bluuebunny/crossref_metadata_2025_split huggingface dataset:
Optogenetic activation of axon guidance receptors controls direction of neurite outgrowth
Authors: Endo M. , Hattori M. , Toriyabe H. , Ohno H. , Kamiguchi H. , Iino Y. , Ozawa T. 
Published: April 2016

AbstractGrowth cones of extending axons navigate to correct targets by sensing a guidance cue gradient via membrane protein receptors. Although most signaling mechanisms have been clarified using an in vitro approach, it is still difficult to investigate the growth cone behavior in complicated extracellular environment of living animals due to the lack of tools. We develop a system for the light-dependent activation of a guidance receptor, Deleted in Colorectal Cancer (DCC), using Arabidopsis thaliana Cryptochrome 2, which oligomerizes upon blue-light absorption. Blue-light illumination transiently activates DCC via its oligomerization, which initiates downstream signaling in the illuminated subcellular region. The extending axons are attracted by illumination in cultured chick dorsal root ganglion neurons. Moreover, light-mediated navigation of the growth cones is achieved in living Caenorhabditis elegans. The photo-manipulation system is applicable to investigate the relationship between the growth cone behavior and its surrounding environment in living tissue.
Enoyl-CoA hydratase mediates polyhydroxyalkanoate mobilization in Haloferax mediterranei
Authors: Liu Guiming , Cai Shuangfeng , Hou Jing , Zhao Dahe , Han Jing , Zhou Jian , Xiang Hua 
Published: April 2016

AbstractAlthough polyhydroxyalkanoate (PHA) accumulation and mobilization are one of the most general mechanisms for haloarchaea to adapt to the hypersaline environments with changeable carbon sources, the PHA mobilization pathways are still not clear for any haloarchaea. In this study, the functions of five putative (R)-specific enoyl-CoA hydratases (R-ECHs) in Haloferax mediterranei, named PhaJ1 to PhaJ5, respectively, were thoroughly investigated. Through gene deletion and complementation, we demonstrated that only certain of these ECHs had a slight contribution to poly(3-hydroxybutyrate-co-3-hydroxyvalerate) (PHBV) biosynthesis. But significantly, PhaJ1, the only R-ECH that is associated with PHA granules, was shown to be involved in PHA mobilization in this haloarchaeon. PhaJ1 catalyzes the dehydration of (R)-3-hydroxyacyl-CoA, the common product of PHA degradation, to enoyl-CoA, the intermediate of the β-oxidation cycle, thus could link PHA mobilization to β-oxidation pathway in H. mediterranei. This linkage was further indicated from the up-regulation of the key genes of β-oxidation under the PHA mobilization condition, as well as the obvious inhibition of PHA degradation upon inhibition of the β-oxidation pathway. Interestingly, 96% of phaJ-containing haloarchaeal species possess both phaC (encoding PHA synthase) and the full set genes of β-oxidation, implying that the mobilization of carbon storage in PHA through the β-oxidation cycle would be general in haloarchaea.
Vegetation and Cold Trapping Modulating Elevation-dependent Distribution of Trace Metals in Soils of a High Mountain in Eastern Tibetan Plateau
Authors: Bing Haijian , Wu Yanhong , Zhou Jun , Li Rui , Luo Ji , Yu Dong 
Published: April 2016

AbstractTrace metals adsorbed onto fine particles can be transported long distances and ultimately deposited in Polar Regions via the cold condensation effect. This study indicated the possible sources of silver (Ag), cadmium (Cd), copper (Cu), lead (Pb), antimony (Sb) and zinc (Zn) in soils on the eastern slope of Mt. Gongga, eastern Tibetan Plateau and deciphered the effects of vegetation and mountain cold condensation on their distributions with elevation. The metal concentrations in the soils were comparable to other mountains worldwide except the remarkably high concentrations of Cd. Trace metals with high enrichment in the soils were influenced from anthropogenic contributions. Spatially, the concentrations of Cu and Zn in the surface horizons decreased from 2000 to 3700 m a.s.l. and then increased with elevation, whereas other metals were notably enriched in the mid-elevation area (approximately 3000 m a.s.l.). After normalization for soil organic carbon, high concentrations of Cd, Pb, Sb and Zn were observed above the timberline. Our results indicated the importance of vegetation in trace metal accumulation in an alpine ecosystem and highlighted the mountain cold trapping effect on trace metal deposition sourced from long-range atmospheric transport.
A novel approach for modelling vegetation distributions and analysing vegetation sensitivity through trait-climate relationships in China
Authors: Yang Yanzheng , Zhu Qiuan , Peng Changhui , Wang Han , Xue Wei , Lin Guanghui , Wen Zhongming , Chang Jie , Wang Meng , Liu Guobin , Li Shiqing 
Published: April 2016

