cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.25218113.v1
title: Current and suspended sediment concentration in the Bohai Strait during both ice-covered and ice-free conditions.

description: Current and suspended sediment concentration in the Bohai Strait during both ice-covered and ice-free conditions.
DOI: 10.6084/m9.figshare.7560533.v2
title: Table S4 from An integrative phylogenomic approach illuminates the evolutionary history of cockroaches and termites (Blattodea).

description: Groups defined for generating the decisive amino-acid dataset.
DOI: 10.5281/zenodo.10454473
title: Supplement files to "The global genetic diversity of planktonic foraminifera reveals the structure of cryptic speciation in plankton"

description: Supplement to the manuscript The global genetic diversity of planktonic foraminifera reveals the structure of cryptic speciation in plankton (https://doi.org/10.1111/brv.13065). 

Table S1. Planktonic Foraminifera Ribosomal Reference (PFR²) database v.2., with collection details, taxonomic attribution, and Sanger sequences of planktonic foraminifera.

Table S2. Genotyping data of the species Orbulina universa, Globorotalia truncatulinoides, Globorortalia inflata, Globigerina bulloides, Pulleniatina obliquiloculata, Neogloboquadrina pachyderma and Globigerinella siphonifera with collection details.

Table S3. Updated version of the PR2_V9 reference database used in this study to re-assign the metabarcoding data set of Cordier et al. (2022). The description of the fields can be found at: https://zenodo.org/records/376895.

Table S4. Collection details of samples included in the study consisting of geographic coordinates, date, depth, size fraction associated with biogeographic region and climatology data.

Table S5. Molecular nomenclature resulting from the automated delimitation methods, with the correspondence of the newly defined molecular operational taxonomic units (MOTUs) with the labels existing in the literature and the genotyping data also provided.

Table S6. Occurrence table of planktonic foraminifera amplicon sequence variants (ASVs) in the metabarcoding data set of Cordier et al. (2022) with their sequences and taxonomic assignment to the molecular nomenclature.

Table S7. List of the occurrences of molecular operational taxonomic units (MOTUs) at each level of the nomenclature in the data set for individual samples.
DOI: 10.5281/zenodo.10454474
title: Supplement files to "The global genetic diversity of planktonic foraminifera reveals the structure of cryptic speciation in plankton"

description: Supplement to the manuscript The global genetic diversity of planktonic foraminifera reveals the structure of cryptic speciation in plankton (https://doi.org/10.1111/brv.13065). 

Table S1. Planktonic Foraminifera Ribosomal Reference (PFR²) database v.2., with collection details, taxonomic attribution, and Sanger sequences of planktonic foraminifera.

Table S2. Genotyping data of the species Orbulina universa, Globorotalia truncatulinoides, Globorortalia inflata, Globigerina bulloides, Pulleniatina obliquiloculata, Neogloboquadrina pachyderma and Globigerinella siphonifera with collection details.

Table S3. Updated version of the PR2_V9 reference database used in this study to re-assign the metabarcoding data set of Cordier et al. (2022). The description of the fields can be found at: https://zenodo.org/records/376895.

Table S4. Collection details of samples included in the study consisting of geographic coordinates, date, depth, size fraction associated with biogeographic region and climatology data.

Table S5. Molecular nomenclature resulting from the automated delimitation methods, with the correspondence of the newly defined molecular operational taxonomic units (MOTUs) with the labels existing in the literature and the genotyping data also provided.

Table S6. Occurrence table of planktonic foraminifera amplicon sequence variants (ASVs) in the metabarcoding data set of Cordier et al. (2022) with their sequences and taxonomic assignment to the molecular nomenclature.

Table S7. List of the occurrences of molecular operational taxonomic units (MOTUs) at each level of the nomenclature in the data set for individual samples.
DOI: 10.6084/m9.figshare.21192009
title: Additional file 3 of Longitudinal disease-associated gut microbiome differences in infants with food protein-induced allergic proctocolitis

description: Additional file 3: Supplemental Table 2. Summary table of all significant MaAsLin results. All MaAsLin results from 16S rRNA gene sequencing with q-values for significant taxa which met our predetermined threshold for significance (q&lt;0.20). Mixed effects linear models using arcsine transform on relative abundances were used to determine significance. p-values were adjusted for multiple comparisons using the Benjamini-Hochberg false discovery rate (FDR) method with FDR set at &lt;0.20. (XLS 224 kb)
DOI: 10.6084/m9.figshare.7560569
title: Table S8 from An integrative phylogenomic approach illuminates the evolutionary history of cockroaches and termites (Blattodea).

