bluuebunny/crossref_metadata_2025_split huggingface dataset:
Type IV pilin post-translational modifications modulate materials properties of bacterial colonies
Authors: Zöllner R. , Cronenberg T. , Kouzel N. , Welker A. , Koomey M. , Maier B. 
Published: August 2018

AbstractBacterial type 4 pili (T4P) are extracellular polymers that initiate the formation of microcolonies and biofilms. T4P continuously elongate and retract. These pilus dynamics crucially affects the local order, shape, and fluidity of microcolonies. The major pilin subunit of the T4P bears multiple post-translational modifications. By interfering with different steps of the pilin glycosylation and phosphoform modification pathways, we investigated the effect of pilin post-translational modification on the shape and dynamics of microcolonies formed by Neisseria gonorrhoeae. Deleting the phosphotransferase responsible for phosphoethanolamine modification at residue serine 68 (S68) inhibits shape relaxations of microcolonies after pertubation and causes bacteria carrying the phosphoform modification to segregate to the surface of mixed colonies. We relate these mesoscopic phenotypes to increased attractive forces generated by T4P between cells. Moreover, by deleting genes responsible for the pilin glycan structure, we show that the number of saccharides attached at residue serine 63 (S63) affect the ratio between surface tension and viscosity and cause sorting between bacteria carrying different pilin glycoforms. We conclude that different pilin post-translational modifications moderately affect the attractive forces between bacteria but have severe effects on the materials properties of microcolonies.
Latent Structure of Risk Perception
Authors: Pabon Elisa , MacKillop James , Palmer Abraham A. , de Wit Harriet 
Published: August 2018

AbstractRisk-taking behavior affects many aspects of life, including maladaptive behaviors such as illicit substance use, unsafe driving, and risky sexual behavior. Risk-taking has been measured using both self-report measures and behavioral tasks designed for the purpose, but there is little consensus in the associations among measures and our understanding of the latent constructs underlying different forms of risk is limited. In the present study we examined the construct of risk using data from over 1000 young adults who completed measures of risk-taking, including self-reports of perception of risk, propensity to engage in risky behaviors and performance on behavioral tasks designed to measure risk. To examine the latent structure of risk preferences, we conducted a principal component analysis (PCA). The PCA revealed a latent structure of three distinct components of risk-taking behavior: “Lifestyle Risk Sensitivity”, “Financial Risk Sensitivity”, and “Behavioral Risk Sensitivity”,which consisted only of the Balloon Analogue Risk Task (BART; Lejuez et al., 2002). As expected, risk-taking and perception of risk differed in men and women. Yet, the PCA components were similar in men and women. Future work utilizing additional measures of risk-taking behavior in more heterogeneous samples will help to identify the true biobehavioral constructs underlying these behaviors.
Expected patterns of local ancestry in a hybrid zone
Authors: Smith Joel , Payseur Bret , Novembre John 
Published: August 2018

1AbstractThe initial drivers of reproductive isolation between species are poorly characterized. In cases where partial reproductive isolation exists, genomic patterns of variation in hybrid zones may provide clues about the barriers to gene flow which arose first during the early stages of speciation. Purifying selection against incompatible substitutions that reduce hybrid fitness has the potential to distort local patterns of ancestry relative to background patterns across the genome. The magnitude and qualitative properties of this pattern are dependent on several factors including migration history and the relative fitnesses for different combinations of incompatible alleles. We present a model which may account for these factors and highlight the potential for its use in verifying the action of natural selection on candidate loci implicated in reducing hybrid fitness.
Preliminary prediction of the potential distribution and consequences of Haemaphysalis longicornis using a simple rule-based climate envelope model
Authors: Magori Krisztian 
Published: August 2018

AbstractHaemaphysalis longicornis, the Asian longhorned (or bush) tick has been detected on a sheep in August 2017 in Hunterdon County, New Jersey. By October 26, 2018, this tick has been detected in 44 counties in 9 states along the Atlantic coast of the United States, with the first detection backdated to 2010. Here, I use a simple rule-based climate envelope model, based on a prior analysis in New Zealand, to provide a preliminary analysis of the potential range of this introduced tick species in North America. After validating this model against the counties where the tick has been already detected, I highlight the counties where this tick might cause considerable economic harm. I discuss the many limitations of this simple approach, and potential remedies for these limitations, and more sophisticated approaches. Finally, I conclude that substantial areas of the US, especially along the Gulf and Atlantic coast, are suitable for the establishment of this tick, putting millions of heads of livestock potentially at risk.
Reconstructing B cell receptor sequences from short-read single cell RNA-sequencir with BRAPeS
Authors: Afik Shaked , Raulet Gabriel , Yosef Nir 
Published: August 2018

