bluuebunny/crossref_metadata_2025_split huggingface dataset:
Neuroimaging of brain trauma
Authors: Douglas David B. , Muldermans Jonathan L. , Wintermark Max 
Published: June 2018

Purpose of review
The purpose of this review is to provide an update on advanced neuroimaging techniques in traumatic brain injury (TBI). We will focus this review on recent literature published within the last 18 months and the advanced neuroimaging techniques of perfusion imaging and diffusion tensor imaging (DTI).

Recent findings
In the setting of a moderate or severe acute closed head injury (Glasgow Coma Scale <13), the most appropriate neuroimaging study is a noncontrast computed tomography (CT) scan. In the setting of mild TBI, the indication for neuroimaging can be determined using the New Orleans Criteria or Canadian CT Head Rules or National Emergency X-Ray Utilization Study-II clinical criteria. Two advanced neuroimaging techniques that are currently being researched in TBI include perfusion imaging and DTI. Perfusion CT has a higher sensitivity for detecting cerebral contusions than noncontrast CT examinations. DTI is a sensitive at detecting TBI at the group level (TBI-group versus control group), but there is insufficient evidence to suggest that DTI plays a clinical role for diagnosing mild TBI at the individual patient level.

Summary
Future research in advanced neuroimaging techniques including perfusion imaging and DTI may improve the accuracy of the diagnosis and prognosis as well as improve the management of TBI.
Defining the seafloor microbiome of the Gulf of Mexico and its response to oil perturbation
Authors: Overholt Will A. , Schwing Patrick , Raz Kala M. , Hastings David , Hollander David J. , Kostka Joel E. 
Published: June 2018

AbstractThe microbial ecology of oligotrophic deep ocean sediments is understudied relative to their shallow counterparts, and this lack of understanding hampers our ability to predict responses to current and future perturbations. The Gulf of Mexico has experienced two of the largest accidental marine oil spills, the 1979 Ixtoc-1 blowout and the 2010 Deepwater Horizon (DWH) discharge. Here, microbial communities were characterized for 29 sites across multiple years in >700 samples. The composition of the seafloor microbiome was broadly consistent across the region and was well approximated by the overlying water depth and depth within the sediment column, while geographic distance played a limited role. Biogeographical distributions were employed to generate predictive models for over 4000 OTU that leverage easy-to-obtain geospatial variables which are linked to measured sedimentary oxygen profiles. Depth stratification and putative niche diversification are evidenced by the distribution of taxa that mediate the microbial nitrogen cycle. Further, these results demonstrate that sediments impacted by the DWH spill had returned to near baseline conditions after two years. The distributions of benthic microorganisms in the Gulf can be constrained, and moreover deviations from these predictions may pinpoint impacted sites and aid in future response efforts or long-term stability studies.
Mass Mortality of Wood Frogs (Rana sylvatica) in the Ozark National Forest: Is it Acid Rain?
Authors: McCallum Malcolm L. , Klotz Tracy , Stephens William , Bouldin Jennifer , Gillespie Ken , Feldman David , Wheeler Benjamin A. , Trauth Stanley E. 
Published: June 2018

AbstractWe describe observations of a continuing mass mortality event primarily involving wood frogs, but involving other amphibians to a lesser degree. The investigation took place from Spring 2000 through Spring 2004. No definitive correlations between environmental variables and mortality could be identified. Forensic analysis could not isolate causal pathogens. Although mortality fluctuated during the study, it may have spread to other species. Our report identifies population level problems in the eastern part of the Ozark National Forest but is unable to identify a cause. Future studies that more thoroughly address contaminants, pathogens/parasites, and other potential environmental problems in the Ozark National Forest are warranted.
Molecular tools for phytoplankton monitoring samples
Authors: Frazão Bárbara , Silva Alexandra 
Published: June 2018