description: Selected fossil calibrations used in our study. (justifications are provided in Suppl. material S2).
DOI: 10.6084/m9.figshare.7565276
title: Chemical constituents isolated from stems of <i>Schisandra chinensis</i> and their antifeedant activity against <i>Tribolium castaneum</i>

description: One new sesquiterpene (α-iso-cubebenol acetate, <b>8</b>), together with 9 known compounds (1-7, 9, 10) were isolated from the stems of <i>Schisandra chinensis</i> (Turcz.) Baill. by repeated silica gel column chromatography. Based on the results of MS, NMR spectra and comparing with literature data, the six dibenzocyclooctadiene lignans were identified as schizandrin A to C (1-3), schizandrin (4), schisantherin A (5) and gomisin J (6), the two sesquiterpenes were identified as α-iso-cubebenol (7) and α-iso-cubebenol acetate (8), while the two triterpenic acids were identified as ganwuweizic acid (9) and kadsuric acid (10). The antifeedant activity of the 10 compounds against <i>Tribolium castaneum</i> adults was tested. Gomisin J (6) exhibited activity at 1500 ppm concentration with 40.3% antifeeding index percentages. As for the dibenzocyclooctene lignans (compounds <b>1–3</b>, <b>6</b>), the number of methylenedioxies and the position of hydroxyl groups were the main factors to affect their antifeedant activities.
DOI: 10.6084/m9.figshare.7560554.v1
title: Table S1 from An integrative phylogenomic approach illuminates the evolutionary history of cockroaches and termites (Blattodea)

description: Detailed species list including NCBI accession numbers.
DOI: 10.6084/m9.figshare.11759583
title: Additional file 2 of The evolutionary arms race between transposable elements and piRNAs in Drosophila melanogaster

description: Additional file 2: Table S4. Statistics of correlation analysis between piRNA abundance and TE copy number in the 10 GDL and 16 DGRP strains.
DOI: 10.6084/m9.figshare.7560533.v1
title: Table S4 from An integrative phylogenomic approach illuminates the evolutionary history of cockroaches and termites (Blattodea)

description: Groups defined for generating the decisive amino-acid dataset.
DOI: 10.6084/m9.figshare.11759583.v1
title: Additional file 2 of The evolutionary arms race between transposable elements and piRNAs in Drosophila melanogaster

description: Additional file 2: Table S4. Statistics of correlation analysis between piRNA abundance and TE copy number in the 10 GDL and 16 DGRP strains.
DOI: 10.6084/m9.figshare.7560563
title: Table S12 from An integrative phylogenomic approach illuminates the evolutionary history of cockroaches and termites (Blattodea).

description: Results of ancestral state reconstruction.
DOI: 10.6084/m9.figshare.7560536.v2
title: Table S10 from An integrative phylogenomic approach illuminates the evolutionary history of cockroaches and termites (Blattodea).

description: Presence of <i>Blattabacterium</i> in Blattodea transcriptomes.
DOI: 10.6084/m9.figshare.14897366.v1
title: Additional file 1 of Composition and diversity of gut microbiota in Pomacea canaliculata in sexes and between developmental stages

description: Additional file 1: Datafile S1. Noranked OTUs on genus level using the BLASTn on NCBI nucleotide collection.
DOI: 10.21430/m3sbptfzsn
title: Mild and severe COVID-19

description: We analyzed immune responses in 76 COVID-19 patients and 69 healthy individuals from Hong Kong and Atlanta, Georgia, United States.
DOI: 10.21430/m3t4b7mgv4
title: Cross-Reactive Antibodies to SARS-CoV-2 and MERS-CoV in Pre-COVID-19 Blood Samples from Sierra Leoneans

description: To characterize serological responses to coronaviruses in Sierra Leoneans, we tested blood samples collected before the reports in late 2019 of the first COVID-19 cases in Wuhan, China. We demonstrate that, prior to the COVID-19 pandemic, the percentage of Sierra Leonians with cross-reactive antibodies to SARS-CoV-2, MERS-CoV, and seasonal coronaviruses was higher than in United States blood donors.
DOI: 10.21430/m3t90lw0ca
title: SARS-CoV-2 transmission and impacts of unvaccinated-only screening in populations of mixed vaccination status

description: To evaluate the spread of SARS-CoV-2 in populations of mixed vaccination status, focusing on three critical questions. First, how do vaccinated and unvaccinated populations each contribute to community spread and hospitalizations, second, how do testing-based screening programs focused on unvaccinated individuals alone affect community spread and hospitalizations? third, how effective are delta-era screening strategies likely to be against variants with higher breakthrough and reinfection rates?
DOI: 10.21430/m3tgzsfqzz
title: Shared B cell memory to coronaviruses and other pathogens varies in human age groups and tissues

