bluuebunny/crossref_metadata_2025_split huggingface dataset:
Electrophysiological Assessment and Classification of Motor Pathway Function in Patients With Spinal Dural Arteriovenous Fistula
Authors: Nakanishi Kazuyoshi , Tanaka Nobuhiro , Fujimoto Yoshinori , Nishikawa Koichiro , Kamei Naosuke , Nakamae Toshio , Kotaka Shinji , Adachi Nobuo 
Published: October 2018

Purpose:
The diagnosis of spinal dural arteriovenous fistula (SDAVF) is difficult and often delayed because clinical features are often nonspecific. We assessed the motor function electrophysiologically in patients with SDAVF.

Methods:
Motor-evoked potentials after transcranial magnetic stimulation and compound muscle action potentials and F-waves after electrical stimulation in the ulnar and tibial nerves were measured from the abductor hallucis (AH) muscles in 14 patients with SDAVF (SDAVF group), 12 patients with compressive thoracic myelopathy (CTM group), and 16 normal subjects (control group). The peripheral conduction time determined from abductor hallucis muscles (PCT-AH) and the central motor conduction time determined from abductor hallucis muscles (CMCT-AH) were calculated. According to the neurological findings, patients in the SDAVF group were classified to upper motor neuron (UMN) sign and lower motor neuron (LMN) sign categories.

Results:
CMCT-AH in the SDAVF and CMT groups were significantly longer than those in the control group. PCT-AH in the SDAVF group was significantly longer than that in the control and CMT groups. Twelve patients in the SDAVF group showed abnormal CMCT-AH and/or PCT-AH. Abnormal CMCT-AH and PCT-AH were detected in five cases that exhibited UMN sign and/or LMN sign. Three cases with abnormal CMCT-AH and normal PCT-AH exhibited UMN sign. LMN sign without UMN sign was observed in four cases with abnormal PCT-AH and normal CMCT-AH.

Conclusions:
Our study revealed abnormalities in the corticospinal tract and/or lower motor neurons, and classified the patients with SDAVF into three types: the UMN type, LMN type, and mixed type.
Adaptive walks on high-dimensional fitness landscapes and seascapes with distance-dependent statistics
Authors: Agarwala Atish , Fisher Daniel S. 
Published: October 2018

AbstractThe dynamics of evolution is intimately shaped by epistasis — interactions between genetic elements which cause the fitness-effect of combinations of mutations to be non-additive. Analyzing evolutionary dynamics that involves large numbers of epistatic mutations is intrinsically difficult. A crucial feature is that the fitness landscape in the vicinity of the current genome depends on the evolutionary history. A key step is thus developing models that enable study of the effects of past evolution on future evolution. In this work, we introduce a broad class of high-dimensional random fitness landscapes for which the correlations between fitnesses of genomes are a general function of genetic distance. Their Gaussian character allows for tractable computational as well as analytic understanding. We study the properties of these landscapes focusing on the simplest evolutionary process: random adaptive (uphill) walks. Conventional measures of “ruggedness” are shown to not much affect such adaptive walks. Instead, the long-distance statistics of epistasis cause all properties to be highly conditional on past evolution, determining the statistics of the local landscape (the distribution of fitness-effects of available mutations and combinations of these), as well as the global geometry of evolutionary trajectories. In order to further explore the effects of conditioning on past evolution, we model the effects of slowly changing environments. At long times, such fitness “seascapes” cause a statistical steady state with highly intermittent evolutionary dynamics: populations undergo bursts of rapid adaptation, interspersed with periods in which adaptive mutations are rare and the population waits for more new directions to be opened up by changes in the environment. Finally, we discuss prospects for studying more complex evolutionary dynamics and on broader classes of high-dimensional landscapes and seascapes.
What drives mortality among HIV patients in a conflict setting? A prospective cohort study in the Central African Republic
Authors: Crellen Thomas , Ssonko Charles , Piening Turid , Simaleko Marcel Mbeko , St. Calvaire Diemer Henri , Gieger Karen , Siddiqui M. Ruby 
Published: October 2018

