bluuebunny/crossref_metadata_2025_split huggingface dataset:
Habitat heterogeneity reduces richness of ant species by increasing abundance of the local dominant species
Authors: Travassos-Britto B. , Rocha P. B. L. 
Published: May 2018

AbstractThe effect of environmental heterogeneity on species richness is frequently discussed in ecology. However, the empirical evidence has been contradictory as to the direction of the effect. Although some authors have considered that this might be a methodological problem, we argue that for ants, ecological interactions within the community, as interspecific competition is more important. We analyzed the plausibility of models in explaining the ant richness distribution patterns in a semi-desert environment. We used three predicting variables in the construction of the models to explain ant richness distribution: heterogeneity based on the amount of structures regardless of their type, heterogeneity based on the diversity of structures, and the abundance of individuals of the dominant species. We used ANOVA to chose the best model and corroborated the prediction that in this system abundance of dominant species is the best predictor of ant species richness. Neither of the heterogeneity conceptions contributed much to explain richness distribution. However, in a second analysis, we concluded that heterogeneity could affect the abundance of the dominant species. We conclude that competitive dominance is a better predictor of species richness distribution patterns than structural heterogeneity. However, the structural heterogeneity affects the distribution of dominant individuals. We suggest that some unexplained patterns observed about the relationship between heterogeneity and richness could be due to an indirect effect.
A Scoring System to Evaluate the Impact of SNPs in a Path Related Context to Study Behçet’s Disease Aetiology in Japanese Population
Authors: Ozisik Ozan , Meguro Akira , Mizuki Nobuhisa , Diri Banu , Sezerman Osman Ugur 
Published: May 2018

AbstractMotivationGenome-wide association study (GWAS) is a powerful method that can provide a list of single nucleotide polymorphisms (SNPs) that are significantly related to the pathogenesis of a disease. Even though in Mendelian diseases strong associations can be found for certain SNPs, in most of the complex diseases only modest associations can be identified from the GWAS. Therefore, the main challenge in such studies is to understand how multiple SNPs that have modest association with the phenotype interact and contribute to its aetiology. This can only be done via pathway based analysis of modestly associated SNPs and the genes that are affected by these changes.ResultsIn this study, we propose DAPath, a Disease Associated Path analyzer tool for discovering signaling paths and the pathways that contain these paths which are subjected to cumulative impact of modestly associated variants. We applied our proposed method on Behçet’s disease (BD) GWAS dataset from Japanese population. Antigen Processing and Presentation pathway is ranked first with 16 highly affected paths. Th17 cell differentiation, Natural killer cell mediated cytotoxicity, Jak-STAT signaling, and Circadian rhythm pathways are also found to be containing highly affected paths.AvailabilityThe proposed method is available as a Cytoscape plug-in through https://github.com/ozanozisik/DAPath
Genome-wide sampling suggests island divergence accompanied by cryptic epigenetic plasticity in Canada lynx
Authors: Johnson J.B. , Murray D.L. , Shafer A.B.A. 
Published: May 2018

ABSTRACTDetermining the molecular signatures of adaptive differentiation is a fundamental component of evolutionary biology. A key challenge remains for identifying such signatures in wild organisms, particularly between populations of highly mobile species that undergo substantial gene flow. The Canada lynx (Lynx canadensis) is one species where mainland populations appear largely undifferentiated at traditional genetic markers, despite inhabiting diverse environments and displaying phenotypic variation. Here, we used high-throughput sequencing to investigate both neutral genetic structure and epigenetic differentiation across the distributional range of Canada lynx. Using a customized bioinformatics pipeline we scored both neutral SNPs and methylated nucleotides across the lynx genome. Newfoundland lynx were identified as the most differentiated population at neutral genetic markers, with diffusion approximations of allele frequencies indicating that divergence from the panmictic mainland occurred at the end of the last glaciation, with minimal contemporary admixture. In contrast, epigenetic structure revealed hidden levels of differentiation across the range coincident with environmental determinants including winter conditions, particularly in the peripheral Newfoundland and Alaskan populations. Several biological pathways related to morphology were differentially methylated between populations, with Newfoundland being disproportionately methylated for genes that could explain the observed island dwarfism. Our results indicate that epigenetic modifications, specifically DNA methylation, are powerful markers to investigate population differentiation and functional plasticity in wild and non-model systems.SIGNIFICANCEPopulations experiencing high rates of gene flow often appear undifferentiated at neutral genetic markers, despite often extensive environmental and phenotypic variation. We examined genome-wide genetic differentiation and DNA methylation between three interconnected regions and one insular population of Canada lynx (Lynx canadensis) to determine if epigenetic modifications characterized climatic associations and functional molecular plasticity. Demographic approximations indicated divergence of Newfoundland during the last glaciation, while cryptic epigenetic structure identified putatively functional differentiation that might explain island dwarfism. Our study suggests that DNA methylation is a useful marker for differentiating wild populations, particularly when faced with functional plasticity and low genetic differentiation.
Reducing blood culture contamination using an initial specimen diversion device
Authors: Zimmerman Frederic S. , Assous Marc V. , Zevin Shoshana , Wiener-Well Yonit 
Published: May 2018

