VCF file was generated. Peak SNPs initially identified through GWAS were searched in the VCF file of the Vietnam panel, and alleles at these SNPs were assessed by comparing tuber FC data for allelic groups.
Acknowledgment The authors are grateful to  Marie-Claire Gravillon ,  Christophe Perrot  and  Elie Nudol  for their contribution to the phenotyping. The editorial comments by  Hernán Ceballos  improved greatly the quality of this manuscript. This work was supported by the  CGIAR Research Program on Roots, Tubers and Bananas (CRP-RTB)  and the grant opportunity  INV-008567  (formerly OPP1178942):  Breeding RTB Products for End User Preferences (RTBfoods) , to the  French Agricultural Research Centre for International Development (CIRAD), Montpellier, France , by the  Bill & Melinda Gates Foundation  (BMGF): https://rtbfoods. cirad. fr.
Death certificate assessment. Setting and inclusion/exclusion criteria for participants. Between March and October 2020, 104 inhabitants of the studied community (n = 12,597) died, according to information we obtained from the state office for information and technology in North Rhine-Westphalia (Germany). With permission from the government of North Rhine-Westphalia (Germany), the state attorneys provided us with the death certificates of 77 subjects. Out of the remaining 27 deaths, none was attributed to COVID-19 (Fig. 1a ). Data measurement and variables. All death certificates were assessed by three of the authors (E. R. , D. L. , and H. S. ) and a consensus was achieved by applying the following procedures: We extracted information about gender, date of birth, date of death, COD, comorbidities, and any SARS-CoV-2 infection on record with the corresponding date of the first positive test.
We classified causes of death in the following categories: respiratory failure; sepsis; cardiovascular disease (CVD); liver failure; kidney failure; cancer; other as well as comorbidities in the categories: respiratory; sepsis; CVD; liver malfunction; kidney malfunction; cancer; neurological; diabetes; unknown; other. We also compared the number of deaths attributed to COVID-19 in the data submitted by the authorities to the national death counts versus the number of deaths attributed to COVID-19 after our audit. In attributing deaths to COVID-19 in our audit of death certificates, we followed the guidance of the WHO guidelines. Accordingly, the outcome of a COVID-19-related death is defined as resulting from a clinically compatible illness in a probable or confirmed COVID-19 case, unless there is a clear alternative COD that cannot be related to COVID-19 disease (e.
All confidence intervals were computed using a 95% coverage probability. The statistical analysis was carried out using version 4. 1. 1 of the R Language for Statistical Computing (R Core Team 2021: R: A Language and Environment for Statistical Computing, R Foundation for Statistical Computing, Vienna, Austria). Ethical considerations. There are clear data protection laws in Germany under which circumstances researcher can obtain identifiable information. Under §8 of the regional German burial act, we are allowed to analyze death certificates when there is justifiable public interest. Therefore, this analysis was classified as important and the Ministry of Health in North Rhine-Westphalia (Germany) approved the request for access to the death certificates and the district attorney of every city where the patients died provided the certificate.
The criteria for initial enrollment was described in Streeck et al. 21. Briefly, enrollment was based on a sample of 600 persons contained in the civil register of the community. Sampling was done randomly with the side condition that all 600 persons had different surnames, as it was assumed that different surnames were likely to indicate different households. In total, a dataset from 919 participants was analyzed in the original study. For the seroprevalence follow-up Figure  1. Illustrations depicting the number of decedents for death certificate assessment and study participants for seroprevalence survey. (a) Between March and October 2020, a total of 104 inhabitants of the studied community died, according to information we obtained from the state office for information and technology in North Rhine-Westphalia (Germany).
RT-PCR for two viral targets (E and S genes) was performed on isolated RNA samples via the RealStar® SARS-CoV-2 RT-PCR kit 1. 0 (Altona Diagnostics). Internal control Ct values were within an acceptable range in all assays. Data management and quality control. Planning and conduct of the study were supported by the Clinical Study Core Unit of the Study Center Bonn (SZB). Support included protocol and informed consent development following specifications of the WHO with regards to pandemic events, data management, submission to the ethics committee, clinical trial monitoring and quality control. Study data were collected and managed using REDCap electronic data capture tool. REDCap is a secure, web-based software platform designed to support data capture for research studies, providing (1) an intuitive interface for validated data capture; (2) audit trails for tracking data manipulation and export procedures; (3) automated export procedures for seamless data downloads to common statistical packages; and (4) procedures for data integration and interoperability with external sources.
Questionnaire data were recorded on site using paper case report forms and were entered into the electronic study database using double data entry by trained study personnel. Bias. Especially during the early phase of the SARS-CoV-2 pandemic, poorly or incorrectly executed pharyngeal swabs had a negative impact on the quality and results of SARS-CoV-2 RNA detection via PCR. To prevent differences in quality, all pharyngeal swabs in this study were performed by trained medical personnel to ensure consistent quality. Furthermore, it is known that the IgG-ELISA used from EUROIMMUNE had a sensitivity of 90. 9% and a specificity of 99. 1% according to the manufacture. To eliminate this bias, IgG values were corrected for sensitivity and specificity. Statistical analysis. For sample size calculations, see the previous study  21.
The numbers of SARS-CoV-2-associated deaths in the studied community for given lengths of acquisi-tion periods can be considered fixed as the data acquisition corresponded to a complete survey of all recorded SARS-CoV-2-associated deaths in the community during the study period. In addition, we generated also separate IFR estimates for the ages groups 0-54, 55-74, and > 75 years. Additional statistical analysis is described in the Supplementary Information. All confidence intervals were computed using a 95% coverage probability. The statistical analysis was carried out using version 4. 1. 1 of the R Language for Statistical Computing (R Core Team 2021: R: A Language and Environment for Statistical Computing, R Foundation for Statistical Computing, Vienna, Austria). Ethical considerations and Declaration of Helsinki.
Acknowledgements We would like to thank all the subjects who participated in our repeated seroprevalence surveys. Furthermore, we would like to thank the following people who helped with the study:  Maximilian Baum ,  Celina Beta Schlüter ,  Jasmin Zorn ,  Hannah Proksch ,  Melanie Geiger ,  Annika Breuer ,  Julia König ,  Karola Mai ,  Antonia Büning ,  Paulina.
Electrophysiology The csMEA has been designed for use with the MEA2100-Mini-60-System (Multichannel Systems Gmbh, MCS). The MEA has been designed to fit this particular machine that comprises 60 channels. For extracellular electrophysiology experiments, MEAs with cerebral organoids impaled for 3 or 17 days were placed on the head stage and incubated at 37 °C and 5% CO 2 with an aluminum foil wrap for electrical insulation. The medium was replaced >2 h prior to recording. Spontaneous electrical activity was recorded at a sampling rate of 20 kHz, amplified with the MEA2100-Mini-60-Sytem amplifier, and raw electrical data were recorded using the MCS experimenter software. For analysis, raw data were filtered with a 200-1000 Hz bandpass Butterworth filter using the MCS Analyzer software. Spikes were detected when the recorded voltage crossed a bidirectional threshold of 5 SDs, calculated over a 5 ms moving window.
Acknowledgements A part of this work was supported by the  Isite MUSE of the University of Montpellier (BC) , the  ANR Agence Nationale de la Recherche  ( ANR-21-CE33-0007-03  to BC and RG),  Sidaction  (# 21-1-AEQ-12958  to RG), a  CBS2 doctoral  school fellowship (EP), and the " ANRS-MIE/FRM" program  (# MIE202207016212  to EP and RG). Authors thanks the  MRI microscopy facilities  and  CTM university cleanroom in Montpellier  for technical support.