bluuebunny/crossref_metadata_2025_split huggingface dataset:
Dynamic Changes in Brain Mesenchymal Perivascular Cells Associate with Multiple Sclerosis Disease Duration, Active Inflammation, and Demyelination
Authors: Iacobaeus Ellen , Sugars Rachael V. , Törnqvist Andrén Anton , Alm Jessica J. , Qian Hong , Frantzen Janek , Newcombe Jia , Alkass Kanar , Druid Henrik , Bottai Matteo , Röyttä Matias , Le Blanc Katarina 
Published: September 2017

AbstractVascular changes, including blood brain barrier destabilization, are common pathological features in multiple sclerosis (MS) lesions. Blood vessels within adult organs are reported to harbor mesenchymal stromal cells (MSCs) with phenotypical and functional characteristics similar to pericytes. We performed an immunohistochemical study of MSCs/pericytes in brain tissue from MS and healthy persons. Post-mortem brain tissue from patients with early progressive MS (EPMS), late stage progressive MS (LPMS), and healthy persons were analyzed for the MSC and pericyte markers CD146, platelet-derived growth factor receptor beta (PDGFRβ), CD73, CD271, alpha-smooth muscle actin, and Ki67. The MS samples included active, chronic active, chronic inactive lesions, and normal-appearing white matter. MSC and pericyte marker localization were detected in association with blood vessels, including subendothelial CD146+PDGFRβ+Ki67+ cells and CD73+CD271+PDGFRβ+Ki67– cells within the adventitia and perivascular areas. Both immunostained cell subpopulations were termed mesenchymal perivascular cells (MPCs). Quantitative analyses of immunostainings showed active lesions containing increased regions of CD146+PDGFRβ+Ki67+ and CD73+CD271+PDGFRβ+Ki67– MPC subpopulations compared to inactive lesions. Chronic lesions presented with decreased levels of CD146+PDGFRβ+Ki67+ MPC cells compared to control tissue. Furthermore, LPMS lesions displayed increased numbers of blood vessels harboring greatly enlarged CD73+CD271+ adventitial and perivascular areas compared to control and EPMS tissue. In conclusion, we demonstrate the presence of MPC subgroups in control human brain vasculature, and their phenotypic changes in MS brain, which correlated with inflammation, demyelination and MS disease duration. Our findings demonstrate that brain-derived MPCs respond to pathologic mechanisms involved in MS disease progression and suggest that vessel-targeted therapeutics may benefit patients with progressive MS.
Surgical Site Infections in Emergency Abdominal Surgery at Tamale Teaching Hospital, Ghana
Authors: Tabiri Stephen , Yenli Edwin , Kyere Martin , Anyomih Theophilus T. K. 
Published: September 2017

AbstractBackgroundSurgical site infections (SSIs) result in delayed wound healing, increased use of antibiotics and increased length of hospital stay, putting remarkable physical and financial burden on patients, their relatives and the healthcare facilities. Patient‐related factors, such as pre‐existing colonization with antibiotic‐resistant bacteria, and clinical‐related factors, such as adherence to sterile techniques, contribute to the development of SSIs. The objective of this study, therefore, was to determine the SSI rate and risk factors for emergency abdominal surgeries at Tamale Teaching Hospital, Ghana.MethodsThe study population was composed of patients undergoing emergency abdominal surgery at the Tamale Teaching Hospital between June 2010 and June 2015. Demographic and clinical data were collected and included, but was not limited to, patient age and sex, type of procedure performed, wound class (dirty or contaminated), receipt of perioperative blood transfusion, American Society of Anesthesiologists (ASA) score, presence of SSI, length of hospital stay and outcome of surgery. Standard multiple regression was used to statistically assess the independent variables for their association with SSI, and Pearson correlation coefficient was used to determine the strength of association. The beta (β) values, which had the greatest influence on the overall SSI, indicated the relative influence of the entered variable(s).ResultsA total of 1011 patients underwent various emergency abdominal surgical procedures during the period of study. The β values were 0.008 for perioperative blood transfusion, 0.050 for sex, − 0.048 for ASA risk, − 0.001 for having health insurance, 0.037 for being referred from another health facility and 0.034 for age. Sex was the most distinctive contributor to SSI, while perioperative blood transfusion showed the least influence. Sex and ASA score were the best predictors of SSI occurrence. The coefficients of the P values for wound class and serum haemoglobin level (g/dL) were 0.000 and 0.032, respectively. The outcome of surgery was significantly and strongly associated with overall SSI and vice versa (r = 0.088, P < 0.01 two‐tailed).ConclusionSex, ASA score, perioperative blood transfusion, wound class and haemoglobin level can predispose to SSI.
Annual variability in acorn production and pre‐dispersal damage to acorns of four fagaceous species in two adjacent forest stands with different mixed ratios in western Japan
Authors: Hirayama Kimiko , Imai Tatsuo , Enomoto Kosaku , Tachikawa Chieri 
Published: September 2017

