bluuebunny/crossref_metadata_2025_split huggingface dataset:
Calibration requirements for epoch of reionization 21-cm signal observations – I. Effect of time-correlated gains
Authors: Kumar Jais , Dutta Prasun , Roy Nirupam 
Published: May 2020

ABSTRACT
The residual gain errors add to the systematics of the radio interferometric observations. In case of the high dynamic range observations, these systematic effects dominates over the thermal noise of the observation. In this work, we investigate the effect of time-correlated residual gain errors in the estimation of the power spectrum of the sky brightness distribution in high dynamic range observations. Particularly, we discuss a methodology to estimate the bias in the power spectrum estimator of the redshifted 21-cm signal from neutral hydrogen in the presence of bright extragalactic compact sources. We find, that for the visibility-based power spectrum estimators, particularly those use nearby baseline correlations to avoid noise bias, the bias in the power spectrum arises mainly from the time correlation in the residual gain error. The bias also depends on the baseline distribution for a particular observation. Analytical calculations show that the bias is dominant for certain types of baseline pairs used for the visibility correlation. We perform simulated observation of extragalactic compact sources in the presence of residual gain errors with the Giant Metrewave Radio Telescope like array and estimate the bias in the power spectrum. Our results indicate that in order to estimate the redshifted 21-cm power spectrum, better calibration techniques, and estimator development are required.
Discovery of β Cep pulsations in the eclipsing binary V453 Cygni
Authors: Southworth John , Bowman D M , Tkachenko A , Pavlovski K 
Published: May 2020

ABSTRACT
V453 Cyg is an eclipsing binary containing 14 and 11 $\, {\rm M}_\odot$ stars in an eccentric short-period orbit. We have discovered β Cep-type pulsations in this system using Transiting Exoplanet Survey Satellite data. We identify seven significant pulsation frequencies, between 2.37 and 10.51 d−1, in the primary star. These include six frequencies that are separated by yet significantly offset from harmonics of the orbital frequency, indicating they are tidally perturbed modes. We have determined the physical properties of the system to high precision: V453 Cyg A is the first β Cep pulsator with a precise mass measurement. The system is a vital tracer of the physical processes that govern the evolution of massive single and binary stars.
mmCSM-AB: guiding rational antibody engineering through multiple point mutations
Authors: Myung Yoochan , Pires Douglas E V , Ascher David B 
Published: May 2020

AbstractWhile antibodies are becoming an increasingly important therapeutic class, especially in personalized medicine, their development and optimization has been largely through experimental exploration. While there have been many efforts to develop computational tools to guide rational antibody engineering, most approaches are of limited accuracy when applied to antibody design, and have largely been limited to analysing a single point mutation at a time. To overcome this gap, we have curated a dataset of 242 experimentally determined changes in binding affinity upon multiple point mutations in antibody-target complexes (89 increasing and 153 decreasing binding affinity). Here, we have shown that by using our graph-based signatures and atomic interaction information, we can accurately analyse the consequence of multi-point mutations on antigen binding affinity. Our approach outperformed other available tools across cross-validation and two independent blind tests, achieving Pearson's correlations of up to 0.95. We have implemented our new approach, mmCSM-AB, as a web-server that can help guide the process of affinity maturation in antibody design. mmCSM-AB is freely available at http://biosig.unimelb.edu.au/mmcsm_ab/.
Metagenomic profiling of gut microbiome in early chronic kidney disease
Authors: Sato Noriaki , Kakuta Masanori , Hasegawa Takanori , Yamaguchi Rui , Uchino Eiichiro , Murashita Koichi , Nakaji Shigeyuki , Imoto Seiya , Yanagita Motoko , Okuno Yasushi 
Published: May 2020

Abstract

Background
The relationship between chronic kidney disease (CKD) and the gut microbiome, which interact through chronic inflammation, uraemic toxin production and immune response regulation, has gained interest in the development of CKD therapies. However, reports using shotgun metagenomic analysis of the gut microbiome are scarce, especially for early CKD. Here we characterized gut microbiome differences between non-CKD participants and ones with early CKD using metagenomic sequencing.

Methods
In total, 74 non-CKD participants and 37 participants with early CKD were included based on propensity score matching, controlling for various factors including dietary intake. Stool samples were collected from participants and subjected to shotgun sequencing. Bacterial and pathway abundances were profiled at the species level with MetaPhlAn2 and HUMAnN2, respectively, and overall microbiome differences were determined using Bray–Curtis dissimilarities. Diabetic and non-diabetic populations were analysed separately.

