cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.20381592.v1
title: Supplementary Material for: Phenotyping and Genotyping of HNA: Prevalence, Risk of Alloimmunization, and HNA Incompatibilities in Indians

description: <b><i>Background:</i></b> Antibodies to human neutrophil alloantigens (HNA) are involved in the pathophysiology of several clinical conditions including transfusion-related acute lung injury (TRALI), alloimmune and autoimmune neutropenia, and febrile nonhemolytic transfusion reactions leading to neutropenia. The cognate antigens are polymorphic structures expressed on several glycoproteins on the neutrophils, i.e., antigens HNA-1a, -1b, -1c, and -1d on Fc-γ-receptor IIIb; HNA-2 on CD177; HNA-3a and -3b on choline transporter-like protein 2; HNA-4a and -4b on CD11b/αM subunit of the αMβ2-integrin (CD11b/CD18, Mac-1, CR3); and HNA-5a and -5b on αL-subunit (CD11a) of the αLβ2 integrin (CD11a/CD18), leukocyte function associated molecule (LFA)-1. Currently, there is a lacuna of diagnostic methods for detection of HNA in India. This study aimed to determine the HNA frequencies in Indians, estimate the risk of alloimmunization, and prepare typed neutrophil panels, which can be used to detect HNA antibodies in neutropenia cases. <b><i>Material and Methods:</i></b> EDTA blood samples were collected from random 1,054 blood donors. HNA-2 was phenotyped on fresh EDTA samples using FITC labelled monoclonal anti-CD177 by flowcytometry. HNA-1 (<i>FCGR3B</i>) genotyping was carried out by DNA sequencing and PCR-RFLP. Antigens of HNA-3 (<i>SLC44A2</i>) and HNA-5 (<i>ITGAL</i>) were genotyped by PCR-RFLP using <i>TaqαI</i> and <i>Bsp1286I</i> restriction enzymes, respectively, while HNA-4 (<i>ITGAM</i>) was genotyped by PCR-SSP. <b><i>Results:</i></b> Allele frequencies of <i>FCGR3B</i>*<i>01</i>, <i>FCGR3B</i>*<i>02</i>, and <i>FCGR3B</i>*<i>03</i> were found to be 0.433, 0.444, and 0.087, respectively. FCGR3B*01+*02+*03− was the most common genotype (33.78%). Ten individuals showed deficiency of FCGR3B individuals, while 23 showed hyperexpression, i.e., <i>FCGR3B</i>*<i>01+</i>*<i>02+</i>*<i>03+</i>. <i>FCGR3B</i>*<i>04</i>and *<i>05</i> occurred with a frequency of 0.002 and 0.024. HNA-2 was found to be a high frequency antigen occurring in 98.8% population. Four percent individuals showed atypical expression of CD177 on their neutrophils. Allele frequencies of <i>SLC44A2</i>*<i>01</i> and <i>SLC44A2</i>*<i>02</i>were 0.812 and 0.188, respectively, and that of <i>ITGAM</i>*<i>01</i>, <i>ITGAM</i>*<i>02</i>, <i>ITGAL</i>*<i>01</i>, and <i>ITGAL</i>*<i>02</i> were 0.9546, 0.0454, 0.2372, and 0.7628, respectively. <b><i>Conclusion:</i></b> This is the first study in India to report the frequencies of HNA among blood donors. Typed neutrophil panels identified in the present study will enable us to investigate suspected cases of immune neutropenia in future.
DOI: 10.6084/m9.figshare.20381604
title: Supplementary Material for: An Electronic Health Record Tool Increases Genetic Counseling Referral of Individuals at Hereditary Cancer Risk: An Intervention Study

