bluuebunny/crossref_metadata_2025_split huggingface dataset:
Predicting drug-induced transcriptome responses of a wide range of human cell lines by a novel tensor-train decomposition algorithm
Authors: Iwata Michio , Yuan Longhao , Zhao Qibin , Tabei Yasuo , Berenger Francois , Sawada Ryusuke , Akiyoshi Sayaka , Hamano Momoko , Yamanishi Yoshihiro 
Published: May 2019

Abstract

Motivation
Genome-wide identification of the transcriptomic responses of human cell lines to drug treatments is a challenging issue in medical and pharmaceutical research. However, drug-induced gene expression profiles are largely unknown and unobserved for all combinations of drugs and human cell lines, which is a serious obstacle in practical applications.

Results
Here, we developed a novel computational method to predict unknown parts of drug-induced gene expression profiles for various human cell lines and predict new drug therapeutic indications for a wide range of diseases. We proposed a tensor-train weighted optimization (TT-WOPT) algorithm to predict the potential values for unknown parts in tensor-structured gene expression data. Our results revealed that the proposed TT-WOPT algorithm can accurately reconstruct drug-induced gene expression data for a range of human cell lines in the Library of Integrated Network-based Cellular Signatures. The results also revealed that in comparison with the use of original gene expression profiles, the use of imputed gene expression profiles improved the accuracy of drug repositioning. We also performed a comprehensive prediction of drug indications for diseases with gene expression profiles, which suggested many potential drug indications that were not predicted by previous approaches.

Supplementary information
Supplementary data are available at Bioinformatics online.
Integrating read-based and population-based phasing for dense and accurate haplotyping of individual genomes
Authors: Bansal Vikas 
Published: May 2019

Abstract

Motivation
Reconstruction of haplotypes for human genomes is an important problem in medical and population genetics. Hi-C sequencing generates read pairs with long-range haplotype information that can be computationally assembled to generate chromosome-spanning haplotypes. However, the haplotypes have limited completeness and low accuracy. Haplotype information from population reference panels can potentially be used to improve the completeness and accuracy of Hi-C haplotyping.

Results
In this paper, we describe a likelihood based method to integrate short-range haplotype information from a population reference panel of haplotypes with the long-range haplotype information present in sequence reads from methods such as Hi-C to assemble dense and highly accurate haplotypes for individual genomes. Our method leverages a statistical phasing method and a maximum spanning tree algorithm to determine the optimal second-order approximation of the population-based haplotype likelihood for an individual genome. The population-based likelihood is encoded using pseudo-reads which are then used as input along with sequence reads for haplotype assembly using an existing tool, HapCUT2. Using whole-genome Hi-C data for two human genomes (NA19240 and NA12878), we demonstrate that this integrated phasing method enables the phasing of 97–98% of variants, reduces the switch error rates by 3–6-fold, and outperforms an existing method for combining phase information from sequence reads with population-based phasing. On Strand-seq data for NA12878, our method improves the haplotype completeness from 71.4 to 94.6% and reduces the switch error rate 2-fold, demonstrating its utility for phasing using multiple sequencing technologies.

Availability and implementation
Code and datasets are available at https://github.com/vibansal/IntegratedPhasing.
Unsupervised segmentation of mass spectrometric ion images characterizes morphology of tissues
Authors: Guo Dan , Bemis Kylie , Rawlins Catherine , Agar Jeffrey , Vitek Olga 
Published: May 2019

Abstract

Motivation
Mass spectrometry imaging (MSI) characterizes the spatial distribution of ions in complex biological samples such as tissues. Since many tissues have complex morphology, treatments and conditions often affect the spatial distribution of the ions in morphology-specific ways. Evaluating the selectivity and the specificity of ion localization and regulation across morphology types is biologically important. However, MSI lacks algorithms for segmenting images at both single-ion and spatial resolution.

