bluuebunny/crossref_metadata_2025_split huggingface dataset:
DataTri, a database of American triatomine species occurrence
Authors: Ceccarelli Soledad , Balsalobre Agustín , Medone Paula , Cano María Eugenia , Gurgel Gonçalves Rodrigo , Feliciangeli Dora , Vezzani Darío , Wisnivesky-Colli Cristina , Gorla David E , Marti Gerardo A , Rabinovich Jorge E 
Published: April 2018

AbstractTrypanosoma cruzi, the causative agent of Chagas disease, is transmitted to mammals - including humans - by insect vectors of the subfamily Triatominae. We present the results of a compilation of triatomine occurrence and complementary ecological data that represents the most complete, integrated and updated database (DataTri)available on triatomine species at a continental scale. This database was assembled by collecting the records of triatomine species published from 1904 to 2017, spanning all American countries with triatomine presence. A total of 21815 georeferenced records were obtained from published literature, personal fieldwork and data provided by colleagues. The data compiled includes 24 American countries, 14 genera and 135 species. From a taxonomic perspective, 67.33% of the records correspond to the genusTriatoma, 20.81% toPanstrongylus, 9.01% toRhodniusand the remaining 2.85% are distributed among the other 11 triatomine genera. We encourage usingDataTriinformation in various areas, especially to improve knowledge of the geographical distribution of triatomine species and its variations in time.
Effects of a Tablet-Based Home Practice Program With Telepractice on Treatment Outcomes in Chronic Aphasia
Authors: Kurland Jacquie , Liu Anna , Stokes Polly 
Published: April 2018

Purpose
The aim of this study was to determine if a tablet-based home practice program with weekly telepractice support could enable long-term maintenance of recent treatment gains and foster new language gains in poststroke aphasia.

Method
In a pre–post group study of home practice outcomes, 21 individuals with chronic aphasia were examined before and after a 6-month home practice phase and again at follow-up 4 months later. The main outcome measure studied was change in naming previously treated or untreated, practiced or unpracticed pictures of objects and actions. Individualized home practice programs were created in iBooks Author with semantic, phonemic, and orthographic cueing in pictures, words, and videos in order to facilitate naming of previously treated or untreated pictures.

Results
Home practice was effective for all participants with severity moderating treatment effects, such that individuals with the most severe aphasia made and maintained fewer gains. There was a negative relationship between the amount of training required for iPad proficiency and improvements on practiced and unpracticed pictures and a positive relationship between practice compliance and same improvements.

Conclusion
Unsupervised home practice with weekly video teleconferencing support is effective. This study demonstrates that even individuals with chronic severe aphasia, including those with no prior smart device or even computer experience, can attain independent proficiency to continue practicing and improving their language skills beyond therapy discharge. This could represent a low-cost therapy option for individuals without insurance coverage and/or those for whom mobility is an obstacle to obtaining traditional aphasia therapy.
Gaia Data Release 2
Authors: Riello M. , De Angeli F. , Evans D. W. , Busso G. , Hambly N. C. , Davidson M. , Burgess P. W. , Montegriffo P. , Osborne P. J. , Kewley A. , Carrasco J. M. , Fabricius C. , Jordi C. , Cacciari C. , van Leeuwen F. , Holland G. 
Published: April 2018

