bluuebunny/crossref_metadata_2025_split huggingface dataset:
Maternal high-fat diet induces sex-specific changes to glucocorticoid and inflammatory signaling in response to corticosterone and lipopolysaccharide challenge in adult rat offspring
Authors: Wijenayake Sanoji , Rahman Mouly F. , Lum Christine M.W. , De Vega Wilfred C. , Sasaki Aya , McGowan Patrick O. 
Published: September 2019

ABSTRACTBackgroundAcute elevations in endogenous corticosterone (CORT) with psychosocial stress or exogenous administration potentiate inflammatory gene expression. Maternal obesity as a result of high-fat diet (HFD) consumption has been linked to higher basal levels of neuroinflammation, including increased expression of pro-inflammatory genes in the amygdala. These findings suggest that exposure to maternal HFD may elicit pro-inflammatory responses in the presence of an immune stressor such as lipopolysaccharide (LPS), a component of gram-negative bacteria, as well as acute elevated CORT.MethodsRat offspring were exposed to maternal HFD or control diet (CHD) throughout pre and postnatal development until weaning, when all offspring were provided CHD until adulthood. In adulthood, offspring were ‘challenged’ with administration of exogenous CORT, to simulate an acute physiological stress, LPS, to induce an immune stress, or both. qPCR was used to measure transcript abundance of CORT receptors and downstream inflammatory genes in the amygdala, hippocampus and prefrontal cortex, brain regions that mediate neuroendocrine and behavioral responses to stress.ResultsHFD female offspring exhibited elevations in anti-inflammatory transcripts, whereas HFD male offspring responded with greater pro-inflammatory gene expression to simultaneous CORT and LPS administration.ConclusionsThese findings suggest that exposure to maternal HFD leads to sex-specific alterations that may alter inflammatory responses in the brain, possibly as an adaptive response to basal inflammation.
Risk factors associated with Avian Influenza subtype H9 outbreaks on poultry farms in Kathmandu valley, Nepal
Authors: Gompo Tulsi Ram , Shah Bikash Raj , Karki Surendra , Koirala Pragya , Maharjan Manju , Bhatt Diker Dev 
Published: September 2019

AbstractPoultry sector contributes to four percent in national GDP of Nepal. However, this sector is under threat with periodic outbreaks of Avian Influenza (AI) subtypes H5 and H9 since 2009. This has been both a both public health threat and an economic issue. Since last three years, outbreaks of AI subtype H9 has caused huge economic losses in major poultry producing areas of Nepal. However, the risk factors associated with these outbreaks have not been assessed. A retrospective case-control study was conducted from April 2018 to May 2019 in Kathmandu Valley to understand the risk factors associated with AI subtype H9 outbreaks. Out of 100 farms selected, 50 were “case” farms, confirmed positive to H9 at Central Veterinary Laboratory, Kathmandu, and other 50 farms were “control” farms, matched for farm size and locality within a radius of three km from the case farm. Each farm was visited to collect information using semi-structured questionnaire. Nineteen potential risk factors were included in the questionnaire under the broad categories: birds and farm characteristics, management aspects and biosecurity status of the farms. Univariable and multivariable logistic regression analysis were conducted to calculate corresponding odds ratios. Identified risk factors associated with AI subtype H9 outbreaks in Kathmandu valley were: “Birds of age 31-40 days” (OR= 11.31, 95% CI: 1.31-98.02, p=0.028), “Older farms operating for >5 years” (OR= 10.9, 95% CI: 1.76-66.93, p=0.01), “Commercial layers farms” (OR=36.0, 95% CI: 0.97-1332.40, p=0.052), “Used stream water to water birds (OR= 5.7, 95% CI: 1.10-30.13, p=0.039)”, “Farms without practice of fumigation after each batch of poultry (OR= 4, 95% CI: 1.44-13.13, p=0.009)., “Farm with previous history of AI (OR= 13.8, 95% CI: 1.34-143.63, p = 0.028), “Did not applied farm boots (OR= 2.58, 95% CI: 0.98-6.80, p= 0.055), “Visitors allowed to enter the farms (OR= 2.5, 95% CI: 1.011-6.17, p = 0.047) and “No foot bath at entry of farms (OR= 3.3, 95% CI: 1.29-8.38, p = 0.013). This study depicts that outbreaks of AI subtype H9 in Kathmandu valley was related to poor management practices and biosecurity in the poultry farms. We suggest improving management practices and increase biosecurity in the farms to reduce incidences of AI subtype H9 outbreaks in Kathmandu valley.
Molecular patterning during the development ofPhoronopsis harmerireveals similarities to rhynchonelliform brachiopods
Authors: Andrikou Carmen , Passamaneck Yale J. , Lowe Chris J. , Martindale Mark Q. , Hejnol Andreas 
Published: September 2019

