cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.20011356
title: Identification and verification of differentially expressed key genes in peripheral blood-derived T cells between chronic immune thrombocytopenia patients and healthy controls

description: Immune thrombocytopenia (ITP), characterized by decreased platelet counts, is a complex immune-mediated disorder with unelucidated pathogenesis. Accumulating evidence shows that T cell-mediated platelet destruction is one crucial process during the progression of ITP. Here, we attempted to identify core genes in peripheral blood-derived T-cells of chronic ITP through the analysis of microarray data (GSE43179) and clinical verification, with the aim to further understand the pathogenesis and progression of ITP. Compared with healthy controls, 97 differentially expressed genes (DEGs), including 63 up-regulated and 34 down-regulated were identified in ITP patients. Functional enrichment analysis showed that the DEGs were mainly enriched in innate immune response, inflammatory response, and IL-17 signaling pathway. Among the DEGs, top 15 hub genes ranked by degree score were identified via protein-protein interaction (PPI) network and were further confirmed by quantitative reverse transcription PCR (qRT-PCR). Among top 15 hub genes, the expression levels of 14 DEGs like <i>TLR4, S100A8, S100A9</i>, and <i>S100A12</i> were significantly up-regulated, while one DEG <i>IFNG</i> was down-regulated in ITP patients. Noticeably, <i>TLR4</i> exhibited the highest degree score, and <i>S100A8</i> had the largest fold change in qRT-PCR analysis. Altogether, our results suggested that the pathogenesis and progression of ITP are related with multiple immune-related pathways, and that <i>TLR4</i> and <i>S100A8</i> are likely to play crucial roles.
DOI: 10.6084/m9.figshare.7428461
title: Additional file 2: of NmeCas9 is an intrinsically high-fidelity genome-editing platform

description: Table S5. Targeted deep sequencing read count data for all sgRNAs used and for all off-targets detected by SITE-Seq. (XLSX 144 kb)
DOI: 10.13020/t222-a012
title: Materials to re-create Predicting Surface Oscillations in Lake Superior from Normal Mode Dynamics

description: A recent manuscript examined surface oscillations in Lake Superior using observations and the MIT general circulation model (MITgcm). This submission includes the functions to analyze the observations, the configuration and post-processing files for the MITgcm, and Matlab scripts that recreate the figures in the manuscript.
description: There are three folders (compressed in .zip format). Each folder has an associated plain-text documentation file that includes detailed information about its contents. The folders are: (1) MITgcm, (2) analysis_scripts, and (3) plotting_scripts. The first folder includes all compile-time and run-time options for the MITgcm simulations. It also includes Matlab scripts and functions to generate MITgcm input files and post-process MITgcm output files. The MITgcm source code is available at http://mitgcm.org/. The second folder contains the Matlab scripts to process tide gauge (lake level) data collected by the US and Canadian governments. The third folder contains Matlab scripts and functions that re-create the figures included in Kelly et al. (2024). All of the data needed for these scripts are included in the folder.
DOI: 10.6084/m9.figshare.12671330.v1
title: Additional file 3 of What is the right sequencing approach? Solo VS extended family analysis in consanguineous populations

description: Additional file 3.
DOI: 10.6084/m9.figshare.12671330.v2
title: Additional file 3 of What is the right sequencing approach? Solo VS extended family analysis in consanguineous populations

description: Additional file 3.
DOI: 10.13012/b2idb-9316702_v1
title: Data for SEPP: SATé-Enabled Phylogenetic Placement.