AbstractWe investigated the relationships between the annual variation in acorn production and pre‐dispersal insect damage to acorns for 6 years in co‐occurring fagaceous species (Quercus variabilis, Q. serrata, Q. glauca, and Castanopsis cuspidata) in two adjacent forest stands that had different mixed ratios due to succession: a deciduous broad‐leaved forest stand (DB), and an evergreen broad‐leaved forest stand (EB). In C. cuspidata, the annual number of sound acorns correlated with that of female flowers. In contrast, for three Quercus species, the annual variability in sound acorn production was not correlated with that in female flowers, but was affected by the annual fluctuation in the percentage of insect damage in both the stands. For the three Quercus species, the dominant types of insect damage were different among the species, but similar between the two stands: damaged by moth larvae in Q. variabilis, and sap suction by adult weevils in Q. serrata and Q. glauca. Key factor analyses showed that the contribution of the dominant type of insect damage was similar between the two stands for the reproductive loss in Q. variabilis, but was different between the stands in Q. serrata and Q. glauca. Different mixed ratios of fagaceous species might affect the annual variability in sound acorn production via changes in the impact of a particular type of insect damage, even between adjacent stands.
Working with the Hmong Population in a Genetics Setting: an Interpreter Perspective
Authors: Krieger Meghan , Agather Aime , Douglass Kathryn , Reiser Catherine A. , Petty Elizabeth M. 
Published: September 2017

AbstractThe aim of this pilot qualitative study was to describe the experiences and beliefs of medical interpreters when working with genetic counselors and other genetic providers caring for Hmong patients who are not native English speakers. Specific goals were to identify interpreters’ thoughts and perceptions on (a) their roles during sessions, (b) unique challenges in a genetics session, (c) knowledge genetics providers need when working with Hmong patients and interpreters, and (d) supports and training needed to effectively interpret in a genetics setting. Hmong medical interpreters from Wisconsin and Minnesota were invited by email to participate in the study. Six were interviewed by telephone. Participants had worked with a variety of providers including geneticists, genetic counselors, primary care physicians, and oncologists. Factors identified by Hmong interpreters that made interpretation of content difficult in clinical genetics sessions included: time constraints, technical terms, and unique cultural perspectives of Hmong patients. While all respondents felt their primary role was to interpret session content as close to verbatim as possible, there was notable variation in the description of their interpretation style and other perceived roles in the genetic counseling session. Cultural issues genetics providers could consider when working with Hmong patients and different style issues when working with Hmong interpreters are discussed. Ideas for future studies and suggestions to improve communication with Hmong patients are explored.
Factors associated with abdominal pain in patients submitted to colonoscopy
Authors: Bellei Amanda Colpani , Dacoregio Daniela Ghizoni , Bianchini Flávio , Souza Jaime César Gelosa , Bello João Martiniano Lamim , Kock Kaiser de Souza 
Published: September 2017