description: <b><i>Introduction:</i></b> There is widespread under-identification of individuals at hereditary cancer risk despite national guidelines calling for screening. We evaluated the utilization of a tool embedded in the electronic health record (EHR) to assist primary care providers in screening patients for cancer genetic counseling referral. <b><i>Methods:</i></b> We designed BestPractice Advisories linked to a Genetic Cancer Screening Tool (GCST) in EpicCare Ambulatory. The GCST identifies individuals for evaluation for BRCA1/2, Lynch syndrome, and other risk mutations due to personal and family history. We tested the tool in a 7-week intervention in adult wellness visits at two clinics, one urban and one rural. <b><i>Results:</i></b> Out of 687 eligible patients, the screening survey was completed for 469 (67%), and of these, 150 (32%) screened positive for a personal and/or family history meeting genetic counseling referral criteria. Of individuals screening positive, a referral order was placed for 20 (13%). GCST screen-positive rate varied by patient gender but not race or age. Referral rate varied by provider and clinic but was not significantly affected by patient demographics. In the previous year over an equivalent date range, 0.1% of wellness visits (1 of 1,086) led to a referral, and this rate increased to 2.1% (22 of 1,062) during the intervention. The proportion of providers referring patients also increased, from 3.8% (1 of 26) to 42.3% (11 of 26). <b><i>Discussion/Conclusion:</i></b> Genetic counseling referral of individuals at hereditary cancer risk was increased by use of an EHR-integrated tool. These findings add evidence for the benefit of clinical decision support for cancer genetic risk screening in primary care.
DOI: 10.6084/m9.figshare.20381604.v1
title: Supplementary Material for: An Electronic Health Record Tool Increases Genetic Counseling Referral of Individuals at Hereditary Cancer Risk: An Intervention Study

description: <b><i>Introduction:</i></b> There is widespread under-identification of individuals at hereditary cancer risk despite national guidelines calling for screening. We evaluated the utilization of a tool embedded in the electronic health record (EHR) to assist primary care providers in screening patients for cancer genetic counseling referral. <b><i>Methods:</i></b> We designed BestPractice Advisories linked to a Genetic Cancer Screening Tool (GCST) in EpicCare Ambulatory. The GCST identifies individuals for evaluation for BRCA1/2, Lynch syndrome, and other risk mutations due to personal and family history. We tested the tool in a 7-week intervention in adult wellness visits at two clinics, one urban and one rural. <b><i>Results:</i></b> Out of 687 eligible patients, the screening survey was completed for 469 (67%), and of these, 150 (32%) screened positive for a personal and/or family history meeting genetic counseling referral criteria. Of individuals screening positive, a referral order was placed for 20 (13%). GCST screen-positive rate varied by patient gender but not race or age. Referral rate varied by provider and clinic but was not significantly affected by patient demographics. In the previous year over an equivalent date range, 0.1% of wellness visits (1 of 1,086) led to a referral, and this rate increased to 2.1% (22 of 1,062) during the intervention. The proportion of providers referring patients also increased, from 3.8% (1 of 26) to 42.3% (11 of 26). <b><i>Discussion/Conclusion:</i></b> Genetic counseling referral of individuals at hereditary cancer risk was increased by use of an EHR-integrated tool. These findings add evidence for the benefit of clinical decision support for cancer genetic risk screening in primary care.
DOI: 10.5281/zenodo.6911339
title: Mass spectrometry analysis of DENV-2 Infected HeLa Supernatant

