cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.28408044.v1
title: Generation of cynomolgus monkey capsid-specific positive control cells for IFNγ ELISpot assays for adeno-associated gene therapy applications

description: Cell-mediated immune (CMI) responses to adeno-associated virus (AAV) can lead to tissue damage and loss of therapeutic transgene expression. Identifying robust biomarkers and mechanisms of CMI can aid clinical practice and advancement of AAV gene therapies. The present work evaluated peripheral blood mononuclear cells (PBMC) from non-human primates (NHP) before and after immunization with adenovirus 5 encoding AAV9 capsid antigen. PBMC were stimulated <i>ex vivo</i> with AAV9 capsid peptides to evaluate CMI responses by interferon (IFN)-γ ELISpot, intracellular cytokines/activation markers, secreted cytokines, and RNAseq. AAV peptide stimulation produced a robust IFNγ ELISpot 11 days after immunization and ≈ 4 years after cryopreservation. Flow cytometry revealed increased IFNγ, interleukin (IL)-2, or tumor necrosis factor (TNF)-positive T-cells. Increases in secreted CXCR3 ligands (IP-10, I-TAC) were detected. Robust changes and correlations to ELISpot responses were revealed by RNAseq, including IFNγ, IP-10, and I-TAC, many downstream transcripts, and several IFN-independent pathways. These data from AAV-immunized NHP identify biomarkers that could serve as robust and sensitive supplements/alternatives to ELISpot for early detection of CMI responses. Assessment of these biomarkers in non-clinical and clinical studies is a critical next step to determine the translation of this work to administration of a therapeutic AAV vector.
DOI: 10.6084/m9.figshare.28408093.v1
title: Immunophenotypical characterization of immune checkpoint receptor expression in cynomolgus monkeys and human healthy volunteers in resting and in T-cell stimulatory conditions <i>in vitro</i>

description: Immunotherapeutics targeting immune checkpoint receptors or their ligands (i.e., immune checkpoint inhibitors), have been groundbreaking in the field of oncology, radically changing the approach to treatment and improving the clinical outcomes of an ever-expanding list of solid tumors and hematological malignancies. However, immune checkpoint inhibitors (ICI) are not devoid of side effects, collectively regarded as immune-related adverse events (irAE); they are not easily uncovered in preclinical immunotoxicological investigations and are often due to the very low expression of their targets in immunologically-unchallenged non-clinical species. We have characterized expression of a broad range of immune checkpoint receptors in peripheral blood mononuclear cell (PBMC) subpopulations from cynomolgus monkeys and healthy human volunteers, under resting and T-cell stimulatory conditions by multicolor flow cytometry to inform appropriate species selection for modeling potential irAE in immunotherapeutic preclinical research. Focusing on the response of the main lymphocyte populations to interleukin (IL)-2 alone, or in combination with anti-CD3 and anti-CD28 antibodies, checkpoints with shared similarities and key differences between the two species were identified. The results of this first study provide a database for the expression and response to stimulation for immune checkpoint receptors and can help guide future model selection in the design of preclinical studies involving immunotherapeutics directed against these targets.
DOI: 10.6084/m9.figshare.28596600
title: Insight into the role of DNA methylation in prognosis and treatment response prediction of gastrointestinal cancers

description: Gastrointestinal (GI) cancers impose a significant disease burden, underscoring the critical importance of accurate prognosis prediction and treatment response evaluation. DNA methylation, one of the most extensively studied epigenetic modifications, has gained prominence due to its reliable measurement across various sample types. Numerous studies have reported that DNA methylation was linked to the diagnosis, prognosis and treatment response in malignancies, including GI cancers. While its diagnostic role in GI cancers has been comprehensively reviewed. Recent research has increasingly highlighted its potential in prognosis prediction and treatment response evaluation. However, no existing reviews have exclusively focused on these two aspects. In this review, we retrieved relevant studies and included 230 of them in our discussion, thereby providing an overview of the clinical applicability of aberrant DNA methylation in these two fields among patients with esophageal, gastric, colorectal, pancreatic cancers, and hepatocellular carcinomas. Additionally, we discuss the limitations of the current literature and propose directions for future research. Specifically, we emphasize the need for standardized DNA methylation methodologies and advocate for the integration of gene panels, rather than single genes, to address tumor heterogeneity more effectively.
DOI: 10.6084/m9.figshare.28596600.v1
title: Insight into the role of DNA methylation in prognosis and treatment response prediction of gastrointestinal cancers

