bluuebunny/crossref_metadata_2025_split huggingface dataset:
Resource pulses affect prey selection and reduce dietary diversity of dingoes in arid Australia
Authors: Tatler Jack , Prowse Thomas A. A. , Roshier David A. , Allen Benjamin L. , Cassey Phillip 
Published: May 2019

Abstract

In Australia, the dingo Canis lupus dingo is the largest terrestrial predator. Dingoes contribute to ecological processes and functions throughout their continental geographic range. Their generalist diet enables daily energetic requirements to be met even in the resource‐limited deserts of central Australia, where irregular rainfall drives extreme fluctuations in mammal assemblages. Given that predation is a primary driver of declining mammal populations and failed reintroductions, it is necessary to understand the dietary intake of the continent's apex predator if conservation outcomes are to be achieved.

We performed a meta‐analysis of the mammalian composition of the dingo's diet throughout Australia's arid zone, an area covering c. 5.4 million km2. We used 25 data sets from 11 studies to measure the effects of resource booms and anthropogenic disturbance (pastoralism) on diet. We explored whether the probability of prey species occurring in the diet was related to the size of the prey or to prevailing conditions. We also investigated the similarities in diet between dingo populations from across the arid zone, and how dietary overlap was affected by opposing land uses.

Dingoes primarily consumed medium‐sized (35–5500 g) and large (>5500 g) mammals, whereas most small mammals (<35 g) were consumed infrequently, or not at all.

The composition of the diet changed dramatically during resource booms to exploit irruptive prey species such as long‐haired rats Rattus villosissimus (native; 144 g) and house mice Mus musculus (introduced; 20 g). During resource booms, the consumption of large mammals decreased significantly, whereas the occurrence in the diet of medium‐sized mammals remained high. The diversity of species consumed by dingoes was significantly lower during boom periods than during non‐boom periods.

The dingo's heightened consumption of hyper‐abundant species has the potential to release many non‐target species from direct predation pressure during boom times. This could be advantageous for remnant and reintroduced populations of mammals, which are especially susceptible to predation.
Adaptation of the group A Streptococcus adhesin Scl1 to bind fibronectin type III repeats within wound‐associated extracellular matrix: implications for cancer therapy
Authors: McNitt Dudley H. , Choi Soo Jeon , Allen Jessica L. , Hames River A. , Weed Scott A. , Van De Water Livingston , Berisio Rita , Lukomski Slawomir 
Published: May 2019

SummaryThe human‐adapted pathogen group A Streptococcus (GAS) utilizes wounds as portals of entry into host tissue, wherein surface adhesins interact with the extracellular matrix, enabling bacterial colonization. The streptococcal collagen‐like protein 1 (Scl1) is a major adhesin of GAS that selectively binds to two fibronectin type III (FnIII) repeats within cellular fibronectin, specifically the alternatively spliced extra domains A and B, and the FnIII repeats within tenascin‐C. Binding to FnIII repeats was mediated through conserved structural determinants present within the Scl1 globular domain and facilitated GAS adherence and biofilm formation. Isoforms of cellular fibronectin that contain extra domains A and B, as well as tenascin‐C, are present for several days in the wound extracellular matrix. Scl1‐FnIII binding is therefore an example of GAS adaptation to the host's wound environment. Similarly, cellular fibronectin isoforms and tenascin‐C are present in the tumor microenvironment. Consistent with this, FnIII repeats mediate GAS attachment to and enhancement of biofilm formation on matrices deposited by cancer‐associated fibroblasts and osteosarcoma cells. These data collectively support the premise for utilization of the Scl1‐FnIII interaction as a novel method of anti‐neoplastic targeting in the tumor microenvironment.
Population genomics of an outbreak of the potato late blight pathogen, Phytophthora infestans, reveals both clonality and high genotypic diversity
Authors: Maurice Sundy , Montes Melanie S. , Nielsen Bent J. , Bødker Lars , Martin Michael D. , Jønck Carina G. , Kjøller Rasmus , Rosendahl Søren 
Published: May 2019

