bluuebunny/crossref_metadata_2025_split huggingface dataset:
Treatment of Severe Self-Injurious Behavior in Autism Spectrum Disorder by Neuromodulation
Authors: D'Agati Douglas , Chang Andrew D. , Wachtel Lee E. , Reti Irving M. 
Published: July 2016

Abstract
An increasing number of case reports and series document the safe and effective use of electroconvulsive therapy (ECT) in children, adolescents, and young adults with autism spectrum disorder who engage in severe, intractable, repetitive self-injurious behavior (SIB) without environmental or operant function. Although the treatment is very effective for such patients, they typically remain highly dependent on frequent maintenance ECT (M-ECT) to maintain suppression of the SIB achieved during the acute course. Some patients receive M-ECT as frequently as once every 5 days. Such a regimen is quite burdensome for the patient and the patient's family, and the long-term effects of such regimens, starting as early as childhood, are unknown. In this review, we explore the expanding literature supporting the use of ECT for suppressing severe SIB associated with autism spectrum disorder. We also focus on the possible development of alternate nonconvulsive focal forms of brain stimulation, which might replace frequent M-ECT or reduce how frequently a patient needs to receive it. Although there are scarce clinical data currently available supporting these latter treatments, future studies are clearly indicated.
3D sorghum reconstructions from depth images enable identification of quantitative trait loci regulating shoot architecture
Authors: McCormick Ryan F. , Truong Sandra K. , Mullet John E. 
Published: July 2016

AbstractDissecting the genetic basis of complex traits is aided by frequent and non-destructive measurements. Advances in range imaging technologies enable the rapid acquisition of three-dimensional (3D) data from an imaged scene. A depth camera was used to acquire images ofSorghum bicolor, an important grain, forage, and bioenergy crop, at multiple developmental timepoints from a greenhouse-grown recombinant inbred line population. A semi-automated software pipeline was developed and used to generate segmented, 3D plant reconstructions from the images. Automated measurements made from 3D plant reconstructions identified quantitative trait loci (QTL) for standard measures of shoot architecture such as shoot height, leaf angle and leaf length, and for novel composite traits such as shoot compactness. The phenotypic variability associated with some of the QTL displayed differences in temporal prevalence; for example, alleles closely linked with the sorghumDwarf3gene, an auxin transporter and pleiotropic regulator of both leaf inclination angle and shoot height, influence leaf angle prior to an effect on shoot height. Furthermore, variability in composite phenotypes that measure overall shoot architecture, such as shoot compactness, is regulated by loci underlying component phenotypes like leaf angle. As such, depth imaging is an economical and rapid method to acquire shoot architecture phenotypes in agriculturally important plants like sorghum to study the genetic basis of complex traits.
Zika virus may not be alone: proteomics associates a bovine-like viral diarrhea virus to microcephaly
Authors: Nogueira Fabio CS , Velasquez Erika , Melo Adriana SO , Domont Gilberto B , Sawa Akira 
Published: July 2016

One Sentence SummaryProteomics analysis lead us to suspect the presence of a Bovine-like viral diarrhea virus (BVDV-like) in the brain tissue of fetuses bearing microcephaly during the outbreak in Paraiba State, Brazil, 2015.AbstractNo direct experimental causal evidence confirms that the Zika virus is the sole etiological agent responsible for the development of brain malformations in human fetuses during pregnancy. We used a discovery-driven approach to analyze protein extracts of three Zika positive brains. Shotgun mass spectrometry (MS) proteomics did not identify any Zika protein in all samples. However, MS detected the presence of peptide(s) from the polyprotein of a Bovine-like viral diarrhea virus (BVDV-like) in Zika-positive brains. These results indicate that Zika virus may not be, per se, the only etiological agent responsible for microcephaly and suggests that discovery-driven approaches play an essential role in the screening of fluids or tissues for virus or other etiological agents.
The Forest, the Trees, and the Phylo-diversity Jungle
Authors: Mazel Florent , Tucker Caroline M. , Cadotte Marc W. , Carvalho Silvia B. , Davies T. Jonathan , Fritz Susanne A. , Grenyer Rich , Helmus Matthew R. , Mooers Arne Ø. , Pavoine Sandrine , Purschke Oliver , Rosauer Dan. F. , Winter Marten 
Published: July 2016