description: Gastrointestinal (GI) cancers impose a significant disease burden, underscoring the critical importance of accurate prognosis prediction and treatment response evaluation. DNA methylation, one of the most extensively studied epigenetic modifications, has gained prominence due to its reliable measurement across various sample types. Numerous studies have reported that DNA methylation was linked to the diagnosis, prognosis and treatment response in malignancies, including GI cancers. While its diagnostic role in GI cancers has been comprehensively reviewed. Recent research has increasingly highlighted its potential in prognosis prediction and treatment response evaluation. However, no existing reviews have exclusively focused on these two aspects. In this review, we retrieved relevant studies and included 230 of them in our discussion, thereby providing an overview of the clinical applicability of aberrant DNA methylation in these two fields among patients with esophageal, gastric, colorectal, pancreatic cancers, and hepatocellular carcinomas. Additionally, we discuss the limitations of the current literature and propose directions for future research. Specifically, we emphasize the need for standardized DNA methylation methodologies and advocate for the integration of gene panels, rather than single genes, to address tumor heterogeneity more effectively.
DOI: 10.6084/m9.figshare.29041013
title: tRF5–22-SerGCT-1 protects the heart against myocardial injury by targeting MSK1

description: This study aims to explore the expression profiles and potential functions of tsRNAs in MI. Using a mouse model of MI induced by coronary artery ligation, we used smallRNA array to obtain tsRNAs expression profiles. Reverse transcription quantitative polymerase chain reaction(RT-qPCR), Western Blot, tRF5–22-SerGCT-1 mimics and inhibitors, cell proliferation and apoptosis detection, luciferase reporter assay, and bioinformatics analysis were employed to screen differentially expressed tsRNAs and identify the functions of tsRNAs after MI. A total of 175 significantly different tsRNAs (FC &gt; 1.5, <i>p</i> &lt; 0.05) were identified in MI mice, including 98 upregulated and 77 downregulated tsRNAs. Bioinformatics and target gene prediction revealed that two differentially expressed tsRNAs (5‘tiRNA-34-GlnCTG-4, tRF5–22-SerGCT-1) may be involved in processes like autophagy and apoptosis, as well as in key signaling pathways such as MAPK and autophagy. Further investigation of tRF5–22-SerGCT-1 revealed that its overexpression or inhibition in vitro affected MSK1 levels and cardiomyocytes apoptosis following oxygen–glucose deprivation, providing a protective effect. Dual-luciferase assays confirmed that tRF5–22-SerGCT-1 targets MSK1. We found differentially expressed tsRNAs in MI. In addition, our research showed first that tRF5–22-SerGCT-1 might be involved in the MAPK pathways by targeting the MSK1, modulating apoptosis.
DOI: 10.6084/m9.figshare.29041013.v1
title: tRF5–22-SerGCT-1 protects the heart against myocardial injury by targeting MSK1

