cometadata/datacite-rtg-text-other-reclassification-records huggingface dataset:
Impact of health insurance status among migrants from sub-Saharan Africa on access to health care and HIV testing in Germany: a participatory cross-sectional survey
Creators: name: Müllerschön, Johanna
name: Koschollek, Carmen
name: Santos-Hövener, Claudia
name: Kuehne, Anna
name: Müller-Nordhorn, J.
name: Bremer, Viviane
Publisher: name: Robert Koch-Institut
Year: 2019
Subjects: subject: Transients and migrants
subject: Human migration
subject: Health insurance
subject: Access to health care
subject: Health care utilization
subject: HIV
subject: 610 Medizin und Gesundheit

description: Background Among all newly diagnosed HIV cases in Germany in 2015, 16% originated from sub-Saharan Africa. Twelve percent of these infections were contracted within Germany and migrants from sub-Saharan Africa (misSA) are diagnosed later than Germans. Migrants, specifically those without health insurance, face many barriers accessing health care due to their residence status and cultural, socio-economic, legal and linguistic barriers. We assessed whether misSAs’ access to healthcare and utilization of HIV testing services depends on their health insurance status to inform prevention strategies. Methods From January 2015 to February 2016, we conducted a cross-sectional survey on knowledge, attitude, behavior, practice (KABP) regarding HIV, viral hepatitis and sexually transmitted infections among misSA in Germany. The survey was a community-based participatory research project; trained peer researchers recruited participants through outreach. To detect differences between participants with a regular health insurance card compared to asylum seekers with a medical treatment voucher or participants without health insurance or medical treatment voucher, unadjusted and adjusted Odds Ratios, chi-squared tests and 95% confidence intervals were calculated. Results A total of 1919 cases were considered. Overall, 83% had a health insurance card, 10% had a medical treatment voucher and 6% had no health insurance. Participants living in Germany for less than 5 years were less likely to have a health insurance card and more likely to have lower German language skills. Participants without health insurance visited a physician in case of health problems less often than participants with medical treatment voucher or a health insurance card (41.2% vs. 66.1% vs. 90%). Participants without health insurance reported less frequently visiting physicians or hospitals and were less likely to undergo a HIV test. Conclusion Having no health insurance or medical treatment voucher decreased the odds of contact with the healthcare system more than other socio-demographic characteristics. Furthermore, misSA without health insurance had lower odds of ever having done an HIV test than participants with health insurance. To increase health care utilization and testing and to ensure adequate medical care, all migrants should get access to health insurance without increasing costs and consequences for residence status.
Nidān: International Journal for the Study of Hinduism
Creators: name: Editorial Team, The
Publisher: name: Nidān: International Journal for Indian Studies
Year: 2023

description: Complete issue of Nidān 19(1) December 2007
description: Nidān: International Journal for Indian Studies, Vol. 19 No. 1 (2007): Nidān: International Journal for the Study of Hinduism
Additional file 3 of Interdisciplinary clinicians’ attitudes, challenges, and success strategies in providing care to transgender people: a qualitative descriptive study
Creators: name: Soled, Kodiak Ray Sung
name: Dimant, Oscar E.
name: Tanguay, Jona
name: Mukerjee, Ronica
name: Poteat, Tonia
Publisher: name: figshare
Year: 2022
Subjects: subject: Medicine
subject: Sociology
subject: FOS: Sociology
subject: 69999 Biological Sciences not elsewhere classified
subject: FOS: Biological sciences
subject: Science Policy

description: Additional file 3.
Publishing @ DESY
Creators: name: Köhler, Martin
Publisher: name: Deutsches Elektronen-Synchrotron, DESY, Hamburg
Year: 2023

description: Liebenberg-Meeting, Zoom, DESY, Germany, 13 Feb 2023 - 13 Feb 2023
description: Information on the workflow for publishing @ DESY:1. Open Access rate 100% from 20232. Approval workflow3. New entry level indicators
Nidān: International Journal for the Study of Hinduism
Creators: name: Editorial Team, The
Publisher: name: Nidān: International Journal for Indian Studies
Year: 2023

description: Complete issue of Nidān 20(1) December 2008
description: Nidān: International Journal for Indian Studies, Vol. 20 No. 1 (2008): Nidān: International Journal for the Study of Hinduism
Transcriptome-wide association study of blood cell traits in african ancestry and hispanic/latino populations
Creators: name: Yin, J.
name: Jorgenson, E.
name: Tapia, A.L.
name: Rosen, J.D.
name: Hodonsky, C.J.
name: Shang, L.
name: Qian, H.
name: Xie, M.
name: Buyske, S.
name: Young, K.L.
name: Fornage, M.
name: Wang, T.
name: Smith, J.A.
name: Kowalski, M.H.
name: Li, Y.
name: Avery, C.L.
name: Argos, M.
name: Zhou, X.
name: Raffield, L.M.
name: Rotter, J.I.
name: Shan, Y.
name: Wen, J.
name: Bien, S.A.
name: Loos, R.J.F.
name: Liu, Y.
name: Rich, S.S.
name: Sun, Q.
name: Kooperberg, C.
name: Moon, J.-Y.
name: Choquet, H.
name: Chen, J.
name: North, K.E.
name: Graff, M.
name: Rowland, B.
name: Reiner, A.P.
name: Zhao, W.
Publisher: name: MDPI AG
Year: 2021

