bluuebunny/crossref_metadata_2025 huggingface dataset:
Dynamical behavior of an oscillating bubble initially between two liquids
Authors: Liu Yun-Long , Zhang A-Man , Tian Zhao-Li , Wang Shi-Ping
Published: September 2019

The interaction of an oscillating bubble and a nearby liquid–liquid interface is a complex multiphase problem that has many potential applications. In this work, the behavior of a bubble initially between two different liquids (i.e., with a stand-off distance of zero) is investigated numerically and is shown to exhibit a high degree of nonlinearity. A numerical model based on an Eulerian finite-element method is established. It is validated by simulating a nonspherical collapse of a bubble in the gravity field and comparing the results with those obtained in the experiment. Then, several cases of interaction between an oscillating bubble and a liquid–liquid interface are simulated with different initial conditions. It is confirmed that the density interface tends to induce the bubble to develop a jet that drills into the heavier liquid during the bubble collapse phase. The nondimensional period of oscillation increases with increasing density ratio of the two liquids, and an annular jet impacts, generating a pressure peak, when the density ratio exceeds 1.5. When the effect of gravity is taken into account, it is found that the annular impact is enhanced while the downward jet is weakened. In addition, a significantly sized bubble is split from the main bubble by the impact of the annular jet. When the buoyancy parameter exceeds a threshold value, gravity comes to dominate the bubble motion, and neither an annular jet nor a downward jet will develop. If the buoyancy parameter is large enough, the bubble migrates upward and detaches from the liquid–liquid interface during the collapse phase.
Mobility-limiting Coulomb scattering in nitrided 4H-SiC inversion channel on 11¯00 m-face and 112¯ a-face characterized by Hall effect measurements
Authors: Hirai Hirohisa , Hatakeyama Tetsuo , Sometani Mitsuru , Okamoto Mitsuo , Harada Shinsuke , Okumura Hajime
Published: September 2019

To enhance the performance of 4H-SiC switching devices associated with power electronics, a decrease in the resistivity of the inversion channel at the SiO2/4H-SiC interface is required. It is necessary to increase the free carrier density by eliminating interface traps as well as to increase the free carrier mobility by eliminating interface scattering centers. However, the origin of the dominant scattering centers has not yet been clarified, and its scattering mechanism has not yet been experimentally investigated. Thus, in this study, the dominant scattering mechanism in the inversion channel formed on the m- and a-faces of 4H-SiC by nitridation was studied. To characterize the electron scattering in the inversion channel, temperature dependences of both the Hall effect mobility and the Hall scattering factor (γs) were investigated. Because the interface traps prevent the accurate estimation of the free carrier density by conventional capacitance measurements, evaluating γs for the SiO2/4H-SiC interface requires different approaches. Therefore, we developed and applied the “γsdα method” for regions in which the effect of the interface traps can be ignored. By experimentally observing the temperature dependent change of γs for the interface, it was revealed that the dominant scattering mechanism is Coulomb scattering. The possible origins of the mobility-limiting Coulomb scattering at the interface are discussed, including the ionized impurities in the substrate, trapped electrons at the interface, and potential fluctuations at the 4H-SiC surface.
Compressive and rarefactive solitary structures of coupled kinetic Alfven-acoustic waves in non-Maxwellian space plasmas
Authors: Khalid Saba , Qureshi M. N. S. , Masood W.
Published: September 2019

Linear and nonlinear coupled kinetic Alfvén-acoustic (CKAA) waves have been studied using the two-potential theory in non-Maxwellian plasmas where electrons follow the (r, q) distribution function. For the first time, a comprehensive study has been carried out to ascertain how the formation of compressive and rarefactive solitary structures of CKAA waves depends on the low and high energy parts of the electron distribution function. We have found that the flat-tops at low energies of the electron distribution are responsible for the formation of compressive solitary structures, whereas the spikes at low energies allow the formation of both compressive and rarefactive solitary structures. A detailed comparison of generalized (r, q), kappa, Cairns, and Maxwellian distributions has been given, and important differences have also been highlighted. The relevance of the present study with special reference to space plasmas has also been pointed out.
Extreme nonlinear dynamics in vacuum laser acceleration with a crossed beam configuration
Authors: Robinson A. P. L. , Tangtartharakul K. , Weichman K. , Arefiev A. V.
Published: September 2019