AbstractBackgroundProvision of antiretroviral therapy (ART) during conflict settings is rarely attempted and little is known about the expected patterns of mortality. The Central African Republic (CAR) continues to have a low coverage of ART despite an estimated 120,000 people living with HIV and 11,000 AIDS-related deaths in 2013. We present results from a cohort in Zemio, Haut-Mboumou prefecture. This region had the highest prevalence of HIV nationally (14.8% in 2010) and was subject to repeated attacks by armed groups on civilians during the observed period.MethodsConflict from armed groups can impact cohort mortality rates i) directly if HIV patients are victims of armed conflict, or ii) indirectly if population displacement or fear of movement reduces access to ART. Using monthly counts of civilian deaths, injuries and abductions, we estimated the impact of the conflict on patient mortality. We also determine patient-level risk factors for mortality and how this varies with time spent in the cohort. Model-fitting was performed in a Bayesian framework, using generalised-linear models with terms accounting for temporal autocorrelation.ResultsPatients were recruited and observed from October 2011 to May 2017. Overall 1631 patients were enrolled, giving 4107 person-years and 148 deaths. Our first model shows that patient mortality did not increase during periods of heightened conflict. The monthly risk (probability) of mortality was markedly higher at the beginning of the program (0.047 in November 2011 [95% credible interval; CrI 0.0078, 0.21]) and had declined greater than ten-fold by the end of the observed period (0.0016 in June 2017 [95% CrI 0.00042, 0.0036]). Our second model shows the risk of mortality for individual patients was highest in the first five months spent in the cohort. Male sex was associated with a higher mortality (odds ratio; OR 1.7 [95% CrI 1.2, 2.8]) along with the severity of opportunistic infections at baseline.ConclusionsOur results show that chronic conflict did not appear to adversely affect rates of mortality in this cohort, and that mortality was driven predominantly by patient specific risk factors. In areas initiating ART for the first time, particular attention should be focussed on stabilising patients with advanced symptoms.FundingMédecins Sans Frontières
Fast, volumetric live-cell imaging using high-resolution light-field microscopy
Authors: Li Haoyu , Guo Changliang , Kim-Holzapfel Deborah , Li Weiyi , Altshuller Yelena , Schroeder Bryce , Liu Wenhao , Meng Yizhi , French Jarrod B. , Takamaru Ken-Ichi , Frohman Michael A. , Jia Shu 
Published: October 2018

AbstractVisualizing diverse anatomical and functional traits that span many spatial scales with high spatio-temporal resolution provides insights into the fundamentals of living organisms. Light-field microscopy (LFM) has recently emerged as a scanning-free, scalable method that allows for high-speed, volumetric functional brain imaging. Given those promising applications at the tissue level, at its other extreme, this highly-scalable approach holds great potential for observing structures and dynamics in single-cell specimens. However, the challenge remains for current LFM to achieve subcellular level, near-diffraction-limited 3D spatial resolution. Here, we report high-resolution LFM (HR-LFM) for live-cell imaging with a resolution of 300-700 nm in all three dimensions, an imaging depth of several micrometers, and a volume acquisition time of milliseconds. We demonstrate the technique by imaging various cellular dynamics and structures and tracking single particles. The method may advance LFM as a particularly useful tool for understanding biological systems at multiple spatio-temporal levels.
Bioorthogonal antigens allow the unbiased study of antigen processing and presentation
Authors: Araman Can , Pieper-Pournara Linda , van Leeuwen Tyrza , Kampstra Arieke S. B. , Bakkum Thomas , Marqvorsen Mikkel H. S. , Nascimento Clarissa R. , Mirjam Groenewold G. J. , van der Wulp Willemijn , Camps Marcel G. M. , Overkleeft Herman S. , Ossendorp Ferry A. , Toes René E. M. , van Kasteren Sander I. 
Published: October 2018

