bluuebunny/crossref_metadata_2025_split huggingface dataset:
Transcriptome characterization and differentially expressed genes under flooding and drought stress in the biomass grasses Phalaris arundinacea and Dactylis glomerata
Authors: Klaas Manfred , Haiminen Niina , Grant Jim , Cormican Paul , Finnan John , Arojju Sai Krishna , Utro Filippo , Vellani Tia , Parida Laxmi , Barth Susanne 
Published: May 2019

AbstractBackground and AimsPerennial grasses are a global resource as forage, and for alternative uses in bioenergy and as raw materials for the processing industry. Marginal lands can be valuable for perennial biomass grass production, if perennial biomass grasses can cope with adverse abiotic environmental stresses such as drought and waterlogging.MethodsIn this study, two perennial grass species, reed canary grass (Phalaris arundinacea) and cocksfoot (Dactylis glomerata) were subjected to drought and waterlogging stress to study their responses for insights to improving environmental stress tolerance. Physiological responses were recorded, reference transcriptomes established and differential gene expression investigated between control and stress conditions. We applied a robust non-parametric method, RoDEO, based on rank ordering of transcripts to investigate differential gene expression. Furthermore, we extended and validated vRoDEO for comparing samples with varying sequencing depths.Key ResultsThis allowed us to identify expressed genes under drought and waterlogging whilst using only a limited number of RNA sequencing experiments. Validating the methodology, several differentially expressed candidate genes involved in the stage 3 step-wise scheme in detoxification and degradation of xenobiotics were recovered, while several novel stress-related genes classified as of unknown function were discovered.ConclusionsReed canary grass is a species coping particularly well with flooding conditions, but this study adds novel information on how its transcriptome reacts under drought stress. We built extensive transcriptomes for the two investigated C3 species cocksfoot and reed canary grass under both extremes of water stress to provide a clear comparison amongst the two species to broaden our horizon for comparative studies, but further confirmation of the data would be ideal to obtain a more detailed picture.
ADAPTIVE: leArning DAta-dePendenT, concIse molecular VEctors for fast, accurate metabolite identification from tandem mass spectra
Authors: Nguyen Dai Hai , Nguyen Canh Hao , Mamitsuka Hiroshi 
Published: May 2019

Abstract

Motivation
Metabolite identification is an important task in metabolomics to enhance the knowledge of biological systems. There have been a number of machine learning-based methods proposed for this task, which predict a chemical structure of a given spectrum through an intermediate (chemical structure) representation called molecular fingerprints. They usually have two steps: (i) predicting fingerprints from spectra; (ii) searching chemical compounds (in database) corresponding to the predicted fingerprints. Fingerprints are feature vectors, which are usually very large to cover all possible substructures and chemical properties, and therefore heavily redundant, in the sense of having many molecular (sub)structures irrelevant to the task, causing limited predictive performance and slow prediction.

Results
We propose ADAPTIVE, which has two parts: learning two mappings (i) from structures to molecular vectors and (ii) from spectra to molecular vectors. The first part learns molecular vectors for metabolites from given data, to be consistent with both spectra and chemical structures of metabolites. In more detail, molecular vectors are generated by a model, being parameterized by a message passing neural network, and parameters are estimated by maximizing the correlation between molecular vectors and the corresponding spectra in terms of Hilbert-Schmidt Independence Criterion. Molecular vectors generated by this model are compact and importantly adaptive (specific) to both given data and task of metabolite identification. The second part uses input output kernel regression (IOKR), the current cutting-edge method of metabolite identification. We empirically confirmed the effectiveness of ADAPTIVE by using a benchmark data, where ADAPTIVE outperformed the original IOKR in both predictive performance and computational efficiency.