A relatively simple model problem where a single electron moves in two relativistically strong obliquely intersecting plane wave-packets is studied using a number of different numerical solvers. It is shown that, in general, even the most advanced solvers are unable to obtain converged solutions for more than about 100 fs in contrast to the single plane wave problem, and that some basic metrics of the orbit show enormous sensitivity to the initial conditions. At a bare minimum, this indicates an unusual degree of nonlinearity, and may well indicate that the dynamics of this system are chaotic.
Highly effective activation of Mg-implanted p-type GaN by ultra-high-pressure annealing
Authors: Sakurai Hideki , Omori Masato , Yamada Shinji , Furukawa Yukihiro , Suzuki Hideo , Narita Tetsuo , Kataoka Keita , Horita Masahiro , Bockowski Michal , Suda Jun , Kachi Tetsu
Published: September 2019

A high activation ratio of acceptors to Mg ions implanted into a homoepitaxial GaN layer was achieved through an ultra-high-pressure annealing (UHPA) process. Capless annealing under a nitrogen pressure of 1 GPa in a temperature range of 1573–1753 K activated acceptors without thermally decomposing the GaN layer. Conventional rapid thermal annealing leads to a serious decomposition at 1573 K, even with an AlN protective cap. The sample annealed at 1673 K under UHPA exhibited very intense cathodoluminescence in near-band edge and donor-acceptor-pair band emissions. The intensities were over one order of magnitude higher than those of the sample treated by conventional annealing. A Hall-effect measurement was obtained in the temperature range of 275–500 K for the UHPA sample. The obtained hole concentration and mobility at 300 K were 3.6 × 1016 cm−3 and 24.1 cm2 V−1 s−1, respectively. The mobility value was close to that of an epitaxial p-type GaN with the same doping concentration. An Arrhenius plot of hole concentrations showed that the acceptor concentration and ionization energy were separately estimated to be (2.6 ± 0.8) × 1018 cm−3 and 212 ± 5 meV, respectively. By comparing the Mg concentrations obtained from secondary ion mass spectrometry, the acceptor activation ratio (acceptor concentration/Mg concentration) of the UHPA samples exceeded 70%. These results suggest that the UHPA process as a postimplantation annealing technique is promising for the fabrication of GaN-based power devices with selective area doping.
Multiscale modeling of damaged surface topology in a hypersonic boundary
Authors: Mehta Neil A. , Levin Deborah A.
Published: September 2019

In this work, we used molecular dynamics (MD) to perform trajectory simulations of ice-like argon and amorphous silica aggregates on atomically smooth highly ordered pyrolytic graphite (HOPG) and a comparatively rougher quartz surface. It was found that at all incidence velocities, the quartz surface was stickier than the HOPG surface. The sticking probabilities and elastic moduli obtained from MD were then used to model surface evolution at a micron length scale using kinetic Monte Carlo (kMC) simulations. Rules were derived to control the number of sites available for the process execution in kMC to accurately model erosion of HOPG by atomic oxygen (AO) attack and ice-nucleation on surfaces. It was observed that the effect of defects was to increase the material erosion rate, while that of aggregate nucleation was to lower it. Similarly, simulations were performed to study the effects of AO attack and N2 adsorption-desorption on surface evolution and it was found that N2 adsorption-desorption limits the surface available for erosion by AO attack.
RF current condensation in magnetic islands and associated hysteresis phenomena
Authors: Rodríguez E. , Reiman A. H. , Fisch N. J.
Published: September 2019

The nonlinear RF current condensation effect suggests that magnetic islands might be well controlled with broader deposition profiles than previously thought possible. To assess this possibility, a simplified energy deposition model in a symmetrized 1D slab geometry is constructed. By limiting the RF wave power that can be absorbed through damping, this model also describes the predicted hysteresis phenomena. Compared to the linear model, the nonlinear effects lead to larger temperature variations, narrower deposition widths, and more robust island stabilization. Although, in certain regimes, the island center can be disadvantageously shaded because of the nonlinear effects, in general, the RF condensation effect can take place, with current preferentially generated, advantageously, close to the island center.
Stable axially symmetric atomic impurity in an fcc solid—Ba in rare gases
Authors: Kleshchina Nadezhda N. , Kalinina Inna S. , Leibin Iosif V. , Bezrukov Dmitry S. , Buchachenko Alexei A.
Published: September 2019