Results
For diabetic and non-diabetic participants, the mean estimated glomerular filtration rates of the CKD group were 53.71 [standard deviation (SD) 3.87] and 53.72 (SD 4.44), whereas those of the non-CKD group were 72.63 (SD 7.72) and 76.10 (SD 9.84), respectively. Alpha and beta diversities were not significantly different between groups. Based on taxonomic analysis, butyrate-producing species Roseburia inulinivorans, Ruminococcus torques and Ruminococcus lactaris were more abundant in the non-CKD group, whereas Bacteroides caccae and Bacteroides coprocora were more abundant in the non-diabetic CKD group.

Conclusions
Although gut microbiome changes in individuals with early CKD were subtle, the results suggest that changes related to producing short-chain fatty acids can already be observed in early CKD.
Efficacy and safety of oral tolvaptan in patients undergoing hemodialysis: a Phase 2, double-blind, randomized, placebo-controlled trial
Authors: Ogata Hiroaki , Shimofurutani Naoko , Okada Tadashi , Nagamoto Hisashi , Akizawa Tadao 
Published: May 2020

Abstract

Background
Loop diuretics are used to manage fluid retention in patients with end-stage kidney disease undergoing hemodialysis (HD). This randomized, double-blind, placebo-controlled, Phase 2 trial evaluated the efficacy and safety of tolvaptan, a vasopressin V2 receptor antagonist, in Japanese HD patients.

Methods
A total of 124 patients (24-h urine volume ≥500 mL) on thrice-weekly HD were randomized to receive oral tolvaptan 15 mg/day (n = 40), tolvaptan 30 mg/day (n = 40) or placebo (n = 44) for 24 weeks. Efficacy endpoints were change from baseline in 24-h urine volume, total fluid removal by HD per week and interdialytic weight gain (IDWG). Safety was assessed via the incidence of treatment-emergent adverse events (TEAEs).

Results
At treatment end, the difference (95% confidence interval) from the placebo group in the mean change from baseline in 24-h urine volume was significant in the tolvaptan 15 mg {429.1 mL [95% confidence interval (CI) 231.0, 627.2]; P &lt; 0.0001} and 30 mg [371.6 mL (95% CI 144.1, 599.2); P = 0.0017] groups. The mean changes from baseline in total fluid removal by HD and IDWG were not significantly different in the tolvaptan groups versus the placebo group. Although the proportion of patients with TEAEs was lower in the placebo group (77.3%) than in the tolvaptan groups (92.3%), tolvaptan was safe and well-tolerated during the study period.

Conclusions
Tolvaptan significantly sustained diuretic action for 24 weeks in HD patients but did not reduce total fluid removal by HD per week and IDWG to the same extent.
Differentiating Between 2019 Novel Coronavirus Pneumonia and Influenza Using a Nonspecific Laboratory Marker–Based Dynamic Nomogram
Authors: Wang Linghang , Liu Yao , Zhang Ting , Jiang Yuyong , Yang Siyuan , Xu Yanli , Song Rui , Song Meihua , Wang Lin , Zhang Wei , Han Bing , Yang Li , Fan Ying , Cheng Cheng , Wang Jingjing , Xiang Pan , Pu Lin , Xiong Haofeng , Li Chuansheng , Zhang Ming , Tan Jianbo , Chen Zhihai , Liu Jingyuan , Wang Xianbo 
Published: May 2020

Abstract

Background
There is currently a lack of nonspecific laboratory indicators as a quantitative standard to distinguish between the 2019 coronavirus disease (COVID-19) and an influenza A or B virus infection. Thus, the aim of this study was to establish a nomogram to detect COVID-19.

Methods
A nomogram was established using data collected from 457 patients (181 with COVID-19 and 276 with influenza A or B infection) in China. The nomogram used age, lymphocyte percentage, and monocyte count to differentiate COVID-19 from influenza.

Results
Our nomogram predicted probabilities of COVID-19 with an area under the receiver operating characteristic curve of 0.913 (95% confidence interval [CI], 0.883–0.937), greater than that of the lymphocyte:monocyte ratio (0.849; 95% CI, 0.812–0.880; P = .0007), lymphocyte percentage (0.808; 95% CI, 0.768–0.843; P &lt; .0001), monocyte count (0.780; 95% CI, 0.739–0.817; P &lt; .0001), or age (0.656; 95% CI, 0.610–0.699; P &lt; .0001). The predicted probability conformed to the real observation outcomes of COVID-19, according to the calibration curves.

