bluuebunny/crossref_metadata_2025_split huggingface dataset:
The Impact of Socioeconomic Status on the Incidence and Stage of Melanoma in China
Authors: Zheng Shaoluan , Feng Jia , Chen Zhiwei , Wei Chuanyuan , Pan Yuyan , Liu Jiaqi 
Published: May 2024

Background
The role of high socioeconomic status (SES) as an established risk factor for melanoma has been well documented in Western countries and regions. However, research on the association between melanoma and SES in China remains limited. This study aimed to investigate the association between SES and melanoma incidence and stage in China.

Methods
Five measures of SES were accessed, including education level, ethnic background, per capita household income, occupation, and medical insurance coverage. A scoring system based on the Kuppuswamy Socio-Economic Scale was used to create a quantitative assessment of SES. To improve clarity and precision, we refined the language in the original text. Clinical stage at diagnosis was classified according to the Chinese Society Oncology Melanoma Guidelines.

Results
A total of 122 patients with pathologic melanoma were enrolled in this study from January 2013 to December 2017. Of these patients, 58 (48%) were male and 64 (52%) were female, with a mean age of 59.23 ± 9.91 years. Patients in the age groups of 45–59 and 60–73 had a higher incidence of melanoma compared to other age groups. Acral lentiginous melanoma was the most commonly observed subtype, accounting for 48% of cases. Patients with a low level of education (middle school and below) and a low level of monthly household income (<3000 CNY) had a higher risk of developing melanoma, as did those who were unemployed. Interestingly, a higher proportion of melanoma diagnoses were made in patients with medical insurance than those without. However, no significant differences in melanoma staging were found based on education level (P = 0.153), monthly household income (P = 0.507), occupation (P = 0.687), or insurance status (P = 0.537). According to the Kuppuswamy Socio-Economic Scale, there were 0 in upper class, 50 in upper middle class, 44 in lower middle class, 28 in upper lower class, 0 in lower class. The mean K-score was 13.85. No statistically significant interaction was observed between K-score and tumor stage.

Conclusions
Patients with lower SES have a higher risk of developing melanoma. However, no significant differences were found in melanoma staging based on SES.
Systems Immunology Approaches to Understanding Immune Responses in Acute Infection of Yellow Fever Patients
Authors: Gonçalves André N. A. , Costa Priscilla R. , Thomazella Mateus V. , Correia Carolina A. , Marmorato Mariana P. , Dias Juliana Z. C. , Silveira Cassia G. T. , Maestri Alvino , Cerqueira Natalia B. , Moreira Carlos H. V. , Buccheri Renata , Félix Alvina C. , Martins Felipe M. , Maso Vanessa E. , Ferreira Frederico M. , Araújo José D. A. , Vasconcelos Amanda P. , Gonzalez-Dias Patrícia , Sékaly Rafick-Pierre , Cabral-Marques Otavio , Coelho-dos-Reis Jordana G. A. , Ferreira Daniela M. , Kallas Esper G. , Nakaya Helder I. 
Published: May 2024

SummaryIn the 2018 yellow fever (YF) outbreak in Brazil, we generated new transcriptomic data and combined it with clinical and immunological data to decode the pathogenesis of YF. Our analysis of 79 patients highlighted distinct gene expression patterns between acute YF infections, other viral infections, and the milder infection induced by the live-attenuated YF-17D vaccine. We identified a critical role for low-density, immature neutrophils in severe outcomes, marked by the downregulation of genes such as PADI4, CSF3R, and ICAM1 in deceased patients. These genes are essential for neutrophil migration and maturation, suggesting their pivotal role in disease progression. Furthermore, our study revealed a complex interaction among inflammation-related genes: increased expression of CXCL10 in the acute phase was accompanied by decreased expression of IL-1b and an increase in IL1R2, a decoy receptor that binds to IL-1 to inhibit its activity. The diminished expression of HLA class II genes suggests an impairment in antigen presentation. These insights underscore the delicate balance of immune responses in YF pathogenesis and provide a foundation for future therapeutic and diagnostic advancements in managing YF.Highlights●PBMC transcriptome analysis in acute YFV highlights different immune responses between survivors and deceased patients.●Decreased expression of HLA class II genes in dendritic cells of deceased YFV patients indicates a critical impairment in antigen presentation and innate immunity.●Elevated B cell activation markers, such as BLNK and TNFRSF13B, in fatal YFV cases suggest an overactive, potentially dysregulated B cell response.●Increased expression of neutrophil-related genes, including DEFA1B and MMP9, in deceased YFV patients highlights neutrophils’ role in aggravating inflammation and tissue damage.Graphical Abstract
Spatial risk of disease transmission between wild bovids and livestock in Thailand
Authors: Horpiencharoen Wantida , Marshall Jonathan C. , Muylaert Renata L. , John Reju Sam , Hayman David T. S. 
Published: May 2024

