bluuebunny/crossref_metadata_2025_split huggingface dataset:
Delirium Assessment in Acute Stroke: A Systematic Review and Meta-Analysis of Incidence, Assessment Tools, and Assessment Frequencies
Authors: Stokholm Jannik , Steenholt Janni Vagner , Csilag Claudio , Kjær Troels Wesenberg , Christensen Thomas 
Published: December 2019

Purpose: The purpose of this systematic literature review was to examine whether different assessment methods contribute to the variance in delirium incidence detected in populations of patients with acute stroke. Specifically, the aim was to address the influence of (1) choice of assessment tool, (2) frequency of assessment, and (3) type of health professional doing the assessment. Methods: We searched MEDLINE, EMBASE, and PsycINFO and included pro- and retrospective cohort studies assessing delirium during hospitalization of adult acute stroke patients. Results: In 30 articles, 24 unique populations were identified and included in the review. Delirium incidence ranged from 1.4% to 75.6% in total and a chi-square test showed a significant heterogeneity across studies (χ2 = 536.5, df = 23, P < .0001). No studies had an assessment for delirium before a patient entered the study. No specific patterns regarding the influence of tool, assessment frequency or health professional were discernible. Discussion: Subgroups analyses were not conducted due to the heterogeneity across studies. Studies comparing delirium assessment tools directly with each other are needed. Conclusions: Delirium is a common complication in acute stroke. No firm conclusions about a possible correlation of choice of tool, assessment frequency, and delirium incidence could be made due to the great heterogeneity of the study populations. Only 1 study compared 2 tools directly with each other. Further studies comparing delirium assessment tools directly with each other are needed.
Hidradenitis suppurativa: infection, autoimmunity, or both?
Authors: Constantinou Costas A , Fragoulis George E , Nikiphorou Elena 
Published: December 2019

Hidradenitis suppurativa (HS) is a chronic inflammatory skin disease mainly affecting areas rich in apocrine glands. Clinically, is characterized by painful subcutaneous nodules and if left untreated to pus secretion, abscess and fistula formation. Its frequency is estimated to be 0.5–4% of the general population, affecting women more often. Pathogenesis of HS is still not clearly defined. It seems to be a combination of genetic factors with alterations in the skin microbiome. Furthermore, at tissue (i.e. skin) as well as at serum level, several inflammatory cytokines are upregulated. The most important of the latter are tumor necrosis factor (TNF), interleukin (IL)-1, IL-17, and IL-23. Adding another level of complexity, it has been suggested that keratinocytes might be intrinsically activated, contributing also to the observed inflammation. Interestingly, it has been noted that frequency of HS is increased in some autoimmune rheumatic diseases, such as spondyloarthropathies (SpA). Of note, both HS and SpA have relatively strong association with metabolic diseases and obesity implying that there are indeed some common underlying pathophysiological pathways. Although no specific microbe has been identified, alterations in the microbiome of the skin of these patients have been reported. Of note, microbes with a capability for biofilm formation are abundant. Treatment of HS among others, include antibiotics as well as biologic drugs targeting TNF and other cytokines and used for autoimmune rheumatic diseases. Herein, we review the current evidence on links between HS and autoimmune diseases and infectious diseases with a focus on epidemiology and pathophysiology.
Effects of PM2.5 and PM10 on congenital hypothyroidism in Qingdao, China, 2014–2017: a quantitative analysis
Authors: Pan Silin , Ni Wei , Li Wenjie , Li Guoju , Xing Quansheng 
Published: December 2019

Background: We aimed to quantify the impact of PM2.5 and PM10 pollution on congenital hypothyroidism (CH) in Qingdao in the period 2014–2017. Methods: A generalized additive mixed model (GAMM) with time-series Poisson regression was conducted to quantify the association between PM2.5 and PM10 variables in the month when cases of CH were born or in the two preceding the months (lag0, lag1 and lag2) and monthly morbidity of people with CH across different populations. Results: A total of 480,633 newborns were screened for CH during 2014–2017 in Qingdao, and there were 268 cases of CH diagnosed. The count of days per month for which average concentrations of PM2.5 and PM10 exceed legal limits were positively associated with monthly CH morbidity at lag1 month among all the populations, and the adjusted relative risks (RRs) with exposure per 10 μg/m3 were close among different populations. However, the number of days per month of PM2.5 and PM10 concentrations exceeding limits were negatively associated with CH morbidity. Additionally, the RRs of CH increase with worsening air pollution. Conclusions: Concentrations of PM2.5 and PM10 exceeding the legal limits are significantly associated with CH in Qingdao. Moreover, it suggests that sudden and short-term particulate matter pollution events with high levels of particulates exceeding the legal limits may be related to risk of CH.
Organizing a Victory: A Review Essay on the BJP’s 2014 Electoral Success
Authors: Singh Rajkamal , Goel Garima 
Published: December 2019