AbstractHABs can have severe impacts in fisheries or human health by the consumption of contaminated bivalves. Monitoring assessment (quantitative and qualitative identification) of these organisms, is routinely accomplished by microscopic identification and counting of these organisms. Nonetheless, molecular biology techniques are gaining relevance, once these approaches can easily identify phytoplankton organisms at species level and even cell number quantifications. This work tests 12 methods/kits for genomic DNA extraction and seven DNA polymerases to determine which is the best method for routinely use in a common molecular laboratory, for phytoplankton monitoring samples analyses. From our work, Direct PCR master mix for tissue samples, proved to be the most adequate by its velocity of processivity, practicability, reproducibility, sensitiveness and robustness. However, brands such as Omega Biotek, GRISP, Qiagen and MP Biomedicals also showed good results for conventional DNA extraction as well as all the Taq brands tested (GRISP, GE Healthcare Life Sciences, ThermoFisher Scientific and Promega). Lugol’s solution, with our tested kits did not show negative interference in DNA amplification. The same can be said about mechanical digestion, with no significant differences among kits with or without this homogenization step.
Transmission cycles generate diversity in pathogenic viruses
Authors: Sigal Daniel , Reid J.N.S. , Wahl L.M. 
Published: June 2018

AbstractWe investigate the fate ofde novomutations that occur during the in-host replication of a pathogenic virus, predicting the probability that such mutations are passed on during disease transmission to a new host. Using influenza A virus as a model organism, we develop a life-history model of the within-host dynamics of the infection, using a multitype branching process with a coupled deterministic model to capture the population of available target cells. We quantify the fate of neutral mutations and mutations affecting five life-history traits: clearance, attachment, budding, cell death, and eclipse phase timing. Despite the severity of disease transmission bottlenecks, our results suggest that in a single transmission event, several mutations that appearedde novoin the donor are likely to be transmitted to the recipient. Even in the absence of a selective advantage for these mutations, the sustained growth phase inherent in each disease transmission cycle generates genetic diversity that is not eliminated during the transmission bottleneck.
Differential Expression of Immune Related Genes in Taste Buds of Fed and Fasted Mice
Authors: Crosson SM , Currlin S , Moskalenko O , Yegorova S , Dotson CD , Zolotukhin S 
Published: June 2018

AbstractTo study the effects of feeding on taste receptor cell transcriptional regulation, we performed RNA-seq analysis of circumvallate taste buds isolated from mice before or after food consumption. Here we report and compare the taste bud transcriptomes obtained from food-deprived, satiated, and ad libitum fed control mice. Despite sample heterogeneity inherent to the whole taste bud transcriptome, bioinformatics analysis yielded 144 differentially expressed transcripts associated with immunity, cytoskeletal structure, and protein folding between these groups. We also profiled the transcriptome obtained from ad libitum fed control mice based on receptor related gene ontology terms, demonstrating a use of this dataset in the identification of novel TRC receptors. The data presented here suggest that transcriptional regulation of immune cytokine signaling occurs in TRCs shortly after meal consumption, though additional analysis is required to confirm this hypothesis.
Effect of mounding, drainage and fertilization on CH4 fluxes and methane-cycling functional genes in waterlogged forest stands
Authors: Levy-Booth David J. , Prescott Cindy E. , Grayston Susan J. 
Published: June 2018

AbstractSite preparation techniques including mounding, drainage and nitrogen (N) fertilization can enhance seedling survival and site productivity, particularly in waterlogged, low-productivity forest stands. However, practices that alter soil conditions and site hydrology can lead to the unintended alteration of biogeochemical process rates, such as CH4 fluxes. This study sought to measure CH4 fluxes measured using static closed chambers at a sub-boreal spruce site and a coastal cedar-hemlock site that underwent mounding and drainage, respectively, to manipulate water table depth relative to planted seedlings, as well as fertilization. The abundance of methyl coenzyme M reductase (mcrA) gene found in methanogenic archaea and the particulate methane monooxygenase (pmoA) gene found in methane-oxidizing bacteria (MOB) were examined. The use of sulphate as a potential method to stimulate sulphate-reducing bacteria (SRB) and reduce methanogen activity was also investigated using the dissimilatory sulfite reductase β-subunit (dsrB) gene. qPCR was used to link mcrA,pmoA and dsrB gene abundance to soil factors and GHG fluxes. Mounding created hot-spots of CH4 emissions at the spruce site. Drainage improved soil aeration at the coastal cedar-hemlock site and reduced CH4 emission rates. Fertilization did not affect CH4 emissions from either site. CH4 rates were influenced by soil water content and mcrA abundance. Measurements of microbial functional genes can elucidate the effects of site preparation on GHG fluxes in waterlogged forest stands.
Pinetree: a step-wise gene expression simulator with codon-specific translation rates
Authors: Jack Benjamin R. , Wilke Claus O. 
Published: June 2018

