cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5281/zenodo.10657538
title: Peer Review resources - crowdsourced

description: We herewith initiate a crowd-sourced mapping of Peer Review resources for a global research community to be informed and continue to co-create what we see as useful best practices and community standards.

 

Objective

The primary aim of this proposal is to establish a comprehensive and efficient peer review system that filters through marketing noise, emphasizing the distillation of peer review best practices. By identifying and promoting resources that adhere to rigorous standards, we aim to contribute to a culture of accountability and reproducibility, aligning with the principles that the Open Science (OS) community has brought to the forefront.

 

Contributions

Conceptualization and Writing: MJM, GD, JH (per CRediT taxonomy)

Project description: 10.21428/51e64700.fcd86e15



Contact

MJM: stories4sci@gmail.comJH: info@access2perspectives.org
DOI: 10.5281/zenodo.10657539
title: Peer Review resources - crowdsourced

description: We herewith initiate a crowd-sourced mapping of Peer Review resources for a global research community to be informed and continue to co-create what we see as useful best practices and community standards.

 

Objective

The primary aim of this proposal is to establish a comprehensive and efficient peer review system that filters through marketing noise, emphasizing the distillation of peer review best practices. By identifying and promoting resources that adhere to rigorous standards, we aim to contribute to a culture of accountability and reproducibility, aligning with the principles that the Open Science (OS) community has brought to the forefront.

 

Contributions

Conceptualization and Writing: MJM, GD, JH (per CRediT taxonomy)

Project description: 10.21428/51e64700.fcd86e15



Contact

MJM: stories4sci@gmail.comJH: info@access2perspectives.org
DOI: 10.6084/m9.figshare.6530339.v1
title: Additional file 2: of Intrachromosomal colocalization strengthens co-expression, co-modification and evolutionary conservation of neighboring genes

description: Table S2. Always-neighboring gene pairs without intrachromosomal colocalization. (XLSX 295 kb)
DOI: 10.6084/m9.figshare.25219448
title: The Use of Prediction Markets and Corporate Lobbying in Climate Policy Research

description: Data and code related to the titled research paper.
DOI: 10.15139/s3/ciym4b
title: A novel high throughput microwell outgrowth assay for HIV infected cells.

description: These files are the underlying data for the figures in the publication "A novel high throughput microwell outgrowth assay for HIV infected cells." in the Journal of Virology.
DOI: 10.6084/m9.figshare.21749622
title: Development of a novel circular mRNA vaccine of six protein combinations against <i>Staphylococcus aureus</i>

description: <i>Staphylococcus aureus</i> is an extraordinarily versatile pathogen, which is currently the most common cause of nosocomial and community infections. Considering that increased antibiotic resistance may hasten the spread of <i>S. aureus</i>, developing an effective vaccine can possibly aid in its control. The RNA vaccine coding immunodominance epitopes from bacteria provide a potential method to induce T and B cell immune responses by translating them into cells. Furthermore, using bioinformatics to create circular RNA vaccines can ensure that the translation of the vaccine is potent and durable. In this study, 7 cytotoxic T lymphocyte (CTL) epitopes, 4 helper T lymphocyte (HTL) epitopes, and 15 B cell epitopes from 6 proteins that are closely associated with the <i>S. aureus</i> virulence and invasion and critical to natural immune responses were mapped. To verify their interactions, all epitopes were docked with the corresponding MHC alleles. The final vaccine was composed of 26 epitopes and the adjuvant β-defencin, and a disulfide bond was also introduced to improve its stability. After the prediction of structure and characteristics, the developed vaccine was docked with TLR2 and TLR4, which induce immunological responses in <i>S. aureus</i> infection. According to the molecular dynamic simulation, the vaccine might interact strongly with TLRs. Meanwhile, it performed well in immunological simulation and population coverage prediction. Finally, the vaccine was converted into a circular RNA using a series of helper sequences to aid in vaccine circulation translation. Hopefully, this proposed structure will be proven to serve a viable vaccine against <i>S. aureus</i>. Communicated by Ramaswamy H. Sarma
DOI: 10.6084/m9.figshare.7593998
title: Duan_et_al. (2019) Submitted to JGR oceans_ model_data

