bluuebunny/crossref_metadata_2025_split huggingface dataset:
Genetic Variation in Piciform Birds: Monophyly and Generic and Familial Relationships
Authors: Lanyon Scott M. , Zink Robert M. 
Published: October 2019

Abstract
Inter and intrafamilial relationships within the New World Piciformes were examined through an electrophoretic analysis of 20 protein-coding loci (19 of which varied between taxa). One individual from each of 26 species representing 25 genera and 5 families was analyzed; Monotus momota (Coraciiformes, Momotidae) was used as an outgroup. Although levels of genetic differentiation were high (the mean Nei's unbiased distance was 1.07), the data proved useful for phylogenetic inference. The jackknife technique was used to estimate the robustness of phylogenetic hypotheses. At the interfamilial level, the results suggest the following groupings: [[[(Bucconidae) (Galbulidae)]{(Picidae)[(Capitonidae) (Ramphastidae)]}]]. These results were consistent with hypotheses of familial relationships proposed by two recent cladistic analyses of morphological character complexes (Simpson and Cracraft 1981, Swierczewski and Raikow 1981). Our data challenge the currently accepted monophyly of the Piciformes, however, in much the same way as do DNA-DNA hybridization data. Agreement among independently derived hypotheses of interfamilial relationships suggests confidence in our knowledge of evolutionary patterns among piciform taxa. Hypotheses of intrafamilial relationships, some of which agreed with morphological patterns obtained in other studies, were presented. This study shows that starch-gel electrophoresis may be useful at higher taxonomic levels.
Annual Reproductive Yield in the Cooperative Pygmy Nuthatch (Sitta pygmaea)
Authors: Sydeman William J. , Güntert Marcel , Balda Russell P. 
Published: October 2019

Abstract
We studied cooperative-breeding Pygmy Nuthatches (Sitta pygmaea) for 4 yr in northern Arizona. Breeding units contained 2-5 birds. Helpers were found at about 30% of all nests. All helpers that later bred on the study area were male. Helpers were mostly yearlings, and offspring or siblings of the birds that they aided, but often aided at least one unrelated breeder. Breeding units with helpers produced significantly more young than those without helpers. Breeding units in habitats with the greatest floral diversity and structural maturity fledged significantly more young than those in other habitats. Habitat did not influence the effect of helpers. Year effects increased the strength of the relationship between helpers and annual reproductive output. Previous breeding experience and pair-bond duration were not related to reproductive success. Total brood loss, although rare, was responsible for the difference in reproductive output among pairs with and without helpers and between habitats.
Breeding birds with helpers benefit by an increase in direct fitness. The advantage to the helpers is not clear but may be an increase in indirect fitness associated with aiding relatives. Helpers may benefit directly, however, by sharing roosting cavities on a group territory thereby enhancing overwinter survival.
Dominance Relationships in Harems of Female Red-Winged Blackbirds
Authors: Roberts Laurel B. , Searcy William A. 
Published: October 2019

Abstract
We investigated the factors determining dominance in aggressive encounters between female Red-winged Blackbirds (Agelaius phoeniceus) resident on territories of single males. Three male territories were observed, with harems of 5, 5, and 3 females. Feeding platforms were placed on the territories to increase the sample of observable encounters between residents. Order of settlement on the territory was strongly related to dominance; in 19 of 23 dyads the earlier settler won the majority of encounters. Proximity to the nest at the encounter site was also related to dominance; in 30 of 45 dyads the female closer to her nest won the majority of interactions. The effect of proximity on dominance also was shown experimentally by moving the platforms from near one nest to near another, which caused the dominance relationships between the pairs of females to reverse. In a partial correlation analysis, both order of settlement and proximity to nest correlated independently with the percentage of encounters won within dyads. Size, age, and nesting stage were not related to dominance.
Breeding Biology of the Puerto Rican Sharp-Shinned Hawk (Accipiter Striatus Venator)
Authors: Delannoy Carlos A. , Cruz Alexander 
Published: October 2019

