bluuebunny/crossref_metadata_2025_split huggingface dataset:
Exploring the use of mobile phone data for national migration statistics
Authors: Lai Shengjie , Erbach-Schoenberg Elisabeth zu , Pezzulo Carla , Ruktanonchai Nick W. , Sorichetta Alessandro , Steele Jessica , Li Tracey , Dooley Claire A. , Tatem Andrew J. 
Published: March 2019

AbstractStatistics on internal migration are important for keeping estimates of subnational population numbers up-to-date, as well as urban planning, infrastructure development, and impact assessment, among other applications. However, migration flow statistics typically remain constrained by the logistics of infrequent censuses or surveys. The penetration rate of mobile phones is now high across the globe with rapid recent increases in ownership in low-income countries. Analyzing the changing spatiotemporal distribution of mobile phone users through anonymized call detail records (CDRs) offers the possibility to measure migration at multiple temporal and spatial scales. Based on a dataset of 72 billion anonymized CDRs in Namibia from October 2010 to April 2014, we explore how internal migration estimates can be derived and modeled from CDRs at subnational and annual scales, and how precision and accuracy of these estimates compare to census-derived migration statistics. We also demonstrate the use of CDRs to assess how migration patterns change over time, with a finer temporal resolution compared with censuses. Moreover, we show how gravity-type spatial interaction models built using CDRs can accurately capture migration flows. The results highlight that estimates of migration flows made using mobile phone data is a promising avenue for complementing more traditional national migration statistics and obtaining more timely and local data.
A natural anti-periodontitis agent, epimedokoreanin B, inhibits virulence activities of gingipains from Porphyromonas gingivalis
Authors: Kariu Toru , Ikeda Tsuyoshi , Nakashima Keisuke , Potempa Jan , Imamura Takahisa 
Published: March 2019

ABSTRACT
Gingipains are potent virulence cysteine proteases secreted by Porphyromonas gingivalis, a major pathogen of periodontitis. We previously reported that epimedokoreanin B inhibits the activities of gingipains. In this report, we show that epimedokoreanin B inhibits the virulence of gingipains-containing P. gingivalis culture supernatants, indicating the potential use of this prenylated flavonoid as a new agent to combat against periodontal pathogens.
Ingestion of difructose anhydride III partially suppresses the deconjugation and 7α-dehydroxylation of bile acids in rats fed with a cholic acid-supplemented diet
Authors: Lee Dong Geun , Hori Shota , Kohmoto Ohji , Kitta Shinri , Yoshida Ryo , Tanaka Yasutake , Shimizu Hidehisa , Takahashi Keisuke , Nagura Taizo , Uchino Hirokatsu , Fukiya Satoru , Yokota Atsushi , Ishizuka Satoshi 
Published: March 2019

ABSTRACT
Difructose anhydride III (DFAIII) is a prebiotic involved in the reduction of secondary bile acids (BAs). We investigated whether DFAIII modulates BA metabolism, including enterohepatic circulation, in the rats fed with a diet supplemented with cholic acid (CA), one of the 12α-hydroxylated BAs. After acclimation, the rats were fed with a control diet or a diet supplemented with DFAIII. After 2 weeks, each group was further divided into two groups and was fed diet with or without CA supplementation at 0.5 g/kg diet. BA levels were analyzed in aortic and portal plasma, liver, intestinal content, and feces. As a result, DFAIII ingestion reduced the fecal deoxycholic acid level via the partial suppression of deconjugation and 7α-dehydroxylation of BAs following CA supplementation. These results suggest that DFAIII suppresses production of deoxycholic acid in conditions of high concentrations of 12α-hydroxylated BAs in enterohepatic circulation, such as obesity or excess energy intake.
Abbreviation: BA: bile acid; BSH: bile salt hydrolase; CA: cholic acid; DCA: deoxycholic acid; DFAIII: difructose anhydride III; MCA: muricholic acid; MS: mass spectrometry; NCDs: non-communicable diseases; LC: liquid chromatography; SCFA: short-chain fatty acid; TCA: taurocholic acid; TCDCA: taurochenodeoxycholic acid; TDCA: taurodeoxycholic acid; TUDCA: tauroursodeoxychlic acid; TαMCA: tauro-α-muricholic acid; TβMCA: tauro-β-muricholic acid; TωMCA: tauro-ω-muricholic acid
Kinpute: using identity by descent to improve genotype imputation
Authors: Abney Mark , ElSherbiny Aisha 
Published: March 2019