description: II.15 Supernatant harvest for HeLa stimulation experiments HeLa were seeded at a density of 1x10<sup>6</sup> cells in a 75 cm<sup>3</sup> vented flask in complete media and incubated for 24 hr at 37 °C, 5% CO<sub>2</sub>. Following incubation, cells had media removed and were either inoculated with DENV-2 prepared (MOI=1) in 5 mL DMEM or received 5 mL DMEM only, rocking every 15 min for 90 min. Inoculum was then removed and cells received 20 mL of complete media. Cells were left to incubate for 48 hr at 37 °C, 5% CO<sub>2</sub>. Following incubation, cell culture media was harvested, and cells lysed in TRIzol for RT-qPCR to confirm DENV infection. Harvested supernatant was clarified by centrifugation at 2,600 x <em>g </em>for 5 minutes before storing at -80°C. Conditioned media is the term given to the supernatant of cells generated in the absence of DENV-infection. II.16 Sized based fractionation of DENV-infected HeLa supernatant Supernatants were either unfiltered or fractionated into large (&gt;50 kDa) and small (&lt;50 kDa) proteins by Ultra-15, MWCO 50 kDa centrifugal filters (Amicon) for 15 min at RT, at 2,600 x <em>g</em>. Supernatant fractions were then reconstituted to the starting volume (20 mL) in DMEM. II.18 Serum free fractionated supernatant generation and mass spectrometry analysis For mass spectrometry analysis, HeLa were infected in a 75 cm<sup>3</sup> vented flask in the absence of FCS and then had supernatant protein quantitated by BioRad protein assay. 10 μg of protein from supernatants was prepared by Sera-Mag Carboxylate SpeedBeads (Cytiva) clean up as per manufacturer’s instructions to remove contaminating salts and detergents. Protein was then digested using 0.5 μg trypsin gold (Promega Corporation, Alexandria, NSW, Australia) overnight at 37 °C. Peptide clean-up was performed for further salt removal using Sera-Mag Carboxylate SpeedBeads which were then dissociated from peptides as per manufacturer’s instructions in preparation for analysis. Peptides were analysed by the Flinders Proteomics Facility, performed by Dr Alex Colella using Mass spectrometry (TSQ Altis™ Triple Quadrupole Mass Spectrometer, Thermo Scientific) as previously described by Sharma et. al (2009).<sup>223</sup>
DOI: 10.5281/zenodo.6911338
title: Mass spectrometry analysis of DENV-2 Infected HeLa Supernatant

description: II.15 Supernatant harvest for HeLa stimulation experiments HeLa were seeded at a density of 1x10<sup>6</sup> cells in a 75 cm<sup>3</sup> vented flask in complete media and incubated for 24 hr at 37 °C, 5% CO<sub>2</sub>. Following incubation, cells had media removed and were either inoculated with DENV-2 prepared (MOI=1) in 5 mL DMEM or received 5 mL DMEM only, rocking every 15 min for 90 min. Inoculum was then removed and cells received 20 mL of complete media. Cells were left to incubate for 48 hr at 37 °C, 5% CO<sub>2</sub>. Following incubation, cell culture media was harvested, and cells lysed in TRIzol for RT-qPCR to confirm DENV infection. Harvested supernatant was clarified by centrifugation at 2,600 x <em>g </em>for 5 minutes before storing at -80°C. Conditioned media is the term given to the supernatant of cells generated in the absence of DENV-infection. II.16 Sized based fractionation of DENV-infected HeLa supernatant Supernatants were either unfiltered or fractionated into large (&gt;50 kDa) and small (&lt;50 kDa) proteins by Ultra-15, MWCO 50 kDa centrifugal filters (Amicon) for 15 min at RT, at 2,600 x <em>g</em>. Supernatant fractions were then reconstituted to the starting volume (20 mL) in DMEM. II.18 Serum free fractionated supernatant generation and mass spectrometry analysis For mass spectrometry analysis, HeLa were infected in a 75 cm<sup>3</sup> vented flask in the absence of FCS and then had supernatant protein quantitated by BioRad protein assay. 10 μg of protein from supernatants was prepared by Sera-Mag Carboxylate SpeedBeads (Cytiva) clean up as per manufacturer’s instructions to remove contaminating salts and detergents. Protein was then digested using 0.5 μg trypsin gold (Promega Corporation, Alexandria, NSW, Australia) overnight at 37 °C. Peptide clean-up was performed for further salt removal using Sera-Mag Carboxylate SpeedBeads which were then dissociated from peptides as per manufacturer’s instructions in preparation for analysis. Peptides were analysed by the Flinders Proteomics Facility, performed by Dr Alex Colella using Mass spectrometry (TSQ Altis™ Triple Quadrupole Mass Spectrometer, Thermo Scientific) as previously described by Sharma et. al (2009).<sup>223</sup>
DOI: 10.5281/zenodo.6911659
title: CFH and CFHR1-5 predicted TF binding sites

description: TF binding sites for CFH, CFHR1-5 as determined by PROMO (Alggen) for -1100bp to +100bp relative to transcription start site.
DOI: 10.5281/zenodo.6911658
title: CFH and CFHR1-5 predicted TF binding sites