description: This dataset provides the data for Mirarab, Siavash, Nam Nguyen, and Tandy Warnow. "SEPP: SATé-enabled phylogenetic placement." Biocomputing 2012. 2012. 247-258.
DOI: 10.6084/m9.figshare.7428461.v1
title: Additional file 2: of NmeCas9 is an intrinsically high-fidelity genome-editing platform

description: Table S5. Targeted deep sequencing read count data for all sgRNAs used and for all off-targets detected by SITE-Seq. (XLSX 144 kb)
DOI: 10.6084/m9.figshare.12671339.v1
title: Additional file 3 of Comparative transcriptomics analysis revealing flower trichome development during flower development in two Lonicera japonica Thunb. cultivars using RNA-seq

description: Additional file 3: Table S1. Comparison of the density of glandular and non-glandular hairs in ‘Damaohua’ and ‘Yujin 1’ (mm-2). Table S2. Comparison of the lengths of glandular and non-glandular hairs in ‘Damaohua’ and ‘Yujin 1’ (μm). Table S3. Assembly summary of transcriptomic data. Table S4. Preprocessing results of sequencing data quality. Table S5. Annotation results of the unigenes. Table S6. Summary of top 10 GO terms and top 20 KEGG pathway assignments for the L. japonica flower transcriptome. Table S7. DEGs involved in trichome development. Table S8. Primers used for analysis of gene expression by qRT-PCR. Table S9. DEGs involved in signal transduction. Table S10. DEGs involved in secondary metabolites. Table S11. DEGs involved in plant resistance.
DOI: 10.6084/m9.figshare.7428443
title: Additional file 10: of NmeCas9 is an intrinsically high-fidelity genome-editing platform

description: Table S3. Targeted deep sequencing read count data for all sgRNAs used and for all off-targets detected by GUIDE-seq. (XLSX 44 kb)
DOI: 10.6084/m9.figshare.7428479.v1
title: Additional file 3: of NmeCas9 is an intrinsically high-fidelity genome-editing platform

description: Table S2. Summary of potential off-target sites detected by GUIDE-seq analysis using the Bioconductor package GUIDE-seq. The table includes sites for both NmeCas9 (with N4GN3 PAM sequences) and SpyCas9 (with NGG, NGA, and NAG PAM sequences) for the DTS3, DTS7 and DTS8 sgRNAs, as well as for NmeCas9 with the other sgRNAs used in this study. (XLSX 105 kb)
DOI: 10.6084/m9.figshare.7428503
title: Additional file 4: of NmeCas9 is an intrinsically high-fidelity genome-editing platform

description: Table S1. List of off-target sites with canonical and variant SpyCas9 and NmeCas9 PAMs predicted by CRISPRseek, for all guides used in this study. (XLSX 42214 kb)
DOI: 10.6084/m9.figshare.12671182.v1
title: Additional file 4 of Combined signaling of NF-kappaB and IL-17 contributes to Mesenchymal stem cells-mediated protection for Paraquat-induced acute lung injury

description: Additional file 4.
DOI: 10.6084/m9.figshare.7428443.v1
title: Additional file 10: of NmeCas9 is an intrinsically high-fidelity genome-editing platform

description: Table S3. Targeted deep sequencing read count data for all sgRNAs used and for all off-targets detected by GUIDE-seq. (XLSX 44 kb)
DOI: 10.6084/m9.figshare.7428599
title: Additional file 8: of NmeCas9 is an intrinsically high-fidelity genome-editing platform

description: Table S8. Primer sequences used for on- and off-target deep sequencing analysis for all genomic editing sites analyzed by SITE-Seq. (XLSX 48 kb)
DOI: 10.6084/m9.figshare.7428587
title: Additional file 7: of NmeCas9 is an intrinsically high-fidelity genome-editing platform

description: Table S6. GUIDE-seq primer index sequences used in this study. (XLSX 45 kb)
DOI: 10.6084/m9.figshare.7428587.v1
title: Additional file 7: of NmeCas9 is an intrinsically high-fidelity genome-editing platform

description: Table S6. GUIDE-seq primer index sequences used in this study. (XLSX 45 kb)
DOI: 10.6084/m9.figshare.4807021.v1
title: Teaching Ethics in a Statistics Curriculum with a Cross-Cultural Emphasis

