bluuebunny/crossref_metadata_2025_split huggingface dataset:
Association of residual feed intake with growth performance, carcass traits, meat quality, and blood variables in native chickens
Authors: Yang Lei , Wang Xiaolong , He Tingting , Xiong Fengliang , Chen Xianzhen , Chen Xingyong , Jin Sihua , Geng Zhaoyu 
Published: April 2020

Abstract
Improving feed efficiency is a primary goal in poultry breeding strategies. Residual feed intake (RFI) in chickens typically calculated during the growing period is a measure of feed efficiency that is independent of the level of production. The objective of this study was to evaluate phenotypic correlations of growth performance, carcass traits, meat quality, and blood variables with RFI in growing native chickens. A total of 1,008 chickens were selected for the experiment to derive RFI. After the RFI measurement period of 42 d, 25 chickens with low RFI values, 25 chickens with medium RFI values, and 25 chickens with high RFI values were selected. The RFI was significantly positively correlated with feed conversion ratio and average daily feed intake, while it was not significantly correlated with initial body weight (BW), final BW, average daily body weight gain, and metabolic BW0.75. The abdominal fat weight and yield of high RFI group were significantly greater than those of medium and low RFI groups, and the abdominal fat yield was significantly positively correlated with RFI. Moreover, the plasma insulin-like growth factor 1 (IGF-1) content of low RFI group was significantly greater than those of high and medium RFI groups. The plasma concentrations of adrenocorticotropic hormone, triiodothyronine (T3), and cortisol of high RFI birds were significantly greater than that of low RFI birds. RFI was significantly positively correlated with plasma concentrations of T3 and cortisol, while it was significantly negatively correlated with plasma concentration of IGF-1. In addition, the serum levels of glucose and triglyceride of high RFI birds were significantly lower than that of low RFI birds. The serum low-density lipoprotein cholesterol (LDL-C) content of high RFI group was significantly greater than that of medium and low RFI groups, and it was significantly positively correlated with RFI. Our data suggested that selection of chickens with low RFI values may be beneficial to reduce fat deposition in native chickens without affecting the meat quality. Circulating IGF-1, T3, cortisol, and LDL-C concentrations can be used as indirect selection indicators of feed efficiency in native chickens. The effect of IGF-1, T3, cortisol, and LDL-C on feed efficiency of native chickens should be carefully examined and validated in future breeding programs.
Low Homeownership in Germany—a Quantitative Exploration
Authors: Kaas Leo , Kocharkov Georgi , Preugschat Edgar , Siassi Nawid 
Published: April 2020

AbstractThe homeownership rate in Germany is one of the lowest among advanced economies. To better understand this fact, we evaluate the role of specific housing policies that tend to discourage homeownership. In comparison to other countries with higher homeownership such as the United States, Germany has an extensive social housing sector with broad eligibility criteria, high transfer taxes when buying real estate, and no tax deductions for mortgage interest payments by owner-occupiers. We build a life-cycle model with uninsurable income and housing risks and endogenous homeownership in order to quantify the policy impact on homeownership and welfare. Adjusting all three policies has a strong impact on housing tenure choices, closing the gap in homeownership rates between Germany and the United States by about two thirds. At the same time, household welfare would be reduced by moving to a policy regime with low transfer taxes, but it would improve in the absence of social housing, in particular, when coupled with housing subsidies for low-income households.
Fever Without a Source in an Infant Due to Severe Acute Respiratory Syndrome Coronavirus-2
Authors: Kan Matthew J , Grant Lauren M C , Muña Martha A , Greenhow Tara L 
Published: April 2020

Abstract
A 5-week-old infant female admitted for fever without a source subsequently tested positive for severe acute respiratory syndrome coronavirus 2. She had a mild hospital course without respiratory distress. This unexpected presentation changed regional hospital screening for coronavirus disease 2019 and personal protective equipment use by medical providers who evaluate febrile infants.
On ageing star clusters using red supergiants independent of the fraction of interacting binary stars
Authors: Eldridge J J , Beasor Emma R , Britavskiy N 
Published: April 2020