Closed-shell metal atoms in rare gas solids tend to occupy highly symmetric polyhedral crystal sites, as follows from the generic triplet Jahn-Teller splitting of the S → P excitation bands and complies with the isotropic nature of the dispersion forces. Atypical 2 + 1 Jahn-Teller splitting inherent to axially symmetric sites observed recently for Ba atoms has been therefore interpreted as the defect accommodation. By modeling the structure, stability, and spectra of the Ba atom in the face-centered cubic rare gas crystals, we identify thermodynamically stable crystal site of axial C3v symmetry that explains experimental observations. We also demonstrate the dramatic effect of the interaction anisotropy on the trapping site structure and stability for an excited P-state atom. Our results provide strong evidence for stable axially symmetric accommodation of isotropic impurity in a close-packed lattice.
The large-time behavior of the multi-dimensional hyperbolic-parabolic model arising from chemotaxis
Authors: Xu Fuyi , Li Xinliang , Wang Chengli
Published: September 2019

The present paper is dedicated to the study of large-time behavior of global strong solutions to the initial value problem for the hyperbolic-parabolic system derived from chemotaxis models in any dimension d ≥ 2. Under a suitable additional decay assumption involving only the low frequencies of the data and in L2-critical regularity framework, we exhibit the decay rates of strong solutions to the system for initial data close to a stable equilibrium state. The proof relies on a refined time-weighted energy functional in the Fourier space and the Littlewood-Paley decomposition technology.
A dynamical (e,2e) investigation into the ionization of the outermost orbitals of R-carvone
Authors: Jones D. B. , Ali E. , Ning C. G. , Ferreira da Silva F. , Ingólfsson O. , Lopes M. C. A. , Chakraborty H. S. , Madison D. H. , Brunger M. J.
Published: September 2019

We report an experimental and theoretical investigation into the dynamics of electron-impact ionization of R-carvone. Experimental triple differential cross sections are obtained in asymmetric coplanar kinematic conditions for the ionization of the unresolved combination of the three outermost molecular orbitals (41a-39a) of R-carvone. These cross sections are compared with theoretical cross sections calculated within a molecular 3-body distorted wave (M3DW) framework employing either a proper orientation average or orbital average to account for the random orientation of the molecule probed in the experiment. Here, we observe that the overall scattering behavior observed in the experiment is fairly well reproduced within the M3DW framework when implementing the proper average over orientations. The character of the ionized orbitals also provides some qualitative explanation for the observed scattering behavior. This represents substantial progress when trying to describe the scattering dynamics observed for larger molecules under intermediate-impact energy and asymmetric energy sharing scattering conditions.
Assembly and comparative analyses of the mitochondrial genome of Castanospermum australe (Papilionoideae, Leguminosae)
Authors: Zhang Rong , Jin Jian-Jun , Moore Michael J. , Yi Ting-Shuang
Published: September 2019

Plant mitochondrial genomes are often difficult to assemble because of frequent recombination mediated by repeats. Only a few mitochondrial genomes have been characterised in subfamily Papilionoideae of Leguminosae. Here, we report the complete mitochondrial genome of Castanospermum australe A.Cunn. & C.Fraser, an important medicinal and ornamental species in the Aldinoid clade of Papilionoideae. By mapping paired-end reads, seven hypothetical subgenomic conformations were rejected and two hypothetical complete isometric mitochondrial genome conformations that differed by a 64-kb inversion were strongly supported. Quantitative assessment of repeat-spanning read pairs showed a major conformation (MC1) and a minor conformation (MC2). The complete mitochondrial genome of C. australe was, thus, generated as 542 079 bp in length, with a high depth of coverage (~389.7×). Annotation of this mitochondrial genome yielded 58 genes encoding 37 proteins, 18 tRNAs and three rRNAs, as well as 17 introns and three medium-sized repeats (133, 119 and 114 bp). Comparison of 10 mitochondrial genomes from Papilionoideae demonstrated significant variation in genome size, structure, gene content and RNA editing sites. In addition, mitochondrial genes were shown to be potentially useful in resolving the deep relationships of Papilionoideae.
Towards a new online species-information system for legumes
Authors: Bruneau Anne , Borges Leonardo M. , Allkin Robert , Egan Ashley N. , de la Estrella Manuel , Javadi Firouzeh , Klitgaard Bente , Miller Joseph T. , Murphy Daniel J. , Sinou Carole , Vatanparast Mohammad , Zhang Rong
Published: September 2019