description: TF binding sites for CFH, CFHR1-5 as determined by PROMO (Alggen) for -1100bp to +100bp relative to transcription start site.
DOI: 10.6084/m9.figshare.20381574
title: qualitativeplacesignatures.zip

description: This provides the data and code to support the paper submission of 'Location retrieval using qualitative place signatures of visible landmarks'
DOI: 10.6084/m9.figshare.20381574.v1
title: qualitativeplacesignatures.zip

description: This provides the data and code to support the paper submission of 'Location retrieval using qualitative place signatures of visible landmarks'
DOI: 10.6084/m9.figshare.20381622
title: Research data

description: Research data for the grounded theory developed in the study named "<strong>Building (and breaking) a vicious cycle among extreme working conditions, work intensification and perceived well-being: A study of dirty workers in Brazilian favelas"</strong>
DOI: 10.6084/m9.figshare.20381622.v1
title: Research data

description: Research data for the grounded theory developed in the study named "<strong>Building (and breaking) a vicious cycle among extreme working conditions, work intensification and perceived well-being: A study of dirty workers in Brazilian favelas"</strong>
DOI: 10.6084/m9.figshare.20381646
title: Supplementary table

description: Supplementary table
DOI: 10.6084/m9.figshare.20381646.v1
title: Supplementary table

description: Supplementary table
DOI: 10.6084/m9.figshare.20381637
title: Time-lapse fluorescence intensity plots of the CRY2olig clusters in a specific region

description: The quantification of the time-lapse fluorescence intensity of the marked clusters of a specific region activated by a single Bessel beam.
DOI: 10.6084/m9.figshare.20381637.v1
title: Time-lapse fluorescence intensity plots of the CRY2olig clusters in a specific region

description: The quantification of the time-lapse fluorescence intensity of the marked clusters of a specific region activated by a single Bessel beam.
DOI: 10.6084/m9.figshare.20381697
title: Additional file 2 of A systematic analysis of splicing variants identifies new diagnoses in the 100,000 Genomes Project

description: Additional file 2. Table S1. Prioritised variants.
DOI: 10.6084/m9.figshare.20381697.v1
title: Additional file 2 of A systematic analysis of splicing variants identifies new diagnoses in the 100,000 Genomes Project

description: Additional file 2. Table S1. Prioritised variants.
DOI: 10.6084/m9.figshare.20381700
title: Additional file 3 of A systematic analysis of splicing variants identifies new diagnoses in the 100,000 Genomes Project

description: Additional file 3. Table S2. Candidate variants.
DOI: 10.6084/m9.figshare.20381700.v1
title: Additional file 3 of A systematic analysis of splicing variants identifies new diagnoses in the 100,000 Genomes Project

description: Additional file 3. Table S2. Candidate variants.
DOI: 10.6084/m9.figshare.20381703
title: Additional file 4 of A systematic analysis of splicing variants identifies new diagnoses in the 100,000 Genomes Project

description: Additional file 4. Table S3. Experimentally validated branchpoints.
DOI: 10.6084/m9.figshare.20381703.v1
title: Additional file 4 of A systematic analysis of splicing variants identifies new diagnoses in the 100,000 Genomes Project

description: Additional file 4. Table S3. Experimentally validated branchpoints.
DOI: 10.6084/m9.figshare.20381781.v1
title: Additional file 1 of Microbial ecology of sand fly breeding sites: aging and larval conditioning alter the bacterial community composition of rearing substrates

description: Additional file 1: Dataset S1. Number of reads for each ASV (tab 1) and percent relative abundance of ASVs clustered to level-7 taxonomy, e.g., “species” (tab 2).
DOI: 10.6084/m9.figshare.20381781
title: Additional file 1 of Microbial ecology of sand fly breeding sites: aging and larval conditioning alter the bacterial community composition of rearing substrates

description: Additional file 1: Dataset S1. Number of reads for each ASV (tab 1) and percent relative abundance of ASVs clustered to level-7 taxonomy, e.g., “species” (tab 2).
DOI: 10.5281/zenodo.6908294
title: The rest 5 files of WHUS2-CR

