bluuebunny/crossref_metadata_2025_split huggingface dataset:
An experimental test of the effect of male attractiveness on maternal investment in Dark-eyed Juncos
Authors: Ferree Elise D 
Published: June 2019

AbstractWhile social mate choice is an obvious point where sexual selection acts on males, cryptic selection can occur based on how much females invest in a male’s offspring. I tested 4 hypotheses about the relationship between female investment and social mate attractiveness by manipulating a sexually selected trait, white tail feathers (“tail white”), in male Dark-eyed Juncos (Junco hyemalis thurberi): (1) the differential allocation hypothesis predicts that females optimize lifetime reproductive success by maximizing parental investment in the offspring of ornamented mates and minimizing investment when mated to less attractive males; (2) instead of positive differential allocation, females could show negative differential allocation by investing more in less attractive males to compensate for their lower quality; (3) female care could also be influenced directly by paternal investment, in particular what appears to be positive differential allocation could be compensation for reduced care by attractive males; or (4) females could reduce care when paired with socially attractive males that are “good parents”. To evaluate these hypotheses, I examined the impact of tail white manipulation on clutch size, female incubation and brooding, and female and male provisioning. Females did not differentially allocate in relation to social mate attractiveness, nor were females responsive to patterns of male investment, even although artificially attractive males provisioned offspring significantly more than did controls. Naturally bright males, who were also the largest males, did not provision at higher rates, highlighting the need to experimentally separate the role of specific traits from other correlated factors. Tail white-manipulated males were involved in rare cases of polygyny and at times were actively guarded by their mates. Together, these results suggest that tail white influences reproductive behaviors in this junco population, but because of the potential for extrapair paternity, additional data are needed to accurately investigate the trait’s role in female investment.
Male social plasticity influences transient dynamics in the emergence of alternative mating systems in water striders
Authors: Perez Adrian , Montiglio Pierre-Olivio , Wey Tina W , Sih Andrew 
Published: June 2019

AbstractAnimal mating systems are often studied with the goal of understanding why species, populations, or groups vary from one another in the system they display. Although these differences are often treated as basically stable, it is also known that mating systems may shift over time (e.g., from one breeding season to the next). There has been some study of how ecological factors correlate with these changes; however, few, if any, studies have investigated how the phenotypic composition of a group governs the timing and probability of these mating system transitions. Groups of stream water striders (Aquarius remigis) can experience rapid changes in mating system dynamics, with small groups often transitioning into a system in which a single, large male monopolizes mating opportunities. We asked if variation in individual- and group-level traits associated with morphology and behavior (e.g., size of the largest individual, average activity behavioral type in the group) could partially explain the variability in how rapidly groups make this transition, if they make it at all. We show that groups with males that exhibit higher social plasticity tended to take longer to transition to a mating system dominated by a single male. Our results, therefore, suggest that groups in identical ecological conditions can diverge in their mating systems based on how much individuals in the group change their behavior in response to the behavior of other members of the group.
Behavioral, energetic, and color trait integration in male guppies: testing the melanocortin hypothesis
Authors: Santostefano Francesca , Fanson Kerry V , Endler John A , Biro Peter A 
Published: June 2019

AbstractIndividuals of the same population differ consistently from each other in the average expression of behavioral and physiological traits. Often, such traits are integrated and thus correlated with each other. However, the underlying proximate mechanisms generating and maintaining this among-individual covariation are still poorly understood. The melanocortin hypothesis suggests that the melanocortin pathways can have pleiotropic effects linking the expression of melanin-based coloration with physiological and behavioral traits. In the present study, we test this hypothesis in adult male guppies (Poecilia reticulata), by estimating among individual correlations between behaviors (activity, feeding, boldness, display, and chase during courtship), stress response (peak metabolic rate), and coloration (black spot, fuzzy black, and orange). The lack of correlation of any behavior or metabolism with black coloration indicates that the melanocortin hypothesis is not supported in this species. However, we observed covariation among coloration traits, as well as among behavioral traits. Our findings suggest that, although there appear to be constraints within sets of related traits, coloration, physiology, and behaviors can potentially evolve as independent modules in response to selection in this species.
Artificial selection on walking distance suggests a mobility-sperm competitiveness trade-off
Authors: Matsumura Kentarou , Archer C Ruth , Hosken David J , Miyatake Takahisa 
Published: June 2019