SummaryAn outbreak of the potato late blight pathogen Phytophthora infestans in Denmark was characterized in order to resolve the population structure and determine to what extent sexual reproduction was occurring. A standard set of microsatellite simple sequence repeats (SSRs) and single nucleotide polymorphism (SNP) markers generated using restriction site‐associated DNA sequencing (RAD‐seq) were employed in parallel. A total of 83 individuals, isolated from seven different potato fields in 2014, were analysed together with five Danish whole‐genome sequenced isolates, as well as two Mexican individuals used as an outgroup. From a filtered dataset of 55 288 SNPs, population genomics analyses revealed no sign of recombination, implying clonality. In spite of this, multilocus genotypes were unique to individual potato fields, with little evidence of gene flow between fields. Ploidy analysis performed on the SNPs dataset indicated that the majority of isolates were diploid. These contradictory results with clonality and high genotypic diversity may suggest that rare sexual events likely still contribute to the population. Comparison of the results generated by SSRs vs SNPs data indicated that large marker sets, generated by RAD‐seq, may be advised going forward, as it provides a higher level of genetic discrimination than SSRs.
A systems genetics analysis in Eucalyptus reveals coordination of metabolic pathways associated with xylan modification in wood‐forming tissues
Authors: Wierzbicki Martin P. , Christie Nanette , Pinard Desré , Mansfield Shawn D. , Mizrachi Eshchar , Myburg Alexander A. 
Published: May 2019

Summary

Acetyl‐ and methylglucuronic acid decorations of xylan, the dominant hemicellulose in secondary cell walls (SCWs) of woody dicots, affect its interaction with cellulose and lignin to determine SCW structure and extractability. Genes and pathways involved in these modifications may be targets for genetic engineering; however, little is known about the regulation of xylan modifications in woody plants.

To address this, we assessed genetic and gene expression variation associated with xylan modification in developing xylem of Eucalyptus grandis × Eucalyptus urophylla interspecific hybrids. Expression quantitative trait locus (eQTL) mapping identified potential regulatory polymorphisms affecting gene expression modules associated with xylan modification.

We identified 14 putative xylan modification genes that are members of five expression modules sharing seven trans‐eQTL hotspots. The xylan modification genes are prevalent in two expression modules. The first comprises nucleotide sugar interconversion pathways supplying the essential precursors for cellulose and xylan biosynthesis. The second contains genes responsible for phenylalanine biosynthesis and S‐adenosylmethionine biosynthesis required for glucuronic acid and monolignol methylation. Co‐expression and co‐regulation analyses also identified four metabolic sources of acetyl coenxyme A that appear to be transcriptionally coordinated with xylan modification.

Our systems genetics analysis may provide new avenues for metabolic engineering to alter wood SCW biology for enhanced biomass processability.
An integrated overview of AV node physiology
Authors: Billette Jacques , Tadros Rafik 
Published: May 2019

AbstractThe atrioventricular (AV) node generates half of the AV delay needed for blood pumping and filters atrial impulses that could otherwise induce life‐threatening ventricular arrhythmias. It is also a pacemaker and a key target in the treatment of cardiac arrhythmias. The special roles of the AV node primarily arise from its slow conduction, long refractory period, and cellular automaticity. However, efforts to establish the dynamics of these properties and their interaction led to many controversies. In fact, the AV node's behavior is so complex that it seems to escape broadly applicable rules. This review summarizes progresses made in resolving these issues and in integrating the multiple roles of the AV node within a common functional model. Presented evidence shows that the rate‐dependent conduction and refractory properties of the AV node can be reliably characterized and reconciled from nodal responses to S1S2S3 protocols. It also supports the concept that dual pathways constitute a feature of the normal AV node and account for its overall conduction and refractory properties. In this model, the posterior extension and compact node provide the core of the slow and fast pathway, respectively. The transitional tissues and lower nodal bundle provide a common proximal and distal pathway, respectively. These pathways would also support bidirectional conduction. The dual pathway involvement can also be extended to widely variable AV nodal responses, such as Wenckebach cycles, hysteresis, and ventricular response to atrial fibrillation. In brief, the intricate AV nodal behavior may obey a limited set of accessible and definable rules.
Genetic relatedness and the ratio of subpopulation‐common alleles are related in genomic prediction across structured subpopulations in maize
Authors: Li Dongdong , Wang Pingxi , Gu Riliang , Fu Junjie , Xu Zhenxiang , Lyle Demar , Peng Yunling , Wang Guoying , Zhang Hongwei 
Published: May 2019