description: This study aims to explore the expression profiles and potential functions of tsRNAs in MI. Using a mouse model of MI induced by coronary artery ligation, we used smallRNA array to obtain tsRNAs expression profiles. Reverse transcription quantitative polymerase chain reaction(RT-qPCR), Western Blot, tRF5–22-SerGCT-1 mimics and inhibitors, cell proliferation and apoptosis detection, luciferase reporter assay, and bioinformatics analysis were employed to screen differentially expressed tsRNAs and identify the functions of tsRNAs after MI. A total of 175 significantly different tsRNAs (FC &gt; 1.5, <i>p</i> &lt; 0.05) were identified in MI mice, including 98 upregulated and 77 downregulated tsRNAs. Bioinformatics and target gene prediction revealed that two differentially expressed tsRNAs (5‘tiRNA-34-GlnCTG-4, tRF5–22-SerGCT-1) may be involved in processes like autophagy and apoptosis, as well as in key signaling pathways such as MAPK and autophagy. Further investigation of tRF5–22-SerGCT-1 revealed that its overexpression or inhibition in vitro affected MSK1 levels and cardiomyocytes apoptosis following oxygen–glucose deprivation, providing a protective effect. Dual-luciferase assays confirmed that tRF5–22-SerGCT-1 targets MSK1. We found differentially expressed tsRNAs in MI. In addition, our research showed first that tRF5–22-SerGCT-1 might be involved in the MAPK pathways by targeting the MSK1, modulating apoptosis.
DOI: 10.15468/dl.pv53eb
title: Occurrence Download

description: A dataset containing 1450 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Miconia racemosa"
 ]
}

 The dataset includes 1450 records from 87 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0002307-260120142942310/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.6084/m9.figshare.26181888
title: Association of self-esteem and school connectedness with substance use among street children in southwestern Nigeria

description: The study aimed to determine the relationship between substance use, self-esteem and school connectedness among street children in southwestern Nigeria. A cross-sectional survey of 358 street children in Oyo State Nigeria, was carried out. Data was collected using a semi-structured questionnaire. Appropriate scoring systems were used to assess the degree of self-esteem and school connectedness. The 50<sup>th</sup> centile was used as the cutoff point to define good self-esteem and school connectedness. Participants were aged 9–17 years, with a mean age of 16.2 ± 1.3 years; 208 (58.1%) were males. More than three-quarters (77.9%) had used psychoactive substances at some point in their lives, with local (herbal) psychoactive substances being the most frequent, followed by central nervous system depressants. One hundred and eighty (50.3%) of them were currently using psychoactive substances. The females had better self-esteem and school connectedness compared with the males, whereas substance use was more prevalent among the males. Good school connectedness was associated with lower use of psychoactive substances, but good self-esteem was associated only with reduced use of inhalants. Promoting good school connectedness among street children may help in reducing the use of psychoactive substances among them.
DOI: 10.6084/m9.figshare.26181888.v1
title: Association of self-esteem and school connectedness with substance use among street children in southwestern Nigeria

description: The study aimed to determine the relationship between substance use, self-esteem and school connectedness among street children in southwestern Nigeria. A cross-sectional survey of 358 street children in Oyo State Nigeria, was carried out. Data was collected using a semi-structured questionnaire. Appropriate scoring systems were used to assess the degree of self-esteem and school connectedness. The 50<sup>th</sup> centile was used as the cutoff point to define good self-esteem and school connectedness. Participants were aged 9–17 years, with a mean age of 16.2 ± 1.3 years; 208 (58.1%) were males. More than three-quarters (77.9%) had used psychoactive substances at some point in their lives, with local (herbal) psychoactive substances being the most frequent, followed by central nervous system depressants. One hundred and eighty (50.3%) of them were currently using psychoactive substances. The females had better self-esteem and school connectedness compared with the males, whereas substance use was more prevalent among the males. Good school connectedness was associated with lower use of psychoactive substances, but good self-esteem was associated only with reduced use of inhalants. Promoting good school connectedness among street children may help in reducing the use of psychoactive substances among them.
DOI: 10.5517/cc6d36w
title: CCDC 190377: Experimental Crystal Structure Determination

description: Related Article: F.Chalier, P.Tordo|2002|J.Chem.Soc.,Perkin Trans.2||2110|doi:10.1039/b206909c
description: An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
DOI: 10.6084/m9.figshare.27237726
title: The effects of emotional expressivity and self-efficacy levels of individuals with substance addiction on treatment compliance