AbstractBackgroundAnswering the question how conserved patterning systems are across evolutionary lineages requires a broad taxon sampling. Phoronid development has previously been studied using fate mapping and morphogenesis, yet molecular descriptions are missing. Here we report the expression patterns of the evolutionarily conserved anterior (otx, gsc, six3/6, nk2.1), posterior (cdx, bra) and endomesodermal (foxA, gata4/5/6, twist) markers in the phoronidPhoronopsis harmeri.ResultsThe transcription factorsfoxA, gata4/5/6andcdxshow conserved expression in patterning the development and regionalization of the phoronid embryonic gut, withfoxAexpressed in the presumptive foregut,gata4/5/6demarcating the midgut andcdxconfined to the hindgut. Surprisingly,brachyury, an evolutionary conserved transcription factor often associated with gastrulation movements and patterning of the mouth and hindgut, seems to be unrelated with gastrulation and mouth patterning in phoronids. Furthermore,six3/6, a well-conserved anterior marker, shows a remarkably dynamic expression, demarcating not only the apical organ and the oral ectoderm, but also clusters of cells of the developing midgut and the anterior mesoderm, similar to what has been reported for brachiopods, bryozoans and some deuterostome Bilateria.ConclusionsOur comparison of gene expression patterns with other studied Bilateria reveals that the timing of axis determination and cell fate distribution of the phoronid shows highest similarities to rhynchonelliform brachiopods. Despite these similarities, the phoronidP. harmerishows also particularities in its development, which hint to divergences in the arrangement of gene regulatory networks responsible for germ layer formation and axis specification.
Rapid evolution at the Drosophila telomere: transposable element dynamics at an intrinsically unstable locus
Authors: McGurk Michael P , Dion-Côté Anne-Marie , Barbash Daniel A 
Published: September 2019

ABSTRACTDrosophila telomeres have been maintained by three families of active transposable elements (TEs),HeT-A, TAHREandTART, collectively referred to as HTTs, for tens of millions of years, which contrasts with an unusually high degree of HTT interspecific variation. While the impacts of conflict and domestication are often invoked to explain HTT variation, the telomeres are unstable structures such that neutral mutational processes and evolutionary tradeoffs may also drive HTT evolution. We leveraged population genomic data to analyze nearly 10,000 HTT insertions in 85D. melanogastergenomes and compared their variation to other more typical TE families. We observe that occasional large-scale copy number expansions of both HTTs and other TE families occur, highlighting that the HTTs are, like their feral cousins, typically repressed but primed to take over given the opportunity. However, large expansions of HTTs are not caused by the runaway activity of any particular HTT subfamilies or even associated with telomere-specific TE activity, as might be expected if HTTs are in strong genetic conflict with their hosts. Rather than conflict, we suggest instead that distinctive aspects of HTT copy number variation and sequence diversity largely reflect telomere instability, with HTT insertions being lost at much higher rates than other TEs elsewhere in the genome. We extend previous observations that telomere deletions occur at a high rate, and surprisingly discover that more than a third do not appear to have been healed with an HTT insertion. We also report that some HTT families may be preferentially activated by the erosion of whole telomeres, implying the existence of HTT-specific host control mechanisms. We further suggest that the persistent telomere localization of HTTs may reflect a highly successful evolutionary strategy that trades away a stable insertion site in order to have reduced impact on the host genome. We propose that HTT evolution is driven by multiple processes with niche specialization and telomere instability being previously underappreciated and likely predominant.
Two parallel arms of the heterochronic pathway direct coordinated juvenile-to-adult transition through distinct LIN-29 isoforms
Authors: Azzi Chiara , Aeschimann Florian , Neagu Anca , Großhans Helge 
Published: September 2019