description: This is the model data for article submitted to AGU JGR Oceans; If you any question or want use this dataset, please contact Dr. Jing Duan (jingduan@qdio.ac.cn)
DOI: 10.6084/m9.figshare.13346137
title: Additional file 10 of The genetic control of leaf and petal allometric variations in Arabidopsis thaliana

description: Additional file 10: Table S9. The estimated value for each of the 19 parental alleles at each detected QTL for life-history traits.
DOI: 10.6084/m9.figshare.13346143.v1
title: Additional file 2 of The genetic control of leaf and petal allometric variations in Arabidopsis thaliana

description: Additional file 2: Table S1. The phenotype data for all traits used for QTL analysis.
DOI: 10.6084/m9.figshare.13346146.v1
title: Additional file 3 of The genetic control of leaf and petal allometric variations in Arabidopsis thaliana

description: Additional file 3: Table S2. Significant QTL detected for the leaf and petal allometry models.
DOI: 10.6084/m9.figshare.13346146
title: Additional file 3 of The genetic control of leaf and petal allometric variations in Arabidopsis thaliana

description: Additional file 3: Table S2. Significant QTL detected for the leaf and petal allometry models.
DOI: 10.6084/m9.figshare.13346152.v1
title: Additional file 5 of The genetic control of leaf and petal allometric variations in Arabidopsis thaliana

description: Additional file 5: Table S4. The candidate genes account for leaf and petal allometry variation.
DOI: 10.6084/m9.figshare.13346155.v1
title: Additional file 6 of The genetic control of leaf and petal allometric variations in Arabidopsis thaliana

description: Additional file 6: Table S5. Significant QTL detected for the leaf and petal allometry covariation.
DOI: 10.6084/m9.figshare.13346161
title: Additional file 8 of The genetic control of leaf and petal allometric variations in Arabidopsis thaliana

description: Additional file 8: Table S7. The candidate genes account for leaf and petal allometry covariation.
DOI: 10.6084/m9.figshare.13346149
title: Additional file 4 of The genetic control of leaf and petal allometric variations in Arabidopsis thaliana

description: Additional file 4: Table S3. The estimated value for each of the 19 parental alleles at each detected QTL for leaf and petal allometry models.
DOI: 10.6084/m9.figshare.13346164
title: Additional file 9 of The genetic control of leaf and petal allometric variations in Arabidopsis thaliana

description: Additional file 9: Table S8. The significant QTL detected for life-history traits in MAGIC lines.
DOI: 10.6084/m9.figshare.13346158
title: Additional file 7 of The genetic control of leaf and petal allometric variations in Arabidopsis thaliana

description: Additional file 7: Table S6. The estimated value for each of the 19 parental alleles at each detected QTL for leaf and petal allometry covariation.
DOI: 10.6084/m9.figshare.13346161.v1
title: Additional file 8 of The genetic control of leaf and petal allometric variations in Arabidopsis thaliana

description: Additional file 8: Table S7. The candidate genes account for leaf and petal allometry covariation.
DOI: 10.6084/m9.figshare.11264441
title: Chromosome-level genome assembly of the brown alga Undaria pinnatifida using PacBio and Hi-C technologies