Availability and implementation
The code will be accessed through http://www.bic.kyoto-u.ac.jp/pathway/tools/ADAPTIVE after the acceptance of this article.
Minnow: a principled framework for rapid simulation of dscRNA-seq data at the read level
Authors: Sarkar Hirak , Srivastava Avi , Patro Rob 
Published: May 2019

Abstract

Summary
With the advancements of high-throughput single-cell RNA-sequencing protocols, there has been a rapid increase in the tools available to perform an array of analyses on the gene expression data that results from such studies. For example, there exist methods for pseudo-time series analysis, differential cell usage, cell-type detection RNA-velocity in single cells, etc. Most analysis pipelines validate their results using known marker genes (which are not widely available for all types of analysis) and by using simulated data from gene-count-level simulators. Typically, the impact of using different read-alignment or unique molecular identifier (UMI) deduplication methods has not been widely explored. Assessments based on simulation tend to start at the level of assuming a simulated count matrix, ignoring the effect that different approaches for resolving UMI counts from the raw read data may produce. Here, we present minnow, a comprehensive sequence-level droplet-based single-cell RNA-sequencing (dscRNA-seq) experiment simulation framework. Minnow accounts for important sequence-level characteristics of experimental scRNA-seq datasets and models effects such as polymerase chain reaction amplification, cellular barcodes (CB) and UMI selection and sequence fragmentation and sequencing. It also closely matches the gene-level ambiguity characteristics that are observed in real scRNA-seq experiments. Using minnow, we explore the performance of some common processing pipelines to produce gene-by-cell count matrices from droplet-bases scRNA-seq data, demonstrate the effect that realistic levels of gene-level sequence ambiguity can have on accurate quantification and show a typical use-case of minnow in assessing the output generated by different quantification pipelines on the simulated experiment.

Supplementary information
Supplementary data are available at Bioinformatics online.
Adversarial domain adaptation for cross data source macromolecule in situ structural classification in cellular electron cryo-tomograms
Authors: Lin Ruogu , Zeng Xiangrui , Kitani Kris , Xu Min 
Published: May 2019

Abstract

Motivation
Since 2017, an increasing amount of attention has been paid to the supervised deep learning-based macromolecule in situ structural classification (i.e. subtomogram classification) in cellular electron cryo-tomography (CECT) due to the substantially higher scalability of deep learning. However, the success of such supervised approach relies heavily on the availability of large amounts of labeled training data. For CECT, creating valid training data from the same data source as prediction data is usually laborious and computationally intensive. It would be beneficial to have training data from a separate data source where the annotation is readily available or can be performed in a high-throughput fashion. However, the cross data source prediction is often biased due to the different image intensity distributions (a.k.a. domain shift).

Results
We adapt a deep learning-based adversarial domain adaptation (3D-ADA) method to timely address the domain shift problem in CECT data analysis. 3D-ADA first uses a source domain feature extractor to extract discriminative features from the training data as the input to a classifier. Then it adversarially trains a target domain feature extractor to reduce the distribution differences of the extracted features between training and prediction data. As a result, the same classifier can be directly applied to the prediction data. We tested 3D-ADA on both experimental and realistically simulated subtomogram datasets under different imaging conditions. 3D-ADA stably improved the cross data source prediction, as well as outperformed two popular domain adaptation methods. Furthermore, we demonstrate that 3D-ADA can improve cross data source recovery of novel macromolecular structures.

Availability and implementation
https://github.com/xulabs/projects

Supplementary information
Supplementary data are available at Bioinformatics online.
TideHunter: efficient and sensitive tandem repeat detection from noisy long-reads using seed-and-chain
Authors: Gao Yan , Liu Bo , Wang Yadong , Xing Yi 
Published: May 2019

Abstract

Motivation
Pacific Biosciences (PacBio) and Oxford Nanopore Technologies (ONT) sequencing technologies can produce long-reads up to tens of kilobases, but with high error rates. In order to reduce sequencing error, Rolling Circle Amplification (RCA) has been used to improve library preparation by amplifying circularized template molecules. Linear products of the RCA contain multiple tandem copies of the template molecule. By integrating additional in silico processing steps, these tandem sequences can be collapsed into a consensus sequence with a higher accuracy than the original raw reads. Existing pipelines using alignment-based methods to discover the tandem repeat patterns from the long-reads are either inefficient or lack sensitivity.