AbstractRobust organismal development relies on temporal coordination of disparate physiological processes. InCaenorhabditis elegans, the timely transition from juvenile to adult is controlled by the heterochronic pathway, a regulatory cascade of conserved proteins and small RNAs. The heterochronic pathway culminates in accumulation of the transcription factor LIN-29, which triggers coordinated execution of juvenile-to-adult (J/A) transition events. Here, we reveal that two LIN-29 isoforms fulfill distinct functions during the J/A transition. We show that the functional differences between the isoforms do not stem from differences in their sequences, but from their distinct spatiotemporal expression, and we propose that distinct LIN-29 dose sensitivities of the individual J/A transition events help to ensure their temporal ordering. We demonstrate that uniquelin-29isoform expression patterns are generated by the RNA-binding protein LIN-41 forlin-29a, and the transcription factor HBL-1 forlin-29b. By regulating both HBL-1 and LIN-41, the RNA-binding protein LIN-28 coordinates LIN-29 isoform activity. Thus, our findings reveal that a coordinated transition from juvenile to adult involves branching of a linear pathway to achieve timely control of multiple events.
In silico analysis of long non-coding RNAs in medulloblastoma and its subgroups
Authors: Joshi Piyush , Perera Ranjan J. 
Published: September 2019

AbstractMedulloblastoma is the most common malignant pediatric brain tumor with high fatality rate. Recent large-scale studies utilizing genome-wide technologies have sub-grouped medulloblastomas into four major subgroups: wingless (WNT), sonic hedgehog (SHH), group 3, and group 4. However, there has yet to be a global analysis of long non-coding RNAs, a crucial part of the regulatory transcriptome, in medulloblastoma. Here, we performed bioinformatic analysis of RNA-seq data from 175 medulloblastoma patients. Differential lncRNA expression sub-grouped medulloblastomas into the four main molecular subgroups. Some of these lncRNAs were subgroup-specific, with a random forest-based machine-learning algorithm identifying an 11-lncRNA diagnostic signature. We also validated the diagnostic signature in patient derived xenograft (PDX) models. We further identified a 17-lncRNA prognostic model using LASSO based penalized Cox’ PH model (Score HR= 13.6301, 95% CI= 8.857-20.98, logrank p-value=< 2e-16). Our analysis represents the first global lncRNA analysis in medulloblastoma. Our results identify putative candidate lncRNAs that could be evaluated for their functional role in medulloblastoma genesis and progression or as diagnostic and prognostic biomarkers.
Hedgehog pathway activation through conformational blockade of the Patched sterol conduit
Authors: Zhang Yunxiao , Lu Wan-Jin , Bulkley David P. , Liang Jiahao , Ralko Arthur , Roberts Kelsey J. , Li Anping , Cho Wonhwa , Cheng Yifan , Manglik Aashish , Beachy Philip A. 
Published: September 2019

AbstractActivation of the Hedgehog pathway may have therapeutic value for improved bone healing, taste receptor cell regeneration, and alleviation of colitis or other conditions. Systemic pathway activation, however, may be detrimental and therapeutic application has been difficult for lack of agents amenable to tissue targeting. We have developed a novel agonist, a conformation-specific nanobody against the Hedgehog receptor Patched1. This nanobody potently activates the Hedgehog pathway in vitro and in vivo by stabilizing an alternative conformation of a Patched1 “switch helix”, as revealed by cryo-EM structure determination. Although this conformation likely constitutes part of the transport cycle, nanobody-trapping disrupts the cycle and prevents substrate movement through the Patched1 sterol conduit. Our conformation-selective nanobody approach provides a new route to the development of transporter-related pharmacologic agents and may be generally applicable to the study of other transporters.
Adaptive Tree Proposals for Bayesian Phylogenetic Inference
Authors: Meyer X. 
Published: September 2019

