bluuebunny/crossref_metadata_2025_split huggingface dataset:
Jasmine: a Java pipeline for isomiR characterization in miRNA-Seq data
Authors: Zhong Xiangfu , Pla Albert , Rayner Simon 
Published: October 2019

Abstract

Motivation
The existence of complex subpopulations of miRNA isoforms, or isomiRs, is well established. While many tools exist for investigating isomiR populations, they differ in how they characterize an isomiR, making it difficult to compare results across different tools. Thus, there is a need for a more comprehensive and systematic standard for defining isomiRs. Such a standard would allow investigation of isomiR population structure in progressively more refined sub-populations, permitting the identification of more subtle changes between conditions and leading to an improved understanding of the processes that generate these differences.

Results
We developed Jasmine, a software tool that incorporates a hierarchal framework for characterizing isomiR populations. Jasmine is a Java application that can process raw read data in fastq/fasta format, or mapped reads in SAM format to produce a detailed characterization of isomiR populations. Thus, Jasmine can reveal structure not apparent in a standard miRNA-Seq analysis pipeline.

Availability and implementation
Jasmine is implemented in Java and R and freely available at bitbucket https://bitbucket.org/bipous/jasmine/src/master/.

Supplementary information
Supplementary data are available at Bioinformatics online.
Influenza classification from short reads with VAPOR facilitates robust mapping pipelines and zoonotic strain detection for routine surveillance applications
Authors: Southgate Joel A , Bull Matthew J , Brown Clare M , Watkins Joanne , Corden Sally , Southgate Benjamin , Moore Catherine , Connor Thomas R 
Published: October 2019

Abstract

Motivation
Influenza viruses represent a global public health burden due to annual epidemics and pandemic potential. Due to a rapidly evolving RNA genome, inter-species transmission, intra-host variation, and noise in short-read data, reads can be lost during mapping, and de novo assembly can be time consuming and result in misassembly. We assessed read loss during mapping and designed a graph-based classifier, VAPOR, for selecting mapping references, assembly validation and detection of strains of non-human origin.

Results
Standard human reference viruses were insufficient for mapping diverse influenza samples in simulation. VAPOR retrieved references for 257 real whole-genome sequencing samples with a mean of &gt;99.8% identity to assemblies, and increased the proportion of mapped reads by up to 13.3% compared to standard references. VAPOR has the potential to improve the robustness of bioinformatics pipelines for surveillance and could be adapted to other RNA viruses.

Availability and implementation
VAPOR is available at https://github.com/connor-lab/vapor.

Supplementary information
Supplementary data are available at Bioinformatics online.
Generalized Born radii computation using linear models and neural networks
Authors: Mahmoud Saida Saad Mohamed , Esposito Gennaro , Serra Giuseppe , Fogolari Federico 
Published: October 2019

Abstract

Motivation
Implicit solvent models play an important role in describing the thermodynamics and the dynamics of biomolecular systems. Key to an efficient use of these models is the computation of generalized Born (GB) radii, which is accomplished by algorithms based on the electrostatics of inhomogeneous dielectric media. The speed and accuracy of such computations are still an issue especially for their intensive use in classical molecular dynamics. Here, we propose an alternative approach that encodes the physics of the phenomena and the chemical structure of the molecules in model parameters which are learned from examples.

Results
GB radii have been computed using (i) a linear model and (ii) a neural network. The input is the element, the histogram of counts of neighbouring atoms, divided by atom element, within 16 Å. Linear models are ca. 8 times faster than the most widely used reference method and the accuracy is higher with correlation coefficient with the inverse of ‘perfect’ GB radii of 0.94 versus 0.80 of the reference method. Neural networks further improve the accuracy of the predictions with correlation coefficient with ‘perfect’ GB radii of 0.97 and ca. 20% smaller root mean square error.

Availability and implementation
We provide a C program implementing the computation using the linear model, including the coefficients appropriate for the set of Bondi radii, as Supplementary Material. We also provide a Python implementation of the neural network model with parameter and example files in the Supplementary Material as well.

