bluuebunny/crossref_metadata_2025_split huggingface dataset:
Demography of Bell's Vireos in Missouri Grassland-Shrub Habitats
Authors: Budnik Joel M. , Ryan Mark R. , Thompson III Frank R. 
Published: September 2019

Abstract
Numbers of Bell's Vireos (Vireo bellii) have declined throughout much of the breeding range in recent years, yet little information exists to determine factors that are causing these declines. We studied Bell's Vireos nesting in grassland-shrub habitats at two study areas in central Missouri to determine reproductive performance, survival, and population growth potential. Birds were color banded and observed during the breeding seasons of 1996, 1997, and 1998 to determine seasonal fecundity. We monitored 124 breeding pairs (127 pair years) and 213 nests. Density declined from 1.00 to 0.80 territories per 10 ha at the first site and increased from 1.11 to 1.33 at the second site during the study. Mean nesting success was 31 ± SE of 0.03% overall and ranged from 13 to 42% among years and study areas; 57% of the pairs fledged at least one young. Low annual production was a function of high rates of nest predation (41% of all nests observed, accounting for 44 to 78% of daily nest mortality annually) and nest parasitism by Brown-headed Cowbirds (Molothrus ater; 29% of nests observed, 17 to 37% of daily nest mortality annually). Mean seasonal fecundity was 1.60 young fledged per pair per year (range 1.00 to 1.79). Annual survival of adults was 61 ± 0.04% and was higher than previously reported. We used our estimates of seasonal fecundity and annual survival of adults to determine the finite rate of increase (λ) for our study population. Our study areas seemingly comprised sink habitats (λ = 0.85). Thus, the vireos on our study areas likely were limited by low reproductive success. Population declines also may be caused by habitat loss, which highlights the need for investigation of historical and current rates of loss of grassland-shrub habitat.
A New Species of Tody-Tyrant (Tyrannidae: Poecilotriccus) From Northern Peru
Authors: Johnson Ned K. , Jones Robert E. 
Published: September 2019

Abstract
We describe a new species of tody-tyrant of the genus Poecilotriccus, isolated in midelevation forests of the Cordillera de Colán and nearby mountains to the east in the northeastern Andes of Peru. The new species is allopatric from, and forms a probable superspecies with, the Rufous-crowned Tody-Tyrant (P. ruficeps), the nearest known populations of which inhabit the Cerro Chinguela of northern Peru. The geographic ranges of those sister taxa are divided by the North Peruvian Low, occupied by the Río Marañón, the major break in east-slope Andean forest between Venezuela and Bolivia. The new species and its allospecies, P. ruficeps are identical in color of the back and in lightness and hue of the crown, but are 100% separable in lightness, chroma, and hue of the belly; in color and pattern of the face; and in song. We infer that differences in vocalizations and facial markings would serve as premating reproductive isolating mechanisms should the two forms become sympatric.
Response of Passerine Birds to Forest Edge in Coast Redwood Forest Fragments
Authors: Brand L. Arriana , George T. Luke 
Published: September 2019

Abstract
The response of passerine birds to forest edge was examined in old-growth and mature second-growth coast redwood (Sequoia sempivirens) forest in northern California. The study objectives were to determine which common passerine species are sensitive to edges during the breeding season and to estimate edge width for forest interior species. Response to edge was measured along twelve 100 × 400 m plots extending from the edge into the forest interior to obtain relative density of birds. Plots were surveyed 4 to 5 times in 1996 and 8 to10 times in 1997. We found that 14 common passerines showed a gradient of edge sensitivity. Steller's Jay (Cyanocitta stelleri) and Swainson's Thrush (Catharus ustulatus) had higher relative densities near edges than in the forest interior (P < 0.05) and were categorized as edge species. Brown Creeper (Certhia americana), Winter Wren (Troglodytes troglodytes), Pacific-slope Flycatcher (Empidonax difficilis), and Varied Thrush (Ixoreus naevius) had lower relative densities near edges (P < 0.05) and were categorized as interior birds. Based on exponential regression models, estimated edge widths were 140 m for Varied Thrushes, 85 m for Brown Creepers, 120 m for Winter Wrens, and 125 m for Pacific-slope Flycatchers. Creation of edges would probably benefit Steller's Jays (which may be a nest predator), may not benefit Swainson's Thrushes, and may be detrimental to species that avoid edges. We recommend that edge effects be taken into consideration when planning for the conservation of bird species in the region.
Foraging Decisions of Sandwich Terns in the Presence of Kleptoparasitising Gulls
Authors: Stienen Eric W. M. , Brenninkmeijer Alex 
Published: September 2019