AbstractFalse positive blood cultures result from contamination, consuming microbiological laboratory resources and causing unnecessary antibiotic treatment and lengthened hospitalizations. Skin sterilization has been shown to reduce contamination; however, bacteria do not only colonize the surface of human skin, but are also found in deeper tissues, requiring additional techniques to reduce contamination. An initial specimen diversion device diverts the initial 1-2 ml of blood so as to remove any potentially contaminated skin plug, thus potentially further reducing culture contamination. The device has been associated with a reduction in culture contamination over short study periods in certain populations. However, more study is needed to understand whether the effect continues over longer periods of time and in hospitalized patients. Thus, in this prospective, controlled pragmatic study, cultures were obtained from hospitalized patients using the initial specimen diversion device, with cultures taken using standard methods serving as control. In total, 671 blood cultures were obtained: 207 cultures were taken using an initial specimen diversion device, with 2 (1.0%) contaminated cultures and 464 cultures were taken without the device, with 24 (5.2%) contaminated cultures (p < 0.008). No significant difference was shown in the rate of true positive cultures. Thus, use of a diversion device was associated with reduced culture contamination in hospitalized patients over a six month period without concomitant reduction in true positive cultures. This intervention may result in a reduction in costs, antibiotic use and duration of hospitalization.
Structural variability and functional association in the epiphytic bacteria assemblies of freshwater macrophytes (Myriophyllum spicatum)
Authors: Xian Ling , Wan Tao , Cao Yu , Sun Junyao , Wu Ting , Zhao Suting , Apudo Andrew Apudo , Li Wei , Liu Fan 
Published: May 2018

AbstractThe underlying principles influencing bacteria community assembly have long been of interest in the field of microbial ecology. Environmental heterogeneity is believed to be important in controlling the uniqueness and variability of communities. However, little is known about the influence of the host macrophytes on epiphytic bacteria assembly processe. Here, we produced two contrasting artificial water environments (eutrophic and oligotrophic) for reciprocal transplant experiment ofMyriophyllum spicatum, to recover the colonization of epiphytic bacteria accompanied with plants growth. Comparative analysis addressed a higher species diversity in epiphytic bacteria than in bacterioplankton, and the highest microbiome richness in sediment. Our data revealed that the organization of epiphytic bacterial community was interfered by both plant status (i.e. branch number, net photosynthesis rate etc.) and water bodies (i.e. total phosphate, total nitrogen, pH etc.) while plant status effected the assembly in priority to water. 16S rRNA sequencing further indicated that the epiphytic assemblies were motivated by functionalization and interplay with hosts as a whole. The results complemented new evidences for the ‘lottery process’ in the epiphytic bacteria assembly traits and shed insights into the assembly patterns referring to functional adaptation across epiphytic bacteria and macrophytes.ImportanceA robust understanding of inter-adaptation between microbiome and the host plants have been established basing on vast majority of researches. However, great efforts were made mostly on rhizosphere microbiome. By contrast, referring to another representative group, macrophytes who composed of the freshwater ecosystem were relatively less investigated on such issue. Our study pioneered the experimental operation to interrogate the triadic relationship among macrophytes, epiphytic bacteria and water body. The research present here showed significant exemplar on discussion of plant associate bacteria adaptation taking account of host colonization as well as the epiphytes. The results expand the hypotheses of bacteria assembly principle and provides potential leads on understanding of plant - microbe interactions.
TrackingBorrelia afzeliifrom infectedIxodes ricinusnymphs to mice suggests a direct ‘gut-to-mouth’ route of Lyme disease transmission
Authors: Pospisilova Tereza , Urbanova Veronika , Hes Ondrej , Kopacek Petr , Hajdusek Ondrej , Sima Radek 
Published: May 2018