Suhas Palshikar, Sanjay Kumar and Sanjay Lodha (Eds.), Electoral Politics in India: The Resurgence of the Bharatiya Janata Party. London and New York: Routledge. 2017. 312 pages. ₹995. Ashutosh Kumar and Yatindra Singh Sisodia (Eds.), How India Votes: A State-by-State Look. New Delhi: Orient BlackSwan. 2019. 443 pages. ₹1395. Prashant Jha, How the BJP Wins: Inside India’s Greatest Election Machine. New Delhi: Juggernaut Books. 2017. 235 pages. ₹399. Rajdeep Sardesai, ‘2014: The Election that Changed India’. Gurgaon: Penguin Books India. 378 pages. ₹399.
High Tibial Osteotomy Survivorship: A Population-Based Study
Authors: Pannell William C. , Heidari Keemia Soraya , Mayer Erik Norman , Zimmerman Kathrin , Heckmann Nathanael , McKnight Braden , Hill Jeffrey Ryan , Vangsness Carleton Thomas , Hatch George Frederick , Weber Alexander Evan 
Published: December 2019

Background: High tibial osteotomy (HTO) was developed to treat early medial compartment osteoarthritis in varus knees. Purpose: To evaluate the midterm and long-term outcomes of HTO in a large population-based cohort of patients. Study Design: Case-control study; Level of evidence, 3. Methods: Data from the California Office of Statewide Health Planning and Development were used to identify patients undergoing HTO from 2000 to 2014. Patients with infectious arthritis, rheumatological disease, congenital deformities, malignancy, concurrent arthroplasty, or skeletal trauma were excluded. Demographic information was assessed for every patient. Failure was defined as conversion to total or unicompartmental knee arthroplasty. Differences between patients requiring arthroplasty and those who did not were identified using univariate analysis. Multivariate analysis was performed, and Kaplan-Meier survivorship estimates for 5- and 10-year survival were computed. Results: A total of 1576 procedures were identified between 2000 and 2014; of these, 358 procedures were converted to arthroplasty within 10 years. Patients who went on to arthroplasty after HTO were older (48.23 ± 6.76 vs 42.66 ± 9.80 years, respectively; P < .001), had a higher incidence of hypertension (25.42% vs 17.82%, respectively; P = .001), and had a higher likelihood of having ≥1 comorbidity (38.0% vs 31.4%, respectively; P = .044). Patients were 8% more likely to require arthroplasty for each additional year in age (relative risk [RR], 1.08). Female patients were also at an increased risk of conversion to arthroplasty compared with male patients (RR, 1.38). Survivorship at 5 and 10 years was 80% and 56%, respectively, and the median time to failure was 5.1 years. Conclusion: HTO may provide long-term survival in select patients. Careful consideration should be given to patient age, sex, and osteoarthritis of the knee when selecting patients for this procedure.
Biomarkers of meat and seafood intake: an extensive literature review
Authors: Cuparencu Cătălina , Praticó Giulia , Hemeryck Lieselot Y. , Sri Harsha Pedapati S. C. , Noerman Stefania , Rombouts Caroline , Xi Muyao , Vanhaecke Lynn , Hanhineva Kati , Brennan Lorraine , Dragsted Lars O. 
Published: December 2019