description: The present study was conducted to determine the effects of emotional expressivity and self-efficacy levels of individuals with substance addiction on treatment compliance. A total of 183 patients who were receiving substance addiction treatment were included in this cross-sectional study. The data were collected by using the Personal Information Form, EmotionalExpressivity Scale (EES), Self-Efficacy Scale (SES), and Treatment Compliance Scale (TCS). In the present study, the emotional expressivity total score average of the participants was found to be 26.53 ± 9.03, their self-efficacy/sufficiency total score average was 74.15 ± 14.84, and their treatment compliance total score average was 85.27 ± 17.25. A negative and significant relationship was detected between the TCS total score and the EES total score of the participants, and there was a positive and significant relationship with the SES total score average (<i>p</i> &lt; .05). When the total scores that were received from the scales were evaluated, the participants’ emotional expressivity scores, self-efficacy perceptions, and treatment compliance were at moderate levels. It was concluded that as the level of emotional expressivity decreased, the treatment motivation levels of the individuals increased and the increase in the self-efficacy levels was a factor that boosted individuals’ treatment compliance. Reducing emotional expression increases patients’ compliance with treatment.Patients with high self-efficacy levels also have high treatment compliance.Self-efficacy and treatment compliance levels of patients with substance addiction were found to be at moderate levels. Reducing emotional expression increases patients’ compliance with treatment. Patients with high self-efficacy levels also have high treatment compliance. Self-efficacy and treatment compliance levels of patients with substance addiction were found to be at moderate levels.
DOI: 10.6084/m9.figshare.27237726.v3
title: The effects of emotional expressivity and self-efficacy levels of individuals with substance addiction on treatment compliance

description: The present study was conducted to determine the effects of emotional expressivity and self-efficacy levels of individuals with substance addiction on treatment compliance. A total of 183 patients who were receiving substance addiction treatment were included in this cross-sectional study. The data were collected by using the Personal Information Form, EmotionalExpressivity Scale (EES), Self-Efficacy Scale (SES), and Treatment Compliance Scale (TCS). In the present study, the emotional expressivity total score average of the participants was found to be 26.53 ± 9.03, their self-efficacy/sufficiency total score average was 74.15 ± 14.84, and their treatment compliance total score average was 85.27 ± 17.25. A negative and significant relationship was detected between the TCS total score and the EES total score of the participants, and there was a positive and significant relationship with the SES total score average (<i>p</i> &lt; .05). When the total scores that were received from the scales were evaluated, the participants’ emotional expressivity scores, self-efficacy perceptions, and treatment compliance were at moderate levels. It was concluded that as the level of emotional expressivity decreased, the treatment motivation levels of the individuals increased and the increase in the self-efficacy levels was a factor that boosted individuals’ treatment compliance. Reducing emotional expression increases patients’ compliance with treatment.Patients with high self-efficacy levels also have high treatment compliance.Self-efficacy and treatment compliance levels of patients with substance addiction were found to be at moderate levels. Reducing emotional expression increases patients’ compliance with treatment. Patients with high self-efficacy levels also have high treatment compliance. Self-efficacy and treatment compliance levels of patients with substance addiction were found to be at moderate levels.
DOI: 10.6084/m9.figshare.25909868
title: Prenatal opioid exposure and the early life epigenome: results from ECHO

description: Prenatal opioid exposure has been associated with adverse child health outcomes. Changes to the epigenome provide a plausible mechanism through which effects may be elicited. We investigated whether prenatal opioid exposure was associated with locus-specific changes in umbilical cord blood DNA methylation (DNAm) and gestational epigenetic age. We leveraged data from the Environmental influences on Child Health Outcomes cohort. Prenatal opioid data was obtained from maternal self-report and/or medical record data. DNAm measures were generated from blood biospecimens collected at birth. Linear regression models tested associations between prenatal maternal opioid exposure and epigenetic outcomes in crude and fully adjusted models. We tested the association between prenatal opioid exposure and cord blood DNAm at 15 CpG sites in 385 (<i>n</i> = 25 exposed, <i>n</i> = 360 unexposed) individuals from three cohorts. We identified a single CpG site (cg14303187) that was nominally associated with prenatal opioid exposure (<i>p</i> = 0.02, β = −0.012; 95% CI, −0.023 to −0.0012). No significant associations between exposure and gestational epigenetic age were found (<i>n</i> = 716 individuals from eight cohorts; <i>n</i> = 29 exposed, <i>n</i> = 687 unexposed). We identified a nominally significant association between prenatal opioid exposure and DNAm at one CpG site. Future studies should continue investigating the effect of this exposure on the epigenome.
DOI: 10.6084/m9.figshare.25909868.v3
title: Prenatal opioid exposure and the early life epigenome: results from ECHO