AbstractWe studied prey selection of Sandwich Terns (Sterna sandvicensis) in the presence of kleptoparasitising Black-headed Gulls (Larus ridibundus) on Griend, Dutch Wadden Sea, from 1992 to 1998. Most often, gulls robbed larger sandeels rather than herring from terns. Provided that one parent attends the chick, energy intake would be too low for the chicks' survival if exclusively fed on sandeel. By provisioning an increasing proportion of herring, parent terns could theoretically overcome a potential food shortage when the chicks grow older. However, the proportion of herring did not increase with age of chicks in most years. Instead, parents increased their foraging effort with the growth of their offspring. In years with high proportions of food loss, parents left their chicks unattended at the nest more often. In that way, parents were largely able to counterbalance food shortage of offspring. In 1992 and 1996, when diet composition was unfavorable and food losses to gulls were high, parents left their chicks unattended at the nest for ∼80% of the daylight period. It is argued that the present working level of parents might be higher than in the 1960s.
Life-History Implications of Large-Scale Spatial Variation in Adult Survival of Black Brant (Branta Bernicla Nigricans)
Authors: Sedinger James S. , Chelgren Nathan D. , Lindberg Mark S. , Obritchkewitch Tim , Kirk Morgan T. , Martin Philip , Anderson Betty A. , Ward David H. 
Published: September 2019

Abstract
We used capture–recapture methods to estimate adult survival rates for adult female Black Brant (Branta bernicla nigricans; hereafter “brant”) from three colonies in Alaska, two on the Yukon-Kuskokwim Delta, and one on Alaska's Arctic coast. Costs of migration and reproductive effort varied among those colonies, enabling us to examine variation in survival in relation to variation in these other variables. We used the Barker model in program MARK to estimate true annual survival for brant from the three colonies. Models allowing for spatial variation in survival were among the most parsimonious models but were indistinguishable from a model with no spatial variation. Point estimates of annual survival were slightly higher for brant from the Arctic (0.90 ± 0.036) than for brant from either Tutakoke River (0.85 ± 0.004) or Kokechik Bay (0.86 ± 0.011). Thus, our survival estimates do not support a hypothesis that the cost of longer migrations or harvest experienced by brant from the Arctic reduced their annual survival relative to brant from the Yukon-Kuskokwim Delta. Spatial variation in survival provides weak support for life-history theory because brant from the region with lower reproductive investment had slightly higher survival.
Sexual Differences in Gap-Crossing Ability of a Forest Songbird in a Fragmented Landscape Revealed Through Radiotracking
Authors: Norris D. Ryan , Stutchbury Bridget J. M. 
Published: September 2019

Abstract
We used radio telemetry to examine extraterritorial movements of female Hooded Warblers (Wilsonia citrina) breeding in small, isolated woodlots. Only 44% of the nine females tracked left their woodlots (n = 6 forays in total). Compared to males followed in the same fragments (Norris and Stutchbury 2001), females spent significantly less time off territory and traveled shorter distances across nonforested gaps. Unlike males in fragmented habitat and females in continuous forest, we found no evidence that females were actively seeking extrapair copulations. We conclude females are relatively more restricted to isolated fragments during the breeding season and suggest that the lack of extrapair copulation opportunity could contribute to female avoidance of fragmented habitat, resulting in a high number of unmated males. This study emphasizes the importance of examining the potential effects of fragmentation in both sexes.
Daily Energy Expenditure of Ovenbirds (Seiurus aurocapillus) Feeding Nestlings
Authors: Vander Haegen W. Matthew , DeGraaf Richard M. 
Published: September 2019