Supplementary information
Supplementary data are available at Bioinformatics online.
Next generation of power electronic-converter application for energy-conversion and storage units and systems
Authors: Jørgensen Kasper Lüthje , Zhang Zhe , Andersen Michael A E 
Published: October 2019

Abstract
By a rearrangement of the traditional supply-converter-load system connection, partial-power-processing-based converters can be used to achieve a reduction in size and cost, increase in system efficiency and lower device power rating. The concept is promising for different applications such as photovoltaic arrays, electric vehicles and electrolysis. For photovoltaic applications, it can drive each cell in the array to its maximum power point with a relatively smaller converter; for electric-vehicle applications, both an onboard charger with reduced weight and improved efficiency as well as a fast charger station handling higher power can be considered. By showing different examples of partial-power-processing application for energy-conversion and storage units and systems, this paper discusses key limitations of partial-power-processing and related improvements from different perspectives to show the potential in future power electronic systems.
Enhancing Plasticity Mechanisms in the Mouse Motor Cortex by Anodal Transcranial Direct-Current Stimulation: The Contribution of Nitric Oxide Signaling
Authors: Barbati Saviana Antonella , Cocco Sara , Longo Valentina , Spinelli Matteo , Gironi Katia , Mattera Andrea , Paciello Fabiola , Colussi Claudia , Podda Maria Vittoria , Grassi Claudio 
Published: October 2019

AbstractConsistent body of evidence shows that transcranial direct-current stimulation (tDCS) over the primary motor cortex (M1) facilitates motor learning and promotes recovery after stroke. However, the knowledge of molecular mechanisms behind tDCS effects needs to be deepened for a more rational use of this technique in clinical settings. Here we characterized the effects of anodal tDCS of M1, focusing on its impact on glutamatergic synaptic transmission and plasticity. Mice subjected to tDCS displayed increased long-term potentiation (LTP) and enhanced basal synaptic transmission at layer II/III horizontal connections. They performed better than sham-stimulated mice in the single-pellet reaching task and exhibited increased forelimb strength. Dendritic spine density of layer II/III pyramidal neurons was also increased by tDCS. At molecular level, tDCS enhanced: 1) BDNF expression, 2) phosphorylation of CREB, CaMKII, and GluA1, and 3) S-nitrosylation of GluA1 and HDAC2. Blockade of nitric oxide synthesis by L-NAME prevented the tDCS-induced enhancement of GluA1 phosphorylation at Ser831 and BDNF levels, as well as of miniature excitatory postsynaptic current (mEPSC) frequency, LTP and reaching performance. Collectively, these findings demonstrate that anodal tDCS engages plasticity mechanisms in the M1 and highlight a role for nitric oxide (NO) as a novel mediator of tDCS effects.
Validation of an UHPLC–MS/MS Method for the Determination of Glaucocalyxin A, a Novel Potent Negative Akt Regulator in Rat Plasma, Lung and Brain Tissues: Application to a Pharmacokinetic Study
Authors: Deng Zhipeng , Liu Qian , He Jixiang , Zhang Sixi , Zhou Wei 
Published: October 2019

AbstractGlaucocalyxin A, a novel potent negative Akt regulator, is a major active constituent of Rabdosia japonica. A simple, specific and sensitive ultra-high pressure liquid chromatography tandem mass spectrometry (UHPLC–MS/MS) method was developed and validated for the quantification of glaucocalyxin A in rat plasma, lung and brain tissues after intravenous administration. Sample preparation was carried out through a simple liqiud–liquid extraction with ethyl acetate using bullatine A as internal standard. The chromatographic separation was achieved by using an Agilent ZORBAX Eclipse Plus C18 column (3.0 mm × 100 mm, 1.8 μm) with a mobile phase of acetonitrile and water containing 0.1% formic acid in a gradient elution. Mass spectrometry analysis was conducted in positive ionization mode with multiple reaction monitoring transitions at m/z 333.2 → 157.1 for glaucocalyxin A and m/z 344.2 → 128.1 for IS. Calibration curves were linear over the ranges of 20.0–4000 ng/mL for both plasma and tissue samples (r2 &gt; 0.99). The Lower limit of quantification (LLOQ) was 0.284 ng/mL. The intra-day and inter-day precision relative standard deviation (RSD%) were &lt;14.9%, while the accuracy ranged from −12.5 to 17.0% for LLOQ and quality control samples. This UHPLC–MS/MS method was successfully applied in the pharmacokinetics, lung and brain tissue distributions of glaucocalyxin A after intravenous administration.
Myocardial overexpression of ANKRD1 causes sinus venosus defects and progressive diastolic dysfunction
Authors: Piroddi Nicoletta , Pesce Paola , Scellini Beatrice , Manzini Stefano , Ganzetti Giulia S , Badi Ileana , Menegollo Michela , Cora Virginia , Tiso Simone , Cinquetti Raffaella , Monti Laura , Chiesa Giulia , Bleyl Steven B , Busnelli Marco , Dellera Federica , Bruno Daniele , Caicci Federico , Grimaldi Annalisa , Taramelli Roberto , Manni Lucia , Sacerdoti David , Tesi Chiara , Poggesi Corrado , Ausoni Simonetta , Acquati Francesco , Campione Marina 
Published: October 2019