AbstractThe livestock-wildlife interface is one of the most essential issues threatening wildlife conservation and public health. Identifying interface areas can help to prioritise disease surveillance and implement mitigation measures and control programs for targeting threatened wildlife. We predicted interface areas which were assumed to be areas at risk of infectious disease transmission based on the spatial overlap between three Thai wild bovids (including gaur, banteng and wild water buffalo) habitat suitability and domestic cattle. We assumed that domestic cattle are the reservoir of bovine infectious disease, and that high cattle density is a proxy for a higher risk of disease transmission. Our study indicated that the highest risk areas for the native species are at the forest edges where overlap exists between high habitat suitability and high cattle density. Wild water buffalo showed the largest proportion of high-risk areas (8%), while gaur and banteng showed similar risk areas (4%) in Thailand. The largest proportion of risk areas overlapping with protected areas was Namtok Sam Lan PAs at 89% for gaur, 84% for banteng and 65% for wild water buffalo. Kuiburi NP has the largest risk area around 274 km2(around 28% of the total protected area) for gaur and banteng, whereas wild water buffalo has the largest risk area overlapping with Huai Thabthan-Had Samran around 126 km2(10% of the PA). Kaengkrachan Forest Complex showed the second largest risk area from 249 km2for gaur and 273 km2for banteng (8-9% of the PA). Our results address how habitat suitability might be helpful for infectious disease prevention and control strategies focused on native fauna and One Health. Furthermore, this work may also support the wild bovid habitat conservation initiatives and land use planning by informing decision-making about balancing wildlife habitats and livestock farming.
LUKB: Preparing Local UK Biobank Data for Analysis
Authors: Li Xiangnan , Wang Shuming , Zhang Hui , Hu Zixin 
Published: May 2024

AbstractBackgroundWhile UK Biobank data holds immense potential for human health research, its complex pre-processing steps involving decryption, extraction, and code mapping often act as a barrier for researchers, diverting them from their core research questions. A freely available tool for preparing UK Biobank data would reduce the workload of researchers and the costs produced by alternatively using UK Biobank Research Analysis Platform (RAP).ResultsWe developed LUKB, an R Shiny-based web tool that simplifies UK Biobank data preparation by automating pre-processing tasks. Through simple actions, researchers can add downloaded UK Biobank data to LUKB, achieving rapid data decryption, efficient extraction, and accurate code mapping effortlessly.ConclusionLUKB reduces pre-processing time, allowing researchers to dedicate more time to their scientific endeavors, and provide an alternative to UK Biobank RAP to minimize costs. LUKB is freely available at Github (https://github.com/HaiGenBuShang/LUKB).
Genetic variants associated with cell-type-specific intra-individual gene expression variability reveal new mechanisms of genome regulation
Authors: Xue Angli , Yazar Seyhan , Alquicira-Hernández José , Cuomo Anna S E , Senabouth Anne , Gordon Gracie , Kathail Pooja , Ye Chun Jimme , Hewitt Alex W. , Powell Joseph E. 
Published: May 2024