AbstractIncreasing evidence indicates that current dynamic global vegetation models (DGVMs) have suffered from insufficient realism and are difficult to improve, particularly because they are built on plant functional type (PFT) schemes. Therefore, new approaches, such as plant trait-based methods, are urgently needed to replace PFT schemes when predicting the distribution of vegetation and investigating vegetation sensitivity. As an important direction towards constructing next-generation DGVMs based on plant functional traits, we propose a novel approach for modelling vegetation distributions and analysing vegetation sensitivity through trait-climate relationships in China. The results demonstrated that a Gaussian mixture model (GMM) trained with a LMA-Nmass-LAI data combination yielded an accuracy of 72.82% in simulating vegetation distribution, providing more detailed parameter information regarding community structures and ecosystem functions. The new approach also performed well in analyses of vegetation sensitivity to different climatic scenarios. Although the trait-climate relationship is not the only candidate useful for predicting vegetation distributions and analysing climatic sensitivity, it sheds new light on the development of next-generation trait-based DGVMs.
Knots cascade detected by a monotonically decreasing sequence of values
Authors: Liu Xin , Ricca Renzo L. 
Published: April 2016

AbstractDue to reconnection or recombination of neighboring strands superfluid vortex knots and DNA plasmid torus knots and links are found to undergo an almost identical cascade process, that tend to reduce topological complexity by stepwise unlinking. Here, by using the HOMFLYPT polynomial recently introduced for fluid knots, we prove that under the assumption that topological complexity decreases by stepwise unlinking this cascade process follows a path detected by a unique, monotonically decreasing sequence of numerical values. This result holds true for any sequence of standardly embedded torus knots T(2, 2n + 1) and torus links T(2, 2n). By this result we demonstrate that the computation of this adapted HOMFLYPT polynomial provides a powerful tool to measure topological complexity of various physical systems.
Potential use of bacterial community succession for estimating post-mortem interval as revealed by high-throughput sequencing
Authors: Guo Juanjuan , Fu Xiaoliang , Liao Huidan , Hu Zhenyu , Long Lingling , Yan Weitao , Ding Yanjun , Zha Lagabaiyila , Guo Yadong , Yan Jie , Chang Yunfeng , Cai Jifeng 
Published: April 2016

AbstractDecomposition is a complex process involving the interaction of both biotic and abiotic factors. Microbes play a critical role in the process of carrion decomposition. In this study, we analysed bacterial communities from live rats and rat remains decomposed under natural conditions, or excluding sarcosaphagous insect interference, in China using Illumina MiSeq sequencing of 16S rRNA gene amplicons. A total of 1,394,842 high-quality sequences and 1,938 singleton operational taxonomic units were obtained. Bacterial communities showed notable variation in relative abundance and became more similar to each other across body sites during the decomposition process. As decomposition progressed, Proteobacteria (mostly Gammaproteobacteria) became the predominant phylum in both the buccal cavity and rectum, while Firmicutes and Bacteroidetes in the mouth and rectum, respectively, gradually decreased. In particular, the arrival and oviposition of sarcosaphagous insects had no obvious influence on bacterial taxa composition, but accelerated the loss of biomass. In contrast to the rectum, the microbial community structure in the buccal cavity of live rats differed considerably from that of rats immediately after death. Although this research indicates that bacterial communities can be used as a “microbial clock” for the estimation of post-mortem interval, further work is required to better understand this concept.
Supramolecular Chemistry at Surfaces
Authors: Amabilino David B 
Published: April 2016