ABSTRACT
We use the Binary Population and Spectral Synthesis models to test the recent suggestion that red supergiants can provide an accurate age estimate of a coeval stellar population that is unaffected by interacting binary stars. Ages are estimated by using both the minimum luminosity of red supergiants and the mean luminosity of red supergiants in a cluster. We test these methods on a number of observed star clusters and find our results in agreement with previous estimates. Importantly, we find the difference between the ages derived from stellar population models with and without a realistic population of interacting binary stars is only a few hundred thousand years at most. We find that the mean luminosity of red supergiants in a cluster is the best method to determine the age of a cluster because it is based on the entire red supergiant population rather than using only the least luminous red supergiant.
A critical role of telomere chromatin compaction in ALT tumor cell growth
Authors: Shi Guang , Hu Yang , Zhu Xing , Jiang Yuanling , Pang Junjie , Wang Chuanle , Huang Wenjun , Zhao Yong , Ma Wenbin , Liu Dan , Huang Junjiu , Songyang Zhou 
Published: April 2020

Abstract
ALT tumor cells often contain abundant DNA damage foci at telomeres and rely on the alternative lengthening of telomeres (ALT) mechanism to maintain their telomeres. How the telomere chromatin is regulated and maintained in these cells remains largely unknown. In this study, we present evidence that heterochromatin protein 1 binding protein 3 (HP1BP3) can localize to telomeres and is particularly enriched on telomeres in ALT cells. HP1BP3 inhibition led to preferential growth inhibition of ALT cells, which was accompanied by telomere chromatin decompaction, increased presence of C-circles, more pronounced ALT-associated phenotypes and elongated telomeres. Furthermore, HP1BP3 appeared to participate in regulating telomere histone H3K9me3 epigenetic marks. Taken together, our data suggest that HP1BP3 functions on telomeres to maintain telomere chromatin and represents a novel target for inhibiting ALT cancer cells.
Regulation of alternative polyadenylation in the yeast Saccharomyces cerevisiae by histone H3K4 and H3K36 methyltransferases
Authors: Kaczmarek Michaels Katarzyna , Mohd Mostafa Salwa , Ruiz Capella Julia , Moore Claire L 
Published: April 2020

AbstractAdjusting DNA structure via epigenetic modifications, and altering polyadenylation (pA) sites at which precursor mRNA is cleaved and polyadenylated, allows cells to quickly respond to environmental stress. Since polyadenylation occurs co-transcriptionally, and specific patterns of nucleosome positioning and chromatin modifications correlate with pA site usage, epigenetic factors potentially affect alternative polyadenylation (APA). We report that the histone H3K4 methyltransferase Set1, and the histone H3K36 methyltransferase Set2, control choice of pA site in Saccharomyces cerevisiae, a powerful model for studying evolutionarily conserved eukaryotic processes. Deletion of SET1 or SET2 causes an increase in serine-2 phosphorylation within the C-terminal domain of RNA polymerase II (RNAP II) and in the recruitment of the cleavage/polyadenylation complex, both of which could cause the observed switch in pA site usage. Chemical inhibition of TOR signaling, which causes nutritional stress, results in Set1- and Set2-dependent APA. In addition, Set1 and Set2 decrease efficiency of using single pA sites, and control nucleosome occupancy around pA sites. Overall, our study suggests that the methyltransferases Set1 and Set2 regulate APA induced by nutritional stress, affect the RNAP II C-terminal domain phosphorylation at Ser2, and control recruitment of the 3′ end processing machinery to the vicinity of pA sites.
A splice site-sensing conformational switch in U2AF2 is modulated by U2AF1 and its recurrent myelodysplasia-associated mutation
Authors: Warnasooriya Chandani , Feeney Callen F , Laird Kholiswa M , Ermolenko Dmitri N , Kielkopf Clara L 
Published: April 2020

