bluuebunny/crossref_metadata_2025_split huggingface dataset:
A High Prevalence Rate of a Positive Screen for Cognitive Impairment in Patients With Human Immunodeficiency Virus Attending an Irish Clinic
Authors: McNamara Patricia H. , Coen Robert , Redmond Janice , Doherty Colin P. , Bergin Colm 
Published: December 2016

Abstract

Background
Human immunodeficiency virus (HIV)-associated neurocognitive disorders occurs in 20%–50% of HIV-positive patients. We undertook this study to assess the prevalence of a positive screen for cognitive impairment in the clinic population at our institution and to demonstrate the feasibility of implementing a screening program in routine clinical encounters.

Methods
This was a cross-sectional study, and patients were recruited prospectively between December 2010 and February 2013. Inclusion criteria were as follows: patients were HIV positive, over the age of 18, capable of giving informed consent, and had sufficient ability to communicate in English. Patients were screened for cognitive impairment using the Brief Neurocognitive Screen.

Results
A total of 604 patients were recruited, and 51.5% had a positive screen for cognitive impairment. The majority of the study cohort were male (78.8%), mean age was 40.9 (standard deviation, 10.2) years, 70.9% were Irish, the most common mode of transmission was men who have sex with men (49.3%), 83% were on antiretroviral therapy, and 88.7% were virally suppressed. Logistic regression showed that the main factors predictive of a positive screen for cognitive impairment were the endorsement of cognitive symptoms (P = .024), being born in Africa (P &lt; .000001), the use of benzodiazepines (P = .00341), being unemployed (P = .008), and consumption of more than 40 units of alcohol weekly (P = .035). There was a positive screen for depression in 9.1% and a positive screen for anxiety in 24.5%.

Conclusions
The study highlights the necessity for a structured, prospective, large-scale screening program for cognitive impairment across countries with limited resources and demonstrates the feasibility of easily implementing this with minimal training.
The food web of Potter Cove (Antarctica): complexity, structure and function
Authors: Marina Tomás I. , Salinas Vanesa , Cordone Georgina , Campana Gabriela , Moreira María Eugenia , Deregibus Dolores , Torre Luciana , Sahade Ricardo , Tatián Marcos , Oro Esteban Barrera , De Troch Marleen , Doyle Santiago , Quartino María Liliana , Saravia Leonardo A. , Momo Fernando R. 
Published: December 2016

AbstractKnowledge of the food web structure and complexity are central to better understand ecosystem functioning. A food-web approach includes both species and energy flows among them, providing a natural framework for characterizing species’ ecological roles and the mechanisms through which biodiversity influences ecosystem dynamics. Here we present for the first time a high-resolution food web for a marine ecosystem at Potter Cove (northern Antarctic Peninsula). Eleven food web properties were analyzed in order to document network complexity, structure and topology. We found a low linkage density (3.4), connectance (0.04) and omnivory percentage (45), as well as a short path length (1.8) and a low clustering coefficient (0.08). Furthermore, relating the structure of the food web to its dynamics, an exponential degree distribution (in- and out-links) was found. This suggests that the Potter Cove food web may be vulnerable if the most connected species became locally extinct. For two of the three more connected functional groups, competition overlap graphs imply high trophic interaction between demersal fish and niche specialization according to feeding strategies in amphipods. On the other hand, the prey overlap graph shows also that multiple energy pathways of carbon flux exist across benthic and pelagic habitats in the Potter Cove ecosystem. Although alternative food sources might add robustness to the web, network properties (low linkage density, connectance and omnivory) suggest fragility and potential trophic cascade effects.
Rescuing Troves of Data to Tackle Emerging Mosquito-Borne Diseases
Authors: Rund Samuel S.C. , Martinez Micaela Elvira 
Published: December 2016