AbstractMotivationStochastic gene expression simulations often assume steady-state transcript levels, or they model transcription in more detail than translation. Moreover, they lack accessible programming interfaces, which limits their utility.ResultsWe present Pinetree, a step-wise gene expression simulator with codon-specific translation rates. Pinetree models both transcription and translation in a stochastic framework with individual polymerase and ribosome-level detail. Written in C++ with a Python front-end, any user familiar with Python can specify a genome and simulate gene expression. Pinetree was designed to be efficient and scale to simulate large plasmids or viral genomes.AvailabilityPinetree is available on GitHub (https://github.com/benjaminjack/pinetree) and the Python Package Index (https://pypi.org/project/pinetree/).
Associations between Afrotropical bats, parasites, and microbial symbionts
Authors: Lutz Holly L. , Jackson Elliot W. , Dick Carl W. , Webala Paul W. , Babyesiza Waswa S. , Kerbis Peterhans Julian C. , Demos Terrence C. , Patterson Bruce D. , Gilbert Jack A. 
Published: June 2018

ABSTRACTBats are among the most diverse animals on the planet and harbor numerous bacterial, viral, and eukaryotic symbionts. The interplay between bacterial community composition and parasitism in bats is not well understood and may have important implications for studies of similar systems. Here we present a comprehensive survey of dipteran and haemosporidian parasites, and characterize the gut, oral, and skin microbiota of Afrotropical bats. We identify significant correlations between bacterial community composition of the skin and dipteran ectoparasite prevalence across four major bat lineages, as well as links between the oral microbiome and malarial parasitism, suggesting a potential mechanism for host selection and vector-borne disease transmission in bats. In contrast to recent studies of host-microbe phylosymbiosis in mammals, we find no correlation between chiropteran phylogenetic distances and bacterial community dissimilarity across the three anatomical sites, suggesting that host environment is more important than shared ancestry in shaping the composition of bat-associated bacterial communities.SIGNIFICANCEAnimals rely on bacterial symbionts for numerous biological functions, such as digestion and immune system development. Increasing evidence suggests that host-associated microbes may play a role in mediating parasite burden. This study is the first to provide a comprehensive survey of bacterial symbionts from multiple anatomical sites across a broad taxonomic range of Afrotropical bats, demonstrating significant associations between the bat microbiome and parasite prevalence. This study provides a framework for future approaches to systems biology of host-symbiont interactions across broad taxonomic scales, emphasizing the interdependence between microbial symbionts and vertebrate health in the study of wild organisms and their natural history.
Characterisation and structure determination of a llama-derived nanobody targeting the J-base binding protein 1
Authors: Van Beusekom Bart , Heidebrecht Tatjana , Adamopoulos Athanassios , Fish Alexander , Pardon Els , Steyaert Jan , Joosten Robbie P. , Perrakis Anastassis 
Published: June 2018