Results
We present a novel tandem repeat detection and consensus calling tool, TideHunter, to efficiently discover tandem repeat patterns and generate high-quality consensus sequences from amplified tandemly repeated long-read sequencing data. TideHunter works with noisy long-reads (PacBio and ONT) at error rates of up to 20% and does not have any limitation of the maximal repeat pattern size. We benchmarked TideHunter using simulated and real datasets with varying error rates and repeat pattern sizes. TideHunter is tens of times faster than state-of-the-art methods and has a higher sensitivity and accuracy.

Availability and implementation
TideHunter is written in C, it is open source and is available at https://github.com/yangao07/TideHunter
epiTAD: a web application for visualizing chromosome conformation capture data in the context of genetic epidemiology
Authors: Creed Jordan H , Aden-Buie Garrick , Monteiro Alvaro N , Gerke Travis A 
Published: May 2019

Abstract

Summary
Complementary advances in genomic technology and public data resources have created opportunities for researchers to conduct multifaceted examination of the genome on a large scale. To meet the need for integrative genome wide exploration, we present epiTAD. This web-based tool enables researchers to compare genomic 3D organization and annotations across multiple databases in an interactive manner to facilitate in silico discovery.

Availability and implementation
epiTAD can be accessed at https://apps.gerkelab.com/epiTAD/ where we have additionally made publicly available the source code and a Docker containerized version of the application.
Fatal Yellow Fever in a Kidney Transplant Patient
Authors: Pierrotti Lígia C , Duarte-Neto Amaro N , Song Alice T W , Ventura Carlucci G , David-Neto Elias , Azevedo Luiz S 
Published: May 2019

Abstract
A kidney-transplanted patient, unvaccinated against yellow fever (YF), developed high fever, progressed rapidly to hepatic insufficiency and coma, and died 8 days later. Real-time polymarase chain reaction for YF virus collected on the seventh day of symptoms was positive. Autopsy showed disseminated infection and midzonal hepatitis with apoptotic hepatocytes and minimal inflammatory reaction.
Laparoscopic magnetic sphincter augmentation versus fundoplication for gastroesophageal reflux disease: systematic review and pooled analysis
Authors: Guidozzi Nadia , Wiggins Tom , Ahmed Ahmed R , Hanna George B , Markar Sheraz R 
Published: May 2019

SUMMARY
Magnetic sphincter augmentation (MSA) has been proposed as a less invasive, more appealing alternative intervention to fundoplication for the treatment of gastroesophageal reflux disease (GERD). The aim of this study was to evaluate clinical outcomes following MSA for GERD control in comparison with laparoscopic fundoplication. A systematic electronic search for articles was performed in Medline, Embase, Web of Science, and Cochrane Library for single-arm cohort studies or comparative studies (with fundoplication) evaluating the use of MSA. A random-effects meta-analysis for postoperative proton pump inhibitor (PPI) use, GERD-health-related quality of life (GERD-HRQOL), gas bloating, ability to belch, dysphagia, and reoperation was performed. The systematic review identified 6 comparative studies of MSA versus fundoplication and 13 single-cohort studies. Following MSA, only 13.2% required postoperative PPI therapy, 7.8% dilatation, 3.3% device removal or reoperation, and esophageal erosion was seen in 0.3%. There was no significant difference between the groups in requirement for postoperative PPI therapy (pooled odds ratio, POR = 1.08; 95%CI 0.40–2.95), GERD-HRQOL score (weighted mean difference, WMD = 0.34; 95%CI −0.70–1.37), dysphagia (POR = 0.94; 95%CI 0.57–1.55), and reoperation (POR = 1.23; 95%CI 0.26–5.8). However, when compared to fundoplication MSA was associated with significantly less gas bloating (POR = 0.34; 95%CI 0.16–0.71) and a greater ability to belch (POR = 12.34; 95%CI 6.43–23.7). In conclusion, magnetic sphincter augmentation achieves good GERD symptomatic control similar to that of fundoplication, with the benefit of less gas bloating. The safety of MSA also appears acceptable with only 3.3% of patients requiring device removal. There is an urgent need for randomized data directly comparing fundoplication with MSA for the treatment of GERD to truly evaluate the efficacy of this treatment approach.
Prognostic implications of global, left ventricular myocardial work efficiency before cardiac resynchronization therapy
Authors: van der Bijl Pieter , Vo Ngoc Mai , Kostyukevich Marina V , Mertens Bart , Ajmone Marsan Nina , Delgado Victoria , Bax Jeroen J 
Published: May 2019

Abstract

Aims
Cardiac resynchronization therapy (CRT) restores mechanical efficiency to the failing left ventricular (LV) by resynchronization of contraction. Global, LV myocardial work efficiency (GLVMWE) can be quantified non-invasively with echocardiography. The prognostic implication of GLVMWE remains unexplored, and we therefore related GLVMWE before CRT to long-term prognosis.

