dataesr/scientific-paragraphs-categorization huggingface dataset:
No reuse allowed without permission. The copyright holder for this this version posted February 7, 2020. ; https://doi. org/10. 1101/2020. 02. 06. 937128 doi: bioRxiv preprint into 35 population-level bins of relatively high contamination. This approach was undertaken to correctly assign phylum-level taxonomy to the resulting contigs. Subsequently, the bin refinement module integrated in MetaWRAP was used to fine-tune the resulting bins (MAGs) to the species/strain levels  54. The completeness and contamination of the generated MAGs were assessed with checkM  55. Taxonomic affiliation was assessed with PhyloPhlan  56. Similarity to the previously reconstructed MAGs was verified with the FastANI  57. MAGs abundance within the reconstructed metagenome was calculated as average of contigs metagenomic abundance (DNA-RPKMs, see above) assigned to a specific MAG.
De novo metatranscriptomics, host transcriptomics and data analysis For three selected samples (LM1-1, LM1-2 and LM1-8) the (meta)transcriptomic analysis was performed using an optimised approach described earlier  11. Ribo-Zero Gold rRNA Removal Kit "Epidemiology" (Illumina) was used to enrich the sample for prokaryotic and eukaryotic mRNA. Enriched mRNA was purified using Agencourt RNAClean XP Kit and analyzed with Bioanalyser RNA 6000 Pico Kit (Agilent). In continuation, SMARTer Stranded RNA-Seq Kit (Clontech) was used according to the manufacturer's instructions to prepare sequencing libraries. Final libraries were quantified with High Sensitivity DNA Kit (Agilent) and KAPA SYBR FAST Universal qPCR Kit. Libraries were pair-end sequenced at the Luxembourg Centre for Systems Biomedicine (University of Luxembourg) using Illumina NextSeq 500/550 High Output v2-300 Kit.
Raw sequencing reads are available in the SRA database under the project number PRJNA587406. Over 285 M raw reads were quality trimmed in CLC Genomics Workbench v. 9. 5. 2, using a phred quality score of 20, minimum length of 50 and allowing no ambiguous nucleotides, resulting in close to 214 M quality-trimmed reads. Contaminating rRNA reads were removed using SortMeRNA 2. 0 software  60. The resulting non-preprint (which was not certified by peer review) is the author/funder. All rights reserved. No reuse allowed without permission. The copyright holder for this this version posted February 7, 2020. ; https://doi. org/10. 1101/2020. 02. 06. 937128 doi: bioRxiv preprint rRNA reads were used to perform de novo (meta)transcriptome co-assembly using the CLC assembly algorithm in mapping mode with default parameters, except for minimum contig length of 200, length fraction of 0.
90 and similarity fraction 0. 95. As a result, nearly 2 M contigs were assembled. Obtained contigs were further submitted to IMG/MER for taxonomic and functional annotation  51. Following the taxonomic assignment, 759,451 transcripts of putative prokaryotic origin were selected for further analysis. Initial IMG/MER taxonomic annotation resulted in over-representation of transcripts of putative Firmicutes origin (Supplementary Fig. 4 ). As nearly no Firmicutes OTUs were detected using the 16S rRNA gene amplicon sequencing, transcripts were re-annotated based on the de-novo assembled metagenome and contig binnig, resulting in re-classification of virtually all Firmicutes-assigned contigs to Fibrobacteres and Spirochaetae. To complement the study and to characterise potential contribution of the termite host to Miscanthus digestion, transcripts of eukaryotic origin and taxonomically assigned to Insecta (based on the IMG/MER annotation) were further evaluated for the completeness of the de novo reconstructed transcriptome with the BUSCO pipeline  26  and using the Eukaryota database (odb9).
Identification of cazymes, heterologous protein production, purification and activity testing Genes (metagenomics) and gene transcripts (metatranscriptomics) encoding for carbohydrate active enzymes were detected using dbCAN (dbCAN-fam-HMMs. txt. v6; ref. 61  ) and CAZy database  62. Using the threshold of e-value of < 1e  -18  and coverage > 0. 35 recommended for prokaryotic CAZymes resulted in removal of a high number of putative CAZymes, therefore additional manual curation preprint (which was not certified by peer review) is the author/funder. All rights reserved. No reuse allowed without permission. The copyright holder for this this version posted February 7, 2020. ; https://doi. org/10. 1101/2020. 02. 06. 937128 doi: bioRxiv preprint 20 was performed to maximise the number of entries retained for further analysis.