AbstractProteolysis is fundamental to many biological processes. In the immune system, it underpins the activation of the adaptive immune response: degradation of antigenic material into short peptides and presentation thereof on major histocompatibility complexes, leads to activation of T-cells. This initiates the adaptive immune response against many pathogens.
An inexpensive air stream temperature controller and its use to facilitate temperature controlled behavior in livingDrosophila
Authors: Sangston Ryan , Hirsh Jay 
Published: October 2018

AbstractControlling the environment of an organism has many biologically relevant applications. Temperature-dependent inducible biological reagents have proven invaluable for elucidating signaling cascades and dissection of neural circuits. Here we develop a simple and affordable system for rapidly changing temperature in a chamber housing adultDrosophilamelanogaster. Utilizing flies expressing the temperature inducible channel dTrpA1 in dopaminergic neurons, we show rapid and reproducible changes in locomotor behavior. This device should have wide application to temperature modulated biological reagents.Method SummaryWe develop widely applicable and affordable solution to rapidly changing temperature within an enclosed chamber using commercially available components.
The influence of molecular reach and diffusivity on the efficacy of membrane-confined reactions
Authors: Zhang Ying , Clemens Lara , Goyette Jesse , Allard Jun , Dushek Omer , Isaacson Samuel. A. 
Published: October 2018

AbstractSignalling by surface receptors often relies on tethered reactions whereby an enzyme bound to the cytoplasmic tail of a receptor catalyses reactions on substrates within reach. The overall length and stiffness of the receptor tail, the enzyme, and the substrate determine a biophysical parameter termed the molecular reach of the reaction. This parameter determines the probability that the receptor-tethered-enzyme will contact the substrate, in the volume proximal to the membrane, when separated by different distances within the membrane plane. In this work we develop particle-based stochastic reaction-diffusion models to study the interplay between molecular reach and diffusion. We find that increasing the molecular reach can increase reaction efficacy for slowly diffusing receptors, while for rapidly diffusing receptors increasing molecular reach reduces reaction efficacy. In contrast, if reactions are forced to take place within the 2D plasma membrane instead of the 3D volume proximal to it, or if molecules diffuse in 3D, increasing molecular reach increases reaction efficacy for all diffusivities. We show results in the context of immune checkpoint receptors (PD-1 dephosphorylating CD28), a standard opposing kinase-phosphatase reaction, and a minimal two-particle model. The work highlights the importance of the 3D nature of many 2D membrane-confined interactions, illustrating a role for molecular reach in controlling biochemical reactions.
Multi-allele species reconstruction using ASTRAL
Authors: Rabiee Maryam , Sayyari Erfan , Mirarab Siavash 
Published: October 2018

AbstractGenome-wide phylogeny reconstruction is becoming increasingly common, and one driving factor behind these phylogenomic studies is the promise that the potential discordance between gene trees and the species tree can be modeled. Incomplete lineage sorting is one cause of discordance that bridges population genetic and phylogenetic processes. ASTRAL is a species tree reconstruction method that seeks to find the tree with minimum quartet distance to an input set of inferred gene trees. However, the published ASTRAL algorithm only works with one sample per species. To account for polymorphisms in present-day species, one can sample multiple individuals per species to create multi-allele datasets. Here, we introduce how ASTRAL can handle multi-allele datasets. We show that the quartet-based optimization problem extends naturally, and we introduce heuristic methods for building the search space specifically for the case of multi-individual datasets. We study the accuracy and scalability of the multi-individual version of ASTRAL-III using extensive simulation studies and compare it to NJst, the only other scalable method that can handle these datasets. We do not find strong evidence that using multiple individuals dramatically improves accuracy. When we study the trade-off between sampling more genes versus more individuals, we find that sampling more genes is more effective than sampling more individuals, even under conditions that we study where trees are shallow (median length: ≈ 1Ne) and ILS is extremely high.
A phylum-wide survey reveals multiple independent gains of head regeneration ability in Nemertea
Authors: Zattara Eduardo E. , Fernández-Álvarez Fernando A. , Hiebert Terra C. , Bely Alexandra E. , Norenburg Jon L. 
Published: October 2018

