bluuebunny/crossref_metadata_2025_split huggingface dataset:
Die Grenzen der selektiven Lasertrabekuloplastik zur Behandlung des Glaukoms
Authors: Filev F. , Gesser C. , Kromer R. , Klemm M. 
Published: September 2016

Zusammenfassung
Einleitung: Ziel dieser Studie ist es, den Stellenwert der selektiven Lasertrabekuloplastik (SLT) in einer Klinik der Tertiärversorgung darzustellen.
Material und Methoden: Wir führten eine retrospektive Datenanalyse von Patienten, die an der Universitätsaugenklinik Hamburg Eppendorf behandelt wurden, durch. 113 Augen von 113 Patienten mit primär chronischem Offenwinkelglaukom, die zwischen 03/2011 und 01/2014 eine SLT-Therapie bekamen und ein Follow-up von mindestens 4 Monate aufwiesen, wurden eingeschlossen.
Ergebnisse: Es zeigte sich eine mittlere Drucksenkung von 1,08 mmHg oder 7 % im Zeitraum von 4 bis 6 Monaten nach der Behandlung. Bei 43,7 % der Augen war innerhalb von 12 Monaten eine weitere drucksenkende Maßnahme (Intensivierung der topischen drucksenkenden Therapie oder drucksenkender Eingriff) erforderlich.
Diskussion: Wir stellten fest, dass bei einem konservativ oder operativ vorbehandelten Patientenkollektiv mit niedrigem Ausgangsdruck und niedrigem Zieldruck durch eine alleinige SLT keine hinreichende und dauerhafte Drucksenkung zu erzielen war.
Role of dystroglycan in limiting contraction-induced injury to the sarcomeric cytoskeleton of mature skeletal muscle
Authors: Rader Erik P. , Turk Rolf , Willer Tobias , Beltrán Daniel , Inamori Kei-ichiro , Peterson Taylor A. , Engle Jeffrey , Prouty Sally , Matsumura Kiichiro , Saito Fumiaki , Anderson Mary E. , Campbell Kevin P. 
Published: September 2016

Significance
Dystroglycan (DG) is an extracellular matrix receptor that is linked to the cytoskeleton and critical for the development of skeletal muscle. DG deficiency throughout development is associated with multiple pathological features and muscular dystrophy. However, the direct consequence of DG disruption in mature muscle is not known. Here, we investigate muscles of transgenic mice after genetic knockdown of DG at maturity. The results demonstrate early susceptibility to contraction-induced injury accompanied by reduced passive tension and decreased titin immunostaining, rather than increased necrosis, excitation–contraction uncoupling, or sarcolemmal fragility. These results suggest a need for critical rethinking of both current theories regarding contraction-induced injury in muscular dystrophy and therapeutic strategies.
High-throughput single-cell gene-expression profiling with multiplexed error-robust fluorescence in situ hybridization
Authors: Moffitt Jeffrey R. , Hao Junjie , Wang Guiping , Chen Kok Hao , Babcock Hazen P. , Zhuang Xiaowei 
Published: September 2016

Significance
Image-based approaches to single-cell transcriptomics offer the ability to quantify not only the copy number of RNAs within cells but also the intracellular RNA location and the spatial organization of cells within cultures or tissues. Here we report advances in multiplexed error-robust fluorescence in situ hybridization (MERFISH) that increase the measurement throughput by two orders of magnitude and allow gene expression profiling of ∼40,000 human cells in a single 18-h measurement. This drastic increase in throughput should facilitate the identification and study of rare populations of cells as well as the characterization of transcriptionally distinct cell types within large tissue regions.
Assessment of cancer and virus antigens for cross-reactivity in human tissues
Authors: Jaravine Victor , Raffegerst Silke , Schendel Dolores J , Frishman Dmitrij 
Published: September 2016

Abstract

Motivation
Cross-reactivity (CR) or invocation of autoimmune side effects in various tissues has important safety implications in adoptive immunotherapy directed against selected antigens. The ability to predict CR (on-target and off-target toxicities) may help in the early selection of safer therapeutically relevant target antigens.

