bluuebunny/crossref_metadata_2025_split huggingface dataset:
Genetic Identification of Eggs Purportedly From the Extinct Labrador Duck (Camptorhynchus Labradorius)
Authors: Chilton Glen , Sorenson Michael D. 
Published: September 2019

AbstractMaterial extracted from inside the shells of nine purported Labrador Duck (Camptorhynchus labradorius) eggs was subjected to DNA extraction and polymerase chain reaction (PCR) amplification. For each egg, partial sequences of one to three mitochondrial genes (12S, ND2, and control region) were compared with sequences derived from a Labrador Duck specimen and representatives of several other waterfowl species. Sequences from six eggs were consistent with those of the Red-breasted Merganser (Mergus serrator), whereas the sequences from one egg was most consistent with that of the Common Eider (Somateria mollissima). The remaining two eggs yielded sequences consistent with that of the Mallard (Anas platyrhynchos) or a domestic duck. Regrettably, none of the eggs provided additional information about the breeding grounds of the extinct Labrador Duck. To our knowledge, this is the first report of DNA extraction and amplification from old eggshells of birds.Identification génétique d'œufs présumés provenir de l'espèce disparue Camptorhynchus labradorius
Distinctiveness, Use, and Value of Midwestern Oak Savannas and Woodlands as Avian Habitats
Authors: Grundel Ralph , Pavlovic Noel B. 
Published: September 2019

AbstractOak savannas and woodlands historically covered millions of hectares in the midwestern United States but are rare today. We evaluated the ecological distinctiveness and conservation value of savannas and woodlands by examining bird distributions across a fire-maintained woody-vegetation gradient in northwest Indiana encompassing five habitats—open habitats with low canopy cover, savannas, woodlands, scrublands, and forests—during migration, breeding, and overwintering. Savannas and woodlands were significantly different in overall bird species composition from open and forest habitats but were often intermediate between open and forest in guild densities. Few bird species were consistently and highly concentrated in savannas or woodlands, and the Red-headed Woodpecker (Melanerpes erythrocephalus) was the only species significantly more abundant in savannas and woodlands than in open, scrub, and forest habitats. Fire frequency over a 15-year interval was a significant predictor of bird community composition and was positively related to species diversity, spring transient migrant density, and density of the most threatened species. Each habitat type had characteristics potentially important for avian conservation. Scrub had the highest density of transient migrants, which suggests it plays an important role as migration stopover habitat. More species were significantly concentrated in open or forest habitats than in the other habitats. Lack of species concentration and intermediate community composition suggested that birds experienced savannas and woodlands more as ecotones than as habitats distinct from forests or grasslands. However, this intermediate character can benefit conservation, as evidenced by savannas and woodlands having the highest density of the most threatened species along this woody-vegetation gradient.Características Únicas, Uso y Valor de las Sabanas y Bosques Abiertos de Roble del Oeste Central como Hábitats para las Aves
Experimental Analysis of The Auditory Detection Process on Avian Point Counts
Authors: Simons Theodore R. , Alldredge Mathew W. , Pollock Kenneth H. , Wettroth John M. 
Published: September 2019

AbstractWe have developed a system for simulating the conditions of avian surveys in which birds are identified by sound. The system uses a laptop computer to control a set of amplified MP3 players placed at known locations around a survey point. The system can realistically simulate a known population of songbirds under a range of factors that affect detection probabilities. The goals of our research are to describe the sources and range of variability affecting point-count estimates and to find applications of sampling theory and methodologies that produce practical improvements in the quality of bird-census data. Initial experiments in an open field showed that, on average, observers tend to undercount birds on unlimited-radius counts, though the proportion of birds counted by individual observers ranged from 81% to 132% of the actual total. In contrast to the unlimited-radius counts, when data were truncated at a 50-m radius around the point, observers overestimated the total population by 17% to 122%. Results also illustrate how detection distances decline and identification errors increase with increasing levels of ambient noise. Overall, the proportion of birds heard by observers decreased by 28 ± 4.7% under breezy conditions, 41 ± 5.2% with the presence of additional background birds, and 42 ± 3.4% with the addition of 10 dB of white noise. These findings illustrate some of the inherent difficulties in interpreting avian abundance estimates based on auditory detections, and why estimates that do not account for variations in detection probability will not withstand critical scrutiny.Análisis Experimentales del Proceso de Detección Auditiva en Puntos de Conteo de Aves
Breeding Habitat Requirements and Selection by Olrog's Gull (Larus Atlanticus), A Threatened Species
Authors: Borboroglu Pablo García , Yorio Pablo 
Published: September 2019

