cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.13082059.v1
title: The SWI/SNF ATPase BRG1 stimulates DNA end resection and homologous recombination by reducing nucleosome density at DNA double strand breaks and by promoting the recruitment of the CtIP nuclease

description: DNA double strand breaks (DSBs) are among the most toxic DNA lesions and can be repaired accurately through homologous recombination (HR). HR requires processing of the DNA ends by nucleases (DNA end resection) in order to generate the required single-stranded DNA (ssDNA) regions. The SWI/SNF chromatin remodelers are 10–15 subunit complexes that contain one ATPase (BRG1 or BRM). Multiple subunits of these complexes have recently been identified as a novel family of tumor suppressors. These complexes are capable of remodeling chromatin by pushing nucleosomes along the DNA. More recent studies have identified these chromatin remodelers as important factors in DNA repair. Using the DR-U2OS reporter system, we show that the down regulation of BRG1 significantly reduces HR efficiency, while BRM has a minor effect. Inactivation of BRG1 impairs DSB repair and results in a defect in DNA end resection, as measured by the amount of BrdU-containing ssDNA generated after DNA damage. Inactivation of BRG1 also impairs the activation of the ATR kinase, reduces the levels of chromatin-bound RPA, and reduces the number of RPA and RAD51 foci after DNA damage. This defect in DNA end resection is explained by the defective recruitment of GFP-CtIP to laser-induced DSBs in the absence of BRG1. Importantly, we show that BRG1 reduces nucleosome density at DSBs. Finally, inactivation of BRG1 renders cells sensitive to anti-cancer drugs that induce DSBs. This study identifies BRG1 as an important factor for HR, which suggests that BRG1-mutated cancers have a DNA repair vulnerability that can be exploited therapeutically.
DOI: 10.6084/m9.figshare.13082059
title: The SWI/SNF ATPase BRG1 stimulates DNA end resection and homologous recombination by reducing nucleosome density at DNA double strand breaks and by promoting the recruitment of the CtIP nuclease

description: DNA double strand breaks (DSBs) are among the most toxic DNA lesions and can be repaired accurately through homologous recombination (HR). HR requires processing of the DNA ends by nucleases (DNA end resection) in order to generate the required single-stranded DNA (ssDNA) regions. The SWI/SNF chromatin remodelers are 10–15 subunit complexes that contain one ATPase (BRG1 or BRM). Multiple subunits of these complexes have recently been identified as a novel family of tumor suppressors. These complexes are capable of remodeling chromatin by pushing nucleosomes along the DNA. More recent studies have identified these chromatin remodelers as important factors in DNA repair. Using the DR-U2OS reporter system, we show that the down regulation of BRG1 significantly reduces HR efficiency, while BRM has a minor effect. Inactivation of BRG1 impairs DSB repair and results in a defect in DNA end resection, as measured by the amount of BrdU-containing ssDNA generated after DNA damage. Inactivation of BRG1 also impairs the activation of the ATR kinase, reduces the levels of chromatin-bound RPA, and reduces the number of RPA and RAD51 foci after DNA damage. This defect in DNA end resection is explained by the defective recruitment of GFP-CtIP to laser-induced DSBs in the absence of BRG1. Importantly, we show that BRG1 reduces nucleosome density at DSBs. Finally, inactivation of BRG1 renders cells sensitive to anti-cancer drugs that induce DSBs. This study identifies BRG1 as an important factor for HR, which suggests that BRG1-mutated cancers have a DNA repair vulnerability that can be exploited therapeutically.
DOI: 10.6084/m9.figshare.9947696
title: RETRACTED ARTICLE: Long non-coding RNA <i>SNHG4</i> promotes cervical cancer progression through regulating c-Met via targeting miR-148a-3p

description: We, the Editors and Publisher of the journal <i>Cell Cycle</i>, have retracted the following article: Hanchen Li, Jiang Hong and Walimuni Sandaroo Mendis Abeysekara Wijayakulathilaka. Long non-coding RNA SNHG4 promotes cervical cancer progression through regulating c-Met via targeting miR-148a-3p. Cell Cycle. 2019;18(23):3313-3324. doi: 10.1080/15384101.2019.1674071 Since publication, significant concerns have been raised about the integrity of the data and reported results in the article. When approached for an explanation, the authors did not provide their original data or any necessary supporting information. As verifying the validity of published work is core to the integrity of the scholarly record, we are therefore retracting the article. The corresponding author listed in this publication has been informed. We have been informed in our decision-making by our policy on publishing ethics and integrity and the COPE guidelines on retractions. The retracted article will remain online to maintain the scholarly record, but it will be digitally watermarked on each page as ‘Retracted’.
DOI: 10.6084/m9.figshare.13134837.v1
title: LncRNA GAS5/miR‑4465 axis regulates the malignant potential of nasopharyngeal carcinoma by targeting COX2