AbstractGene expression levels can vary substantially across cells, even in a seemingly homogeneous cell population. Identifying the relationships between genetic variation and gene expression is critical for understanding the mechanisms of genome regulation. However, the genetic control of gene expression variability among the cellswithinindividuals has yet to be extensively examined. This is primarily due to the statistical challenges, such as the need for sufficiently powered cohorts and adjusting mean-variance dependence. Here, we introduce MEOTIVE (Mapping genetic Effects On inTra-Individual Variability of gene Expression), a novel statistical framework to identify genetic effects on the gene expression variability (sc-veQTL) accounting for the mean-variance dependence. Using single-cell RNA-seq data of 1.2 million peripheral blood mononuclear cells from 980 human donors, we identified 14 – 3,488 genes with significant sc-veQTLs (study-wideq-value < 0.05) across different blood cell types, 2,103 of which were shared across more than one cell type. We further detected 55 SNP-gene pairs (in 34 unique genes) by directly linking genetic variations with gene expression dispersion (sc-deQTL) regardless of mean-variance dependence, and these genes were enriched in biological processes relevant to immune response and viral infection. An example is rs1131017 (p<9.08×10−52), a sc-veQTL in the 5’UTR ofRPS26, which shows a ubiquitous dispersion effect across cell types, with higher dispersion levels associated with lower auto-immune disease risk, including rheumatoid arthritis and type 1 diabetes. Another example isLYZ, which is associated with antibacterial activity against bacterial species and was only detected with a monocyte-specific deQTL (rs1384) located at the 3’ UTR region (p=1.48×10−11) and replicated in an independent cohort. Our results demonstrate an efficient and robust statistical method to identify genetic effects on gene expression variability and how these associations and their involved pathways confer auto-immune disease risk. This analytical framework provides a new approach to unravelling the genetic regulation of gene expression at the single-cell resolution, advancing our understanding of complex biological processes.
An in-depth analysis and exploreation with focus on the biofilm inStaphylococcus aureus
Authors: Zhang Zhiyuan , Chen Guozhong , Pan Yuanyuan , Yang Zhu , Liu Yin , Li Erguang 
Published: May 2024

ABSTRACTResearch into the biolfilm formation inStaphylococcus aureushas benefited greatly from the generation of high-throughput sequencing data to drive molecular analyses. The accumulation of these data, particularly transcriptomic data, offers a unique opportunity to unearth the network and constituent genes involved in the biofilm formation ofStaphylococcus aureusthrough machine learning strategies and co-expression analyses. Herein, we harnessed all available RNA sequencing data related toStaphylococcus aureusbiofilm studies and identified influenced functional pathways and corresponding genes in the process of the transition of bacteria from planktonic to biofilm state via employing machine learning and differential expression analyses. By weighted gene co-expression analysis and our previously developed predictor, important functional modules, potential biofilm-associated proteins and subnetwork of biofilm formation pathway were found. By constructing a protein-protein interaction (PPI) network, we discovered several hitherto unreported novel protein interactions within these functional modules. To make these data more straightforward to experimental biologists, an online database named SAdb was developed (http://sadb.biownmcli.info/).IMPORTANCEIn this work, we conducted a comprehensive and in-depth exploration of RNA sequencing data in biofilm research through differential expression analysis, machine learning, WGCNA, and biofilm-associated protein predictive analysis, which has also illuminated novel analytical perspective for other research into bacterial phenotypes. And, to provide researchers with unimpeded access to these data, we developed a database name SAdb for the storage and analysis ofStaphylococcus aureusomics data. We believe that this study will captivate the interest of researchers in the field of bacteriology, particularly those studying biofilms, which play a crucial role in bacterial growth, pathogenicity, and drug resistance.
Placental PFAS concentrations are associated with perturbations of placental DNA methylation at loci with important roles on cardiometabolic health
Authors: Everson Todd M. , Sehgal Neha , Barr Dana Boyd , Panuwet Parinya , Yakimavets Volha , Perez Cynthia , Shankar Kartik , Eick Stephanie M. , Pearson Kevin J. , Andres Aline 
Published: May 2024