Abstract
We studied the breeding biology of the Sharp-shinned Hawk (Accipiter striatus venator ) in Maricao forest of western Puerto Rico from 1978 to 1985. Sharp-shinned Hawks are year-round residents and establish nesting territories only during the breeding season, which coincides with the dry and beginning of the wet seasons. Nesting sites were occupied in December and January every year and reoccupancy rates were 50% or higher. Prolonged and intense territorial conflicts between mated and unmated males were common. The onset of egg-laying was in late March or early April approximately 3-4 months after occupancy of nesting sites. Laying of first clutches peaked in early April and spanned 38 days (n = 19 clutches). Laying of second clutches occurred irregularly and spanned 55 days (n = 8 clutches). Females renested only after the initial clutch or brood was lost. The incubation period was 32 days (n = 13 clutches), similar to the duration reported in temperate North America. Nestling females attained larger asymptotic mass than males, but the latter grew faster; although the slopes of the regression lines were statistically homogeneous. Males fledged at an average age of 28.2 days and females at 32.1 days. Young were slightly heavier than adults at fledging, but the wing chord and tail lengths were approximately 50% shorter than those of adults. Fledging occurred at the peak of prey abundance. The breeding cycle in Puerto Rico was approximately 2 months longer than that recorded in Oregon and Utah. The time that elapsed from occupancy of nesting sites to egg laying accounted for the differences. Juveniles departed from nesting sites when prey was still abundant but delivery rates had declined considerably. A total of 105 eggs was laid in 40 nests (average clutch size 2.6), of which 63% hatched and 47% of the nestlings fledged. A total of 0.8 young fledged per breeding attempt. Overall nest success was 29%, 36% (n = 33 nests) in first nesting attempts and 0% in second nesting attempts (n = 9 nests). Most reproductive losses in 28 nests resulted from nestling mortality from Philornis sp. (Diptera, Muscidae) (n = 9) and desertion of clutches (n = 11). Fecundity and reproductive success was lower in Puerto Rico than in Oregon, Utah, and Wyoming. Despite low reproductive success in Maricao forest, the breeding population did not decline during our study.
On the Origin of Darwin's Finches
Authors: Baptista Luis F. , Trail Pepper W. 
Published: October 2019

Abstract
We critically reviewed recent attempts to identify the ancestor of Darwin's finches (Emberizidae, "Geospizinae"), and summarized new information on taxa that have been suggested as sister groups of the geospizines, specifically the emberizines Tiaris, Melanospiza, and Volatinia. Reproductive behaviors and displays are conservative among Darwin's finches, and have been neglected in discussions of the ancestry of the group. We concentrate on these characters. We found that Tiaris and Melanospiza share a large number of apparently derived epigamic behaviors with the geospizines, none of which are exhibited by Volatinia.
WASPS: web-assisted symbolic plasmid synteny server
Authors: Badel Catherine , Da Cunha Violette , Catchpole Ryan , Forterre Patrick , Oberto Jacques 
Published: October 2019

Abstract

Motivation
Comparative plasmid genome analyses require complex tools, the manipulation of large numbers of sequences and constitute a daunting task for the wet bench experimentalist. Dedicated plasmid databases are sparse, only comprise bacterial plasmids and provide exclusively access to sequence similarity searches.

Results
We have developed Web-Assisted Symbolic Plasmid Synteny (WASPS), a web service granting protein and DNA sequence similarity searches against a database comprising all completely sequenced natural plasmids from bacterial, archaeal and eukaryal origin. This database pre-calculates orthologous protein clustering and enables WASPS to generate fully resolved plasmid synteny maps in real time using internal and user-provided DNA sequences.

Availability and implementation
WASPS queries befit all current browsers such as Firefox, Edge or Safari while the best functionality is achieved with Chrome. Internet Explorer is not supported. WASPS is freely accessible at https://archaea.i2bc.paris-saclay.fr/wasps/.

Supplementary information
Supplementary data are available at Bioinformatics online.
RNAIndel: discovering somatic coding indels from tumor RNA-Seq data
Authors: Hagiwara Kohei , Ding Liang , Edmonson Michael N , Rice Stephen V , Newman Scott , Easton John , Dai Juncheng , Meshinchi Soheil , Ries Rhonda E , Rusch Michael , Zhang Jinghui 
Published: October 2019

Abstract

Motivation
Reliable identification of expressed somatic insertions/deletions (indels) is an unmet need due to artifacts generated in PCR-based RNA-Seq library preparation and the lack of normal RNA-Seq data, presenting analytical challenges for discovery of somatic indels in tumor transcriptome.