description: Nasopharyngeal carcinoma is a malignant tumor that not only negatively affects the physical and mental health but also the quality of life of the patients. Growth arrest-specific transcript 5 (GAS5) is a common long-chain non-coding RNA (lncRNA) that has been reported to participate in the development of various cancers. However, the biological functions of lncRNA GAS5 in the occurrence and development of nasopharyngeal carcinoma are elusive. The expression of lncRNA GAS5 in nasopharyngeal carcinoma and normal samples were analyzed. Bioinformatic tool was utilized to predict the potential function of lncRNA in nasopharyngeal carcinoma. Transplanted mice were used for in vivo experiments. We observed that the expression of lncRNA GAS5 was upregulated in nasopharyngeal carcinoma tissues and cells. Down-regulation of lncRNA GAS5 inhibited the proliferation and promoted apoptosis of nasopharyngeal carcinoma cells. The expression of miR–4465 was down regulated in nasopharyngeal carcinoma tissues and cells. LncRNA GAS5 could directly bind to miR–4465 and regulated the expression of miR–4465. It was further confirmed that miR–4465 could directly bind with COX2 and inhibit the expression of COX2. Down-regulation of lncRNA GAS5 suppressed tumor growth, promoted the expression levels of miR–18a–5p and suppressed the expression of COX2 in vivo. LncRNA GAS5 regulated nasopharyngeal carcinoma malignancy through targeting miR–4465 and modulating COX2. The GAS5/miR–4465/COX2 axis in nasopharyngeal carcinoma pathogenesis was confirmed, which would provide a new therapeutic target for nasopharyngeal carcinoma.
DOI: 10.6084/m9.figshare.13168167
title: Single-cell analysis of copy-number alterations in serous ovarian cancer reveals substantial heterogeneity in both low- and high-grade tumors

description: Unusually high aneuploidy is a hallmark of epithelial serous ovarian cancer (SOC). Previous analyses have focused on aneuploidy on average across all tumor cells. With the expansion of single-cell sequencing technologies, however, an analysis of copy number heterogeneity cell-to-cell is now technically feasible. Here, we describe an analysis of single-cell RNA sequencing (scRNA-seq) data to infer arm-level aneuploidy in individual serous ovarian cancer cells. By first clustering high-quality sequenced epithelial versus non-epithelial cells, high-confidence tumor cell populations were identified. InferCNV was used to predict segmented copy-number alterations (CNAs), which were then used to determine arm-level aneuploidy at the single-cell level. Control comparisons of normal cells to normal cells showed zero arm-level aneuploidy, whereas a median of four aneuploid events were detectable in cancer cells. A heterogeneity analysis of high-grade tumor cells compared to low-grade tumor cells showed similar levels of cell-to-cell variation between cancer grades. Metastatic tumors potentially showed selection pressure with reduced cell-to-cell variation compared to cells from primary tumors. Minor cell populations with CNAs similar to metastatic cells were identified within the matched primary tumors. Taken together, these results provide a minimum estimate for single-cell aneuploidy in serous ovarian cancer and demonstrate the utility of single-cell sequencing for CNA analysis.
DOI: 10.6084/m9.figshare.13168167.v1
title: Single-cell analysis of copy-number alterations in serous ovarian cancer reveals substantial heterogeneity in both low- and high-grade tumors

description: Unusually high aneuploidy is a hallmark of epithelial serous ovarian cancer (SOC). Previous analyses have focused on aneuploidy on average across all tumor cells. With the expansion of single-cell sequencing technologies, however, an analysis of copy number heterogeneity cell-to-cell is now technically feasible. Here, we describe an analysis of single-cell RNA sequencing (scRNA-seq) data to infer arm-level aneuploidy in individual serous ovarian cancer cells. By first clustering high-quality sequenced epithelial versus non-epithelial cells, high-confidence tumor cell populations were identified. InferCNV was used to predict segmented copy-number alterations (CNAs), which were then used to determine arm-level aneuploidy at the single-cell level. Control comparisons of normal cells to normal cells showed zero arm-level aneuploidy, whereas a median of four aneuploid events were detectable in cancer cells. A heterogeneity analysis of high-grade tumor cells compared to low-grade tumor cells showed similar levels of cell-to-cell variation between cancer grades. Metastatic tumors potentially showed selection pressure with reduced cell-to-cell variation compared to cells from primary tumors. Minor cell populations with CNAs similar to metastatic cells were identified within the matched primary tumors. Taken together, these results provide a minimum estimate for single-cell aneuploidy in serous ovarian cancer and demonstrate the utility of single-cell sequencing for CNA analysis.
DOI: 10.6084/m9.figshare.9947696.v4
title: RETRACTED ARTICLE: Long non-coding RNA <i>SNHG4</i> promotes cervical cancer progression through regulating c-Met via targeting miR-148a-3p