Results
We developed a methodology for the calculation of quantitative CR for any defined peptide epitope. Using this approach, we performed assessment of 4 groups of 283 currently known human MHC-class-I epitopes including differentiation antigens, overexpressed proteins, cancer-testis antigens and mutations displayed by tumor cells. In addition, 89 epitopes originating from viral sources were investigated. The natural occurrence of these epitopes in human tissues was assessed based on proteomics abundance data, while the probability of their presentation by MHC-class-I molecules was modelled by the method of Keşmir et al. which combines proteasomal cleavage, TAP affinity and MHC-binding predictions. The results of these analyses for many previously defined peptides are presented as CR indices and tissue profiles. The methodology thus allows for quantitative comparisons of epitopes and is suggested to be suited for the assessment of epitopes of candidate antigens in an early stage of development of adoptive immunotherapy.

Availability and Implementation
Our method is implemented as a Java program, with curated datasets stored in a MySQL database. It predicts all naturally possible self-antigens for a given sequence of a therapeutic antigen (or epitope) and after filtering for predicted immunogenicity outputs results as an index and profile of CR to the self-antigens in 22 human tissues. The program is implemented as part of the iCrossR webserver, which is publicly available at http://webclu.bio.wzw.tum.de/icrossr/.

Supplementary information
Supplementary data are available at Bioinformatics online.
Nanocall: an open source basecaller for Oxford Nanopore sequencing data
Authors: David Matei , Dursi L J , Yao Delia , Boutros Paul C , Simpson Jared T 
Published: September 2016

Abstract

Motivation
The highly portable Oxford Nanopore MinION sequencer has enabled new applications of genome sequencing directly in the field. However, the MinION currently relies on a cloud computing platform, Metrichor (metrichor.com), for translating locally generated sequencing data into basecalls.

Results
To allow offline and private analysis of MinION data, we created Nanocall. Nanocall is the first freely available, open-source basecaller for Oxford Nanopore sequencing data and does not require an internet connection. Using R7.3 chemistry, on two E.coli and two human samples, with natural as well as PCR-amplified DNA, Nanocall reads have ∼68% identity, directly comparable to Metrichor ‘1D’ data. Further, Nanocall is efficient, processing ∼2500 Kbp of sequence per core hour using the fastest settings, and fully parallelized. Using a 4 core desktop computer, Nanocall could basecall a MinION sequencing run in real time. Metrichor provides the ability to integrate the ‘1D’ sequencing of template and complement strands of a single DNA molecule, and create a ‘2D’ read. Nanocall does not currently integrate this technology, and addition of this capability will be an important future development. In summary, Nanocall is the first open-source, freely available, off-line basecaller for Oxford Nanopore sequencing data.

Availability and Implementation
Nanocall is available at github.com/mateidavid/nanocall, released under the MIT license.

Supplementary information
Supplementary data are available at Bioinformatics online.
The OGCleaner: filtering false-positive homology clusters
Authors: Fujimoto M Stanley , Suvorov Anton , Jensen Nicholas O , Clement Mark J , Snell Quinn , Bybee Seth M 
Published: September 2016

Abstract

Summary
Detecting homologous sequences in organisms is an essential step in protein structure and function prediction, gene annotation and phylogenetic tree construction. Heuristic methods are often employed for quality control of putative homology clusters. These heuristics, however, usually only apply to pairwise sequence comparison and do not examine clusters as a whole. We present the Orthology Group Cleaner (the OGCleaner), a tool designed for filtering putative orthology groups as homology or non-homology clusters by considering all sequences in a cluster. The OGCleaner relies on high-quality orthologous groups identified in OrthoDB to train machine learning algorithms that are able to distinguish between true-positive and false-positive homology groups. This package aims to improve the quality of phylogenetic tree construction especially in instances of lower-quality transcriptome assemblies.