Conclusions
We found that age, lymphocyte percentage, and monocyte count are risk factors for the early-stage prediction of patients infected with the 2019 novel coronavirus. As such, our research provides a useful test for doctors to differentiate COVID-19 from influenza.
Modifying and Evaluating the Opioid Overdose Knowledge Scale for Prescription Opioids: A Pilot Study of the Rx-OOKS
Authors: Shoup Jo Ann , Mueller Shane R , Binswanger Ingrid A , Williams Anna V , Strang John , Glanz Jason M 
Published: May 2020

Abstract

Objective
To develop a validated instrument that measures knowledge about prescription opioid overdose.

Methods
Within an integrated health care system, we adapted, piloted, and tested the reliability and predictive validity of a modified Opioid Overdose Knowledge Scale (OOKS) instrument specific to prescription opioids (Rx-OOKS) with a patient population prescribed long-term opioid therapy and potentially at risk of opioid overdose. We used an interdisciplinary team approach and patient interviews to adapt the instrument. We then piloted the survey on a patient sample and assessed it using Cronbach’s alpha and logistic regression.

Results
Rx-OOKS (N = 56) resulted in a three-construct, 25-item instrument. Internal consistency was acceptable for the following constructs: “signs of an overdose” (10 items) at α = 0.851, “action to take with opioid overdose” (seven items) at α = 0.692, and “naloxone use knowledge” (eight items) at α = 0.729. One construct, “risks of an overdose” (three items), had an α of 0.365 and was subsequently eliminated from analysis due to poor performance. We conducted logistic regression to determine if any of the constructs was strongly associated with future naloxone receipt. Higher scores on “actions to take in an overdose” had nine times the odds of receiving naloxone (odds ratio [OR] = 9.00, 95% confidence interval [CI] = 1.42–57.12); higher “naloxone use knowledge” scores were 15.8 times more likely to receive naloxone than those with lower scores (OR = 15.83, 95% CI = 1.68–149.17).

Conclusions
The Rx-OOKS survey instrument can reliably measure knowledge about prescription opioid overdose recognition and naloxone use. Further, knowledge about actions to take during an opioid overdose and naloxone use were associated with future receipt of naloxone.
Occupational class and educational level inequalities in major cardiovascular risk factors in Turkey: 2008–2016
Authors: Erkoyun Erdem , Mackenbach J P 
Published: May 2020

Abstract

Background
We aimed to investigate the magnitude of occupational class (OC) and educational level (EL) inequalities in cardiovascular risk factors in Turkey from 2008 to 2016 and compare these inequalities with neighbouring European countries.

Methods
We used the Turkey Health Survey among a representative sample of the Turkish population. We estimated relative index of inequality (RII) for four cardiovascular risk factors (obesity/overweight, hypertension, diabetes, smoking) by OC/EL with an interaction term for survey year and compared selected results with neighbouring countries.

Results
Men with lower OC and EL smoked more (e.g. RII for EL = 1.40 [1.26–1.55]); however, the remaining risk factors were mostly lower in these groups. Women in lower socio-economic groups smoked less (e.g. RII for EL = 0.36 [0.29–0.44]), however, had higher prevalence of the remaining risk factors. Significant interactions with survey year were only found in a few cases. The pattern of inequalities in Turkey is largely similar to neighbouring countries.

Conclusions
Inequalities in cardiovascular risk factors are less systematic in Turkey than in most high-income countries, but ongoing trends suggest that this may change in the future.
Does Herding Undermine the Trust Enhancing Effect of Reputation? An Empirical Investigation with Online-Auction Data
Authors: Przepiorka Wojtek , Aksoy Ozan 
Published: May 2020