AbstractGenomic prediction (GP), which could predict the breeding value of crop plants genotyped with molecular markers, has been carried out in multiple species. Prediction accuracy (PA) of GP depends on various factors, including genetic relatedness and genetic basis. In this study, we examined the rationale for the low PA of GP when the training and validation populations were distinct using 170 temperate inbred lines and 210 tropical and subtropical inbred lines, respectively. All inbred lines were evaluated for 17 traits and genotyped with 550K high‐density markers. The results show that: (a) the influences of heritability and marker number on PA reflected variations in phenotypic variance captured by the genetic information; (b) the low PA of GP when the training and validation populations represent structured subpopulation is related to the ratio of subpopulation‐common alleles (RSCA) and the genetic relatedness between the two subpopulations; (c) RSCA and PA increased with the increase of genetic relatedness, suggesting that these three factors were related. Our findings would provide references when performing GP, and guidance when designing breeding populations.
“In vitro” capacitation and further progesterone‐induced acrosome exocytosis are linked to specific changes in the expression and location of threonine phosphorylation of boar spermatozoa
Authors: Ramió‐Lluch Laura , Prieto Olga Blanco , Ramírez Alfredo , Fernández‐Novell Josep M. , Peña Alejandro , Rodríguez‐Gil Joan Enric 
Published: May 2019

AbstractThe aim of this study was to determine if the achievement of the “in vitro” capacitation (IVC) status and subsequent progesterone‐induced “in vitro” acrosome exocytosis (IVAE) was accompanied with overall changes in threonine phosphorylation (pThre) of boar spermatozoa. For this purpose, mono‐ and bi‐dimensional Western blot analyses as well as immunocytochemistry studies against pThre were performed in boar sperm subjected to IVC and subsequent IVAE. Mono‐dimensional Western blot in non‐capacitated samples showed that launching of IVC did induce an overall increase in signal intensity in all observed bands that was followed by a subsequent decrease afterwards. Bi‐dimensional Western blot analysis showed the presence of four main signal protein clusters. The attainment of IVC induced an overall decrease in the number and intensity of spots of Clusters A, B and C and a concomitant increase in the intensity of spots of Cluster D. The IVAE launching caused a rapid increase in the intensity of spots of Clusters B, C and D, which was followed by a subsequent decrease of the intensity together with a concomitant pI displacement of Cluster C. Finally, immunocytochemistry showed that the pThre signal of non‐capacitated cells was located at the whole sperm. The IVC did not induce prominent changes in this location. In contrast, the induction of IVAE caused the appearance of an additional an intense acrosome and tail pThre signal that subsequently decreased. In conclusion, our results indicate that IVC and further IVAE induced specific changes in the intensity and appearance of pThre protein phosphorylation which were linked to changes of specific protein characteristics as pI. These results support, thus, the existence of a specific role of pThre in IVC/IVAE of boar sperm.
Rural Livelihood Diversification: A Solution for Poverty in the Post‐Soviet Rural Baltic States?
Authors: Žakevičiūtė Rasa 
Published: May 2019

AbstractThis article analyses rural livelihood diversification through a longitudinal follow‐up survey, that targets former collective farm workers in Estonia, Latvia and Lithuania. It argues, that between 1995 and 2010 the former collective farm workers employed three distinct livelihood diversification strategies in order to create their living. A wage‐based livelihood diversification strategy, which does not include any agricultural practices, was more common among the better‐off households. A farm‐based livelihood diversification strategy, which does not rely on salaries, was more often employed by the poor. A mixed strategy, that combines both wage income and farm activities, was used by both better‐off (above the poverty line) and poor households (below the poverty line). The paper also finds that livelihood diversification and poverty among the researched households have country specific patterns, which coincide with the general rural development in Baltic states.
Phylogenetics and comparative analysis of the mitochondrial genomes of three violet‐ringed octopuses
Authors: Tang Yan , Zheng Xiaodong , Zhong Hong , Li Qi 
Published: May 2019