Context. The second Gaia data release is based on 22 months of mission data with an average of 0.9 billion individual CCD observations per day. A data volume of this size and granularity requires a robust and reliable but still flexible system to achieve the demanding accuracy and precision constraints that Gaia is capable of delivering.
Aims. We aim to describe the input data, the treatment of blue photometer/red photometer (BP/RP) low-resolution spectra required to produce the integrated GBP and GRP fluxes, the process used to establish the internal Gaia photometric system, and finally, the generation of the mean source photometry from the calibrated epoch data for Gaia DR2.
Methods. The internal Gaia photometric system was initialised using an iterative process that is solely based on Gaia data. A set of calibrations was derived for the entire Gaia DR2 baseline and then used to produce the final mean source photometry. The photometric catalogue contains 2.5 billion sources comprised of three different grades depending on the availability of colour information and the procedure used to calibrate them: 1.5 billion gold, 144 million silver, and 0.9 billion bronze. These figures reflect the results of the photometric processing; the content of the data release will be different due to the validation and data quality filters applied during the catalogue preparation. The photometric processing pipeline, PhotPipe, implements all the processing and calibration workflows in terms of Map/Reduce jobs based on the Hadoop platform. This is the first example of a processing system for a large astrophysical survey project to make use of these technologies.
Results. The improvements in the generation of the integrated G–band fluxes, in the attitude modelling, in the cross-matching, and and in the identification of spurious detections led to a much cleaner input stream for the photometric processing. This, combined with the improvements in the definition of the internal photometric system and calibration flow, produced high-quality photometry. Hadoop proved to be an excellent platform choice for the implementation of PhotPipe in terms of overall performance, scalability, downtime, and manpower required for operations and maintenance.
Preventive effect of mesenchymal stem cell culture supernatant on luminal stricture after endoscopic submucosal dissection in the rectum of pigs
Authors: Tsuda Momoko , Ohnishi Shunsuke , Mizushima Takeshi , Hosono Hidetaka , Yamahara Kenichi , Ishikawa Marin , Abiko Satoshi , Katsurada Takehiko , Shimizu Yuichi , Sakamoto Naoya 
Published: April 2018

Abstract
Background Mesenchymal stem cells (MSCs) are valuable in regenerative medicine, and MSC culture supernatant (MSC-CS) reportedly inhibits inflammation and fibrosis. We investigated whether colorectal luminal stricture develops after circumferential endoscopic submucosal dissection (ESD) in the colorectum, and whether the development of luminal stricture could be prevented by using MSC-CS enema.
Methods In the first experiment, we performed circumferential ESD in the rectums or distal colons of pigs (n = 4 in each group). We sacrificed the pigs on Day 22 and measured the degree of luminal stricture. In the second experiment, we performed circumferential ESD in the rectums of pigs and administered an MSC-CS gel or a control gel enema after ESD for 4 days. We sacrificed the pigs on Day 8 (n = 3 in each group) or 22 (n = 3 in each group) to measure the degree of luminal stricture, and performed histological analysis.
Results Severe luminal stricture was observed in the rectum but not in the distal colon. Moreover, fiber accumulation in the submucosa and hypertrophy of the muscularis propria were observed in the rectum but not in the distal colon. The degree of luminal stricture in the rectum was significantly lower in the MSC-CS group than in the control group. Furthermore, MSC-CS attenuated myofibroblast activation and hypertrophy of the muscularis propria on Day 22, and reduced inflammatory cell infiltration on Day 8.
Conclusions Luminal stricture after ESD developed only in the rectum because of the difference in myofibroblast activation and fiber accumulation. In addition, MSC-CS enema prevented luminal stricture after ESD, possibly by inhibiting the inflammatory reaction and fibrosis.
Is Low-field NMR a Complementary Tool to GC-MS in Quality Control of Essential Oils? A Case Study: Patchouli Essential Oil
Authors: Krause Andre , Wu Yu , Tian Runtao , van Beek Teris 
Published: April 2018

AbstractHigh-field NMR is an expensive and important quality control technique. In recent years, cheaper and simpler low-field NMR has become available as a new quality control technique. In this study, 60 MHz 1H-NMR was compared with GC-MS and refractometry for the detection of adulteration of essential oils, taking patchouli essential oil as a test case. Patchouli essential oil is frequently adulterated, even today. In total, 75 genuine patchouli essential oils, 10 commercial patchouli essential oils, 10 other essential oils, 17 adulterants, and 1 patchouli essential oil, spiked at 20% with those adulterants, were measured. Visual inspection of the NMR spectra allowed for easy detection of 14 adulterants, while gurjun and copaiba balsams proved difficult and one adulterant could not be detected. NMR spectra of 10 random essential oils differed not only strongly from patchouli essential oil but also from one another, suggesting that fingerprinting by low-field NMR is not limited to patchouli essential oil. Automated chemometric evaluation of NMR spectra was possible by similarity analysis (Mahalanobis distance) based on the integration from 0.1 – 8.1 ppm in 0.01 ppm increments. Good quality patchouli essential oils were recognised as well as 15 of 17 deliberate adulterations. Visual qualitative inspection by GC-MS allowed for the detection of all volatile adulterants. Nonvolatile adulterants, and all but one volatile adulterant, could be detected by semiquantitation. Different chemometric approaches showed satisfactory results. Similarity analyses were difficult with nonvolatile adulterants. Refractive index measurements could detect only 8 of 17 adulterants. Due to advantages such as simplicity, rapidity, reproducibility, and ability to detect nonvolatile adulterants, 60 MHz 1H-NMR is complimentary to GC-MS for quality control of essential oils.
Depression im Alter – Diagnostik, Pathophysiologie und therapeutische Strategien
Authors: Dafsari Forugh S. , Jessen Frank 
Published: April 2018