AbstractIn today’s online markets, the reputation mechanism undergoes its most successful propagation in human history. Online reputation systems substitute informal sanctioning mechanisms at work in close-knit groups and enable complete strangers to trade with each other across large geographic distances. The organizational features of online markets support actors in solving three problems that hamper mutually beneficial market exchange: the value, competition, and cooperation problems. However, due to the plethora of trading opportunities available online, actors face a problem of excess, i.e., the difficulty of choosing a trading partner. Imitation of other actors’ choices of trading partners (i.e., herding) can solve the problem of excess but at the same time lead to the neglect of information about these trading partners’ trustworthiness. Using a large set of online-auction data (N ≈ 88 k), we investigate whether herding as a strategy for solving the problem of excess undermines the reputation mechanism in solving the cooperation problem. Our analysis shows that although buyers follow others in their decisions of which offers to consider, they do not follow others at any price and refer to sellers’ reputations to establish seller trustworthiness. Our results corroborate that reputation systems are viable organizational features that promote mutually beneficial exchanges in anonymous online markets.
Electroencephalographic changes associated with subjective under- and overestimation of sleep duration
Authors: Lecci Sandro , Cataldi Jacinthe , Betta Monica , Bernardi Giulio , Heinzer Raphaël , Siclari Francesca 
Published: May 2020

Abstract
Feeling awake although sleep recordings indicate clear-cut sleep sometimes occurs in good sleepers and to an extreme degree in patients with so-called paradoxical insomnia. It is unknown what underlies sleep misperception, as standard polysomnographic (PSG) parameters are often normal in these cases. Here we asked whether regional changes in brain activity could account for the mismatch between objective and subjective total sleep times (TST). To set cutoffs and define the norm, we first evaluated sleep perception in a population-based sample, consisting of 2,092 individuals who underwent a full PSG at home and estimated TST the next day. We then compared participants with a low mismatch (normoestimators, n = 1,147, ±0.5 SD of mean) with those who severely underestimated (n = 52, &lt;2.5th percentile) or overestimated TST (n = 53, &gt;97.5th percentile). Compared with normoestimators, underestimators displayed higher electroencephalographic (EEG) activation (beta/delta power ratio) in both rapid eye movement (REM) and non-rapid eye movement (NREM) sleep, while overestimators showed lower EEG activation (significant in REM sleep). To spatially map these changes, we performed a second experiment, in which 24 healthy subjects and 10 insomnia patients underwent high-density sleep EEG recordings. Similarly to underestimators, patients displayed increased EEG activation during NREM sleep, which we localized to central-posterior brain areas. Our results indicate that a relative shift from low- to high-frequency spectral power in central-posterior brain regions, not readily apparent in conventional PSG parameters, is associated with underestimation of sleep duration. This challenges the concept of sleep misperception, and suggests that instead of misperceiving sleep, insomnia patients may correctly perceive subtle shifts toward wake-like brain activity.
Effects of grinding method and particle size of wheat grain on energy and nutrient digestibility in growing and finishing pigs
Authors: Acosta Jesus A , Petry Amy L , Gould Stacie A , Jones Cassandra K , Stark Charles R , Fahrenholz Adam , Patience John F 
Published: May 2020

Abstract
Feed grains are processed to improve their value in pig diets by exposing kernel contents to enzymatic and microbial action. The objective of this study was to quantify the effect of reducing mean particle size (PS) of wheat grain ground with two different grinding methods (GMs) on the apparent total tract digestibility (ATTD) of nutrients and energy in growing and finishing pigs. Forty-eight barrows were housed in individual pens for 11 d for two periods. Pigs were randomly assigned to a 3 × 2 × 2 factorial experimental design: three target mean PS of wheat grain (300, 500, and 700 µm), two GMs (roller mill and hammermill), and two body weight (BW) periods (growing period; initial BW of 54.9 ± 0.6 kg and finishing period; initial BW of 110.7 ± 1.4 kg). Diets contained one of six hard red wheat grain samples, vitamins, minerals, and titanium dioxide as an indigestible marker. Feed allowance provided 2.5 (for the two lightest pigs in each treatment) or 2.7 (for the remaining six pigs in each treatment) times the estimated daily maintenance energy requirement for each growth stage. Fecal samples were collected for the last 3 d of each period. Data were analyzed as a linear mixed model with pig as a random effect and PS, GM, and BW period and their interactions as fixed effects utilizing the MIXED procedure of SAS. Growing pigs had greater (P &lt; 0.05) ATTD of dry matter (DM), gross energy (GE), N, acid hydrolyzed ether extract (AEE), and neutral detergent fiber (NDF) by lowering mean PS from 700 to 500 μm using either a roller mill or a hammermill. However, digestibility did not increase when PS was reduced from 500 to 300 μm, except for AEE (P &lt; 0.05). Finishing pigs had greater ATTD of DM, GE, N, AEE, and NDF by lowering mean PS with a hammermill from 700 to 500 μm (P &lt; 0.05), but it was greater for 500 μm than for 300 μm (P &lt; 0.05). Using a roller mill reduced the ATTD of DM and NDF by lowering PS from 700 to 300 μm (P &lt; 0.05). The ATTD of GE decreased by lowering PS from 700 to 500 μm with a roller mill (P &lt; 0.05) for finishing pigs. The ATTD of N and AEE for finishing pigs were similar from 700 to 300 μm when ground by a roller mill. These data suggest that the PS that maximized digestibility for a hammermill is 500 μm for both growing and finishing pigs. However, for the roller mill, the PS resulting in the best digestibility were 500 and 700 μm for growing and finishing pigs, respectively.
Genetic Determinants of Reduced Arsenic Metabolism Efficiency in the 10q24.32 Region Are Associated With ReducedAS3MTExpression in Multiple Human Tissue Types
Authors: Chernoff Meytal , Tong Lin , Demanelis Kathryn , Vander Griend Donald , Ahsan Habib , Pierce Brandon L 
Published: May 2020