AbstractThe joint use of phylogenetic trees and ecological data has proven useful for many aspects of ecology. However, there are a multitude of phylo-diversity metrics with complex interdependencies and mathematical redundancies (the so-called ‘jungle’ of metrics). Several recentpapers have been trying to ‘map’ this jungle but appear at a first glance to contradict each other. We suggest that these contradictory results are in fact complementary and reflect two approaches to understand diversity metrics: the first focuses on general mathematical properties,the second focuses on assessing metric performance in relation to particular questions.In this manuscript, we discuss the complementarity of the two approaches and in particular how recent papers fit into this categorisation.
Detecting the impact of temperature on transmission of Zika, dengue and chikungunya using mechanistic models
Authors: Mordecai Erin A. , Cohen Jeremy M. , Evans Michelle V. , Gudapati Prithvi , Johnson Leah R. , Lippi Catherine A. , Miazgowicz Kerri , Murdock Courtney C. , Rohr Jason R. , Ryan Sadie J. , Savage Van , Shocket Marta S. , Ibarra Anna Stewart , Thomas Matthew B. , Weikel Daniel P. 
Published: July 2016

AbstractRecent epidemics of Zika, dengue, and chikungunya have heightened the need to understand the seasonal and geographic range of transmission byAedes aegyptiandAe. albopictusmosquitoes. We use mechanistic transmission models to derive predictions for how the probability and magnitude of transmission for Zika, chikungunya, and dengue change with mean temperature, and we show that these predictions are well matched by human case data. Across all three viruses, models and human case data both show that transmission occurs between 18-34°C with maximal transmission occurring in a range from 26-29°C. Controlling for population size and two socioeconomic factors, temperature-dependent transmission based on our mechanistic model is an important predictor of human transmission occurrence and incidence. Risk maps indicate that tropical and subtropical regions are suitable for extended seasonal or year-round transmission, but transmission in temperate areas is limited to at most three months per year even if vectors are present. Such brief transmission windows limit the likelihood of major epidemics following disease introduction in temperate zones.Author SummaryUnderstanding the drivers of recent Zika, dengue, and chikungunya epidemics is a major public health priority. Temperature may play an important role because it affects mosquito transmission, affecting mosquito development, survival, reproduction, and biting rates as well as the rate at which they acquire and transmit viruses. Here, we measure the impact of temperature on transmission by two of the most common mosquito vector species for these viruses,Aedes aegyptiandAe. albopictus. We integrate data from several laboratory experiments into a mathematical model of temperature-dependent transmission, and find that transmission peaks at 26-29°C and can occur between 18-34°C. Statistically comparing model predictions with recent observed human cases of dengue, chikungunya, and Zika across the Americas suggests an important role for temperature, and supports model predictions. Using the model, we predict that most of the tropics and subtropics are suitable for transmission in many or all months of the year, but that temperate areas like most of the United States are only suitable for transmission for a few months during the summer (even if the mosquito vector is present).
The metabolic profile of lag and exponential phases ofSaccharomyces cerevisiaegrowth changes continuously
Authors: Bento Rafael N. , Aradhya Miguel A. , Semedo Valdir A. R. , Bernardes Carlos E. S. , Piedade Manuel E. M. , Antunes Fernando 
Published: July 2016

AbstractCellular growth is usually separated in well-defined phases. For microorganism likeSaccharomyces cerevisiae,two phases usually defined are (1) a lag phase, in which no growth is observed and cells adapt to a new environment, followed by (2) an exponential phase, in which rapid proliferation occurs. Here we investigate whether these well-defined phases are uniform. By using flow-microcalorimetry, we found that the metabolic profile of the culture is continuously changing, both in the lag and exponential phases of growth. Along the lag phase there is a continuous increase in the energy that is dissipated irreversibly as heat, while in the exponential phase the opposite occurs. We also confirm recent observations that the oxidative component of metabolism decreases along the exponential phase. Interestingly, nutrient limitation further decreases the amount of energy that is dissipated irreversibly. Altogether, this points to a picture in which cells respond rapidly to minute environmental changes by adjusting their metabolic profile.
MIGS: Methylation Interpolated Gene Signatures Determine Associations Between Differential Methylation and Gene Expression
Authors: Schlosberg Christopher E , VanderKraats Nathan D , Edwards John R 
Published: July 2016