AbstractQuantitative tracking ofBorrelia afzeliihas shown that its transmission cycle differs from the salivary route ofB. burgdorferitransmission byIxodes scapularis.Borrelia afzeliiare abundant in the guts of unfedIxodes ricinusnymphs and their numbers continuously decrease during feeding. In contrast, spirochetes are not present in the salivary glands.Borrelia afzeliitransmission starts during the early stages of feeding, spirochetes could be detected in murine skin within 1 day of tick attachment. Tick saliva is not essential forB. afzeliiinfectivity, the main requirement for successful host colonization being a change in outer surface protein expression that occurs in the tick gut during feeding. Spirochetes in vertebrate mode are able to survive within the host even if the tick is not present. On the basis of our data we propose that a direct ‘gut-to-mouth’ route of infection appears to be the main route ofB. afzeliitransmission.ImportanceLyme borreliosis is the most common vector-borne disease in the USA and Europe. The disease is caused by theBorreliaspirochetes and is transmitted throughIxodesticks. A better understanding of howBorreliaspirochetes are transmitted is crucial for development of efficient vaccines for preventing Lyme borreliosis. Here we present that the transmission of EuropeanB. afzeliispirochetes byI. ricinusticks significantly differs from the model transmission cycle described for AmericanB. burgdorferi/I. scapularis. We suggest thatB. afzeliiis not transmitted via salivary glands but most likely through the ‘midgut to mouthpart’ route. We further demonstrate that tick saliva is not important forB. afzeliitransmission and infectivity. Therefore, we support early studies by Willy Burgdorfer, who proposed thatBorreliatransmission occurs by regurgitation of infected gut contents. Our findings collectively point to theBorrelia-tick midgut interface as the correct target in our endeavours to combat Lyme borreliosis.
DeepRibo: precise gene annotation of prokaryotes using deep learning and ribosome profiling data
Authors: Clauwaerts Jim , Menschaert Gerben , Waegeman Willem 
Published: May 2018

AbstractAnnotation of gene expression in prokaryotes often finds itself corrected due to small variations of the annotated gene regions observed between different (sub-species. It has become apparent that traditional sequence alignment algorithms, used for the curation of genomes, are not able to map the full complexity of the genomic landscape. We present DeepRibo, a novel neural network applying ribosome profiling data that shows to be a precise tool for the delineation and annotation of expressed genes in prokaryotes. The neural network combines recurrent memory cells and convolutional layers, adapting the information gained from both the high-throughput ribosome profiling data and Shine-Dalgarno region into one model. DeepRibo is designed as a single model trained on a variety of ribosome profiling experiments, and is therefore evaluated on independent datasets. Through extensive validation of the model, including the use of multiple species sequence similarity and mass spectrometry, the effectiveness of the model is highlighted.
Iodine status of children and Knowledge, Attitude, Practice of Iodised salt use in a remote community in Kerema district, Gulf province, Papua New Guinea
Authors: Goris Janny M , Temple Victor J , Zomerdijk Nienke , Codling Karen 
Published: May 2018

ABSTRACTIodine deficiency is the single most common cause of preventable mental impairment in communities with suboptimal iodine intake. Objective of the present study was to assess in more detail the iodine status and knowledge, attitudes and practice (KAP) relating to use of iodised salt in a remote community in Kotidanga area, Kerema district, Gulf province, Papua New Guinea. This prospective school and community based cross-sectional study was carried out in 2017. Simple random sampling was used to select schools. Multistage sampling was used to randomly select 291 children aged 6 to 12 years. Salt samples were collected for analysis from children’s households as well as a single urine sample of selected children. Salt iodine content and Urinary iodine concentration (UIC) were analysed. A semi-structured FAO questionnaire was used to assess KAP of three different community groups. Only 64% of households had salt on the day of data collection. Mean iodine content in household salt samples was 29.0 ± 19.1 ppm. Iodine content was below 30.0 ppm in 54.8% and below 15.0 ppm in 31.2% of salt samples. Mean per capita discretionary intake of household salt was 2.9 ± 1.8 g/day. Median UIC was 25.5 μg/L and Interquartile Range was 15.0 to 47.5 μg/L; 75.9% (221/291) of the children had UIC below 50.0 μg/L, indicating moderate status iodine nutrition. Median UIC was 34.3μg/L for children in households with salt, compared to 15.5 μg/L for children in households without salt, indicating severe iodine deficiency in the latter group. The three community groups had limited knowledge about importance of using iodised salt and consequences of iodine deficiency on health outcomes. This remote community has limited access to adequately iodised household salt due to high cost, inappropriate packaging, storage and food preparation, resulting in iodine deficiency. Strategies to increase iodine intake are needed.
Nurtured by nature: Considering the role of environmental and parental legacies in coral ecological performance
Authors: Putnam Hollie M. , Ritson-Williams Raphael , Cruz Jolly Ann , Davidson Jennifer M. , Gates Ruth D. 
Published: May 2018