description: Like most professional disciplines, the ASA has adopted ethical guidelines for its practitioners. To promote these guidelines, as well as to meet governmental and institutional mandates, U.S. universities are demanding more training on ethics within existing statistics graduate student curricula. Most of this training is based on the teachings of Western philosophers. However, many statistics graduate students are from Eastern cultures (particularly Chinese), and cultural and linguistic evidence indicates that Western ethics may be difficult to translate into the philosophical concepts common to students from different cultural backgrounds. This article describes how to teach cross-cultural ethics, with emphasis on the ASA Ethical Guidelines, within a graduate-level statistical consulting course. In particular, we present content that can help students overcome cultural and language barriers to gain an understanding of ethical decision-making that is compatible with both Western and Eastern philosophical models. Supplementary materials for this article are available online.
DOI: 10.6084/m9.figshare.4807021
title: Teaching Ethics in a Statistics Curriculum with a Cross-Cultural Emphasis

description: Like most professional disciplines, the ASA has adopted ethical guidelines for its practitioners. To promote these guidelines, as well as to meet governmental and institutional mandates, U.S. universities are demanding more training on ethics within existing statistics graduate student curricula. Most of this training is based on the teachings of Western philosophers. However, many statistics graduate students are from Eastern cultures (particularly Chinese), and cultural and linguistic evidence indicates that Western ethics may be difficult to translate into the philosophical concepts common to students from different cultural backgrounds. This article describes how to teach cross-cultural ethics, with emphasis on the ASA Ethical Guidelines, within a graduate-level statistical consulting course. In particular, we present content that can help students overcome cultural and language barriers to gain an understanding of ethical decision-making that is compatible with both Western and Eastern philosophical models. Supplementary materials for this article are available online.
DOI: 10.6084/m9.figshare.12671420
title: Additional file 1 of Plasma circulating tumor DNA assessment reveals KMT2D as a potential poor prognostic factor in extranodal NK/T-cell lymphoma

description: Additional file 1: Table S1. The mutant allele frequencies in each gene of each sample.
DOI: 10.6084/m9.figshare.12671420.v1
title: Additional file 1 of Plasma circulating tumor DNA assessment reveals KMT2D as a potential poor prognostic factor in extranodal NK/T-cell lymphoma

description: Additional file 1: Table S1. The mutant allele frequencies in each gene of each sample.
DOI: 10.6084/m9.figshare.20011555
title: Proliferation rate and expression of stem cells markers during expansion in primary culture of pulp cells

description: Abstract: The aim of the present study was to evaluate the proliferation rate and the expression of stem cells markers during expansion in primary culture of dental pulp stem cells (DPSCs), comparing different techniques (explant and enzymatic digestion), subject ages (up to 40 and over 40) and cell passages (#2, #5 and #8). DPSCs were isolated using either the enzymatic digestion (ED) or explant (EX) technique. The number of days needed for the cells to reach confluence was determined. Immunophenotyping was performed by immunofluorescence and flow cytometry analysis using antibodies specific for nestin, vimentin, CD44, CD146, Oct3/4 and CD34. Data were subjected to three-way analysis of variance (n = 6/group). The ANOVA tests were complemented by Tukey's or t-tests (p &lt; 0.05). The variables “donor age” and “technique” were analyzed to define the optimal desirability value using a response optimization. DPSCs presented a high proliferation rate from passages 2 to 5 while cells from passage 8 proliferated at a slower rate. For all markers, no significant difference was observed among passages, irrespective of the technique used or the donor's age. The mean fraction of specific antibodies was 73.7% (± 11.5), 49.0% (± 18.7), 80.1% (± 8.0), 45.2% (± 13.7), 64.7% (± 5.3) and 2.0% (± 1.5) for CD44, OCT, vimentin, nestin, CD146 and CD34, respectively. The highest optimal desirability value was obtained using the ED technique and cells from younger patients (d = 0.92). However, it was concluded that neither the isolation technique nor the donor age or cell passage significantly interfered with the stem cell phenotype and proliferation rate during cell expansion.
DOI: 10.17028/rd.lboro.22633237
title: Supplementary information files for: A light-management film layer induces dramatically enhanced acetate production in photo-assisted microbial electrosynthesis systems