AbstractWe studied habitat requirements and selection of Olrog's Gulls (Larus atlanticus) breeding at six colonies along 2,500 km of coastline in central Argentina that encompasses its entire distributional range. Colonies were located only on islands that ranged in size between 0.4 and 125.8 ha, and the islands' distance to the mainland varied from 0.12 to 16.7 km. Colonies ranged in size between 12 and 341 nests. In three of the colonies, gulls nested in subcolonies (range: 8–239 nests). They nested at relatively high densities, with a mean inter-nest distance of 0.66 ± 0.25 m. Logistic regression analysis to compare nest and random-site characteristics at each colony showed that Olrog's Gulls selected sites that were close to the high-tide line, at a lower height above sea level, far from available vegetation, and had lower vegetation cover over the nest. Olrog's Gulls showed a significant positive association with Kelp Gulls (L. dominicanus), an expanding generalist species that also nests in similar habitats. Current trends in coastal development, particularly in the Olrog's Gulls' main breeding grounds of southern Buenos Aires, indicate the urgent need for habitat-protection guidelines for this threatened species. Moreover, its breeding association with Kelp Gulls suggests a potential spatial conflict and highlights the need for increased monitoring and management actions.Selección y Requerimientos de Hábitat Reproductivo en Larus atlanticus, una Especie Amenazada
Small-Prey Profitability: Field Analysis of Shorebirds’ use of Surface Tension of Water to Transport Prey
Authors: Estrella Sora M. , Masero José A. , Pérez-Hurtado Alejandro 
Published: September 2019

AbstractPrevious laboratory studies have shown that Red-necked Phalarope (Phalaropus lobatus), Wilson’s Phalarope (P. tricolor), Western Sandpiper (Calidris mauri), and Least Sandpiper (C. minutilla) use the surface tension of water surrounding a prey item to transport it from bill tip to mouth. Although such experimental work suggests that many species of shorebird may be capable of surface-tension feeding, no field studies have been done that examine this possibility. We studied the occurrence and interspecific variation in the performance of surface-tension transport (STT) in wild shorebirds feeding on identical prey items in shallow water. All shorebirds videotaped—Little Stint (C. minuta), Dunlin (C. alpina), Sanderling (C. alba), Curlew Sandpiper (C. ferruginea), Common Redshank (Tringa totanus), and Black-winged Stilt (Himantopus himantopus)—used STT to feed on small prey items. Individuals employing STT used one or several cycles of jaw spreading to transport the prey contained in a drop of water upward along the bill cavity, an action indicative of STT. Two distinct types of prey transport were observed: (1) use of STT in isolation by calidridine species following the description given in previous studies (i.e., an absence of other feeding mechanisms such as tongue movements, suction, or inertial transport), and (2) STT aided by inertial transport (head jerks) as seen in Common Redshank and Black-winged Stilt. Measured prey-transport variables (number of cycles, total time, and speed of transport) varied among species. The absence of significant relationships between these variables and measures of external morphology (bill length, bill length-to-width ratio, and bill length-to-depth ratio) suggests that some interspecific variations in STT performance may be attributable to differences in internal bill morphology. We show that STT is a common feeding mechanism in small or medium- sized shorebird species that feed on small prey items in shallow water. Birds using STT transported ≤3.6× faster than the theoretical value predicted by a previous model and can achieve high intake rates when foraging on high densities of available small prey items.Ventajas de las Presas Pequeñas: Análisis de Campo del Uso de la Tensión Superficial del Agua por las Aves Playeras para Transportar las Presas
Malaria Prevalence and White-Blood-Cell Response to Infection in a Tropical and in a Temperate Thrush
Authors: Ricklefs Robert E. , Sheldon Kimberly S. 
Published: September 2019