Methods and results
Data were analysed from an ongoing registry of patients with Class I indications for CRT. GLVMWE was defined as the ratio of constructive work in all LV segments, divided by the sum of constructive and wasted work in all LV segments, as a percentage. It was derived from speckle tracking strain echocardiography and non-invasive blood pressure measurements, taken pre-CRT. Patients were dichotomized according to baseline, median GLVMWE [75%; interquartile range (IQR) 66–81%]. A total of 153 patients (66 ± 10 years, 72% male, 48% ischaemic heart disease) were analysed. After a median follow-up of 57 months (IQR 28–76 months), 31% of patients died. CRT recipients with less efficient baseline energetics (GLVMWE &lt;75%) demonstrated lower event rates than patients with more efficient baseline energetics (GLVMWE ≥75%) (log-rank test, P = 0.029). On multivariable analysis, global LV wasted work ratio &lt;75% pre-CRT was independently associated with a decreased risk of all-cause mortality (hazard ratio 0.48, 95% confidence interval 0.25–0.92; P = 0.027), suggesting that the potential for improvement in LV efficiency is important for CRT benefit.

Conclusion
GLVMWE can be derived non-invasively from speckle tracking strain echocardiography and non-invasive blood pressure recordings. A lower GLVMWE before CRT is independently associated with improved long-term outcome.
Effects of mesenchymal stem cell transfer on orthodontically induced root resorption and orthodontic tooth movement during orthodontic arch expansion protocols: an experimental study in rats
Authors: Gul Amuk Nisa , Kurt Gokmen , Karsli Erol , Ozcan Servet , Acar Mustafa Burak , Amuk Mehmet , Lekesizcan Ayca , Gurgan Cem Abdulkadir 
Published: May 2019

SummaryObjectivesThe aim was to evaluate the effects of mesenchymal stem cell (MSC) transfer to periodontal ligament (PDL) on the inhibition and/or repair of orthodontically induced root resorption (OIRR) during and after arch expansion and on the orthodontic tooth movement (OTM) rate of the maxillary first molar teeth of rats.Material and methodsSixty Wistar rats were divided into three groups as the untreated group, MSC and control injections during the expansion period group (EMSC-EC), and MSC and control injections at the retention period group (RMSC-RC). Fifty grams of orthodontic force was applied to the maxillary first molar teeth of the rats for 14 days in the vestibular direction, and then, 20 days of retention was carried out. MSCs and control injections were performed every 3 days in the EC, RC, EMSC, and RMSC groups. At the end of the experiment, samples were prepared for OTM evaluation, mRNA expression analysis, micro-computed tomography measurements, cementum thickness calculations, and structural examinations.ResultsThe amount of OTM in EMSC group was significantly higher than in EC group (P &lt; 0.001). MSC transfer during the expansion and retention periods reduced the number of resorption lacunae, volumetric and linear resorptive measurements, and cyclooxygenase-2 and receptor activator of nuclear factor kappa B ligand (RANKL) mRNA expression levels, and increased the osteoprotegerin (OPG) expression levels, OPG/RANKL ratio, and cementum thickness in the EMSC and RMSC groups.ConclusionsMSC transfer to PDL during expansion increased the amount of OTM. Injection of MSC during the retention period was found to be slightly more effective in prevention and/or repair of OIRR than MSC transfer during the expansion period.
Impact of DNA extraction methods on the observed microbial communities from the intestinal flora of the penaeid shrimp Litopenaeus vannamei
Authors: Jiang Boyun , Sun Jingfeng , Lv Aijun , Hu Xiucai , Shi Hongyue , Sung YeongYik , Wang Qingkui , Wang Yang 
Published: May 2019

