bluuebunny/crossref_metadata_2025_split huggingface dataset:
Experimental Evidence for Sibling Recognition in Common Terns (Sterna Hirundo)
Authors: Burger J. , Gochfeld M. , Boarman W. I. 
Published: October 2019

Abstract
Young Common Terns (Sterna hirundo) did not respond preferentially to calls of siblings at 8 and 9 days of age, but did so by 12 days of age. In experiments with and without visual isolation, and with use of playback, we demonstrated a tendency to approach sibling begging calls. This differential response indicated sibling-recognition occurred, was based on experience, and involved vocal cues.
A Mechanism of Sexual Segregation by Habitat in American Kestrels (Falco sparverius) Wintering in South-Central Florida
Authors: Smallwood John A. 
Published: October 2019

Abstract
I observed the establishment of 240 winter territories by American Kestrels (Falco sparverius) on a 293-km census route in south-central Florida during autumn 1985. Most females arrived before males. Analysis of banding records revealed that immatures of both sexes and adult females preceded adult males in autumn migration in eastern North America; thus, the sex ratio of early arrivals was skewed toward females. In south Florida territorial kestrels occupied habitats in decreasing order of foraging quality, as measured by percentage cover of suitable hunting substrate (grasses or weedy forbs < 25 cm in height) and woody canopy cover (which was correlated negatively with suitable hunting substrate and obstructed the view of hunting kestrels). Early-arriving males also occupied habitats of superior foraging quality and were as successful as females in defending territories against same-sex and opposite-sex kestrels as high-quality habitats became limited. Results of experiments in which free-flying intruder kestrels were released onto defended territories suggested that males defended winter territories more tenaciously than did females. Because there was no evidence of male submissiveness on the wintering grounds, the female-dominance hypothesis is not a plausible explanation for sexual segregation by habitat in wintering kestrels. Each kestrel's arrival date was apparently the principal determinant of the foraging quality of habitats still available for occupancy; foraging quality was correlated negatively with arrival date for the adult males and for the females and immatures. A delayed molt in adult males, associated with differential sex roles on the breeding grounds, may delay the migratory departure, resulting in the late arrival on the wintering grounds.
Nuclear DNA Evolution and Phylogeny of the New World Nine-Primaried Oscines
Authors: Bledsoe Anthony H. 
Published: October 2019

Abstract
Estimates of phylogeny were derived from measures of dissimilarity of single-copy nuclear-DNA sequences for 13 species that represent the currently recognized major groups of New World nine-primaried oscines and an outgroup (Passer). The dissimilarity coefficients (delta mode and delta T50H) calculated from thermal dissociation curves of reassociated DNA sequences exhibited the properties of a metric. No statistically significant increase in goodness-of-fit of the raw data to a phylogeny estimated from a least-squares analysis of the 13 × 13 matrix of distances was achieved when the lengths of sister branches were allowed to vary. "Jackknife" and negative branch-length analyses identified unstable stems that resulted from non-additivity caused in part by measurement error. Such stems were collapsed to produce a more robust topology, which served as the basis for estimating the positions of taxa not included in the 13 × 13 matrix.
The clade that subsumed several "typical" tanagers (e.g. Tachyphonus rufus) also included Sicalis luteola and Diuca diuca (usually allied with the North American emberizine sparrows); Cyanerpes cyaneus, two species of Diglossa, and Coereba flaveola (often split among several major groups); and Tersina viridis, Catamblyrhynchus diadema, and Nephelornis oneilli (whose affinities are often considered uncertain). This "tanager" clade and its sister group, the cardinals (represented by Cardinalis cardinalis), together formed one fork of a trichotomy. Several emberizine sparrows (e.g. Pooecetes gramineus) formed the second fork, and wood-warblers (e.g. Dendroica striata) and New World orioles (e.g. Psarocolius angustifrons) formed the third. The chaffinches (represented by Fringilla coelebs) and several cardueline finches (e.g. Carduelis pinus) together formed the sister group of the other New World nine-primaried oscines included in the study. This phylogeny implies that convergence in feeding specializations among lineages is more extensive than traditional arrangements of the assemblage would suggest.
Heightened perception of competition hastens courtship
Authors: Santori Claudia , Bussière Luc F , Houslay Thomas M 
Published: October 2019