AbstractAimsIncreased Ankyrin Repeat Domain 1 (ANKRD1) levels linked to gain of function mutations have been associated to total anomalous pulmonary venous return and adult cardiomyopathy occurrence in humans. The link between increased ANKRD1 level and cardiac structural and functional disease is not understood. To get insight into this problem, we have generated a gain of function ANKRD1 mouse model by overexpressing ANKRD1 in the myocardium.Methods and resultsAnkrd1 is expressed non-homogeneously in the embryonic myocardium, with a dynamic nucleo-sarcomeric localization in developing cardiomyocytes. ANKRD1 transgenic mice present sinus venosus defect, which originates during development by impaired remodelling of early embryonic heart. Adult transgenic hearts develop diastolic dysfunction with preserved ejection fraction, which progressively evolves into heart failure, as shown histologically and haemodynamically. Transgenic cardiomyocyte structure, sarcomeric assembly, and stability are progressively impaired from embryonic to adult life. Postnatal transgenic myofibrils also present characteristic functional alterations: impaired compliance at neonatal stage and impaired lusitropism in adult hearts. Altogether, our combined analyses suggest that impaired embryonic remodelling and adult heart dysfunction in ANKRD1 transgenic mice present a common ground of initial cardiomyocyte defects, which are exacerbated postnatally. Molecular analysis showed transient activation of GATA4-Nkx2.5 transcription in early transgenic embryos and subsequent dynamic transcriptional modulation within titin gene.ConclusionsANKRD1 is a fine mediator of cardiomyocyte response to haemodynamic load in the developing and adult heart. Increased ANKRD1 levels are sufficient to initiate an altered cellular phenotype, which is progressively exacerbated into a pathological organ response by the high ventricular workload during postnatal life. Our study defines for the first time a unifying picture for ANKRD1 role in heart development and disease and provides the first mechanistic link between ANKRD1 overexpression and cardiac disease onset.
Reverse takotsubo cardiomyopathy– life-threatening symptom of an incidental pheochromocytoma: a case report
Authors: Mierke Johannes , Loehn Tobias , Linke Axel , Ibrahim Karim 
Published: October 2019

Abstract

Background
Cardiogenic shock (CS) due to takotsubo cardiomyopathy (TTC) is a life-threatening condition. Therapy is challenging because of the ambivalent effects of catecholamines. Catecholamines are required to stabilize blood pressure but might aggravate TTC. Cardiac assist devices could be a suitable solution for conserving catecholamines and the prevention of TTC perpetuation.

Case summary
We report the case of a male patient with refractory CS and severe respiratory insufficiency as a result of a reverse TTC, which involved both ventricles. Simultaneous circulatory support with an Impella CP® and veno-arterial extracorporeal membrane oxygenation was initiated for cardiopulmonary stabilization and catecholamine weaning. A giant, incidental pheochromocytoma was diagnosed as the cause of TTC. After drug treatment and resection of the tumour, biventricular function completely recovered within 7 weeks.

