bluuebunny/crossref_metadata_2025_split huggingface dataset:
Character evaluation and selection of tropical wheat lines in the long period of the dry season and high temperature
Authors: Syahruddin K , Nur A , Azrai M , Larekeng S H 
Published: May 2019

Abstract
The problem in the development of wheat crops today is climate change that reduces wheat production in almost all regions of the world. It has an impact on rising temperatures and limited water supplies that can cause drought stress. These problems became the main issue of world wheat crop development. Therefore, the assembly of adapted varieties of wheat that adapted to climate change is crucial. This study aims to evaluate characters and select wheat lines based on the yield and yield component characters and to obtain tolerant wheat lines under those natural stress in tropical environments. The study used 56 wheat lines and 6 released varieties for controls, 3 replications with Randomized Block Design. Character evaluation shows significant differences in a large number of observational characters except for the number of seeds/spike and moisture content. Characters that can be used for selection and evaluation of promising lines are all characteristics of the yield and yield components except the Number of Seed Per spike (NSS) and Water Content (WC) characters. Promising lines were G5, G8 and G11 became potential selection lines with potential yields of 3, 3.39 and 3.03.
Publishing without belief
Authors: Plakias Alexandra 
Published: May 2019

AbstractIs there anything wrong with publishing philosophical work which one does not believe (publishing without belief, henceforth referred to as ‘PWB’)? I argue that there is not: the practice isn’t intrinsically wrong, nor is there a compelling consequentialist argument against it. Therefore, the philosophical community should neither proscribe nor sanction it. The paper proceeds as follows. First, I’ll clarify and motivate the problem, using both hypothetical examples and a recent real-world case. Next, I’ll look at arguments that there is something wrong with PWB, and show that none is sound. Then, I’ll give some reasons for thinking a norm against PWB is detrimental to the profession. Do I believe these arguments? If I’m right, it shouldn’t matter.
Occupational Exposure to Antibiotics in Poultry Feeding Farms
Authors: Paul Roland , Gerling Susanne , Berger Marion , Blümlein Katharina , Jäckel Udo , Schuchardt Sven 
Published: May 2019

Abstract
Today, antibiotics are essential for effective treatment of infectious diseases both in human and veterinary medicine. The increasing development and distribution of antibiotic-resistant microorganisms are subject of concern. In some sectors of animal agriculture, such as poultry feeding farms, the application of antibiotics and hence occupational exposure is inevitable. In the past, numerous studies focussed on the occurrence of antibiotic-resistant bacteria in livestock farming, but little attention was paid to the employees. The exposure of workers to antibiotics was the focus of the study detailed in this article. Four biomonitoring campaigns monitoring systemic exposure of workers to antibiotics were run at two farms over four fattening periods. Urine samples of potentially affected employees were sampled and analysed for the antibiotics of interest by liquid chromatography–mass spectrometry. The highest antibiotic concentrations detected in urine samples exceeded the minimum inhibitory concentration of some bacteria strains. In some cases, the amount of antibiotics excreted over a time-period of 24 h indicated the exceedance of the tolerable daily intake.
Plasticity of phenotype and heteroblasty in contrasting populations of Acacia koa
Authors: Rose Kyle M E , Mickelbart Michael V , Jacobs Douglass F 
Published: May 2019