Acknowledgements This research was funded through FNR 2014  CORE  project  OPTILYS  (Exploring the higher termite lignocellulolytic system to optimize the conversion of biomass into energy and useful platform molecules/ C14/SR/8286517 ), and co-funded through the grant  PDR T. 0065. 15from the  Belgian F. R. S. -FNRS. We are grateful to  Philippe Cerdan ,  Régis Vigouroux  and the staff of the  Laboratoire Environnement HYDRECO of Petit Saut (EDF-CNEH)  for logistic support during the field work.
How has the performance of the European regional register of the European IVF-monitoring Consortium (EIM)/ European Society of Human Reproduction and Embryology (ESHRE) evolved from 1997 to 2016, as compared to the register of the Centres for Disease Control and Prevention (CDC) of the USA and the Australia and New Zealand Assisted Reproduction Database (ANZARD)? SUMMARY ANSWER: It was found that coherent and analogous changes are recorded in the three regional registers over time, with a different intensity and pace, that new technologies are taken up with considerable delay and that incidental complications and adverse events are only recorded sporadically. WHAT IS KNOWN ALREADY: European data on ART have been collected since 1997 by EIM. Data collection on ART in Europe is particularly difficult due to its fragmented political and legal landscape.
In 1997, approximately 78. 1% of all known institutions offering ART services in 23 European countries submitted data and in 2016 this number rose to 91. 8% in 40 countries. STUDY DESIGN, SIZE, DURATION: We compared the changes in European ART data as published in the EIM reports (2001)(2002)(2003)(2004)(2005)(2006)(2007)(2008)(2009)(2010)(2011)(2012)(2013)(2014)(2015)(2016)(2017)(2018)(2019)(2020) with those of the USA, as published by CDC, and with those of Australia and New Zealand, as published by ANZARD. PARTICIPANTS/MATERIALS, SETTING, METHODS: We performed a retrospective analysis of the published EIM data sets spanning the 20 years observance period from 1997 to 2016, together with the published data sets of the USA as well as of Australia and New Zealand. By comparing the data sets in these three large registers, we analysed differences in the completeness of the recordings together with differences in the time intervals on the occurrence of important trends in each of them.
Europe currently consists of 51 independent countries with very diverse cultural, political, economic and legal systems, often lacking national data registers dealing with reproduction, rendering the Europe-wide registration of activities in ART difficult. Whereas the first report contained data from 18 countries  (Nygren and Andersen, 2001) , EIM currently manages the largest global register, dealing with ART reported by 40 European countries  (Wyns et al. , 2020). One way to analyse the quality of the European data register as managed by EIM is to compare it with large data sets provided by other sizeable registries that have been active during the same time period. Similarities and discrepancies between such registries are likely to be useful to further improve data recording and interpretation.
For that reason, the trends observed in Europe during the time interval from 1997 to 2016 were compared with those of other large registers, such as that of the USA (Centres for Disease Control and Prevention (CDC), with the first data set collected in 1996) and of Australia and New Zealand (National Perinatal Epidemiology and Statistics Unit, first data set available online 1996, since 2004 known as the Australia and New Zealand Assisted Reproduction Database (ANZARD)). The retrospective analysis of the data sets spanning the 20-year observance period from 1997 to 2016 could help to identify timely trends in the various techniques of ART.
Periodic unannounced inspections of all institutions, including the records, as part of the accreditation system are imposed by public law. The Australian and New Zealand database on ART (ANZARD) was initiated in 2004 by the national perinatal epidemiology and statistics unit (NPSU), now located at the University of New South Wales, Australia, in collaboration with the Fertility Society of Australia. Australia was the first country worldwide to establish a data registry in 1992 for the purpose of surveillance in ART. The data on ART starting in 1992 and going up to 2016 are all available online (www. npesu. unsw. edu. au). Details of the history and current settings of surveillance in ART in Australia and New Zealand, as carried out by ANZARD, have been published recently  (Chambers et al.
