bluuebunny/crossref_metadata_2025_split huggingface dataset:
MHC-associated mate choice under competitive conditions in captive versus wild Tasmanian devils
Authors: Day Jenna , Gooley Rebecca M , Hogg Carolyn J , Belov Katherine , Whittington Camilla M , Grueber Catherine E 
Published: May 2019

AbstractMate choice contributes to driving evolutionary processes when animals choose breeding partners that confer genetic advantages to offspring, such as increased immunocompetence. The major histocompatibility complex (MHC) is an important group of immunological molecules, as MHC antigens bind and present foreign peptides to T-cells. Recent studies suggest that mates may be selected based on their MHC profile, leading to an association between an individual’s MHC diversity and their breeding success. In conservation, it may be important to consider mate choice in captive breeding programs, as this mechanism may improve reproductive rates. We investigated the reproductive success of Tasmanian devils in a group housing facility to determine whether increased MHC-based heterozygosity led individuals to secure more mating partners and produce more offspring. We also compared the breeding success of captive females to a wild devil population. MHC diversity was quantified using 12 MHC-linked microsatellite markers, including 11 previously characterized markers and one newly identified marker. Our analyses revealed that there was no relationship between MHC-linked heterozygosity and reproductive success either in captivity or the wild. The results of this study suggest that, for Tasmanian devils, MHC-based heterozygosity does not produce greater breeding success and that no specific changes to current captive management strategies are required with respect to preserving MHC diversity.
Presence of kin-biased social associations in a lizard with no parental care: the eastern water dragon (Intellagama lesueurii)
Authors: Piza-Roca Carme , Strickland Kasha , Kent Nicola , Frere Celine H 
Published: May 2019

AbstractNumerous studies have observed kin-biased social associations in a variety of species. Many of these studies have focused on species exhibiting parental care, which may facilitate the transmission of the social environment from parents to offspring. This becomes problematic when disentangling whether kin-biased associations are driven by kin recognition, or are a product of transmission of the social environment during ontogeny, or a combination of both. Studying kin-biased associations in systems that lack parental care may aid in addressing this issue. Furthermore, when studying kin-biased social associations, it is important to differentiate whether these originate from preferential choice or occur randomly as a result of habitat use or limited dispersal. Here, we combined high-resolution single-nucleotide polymorphism data with a long-term behavioral data set of a reptile with no parental care to demonstrate that eastern water dragons (Intellagama lesueurii) bias their nonrandom social associations toward their kin. In particular, we found that although the overall social network was not linked to genetic relatedness, individuals associated with kin more than expected given availability in space and also biased social preferences toward kin. This result opens important opportunities for the study of kinship-driven associations without the confounding effect of vertical transmission of social environments. Furthermore, we present a robust multiple-step approach for determining whether kin-biased social associations are a result of active social decisions or random encounters resulting from habitat use and dispersal patterns.
EROS-DOCK: protein–protein docking using exhaustive branch-and-bound rotational search
Authors: Ruiz Echartea Maria Elisa , Chauvot de Beauchêne Isaure , Ritchie David W 
Published: May 2019

Abstract

Motivation
Protein–protein docking algorithms aim to predict the 3D structure of a binary complex using the structures of the individual proteins. This typically involves searching and scoring in a 6D space. Many docking algorithms use FFT techniques to exhaustively cover the search space and to accelerate the scoring calculation. However, FFT docking results often depend on the initial protein orientations with respect to the Fourier sampling grid. Furthermore, Fourier-transforming a physics-base force field can involve a serious loss of precision.

Results
Here, we present EROS-DOCK, an algorithm to rigidly dock two proteins using a series of exhaustive 3D rotational searches in which non-clashing orientations are scored using the ATTRACT coarse-grained force field model. The rotational space is represented as a quaternion ‘π-ball’, which is systematically sub-divided in a ‘branch-and-bound’ manner, allowing efficient pruning of rotations that will give steric clashes. The algorithm was tested on 173 Docking Benchmark complexes, and results were compared with those of ATTRACT and ZDOCK. According to the CAPRI quality criteria, EROS-DOCK typically gives more acceptable or medium quality solutions than ATTRACT and ZDOCK.

Availability and implementation
The EROS-DOCK program is available for download at http://erosdock.loria.fr.