Results
We present RNAIndel, a tool for predicting somatic, germline and artifact indels from tumor RNA-Seq data. RNAIndel leverages features derived from indel sequence context and biological effect in a machine-learning framework. Except for tumor samples with microsatellite instability, RNAIndel robustly predicts 88–100% of somatic indels in five diverse test datasets of pediatric and adult cancers, even recovering subclonal (VAF range 0.01–0.15) driver indels missed by targeted deep-sequencing, outperforming the current best-practice for RNA-Seq variant calling which had 57% sensitivity but with 14 times more false positives.

Availability and implementation
RNAIndel is freely available at https://github.com/stjude/RNAIndel.

Supplementary information
Supplementary data are available at Bioinformatics online.
iATC-NRAKEL: an efficient multi-label classifier for recognizing anatomical therapeutic chemical classes of drugs
Authors: Zhou Jian-Peng , Chen Lei , Guo Zi-Han 
Published: October 2019

Abstract

Motivation
The anatomical therapeutic chemical (ATC) classification system plays an increasingly important role in drug repositioning and discovery. The correct identification of classes in each level of such system that a given drug may belong to is an essential problem. Several multi-label classifiers have been proposed in this regard. Although they provided satisfactory performance, the feature extraction procedures were still rough. More refined features may further improve the predicted quality.

Results
In this article, we provide a novel multi-label classifier, called iATC-NRAKEL, to predict drug ATC classes in the first level. To obtain more informative drug features, we employed the drug association information in STITCH and KEGG, which was organized by seven drug networks. The powerful network embedding algorithm, Mashup, was adopted to extract informative drug features. The obtained features were fed into the RAndom k-labELsets (RAKEL) algorithm with support vector machine as the basic classification algorithm to construct the classifier. The 10-fold cross-validation of the benchmark dataset with 3883 drugs showed that the accuracy and absolute true were 76.56 and 74.51%, respectively. The comparison results indicated that iATC-NRAKEL was much superior to all previous reported classifiers. Finally, the contribution of each network was analyzed.

Availability and implementation
The codes of iATC-NRAKEL are available at https://github.com/zhou256/iATC-NRAKEL.
From “Mine” to “Ours”: Gendered Hierarchies of Authorship and the Limits of Taylor Swift’s Paratextual Feminism
Authors: McNutt Myles 
Published: October 2019

AbstractThis article analyzes paratextual strategies deployed by Taylor Swift in her transition from country to pop in the context of her articulation of her authorship as a female songwriter. This was a transition complicated by the gendered hierarchies of pop music, wherein male producers carry significant discursive weight. The article frames the “Voice Memos” included with her 2014 album 1989 as a form of paratextual feminism, reiterating the authenticity she developed as a country star and pushing back against claims her collaboration with male producers like Max Martin and Ryan Tedder threaten her autonomy as a female voice in the music industry. However, the article goes on to consider how these and other paratextual feminisms are inherently tied to neoliberal values of post-feminism, demonstrating that their potential as a gendered critique of the media industries is limited by the lack of actualization within Swift’s broader star text and industry practice.
A Model of Brain Folding Based on Strong Local and Weak Long-Range Connectivity Requirements
Authors: Groden Moritz , Weigand Marvin , Triesch Jochen , Jedlicka Peter , Cuntz Hermann 
Published: October 2019

AbstractThroughout the animal kingdom, the structure of the central nervous system varies widely from distributed ganglia in worms to compact brains with varying degrees of folding in mammals. The differences in structure may indicate a fundamentally different circuit organization. However, the folded brain most likely is a direct result of mechanical forces when considering that a larger surface area of cortex packs into the restricted volume provided by the skull. Here, we introduce a computational model that instead of modeling mechanical forces relies on dimension reduction methods to place neurons according to specific connectivity requirements. For a simplified connectivity with strong local and weak long-range connections, our model predicts a transition from separate ganglia through smooth brain structures to heavily folded brains as the number of cortical columns increases. The model reproduces experimentally determined relationships between metrics of cortical folding and its pathological phenotypes in lissencephaly, polymicrogyria, microcephaly, autism, and schizophrenia. This suggests that mechanical forces that are known to lead to cortical folding may synergistically contribute to arrangements that reduce wiring. Our model provides a unified conceptual understanding of gyrification linking cellular connectivity and macroscopic structures in large-scale neural network models of the brain.
Effect of Endogenous Clostridioides difficile Toxin Antibodies on Recurrence of C. difficile Infection
Authors: Kelly Ciarán P , Poxton Ian R , Shen Judong , Wilcox Mark H , Gerding Dale N , Zhao Xuemei , Laterza Omar F , Railkar Radha , Guris Dalya , Dorr Mary Beth 
Published: October 2019