AbstractA large number of genomic studies are underway to determine which genes are abnormally regulated by methylation in disease. However, our understanding of how disease-specific methylation changes potentially affect expression is poorly understood. We need better tools to explain specific variation in methylation that potentially affects gene expression in clinical sequencing. We have developed a model, Methylation Interpolated Gene Signatures (MIGS), that captures the complexity of DNA methylation changes around a gene promoter. Using data from the Roadmap Epigenomics Project, we show that MIGS significantly outperforms current methods to use methylation data to predict differential expression. We find that methylation changes at the TSS and downstream ~2kb are most predictive of expression change. MIGS will be an invaluable tool to analyze genome-wide methylation data as MIGS produces a longer and more accurate list of genes with methylation-associated expression changes.
Falco: A quick and flexible single-cell RNA-seq processing framework on the cloud
Authors: Yang Andrian , Troup Michael , Lin Peijie , Ho Joshua W. K. 
Published: July 2016

AbstractSummarySingle-cell RNA-seq (scRNA-seq) is increasingly used in a range of biomedical studies. Nonetheless, current RNA-seq analysis tools are not specifically designed to efficiently process scRNA-seq data due to their limited scalability. Here we introduce Falco, a cloud-based framework to enable paralellisation of existing RNA-seq processing pipelines using big data technologies of Apache Hadoop and Apache Spark for performing massively parallel analysis of large scale transcriptomic data. Using two public scRNA-seq data sets and two popular RNA-seq alignment/feature quantification pipelines, we show that the same processing pipeline runs 2.6 – 145.4 times faster using Falco than running on a highly optimised single node analysis. Falco also allows user to the utilise low-cost spot instances of Amazon Web Services (AWS), providing a 65% reduction in cost of analysis.AvailabilityFalco is available via a GNU General Public License athttps://github.com/VCCRI/Falco/Contactj.ho@victorchang.edu.auSupplementary informationSupplementary data are available atBioRXivonline.
Metabolic complementation in bacterial communities: necessary conditions and optimality
Authors: Mori Matteo , Ponce-de-León Miguel , Peretó Juli , Montero Francisco Montero 
Published: July 2016

AbstractBacterial communities may display metabolic complementation, in which different members of the association partially contribute to the same biosynthetic pathway. In this way, the end product of the pathway is synthesized by the community as a whole. However, the emergence and the benefits of such complementation are poorly understood. Herein we present a simple model to analyze the metabolic interactions among bacteria, including the host in the case of endosymbiotic bacteria. The model considers two cell populations, with both cell types encoding for the same linear biosynthetic pathway. We have found that, for metabolic complementation to emerge as an optimal strategy, both product inhibition and large permeabilities are needed. In the light of these results, we then consider the patterns found in the case of tryptophan biosynthesis in the endosymbiont consortium hosted by the aphidCinara cedri.Using in-silico computed physicochemical properties of metabolites of this and other biosynthetic pathways, we verified that the splitting point of the pathway corresponds to themost permeable intermediate.
Antibody-Based Affinity Cryo-Electron Microscopy at 2.6 Å Resolution
Authors: Yu Guimei , Li Kunpeng , Huang Pengwei , Jiang Xi , Jiang Wen 
Published: July 2016

AbstractThe affinity cryo-electron microscopy (cryo-EM) approach has been explored in recent years to simplify and improve the sample preparation for cryo-EM. Despite the demonstrated successes for low-concentration and unpurified specimens, the lack of near-atomic structures using this approach has led to a common perception of affinity cryo-EM as a niche technique incapable of reaching high resolutions. Here, we report a ~2.6 Å structure solved using the antibody-based affinity grid approach with a Tulane virus sample of low concentration. This is the first near-atomic structure solved using the affinity cryo-EM approach. Quantitative analyses of the structure indicate data and reconstruction quality comparable to conventional grid preparation method using samples at high concentration. With the shifting of bottlenecks of cryo-EM structural studies to sample grid preparation, our demonstration of the sub-3 Å capability of affinity cryo-EM approach indicates its potential in revolutionizing cryo-EM sample preparation for a broader spectrum of specimens.
Functional genetic characterization by CRISPR-Cas9 of two enhancers ofFOXP2in a child with speech and language impairment
Authors: Torres-Ruiz R. , Benitez-Burraco A. , Martínez-Lage M. , Rodríguez-Perales S. , García-Bellido P. 
Published: July 2016