description: Background: Thousands of genetic variants have been associated with hematological traits, though target genes remain unknown at most loci. Moreover, limited analyses have been conducted in African ancestry and Hispanic/Latino populations; hematological trait associated variants more common in these populations have likely been missed. Methods: To derive gene expression prediction models, we used ancestry-stratified datasets from the Multi-Ethnic Study of Atherosclerosis (MESA, including n = 229 African American and n = 381 Hispanic/Latino participants, monocytes) and the Depression Genes and Networks study (DGN, n = 922 European ancestry participants, whole blood). We then performed a transcriptome-wide association study (TWAS) for platelet count, hemoglobin, hematocrit, and white blood cell count in African (n = 27,955) and Hispanic/Latino (n = 28,324) ancestry participants. Results: Our results revealed 24 suggestive signals (p < 1 × 10−4 ) that were conditionally distinct from known GWAS identified variants and successfully replicated these signals in European ancestry subjects from UK Biobank. We found modestly improved correlation of predicted and measured gene expression in an independent African American cohort (the Genetic Epidemiology Network of Arteriopathy (GENOA) study (n = 802), lymphoblastoid cell lines) using the larger DGN reference panel; however, some genes were well predicted using MESA but not DGN. Conclusions: These analyses demonstrate the importance of performing TWAS and other genetic analyses across diverse populations and of balancing sample size and ancestry background matching when selecting a TWAS reference panel.
Nidān: International Journal for the Study of Hinduism
Creators: name: Editorial Team, The
Publisher: name: Nidān: International Journal for Indian Studies
Year: 2023

description: Complete issue of Nidān 21(1) December 2009
description: Nidān: International Journal for Indian Studies, Vol. 21 No. 1 (2009): Nidān: International Journal for the Study of Hinduism
Additional file 4 of Interdisciplinary clinicians’ attitudes, challenges, and success strategies in providing care to transgender people: a qualitative descriptive study
Creators: name: Soled, Kodiak Ray Sung
name: Dimant, Oscar E.
name: Tanguay, Jona
name: Mukerjee, Ronica
name: Poteat, Tonia
Publisher: name: figshare
Year: 2022
Subjects: subject: Medicine
subject: Sociology
subject: FOS: Sociology
subject: 69999 Biological Sciences not elsewhere classified
subject: FOS: Biological sciences
subject: Science Policy

description: Additional file 4.
Bounding linear head reduction and visible interaction through skeletons
Creators: name: Clairambault, Pierre
Publisher: name: arXiv
Year: 2015
Subjects: subject: Logic in Computer Science (cs.LO)
subject: FOS: Computer and information sciences

description: In this paper, we study the complexity of execution in higher-order programming languages. Our study has two facets: on the one hand we give an upper bound to the length of interactions between bounded P-visible strategies in Hyland-Ong game semantics. This result covers models of programming languages with access to computational effects like non-determinism, state or control operators, but its semantic formulation causes a loose connection to syntax. On the other hand we give a syntactic counterpart of our semantic study: a non-elementary upper bound to the length of the linear head reduction sequence (a low-level notion of reduction, close to the actual implementation of the reduction of higher-order programs by abstract machines) of simply-typed lambda-terms. In both cases our upper bounds are proved optimal by giving matching lower bounds. These two results, although different in scope, are proved using the same method: we introduce a simple reduction on finite trees of natural numbers, hereby called interaction skeletons. We study this reduction and give upper bounds to its complexity. We then apply this study by giving two simulation results: a semantic one measuring progress in game-theoretic interaction via interaction skeletons, and a syntactic one establishing a correspondence between linear head reduction of terms satisfying a locality condition called local scope and the reduction of interaction skeletons. This result is then generalized to arbitrary terms by a local scopization transformation.
Nidān: International Journal for the Study of Hinduism
Creators: name: Editorial Team, The
Publisher: name: Nidān: International Journal for Indian Studies
Year: 2023

description: Complete issue of Nidān 22(1) December 2010: Hindu Studies: Studies of Past-Present
description: Nidān: International Journal for Indian Studies, Vol. 22 No. 1 (2010): Nidān: International Journal for the Study of Hinduism
MRLocus: Identifying causal genes mediating a trait through Bayesian estimation of allelic heterogeneity
Creators: name: Ibrahim, J.G.
name: Li, Y.
name: Love, M.I.
name: Tapia, A.L.
name: Stein, J.L.
name: Matoba, N.
name: Wilson, E.P.
name: Zhu, A.
Publisher: name: Public Library of Science
Year: 2021

description: Expression quantitative trait loci (eQTL) studies are used to understand the regulatory function of non-coding genome-wide association study (GWAS) risk loci, but colocalization alone does not demonstrate a causal relationship of gene expression affecting a trait. Evidence for mediation, that perturbation of gene expression in a given tissue or developmental context will induce a change in the downstream GWAS trait, can be provided by two-sample Mendelian Randomization (MR). Here, we introduce a new statistical method, MRLocus, for Bayesian estimation of the gene-to-trait effect from eQTL and GWAS summary data for loci with evidence of allelic heterogeneity, that is, containing multiple causal variants. MRLocus makes use of a colocalization step applied to each nearly-LD-independent eQTL, followed by an MR analysis step across eQTLs. Additionally, our method involves estimation of the extent of allelic heterogeneity through a dispersion parameter, indicating variable mediation effects from each individual eQTL on the downstream trait. Our method is evaluated against other state-of-the-art methods for estimation of the gene-to-trait mediation effect, using an existing simulation framework. In simulation, MRLocus often has the highest accuracy among competing methods, and in each case provides more accurate estimation of uncertainty as assessed through interval coverage. MRLocus is then applied to five candidate causal genes for mediation of particular GWAS traits, where gene-to-trait effects are concordant with those previously reported. We find that MRLocus’s estimation of the causal effect across eQTLs within a locus provides useful information for determining how perturbation of gene expression or individual regulatory elements will affect downstream traits. The MRLocus method is implemented as an R package available at https://mikelove.github.io/ mrlocus.
RESEARCH AND DEVELOPMENT OF ELECTRIC MICRO-BUS VEHICLE CHASSIS
Creators: name: Coovert, Benjamin
Publisher: name: Purdue University Graduate School
Year: 2023
Subjects: Numerical modelling and mechanical characterisation