AbstractWhen animals use costly labile display or signal traits to display to the opposite sex, they face complex decisions regarding the degree and timing of their investment in separate instances of trait expression. Such decisions may be informed by not only the focal individual’s condition (or pool of available resources) but also aspects of the social environment, such as perceptions of same-sex competition or the quality of available mates. However, the relative importance of these factors to investment decisions remains unclear. Here, we use manipulations of condition (through dietary nutrition), recent social environment (exposure to a silenced male, nonsilenced male, female, or isolation), and female mating history (single or multiple male) to test how quickly male decorated crickets (Gryllodes sigillatus) decide to begin courting an available female. We find that males that were previously housed with nonsilenced males started courting the female earlier than other males. Females only mounted males after courtship began. Our results suggest a strong effect of the perception of competition on the decision to invest resources in sexual signaling behavior and that females might exert directional selection on its timing.
VISOR: a versatile haplotype-aware structural variant simulator for short- and long-read sequencing
Authors: Bolognini Davide , Sanders Ashley , Korbel Jan O , Magi Alberto , Benes Vladimir , Rausch Tobias 
Published: October 2019

Abstract

Summary
VISOR is a tool for haplotype-specific simulations of simple and complex structural variants (SVs). The method is applicable to haploid, diploid or higher ploidy simulations for bulk or single-cell sequencing data. SVs are implanted into FASTA haplotypes at single-basepair resolution, optionally with nearby single-nucleotide variants. Short or long reads are drawn at random from these haplotypes using standard error profiles. Double- or single-stranded data can be simulated and VISOR supports the generation of haplotype-tagged BAM files. The tool further includes methods to interactively visualize simulated variants in single-stranded data. The versatility of VISOR is unmet by comparable tools and it lays the foundation to simulate haplotype-resolved cancer heterogeneity data in bulk or at single-cell resolution.

Availability and implementation
VISOR is implemented in python 3.6, open-source and freely available at https://github.com/davidebolo1993/VISOR. Documentation is available at https://davidebolo1993.github.io/visordoc/.

Supplementary information
Supplementary data are available at Bioinformatics online.
ReQTL: identifying correlations between expressed SNVs and gene expression using RNA-sequencing data
Authors: Spurr Liam F , Alomran Nawaf , Bousounis Pavlos , Reece-Stremtan Dacian , Prashant N M , Liu Hongyu , Słowiński Piotr , Li Muzi , Zhang Qianqian , Sein Justin , Asher Gabriel , Crandall Keith A , Tsaneva-Atanasova Krasimira , Horvath Anelia 
Published: October 2019

Abstract

Motivation
By testing for associations between DNA genotypes and gene expression levels, expression quantitative trait locus (eQTL) analyses have been instrumental in understanding how thousands of single nucleotide variants (SNVs) may affect gene expression. As compared to DNA genotypes, RNA genetic variation represents a phenotypic trait that reflects the actual allele content of the studied system. RNA genetic variation at expressed SNV loci can be estimated using the proportion of alleles bearing the variant nucleotide (variant allele fraction, VAFRNA). VAFRNA is a continuous measure which allows for precise allele quantitation in loci where the RNA alleles do not scale with the genotype count. We describe a method to correlate VAFRNA with gene expression and assess its ability to identify genetically regulated expression solely from RNA-sequencing (RNA-seq) datasets.

Results
We introduce ReQTL, an eQTL modification which substitutes the DNA allele count for the variant allele fraction at expressed SNV loci in the transcriptome (VAFRNA). We exemplify the method on sets of RNA-seq data from human tissues obtained though the Genotype-Tissue Expression (GTEx) project and demonstrate that ReQTL analyses are computationally feasible and can identify a subset of expressed eQTL loci.

Availability and implementation
A toolkit to perform ReQTL analyses is available at https://github.com/HorvathLab/ReQTL.