description: We evaluated pediatric and adult blood and deceased adult organ donor tissues to determine convergent antigen-specific antibody genes of similar sequences shared between individuals. B cell memory varied for different pathogens. Polysaccharide antigenspecific clones were not exclusive to the spleen. Adults had higher clone frequencies and greater class switching in lymphoid tissues than blood, while pediatric blood had abundant class-switched convergent clones. Consistent with reported serology, prepandemic children had class-switched convergent clones to severe acute respiratory syndrome coronavirus 2 with weak cross-reactivity to other coronaviruses, while adult blood or tissues showed few such clones. These results highlight the prominence of early childhood B cell clonal expansions and cross-reactivity for future responses to novel pathogens.
DOI: 10.21430/m3thy9wl9x
title: Cross-tissue, single-cell stromal atlas identifies shared pathological fibroblast phenotypes in four chronic inflammatory diseases

description: Pro-inflammatory fibroblasts are critical to pathogenesis in rheumatoid arthritis, inflammatory bowel disease, interstitial lung disease, and Sjogren's syndrome, and represent a novel therapeutic target for chronic inflammatory disease. However, the heterogeneity of fibroblast phenotypes, exacerbated by the lack of a common cross-tissue taxonomy, has limited the understanding of which pathways are shared by multiple diseases. To investigate, we profiled patient-derived fibroblasts from inflamed and non-inflamed synovium, intestine, lung, and salivary glands with single-cell RNA-sequencing. We integrated all fibroblasts into a multi-tissue atlas to characterize shared and tissue-specific phenotypes. Two shared clusters, CXCL10+CCL19+ immune-interacting and SPARC+COL3A1+ vascular-interacting fibroblasts were expanded in all inflamed tissues and additionally mapped to dermal analogues in a public atopic dermatitis atlas. We further confirmed these human pro-inflammatory fibroblasts in animal models of lung, joint, and intestinal inflammation. This work represents the first cross-tissue, single-cell fibroblast atlas revealing shared pathogenic activation states across four chronic inflammatory diseases.
DOI: 10.21430/m3ui1hk603
title: The Non-pregnant and Pregnant Human Cervix: a Systematic Proteomic Analysis

description: The study utilized a systematic proteomic approach to understand which soluble ECM and cellular proteins exist in the different regions of the human cervix and how the proteomic profiles change from the non-pregnant (NP) to the pregnant (PG) state. The human cervix proteome with at least 4548 proteins was identified and the differential proteome patterns between the NP and PG human cervix were established. The proteins involved with elastic fiber formation and ECM organization/degradation were significantly increased while proteins involved in RNA polymerase I/promoter opening, DNA methylation, senescence, immune system, and compliment activation were decreased in the pregant (PG) vs non-pregnant (NP) cervix.
DOI: 10.21430/m3v1zyuvbn
title: Early non-neutralizing, afucosylated antibody responses are associated with COVID-19 severity

description: To study the biology of afucosylated IgG immune complexes
DOI: 10.21430/m3vpy49egu
title: Mass cytometry analysis of PBMCs from peanut-sensitized tolerant and clinically allergic infants

description: In this study, we performed mass cytometry on unstimulated, peanut-stimulated and PMA/ionomycin stimulated PBMCs of 1-year old infants from the HealthNuts study to define the circulating immune cell signatures associated with peanut sensitized tolerance, clinical peanut allergy, and non-food allergic healthy controls.
DOI: 10.21430/m3w5sk65xi
title: Generation of human long-lived plasma cells by developmentally regulated epigenetic imprinting

description: Our study demonstrates that early-minted blood ASCs in the BM microniche must undergo morphological, transcriptional, and epigenetic changes to mature into apoptotic-resistant LLPCs.
DOI: 10.21430/m3wiutt8od
title: Corticosteroid treatment in COVID-19 modulates host inflammatory responses and transcriptional signatures of immune dysregulation

description: In this study, a cross-sectional and longitudinal analysis of Ab, soluble immune mediators, and transcriptional responses in young (< or = 65 years) and aged (>65 years) diabetic males with obesity hospitalized with acute severe COVID-19 was conducted. Additionally, the transcriptional profiles in samples obtained before and after corticosteroids became standard of care were compared. The analysis indicates that severe COVID-19 is characterized by robust Ab responses, heightened systemic inflammation, increased expression of genes related to inflammatory and pro-apoptotic processes, and reduced expression of those important for adaptive immunity regardless of age. In contrast, COVID-19 patients receiving steroids did not show high levels of systemic immune mediators and lacked transcriptional indicators of heightened inflammatory and apoptotic responses. Overall, these data suggest that inflammation and cell death are key drivers of severe COVID-19 pathogenesis in the absence of corticosteroid therapy.
DOI: 10.21430/m3wylovykd
title: Common Cervicovaginal Microbial Supernatants Alter Cervical Epithelial Function