AbstractMeat, including fish and shellfish, represents a valuable constituent of most balanced diets. Consumption of different types of meat and fish has been associated with both beneficial and adverse health effects. While white meats and fish are generally associated with positive health outcomes, red and especially processed meats have been associated with colorectal cancer and other diseases.The contribution of these foods to the development or prevention of chronic diseases is still not fully elucidated. One of the main problems is the difficulty in properly evaluating meat intake, as the existing self-reporting tools for dietary assessment may be imprecise and therefore affected by systematic and random errors. Dietary biomarkers measured in biological fluids have been proposed as possible objective measurements of the actual intake of specific foods and as a support for classical assessment methods. Good biomarkers for meat intake should reflect total dietary intake of meat, independent of source or processing and should be able to differentiate meat consumption from that of other protein-rich foods; alternatively, meat intake biomarkers should be specific to each of the different meat sources (e.g., red vs. white; fish, bird, or mammal) and/or cooking methods. In this paper, we present a systematic investigation of the scientific literature while providing a comprehensive overview of the possible biomarker(s) for the intake of different types of meat, including fish and shellfish, and processed and heated meats according to published guidelines for biomarker reviews (BFIrev). The most promising biomarkers are further validated for their usefulness for dietary assessment by published validation criteria.
The exploration of disease-specific gene regulatory networks in esophageal carcinoma and stomach adenocarcinoma
Authors: Qin Guimin , Yang Luqiong , Ma Yuying , Liu Jiayan , Huo Qiuyan 
Published: December 2019

Abstract
Background
Feed-forward loops (FFLs), consisting of miRNAs, transcription factors (TFs) and their common target genes, have been validated to be important for the initialization and development of complex diseases, including cancer. Esophageal Carcinoma (ESCA) and Stomach Adenocarcinoma (STAD) are two types of malignant tumors in the digestive tract. Understanding common and distinct molecular mechanisms of ESCA and STAD is extremely crucial.

Results
In this paper, we presented a computational framework to explore common and distinct FFLs, and molecular biomarkers for ESCA and STAD. We identified FFLs by combining regulation pairs and RNA-seq data. Then we constructed disease-specific co-expression networks based on the FFLs identified. We also used random walk with restart (RWR) on disease-specific co-expression networks to prioritize candidate molecules. We identified 148 and 242 FFLs for these two types of cancer, respectively. And we found that one TF, E2F3 was related to ESCA, two genes, DTNA and KCNMA1 were related to STAD, while one TF ESR1 and one gene KIT were associated with both of the two types of cancer.

Conclusions
This proposed computational framework predicted disease-related biomolecules effectively and discovered the correlation between two types of cancers, which helped develop the diagnostic and therapeutic strategies of Esophageal Carcinoma and Stomach Adenocarcinoma.
Modelling TERT regulation across 19 different cancer types based on the MIPRIP 2.0 gene regulatory network approach
Authors: Poos Alexandra M. , Kordaß Theresa , Kolte Amol , Ast Volker , Oswald Marcus , Rippe Karsten , König Rainer 
Published: December 2019

AbstractBackgroundReactivation of the telomerase reverse transcriptase geneTERTis a central feature for unlimited proliferation of the majority of cancers. However, the underlying regulatory processes are only partly understood.ResultsWe assembled regulator binding information from serveral sources to construct a generic human and mouse gene regulatory network. Advancing our “Mixed Integer linear Programming based Regulatory Interaction Predictor” (MIPRIP) approach, we identified the most common and cancer-type specific regulators ofTERTacross 19 different human cancers. The results were validated by using the well-knownTERTregulation by the ETS1 transcription factor in a subset of melanomas with mutations in theTERTpromoter.Our improved MIPRIP2 R-package and the associated generic regulatory networks are freely available athttps://github.com/KoenigLabNM/MIPRIP.ConclusionMIPRIP 2.0 identified common as well as tumor type specific regulators ofTERT. The software can be easily applied to transcriptome datasets to predict gene regulation for any gene and disease/condition under investigation.
ZDOG: zooming in on dominating genes with mutations in cancer pathways
Authors: Alberts Rudi , Chen Jinyu , Zhang Louxin 
Published: December 2019

Abstract
Background
Inference of cancer-causing genes and their biological functions are crucial but challenging due to the heterogeneity of somatic mutations. The heterogeneity of somatic mutations reveals that only a handful of oncogenes mutate frequently and a number of cancer-causing genes mutate rarely.