description: <i>Undaria
pinnatifida</i> is an important economic kelp species in East Asia.
In recent decades it has drawn increasing attention due to its worldwide spread
as an invasive species. Lack of genome sequence hinders crucial fundamental
researches in this alga. Herein, we present the whole genome sequence of a male
gametophyte of <i>U. pinnatifida</i>, the
first reference genome of the family Alariaceae. The genome, which was assembled
based on the clean data produced by the Pacific Biosciences sequencing platform,
was 511.0 Mb with contig N50 length of 1.7 Mb. We then assembled the contigs
into chromosome-level scaffolds with an N50 length of 16.5 Mb using the high-throughput
chromosome conformation capture (Hi-C) technology. In total 502.8 Mb genomic
sequences were located on 30 chromosomes, accounting for 98.4% of the whole
assembled length. A total of 12,402 protein-coding genes were annotated in the
reference genome. This chromosome-level genome will provide valuable
information for molecular biological studies in <i>U. pinnatifida</i> and comparative genomic studies with other brown
algae.<br>
DOI: 10.6084/m9.figshare.13346383.v1
title: Additional file 1 of Perioperative Dexmedetomidine attenuates brain ischemia reperfusion injury possibly via up-regulation of astrocyte Connexin 43

description: Additional file 1.
DOI: 10.6084/m9.figshare.13346383
title: Additional file 1 of Perioperative Dexmedetomidine attenuates brain ischemia reperfusion injury possibly via up-regulation of astrocyte Connexin 43

description: Additional file 1.
DOI: 10.6084/m9.figshare.17031708
title: Cyclin-Dependent Kinase 4 is expected to be a therapeutic target for hepatocellular carcinoma metastasis using integrated bioinformatic analysis

description: Hepatocellular carcinoma (HCC) is the third leading cause of cancer-related mortality worldwide. HCC cells possess biological characteristics of high invasion and metastasis. In this respect, to prevent cancer cell invasion and metastasis and early active intervention, we herein screened through the TCGA database for further prognostic analysis including overall survival and disease-free survival . The Kaplan-Meier curve suggested that Cyclin-Dependent Kinase 4 (CDK4) might be an independent prognostic factor for HCC. Moreover, we performed mRNA expression analysis to measure CDK4 levels in normal liver tissues and HCC tissues, and immunohistochemistry analysis to detect protein level of CDK4 in Non-tumor tissue and HCC tissues . Our findings indicated that the expression of CDK4 was significantly higher in tumor tissues compared with Non-tumor tissue in HCC, which increased from HCC stage 1 to 3. Furthermore, the results of transwell-assay indicated that knocking down CDK4 significantly suppresses the invasion and migration of HCC cells, and the results of bioinformatics analysis revealed that genes closely associated with CDK4 are potentially worthy of further investigation. Additionally, the results of Western Blot indicated CDK4 regulates epithelial mesenchymal transition in HCC,and CDK4 appears to regulate EMT and HCC progression via the Wnt/β-catenin pathway. Collectively, this study found the key target gene through bioinformatic analysis and further functional validation through cell experiments. In particular, CDK4 is anticipated to become a crucial hub gene to snipe the metastasis of cancer cells in HCC. <b>Abbreviations</b>: Hepatocellular carcinoma (HCC);Cyclin-Dependent Kinase 4(CDK4);Genomic Data Commons (GDC); genes; EC, Endometrial cancer; GEO, gene expression omnibus; GO, Gene Ontology; GSEA, Gene set enrichment analysis; KEGG, Database; TCGA, The Cancer Genome Atlas; TSGs, tumor suppressor genes;epithelial mesenchymal transition (EMT).
DOI: 10.6084/m9.figshare.13346385
title: Additional file 1 of Identification of Novel Alleles of the Rice Blast-Resistance Gene Pi9 through Sequence-Based Allele Mining

description: Additional file 1: Supplementary Table 1. Primers for sequence analysis of Pi9, Pi2, Pigm and Pizt allele genes in rice.Among them, the alleles of Pi2, Pigm and Piz-t share a set of primers for amplification and sequencing; the alleles of Pi9 use a unique set of primers for amplification and sequencing. The primers used for PCR amplification and sequencing were clearly labelled and listed in the table
DOI: 10.6084/m9.figshare.13346400.v1
title: Additional file 6 of Identification of Novel Alleles of the Rice Blast-Resistance Gene Pi9 through Sequence-Based Allele Mining