ABSTRACT
Two DNA extraction methods, the Zirmil-beating cell disruption method (ZBC) and the QIAamp fast DNA stool mini kit (QIA), were used to extract DNA from the intestinal flora of the penaeid shrimp Litopenaeus vannamei, and their microbial communities were analyzed using 16S rDNA high-throughput sequencing. Results were obtained in terms of the number of reads, alpha diversity indexes, beta diversity indexes and taxonomic composition. The alpha diversity indexes of the community, according to the ZBC method, were higher than those according to the QIA method. Furthermore, results from the three samples using the ZBC method were less consistent than those where the QIA method was used. Further, using the latter method led to substantive clustering. It is suggested that the QIA method is more stable and repeatable than the ZBC method. Although the two extraction methods shared the major abundant microflora based on 16S rDNA high-throughput sequencing, bias associated with diversity analysis indexes and certain species was observed.
Social Integration and Terminal Decline in Life Satisfaction Among Older Japanese
Authors: Nakagawa Takeshi , Hülür Gizem 
Published: May 2019

Abstract

Objectives
Well-being typically exhibits pronounced deteriorations with approaching death, with sizeable interindividual variations in levels and changes. It is less well understood how psychosocial factors contribute to these individual differences. We examined whether and how social integration is associated with terminal trajectories of well-being, indexed as life satisfaction.

Method
Data were drawn from 1,119 deceased Japanese participants of a 15-year longitudinal study (age at death: M = 79.2 years; SD = 7.7 years; 43.1% women). Life satisfaction, structural and functional features of social integration (e.g., frequency of contact with family and nonfamily, and perceived overall support, respectively), sociodemographic characteristics, and physical function were assessed.

Results
Social integration predicted individual differences in terminal decline in life satisfaction, after controlling for age at death, gender, education, and physical function: More diverse social relationships were associated with higher levels of life satisfaction at 1 year before death. In addition, individuals who exhibited more decline in social participation and perceived less support showed more pronounced decline with increasing proximity of death.

Discussion
This study suggests that social integration plays a protective role in late-life well-being and that sustaining an active social life and supportive social interactions may help mitigate terminal decline in well-being.
Perceptual Inhibition Is Not a Specific Component of the Sensory Integration Process Necessary for a Rapid Voluntary Step Initiation in Healthy Older Adults
Authors: Magnard Justine , Berrut Gilles , Couturier Catherine , Cattagni Thomas , Cornu Christophe , Deschamps Thibault 
Published: May 2019

Abstract

Objectives
We investigated whether performing step initiation during a proprioceptive perturbation would require greater perceptual or motor inhibitory control in older adults.

Method
Fifty-two healthy adults (young: n = 26, mean age 22.5 years vs. older: n = 26, mean age 70.1 years) performed a stepping reaction time task, with different inhibition requirements (i.e., perceptual vs. motor inhibitory conflict), with two proprioceptive configurations: with and without application of Achilles tendon vibrations.

Results
Beyond a systematically greater stepping reaction time in older adults (p &lt; .01), no difference was found between the perceptual versus motor inhibitory conflict resolution, regardless of age and proprioceptive configuration. Furthermore, slower reaction time was observed for young participants in the presence of Achilles tendon vibrations unlike older adults, who showed the same reactive stepping performance with or without vibrations (p &lt; .05).

Discussion
These findings show that perceptual inhibition cannot be considered as specifically involved in the central processing of proprioceptive signals, at least not in active older adults. Rather than motor system malfunctioning or a reduced amount of proprioceptive afference, we propose that cortical-proprioceptive processing in older adults remains as effective as in young adults, regardless of the high attentional requirements for step responses.
Valve-sparing root reimplantation in anomalous right coronary origin
Authors: Ram Duvuru , Lund Jens Teglgaard 
Published: May 2019

Abstract
Anomalous origin of coronary artery is a rare anomaly. Performing valve-sparing root reimplantation for aortic root pathology in these patients is challenging. There are modified techniques for performing valve-sparing procedures in this rare subset of patients. Herein, we present a case of anomalous right coronary origin from left ostium managed by conventional valve-sparing root reimplantation.