AbstractThe placenta is crucial for fetal development, is affected by PFAS toxicity, and evidence is accumulating that gestational PFAS perturb the epigenetic activity of the placenta. Gestational PFAS exposure is can adversely affect offspring, yet individual and cumulative impacts of PFAS on the placental epigenome remain underexplored. Here, we conducted an epigenome-wide association study (EWAS) to examine the relationships between placental PFAS levels and DNA methylation in a cohort of mother-infant dyads in Arkansas. We measured 17 PFAS in human placental tissues and quantified placental DNA methylation levels via the Illumina EPIC Microarray. We tested for differential DNA methylation with individual PFAS, and with mixtures of multiple PFAS. Our results demonstrated that numerous epigenetic loci were perturbed by PFAS, with PFHxS exhibiting the most abundant effects. Mixture analyses suggested cumulative effects of PFOA and PFOS, while PFHxS may act more independently. We additionally explored whether sex-specific effects may be present and concluded that future large studies should explicitly test for sex-specific effects. The genes that are annotated to our PFAS-associated epigenetic loci are primarily involved in growth processes and cardiometabolic health, while some genes are involved in neurodevelopment. These findings shed light on how prenatal PFAS exposures affect birth outcomes and children’s health, emphasizing the importance of understanding PFAS mechanisms in the in-utero environment.
Remote automated delivery of mechanical stimuli coupled to brain recordings in behaving mice
Authors: Burdge Justin , Jhumka Anissa , Ogundare Simon , Baer Nicholas , Fulton Sasha , Bistis Brittany , Foster William , Toussaint Andre , Li Miao , Morizawa Yosuke M. , Yadessa Leah , Khan Ashar , Delinois Abednego , Mayiseni Wadzanayi , Loran Noah , Yang Guang , Abdus-Saboor Ishmail 
Published: May 2024

SummaryThe canonical framework for testing pain and mechanical sensitivity in rodents is manual delivery of stimuli to the paw. However, this approach can produce variability in results, requires significant training, and is ergonomically unfavorable to the experimenter. To circumvent limitations in manual delivery of stimuli, we have created a device called the ARM (AutomatedReproducibleMechano-stimulator). Built using a series of linear stages, cameras, and stimulus holders, the ARM is more accurate at hitting the desired target, delivers stimuli faster, and decreases variability in delivery of von Frey hair filaments. We demonstrate that the ARM can be combined with traditional measurements of pain behavior and automated machine-learning based pipelines. Importantly, the ARM enables remote testing of mice with experimenters outside the testing room. Using remote testing, we found that mice appeared to habituate more quickly when an experimenter was not present and experimenter presence leads to significant sex-dependent differences in withdrawal behavior. Lastly, to demonstrate the utility of the ARM for neural circuit dissection of pain mechanisms, we combined the ARM with cellular-resolved microendoscopy in the amygdala, linking stimulus, behavior, and brain activity of amygdalar neurons that encode negative pain states. Taken together, the ARM improves speed, accuracy, and robustness of mechanical pain assays and can be combined with automated pain detection systems and brain recordings to map pain sensation and affect.
Explainable models using transcription factor binding and epigenome patterns at promoters reveal disease-associated genes and their regulators in the context of cell-types
Authors: Chandra Omkar , Pramanik Durjay , Gautam Srishti , Sharma Madhu , Dubey Niharika , Mahato Biswarup , Orlov Yuriy L , Kumar Vibhor 
Published: May 2024

