bluuebunny/crossref_metadata_2025_split huggingface dataset:
Condensin-dependent chromatin condensation represses transcription globally during quiescence
Authors: Swygert Sarah G. , Kim Seungsoo , Wu Xiaoying , Fu Tianhong , Hsieh Tsung-Han , Rando Oliver J. , Eisenman Robert N. , Shendure Jay , McKnight Jeffrey N. , Tsukiyama Toshio 
Published: May 2018

SUMMARYQuiescence is a stress-resistant state in which cells reversibly exit the mitotic cell cycle and suspend most cellular processes. Quiescence is essential for stem cell maintenance and its misregulation is implicated in tumor formation. One of the conserved hallmarks of quiescent cells, from Saccharomyces cerevisiae to humans, is highly condensed chromatin. Here, we use Micro-C XL to map chromatin contacts at single-nucleosome resolution genome-wide to elucidate mechanisms and functions of condensed chromatin in quiescent S. cerevisiae cells. We describe previously uncharacterized chromatin domains on the order of 10-60 kilobases that in quiescent cells are formed by condensin-mediated chromatin loops. Conditional depletion of condensin prevents chromatin condensation during quiescence entry and leads to widespread transcriptional de-repression. We further demonstrate that condensin-dependent chromatin compaction is conserved in quiescent human fibroblasts. We propose that condensin-dependent condensation of chromatin represses transcription throughout the quiescent cell genome.
PKMζ in the nucleus accumbens acts to dampen cocaine seeking
Authors: McGrath Anna G. , Lenz Jeffrey D. , Briand Lisa A. 
Published: May 2018

AbstractThe constitutively active, atypical protein kinase C, protein kinase M-ζ (PKMζ), is exclusively expressed in the brain and its expression increases following exposure to drugs of abuse. However, the limitations of currently available tools have made it difficult to examine the role of PKMζ in cocaine addiction. The current study demonstrates that constitutive deletion of PKMζ potentiates cue-induced reinstatement of cocaine seeking and increases both food and cocaine taking, without affecting cue-driven food seeking in both male and female mice. Conditional deletion of PKMζ within the nucleus accumbens recapitulated the increase in cocaine taking and seeking seen in the constitutive knockout mice, but only in male animals. Site-specific knockdown of PKMζ in the nucleus accumbens had no effect on cocaine or natural reward behaviors in female mice. Taken together these results indicate that PKMζ may act to dampen addictive phenotypes. Furthermore, these results indicate that PKMζ is playing divergent roles in reward seeking in males and females.
Inhibition of cell fate repressors secures the differentiation of the touch receptor neurons ofCaenorhabditis elegans
Authors: Zheng Chaogu , Jin Felix Qiaochu , Trippe Brian Loeber , Wu Ji , Chalfie Martin 
Published: May 2018

AbstractTerminal differentiation generates the specialized features and functions that allow postmitotic cells to acquire their distinguishing characteristics. This process is thought to be controlled by transcription factors called “terminal selectors” that directly activate a set of downstream effector genes. InCaenorhabditis elegansthe differentiation of both the mechanosensory touch receptor neurons (TRNs) and the multidendritic nociceptor FLP neurons utilize the terminal selectors UNC-86 and MEC-3. The FLP neurons fail to activate TRN genes, however, because a complex of two transcriptional repressors (EGL-44/EGL-46) prevents their expression. Here we show that the ZEB family transcriptional factor ZAG-1 promotes TRN differentiation not by activating TRN genes but by preventing the expression of EGL-44/EGL-46. Since EGL-44/EGL-46 also inhibits the production of ZAG-1, these proteins form a bistable, negative feedback loop that regulates the choice between the two neuronal fates.Summary statement:Transcriptional repressors regulate binary fate choices through reciprocal inhibition during terminal neuronal differentiation. Specifically, ZEB family transcription factor safeguards fate specification of touch receptor neuron by inhibiting TEA domain-containing repressor.
Evaluating the information content of shallow shotgun metagenomics
Authors: Hillmann Benjamin , Al-Ghalith Gabriel A. , Shields-Cutler Robin R. , Zhu Qiyun , Gohl Daryl M. , Beckman Kenneth B. , Knight Rob , Knights Dan 
Published: May 2018