Abstract

Background
Endogenous antibodies (eAbs) against Clostridioides (Clostridium) difficile toxins may protect against recurrence of C. difficile infection (rCDI). This hypothesis was tested using placebo group data from MODIFY (Monoclonal Antibodies for C. difficile Therapy) I and II (NCT01241552 and NCT01513239, respectively), global, randomized phase 3 trials that assessed the efficacy and safety of the antitoxin monoclonal antibodies bezlotoxumab and actoxumab in participants receiving antibiotic therapy for CDI.

Methods
A placebo infusion (normal saline) was administered on study day 1. Serum samples were collected on day 1, week 4, and week 12, and eAb-A and eAb-B titers were measured by 2 validated electrochemiluminescence immunoassays. Rates of initial clinical cure and rCDI were summarized by eAb titer category (low, medium, high) at each time point.

Results
Serum eAb titers were available from a total of 773 participants. The proportion of participants with high eAb-A and eAb-B titers increased over time. Rates of initial clinical cure were similar across eAb titer categories. There was no correlation between eAb-A titers and rCDI rate at any time point. However, there was a negative correlation between rCDI and eAb-B titer on day 1 and week 4. rCDI occurred in 22% of participants with high eAb-B titers at baseline compared with 35% with low or medium titers (P = .015).

Conclusions
Higher eAb titers against toxin B, but not toxin A, were associated with protection against rCDI. These data are consistent with the observed efficacy of bezlotoxumab, and lack of efficacy of actoxumab, in the MODIFY trials.

Clinical Trials Registration
NCT01241552 and NCT01513239.
Consensus Report on Shigella Controlled Human Infection Model: Conduct of Studies
Authors: Talaat Kawsar R , Bourgeois A Louis , Frenck Robert W , Chen Wilbur H , MacLennan Calman A , Riddle Mark S , Suvarnapunya Akamol E , Brubaker Jessica L , Kotloff Karen L , Porter Chad K 
Published: October 2019

AbstractShigella causes morbidity and mortality worldwide, primarily affecting young children living in low-resource settings. It is also of great concern due to increasing antibiotic resistance, and is a priority organism for the World Health Organization. A Shigella vaccine would decrease the morbidity and mortality associated with shigellosis, improve child health, and decrease the need for antibiotics. Controlled human infection models (CHIMs) are useful tools in vaccine evaluation for early up- or down-selection of vaccine candidates and potentially useful in support of licensure. Over time, the methods employed in these models have become more uniform across sites performing CHIM trials, although some differences in conduct persist. In November 2017, a Shigella CHIM workshop was convened in Washington, District of Columbia. Investigators met to discuss multiple aspects of these studies, including study procedures, clinical and immunological endpoints, and shared experiences. This article serves as a uniform procedure by which to conduct Shigella CHIM studies.
Consensus Report on Shigella Controlled Human Infection Model: Immunological Assays
Authors: Kaminski Robert W , Pasetti Marcela F , Aguilar Ana Older , Clarkson Kristen A , Rijpkema Sjoerd , Bourgeois A Louis , Cohen Dani , Feavers Ian , MacLennan Calman A 
Published: October 2019

AbstractModerate to severe diarrhea caused by Shigella is a global health concern due to its substantial contribution to morbidity and mortality in children aged &lt;5 years in low- and middle-income countries. Although antibiotic treatment can be effective, emerging antimicrobial resistance, limited access, and cost affirm the role of vaccines as the most attractive countermeasure. Controlled human infection models (CHIMs) represent a valuable tool for assessing vaccine efficacy and potentially accelerating licensure. Currently, immunological analysis during CHIM studies is customized based on vaccine type, regimen, and administration route. Additionally, differences in type of immunoassays and procedures used limit comparisons across studies. In November 2017, an expert working group reviewed Shigella CHIM studies performed to date and developed consensus guidelines on prioritization of immunoassays, specimens, and collection time points. Immunoassays were ranked into 3 tiers, with antibodies to Shigella lipopolysaccharide (LPS) being the highest priority. To facilitate comparisons across clinical studies, a second workshop was conducted in December 2017, which focused on the pathway toward a recognized enzyme-linked immunosorbent assay (ELISA) to determine serum immunoglobulin G titers against Shigella LPS. The consensus of the meeting was to establish a consortium of international institutions with expertise in Shigella immunology that would work with the National Institute for Biological Standards and Control to establish a harmonized ELISA, produce a reference sera, and identify a reliable source of Shigella LPS for global utilization. Herein we describe efforts toward establishing common procedures to advance Shigella vaccine development, support licensure, and ultimately facilitate vaccine deployment and uptake.
Long-term Persistence of an Extensively Drug-Resistant Subclade of Globally Distributed Pseudomonas aeruginosa Clonal Complex 446 in an Academic Medical Center
Authors: Pincus Nathan B , Bachta Kelly E R , Ozer Egon A , Allen Jonathan P , Pura Olivia N , Qi Chao , Rhodes Nathaniel J , Marty Francisco M , Pandit Alisha , Mekalanos John J , Oliver Antonio , Hauser Alan R 
Published: October 2019