description: Additional file 6: Supplementary Table 6. Primers for sequence analysis of AvrPi9 and AvrPiz-t genes in M. oryzae.The AvrPi9 and AvrPiz-t genes each use a unique set of primers for amplification and sequencing. The primers used for PCR amplification and sequencing were labelled and listed in the table.
DOI: 10.6084/m9.figshare.13346391
title: Additional file 3 of Identification of Novel Alleles of the Rice Blast-Resistance Gene Pi9 through Sequence-Based Allele Mining

description: Additional file 3: Supplementary Table 3. List of 107 rice varieties used for allele mining. Approximately 1883 varieties were grown at trial nurseries of Enshi and Yichang, Hubei Province. We identified 361 varieties from nurseries at Enshi or Yichang that displayed HR or R resistance phenotypes. A PCR-based screen for the presence of Pi2, Pi9, Pigm, or Piz-t identified 107 varieties as candidates for allele mining. The sequencing results of all 107 materials are shown in this table
DOI: 10.6084/m9.figshare.13346391.v1
title: Additional file 3 of Identification of Novel Alleles of the Rice Blast-Resistance Gene Pi9 through Sequence-Based Allele Mining

description: Additional file 3: Supplementary Table 3. List of 107 rice varieties used for allele mining. Approximately 1883 varieties were grown at trial nurseries of Enshi and Yichang, Hubei Province. We identified 361 varieties from nurseries at Enshi or Yichang that displayed HR or R resistance phenotypes. A PCR-based screen for the presence of Pi2, Pi9, Pigm, or Piz-t identified 107 varieties as candidates for allele mining. The sequencing results of all 107 materials are shown in this table
DOI: 10.6084/m9.figshare.13346400
title: Additional file 6 of Identification of Novel Alleles of the Rice Blast-Resistance Gene Pi9 through Sequence-Based Allele Mining

description: Additional file 6: Supplementary Table 6. Primers for sequence analysis of AvrPi9 and AvrPiz-t genes in M. oryzae.The AvrPi9 and AvrPiz-t genes each use a unique set of primers for amplification and sequencing. The primers used for PCR amplification and sequencing were labelled and listed in the table.
DOI: 10.6084/m9.figshare.13346403
title: Additional file 7 of Identification of Novel Alleles of the Rice Blast-Resistance Gene Pi9 through Sequence-Based Allele Mining

description: Additional file 7: Supplementary Table 7. List the presence of AvrPi9 and AvrPiz-t genes in 34 M. oryzae.+, the gene is present in the M. oryzae; −, the gene does not exist in the M. oryzae.
DOI: 10.6084/m9.figshare.9691775
title: Additional file 2: of Transcriptome clarifies mechanisms of lesion genesis versus progression in models of Ccm3 cerebral cavernous malformations

description: Table S1. List of identified differentially expressed genes in each of three models (fold change |FC| ≥ 2, p &lt; 0.05, false discovery rate corrected). (XLSX 643 kb)
DOI: 10.6084/m9.figshare.9691775.v1
title: Additional file 2: of Transcriptome clarifies mechanisms of lesion genesis versus progression in models of Ccm3 cerebral cavernous malformations

description: Table S1. List of identified differentially expressed genes in each of three models (fold change |FC| ≥ 2, p &lt; 0.05, false discovery rate corrected). (XLSX 643 kb)
DOI: 10.6084/m9.figshare.9691781
title: Additional file 3: of Transcriptome clarifies mechanisms of lesion genesis versus progression in models of Ccm3 cerebral cavernous malformations

description: Table S2. Top 20 genes by fold change for acute in vivo neurovascular units (NVUs), chronic in vivo NVUs and in vitro brain microvascular endothelial cells models (fold change |FC| ≥ 2; p &lt; 0.05, false discovery rate corrected). (XLSX 18 kb)
DOI: 10.6084/m9.figshare.9691781.v1
title: Additional file 3: of Transcriptome clarifies mechanisms of lesion genesis versus progression in models of Ccm3 cerebral cavernous malformations