ABSTRACTAlthough microbial communities are associated with many aspects of human, environmental, plant, and animal health, there exists no cost-effective method for precisely characterizing species and genes present in such communities. While deep whole-genome shotgun (WGS) sequencing provides the highest-level of taxonomic and functional resolution, it is often prohibitively expensive for large-scale studies. The prevailing alternative, high-throughput 16S rRNA gene amplicon sequencing (16S), often does not resolve taxonomy past the genus level and provides only moderately accurate predictions of the functional profile; thus, there is currently no widely accepted approach to affordable, high-resolution, taxonomic and functional microbiome analysis. To address this technology gap, we evaluated the information content of shallow shotgun sequencing with as low as 0.5 million sequences per sample as an alternative to 16S sequencing for large human microbiome studies. We describe a library preparation protocol enabling shallow shotgun sequencing at approximately the same per-sample cost as 16S. We analyzed multiple real and simulated biological data sets, including two novel human stool samples with ultra-deep sequencing of 2.5 billion sequences per sample, and found that shallow shotgun recovers accurate species-level taxonomic and functional profiles of the human microbiome. We recognize and discuss some of the inherent limitations of shallow shotgun sequencing, and note that 16S sequencing remains a valuable and important method for taxonomic profiling of novel environments. Although deep WGS remains the gold standard for high-resolution microbiome analysis, we recommend that researchers consider shallow shotgun sequencing as a useful alternative to 16S for large-scale human microbiome research studies.
Species distribution, virulence factors and antimicrobial resistance of Acinetobacter spp. isolates from dogs and cats: a preliminary study
Authors: Kimura Yui , Harada Kazuki , Shimizu Takae , Sato Tomomi , Kajino Akari , Usui Masaru , Tamura Yutaka , Tsuyuki Yuzo , Miyamoto Tadashi , Ohki Asami , Watarai Masahisa 
Published: May 2018

ABSTRACTIn this study, the prevalence of virulence factors and antimicrobial resistance among 67 Acinetobacter spp. isolates, consisting of 21 Acinetobacter baumannii and 46 non‐baumannii Acinetobacter obtained from companion animals, was investigated. PCR analysis showed that the most prevalent virulence gene was afa/draBC (29.9%), followed by papC (22.4%) and cvaC (20.9%). Antimicrobial susceptibility testing revealed that resistance to gentamicin (14.9%) and ciprofloxacin (11.9%) was relatively prevalent. Five gentamicin‐ and/or ciprofloxacin‐resistant A. baumannii strains were assigned to ST25, ST149, ST164, ST203 and ST1198. All ciprofloxacin‐resistant isolates harbored point mutations in gyrA and/or parC. To the best of our knowledge, this is the first report of preliminary monitoring of animal‐origin Acinetobacter spp. in Japan.
Experience during development triggers between‐individual variation in behavioural plasticity
Authors: Urszán Tamás János , Garamszegi László Zsolt , Nagy Gergely , Hettyey Attila , Török János , Herczeg Gábor 
Published: May 2018

Abstract

Behavioural consistency within and across behaviours (animal personality and behavioural syndrome, respectively) has been vigorously studied in the last decade, leading to the emergence of “animal personality” research. It has been proposed recently that not only mean behaviour (behavioural type), but the environmentally induced behavioural change (behavioural plasticity) might also differ between individuals within populations.

While case studies presenting between‐individual variation in behavioural plasticity have started to accumulate, the mechanisms behind its emergence are virtually unknown. We have recently demonstrated that ecologically relevant environmental stimuli during ontogeny are necessary for the development of animal personality and behavioural syndromes. However, it is unknown whether between‐individual variation in behavioural plasticity is hard‐wired or induced.