Results
We develop a Cytoscape app, named ZDOG, for visualization of the extent to which mutated genes may affect cancer pathways using the dominating tree model. The dominator tree model allows us to examine conveniently the positional importance of a gene in cancer signalling pathways. This tool facilitates the identification of mutated “master” regulators even with low mutation frequency in deregulated signalling pathways.

Conclusions
We have presented a model for facilitating the examination of the extent to which mutation in a gene may affect downstream components in a signalling pathway through its positional information. The model is implemented in a user-friendly Cytoscape app which will be freely available upon publication.

Availability
Together with a user manual, the ZDOG app is freely available at GitHub (https://github.com/rudi2013/ZDOG). It is also available in the Cytoscape app store (http://apps.cytoscape.org/apps/ZDOG) and users can easily install it using the Cytoscape App Manager.
Detection and application of genome-wide variations in peach for association and genetic relationship analysis
Authors: Guan Liping , Cao Ke , Li Yong , Guo Jian , Xu Qiang , Wang Lirong 
Published: December 2019

Abstract
Background
Peach (Prunus persica L.) is a diploid species and model plant of the Rosaceae family. In the past decade, significant progress has been made in peach genetic research via DNA markers, but the number of these markers remains limited.

Results
In this study, we performed a genome-wide DNA markers detection based on sequencing data of six distantly related peach accessions. A total of 650,693~1,053,547 single nucleotide polymorphisms (SNPs), 114,227~178,968 small insertion/deletions (InDels), 8386~12,298 structure variants (SVs), 2111~2581 copy number variants (CNVs) and 229,357~346,940 simple sequence repeats (SSRs) were detected and annotated. To demonstrate the application of DNA markers, 944 SNPs were filtered for association study of fruit ripening time and 15 highly polymorphic SSRs were selected to analyze the genetic relationship among 221 accessions.

Conclusions
The results showed that the use of high-throughput sequencing to develop DNA markers is fast and effective. Comprehensive identification of DNA markers, including SVs and SSRs, would be of benefit to genetic diversity evaluation, genetic mapping, and molecular breeding of peach.
Investigating the role of super-enhancer RNAs underlying embryonic stem cell differentiation
Authors: Chang Hao-Chun , Huang Hsuan-Cheng , Juan Hsueh-Fen , Hsu Chia-Lang 
Published: December 2019

Abstract
Background
Super-enhancer RNAs (seRNAs) are a kind of noncoding RNA transcribed from super-enhancer regions. The regulation mechanism and functional role of seRNAs are still unclear. Although super-enhancers play a critical role in the core transcriptional regulatory circuity of embryonic stem cell (ESC) differentiation, whether seRNAs have similar properties should be further investigated.

Results
We analyzed cap analysis gene expression sequencing (CAGE-seq) datasets collected during the differentiation of embryonic stem cells (ESCs) to cardiomyocytes to identify the seRNAs. A non-negative matrix factorization algorithm was applied to decompose the seRNA profiles and reveal two hidden stages during the ESC differentiation. We further identified 95 and 78 seRNAs associated with early- and late-stage ESC differentiation, respectively. We found that the binding sites of master regulators of ESC differentiation, including NANOG, FOXA2, and MYC, were significantly observed in the loci of the stage-specific seRNAs. Based on the investigation of genes coexpressed with seRNA, these stage-specific seRNAs might be involved in cardiac-related functions such as myofibril assembly and heart development and act in trans to regulate the co-expressed genes.

Conclusions
In this study, we used a computational approach to demonstrate the possible role of seRNAs during ESC differentiation.
Sketch distance-based clustering of chromosomes for large genome database compression
Authors: Tang Tao , Liu Yuansheng , Zhang Buzhong , Su Benyue , Li Jinyan 
Published: December 2019