description: The study investigated the biological, molecular, and epigenetic effects of Cervicovaginal (CV) microbiota (specifically : Lactobacillus crispatus (Lc), Lactobacillus iners (Li), and Gardnerella vaginalis (Gv)) on the cervical epithelial barrier function and determined whether Lc mitigates the effects of lipopolysaccharide (LPS) and Gv on the cervical epithelial barrier as a possible mechanism by which CV microbiota mitigates disease risk. Ectocervical and endocervical cells treated with Lc, Lv, and Gv bacteria-free supernatants alone or combined were used to measure cell permeability, adherens junction proteins, inflammatory mediators, and miRNAs. FINDINGS: L. crispatus mitigated the LPS or G. vaginalis-induced disruption of the cervical epithelial barrier and reversed the G. vaginalis-mediated increase in miRNA expression. G. vaginalis colonization of the CV space of a pregnant C57/B6 mouse resulted in 100% PTB.
DOI: 10.21430/m3xl8x77t6
title: Blood and tissue studies of Tick-borne diseases in adults. Blood and tissue studies of Tick-borne diseases in children. Year1

description: The study is designed to look at how the body responds to infection with Lyme disease spirochete and how this response relates to clinical symptoms and infection outcomes.
DOI: 10.21430/m3xlufomxu
title: Safety, tolerability and immunogenicity in age de-escalation of PfSPZ Vaccine in Equatorial Guinea (EGSPZV2)

description: This trial will evaluate the safety, tolerability, and immunogenicity of PfSPZ Vaccine in healthy Equatoguinean adults, adolescents, children and infants who receive doses of 0.9x10^6, 1.8x10^6 or 2.7x10^6 PfSPZ Vaccine via direct venous inoculation (DVI) compared with control groups receiving normal saline (NS) placebo by DVI. In addition, the study will also assess a second PfSPZ-based vaccination approach known as PfSPZ-CVac- the administration of non-irradiated, infectious PfSPZ (PfSPZ Challenge) (1x10^5 PfSPZ) under anti-malarial chemoprophylaxis (chloroquine) in younger adults ages 18 to 35 years for safety, tolerability, immunogenicity and efficacy against controlled human malaria infection (CHMI).
DOI: 10.21430/m3yd38ifgb
title: Optimization of non-coding regions for a non-modified mRNA COVID-19 vaccine

description: Here we report the results of a head-to-head comparison of the immunogenicity and protective efficacy of CVnCoV and CV2CoV in non-human primates. We immunized 18 cynomolgus macaques with two doses of 12 μg lipid nanoparticle-formulated CVnCoV or CV2CoV or with sham (n = 6 per group). Compared with CVnCoV, CV2CoV induced substantially higher titres of binding and neutralizing antibodies, memory B cell responses and T cell responses as well as more potent neutralizing antibody responses against SARS-CoV-2 variants, including the Delta variant. Moreover, CV2CoV was found to be comparably immunogenic to the BNT162b2 (Pfizer) vaccine in macaques. Although CVnCoV provided partial protection against SARS-CoV-2 challenge, CV2CoV afforded more robust protection with markedly lower viral loads in the upper and lower respiratory tracts. Binding and neutralizing antibody titres were correlated with protective efficacy. These data demonstrate that optimization of non-coding regions can greatly improve the immunogenicity and protective efficacy of a non-modified mRNA SARS-CoV-2 vaccine in non-human primates.
DOI: 10.21430/m3yklkq0ma
title: A shift in lung macrophage composition is associated with COVID-19 severity and recovery

description: Though it has been over 2 years since the start of the Coronavirus Disease 2019 (COVID-19) pandemic, COVID-19 continues to be a worldwide health crisis. Despite the development of preventive vaccines, therapies to treat COVID-19 and other inflammatory diseases remain a major unmet need in medicine. Our study sought to identify drivers of disease severity and mortality to develop tailored immunotherapy strategies to halt disease progression.
DOI: 10.21430/m3yq1sxvs6
title: Durable SARS-CoV-2 B cell immunity after mild or severe disease

