bluuebunny/crossref_metadata_2025_split huggingface dataset:
Chemerin as a modulator of angiogenesis and apoptosis processes in the corpus luteum of pigs: an in vitro study
Authors: Rytelewska Edyta , Kiezun Marta , Zaobidna Ewa , Gudelska Marlena , Kisielewska Katarzyna , Dobrzyn Kamil , Kaminski Tadeusz , Smolinska Nina 
Published: June 2021

AbstractThe corpus luteum (CL) undergoes rapid changes, and its functional capabilities are influenced by processes such as angiogenesis and apoptosis. According to the literature, chemerin-a protein that participates in the regulation of energy homeostasis and the immune response, may also affect angiogenesis and apoptosis. Therefore, the aim of this study was to investigate the in vitro effect of chemerin on angiogenesis and apoptosis in porcine luteal cells (Lc) during specific phases related to CL physiology. Luteal cells were harvested from gilts during the early-, mid-, and late-luteal phases of the estrous cycle. The cells were preincubated for 48 h and incubated for 24 h with chemerin or a serum-free medium (controls). The abundance of angiogenesis- and apoptosis-related proteins was determined by enzyme-linked immunosorbent assay (ELISA) in spent culture media, or by ELISA and Western blot in protein extracts. The current study demonstrated that chemerin stimulates the production of vascular endothelial growth factor A (VEGF-A) and basic fibroblast growth factor (bFGF) by porcine Lc and increases the protein abundance of angiogenic factors’ receptors (VEGFR1, VEGFR2, VEGFR3, FGFR1, FGFR2) in these cells. The study also revealed that chemerin exerts a modulatory effect (stimulatory/inhibitory, depending on the phase of the cycle) on the protein abundance of first apoptosis signal (Fas), Fas ligand, B-cell lymphoma 2, and caspase-3 in porcine Lc. These results imply that chemerin may affect angiogenesis and apoptosis processes in the porcine CL, as evidenced by its modulatory effect of chemerin on the protein abundance of crucial angiogenesis- and apoptosis-related factors, observed in an in vitro study of porcine Lc.
Characterization of transcriptional activity during ZGA in mammalian SCNT embryo
Authors: Deng Mingtian , Chen Baobao , Yang Yingnan , Wan Yongjie , Liu Zifei , Fu Jun , Wang Feng 
Published: June 2021

Abstract
Developmental arrest of somatic cell nuclear transfer (SCNT) embryos first occurs at zygotic/embryonic genome activation (ZGA/EGA), which is critical for preimplantation development. However, study on transcriptome of SCNT embryos during ZGA/EGA is limited. In the present study, we performed RNA sequencing (RNA-seq) of the eight-cell SCNT embryos in goat and provide cross-species analysis of transcriptional activity of SCNT embryos during ZGA/EGA in mice, human, bovine, and goat. RNA-seq data revealed 3966 differentially expressed genes (DEGs) failed to be reprogrammed or activated during EGA of SCNT embryos in goat. Series test of cluster analysis showed four clusters of DEGs and similar changes of the clusters in the four species. Specifically, genes in cluster 3 were somehow upregulated compared with the donor cells and the in vitro fertilization embryo. Moreover, the histone methylation key players and N6-methyladenosine modifiers (SUV39H1, SETDB1, SETD2, KDM5B, IGF2BP1, and YTHDF2) were differentially expressed in SCNT embryos of all species. Finally, we identified three modules correlated with the development of SCNT embryos in mice and screened 288 genes (such as BTG4, WEE1, KLF3, and USP21) that are likely critical for SCNT reprogramming using weighted gene correlation network analysis. Our data will broaden the current understanding of transcriptome activity during stochastic reprogramming events and provide an excellent source for future studies.
The potential role of stress and sex steroids in heritable effects of sevoflurane
Authors: Martynyuk Anatoly E , Ju Ling-Sha , Morey Timothy E 
Published: June 2021