Adverse events 1997-2016 Adverse events are recorded as complications observed during or after ART, such as ovarian hyperstimulation syndrome (OHSS), infections and haemorrhage after oocyte collection, foetal reduction and maternal death (Table  V ). CDC does not deliver any information concerning these complications but mentions the rare occurrence of maternal deaths. In the Austrialia and New Zealand data sets both the incidence of OHSS (only those cases that had to be admitted to a hospital) and of foetal reduction (combined with termination of pregnancy) are provided, albeit intermittently. Over the entire observation period the mean incidence of OHSS in Europe was reported to be 0. 61% and in Australia and New Zealand 0. 71% (X 2 statistic is 171, P < 0. 00001). In recent years the incidence of OHSS has decreased both in Europe and in Australia and New Zealand (Table  V ).
6 ). Whereas the prematurity rates in triplet deliveries were similar in the three geographical areas, reported singleton and twin prematurity rates were highly distinct in the three geographical areas. Australia and New Zealand had the lowest rate of premature births for singleton gestations, but the highest rate for twins and triplets. Since 2006, the reported prematurity rates of singletons in the European data sets rose to incidence levels similar to those in the USA, whereas the reported prematurity rates in twin and triplet pregnancies remained the lowest of the three regions.
Registry data are a valuable adjunct to randomized studies and to meta-analyses, as they have the potential to demonstrate ongoing changes under real-life conditions based on data sets arising from large cohorts. However, the quality of the recorded data must be optimized, particularly in Europe with its very fragmented political and legal landscape  (Calhaz-Jorge et al. , 2020). After 20 years of data collection the steering committee of EIM decided, on behalf of ESHRE, to compare the existing and published EIM data sets with those of two other comparable regional registries, namely CDC and ANZARD, using the annual cross-sectional data sets, all published and freely available online. Whereas in the USA (FCSRCA) and in Australia and New Zealand (Reproductive Technology Accreditation Committee) data registration is compulsory, the regulations in the various European countries continue to be highly diverse (Calhaz-Jorge et al.
, 2020). The asterisks (*) mark the years in which the number of initiated cycles is underreported (Fig. 2 ). 6   The comparison of the three registries revealed a number of deficiencies that are closely linked to the methods used in national and supranational data registries. Although an increasing array of novel technology has been introduced and adopted by the three registries (Tables  I  and II ), large national or supranational registries are slow to initiate recording them. Most if not all emerging novel treatment modalities were initiated after key publications, such as the first birth after ICSI  (Palermo et al. , 1992). ICSI was recorded by all registries from their early beginnings, for example by CDC since 1996, by ANZARD since 1996 and by EIM since 1997. PGT was first introduced for genetic analysis of the X-chromosome in a human embryo  (Handyside et al.
, 1990)  and its use was first recorded by EIM in 2002, by ANZARD in 2004 and by CDC in 2006. The feasibility of eSET was first suggested as an appropriate treatment in 2001  (Tiitinen et al. , 2001)  and its use was registered by CDC in 2008, and by ANZARD in 2010. In the European data sets, the transfer of one embryo is being recorded, but not whether this embryo stems from eSET in particular. Freeze-all was first described 1999  (Ferraretti et al. , 1999)  and was first registered by CDC in 2008, by ANZARD in 2011 and by EIM in 2017. In general, new developments in ART have been picked up by EIM later than CDC and ANZARD. There is no indication that the adoption of novel technology into the recording of data is orchestrated among the three registers.
Number of infants born after ART Europe United States Australia & New Zealand 2. 9 2. 4 2. 2 1. 9 1. 7 1. 6 1. 5 1. 4 1. 1 1. 2 1. 3 1. 1 0. 9 1. 1 1. 7 1. 7 1. 5 1. 6 1. 4 1. 3 1. 9 1. 8 1. 7 1. 7 1. 6 1. 5 1. 5 1. 4 1. 4 1. 3 1. 2 1. 2 1. 0 1. 0 0. In times in which many adjuncts, with limited or no evidence of success, are constantly being introduced into ART  (Harper et al. , 2017) , the complexity of present-day ART is barely reflected by current simplified data recordings. It is crucial that the structure of the published cross-sectional data sets remains comparable from one year to another. Furthermore, the ever more complex mixture of new evolving techniques and treatment options does pose a challenge to any data registry. Gamete and embryo donation, fresh or FET, transfer at different stages of embryonic development, genetic testing options at different levels of gamete and embryonic development, and the extraction of gametes at different stages of development out of the ovaries or from testicular tissue all contribute to the current variability of treatment options.