Abstract

Motivation
Genotype imputation, though generally accurate, often results in many genotypes being poorly imputed, particularly in studies where the individuals are not well represented by standard reference panels. When individuals in the study share regions of the genome identical by descent (IBD), it is possible to use this information in combination with a study-specific reference panel (SSRP) to improve the imputation results. Kinpute uses IBD information—due to recent, familial relatedness or distant, unknown ancestors—in conjunction with the output from linkage disequilibrium (LD) based imputation methods to compute more accurate genotype probabilities. Kinpute uses a novel method for IBD imputation, which works even in the absence of a pedigree, and results in substantially improved imputation quality.

Results
Given initial estimates of average IBD between subjects in the study sample, Kinpute uses a novel algorithm to select an optimal set of individuals to sequence and use as an SSRP. Kinpute is designed to use as input both this SSRP and the genotype probabilities output from other LD-based imputation software, and uses a new method to combine the LD imputed genotype probabilities with IBD configurations to substantially improve imputation. We tested Kinpute on a human population isolate where 98 individuals have been sequenced. In half of this sample, whose sequence data was masked, we used Impute2 to perform LD-based imputation and Kinpute was used to obtain higher accuracy genotype probabilities. Measures of imputation accuracy improved significantly, particularly for those genotypes that Impute2 imputed with low certainty.

Availability and implementation
Kinpute is an open-source and freely available C++ software package that can be downloaded from.

Supplementary information
Supplementary data are available at Bioinformatics online.
FusionLearn: a biomarker selection algorithm on cross-platform data
Authors: Gao Xin , Zhong Yuan 
Published: March 2019

AbstractMotivationIn high dimensional genetic data analysis, the objective is to select important biomarkers which are involved in some biological processes, such as disease progression, immune response, etc. The experimental data are often collected from different platforms including microarray experiments and proteomic experiments. The conventional single-platform approach lacks the capability to learn from multiple platforms, and the resulted lists of biomarkers vary across different platforms. There is a great need to develop an algorithm which can aggregate information across platforms and provide a consolidated list of biomarkers across different platforms.ResultsIn this paper, we introduce an R package FusionLearn, which implements a fusion learning algorithm to analyze cross-platform data. The consolidated list of biomarkers is selected by the technique of group penalization. We first apply the algorithm on a collection of breast cancer microarray experiments from the NCBI (National Centre for Biotechnology Information) microarray database and the resulted list of selected genes have higher classification accuracy rate across different datasets than the lists generated from each single dataset. Secondly, we use the software to analyze a combined microarray and proteomic dataset for the study of the growth phase versus the stationary phase in Streptomyces coelicolor. The selected biomarkers demonstrate consistent differential behavior across different platforms.Availability and implementationR package: https://cran.r-project.org/package=FusionLearn.
parMATT: parallel multiple alignment of protein 3D-structures with translations and twists for distributed-memory systems
Authors: Shegay Maksim V , Suplatov Dmitry A , Popova Nina N , Švedas Vytas K , Voevodin Vladimir V 
Published: March 2019

Abstract

Motivation
Accurate structural alignment of proteins is crucial at studying structure-function relationship in evolutionarily distant homologues. Various software tools were proposed to align multiple protein 3D-structures utilizing one CPU and thus are of limited productivity at large-scale analysis of protein families/superfamilies.

Results
The parMATT is a hybrid MPI/pthreads/OpenMP parallel re-implementation of the MATT algorithm to align multiple protein 3D-structures by allowing translations and twists. The parMATT can be faster than MATT on a single multi-core CPU, and provides a much greater speedup when executed on distributed-memory systems, i.e. computing clusters and supercomputers hosting memory-independent computing nodes. The most computationally demanding steps of the MATT algorithm—the initial construction of pairwise alignments between all input structures and further iterative progression of the multiple alignment—were parallelized using MPI and pthreads, and the concluding refinement step was optimized by introducing the OpenMP support. The parMATT can significantly accelerate the time-consuming process of building a multiple structural alignment from a large set of 3D-records of homologous proteins.

Availability and implementation
The source code is available at https://biokinet.belozersky.msu.ru/parMATT.