Here, we tested whether experience with predation during development affected predator‐induced behavioural plasticity in Rana dalmatina tadpoles. We ran a common garden experiment with two ontogenetic predation treatments: tadpoles developed from hatching in either the presence or absence of olfactory predator stimuli. Then, we assayed all tadpoles repeatedly for activity and risk‐taking both in the absence and presence of olfactory predator stimuli.

We found that (a) between‐individual variation in predator‐induced behavioural plasticity was present only in the group that developed in the presence of olfactory stimuli from predators and (b) previous experience with predatory stimuli resulted in lower plastic response at the group level. The latter pattern resulted from increased between‐individual variation and not from universally lower individual responses. We also found that experience with predation during development increased the predictability (i.e. decreased the within‐individual variation unrelated to environmental change) of activity, but not risk‐taking. In line with this, tadpoles developing under perceived predatory risk expressed their activity with higher repeatability.

We suggest that ecologically relevant environmental stimuli are not only fundamental for the development of animal personality and behavioural syndromes, but also for individual variation in behavioural plasticity. Thus, experience is of central importance for the emergence of individual behavioural variation at many levels.
Influence of prehospital airway management on neurological outcome in patients transferred to a heart attack centre following out‐of‐hospital cardiac arrest
Authors: Edwards Timothy , Williams Julia , Cottee Michaela 
Published: May 2018

AbstractObjectiveTo describe the association between prehospital airway management and neurological outcomes in patients transferred by the ambulance service directly to a heart attack centre (HAC) post‐return of spontaneous circulation (ROSC).MethodsA retrospective observational cohort study in which ambulance records were reviewed to determine prehospital airway management strategy and collect physiological and demographic data. HAC notes were obtained to determine in‐hospital management and quantify neurological outcome via the cerebral performance category (CPC) scale. Statistical analyses were performed via χ2‐test, Mann–Whitney U‐test, odds ratios and binomial logistic regression.ResultsTwo hundred and twenty patients were included between August 2013 and August 2014, with complete outcome data obtained for 209. Median age of patients with complete outcome data was 67 years and 71.3% were male (n = 149). Airway management was provided using a supraglottic airway (SGA) in 72.7% of cases (n = 152) with the remainder undergoing endotracheal intubation (ETI). There was no significant difference in the proportion of patients who had a good neurological outcome (CPC 1 and 2) at discharge between the SGA and ETI groups (P = 0.29). Binomial logistic regression incorporating factors known to influence outcome demonstrated no significant difference in neurological outcomes between the SGA and ETI groups (adjusted OR 0.73, 95% CI 0.34–1.56).ConclusionIn this observational study, there was no significant difference in the proportion of good neurological outcomes in patients managed with SGA versus ETI during cardiac arrest and in the post‐ROSC transfer phase. Further research is required to provide more definitive evidence in relation to the optimal airway management strategy in out‐of‐hospital cardiac arrest.
Diversity and participation in private apartment buildings: a review of the literature
Authors: Liu Edgar , Easthope Hazel , Ho Christina , Buckle Caitlin 
Published: May 2018

AbstractContemporary urban life has been shaped by two momentous shifts over the twentieth century: these shifts are increasing global mobility and increasing housing density, and both have required changes to personal approaches to dwelling. They have been pronounced in Australia, which has moved from an imperial‐colonial century to an Asian century in just over 100 years. Coupled with compact city policies in some regions, increased international migration has resulted in urban populations becoming more ethno‐culturally diverse, and encouraged urban residents to live in closer proximity to each other. Such trends are evident in the expansion of apartment living in cities. In the academic literature, each of these global shifts has been addressed separately, with much less attention being given to the two together. This oversight is especially the case in places where these changes are experienced most profoundly—private multi‐owned residential buildings that many and growing numbers of urban residents call home. The oversight is concerning because successful apartment living requires sustained participation and cooperation—how we dwell with each other matters. Without such forms of engagement and courtesies, apartment communities cannot run effectively or cohesively in terms of associational participation in management or of the everyday encounters of social life. Arguably, because global mobility is now so pronounced, engagement and civility require that people are respectfully observant of ethno‐diversity. Yet our review of the existing literature on multicultural encounters and participation in multi‐owned private apartment buildings suggests the need for more research on the intersections among global mobility, housing density, and apartment living. This paper begins to bridge this gap.
β‐blockers interfere with cell homing receptors and regulatory proteins in a model of spontaneously hypertensive rats
Authors: Eibel Bruna , Kristochek Melissa , Peres Thiago R. , Dias Lucinara D. , Dartora Daniela R. , Casali Karina R. , Kalil Renato A. K. , Lehnen Alexandre M. , Irigoyen Maria Claudia , Markoski Melissa M. 
Published: May 2018