description: The rest 5 files of WHUS2-CR dataset. If you use this dataset for your research, please cite us accordingly: #Reference: [1] J. Li, Z. W, Z. Hu, J. Z, M. Li, L. Mo and M. Molinier, “Thin cloud removal in optical remote sensing images based on generative adversarial networks and physical model of cloud distortion,” ISPRS J. Photogramm. Remote Sens., vol. 166, pp. 373–389, Aug. 2020, doi: 10.1016/j.isprsjprs.2020.06.021. <br> [2] J. Li, Z. Wu, Z. Hu, Z. Li, Y. Wang, and M. Molinier, “Deep learning based thin cloud removal fusing vegetation red edge and short wave infrared spectral information for Sentinel-2A imagery,” Remote Sens., vol. 13, no. 1, p. 157, Jan. 2021, doi: 10.3390/rs13010157.
DOI: 10.6084/m9.figshare.20381820
title: Additional file 2 of Large-scale manipulation of promoter DNA methylation reveals context-specific transcriptional responses and stability

description: Additional file 2: Supplementary Table S1: WGBS stats, S2: Promoter DMRs, S3: Alternative TSS in ZF-D3A-wt, and S4: Alternative TSS in ZF-D3A-mut.
DOI: 10.5281/zenodo.5616752
title: The rest 5 files of WHUS2-CR

description: The rest 5 files of WHUS2-CR dataset. If you use this dataset for your research, please cite us accordingly: #Reference: [1] J. Li, Z. W, Z. Hu, J. Z, M. Li, L. Mo and M. Molinier, “Thin cloud removal in optical remote sensing images based on generative adversarial networks and physical model of cloud distortion,” ISPRS J. Photogramm. Remote Sens., vol. 166, pp. 373–389, Aug. 2020, doi: 10.1016/j.isprsjprs.2020.06.021. <br> [2] J. Li, Z. Wu, Z. Hu, Z. Li, Y. Wang, and M. Molinier, “Deep learning based thin cloud removal fusing vegetation red edge and short wave infrared spectral information for Sentinel-2A imagery,” Remote Sens., vol. 13, no. 1, p. 157, Jan. 2021, doi: 10.3390/rs13010157.
DOI: 10.6084/m9.figshare.20381820.v1
title: Additional file 2 of Large-scale manipulation of promoter DNA methylation reveals context-specific transcriptional responses and stability

description: Additional file 2: Supplementary Table S1: WGBS stats, S2: Promoter DMRs, S3: Alternative TSS in ZF-D3A-wt, and S4: Alternative TSS in ZF-D3A-mut.
DOI: 10.6084/m9.figshare.20381893.v1
title: Additional file 3 of Viral blood-borne infections testing and linkage to care cascade among persons who experience homelessness in the United States: a systematic review and meta-analysis

description: Additional file 3.
DOI: 10.6084/m9.figshare.20381893
title: Additional file 3 of Viral blood-borne infections testing and linkage to care cascade among persons who experience homelessness in the United States: a systematic review and meta-analysis

description: Additional file 3.
DOI: 10.6084/m9.figshare.20381982
title: Additional file 2 of CD26 is a senescence marker associated with reduced immunopotency of human adipose tissue-derived multipotent mesenchymal stromal cells

description: Additional file 2. Excel file with RNA-seq data.
DOI: 10.6084/m9.figshare.20381982.v1
title: Additional file 2 of CD26 is a senescence marker associated with reduced immunopotency of human adipose tissue-derived multipotent mesenchymal stromal cells

description: Additional file 2. Excel file with RNA-seq data.
DOI: 10.6084/m9.figshare.20381985
title: Additional file 1 of Evaluation of an advance care planning training program for practice professionals in Japan incorporating shared decision making skills training: a prospective study of a curricular intervention

description: Additional file 1.
DOI: 10.6084/m9.figshare.20381985.v1
title: Additional file 1 of Evaluation of an advance care planning training program for practice professionals in Japan incorporating shared decision making skills training: a prospective study of a curricular intervention