, 2019). Both EIM and ANZARD reported a mean incidence of OHSS between 0. 61% and 0. 71% per treatment cycle (Table  V ), which suggests under-reporting. In addition to over-and under-reporting of adverse events, the lack of standardization in defining complications in ART is a major obstacle. The international glossary on definitions may help to standardize the reporting of adverse events  (Zegers-Hochschild et al. , 2017). Another example of potential under-reporting is given by the significantly lower reported incidence of premature deliveries in twin and triplet gestations in the European register. In recent years, however, the number of recorded premature twin and triplet deliveries in Europe is now approaching the long-standing incidences reported by CDC and ANZARD (Fig. 6 ). In the beginning of ART data recordings in Australia and New Zealand, some degree of under-reporting of premature twin and triplet pregnancies may have prevailed as well.
Over-reporting may also occur. A comparison of recording ART in the case of normal pregnancies in birth certificates with national ART surveillance data in FL and MA, USA, has demonstrated a clear discordance between both data registries: ART was more often reported for women at risk of adverse pregnancy outcome, but much less so in normal pregnancies  (Cohen et al. , 2014). The higher incidence of premature deliveries in singleton pregnancies in the USA than in Australia and New Zealand may perhaps be explained by some under-reporting of normal delivery outcomes in the US data sets. Even worse than over-or under-reporting, a number of known complications of ART are, even today, still not being registered systematically, such as accidental loss of gametes and embryos (not registered at all), infections and bleedings (recorded only by EIM) and maternal death (recorded annually only by EIM).
Complications during ongoing pregnancies achieved with ART, such as hypertensive disorders after infertility treatment  (Monseur et al. , 2019) , are not being recorded systematically by any register. The health status of the infants is recorded only at the moment of birth, although minor and major malformations or health impairments are more often determined during further infant development. Long-term outcomes of children conceived with ART might be better evaluated through linking of ART data sets with the data sets of other health services, as done in the USA and in the European Nordic countries  (Luke et al. , 2019). Despite these data recording deficiencies, which become apparent when comparing the results of the three registries over a prolonged time interval, much has been achieved in the last 20 years.
not rec. not rec. not rec. not rec. 2014 1996 1996 2005 lated from the raw data sets, made available by the ESHRE office. The a 'not rec. ' means 'not recorded'. total numbers of newborn children and of inhabitants of each partici- b Before 2007, the transfer of a single embryo was recorded only in fresh cycles. It pating European country each year were taken from Wikipedia. was not differentiated between elective and non-elective single embryo transfer. c In the Centres for Disease Control and Prevention (CDC) data sets, the distinction is made between frozen and fresh embryo donation. d The Australia and New Zealand Assisted Reproduction Database (ANZARD) data sets denominate surrogacy by the term 'surrogacy arrangement cycles', whereas the CDC denominates surrogacy by the term 'gestational carrier'.
ANZARD, Australia and New Zealand Assisted Reproduction Database; CDC, the Centres for Disease Control and Prevention; ED, egg donation; EIM, the European IVF-monitoring Consortium; FET, frozen embryo transfer; FOR, frozen oocyte replacement; PGT, preimplantation genetic testing. Comparison of three ART registers, 1997-2016 EIM Registered institutions recorded ART in Europe, as given by EIM CDC Participating institutions % Registered institutions Participating institutions no. IVF versus no. ICSI (ratio) Europe 482 335 335 521 360 360 537 370 370 729 569 78. 1 383 383 740 579 78. 2 385 385 770 631 81. 9 428 391 1008 725 71. 9 437 399 1121 785 70. 0 461 411 1134 923 81. 4 475 422 1160 998 86. 0 483 426 1204 1029 88. 7 485 430 1245 1051 84. 4 475 436 1179 1005 85. 2 481 451 1202 991 82. 4 474 443 1314 1064 81.
Data processing We aligned FASTQ files to the Grch38. p12 genome assembly using STAR v2. 6. 1a. 17 We then used GATK Best Practices  18  for variant calling and FeatureCounts (within the Subread v. 1. 6. 2 package  19  ) to assign fragments to each gene feature included in the Grch38v94 gene transfer format file. For differential isoform usage, we used the STAR v. 2. 6. 1 package in quantMode TranscriptomeSAM mode and used Salmon to obtain isoform expression values. 20 For differential gene expression and differential isoform usage analyses, we used DESeq2 v1. 24,  21  which applies the Benjamini-Hochberg for p value adjustment. We used a false discovery rate threshold of 5%. To perform gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analyses, we used Metascape 3.