description: In this project, a chassis concept has been developed for a small electric vehicle ’minibus’. The vehicle is intended to be used as a transport between agricultural locations in Ethiopia to cities where the products can be sold. The objective is to develop a chassis that can house several different modular structures for the purposes of transporting refrigerated goods, a mobile power grid, or people. Literature studies have been conducted on current electric vehicle markets, battery markets, chassis materials, and optimal cross-sections. The battery housings have also been analyzed from an environmental perspective to account for conditions in Ethiopia. Based on this, it was found that a four-wheeled ’minibus’ design including space for approximately fourteen custom batteries is optimal. It is essential to keep in mind that this project has been carried out both on a conceptual level within the framework of a degree project as well as a production project for use in Ethiopian rural areas. This master thesis project aims to provide a solid benchmark for further development and research within the subject.
Additional file 1 of Household expenditure of smokers and ex-smokers across socioeconomic groups: results from a large nationwide Australian longitudinal survey
Creators: name: Lal, Anita
name: Mohebi, Mohammadreza
name: White, Sarah L.
name: Scollo, Michelle
name: McCaffrey, Nikki
Publisher: name: figshare
Year: 2022
Subjects: subject: Medicine
subject: Biotechnology
subject: 59999 Environmental Sciences not elsewhere classified
subject: FOS: Earth and related environmental sciences
subject: 69999 Biological Sciences not elsewhere classified
subject: FOS: Biological sciences
subject: Cancer
subject: Science Policy

description: Additional file 1.
HiC-ACT: improved detection of chromatin interactions from Hi-C data via aggregated Cauchy test
Creators: name: Hu, M.
name: Lagler, T.M.
name: Lagler, T.M.
name: Abnousi, A.
name: Li, Y.
name: Li, Y.
name: Yang, Y.
name: Hu, M.
name: Yang, Y.
name: Abnousi, A.
Publisher: name: Cell Press
Year: 2021

description: Genome-wide chromatin conformation capture technologies such as Hi-C are commonly employed to study chromatin spatial organization. In particular, to identify statistically significant long-range chromatin interactions from Hi-C data, most existing methods such as Fit-Hi-C/FitHiC2 and HiCCUPS assume that all chromatin interactions are statistically independent. Such an independence assumption is reasonable at low resolution (e.g., 40 kb bin) but is invalid at high resolution (e.g., 5 or 10 kb bins) because spatial dependency of neighboring chromatin interactions is non-negligible at high resolution. Our previous hidden Markov random field-based methods accommodate spatial dependency but are computationally intensive. It is urgent to develop approaches that can model spatial dependence in a computationally efficient and scalable manner. Here, we develop HiC-ACT, an aggregated Cauchy test (ACT)-based approach, to improve the detection of chromatin interactions by post-processing results from methods assuming independence. To benchmark the performance of HiC-ACT, we re-analyzed deeply sequenced Hi-C data from a human lymphoblastoid cell line, GM12878, and mouse embryonic stem cells (mESCs). Our results demonstrate advantages of HiC-ACT in improving sensitivity with controlled type I error. By leveraging information from neighboring chromatin interactions, HiC-ACT enhances the power to detect interactions with lower signal-to-noise ratio and similar (if not stronger) epigenetic signatures that suggest regulatory roles. We further demonstrate that HiC-ACT peaks show higher overlap with known enhancers than Fit-Hi-C/FitHiC2 peaks in both GM12878 and mESCs. HiC-ACT, effectively a summary statistics-based approach, is computationally efficient (∼6 min and ∼2 GB memory to process 25,000 pairwise interactions).
Nidān: International Journal for the Study of Hinduism
Creators: name: Editorial Team, The
Publisher: name: Nidān: International Journal for Indian Studies
Year: 2023

description: Complete issue of Nidān 23(1) December 2011: Hinduism and Materiality
description: Nidān: International Journal for Indian Studies, Vol. 23 No. 1 (2011): Nidān: International Journal for the Study of Hinduism
Super hotspots and super coldspots in the repair of UV-induced DNA damage in the human genome
Creators: name: Li, W.
name: Li, W.
name: Yang, Y.
name: Lindsey-Boltz, L.A.
name: Li, Y.
name: Sancar, A.
name: Li, Y.
name: Yang, Y.
name: Jiang, Y.
name: Sancar, A.
name: Lindsey-Boltz, L.A.
name: Jiang, Y.
Publisher: name: American Society for Biochemistry and Molecular Biology Inc.
Year: 2021

description: The formation of UV-induced DNA damage and its repair are influenced by many factors that modulate lesion formation and the accessibility of repair machinery. However, it remains unknown which genomic sites are prioritized for immediate repair after UV damage induction, and whether these prioritized sites overlap with hotspots of UV damage. We identified the super hotspots subject to the earliest repair for (6-4) pyrimidine- pyrimidone photoproduct by using the eXcision Repairsequencing (XR-seq) method. We further identified super coldspots for (6-4) pyrimidine-pyrimidone photoproduct repair and super hotspots for cyclobutane pyrimidine dimer repair by analyzing available XR-seq time-course data. By integrating datasets of XR-seq, Damage-seq, adductSeq, and cyclobutane pyrimidine dimer-seq, we show that neither repair super hotspots nor repair super coldspots overlap hotspots of UV damage. Furthermore, we demonstrate that repair super hotspots are significantly enriched in frequently interacting regions and superenhancers. Finally, we report our discovery of an enrichment of cytosine in repair super hotspots and super coldspots. These findings suggest that local DNA features together with large-scale chromatin features contribute to the orders of magnitude variability in the rates of UV damage repair.
Safety and efficacy of lumen-apposing metal stents and double-pigtail plastic stents for endoscopic ultrasound-guided drainage of walled-off necrosis; a systematic review and meta-analysis
Creators: name: Khizar, Hayat
name: Yufei, Hu
name: Yanhua, Wu
name: Wangyang, Chen
name: Ying, Bian
name: Chenyu, Le
name: Zhicheng, Huang
name: Ali, Kamran
name: Jianfeng, Yang
Publisher: name: Taylor & Francis
Year: 2023
Subjects: subject: Medicine
subject: Physiology
subject: FOS: Biological sciences
subject: Pharmacology
subject: Biotechnology
subject: Sociology
subject: FOS: Sociology
subject: Developmental Biology
subject: Cancer