ABSTRACTRNA-sequencing of single B cells provides simultaneous measurements of the cell state and its binding specificity. However, in order to uncover the latter further reconstruction of the B cell receptor (BCR) sequence is needed. We present BRAPeS, an algorithm for reconstructing BCRs from short-read paired-end single cell RNA-sequencing. BRAPeS is accurate and achieves a high success rate even at very short (25bp) read length, which can decrease the cost and increase the number of cells that can be analyzed compared to long reads. BRAPeS is publicly available in the following link:https://github.com/YosefLab/BRAPeS.
SNP-ChIP: A versatile and tag-free method to quantify changes in protein binding across the genome
Authors: Vale-Silva Luis A. , Markowitz Tovah E. , Hochwagen Andreas 
Published: August 2018

AbstractChromatin-immunoprecipitation followed by sequencing (ChIP-seq) is the method of choice for mapping genome-wide binding of chromatin-associated factors. However, broadly applicable methods for between-sample comparisons are lacking. Here, we introduce SNP-ChIP, a method that leverages small-scale intra-species polymorphisms, mainly SNPs, for quantitative spike-in normalization of ChIP-seq results. Sourcing spike-in material from the same species ensures antibody cross-reactivity and physiological coherence, thereby eliminating two central limitations of traditional spike-in approaches. We show that SNP-ChIP is robust to changes in sequencing depth and spike-in proportions, and reliably identifies changes in overall protein levels, irrespective of changes in binding distribution. Application of SNP-ChIP to test cases from budding yeast meiosis allowed discovery of novel regulators of the chromosomal protein Red1 and quantitative analysis of the DNA-damage associated histone modificationγ-H2AX. SNP-ChIP is fully compatible with the intra-species diversity of humans and most model organisms and thus offers a general method for normalizing ChIP-seq results.
Inactivation of medial frontal cortex changes risk preference
Authors: Chen Xiaomo , Stuphorn Veit 
Published: August 2018

SummaryHumans and other animals need to make decisions under varying degrees of uncertainty. These decisions are strongly influenced by an individual’s risk preference, however the neuronal circuitry by which risk preference shapes choice is still unclear [1]. Supplementary eye field (SEF), an oculomotor area within primate medial frontal cortex, is thought to be an essential part of the neuronal circuit underlying oculomotor decision-making, including decisions under risk [2–5]. Consistent with this view, risk-related action value and monitoring signals have been observed in SEF [6–8]. However, such activity has also been observed in other frontal areas, including orbitofrontal [9–11], cingulate [12–14], and dorsal lateral frontal cortex [15]. It is thus unknown whether the activity in SEF causally contributes to risky decisions, or if it is merely a reflection of neural processes in other cortical regions. Here, we tested a causal role of SEF in risky oculomotor choices. We found that SEF inactivation strongly reduced the frequency of risky choices. This reduction was largely due to a reduced attraction to reward uncertainty and high reward gain, but not due to changes in the subjective estimation of reward probability or average expected reward. Moreover, SEF inactivation also led to increased sensitivity to differences between expected and actual reward during free choice. Nevertheless, it did not affect adjustments of decisions based on reward history.
Phosphatidylinositol 3,5-Bisphosphate Regulates Yeast Vacuole Fusion at the Transition betweentrans-SNARE Complex Formation and Hemifusion
Authors: Miner Gregory E. , Sullivan Katherine D. , Guo Annie , Jones Brandon C. , Starr Matthew L. , Fratti Rutilio A. 
Published: August 2018