Abstract
Objective The study evaluated factors associated with abdominal pain during colonoscopy.
Methods This was a cross-sectional observational study that evaluated patients who underwent colonoscopy between February 2014 and February 2015. Physical characteristics, surgical history and previous colonoscopies, indication and current examination conditions, fentanyl and midazolam dose, and pain level were analyzed. Significance level adopted: p
< 0.05. Chi-squared test was used for association of categorical variables, Student's t-test was applied for comparison of means, and Spearman's coefficient was used for correlation.
Results A total of 566 women and 391 men with mean age of 54.81 years and mean BMI of 27,064 were evaluated. Of the total, 29 (3.0%) had mild pain, 42 (4.4%) had moderate pain, and 18 (1.9%) had severe pain. Women were less tolerant (p = 0.011) and had longer cecal intubation times (p = 0.001). Mean duration of colonoscopy and mean dose of midazolam were higher in patients with pain (p = 0.001), (p < 0.001*). Among the 39 patients with an incomplete examination, 8 reported pain (p = 0.049).
Conclusion Female gender and prolonged intubation time were significantly associated with abdominal pain during colonoscopy. Patients with discomfort had a higher failure rate on the exam. Additional doses of midazolam given to patients with pain were not effective.
Phandango: an interactive viewer for bacterial population genomics
Authors: Hadfield James , Croucher Nicholas J , Goater Richard J , Abudahab Khalil , Aanensen David M , Harris Simon R 
Published: September 2017

Abstract

Summary
Fully exploiting the wealth of data in current bacterial population genomics datasets requires synthesizing and integrating different types of analysis across millions of base pairs in hundreds or thousands of isolates. Current approaches often use static representations of phylogenetic, epidemiological, statistical and evolutionary analysis results that are difficult to relate to one another. Phandango is an interactive application running in a web browser allowing fast exploration of large-scale population genomics datasets combining the output from multiple genomic analysis methods in an intuitive and interactive manner.

Availability and implementation
Phandango is a web application freely available for use at www.phandango.net and includes a diverse collection of datasets as examples. Source code together with a detailed wiki page is available on GitHub at https://github.com/jameshadfield/phandango.
Domination, Authority, and the Forms of Chinese Power
Authors: Lake David A 
Published: September 2017

Abstract
The debate about China’s rise and future United States–China relations has focused on the purpose to which China’s growing international power will be put. This article focuses on the form of China’s power, distinguishing between domination and authority. Different great powers have, at different times, chosen one, the other, or more commonly differing mixes of the two forms. How China chooses now and in the future will have a significant effect on its relationships with other states, and through them on its relationship with the United States. The first section explores the differences between domination and authority as strategies for the exercise of international power. The second section summarizes a theory of authority with particular relevance to China today. Though necessarily speculative, this section identifies where China is most likely to choose one strategy over the other as its international influence expands. The final section examines the domestic impediments in China to the choice of authority. While both China and the United States might be better off in a world in which the former constructs an international hierarchy to parallel the latter’s, the conclusion draws a relatively pessimistic assessment of the prospects for cooperation between the two emerging superpowers.
Image Desecration in Spilamberto: Jews and Christian Images in Seventeenth-Century Italy
Authors: Aron-Beller Katherine 
Published: September 2017

Abstract
This article explores a series of incidents that took place near Modena between 1632 and 1635, in which members of a Jewish family were accused of desecrating Christian devotional images. It is based on a file in the inquisitorial archive in Modena, with additional information culled from the Archivio della Congregazione per la Dottrina della Fede in Rome. The principal locale of the story is a silk mill which was leased to Simon Sanguinetti and his four sons in 1632, a year after plague had devastated the region. The Sanguinetti were encouraged to take on this enterprise by the mill-owner, Baldassare Rangone, who clearly hoped that an injection of Jewish capital would result in the revival of the business. However, the Jewish tenants-cum-managers were soon accused of desecrating two types of Catholic images—a painted panel and cheap prints of religious subjects. During the investigations, three Jewish suspects were imprisoned for periods of up to four months, and two of them were tortured. The main focus of this article is on the two types of images, their religious and social significance, the Jewish–Christian tensions that were created by them, and their supposed desecration. It illustrates an unstudied aspect of hidden Jewish violence and the actualisation of emotions that might otherwise have remained unnoticed.
TC3A: The Cancer 3′ UTR Atlas
Authors: Feng Xin , Li Lei , Wagner Eric J , Li Wei 
Published: September 2017