Supramolecular chemistry provides a versatile approach for modifying the structure and function of surfaces, including the formation of clusters, monolayers and films. This can be used in a variety of applications from porous surface systems, to modifiers of interface energy and sensor-based systems.
Supramolecular Chemistry at Surfaces covers different methods of preparing and studying self-assembled structures at surfaces and interfaces. The book starts with a general introduction concerning the nature of surfaces followed by specific sections discussing different techniques to characterise surface-based supramolecular systems. Each chapter then goes on to address different surface systems including the surface of water; physisorbed layers at interfaces; chemisorbed layers at interfaces; polyelectrolyte systems; thin films; dynamic systems; and patterning.
Written by a leading expert in the field, this is the first book to give a multidisciplinary view of the supramolecular aspects of interfaces providing the reader with an objective summary of all the deposition methods and their characterisation. The book will appeal to students and researchers in supramolecular chemistry, nanoscience, polymer chemistry and physics, surface science and materials science.
NLRP3 inflammasome plays a redundant role with caspase 8 to promote IL-1β–mediated osteomyelitis
Authors: Gurung Prajwal , Burton Amanda , Kanneganti Thirumala-Devi 
Published: April 2016

SignificanceIL-1 is a pleiotropic cytokine involved in a myriad of autoinflammatory disorders. In proline-serine-threonine phosphatase-interacting protein 2 (Pstpip2cmo) mice, IL-1β provokes autoinflammatory osteomyelitis. Here, we demonstrated the redundant roles of Nod like receptor family, pyrin domain containing 3 (NLRP3) inflammasome with caspase 8 in the processing of IL-1β inPstpip2cmomice. Identification of redundancy between NLRP3 inflammasome and caspase 8 is fundamental in our understanding of the inflammasomes and alternative modes of IL-1β regulation in osteomyelitic disease. Moreover, IL-1β signaling connects distinct compartments in promoting the disease, identifying previously unidentified checkpoints that could be targeted for therapeutic purposes in similar disease settings. Thus, our studies have unraveled the complex IL-1β regulatory network in vivo in a mouse model of osteomyelitis that will be useful for autoinflammatory diseases in general.
Effects of the Antihypertensive Fixed-Dose Combinations on an Early Marker of
Hypertensive Cardiac Damage in Subjects at Low Cardiovascular Risk
Authors: Mazza A. , Schiavon L. , Zuin M. , Lenti S. , Ramazzina E. , Rubello D. , Casiglia E. 
Published: April 2016

Abstract

BACKGROUND
In hypertensive subjects (HTs), isolated left ventricular diastolic dysfunction (LVDD) is an early marker of cardiac damage and is associated with poor prognosis. However, few intervention trials investigated the effects of antihypertensive therapy on isolated LVDD regression. This study investigates the blood pressure (BP)-lowering efficacy and the effect on LVDD of antihypertensive drugs administered as fixed-dose combinations in untreated HTs with isolated LVDD.

METHODS
A total of 168 HTs (23% of them having impaired fasting glucose (IFG)) aged 48±4.2 years were randomized to receive open-label once-daily oral treatment of beta-blocker + diuretic, angiotensin-converting enzyme inhibitor (ACEI) + diuretic, angiotensin II receptor blocker (ARB) + diuretic, ARB + calcium channel blocker (CCB), or ACEI + CCB. Clinic and 24-hour ambulatory BP values were measured before randomization and at the follow-up. Regression of LVDD was defined as normalization of both the E/A (ratio of early-to-late ventricular filling wave velocity) and E/E’ (mitral velocity to early diastolic velocity of the mitral annulus) ratios. Comparisons were made between categorical variables using the χ 2 test and between continuous variables by gender using analysis of variance for repeated measures.

RESULTS
BP reduction did not differ between groups. LVDD regression was significantly more prevalent in the ARB + CCB or ACEI + CCB groups than with other combinations; in HTs with IFG, it was most prevalent (46%) with ACEI + CCB.

CONCLUSIONS
Independently of BP reduction, the fixed-dose combinations ARB + CCB and ACEI + CCB led to regression of isolated LVDD. In those with an IFG, ACEI + CCB was most effective.
Cell-free DNA fragment-size distribution analysis for non-invasive prenatal CNV prediction
Authors: Arbabi Aryan , Rampášek Ladislav , Brudno Michael 
Published: April 2016