AbstractSecuring matings is a key determinant of fitness, and in many species, males are the sex that engages in mate searching. Searching for mates is often associated with increased mobility. This elevated investment in movement is predicted to trade-off with sperm competitiveness, but few studies have directly tested whether this trade-off occurs. Here, we assessed whether artificial selection on mobility affected sperm competitiveness and mating behavior, and if increased mobility was due to increased leg length in red flour beetles (Tribolium castaneum). We found that, in general, males selected for decreased mobility copulated for longer, stimulated females more during mating, and tended to be better sperm competitors. Surprisingly, they also had longer legs. However, how well males performed in sperm competition depended on females. Males with reduced mobility always copulated for longer than males with high mobility, but this only translated into greater fertilization success in females from control populations and not the selection populations (i.e. treatment females). These results are consistent with a mate-searching/mating-duration trade-off and broadly support a trade-off between mobility and sperm competitiveness.
Biological market effects predict cleaner fish strategic sophistication
Authors: Triki Zegni , Wismer Sharon , Rey Olivia , Ann Binning Sandra , Levorato Elena , Bshary Redouan 
Published: June 2019

Abstract
Market-like situations emerge in nature when trading partners exchange goods and services. However, how partner choice option contributes to the expression of social strategic sophistication (i.e., the ability to adjust behavior flexibly given the specifics of a situation) is still poorly understood. A suitable study system to explore this question is the “cleaner” fish Labroides dimidiatus. Cleaners trade parasite removal in exchange for food with a variety of “client” species. Previous research documented strong interindividual variation in two features of their strategic sophistication, namely, the ability to adjust service quality to the presence of an audience and to give priority to clients with access to alternative cleaners (“visitor clients”) over clients lacking such choice options (“resident clients”). Here, we sampled various demes (i.e., group of individuals) of the same population of cleaner fish in order to investigate the extent to which factors describing fish densities and cleaning interaction patterns predict the strategic sophistication in two laboratory experiments. These experiments tested whether cleaners could increase their food intake through reputation management and/or learning to provide service priority to a visitor-like ephemeral food plate. We found that high “outbidding competition,” characterized by high densities of cleaners and visitor clients, along with visitor’s behavior promoting such competition, consistently predicted high strategic sophistication in cleaners. A better understanding of the role of learning versus potential genetic factors, interacting with local market conditions to affect strategic sophistication, is needed to clarify how natural selection has promoted the evolution and maintenance of cooperation in this cleaning mutualism.
GeneNoteBook, a collaborative notebook for comparative genomics
Authors: Holmer Rens , van Velzen Robin , Geurts Rene , Bisseling Ton , de Ridder Dick , Smit Sandra 
Published: June 2019

Abstract

Summary
Analysis and comparison of genomic and transcriptomic datasets have become standard procedures in biological research. However, for non-model organisms no efficient tools exist to visually work with multiple genomes and their metadata, and to annotate such data in a collaborative way. Here we present GeneNoteBook: a web based collaborative notebook for comparative genomics. GeneNoteBook allows experimental and computational researchers to query, browse, visualize and curate bioinformatic analysis results for multiple genomes. GeneNoteBook is particularly suitable for the analysis of non-model organisms, as it allows for comparing newly sequenced genomes to those of model organisms.

Availability and implementation
GeneNoteBook is implemented as a node.js web application and depends on MongoDB and NCBI BLAST. Source code is available at https://github.com/genenotebook/genenotebook. Additionally, GeneNoteBook can be installed through Bioconda and as a Docker image. Full installation instructions and online documentation are available at https://genenotebook.github.io.