The need for scientists to exchange, share and organise data has resulted in a proliferation of biodiversity research-data portals over recent decades. These cyber-infrastructures have had a major impact on taxonomy and helped the discipline by allowing faster access to bibliographic information, biological and nomenclatural data, and specimen information. Several specialised portals aggregate particular data types for a large number of species, including legumes. Here, we argue that, despite access to such data-aggregation portals, a taxon-focused portal, curated by a community of researchers specialising on a particular taxonomic group and who have the interest, commitment, existing collaborative links, and knowledge necessary to ensure data quality, would be a useful resource in itself and make important contributions to more general data providers. Such an online species-information system focused on Leguminosae (Fabaceae) would serve useful functions in parallel to and different from international data-aggregation portals. We explore best practices for developing a legume-focused portal that would support data sharing, provide a better understanding of what data are available, missing, or erroneous, and, ultimately, facilitate cross-analyses and direct development of novel research. We present a history of legume-focused portals, survey existing data portals to evaluate what is available and which features are of most interest, and discuss how a legume-focused portal might be developed to respond to the needs of the legume-systematics research community and beyond. We propose taking full advantage of existing data sources, informatics tools and protocols to develop a scalable and interactive portal that will be used, contributed to, and fully supported by the legume-systematics community in the easiest manner possible.
The mechanism of thin filament regulation: Models in conflict?
Authors: Geeves Michael A. , Lehrer Sherwin S. , Lehman William
Published: September 2019

In a recent JGP article, Heeley et al. (2019. J. Gen. Physiol. https://doi.org/10.1085/jgp.201812198) reopened the debate about two- versus three-state models of thin filament regulation. The authors review their work, which measures the rate constant of Pi release from myosin.ADP.Pi activated by actin or thin filaments under a variety of conditions. They conclude that their data can be described by a two-state model and raise doubts about the generally accepted three-state model as originally formulated by McKillop and Geeves (1993. Biophys. J. https://doi.org/10.1016/S0006-3495(93)81110-X). However, in the following article, we follow Plato’s dictum that “twice and thrice over, as they say, good it is to repeat and review what is good.” We have therefore reviewed the evidence for the three- and two-state models and present our view that the evidence is overwhelmingly in favor of three structural states of the thin filament, which regulate access of myosin to its binding sites on actin and, hence, muscle contractility.
All-optical switch and transistor based on coherent light-controlled single two-level atom coupling with two nanowires*
Authors: Zhang Xin-Qin , Xia Xiu-Wen , Xu Jing-Ping , Cheng Mu-Tian , Yang Ya-Ping
Published: September 2019

Atom–nanowire coupling system is a promising platform for optical quantum information processing. Unlike the previous designing of optical switch and transistor requiring a dedicated multi-level emitter and high fineness microcavity, a new proposal is put forward which contains a single two-level atom asymmetrically coupled with two nanowires. Single-emitter manipulation of photonic signals for bilateral coherent incident is clear now, since we specify atomic saturation nonlinearity into three contributions which brings us a new approach to realizing light-controlled-light at weak light and single-atom levels. An efficient optically controllable switch based on self-matching-induced-block and a concise optical transistor are proposed. Our findings show potential applications in full-optical devices.
School Based Pre-Service (Initial) Teacher Training Programs in the USA and the UK
Authors: Solomon Margaret
Published: September 2019

This article is about School-Based Initial Teacher Training (SBITT) programs practiced in the USA and the UK. The article briefly discusses how US teacher-training programs began in 1839, as Normal School in New England. They then later became university based traditional teacher-training programs across the country. Then it shows how a gradual change in teacher training came into the U.S. in the 1980s with the introduction of school-based teacher training as an alternative route. Although most teachers in the U.S are still trained in colleges and universities, the paper shows that many states still pursue alternative routes to teacher credentialing and focus on school-based training

The next part is a brief narration of the history of school-based teacher training in the UK, which began in the early 19th century. In the later part of 1800s, teacher training was favored at universities in the UK and more colleges were opened to facilitate training teachers at higher education institutions (HEI). In the late 1900s, there was an emergence of School-Based Initial Teacher Training (SBITT) programs developed as a result of a shortage of trained teachers. Finally, a variety of different SBITT programs became the most prominent method of initial teacher training. In 2017–2018, 53% of teachers favored a school-based teacher training program, while 47% preferred a university-based teacher training program
Power and Trade between Qing China and Chosŏn Korea
Authors: Song Nianshen
Published: September 2019