AbstractThe J-base Binding Protein 1 (JBP1) contributes to biosynthesis and maintenance of base J (β-D-glucosyl-hydroxymethyluracil), a modification of thymidine confined to some protozoa. Camelid (llama) single domain antibody fragments (nanobodies) targeting JBP1 were produced for use as crystallization chaperones. Surface plasmon resonance (SPR) screening identified Nb6 as a strong binder, recognising JBP1 with a 1:1 stoichiometry and high affinity (kD=30nM). Crystallisation trials of JBP1 in complex with Nb6, yielded crystals diffracting to 1.47Å resolution.However, the asymmetric unit dimensions and molecular replacement with a nanobody structure, clearly showed that the crystals of the expected complex with JBP1 were of the nanobody alone. Nb6 crystallizes in spacegroup P31 with two molecules in the asymmetric unit; its crystal structure was refined to a final resolution of 1.64Å. Ensemble refinement suggests that on the ligand-free state one of the complementarity determining regions (CDRs) is flexible while the other two adopt well-defined conformations.SynopsisA camelid single domain antibody fragment (nanobody) is shown to have high affinity towards its recognition target, the J-base binding protein 1 (JBP1). The serendipitous crystallisation of this nanobody alone, and its crystal structure solution and refinement to 1.64Å resolution are described. Ensemble refinement suggests that on the ligand-free state one of the complementarity determining regions (CDRs) is flexible while the other two adopt well-defined conformations.
Diverse lineages ofCandida albicanslive on old oaks
Authors: Bensasson Douda , Dicks Jo , Ludwig John M. , Bond Christopher J. , Elliston Adam , Roberts Ian N. , James Stephen A. 
Published: June 2018

AbstractThe human pathogen,Candida albicans, is considered an obligate commensal of animals, yet it is occasionally isolated from trees, shrubs and grass. We generated deep genome sequence data for three strains ofC. albicansthat we isolated from oak trees in an ancient wood-pasture, and compared these to the genomes of the type strain and 21 other clinical strains.C. albicansstrains from oak are similar to clinicalC. albicansin that they are predominantly diploid and can become naturally homozygous at the mating locus through whole-chromosome loss of heterozygosity (LOH). LOH regions in all genomes arose recently suggesting that LOH mutations usually occur transiently inC. albicanspopulations. Oak strains differed from clinical strains in showing less LOH, and higher levels of heterozygosity genome-wide. Using phylogenomic analyses,in silicochromosome painting, and comparisons with thousands moreC. albicansstrains at seven loci, we show that each oak strain is more closely related to strains from humans and other animals than to strains from other oaks. Therefore, the isolation ofC. albicansfrom oak is not easily explained as contamination from a single animal source. The high heterozygosity of oak strains could arise as a result of reduced mitotic recombination in asexual lineages, recent parasexual reproduction or because of natural selection. Regardless of mechanism, the diversity ofC. albicanson oaks implies that they have lived in this environment long enough for genetic differences from clinical strains to arise.
Tobacco TGA7 mediates gene expression dependent and independent of salicylic acid
Authors: Stos-Zweifel Vlatka , Neeley David , Konopka Evelyn , Meissner Meike , Hermann Meike , Maier Felix , Häfner Verena , Pfitzner Artur J.P. , Pfitzner Ursula M. 
Published: June 2018

ABSTRACTBasic region leucine zipper (bZIP) transcription factors of the TGA family control gene expression in response to diverse stimuli. Arabidopsis clade II and clade III TGA factors mediate salicylic acid (SA)-induced expression of PATHOGENESIS-RELATED GENE1 (PR-1) via interplay with NONEXPRESSOR OF PR GENES1 (NPR1, a.k.a. NIM1). Interaction with TGA factors occurs through the central ankyrin repeat domain of NPR1. In a yeast two-hybrid screen with the NPR1 bait, we identified TGA7, a novel member of the tobacco (Nt) TGA family grouping to clade III. TGA7 is most similar to NtTGA1a, and, like NtTGA1a, TGA7 displays transcription activity in yeast. Unexpectedly, TGA7 preferentially and uniquely interacts with the SA-sensitive C-terminal region of NtNPR1, demonstrating that NtNPR1 harbors multiple distinct TGA factor binding sites. Interaction with NPR1 impairs TGA7 transcription activity in yeast. Furthermore, TGA7 binding to the NtNPR1 C-terminus is outcompeted by SA-induced type 2 NIM1-INTERACTING (NIMIN) proteins. In tobacco plants, a TGA7–Gal4 DNA-binding domain chimeric protein (TGA7GBD) mediates SA-responsive reporter gene expression in young leaf tissue and spontaneous reporter activation in older leaves displaying PR-1 gene expression. Astonishingly, TGA7GBD is also able to activate the reporter independent from PR-1 gene expression in noninduced cotyledons of tobacco seedlings. Together, our findings support a model in which TGA7 mediates both SA-dependent and SA-independent gene activation controlled by the plant’s developmental stage and by the C-terminal region of constitutively accumulating NtNPR1.
Determinants of mortgage price affordability: a study of Ghana
Authors: Owusu-Manu DeGraft , Edwards David John , Pärn Erika Anneli , Asiedu Richard Ohene , Aboagye Alex 
Published: June 2018