Abstract
An essential heterodimer of the U2AF1 and U2AF2 pre-mRNA splicing factors nucleates spliceosome assembly at polypyrimidine (Py) signals preceding the major class of 3′ splice sites. U2AF1 frequently acquires an S34F-encoding mutation among patients with myelodysplastic syndromes (MDS). The influence of the U2AF1 subunit and its S34F mutation on the U2AF2 conformations remains unknown. Here, we employ single molecule Förster resonance energy transfer (FRET) to determine the influence of wild-type or S34F-substituted U2AF1 on the conformational dynamics of U2AF2 and its splice site RNA complexes. In the absence of RNA, the U2AF1 subunit stabilizes a high FRET value, which by structure-guided mutagenesis corresponds to a closed conformation of the tandem U2AF2 RNA recognition motifs (RRMs). When the U2AF heterodimer is bound to a strong, uridine-rich splice site, U2AF2 switches to a lower FRET value characteristic of an open, side-by-side arrangement of the RRMs. Remarkably, the U2AF heterodimer binds weak, uridine-poor Py tracts as a mixture of closed and open U2AF2 conformations, which are modulated by the S34F mutation. Shifts between open and closed U2AF2 may underlie U2AF1-dependent splicing of degenerate Py tracts and contribute to a subset of S34F-dysregulated splicing events in MDS patients.
Reciprocal regulation of hnRNP C and CELF2 through translation and transcription tunes splicing activity in T cells
Authors: Mallory Michael J , McClory Sean P , Chatrikhi Rakesh , Gazzara Matthew R , Ontiveros Robert J , Lynch Kristen W 
Published: April 2020

Abstract
RNA binding proteins (RBPs) frequently regulate the expression of other RBPs in mammalian cells. Such cross-regulation has been proposed to be important to control networks of coordinated gene expression; however, much remains to be understood about how such networks of cross-regulation are established and what the functional consequence is of coordinated or reciprocal expression of RBPs. Here we demonstrate that the RBPs CELF2 and hnRNP C regulate the expression of each other, such that depletion of one results in reduced expression of the other. Specifically, we show that loss of hnRNP C reduces the transcription of CELF2 mRNA, while loss of CELF2 results in decreased efficiency of hnRNP C translation. We further demonstrate that this reciprocal regulation serves to fine tune the splicing patterns of many downstream target genes. Together, this work reveals new activities of hnRNP C and CELF2, provides insight into a previously unrecognized gene regulatory network, and demonstrates how cross-regulation of RBPs functions to shape the cellular transcriptome.
Encoding multiple digital DNA signals in a single analog channel
Authors: Yan Yan Helen , Zhang David Yu , Wu Lucia R 
Published: April 2020

AbstractFor many analytic and biomedical applications, the presence of an analyte above or below a critical concentration is more informative for decision making than the actual concentration value. Straightforward analog-to-digital signal conversion does not take full advantage of the precision and dynamic range of modern sensors. Here, we present and experimentally demonstrate an analog-to-multiple-digital signal conversion, reporting digital signals that indicate whether the concentrations of specific DNA sequences exceed respective threshold values. These threshold values can be individually programmed for each target sequence. Experimentally, we showed representation of four DNA targets’ information in a single fluorescence channel.
Acute cognitive effects of the hypocretin receptor antagonist almorexant relative to zolpidem and placebo: a randomized clinical trial
Authors: Neylan Thomas C , Richards Anne , Metzler Thomas J , Ruoff Leslie M , Varbel Jonathan , O’Donovan Aoife , Sivasubramanian Melinda , Motraghi Terri , Hlavin Jennifer , Batki Steven L , Inslicht Sabra S , Samuelson Kristin , Morairty Stephen R , Kilduff Thomas S 
Published: April 2020

Abstract

Study Objectives
Hypnotic medications can adversely affect behavior during unanticipated awakenings during the night. Animals treated with the hypocretin (Hcrt) receptor antagonist almorexant (ALM) have less acute cognitive impairment compared to the GABAA receptor modulator zolpidem (ZOL). This study aimed to determine whether ALM produces less acute cognitive impairment than ZOL in human subjects.

Methods
Healthy, young adult, unmedicated male and female subjects participated in a controlled trial of a single dose of ALM 100 mg (N = 48), ALM 200 mg (N = 53), ZOL 10 mg (N = 49), and placebo (PBO, N = 52).

Results
ZOL and both doses of ALM produced similar levels of subjective sleepiness and impaired the ability of subjects to remain awake in a dark, low-stimulus setting relative to PBO. For most cognitive measures, performance under ZOL was significantly worse than ALM or PBO. For tasks involving verbal memory or visual-motor coordination, ZOL impaired performance, whereas the two doses of ALM were no different than PBO. For tasks involving higher-order executive function, ZOL produced impairment in processing speed and inhibitory control, whereas the two doses of ALM were no different than PBO. Performance decrements for ALM were less than ZOL but greater than PBO for some reaction time measures.