Availability and Implementation
https://github.com/byucsl/ogcleaner

Supplementary information
Supplementary data are available at Bioinformatics online.
Analysis of liver damage from radon, X-ray, or alcohol treatments in mice using a self-organizing map
Authors: Kanzaki Norie , Kataoka Takahiro , Etani Reo , Sasaoka Kaori , Kanagawa Akihiro , Yamaoka Kiyonori 
Published: September 2016

Abstract
In our previous studies, we found that low-dose radiation inhibits oxidative stress–induced diseases due to increased antioxidants. Although these effects of low-dose radiation were demonstrated, further research was needed to clarify the effects. However, the analysis of oxidative stress is challenging, especially that of low levels of oxidative stress, because antioxidative substances are intricately involved. Thus, we proposed an approach for analysing oxidative liver damage via use of a self-organizing map (SOM)—a novel and comprehensive technique for evaluating hepatic and antioxidative function. Mice were treated with radon inhalation, irradiated with X-rays, or subjected to intraperitoneal injection of alcohol. We evaluated the oxidative damage levels in the liver from the SOM results for hepatic function and antioxidative substances. The results showed that the effects of low-dose irradiation (radon inhalation at a concentration of up to 2000 Bq/m3, or X-irradiation at a dose of up to 2.0 Gy) were comparable with the effect of alcohol administration at 0.5 g/kg bodyweight. Analysis using the SOM to discriminate small changes was made possible by its ability to ‘learn’ to adapt to unexpected changes. Moreover, when using a spherical SOM, the method comprehensively examined liver damage by radon, X-ray, and alcohol. We found that the types of liver damage caused by radon, X-rays, and alcohol have different characteristics. Therefore, our approaches would be useful as a method for evaluating oxidative liver damage caused by radon, X-rays and alcohol.
The nature of the X-ray pulsar in M 31: An intermediate-mass X-ray binary?
Authors: Karino Shigeyuki 
Published: September 2016

Abstract
The first finding of the spin period of an accreting neutron star in M 31 was recently reported. The observed spin period is 1.2 s, and it shows 1.27 d modulations due to orbital motion. From the orbital information, the mass donor could not be a giant massive star. On the other hand, its observed properties are very odd as those of typical low-mass X-ray binaries. In this study, we compare the observed binary parameters with theoretical models given by a stellar evolution track, and give a restriction on the possible mass range of the donor. According to the standard stellar evolution model, the donor star should be larger than 1.5 M⊙, which suggests that this system is a new member of a rare category, an intermediate-mass X-ray binary. The magnetic field strength of the neutron star suggested by the spin-up/down tendency in this system supports the possibility of an intermediate-mass donor.
Incidence of Antipsychotic-Associated Side Effects
Authors: Takeuchi Hiroyoshi , Fervaha Gagan , Remington Gary 
Published: September 2016

Objective
This study aimed to compare (1) the detection rates of antipsychotic-associated side effects between clinician and patient ratings and (2) differences as a function of change and absolute score definitions.

Methods
Data from phase 1 of the Clinical Antipsychotic Trials of Intervention Effectiveness (N = 1460) were analyzed. In this trial, 18 adverse events were systematically and concurrently assessed by clinicians and patients using a 4-point severity scale ranging from 0 (absent) to 3 (severe). The incidence of antipsychotic-associated side effects was calculated according to 2 definitions: change score (ie, higher score on the scale versus baseline) and absolute score (a score of 2 or 3 on the scale). In addition, patient and clinician concurrent detection rates were examined.