Discussion
A rare and challenging situation is the coincidence of a nor/epinephrine-secreting tumour, such as a pheochromocytoma, and severe CS complicating TTC. Although percutaneous left ventricular assist devices (pLVAD) are highly complicated and have shown conflicting results in terms of clinical efficacy for CS, its use may prevent the perpetuation of TTC due to reduced catecholamines requirement.
Complete Genome of the Chitin-Degrading Bacterium, Paenibacillus xylanilyticus W4
Authors: Liao Weifang , Liu Pulin , Liao Weijie , Miao Lihong 
Published: October 2019

Abstract
Chitinases possess an extraordinary ability to directly hydrolyze highly insoluble chitin polymers to low-molecular-weight chito-oligomers, which possess particular biological functions, such as elicitor action and antitumor activity. A novel strain, Paenibacillus xylanilyticus W4, which was isolated from soil, showed strong chitin degradation activity. Here, we first reported the complete genome information of P. xylanilyticus. Paenibacillus xylanilyticus W4 contains a 5,532,141 bp single circular chromosome with 47.33% GC content. The genome contains 5,996 genes, including 39 rRNA- and 109 tRNA-coding genes. Phylogenetic analysis and Genome-to-Genome Distance revealed its taxonomic characterization into a separate family. Six glycoside hydrolase 18 (GH18) and 2 GH23 enzymes involved in chitin degradation. Although many of the chitinases were conserved in Paenibacillus, several GH18 chitinases share high similarity with Bacillus circulans. The genome information provided here could benefit for understanding the chitin-degrading properties of P. xylanilyticus as well as its potential application in biotechnological and pharmaceutical fields.
Marine ecosystems model development should be rooted in past experiences, not anchored in old habits
Authors: Maps Frédéric , Record Nicholas R 
Published: October 2019

Abstract
Numerical models of marine ecosystems tend to increase in complexity, incorporating a growing number of functions and parameters. Here, we reflect on the issue of “anchoring” inherent to model development, i.e. the tendency for modellers to take processes, functional forms and parameters from previous studies as granted. We focused on the particular example of the parameterization of temperature-dependent ontogeny in Calanus spp. copepods. We could identify 68 studies that implemented and parameterized this functional relationship. Semantic analysis identified distinct clusters of research scopes and coauthor networks. We showed that biases in parameters origin have the potential to produce misleading results, while recent experimental studies were often not assimilated into contemporary modelling studies. Anchoring involves external constraints in numerical models' development such as conceptual gaps and data scarcity, as well as internal drivers such as academic ontogeny and cultural background of the modeller. Retrospective quantitative literature analyses help identify how biases have worked their way into the collective understanding and help to suggest ways forward for the research community. These involve implementation of revision management systems for parameters and functional forms as already exists for numerical codes, and, as always, a more efficient dialogue between modellers, experimentalists and field ecologists.
Evaluating impacts of bottom trawling and hypoxia on benthic communities at the local, habitat, and regional scale using a modelling approach
Authors: van Denderen P D , Bolam S G , Friedland R , Hiddink J G , Norén K , Rijnsdorp A D , Sköld M , Törnroos A , Virtanen E A , Valanko S 
Published: October 2019

Abstract
Bottom trawling disturbance and hypoxia are affecting marine benthic habitats worldwide. We present an approach to predict their effects on benthic communities, and use the approach to estimate the state, the biomass relative to carrying capacity, of the Baltic Sea at the local, habitat, and regional scale. Responses to both pressures are expected to depend on the longevity of fauna, which is predicted from benthic data from 1558 locations. We find that communities in low-salinity regions mostly consist of short-lived species, which are, in our model, more resilient than those of the saline areas. The model predicts that in 14% of the Baltic Sea region benthic biomass is reduced by at least 50%, whereas an additional 8% of the region has reductions of 10–50%. The effects of hypoxia occur over larger spatial scales and lead to a low state of especially deep habitats. The approach is based on a simple characterization of the benthic community, which comes with high uncertainty, but allows for the identification of benthic habitats that are at greatest risk and prioritization of management actions at the regional scale. This information supports the development of sustainable approaches to manage impact of human activities on benthic ecosystems.
Integrating hepatitis C care for at-risk groups (HepLink): baseline data from a multicentre feasibility study in primary and community care
Authors: Nic An Riogh Eithne , Swan Davina , McCombe Geoff , O’Connor Eileen , Avramovic Gordana , Macías Juan , Oprea Cristiana , Story Alistair , Surey Julian , Vickerman Peter , Ward Zoe , Lambert John S , Tinago Willard , Ianache Irina , Iglesias Maria , Cullen Walter 
Published: October 2019

Abstract

Objectives
To examine HCV prevalence and management among people who inject drugs (PWID) attending primary care and community-based health services at four European sites using baseline data from a multicentre feasibility study of a complex intervention (HepLink).