AbstractAccording to the World Health Organization, every year more than a billion people are infected with vector-borne diseases worldwide. There are no vaccines for most vector-borne diseases. Vector control, therefore, is often the only way to prevent outbreaks. Despite the major impact of vectors on human health, knowledge gaps exist regarding their natural population dynamics. Even the most basic information—such as spatiotemporal abundance— is not available. Mosquitoes transmit malaria and the viruses causing Yellow Fever, West Nile, Dengue, Chikungunya, and Zika in the Americas. The Americas have a long history of mosquito control efforts, including the unsustained but successfulAedes aegyptieradication initiative. In the US, municipalities have independently created agencies for mosquito control and monitoring. We propose that the ensemble of US mosquito control agencies can, and should, be used to develop a national—and potentially international—system for Cross-Scale Vector Monitoring and Control (CSVMaC), in which local level monitoring and control efforts are cross-linked by unified real-time data streaming to build the data capital needed to gain a mechanistic understanding of vector population dynamics. Vectors, and the pathogens they transmit, know no jurisdictions. The vision of CSVMaC is, therefore, to provide data for (i) the general study of mosquito ecology and (ii) to inform vector control during epidemics/outbreaks that impact multiple jurisdictions (i.e., counties, states, etc.). We reveal >1000 mosquito control agencies in the US with enormous troves of data that are hidden among many data silos. For CSVMaC, we propose the creation of a nationally-coordinated open-access database to collate mosquito data. The database would provide scientific and public health communities with highly resolved spatiotemporal data on arboviral disease vectors, empowering new interventions and insights while leveraging pre-existing human efforts, operational infrastructure, and investments already funded by taxpayers.
AmoA-targeted polymerase chain reaction primers for the specific detection and quantification of comammoxNitrospirain the environment
Authors: Pjevac Petra , Schauberger Clemens , Poghosyan Lianna , Herbold Craig W. , van Kessel Maartje A.H.J. , Daebeler Anne , Steinberger Michaela , Jetten Mike S. M. , Sebastian Lücker , Michael Wagner , Holger Daims 
Published: December 2016

AbstractNitrification, the oxidation of ammonia via nitrite to nitrate, has always been considered to be catalyzed by the concerted activity of ammonia- and nitrite-oxidizing microorganisms. Only recently, complete ammonia oxidizers (‘comammox’), which oxidize ammonia to nitrate on their own, were identified in the bacterial genusNitrospira, previously known to contain only canonical nitrite oxidizers.Nitrospiraare widespread in nature, but for assessments of the distribution and functional importance of comammoxNitrospirain ecosystems cultivation-independent tools to distinguish comammox from strictly nitrite-oxidizingNitrospiraare required. Here we developed new PCR primer sets that specifically target theamoAgenes coding for subunit A of the distinct ammonia monooxygenase of comammoxNitrospira. While existing primers capture only a fraction of the known comammoxamoAdiversity, the new primer sets cover as much as 95% of the comammoxamoAclade A and 92% of the clade B sequences in a reference database containing 326 comammoxamoAgenes with sequence information at the primer binding sites. Application of the primers to 13 samples from engineered systems (a groundwater well, drinking water treatment and wastewater treatment plants) and other habitats (rice paddy and forest soils, rice rhizosphere, brackish lake sediment and freshwater biofilm) detected comammoxNitrospirain all samples and revealed a considerable diversity of comammox in most habitats. Excellent primer specificity for comammoxamoAwas achieved by avoiding the use of highly degenerate primer preparations and by using equimolar mixtures of oligonucleotides that match existing comammoxamoAgenes. Quantitative PCR with these equimolar primer mixtures was highly sensitive and specific, and enabled the efficient quantification of clade A and clade B comammoxamoAgene copy numbers in environmental samples. Thus, the new comammoxamoA-targeted primers will enable more encompassing studies of nitrifying microorganisms in diverse ecosystems.
Natural Selection on MHC IIb in Parapatric Lake and Stream Stickleback: Balancing, Divergent, Both, or Neither?
Authors: E. Stutz William , Bolnick Daniel I. 
Published: December 2016