description: Patients with walled-off necrosis (WON) are still challenging to treat safely and effectively. Recently, double-pigtail plastic stents (DPS), bi-flanged metallic stents (BFMS), and lumen-apposing metal stents (LAMS) have been employed with endoscopic ultrasound-guided (EUS-guided) drainage. However, there is little solid evidence to support the effectiveness and safety of using stents. This study aims to compare the outcomes of the LAMS and the PS. Till July 2022, a thorough database search was done, and studies that met the criteria were chosen. By using the RevMan software, the technical and clinical success and other secondary outcomes were calculated. Subgroup analysis was performed between the LAMS and the BFMS. Fifteen studies (two randomized controlled trials and thirteen observational) with 687 patients receiving metal stents and 771 patients receiving plastic stents were selected for final analysis. There was no significant risk of bias or publication bias. The odds ratios (OR) for technical and clinical success were 0.36 (95% confidence interval (95% CI) 0.08, 1.52) and 2.26 (95%CI 1.62, 3.15), respectively. The OR for overall adverse events was 0.74 (95% CI 0.41, 1.34). In subgroup analysis, the LAMS and the BFMS showed the same outcomes. Compared to DPS, LAMS had better clinical outcomes and fewer side effects when treating patients with WON. What is the best endoscopic treatment option for the walled-off necrosis (WON)?A brief comparison of lumen-apposing metal stents (LAMS), bi-flanged metallic stents (BFMS) and double-pigtail plastic stents (DPS) for the treatment of WON patients.How can we limit the adverse events and provide better treatment. What is the best endoscopic treatment option for the walled-off necrosis (WON)? A brief comparison of lumen-apposing metal stents (LAMS), bi-flanged metallic stents (BFMS) and double-pigtail plastic stents (DPS) for the treatment of WON patients. How can we limit the adverse events and provide better treatment.
FIREcaller: Detecting frequently interacting regions from Hi-C data
Creators: name: Hu, M.
name: Abnousi, A.
name: Crowley, C.
name: Wu, D.
name: Plewczyński, D.
name: Hu, B.
name: Lipiński, J.
name: Abnousi, A.
name: Plewczyński, D.
name: Ren, B.
name: Won, H.
name: Lipiński, J.
name: Yang, Y.
name: Wu, D.
name: Qiu, Y.
name: Crowley, C.
name: Hu, M.
name: Li, Y.
name: Qiu, Y.
name: Hu, B.
name: Ren, B.
name: Won, H.
name: Li, Y.
name: Yang, Y.
Publisher: name: Elsevier B.V.
Year: 2021

description: Hi-C experiments have been widely adopted to study chromatin spatial organization, which plays an essential role in genome function. We have recently identified frequently interacting regions (FIREs) and found that they are closely associated with cell-type-specific gene regulation. However, computational tools for detecting FIREs from Hi-C data are still lacking. In this work, we present FIREcaller, a stand-alone, user-friendly R package for detecting FIREs from Hi-C data. FIREcaller takes raw Hi-C contact matrices as input, performs within-sample and cross-sample normalization, and outputs continuous FIRE scores, dichotomous FIREs, and super-FIREs. Applying FIREcaller to Hi-C data from various human tissues, we demonstrate that FIREs and super-FIREs identified, in a tissue-specific manner, are closely related to gene regulation, are enriched for enhancer-promoter (E-P) interactions, tend to overlap with regions exhibiting epigenomic signatures of cis-regulatory roles, and aid the interpretation or GWAS variants. The FIREcaller package is implemented in R and freely available at https://yunliweb.its.unc.edu/FIREcaller.
Nidān: International Journal for the Study of Hinduism
Creators: name: Editorial Team, The
Publisher: name: Nidān: International Journal for Indian Studies
Year: 2023

description: Complete issue of Nidān 24(1) December 2012: Fierce Goddesses of South Asia
description: Nidān: International Journal for Indian Studies, Vol. 24 No. 1 (2012): Nidān: International Journal for the Study of Hinduism
Additional file 2 of Household expenditure of smokers and ex-smokers across socioeconomic groups: results from a large nationwide Australian longitudinal survey
Creators: name: Lal, Anita
name: Mohebi, Mohammadreza
name: White, Sarah L.
name: Scollo, Michelle
name: McCaffrey, Nikki
Publisher: name: figshare
Year: 2022
Subjects: subject: Medicine
subject: Biotechnology
subject: 59999 Environmental Sciences not elsewhere classified
subject: FOS: Earth and related environmental sciences
subject: 69999 Biological Sciences not elsewhere classified
subject: FOS: Biological sciences
subject: Cancer
subject: Science Policy