Abstract
Most surgical procedures require general anesthesia, which is a reversible deep sedation state lacking all perception. The induction of this state is possible because of complex molecular and neuronal network actions of general anesthetics (GAs) and other pharmacological agents. Laboratory and clinical studies indicate that the effects of GAs may not be completely reversible upon anesthesia withdrawal. The long-term neurocognitive effects of GAs, especially when administered at the extremes of ages, are an increasingly recognized health concern and the subject of extensive laboratory and clinical research. Initial studies in rodents suggest that the adverse effects of GAs, whose actions involve enhancement of GABA type A receptor activity (GABAergic GAs), can also extend to future unexposed offspring. Importantly, experimental findings show that GABAergic GAs may induce heritable effects when administered from the early postnatal period to at least young adulthood, covering nearly all age groups that may have children after exposure to anesthesia. More studies are needed to understand when and how the clinical use of GAs in a large and growing population of patients can result in lower resilience to diseases in the even larger population of their unexposed offspring. This minireview is focused on the authors’ published results and data in the literature supporting the notion that GABAergic GAs, in particular sevoflurane, may upregulate systemic levels of stress and sex steroids and alter expressions of genes that are essential for the functioning of these steroid systems. The authors hypothesize that stress and sex steroids are involved in the mediation of sex-specific heritable effects of sevoflurane.
A Clinical Prediction Model for Unsuccessful Pulmonary Tuberculosis Treatment Outcomes
Authors: Peetluk Lauren S , Rebeiro Peter F , Ridolfi Felipe M , Andrade Bruno B , Cordeiro-Santos Marcelo , Kritski Afranio , Durovni Betina , Calvacante Solange , Figueiredo Marina C , Haas David W , Liu Dandan , Rolla Valeria C , Sterling Timothy R ,   Regional Prospective Observational Research in Tuberculosis (RePORT)-Brazil Network, Spener-Gomes Renata , de Souza Alexandra Brito , Silva Jesus Jaquelane , Benjamin Aline , Marinho Sant’Anna Flavia , Peixoto Ignácio Francine , Cristina Lourenço Maria , Gomes-Silva Adriano , de Oliveira Jamile G , Moreira Adriana S R , Calçada Carvalho Anna Cristina , Silva Elisangela C , Mello Mayla , Rocha Michael S , Nogueira Betania , Nascimento Vanessa , Nery Saulo , Andrade Alice M S , Malta-Santos Hayna , Rebouças-Silva Jéssica , Ramos André M C , Melo Sayonara , Cubillos-Angulo Juan M , de Moraes Laise 
Published: June 2021

Abstract

Background
Despite widespread availability of curative therapy, tuberculosis (TB) treatment outcomes remain suboptimal. Clinical prediction models can inform treatment strategies to improve outcomes. Using baseline clinical data, we developed a prediction model for unsuccessful TB treatment outcome and evaluated the incremental value of human immunodeficiency virus (HIV)–related severity and isoniazid acetylator status.

Methods
Data originated from the Regional Prospective Observational Research for Tuberculosis Brazil cohort, which enrolled newly diagnosed TB patients in Brazil from 2015 through 2019. This analysis included participants with culture-confirmed, drug-susceptible pulmonary TB who started first-line anti-TB therapy and had ≥12 months of follow-up. The end point was unsuccessful TB treatment: composite of death, treatment failure, regimen switch, incomplete treatment, or not evaluated. Missing predictors were imputed. Predictors were chosen via bootstrapped backward selection. Discrimination and calibration were evaluated with c-statistics and calibration plots, respectively. Bootstrap internal validation estimated overfitting, and a shrinkage factor was applied to improve out-of-sample prediction. Incremental value was evaluated with likelihood ratio–based measures.

Results
Of 944 participants, 191 (20%) had unsuccessful treatment outcomes. The final model included 7 baseline predictors: hemoglobin, HIV infection, drug use, diabetes, age, education, and tobacco use. The model demonstrated good discrimination (c-statistic = 0.77; 95% confidence interval, .73–.80) and was well calibrated (optimism-corrected intercept and slope, –0.12 and 0.89, respectively). HIV-related factors and isoniazid acetylation status did not improve prediction of the final model.