Supplementary information
Supplementary data are available at Bioinformatics online.
EnImpute: imputing dropout events in single-cell RNA-sequencing data via ensemble learning
Authors: Zhang Xiao-Fei , Ou-Yang Le , Yang Shuo , Zhao Xing-Ming , Hu Xiaohua , Yan Hong 
Published: May 2019

Abstract

Summary
Imputation of dropout events that may mislead downstream analyses is a key step in analyzing single-cell RNA-sequencing (scRNA-seq) data. We develop EnImpute, an R package that introduces an ensemble learning method for imputing dropout events in scRNA-seq data. EnImpute combines the results obtained from multiple imputation methods to generate a more accurate result. A Shiny application is developed to provide easier implementation and visualization. Experiment results show that EnImpute outperforms the individual state-of-the-art methods in almost all situations. EnImpute is useful for correcting the noisy scRNA-seq data before performing downstream analysis.

Availability and implementation
The R package and Shiny application are available through Github at https://github.com/Zhangxf-ccnu/EnImpute.

Supplementary information
Supplementary data are available at Bioinformatics online.
A simple skeletal measurement effectively predicts climbing behaviour in a diverse clade of small mammals
Authors: Nations Jonathan A , Heaney Lawrence R , Demos Terrence C , Achmadi Anang S , Rowe Kevin C , Esselstyn Jacob A 
Published: May 2019

AbstractArboreal locomotion allows access to above-ground resources and might have fostered the diversification of mammals. Nevertheless, simple morphological measurements that consistently correlate with arboreality remain indefinable. As such, the climbing habits of many species of mammals, living and extinct, remain speculative. We collected quantitative data on the climbing tendencies of 20 species of murine rodents, an ecologically and morphologically diverse clade. We leveraged Bayesian phylogenetic mixed models (BPMMs), incorporating intraspecific variation and phylogenetic uncertainty, to determine which, if any, traits (17 skeletal indices) predict climbing frequency. We used ordinal BPMMs to test the ability of the indices to place 48 murine species that lack quantitative climbing data into three qualitative locomotor categories (terrestrial, general and arboreal). Only two indices (both measures of relative digit length) accurately predict locomotor styles, with manus digit length showing the best fit. Manus digit length has low phylogenetic signal, is largely explained by locomotor ecology and might effectively predict locomotion across a multitude of small mammals, including extinct species. Surprisingly, relative tail length, a common proxy for locomotion, was a poor predictor of climbing. In general, detailed, quantitative natural history data, such as those presented here, are needed to enhance our understanding of the evolutionary and ecological success of clades.
Novel HILIC-ESI-MS method for urinary profiling of MSUD and methylmalonic aciduria biomarkers
Authors: Mathew Elizabeth Mary , Lewis Leslie , Rao Pragna , Nalini K , Kamath Asha , Moorkoth Sudheer 
Published: May 2019

AbstractMethyl malonic acid and branched-chain keto acids are important biomarkers for the diagnosis of cobalamin deficiencies and maple syrup urine disease. We report the development and validation of a HILIC-ESI-MS2 method for the quantification of these organic acids from neonatal urine. The samples were 100 times diluted and analyzed on a ZIC-HILIC column with 25-mM formic acid in water: 25-mM formic acid in acetonitrile (45:55) at a flow rate of 0.8 mL/min with a runtime of only 6 minutes. The method demonstrated a lower limit of detection of 10 ng/mL, Limit of Quantification (LOQ) of 50 ng/mL, linearity of r2 ≥ 0.990 and recoveries of 87–105% for all analytes. The intraday and interday precision CV’s were <10% and 12%, respectively. Extensive stability studies demonstrated the analytes to be stable in stock and in matrix with a percent change within ±15%. The Bland–Altman analysis of the developed method with the gold standard GCMS method demonstrated a bias of 0.44, 0.11, 0.009 and –0.19 for methyl malonic acid, 3-methyl-2-oxovaleric acid, 2-hydroxy-3methylbutyric acid and 4-methyl-2-oxovaleric acid, respectively, proving the methods are comparable. The newly developed method involves no derivatization and has a simple sample preparation and a low runtime, enabling it to be easily automated with a high sample throughput in a cost-effective manner.
Developing a High-Performance Liquid Chromatography (HPLC) Method for Simultaneous Determination of Oxytetracycline, Tinidazole and Esomeprazole in Human Plasma
Authors: Sebaiy Mahmoud M , Hassan Wafaa S , Elhennawy Mostafa E 
Published: May 2019