description: Additional file 2.
CUE: CpG impUtation ensemble for DNA methylation levels across the human methylation450 (HM450) and EPIC (HM850) BeadChip platforms
Creators: name: Li, Y.
name: Fry, R.C.
name: Fry, R.C.
name: O'Shea, T.M.
name: Li, G.
name: Santos, H.P., Jr.
name: Miller, M.W.
name: Raffield, L.
name: Logue, M.
name: Miller, M.W.
name: Li, Y.
name: O'Shea, T.M.
name: Santos, H.P., Jr.
name: Logue, M.
name: Raffield, L.
name: Li, G.
Publisher: name: Bellwether Publishing, Ltd.
Year: 2021

description: DNA methylation at CpG dinucleotides is one of the most extensively studied epigenetic marks. With technological advancements, geneticists can profile DNA methylation with multiple reliable approaches. However, profiling platforms can differ substantially in the CpGs they assess, consequently hindering integrated analysis across platforms. Here, we present CpG impUtation Ensemble (CUE), which leverages multiple classical statistical and modern machine learning methods, to impute from the Illumina HumanMethylation450 (HM450) BeadChip to the Illumina HumanMethylationEPIC (HM850) BeadChip. Data were analysed from two population cohorts with methylation measured both by HM450 and HM850: the Extremely Low Gestational Age Newborns (ELGAN) study (n = 127, placenta) and the VA Boston Posttraumatic Stress Disorder (PTSD) genetics repository (n = 144, whole blood). Cross-validation results show that CUE achieves the lowest predicted root-mean-square error (RMSE) (0.026 in PTSD) and the highest accuracy (99.97% in PTSD) compared with five individual methods tested, including k-nearest-neighbours, logistic regression, penalized functional regression, random forest, and XGBoost. Finally, among all 339,033 HM850-only CpG sites shared between ELGAN and PTSD, CUE successfully imputed 289,604 (85.4%) sites, where success was defined as RMSE < 0.05 and accuracy >95% in PTSD. In summary, CUE is a valuable tool for imputing CpG methylation from the HM450 to HM850 platform.
Nidān: International Journal for the Study of Hinduism
Creators: name: Editorial Team, The
Publisher: name: Nidān: International Journal for Indian Studies
Year: 2023

description: Complete issue of Nidān 25(1) December 2013
description: Nidān: International Journal for Indian Studies, Vol. 25 No. 1 (2013): Nidān: International Journal for the Study of Hinduism
Nidān: International Journal for the Study of Hinduism
Creators: name: Editorial Team, The
Publisher: name: Nidān: International Journal for Indian Studies
Year: 2023

description: Complete issue of Nidān 26(1) July 2014
description: Nidān: International Journal for Indian Studies, Vol. 26 No. 1 (2014): Nidān: International Journal for the Study of Hinduism
Cell-type-specific 3D epigenomes in the developing human cortex
Creators: name: Jones, I.R.
name: Maliskova, L.s
name: Juric, I.
name: Yang, X.
name: Choudhary, M.N.K.
name: Wang, T.
name: Abnousi, A.
name: Li, Y.
name: Lee, J.
name: Bergenholtz, S.
name: Yang, X.
name: Pebworth, M.-P.
name: Lee, J.
name: Li, B.
name: Li, Y.
name: Kriegstein, A.R.
name: Abnousi, A.
name: Song, M.
name: Fan, C.
name: Wang, T.
name: Hu, M.
name: Shen, Y.
name: Rosen, J.D.
name: Maliskova, L.s
name: Liu, W.
name: Bergenholtz, S.
name: Rosen, J.D.
name: Pollen, A.A.
name: Kriegstein, A.R.
name: Hu, M.
name: Pebworth, M.-P.
name: Li, B.
name: Cui, X.
name: Wen, J.
name: Pollen, A.A.
name: Cui, X.
name: Eze, U.C.
name: Shen, Y.
name: Eze, U.C.
name: Liu, W.
name: Jones, I.R.
name: Juric, I.
name: Wen, J.
name: Song, M.
name: Choudhary, M.N.K.
name: Fan, C.
Publisher: name: Nature Research
Year: 2020

description: Lineage-specific epigenomic changes during human corticogenesis have been difficult to study owing to challenges with sample availability and tissue heterogeneity. For example, previous studies using single-cell RNA sequencing identified at least 9 major cell types and up to 26 distinct subtypes in the dorsal cortex alone1,2. Here we characterize cell-type-specific cis-regulatory chromatin interactions, open chromatin peaks, and transcriptomes for radial glia, intermediate progenitor cells, excitatory neurons, and interneurons isolated from mid-gestational samples of the human cortex. We show that chromatin interactions underlie several aspects of gene regulation, with transposable elements and disease-associated variants enriched at distal interacting regions in a cell-type-specific manner. In addition, promoters with increased levels of chromatin interactivity—termed super-interactive promoters—are enriched for lineage-specific genes, suggesting that interactions at these loci contribute to the fine-tuning of transcription. Finally, we develop CRISPRview, a technique that integrates immunostaining, CRISPR interference, RNAscope, and image analysis to validate cell-type-specific cis-regulatory elements in heterogeneous populations of primary cells. Our findings provide insights into cell-type-specific gene expression patterns in the developing human cortex and advance our understanding of gene regulation and lineage specification during this crucial developmental window.
Dolomìa: a digital platform for migrant associations in South Tyrol
Creators: name: Obukhova, Kseniia
name:  Marti, Hannah Verena
name: Scroppo, Sofia
Publisher: name: Eurac Research
Year: 2022