description: Prenatal opioid exposure has been associated with adverse child health outcomes. Changes to the epigenome provide a plausible mechanism through which effects may be elicited. We investigated whether prenatal opioid exposure was associated with locus-specific changes in umbilical cord blood DNA methylation (DNAm) and gestational epigenetic age. We leveraged data from the Environmental influences on Child Health Outcomes cohort. Prenatal opioid data was obtained from maternal self-report and/or medical record data. DNAm measures were generated from blood biospecimens collected at birth. Linear regression models tested associations between prenatal maternal opioid exposure and epigenetic outcomes in crude and fully adjusted models. We tested the association between prenatal opioid exposure and cord blood DNAm at 15 CpG sites in 385 (<i>n</i> = 25 exposed, <i>n</i> = 360 unexposed) individuals from three cohorts. We identified a single CpG site (cg14303187) that was nominally associated with prenatal opioid exposure (<i>p</i> = 0.02, β = −0.012; 95% CI, −0.023 to −0.0012). No significant associations between exposure and gestational epigenetic age were found (<i>n</i> = 716 individuals from eight cohorts; <i>n</i> = 29 exposed, <i>n</i> = 687 unexposed). We identified a nominally significant association between prenatal opioid exposure and DNAm at one CpG site. Future studies should continue investigating the effect of this exposure on the epigenome.
DOI: 10.6084/m9.figshare.27099132.v1
title: Sex differences in state level prevalence of alcohol use among Black women and men in the United States

description: To investigate differences in alcohol use among Black men and women across U.S. states, using data from the Behavioral Risk Factor Surveillance System. Measured any alcohol use, heavy drinking (i.e., 8+/15+ drinks for women/men in a 7-day period), and binge drinking (i.e., 4+/5+ drinks in one session). Weighted prevalence estimates were age-standardized to the 2000 US population. Binge drinking among Black men in Midwestern states was high, ranging from 40% in Minnesota to 45.8% in Iowa. Black women in Southern states had 6–10% points higher prevalence of heavy drinking than Black men. Drinking prevalence in Southern states was higher than expected, especially among Black women.
DOI: 10.6084/m9.figshare.25909868.v2
title: Prenatal opioid exposure and the early life epigenome: results from ECHO

description: Prenatal opioid exposure has been associated with adverse child health outcomes. Changes to the epigenome provide a plausible mechanism through which effects may be elicited. We investigated whether prenatal opioid exposure was associated with locus-specific changes in umbilical cord blood DNA methylation (DNAm) and gestational epigenetic age. We leveraged data from the Environmental influences on Child Health Outcomes cohort. Prenatal opioid data was obtained from maternal self-report and/or medical record data. DNAm measures were generated from blood biospecimens collected at birth. Linear regression models tested associations between prenatal maternal opioid exposure and epigenetic outcomes in crude and fully adjusted models. We tested the association between prenatal opioid exposure and cord blood DNAm at 15 CpG sites in 385 (<i>n</i> = 25 exposed, <i>n</i> = 360 unexposed) individuals from three cohorts. We identified a single CpG site (cg14303187) that was nominally associated with prenatal opioid exposure (<i>p</i> = 0.02, β = −0.012; 95% CI, −0.023 to −0.0012). No significant associations between exposure and gestational epigenetic age were found (<i>n</i> = 716 individuals from eight cohorts; <i>n</i> = 29 exposed, <i>n</i> = 687 unexposed). We identified a nominally significant association between prenatal opioid exposure and DNAm at one CpG site. Future studies should continue investigating the effect of this exposure on the epigenome.