AbstractBackground and AimsHeteroblastic plant species, whose morphology or growth habit changes suddenly during development, offer unique opportunities to investigate the role of selection in canalizing development or increasing the adaptive importance of plasticity. Leaf forms of the Hawaiian tree Acacia koa (koa) change morphologically and physiologically during the first year of growth, providing time to study abiotic factors influencing transition rates relative to other Acacia species.MethodsThe roles of light and water availability in triggering transition to the mature leaf form in contrasting (wet/dry) ecotypes of koa were investigated using a novel modelling technique to distinguish between chronological and ontogenetic controls in triggering transition. A light quality treatment was included to test interactions of heterophylly (the presence of multiple leaf forms) with heteroblastic processes on the resulting phenotype at transition.Key ResultsIncreased light intensity increased transition rates, but reduced red to far-red light (R:FR) ratios did not affect transition rates, solidifying the current paradigm of heteroblasty. However, evidence was found for earlier transition ontogenetically under water stress, which is not part of the current paradigm and could differentiate the role of heteroblasty in some Acacia species versus other heteroblastic species. Ecotypic responses also indicate that plasticity of development could vary across koa’s range and the adaptive significance of heteroblasty could be marginalized or amplified dependent on the disparate selective pressures present across koa’s range.ConclusionsThe use of novel survival functions and a species with an elongated transition time helped to elucidate abiotic modifiers of ontogenetic trajectories. Differences in ontogenetic trajectories between contrasting ecotypes suggest that ongoing climate and land use change will have non-uniform effects on koa regeneration and establishment dynamics across its range.
Large scale microbiome profiling in the cloud
Authors: Valdes Camilo , Stebliankin Vitalii , Narasimhan Giri 
Published: May 2019

Abstract

Motivation
Bacterial metagenomics profiling for metagenomic whole sequencing (mWGS) usually starts by aligning sequencing reads to a collection of reference genomes. Current profiling tools are designed to work against a small representative collection of genomes, and do not scale very well to larger reference genome collections. However, large reference genome collections are capable of providing a more complete and accurate profile of the bacterial population in a metagenomics dataset. In this paper, we discuss a scalable, efficient and affordable approach to this problem, bringing big data solutions within the reach of laboratories with modest resources.

Results
We developed Flint, a metagenomics profiling pipeline that is built on top of the Apache Spark framework, and is designed for fast real-time profiling of metagenomic samples against a large collection of reference genomes. Flint takes advantage of Spark’s built-in parallelism and streaming engine architecture to quickly map reads against a large (170 GB) reference collection of 43 552 bacterial genomes from Ensembl. Flint runs on Amazon’s Elastic MapReduce service, and is able to profile 1 million Illumina paired-end reads against over 40 K genomes on 64 machines in 67 s—an order of magnitude faster than the state of the art, while using a much larger reference collection. Streaming the sequencing reads allows this approach to sustain mapping rates of 55 million reads per hour, at an hourly cluster cost of $8.00 USD, while avoiding the necessity of storing large quantities of intermediate alignments.

Availability and implementation
Flint is open source software, available under the MIT License (MIT). Source code is available at https://github.com/camilo-v/flint.

Supplementary information
Supplementary data are available at Bioinformatics online.
Model-based optimization of subgroup weights for survival analysis
Authors: Richter Jakob , Madjar Katrin , Rahnenführer Jörg 
Published: May 2019

AbstractMotivationTo obtain a reliable prediction model for a specific cancer subgroup or cohort is often difficult due to limited sample size and, in survival analysis, due to potentially high censoring rates. Sometimes similar data from other patient subgroups are available, e.g. from other clinical centers. Simple pooling of all subgroups can decrease the variance of the predicted parameters of the prediction models, but also increase the bias due to heterogeneity between the cohorts. A promising compromise is to identify those subgroups with a similar relationship between covariates and target variable and then include only these for model building.ResultsWe propose a subgroup-based weighted likelihood approach for survival prediction with high-dimensional genetic covariates. When predicting survival for a specific subgroup, for every other subgroup an individual weight determines the strength with which its observations enter into model building. MBO (model-based optimization) can be used to quickly find a good prediction model in the presence of a large number of hyperparameters. We use MBO to identify the best model for survival prediction of a specific subgroup by optimizing the weights for additional subgroups for a Cox model. The approach is evaluated on a set of lung cancer cohorts with gene expression measurements. The resulting models have competitive prediction quality, and they reflect the similarity of the corresponding cancer subgroups, with both weights close to 0 and close to 1 and medium weights.Availability and implementationmlrMBO is implemented as an R-package and is freely available at http://github.com/mlr-org/mlrMBO.
Omadacycline: A Modernized Tetracycline
Authors: Gallagher Jason C 
Published: May 2019