Supplementary information
Supplementary data are available at Bioinformatics online.
Parallel repulsive logic regression with biological adjacency
Authors: Yoneoka Daisuke , Im Cindy , Yasui Yutaka 
Published: March 2019

Summary
Logic regression, an extension of generalized linear models with Boolean combinations of binary variables as predictors, is a useful tool in exploring interactions among single-nucleotide polymorphisms (SNPs) in genome-wide association studies. However, since the search space defined by all possible combinations of SNPs, their complements, and logical operators in Boolean expressions can be exceedingly large in such studies, objective function optimization is slow and likely to be trapped in many local solutions, resulting in model over-fitting. We introduce a new search algorithm, parallel repulsive logic regression (PRLR), to efficiently estimate parameters of a logic regression to find a best model within the large space of SNP interactions by incorporating: (i) relevant biological adjacency matrix between SNPs to define similarity of estimation paths or trees, which are derived from physical SNP positions on chromosomes and/or memberships in biological gene pathways; and (ii) two repulsive forces to counter the similarity between and within estimation paths considered in parallel, which are introduced as penalty terms in the objective function. We compare our method’s performance for identifying biologically-meaningful SNP interactions through simulations and with real genetic-epidemiological data. PRLR’s detection-accuracy measures outperform existing approaches, especially in terms of positive predictive value and sensitivity for detecting SNP–SNP interactions.
The presence of residents during orthopedic operation exerts no negative influence on outcome
Authors: Giordano Lorenzo , Oliviero Antonio , Peretti Giuseppe M , Maffulli Nicola 
Published: March 2019

Abstract

Background
Operative procedural training is a key component of orthopedic surgery residency. It is unclear how and whether residents participation in orthopedic surgical procedures impacts on post-operative outcomes.

Sources of data
A systematic search was performed to identify articles in which the presence of a resident in the operating room was certified, and was compared with interventions without the presence of residents.

Areas of agreement
There is a likely beneficial role of residents in the operating room, and there is only a weak association between the presence of a resident and a worse outcome for orthopedic surgical patients

Areas of controversy
Most of the studies were undertaken in USA, and this represents a limit from the point of view of comparison with other academic and clinical realities.

Growing point
The data provide support for continued and perhaps increased involvement of resident in orthopedic surgery.

Areas of research
To clarify the role of residents on clinically relevant outcomes in orthopedic patients, appropriately powered randomized control trials should be planned.
Severe Illnesses Associated With Outbreaks of Respiratory Syncytial Virus and Influenza in Adults
Authors: Zhou James A , Schweinle Jo Ellen , Lichenstein Richard , Walker Robert E , King James C 
Published: March 2019

Abstract

Background
Recent reports have described the contribution of adult respiratory syncytial virus (RSV) infections to the use of advanced healthcare resources and death.

Methods
Data regarding patients aged ≥18 years admitted to any of Maryland’s 50 acute-care hospitals were evaluated over 12 consecutive years (2001–2013). We examined RSV and influenza (flu) surveillance data from the US National Respiratory and Enteric Virus Surveillance System and the Centers for Disease Control and Prevention and used this information to define RSV and flu outbreak periods in the Maryland area. Outbreak periods consisted of consecutive individual weeks during which at least 10% of RSV and/or flu diagnostic tests were positive. We examined relationships of RSV and flu outbreaks to occurrence of 4 advanced medical outcomes (hospitalization, intensive care unit admission, intubated mechanical ventilation, and death) due to medically attended acute respiratory illness (MAARI).

Results
Occurrences of all 4 MAARI-related hospital advanced medical outcomes were consistently greater for all adult ages during RSV, flu, and combined RSV–flu outbreak periods compared to nonoutbreak periods and tended to be greatest in adults aged ≥65 years during combined RSV–flu outbreak periods. Rate ratios for all 4 MAARI-related advanced medical outcomes ranged from 1.04 to 1.38 during the RSV, flu, or combined RSV–flu outbreaks compared to the nonoutbreak periods, with all 95% lower confidence limits &gt;1.