description: We, the Editors and Publisher of the journal <i>Cell Cycle</i>, have retracted the following article: Hanchen Li, Jiang Hong and Walimuni Sandaroo Mendis Abeysekara Wijayakulathilaka. Long non-coding RNA SNHG4 promotes cervical cancer progression through regulating c-Met via targeting miR-148a-3p. Cell Cycle. 2019;18(23):3313-3324. doi: 10.1080/15384101.2019.1674071 Since publication, significant concerns have been raised about the integrity of the data and reported results in the article. When approached for an explanation, the authors did not provide their original data or any necessary supporting information. As verifying the validity of published work is core to the integrity of the scholarly record, we are therefore retracting the article. The corresponding author listed in this publication has been informed. We have been informed in our decision-making by our policy on publishing ethics and integrity and the COPE guidelines on retractions. The retracted article will remain online to maintain the scholarly record, but it will be digitally watermarked on each page as ‘Retracted’.
DOI: 10.6084/m9.figshare.23197985
title: Source data and uncropped blots corresponding to "Sympathetic tone dictates the impact of lipolysis on FABP4 secretion"

description: Source data and uncropped blots corresponding to article: Prentice KJ, Lee A, Cedillo P, Inouye KE, Ertunc ME, Riveros JK, Lee GY, Hotamisligil GS. Sympathetic tone dictates the impact of lipolysis on FABP4 secretion. J Lipid Res. 2023 May 10:100386. doi: 10.1016/j.jlr.2023.100386. Epub ahead of print. PMID: 37172691
DOI: 10.6084/m9.figshare.13168165
title: Silencing miR-125b-5p attenuates inflammatory response and apoptosis inhibition in mycobacterium tuberculosis-infected human macrophages by targeting DNA damage-regulated autophagy modulator 2 (DRAM2)

description: Tuberculosis is one of the most important infectious diseases worldwide and macrophage apoptosis is the major host defense mechanism against TB. We attempted to characterize the role of miRNA (miR)-125b-5p on mycobacterium tuberculosis (Mtb) infection and macrophages behaviors <i>in vitro</i>. According to fluorescence-activated cell separation (FACS), primary monocytes (CD14<sup>+</sup>) in TB patients were accumulated, and apoptotic monocytes were decreased. Peripheral blood mononuclear cells (PBMCs)-derived macrophages (MDMs) and monocytic cells THP-1-derived macrophage-like cells (TDMs) <i>in vitro</i> were used to be infected with H37Rv. After infection, colony-forming units assay revealed the increase of bacterial activity, FACS demonstrated the decrease of apoptosis rate of MDMs and TDMs, as well as promoted levels of IL-6, TNF-α, Bax, and Bim and suppressed levels of IL-10 and Bcl-2, examined by enzyme-linked immunosorbent assay (ELISA) and western blot assay. Expression of miR-125b-5p and DNA damage-regulated autophagy modulator 2 (DRAM2) was examined, and real-time PCR and western blot assay showed that miR-125b-5p was upregulated, whereas DRAM2 was downregulated in primary monocytes and H37Rv-infected macrophages (MDMs and TDMs). Moreover, blocking miR-125b-5p could attenuated H37Rv-induced bacterial activity and inflammatory response of MDMs and TDMs, accompanied with apoptosis inhibition. Whereas these effects of miR-125b-5p knockdown were abolished by downregulating DRAM2. In mechanism, DRAM2 was a downstream target of miR-125b-5p, as evidenced by dual-luciferase reporter assay. Collectively, silencing miR-125b-5p could protect human macrophages against Mtb infection through promoting apoptosis and inhibiting inflammatory response via targeting DRAM2, suggesting a novel target for Mtb eliminating. <b>Abbreviations:</b> TB: tuberculosis; PBMCs: peripheral blood mononuclear cells; Mtb: mycobacterium tuberculosis; AFB: acid fast bacilli; FITC: fluorescein isothiocyanate; MDMs: monocytes-derived macrophages; TDMs: THP-1-derived macrophage-like cells; ERFP: Mtb-enhanced red fluorescent protein; CFU: colony-forming units; ELISA: enzyme-linked immunosorbent assay; FACS: fluorescence-activated cell separation; PI: propidium iodide; DRAM2: DNA damage-regulated autophagy modulator 2; Real-time PCR: real-time polymerase chain reaction; in-miR-125b-5p: miR-125b-5p inhibitor; si-DRAM2: siRNA against DRAM2
DOI: 10.6084/m9.figshare.13168165.v1
title: Silencing miR-125b-5p attenuates inflammatory response and apoptosis inhibition in mycobacterium tuberculosis-infected human macrophages by targeting DNA damage-regulated autophagy modulator 2 (DRAM2)