Conclusions
The data provide support for the hypothesis that Hcrt receptor antagonists produce less functional impairment than a benzodiazepine receptor agonist (BzRA). These observations are particularly relevant to patients treated with sedative-hypnotics who are at elevated risk for falls and other untoward events during the intended hours for sleep.
Help-Seeking Behaviors as Cultural Capital: Cultural Guides and the Transition from High School to College among Low-Income First Generation Students
Authors: Richards Bedelia Nicola 
Published: April 2020

AbstractThis article argues that educational institutions can transmit cultural capital in the form of help-seeking dispositions (feeling empowered to ask for and receive help) and specialized knowledge (information about how to gain access to resources) that can positively impact students’ academic outcomes. Additionally, this article questions the perception that educational institutions function primarily as agents of social reproduction, by showing that institutional agents such as high school teachers and administrators can function as “cultural guides” to bolster students’ opportunities for social mobility. Drawing on interviews with graduates of King and Chavez, two early college high schools which target low-income, first-generation college students, I find that King graduates were more strategic help-seekers and were more likely to use campus-based resources than their counterparts at Chavez, in part because their school’s curriculum explicitly and systematically taught this skill. This article challenges the perception that teachers and administrators function exclusively as gatekeepers in educational institutions. Instead, the data presented show that these institutional agents can also function as “cultural guides” who transmit cultural capital in the form of help-seeking values and behaviors to students from economically marginalized communities; promoting their upward mobility.
The Dynamics of Bird Diversity in the New World
Authors: Machac Antonin 
Published: April 2020

AbstractThree prominent explanations have been proposed to explain the dramatic differences in species richness across regions and elevations, (i) time for speciation, (ii) diversification rates, and (iii) ecological limits. But the relative importance of these explanations and, especially, their interplay and possible synthesis remain largely elusive. Integrating diversification analyses, null models, and geographic information systems, I study avian richness across regions and elevations of the New World. My results reveal that even though the three explanations are differentially important (with ecological limits playing the dominant role), each contributes uniquely to the formation of richness gradients. Further, my results reveal the likely interplay between the explanations. They indicate that ecological limits hinder the diversification process, such that the accumulation of species within a region gradually slows down over time. Yet, it does not seem to converge toward a hard ceiling on regional richness. Instead, species-rich regions show suppressed, but continued, diversification, coupled with signatures of possible competition (esp. Neotropical lowlands). Conversely, species-poor, newly-colonized regions show fast diversification and weak to no signs of competition (esp. Nearctic highlands). These results held across five families of birds, across grid cells, biomes, and elevations. Together, my findings begin to illuminate the rich, yet highly consistent, interplay of the mechanisms that together shape richness gradients in the New World, including the most species-rich biodiversity hotspots on the planet, the Andes and the Amazon. [Biogeography; community; competition; macroevolution; phylogenetics; richness gradient.]
S. mediterranea Ataxia telangiectasia and Rad3‐related kinase (SmedATR) May be Required to Prevent DNA Replication Stress
Authors: Ishaq Ariana , Nguyen Lillian , Sheppard Taylor , Velasquez Elizabeth , Ahmed Youssef , Montes Patricia , Arroyo Jimena , Tirgar Reyehana , Shamoon Ushna , Akapti Lois , Nam Edward 
Published: April 2020