AbstractA high performance liquid chromatography method had been developed and validated for rapid simultaneous separation and determination of three anti-helicobacter drugs, oxytetracycline (OXY), tinidazole (TIN) and esomeprazole (ESM) in human plasma within 6 minutes. Drugs extraction method from plasma was based on protein precipitation technique. Separation was carried out on a Equisil BDS C18 column (5 μm, 150 × 4.60 mm) using a mobile phase of acetonitrile: 0.025 M KH2PO4 (25: 75, v/v) adjusted to pH 3.50 with ortho-phosphoric acid at ambient temperature. The flow rate was 1 mL/min and maximum absorption was measured using Diode Array (DAD) detector at 285 nm. The retention times of OXY, TIN and ESM were recorded to be 2.68, 3.52 and 5.17 minutes, respectively, indicating a shorter analysis time. Limits of detection were also reported to be 0.10, 0.07 and 0.04 μg/mL for OXY, TIN and ESM, respectively, showing a high degree of the method sensitivity. The method was then validated according to FDA guidelines for the determination of the drugs clinically in human plasma specially regarding pharmacokinetic and bioequivalence studies.
Low hemoglobin at hemodialysis initiation: an international study of anemia management and mortality in the early dialysis period
Authors: Karaboyas Angelo , Morgenstern Hal , Waechter Sandra , Fleischer Nancy L , Vanholder Raymond , Jacobson Stefan H , Sood Manish M , Schaubel Douglas E , Inaba Masaaki , Pisoni Ronald L , Robinson Bruce M 
Published: May 2019

AbstractBackgroundAnemia at hemodialysis (HD) initiation is common. Correcting low hemoglobin (Hgb) before HD initiation may improve survival by avoiding potential harms of chronic anemia, high doses of erythropoiesis-stimulating agents (ESAs) and intravenous (IV) iron in the early HD period, and/or rapid Hgb rise.MethodsWe included 4604 incident HD patients from 21 countries in the Dialysis Outcomes and Practice Patterns Study Phases 4–5 (2009–15). Because low Hgb at HD start may reflect comorbidity or ESA hyporesponse, we restricted our analysis to the 80% of patients who achieved Hgb ≥10 g/dL 91–120 days after HD start (Month 4).ResultsAbout 53% of these patients had Hgb &lt;10 g/dL in Month 1 (&lt;30 days after HD start); they were younger with a similar comorbidity profile (versus Hgb ≥10 g/dL). Month 1 Hgb was associated with first-year HD mortality (adjusted hazard ratio for 1 g/dL higher Hgb was 0.89; 95% confidence interval: 0.81–0.97), despite minimal differences in Month 4 Hgb. Patients with lower Hgb in Month 1 received higher doses of ESA, but not IV iron, over the first 3 months of HD. Results were consistent when excluding catheter users or adjusting for IV iron and ESA dose over the first 3 months.ConclusionsEven among patients with Hgb ≥10 g/dL 3 months later, anemia at HD initiation was common and associated with elevated mortality. A more proactive approach to anemia management in advanced chronic kidney disease (CKD) may thus improve survival on HD, though long-term prospective studies of non-dialysis CKD patients are needed.
A loosening prosthesis in a dialysis patient
Authors: Cailleaux Pierre-Emmanuel , Benarbia Seddik , Allard Guillaume , Ureña-Torres Pablo , Cohen-Solal Martine 
Published: May 2019

Abstract
A haemodialysis patient with periprosthetic fractures and a history of corticosteroid use was referred for assessment for bone mineral disorders. Mixed renal osteodystrophy was diagnosed following a bone biopsy. Correction for vitamin D insufficiency did not improve the clinical signs, which prompted a potential diagnosis of hypophosphataemic osteomalacia to be considered. No causes for hypophosphataemia were found, except for phosphate dietary restrictions. Phosphorus supplementation was administered, resulting in an upturn in bone biochemical and histological parameters and increased bone mineral density, thus confirming the diagnosis of hypophosphataemic osteomalacia due to low phosphate intake. Characteristic features related to this diagnosis are shown from three repeated bone biopsies performed during the course of patient follow-up.
Male courtship signal modality and female mate preference in the wolf spider Schizocosa ocreata: results of digital multimodal playback studies
Authors: Kozak Elizabeth C , Uetz George W 
Published: May 2019