Supplementary information
Supplementary data are available at Bioinformatics online.
iScore: a novel graph kernel-based function for scoring protein–protein docking models
Authors: Geng Cunliang , Jung Yong , Renaud Nicolas , Honavar Vasant , Bonvin Alexandre M J J , Xue Li C 
Published: June 2019

AbstractMotivationProtein complexes play critical roles in many aspects of biological functions. Three-dimensional (3D) structures of protein complexes are critical for gaining insights into structural bases of interactions and their roles in the biomolecular pathways that orchestrate key cellular processes. Because of the expense and effort associated with experimental determinations of 3D protein complex structures, computational docking has evolved as a valuable tool to predict 3D structures of biomolecular complexes. Despite recent progress, reliably distinguishing near-native docking conformations from a large number of candidate conformations, the so-called scoring problem, remains a major challenge.ResultsHere we present iScore, a novel approach to scoring docked conformations that combines HADDOCK energy terms with a score obtained using a graph representation of the protein–protein interfaces and a measure of evolutionary conservation. It achieves a scoring performance competitive with, or superior to, that of state-of-the-art scoring functions on two independent datasets: (i) Docking software-specific models and (ii) the CAPRI score set generated by a wide variety of docking approaches (i.e. docking software-non-specific). iScore ranks among the top scoring approaches on the CAPRI score set (13 targets) when compared with the 37 scoring groups in CAPRI. The results demonstrate the utility of combining evolutionary, topological and energetic information for scoring docked conformations. This work represents the first successful demonstration of graph kernels to protein interfaces for effective discrimination of near-native and non-native conformations of protein complexes.Availability and implementationThe iScore code is freely available from Github: https://github.com/DeepRank/iScore (DOI: 10.5281/zenodo.2630567). And the docking models used are available from SBGrid: https://data.sbgrid.org/dataset/684).Supplementary informationSupplementary data are available at Bioinformatics online.
Dissociable and Paradoxical Roles of Rat Medial and Lateral Orbitofrontal Cortex in Visual Serial Reversal Learning
Authors: Hervig M E , Fiddian L , Piilgaard L , Božič T , Blanco-Pozo M , Knudsen C , Olesen S F , Alsiö J , Robbins T W 
Published: June 2019

ABSTRACT
Much evidence suggests that reversal learning is mediated by cortico-striatal circuitries with the orbitofrontal cortex (OFC) playing a prominent role. The OFC is a functionally heterogeneous region, but potential differential roles of lateral (lOFC) and medial (mOFC) portions in visual reversal learning have yet to be determined. We investigated the effects of pharmacological inactivation of mOFC and lOFC on a deterministic serial visual reversal learning task for rats. For reference, we also targeted other areas previously implicated in reversal learning: prelimbic (PrL) and infralimbic (IL) prefrontal cortex, and basolateral amygdala (BLA). Inactivating mOFC and lOFC produced opposite effects; lOFC impairing, and mOFC improving, performance in the early, perseverative phase specifically. Additionally, mOFC inactivation enhanced negative feedback sensitivity, while lOFC inactivation diminished feedback sensitivity in general. mOFC and lOFC inactivation also affected novel visual discrimination learning differently; lOFC inactivation paradoxically improved learning, and mOFC inactivation had no effect. We also observed dissociable roles of the OFC and the IL/PrL. Whereas the OFC inactivation affected only perseveration, IL/PrL inactivation improved learning overall. BLA inactivation did not affect perseveration, but improved the late phase of reversal learning. These results support opponent roles of the rodent mOFC and lOFC in deterministic visual reversal learning.
Reduced Mortality of Staphylococcus aureus Bacteremia in a Retrospective Cohort Study of 2139 Patients: 2007–2015
Authors: Austin Eloise D , Sullivan Sean S , Macesic Nenad , Mehta Monica , Miko Benjamin A , Nematollahi Saman , Shi Qiuhu , Lowy Franklin D , Uhlemann Anne-Catrin 
Published: June 2019