Results
The differences in incidence of antipsychotic-associated side effects between clinician and patient ratings were as small as 5.7% across the 2 definitions. The incidence of all side effects across clinician and patient ratings was approximately 2 times higher when using the change versus absolute score definition. Among the side effects detected by patients, 11 side effects were identified more frequently by clinicians, with 14.3% to 30.2% differences when using the change versus absolute score definition. Conversely, there was no difference of 10% or greater in patient or clinician concurrent detection rate on any item when using the absolute versus change score definition.

Conclusions
Our findings suggest that patient ratings are in line with clinician ratings and that the change score definition may be superior for the assessment of antipsychotic-associated side effects in clinical studies.
Close genetic relationships between a spousal pair with autism-affected children and high minor allele content in cases in autism-associated SNPs
Authors: Zhu Zuobin , Lu Xitong , Yuan Dejian , Huang Shi 
Published: September 2016

AbstractParents of children affected with autism spectrum disorders (ASD) often have mild forms of autistic-like characteristics. Past studies have focused on searching for individual genetic risk loci of ASD. Here we studied the overall properties of the genomes of ASD trios by using previously published genome-wide data for common SNPs. The pairwise genetic distance (PGD) between a spousal pair with ASD-affected children was found smaller than that of a random pair selected among the spouses in the ASD trios, and spousal relatedness correlated with severe forms of ASD. Furthermore, for a set of 970 ASD associated SNPs, cases showed higher homozygous minor allele content than parents. These results indicate new genetic elements in the broad phenotypes of parents with ASD-affected offspring and in ASD pathogenesis.HighlightsThe overall properties of the genomes of ASD trios show ASD specific features.A spousal pair with ASD-affected children showed smaller genetic distance than that of a randomly selected pair among the spouses in the ASD trios.Minor allele contents in ASD-associated SNPs in ASD cases were greater than those in the parents of cases.
MathIOmica: an integrative platform for dynamic omics
Authors: Mias George I. , Yusufaly Tahir , Roushangar Raeuf , Brooks Lavida R. K. , Singh Vikas V. , Christou Christina 
Published: September 2016

AbstractMultiple omics data are rapidly becoming available, necessitating the use of new methods to integrate different technologies and interpret the results arising from multimodal assaying. The MathIOmica package forMathematicaprovides one of the first extensive introductions to the use of the Wolfram Language to tackle such problems in bioinformatics. The package particularly addresses the necessity to integrate multiple omics information arising from dynamic profiling in a personalized medicine approach. It provides multiple tools to facilitate bioinformatics analysis, including importing data, annotating datasets, tracking missing values, normalizing data, clustering and visualizing the classification of data, carrying out annotation and enumeration of ontology memberships and pathway analysis. We anticipate MathIOmica to not only help in the creation of new bioinformatics tools, but also in promoting interdisciplinary investigations, particularly from researchers in mathematical, physical science and engineering fields transitioning into genomics, bioinformatics and omics data integration.
A phenomenological spatial model for macro-ecological patterns in species-rich ecosystems
Authors: Peruzzo Fabio , Azaele Sandro 
Published: September 2016

Over the last few decades, ecologists have come to appreciate that key ecological patterns, which describe ecological communities at relatively large spatial scales, are not only scale dependent, but also intimately intertwined. The relative abundance of species – which informs us about the commonness and rarity of species – changes its shape from small to large spatial scales. The average number of species as a function of area has a steep initial increase, followed by decreasing slopes at large scales. Finally, if we find a species in a given location, it is more likely we find an individual of the same species close-by, rather than farther apart. Such spatial turnover depends on the geographical distribution of species, which often are spatially aggregated. This reverberates on the abundances as well as the richness of species within a region, but so far it has been difficult to quantify such relationships.Within a neutral framework – which considers all individuals competitively equivalent – we introduce a spatial stochastic model, which phenomenologically accounts for birth, death, immigration and local dispersal of individuals. We calculate the pair correlation function – which encapsulates spatial turnover – and the conditional probability to find a species with a certain population within a given circular area. Also, we calculate the macro-ecological patterns, which we have referred to above, and compare the analytical formulæ with the numerical integration of the model. Finally, we contrast the model predictions with the empirical data for two lowland tropical forest inventories, showing always a good agreement.
Properties of compostite feedback-feedforward pulse generating motifs
Authors: Iyengar Bharat Ravi 
Published: September 2016

