bluuebunny/crossref_metadata_2025_split huggingface dataset:
Live tracking of Moving samples in confocal microscopy for vertically grown roots tips
Authors: von Wangenheim Daniel , Hauschild Robert , Fendrych Matyáš , Barone Vanessa , Friml Jiří 
Published: March 2017

AbstractRoots navigate through soil integrating environmental signals to orient their growth. TheArabidopsisroot is a widely used model for developmental, physiological and cell biological studies. Live imaging greatly aids these efforts, but the horizontal sample position and continuous root tip displacement present significant difficulties. Here, we develop a confocal microscope setup for vertical sample mounting and integrated directional illumination. We present TipTracker - a custom software for automatic tracking of diverse moving objects usable on various microscope setups. Combined, this enables observation of root tips growing along the natural gravity vector over prolonged periods of time, as well as the ability to induce rapid gravity or light stimulation. We also track migrating cells in the developing zebrafish embryo, demonstrating the utility of this system in the acquisition of high resolution data sets of dynamic samples. We provide detailed descriptions of the tools enabling the easy implementation on other microscopes.
Solution structure of human STARD1 protein and its interaction with fluorescently-labeled cholesterol analogues with different position of the NBD-group
Authors: Tugaeva Kristina V. , Faletrov Yaroslav V. , Allakhverdiev Elvin S. , Maksimov Eugene G. , Sluchanko Nikolai N. 
Published: March 2017

AbstractIntracellular cholesterol transfer to mitochondria, a bottleneck of adrenal and gonadal steroidogenesis, relies on the functioning of the steroidogenic acute regulatory protein (StAR, STARD1), for which many disease-associated mutations have been described. Despite significant progress in the field, the exact mechanism of cholesterol binding and transfer by STARD1 remains debatable, and the solution conformation of STARD1 is insufficiently characterized, partially due to its poor solubility. Although cholesterol binding to STARD1 was widely studied by commercially available fluorescent NBD-analogues, the effect of the NBD group position on binding remained unexplored. Here, we analyzed in detail the hydrodynamic properties and solution conformation of STARD1 and its interaction with cholesterol-like steroids bearing 7-nitrobenz-2-oxa-1,3-diazol-4-yl (NBD) group in different position, namely 22-NBD-cholesterol (22NC), 25-NBD-cholesterol (25NC), 20-((NBDamino)-pregn-5-en-3-ol (20NP) and 3-(NBDamino)-cholestane (3NC). The small-angle X-ray scattering (SAXS)-based modeling and docking simulations show that, apart from movements of the flexible Ω1-loop, STARD1 unlikely undergoes significant structural rearrangements proposed earlier as a gating mechanism for cholesterol binding. While being able to stoichiometrically bind 22NC and 20NP with high fluorescence yield and quantitative exhaustion of fluorescence of some protein tryptophans, STARD1 binds 25NC and 3NC with much lower affinity and poor fluorescence yield. In contrast to 3NC, binding of 20NP leads to STARD1 stabilization and increases the NBD fluorescence lifetime. Remarkably, in terms of fluorescence response, 20NP outperforms commonly used 22NC and is recommended for future studies. Our study benefits from state-of-the-art techniques and revisits the results of the STARD1 research over the last 20 years, revealing important novel information.
Management of Mendelian Traits in Breeding Programs by Gene Editing: A Simulation Study
Authors: Cole John B. 
Published: March 2017