AbstractBackgroundUnderstanding the changing epidemiology of Staphylococcus aureus bacteremia, as well as the variables associated with poor outcomes, can yield insight into potential interventions.MethodsThis study was a retrospective, observational cohort study of adult patients at an academic medical center in New York City who had S. aureus bloodstream infections between 1 January 2007 and 31 December 2015. Participants were divided into 3 periods: group 1 (2007–2009), group 2 (2010–2012), and group 3 (2013–2015) for trend analysis. All clinical strains were genotyped (spa.). The main outcome was 30-day all-cause mortality.ResultsThere were 1264 episodes of methicillin-susceptible S. aureus (MSSA) and 875 episodes of methicillin-resistant S. aureus (MRSA) bacteremia, with a rising proportion due to MSSA (55% group 1; 59% group 2; 63% group 3; P = .03.) There were no significant changes in average age, gender, Charlson score, and distribution of strain genotypes. Mortality in MRSA infection was unchanged (25% group 1; 25% group 2; 26% group 3), while mortality in MSSA infection significantly declined (18% group 1; 18% group 2; 13% group 3). The average time to antistaphylococcal therapy (AST) in MSSA infection declined during the study (3.7 days group 1; 3.5 group 2; 2.2 group 3). In multivariate analysis, AST within 7 days of initial positive MSSA culture was associated with survival.ConclusionsMortality in MSSA bloodstream infection is declining, associated with a decrease in time to targeted therapy. These results emphasize the potential for rapid diagnostics and early optimization of treatment to impact outcomes in MSSA bacteremia.
Dengue Infection Complicated by Hemophagocytic Lymphohistiocytosis: Experiences From 180 Patients With Severe Dengue
Authors: Kan Foong Kee , Tan Cheng Cheng , Von Bahr Greenwood Tatiana , Khalid Khairil E , Supramaniam Premaa , Hed Myrberg Ida , Tan Lian Huat , Henter Jan-Inge 
Published: June 2019

Abstract

Background
Globally, ~500 000 people with severe dengue (SD) require hospitalization yearly; ~12 500 (2.5%) die. Secondary hemophagocytic lymphohistiocytosis (sHLH) is a potentially fatal hyperinflammatory condition for which HLH-directed therapy (as etoposide and dexamethasone) can be life-saving. Prompted by the high mortality in SD and the increasing awareness that patients with SD may develop sHLH, our objectives were to (1) determine the frequency of dengue-HLH in SD, (2) describe clinical features of dengue-HLH, (3) assess mortality rate in SD and dengue-HLH, and (4) identify mortality-associated risk factors in SD.

Methods
A 5-year retrospective single-center study in all adult patients with SD admitted to a tertiary intensive care unit in Malaysia.

Results
Thirty-nine of 180 (22%) patients with SD died. Twenty-one of 180 (12%) had HLH defined as an HLH probability ≥70% according to histo score (HScore); 9 (43%) died. Similarly, 12 of 31 (39%) fulfilling ≥4 and 7 of 9 (78%) fulfilling ≥5 HLH-2004 diagnostic criteria died. Peak values of aspartate aminotransferase (AST), alanine aminotransferase, lactate dehydrogenase, and creatinine correlated to fatality (odds ratios [ORs], 2.9, 3.4, 5.8, and 31.9; all P &lt; .0001), as did peak ferritin (OR, 2.5; P = .0028), nadir platelets (OR, 1.9; P = .00068), hepatomegaly (OR, 2.9; P = .012), and increasing age (OR, 1.2; P = .0043). Multivariable logistic regression revealed peak AST (OR, 2.8; P = .0019), peak creatinine (OR, 7.3; P = .0065), and SOFA (Sequential Organ Failure Assessment) score (OR, 1.4; P = .0051) as independent risk factors of death.

Conclusions
Be observant of dengue-HLH due to its high mortality. A prospective study is suggested on prompt HLH-directed therapy in SD patients with hyperinflammation and evolving multiorgan failure at risk of developing dengue-HLH.
Tuberculosis Preventive Therapy for Individuals Exposed to Drug-resistant Tuberculosis: Feasibility and Safety of a Community-based Delivery of Fluoroquinolone-containing Preventive Regimen
Authors: Malik Amyn A , Fuad Junaid , Siddiqui Sara , Amanullah Farhana , Jaswal Maria , Barry Zainab , Jabeen Farhat , Fatima Razia , Yuen Courtney M , Salahuddin Naseem , Khan Aamir J , Keshavjee Salmaan , Becerra Mercedes C , Hussain Hamidah 
Published: June 2019

Abstract

Background
Observational studies have demonstrated the effectiveness of a fluoroquinolone-based regimen to treat individuals presumed to be infected with drug-resistant tuberculosis (DR-TB). We sought to assess the feasibility of this approach in an urban setting in South Asia.