To this aim, we downloaded the medial temporal gyrus snRNAseq data derived from the Allen Brain Atlas, which includes 15,928 cells from 8 human tissue donors. We selected this data set as it contains double the number of nuclei than the primary visual cortex and the anterior cingulate cortex, also contained in the database. 10 The third data set comprised 10,319 cells derived from the frontal cortex of 4 individuals. 11 Cell type deconvolution of cellular subpopulations was performed using the ROSMAP data as reference.
Weighted gene coexpression network analyses We accounted for genes with more than 10 counts across all individuals. DESeq2 was then used to normalize the input data to construct coexpression networks using the weighted gene coexpression network analyses (WGCNA) package. 24 e then constructed the signed weighted correlation network, which takes into account both negative and positive correlations, using the manual function in WGCNA, applying the biweight midcorrelation, selecting a power of 7 (the lowest possible power term where topology fits a scale free network), and run in a single block analysis. We defined all modules by the hybrid treecutting option with deepsplit parameter = 2, applying a minimal module size of 30 genes and merging modules with a cutHeight ≤0. 25. Module eigengenes (first principal component as a summary of each module) summarized the modules and correlations performed using spearman correlation for continuous traits and Pearson correlation for binary traits (bicor and corPvalueStudent, included in the WGCNA package).
Quantification analysis We obtained full-section immunohistochemistry (IHC) images with Pannoramic MIDI II (3DHistech). Blinded to the neuropathologic diagnoses, we delimited 6 gray matter areas of the motor cortex from each case, and for each gray matter area, we randomly generated 6 regions of interest (ROIs) with the same size using the multicrop. m script. We used the Iba1. m script to quantify densities for Iba1 staining in each ROI, which represents a total of 36 images per individual. This algorithm binarizes the random images and compute densities of protein expression to quantify the number of immunoreactive objects. Both in-house algorithms can be freely accessed at github. com/Memo-ryUnitSantPau. We used MATLAB R2017b software to develop the algorithm (The MathWorks Inc. , Natick, MA).
Statistical analysis We used the Shapiro-Wilk test to test for deviation from a standard distribution. For correlation analyses, we determined the Pearson or Spearman correlation coefficients using the ggscatter function within the ggpubr package in R. We performed mean comparison analyses through the Student t test or Student test with Welch correction (using t. test function in R), depending on data distribution. Statistical significance for all tests was set at 5% (α = 0. 05), and all statistical tests were 2 sided. We used R version 3. 6. 2 to perform all statistical analyses.
lww. com/NXI/A280). Enrichment analyses revealed the involvement of postsynaptic density and immune response as dominant pathways (figure e-1, links. lww. com/NXI/A279). To further characterize and confirm the synaptic involvement, we used the SynGO database, which provides an expertcurated resource for synaptic function and gene enrichment analysis. 23 This analysis confirmed the enrichment of postsynaptic components in our list of differentially expressed isoforms (table e-5, links. lww. com/NXI/A280). Among the list of altered genes identified by the differential isoform expression and gene expression models, 32 of them overlapped between both approaches (table e-6, links. lww. com/NXI/ A280). The involvement of synaptic-related changes was confirmed from the differential isoform usage analysis (figure e-2, links.
Cell type deconvolution To characterize the variability of cell types and compare cellular proportions between groups, we applied the recently developed MuSiC algorithm. As reference, we used data from the first and most comprehensive human snRNAseq study performed in brain tissue of individuals with a neurodegenerative disease, which includes 24 patients with Alzheimer disease and 24 HCs. 12 Cell type deconvolution revealed an overrepresentation of microglial cells in the ALS motor cortex compared with HC (p = 0. 025, fold change = 1. 65) and a reduction in excitatory neurons (p = 0. 101, fold change = -0. 85) (figure  2 ). We confirmed microglial upregulation using 2 additional independent reference data sets. 10, 11 In both cases, we found the same pattern of downregulation of excitatory neurons (figures e-4 and e-5, links.