AbstractWhen tetracyclines were introduced in the 1940s, these antibiotics offered a broad spectrum of activity against multiple types of pathogens. However, their utility waned after the selection of tetracycline resistance in the pathogens against which they were effective. Omadacycline is a semisynthetic aminomethylcycline antibacterial derived from the tetracycline class of antibiotics that is unaffected by these resistance mechanisms. It has an appropriate spectrum of activity for community-acquired infections, including those caused by many resistant organisms. Omadacycline offers a well-tolerated treatment for acute bacterial skin and skin structure infections and community-acquired bacterial pneumonia. Omadacycline has minimal known drug–drug interactions, and should be administered in a fasting state, avoiding dairy and cation-containing products for at least 4 hours after dosing. It does not require dose adjustments for sex, age, or hepatic or renal impairment, and has a safety profile similar to that of other oral tetracyclines. Because omadacycline can be administered effectively orally, it can help reduce hospitalization costs associated with intravenous antibiotic administration. This special supplement to Clinical Infectious Diseases offers an in-depth examination of omadacycline development, including discussions of pharmacokinetic and pharmacodynamic trials, spectrum of activity and preclinical data, early clinical trials, phase III clinical trials, and an integrated safety summary.
Microbiology and Preclinical Review of Omadacycline
Authors: Karlowsky James A , Steenbergen Judith , Zhanel George G 
Published: May 2019

AbstractOmadacycline is a novel aminomethylcycline antimicrobial and semisynthetic derivative of tetracycline. In vitro, omadacycline displays potent activity against gram-positive and many gram-negative bacteria, including methicillin-resistant Staphylococcus aureus, Streptococcus pneumoniae, β-hemolytic streptococci, vancomycin-resistant Enterococcus, and Enterobacteriaceae. Omadacycline is also active against atypical and anaerobic pathogens, including Legionella pneumophila, Mycoplasma spp., Ureaplasma spp., Bacteroides spp., and Clostridioides difficile. This review outlines the microbiology and preclinical studies of omadacycline, including its mechanism of action; spectrum of activity; protein binding; activity in the presence of surfactant, serum, normal, and pH-adjusted urine, or bacterial biofilms; postantibiotic effect; pharmacodynamic properties; and in vitro and in vivo efficacy. The results of in vitro and in vivo animal studies support the observations made in phase III clinical trials and the clinical development of omadacycline.
Validation of distinct pathogenic patterns in a cohort of membranoproliferative glomerulonephritis patients by cluster analysis
Authors: Garam Nóra , Prohászka Zoltán , Szilágyi Ágnes , Aigner Christof , Schmidt Alice , Gaggl Martina , Sunder-Plassmann Gere , Bajcsi Dóra , Brunner Jürgen , Dumfarth Alexandra , Cejka Daniel , Flaschberger Stefan , Flögelova Hana , Haris Ágnes , Hartmann Ágnes , Heilos Andreas , Mueller Thomas , Rusai Krisztina , Arbeiter Klaus , Hofer Johannes , Jakab Dániel , Sinkó Mária , Szigeti Erika , Bereczki Csaba , Janko Viktor , Kelen Kata , Reusz György S , Szabó Attila J , Klenk Nóra , Kóbor Krisztina , Kojc Nika , Knechtelsdorfer Maarten , Laganovic Mario , Lungu Adrian Catalin , Meglic Anamarija , Rus Rina , Kersnik-Levart Tanja , Macioniene Ernesta , Miglinas Marius , Pawłowska Anna , Stompór Tomasz , Podracka Ludmila , Rudnicki Michael , Mayer Gert , Rysava Romana , Reiterova Jana , Saraga Marijan , Seeman Tomáš , Zieg Jakub , Sládková Eva , Szabó Tamás , Capitanescu Andrei , Stancu Simona , Tisljar Miroslav , Galesic Kresimir , Tislér András , Vainumäe Inga , Windpessl Martin , Zaoral Tomas , Zlatanova Galia , Csuka Dorottya 
Published: May 2019