AbstractThe persistence of reef building corals is threatened by human-induced environmental change. Maintaining coral reefs into the future requires not only the survival of adults, but also the influx of recruits to promote genetic diversity and retain cover following adult mortality. Few studies examine the linkages among multiple life stages of corals, despite a growing knowledge of carryover effects in other systems. We provide a novel test of coral parental preconditioning to ocean acidification (OA) to better understand impacts on the processes of offspring recruitment and growth. Coral planulation was tracked for three months following adult exposure to high pCO2and offspring from the second month were reciprocally exposed to ambient and high pCO2. Offspring of parents exposed to high pCO2had greater settlement and survivorship immediately following release, retained survivorship benefits during one and six months of continued exposure, and further displayed growth benefits to at least one month post release. Enhanced performance of offspring from parents exposed to high conditions was maintained despite the survivorship in both treatments declining in continued exposure to OA. Preconditioning of the adults while they brood their larvae may provide a form of hormetic conditioning, or environmental priming that elicits stimulatory effects. Defining mechanisms of positive carryover effects, or positive trans-generational plasticity, is critical to better understanding ecological and evolutionary dynamics of corals under regimes of increasing environmental disturbance. Considering parental and environmental legacies in ecological and evolutionary projections may better account for coral reef response to the chronic stress regimes characteristic of climate change.
Mixed-cropping systems of different rice cultivars have grain yield and quality advantages over mono-cropping systems
Authors: Li Meijuan , Zhang Jiaen , Liu Shiwei , Ashraf Umair , Qiu Shuqing 
Published: May 2018

AbstractMixed-cropping system is a centuries-old cropping technique that is still widely practiced in the farmers’ field over the globe. Increased plant diversity enhances farmland biodiversity, which would improve grain yield and quality; however, the impacts of growing different rice cultivars simultaneously were rarely investigated. In present study, five popular rice cultivars were selected and ten mixture combinations were made according to the growth period, plant height, grain yield and quality, and pest and disease resistance. Seedlings of the five cultivars and ten mixture combinations (mixed-sowing of the seeds in an equal ratio, then mixed-transplanting and finally mixed-harvesting) were grown in plastic pots under greenhouse during the early and late growing seasons in 2016. Results showed that, compared with the corresponding mono-cropping systems, almost all combinations of the mixed-cropping systems have advantages in yield related traits and grain quality. Compared with the mono-cropping systems in the early and late growing seasons in 2016, mixed-cropping systems increased the number of spikelets per panicle, seed-setting rate, and grain weight per pot and harvest index by 19.52% and 5.77%, 8.53% and 4.41%, 8.31% and 4.61%, and 10.26% and 6.98%, respectively (paired t-test). In addition, mixed-cropping systems reduced chalky rice rate and chalkiness degree by 33.12% and 43.42% and by 30.11% and 48.13% in the early and late growing seasons, respectively (paired t-test). These results may be due to enhanced SPAD indexes and photosynthetic rates at physiology maturity in mixed-cropping systems. In general, it was found that mixed-cropping with different rice cultivars have potential for increasing grain yield and improving grain quality.
Optogenetic dissection of Rac1 and Cdc42 gradient shaping
Authors: De Beco S. , Vaidžiulytė K. , Manzi J. , Dalier F. , di Federico F. , Cornilleau G. , Dahan M. , Coppey M. 
Published: May 2018

AbstractDuring migration, cells present a polarized activity that is aligned with the direction of motion. This cell polarity is established by an internal molecular circuitry, without the requirement of extracellular cues. At the heart of this circuitry, Rho GTPases spontaneously form spatial gradients that define the front and back of migrating cells. At the front of the cell, active Cdc42 forms a steep gradient whereas active Rac1 forms a more extended pattern peaking a few microns away from the cell tip. What are the mechanisms shaping these gradients, and what is the functional role of the shape of these gradients? Combining optogenetics and cell micopatterning, we show that Cdc42 and Rac1 gradients are set by spatial patterns of activators and deactivators and not directly by advection or diffusion mechanisms. Cdc42 simply follows the distribution of GEFs thanks to a uniform GAP activity, whereas Rac1 shaping requires the activity of an additional GAP, β2-chimaerin, which is sharply localized at the tip of the cell. We find that β2-chimaerin recruitment depends on feedbacks from Cdc42 and Rac1. Functionally, the extent -neither the slope nor the amplitude- of RhoGTPases gradients governs cell migration. A Cdc42 gradient with a short spatial extent is required to maximize directionality during cell migration while an extended Rac1 gradient controls the speed of the cell.