AbstractTo evaluate the possibilities and limitations of using white-blood-cell (WBC) counts to characterize investment in immune-system function, we compared the prevalence and intensity of malaria infections and concentrations of WBCs in the American Robin (Turdus migratorius) in Michigan and Missouri and in the Clay- colored Robin (T. grayi) in central Panama. We ascertained infection by polymerase chain reaction (PCR) screening and quantified infection intensity and WBC concentrations by visual inspection of blood smears. Because few parasites were observed on smears, we assumed that most cases of malaria represented chronic, rather than acute, infections. Prevalence of haemosporidian infection (Panama 41%, Missouri 57%, Michigan 63%) did not differ significantly between locations. However, most infections in Panama were undetected on blood smears, whereas more than half were apparent on smears in Michigan and Missouri. Among WBCs, lymphocytes were the most abundant type, followed by heterophils; eosinophils and lymphocytes were more common in the North American sample than in Panama, and their numbers in Michigan were significantly higher in infected than in noninfected individuals. Tropical T. grayi apparently maintained infections at lower intensities but appeared to accomplish this in spite of lower abundances of immune-system cells. Furthermore, analyses of blood smears of Turdus spp. from elsewhere in the tropics revealed a wide range of prevalence, which suggests that either the regional presence of haemosporidians or the ability of hosts to control infections cannot be learned from limited samples. Additional species surveyed in Michigan and Panama revealed no consistent pattern in either infection intensity or WBC concentrations. Infection and response appear to be highly idiosyncratic. In agreement with other authors, we caution that blood parameters are difficult both to interpret and to sam- ple adequately in tests of regional or other effects.Prevalencia de Malaria y Respuesta de Glóbulos Blancos a la Infección en un Zorzal de la Zona Tropical y Uno de la Zona Templada
Nesting Success of Acadian Flycatchers (Empidonax Virescens) in Floodplain Forest Corridors
Authors: Chapa-Vargas Leonardo , Robinson Scott K. 
Published: September 2019

AbstractReconnecting forest patches, including those of floodplain forest, often involves the creation of long, narrow corridors that have the potential to act as ecological traps for wildlife. We examined the effect of forest width and habitat composition of the landscapes immediately around nest patches on survival and parasitism of 359 Acadian Flycatcher (Empidonax virescens) nests in the Cache River Bioreserve in southern Illinois. Nests were distributed among 19 floodplain forest corridors along a small river system that is being restored and reconnected along its original floodplain. The corridors spanned a range of widths (80–3,170 m) and varied with the presence or absence of natural water-related habitats (beaver ponds, backwater swamps, and creeks). Although nest success varied slightly between stages of the breeding cycle, confidence intervals overlapped, which suggests constant nest success throughout the breeding cycle. Nest survival was relatively high by regional standards but did not vary significantly with any of the landscape variables measured. Contrary to predictions, probabilities of brood parasitism decreased with increasing proportions of anthropogenic habitats surrounding nests. Probabilities of brood parasitism also decreased, but only slightly, as the breeding season progressed. Finally, Acadian Flycatcher nests were located significantly more often near natural (forest-water interface) edges than expected at random. Narrow corridors such as those along floodplain restoration projects do not necessarily create ecological traps for all forest species. Acadian Flycathcers, however, are one of the only forest-nesting Neotropical migrants that nest in narrow corridors and, therefore, may be less vulnerable to negative effects of fragmentation.Éxito de Nidificación de Empidonax virescens en Corredores de Bosque de Planicies Inundables
Survival and Breeding Advantages of Larger Black Brant (Branta Bernicla Nigricans) Goslings: Within- and Among-Cohort Variation
Authors: Sedinger James S. , Chelgren Nathan D. 
Published: September 2019