AbstractBayesian inference of phylogenies with MCMC is without a doubt a staple in the study of evolution. Yet, this method still suffers from a practical challenge identified more than two decades ago: designing tree topology proposals that efficiently sample the tree space. In this article, I introduce the concept of tree topology proposals that adapt to the posterior distribution as it is estimated. I use this concept to elaborate two adaptive variants of existing proposals and an adaptive proposal based on a novel design philosophy in which the structure of the proposal is informed by the posterior distribution of trees. I investigate the performance of these proposals by first presenting a metric that captures the performance of each proposals within a mixture. Using this metric, I then compare the adaptive proposals performance to the performance of standard and parsimony-guided proposals on 11 empirical datasets. Using adaptive proposals led to consistent performance gains and resulted in up to 18-fold increases in mixing efficiency and 6-fold increases in converge rate without increasing the computational cost of these analyses. [Bayesian inference; Adaptive tree proposals; Markov chain Monte Carlo; phylogenetics; posterior probability distribution.]
A native prokaryotic voltage-dependent calcium channel with a novel selectivity filter sequence
Authors: Shimomura Takushi , Yonekawa Yoshiki , Nagura Hitoshi , Tateyama Michihiro , Fujiyoshi Yoshinori , Irie Katsumasa 
Published: September 2019

AbstractVoltage-dependent Ca2+ channels (Cavs) are indispensable for coupling action potentials with Ca2+ signaling in living organisms. The structure of Cavs is similar to that of voltage-dependent Na+ channels (Navs). It is known that prokaryotic Navs can obtain Ca2+ selectivity by negative charge mutations of the selectivity filter, but native prokaryotic Cavs had not yet been identified.Here, we report the first identification of a native prokaryotic Cav, CavMr, and its relative, NavPp. Although CavMr contains a smaller number of negatively charged residues in the selectivity filter than artificial prokaryotic Cavs, CavMr exhibits high Ca2+ selectivity. In contrast, NavPp, which has similar filter sequence to artificial Cavs, mainly allows Na+ to permeate. Interestingly, a NavPp mutant whose selectivity filter was replaced with that of CavMr exhibits high Ca2+ selectivity. Mutational analyses revealed that the glycine residue of the CavMr selectivity filter is a determinant for Ca2+ selectivity. This glycine residue is well conserved among subdomains I and III of eukaryotic Cavs.These findings provide new insight into the Ca2+ selectivity mechanism conserved from prokaryotes to eukaryotes.
Effects of active dry yeast on growth performance, rumen fermentation characteristics and slaughter performance in beef cattle
Authors: Liu Siqiang , Yuan Mei , Kang Kun , Wang Zhisheng , Wang Lizhi , Xue Bai , Tian Gang , Zou Huawei , Shah Ali Mujtaba , Zhang Xiangfei , Yu Peiqiang , Wang Hongze , Peng Quanhui 
Published: September 2019

AbstractThis study aimed to investigate the effects of active dry yeast (ADY) on rumen microbial composition and slaughter performance of beef cattle. Thirty-two finishing beef cattle (simmental crossbred cattle ♂ × cattle-yaks ♀), with an average body weight of 110 ± 12.85 kg, were randomly assigned to one of four treatments: the low plane of nutrition group (Control), low plane of nutrition group + ADY 2 g/head/d (ADY2), low plane of nutrition group + ADY 4 g/head/d (ADY4) and high plane of nutrition group (HPN). ADY supplementation increased average daily gain (P<0.001), and the carcass weight of ADY4 group had no significant difference with HPN group (P>0.05). The serum glutamic-pyruvic transaminase activity in control and ADY4 group was higher than HPN group (P=0.001). The neutral detergent fiber (P=0.022) and acid detergent fiber (P=0.043) digestibility in HPN group was greater than control, but no difference was obtained among ADY2, ADY4 and HPN group (P>0.05). The rumen ammonium nitrogen content in control was greater than ADY2 and ADY4 group (P=0.003), and no difference was obtained ADY2, ADY4 and HPN group (P>0.05). The propionic acid content in the rumen in ADY2, ADY4, and HPN group were greater than control group (P<0.001). The simpson (P=0.014) and shannon (P=0.045) indexes in control and HPN group were greater than ADY4 group. At the phylum level, the relative abundance of Firmicutes in the HPN group was higher than ADY4 group (P=0.015). At the genus level, HPN and ADY4 were clustered together, and the relative abundance of Ruminococcaceae UCG-002 in ADY4 group was higher than control and HPN group (P=0.004). In conclusion, supplementation ADY 4 g/head/d shift the rumen microbial composition of beef cattle fed low plane of nutrition to a more similar level with cattle fed with HPN diet, produced comparable carcass weight with HPN diet.
Chilling induces unidirectional solute leak through the locust gut epithelia
Authors: Brzezinski Kaylen , MacMillan Heath A. 
Published: September 2019