AbstractThe doubly labeled water method was used to measure daily energy expenditure of adult Ovenbirds (Seiurus aurocapillus) feeding nestlings in large and small forests in northern New England. Carbon dioxide production for all birds averaged 7.67 ± 1.29 mL g−1 hr−1 (n = 27), equivalent to 90.1 ± 15.0 kJ day−1. Carbon dioxide production did not differ between males and females within the same pair measured over the same period. Ratio of daily energy expenditure to basal metabolic rate (BMR) for Ovenbirds (3.4) was closer to the mean value derived for aerial foragers (3.8) than that for ground foragers (2.3) in a sample of passerines feeding nestlings. High daily energy expenditure for Ovenbirds may be related to their relatively brief breeding season in northern climates and their use of cool, closed-canopy forests. Although daily energy expenditure for Ovenbirds was high when compared to other ground-foraging passerines, most individuals were not working near the hypothetical maximum of 4× BMR (Drent and Daan 1980). Daily energy expenditure for Ovenbirds feeding young was greater in large forests than small forests, although the difference was not statistically significant. We speculate that time used for foraging (and hence energy expenditure) may be lower in small forests as a result of increased prey density, or alternatively, greater risk of nest predation in forest fragments leads to greater vigilance at the nest site and less time available for foraging. Further studies of avian energetics in large and small forests, including detailed time–activity budgets, may reveal hidden costs of forest fragmentation.
A Geometric Method for Determining Shape of Bird Eggs
Authors: Baker Douglas E. 
Published: September 2019

Abstract
Precise quantification of the oval of a bird egg can provide a powerful tool for the analysis of egg shape for various biological problems. A new approach to the geometry of a bird egg oval is presented here using a simple algebraic equation to fit all normal bird egg shapes. Only two parameters are needed in the equation for complete shape description of an egg oval to quantify the equation's capacity for curve fitting all species and shapes of bird egg ovals. The equation was fitted to egg silhouettes from a sample of 250 different bird egg species containing one egg per species. Standard regression analysis was used to fit the equation to each egg profile. The 99% CI for the curve fit acceptance rate was calculated to determine the equation's statistical significance for all species of bird eggs. Compared to the power series multiequation models (Preston 1968, Todd and Smart 1984), the equation used here is the simplest analytic description of a bird egg oval.
BioBERT: a pre-trained biomedical language representation model for biomedical text mining
Authors: Lee Jinhyuk , Yoon Wonjin , Kim Sungdong , Kim Donghyeon , Kim Sunkyu , So Chan Ho , Kang Jaewoo 
Published: September 2019

Abstract

Motivation
Biomedical text mining is becoming increasingly important as the number of biomedical documents rapidly grows. With the progress in natural language processing (NLP), extracting valuable information from biomedical literature has gained popularity among researchers, and deep learning has boosted the development of effective biomedical text mining models. However, directly applying the advancements in NLP to biomedical text mining often yields unsatisfactory results due to a word distribution shift from general domain corpora to biomedical corpora. In this article, we investigate how the recently introduced pre-trained language model BERT can be adapted for biomedical corpora.

Results
We introduce BioBERT (Bidirectional Encoder Representations from Transformers for Biomedical Text Mining), which is a domain-specific language representation model pre-trained on large-scale biomedical corpora. With almost the same architecture across tasks, BioBERT largely outperforms BERT and previous state-of-the-art models in a variety of biomedical text mining tasks when pre-trained on biomedical corpora. While BERT obtains performance comparable to that of previous state-of-the-art models, BioBERT significantly outperforms them on the following three representative biomedical text mining tasks: biomedical named entity recognition (0.62% F1 score improvement), biomedical relation extraction (2.80% F1 score improvement) and biomedical question answering (12.24% MRR improvement). Our analysis results show that pre-training BERT on biomedical corpora helps it to understand complex biomedical texts.

Availability and implementation
We make the pre-trained weights of BioBERT freely available at https://github.com/naver/biobert-pretrained, and the source code for fine-tuning BioBERT available at https://github.com/dmis-lab/biobert.
Sex and Age Determination of Short- Eared Owl Nestlings
Authors: Arroyo Beatriz E. , DeCornulier Thomas , Bretagnolle Vincent 
Published: September 2019

Abstract
We studied plumage patterns of known-sex nestling and juvenile Short-eared Owls (Asio flammeus) to develop a sexing technique for nestlings in the field. Markings on the secondaries varied according to sex, and differences were apparent from about 10–15 days of age. We also provide aging formulas based on mass for nestlings up to 15 days of age and on wing length for nestlings older than that age. Finally, we evaluate growth parameters according to sex. The asymptotes of body mass, wing length, and tarsus length growth curves were higher in females than males. The inflexion point was attained earlier by males than by females.
First-in-man explantation of a HeartMate 3 left ventricular assist device via customized plug
Authors: Hanke Jasmin S , Dogan Günes , Haverich Axel , Schmitto Jan D 
Published: September 2019