AbstractUnderstanding genome-wide epigenetic regulation of diseases is important in establishing pathogenic factors and could aid in disease diagnosis, prognosis, and therapeutics. In this study, we have utilized transcription factors (TFs) and co-factor profiles (n=823) as features in machine learning models to link them to various diseases. Further, along with TFs and co-factor profiles, histone modifications ChIP-seq (n = 621), cap analysis gene expression (CAGE) tags (n = 255), and DNase hypersensitivity profiles (n = 255) as features allowed for the modeling of association of coding and non-coding genes to diseases. Such predicted associations could be independently validated using genome-wide association data and survival analysis. However, the unique aspect of our approach is that it highlights the link between TF binding patterns and diseases in the context of cell types. Besides highlighting relevant TF-binding in known cell-types associated with diseases, it also provided their surprising link with TFs expressed in immune cells and other seemingly non-related cells. Further investigation revealed such links to be genuine and potentially useful for prognosis, further revealing the need to deconvolve a set of known genes associated with diseases.
Generic workflow for a rapid and easy design of strain-specific PCR and qPCR primers, applied to the assessment of bacterial strains survival in soil
Authors: Polrot A. , Béguet J. , Devers-Lamrani M. , Martin-Laurent F. , Spor A. 
Published: May 2024

AbstractBackgroundDetecting bacteria at the strain level is crucial in microbiology. Although qPCR is widely used, designing strain-specific primers remains a challenge due to nucleotide sequence similarities among related strains.Methods and ResultsThis paper introduces a simplified, web-based workflow for designing strain-specific primers using publicly available microbial genomes. The method does not require advanced bioinformatics skills and can be applied using a basic computer. Primers designed using this workflow are applied to assess the survival of two closeBacillusstrains in soil microcosms.ConclusionThe workflow offers an accessible solution for accurate bacterial strain detection, and fills a gap for researchers without specialized training in bioinformatics.
Investigation of the mechanism of accelerated biodegradation ofParacoccus-KDSPL-02
Authors: Wang Peng , Xu Shanxiang , Shen Chen , Ma Jiewen , Cheng Feiyu , Liu Jingyu 
Published: May 2024

AbstractParacoccus-KDSPL-02can accelerate to degrade penicillin G under light remain poorly understood, largely due to the lack of high-throughput genome engineering tools. Firstly, this study sequenced the genome ofParacoccus-KDSPL-02and mined the genes that might be involved, and in order to understand in detail whether the expression of the mined genes changed during light. Further, for genes with altering transcriptional levels under light, this study obtained PROKKA_01468 which a photoreceptor protein inParacoccus-KDSPL-02. In the end, for validating the function of PROKKA_01468, this study knocked down the sequence of the PROKKA_01468 by applying gene editing system, and the knockdown strain showed significant change in the rate of degradation of phenylacetic acid, which is the intermediate product of penicillin G degradation, by light compared with darkness, so that the PROKKA_01468 is the most effective photoreceptor protein inParacoccus-KDSPL-02.SynopsisThis research elucidates a molecular mechanism capable of accelerating penicillin G degradation in wastewater, with significant implications for environmental science.
Assessing the Risk of Depression Among U.S. Adults with Resolved Thyroid Dysfunction--data analysis from the National Health and Nutrition Examination Survey (2013–2018)
Authors: Zhan Denghuang , Chen Pinyu , Karim Ehsan 
Published: May 2024

AbstractBackgroundDepression is a highly-prevalent disease among US adults. The positive association between thyroid dysfunction and depression has been identified in many studies, but whether the thyroid dysfunction history (have recovered) is still associated with depression, and whether this association is modified by gender is still unknown. This finding can be important for depression preventions.MethodsWe applied design-adjusted multivariable logistic regression to examine the adjusted association between thyroid dysfunction history and depression by using data from the National Health and Nutrition Examination Survey from 2013 to 2018.ResultsOf 11975 respondents with complete responses included in this study, 8.4% (n = 1007) of the respondents have depression. The design-adjusted analysis shows no significant association between the thyroid dysfunction history and depression but shows gender as a significant effect modifier of the association. The association is 3.31(odds ratio, 95% CI: [1.38,7.93]) for males and 1.15 (odds ratio, 95% CI: [0.72, 1.84]) for females.ConclusionPeople who had thyroid dysfunction but recovered will still have a higher risk of getting depression, and it differs in genders. More suggestions and actions are needed for those who recovered from the thyroid dysfunction in order to prevent depression, especially for the males.