description: Supplementary files for article A light-management film layer induces dramatically enhanced acetate production in photo-assisted microbial electrosynthesis systems.
 A light-management system consisting of a Al-doped ZnO (AZO) film layer was combined for the first time with different bio-photocathodes (<em>Serratia marcescens</em> Q1 electrotroph immobilized on g-C<sub>3</sub>N<sub>4</sub>, MnFe<sub>2</sub>O<sub>4</sub> or MnFe<sub>2</sub>O<sub>4</sub>/g-C<sub>3</sub>N<sub>4</sub>) to significantly enhance acetate production from bicarbonate in photo-assisted microbial electrosynthesis systems (MES). The AZO light-management system exhibiting optical properties independent of the light incident angle mitigated the shielding effect of light by electrotrophs, increasing light trapping and decreasing light reflection, ultimately allowing higher rates of photon absorption and redistributions of photons over the photo-active layers. As a result, more reducing equivalents as H<sub>2</sub> produced up to 242% (g-C<sub>3</sub>N<sub>4</sub>/AZO-filter) and 543% (g-C<sub>3</sub>N<sub>4</sub>/AZO) increase in acetate production at coulombic efficiencies of 70% (g-C<sub>3</sub>N<sub>4</sub>/AZO-filter) and 81% (g-C<sub>3</sub>N<sub>4</sub>/AZO). The record high solar-to-acetate efficiency obtained with the MnFe<sub>2</sub>O<sub>4</sub>/g-C<sub>3</sub>N<sub>4</sub>/AZO biocathode was 3.20%. The light-management system proposed in this study opens a new promising way to construct efficient bio-photocathodes for inorganic carbon reduction in photo-assisted MES.
DOI: 10.6084/m9.figshare.20011555.v1
title: Proliferation rate and expression of stem cells markers during expansion in primary culture of pulp cells

description: Abstract: The aim of the present study was to evaluate the proliferation rate and the expression of stem cells markers during expansion in primary culture of dental pulp stem cells (DPSCs), comparing different techniques (explant and enzymatic digestion), subject ages (up to 40 and over 40) and cell passages (#2, #5 and #8). DPSCs were isolated using either the enzymatic digestion (ED) or explant (EX) technique. The number of days needed for the cells to reach confluence was determined. Immunophenotyping was performed by immunofluorescence and flow cytometry analysis using antibodies specific for nestin, vimentin, CD44, CD146, Oct3/4 and CD34. Data were subjected to three-way analysis of variance (n = 6/group). The ANOVA tests were complemented by Tukey's or t-tests (p &lt; 0.05). The variables “donor age” and “technique” were analyzed to define the optimal desirability value using a response optimization. DPSCs presented a high proliferation rate from passages 2 to 5 while cells from passage 8 proliferated at a slower rate. For all markers, no significant difference was observed among passages, irrespective of the technique used or the donor's age. The mean fraction of specific antibodies was 73.7% (± 11.5), 49.0% (± 18.7), 80.1% (± 8.0), 45.2% (± 13.7), 64.7% (± 5.3) and 2.0% (± 1.5) for CD44, OCT, vimentin, nestin, CD146 and CD34, respectively. The highest optimal desirability value was obtained using the ED technique and cells from younger patients (d = 0.92). However, it was concluded that neither the isolation technique nor the donor age or cell passage significantly interfered with the stem cell phenotype and proliferation rate during cell expansion.
DOI: 10.6084/m9.figshare.20011356.v1
title: Identification and verification of differentially expressed key genes in peripheral blood-derived T cells between chronic immune thrombocytopenia patients and healthy controls