AbstractAnimals vary widely in their ability to regenerate, suggesting that regenerative abilities have a rich evolutionary history. However, our understanding of this history remains limited because regeneration ability has only been evaluated in a tiny fraction of species. Available comparative regeneration studies have identified losses of regenerative ability, yet clear documentation of gains is lacking. We surveyed regenerative ability in 34 species spanning the phylum Nemertea, assessing the ability to regenerate heads and tails either through our own experiments or from literature reports. Our sampling included representatives of the 10 most diverse families and all three orders comprising this phylum. We generated a phylogenetic framework using sequence data to reconstruct the evolutionary history of head and tail regeneration ability across the phylum and found that while all evaluated species can remake a posterior end, surprisingly few could regenerate a complete head. Our analysis reconstructs a nemertean ancestor unable to regenerate a head and indicates at least four separate lineages have independently gained head regeneration ability, one such gains reconstructed as taking place within the last 10-15 mya. Our study highlights nemerteans as a valuable group for studying evolution of regeneration and identifying mechanisms associated with repeated gains of regenerative ability.
Crop Information Engine and Research Assistant (CIERA) for managing genealogy, phenotypic and genotypic data for breeding programs
Authors: Yates Shawn , Lagüe Martin , Knox Ron , Cuthbert Richard , Clarke Fran , Clarke John , Ruan Yuefeng , Sangha Jatinder , Bhadauria Vijai 
Published: October 2018

AbstractBackgroundWith the advent of next-generation marker platforms and phenomics in crop breeding programs, the volume of both the genotypic and phenotypic data produced has increased exponentially. Often the data remain underutilized if not properly collated, managed and accessed. Effective management of the data is paramount to making sound and timely decision on cross planning in order to accelerate genetic gain (ΔG) in crops for disease resistance, agronomic and end-use quality traits.ResultsTo address the challenges in managing and efficient utilization of the sheer volume of data generated in a crop breeding program, we developed an electronic information system called the Crop Information Engine and Research Assistant (CIERA). The CIERA, written in Visual Basic, runs on the Microsoft Windows operating system and requires the .Net Framework 4.7 as well as the MySQL Community Server 5.7. The highly intuitive graphical user interface of CIERA includes user-friendly query tools to facilitate the collation of data across relevant phenotypic environments from its phenotypic data management database and can combine that information with the genealogy and genetic data from its genealogy management and genetic data management databases, respectively.ConclusionsUsing CIERA, breeders can build a comprehensive profile of germplasm, within a few minutes, to assist them in planning crosses for enhancing genetic gain by selecting superior lines for crosses.
Differential Metabolic and Multi-tissue Transcriptomic Responses to Fructose Consumption among Genetically Diverse Mice
Authors: Zhang Guanglin , Byun Hyae Ran , Ying Zhe , Blencowe Montgomery , Zhao Yuqi , Hong Jason , Shu Le , Krishnan Karthick Chella , Gomez-Pinilla Fernando , Yang Xia 
Published: October 2018

AbstractHigh fructose intake is a major risk for metabolic syndrome; however, its effects seem to vary across individuals. To determine main factors involved in the inter-individual responses to fructose, we fed inbred mouse strains C57BL/6J (B6), DBA/2J (DBA) and FVB/NJ (FVB) with fructose. DBA mice showed the highest susceptibility to gain adiposity and glucose intolerance. Elevated insulin was found in DBA and FVB mice, and cholesterol levels were uniquely elevated in B6 mice. The transcriptional profiles of liver, hypothalamus, and adipose tissues showed strain- and tissue-specific pathways altered by fructose, such as fatty acid and cholesterol pathways for B6 and PPAR signaling for DBA in liver, and oxidative phosphorylation for B6 and protein processing for DBA in hypothalamus. Using network modeling, we predicted potential strain-specific key regulators of fructose response such as Fgf21 (DBA) and Lss (B6) in liver, and validated strain-biased responses as well as the regulatory actions of Fgf21 and Lss in primary hepatocytes. Our findings support that fructose perturbs individualized tissue networks and pathways and associates with distinct features of metabolic dysfunctions across genetically diverse mice. Our results elucidate the molecular pathways and gene regulatory mechanisms underlying inter-individual variability in response to high fructose diet.
Microbial contamination screening and interpretation for biological laboratory environments
Authors: Li Xi , Zhu Xue , Wang Wenjie , Ning Kang 
Published: October 2018