Methods
Primary care and community-based health services in Dublin, London, Bucharest and Seville were recruited from the professional networks of the HepLink consortium. Patients were eligible to participate if aged ≥18 years, on opioid substitution treatment or at risk of HCV (i.e. injecting drug use, homeless or incarcerated), and attended the service. Data on patient demographics and prior HCV management were collected on participants at baseline.

Results
Twenty-nine primary care and community-based health services and 530 patients were recruited. Baseline data were collected on all participants. Participants’ mean age ranged from 35 (Bucharest) to 51 years (London), with 71%–89% male. Prior lifetime HCV antibody testing ranged from 65% (Bucharest) to 95% (Dublin) and HCV antibody positivity among those who had been tested ranged from 78% (Dublin) to 95% (Bucharest). Prior lifetime HCV RNA testing among HCV antibody-positive participants ranged from 17% (Bucharest) to 84% (London). Among HCV antibody- or RNA-positive participants, prior lifetime attendance at a hepatology/infectious disease service ranged from 6% (London) to 50% (Dublin) and prior lifetime HCV treatment initiation from 3% (London) to 33% (Seville).

Conclusions
Baseline assessment of the HCV cascade of care among PWID attending primary care and community-based health services at four European sites identified key aspects of the care cascade at each site that need to be improved.
Consumers Make Different Inferences and Choices When Product Uncertainty Is Attributed to Forgetting Rather than Ignorance
Authors: Walters Daniel J , Hershfield Hal E 
Published: October 2019

AbstractWhen a consumer realizes that information relevant to a consumption decision is missing, such uncertainty can be attributed to ignorance (i.e., the information has never been observed and is unknown) or to memory failure (i.e., the information has been observed and is forgotten). Although research has examined inferences about unknown attributes, no prior work has examined inferences about forgotten attributes. Across six experiments in the lab and in the field, we find that when uncertainty is attributed to ignorance, consumers often make inferences about unknown attributes based on existing correlational evidence (e.g., a brand comparison sheet that could indicate a positive or negative correlation between the unknown attribute and observable attributes). However, when uncertainty is attributed to memory failure, consumers tend to ignore such existing correlational evidence and instead make inferences about forgotten attributes that tend to be positively correlated with known attributes. This process occurs partly because when consumers believe that an attribute was forgotten, they falsely retrieve an impression about the attribute that tends to be consistent with their overall product evaluation. Overall, believing that an attribute is forgotten and believing that it is unknown can lead to opposite inferences and choices.
Effects of Climate and Host Age on Flight Activity, Infestation Percentage, and Intensity by Coptoborus ochromactonus (Coleoptera: Curculionidae: Scolytinae) in Commercial Balsa Plantations of Ecuador
Authors: Martínez Malena , Cognato Anthony I , Guachambala Marcelino , Urdanigo Juan Pablo , Boivin Thomas 
Published: October 2019

AbstractCoptoborus ochromactonus (Smith and Cognato) is one of the most common and important pests of balsa, Ochroma pyramidale (Cav. Ex Lam. Urb.), an economic pillar of the wood industry in Ecuador. Commercial balsa plantations have been expanded from humid to dry climate areas to limit insect damage, but basic knowledge is still lacking on the interaction of C. ochromactonus activity with variation in climate and plantation age. We investigated the effects of climate and host age on the seasonal flight activity of C. ochromactonus and its infestation rate and intensity, as well as the effect of age and individual infestation intensity on balsa dieback. Experiments were conducted in 1-, 2-, and 3-yr-old commercial balsa plantations located in areas of humid or dry climates. Seasonal flight activity (monitored with baited traps) differed between study sites and seasons. Increased flight activity was significantly correlated with higher relative humidity, higher mean temperature, and reduced precipitation during the dry season in the humid site and with increased mean and minimum temperature and increased precipitation during the rainy season in the dry site. Infestation rates by C. ochromactonus significantly increased with plantation age, especially in the humid site. Intensity of individual infestations (measured as number of successful insect entry holes per tree) was significantly influenced by both climate and plantation age, and it was particularly severe on 3-yr-old trees in the dry site. Percentage of foliage loss significantly increased with infestation intensity. Overall, our results can be relevant for devising preventive measures and suitable management strategies for this emerging pest in Ecuadorian wood plantations.