AbstractWe examined the relationship between mass late in the first summer and survival and return to the natal breeding colony for 12 cohorts (1986-1997) of female Black Brant (Branta bernicla nigricans). We used Cormack-Jolly-Seber methods and the program MARK to analyze capture-recapture data. Models included two kinds of residuals from regressions of mass on days after peak of hatch when goslings were measured; one based on the entire sample (12 cohorts) and the other based only on individuals in the same cohort. Some models contained date of peak of hatch (a group covariate related to lateness of nesting in that year) and mean cohort residual mass. Finally, models allowed survival to vary among cohorts. The best model of encounter probability included an effect of residual mass on encounter probability and allowed encounter probability to vary among age classes and across years. All competitive models contained an effect of one of the estimates of residual mass; relatively larger goslings survived their first year at higher rates. Goslings in cohorts from later years in the analysis tended to have lower first-year survival, after controlling for residual mass, which reflected the generally smaller mean masses for these cohorts but was potentially also a result of population-density effects additional to those on growth. Variation among cohorts in mean mass accounted for 56% of variation among cohorts in first-year survival. Encounter probabilities, which were correlated with breeding probability, increased with relative mass, which suggests that larger goslings not only survived at higher rates but also bred at higher rates. Although our findings support the well-established linkage between gosling mass and fitness, they suggest that additional environmental factors also influence first-year survival.Supervivencia y Ventajas Reproductivas de los Pichones de Mayor Tamaño de Branta bernicla nigricans: Variación entre y dentro de las Cohortes
Modeling Population Growth of The Ovenbird (Seiurus Aurocapilla) in the Southern Appalachians
Authors: Podolsky Andrei L. , Simons Theodore R. , Collazo Jaime A. 
Published: September 2019

AbstractStudies of source-sink dynamics are often prompted by concerns about negative population trends. Estimates of population trajectories are usually based on assumptions about survival rates and empirical measures of fecundity. Most models ignore the influence of the rates of renesting and multiple brooding. We used the Ovenbird (Seiurus aurocapilla) as a model Neotropical migratory songbird species to investigate the relative effects of annual female survival and components of annual fecundity on population growth rates. We applied productivity data from a three- year field study and data from Hann (1937) to several models of annual fecundity to examine the sensitivity of lambda to variations in annual female survival and the likelihood of renesting and double-brooding. Our simulations illustrate the importance of incorporating estimates of annual survival and rates of additional breeding attempts in songbird population models because population growth rates are quite sensitive to variations in these parameters. Lambda is especially sensitive to survival estimates and changes with them at the same order of magnitude. Whenever feasible, female survival and probabilities of additional breeding attempts should be estimated by direct methods. The indirect methods used in our study (annual female survival estimated from the age ratio of breeding females, and rates of renesting and double- brooding determined from the timing of reproduction) probably underestimated these parameters.Modelado del Crecimiento Poblacional de Seiurus aurocapilla en el Sur de los Apalaches
Sex, Wingtip Shape, and Wing-Loading Predict Arrival Date at a Stopover Site in the Swainson's Thrush (Catharus Ustulatus)
Authors: Bowlin Melissa S. 
Published: September 2019