description: Table S2. Top 20 genes by fold change for acute in vivo neurovascular units (NVUs), chronic in vivo NVUs and in vitro brain microvascular endothelial cells models (fold change |FC| ≥ 2; p &lt; 0.05, false discovery rate corrected). (XLSX 18 kb)
DOI: 10.6084/m9.figshare.9691784
title: Additional file 1: of Tigecycline-induced sustained severe hypoglycemia: a case report

description: The CARE checklist. (XLSX 11 kb)
DOI: 10.6084/m9.figshare.9691784.v1
title: Additional file 1: of Tigecycline-induced sustained severe hypoglycemia: a case report

description: The CARE checklist. (XLSX 11 kb)
DOI: 10.6084/m9.figshare.9691790
title: Additional file 4: of Transcriptome clarifies mechanisms of lesion genesis versus progression in models of Ccm3 cerebral cavernous malformations

description: Table S3. List of enriched gene ontology functions for top 20 genes by fold change in each model (p &lt; 0.05, false discovery rate corrected). (XLSX 14 kb)
DOI: 10.6084/m9.figshare.9691790.v1
title: Additional file 4: of Transcriptome clarifies mechanisms of lesion genesis versus progression in models of Ccm3 cerebral cavernous malformations

description: Table S3. List of enriched gene ontology functions for top 20 genes by fold change in each model (p &lt; 0.05, false discovery rate corrected). (XLSX 14 kb)
DOI: 10.6084/m9.figshare.9691793
title: Additional file 5: of Transcriptome clarifies mechanisms of lesion genesis versus progression in models of Ccm3 cerebral cavernous malformations

description: Table S4. List of unique differentially expressed genes for all models according to the Venn diagram of the models (fold change |FC| ≥ 2.0; p &lt; 0.05, false discovery rate corrected). (XLSX 745 kb)
DOI: 10.6084/m9.figshare.9691793.v1
title: Additional file 5: of Transcriptome clarifies mechanisms of lesion genesis versus progression in models of Ccm3 cerebral cavernous malformations

description: Table S4. List of unique differentially expressed genes for all models according to the Venn diagram of the models (fold change |FC| ≥ 2.0; p &lt; 0.05, false discovery rate corrected). (XLSX 745 kb)
DOI: 10.6084/m9.figshare.9691796
title: Additional file 6: of Transcriptome clarifies mechanisms of lesion genesis versus progression in models of Ccm3 cerebral cavernous malformations

description: Table S5. List of gene ontology terms for acute in vivo neurovascular units (NVUs) only and chronic in vivo NVUs only (p &lt; 0.01, false discovery rate corrected). (XLSX 160 kb)
DOI: 10.6084/m9.figshare.9691796.v1
title: Additional file 6: of Transcriptome clarifies mechanisms of lesion genesis versus progression in models of Ccm3 cerebral cavernous malformations

description: Table S5. List of gene ontology terms for acute in vivo neurovascular units (NVUs) only and chronic in vivo NVUs only (p &lt; 0.01, false discovery rate corrected). (XLSX 160 kb)
DOI: 10.6084/m9.figshare.9691799
title: Additional file 7: of Transcriptome clarifies mechanisms of lesion genesis versus progression in models of Ccm3 cerebral cavernous malformations

description: Table S6. 1876 gene ontology (GO) terms used for generating the heatmap. (XLSX 157 kb)
DOI: 10.6084/m9.figshare.9691799.v1
title: Additional file 7: of Transcriptome clarifies mechanisms of lesion genesis versus progression in models of Ccm3 cerebral cavernous malformations

description: Table S6. 1876 gene ontology (GO) terms used for generating the heatmap. (XLSX 157 kb)
DOI: 10.6084/m9.figshare.9691802
title: Additional file 8: of Transcriptome clarifies mechanisms of lesion genesis versus progression in models of Ccm3 cerebral cavernous malformations