ABSTRACTPhosphoinositides (PIs) regulate myriad cellular functions including membrane fusion, as exemplified by the yeast vacuole, which uses various PIs at different stages of fusion. In light of this, the effect of phos-phatidylinositol 3,5-bisphosphate [PI(3,5)P2] on vacuole fusion remains unknown. PI(3,5)P2is made by the PI3P 5-kinase Fab1/PIKfyve and has been characterized as a regulator of vacuole fission during hyperosmotic shock where it interacts with the TRP family Ca2+channel Yvc1. Here we demonstrate that exogenously added dioctanoyl (C8) PI(3,5)P2abolishes homotypic vacuole fusion. This effect was not linked to interactions with Yvc1, as fusion was equally affected usingyvc1Δvacuoles. Thus, the effects of C8-PI(3,5)P2on fusion versus fission operate through distinct mechanisms. Further testing showed that C8-PI(3,5)P2inhibited vacuole fusion after the formation oftrans-SNARE pairs. Although SNARE complex formation was unaffected we found that C8-PI(3,5)P2strongly inhibited hemifusion. Overproduction of endogenous PI(3,5)P2by thefab1T2250Ahyperactive kinase mutant also inhibited at the hemifusion stage, bolstering the model in which PI(3,5)P2inhibits fusion when present elevated levels. Taken together, this work identifies a novel function for PI(3,5)P2as a negative regulator of vacuolar fusion. Moreover, it suggests that this lipid acts as a molecular switch between fission and fusion.
Avian predation intensity as a driver of clinal variation in colour morph frequency
Authors: Matthews Genevieve , Goulet Celine T. , Delhey Kaspar , Atkins Zak S. , While Geoffrey M. , Gardner Michael G. , Chapple David G. 
Published: August 2018

Abstract

Phenotypic variation provides the framework for natural selection to work upon, enabling adaptive evolution. One of the most discernible manifestations of phenotypic variability is colour variation. When this variation is discrete, genetically based colour pattern morphs occur simultaneously within a population.

Why and how colour polymorphisms are maintained is an evolutionary puzzle. Several evolutionary drivers have been hypothesized as influencing clinal patterns of morph frequency, with spatial variation in climate and predation being considered especially important. Despite this, no study has examined both of their roles simultaneously. The aims of this study were to: (a) examine the covariation of physiology, environmental variables and colouration at a local scale; and (b) determine if these factors and their interplay explain broad clinal variation in morph frequency.

We used the lizard Liopholis whitii as a model system, as this species displays a discrete, heritable polymorphism for colour pattern (plain‐backed, patterned morphs) whose morph frequency varies latitudinally. We measured reflectance, field activity temperatures and microhabitat structure to test for differences in crypsis, thermal biology and microhabitat selection of patterned and plain‐backed morphs within a single population where colour morphs occur sympatrically. We then used data from the literature to perform a broad‐scale analysis to identify whether these factors also explained the latitudinal variation of morph frequency in this species.

At the local scale, plain‐backed morphs were found to be less cryptic than patterned morphs while no other differences were detected in terms of thermal biology, dorsal reflectance and microhabitat use. At a broader scale, predation was the most influential factor mediating morph frequency across latitudes. However, the observed pattern of morph frequency is opposite to what the modelling results suggest in that the incidence of the least cryptic morph is highest where predation pressure is most severe. Clinal variation in the level of background matching between morphs or the potential reproductive advantage by the plain‐backed morph may, instead, be driving the observed morph frequency.

Together, these results provide key insights into the evolution of local adaptation as well as the ecological forces involved in driving the dynamics of colour polymorphism.
Towards the development of general rules describing landscape heterogeneity–multifunctionality relationships
Authors: van der Plas Fons , Allan Eric , Fischer Markus , Alt Fabian , Arndt Hartmut , Binkenstein Julia , Blaser Stefan , Blüthgen Nico , Böhm Stefan , Hölzel Norbert , Klaus Valentin H. , Kleinebecker Till , Morris Kathryn , Oelmann Yvonne , Prati Daniel , Renner Swen C. , Rillig Matthias C. , Schaefer H. Martin , Schloter Michael , Schmitt Barbara , Schöning Ingo , Schrumpf Marion , Solly Emily F. , Sorkau Elisabeth , Steckel Juliane , Steffan‐Dewenter Ingolf , Stempfhuber Barbara , Tschapka Marco , Weiner Christiane N. , Weisser Wolfgang W. , Werner Michael , Westphal Catrin , Wilcke Wolfgang , Manning Peter 
Published: August 2018

Abstract

Rapid growth of the world's human population has increased pressure on landscapes to deliver high levels of multiple ecosystem services, including food and fibre production, carbon storage, biodiversity conservation, and recreation. However, we currently lack general principles describing how to achieve this landscape multifunctionality.