description: Immune thrombocytopenia (ITP), characterized by decreased platelet counts, is a complex immune-mediated disorder with unelucidated pathogenesis. Accumulating evidence shows that T cell-mediated platelet destruction is one crucial process during the progression of ITP. Here, we attempted to identify core genes in peripheral blood-derived T-cells of chronic ITP through the analysis of microarray data (GSE43179) and clinical verification, with the aim to further understand the pathogenesis and progression of ITP. Compared with healthy controls, 97 differentially expressed genes (DEGs), including 63 up-regulated and 34 down-regulated were identified in ITP patients. Functional enrichment analysis showed that the DEGs were mainly enriched in innate immune response, inflammatory response, and IL-17 signaling pathway. Among the DEGs, top 15 hub genes ranked by degree score were identified via protein-protein interaction (PPI) network and were further confirmed by quantitative reverse transcription PCR (qRT-PCR). Among top 15 hub genes, the expression levels of 14 DEGs like <i>TLR4, S100A8, S100A9</i>, and <i>S100A12</i> were significantly up-regulated, while one DEG <i>IFNG</i> was down-regulated in ITP patients. Noticeably, <i>TLR4</i> exhibited the highest degree score, and <i>S100A8</i> had the largest fold change in qRT-PCR analysis. Altogether, our results suggested that the pathogenesis and progression of ITP are related with multiple immune-related pathways, and that <i>TLR4</i> and <i>S100A8</i> are likely to play crucial roles.
DOI: 10.6084/m9.figshare.12671330
title: Additional file 3 of What is the right sequencing approach? Solo VS extended family analysis in consanguineous populations

description: Additional file 3.
DOI: 10.6084/m9.figshare.12671339
title: Additional file 3 of Comparative transcriptomics analysis revealing flower trichome development during flower development in two Lonicera japonica Thunb. cultivars using RNA-seq

description: Additional file 3: Table S1. Comparison of the density of glandular and non-glandular hairs in ‘Damaohua’ and ‘Yujin 1’ (mm-2). Table S2. Comparison of the lengths of glandular and non-glandular hairs in ‘Damaohua’ and ‘Yujin 1’ (μm). Table S3. Assembly summary of transcriptomic data. Table S4. Preprocessing results of sequencing data quality. Table S5. Annotation results of the unigenes. Table S6. Summary of top 10 GO terms and top 20 KEGG pathway assignments for the L. japonica flower transcriptome. Table S7. DEGs involved in trichome development. Table S8. Primers used for analysis of gene expression by qRT-PCR. Table S9. DEGs involved in signal transduction. Table S10. DEGs involved in secondary metabolites. Table S11. DEGs involved in plant resistance.
DOI: 10.6084/m9.figshare.7428503.v1
title: Additional file 4: of NmeCas9 is an intrinsically high-fidelity genome-editing platform

description: Table S1. List of off-target sites with canonical and variant SpyCas9 and NmeCas9 PAMs predicted by CRISPRseek, for all guides used in this study. (XLSX 42214 kb)
DOI: 10.25403/upresearchdata.25187834
title: Investigating the seroprevalence of <i>Toxoplasma gondii</i> and determining the knowledge and practices in an interface area in Mpumalanga, South Africa

