cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5281/zenodo.10794360
title: Natural history specimens collected and/or identified and deposited.

description: Natural history specimen data collected and/or identified by Richard Haensch, http://www.wikidata.org/entity/Q636119. Claims or attributions were made on Bionomia, https://bionomia.net using specimen data from the Global Biodiversity Information Facility, https://gbif.org.
description: http://www.wikidata.org/entity/Q636119
DOI: 10.5281/zenodo.10806676
title: Natural history specimens collected and/or identified and deposited.

description: Natural history specimen data collected and/or identified by Richard Haensch, http://www.wikidata.org/entity/Q636119. Claims or attributions were made on Bionomia, https://bionomia.net using specimen data from the Global Biodiversity Information Facility, https://gbif.org.
description: http://www.wikidata.org/entity/Q636119
DOI: 10.6084/m9.figshare.25387522
title: Data obtained for publication Mat Res Bull 167 (2023) 112438

description: Data obtained for publication Mat Res Bull 167 (2023) 112438
DOI: 10.6084/m9.figshare.25387522.v1
title: Data obtained for publication Mat Res Bull 167 (2023) 112438

description: Data obtained for publication Mat Res Bull 167 (2023) 112438
DOI: 10.5281/zenodo.10805292
title: Natural history specimens collected and/or identified and deposited.

description: Natural history specimen data collected and/or identified by Egmont Rett, http://www.wikidata.org/entity/Q124811396. Claims or attributions were made on Bionomia, https://bionomia.net using specimen data from the Global Biodiversity Information Facility, https://gbif.org.
description: http://www.wikidata.org/entity/Q124811396
DOI: 10.5281/zenodo.10805293
title: Natural history specimens collected and/or identified and deposited.

description: Natural history specimen data collected and/or identified by Egmont Rett, http://www.wikidata.org/entity/Q124811396. Claims or attributions were made on Bionomia, https://bionomia.net using specimen data from the Global Biodiversity Information Facility, https://gbif.org.
description: http://www.wikidata.org/entity/Q124811396
DOI: 10.5281/zenodo.10806677
title: Natural history specimens collected and/or identified and deposited.

description: Natural history specimen data collected and/or identified by Egmont Rett, http://www.wikidata.org/entity/Q124811396. Claims or attributions were made on Bionomia, https://bionomia.net using specimen data from the Global Biodiversity Information Facility, https://gbif.org.
description: http://www.wikidata.org/entity/Q124811396
DOI: 10.5281/zenodo.10805299
title: Natural history specimens collected and/or identified and deposited.

description: Natural history specimen data collected and/or identified by François Alexandre Pelvet, http://www.wikidata.org/entity/Q124811289. Claims or attributions were made on Bionomia, https://bionomia.net using specimen data from the Global Biodiversity Information Facility, https://gbif.org.
description: http://www.wikidata.org/entity/Q124811289
DOI: 10.5281/zenodo.10805300
title: Natural history specimens collected and/or identified and deposited.

description: Natural history specimen data collected and/or identified by François Alexandre Pelvet, http://www.wikidata.org/entity/Q124811289. Claims or attributions were made on Bionomia, https://bionomia.net using specimen data from the Global Biodiversity Information Facility, https://gbif.org.
description: http://www.wikidata.org/entity/Q124811289
DOI: 10.5281/zenodo.10806678
title: Natural history specimens collected and/or identified and deposited.

description: Natural history specimen data collected and/or identified by François Alexandre Pelvet, http://www.wikidata.org/entity/Q124811289. Claims or attributions were made on Bionomia, https://bionomia.net using specimen data from the Global Biodiversity Information Facility, https://gbif.org.
description: http://www.wikidata.org/entity/Q124811289
DOI: 10.5281/zenodo.8384850
title: 263 MAG annotations for three nested metagenomic studies describe crop-shrub-microbe interactions in an agroecology system in the Sahel