description: Migration studies consider the voluntary sector as a fundamental element of integration and inclusion processes. Not only do new citizens participate in and benefit from the activities of local voluntary associations, but they are also the protagonists/founders of new associations. In a recent local project in South Tyrol, we asked ourselves: what instruments are best suited to support these organizations?
Spatial access to Emergency General Surgery (EGS) services and EGS bypass behaviours in California
Creators: name: Han, Jiuying
name: Wan, Neng
name: Brewer, Simon C.
name: McCrum, Marta
Publisher: name: Taylor & Francis
Year: 2023
Subjects: subject: Medicine
subject: 59999 Environmental Sciences not elsewhere classified
subject: FOS: Earth and related environmental sciences
subject: Sociology
subject: FOS: Sociology
subject: 69999 Biological Sciences not elsewhere classified
subject: FOS: Biological sciences
subject: 80699 Information Systems not elsewhere classified
subject: FOS: Computer and information sciences
subject: Cancer
subject: Science Policy

description: Hospital bypass behaviours (i.e. people go to faraway hospitals instead of close ones) of Emergency General Surgery (EGS) patients may cause treatment delays and worsened health outcomes. This study aimed to find the associations between EGS bypass behaviours and spatial access to EGS services as well as other factors at the individual level and ZIP Code Tabulation Area (ZCTA) level in California. We used a gravity model to calculate spatial access to EGS services at the ZCTA level. A Bayesian hierarchical spatial model was used to access associated variables of EGS bypass while accounting for spatial autocorrelation. Results show that better spatial access to EGS hospitals was associated with lower likelihood of EGS bypass. Other factors such as rural–urban status, health insurance type and race/ethnicity were also related to EGS bypass behaviours. Besides, people with similar EGS bypass behaviours seemed to cluster together due to spatial effect. Our results have important implications for EGS resource allocation, utilization and EGS disparity alleviation.
Additional file 1 of Scalable, ultra-fast, and low-memory construction of compacted de Bruijn graphs with Cuttlefish 2
Creators: name: Khan, Jamshed
name: Kokot, Marek
name: Deorowicz, Sebastian
name: Patro, Rob
Publisher: name: figshare
Year: 2022
Subjects: subject: Space Science
subject: Genetics
subject: FOS: Biological sciences
subject: 69999 Biological Sciences not elsewhere classified
subject: 80699 Information Systems not elsewhere classified
subject: FOS: Computer and information sciences
subject: 19999 Mathematical Sciences not elsewhere classified
subject: FOS: Mathematics
subject: 110309 Infectious Diseases
subject: FOS: Health sciences

description: Additional file 1. Supplementary material for “Scalable, ultra-fast, and low-memory construction of compacted de Bruijn graphs with Cuttlefish 2”. References [84–88] are cited in order in the supplementary material.
The circadian clock shapes the Arabidopsis transcriptome by regulating alternative splicing and alternative polyadenylation
Creators: name: Li, Y.
name: Yang, Y.
name: Li, Y.
name: Oztas, O.
name: Sancar, A.
name: Yang, Y.
name: Oztas, O.
name: Sancar, A.
Publisher: name: American Society for Biochemistry and Molecular Biology Inc.
Year: 2020

description: The circadian clock in plants temporally coordinates biological processes throughout the day, synchronizing gene expression with diurnal environmental changes. Circadian oscillator proteins are known to regulate the expression of clock-controlled plant genes by controlling their transcription. Here, using a high-throughput RNA-Seq approach, we examined genome-wide circadian and diurnal control of the Arabidopsis transcriptome, finding that the oscillation patterns of different transcripts of multitranscript genes can exhibit substantial differences and demonstrating that the circadian clock affects posttranscriptional regulation. In parallel, we found that two major posttranscriptional mechanisms, alternative splicing (AS; especially intron retention) and alternative polyadenylation (APA), display circadian rhythmicity resulting from oscillation in the genes involved in AS and APA. Moreover, AS-related genes exhibited rhythmic AS and APA regulation, adding another layer of complexity to circadian regulation of gene expression. We conclude that the Arabidopsis circadian clock not only controls transcription of genes but also affects their posttranscriptional regulation by influencing alternative splicing and alternative polyadenylation.
Nidān: International Journal for the Study of Hinduism
Creators: name: Editorial Team, The
Publisher: name: Nidān: International Journal for Indian Studies
Year: 2023

description: Complete issue of Nidān 26(2) December 2014
description: Nidān: International Journal for Indian Studies, Vol. 26 No. 2 (2014): Nidān: International Journal for the Study of Hinduism
Optimal search strategies of space-time coupled random walkers with finite lifetimes
Creators: name: Campos, D.
name: Abad, E.
name: Méndez, V.
name: Yuste, S. B.
name: Lindenberg, K.
Publisher: name: arXiv
Year: 2015
Subjects: subject: Statistical Mechanics (cond-mat.stat-mech)
subject: FOS: Physical sciences

description: We present a simple paradigm for detection of an immobile target by a space-time coupled random walker with a finite lifetime. The motion of the walker is characterized by linear displacements at a fixed speed and exponentially distributed duration, interrupted by random changes in the direction of motion and resumption of motion in the new direction with the same speed. We call these walkers "mortal creepers". A mortal creeper may die at any time during its motion according to an exponential decay law characterized by a finite mean death rate $ω_m$. While still alive, the creeper has a finite mean frequency $ω$ of change of the direction of motion. In particular, we consider the efficiency of the target search process, characterized by the probability that the creeper will eventually detect the target. Analytic results confirmed by numerical results show that there is an $ω_m$-dependent optimal frequency $ω=ω_{opt}$ that maximizes the probability of eventual target detection. We work primarily in one-dimensional ($d=1$) domains and examine the role of initial conditions and of finite domain sizes. Numerical results in $d=2$ domains confirm the existence of an optimal frequency of change of direction, thereby suggesting that the observed effects are robust to changes in dimensionality. In the $d=1$ case, explicit expressions for the probability of target detection in the long time limit are given. In the case of an infinite domain, we compute the detection probability for arbitrary times and study its early- and late-time behavior. We further consider the survival probability of the target in the presence of many independent creepers beginning their motion at the same location and at the same time. We also consider a version of the standard "target problem" in which many creepers start at random locations at the same time.
description: 18 pages, 7 figures. The title has been changed with respect to the one in the previous version
Additional file 2 of Scalable, ultra-fast, and low-memory construction of compacted de Bruijn graphs with Cuttlefish 2
Creators: name: Khan, Jamshed
name: Kokot, Marek
name: Deorowicz, Sebastian
name: Patro, Rob
Publisher: name: figshare
Year: 2022
Subjects: subject: Space Science
subject: Genetics
subject: FOS: Biological sciences
subject: 69999 Biological Sciences not elsewhere classified
subject: 80699 Information Systems not elsewhere classified
subject: FOS: Computer and information sciences
subject: 19999 Mathematical Sciences not elsewhere classified
subject: FOS: Mathematics
subject: 110309 Infectious Diseases
subject: FOS: Health sciences