AbstractBackgroundAntimicrobial resistance (AMR) is a major challenge in the treatment of infections caused by Pseudomonas aeruginosa. Highly drug-resistant infections are disproportionally caused by a small subset of globally distributed P. aeruginosa sequence types (STs), termed “high-risk clones.” We noted that clonal complex (CC) 446 (which includes STs 298 and 446) isolates were repeatedly cultured at 1 medical center and asked whether this lineage might constitute an emerging high-risk clone.MethodsWe searched P. aeruginosa genomes from collections available from several institutions and from a public database for the presence of CC446 isolates. We determined antibacterial susceptibility using microbroth dilution and examined genome sequences to characterize the population structure of CC446 and investigate the genetic basis of AMR.ResultsCC446 was globally distributed over 5 continents. CC446 isolates demonstrated high rates of AMR, with 51.9% (28/54) being multidrug-resistant (MDR) and 53.6% of these (15/28) being extensively drug-resistant (XDR). Phylogenetic analysis revealed that most MDR/XDR isolates belonged to a subclade of ST298 (designated ST298*) of which 100% (21/21) were MDR and 61.9% (13/21) were XDR. XDR ST298* was identified repeatedly and consistently at a single academic medical center from 2001 through 2017. These isolates harbored a large plasmid that carries a novel antibiotic resistance integron.ConclusionsCC446 isolates are globally distributed with multiple occurrences of high AMR. The subclade ST298* is responsible for a prolonged epidemic (≥16 years) of XDR infections at an academic medical center. These findings indicate that CC446 is an emerging high-risk clone deserving further surveillance.
Modelling temperature and humidity effects on web performance: implications for predicting orb-web spider (Argiope spp.) foraging under Australian climate change scenarios
Authors: Blamires S J , Sellers W I 
Published: October 2019

Lay Summary.How climate change impacts animal extended phenotypes (EPs) is poorly understood. We modelled how temperature and humidity affects the ability of spider webs to intercept prey. We found humidity had negative effects at the extremes. Temperature, however, likely interacts with humidity to affect web tension and prey retention.
Control of sinus venous valve and sinoatrial node development by endocardial NOTCH1
Authors: Wang Yidong , Lu Pengfei , Jiang Liping , Wu Bingruo , Zhou Bin 
Published: October 2019

AbstractAimsSinus venous valve (SVV) and sinoatrial node (SAN) develop together at the sinoatrial junction during embryogenesis. SVV ensures unidirectional cardiac input and SAN generates sinus rhythmic contraction, respectively; both functions are essential for embryonic survival. We aim to reveal the potential role of endocardial NOTCH signalling in SVV and SAN formation.Methods and resultsWe specifically deleted Notch1 in the endocardium using an Nfatc1Cre line. This deletion resulted in underdeveloped SVV and SAN, associated with reduced expression of T-box transcription factors, Tbx5 andTbx18, which are essential for the formation of SVV and SAN. The deletion also led to decreased expression of Wnt2 in myocardium of SVV and SAN. WNT2 treatment was able to rescue the growth defect of SVV and SAN resulted from the Notch1 deletion in whole embryo cultures. Furthermore, the Notch1 deletion reduced the expression of Nrg1 in the SVV myocardium and supplement of NRG1 restored the growth of SVV in cultured Notch1 knockout embryos.ConclusionOur findings support that endocardial NOTCH1 controls the development of SVV and SAN by coordinating myocardial WNT and NRG1 signalling functions.