Abstract
Females must be able to perceive and assess male signals, especially when they occur simultaneously with those of other males. Previous studies show female Schizocosa ocreata wolf spiders display receptivity to isolated visual or vibratory courtship signals, but increased receptivity to multimodal courtship. It is unknown whether this is true when females are presented with a choice between simultaneous multimodal and isolated unimodal male courtship. We used digital playback to present females with a choice simulating simultaneous male courtship in different sensory modes without variation in information content: 1) isolated unimodal visual versus vibratory signals; 2) multimodal versus vibratory signals; and 3) multimodal versus visual signals. When choosing between isolated unimodal signals (visual or vibratory), there were no significant differences in orientation latency and number of orientations, approaches or receptive displays directed to either signal. When given a choice between multimodal versus vibratory-only male courtship signals, females were more likely to orient to the multimodal stimulus, and directed significantly more orients, approaches and receptivity behaviors to the multimodal signal. When presented with a choice between multimodal and visual-only signals, there were significantly more orients and approaches to the multimodal signal, but no significant difference in female receptivity. Results suggest that signal modes are redundant and equivalent in terms of qualitative responses, but when combined, multimodal signals quantitatively enhance detection and/or reception. This study confirms the value of testing preference behavior using a choice paradigm, as female preferences may depend on the context (e.g., environmental context and social context) in which they are presented with male signals.
High human disturbance decreases individual variability in skink escape behavior
Authors: Williams Dana M , Nguyen Phat-Tan , Chan Kemal , Krohn Madeleine , Blumstein Daniel T 
Published: May 2019

Abstract
Animals living around people may modify their antipredator behavior as a function of proximity to humans, and this response has profound implications for whether or not a population can coexist with humans. We asked whether inland blue-tailed skinks Emoia impar modified their individual antipredator behavior as a function of differential exposure to humans. We conducted multiple consecutive flushes and recorded 2 measures of antipredator response: flight initiation distance (FID), the distance from a threatening stimulus at which an individual flees, and distance fled, the distance an individual fled after a flush. We used a multiple model comparison approach to quantify variation in individual escape behavior across multiple approaches and to test for differences in between-individual variation among populations. We found that individuals tolerated closer approach and fled shorter distances at locations with relatively less human disturbance than at locations with medium and high human disturbance, respectively. In addition, skinks living at high human disturbance sites had less variable FIDs than at low human disturbance sites. Two theories may explain these results. Selection against less favorable phenotypes has reduced behavioral variation in urban habitats and behavioral plasticity allows individuals to flexibly adjust their behavioral patterns in response to human disturbance. These results highlight the importance of studying variation within populations, at the individual level, which may better elucidate the impact that human disturbance has on the behavioral composition of populations.
Anatomy of mitral annulus insights from non-invasive imaging techniques
Authors: Faletra Francesco F , Leo Laura Anna , Paiocchi Vera Lucia , Caretta Alessandro , Viani Giacomo Maria , Schlossbauer Susanne Anna , Demertzis Stefanos , Ho Siew Yen 
Published: May 2019

AbstractThe mitral annulus (MA) is not a continuous ring of connective tissue from which are suspended mitral leaflets. Instead, it is a much more complex structure made up of a mix of fibrous, muscular, and adipose tissues. MA is a key structure in any type of mitral valve repair and recently it has been targeted for transcutaneous devices. Thus, a deep understanding of MA anatomy has never been more important. Traditionally, cardiac anatomy has been described using anatomic specimens. Currently, sophisticated non-invasive techniques allow imaging of MA with a richness of anatomical details unimaginable only two decades ago. The aim of this review is to provide a better understanding of the peculiar aspects of MA as they are revealed through these imaging techniques and discuss clinical implications related to this complex structure.
The Rosa Lee phenomenon and its consequences for fisheries advice on changes in fishing mortality or gear selectivity
Authors: Kraak Sarah B M , Haase Stefanie , Minto Cóilín , Santos Juan 
Published: May 2019