ZusammenfassungDepressionen zählen zu den häufigsten psychischen Erkrankungen im höheren Lebensalter. Sie führen zu einer starken Inanspruchnahme von Gesundheitsleistungen und
gehen mit erhöhter Morbidität und Mortalität einher. Mit Blick auf den demografischen Wandel stellt die Altersdepression eine große Herausforderung der
alternden Gesellschaft dar. Der frühzeitigen Diagnostik und spezifischen Behandlung kommt eine besondere Bedeutung zu.
Spatial and temporal organization of cadherin in punctate adherens junctions
Authors: Indra Indrajyoti , Choi Jongho , Chen Chi-Shuo , Troyanovsky Regina B. , Shapiro Lawrence , Honig Barry , Troyanovsky Sergey M. 
Published: April 2018

Significance
Adherens junctions (AJs) are major intercellular adhesive structures in vertebrates. Despite the critical role of AJs in tissue integrity and morphogenesis, the detailed organization of their key protein E-cadherin, inside and outside of AJs, remains controversial. Using superresolution microscopy approaches, we show that AJs can reach more than 1 μm in length and consist of tightly packed E-cadherin clusters with crystal-like density interspersed within sparser cadherin regions. No clusters were found outside of AJs. E-cadherin tracking showed that these crystal-like pAJ clusters are transient and their cadherin is reused for new clusters. Our results thus modify the classical view of AJs by depicting them as mosaics of cadherin clusters, whose short lifetimes enable stable overall morphology combined with rapid internal rearrangements.
Suppression of costimulation by human cytomegalovirus promotes evasion of cellular immune defenses
Authors: Wang Eddie C. Y. , Pjechova Mariana , Nightingale Katie , Vlahava Virginia-Maria , Patel Mihil , Ruckova Eva , Forbes Simone K. , Nobre Luis , Antrobus Robin , Roberts Dawn , Fielding Ceri A. , Seirafian Sepehr , Davies James , Murrell Isa , Lau Betty , Wilkie Gavin S. , Suárez Nicolás M. , Stanton Richard J. , Vojtesek Borivoj , Davison Andrew , Lehner Paul J. , Weekes Michael P. , Wilkinson Gavin W. G. , Tomasec Peter 
Published: April 2018

SignificanceHuman cytomegalovirus (HCMV) is the major infectious cause of developmental disorders in babies due to its capacity to cross the placenta. HCMV is also a major pathogen in transplant recipients and HIV–AIDS patients. Despite inducing the strongest immune responses observed for any human pathogen, HCMV evades host defenses and persists for life. Herein, we report another viral stealth strategy. HCMV UL148 reduces surface expression of a key cell adhesion molecule (CD58), impairing the ability of NK and T cells to be activated by HCMV-infected cells. Our findings highlight a role for CD58 in recognition of HCMV-infected cells and may be relevant for development of future antiviral therapies.
Control of motor coordination by astrocytic tonic GABA release through modulation of excitation/inhibition balance in cerebellum
Authors: Woo Junsung , Min Joo Ok , Kang Dae-Si , Kim Yoo Sung , Jung Guk Hwa , Park Hyun Jung , Kim Sunpil , An Heeyoung , Kwon Jea , Kim Jeongyeon , Shim Insop , Kim Hyung-Gun , Lee C. Justin , Yoon Bo-Eun 
Published: April 2018