Methods
From February 2016 until March 2017, all household contacts of DR-TB patients enrolled at the Indus Hospital were screened for TB symptoms at home. Children aged 0–17 years, symptomatic adults, and those with an immunocompromising condition (human immunodeficiency virus, diabetes, or malnutrition) were evaluated for TB disease. Contacts diagnosed with TB disease were started on treatment. Contacts without TB disease aged &lt;5 years, contacts aged between 5 and 17 years with either a positive tuberculin skin test or an immunocompromising condition, or contacts aged ≥18 years with an immunocompromising condition were offered 6 months of treatment with a fluoroquinolone.

Results
One hundred households with 800 contacts were enrolled: 353 (44.1%) individuals aged ≤17 years with a median age of 19 years (interquartile range, 10–32); 423 (52.9%) were males. In total, 737 (92.1%) individuals were screened, of which 8 were already on treatment for TB (1.1%); another 3 (0.4%) contacts were diagnosed with TB disease and started on treatment. Of 215 eligible for infection treatment, 172 (80.0%) contacts initiated and 121 (70.3%) completed treatment. No TB disease or significant adverse events were observed during 12 months of follow-up.

Conclusions
Fluoroquinolone-based treatment for contacts with presumed DR-TB infection is feasible and well tolerated in a high TB burden setting.
Proximity to unconventional shale gas infrastructure alters breeding bird abundance and distribution
Authors: Farwell Laura S , Wood Petra B , Brown Donald J , Sheehan James 
Published: June 2019

AbstractUnconventional shale gas development is a rapidly expanding driver of forest loss and fragmentation in the central Appalachian region. We evaluated the relationship between breeding passerine abundances and distance from shale gas development at a long-term (2008–2017) study site in northern West Virginia, USA. We examined responses of 27 species within 3 habitat guilds: forest interior, early successional, and synanthropic. More than half of the species evaluated showed sensitivity to distance from unconventional shale gas infrastructure (e.g., well pads, access roads, pipelines). Five forest interior species occurred in greater abundances farther from shale gas development, whereas 3 forest interior gap specialists increased in abundance closer to shale gas. Early successional and synanthropic species, including the nest-parasitic Brown-headed Cowbird (Molothrus ater), generally occurred in greater abundances closer to shale gas infrastructure. We used interpolated distributions of 4 focal species to assess their spatial response to unconventional shale gas development over time. Our results indicate that breeding passerine distributions and community composition are changing with forest disturbance driven by unconventional shale gas energy development.
Thyroid hormone concentrations associated with age, sex, reproductive status and apparent reproductive failure in the Amazon river dolphin (Inia geoffrensis)
Authors: Robeck T R , Amaral R S , da Silva V M F , Martin A R , Montano G A , Brown J L 
Published: June 2019

AbstractThis study was conducted to characterize immunoreactive thyroid hormone concentrations in wild Amazon river dolphins, also called boto (Inia geoffrensis) by age group, sex, pregnancy and lactation status, and to determine if thyroid hormone concentration differences could be detected between pregnant females with and without successful parturition outcomes. Radioimmunoassays were used to analyse total T3 and total T4 in 182 serum samples collected from 172 botos living in the Mamirauá Sustainable Development Reserve, in the Brazilian Amazon from 2003 through 2015. Age significantly affected tT3 and tT4 concentrations in males, with values in immature males and females being significantly lower than those in adult males, whereas no age effects were noted between immature females and adult non-pregnant, non-lactating females. Significant sex differences were noted in tT3 concentrations between immature males and females and in tT4 concentrations between adult males and females. These resulted in significant differences in the tT3:tT4 ratio between males and females within the immature and adult groups. Lactating and non-pregnant adult females had significantly higher tT3 concentrations than pregnant females, and this difference was primarily driven by a 12% drop in tT3 concentrations during the last two-thirds of pregnancy. No differences in thyroid hormone concentrations were detected between females diagnosed as pregnant and later found to have or not have a live calf. These results are the first to define thyroid hormone reference intervals and normal physiological variations in a wild population of river dolphins.