description: The Sahel region of West Africa is a vulnerable eco-region, where climate change induced drought and a rapidly growing population pose serious threats to food security and contribute to soil degradation. Local and biologically based systems are necessary to maintain crop yields and soil health, and intercropping with native woody shrubs Guiera senegalensis has been discovered as a solution. We have previously shown that soil microbial communities are significantly altered by the presence of shrubs, and that these organisms may have plant growth promoting properties. Here, we augment those data with metagenomic and metatranscriptomic data across three nested experiments: a landscape scale experiment across a rainfall and soil type gradient, a long-term experimental site, and a growth chamber simulated drought experiment.  We  recovered 263 95% ANI dereplicated metagenome-assembled genomes (MAGs)  of medium and high quality to evaluate their relative enrichment and what their encoded metabolisms reveal about mechanisms of microbiome millet support. These data contribute to our understanding of the role of the microbial community crop drought resilience in the Sahel and in semi-arid cropping systems globally. Here we present the DRAM annotations of each MAG, all associated metadata, viral genes and vOTUs from the Optimized Shrub Intercropping Study (OSS), and eukaryotic contigs from the OSS
DOI: 10.5281/zenodo.8384851
title: 263 MAG annotations for three nested metagenomic studies describe crop-shrub-microbe interactions in an agroecology system in the Sahel

description: The Sahel region of West Africa is a vulnerable eco-region, where climate change induced drought and a rapidly growing population pose serious threats to food security and contribute to soil degradation. Local and biologically based systems are necessary to maintain crop yields and soil health, and intercropping with native woody shrubs Guiera senegalensis has been discovered as a solution. We have previously shown that soil microbial communities are significantly altered by the presence of shrubs, and that these organisms may have plant growth promoting properties. Here, we augment those data with metagenomic and metatranscriptomic data across three nested experiments: a landscape scale experiment across a rainfall and soil type gradient, a long-term experimental site, and a growth chamber simulated drought experiment.  We  recovered 263 95% ANI dereplicated metagenome-assembled genomes (MAGs)  of medium and high quality to evaluate their relative enrichment and what their encoded metabolisms reveal about mechanisms of microbiome millet support. These data contribute to our understanding of the role of the microbial community crop drought resilience in the Sahel and in semi-arid cropping systems globally. Here we present the DRAM annotations of each MAG, all associated metadata, viral genes and vOTUs from the Optimized Shrub Intercropping Study (OSS), and eukaryotic contigs from the OSS
DOI: 10.15131/shef.data.21198070
title: Visual Odometry for Robot Localisation in Feature-Sparse Sewer Pipes Using Joint and Manhole Detections -- Data

description: Video data captured by robotic inspection platforms within sewer pipes along with ground truth odometry data and manhole locations.
DOI: 10.18112/openneuro.ds005028.v1.0.0
title: Comparing P300 Flashing paradigms in online typing with language models
DOI: 10.15131/shef.data.21197800
title: A comparison of combined sound-meaning vocabulary instruction versus semantic instruction on vocabulary, phonemic awareness and decoding in 5-6 year olds

description: The dataset relates to an experimental PhD study of 273 pupils aged 5-6 in the UK.  Background information was gathered on each child, followed by testing of vocabulary, phonological processing and literacy skills at three timepoints.  T1 assessment took place prior to a vocabulary teaching intervention, T2 assessment was directly afterwards and T3 was four months later.  Ethical approval was granted by the University of Sheffield Reference Number 019719.
DOI: 10.15131/shef.data.21197800.v1
title: A comparison of combined sound-meaning vocabulary instruction versus semantic instruction on vocabulary, phonemic awareness and decoding in 5-6 year olds

description: The dataset relates to an experimental PhD study of 273 pupils aged 5-6 in the UK.  Background information was gathered on each child, followed by testing of vocabulary, phonological processing and literacy skills at three timepoints.  T1 assessment took place prior to a vocabulary teaching intervention, T2 assessment was directly afterwards and T3 was four months later.  Ethical approval was granted by the University of Sheffield Reference Number 019719.
DOI: 10.17608/k6.auckland.25387837
title: Data for Symplegma manuscript

description: The global increase in frequency and severity of marine heatwaves (MHWs) is highlighting the impact these extreme climatic events can have on marine ecosystems. Throughout the summer of 2021/2022 northeastern Aotearoa/New Zealand suffered an unprecedented MHW. Worst impacted areas, such as the semi-enclosed Te Moananui-ā-Toi/Hauraki Gulf, experienced more than three continual months of temperatures at or above the climatological mean maximum (20.7°C). During this period, we observed a rapid increase in the abundance and cover of the invasive, warm-affinity colonial ascidian <i>Symplegma brakenhielmi</i> on temperate rocky reef<i>. </i>Population expansion of this species has not previously been linked to MHW events. Benthic monitoring as water temperatures cooled showed a sharp decrease in <i>S. brakenhielmi</i> abundance, but not complete disappearance, and the coverage of individually monitored colonies also declined. There was no observed increase in abundance or cover throughout the summer of 2022/2023, a potential consequence of cooler water temperatures and multiple cyclones. Observed impacts included the growth of <i>S. brakenhielmi</i> over other sessile invertebrate and macroalgal species, as well as on highly mobile spiny lobster, suggesting that this species can have a variety of impacts on temperate rocky reefs. These findings highlight how MHW can facilitate the rapid expansion and integration of non-native, warm-affinity species into temperate reef ecosystems and provide insight into what we can expect in the future as ocean temperatures continue to warm.
DOI: 10.17608/k6.auckland.25387837.v1
title: Data for Symplegma manuscript