Supplementary information
Supplementary data are available at Bioinformatics online.
Role of Narrative and Social Networks in Thwarting Violence and Sexual Abuse in Young People’s Lives
Authors: Hydén Margareta , Gadd David , Grund Thomas 
Published: October 2019

AbstractCombining narrative analysis with social network analysis, this article analyses the case of a young Swedish female who had been physically and sexually abused. We show how she became trapped in an abusive relationship at the age of fourteen years following social work intervention in her family home, and how she ultimately escaped from this abuse aged nineteen years. The analysis illustrates the significance of responses to interpersonal violence from the social networks that surround young people; responses that can both entrap them in abusive relationships by blaming them for their problems and enable them to escape abuse by recognising their strengths and facilitating their choices. The article argues that the case for social work approaches that envision young people’s social networks after protective interventions have been implemented. The article explains that such an approach has the potential to reconcile the competing challenges of being responsive to young people’s needs while anticipating the heightened risk of being exposed to sexual abuse young people face when estranged from their families or after their trust in professionals has been eroded.
Cyclin-like proteins tip regenerative balance in the liver to favour cancer formation
Authors: Fifield Bre-Anne , Talia John , Stoyanovich Carlee , Elliott Mitchell J , Bakht Martin K , Basilious Amy , Samsoondar Joshua P , Curtis Madison , Stringer Keith F , Porter Lisa A 
Published: October 2019

Abstract
Hepatocellular carcinoma (HCC) is one of the leading causes of cancer-related deaths worldwide. A variety of factors can contribute to the onset of this disease, including viral infection, obesity, alcohol abuse and non-alcoholic fatty liver disease (NAFLD). These stressors predominantly introduce chronic inflammation leading to liver cirrhosis and finally the onset of HCC; however, approximately 20% of HCC cases arise in the absence of cirrhosis via a poorly defined mechanism. The atypical cyclin-like protein Spy1 is capable of overriding cell cycle checkpoints, promoting proliferation and has been implicated in HCC. We hypothesize that Spy1 promotes sustained proliferation making the liver more susceptible to accumulation of deleterious mutations, leading to the development of non-cirrhotic HCC. We report for the first time that elevation of Spy1 within the liver of a transgenic mouse model leads to enhanced spontaneous liver tumourigenesis. We show that the abundance of Spy1 enhanced fat deposition within the liver and decreased the inflammatory response. Interestingly, Spy1 transgenic mice have a significant reduction in fibrosis and sustained rates of hepatocyte proliferation, and endogenous levels of Spy1 are downregulated during the normal fibrotic response. Our results provide support that abnormal regulation of Spy1 protein drives liver tumorigenesis in the absence of elevated fibrosis and, hence, may represent a potential mechanism behind non-cirrhotic HCC. This work may implicate Spy1 as a prognostic indicator and/or potential target in the treatment of diseases of the liver, such as HCC.
The cyclin-like protein Spy1 enhances lipid deposition and reduces fibrosis in the liver. Spy1 also promotes increased hepatocyte proliferation and onset of non-cirrhotic hepatocellular carcinoma (HCC). Thus, Spy1 may be used as a potential target in the treatment of HCC.
Virtual Infrastructure Orchestration For Cloud Service Deployment
Authors: Qadeer Arslan , Waqar Malik Asad , Ur Rahman Anis , Mian Muhammad Hamayun , Ahmad Arsalan 
Published: October 2019

AbstractCloud adoption has significantly increased using the infrastructure-as-a-service (IaaS) paradigm, in order to meet the growing demands of computing, storage and networking, in small as well as large enterprises. Different vendors provide their customized solutions for OpenStack deployment on bare metal or virtual infrastructure. Among these many available IaaS solutions, OpenStack stands out as being an agile and open-source platform. However, its deployment procedure is a time-taking and complex process with a learning curve. This paper addresses the lack of basic infrastructure automation in almost all of the OpenStack deployment projects. We propose a flexible framework to automate the process of infrastructure bring up for deployment of several OpenStack distributions, as well as resolving dependencies for a successful deployment. Our experimental results demonstrate the effectiveness of the proposed framework in terms of automation status and deployment time, that is, reducing the time spent in preparing a basic virtual infrastructure by four times, on average.
High sensitivity of a keystone forage fish to elevated CO2 and temperature
Authors: Murray Christopher S , Wiley David , Baumann Hannes 
Published: October 2019