Results
This article contributes spatial-Dirichlet Gaussian mixture model (DGMM), an algorithm and a workflow for the analyses of MSI experiments, that detects components of single-ion images with homogeneous spatial composition. The approach extends DGMMs to account for the spatial structure of MSI. Evaluations on simulated and experimental datasets with diverse MSI workflows demonstrated that spatial-DGMM accurately segments ion images, and can distinguish ions with homogeneous and heterogeneous spatial distribution. We also demonstrated that the extracted spatial information is useful for downstream analyses, such as detecting morphology-specific ions, finding groups of ions with similar spatial patterns, and detecting changes in chemical composition of tissues between conditions.

Availability and implementation
The data and code are available at https://github.com/Vitek-Lab/IonSpattern.

Supplementary information
Supplementary data are available at Bioinformatics online.
Efficient merging of genome profile alignments
Authors: Hennig André , Nieselt Kay 
Published: May 2019

Abstract

Motivation
Whole-genome alignment (WGA) methods show insufficient scalability toward the generation of large-scale WGAs. Profile alignment-based approaches revolutionized the fields of multiple sequence alignment construction methods by significantly reducing computational complexity and runtime. However, WGAs need to consider genomic rearrangements between genomes, which make the profile-based extension of several whole-genomes challenging. Currently, none of the available methods offer the possibility to align or extend WGA profiles.

Results
Here, we present genome profile alignment, an approach that aligns the profiles of WGAs and that is capable of producing large-scale WGAs many times faster than conventional methods. Our concept relies on already available whole-genome aligners, which are used to compute several smaller sets of aligned genomes that are combined to a full WGA with a divide and conquer approach. To align or extend WGA profiles, we make use of the SuperGenome data structure, which features a bidirectional mapping between individual sequence and alignment coordinates. This data structure is used to efficiently transfer different coordinate systems into a common one based on the principles of profiles alignments. The approach allows the computation of a WGA where alignments are subsequently merged along a guide tree. The current implementation uses progressiveMauve and offers the possibility for parallel computation of independent genome alignments. Our results based on various bacterial datasets up to several hundred genomes show that we can reduce the runtime from months to hours with a quality that is negligibly worse than the WGA computed with the conventional progressiveMauve tool.

Availability and implementation
GPA is freely available at https://lambda.informatik.uni-tuebingen.de/gitlab/ahennig/GPA. GPA is implemented in Java, uses progressiveMauve and offers a parallel computation of WGAs.

Supplementary information
Supplementary data are available at Bioinformatics online.
Ecological Effects of Free-Roaming Horses in North American Rangelands
Authors: Davies Kirk W , Boyd Chad S 
Published: May 2019

Abstract
Free-roaming horses are a widespread conservation challenge. Horse use (grazing and related impacts) is largely unmanaged, leading to concerns about its impact on native plant communities and ecosystem function. We synthesized the literature to determine the ecological effects of free-roaming horses in North American rangelands. Largely unmanaged horse use can alter plant community composition, diversity, and structure and can increase bare ground and erosion potential. Free-roaming-horse use has also been linked to negative impacts on native fauna. Horses have repeatedly been shown to limit and even exclude native wildlife's use of water sources. These effects would likely be greatly reduced if the horse populations were better managed, but sociopolitical factors often preclude improved management. Using rigorous ecological research to educate politicians and the general public may facilitate the development of science-based management of free-roaming horses; however, ecological effects may have to become more severe before such changes can be realized.
Subtherapeutic Rifampicin Concentration Is Associated With Unfavorable Tuberculosis Treatment Outcomes
Authors: Ramachandran Geetha , Chandrasekaran Padmapriyadarshini , Gaikwad Sanjay , Agibothu Kupparam Hemanth Kumar , Thiruvengadam Kannan , Gupte Nikhil , Paradkar Mandar , Dhanasekaran Kavitha , Sivaramakrishnan Gomathi Narayan , Kagal Anju , Thomas Beena , Pradhan Neeta , Kadam Dileep , Hanna Luke Elizabeth , Balasubramanian Usha , Kulkarni Vandana , Murali Lakshmi , Golub Jonathan , Gupte Akshay , Shivakumar Shri Vijay Bala Yogendra , Swaminathan Soumya , Dooley Kelly E , Gupta Amita , Mave Vidya 
Published: May 2019

Abstract

Background
The relationships between first-line drug concentrations and clinically important outcomes among patients with tuberculosis (TB) remain poorly understood.