Abstract

Background
A novel data-driven cluster analysis identified distinct pathogenic patterns in C3-glomerulopathies and immune complex-mediated membranoproliferative glomerulonephritis. Our aim was to replicate these observations in an independent cohort and elucidate disease pathophysiology with detailed analysis of functional complement markers.

Methods
A total of 92 patients with clinical, histological, complement and genetic data were involved in the study, and hierarchical cluster analysis was done by Ward method, where four clusters were generated.

Results
High levels of sC5b-9 (soluble membrane attack complex), low serum C3 levels and young age at onset (13 years) were characteristic for Cluster 1 with a high prevalence of likely pathogenic variations (LPVs) and C3 nephritic factor, whereas for Cluster 2—which is not reliable because of the small number of cases—strong immunoglobulin G staining, low C3 levels and high prevalence of nephritic syndrome at disease onset were observed. Low plasma sC5b-9 levels, decreased C3 levels and high prevalence of LPV and sclerotic glomeruli were present in Cluster 3, and patients with late onset of the disease (median: 39.5 years) and near-normal C3 levels in Cluster 4. A significant difference was observed in the incidence of end-stage renal disease during follow-up between the different clusters. Patients in Clusters 3–4 had worse renal survival than patients in Clusters 1–2.

Conclusions
Our results confirm the main findings of the original cluster analysis and indicate that the observed, distinct pathogenic patterns are replicated in our cohort. Further investigations are necessary to analyse the distinct biological and pathogenic processes in these patient groups.
The Association Between Self-Reported and Performance-Based Physical Function With Activities of Daily Living Disability in the Canadian Longitudinal Study on Aging
Authors: Mayhew Alexandra J , Griffith Lauren E , Gilsing Anne , Beauchamp Marla K , Kuspinar Ayse , Raina Parminder 
Published: May 2019

Abstract

Background
Physical function limitations precede disability and are a target to prevent or delay disability in aging adults. The objective of this article was to assess the relationship between self-report and performance-based measures of physical function with disability.

Methods
Baseline data (2012–2015) from the Canadian Longitudinal Study on Aging (n = 51,338) was used. Disability was defined as having a limitation for at least one of 14 activities of daily living. Physical function was measured using 14 questions across three domains (upper body, lower body, and dexterity) and five performance-based tests (gait speed, timed up and go, single leg stance, chair rise, and grip strength). Logistic regression was used to assess the relationship between physical function operationalized as (i) at least one limitation, (ii) presence or absence of limitations in each individual domain/test, and (iii) number of domains/tests with limitations, with disability.

Results
In the 21,241 participants with self-reported function data, the odds of disability were 1.87 (95% CI: 1.56–2.24), 6.78 (5.68–8.08), and 14.43 (11.50–18.1) for one, two, and three limited domains, respectively. In the 30,097 participants with performance-based measures of function, the odds of disability ranged from 1.53 (1.33–1.76) for one test limited to 14.91 (11.56–19.26) for all five tests limited.

Conclusions
Both performance-based and self-report measures of physical function were associated with disability. Each domain and performance test remained associated with disability after adjustment for the other domains and tests. Disability risk was higher when the number of self-report domains and performance-based limitations increased.
Prader–Willi syndrome imprinting centre deletion mice have impaired baseline and 5-HT2CR-mediated response inhibition
Authors: Davies Jennifer R , Wilkinson Lawrence S , Isles Anthony R , Humby Trevor 
Published: May 2019