description: Table S7. List of gene ontology terms for lesional neurovascular units excluding in vitro brain microvascular endothelial cell (BMEC) differentially expressed genes (p &lt; 0.01, false discovery rate (FDR) corrected) and in vitro BMECs (p &lt; 0.05, FDR corrected). (XLSX 145 kb)
DOI: 10.6084/m9.figshare.9691802.v1
title: Additional file 8: of Transcriptome clarifies mechanisms of lesion genesis versus progression in models of Ccm3 cerebral cavernous malformations

description: Table S7. List of gene ontology terms for lesional neurovascular units excluding in vitro brain microvascular endothelial cell (BMEC) differentially expressed genes (p &lt; 0.01, false discovery rate (FDR) corrected) and in vitro BMECs (p &lt; 0.05, FDR corrected). (XLSX 145 kb)
DOI: 10.6084/m9.figshare.9691805
title: Additional file 9: of Transcriptome clarifies mechanisms of lesion genesis versus progression in models of Ccm3 cerebral cavernous malformations

description: Table S8. List of 105 putative targets of mmu-miR-3472a within the differentially expressed genes common between acute and chronic in vivo neurovascular units. (XLSX 34 kb)
DOI: 10.6084/m9.figshare.9691805.v1
title: Additional file 9: of Transcriptome clarifies mechanisms of lesion genesis versus progression in models of Ccm3 cerebral cavernous malformations

description: Table S8. List of 105 putative targets of mmu-miR-3472a within the differentially expressed genes common between acute and chronic in vivo neurovascular units. (XLSX 34 kb)
DOI: 10.6084/m9.figshare.13346454
title: Additional file 1 of Randomized controlled multicentre study of albumin replacement therapy in septic shock (ARISS): protocol for a randomized controlled trial

description: Additional file 1.
DOI: 10.6084/m9.figshare.13346454.v1
title: Additional file 1 of Randomized controlled multicentre study of albumin replacement therapy in septic shock (ARISS): protocol for a randomized controlled trial

description: Additional file 1.
DOI: 10.15156/bio/sh3440205.08fu
title: SH3440205.08FU

description: UNITE provides a unified way for delimiting, identifying, communicating, and working with DNA-based Species Hypotheses (SH). All fungal ITS sequences in the international nucleotide sequence databases are clustered to approximately the species level by applying a set of dynamic distance values (<0.5 - 3.0%). All species hypotheses are given a unique, stable name in the form of a DOI, and their taxonomic and ecological annotations are verified through distributed, web-based third-party annotation efforts. SHs are connected to a taxon name and its classification as far as possible (phylum, class, order, etc.) by taking into account identifications for all sequences in the SH. An automatically or manually designated sequence is chosen to represent each such SH. These sequences are released (https://unite.ut.ee/repository.php) for use by the scientific community in, for example, local sequence similarity searches and next-generation sequencing analysis pipelines. The system and the data are updated automatically as the number of public fungal ITS sequences grows.
DOI: 10.15156/bio/sh3440206.08fu
title: SH3440206.08FU

description: UNITE provides a unified way for delimiting, identifying, communicating, and working with DNA-based Species Hypotheses (SH). All fungal ITS sequences in the international nucleotide sequence databases are clustered to approximately the species level by applying a set of dynamic distance values (<0.5 - 3.0%). All species hypotheses are given a unique, stable name in the form of a DOI, and their taxonomic and ecological annotations are verified through distributed, web-based third-party annotation efforts. SHs are connected to a taxon name and its classification as far as possible (phylum, class, order, etc.) by taking into account identifications for all sequences in the SH. An automatically or manually designated sequence is chosen to represent each such SH. These sequences are released (https://unite.ut.ee/repository.php) for use by the scientific community in, for example, local sequence similarity searches and next-generation sequencing analysis pipelines. The system and the data are updated automatically as the number of public fungal ITS sequences grows.