AbstractBackgroundGenotypes based on high-density single nucleotide polymorphisms have recently been used to identify a number of novel recessive mutations that adversely affect fertility in dairy cattle as well as to track conditions such as polledness. The use of sequential mate allocation strategies that account for increases in genomic inbreeding and the economic impact of affected matings may result in faster allele frequency changes than strategies that do not consider inbreeding and monetary losses. However, the effect of gene editing on selection programs also should be considered because gene editing has the potential to dramatically change allele frequencies in livestock populations.MethodsA simulation program developed to evaluate dairy cattle breeding schemes was extended to include the use of clustered regularly interspaced short palindromic repeat (CRISPR), transcription activator-like effector nuclease (TALEN), and zinc finger nuclease (ZFN) technologies for gene editing. A hypothetical technology with a perfect success rate was used to establish an upper limit on attainable progress, and a scenario with no editing served as a baseline for comparison.ResultsThe technologies differed in the rate of success of gene editing as well as the success rate of embryo transfer based on literature estimates. The number of edited alleles was assumed to have no effect on success rate. The two scenarios evaluated considered only the horned locus or 12 recessive alleles that currently are segregating in the U.S. Holstein population. The top 1, 5, or 10% of bulls were edited each generation, and either no cows or the top 1% of cows were edited. Inefficient editing technologies produced less cumulative genetic gain and lower inbreeding than efficient ones. Gene editing was very effective at reducing the frequency of the horned haplotype (increasing the frequency of polled animals in the population), and allele frequencies of the 12 recessives segregating in the U.S. Holstein population decreased faster with editing than without.ConclusionsGene editing can be an effective tool for reducing the rate of harmful alleles in a dairy cattle population even if only a small proportion of elite animals are modified.
Why concatenation fails in the anomaly zone
Authors: Mendes Fábio K. , Hahn Matthew W. 
Published: March 2017

AbstrctGenome-scale sequencing has been of great benefit in recovering species trees, but has not provided final answers. Despite the rapid accumulation of molecular sequences, resolving short and deep branches of the tree of life has remained a challenge, and has prompted the development of new strategies that can make the best use of available data. One such strategy – the concatenation of gene alignments – can be successful when coupled with many tree estimation methods, but has also been shown to fail when there are high levels of incomplete lineage sorting. Here, we focus on the failure of likelihood-based methods in retrieving a rooted, asymmetric four-taxon species tree from concatenated data when the species tree is in or near the anomaly zone – a region of parameter space where the most common gene tree does not match the species tree because of incomplete lineage sorting. First, we use coalescent theory to prove that most informative sites will support the species tree in the anomaly zone, and that as a consequence maximum-parsimony succeeds in recovering the species tree from concatenated data. We further show that maximum-likelihood tree estimation from concatenated data fails both inside and outside the anomaly zone, and that this failure is unconnected to the frequency of the most common gene tree. We provide support for a hypothesis that likelihood-based methods fail in and near the anomaly zone because discordant sites on the species tree have a lower likelihood than those that are discordant on alternative topologies. Our results confirm and extend previous reports of the failure and success of likelihood- and parsimony-based methods, and highlight avenues for future work improving the performance of methods aimed at recovering species tree.
Severe infections emerge from the microbiome by adaptive evolution
Authors: Young Bernadette C. , Wu Chieh-Hsi , Claire Gordon N. , Cole Kevin , Price James R. , Liu Elian , Sheppard Anna E. , Perera Sanuki , Charlesworth Jane , Golubchik Tanya , Iqbal Zamin , Bowden Rory , Massey Ruth C. , Paul John , Crook Derrick W. , Peto Timothy E. A. , Sarah Walker A. , Llewelyn Martin J. , Wyllie David H. , Wilson Daniel J. 
Published: March 2017

AbstractBacteria responsible for the greatest global mortality colonize the human microbiome far more frequently than they cause severe infections. Whether mutation and selection within the microbiome accompany infection is unknown. We investigatedde novomutation in 1163Staphylococcus aureusgenomes from 105 infected patients with nose-colonization. We report that 72% of infections emerged from the microbiome, with infecting and nose-colonizing bacteria showing parallel adaptive differences. We found 2.8-to-3.6-fold enrichments of protein-altering variants in genes responding torsp, which regulates surface antigens and toxicity;agr, which regulates quorum-sensing, toxicity and abscess formation; and host-derived antimicrobial peptides. Adaptive mutations in pathogenesis-associated genes were 3.1-fold enriched in infecting but not nose-colonizing bacteria. None of these signatures were observed in healthy carriers nor at the species-level, suggesting disease-associated, short-term, within-host selection pressures. Our results show that infection, like a cancer of the microbiome, emerges through spontaneous adaptive evolution, raising new possibilities for diagnosis and treatment.One Sentence SummaryLife-threateningS. aureusinfections emerge from nose microbiome bacteria in association with repeatable adaptive evolution.
DLPFC Transcriptome Defines Two Molecular Subtypes of Schizophrenia
Authors: Rhodes C. Harker , Bowen Elijah F. W. , Burgess Jack L. , Granger Richard 
Published: March 2017