Abstract
Prader–Willi syndrome (PWS) is a neurodevelopmental disorder caused by deletion or inactivation of paternally expressed imprinted genes on human chromosome 15q11–q13. In addition to endocrine and developmental issues, PWS presents with behavioural problems including stereotyped behaviour, impulsiveness and cognitive deficits. The PWS genetic interval contains several brain-expressed small nucleolar (sno) RNA species that are subject to genomic imprinting, including snord115 that negatively regulates post-transcriptional modification of the serotonin 2C receptor (5-HT2CR) pre-mRNA potentially leading to a reduction in 5-HT2CR function. Using the imprinting centre deletion mouse model for PWS (PWSICdel) we have previously shown impairments in a number of behaviours, some of which are abnormally sensitive to 5-HT2CR-selective drugs. In the stop-signal reaction time task test of impulsivity, PWSICdel mice showed increased impulsivity relative to wild-type (WT) littermates. Challenge with the selective 5-HT2CR agonist WAY163909 reduced impulsivity in PWSICdel mice but had no effect on WT behaviour. This behavioural dissociation in was also reflected in differential patterns of immunoreactivity of the immediate early gene c-Fos, with a blunted response to the drug in the orbitofrontal cortex of PWSICdel mice, but no difference in c-Fos activation in the nucleus accumbens. These findings suggest specific facets of response inhibition are impaired in PWSICdel mice and that abnormal 5-HT2CR function may mediate this dissociation. These data have implications for our understanding of the aetiology of PWS-related behavioural traits and translational relevance for individuals with PWS who may seek to control appetite with the new obesity treatment 5-HT2CR agonist lorcaserin.
Is Strategic Studies Rationalist, Materialist, and A-Critical? Reconnecting Security and Strategy
Authors: Vennesson Pascal 
Published: May 2019

AbstractBetween the 1940s and the 1960s, strategy was at the heart of security studies and closely intertwined with International Relations (IR). Over the past three decades, however, the study of strategy has been relegated to a secondary position in the international security subfield and marginalized in IR theorizing. One important source of this disconnect is the challenge mounted by critical security advocates, who sought to reorient the study of security away from strategic studies. They reached into the philosophy of science and pulled out three familiar dichotomies, rationalism/constructivism, materialism/idealism, and problem-solving/critical theorizing, that they could utilize within security debates. Specifically, they argue that strategic studies leaves out too much of what is really important for security and world politics because it is rationalist, materialist, and retains an uncritical view of knowledge production. In this article, I turn the critical security conventional wisdom on its head and show that strategic studies, exemplified by the ideas of Carl von Clausewitz and Thomas Schelling, actually transcends these dichotomies and hence offers an indispensable source of insights for both security studies and IR.
EpiAlignment: alignment with both DNA sequence and epigenomic data
Authors: Lu Jia , Cao Xiaoyi , Zhong Sheng 
Published: May 2019

Abstract
Comparative epigenomics, which subjects both epigenome and genome to interspecies comparison, has become a powerful approach to reveal regulatory features of the genome. Thus elucidated regulatory features surpass the information derived from comparison of genomic sequences alone. Here, we present EpiAlignment, a web-based tool to align genomic regions with both DNA sequence and epigenomic data. EpiAlignment takes DNA sequence and epigenomic profiles derived by ChIP-seq from two species as input data, and outputs the best semi-global alignments. These alignments are based on EpiAlignment scores, computed by a dynamic programming algorithm that accounts for both sequence alignment and epigenome similarity. For timely response, the EpiAlignment web server automatically initiates up to 140 computing threads depending on the size of user input data. For users’ convenience, we have pre-compiled the comparable human and mouse epigenome datasets in matched cell types and tissues from the Roadmap Epigenomics and ENCODE consortia. Users can either upload their own data or select pre-compiled datasets as inputs for EpiAlignment analyses. Results are presented in graphical and tabular formats where the entries can be interactively expanded to visualize additional features of these aligned regions. EpiAlignment is available at https://epialign.ucsd.edu/.