description: Additional file 1.
DOI: 10.6084/m9.figshare.20382006
title: Additional file 1 of DNA methylation and transcriptomic features are preserved throughout disease recurrence and chemoresistance in high grade serous ovarian cancers

description: Additional file 1: Supplementary Table 1. Clinical features of the cohort. Supplementary Table 2. PostQC sample information. Supplementary Table 3. PMD genome coverage per sample. Supplementary Table 4. PMDs common to ovarian cancer (ovcaPMDs). Supplementary Table 5. Enriched pathways for genes in PMDs. Supplementary Table 6. DMRs from Primary vs Recurrent. Negative values indicate regions hypermethylated in recurrent samples. Supplementary Table 7. DEGs from Primary vs Recurrent. Supplementary Table 8. Genes near Primary vs Recurrent DMRs intersecting DEGs. Supplementary Table 9. DMRs from BC vs NC. Supplementary Table 10. DMRs from BC vs NC (hg19) that overlap 450k probes within 300bp. Supplementary Table 11. DEGs from BC vs NC. Supplementary Table 12. Genes near BC vs NC DMRs intersecting DEGs
DOI: 10.6084/m9.figshare.20382006.v1
title: Additional file 1 of DNA methylation and transcriptomic features are preserved throughout disease recurrence and chemoresistance in high grade serous ovarian cancers

description: Additional file 1: Supplementary Table 1. Clinical features of the cohort. Supplementary Table 2. PostQC sample information. Supplementary Table 3. PMD genome coverage per sample. Supplementary Table 4. PMDs common to ovarian cancer (ovcaPMDs). Supplementary Table 5. Enriched pathways for genes in PMDs. Supplementary Table 6. DMRs from Primary vs Recurrent. Negative values indicate regions hypermethylated in recurrent samples. Supplementary Table 7. DEGs from Primary vs Recurrent. Supplementary Table 8. Genes near Primary vs Recurrent DMRs intersecting DEGs. Supplementary Table 9. DMRs from BC vs NC. Supplementary Table 10. DMRs from BC vs NC (hg19) that overlap 450k probes within 300bp. Supplementary Table 11. DEGs from BC vs NC. Supplementary Table 12. Genes near BC vs NC DMRs intersecting DEGs
DOI: 10.6084/m9.figshare.20382055
title: Additional file 1 of Drug cost avoidance analysis of cancer clinical trials in Spain: a study on cost contributors and their impact

description: Additional file 1: Supplementary Table 1. Sensitivity Analysis
DOI: 10.6084/m9.figshare.20382055.v1
title: Additional file 1 of Drug cost avoidance analysis of cancer clinical trials in Spain: a study on cost contributors and their impact

description: Additional file 1: Supplementary Table 1. Sensitivity Analysis
DOI: 10.6084/m9.figshare.20382057.v1
title: Additional file 5 of Exploring the lncRNA localization landscape within the retinal pigment epithelium under normal and stress conditions

description: Additional file 5: Table S1. Localization changes of lncRNAs expressed in both BXS and BXS-H2O2.
DOI: 10.6084/m9.figshare.20382054.v1
title: Additional file 4 of Exploring the lncRNA localization landscape within the retinal pigment epithelium under normal and stress conditions

description: Additional file 4: Supplementary Figure 4. Analysis of ADAR1 expression and localization. (A) Detection of ADAR1 by western blotting of lysates from ARPE-19 cells that were treated with H2O2 or left untreated. Blot images are cropped for clarity and conciseness. (B) Immunofluorescent staining of ADAR1 in ARPE-19 cells that were treated with H2O2 or left untreated. (C) Immunofluorescent detection of ADAR1-p110 in ARPE-19 cells that were treated with H2O2 or left untreated and that were transfected with either only ZsGreen mRNA (Neg. Control) or ZsGreen mRNA plus ADAR1-p110-Flag mRNA (ADAR1-p110). Successful transfection was visualized by fluorescence of the ZsGreen protein, and ADAR1-p110 expression was visualized via an anti-flag antibody.