Methods
We enrolled a prospective cohort of patients with new pulmonary TB receiving thrice-weekly treatment in India. The maximum plasma concentration of each drug was determined at months 1 and 5 using blood samples drawn 2 hours postdose. Subtherapeutic cutoffs were: rifampicin &lt;8 µg/mL, isoniazid &lt;3 µg/mL, and pyrazinamide &lt;20 µg/mL. Factors associated with lower log-transformed drug concentrations, unfavorable outcomes (composite of treatment failure, all-cause mortality, and recurrence), and individual outcomes were examined using Poisson regression models.

Results
Among 404 participants, rifampicin, isoniazid, and pyrazinamide concentrations were subtherapeutic in 85%, 29%, and 13%, respectively, at month 1 (with similar results for rifampicin and isoniazid at month 5). Rifampicin concentrations were lower with human immunodeficiency virus coinfection (median, 1.6 vs 4.6 µg/mL; P = .015). Unfavorable outcome was observed in 19%; a 1-μg/mL decrease in rifampicin concentration was independently associated with unfavorable outcome (adjusted incidence rate ratio [aIRR], 1.21 [95% confidence interval {CI}, 1.01–1.47]) and treatment failure (aIRR, 1.16 [95% CI, 1.05–1.28]). A 1-μg/mL decrease in pyrazinamide concentration was associated with recurrence (aIRR, 1.05 [95% CI, 1.01–1.11]).

Conclusions
Rifampicin concentrations were subtherapeutic in most Indian patients taking a thrice-weekly TB regimen, and low rifampicin and pyrazinamide concentrations were associated with poor outcomes. Higher or more frequent dosing is needed to improve TB treatment outcomes in India.
Vedolizumab Treatment in Extra-Intestinal Manifestations in Inflammatory Bowel Disease: A Systematic Review
Authors: Chateau Thomas , Bonovas Stefanos , Le Berre Catherine , Mathieu Nicolas , Danese Silvio , Peyrin-Biroulet Laurent 
Published: May 2019

AbstractBackground and AimsWe aimed to summarize existing data on the effectiveness of vedolizumab in extra-intestinal manifestations [EIMs] in inflammatory bowel disease [IBD].MethodsWe conducted a systematic literature search in PubMed and the Cochrane Library, up to October 2018. Interventional and non-interventional studies as well as case-series studying vedolizumab and EIMs in adult patients with IBD were considered eligible.ResultsThree interventional studies [one randomized trial, n = 1032; and two open-label trials, n = 347], five non-interventional studies [n = 1496] and three case-series [n = 17] were included. Vedolizumab did not show any effectiveness in primary sclerosing cholangitis [PSC]. While no effect was seen in pre-existing manifestations regarding arthralgia and arthritis, the occurrence of new rheumatic symptoms was lower among vedolizumab users compared to placebo; occurrence was higher, however, with vedolizumab than with tumour necrosis factor inhibitors. Finally, vedolizumab appears not to be efficacious for the treatment of cutaneous manifestations.ConclusionsThere is no strong evidence to suggest that vedolizumab may be efficacious for the treatment of pre-existing EIMs [especially PSC, rheumatic and cutaneous manifestations], although it may reduce the occurrence of new EIMs.
The Individual in Context(s): Research Potentials of the Socio-Economic Panel Study (SOEP) in Sociology
Authors: Giesselmann Marco , Bohmann Sandra , Goebel Jan , Krause Peter , Liebau Elisabeth , Richter David , Schacht Diana , Schröder Carsten , Schupp Jürgen , Liebig Stefan 
Published: May 2019

AbstractThe German Socio-Economic Panel (SOEP) study is a rich resource for sociologists, mainly because it offers direct measures of respondents’ contexts. The SOEP data provide (i) information retrieved from individuals themselves, (ii) direct information retrieved from their parents, partners, and organizations, (iii) prospectively collected information on past characteristics, and (iv) regional and spatial identifiers allowing researchers to link the data with regional-level characteristics. As the study has been in the field since 1984, the data also reflect variation in institutional and structural settings over time. Regular refreshment samples provide options to identify cohort effects. Together, these features allow multi-layered contextual designs that offer substantive insights into the effects of formal and informal institutions on individual behaviour and living conditions. This article introduces the main types of SOEP-based sociological research designs and discusses their survey methodological origins. It also points to underexplored potentials as well as limitations of the SOEP. Finally, it offers basic suggestions for approaching the data in each of the research designs presented.
Prevalence and genetic diversity of Vibrio parahaemolyticus strains from salmon in Chinese markets
Authors: Xie Tengfei , Wu Gang , He Xujun , Lai Zengzhe , Zhang Huatong , Zhao Jing 
Published: May 2019