AbstractBackgroundThe rapid development of Next-Generation Sequencing technologies enables sequencing genomes with low cost. The dramatically increasing amount of sequencing data raised crucial needs for efficient compression algorithms. Reference-based compression algorithms have exhibited outstanding performance on compressing single genomes. However, for the more challenging and more useful problem of compressing a large collection ofngenomes, straightforward application of these reference-based algorithms suffers a series of issues such as difficult reference selection and remarkable performance variation.ResultsWe propose an efficient clustering-based reference selection algorithm for reference-based compression within separate clusters of thengenomes. This method clusters the genomes into subsets of highly similar genomes using MinHash sketch distance, and uses the centroid sequence of each cluster as the reference genome for an outstanding reference-based compression of the remaining genomes in each cluster. A final reference is then selected from these reference genomes for the compression of the remaining reference genomes. Our method significantly improved the performance of the-state-of-art compression algorithms on large-scale human and rice genome databases containing thousands of genome sequences. The compression ratio gain can reach up to 20-30% in most cases for the datasets from NCBI, the 1000 Human Genomes Project and the 3000 Rice Genomes Project. The best improvement boosts the performance from 351.74 compression folds to 443.51 folds.ConclusionsThe compression ratio of reference-based compression on large scale genome datasets can be improved via reference selection by applying appropriate data preprocessing and clustering methods. Our algorithm provides an efficient way to compress large genome database.
Human protein-RNA interaction network is highly stable across mammals
Authors: Ramakrishnan Aarthi , Janga Sarath Chandra 
Published: December 2019

Abstract
Background
RNA-binding proteins (RBPs) are crucial in modulating RNA metabolism in eukaryotes thereby controlling an extensive network of RBP-RNA interactions. Although previous studies on the conservation of RBP targets have been carried out in lower eukaryotes such as yeast, relatively little is known about the extent of conservation of the binding sites of RBPs across mammalian species.

Results
In this study, we employ CLIP-seq datasets for 60 human RBPs and demonstrate that most binding sites for a third of these RBPs are conserved in at least 50% of the studied vertebrate species. Across the studied RBPs, binding sites were found to exhibit a median conservation of 58%, ~ 20% higher than random genomic locations, suggesting a significantly higher preservation of RBP-RNA interaction networks across vertebrates. RBP binding sites were highly conserved across primates with weak conservation profiles in birds and fishes. We also note that phylogenetic relationship between members of an RBP family does not explain the extent of conservation of their binding sites across species. Multivariate analysis to uncover features contributing to differences in the extents of conservation of binding sites across RBPs revealed RBP expression level and number of post-transcriptional targets to be the most prominent factors. Examination of the location of binding sites at the gene level confirmed that binding sites occurring on the 3′ region of a gene are highly conserved across species with 90% of the RBPs exhibiting a significantly higher conservation of binding sites in 3′ regions of a gene than those occurring in the 5′. Gene set enrichment analysis on the extent of conservation of binding sites to identify significantly associated human phenotypes revealed an enrichment for multiple developmental abnormalities.

Conclusions
Our results suggest that binding sites of human RBPs are highly conserved across primates with weak conservation profiles in lower vertebrates and evolutionary relationship between members of an RBP family does not explain the extent of conservation of their binding sites. Expression level and number of targets of an RBP are important factors contributing to the differences in the extent of conservation of binding sites. RBP binding sites on 3′ ends of a gene are the most conserved across species. Phenotypic analysis on the extent of conservation of binding sites revealed the importance of lineage-specific developmental events in post-transcriptional regulatory network evolution.
SMaSH: Sample matching using SNPs in humans
Authors: Westphal Maximillian , Frankhouser David , Sonzone Carmine , Shields Peter G. , Yan Pearlly , Bundschuh Ralf 
Published: December 2019

AbstractBackgroundInadvertent sample swaps are a real threat to data quality in any medium to large scale omics studies. While matches between samples from the same individual can in principle be identified from a few well characterized single nucleotide polymorphisms (SNPs), omics data types often only provide low to moderate coverage, thus requiring integration of evidence from a large number of SNPs to determine if two samples derive from the same individual or not.MethodsWe select about six thousand SNPs in the human genome and develop a Bayesian framework that is able to robustly identify sample matches between next generation sequencing data sets.ResultsWe validate our approach on a variety of data sets. Most importantly, we show that our approach can establish identity between different omics data types such as Exome, RNA-Seq, and MethylCap-Seq. We demonstrate how identity detection degrades with sample quality and read coverage, but show that twenty million reads of a fairly low quality RNA-Seq sample are still sufficient for reliable sample identification.ConclusionOur tool, SMASH, is able to identify sample mismatches in next generation sequencing data sets between different sequencing modalities and for low quality sequencing data.