description: Tuberculosis is one of the most important infectious diseases worldwide and macrophage apoptosis is the major host defense mechanism against TB. We attempted to characterize the role of miRNA (miR)-125b-5p on mycobacterium tuberculosis (Mtb) infection and macrophages behaviors <i>in vitro</i>. According to fluorescence-activated cell separation (FACS), primary monocytes (CD14<sup>+</sup>) in TB patients were accumulated, and apoptotic monocytes were decreased. Peripheral blood mononuclear cells (PBMCs)-derived macrophages (MDMs) and monocytic cells THP-1-derived macrophage-like cells (TDMs) <i>in vitro</i> were used to be infected with H37Rv. After infection, colony-forming units assay revealed the increase of bacterial activity, FACS demonstrated the decrease of apoptosis rate of MDMs and TDMs, as well as promoted levels of IL-6, TNF-α, Bax, and Bim and suppressed levels of IL-10 and Bcl-2, examined by enzyme-linked immunosorbent assay (ELISA) and western blot assay. Expression of miR-125b-5p and DNA damage-regulated autophagy modulator 2 (DRAM2) was examined, and real-time PCR and western blot assay showed that miR-125b-5p was upregulated, whereas DRAM2 was downregulated in primary monocytes and H37Rv-infected macrophages (MDMs and TDMs). Moreover, blocking miR-125b-5p could attenuated H37Rv-induced bacterial activity and inflammatory response of MDMs and TDMs, accompanied with apoptosis inhibition. Whereas these effects of miR-125b-5p knockdown were abolished by downregulating DRAM2. In mechanism, DRAM2 was a downstream target of miR-125b-5p, as evidenced by dual-luciferase reporter assay. Collectively, silencing miR-125b-5p could protect human macrophages against Mtb infection through promoting apoptosis and inhibiting inflammatory response via targeting DRAM2, suggesting a novel target for Mtb eliminating. <b>Abbreviations:</b> TB: tuberculosis; PBMCs: peripheral blood mononuclear cells; Mtb: mycobacterium tuberculosis; AFB: acid fast bacilli; FITC: fluorescein isothiocyanate; MDMs: monocytes-derived macrophages; TDMs: THP-1-derived macrophage-like cells; ERFP: Mtb-enhanced red fluorescent protein; CFU: colony-forming units; ELISA: enzyme-linked immunosorbent assay; FACS: fluorescence-activated cell separation; PI: propidium iodide; DRAM2: DNA damage-regulated autophagy modulator 2; Real-time PCR: real-time polymerase chain reaction; in-miR-125b-5p: miR-125b-5p inhibitor; si-DRAM2: siRNA against DRAM2
DOI: 10.6084/m9.figshare.9947696.v3
title: Long non-coding RNA <i>SNHG4</i> promotes cervical cancer progression through regulating c-Met via targeting miR-148a-3p

description: Long non-coding RNA (lncRNA) <i>SNHG4</i> has been shown to be associated with the development of a variety of cancers. The purpose of this study was to investigate the effect of <i>SNHG4</i> on cervical cancer (CC) and the corresponding mechanism. The qRT-PCR was used to determine the expressions of SNHG4 and <i>miR-148a-3p</i> in CC cell lines and tissues. Cell apoptosis and proliferation were measured by flow cytometry and MTT assay, respectively. The interaction between SNHG4, <i>miR-148a-3p</i> and <i>c-Met</i> was verified by bioinformatics, dual-luciferase reporter gene and RNA immunoprecipitation (RIP), and the effect of <i>SNHG4</i> on the growth of CC tumor <i>in vivo</i> was explored. The expression of <i>SNHG4</i> was increased in both CC cell lines and tissues, while the expression of <i>miR-148a-3p</i> was down-regulated. Meanwhile, silencing SNHG4 remarkably inhibited CC cell proliferation and promoted apoptosis. In addition, miR-148a-3p was a direct target gene of <i>SNHG4</i>, and down-regulation of miR-148a-3p could observably reverse the effect of silencing <i>SNHG4</i> on the proliferation and apoptosis of CC cells. More importantly, <i>SNHG4</i> could up-regulate the expression of <i>c-Met</i> by targeting and interacting with <i>miR-148a-3p</i>. Finally, <i>in vivo</i> experiments confirmed that silence SNHG4 down-regulated the expression of <i>c-Met</i> by promoting <i>miR-148a-3p</i>, and ultimately suppressed the growth of CC tumor <i>in vivo</i>. In conclusion, <i>SNHG4</i> could be used as a competitive endogenous RNA to bind to miR-148a-3p, thereby up-regulating the expression of <i>c-Met</i> and ultimately promoting the progression of CC, which provided a potential therapeutic target for the targeted treatment of CC.
DOI: 10.5281/zenodo.7971761
title: Supplementary dataset for a talk about russian journals and publishers