AbstractWidespread alternative polyadenylation (APA) occurs during enhanced cellular proliferation and transformation. Recently, we demonstrated that CFIm25-mediated 3′ UTR shortening through APA promotes glioblastoma tumor growth in vitro and in vivo, further underscoring its significance to tumorigenesis. Here, we report The Cancer 3′ UTR Atlas (TC3A), a comprehensive resource of APA usage for 10,537 tumors across 32 cancer types. These APA events represent potentially novel prognostic biomarkers and may uncover novel mechanisms for the regulation of cancer driver genes. TC3A is built on top of the now de facto standard cBioPortal. Therefore, the large community of existing cBioPortal users and clinical researchers will find TC3A familiar and immediately usable. TC3A is currently fully functional and freely available at http://tc3a.org.
Database Resources of the BIG Data Center in 2018
Authors:   BIG Data Center Members, Xu Xingjian , Hao Lili , Zhu Junwei , Tang Bixia , Zhou Qing , Song Fuhai , Chen Tingting , Zhang Sisi , Dong Lili , Lan Li , Wang Yanqing , Sang Jian , Hao Lili , Liang Fang , Cao Jiabao , Liu Fang , Liu Lin , Wang Fan , Ma Yingke , Xu Xingjian , Zhang Lijuan , Chen Meili , Tian Dongmei , Li Cuiping , Dong Lili , Du Zhenglin , Yuan Na , Zeng Jingyao , Zhang Zhewen , Wang Jinyue , Shi Shuo , Zhang Yadong , Pan Mengyu , Tang Bixia , Zou Dong , Song Shuhui , Sang Jian , Xia Lin , Wang Zhennan , Li Man , Cao Jiabao , Niu Guangyi , Zhang Yang , Sheng Xin , Lu Mingming , Wang Qi , Xiao Jingfa , Zou Dong , Wang Fan , Hao Lili , Liang Fang , Li Mengwei , Sun Shixiang , Zou Dong , Li Rujiao , Yu Chunlei , Wang Guangyu , Sang Jian , Liu Lin , Li Mengwei , Li Man , Niu Guangyi , Cao Jiabao , Sun Shixiang , Xia Lin , Yin Hongyan , Zou Dong , Xu Xingjian , Ma Lina , Chen Huanxin , Sun Yubin , Yu Lei , Zhai Shuang , Sun Mingyuan , Zhang Zhang , Zhao Wenming , Xiao Jingfa , Bao Yiming , Song Shuhui , Hao Lili , Li Rujiao , Ma Lina , Sang Jian , Wang Yanqing , Tang Bixia , Zou Dong , Wang Fan 
Published: September 2017

Abstract
The BIG Data Center at Beijing Institute of Genomics (BIG) of the Chinese Academy of Sciences provides freely open access to a suite of database resources in support of worldwide research activities in both academia and industry. With the vast amounts of omics data generated at ever-greater scales and rates, the BIG Data Center is continually expanding, updating and enriching its core database resources through big-data integration and value-added curation, including BioCode (a repository archiving bioinformatics tool codes), BioProject (a biological project library), BioSample (a biological sample library), Genome Sequence Archive (GSA, a data repository for archiving raw sequence reads), Genome Warehouse (GWH, a centralized resource housing genome-scale data), Genome Variation Map (GVM, a public repository of genome variations), Gene Expression Nebulas (GEN, a database of gene expression profiles based on RNA-Seq data), Methylation Bank (MethBank, an integrated databank of DNA methylomes), and Science Wikis (a series of biological knowledge wikis for community annotations). In addition, three featured web services are provided, viz., BIG Search (search as a service; a scalable inter-domain text search engine), BIG SSO (single sign-on as a service; a user access control system to gain access to multiple independent systems with a single ID and password) and Gsub (submission as a service; a unified submission service for all relevant resources). All of these resources are publicly accessible through the home page of the BIG Data Center at http://bigd.big.ac.cn.
Food environments and obesity – can’t see the fat for the restaurants?
Authors: Speakman John R , Mazidi Mohsen 
Published: September 2017