Conclusions
Both RSV and flu outbreaks were associated with surges in MAARI-related advanced medical outcomes (hospitalization, intensive care unit admission, intubated mechanical ventilation, and death) for adults of all ages.
Molecular Approach to Diagnosis of Cardiovascular Implantable Electronic Device Infection
Authors: Esquer Garrigos Zerelda , Sohail M Rizwan , Greenwood-Quaintance Kerryl E , Cunningham Scott A , Vijayvargiya Prakhar , Fida Madiha , Friedman Paul A , Mandrekar Jayawant , DeSimone Daniel C , Baddour Larry M , Patel Robin 
Published: March 2019

Abstract

Background
Sonicate fluid (SF), a solution derived from vortexing and sonication of explanted cardiovascular implantable electronic devices (CIEDs), is a higher-yield specimen compared with swabs or tissues for culture-based detection of microorganisms associated with CIED infection. Despite this, SF culture fails to identify a causative organism in ~50% of cases. We aimed to evaluate the diagnostic performance of 16S ribosomal RNA gene (rRNA) polymerase chain reaction (PCR)/sequencing of SF and compare it with that of SF culture.

Methods
We identified 322 SF specimens from extracted CIEDs and reviewed clinical data for each patient. Subjects were classified as having or not having CIED infection. Cases were subcategorized as culture negative if no significant growth was reported from SF cultures and as culture positive if an organism was detected above predefined thresholds. 16S rRNA PCR/sequencing was performed, with the organisms identified reported according to Clinical and Laboratory Standards Institute guidelines for sequence data interpretation.

Results
A total of 278 SF samples corresponded to infected cases, of which 160 were culture positive and 118 culture negative. The remaining 44 were from noninfected cases, of which 2 were culture positive. Compared with SF culture, the sensitivity of 16S rRNA PCR/sequencing was higher (64% vs 57.5%, P = .003). 16S rRNA PCR/sequencing detected a potential pathogen in 28 of 118 culture-negative cases, identifying staphylococci in the majority (18/28).

Conclusions
16S rRNA PCR/sequencing has higher sensitivity to detect bacteria in SF from extracted CIEDs than does SF culture.
YeasTSS: an integrative web database of yeast transcription start sites
Authors: McMillan Jonathan , Lu Zhaolian , Rodriguez Judith S , Ahn Tae-Hyuk , Lin Zhenguo 
Published: March 2019

Abstract
The transcription initiation landscape of eukaryotic genes is complex and highly dynamic. In eukaryotes, genes can generate multiple transcript variants that differ in 5′ boundaries due to usages of alternative transcription start sites (TSSs), and the abundance of transcript isoforms are highly variable. Due to a large number and complexity of the TSSs, it is not feasible to depict details of transcript initiation landscape of all genes using text-format genome annotation files. Therefore, it is necessary to provide data visualization of TSSs to represent quantitative TSS maps and the core promoters (CPs). In addition, the selection and activity of TSSs are influenced by various factors, such as transcription factors, chromatin remodeling and histone modifications. Thus, integration and visualization of functional genomic data related to these features could provide a better understanding of the gene promoter architecture and regulatory mechanism of transcription initiation. Yeast species play important roles for the research and human society, yet no database provides visualization and integration of functional genomic data in yeast. Here, we generated quantitative TSS maps for 12 important yeast species, inferred their CPs and built a public database, YeasTSS (www.yeastss.org). YeasTSS was designed as a central portal for visualization and integration of the TSS maps, CPs and functional genomic data related to transcription initiation in yeast. YeasTSS is expected to benefit the research community and public education for improving genome annotation, studies of promoter structure, regulated control of transcription initiation and inferring gene regulatory network.
A clampless anastomosis technique using the aortic cannula mounted by a prosthetic graft for a severely calcified aorta in a patient with subclavian steal syndrome
Authors: Sumi Kohei , Yoshida Shigehiko , Okamura Yoshitaka , Kunimoto Hideki 
Published: March 2019

Abstract
Patients with severely calcified aorta are at high risk of embolic stroke during surgery and it is not feasible to clamp the aorta, necessitating alternative surgical strategies. We present a clampless anastomosis technique using the aortic cannula mounted by a prosthetic graft for a severely calcified aorta in a patient with subclavian–vertebral artery steal syndrome.
Mycobacterium tuberculosisinfection of host cells in space and time
Authors: Bussi Claudio , Gutierrez Maximiliano G 
Published: March 2019