Scholars often regard the Qing-Korean relationship as the most representative instance of the so-called tributary system, the Sino-centric hierarchical world order in early modern East Asia. It was also the most stable one, established in 1637 and ending as late as 1895 after the Qing’s total defeat in the first Sino-Japanese War. Precisely because this bilateral relationship was so typical and so stable, it was also unique in many ways. Although the Manchu regime largely inherited Ming China’s institutions in dealing with Korea (and, later, with other foreign states), this legacy revealed new meanings in the context of the Manchu conquest of China. As the Qing’s first and last subordinate state in the region, Chosŏn Korea served as both an ideological and a practical model in shaping the Qing’s geopolitical construction.

Beginning and ending with military clashes, the Qing-Chosŏn hierarchical relationship from the early 17th to the late 19th centuries was nourished and solidified by more peaceful interactions. Generally conducted under the Confucian zongfan (宗藩) principles, these interactions included rituals, diplomatic missions, trade, negotiations, cross-border jurisdiction, and cultural exchanges. Far from being imposed unilaterally by the Qing, the bilateral relationship was mutually constructed in a long process in which the Korean government and literati played a proactive role. During this time, the Korean attitude toward the Qing underwent a gradual change, from hostility to nuanced acceptance. In the late 19th century the two countries tried but failed to adjust their relationship in order to survive the geopolitical threat from industrialized, colonial powers. The collapse of the Qing-Chosŏn hierarchy eventually led to the rise of new national identities in both China and the Korean Peninsula in the 20th century.
Slowly but surely: gradual diversification and phenotypic evolution in the hyper-diverse tree fern family Cyatheaceae
Authors: Loiseau Oriane , Weigand Anna , Noben Sarah , Rolland Jonathan , Silvestro Daniele , Kessler Michael , Lehnert Marcus , Salamin Nicolas
Published: September 2019

Background and Aims

The tremendously unbalanced distribution of species richness across clades in the tree of life is often interpreted as the result of variation in the rates of diversification, which may themselves respond to trait evolution. Even though this is likely a widespread pattern, not all diverse groups of organisms exhibit heterogeneity in their dynamics of diversification. Testing and characterizing the processes driving the evolution of clades with steady rates of diversification over long periods of time are of importance in order to have a full understanding of the build-up of biodiversity through time.

Methods

We studied the macroevolutionary history of the species-rich tree fern family Cyatheaceae and inferred a time-calibrated phylogeny of the family including extinct and extant species using the recently developed fossilized birth–death method. We tested whether the high diversity of Cyatheaceae is the result of episodes of rapid diversification associated with phenotypic and ecological differentiation or driven by stable but low rates of diversification. We compared the rates of diversification across clades, modelled the evolution of body size and climatic preferences and tested for trait-dependent diversification.

Key Results

This ancient group diversified at a low and constant rate during its long evolutionary history. Morphological and climatic niche evolution were found to be overall highly conserved, although we detected several shifts in the rates of evolution of climatic preferences, linked to changes in elevation. The diversification of the family occurred gradually, within limited phenotypic and ecological boundaries, and yet resulted in a remarkable species richness.

Conclusions

Our study indicates that Cyatheaceae is a diverse clade which slowly accumulated morphological, ecological and taxonomic diversity over a long evolutionary period and provides a compelling example of the tropics as a museum of biodiversity.
Plants are intelligent, here’s how
Authors: Calvo Paco , Gagliano Monica , Souza Gustavo M , Trewavas Anthony
Published: September 2019

Hypotheses

The drive to survive is a biological universal. Intelligent behaviour is usually recognized when individual organisms including plants, in the face of fiercely competitive or adverse, real-world circumstances, change their behaviour to improve their probability of survival.

Scope

This article explains the potential relationship of intelligence to adaptability and emphasizes the need to recognize individual variation in intelligence showing it to be goal directed and thus being purposeful. Intelligent behaviour in single cells and microbes is frequently reported. Individual variation might be underpinned by a novel learning mechanism, described here in detail. The requirements for real-world circumstances are outlined, and the relationship to organic selection is indicated together with niche construction as a good example of intentional behaviour that should improve survival. Adaptability is important in crop development but the term may be complex incorporating numerous behavioural traits some of which are indicated.