description: The global increase in frequency and severity of marine heatwaves (MHWs) is highlighting the impact these extreme climatic events can have on marine ecosystems. Throughout the summer of 2021/2022 northeastern Aotearoa/New Zealand suffered an unprecedented MHW. Worst impacted areas, such as the semi-enclosed Te Moananui-ā-Toi/Hauraki Gulf, experienced more than three continual months of temperatures at or above the climatological mean maximum (20.7°C). During this period, we observed a rapid increase in the abundance and cover of the invasive, warm-affinity colonial ascidian <i>Symplegma brakenhielmi</i> on temperate rocky reef<i>. </i>Population expansion of this species has not previously been linked to MHW events. Benthic monitoring as water temperatures cooled showed a sharp decrease in <i>S. brakenhielmi</i> abundance, but not complete disappearance, and the coverage of individually monitored colonies also declined. There was no observed increase in abundance or cover throughout the summer of 2022/2023, a potential consequence of cooler water temperatures and multiple cyclones. Observed impacts included the growth of <i>S. brakenhielmi</i> over other sessile invertebrate and macroalgal species, as well as on highly mobile spiny lobster, suggesting that this species can have a variety of impacts on temperate rocky reefs. These findings highlight how MHW can facilitate the rapid expansion and integration of non-native, warm-affinity species into temperate reef ecosystems and provide insight into what we can expect in the future as ocean temperatures continue to warm.
DOI: 10.15131/shef.data.21310758
title: The Staphylococcus aureus cell division protein, DivIC, interacts with the cell wall and controls its biosynthesis. Supplementary information. Supplementary Fig. 4b, AFM data

description:   
The Staphylococcus aureus cell division protein, DivIC, interacts with the cell wall and controls its biosynthesis. Supplementary information. Supplementary Fig. 4b, AFM data to generate images shown on Supp. fig. 4b
DOI: 10.15131/shef.data.21310758.v1
title: The Staphylococcus aureus cell division protein, DivIC, interacts with the cell wall and controls its biosynthesis. Supplementary information. Supplementary Fig. 4b, AFM data

description:   
The Staphylococcus aureus cell division protein, DivIC, interacts with the cell wall and controls its biosynthesis. Supplementary information. Supplementary Fig. 4b, AFM data to generate images shown on Supp. fig. 4b
DOI: 10.15131/shef.data.21310773
title: The Staphylococcus aureus cell division protein, DivIC, interacts with the cell wall and controls its biosynthesis. Supplementary information. Supplementary Fig. 4d, AFM data

description: The Staphylococcus aureus cell division protein, DivIC, interacts with the cell wall and controls its biosynthesis. Supplementary information. Supplementary Fig. 4d, AFM data to generate images shown on Supp. fig. 4d
DOI: 10.15131/shef.data.21310803
title: The Staphylococcus aureus cell division protein, DivIC, interacts with the cell wall and controls its biosynthesis. Supplementary information. Fluorescence microscopy raw images Fig. 1d; 2a,c; 4a, c, e; 5d, f; 6c. ATM raw images Fig. 3a

description: The Staphylococcus aureus cell division protein, DivIC, interacts with the cell wall and controls its biosynthesis. Supplementary information. Fluorescence microscopy raw images Fig. 1d; 2a,c; 4a. c. e 5d, f; 6c. TEM raw images Fig. 3a
DOI: 10.5281/zenodo.10806701
title: Whole Cancer Cell Vaccine Protects Ovarian Functions in Tumor-bearing Mice through Downregulating CXCL10