AbstractAimTo examine the interference of β‐blockers with the chemokine stromal cell‐derived factor‐1 (SDF‐1) found in cell homing receptors, C‐X‐C chemokine receptor type 4 (CXCR‐4) and CXCR‐7, and regulatory proteins of homing pathways, we administered atenolol, carvedilol, metoprolol, and propranolol for 30 days using an orogastric tube to hypertensive rats.MethodWe collected blood samples before and after treatment and quantified the levels of SDF‐1 with enzyme‐linked immunosorbent assay (ELISA). On day 30 of treatment, the spontaneously hypertensive rats (SHR) were euthanized, and heart, liver, lung, and kidney tissues were biopsied. Proteins were isolated for determining the expression of CXCR‐4, CXCR‐7, GRK‐2 (G protein‐coupled receptors kinase 2), β‐arrestins (β1‐AR and β2‐AR), and nuclear factor kappa B (NFκB).ResultsWe found that the study drugs modulated these proteins, and metoprolol and propranolol strongly affected the expression of β1‐AR (P = .0102) and β2‐AR (P = .0034).Conclusionβ‐blockers modulated tissue expression of the proteins and their interactions following 30 days of treatment. It evidences that this class of drugs can interfere with proteins of cell homing pathways.
In situ simulation of sea‐level rise impacts on coastal wetlands using a flow‐through mesocosm approach
Authors: Stachelek Jemma , Kelly Stephen P. , Sklar Fred H. , Coronado‐Molina Carlos , Troxler Tiffany , Bauman Laura 
Published: May 2018

AbstractThe impact of sea level rise (SLR) on coastal wetlands is dependent on the net effects of increased inundation and saltwater intrusion. The need for accurate projections ofSLRimpacts has motivated several experimental mesocosm studies aimed at detailed investigations on wetland biogeochemical cycling. However, the degree with which they accurately reproduce field conditions remains unknown because they have primarily been laboratory based using relatively small sediment volumes (10–200 L) treated over short time periods.As a first step towards addressing these issues, we present a novel mesocosm device and portable methodology for long‐termSLRsimulation via in situ saltwater additions to relatively large sediment volumes (approximately 1,000 L). The device (chamber) consists of two interlocking polycarbonate cylinders with an internal diameter of 1.4 m. Each cylinder has holes drilled in the side to facilitate water exchange. The outer cylinder (collar) can be rotated to one of two possible positions. The first position produces alignment of the inner cylinder holes with the collar holes, whereas the second position offsets the holes to eliminate water exchange and contain salt additions (doses).Our device design and dosing scheme produced higher porewater salinities in the sediments of treatment mesocosms relative to control mesocosm sediments. In addition, we observed low incidence of elevated porewater salinity outside of the chamber walls and no measurable salt contamination of control plots.WidespreadSLRsimulations in a variety of geographical settings, whether with our proposed design or some other design, would likely help reduce some of the general uncertainties regarding the sensitivity of coastal wetlands toSLRand saltwater intrusion.
RRPP: An r package for fitting linear models to high‐dimensional data using residual randomization
Authors: Collyer Michael L. , Adams Dean C. 
Published: May 2018

Abstract

Residual randomization in permutation procedures (RRPP) is an appropriate means of generating empirical sampling distributions for ANOVA statistics and linear model coefficients, using ordinary or generalized least‐squares estimation. This is an especially useful approach for high‐dimensional (multivariate) data.