description: Most SARS-CoV-2-infected individuals develop S-RBD specific, class-switched rMBCs that resemble germinal center derived B cells induced by effective vaccination against other pathogens, providing evidence for durable B cell mediated immunity against SARS-CoV-2 after mild or severe disease.
DOI: 10.21430/m3yr3w2eba
title: 35th Multicenter Airway Research Collaboration (MARC-35):  dual transcriptomic profile of nasopharyngeal aspirates

description: As part of MARC-35, we aimed to identify biologically-distinct nasopharyngeal microbiome and host immune profiles among infants (age <1 year) hospitalized for bronchiolitis.
DOI: 10.21430/m3z6v3i3qm
title: Heterogeneity of human anti-viral immunity shaped by virus, tissue, age, and sex

description: Focusing on CD8+ T cells, we elucidate the factors that shape the maintenance and function of anti-viral T cell immunity by comprehensive profiling of virus-specific T cells across blood, lymphoid organs, and mucosal tissues of organ donors.
DOI: 10.21430/m3zinj9x7n
title: Vascular Disease and Thrombosis in SARS-CoV-2-Infected Rhesus Macaques

description: In this study, we demonstrate endothelial disruption and vascular thrombosis in histopathologic sections of lungs from both humans and rhesus macaques infected with SARS-CoV-2. The results suggest a model in which critical interactions between inflammatory and thrombosis pathways lead to SARS-CoV-2-induced vascular disease. Our findings suggest potential therapeutic targets for COVID-19.
DOI: 10.21430/m3zk51u9th
title: Quantitative chest CT combined with plasma cytokines predicts outcomes in COVID-19 patients

description: To assess the performance of a chest CT qualitative score and a quantitative analyses alone and in combination with plasma cytokines for prediction of survival and maximum severity degree in COVID-19 patients.
DOI: 10.21430/m3zqi9uohm
title: Role of Transcriptomics of Acute DENV-Specific CD8+ T Cells in Disease Severity

description: CD3+CD8+ T-cells were isolated from the peripheral blood of patients hospitalized with either dengue fever (DF) or dengue hemorrhagic fever (DHF) and their transcriptomic profile was analyzed for differences correlating with disease severity.
DOI: 10.21430/m3zv06eam0
title: Repeated cross-sectional sero-monitoring of SARS-CoV-2 in New York City

description: Here, to understand seroprevalence dynamics, we conduct a retrospective, repeated cross-sectional analysis of anti-SARS-CoV-2 spike antibodies in weekly intervals from the beginning of February to July 2020 using more than 10,000 plasma samples from patients at Mount Sinai Hospital in New York City. We describe the dynamics of seroprevalence in an 'urgent care' group, which is enriched in cases of COVID-19 during the epidemic, and a 'routine care' group, which more closely represents the general population. Our data suggest that SARS-CoV-2 was introduced in New York City earlier than previously documented and describe the dynamics of seroconversion over the full course of the first wave of the pandemic in a major metropolitan area.
DOI: 10.21430/m3zxhxs7fv
title: Direct on-swab metabolic profiling of vaginal microbiome host interactions

description: The study applied direct on-swab metabolic profiling by DESI-MS as an innovative approach for preterm birth risk stratification through rapid assessment of vaginal microbiota-host dynamics. The sample preparation-free characterisation of the cervicovaginal metabolome in two independent pregnancy cohorts (VMET, n = 160; 455 swabs; VMET II, n = 205; 573 swabs) were examined. By integrating metataxonomics and immune profiling data from matched samples, the study revealed specific metabolome signatures can be used to robustly predict simultaneously both the composition of the vaginal microbiome and host inflammatory status.
DOI: 10.21430/mmm
title: Mild and severe COVID-19

description: We analyzed immune responses in 76 COVID-19 patients and 69 healthy individuals from Hong Kong and Atlanta, Georgia, United States.
DOI: 10.21430/m301ki6wve
title: Safety and immunogenicity of an inactivated recombinant Newcastle disease virus vaccine expressing SARS-CoV-2 spike: Interim results of a randomised, placebo-controlled, phase 1 trial

description: To assess safety and immunogenicity of an affordable egg-based recombinant Newcastle disease virus vaccine (NDV-HXP-S) expressing the spike (S) protein of SARS-CoV-2
DOI: 10.21430/m31zdulpah
title: Household Transmission of Severe Acute Respiratory Syndrome Coronavirus 2 in the United States: Living Density, Viral Load, and Disproportionate Impact on Communities of Color

description: To measure the secondary household attack rates of SARS-CoV-2 in vulnerable communities and to indentify risk factors for transmission.