Abstract
Background: Non-invasive detection of aneuploidies in a fetal genome through analysis of cell-free DNA circulating in the maternal plasma is becoming a routine clinical test. Such tests, which rely on analyzing the read coverage or the allelic ratios at single-nucleotide polymorphism (SNP) loci, are not sensitive enough for smaller sub-chromosomal abnormalities due to sequencing biases and paucity of SNPs in a genome.
Results: We have developed an alternative framework for identifying sub-chromosomal copy number variations in a fetal genome. This framework relies on the size distribution of fragments in a sample, as fetal-origin fragments tend to be smaller than those of maternal origin. By analyzing the local distribution of the cell-free DNA fragment sizes in each region, our method allows for the identification of sub-megabase CNVs, even in the absence of SNP positions. To evaluate the accuracy of our method, we used a plasma sample with the fetal fraction of 13%, down-sampled it to samples with coverage of 10X–40X and simulated samples with CNVs based on it. Our method had a perfect accuracy (both specificity and sensitivity) for detecting 5 Mb CNVs, and after reducing the fetal fraction (to 11%, 9% and 7%), it could correctly identify 98.82–100% of the 5 Mb CNVs and had a true-negative rate of 95.29–99.76%.
Availability and implementation: Our source code is available on GitHub at https://github.com/compbio-UofT/FSDA.
Contact: brudno@cs.toronto.edu
Mass segregation in star clusters is not energy equipartition
Authors: Parker Richard J. , Goodwin Simon P. , Wright Nicholas J. , Meyer Michael R. , Quanz Sascha P. 
Published: April 2016

Abstract
Mass segregation in star clusters is often thought to indicate the onset of energy equipartition, where the most massive stars impart kinetic energy to the lower-mass stars and brown dwarfs/free-floating planets. The predicted net result of this is that the centrally concentrated massive stars should have significantly lower velocities than fast-moving low-mass objects on the periphery of the cluster. We search for energy equipartition in initially spatially and kinematically substructured N-body simulations of star clusters with N = 1500 stars, evolved for 100 Myr. In clusters that show significant mass segregation we find no differences in the proper motions or radial velocities as a function of mass. The kinetic energies of all stars decrease as the clusters relax, but the kinetic energies of the most massive stars do not decrease faster than those of lower-mass stars. These results suggest that dynamical mass segregation – which is observed in many star clusters – is not a signature of energy equipartition from two-body relaxation.
Acceptability of Rapid Point-of-Care Hepatitis C Tests Among People Who Inject Drugs and Utilize Syringe-Exchange Programs
Authors: Barocas Joshua A. , Linas Benjamin P. , Kim Arthur Y. , Fangman John , Westergaard Ryan P. 
Published: April 2016

Abstract
People who inject drugs may benefit from point-of-care hepatitis C virus (HCV) testing offered at syringe exchanges. We sought to understand whether this population would be willing to undergo rapid HCV testing. We found that there was broad support for rapid HCV testing, especially among younger people who inject drugs with high perceived risk.
Earth rotation derived from occultation records
Authors: Sôma Mitsuru , Tanikawa Kiyotaka 
Published: April 2016

Abstract
We determined the values of the Earth's rotation parameter, ΔT = T T − UT, around AD 500 after confirming that the value of the tidal acceleration, $\dot{n}$, of the lunar motion remained unchanged during the period between ancient times and the present. For determining of ΔT, we used contemporaneous occultations of planets by the Moon. In general, occultation records are not useful. However, there are some records that give us a stringent condition for the range of ΔT. Records of the lunar occultations in AD 503 and AD 513 are such examples. In order to assure the usefulness of this occultation data, we used contemporaneous annular and total solar eclipses, which have not been used in the preceding work. This is the first work in which the lunar occultation data have been used as primary data to determine the value of ΔT together with auxiliary contemporaneous annular and total solar eclipses. Our ΔT value is less than a smoothed value (Stephenson 1997) by at least 450 s. The result is consistent with our earlier results obtained from solar eclipses.
Selecting Reads for Haplotype Assembly
Authors: Fischer Sarah O. , Marschall Tobias 
Published: April 2016

AbstractHaplotype assembly or read-based phasingis the problem of reconstructing both haplotypes of a diploid genome from next-generation sequencing data. This problem is formalized as the Minimum Error Correction (MEC) problem and can be solved using algorithms such as WhatsHap. The runtime of WhatsHap is exponential in the maximum coverage, which is hence controlled in a pre-processing step that selects reads to be used for phasing. Here, we report on a heuristic algorithm designed to choose beneficial reads for phasing, in particular to increase the connectivity of the phased blocks and the number of correctly phased variants compared to the random selection previously employed in by WhatsHap. The algorithm we describe has been integrated into the WhatsHap software, which is available under MIT licence fromhttps://bitbucket.org/whatshap/whatshap.
Human CODIS STR Loci Profiling from HTS Data
Authors: Ricke Darrell O. , Petrovick Martha , Bobrow Johanna , Boettcher Tara , Zook Christina , Harper James , Wack Edward , Schwoebel Eric 
Published: April 2016