Purpose
While mortgage markets have gradually emerged in many African countries, substantial barriers still hinder their growth and expansion. Affordability has been widely cited as a prominent issue that doggedly remains at the core of urban housing problems. Hence, this paper aims to investigate the determinants of mortgage price affordability.

Design/methodology/approach
Data were gathered using semi-structured questionnaires obtained from a sample drawn from three major West African mortgage financing institutions. Respondents rated the variables using a five-point Likert item rating. The survey results were analysed using exploratory factor analysis.

Findings
In total, 11 variables that influence mortgage affordability were categorised within five principal components, namely, economic factors, financial factors, property characteristics, developmental factors and geographical factors.

Practical implications
The results provide insightful guidance to policymakers and practitioners on how to mitigate affordability issues within Ghana’s fledgling mortgage market. Failure to address the mortgage price affordability conundrum will place enormous pressure upon social housing and rental accommodation.

Originality/value
The research findings expand existing frontiers of knowledge by investigating and reporting upon the determinants of mortgage price affordability. The work also engenders wider debate on the need to establish mortgage packages targeted at low-to-middle-income earners. The culmination of analysis and debate will provide a robust basis for developing a future housing policy framework.
Assessing the strategic needs of local territorial systems (LTSs)
Authors: Pino Giovanni , Guido Gianluigi , Peluso Alessandro M. , Pichierri Marco 
Published: June 2018

Purpose
This paper aims to contribute to the literature on place marketing by focusing on the concept of strategic needs, i.e. the set of strategic priorities that a place could achieve in a medium- to long-term horizon to improve its development.

Design/methodology/approach
The research examines the strategic needs of four local territorial systems (LTSs), i.e. clusters of municipalities that share social, economic and spatial similarities, located in a southern Italian province, through an analysis of their competitive positioning over three temporal instants.

Findings
For each LTS, the analysis identified a number of development goals that local policymakers could pursue and the strategies most suitable to achieve the said goals.

Originality/value
This paper proposes a new methodological approach to set the development goals of local areas based on the simultaneous assessment of their attractiveness and competitive capacity.
University entrepreneurship: how to trigger entrepreneurial intent of undergraduate students
Authors: Rodríguez Gutiérrez Paola Isabel , Pastor Pérez María del Pilar , Alonso Galicia Patricia Esther 
Published: June 2018

Purpose
The purpose of this paper is to describe the elements and relationships that explain the entrepreneurial intent in university students, evaluating possible gender and degree differences.

Design/methodology/approach
The study is of quantitative approach, survey research design and cross-sectional method. The instrument used was a self-administered questionnaire answered by undergraduate university students enrolled in a public university. The sampling was stratified random, with a representative sample size of 734 cases. For data analysis and hypothesis testing, a confirmatory factor analysis and structural equation model were made.

Findings
The results show that the entrepreneurial self-efficacy attribute largely explains the entrepreneurial intent, while all other variables, such as entrepreneurial identity aspirations and outcome expectations, play a less important role but maintain some influence.

Research limitations/implications
According to the findings of this research, institutions of higher education should direct efforts to improve the entrepreneurial skills of students, especially for women. And the creation of an institutional entrepreneurial culture should also be emphasized so that the university students are able to build an entrepreneurial identity.

Originality/value
The value of the research is the proposed integrative model that explains how to trigger entrepreneurial intent, shows the prominent role of entrepreneurial self-efficacy as a predictor variable of entrepreneurial intent and the role of entrepreneur identity aspirations and entrepreneurial self-efficacy as mediating variables. Additionally, this research identifies differences in the model of entrepreneurial intent derived from the variables of gender and degrees.