Significance
Tonic inhibition plays critical roles in cognitive functions under physiological and pathological conditions by controlling neuronal excitability. Although we have previously reported that cerebellar tonic inhibition is critically dependent on both the synthesis of GABA through monoamine oxidase B (MAOB) enzyme and the release via the bestrophin 1 (Best1) channel, the role of astrocytic GABA in cerebellar function in vivo has remained elusive. Here, we report that a reduction of tonic GABA release by genetic or pharmacological removal of Best1 or MAOB caused enhanced neuronal excitability, synaptic transmission, and motor performance on the rotarod test, whereas an augmentation of tonic GABA release by astrocyte-specific overexpression of MAOB caused opposite results. Our findings suggest the actions of astrocytic GABA in excitation/inhibition balance and motor coordination.
Phenomenal intentionality: reductionism vs. primitivism
Authors: Woodward Philip 
Published: April 2018

AbstractThis paper explores the relationship between phenomenal properties and intentional properties. In recent years a number of philosophers have argued that intentional properties are sometimes necessitated by phenomenal properties, but have not explained why or how. Exceptions can be found in the work of Katalin Farkas and Farid Masrour, who develop versions of reductionism regarding phenomenally-necessitated intentionality (or ‘phenomenal intentionality’). I raise two objections to reductive theories of the sort they develop. Then I propose a version of primitivism regarding phenomenal intentionality. I argue that primitivism avoids the pitfalls of reductionism while promising broad explanatory payoffs.
Scalable preprocessing for sparse scRNA-seq data exploiting prior knowledge
Authors: Mukherjee Sumit , Zhang Yue , Fan Joshua , Seelig Georg , Kannan Sreeram 
Published: April 2018

Abstract

Motivation
Single cell RNA-seq (scRNA-seq) data contains a wealth of information which has to be inferred computationally from the observed sequencing reads. As the ability to sequence more cells improves rapidly, existing computational tools suffer from three problems. (i) The decreased reads-per-cell implies a highly sparse sample of the true cellular transcriptome. (ii) Many tools simply cannot handle the size of the resulting datasets. (iii) Prior biological knowledge such as bulk RNA-seq information of certain cell types or qualitative marker information is not taken into account. Here we present UNCURL, a preprocessing framework based on non-negative matrix factorization for scRNA-seq data, that is able to handle varying sampling distributions, scales to very large cell numbers and can incorporate prior knowledge.

Results
We find that preprocessing using UNCURL consistently improves performance of commonly used scRNA-seq tools for clustering, visualization and lineage estimation, both in the absence and presence of prior knowledge. Finally we demonstrate that UNCURL is extremely scalable and parallelizable, and runs faster than other methods on a scRNA-seq dataset containing 1.3 million cells.

Availability and implementation
Source code is available at https://github.com/yjzhang/uncurl_python.

Supplementary information
Supplementary data are available at Bioinformatics online.
BlockFeST: Bayesian calculation of region-specific FST to detect local adaptation
Authors: Pfeifer Bastian , Lercher Martin J 
Published: April 2018

Abstract

Summary
The fixation index FST can be used to identify non-neutrally evolving loci from genome-scale SNP data across two or more populations. Recent years have seen the development of sophisticated approaches to estimate FST based on Markov-Chain Monte-Carlo simulations. Here, we present a vectorized R implementation of an extension of the widely used BayeScan software for codominant markers, adding the option to group individual SNPs into pre-defined blocks. A typical application of this new approach is the identification of genomic regions, genes, or gene sets containing SNPs that evolved under directional selection.

Availability and implementation
The R implementation of our method, which builds on the powerful population genetics and genomics software PopGenome, is available freely from CRAN.

Supplementary information
Supplementary data are available at Bioinformatics online.
Predicting gene structure changes resulting from genetic variants via exon definition features
Authors: Majoros William H , Holt Carson , Campbell Michael S , Ware Doreen , Yandell Mark , Reddy Timothy E 
Published: April 2018