description: Young female patients with cancer are likely to become sub-fertile or infertile even if they ultimately overcome cancer through various therapies. Cancer immunotherapy has recently emerged as a promising novel therapy against cancers with high malignancy and lethality, but it is unclear whether cancer immunotherapy affects female fertility. This study employed MCA205 cell-allotransplanted B6 mice as a model to investigate whether two popular immunotherapies—PD-1 monoclonal antibody (PD-1) therapy and whole cancer cell vaccine (WCV) therapy—affect ovarian function. MCA205 allotransplanted (M) mice exhibited decreased follicle numbers at each stage, decreased proliferation, increased apoptosis, and a decreased oocyte maturation rate. WCV treatment significantly reversed these abnormalities, whereas PD-1 did not. RNA sequencing of the ovaries revealed that multiple differentially expressed genes (DEGs) were involved in inflammation pathways. Furthermore, cytokine microarray characterized CXCL10 with both biggest increment in M group and best rescue in WCV group. Next, CXCL10 antibody Immunoprecipitation in ovarian lysate and LC-MS baited the only receptor IL18R1. Furthermore, we found that CXCL10 impaired ovarian function through three pathways: inducing ovarian fibrosis through CXCL10→IL18R1→p-JNK→COL1A1, promoting primordial follicle overactivation through CXCL10→IL18R1→p-AKT, and increasing ovarian inflammation through CXCL10→IL18R1→p-P65. Finally, we rescued the decreased ovarian function in the M group by blocking the CXCL10→IL18R1 pathway with CXCL10 antibody or a CXCL10–IL18R1 interface peptide, CIBB. This study provides mechanical evidence and translational strategies for WCVs to achieve the dual functions of suppressing tumor progression while protecting ovarian function.

Supplementary dataset 1

Related to Fig. 3A and 3B. This file includes two sheets. “All_samples-fpkm” includes FPKM values of all identified genes in ovaries from CTR, M, VM, and PM group (three repeats per group); “heat map” includes all average log2 values (from three repeats per group) of 435 DEGs (differentially expressed genes) at the threshold of |log2(M/CTR)| ≥ 1.

Supplementary dataset 2

Related to Fig. 3C. This file includes 33 sheets. “summary” includes all conc. values (pg/ml) of 31 plasma DECs (differentially expressed cytokines); “Curves” includes standard curves for all 31 cytokines; each of the other 31 sheets include the detailed assays for each plasma cytokine for CTR, M, VM, and PM group (five repeats per group).

Supplementary dataset 3

Related to Fig. 4A. This file includes two sheets. “peptides” includes all related values of all identified peptides; “Protein Groups” includes the related info. Of all proteins corresponding to the identified peptides
DOI: 10.5281/zenodo.10806702
title: Whole Cancer Cell Vaccine Protects Ovarian Functions in Tumor-bearing Mice through Downregulating CXCL10

description: Young female patients with cancer are likely to become sub-fertile or infertile even if they ultimately overcome cancer through various therapies. Cancer immunotherapy has recently emerged as a promising novel therapy against cancers with high malignancy and lethality, but it is unclear whether cancer immunotherapy affects female fertility. This study employed MCA205 cell-allotransplanted B6 mice as a model to investigate whether two popular immunotherapies—PD-1 monoclonal antibody (PD-1) therapy and whole cancer cell vaccine (WCV) therapy—affect ovarian function. MCA205 allotransplanted (M) mice exhibited decreased follicle numbers at each stage, decreased proliferation, increased apoptosis, and a decreased oocyte maturation rate. WCV treatment significantly reversed these abnormalities, whereas PD-1 did not. RNA sequencing of the ovaries revealed that multiple differentially expressed genes (DEGs) were involved in inflammation pathways. Furthermore, cytokine microarray characterized CXCL10 with both biggest increment in M group and best rescue in WCV group. Next, CXCL10 antibody Immunoprecipitation in ovarian lysate and LC-MS baited the only receptor IL18R1. Furthermore, we found that CXCL10 impaired ovarian function through three pathways: inducing ovarian fibrosis through CXCL10→IL18R1→p-JNK→COL1A1, promoting primordial follicle overactivation through CXCL10→IL18R1→p-AKT, and increasing ovarian inflammation through CXCL10→IL18R1→p-P65. Finally, we rescued the decreased ovarian function in the M group by blocking the CXCL10→IL18R1 pathway with CXCL10 antibody or a CXCL10–IL18R1 interface peptide, CIBB. This study provides mechanical evidence and translational strategies for WCVs to achieve the dual functions of suppressing tumor progression while protecting ovarian function.

Supplementary dataset 1

Related to Fig. 3A and 3B. This file includes two sheets. “All_samples-fpkm” includes FPKM values of all identified genes in ovaries from CTR, M, VM, and PM group (three repeats per group); “heat map” includes all average log2 values (from three repeats per group) of 435 DEGs (differentially expressed genes) at the threshold of |log2(M/CTR)| ≥ 1.