Conclusions
Using information readily available at treatment initiation, the prediction model performed well in this population. The findings may guide future work to allocate resources or inform targeted interventions for high-risk patients.
Conditional Cash Transfers to Incentivize Tuberculosis Screening: Description of a Novel Strategy for Contact Investigation in Rural South Africa
Authors: Baik Yeonsoo , Hanrahan Colleen F , Mmolawa Lesego , Nonyane Bareng A S , Albaugh Nicholas W , Lebina Limakatso , Siwelana Tsundzukani , Martinson Neil , Dowdy David W 
Published: June 2021

Abstract

Background
Providing incentives to screen close contacts for tuberculosis (TB) is an alternative to household-based contact investigation. We aimed to characterize patients and contexts where this incentive-based strategy might be preferred.

Methods
This is a secondary analysis of a cluster randomized trial of TB contact investigation in Limpopo District, South Africa, conducted between 2016 and 2020. Twenty-eight clinics were randomly allocated to household-based vs incentive-based contact investigation. In the incentive-based arm, index participants and contacts received transport reimbursement and incentives for TB screening and microbiological diagnosis of contacts. We estimated differences in mean number of contacts per index participant with household-based vs incentive-based contact investigation overall and within subgroups of index participants.

Results
A total of 3776 contacts (1903 in the incentive-based and 1873 in the household-based arm) were referred by 2501 index participants. A higher proportion of contacts in the incentive-based than household-based arm were adults (72% vs 59%), reported chronic TB symptoms (25% vs 16%) or ever smoking (23% vs 11%). Index participants who walked or bicycled to a clinic referred 1.03 more contacts per index (95% confidence interval [CI], .48 to 1.57) through incentive-based than household-based investigation. Index participants living with &gt;5 household members referred 0.48 more contacts per index (95% CI, .03 to .94) through household-based than incentive-based investigation.

Conclusions
Relative to household-based investigation, incentive-based investigation identifies contacts likely at higher risk for active TB. Incentive-based investigation may be more appropriate for index participants who can easily access clinics, versus household-based investigation for patients with large households.
Clinical Trials Registration. NCT02808507.
Learning Representation From Concurrence-Words Graph For Aspect Sentiment Classification
Authors: Lu Guangquan , Huang Jihong 
Published: June 2021

Abstract
Aspect sentiment classification is an important research topic in natural language processing and computational linguistics, assisting in automatically review analysis and emotional tendency judgement. Different from extant methods that focus on text sequence representations, this paper presents a network framework to learn representation from concurrence-words relation graph (LRCWG), so as to improve the Macro-F1 and accuracy. The LRCWG first employs the multi-head attention mechanism to capture the sentiment representation from the sentences which can learn the importance of text sequence representation. And then, it leverages the priori sentiment dictionary information to construct the concurrence relations of sentiment words with Graph Convolution Network (GCN). This assists in that the learnt context representation can keep both the semantics integrity and the features of sentiment concurrence-words relations. The designed algorithm is experimentally evaluated with all the five benchmark datasets and demonstrated that the proposed aspect sentiment classification can significantly improve the prediction performance of learning task.
The Progenetix oncogenomic resource in 2021
Authors: Huang Qingyao , Carrio-Cordo Paula , Gao Bo , Paloots Rahel , Baudis Michael 
Published: June 2021

Abstract
In cancer, copy number aberrations (CNAs) represent a type of nearly ubiquitous and frequently extensive structural genome variations. To disentangle the molecular mechanisms underlying tumorigenesis as well as identify and characterize molecular subtypes, the comparative and meta-analysis of large genomic variant collections can be of immense importance. Over the last decades, cancer genomic profiling projects have resulted in a large amount of somatic genome variation profiles, however segregated in a multitude of individual studies and datasets. The Progenetix project, initiated in 2001, curates individual cancer CNA profiles and associated metadata from published oncogenomic studies and data repositories with the aim to empower integrative analyses spanning all different cancer biologies. During the last few years, the fields of genomics and cancer research have seen significant advancement in terms of molecular genetics technology, disease concepts, data standard harmonization as well as data availability, in an increasingly structured and systematic manner. For the Progenetix resource, continuous data integration, curation and maintenance have resulted in the most comprehensive representation of cancer genome CNA profiling data with 138 663 (including 115 357 tumor) copy number variation (CNV) profiles. In this article, we report a 4.5-fold increase in sample number since 2013, improvements in data quality, ontology representation with a CNV landscape summary over 51 distinctive National Cancer Institute Thesaurus cancer terms as well as updates in database schemas, and data access including new web front-end and programmatic data access.
Database URL: progenetix.org
Minimally invasive oesophagectomy in the prone versus lateral decubitus position: a systematic review and meta-analysis
Authors: Schizas Dimitrios , Papaconstantinou Dimitrios , Krompa Anastasia , Athanasiou Antonios , Triantafyllou Tania , Tsekrekos Andrianos , Ruurda Jelle P , Rouvelas Ioannis 
Published: June 2021