AbstractChill-susceptible insects, like the migratory locust, often die when exposed to low temperatures from an accumulation of tissue damage that is unrelated to freezing (chilling injuries). Chilling injury is consistently associated with ion imbalance across the gut epithelia. It has recently been suggested that this imbalance is at least partly caused by a cold-induced disruption of epithelial barrier function. Here, we aim to test this hypothesis in the migratory locust (L. migratoria). First, chill tolerance was quantified by exposing locusts to −2°C for various durations and monitored for chill coma recovery time and survival 24h post-cold exposure. Longer exposure times significantly increased recovery time and caused injury and death. Ion-selective microelectrodes were also used to determine the presence of cold-induced ion imbalance. We found a significant increase and decrease of hemolymph K+and Na+concentrations over time, respectively. Next, barrier failure along the gut was tested by monitoring the movement of an epithelial barrier marker (FITC-dextran) across the gut epithelia during exposure to −2°C. We found minimal marker movement across the epithelia in the serosal to mucosal direction, suggesting that locust gut barrier function remains generally conserved during chilling. However, when tested in the mucosal to serosal direction, we saw significant increases of FITC-dextran with chilling. This instead suggests that while cold-induced barrier disruption is present, it is likely unidirectional. It is important to note that these data reveal only the phenomenon itself. The location of this leak as well as the underlying mechanisms remain unclear and require further investigation.Summary statementIn this study, we provide the first evidence for the presence of cold-induced paracellular leak along the gut of the migratory locust, and that this leak is strongest in the mucosal to serosal direction.
Identification of four unconventional kinetoplastid kinetochore proteins KKT22–25 in Trypanosoma brucei
Authors: Nerusheva Olga O. , Ludzia Patryk , Akiyoshi Bungo 
Published: September 2019

SummaryThe kinetochore is a multi-protein complex that drives chromosome segregation in eukaryotes. It assembles onto centromere DNA and interacts with spindle microtubules during mitosis and meiosis. Although most eukaryotes have canonical kinetochore proteins, kinetochores of evolutionarily divergent kinetoplastid species consist of at least 20 unconventional kinetochore proteins (KKT1–20). In addition, twelve proteins (KKIP1–12) are known to localize at kinetochore regions during mitosis. It remains unclear whether KKIP proteins interact with KKT proteins. Here, we report the identification of four additional kinetochore proteins, KKT22–25, in Trypanosoma brucei. KKT22 and KKT23 constitutively localize at kinetochores, while KKT24 and KKT25 localize from S phase to anaphase. KKT23 has a Gcn5-related N-acetyltransferase (GNAT) domain, which is not found in any kinetochore protein known to date. We also show that KKIP1 co-purifies with KKT proteins, but not with KKIP proteins. Finally, our affinity purification of KKIP2/3/4/6 identifies a number of proteins as their potential interaction partners, many of which are implicated in RNA binding or processing. These findings further support the idea that kinetoplastid kinetochores are unconventional.
Is integrated reporting associated with corporate financing decisions? Some empirical evidence
Authors: Lemma Tesfaye T. , Khan Arifur , Muttakin Mohammad Badrul , Mihret Dessalegn Getie 
Published: September 2019

PurposeThe emerging practice of integrated reporting (IR) has raised curiosity regarding how it impacts on firms and their stakeholders. The purpose of this paper is to examine whether a firm’s decision to provide integrated reports is associated with its financing decisions and whether financial reporting quality mediates the relationship.Design/methodology/approachA usable sample of 832 firm-year observations was employed based on a dataset drawn from companies listed on the Johannesburg Securities Exchange (JSE) for the period between 2009 and 2015.FindingsThe findings show that firms that provide integrated reports tend to have lower levels of leverage, and this effect is partially mediated through financial reporting quality. We further document that the partial effect of financial reporting quality on leverage is stronger for firms that provide integrated reports than is the case for other firms. The findings suggest that IR enables firms to employ equity financing, which is a more informationally-sensitive source of capital than debt financing.Originality/valueThis study is the first to document evidence suggesting that management can draw on IR in devising optimal financing strategy.