AbstractMajor histocompatibility (MHC) genes encode proteins that play a central role in vertebrates’ adaptive immunity to parasites. MHC loci are among the most polymorphic in vertebrates’ genomes, inspiring many studies to identify evolutionary processes driving MHC polymorphism within populations, and divergence between populations. Leading hypotheses include balancing selection favoring rare alleles within populations, and spatially divergent selection. These hypotheses do not always produce diagnosably distinct predictions, causing many studies of MHC to yield inconsistent or ambiguous results. We suggest a novel strategy to distinguish balancing versus divergent selection on MHC, taking advantage of natural admixture between parapatric populations. With divergent selection, immigrant alleles will be more infected and less fit because they are susceptible to novel parasites in their new habitat. With balancing selection, locally-rare immigrant alleles will be more fit (less infected). We tested these contrasting predictions using threespine stickleback from three replicate pairs of parapatric lake and stream habitats. We found numerous positive and negative associations between particular MHC IIβ alleles and particular parasite taxa. A few allele-parasite comparisons supported balancing selection, others supported divergent selection between habitats. But, there was no overall tendency for fish with immigrant MHC alleles to be more or less heavily infected. Instead, locally rare MHC alleles (not necessarily immigrants) were associated with heavier infections. Our results illustrate the complex relationship between MHC IIβ allelic variation and spatially varying multi-species parasite communities: different hypotheses may be concurrently true for different allele-parasite combinations.
tensorBF: an R package for Bayesian tensor factorization
Authors: Khan Suleiman A. , Ammad-ud-din Muhammad 
Published: December 2016

AbstractWith recent advancements in measurement technologies, many multi-way and tensor datasets have started to emerge. Exploiting the natural tensor structure in the data has been shown to be advantageous for both explorative and predictive studies in several application areas of bioinformatics and computational biology. Therefore, there has subsequently arisen a need for robust and flexible tools for effectively analyzing tensor data sets. We present the R package tensorBF, which is the first R package providing Bayesian factorization of a tensor. Our package implements a generative model that automatically identifies the number of factors needed to explain the tensor, overcoming a key limitation of traditional tensor factorizations. We also recommend best practices when using tensor factorizations for both, explorative and predictive analysis with an example application on drug response dataset. The package also implements tools related to the normalization of data, informative noise priors and visualization. Availability: The package is available athttps://cran.r-project.org/package=tensorBF.
Prestack amplitude versus angle inversion for Young's modulus and Poisson's ratio based on the exact Zoeppritz equations
Authors: Zhou Lin , Li Jingye , Chen Xiaohong , Liu Xingye , Chen Li 
Published: December 2016

ABSTRACTElastic parameters such as Young's modulus, Poisson's ratio, and density are very important characteristic parameters that are required to properly characterise shale gas reservoir rock brittleness, evaluate gas characteristics of reservoirs, and directly interpret lithology and oil‐bearing properties. Therefore, it is significant to obtain accurate information of these elastic parameters. Conventionally, they are indirectly calculated by the rock physics method or estimated by approximate formula inversion. The cumulative errors caused by the indirect calculation and low calculation accuracy of the approximate Zoeppritz equations make accurate estimation of Young's modulus, Poisson's ratio, and density difficult in the conventional method. In this paper, based on the assumption of isotropy, we perform several substitutions to convert the Zoeppritz equations from the classical form to a new form containing the chosen elastic constants of Young's modulus, Poisson's ratio, and density. The inversion objective function is then constructed by utilising Bayesian theory. Meanwhile, the Cauchy distribution is introduced as a priori information. We then combine the idea of generalised linear inversion with an iterative reweighed least squares algorithm in order to solve the problem. Finally, we obtain the iterative updating formula of the three elastic parameters and achieve the direct inversion of these elastic parameters based on the exact Zoeppritz equations. Both synthetic and field data examples show that the new method is not only able to obtain the two elastic parameters of Young's modulus and Poisson's ratio stably and reasonably from prestack seismic data but also able to provide an accurate estimation of density information, which demonstrates the feasibility and effectiveness of the proposed method. The proposed method offers an efficient seismic method to identify a “sweet spot” within a shale gas reservoir.
Bottom‐up and trait‐mediated effects of resource quality on amphibian parasitism
Authors: Stephens Jeffrey P. , Altman Karie A. , Berven Keith A. , Tiegs Scott D. , Raffel Thomas R. 
Published: December 2016