AbstractLittle is known about the molecular pathogenesis of schizophrenia, possibly because of unrecognized heterogeneity in diagnosed patient populations. We analyzed gene expression data collected from the dorsolateral prefrontal cortex (DLPFC) of post-mortem frozen brains of 189 adult diagnosed schizophrenics and 206 matched controls. Transcripts from 633 genes are differentially expressed in the DLPFC of schizophrenics as compared to controls at Bonferroni-corrected significance levels. Seventeen of those genes are differentially expressed at very high significance levels (< 10−8after Bonferroni correction).Weighted Gene Co-expression Network Analysis (WGCNA) of the schizophrenic subjects, based on the transcripts differentially expressed in the schizophrenics as compared to controls, divides them into two groups: "Type 1" schizophrenics, have a DLPFC transcriptome similar to that of controls with no expressed genes identified in this subcohort while the "type 2" schizophrenics have a DLPFC transcriptome dramatically different from that of controls, with 3,652 expression array probes to 3,200 genes detecting transcripts that are differentially expressed at very high significance levels. These findings were re-tested and replicated in a separate independent cohort, using the RNAseq data from the DLPFC of an independent set of schizophrenics and control subjects.We suggest the hypothesis that these striking differences in DLPFC transcriptomes, identified and replicated in two populations, imply a fundamental biologic difference between these two groups of patients who have been diagnosed as schizophrenic.
Postmating sexual selection and the enigmatic jawed genitalia ofCallosobruchus subinnotatus
Authors: van Haren Merel M. , Liljestrand Rönn Johanna , Schilthuizen Menno , Arnqvist Göran 
Published: March 2017

SummaryInsect genitalia exhibit rapid divergent evolution. Truly extraordinary structures have evolved in some groups, presumably as a result of post-mating sexual selection. To increase our understanding of this phenomenon, we studied the function of one such structure. The male genitalia ofCallosobruchus subinnotatus(Coleoptera: Bruchinae) contain a pair of jaw-like structures with unknown function. Here, we used phenotypic engineering to ablate the teeth on these jaws. We then experimentally assessed the effects of ablation of the genital jaws on mating duration, ejaculate weight, male fertilization success and female fecundity, using a double-mating experimental design. We predicted that copulatory wounding in females should be positively related to male fertilization success. However, we found no significant correlation between genital tract scarring in females and male fertilization success. Male fertilization success was, however, positively related to the amount of ejaculate transferred by males and negatively related to female ejaculate dumping. Ablation of male genital jaws did not affect male relative fertilization success but resulted in a reduction in female egg production. Our results suggest that postmating sexual selection in males indeed favors these genital jaws, but not primarily through an elevated relative success in sperm competition but by increasing female egg production.
Optimal construction of army ant living bridges
Authors: Graham Jason M. , Kao Albert B. , Wilhelm Dylana A. , Garnier Simon 
Published: March 2017

AbstractIntegrating the costs and benefits of collective behaviors is a fundamental challenge to understanding the evolution of group living. These costs and benefits can rarely be quantified simultaneously due to the complexity of the interactions within the group, or even compared to each other because of the absence of common metrics between them. The construction of ‘living bridges’ by New World army ants - which they use to shorten their foraging trails - is a unique example of a collective behavior where costs and benefits have been experimentally measured and related to each other. As a result, it is possible to make quantitative predictions about when and how the behavior will be observed. In this paper, we extend a previous mathematical model of these costs and benefits into a general framework for analyzing the optimal formation, and final configuration, of army ant living bridges. We provide experimentally testable predictions of the final bridge position, as well as the optimal formation process for certain cases, for a wide range of scenarios, which more closely resemble common terrain obstacles that ants encounter in nature. As such, our framework offers a rare benchmark for determining the evolutionary pressures governing the evolution of a naturally occurring collective animal behavior.
The Junction Usage Model (JUM): A method for comprehensive annotation-free analysis of alternative pre-mRNA splicing patterns
Authors: Wang Qingqing , Rio Donald C. 
Published: March 2017