We combine theoretical simulations and empirical data on 14 ecosystem services measured across 150 grasslands in three German regions. In doing so, we investigate the circumstances under which spatial heterogeneity in a driver of ecosystem functioning (an “ecosystem‐driver,” e.g., the presence of keystone species, land‐use intensification, or habitat types) increases landscape‐level ecosystem multifunctionality.

Simulations based on theoretical data demonstrated that relationships between heterogeneity and landscape multifunctionality are highly variable and can range from nonsignificant to strongly positive. Despite this variability, we could identify criteria under which heterogeneity‐landscape multifunctionality relationships were most strongly positive: this happened when multiple ecosystem services responded contrastingly (both positively and negatively) to an ecosystem‐driver.

These findings were confirmed using empirical data, which showed that heterogeneity in land‐use intensity (LUI) promoted landscape multifunctionality in cases where functions with both positive (e.g., plant biomass) and negative (e.g., flower cover) responses to land use intensification were included. For example, the simultaneous provisioning of ecosystem functions related to forage production (generally profiting from land‐use intensification), biodiversity conservation and recreation (generally decreasing with land‐use intensification) was highest in landscapes consisting of sites varying in LUI.

Synthesis and applications. Our findings show that there are general principles governing landscape multifunctionality. A knowledge of these principles may support land management decisions. For example, knowledge of relationships between ecosystem services and their drivers, such as land use type, can help estimate the consequences of increasing or decreasing heterogeneity for landscape‐level ecosystem service supply, although interactions between landscape units (e.g., the movement of pollinators) must also be considered.
Winter cover crop legacy effects on litter decomposition act through litter quality and microbial community changes
Authors: Barel Janna M. , Kuyper Thomas W. , Paul Jos , de Boer Wietse , Cornelissen Johannes H. C. , De Deyn Gerlinde B. 
Published: August 2018

AbstractIn agriculture, winter cover crop (WCC) residues are incorporated into the soil to improve soil quality, as gradual litter decomposition can improve fertility. Decomposition rate is determined by litter quality, local soil abiotic and biotic properties. How these factors are interlinked and influenced by cropping history is, however, unclear.We grewWCCmonocultures and mixtures in rotation with main cropsAvena sativa(oat) andCichorium endivia(endive) and tested how crop rotation influencesWCClitter quality, abiotic and biotic soil conditions, and litter decomposition rates. To disentangleWCClitter quality effects fromWCCsoil legacy effects on decomposition, we tested how rotation history influences decomposition of standard substrates and explored the underlying mechanisms.In a common environment (e.g. winter fallow plots),WCCdecomposition rate constants (k) correlated negatively with litter C, lignin and, surprisingly, N content, due to strong positive correlations among these traits. Plots with a history of fast‐decomposingWCCs exhibited faster decomposition of their own litters as well as of the standard substrates filter paper and rooibos tea, as compared to winter fallow plots.WCCtreatments differentially affected soil microbial biomass, as well as soil organic matter and mineral nitrogen content.WCC‐induced soil changes affected decomposition rates. Depending on the main crop rotation treatment, legacy effects were attributed to biomass input ofWCCs and their litter quality or changes in microbial biomass.Synthesis and applications. These results demonstrate that decomposition in cropping systems is influenced directly through crop residues, as well as through crop‐induced changes in soil biotic properties. Rotation history influences decomposition, wherein productive winter cover crops (WCC) with low lignin content decompose fast and stimulate the turnover of both own and newly added residues via their knock‐on effect on the soil microbial community. Thus, WCC have promise for sustainable carbon‐ and nutrient‐cycling management through litter feedbacks.
Rising pregabalin use and misuse in Australia: trends in utilization and intentional poisonings
Authors: Cairns Rose , Schaffer Andrea L. , Ryan Nicole , Pearson Sallie‐Anne , Buckley Nicholas A. 
Published: August 2018