description: Additional file 2. Review history.
Age-related DNA hydroxymethylation is enriched for gene expression and immune system processes in human peripheral blood
Creators: name: Kiel, D.P.
name: Huang, L.
name: Li, R.
name: Yang, Y.
name: Yang, Y.
name: Jin, P.
name: Huang, L.
name: Li, R.
name: Murabito, J.M.
name: Johnson, N.D.
name: Grant, C.
name: Whitsel, E.A.
name: Jin, P.
name: Murabito, J.M.
name: Wu, H.
name: Johnson, N.D.
name: Conneely, K.N.
name: Kim, H.R.
name: Li, Y.
name: Li, Y.
name: Baccarelli, A.A.
name: Kim, H.R.
name: Wu, H.
name: Kiel, D.P.
name: Baccarelli, A.A.
name: Whitsel, E.A.
name: Conneely, K.N.
name: Grant, C.
Publisher: name: Taylor and Francis Inc.
Year: 2020

description: DNA methylation (DNAm) has a well-established association with age in many tissues, including peripheral blood mononuclear cells (PBMCs). Compared to DNAm, the closely related epigenetic modification known as DNA hydroxymethylation (DNAhm) was much more recently discovered in mammals. Preliminary investigations have observed a positive correlation between gene body DNAhm and cis-gene expression. While some of these studies have observed an association between age and global DNAhm, none have investigated region-specific age-related DNAhm in human blood samples. In this study, we investigated DNAhm and gene expression in PBMCs of 10 young and 10 old, healthy female volunteers. Thousands of regions were differentially hydroxymethylated in the old vs. young individuals in gene bodies, exonic regions, enhancers, and promoters. Consistent with previous work, we observed directional consistency between age-related differences in DNAhm and gene expression. Further, age-related DNAhm and genes with high levels of DNAhm were enriched for immune system processes which may support a role of age-related DNAhm in immunosenescence.
Inferring Regulatory Networks From Mixed Observational Data Using Directed Acyclic Graphs
Creators: name: Dong, L.
name: Li, Q.
name: Li, Y.
name: Wu, D.
name: Dong, L.
name: Poston, T.B.
name: Mohlke, K.L.
name: Spracklen, C.N.
name: Zheng, X.
name: Li, Q.
name: Poston, T.B.
name: Zhong, W.
name: Darville, T.
name: Zheng, X.
name: Darville, T.
name: Wu, D.
name: Li, Y.
name: Mohlke, K.L.
name: Zhong, W.
name: Spracklen, C.N.
Publisher: name: Frontiers Media S.A.
Year: 2020

description: Construction of regulatory networks using cross-sectional expression profiling of genes is desired, but challenging. The Directed Acyclic Graph (DAG) provides a general framework to infer causal effects from observational data. However, most existing DAG methods assume that all nodes follow the same type of distribution, which prohibit a joint modeling of continuous gene expression and categorical variables. We present a new mixed DAG (mDAG) algorithm to infer the regulatory pathway from mixed observational data containing both continuous variables (e.g. expression of genes) and categorical variables (e.g. categorical phenotypes or single nucleotide polymorphisms). Our method can identify upstream causal factors and downstream effectors closely linked to a variable and generate hypotheses for causal direction of regulatory pathways. We propose a new permutation method to test the conditional independence of variables of mixed types, which is the key for mDAG. We also utilize an L1 regularization in mDAG to ensure it can recover a large sparse DAG with limited sample size. We demonstrate through extensive simulations that mDAG outperforms two well-known methods in recovering the true underlying DAG. We apply mDAG to a cross-sectional immunological study of Chlamydia trachomatis infection and successfully infer the regularity network of cytokines. We also apply mDAG to a large cohort study, generating sensible mechanistic hypotheses underlying plasma adiponectin level. The R package mDAG is publicly available from CRAN at https://CRAN.R-project.org/package=mDAG.
Additional file 1 of Protein citrullination marks myelin protein aggregation and disease progression in mouse ALS models
Creators: name: Yusuf, Issa O.
name: Qiao, Tao
name: Parsi, Sepideh
name: Tilvawala, Ronak
name: Thompson, Paul R.
name: Xu, Zuoshang
Publisher: name: figshare
Year: 2022
Subjects: subject: Biophysics
subject: Biochemistry
subject: Medicine
subject: Genetics
subject: FOS: Biological sciences
subject: Molecular Biology
subject: Neuroscience
subject: Physiology
subject: 39999 Chemical Sciences not elsewhere classified
subject: FOS: Chemical sciences
subject: Cancer
subject: Hematology