description: This supplementary dataset for a talk about Russian journals and publishers in Scopus contains ids and 2020-23 publication counts for ca 700 Russian journals along with data on the share of internationally coauthored publications, and a simple publisher taxonomy.
DOI: 10.5281/zenodo.7971760
title: Supplementary dataset for a talk about russian journals and publishers

description: This supplementary dataset for a talk about Russian journals and publishers in Scopus contains ids and 2020-23 publication counts for ca 700 Russian journals along with data on the share of internationally coauthored publications, and a simple publisher taxonomy.
DOI: 10.5066/p9ljfgw5
title: The Oysters of Chicopit Bay, Florida, 2016-2018

description: This data set was generated to evaluate the status and response of oysters within Chicopit Bay, FL, in the Timucuan Ecological and Historic Preserve during and following dredging completed by the Army Corps of Engineers for the Mile Point Project.� It includes live oyster area estimates from aerial images collected in 2016-2018.
DOI: 10.6084/m9.figshare.20997910
title: Spider and caterpillar abundance, tree size, and canopy closure metrics in a tree diversity experiment

description: This data set includes spider abundances recorded on focal trees in a large-scale forest diversity manipulation at the Smithsonian Environmental Research Center in Edgewater, MD, USA. We repeatedly sampled spiders on 540 trees of 15 species planted in single or mixed species combinations (4 or 12) in June and August of 2019 and 2021. We took caterpillar abundance data, measured tree height, and took canopy closure measurements on each tree in 2021. <br> Data associated with the paper: <strong>Positive tree diversity effects on arboreal spider abundance are tied to canopy cover in a forest experiment</strong> published in Ecology
DOI: 10.7281/t1/awjugz/dvbnix
title: readme.txt

description: A readme file for dry_model_output.zip folder.
DOI: 10.7281/t1/awjugz/c7uglm
title: dry_model_output.zip

description: Dry model output and readme for the paper “Yang et al., (2019), Dependence of Atmospheric Transport into the Arctic on Extent of the Hadley Cell”.
DOI: 10.18128/m130-007.2023-04
title: Sexism-state-abortion access

description: The state-level abortion access measure r eports the proportion of a state's females aged 15-44 who reside in counties with an abortion provider by year and month from 2009-2022.
DOI: 10.5519/qd.wh9w0zmm
title: Query on the Natural History Museum Data Portal (data.nhm.ac.uk) (23 records)
DOI: 10.18128/m130-015.2023-04
title: Politics-state-county presidential results

description: The county presidential election results measure provides the proportion of votes cast for the Democratic candidate (Joseph R. Biden) or the Republican candidate (Donald J. Trump) in the 2020 presidential election.
DOI: 10.18128/m130-014.2023-04
title: Politics-state-state presidential results

description: The state presidential election results measure provides the proportion of votes cast for the Democratic candidate (Joseph R. Biden) or the Republican candidate (Donald J. Trump) in the 2020 presidential election.
DOI: 10.18128/m130-013.2023-04
title: Racism-county-residential segregation-index of dissimilarity

description: Residential segregation measures the physical separation of population groups into different areas (i.e., neighborhoods) in a geographic unit (i.e., a county or city). We report the index of dissmilarity(D) for United States counties in our data file. The index of dissimilarity is a measure of evenness and measures the proportion of a group's population that must move so that each sub-county geographic unit in a county has the same proportion of that group as the county. We use census tracts as our sub-county geographic unit because census tracts nest within counties. D is typically calculated using two population groups. We have computed the index of dissimilarity for the following groups: (1) White alone, not Hispanic or Latino : Black alone, (2) White alone, not Hispanic or Latino : Asian alone, (3) White alone, not Hispanic or Latino : Hispanic or Latino.