Abstract
When size-selective fishing removes faster-growing individuals at higher rates than slower-growing fish, the surviving populations will become dominated by slower-growing individuals. When this “Rosa Lee phenomenon” is ignored, bias may occur in catch and stock projections. In a length-and-age-based model we quantified the effects through simulations of a simplified fishery on a stock that resembles Western Baltic cod. We compared outcomes of runs with and without taking account of the Rosa Lee phenomenon in scenarios of changes in fishing mortality. We found that, when only fishing rate was changed, the biases in predictions of spawning-stock biomass (SSB), yield and catches of undersized fish were relatively small (&lt;10% in absolute values). When the selectivity parameters of the gear were increased, the bias in the prediction of the catches of undersized fish was very substantial (+120 to 160%). When the selectivity parameters were decreased, the biases in the predictions of SSB, yield and catches of undersized fish, were substantial (25–50% in absolute values). With slower mean growth the biases became more pronounced. We conclude that in short-term forecasts, medium-term projections, and MSE simulations featuring selectivity changes, the Rosa Lee phenomenon should be accounted for, ideally by using length-based models.
Concealing Disease: Trade and Travel Barriers and the Timeliness of Outbreak Reporting
Authors: Worsnop Catherine Z 
Published: May 2019

AbstractSlow outbreak reporting by states is a key challenge to effectively responding to global health emergencies like Zika, Ebola, and H1N1. Current policy focuses on improving domestic outbreak surveillance capacity globally in order to reduce reporting lags. However, governments also face economic and political incentives to conceal outbreaks, and these incentives largely are ignored in policy discussions. In spite of the policy implications for outbreak response, the “capacity” and “will” explanations have not been systematically examined. Analysis of a dataset coding the timeliness of outbreak reporting from 1996–2014 finds evidence that states’ unwillingness to report—rather than just their inability—leads to delayed reporting. The findings suggest that though building surveillance capacity is critical, doing so may not be sufficient to reduce reporting lags. Policy aimed at encouraging rapid reporting must also mitigate the associated economic and political costs.
Effect of gestation dietary methionine/lysine ratio on placental angiogenesis and reproductive performance of sows1
Authors: Xia Mao , Pan Ye , Guo Liangliang , Wei Xiaowei X , Xiong Jia , Wang Liu , Peng Jie , Wang Chao , Peng Jian , Wei H K 
Published: May 2019

Abstract
The current study aims to evaluate the effects of different gestation dietary Met/Lys (methionine, Met/lysine) ratios on the production performance of sows. Specifically, it measured the effect of Met on plasma urea and AA concentrations and placental vascular density of pregnant sows. A total of 325 multiparous sows (third parity, Large × White) were randomly allocated to five dietary treatments (n = 65) with five dietary Met/Lys ratios 0.27 (nutrient requirements of swine [NRC] 2012 level), 0.32, 0.37, 0.42, and 0.47). The litter size and weight at birth were measured and recorded. Blood samples were obtained on days 0, 40, 90, and 114 of gestation, and placenta samples were collected at parturition. The effects of different dietary Met/Lys ratios on the reproductive performance were evaluated based on the prolificacy of sows as either high (≥13 total piglets born) or low (<13 total piglets born). The results showed that dietary Met/Lys ratio had no significant effect on the reproductive performance of lower prolificacy sows (P > 0.05). However, for high-prolificacy sows, litter weight of born alive significantly increased in 0.37 Met/Lys ratios group compared with control group (P < 0.05). The gestation dietary Met/Lys ratio showed significant quadratic effects on the litter birth weight and percentage of piglets born with weight <0.9 kg (P < 0.05), and the Met/Lys ratios to achieve the best reproductive performance determined to be 0.37. Furthermore, plasma urea concentrations of sows also changed with Met/Lys ratios quadratically (P < 0.05). Increasing dietary Met/Lys ratios elevated the concentration of most plasma AA. Although the dietary Met/Lys ratio had no significant effect on the placental vascular density (P > 0.05), the gestation dietary Met/Lys ratio showed significant quadratic effects on the placental vascular density (P < 0.05). In addition, the birth weight of piglets of high-prolificacy sows was positively correlated with the placental vascular density (P < 0.01). Taken as a whole, the dietary Met/Lys ratio showed a quadratic curve relation with birth weight performance and placental angiogenesis performance, to which 0.37 ratio contributed to the best performance of high-prolificacy sows.