AbstractApproximately 140 million people worldwide are exposed to inorganic arsenic through contaminated drinking water. Chronic exposure increases risk for cancers as well as cardiovascular, respiratory, and neurologic diseases. Arsenic metabolism involves the AS3MT (arsenic methyltransferase) gene, and arsenic metabolism efficiency (AME, measured as relative concentrations of arsenic metabolites in urine) varies among individuals. Inherited genetic variation in the 10q24.32 region, containing AS3MT, influences AME, but the mechanisms remain unclear. To better understand these mechanisms, we use tissue-specific expression data from GTEx (Genotype-tissue Expression project) to identify cis-eQTLs (expression quantitative trait loci) for AS3MT and other nearby genes. We combined these data with results from a genome-wide association study of AME using “colocalization analysis,” to determine if 10q24.32 SNPs (single nucleotide polymorphisms) that affect AME also affect expression of AS3MT or nearby genes. These analyses identified cis-eQTLs for AS3MT in 38 tissue types. Colocalization results suggest that the casual variant represented by AME lead SNP rs4919690 impacts expression of AS3MT in 13 tissue types (&gt; 80% probability). Our results suggest this causal SNP also regulates/coregulates expression of nearby genes: BORCS7 (43 tissues), NT5C2 (2 tissues), CYP17A1-AS1 (1 tissue), and RP11-724N1.1 (1 tissue). The rs4919690 allele associated with decreased AME is associated with decreased expression of AS3MT (and other coregulated genes). Our study provides a potential biological mechanism for the association between 10q24.32 variation and AME and suggests that the causal variant, represented by rs4919690, may impact AME (as measured in urine) through its effects on arsenic metabolism occurring in multiple tissue types.
Altered oligodendroglia and astroglia in chronic traumatic encephalopathy
Authors: Chancellor K. Blake , Chancellor Sarah E. , Duke-Cohan Joseph E. , Huber Bertrand R. , Stein Thor D. , Alvarez Victor E. , Okaty Benjamin W. , Dymecki Susan M. , McKee Ann C. 
Published: May 2020

SUMMARYChronic traumatic encephalopathy (CTE) is a progressive tauopathy found in contact sport athletes, military veterans, and others exposed to repetitive head impacts (RHI)1–6. White matter atrophy and axonal loss have been reported in CTE but have not been characterized on a molecular or cellular level2,7,8. Here, we present RNA sequencing profiles of cell nuclei from postmortem dorsolateral frontal white matter from eight individuals with neuropathologically confirmed CTE and eight age- and sex-matched controls. Analyzing these profiles using unbiased clustering approaches, we identified eighteen transcriptomically distinct cell groups (clusters), reflecting cell types and/or cell states, of which a subset showed differences between CTE and control tissue. Independent in situ methods applied on tissue sections adjacent to that used in the single-nucleus RNA-seq work yielded similar findings. Oligodendrocytes were found to be most severely affected in the CTE white matter samples; they were diminished in number and altered in relative proportions across subtype clusters. Further, the CTE-enriched oligodendrocyte population showed greater abundance of transcripts relevant to iron metabolism and cellular stress response. CTE tissue also demonstrated excessive iron accumulation histologically. Astrocyte alterations were more nuanced; total astrocyte number was indistinguishable between CTE and control samples, but transcripts associated with neuroinflammation were elevated in the CTE astrocyte groups as compared to controls. These results demonstrate specific molecular and cellular differences in CTE oligodendrocytes and astrocytes and may provide a starting point for the development of diagnostics and therapeutic interventions.