AbstractNegative feedbacks and incoherent feedforward loops are known to give rise to a pulse in response to a step change in the input. In this article, I present a study of composite motifs made of coupled feedback and feedforward loops, acting via different regulatory mechanisms. In these motifs, the effect of input and output on the controller is realized via either an AND-gate or an OR-gate. Using a simplistic model of gene expression and a common parameter set, I have studied the effect of global parameter variation on the dynamic and steady-state properties of different motifs, in response to a step change in the input. These metrics include steady state gain, response time, overshoot, peak time and peak duration. For the motifs with a negative feedback component, it can be seen that AND-gated motifs show a “feedforward-like” property whereas the OR-gated motifs show a “feedback-like” property. Motifs with a positive feedback component show hypersensitivity of gain, to parameters. Overshoot correlates negatively with peak time whereas peak duration correlates concavely with peak time, a property that is also observed for uncoupled feedback and feedforward motifs. This indicates that this relationship between overshoot, peak duration and peak time, seems to be a universal property of pulse-generating motifs.
Simulation model for dynamics of three types of annual plants
Authors: Pękalski Andrzej 
Published: September 2016

AbstractA Monte Carlo type model describing dynamics of three pairs of annual plants living in a homogeneous habitat is presented and discussed. Each plant follows its own history with growing, fecundity and survival chances determined individually as functions of the plant’s condition and environment. The three plants -Valerianella locusta, Mysotis ramosissimaandCerastium semidecandrumdiffer by the weight of their seeds, which in the model determines the competition preference. Heavier seeds have a better chance for germination from a site containing seeds of different plants. Better colonisers produce more seeds and disperse them over a larger distance. I show that without absolute asymmetry in the impact effects between better competitors and better colonisers and in a spatially and temporarily homogeneous habitat, coexistence of species is possible, however only in a limited time. This is different from statements coming from models using mean-field type methods. I demonstrate also that in a system of two species clustering of plants of the same type are more frequent. From the calculated survival chances of seedlings and adult plants it follows that elimination of plants occur mostly at the early stages of the plants life cycle, which agrees with the field data.I show that this competition/colonisation trade-off model is sufficient to maintain coexistence and I determine the conditions for dominance of one type of plants. I show that the time of extinction of the weaker species goes down with increasing observation time as a power function with the exponent independent of the type of plants.
ANumerusPopulation Viability and Harvesting Analyses Web App
Authors: Getz Wayne M. , Muellerklein Oliver , Salter Richard , Carlson Colin J. , Lyons Andrew J. , Seidel Dana 
Published: September 2016

AbstractPopulation viability analysis (PVA) is used to assess the probability that a biological population will persist for a specified period of time. Such models are typically cast as Markov processes that may include age, stage, sex and metapopulation structures, density-dependence and ecological interaction processes. They may also include harvesting, stocking, and thresholds that trigger interventions. Here we present Numerus PVA, which is a web app that includes extensible user-selected options. Specifically, Numerus PVA allows for the specification of one to ten age classes, one or two sexes, single population or metapopulation configurations with 2 or 3 subpopulations, as well as density-dependent settings for inducing region-specific carrying capacities. Movement among subpopulations can be influenced by age, metapopulation connectivity, and attractivity of regions based on the relative fitness of the youngest age classes in each region. Simulations can be carried out deterministically or stochastically, with a user-specified combination of demographic and environmental processes. Numerus PVA is freely available athttp://www.numerusinc.com/webapps/pvafor running directly on any browser and device. Numerus PVA is easily modified by users familiar with the NovaModeler Software Platform.