ABSTRACT
Consumption of contaminated salmon in China has led to pathogenic Vibrio parahaemolyticus infections in humans. In this study, 420 salmon samples were collected from supermarkets and restaurants in China that showed a contamination rate of 9.05 and 15.24%, respectively. Eighteen antibiotics were used to test the antibiotic susceptibility of all 51 isolates. The most common resistance was observed to β-lactam antibiotics and aminoglycosides, including ampicillin (92.16%), streptomycin (88.24%), kanamycin (45.10%) and cephazolin (45.10%). Meanwhile, many strains were resistant to more than two antibiotics (48/51, 94.12%). Only two and five isolates were positive for tdh and trh, respectively. Serotyping results demonstrated that O2 was most prevalence serotype (15/51, 29.41%). Molecular typing (enterobacterial repetitive intergenic consensus sequence polymerase chain reaction and multilocus sequence typing) allowed classification of all the isolates into 5 clusters and 44 sequence types, highlighting genetic variation and relatedness. In general, the high antibiotic resistance is alarming and raises public health concerns. Frequent monitoring of salmon for V. parahaemolyticus contamination, genetic diversity and antibiotic susceptibility is essential to improve seafood safety.
Misinformation Effect in Aging: A New Light with Equivalence Testing
Authors: Tessoulin Marine , Galharret Jean-Michel , Gilet Anne-Laure , Colombel Fabienne 
Published: May 2019

Abstract

Objectives
To better characterize the formation of false memories in older adults, we conducted a study using a French adaptation of the misinformation paradigm from Loftus, Levidow, and Duensing (1992). We aimed to show higher false memory production in older than in younger adults.

Method
One hundred and four younger adults (18–30 years) and 104 older adults (70–95 years) took part in the study. Participants were presented with a misinformation paradigm through the viewing of a short video followed by a questionnaire containing misinformation about the film. After a short delay (45 min), they performed a recognition task.

Results
Contrary to our hypothesis, the results analyzed with a Welch t test did not reveal a greater misinformation effect in older adults than in younger adults. Results were reanalyzed using the equivalence test which indicated that younger and older adults are statistically equivalent and not statistically different.

Discussion
The equivalence test helped to clarify the contradictory results of the literature. Furthermore, such results show the interest to reconsider misinformation effect in aging.
A Spider’s Vibration Landscape: Adaptations to Promote Vibrational Information Transfer in Orb Webs
Authors: Mortimer B 
Published: May 2019

Abstract
Spider orb webs are used not only for catching prey, but also for transmitting vibrational information to the spider. Vibrational information propagates from biological sources, such as potential prey or mates, but also abiotic sources, such as wind. Like other animals, the spider must cope with physical constraints acting on the propagation of vibrational information along surfaces and through materials—including loss of energy, distortion, and filtering. The spider mitigates these physical constraints by making its orb web from up to five different types of silks, closely controlling silk use and properties during web building. In particular, control of web geometry, silk tension, and silk stiffness allows spiders to adjust how vibrations spread throughout the web, as well as their amplitude and speed of propagation, which directly influences energy loss, distortion, and filtering. Turning to how spiders use this information, spiders use lyriform organs distributed across their eight legs as vibration sensors. Spiders can adjust coupling to the silk fibers and use posture to modify vibrational information as it moves from the web to the sensors. Spiders do not sense all vibrations equally—they are least sensitive to low frequencies (&lt;30 Hz) and most sensitive to high frequencies (ca. 1 kHz). This sensitivity pattern cannot be explained purely by the frequency range of biological inputs. The role of physical and evolutionary constraints is discussed to explain spider vibration sensitivity and a role of vibration sensors to detect objects on the web as a form of echolocation is also discussed.
Testing for Betel Nut Alkaloids in Hair of Papuans Abusers using UPLC–MS/MS and UPLC–Q-Tof-MS
Authors: Gheddar Laurie , Ricaut François-Xavier , Ameline Alice , Brucato Nicolas , Tsang Roxanne , Leavesley Matthew , Raul Jean-Sébastien , Kintz Pascal 
Published: May 2019