Abstract
The thoracic phase of minimally invasive esophagectomy was initially performed in the lateral decubitus position (LDP); however, many experts have gradually transitioned to a prone position (PP) approach. The aim of the present systematic review and meta-analysis is to quantitatively compare the two approaches. A systematic literature search of the MEDLINE, Embase, Google Scholar, Web of Knowledge, China National Knowledge Infrastructure and ClinicalTrials.gov databases was undertaken for studies comparing outcomes between patients undergoing minimally invasive esophageal surgery in the PP versus the LDP. In total, 15 studies with 1454 patients (PP; n = 710 vs. LDP; n = 744) were included. Minimally invasive esophagectomy in the PP provides statistically significant reduction in postoperative respiratory complications (Risk ratios 0.5, 95% confidence intervals [CI] 0.34–0.76, P &lt; 0.001), blood loss (weighted mean differences [WMD] –108.97, 95% CI –166.35 to −51.59 mL, P &lt; 0.001), ICU stay (WMD –0.96, 95% CI –1.7 to −0.21 days, P = 0.01) and total hospital stay (WMD –2.96, 95% CI –5.14 to −0.78 days, P = 0.008). In addition, prone positioning increases the overall yield of chest lymph node dissection (WMD 2.94, 95% CI 1.54–4.34 lymph nodes, P &lt; 0.001). No statistically significant difference in regards to anastomotic leak rate, mortality and 5-year overall survival was encountered. Subgroup analysis revealed that the protective effect of prone positioning against pulmonary complications was more pronounced for patients undergoing single-lumen tracheal intubation. A head to head comparison of minimally invasive esophagectomy in the prone versus the LDP reveals superiority of the former method, with emphasis on the reduction of postoperative respiratory complications and reduced length of hospitalization. Long-term oncologic outcomes appear equivalent, although validation through prospective studies and randomized controlled trials is still necessary.
Urbanisation and the Onset of Modern Economic Growth
Authors: Brunt Liam , García-Peñalosa Cecilia 
Published: June 2021

AbstractA large literature characterises urbanisation as resulting from productivity growth attracting rural workers to cities. Incorporating economic geography elements into a growth model, we suggest that causation runs the other way: when rural workers move to cities, the resulting urbanisation produces technological change and productivity growth. Urban density leads to knowledge exchange and innovation, thus creating a positive feedback loop between city size and productivity that initiates sustained economic growth. This model is consistent with the fact that urbanisation rates in western Europe, most notably England, reached unprecedented levels by the mid-eighteenth century, the eve of the Industrial Revolution.
Adaptation of the Communities That Care Youth Survey for use in Brazil: A pilot study
Authors: de Oliveira Corrêa Arthur , Brown Eric C , Murta Sheila Giardini , Briney John S 
Published: June 2021

Summary
Substance use and violence are serious problems affecting Brazilian youth, prompting local authorities to invest in adapting and implementing evidence-based prevention programs developed abroad. To ensure that interventions are effective, valid and reliable measures of risk factors for substance use and violence are needed. We conducted a pilot examination of the measurement properties of risk factors in the Communities That Care Youth Survey (CTCYS), a school-based survey developed in the United States. The Brazilian-adapted CTCYS included 25 risk factors as well as measures of substance use and antisocial behaviors. The survey was translated into Brazilian Portuguese and adapted for use in Brazil, incorporating suggestions from local experts. The survey was administered to 926 students in one Brazilian community. Results indicate that scale internal consistency was acceptable for all but two scales: (i) Academic Failure and (ii) Rebelliousness. Confirmatory factor analyses suggested good model fit for most measurement models albeit with minor modifications for most scales. Findings from this pilot study provide a foundation for the use of the CTCYS in Brazil to assess community levels of adolescent risk and evaluate prevention programs.
Integrative DNA Methylation and Gene Expression Analysis in the Prefrontal Cortex of Mexicans Who Died by Suicide
Authors: Romero-Pimentel Ana L , Almeida Daniel , Muñoz-Montero Said , Rangel Claudia , Mendoza-Morales Roberto , Gonzalez-Saenz Eli E , Nagy Corina , Chen Gary , Aouabed Zahia , Theroux Jean-Francois , Turecki Gustavo , Martinez-Levy Gabriela , Walss-Bass Consuelo , Monroy-Jaramillo Nancy , Fernández-Figueroa Edith A , Gómez-Cotero Amalia , García-Dolores Fernando , Morales-Marin Mirna E , Nicolini Humberto 
Published: June 2021