AbstractBackground and aimsPregabalin is a gamma‐aminobutyric acid (GABA) analogue, used to treat neuropathic pain and epilepsy. Pregabalin was registered in Australia in 2005, and subsidized publically in 2013. We aimed to describe Australian patterns of pregabalin use and intentional poisoning, and identify people potentially at high risk of misuse.Design and settingPopulation‐based retrospective cohort study of dispensings in the 10% sample of Australian Pharmaceutical Benefits Scheme (July 2012–February 2017); intentional poisoning calls to New South Wales Poisons Information Centre (NSWPIC) (2004–2016); intentional poisonings in two Australian toxicology service databases; and poisoning fatalities in NSW coronial records (2005–2016).ParticipantsA total of 122 572 people dispensed pregabalin, people with intentional pregabalin overdoses managed by NSWPIC and the toxicology services and pregabalin‐associated deaths referred to the NSW coroner.MeasurementsTrends in dispensing, poisoning, death; demographics and patient characteristics, proportion of users at high risk of misuse (latent class analysis, LCA) and characteristics of high‐risk users.FindingsPregabalin dispensing increased by 73 424 per year [95% confidence interval (CI) = 61726–85 121 P < 0.001] between 2013 and 2016. NSWPIC received 1158 reports of intentional pregabalin poisonings, with a 53.8% increase per year, 2005–2016 (95% CI = 44.0–64.2%, P < 0.001). We identified 88 pregabalin‐associated deaths, 57.8% yearly increase (95% CI = 30.0–91.6%, P < 0.001). Patients overdosing on pregabalin commonly co‐ingested opioids, benzodiazepines and illicit drugs, and had high rates of psychiatric and substance use comorbidities; 14.7% of pregabalin users were classed by the LCA as at high risk of misuse, and were more likely to be younger, male, co‐prescribed benzodiazepines or opioids, have more individual prescribers and higher pregabalin strengths dispensed.ConclusionsThere has been a dramatic increase in pregabalin use, poisonings and deaths in Australia since it became subsidized publicly in 2013. One in seven Australians dispensed pregabalin appears to be at high risk of misuse.
Patterns of use and optimal timing of antenatal corticosteroids in twin compared with singleton pregnancies
Authors: Rottenstreich Amihai , Levin Gabriel , Kleinstern Geffen , Haj Yahya Rani , Rottenstreich Misgav , Yagel Simcha , Elchalal Uriel 
Published: August 2018

AbstractIntroductionPrevious reports have shown that suboptimal antenatal corticosteroids administration occurs in most cases. However, as multifetal gestations were either excluded or constituted a small proportion of the participants in these studies, little is known about the patterns of use of antenatal corticosteroids in twin pregnancies.Material and methodsWe reviewed the records of women who received antenatal corticosteroids and delivered between 240/7 and 346/7 weeks of gestation during 2015‐2017 at 2 university hospitals. Optimal antenatal corticosteroids timing was defined as delivery ≥24 hours ≤7 days from the previous antenatal corticosteroids course.ResultsOf 424 pregnancies, 307 (72.4%) were singleton and 117 were (27.6%) twin. For twin compared with singleton pregnancies, gestational age at initial antenatal corticosteroids administration was lower (P = 0.02), the proportion of deliveries within the optimal window of the initial antenatal corticosteroids course was lower (19.7% vs 33.2%, P = 0.001), and the proportion of women eligible for a rescue antenatal corticosteroids course was higher (58.1% vs 32.9%, P < 0.0001). However, despite similar rates of rescue antenatal corticosteroids administration (P = 0.64), the overall rate of delivery within any optimal window (either initial or rescue course) was lower in twin than singleton pregnancies (26.5% vs 42.3%, P = 0.004), and the antenatal corticosteroids‐to‐delivery interval was longer (median 6.9 vs 4.2 days, P = 0.0009). In multivariate analysis, optimal antenatal corticosteroids administration was negatively associated with twin pregnancy (P = 0.04) and preterm labor (P = 0.05), and positively associated with the presence of gestational hypertensive disorders (P = 0.03).ConclusionsTwin pregnancy is an independent risk factor for suboptimal antenatal corticosteroids administration. Directed efforts should be made to improve the utilization of antenatal corticosteroids in this vulnerable group of women.