AbstractAlternative pre-mRNA splicing (AS) greatly diversifies metazoan transcriptomes and proteomes and is crucial for gene regulation. Current computational analysis methods of AS from Illumina RNA-seq data rely on pre-annotated libraries of known spliced transcripts, which hinders AS analysis with poorly annotated genomes and can further mask unknown AS patterns. To address this critical bioinformatics problem, we developed a method called the Junction Usage Model (JUM) that uses a bottom-up approach to identify, analyze and quantitate global AS profiles without any prior transcriptome annotations. JUM accurately reports global AS changes in terms of the five conventional AS patterns and an additional “Composite” category composed of inseparable combinations of conventional patterns. JUM stringently classifies the difficult and disease-relevant pattern of intron retention, reducing the false positive rate of IR detection commonly seen in other annotation-based methods to near negligible rates. When analyzing AS in RNA-samples derived from Drosophila heads, human tumors and human cell lines bearing cancer-associated splicing factor mutations, JUM consistently identified ~ twice the number of novel AS events missed by other methods. Computational simulations showed JUM exhibits a 1.2-4.8 times higher true positive rate at a fixed cut-off of 5% false discovery rate. In summary, JUM provides a new framework and improved method that removes the necessity for transcriptome annotations and enables the detection, analysis and quantification of AS patterns in complex metazoan transcriptomes with superior accuracy.
A review of diagnostic approaches to medullary thyroid carcinoma
Authors: Borhani Soheila , Hedayati Mehdi 
Published: March 2017

AbstractMedullary thyroid carcinoma (MTC), occurring sporadically or as an autosomal dominant trait, accounts for 5-10% of all thyroid gland neoplasms. While the sporadic variant originates from somatic rearranged-during-transfection (RET) mutations, the inherited variant is preceded by germ-line mutations of the RET proto-oncogene. Analysis of the transformations of this certain gene is the cornerstone of diagnostic and prognostic approaches in MTC. Additionally, a panel of histopathological evaluations, biochemical markers, and imaging procedures play a pivotal role in the management of MTC. The survival rate of MTC is relatively low compared to differentiated thyroid neoplasia and is highly influenced by the stage of tumors. Improvement in MTC surveillance significantly depends on early diagnosis as well as implementation of proper screening modalities in hereditary subtypes. The present review addresses medullary thyroid carcinoma, and in particular, the current diagnostic approaches to this challenging malignancy.
The self-healing evaluation of microcapsule-based epoxy coatings applied on AA6061 Al alloy in 3.5% NaCl solution
Authors: Shahidi Zandi Mehdi , Hasanzadeh Majdeh 
Published: March 2017

Purpose
The aim of this work is to investigate the self-healing performance of epoxy coatings containing microcapsules. The microcapsule-based coatings were applied on AA6061 Al alloy and immersed in 3.5 per cent NaCl solution.

Design/methodology/approach
Microcapsules with urea–formaldehyde as the shell and linseed oil as the healing agent were prepared by in situ polymerization in an oil-in-water emulsion. For the sake of an optimum self-healing system, some coating samples were prepared by using different microcapsule concentrations: 0, 5, 10 and 20 Wt.%. The scratch-filling efficiency as the theoretical estimate of the self-healing performance was calculated for the coating samples with different microcapsule concentrations. The scratch-sealing efficiency (SSE) as a particularly crucial parameter in the self-healing evaluation of coatings was measured by both electrochemical impedance spectroscopy (EIS) and electrochemical noise (EN) techniques.