Here, we present an r package that provides a comprehensive suite of tools for applying RRPP to linear models. Important available features include choices for OLS or GLS coefficient estimation, data or dissimilarity matrix analysis capability, choice among types I, II, or III sums of squares and cross‐products, various effect size estimation methods, and an ability to perform mixed‐model ANOVA.

The lm.rrpp function is similar to the lm function in many regards, but provides coefficient and ANOVA statistics estimates over many random permutations. The S3 generic functions commonly used with lm also work with lm.rrpp. Additionally, a pairwise function provides statistical tests for comparisons of least‐squares means or slopes, among designated groups. Users have many options for varying random permutations. Compared to similar available packages and functions, RRPP is extremely fast and yields comprehensive results for downstream analyses and graphics, following model fits with lm.rrpp.

The RRPP package facilitates analysis of both univariate and multivariate response data, even when the number of variables exceeds the number of observations.
How have US banks adopted the Financial Accounting Standards Board's Level 3 fair value disclosure rules?
Authors: Keshk Walied , Lu Hung‐Yuan (Richard) , Mande Vivek 
Published: May 2018

AbstractWe examine how banks have complied with the Financial Accounting Standards Board's disclosure rules on Level 3 recurring fair value measurements. We document widespread noncompliance with the basic disclosure requirements. We also find that the noncompliant banks are smaller in size and are associated with lower audit quality, lower institutional ownership and less effective internal controls. Our results should be of use to regulators, auditors and audit committees in the United States, Australia and other countries for assessing the likelihood of noncompliance with fair value disclosure rules and improving the quality of fair value disclosures provided to investors.
Predicting FTSE 100 returns and volatility using sentiment analysis
Authors: Johnman Mark , Vanstone Bruce James , Gepp Adrian 
Published: May 2018

AbstractWe investigate the statistical and economic effect of positive and negative sentiment on daily excess returns and volatility in the FTSE 100 index, using business news articles published by the Guardian Media Group between 01/01/2000 and 01/06/2016. The analysis indicates that while business news sentiment derived from articles aimed at retail traders does not influence excess returns in the FTSE 100 index, it does affect volatility, with negative sentiment increasing volatility and positive sentiment reducing it. Further, an ETF‐based trading strategy based on these findings is found to outperform the naïve buy‐and‐hold approach.
The role of intellectual property rights in seed technology transfer through trade: evidence from U.S. field crop seed exports
Authors: Zhou Minyu , Sheldon Ian , Eum Jihyun 
Published: May 2018

AbstractA panel of 134 countries over the period 1985–2010 is used to evaluate the effect of intellectual property rights (IPRs) on field crop seed imports from the United States. Based on estimating a gravity equation using the Heckman selection and Poisson fixed‐effects panel econometric methods, the results indicate that membership of countries in both the International Union for the Protection of New Varieties of Plants and the Trade‐Related Aspects of Intellectual Property Rights Agreement of the World Trade Organization have a positive and statistically significant effect on their imports of U.S. field crop seeds. These results, however, are also sensitive to both income level of importing countries and better enforcement of IPRs by those countries.
Renters, landlords, and farmland stewardship
Authors: Deaton B. James , Lawley Chad , Nadella Karthik 
Published: May 2018

AbstractAre farmers better stewards of the land they own than the land they rent from others? We answer this question using a data set that identifies Ontario farmers’ conservation practices on their own land as well as the land they rent. Using a fixed‐effects regression approach, we find that the role of tenure varies for different types of conservation practices. Farmers were found to be just as likely to adopt a machinery‐related practice such as conservation tillage on their rented land as that land which they own. On the other hand, farmers were found to be less likely to adopt site‐specific conservation practices such as planting cover crops on rented land. However, this effect diminishes as the expected length of the rental relationship increases when the landlord has a farming background.