AbstractSimilar morphological characters and little molecular data ofAmphioctopus rex,A. neglectusandA. cf. ovulumresulted in their unknown phylogenetic statuses and equivocal relationships. In this study, the complete mitochondrial genomes of these three species collected in Chinese waters were sequenced and compared with each other to clarify the relationships among them. The lengths of the mitochondrial genomes varied from 15,646 bp to 15,814 bp, and the A + T content and GC skew for protein‐coding genes showed little variation. In contrast, both a dendrogram based on codon usage and the gene arrangements of the three octopuses showed thatA. rexwas more closely related toA. neglectusthan toA. cf. ovulum. Five data sets and two methods (maximum likelihood and Bayesian inference) were utilized for the first time to explore the phylogenetic relationships among these three species in Octopodidae. The results indicated that a data set combining protein‐coding genes and RNA genes (PR) was optimal for analysing the relationships among 43 cephalopods. All of the phylogenetic trees divided the cephalopods into 10 taxa and supported the monophyly of Oegopsida, Myopsida, Sepiidae and Octopodidae. In this study, Idiosepiidae was classified as sister to Sepiolidae. Trees constructed using all data sets robustly supported the monophyly of the genusAmphioctopus. Notably,A. rexwas more closely related toA. neglectusthan toA. cf. ovulum, although these three species share the characteristic of violet rings on dark ocelli.
Coenzyme Q10 supplementation in traumatic brain injury: a scoping review protocol
Authors: Allan Kaylee , Hayes Kati , Thomas Matt , Barnard Katie 
Published: May 2019

ABSTRACT

Objective:
The objective of this review is to map evidence on coenzyme Q10 (CoQ10) use in traumatic brain injury (TBI).

Introduction:
Traumatic brain injury is an insult to the brain structure caused by external force and resulting in physiological disruption to brain function. Globally, 60% of all TBIs occur from road traffic accidents. In 2016, the World Health Organization reported that road traffic accidents were among the top 10 leading causes of death. Following the initial brain injury, a secondary injury can occur due primarily to a significant increase in production of free radicals causing oxidative stress, which can dictate the patient's ability to survive. Coenzyme Q10 is known to protect neuronal cells from oxidative stress; the mechanism for this has been examined in studies using rats. This review will examine what is known about CoQ10 in TBI and identify gaps in the literature, which may guide future research.

Inclusion criteria:
The review will include both human and animal subjects who have experienced a TBI in the acute/laboratory-controlled setting and where CoQ10 is supplemented. Animal studies will be included. The review will consider experimental and quasi-experimental study designs including randomized controlled trials, non-randomized controlled trials, before and after studies, and interrupted time-series studies. Studies published in English will be considered, with no date restriction.

Methods:
Searches will be conducted in the Cochrane Library, MEDLINE, Embase, CINAHL and trial registries. Data will be extracted and presented on details about the population, concept, context, study methods and key findings.
A molecular rheostat: Kv2.1 currents maintain or suppress repetitive firing in motoneurons
Authors: Romer Shannon H. , Deardorff Adam S. , Fyffe Robert E. W. 
Published: May 2019