AbstractMotivationGenetic variation that disrupts gene function by altering gene splicing between individuals can substantially influence traits and disease. In those cases, accurately predicting the effects of genetic variation on splicing can be highly valuable for investigating the mechanisms underlying those traits and diseases. While methods have been developed to generate high quality computational predictions of gene structures in reference genomes, the same methods perform poorly when used to predict the potentially deleterious effects of genetic changes that alter gene splicing between individuals. Underlying that discrepancy in predictive ability are the common assumptions by reference gene finding algorithms that genes are conserved, well-formed and produce functional proteins.ResultsWe describe a probabilistic approach for predicting recent changes to gene structure that may or may not conserve function. The model is applicable to both coding and non-coding genes, and can be trained on existing gene annotations without requiring curated examples of aberrant splicing. We apply this model to the problem of predicting altered splicing patterns in the genomes of individual humans, and we demonstrate that performing gene-structure prediction without relying on conserved coding features is feasible. The model predicts an unexpected abundance of variants that create de novo splice sites, an observation supported by both simulations and empirical data from RNA-seq experiments. While these de novo splice variants are commonly misinterpreted by other tools as coding or non-coding variants of little or no effect, we find that in some cases they can have large effects on splicing activity and protein products and we propose that they may commonly act as cryptic factors in disease.Availability and implementationThe software is available from geneprediction.org/SGRF.Supplementary informationSupplementary information is available at Bioinformatics online.
Latent variable modeling for the microbiome
Authors: Sankaran Kris , Holmes Susan P 
Published: April 2018

SummaryThe human microbiome is a complex ecological system, and describing its structure and function under different environmental conditions is important from both basic scientific and medical perspectives. Viewed through a biostatistical lens, many microbiome analysis goals can be formulated as latent variable modeling problems. However, although probabilistic latent variable models are a cornerstone of modern unsupervised learning, they are rarely applied in the context of microbiome data analysis, in spite of the evolutionary, temporal, and count structure that could be directly incorporated through such models. We explore the application of probabilistic latent variable models to microbiome data, with a focus on Latent Dirichlet allocation, Non-negative matrix factorization, and Dynamic Unigram models. To develop guidelines for when different methods are appropriate, we perform a simulation study. We further illustrate and compare these techniques using the data of Dethlefsen and Relman (2011, Incomplete recovery and individualized responses of the human distal gut microbiota to repeated antibiotic perturbation. Proceedings of the National Academy of Sciences108, 4554–4561), a study on the effects of antibiotics on bacterial community composition. Code and data for all simulations and case studies are available publicly.
SILAC-based phosphoproteomics reveals new PP2A-Cdc55-regulated processes in budding yeast
Authors: Baro Barbara , Játiva Soraya , Calabria Inés , Vinaixa Judith , Bech-Serra Joan-Josep , de LaTorre Carolina , Rodrigues João , Hernáez María Luisa , Gil Concha , Barceló-Batllori Silvia , Larsen Martin R , Queralt Ethel 
Published: April 2018

Abstract

Background
Protein phosphatase 2A (PP2A) is a family of conserved serine/threonine phosphatases involved in several essential aspects of cell growth and proliferation. PP2ACdc55 phosphatase has been extensively related to cell cycle events in budding yeast; however, few PP2ACdc55 substrates have been identified. Here, we performed a quantitative mass spectrometry approach to reveal new substrates of PP2ACdc55 phosphatase and new PP2A-related processes in mitotic arrested cells.

Results
We identified 62 statistically significant PP2ACdc55 substrates involved mainly in actin-cytoskeleton organization. In addition, we validated new PP2ACdc55 substrates such as Slk19 and Lte1, involved in early and late anaphase pathways, and Zeo1, a component of the cell wall integrity pathway. Finally, we constructed docking models of Cdc55 and its substrate Mob1. We found that the predominant interface on Cdc55 is mediated by a protruding loop consisting of residues 84–90, thus highlighting the relevance of these aminoacids for substrate interaction.

Conclusions
We used phosphoproteomics of Cdc55-deficient cells to uncover new PP2ACdc55 substrates and functions in mitosis. As expected, several hyperphosphorylated proteins corresponded to Cdk1-dependent substrates, although other kinases' consensus motifs were also enriched in our dataset, suggesting that PP2ACdc55 counteracts and regulates other kinases distinct from Cdk1. Indeed, Pkc1 emerged as a novel node of PP2ACdc55 regulation, highlighting a major role of PP2ACdc55 in actin cytoskeleton and cytokinesis, gene ontology terms significantly enriched in the PP2ACdc55-dependent phosphoproteome.