AbstractLeaf litter subsidies are important resources for aquatic consumers like tadpoles and snails, causing bottom‐up effects on wetland ecosystems. Recent studies have shown that variation in litter nutritional quality can be as important as litter quantity in driving these bottom‐up effects. Resource subsidies likely also have indirect and trait‐mediated effects on predation and parasitism, but these potential effects remain largely unexplored.We generated predictions for differential effects of litter nutrition and secondary polyphenolic compounds on tadpole (Lithobates sylvatica) exposure and susceptibility toRibeiroia ondatrae, based on ecological stoichiometry and community‐ecology theory. We predicted direct and indirect effects on key traits of the tadpole host (rates of growth, development and survival), the trematode parasite (production of the cercaria infective stages) and the parasite's snail intermediate host (growth and reproduction).To test these predictions, we conducted a large‐scale mesocosm experiment using a natural gradient in the concentrations of nutrients (nitrogen) and toxic secondary compounds (polyphenolics) of nine leaf litter species. To differentiate between effects on exposure vs. susceptibility to infection, we included multiple infection experiments including one with constant per capita exposure.We found that increased litter nitrogen increased tadpole survival, and also increased cercaria production by the snail intermediate hosts, causing opposing effects on tadpole per capita exposure to trematode infection. Increased litter polyphenolics slowed tadpole development, leading to increased infection by increasing both their susceptibility to infection and the length of time they were exposed to parasites.Based on these results, recent shifts in forest composition towards more nitrogen‐poor litter species should decrease trematode infection in tadpoles via density‐ and trait‐mediated effects on the snail intermediate hosts. However, these shifts also involve increased abundance of litter species with high polyphenolic levels, which should increase trematode infection via trait‐mediated effects on tadpoles. Future studies will be needed to determine the relative strength of these opposing effects in natural wetland communities. [Correction added after online publication on 5 January 2017: wording changed to ‘which should increase trematode infection via trait‐mediated effects on tadpoles’.]
Moving forward: insights and applications of moving‐habitat models for climate change ecology
Authors: Harsch Melanie A. , Phillips Austin , Zhou Ying , Leung Margaret‐Rose , Rinnan D. Scott , Kot Mark 
Published: December 2016

SummaryPredicting and managing species’ responses to climate change is one of the most significant challenges of our time. Tools are needed to address problems associated with novel climatic conditions, biotic interactions and greater climate velocities.We present a spatially explicit moving‐habitat model (MHM) and demonstrate its versatility in tackling critical questions in climate change research, including dispersal in multiple spatial dimensions, population stage structure, interspecific interactions, asymmetric range shifts, Allee effects and the presence of infectious diseases. The model utilizes integrodifference equations to track changes in population density over time in a habitat that is moving. The model is quite flexible and can accommodate variation in demography, dispersal patterns, biotic interaction and stochasticity in the velocity of climate change.The methods provide a general mechanistic understanding of the underlying ecological processes that drive a system. Field data can be readily incorporated into the model to give insight into specific populations of interest and inform management decisions.Synthesis. Moving‐habitat models unite ecological theory, data‐centred modelling and conservation decision support under a single framework. Their ability to generate testable hypotheses, incorporate data and inform best management practices proves that these models provide a valuable framework for climate change biologists.
Regulation of microvascular flow and metabolism: An overview
Authors: Keske Michelle A , Dwyer Renee M , Russell Ryan D , Blackwood Sarah J , Brown Aascha A , Hu Donghua , Premilovac Dino , Richards Stephen M , Rattigan Stephen 
Published: December 2016