Key points
Kv2 currents maintain and regulate motoneuron (MN) repetitive firing properties.
Kv2.1 channel clustering properties are dynamic and respond to both high and low activity conditions.
The enzyme calcineurin regulates Kv2.1 ion channel declustering.
In patholophysiological conditions of high activity, Kv2.1 channels homeostatically reduce MN repetitive firing.
Modulation of Kv2.1 channel kinetics and clustering allows these channels to act in a variable way across a spectrum of MN activity states.
AbstractKv2.1 channels are widely expressed in the central nervous system, including in spinal motoneurons (MNs) where they aggregate as distinct membrane clusters associated with highly regulated signalling ensembles at specific postsynaptic sites. Multiple roles for Kv2 channels have been proposed but the physiological role of Kv2.1 ion channels in mammalian spinal MNs is unknown. To determine the contribution of Kv2.1 channels to rat α‐motoneuron activity, the Kv2 inhibitor stromatoxin was used to block Kv2 currents in whole‐cell current clamp electrophysiological recordings in rat lumbar MNs. The results indicate that Kv2 currents permit shorter interspike intervals and higher repetitive firing rates, possibly by relieving Na+ channel inactivation, and thus contribute to maintenance of repetitive firing properties. We also demonstrate that Kv2.1 clustering properties in motoneurons are dynamic and respond to both high and low activity conditions. Furthermore, we show that the enzyme calcineurin regulates Kv2.1 ion channel clustering status. Finally, in a high activity state, Kv2.1 channels homeostatically reduce motoneuron repetitive firing. These results suggest that the activity‐dependent regulation of Kv2.1 channel kinetics allows these channels to modulate repetitive firing properties across a spectrum of motoneuron activity states.
CFD-Aided Design of a Transonic Aeroelastic Compressor Rig
Authors: Tian Simeng , Petrie-Repar Paul , Glodic Nenad , Sun Tianrui 
Published: May 2019

Abstract
This paper presents the results of computational fluid dynamics (CFD)-aided design calculations of a transonic linear cascade wind tunnel. The purpose of the wind tunnel is to generate data for the validation of numerical methods employed to calculate aerodynamic damping for forced response cases in transonic compressors. It is common for transonic wind tunnels to use transonic walls (perforated walls with controlled suction) to adjust the transonic flow in the experiment. Unfortunately, perforated walls are difficult to model in CFD simulations, and they complicate the validation process. One of the goals of the new tunnel is not to use perforated walls. The main difficulty in the design of a transonic linear cascade is achieving periodic flow for the central blades due to shock reflections from the side walls and the sensitivity of transonic flow to small changes in geometry. Other design constraints are the maximum available mass flow of 4.5 kg/s and the minimum required blade thickness of 2 mm for instrumentation. The purpose of the current CFD simulations is to determine the optimum geometry (sidewalls, tailboards, and throttle) of the tunnel with the goal of achieving near periodic flow conditions for the central blade channels at the similar condition in a typical transonic compressor.
Computational Modeling of Inertial Effects on Electromechanics of the Heart
Authors: Jaffery Ovais A. , Akhtar Imran , Imran Majeed S. M. , Zaidi Tahir 
Published: May 2019

Abstract
Computational modeling of cardiac function has gradually progressed during the past four decades and now beginning to translate toward clinical use as a noninvasive mean of optimizing cardiac treatment options. Recent experimental findings and numerical investigations have suggested an important role of mechanical and intrinsic properties of cardiac tissues in overall electromechanical dynamics of the heart. The inertial effects, which were usually neglected in earlier computational studies, have now been found to alter cardiac dynamics through stretch activated channels (SAC) and can lead to cardiac disorders under specific set of physiological conditions. Considering possible role of inertia in cardiac dynamics, we have modeled electromechanical activity of the heart with inertia terms for computing pressure volume relation and action potentials over a complete cardiac cycle. To this end, we use the continuum balance laws to capture physiological function of the human left ventricle (LV) on an idealized geometry and solve the resulting equations using a python-based finite element platform. For the same set of pressure boundary conditions, the finite element models for quasi-static (less inertia) and dynamic (with inertia terms) formulation yielded a difference of 4.2% end diastolic volume (EDV), 3.1% ejection fraction, and variations in fiber strain pattern. The mechano-electric transduction channels sensitive to small mechanical perturbations in combination with changes in electrical conductivity due to deformation caused quantitative variations over cardiac electrical activity up to 2.75–5% reduction in action potential duration (APD) at 50% repolarization (APD50) and 3.5–5.75% reduction at 90% repolarization (APD90). Catering the effect of inertia can help the research community to improve future computational models in investigating the electromechanics of the heart.