Abstract
Myocardial recovery in left ventricular assist device patients is a rare opportunity to explant the assist device. Despite myocardial recovery, these patients remain high-risk candidates. Short, effective procedures are the key to successful left ventricular assist device explantation. Conventional methods such as ventriculoplasty are extensive and challenging procedures. Thus, an explantation tool was developed in order to simplify HeartMate 3 (Abbott Cooperation, Abbott Park, Ill, USA) explantation. A customized metal plug was designed to fit into the HeartMate 3-sewing ring. We now report the successful first-in-man use of this novel plug for HeartMate 3 explantation.
Corytophanids Replaced the Pleurodont XY System with a New Pair of XY Chromosomes
Authors: Acosta Armando , Suárez-Varón Gabriel , Rodríguez-Miranda Luis A , Lira-Noriega Andrés , Aguilar-Gómez Diana , Gutiérrez-Mariscal Mariana , Hernández-Gallegos Oswaldo , Méndez-de-la-Cruz Fausto , Cortez Diego 
Published: September 2019

Abstract
Almost all lizard families in the pleurodont clade share the same XY system. This system was meticulously studied in Anolis carolinensis, where it shows a highly degenerated Y chromosome and a male-specific X chromosome dosage compensation mechanism. Corytophanids (casque-headed lizards) have been proposed as the only family in the pleurodont clade to lack the XY system. In this study, we worked with extensive genomic and transcriptomic data from Basiliscus vittatus, a member of the Corytophanidae family that inhabits the tropical rainforests of Mexico. We confirmed that B. vittatus underwent a sex chromosome system turnover, which consisted in the loss of the pleurodont XY system and the gain of a new pair of XY chromosomes that are orthologous to chicken chromosome 17. We estimated the origin of the sex chromosome system to have occurred ∼63 Ma in the ancestor of corytophanids. Moreover, we identified 12 XY gametologues with particular attributes, such as functions related to the membrane and intracellular trafficking, very low expression levels, blood specificity, and incomplete dosage compensation in males.
The molecular chaperone Hsp90 maintains Golgi organization and vesicular trafficking by regulating microtubule stability
Authors: Wu Yuan , Ding Yubo , Zheng Xiudan , Liao Kan 
Published: September 2019

AbstractHsp90 is an abundant and special molecular chaperone considered to be the regulator of many transcription factors and signaling kinases. Its high abundance is indicative of its involvement in some more fundamental processes. In this study, we provide evidence that Hsp90 is required for microtubule stabilization, Golgi organization, and vesicular trafficking. We showed that Hsp90 is bound to microtubule-associated protein 4 (MAP4), which is essential for maintaining microtubule acetylation and stabilization. Hsp90 depletion led to the decrease in MAP4, causing microtubule deacetylation and destabilization. Furthermore, in Hsp90-depleted cells, the Golgi apparatus was fragmented and anterograde vesicle trafficking was impaired, with phenotypes similar to those induced by silencing MAP4. These disruptive effects of Hsp90 depletion could be rescued by the expression of exogenous MAP4 or the treatment of trichostatin A that increases microtubule acetylation as well as stability. Thus, microtubule stability is an essential cellular event regulated by Hsp90.
The Association Between Medicare Low-Income Subsidy and Anticancer Treatment Uptake in Advanced Lung Cancer
Authors: Chou Yi-Ting , Farley Joel F , Stinchcombe Thomas E , Proctor Amber E , Lafata Jennifer Elston , Dusetzina Stacie B 
Published: September 2019

Abstract

Background
High out-of-pocket costs may impact anticancer treatment uptake. The Low-Income Subsidy (LIS) program can reduce patient out-of-pocket cost for Medicare Part D–covered treatments. We examined whether the LIS increased uptake and reduced time to initiate orally administered anticancer drugs in patients with advanced non–small cell lung cancer (NSCLC).

Methods
Using Surveillance, Epidemiology and End Results (SEER)-Medicare data, we identified older adults (aged 65 years and older) diagnosed with advanced NSCLC from 2007 through 2013 and categorized them as full LIS, partial LIS, or non-LIS. We used propensity-score weighted (IPTW) Cox proportional hazards regression to assess the likelihood of and time to initiate Part D treatments. Part B medication uptake was our negative control because supplemental insurance reduces out-of-pocket costs for those drugs. All statistical tests were two-sided.