description: <i>Toxoplasma gondii</i> (<i>T. gondii</i>) is an obligate protozoan parasite from the phylum, Apicomplexa, that causes a disease known as Toxoplasmosis, in warm-blooded animals. Although toxoplasmosis is mostly asymptomatic, in immune compromised humans and animals it can lead to a severe disease. <i>Toxoplasma gondii</i> is of global importance and affects approximately 30-50% of the population worldwide. Although it is of worldwide importance, in most African countries including South Africa (SA), information on the national prevalence of <i>T. gondii</i> is limited in people and animals and has not yet been fully investigated and documented. The data was collected using Therefore the data presents the seroprevalence of <i>T. gondi</i><i>i</i> in humans, domestic and wild animals as well as assessing the knowledge of the parasite and associated practices among the human population in an interface area in South Africa. Serum samples were collected by the National Institute for Communicable Diseases (NICD). Blood samples from chickens, goats and cats were collected from four villages in the area, namely, Athol, Gottenburg, Tlhavekisa and Utah. Initially, systematic sampling was envisaged by sampling households in every second street of these villages. However, due to the lack of availability of informal farmers (household owners), pet owners (household owners) and the targeted livestock and pets in the villages, opportunistic sampling was performed from eligible households per street. All household owners who had informal farms or were pet owners with the targeted animal species were invited to participate in the study. In participating households, a blood sample was collected from targeted animal species. Furthermore, questionnaires (n =384) were conducted in households in the four villages. The questionnaire focused on obtaining information regarding the socio-environmental and husbandry conditions per household as well as knowledge about Toxoplasma. To detect anti-<i>T. gondii</i> antibodies, the MAST® Toxoreagent™ ID rapid latex agglutination commercial kit (Mast Group Ltd., United Kingdom) was used following the manufacturer’s instructions. <br>
DOI: 10.6084/m9.figshare.12671522
title: Additional file 1 of LINC00667/miR-449b-5p/YY1 axis promotes cell proliferation and migration in colorectal cancer

description: Additional file 1: Table S1. Ct value for GAPDH and LINC00667.
DOI: 10.6084/m9.figshare.7428536
title: Additional file 5: of NmeCas9 is an intrinsically high-fidelity genome-editing platform

description: Table S9. Plasmids used in this study (including sequences of synthetic oligonucleotides that were used for sgRNA guide sequence cloning), and primer sequences used for analysis of editing at the corresponding genomic sites by T7E1 and TIDE analyses). (XLSX 30 kb)
DOI: 10.6084/m9.figshare.7428536.v1
title: Additional file 5: of NmeCas9 is an intrinsically high-fidelity genome-editing platform

description: Table S9. Plasmids used in this study (including sequences of synthetic oligonucleotides that were used for sgRNA guide sequence cloning), and primer sequences used for analysis of editing at the corresponding genomic sites by T7E1 and TIDE analyses). (XLSX 30 kb)
DOI: 10.6084/m9.figshare.7428599.v1
title: Additional file 8: of NmeCas9 is an intrinsically high-fidelity genome-editing platform

description: Table S8. Primer sequences used for on- and off-target deep sequencing analysis for all genomic editing sites analyzed by SITE-Seq. (XLSX 48 kb)
DOI: 10.6084/m9.figshare.12671545
title: Additional file 6 of Dynamic light caused less photosynthetic suppression, rather than more, under nitrogen deficit conditions than under sufficient nitrogen supply conditions in soybean

description: Additional file 6. raw data of Fig. 1-5 and Fig. S1-S4.
DOI: 10.6084/m9.figshare.12671545.v1
title: Additional file 6 of Dynamic light caused less photosynthetic suppression, rather than more, under nitrogen deficit conditions than under sufficient nitrogen supply conditions in soybean

description: Additional file 6. raw data of Fig. 1-5 and Fig. S1-S4.
DOI: 10.6084/m9.figshare.12671552
title: Additional file 1 of Integrating RNA-Seq with GWAS reveals novel insights into the molecular mechanism underpinning ketosis in cattle

description: Additional file 1: Table S1. Summary of RNA-Seq data mapping information.
DOI: 10.6084/m9.figshare.20004761.v1
title: Additional file 1 of The histone deacetylase HOS2 controls pathogenicity through regulation of melanin biosynthesis and appressorium formation in Colletotrichum gloeosporioides

description: Additional file 1: Table S1. Nucleotide and deduced amino acid sequences of CgHOS2. Table S2. RNA-seq results. Table S3. Primers used in this study.