Abstract

Background
Suicide represents a major health concern, especially in developing countries. While many demographic risk factors have been proposed, the underlying molecular pathology of suicide remains poorly understood. A body of evidence suggests that aberrant DNA methylation and expression is involved. In this study, we examined DNA methylation profiles and concordant gene expression changes in the prefrontal cortex of Mexicans who died by suicide.

Methods
In collaboration with the coroner’s office in Mexico City, brain samples of males who died by suicide (n = 35) and age-matched sudden death controls (n = 13) were collected. DNA and RNA were extracted from prefrontal cortex tissue and analyzed with the Infinium Methylation480k and the HumanHT-12 v4 Expression Beadchips, respectively.

Results
We report evidence of altered DNA methylation profiles at 4430 genomic regions together with 622 genes characterized by differential expression in cases vs controls. Seventy genes were found to have concordant methylation and expression changes. Metacore-enriched analysis identified 10 genes with biological relevance to psychiatric phenotypes and suicide (ADCY9, CRH, NFATC4, ABCC8, HMGA1, KAT2A, EPHA2, TRRAP, CD22, and CBLN1) and highlighted the association that ADCY9 has with various pathways, including signal transduction regulated by the cAMP-responsive element modulator, neurophysiological process regulated by the corticotrophin-releasing hormone, and synaptic plasticity. We therefore went on to validate the observed hypomethylation of ADCY9 in cases vs control through targeted bisulfite sequencing.

Conclusion
Our study represents the first, to our knowledge, analysis of DNA methylation and gene expression associated with suicide in a Mexican population using postmortem brain, providing novel insights for convergent molecular alterations associated with suicide.
Genome-Wide Correlation of DNA Methylation and Gene Expression in Postmortem Brain Tissues of Opioid Use Disorder Patients
Authors: Liu Andi , Dai Yulin , Mendez Emily F , Hu Ruifeng , Fries Gabriel R , Najera Katherine E , Jiang Shan , Meyer Thomas D , Stertz Laura , Jia Peilin , Walss-Bass Consuelo , Zhao Zhongming 
Published: June 2021

AbstractBackgroundOpioid use disorder (OUD) affects millions of people, causing nearly 50 000 deaths annually in the United States. While opioid exposure and OUD are known to cause widespread transcriptomic and epigenetic changes, few studies in human samples have been conducted. Understanding how OUD affects the brain at the molecular level could help decipher disease pathogenesis and shed light on OUD treatment.MethodsWe generated genome-wide transcriptomic and DNA methylation profiles of 22 OUD subjects and 19 non-psychiatric controls. We applied weighted gene co-expression network analysis to identify genetic markers consistently associated with OUD at both transcriptomic and methylomic levels. We then performed functional enrichment for biological interpretation. We employed cross-omics analysis to uncover OUD-specific regulatory networks.ResultsWe found 6 OUD-associated co-expression gene modules and 6 co-methylation modules (false discovery rate &lt;0.1). Genes in these modules are involved in astrocyte and glial cell differentiation, gliogenesis, response to organic substance, and response to cytokine (false discovery rate &lt;0.05). Cross-omics analysis revealed immune-related transcription regulators, suggesting the role of transcription factor-targeted regulatory networks in OUD pathogenesis.ConclusionsOur integrative analysis of multi-omics data in OUD postmortem brain samples suggested complex gene regulatory mechanisms involved in OUD-associated expression patterns. Candidate genes and their upstream regulators revealed in astrocyte, and glial cells could provide new insights into OUD treatment development.