Findings
According to EIS and EN results, the coating samples containing 5 and 10 per cent microcapsules provided the insignificant self-healing performance, while the coating sample containing 20 per cent microcapsules exhibited the acceptable self-healing performance to AA6061 alloy in the NaCl solution. The measured SSE values confirmed the good agreement of EN data with electrochemical parameters obtained from the EIS technique.

Originality/value
This work is an attempt to evaluate the self-healing performance of microcapsule-based epoxy coatings applied on AA6061 Al alloy in sea water.
Do government administered financial rewards undermine firms’ internal whistle-blowing systems?
Authors: Lee Gladys , Turner Michael J. 
Published: March 2017

Purpose
This paper aims to provide a discussion of the application of the research pitch template developed by Faff (2015, 2016b) to a research topic on whistle-blowing. Specifically, the template was used to develop a research proposal that investigates whether government administered financial rewards undermine a firm’s internal whistle-blowing system. This letter provides a brief commentary on using the pitch template and then discusses personal reflections on the pitch exercise.

Design/methodology/approach
This paper applies the template of Faff (2015) and provides a narrative of the pitching exercise.

Findings
As a first-time user of Faff’s (2015) pitching template, I have found the template very helpful in articulating the essence of this research project and mapping out the fundamentals for the project.

Originality/value
This is a new research idea that is not a pitch retrofitted from published papers or theses. The pitch template was used for the purposes of developing and refining the research idea.
Infrastructure reporting by New Zealand local authorities – perceptions and expectations
Authors: Chatterjee Bikram , Mir Monir Zaman , Eddie Ian A. , Wise Victoria 
Published: March 2017

Purpose
The purpose of this paper is to identify the contextual factors affecting infrastructure reporting by New Zealand local authorities.

Design/methodology/approach
The paper includes a survey and interview of Annual Report Recipients (ARRs) and Infrastructure Information Preparers (IIPs), together with an assessment of the extent of infrastructure information disclosure in the annual reports of New Zealand local authorities.

Findings
This study finds that contrary to the expectations of Lüder’s contingency model (1992), there is an information dissemination gap between the perceptions of ARRs and IIPs regarding infrastructure information reporting in the annual reports of New Zealand local authorities. This finding is consistent with decades of concern about the application of private sector Generally Accepted Accounting Principles to the public sector and the Controller and Auditor General’s (CAG, 2009) concern about the inadequacy of private sector General Purpose Financial Reports in meeting public sector accountability. On the other hand, the study reports that the perceptions of the two groups, ARRs and IIPs, are similar with regard to the importance of infrastructure information items, which is consistent with the expectations of Lüder’s model.

Originality/value
The paper contributes towards theoretical development by adopting Lüder’s (1992) contingency model in the context of infrastructure reporting by New Zealand local authorities and proposing a model of contextual factors by extending Lüder’s model. The practical contribution of the study is in the area of accounting practice and public policy.
Expectations, loss aversion and retirement decisions in the context of the 2009 crisis in Europe
Authors: Sirven Nicolas , Barnay Thomas 
Published: March 2017

PurposeThe purpose of this paper is to estimate a reduced form model of expectations-based reference-dependent preferences to explain job retention of older workers in Europe in the context of the 2009 economic crisis.Design/methodology/approachUsing individual micro-economic longitudinal data from the Survey of Health, Ageing, and Retirement in Europe between 2006 and 2011, the authors derive a measure of “good, bad or no surprise” from workers’ anticipated evolution of their standard of living five years from 2006 (reference point) and from a comparison of their capacity to make ends meet between 2006 and 2011.FindingsThe authors find that the probability to remain on the labour market in 2011 is significantly higher for individuals who experienced a lower than expected standard of living. The effect of a “bad surprise” on job retention is larger than the effect of a “good surprise” once netted out from the effects of expectations at baseline, change in consumption utility, and the usual life-cycle determinants on job retention of older workers.Originality/valueThe authors interpret this result as an evidence of loss aversion in the case the reference point is based on individuals’ expectations. The authors also find that loss aversion is more common among men, risk-averse individuals and those with a higher perceived life expectancy.