AbstractWe recently showed that across the mainland USA there is no association between the density of fast food and full service restaurants and the prevalence of obesity. In a recent editorial it was suggested there are 4 problems with our analysis. The suggested problems were the area of analysis may not reflect adequately the exposure to different outlets, using the absolute numbers of restaurants rather than their ratio, using a global model which assumes the same relationship across all sites and finally the potential for residual confounding. In this short note we address all four of these issues and provide some new analysis of the impact of the ratio of restaurant types on obesity prevalence showing there is only a very weak association (r2= 0.006). We conclude that none of the supposed weaknesses in our original analysis are valid.
Integrative genomics analysis identifiesACVR1Bas a candidate causal gene of emphysema distribution in non-alpha 1-antitrypsin deficient smokers
Authors: Boueiz Adel , Chase Robert , Lamb Andrew , Lee Sool , Naing Zun Zar Chi , Cho Michael H. , Parker Margaret M. , Hersh Craig P. , Crapo James D. , Stergachis Andrew B. , Tal-Singer Ruth , DeMeo Dawn L. , Silverman Edwin K. , Castaldi Peter J. ,   for the COPDGene investigators
Published: September 2017

ABSTRACTBackgroundSeveral genetic risk loci associated with emphysema apico-basal distribution (EABD) have been identified through genome-wide association studies (GWAS), but the biological functions of these variants are unknown. To characterize gene regulatory functions of EABD-associated variants, we integrated EABD GWAS results with 1) a multi-tissue panel of expression quantitative trait loci (eQTL) from subjects with COPD and the GTEx project and 2) epigenomic marks from 127 cell types in the Roadmap Epigenomics project. Functional validation was performed for a variant nearACVR1B.ResultsSNPs from 168 loci with P-values<5x10-5in the largest GWAS meta-analysis of EABD(Boueiz A. et al, AJRCCM 2017)were analyzed. 54 loci overlapped eQTL regions from our multi-tissue panel, and 7 of these loci showed a high probability of harboring a single, shared GWAS and eQTL causal variant (colocalization posterior probability≥0.9). 17 cell types exhibited greater than expected overlap between EABD loci and DNase-I hypersensitive peaks, DNaseI hotspots, enhancer marks, or digital DNaseI footprints (permutation P-value < 0.05), with the strongest enrichment observed in CD4+, CD8+, and regulatory T cells. A region nearACVR1Bdemonstrated significant colocalization with a lung eQTL and overlapped DNase-I hypersensitive regions in multiple cell types, and reporter assays in human bronchial epithelial cells confirmed allele-specific regulatory activity for the lead variant, rs7962469.ConclusionsIntegrative analysis highlights candidate causal genes, regulatory variants, and cell types that may contribute to the pathogenesis of emphysema distribution. These findings will enable more accurate functional validation studies and better understanding of emphysema distribution biology.
Combining radiomics and mathematical modeling to elucidate mechanisms of resistance to immune checkpoint blockade in non-small cell lung cancer
Authors: Saeed-Vafa Daryoush , Bravo Rafael , Dean Jamie A. , El-Kenawi Asmaa , Mon Père Nathaniel , Strobl Maximilian , Daniels Charlie , Stringfield Olya , Damaghi Mehdi , Tunali Ilke , Brown Liam V. , Curtin Lee , Nichol Daniel , Peck Hailee , Gillies Robert J. , Gallaher Jill A. 
Published: September 2017

AbstractImmune therapies have shown promise in a number of cancers, and clinical trials using the anti-PD-L1/PD-1 checkpoint inhibitor in lung cancer have been successful for a number of patients. However, some patients either do not respond to the treatment or have cancer recurrence after an initial response. It is not clear which patients might fall into these categories or what mechanisms are responsible for treatment failure. To explore the different underlying biological mechanisms of resistance, we created a spatially explicit mathematical model with a modular framework. This construction enables different potential mechanisms to be turned on and off in order to adjust specific tumor and tissue interactions to match a specific patient's disease. In parallel, we developed a software suite to identify significant computed tomography (CT) imaging features correlated with outcome using data from an anti-PDL-1 checkpoint inhibitor clinical trial for lung cancer and a tool that extracts these features from both patient CT images and “virtual CT” images created from the cellular density profile of the model. The combination of our two toolkits provides a framework that feeds patient data through an iterative pipeline to identify predictive imaging features associated with outcome, whilst at the same time proposing hypotheses about the underlying resistance mechanisms.