AbstractPointed wingtips and low wing-loading are believed to reduce the amount of energy used during migratory flight. If this is true, individuals with pointed wingtips or consistently low wing-loading should be able to migrate faster than conspecifics and may arrive on the breeding grounds and at stopover sites earlier. To test this hypothesis, I captured 97 Swainson's Thrushes (Catharus ustulatus; hereafter “thrushes”) during May in three consecutive field seasons, 2003-2005, at a stopover site in central Illinois. I used molecular techniques to sex 47 of these thrushes and created a discriminant function analysis using wing, tarsometatarsus, and tail lengths that predicted sex with 80.9% accuracy (P < 0.001). I applied this function to the remaining 50 thrushes so that I could control for any sexual dimorphism in morphology and arrival timing, and then examined seasonal trends in sex and morphology. Male thrushes arrived earlier at my stopover site than females (P < 0.001). After controlling for sex, thrushes with more pointed wingtips (P = 0.002) and lower wing-loading (P = 0.044) arrived earlier than thrushes with more rounded wingtips and higher wing-loading. The general linear model with sex, wingtip pointedness, and wing-loading explained nearly one-third of the variation in arrival date (P < 0.001, r2 = 0.281, n = 90). Pointed wingtips and lower wing-loading may help migratory birds cover distance more quickly and arrive at the breeding grounds sooner; alternatively, thrushes with more pointed wingtips and lower wing-loading may have departed from the wintering grounds earlier. If wing shape and size affect rate of migration, these variables may be important determinants of individual quality in migratory passerines.El Sexo, la Forma de las Puntas de las Alas y la Carga Alar Predicen la Fecha de Arribo de Catharus ustulatus a un Sitio de Escala Migratoria
Pelicans, Cormorants, and Their Relatives: The Pelecaniformes
Authors: Schreiber E. A. 
Published: September 2019

Abstract
The following critiques express the opinions of the individual evaluators regarding the strengths, weaknesses, and value of the books they review. As such, the appraisals are subjective assessments and do not necessarily reflect the opinions of the editors or any official policy of the American Ornithologists’ Union.
Three-dimensional chromosome organization in flowering plants
Authors: Grob Stefan 
Published: September 2019

AbstractResearch on plant three-dimensional (3D) genome architecture made rapid progress over the past 5 years. Numerous Hi-C interaction data sets were generated in a wide range of plant species, allowing for a comprehensive overview on 3D chromosome folding principles in the plant kingdom. Plants lack important genes reported to be vital for chromosome folding in animals. However, similar 3D structures such as topologically associating domains and chromatin loops were identified. Recent studies in Arabidopsis thaliana revealed how chromosomal regions are positioned within the nucleus by determining their association with both, the nuclear periphery and the nucleolus. Additionally, many plant species exhibit high-frequency interactions among KNOT entangled elements, which are associated with safeguarding the genome from invasive DNA elements.Many of the recently published Hi-C data sets were generated to aid de novo genome assembly and remain to date little explored. These data sets represent a valuable resource for future comparative studies, which may lead to a more profound understanding of the evolution of 3D chromosome organization in plants.
Spectrum: fast density-aware spectral clustering for single and multi-omic data
Authors: John Christopher R , Watson David , Barnes Michael R , Pitzalis Costantino , Lewis Myles J 
Published: September 2019

Abstract

Motivation
Clustering patient omic data is integral to developing precision medicine because it allows the identification of disease subtypes. A current major challenge is the integration multi-omic data to identify a shared structure and reduce noise. Cluster analysis is also increasingly applied on single-omic data, for example, in single cell RNA-seq analysis for clustering the transcriptomes of individual cells. This technology has clinical implications. Our motivation was therefore to develop a flexible and effective spectral clustering tool for both single and multi-omic data.

Results
We present Spectrum, a new spectral clustering method for complex omic data. Spectrum uses a self-tuning density-aware kernel we developed that enhances the similarity between points that share common nearest neighbours. It uses a tensor product graph data integration and diffusion procedure to reduce noise and reveal underlying structures. Spectrum contains a new method for finding the optimal number of clusters (K) involving eigenvector distribution analysis. Spectrum can automatically find K for both Gaussian and non-Gaussian structures. We demonstrate across 21 real expression datasets that Spectrum gives improved runtimes and better clustering results relative to other methods.

Availability and implementation
Spectrum is available as an R software package from CRAN https://cran.r-project.org/web/packages/Spectrum/index.html.

Supplementary information
Supplementary data are available at Bioinformatics online.