AbstractSand lances of the genus Ammodytes are keystone forage fish in coastal ecosystems across the northern hemisphere. Because they directly support populations of higher trophic organisms such as whales, seabirds or tuna, the current lack of empirical data and, therefore, understanding about the climate sensitivity of sand lances represent a serious knowledge gap. Sand lances could be particularly susceptible to ocean warming and acidification because, in contrast to other tested fish species, they reproduce during boreal winter months, and their offspring develop slowly under relatively low and stable pCO2 conditions. Over the course of 2 years, we conducted factorial pCO2 × temperature exposure experiments on offspring of the northern sand lance Ammodytes dubius, a key forage species on the northwest Atlantic shelf. Wild, spawning-ripe adults were collected from Stellwagen Bank National Marine Sanctuary (Cape Cod, USA), and fertilized embryos were reared at three pCO2 conditions (400, 1000 and 2100 μatm) crossed with three temperatures (5, 7 and 10 ˚C). Exposure to future pCO2 conditions consistently resulted in severely reduced embryo survival. Sensitivity to elevated pCO2 was highest at 10 ˚C, resulting in up to an 89% reduction in hatching success between control and predicted end-of-century pCO2 conditions. Moreover, elevated pCO2 conditions delayed hatching, reduced remaining endogenous energy reserves at hatch and reduced embryonic growth. Our results suggest that the northern sand lance is exceptionally CO2-sensitive compared to other fish species. Whether other sand lance species with similar life history characteristics are equally CO2-sensitive is currently unknown. But the possibility is a conservation concern, because many boreal shelf ecosystems rely on sand lances and might therefore be more vulnerable to climate change than currently recognized. Our findings indicate that life history, spawning habitat, phenology and developmental rates mediate the divergent early life CO2 sensitivities among fish species.
Does physiological tolerance to acute hypoxia and salinity change explain ecological niche in two intertidal crab species?
Authors: Falconer Thomas R L , Marsden Islay D , Hill Jonathan V , Glover Chris N 
Published: October 2019

Lay summaryIn response to acute salinity change or hypoxia, Hemigrapsus crenulatus exhibited better maintenance of osmoregulatory and cardiovascular function than Hemigrapsus sexdentatus. The greater physiological resilience of H. crenulatus is consistent with its habitation of an ecological niche that promotes greater exposure to environmental stressors than that of H. sexdentatus.
Plato’s queer time: dialogic moments in the life and death of Socrates
Authors: Atack Carol 
Published: October 2019

AbstractCritics, from Athenaeus in the second century CE and Eduard Zeller in the nineteenth, to the present day, have been concerned with problems of authenticity and the dating of Plato’s work, including the inconsistent internal dramatic dates of the dialogues and other anachronisms within them. This article examines the relationship between the imaginary time of the dialogues and Plato’s own context, between the blurring of time and temporal relationships in the dialogues and the arguments that they contain, the construction of anachronistic communities and genealogies within them, through which Plato negotiates his own relationship with Socrates, and the deconstruction and re-negotiation of familial relationships, particularly those between fathers and sons. It uses insights from recent explorations of temporality in queer theory to generate a historicist reading that emphasizes the affective role of time within Plato’s writing. It argues that Plato uses the temporal setting of dialogues to underscore themes of their arguments, and that these anachronic settings can be read as an artefact of Plato’s own reception of Socrates’ life and death, and its context in the turmoil of the Peloponnesian War and the loss and restoration of democracy.
Machine learning approach to literature mining for the genetics of complex diseases
Authors: Schuster Jessica , Superdock Michael , Agudelo Anthony , Stey Paul , Padbury James , Sarkar Indra Neil , Uzun Alper 
Published: October 2019