ABSTRACTTuberculosis (TB) caused by the bacterial pathogen Mycobacterium tuberculosis (Mtb) remains one of the deadliest infectious diseases with over a billion deaths in the past 200 years (Paulson 2013). TB causes more deaths worldwide than any other single infectious agent, with 10.4 million new cases and close to 1.7 million deaths in 2017. The obstacles that make TB hard to treat and eradicate are intrinsically linked to the intracellular lifestyle of Mtb. Mtb needs to replicate within human cells to disseminate to other individuals and cause disease. However, we still do not completely understand how Mtb manages to survive within eukaryotic cells and why some cells are able to eradicate this lethal pathogen. Here, we summarise the current knowledge of the complex host cell-pathogen interactions in TB and review the cellular mechanisms operating at the interface between Mtb and the human host cell, highlighting the technical and methodological challenges to investigating the cell biology of human host cell-Mtb interactions.
Classroom active breaks: a feasibility study in Southern Italy
Authors: Calella Patrizia , Mancusi Caterina , Pecoraro Pierluigi , Sensi Serena , Sorrentino Carmelina , Imoletti Maria , Franzese Adriana , Gallè Francesca , Liguori Giorgio , Valerio Giuliana 
Published: March 2019

Abstract
Though classroom time has been identified as a contributing factor to sedentary behavior, school has been recognized as the main educational setting providing physical activity (PA) opportunities. The purpose of this study was to develop and evaluate the feasibility of a classroom-based intervention which integrates PA during the school time, and assess its potential effect on reducing inactivity in primary school children. The intervention was performed in a sample of 47 children attending a primary school in the south of Italy and it was structured in two sessions of classroom active breaks (CABs) in three school days a week, shared with and supervised by the teachers. CABs showed an overall potential positive effect on the reduction of inactivity of ∼12 min and an equivalent increase in PA levels, of which 5 min were of moderate/vigorous intensity. Girls showed lower time spent in light and moderate PA and higher amount of inactivity than boys and responded better to the intervention. The satisfaction of children and teachers was high. CABs program is a safe tool to reduce inactivity and increase moderate/vigorous PA. Designing structured exercise breaks adapted in a flexible way to meet the needs of the school curriculum program may increase the feasibility of such PA program in the schools.
The association of urine metals and metal mixtures with cardiovascular incidence in an adult population from Spain: the Hortega Follow-Up Study
Authors: Domingo-Relloso Arce , Grau-Perez Maria , Briongos-Figuero Laisa , Gomez-Ariza Jose L , Garcia-Barrera Tamara , Dueñas-Laita Antonio , Bobb Jennifer F , Chaves F Javier , Kioumourtzoglou Marianthi-Anna , Navas-Acien Ana , Redon-Mas Josep , Martin-Escudero Juan C , Tellez-Plaza Maria 
Published: March 2019

AbstractBackgroundThe association of low-level exposure to metals and metal mixtures with cardiovascular incidence in the general population has rarely been studied. We flexibly evaluated the association of urinary metals and metal mixtures concentrations with cardiovascular diseases in a representative sample of a general population from Spain.MethodsUrine antimony (Sb), barium (Ba), cadmium (Cd), chromium (Cr), cobalt (Co), copper (Cu), molybdenum (Mo), vanadium (V) and zinc (Zn) were measured in 1171 adults without clinical cardiovascular diseases, who participated in the Hortega Study. Cox proportional hazard models were used for evaluating the association between single metals and cardiovascular incidence. We used a Probit extension of Bayesian Kernel Machine Regression (BKMR-P) to handle metal mixtures in a survival setting.ResultsIn single-metal models, the hazard ratios [confidence intervals (CIs)] of cardiovascular incidence, comparing the 80th to the 20th percentiles of metal distributions, were 1.35 (1.06, 1.72) for Cu, 1.43 (1.07, 1.90) for Zn, 1.51 (1.13, 2.03) for Sb, 1.46 (1.13, 1.88) for Cd, 1.64 (1.05, 2.58) for Cr and 1.31 (1.01, 1.71) for V. BKMR-P analysis was confirmatory of these findings, supporting that Cu, Zn, Sb, Cd, Cr and V are related to cardiovascular incidence in the presence of the other metals. Cd and Sb showed the highest posterior inclusion probabilities.ConclusionsUrine Cu, Zn, Sb, Cd, Cr and V were independently associated with increased cardiovascular risk at levels relevant for the general population of Spain. Urine metals in the mixture were also jointly associated with cardiovascular incidence, with Cd and Sb being the most important components of the mixture.