Supplementary dataset 2

Related to Fig. 3C. This file includes 33 sheets. “summary” includes all conc. values (pg/ml) of 31 plasma DECs (differentially expressed cytokines); “Curves” includes standard curves for all 31 cytokines; each of the other 31 sheets include the detailed assays for each plasma cytokine for CTR, M, VM, and PM group (five repeats per group).

Supplementary dataset 3

Related to Fig. 4A. This file includes two sheets. “peptides” includes all related values of all identified peptides; “Protein Groups” includes the related info. Of all proteins corresponding to the identified peptides
DOI: 10.15131/shef.data.21311115
title: The Staphylococcus aureus cell division protein, DivIC, interacts with the cell wall and controls its biosynthesis. Supplementary information. Fluorescent microscopy raw images Supp. fig 5a, c, e; Supp. fig 10a. TEM raw files Supp. fig. 3.

description: The Staphylococcus aureus cell division protein, DivIC, interacts with the cell wall and controls its biosynthesis. Supplementary information. Fluorescent microscopy raw images Supp. fig 5a, c, e; Supp. fig 10a. TEM raw files Supp. fig. 3.
DOI: 10.15131/shef.data.21311115.v1
title: The Staphylococcus aureus cell division protein, DivIC, interacts with the cell wall and controls its biosynthesis. Supplementary information. Fluorescent microscopy raw images Supp. fig 5a, c, e; Supp. fig 10a. TEM raw files Supp. fig. 3.

description: The Staphylococcus aureus cell division protein, DivIC, interacts with the cell wall and controls its biosynthesis. Supplementary information. Fluorescent microscopy raw images Supp. fig 5a, c, e; Supp. fig 10a. TEM raw files Supp. fig. 3.
DOI: 10.15131/shef.data.21310764
title: The Staphylococcus aureus cell division protein, DivIC, interacts with the cell wall and controls its biosynthesis. Supplementary information. Supplementary Fig. 4c, AFM data

description: The Staphylococcus aureus cell division protein, DivIC, interacts with the cell wall and controls its biosynthesis. Supplementary information. Supplementary Fig. 4c, AFM data to generate images shown on Supp. fig. 4c
DOI: 10.15131/shef.data.21310764.v1
title: The Staphylococcus aureus cell division protein, DivIC, interacts with the cell wall and controls its biosynthesis. Supplementary information. Supplementary Fig. 4c, AFM data

description: The Staphylococcus aureus cell division protein, DivIC, interacts with the cell wall and controls its biosynthesis. Supplementary information. Supplementary Fig. 4c, AFM data to generate images shown on Supp. fig. 4c
DOI: 10.25550/51-ygx8
title: University of Pittsburgh: Genetics, Genomics and Deep Phenotyping of Orofacial Clefts

description: The overall goal of the Pittsburgh orofacial cleft studies (POFC) is to identify genetic loci and variants involved in CL/P and associated features. Further, through a deep phenotyping paradigm (see “OFC Research Procedures Manual” and associated Forms in the Appendices) POFC investigates a wide variety of phenotypic features in individuals with OFC, their relatives, and unaffected controls. These phenotype measures more accurately define the expression of OFC in participants, and associated features can also refine gene mapping studies of OFC.

The POFC projects include simplex and extended multiplex OFC families ascertained through OFC probands at several sites in the United States (Pennsylvania, Colorado, Iowa. Missouri) and multiple international sites (Europe, Central/South America, Asia, and Africa), as well as unaffected controls.

Basic demographics, medical history, family and pregnancy history, and deep phenotyping were obtained for each research participant. (See “OFC Research Procedures Manual” and associated Appendices). Physical measurements included 3d Facial Images, dental exams, high-resolution ultrasounds of the upper lip to visualize the orbicularis oris muscle, injtra-oral photos and dental casts, height/weight, and others.

Blood or saliva samples were obtained from each study participant for DNA extraction. (See “OFC Research Procedures Manual”, Section 4.6).

To date, the DNA samples have been assessed for genome-wide SNP panels and for whole genome sequencing. See list of publications below for sample results.
DOI: 10.5281/zenodo.8303175
title: no Title

description: No description
DOI: 10.5281/zenodo.10806712
title: no Title

description: No description
DOI: 10.5281/zenodo.8303174
title: no Title

description: No description
DOI: 10.5281/zenodo.10663016
title: Test

description: No description
DOI: 10.5281/zenodo.10663017
title: TR project

description: TR frequency distributions and TR disparity scores.
DOI: 10.5281/zenodo.10806717
title: Test

description: No description