Abstract
Betel nut is the fruit of Areca palm, growing in Papua New Guinea. Mixed with limestone and stick mustard, arecoline and guvacoline, which are present in betel nut, are hydrolyzed into arecaidine and guvacine, respectively. As part of the study on dietary habits of Papuans residents, our laboratory was asked to analyze the four alkaloids in hair to document long-term exposure. Hair samples were collected from 19 adult subjects (males = 11; females = 8), by some of the authors, and were sent to the laboratory for analysis. The four alkaloids have very similar chemical structures. In order to accurately identify the drugs, two methods were developed. First, the compounds were identified using an ultra-high-performance liquid chromatography system coupled to time-of-flight mass spectrometry. Then, they were quantified by an ultra-high-performance liquid chromatography system coupled to tandem mass spectrometry. After decontamination with dichloromethane, hair samples were cut into very small segments and 20 mg were incubated in methanol for 2 h 30 min in an ultrasound bath. After cooling, the methanol was evaporated to dryness in presence of 20-μL octanol to prevent volatilization. Nicotine-d4 was used as an internal standard. Linearity was observed for concentrations ranging from the limit of quantification to 20 ng/mg for arecoline, arecaidine, guvacine and guvacoline. Measured concentrations were in the range 60 pg/mg to 18 ng/mg for arecoline (n = 19), 14 pg/mg to 2.5 ng/mg for guvacoline (n = 11), 63 pg/mg to 3.8 ng/mg for arecaidine (n = 11) and 100 pg/mg to 3.2 ng/mg for guvacine (n = 6). There was no correlation between concentrations of arecoline and arecaidine (ratio from 0.01 to 0.18) and guvacoline and guvacine (ratio from 0.06 to 3.50). However, the identification of these substances in hair is a good marker of consumption of betel nut and allows us to document a local practice that remains difficult to evaluate just by questioning.
Intraday End-of-Day Volume Prediction
Authors: Sancetta Alessio 
Published: May 2019

AbstractA model that predicts the total end-of-day volume and updates the prediction as new intraday information is observed and proposed. This model is a time-varying coefficients model which is estimated using the framework of functional data. Semiparametric constraints such as monotonicity of the time-varying coefficients can be imposed in the estimation. Results that allow us to derive confidence bands under a variety of scenarios including functions that lie at the boundary of the constrained set are given. In the empirical application we consider the end-of-day volume prediction of major Forex futures traded on the Chicago mercantile Exchange and show the benefits of the proposed methodology.
The law of genetic privacy: applications, implications, and limitations
Authors: Clayton Ellen Wright , Evans Barbara J , Hazel James W , Rothstein Mark A 
Published: May 2019

Abstract
Recent advances in technology have significantly improved the accuracy of genetic testing and analysis, and substantially reduced its cost, resulting in a dramatic increase in the amount of genetic information generated, analysed, shared, and stored by diverse individuals and entities. Given the diversity of actors and their interests, coupled with the wide variety of ways genetic data are held, it has been difficult to develop broadly applicable legal principles for genetic privacy. This article examines the current landscape of genetic privacy to identify the roles that the law does or should play, with a focus on federal statutes and regulations, including the Health Insurance Portability and Accountability Act (HIPAA) and the Genetic Information Nondiscrimination Act (GINA). After considering the many contexts in which issues of genetic privacy arise, the article concludes that few, if any, applicable legal doctrines or enactments provide adequate protection or meaningful control to individuals over disclosures that may affect them. The article describes why it may be time to shift attention from attempting to control access to genetic information to considering the more challenging question of how these data can be used and under what conditions, explicitly addressing trade-offs between individual and social goods in numerous applications.