AbstractHuman DNA identification is currently performed by amplifying a small, defined set of short tandem repeat (STR) loci (e.g. CODIS) and analyzing the size of the alleles present at those loci by capillary electrophoresis. High-throughput DNA sequencing (HTS) could enable the simultaneous analysis of many additional STR and single nucleotide polymorphism (SNP) loci, improving accuracy and discrimination. However, it is necessary to demonstrate that HTS can generate accurate data on the CODIS loci to enable backwards compatibility with the FBI NDIS database. Sequencing can also detect novel polymorphisms within alleles that migrate with identical sizes by capillary electrophoresis, improving allele discrimination, and enhancing human identification analysis. All CODIS alleles from an individual can be amplified in a single, multiplex PCR reaction, and combined with additional barcoded samples prior to sequencing. A computational tool for allele identification from multiplexed sequence data has been developed. With longer-read-length platforms, 99.6% allele calling accuracy can be achieved. In the course of STR sequencing protocol development, 12 novel allele sequences have been identified for multiple loci. Sequencing STR loci combined with SNPs will enable new forensic applications.
Stakeholder informed non-traditional student induction: a balanced approach
Authors: Soontiens Werner , Kerr Rosemary , Ang Grace , Scully Glennda 
Published: April 2016

PurposeThe paper considers the evolution of a tailored university induction program over time to establish the change in the nature and content of the program.Design/methodology/approachThe induction program is pitched against the conceptual backdrop of academic norms and conventions, language, integration and the role of mentoring. As an exploratory study of a unique and complex induction program it reports on the basis of discourse analysis over time (from 2009 to 2012).FindingsThe paper establishes that consideration of feedback by students, university staff (academic and professional) and external stakeholders has allowed the program to morph to a balanced content of academic; social; and socio-academic integration activities.Research limitations/implicationsThe paper confirms the framework proposed by Zepke and Leach (2005) and renders a further level of validity to the model when applied in a cross-cultural higher education context.Practical implicationsPractical implications include the value of involving stakeholders as source of knowledge for considering continuous improvements and the notion that a remedial approach to integration of international students proves to be ineffective.Originality/valueArticulation pathways for Chinese university students into Australian universities create a unique set of expectations and challenges to both the students and the Australian universities. A tailor made induction program is a crucial step in addressing these and requires continuous improvement to retain relevance and optimise impact and resources.
Orthopaedic spinal triage
Authors: Kerridge-Weeks Martin , Langridge Neil John 
Published: April 2016

Purpose
– Clinical specialist physiotherapy (CSP)-led musculoskeletal triage clinics have been established in the UK as a means of managing patients referred for outpatient orthopaedic consultation. The purpose of this paper is to determine if a CSP could allocate patients into distinct diagnostic triage categories in line with national and international guidelines. A second aim was to describe the CSPs clinical decision making.

Design/methodology/approach
– A review of 100 spinal patients, consecutively referred between February and April 2013 to a CSP spinal triage clinic was undertaken. Patient demographics (age, gender, employment status), clinical diagnosis and diagnostic triage categories selected for each patient were recorded. Subsequently, if clinical triage led to further investigation or a consultant opinion then the onward management pathway was followed to calculate conversion to consultant surgical intervention.

Findings
– In total, 69 per cent of patients were independently managed by the CSP and discharged back to the General Practitioner or on to therapy. In total, 30 per cent of patients (n=30) were referred for consultant opinion, of these 12 underwent intervention. This represents a conversion rate to consultant intervention of 40 per cent.

Originality/value
– Findings suggest that a significant number of spinal patients referred for an orthopaedic consultation may be managed independently by a CSP. Referral for consultant review was deemed appropriate in terms of conversion to intervention, advice on further imaging, referral to other medical disciplines and patient counselling. This study suggests that CSPs can manage a significant number of patients with spinal conditions whilst providing high-quality referrals to surgical colleagues. This audit provides a novel insight into practitioner behaviour that supports the development of advanced practice for non-medical clinicians.