description: Additional file 1: Table S1. List of Primary Antibodies used in the Study. Table S2. List of Secondary Antibodies used in the Study.
SAME-clustering: Single-cell Aggregated Clustering via Mixture Model Ensemble
Creators: name: Jiang, Y.
name: Shen, Y.
name: Li, Y.
name: Yang, Y.
name: Li, Y.
name: Huh, R.
name: Jiang, Y.
name: Yang, Y.
name: Shen, Y.
name: Huh, R.
Publisher: name: Oxford University Press
Year: 2020

description: Clustering is an essential step in the analysis of single cell RNA-seq (scRNA-seq) data to shed light on tissue complexity including the number of cell types and transcriptomic signatures of each cell type. Due to its importance, novel methods have been developed recently for this purpose. However, different approaches generate varying estimates regarding the number of clusters and the single-cell level cluster assignments. This type of unsupervised clustering is challenging and it is often times hard to gauge which method to use because none of the existing methods outperform others across all scenarios. We present SAME-clustering, a mixture model-based approach that takes clustering solutions from multiple methods and selects a maximally diverse subset to produce an improved ensemble solution. We tested SAME-clustering across 15 scRNA-seq datasets generated by different platforms, with number of clusters varying from 3 to 15, and number of single cells from 49 to 32 695. Results show that our SAME-clustering ensemble method yields enhanced clustering, in terms of both cluster assignments and number of clusters. The mixture model ensemble clustering is not limited to clustering scRNA-seq data and may be useful to a wide range of clustering applications.
title: Diseuse de bonne aventure
title: Fortune teller
Creators: name: Li, Juan
Publisher: name: Pangloss
Year: 2022
Subjects: subject: Linguistique
subject: Tai Lue

description: This is an staged communicative event: the consultant is asked to describe in her own words what she observes regarding the pictoral Totem Field Storyboards called "the Fortune Teller" (Lisa Matthewson, www. totemfieldstoryboards.ca).
Generalized multi-SNP mediation intersection–union test
Creators: name:  Darville, T.
name:  Darville, T.
name:  Zheng, X.
name:  Fine, J.
name:  Zheng, X.
name:  Li, Y.
name: Zhong, W.
name:  Fine, J.
name:  Li, Y.
name: Zhong, W.
Publisher: name: Blackwell Publishing Inc.
Year: 2020

description: To elucidate the molecular mechanisms underlying genetic variants identified from genome-wide association studies (GWAS) for a variety of phenotypic traits encompassing binary, continuous, count, and survival outcomes, we propose a novel and flexible method to test for mediation that can simultaneously accommodate multiple genetic variants and different types of outcome variables. Specifically, we employ the intersection–union test approach combined with the likelihood ratio test to detect mediation effect of multiple genetic variants via some mediator (e.g., the expression of a neighboring gene) on outcome. We fit high-dimensional generalized linear mixed models under the mediation framework, separately under the null and alternative hypothesis. We leverage Laplace approximation to compute the marginal likelihood of outcome and use coordinate descent algorithm to estimate corresponding parameters. Our extensive simulations demonstrate the validity of our proposed methods and substantial, up to 97%, power gains over alternative methods. Applications to real data for the study of Chlamydia trachomatis infection further showcase advantages of our methods. We believe our proposed methods will be of value and general interest in this post-GWAS era to disentangle the potential causal mechanism from DNA to phenotype for new drug discovery and personalized medicine.
SAFE-clustering: Single-cell Aggregated (from Ensemble) clustering for single-cell RNA-seq data
Creators: name:  Love, M.I.
name:  Culpepper, H.W.
name:  Lin, Y.
name:  Li, Y.
name:  Lin, Y.
name: Yang, Y.
name:  Love, M.I.
name:  Li, Y.
name:  Culpepper, H.W.
name: Yang, Y.
name:  Huh, R.
name:  Huh, R.
Publisher: name: Oxford University Press
Year: 2019

description: Motivation: Accurately clustering cell types from a mass of heterogeneous cells is a crucial first step for the analysis of single-cell RNA-seq (scRNA-Seq) data. Although several methods have been recently developed, they utilize different characteristics of data and yield varying results in terms of both the number of clusters and actual cluster assignments. Results: Here, we present SAFE-clustering, single-cell aggregated (From Ensemble) clustering, a flexible, accurate and robust method for clustering scRNA-Seq data. SAFE-clustering takes as input, results from multiple clustering methods, to build one consensus solution. SAFE-clustering currently embeds four state-of-the-art methods, SC3, CIDR, Seurat and t-SNE þ k-means; and ensembles solutions from these four methods using three hypergraph-based partitioning algorithms. Extensive assessment across 12 datasets with the number of clusters ranging from 3 to 14, and the number of single cells ranging from 49 to 32, 695 showcases the advantages of SAFEclustering in terms of both cluster number (18.2-58.1% reduction in absolute deviation to the truth) and cluster assignment (on average 36.0% improvement, and up to 18.5% over the best of the four methods, measured by adjusted rand index). Moreover, SAFE-clustering is computationally efficient to accommodate large datasets, taking <10 min to process 28 733 cells.
title: Choroidal metastasis in a patient with multimetastatic papillary thyroid carcinoma
Creators: name: Christodoulou, Maria Veatriki
Publisher: name: EURORAD
Year: 2024
Subjects: subject: Neuroradiology
subject: CNS
subject: Eyes
subject: Oncology
subject: Thyroid / Parathyroids
subject: CT
subject: MR
subject: Metastases
subject: Clinical Case

description: Clinical History: Thyroidectomy was performed on a 49-year-old woman with multinodular goitre, revealing papillary thyroid cancer (PTC). Despite multiple radioactive iodine (RAI) and systemic therapies, metastases spread to her cervical lymph nodes, lungs and mediastinum. Three years post-diagnosis, she presented with blurred vision of the right eye.

description: 49 years, female