Results
Among 19 746 advanced NSCLC patients, approximately 10% initiated Part D treatments. Patients with partial or no LIS were less likely to initiate Part D treatments than were those with full subsidies (partial LIS vs full LIS HRIPTW = 0.77, 95% confidence interval = 0.62 to 0.97; non-LIS vs full LIS HRIPTW = 0.87, 95% confidence interval  = 0.79 to 0.95). Time to initiate Part D treatments was also slightly shorter among full-LIS patients (full LIS mean [SD] = 10.8 [0.04] months; partial LIS mean [SD] = 11.3 [0.08] months; and non-LIS mean [SD] = 11.1 [0.03] months, P &lt; .001). Conversely, patients with partial or no LIS had shorter time to initiation of Part B drugs.

Conclusions
Patients receiving the full LIS had higher orally administered anticancer treatment uptake than patients without LIS. Notably, patients with partial LIS had the lowest treatment uptake, likely because of their low incomes combined with high expected out-of-pocket spending. High out-of-pocket costs for Part D medications may be a barrier to treatment use for patients without full LIS.
A substructural epistemic resource logic: theory and modelling applications
Authors: Galmiche Didier , Kimmel Pierre , Pym David 
Published: September 2019

AbstractWe present a substructural epistemic logic, based on Boolean BI, in which the epistemic modalities are parametrized on agents’ local resources. The new modalities can be seen as generalizations of the usual epistemic modalities. The logic combines Boolean BI’s resource semantics—we introduce BI and its resource semantics at some length—with epistemic agency. We illustrate the use of the logic in systems modelling by discussing some examples about access control, including semaphores, using resource tokens. We also give a labelled tableaux calculus and establish soundness and completeness with respect to the resource semantics.
The Mayflower and the Slave Ship: Pilgrim-Puritan Origins in the Antebellum Black Imagination
Authors: Gradert Kenyon 
Published: September 2019

AbstractThis essay argues that antebellum black writers claimed America in part by reimagining a national rhetoric of Pilgrim-Puritan origins. Various connections have been drawn between the Puritans and early black writers, including a revised tradition of typological identification with Israel, captivity narratives, and, most frequently, the “black jeremiad.” In addition to these scholarly genealogies, black writers struggled more directly with their spiritual genealogies in an effort to reconcile a growing investment in American and Protestant identity with an emergent sense of black roots. Since Paul Gilroy, a growing number of scholars have examined the importance of origins for antebellum black writers in conversation with dominant Euro-American traditions, yet American Protestantism remains a minor presence in these studies. If early black studies of antiquity, biblical history, and European historiography, for example, were crucial to an emergent sense of black roots, they intertwined in complex ways with black writers’ investment in American Protestantism and its vision of history. Ultimately, black writers further radicalized abolitionists’ revolutionary Puritan genealogy as they made it their own, expanding this spiritual lineage to sanction fugitive slaves, black revolutionaries, and eventually the black troops of the American Civil War, imagined as the culmination of a sacred destiny that was both black and American, traceable to the Mayflower and the slave ship alike.
Developing a unified pipeline for large-scale structure data analysis with angular power spectra – I. The importance of redshift-space distortions for galaxy number counts
Authors: Tanidis Konstantinos , Camera Stefano 
Published: September 2019

ABSTRACT
We develop a cosmological parameter estimation code for (tomographic) angular power spectra analyses of galaxy number counts, for which we include, for the first time, redshift-space distortions (RSDs) in the Limber approximation. This allows for a speed-up in computation time, and we emphasize that only angular scales where the Limber approximation is valid are included in our analysis. Our main result shows that a correct modelling of RSD is crucial not to bias cosmological parameter estimation. This happens not only for spectroscopy-detected galaxies, but even in the case of galaxy surveys with photometric redshift estimates. Moreover, a correct implementation of RSD is especially valuable in alleviating the degeneracy between the amplitude of the underlying matter power spectrum and the galaxy bias. We argue that our findings are particularly relevant for present and planned observational campaigns, such as the Euclid satellite or the Square Kilometre Array, which aim at studying the cosmic large-scale structure and trace its growth over a wide range of redshifts and scales.