AbstractTo generate a parsimonious gene set for understanding the mechanisms underlying complex diseases, we reasoned it was necessary to combine the curation of public literature, review of experimental databases and interpolation of pathway-associated genes. Using this strategy, we previously built the following two databases for reproductive disorders: The Database for Preterm Birth (dbPTB) and The Database for Preeclampsia (dbPEC). The completeness and accuracy of these databases is essential for supporting our understanding of these complex conditions. Given the exponential increase in biomedical literature, it is becoming increasingly difficult to manually maintain these databases. Using our curated databases as reference data sets, we implemented a machine learning-based approach to optimize article selection for manual curation. We used logistic regression, random forests and neural networks as our machine learning algorithms to classify articles. We examined features derived from abstract text, annotations and metadata that we hypothesized would best classify articles with genetically relevant content associated to the disorder of interest. Combinations of these features were used build the classifiers and the performance of these feature sets were compared to a standard ‘Bag-of-Words’. Several combinations of these genetic based feature sets outperformed ‘Bag-of-Words’ at a threshold such that 95% of the curated gene set obtained from the original manual curation of all articles were extracted from the articles classified by machine learning as ‘considered’. The performance was superior in terms of the reduction of required manual curation and two measures of the harmonic mean of precision and recall. The reduction in workload ranged from 0.814 to 0.846 for the dbPTB and 0.301 to 0.371 for the dbPEC. Additionally, a database of metadata and annotations is generated which allows for rapid query of individual features. Our results demonstrate that machine learning algorithms can identify articles with relevant data for databases of genes associated with complex diseases.
Host-Plant Specific Feeding Relationships and Insect Developmental Stage Modulate the Impact of Rainfall on Diamondback Moth Larvae
Authors: Rahman M D Mahbubur , Zalucki Myron P , Furlong Michael J 
Published: October 2019

Abstract
The impact of simulated rainfall on diamondback moth (DBM), Plutella xylostella (L.) (Lepidoptera: Plutellidae), larvae depends on their stage-specific feeding behavior, physical characteristics, and host plants. Neonates released at typical oviposition sites on Chinese cabbage (Brassica rapa var. pekinensis L. [Brassicales: Brassicaceae]) plants moved less (3–72 cm) and spend shorter periods (>1 h) than it has been previously reported for common cabbage (Brassica oleracea var. capitata L. [Brassicales: Brassicaceae]) (>80 cm and >3 h, respectively) before establishing feeding sites. On both host plants, larvae spent longer on the abaxial surfaces of leaves and were more likely to establish mines there than on the adaxial surfaces. On Chinese cabbage plants, ≈40% of neonates were removed when exposed to rainfall (5.6 cm/h for 3 min) within 5 min of release. Larval losses decreased rapidly as the interval between release and rainfall exposure increased and exposure to rainfall 2 h after release did not affect survival. On common cabbage plants, ≈65% of neonates were removed when exposed to rainfall within 30 min of release, losses decreased as the interval between release and rainfall exposure increased, but they decreased more slowly than on Chinese cabbage, and rainfall caused significant larval mortality up to 4 h after release. Rainfall also affected later instar larvae (susceptibility: 2nd> 3rd = 4th) but neither the susceptibility of these larvae nor that of pupae was affected by the host plant. Wet leaf surfaces disrupted movement and feeding site establishment by neonates. When dislodged from plants on to the surface of wet soil, most later stage larvae could relocate host plants, but most neonates could not.
Solidarity between Generations in Extended Families: Old-Age Income as a Way Out of Child Poverty?
Authors: Verbist Gerlinde , Diris Ron , Vandenbroucke Frank 
Published: October 2019

AbstractWe analyse intergenerational solidarity within multigenerational households (MGHs) and assess how the formation of these households is related to poverty across European countries. Our aim is to assess how this type of household is a coping strategy with respect to financial distress for families with children. Using data from EU Statistics on Income and Living Conditions (EU-SILC), we examine three specific empirical questions with regards to this complex form of intergenerational solidarity, notably (i) we identify to what extent co-residence within MGHs is financially beneficial to the young and/or the old generation; (ii) we analyse how the income brought into these households by the old generation impacts on child poverty, and (iii) we test how sensitive this impact is to hypotheses about the way resources are shared in the household. We define MGHs as those households where three generations cohabit. The results indicate that the formation of MGH operates mainly as solidarity from older to younger generations. Although not designed for this purpose, pensions alleviate child poverty in countries where MGH is most prevalent.