ABSTRACTMutations in the coding region ofFOXP2are known to cause speech and language impairment. Microdeletions involving the region downstream the gene have been also associated to speech and cognitive deficits. We recently described a girl harbouring a complex chromosomal rearrangement with one breakpoint downstream the gene that might affect her speech and cognitive abilities via physical separation of distant regulatory DNA elements. In this study, we have used highly efficient targeted chromosomal deletions induced by the CRISPR/Cas9 genome editing tool to demonstrate the functionality of two enhancers, FOXP2-Eproximaland FOXP2-Edistal, located in the intergenic region betweenFOXP2and its adjacentMDFICgene. Deletion of any of these two functional enhancers in the neuroblastomic cell line SK-N-MC downregulatesFOXP2and decreases FOXP2 protein levels, conversely it upregulatesMDFICand increases MDFIC protein levels. This suggests that both regulatory elements may be shared betweenFOXP2andMDFIC. We expect these findings contribute to a deeper understanding of howFOXP2andMDFICare regulated to pace neuronal development supporting speech and language.
Transport efficiency of membrane-anchored kinesin-1 motors depends on motor density and diffusivity
Authors: Grover Rahul , Fischer Janine , Schwarz Friedrich W. , Walter Wilhelm J. , Schwille Petra , Diez Stefan 
Published: July 2016

AbstractIn eukaryotic cells, membranous vesicles and organelles are transported by ensembles of motor proteins. These motors, such as kinesin-1, have been well characterizedin vitroas single molecules or as ensembles rigidly attached to non-biological substrates. However, the collective transport by membrane-anchored motors, i.e. motors attached to a fluid lipid bilayer, is poorly understood. Here, we investigate the influence of motors anchorage to a lipid bilayer on the collective transport characteristics. We reconstituted ‘membrane-anchored’ gliding motility assays using truncated kinesin-1 motors with a streptavidin-binding-peptide tag that can attach to streptavidin-loaded, supported lipid bilayers. We found that the diffusing kinesin-1 motors propelled the microtubules in presence of ATP. Notably, we found the gliding velocity of the microtubules to be strongly dependent on the number of motors and their diffusivity in the lipid bilayer. The microtubule gliding velocity increased with increasing motor density and membrane viscosity, reaching up to the stepping velocity of single-motors. This finding is in contrast to conventional gliding motility assays where the density of surface-immobilized kinesin-1 motors does not influence the microtubule velocity over a wide range. We reason, that the transport efficiency of membrane-anchored motors is reduced because of their slippage in the lipid bilayer, an effect which we directly observed using singlemolecule fluorescence microscopy. Our results illustrate the importance of the motor-cargo coupling, which potentially provides cells with an additional means of regulating the efficiency of cargo transport.
YsbA and LytST are essential for pyruvate utilization in Bacillus subtilis
Authors: van den Esker Marielle H. , Kovács Ákos T. , Kuipers Oscar P. 
Published: July 2016

SummaryThe genome of Bacillus subtilis encodes homologues of the Cid/Lrg network. In other bacterial species, this network consists of holin‐ and antiholin‐like proteins that regulate cell death by controlling murein hydrolase activity. The YsbA protein of B. subtilis is currently annotated as a putative antiholin‐like protein that possibly impedes cell death, whereas YwbH is thought to act as holin‐like protein. However, the actual functions of YsbA and YwbH in B. subtilis have never been characterized. Therefore, we examined the impact of these proteins on growth and cell death in B. subtilis. We did not find a connection to the regulation of programmed cell death, but instead, our experiments reveal that YsbA and its two‐component regulator LytST are essential for growth on pyruvate. Moreover, deletion of ysbA and lytS significantly reduces pyruvate consumption. Our findings suggest that LytST induces ysbA transcription in the presence of pyruvate, and that YsbA is involved in pyruvate utilization presumably by functioning as pyruvate uptake system. We show that B. subtilis excretes pyruvate as overflow metabolite in rich medium, indicating that pyruvate could be a common nutrient in the environment. Hence, YsbA and LytST might play a major role in environmental growth of B. subtilis.
Nomadic lifestyle of Lactobacillus plantarum revealed by comparative genomics of 54 strains isolated from different habitats
Authors: Martino Maria Elena , Bayjanov Jumamurat R. , Caffrey Brian E. , Wels Michiel , Joncour Pauline , Hughes Sandrine , Gillet Benjamin , Kleerebezem Michiel , van Hijum Sacha A.F.T. , Leulier François 
Published: July 2016