SummarySkeletal muscle is an important site for insulin to regulate blood glucose levels. It is estimated that skeletal muscle is responsible for ~80% of insulin‐mediated glucose disposal in the post‐prandial period. The classical action of insulin to increase muscle glucose uptake involves insulin binding to insulin receptors on myocytes to stimulate glucose transporter 4 (GLUT 4) translocation to the cell surface membrane, enhancing glucose uptake. However, an additional role of insulin that is often under‐appreciated is its action to increase muscle perfusion thereby improving insulin and glucose delivery to myocytes. Either of these responses (myocyte and/or vascular) may be impaired in insulin resistance, and both impairments are apparent in type 2 diabetes, resulting in diminished glucose disposal by muscle. The aim of this review is to report on the growing body of literature suggesting that insulin‐mediated control of skeletal muscle perfusion is an important regulator of muscle glucose uptake and that impairment of microvascular insulin action has important physiological consequences early in the pathogenesis of insulin resistance. This work was discussed at the 2015 Australian Physiological Society Symposium “Physiological mechanisms controlling microvascular flow and muscle metabolism”.
Indole‐associated predator–prey interactions between the nematode Caenorhabditis elegans and bacteria
Authors: Lee Jin‐Hyung , Kim Yong‐Guy , Kim Minsu , Kim Eonmi , Choi Hyukjae , Kim Younghoon , Lee Jintae 
Published: December 2016

SummaryIndole is an intercellular and interkingdom signalling molecule found in diverse ecological niches. Caenorhabditis elegans is a bacterivorous nematode that lives in soil and compost environments and a useful model host for studies of host–microbe interactions. Although various bacteria and some plants produce large quantities of extracellular indole, little is known about the effects of indole, its derivatives, or of indole‐producing bacteria on the behaviours of C. elegans or other animals. Here, they show that C. elegans senses and moves toward indole and several indole‐producing bacteria, but avoids non‐indole producing pathogenic bacteria. Furthermore, it was found indole‐producing and non‐indole‐producing bacteria exert divergent effects on the egg‐laying behaviour of C. elegans, and that various indole derivatives also modulate chemotaxis, egg‐laying behaviour and the survival of C. elegans. In contrast, indole at high concentration can kill C. elegans, which in turn, has the ability to detoxify indole by oxidation and glucosylation. Transcriptional analysis showed indole markedly up‐regulated the gene expressions of cytochrome P450s, UDP‐glucuronosyltransferases and glutathione S‐transferase, which well explained the modification of indole by C. elegans while indole down‐regulated the expressions of collagen and F‐box genes. Their findings suggest that indole and its derivatives are important signalling molecules during bacteria–nematode interactions.
Exploration of cultivable fungal communities in deep coal‐bearing sediments from ∼1.3 to 2.5 km below the ocean floor
Authors: Liu Chang‐Hong , Huang Xin , Xie Tian‐Ning , Duan Ning , Xue Ya‐Rong , Zhao Tan‐Xi , Lever Mark A. , Hinrichs Kai‐Uwe , Inagaki Fumio 
Published: December 2016

SummaryAlthough subseafloor sediments are known to harbour a vast number of microbial cells, the distribution, diversity, and origins of fungal populations remain largely unexplored. In this study, we cultivated fungi from 34 of 47 deep coal‐associated sediment samples collected at depths ranging from 1289 to 2457 m below the seafloor (mbsf) off the Shimokita Peninsula, Japan (1118 m water depth). We obtained a total of 69 fungal isolates under strict contamination controls, representing 61 Ascomycota (14 genera, 23 species) and 8 Basidiomycota (4 genera, 4 species). Penicillium and Aspergillus relatives were the most dominant genera within the Ascomycetes, followed by the members of genera Cladosporium, Hamigera, Chaetomium, Eutypella, Acremonium, Aureobasidium, Candida, Eurotium, Exophiala, Nigrospora, Bionectria and Pseudocercosporella. Four Basidiomycota species were identified as genera Schizophyllum, Irpex, Bjerkandera and Termitomyces. Among these isolates, Cladosporium sphaerospermum and Aspergillus sydowii relatives were isolated from a thin lignite coal‐sandstone formation at 2457 mbsf. Our results indicate that these cultivable fungal populations are indigenous, originating from past terrigenous environments, which have persisted, possibly as spores, through ∼20 million years of depositional history.