AbstractAdvances in microbiome researches have led us to the realization that the composition of microbial communities of indoor environment is profoundly affected by the function of buildings, and in turn may bring detrimental effects to the indoor environment and the occupants. Thus investigation is warranted for a deeper understanding of the potential impact of the indoor microbial communities. Among these environments, the biological laboratories stand out because they are relatively clean and yet are highly susceptible to microbial contaminants. In this study, we assessed the microbial compositions of samples from the surfaces of various sites across different types of biological laboratories. We have qualitatively and quantitatively assessed these possible microbial contaminants, and found distinct differences in their microbial community composition. We also found that the type of laboratories has a larger influence than the sampling site in shaping the microbial community, in terms of both structure and richness. On the other hand, the public areas of the different types of laboratories share very similar sets of microbes. Tracing the main sources of these microbes, we identified both environmental and human factors that are important factors in shaping the diversity and dynamics of these possible microbial contaminations in biological laboratories. These possible microbial contaminants that we have identified will be helpful for people who aim to eliminate them from samples.ImportanceMicrobial communities from biological laboratories might hamper the conduction of molecular biology experiments, yet these possible contaminations are not yet carefully investigated. In this work, a metagenomic approach has been applied to identify the possible microbial contaminants and their sources, from the surfaces of various sites across different types of biological laboratories. We have found distinct differences in their microbial community compositions. We have also identified the main sources of these microbes, as well as important factors in shaping the diversity and dynamics of these possible microbial contaminations. The identification and interpretation of these possible microbial contaminants in biological laboratories would be helpful for alleviate their potential detrimental effects.
Comparative whole-genome analysis reveals genetic adaptation of the invasive pinewood nematode
Authors: Li Jiarui , Cheng Xinyue , Lin Runmao , Xiao Shijun , Yi Xinxin , Mao Zhenchuan , Zhang Xi , Ling Jian , Kou Xiaojun , Yan Xia , Luo Ji , Cheng Feixue , Li Yilong , Wang Laifa , Chen Nansheng , Xie Bingyan 
Published: October 2018

AbstractGenetic adaptation to new environments is essential for invasive species. To explore the genetic underpinnings of invasiveness of a dangerous invasive species, the pinewood nematode (PWN)Bursaphelenchus xylophilus, we analysed the genome-wide variations of a large cohort of 55 strains isolated from both the native and introduced regions. Comparative analysis showed abundant genetic diversity existing in the nematode, especially in the native populations. Phylogenetic relationships and principal component analysis indicate a dominant invasive population/group (DIG) existing in China and expansion beyond, with few genomic variations. Putative origin and migration paths at a global scale were traced by targeted analysis of rDNA sequences. A progressive loss of genetic diversity was observed along spread routes. We focused on variations with a low frequency allele (<50%) in the native USA population but fixation in DIG, and a total of 25,992 single nuclear polymorphisms (SNPs) were screened out. We found that a clear majority of these fixation alleles originated from standing variation. Functional annotation of these SNP-harboured genes showed that adaptation-related genes are abundant, such as genes that encode for chemoreceptors, proteases, detoxification enzymes, and proteins involved in signal transduction and in response to stresses and stimuli. Some genes under positive selection were predicted. Our results suggest that adaptability to new environments plays essentially roles in PWN invasiveness. Genetic drift, mutation and strong selection drive the nematode to rapidly evolve in adaptation to new environments, which including local pine hosts, vector beetles, commensal microflora and other new environmental factors, during invasion process.