SummaryThe ability of bacteria to adapt to diverse environmental conditions is well‐known. The process of bacterial adaptation to a niche has been linked to large changes in the genome content, showing that many bacterial genomes reflect the constraints imposed by their habitat. However, some highly versatile bacteria are found in diverse habitats that almost share nothing in common. Lactobacillus plantarum is a lactic acid bacterium that is found in a large variety of habitat. With the aim of unravelling the link between evolution and ecological versatility of L. plantarum, we analysed the genomes of 54 L. plantarum strains isolated from different environments. Comparative genome analysis identified a high level of genomic diversity and plasticity among the strains analysed. Phylogenomic and functional divergence studies coupled with gene–trait matching analyses revealed a mixed distribution of the strains, which was uncoupled from their environmental origin. Our findings revealed the absence of specific genomic signatures marking adaptations of L. plantarum towards the diverse habitats it is associated with. This suggests fundamentally similar trends of genome evolution in L. plantarum, which occur in a manner that is apparently uncoupled from ecological constraint and reflects the nomadic lifestyle of this species.
Oxidation of urea‐derived nitrogen by thaumarchaeota‐dominated marine nitrifying communities
Authors: Tolar Bradley B. , Wallsgrove Natalie J. , Popp Brian N. , Hollibaugh James T. 
Published: July 2016

SummaryUrea nitrogen has been proposed to contribute significantly to nitrification by marine thaumarchaeotes. These inferences are based on distributions of thaumarchaeote urease genes rather than activity measurements. We found that ammonia oxidation rates were always higher than oxidation rates of urea‐derived N in samples from coastal Georgia, USA (means ± SEM: 382 ± 35 versus 73 ± 24 nmol L−1 d−1, Mann‐Whitney U‐test p < 0.0001), and the South Atlantic Bight (20 ± 8.8 versus 2.2 ± 1.7 nmol L−1 d−1, p = 0.026) but not the Gulf of Alaska (8.8 ± 4.0 versus 1.5 ± 0.6, p > 0.05). Urea‐derived N was relatively more important in samples from Antarctic continental shelf waters, though the difference was not statistically significant (19.4 ± 4.8 versus 12.0 ± 2.7 nmol L−1 d−1, p > 0.05). We found only weak correlations between oxidation rates of urea‐derived N and the abundance or transcription of putative Thaumarchaeota ureC genes. Dependence on urea‐derived N does not appear to be directly related to pH or ammonium concentrations. Competition experiments and release of 15NH3 suggest that urea is hydrolyzed to ammonia intracellularly, then a portion is lost to the dissolved pool. The contribution of urea‐derived N to nitrification appears to be minor in temperate coastal waters, but may represent a significant portion of the nitrification flux in Antarctic coastal waters.
Candidate gene analysis of osteochondrosis inSpanishPurebred horses
Authors: Sevane N. , Dunner S. , Boado A. , Cañon J. 
Published: July 2016

SummaryEquine osteochondrosis (OC) is a frequent developmental orthopaedic disease with high economic impact on the equine industry and may lead to premature retirement of the animal as a result of chronic pain and lameness. The genetic background ofOCincludes different genes affecting several locations; however, these genetic associations have been tested in only one or few populations, lacking the validation in others. The aim of this study was to identify the genetic determinants ofOCin theSpanishPurebred horse breed. For that purpose, we used a candidate gene approach to study the association between loci previously implicated in the onset and development ofOCin other breeds and differentOClocations using radiographic data from 144 individuals belonging to the Spanish Purebred horse breed. Of the 48 polymorphisms analysed, three single nucleotide polymorphisms (SNPs) located in theFAF1,FCN3andCOL1A2genes were found to be associated with different locations ofOClesions. These data contribute insights into the complex gene networks underlying the multifactorial diseaseOC, and the associatedSNPs could be used in a marker‐assisted selection strategy to improve horse health, welfare and competitive lifespan.