DNA replication is an important mechanism involved in cellular processes like reproduction, repair, and regeneration. S. mediterranea, a planarian with an amazing regenerative ability, goes through continuous rounds of cell division. Consequently, DNA replication stress occurs with each cell division and must be resolved. From yeast to man, The DNA replication stress response (RSR) is evolutionarily conserved and necessary for life among organisms. The RSR is a signal transduction pathway regulated by Ataxia telangiectasia and Rad3‐related kinase (ATR) and Checkpoint 1 kinase (CHK1) to respond to replication stress, including DNA damage. However, the RSR has not yet been established in the planarian and its involvement in regeneration is currently unknown. We hypothesize that ATR may be essential in replication by preventing and resolving DNA damage. Regeneration experiments were conducted and results indicated that the regenerative ability of planaria were reduced in the presence of hydroxyurea (HU), a replication stress inducing agent. Low HU concentrations (2mM) had similar phenotypic results to the control which suggests that ATR and the RSR may be present in this low dosage to overcome the replication stress. However, when treated with a combination of 2mM HU and ATR inhibitor (ATRi), planarian regeneration was severely hindered. To confirm replication stress shown phenotypically in the regeneration experiments, comet assays were performed to quantify the levels of DNA damage in each experimental group. The ATRi and 2mM HU combination group exhibited the highest average comet tail moment, a parameter used to measure the amounts of fragmented DNA within each planarian cell. The synergistic effects of ATR in combination with HU suggest that ATR is significant in the response to replication stress during regeneration. Additionally, inhibition of CHK1, another kinase in the RSR pathway exhibited similar tail moment values as ATRi. Future experiments will allow us to support the presence of CHK1 and its important role in resolving replication stress. Determining the importance of RSR genes in planarian will elucidate the conserved components and allow us to understand how ATR and the RSR contributes to the incredible regenerative abilities in planarian.Support or Funding InformationUST Committee for Student Research Alvarado Sanchez Lab, Stowers Institute for Medical Research Jim Jenkin for S. mediterranea Department of Education HSI‐STEM grant UST Biology Smith Chair UST Biology Department
Role of PPAR Pathway in Atrial Fibrillation Associated with Heart Valvular Disease: Transcriptomics and Proteomics in the Human Atrial Tissue
Authors: Chen Huan-Xin , Jiang Yi-Yao , Li Ming-Yang , Hou Hai-Tao , Wang Jun , Yang Qin , He Guo-Wei 
Published: April 2020

ObjectiveAtrial fibrillation (AF) is one of the most common cardiac arrhythmias. Previous studies have shown that electrical, contractile, and structural remodeling play the key role in the onset and maintenance of AF. Heart valvular disease (HVD) is associated with an increased risk of thromboembolic events, mainly in patients with AF. However, the molecular mechanism of AF in HVD remains unrevealed, although there was an attempt to discover the plasma biomarkers in HVD.MethodsHuman atrial tissues from patients with HVD in persistent AF preoperatively for at least 6 months or remaining sinus rhythm (as control) undergoing heart valve replacement surgery were studied by combined transcriptomics and proteomics. Owing to the fact that there are maximal 8 Isobaric tags in proteomics analysis by iTRAQ technology, 8 tissue samples were allocated, including left atrial tissues from 3 AF patients (AFLA) and right atrial tissues (3 AFRA and 2 SRRA) from 5 patients. The analysis of transcriptomics and proteomics were from the same samples. Big data obtained from omics study were analyzed by bioinformatics tools. The fold changes of >1.2 (or <0.8) and P value < 0.05 were considered as significant.ResultHierarchical clustering analysis revealed that the genomic expressions of three groups have differences in transcriptomics. Pairwise comparison was performed and differentially expressed genes were identified, including 193 genes up‐regulated and 279 genes down‐regulated. Heat map from differentially expressed proteins in proteomics analysis indicates that there are significant differences in patients with or without AF and between the left and right atrium. Based on Gene ontology (GO) function and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analysis, we found that the expression of genes and proteins associated with PPARα, β/δ, γ was altered in omics study in AF patients. Genes/proteins, such as FATCD36, SCD‐1, FABP, ADIPO, APOA1, APOA2, FATP, FADS2, ACBP, CPT‐1, aP2, CAP, and etc., are included in the PPAR pathway. These genes/proteins may be developed as potential biomarkers for disease pathogenesis and progress in AF.ConclusionOur study provides an integrative analysis of transcriptomics and proteomics in human atrial tissues of AF‐associated HVD patients and reveals that PPAR signaling pathway plays an important role in pathogenesis of AF. Some of differential proteins may become biomarkers and provide new diagnostic and therapeutic methods for AF in the future.Support or Funding InformationThis work was supported by the National Natural Science Foundation of China [81870288 & 81870227]; the Non‐profit Central Research Institute Fund of Chinese Academy of Medical Sciences [2019XK310001& 2018TX31002]; Tianjin Science and Technology Committee[18PTZWHZ00060];Binhai New Area Health Bureau (2018BWKZ005)