Conclusion

There is real biological benefit to regarding plants as intelligent both from the fundamental issue of understanding plant life but also from providing a direction for fundamental future research and in crop breeding.
Taxonomy, Distribution, and Evolution of Golden Plovers (Pluvialis dominica and Pluvialis fulva)
Authors: Connors Peter G.
Published: September 2019

A discriminant function analysis of specimen measurements separates 96% of two forms of Lesser Golden Plover in breeding plumage, previously described as subspecies. The forms breed sympatrically in northwest Alaska and are not isolated by habitat, but the incidence of specimens phenotypically intermediate between two forms is no higher there than in areas of allopatry. The absence of a cline of intergrades or of a hybrid zone indicates that the forms are reproductively isolated through assortative mating and are separate species. To explain the process of speciation in these very similar forms, I propose that the evolution of genetically controlled and markedly different migration routes (Pluvialis dominica to South America and Pluvialis fulva to the central and western Pacific and Indian oceans) during Pleistocene glacial isolation may have selected against hybrids during subsequent secondary contact of populations. This would leat to adaptations in behavior and plumage, such as the difference in male undertail coverts reported here, that would produce assortative mating and reproductive isolation in sympatry. Thus, the requirements of migration and winter range drive the process of speciation.
Clutch Size, Reproductive Success, and Organochlorine Contaminants in Atlantic Coast Black-Crowned Night-Herons
Authors: Custer Thomas W. , Hensler Gary L. , Kaiser T. Earl
Published: September 2019

In 1979, we gathered clutch-size and reproductive-success data on Black-crowned Night-Herons (Nycticorax nycticorax) nesting in three New England and two North Carolina colonies. In 1975, we gathered similar data from one of the New England and one of the North Carolina colonies. Latitudinal differences in clutch initiation were not evident. Mean clutch size was larger in the New England than in the North Carolina colonies. Mean clutch size was smaller in late nests from one New England colony studied in both years and another New England colony studied in 1979; seasonal trends in clutch size for other colonies were not found. In 1979, nest success was greater in two New England colonies than in one North Carolina colony. Within-season differences in nest success occurred but were inconsistent among colonies. In the four instances where statistical comparisons could be made, larger clutches were more successful than smaller ones in two colonies; large and small clutches had similar success in two other colonies. One egg was collected from each of several nests in each colony in 1979 for organochlorine contaminant analysis, and the fate of the remaining eggs was recorded. Concentrations of DDE and PCBs did not differ with clutch size; concentrations of PCBs were lower, however, in eggs laid late in the season. Although the data suggest an effect of DDE on hatching success in the northern more contaminated colonies, the impact of environmental contaminants on overall reproductive success appears to be minimal.
Sexual Roles in the Dot-Winged Antwren (Microrhopias quixensis), a Tropical Forest Passerine
Authors: Greenberg Russell , Gradwohl Judy
Published: September 2019

Dot-winged Antwrens maintain long-term pair bonds on year-long territories in tropical forests and woodland of Central and South America. Pairs partition breeding-related activities nearly equally. Like other antbirds (Formicariidae), both sexes incubate and brood. Both sexes participate equally in territorial maintenance behavior, which primarily involves active border displays. Initial investment in offspring is possibly equalized by long-term nuptial feeding of females by males. Overall, both sexes contribute equally to nestling care, although considerable variation is observed between nests, much of which probably results from variation in the foraging ability of parents. Females feed young consistently less often than do males during the early part of the nestling period and may be recovering from depletion of reserves resulting from egg production. In most pairs females bring more spiders than do males. This difference in prey type is unexpected, because the pair forages close together in the same microhabitat and their bill size is similar. Pairs are distinct in their interactions: some pairs have a rigid feeding order, and others do not.
Age-Related Mortality in a Wintering Population of Dunlin
Authors: Kus Barbara E. , Ashman Philip , Page Gary W. , Stenzel Lynne E.
Published: September 2019

Despite considerable evidence that juvenile shorebirds experience significantly higher annual mortality rates than adults, identification and quantification of the sources of mortality have received little attention. We found that the proportion of juvenile Dunlins (Calidris alpina) in the kills of a Merlin (Falco columbarius) one winter at Bolinas Lagoon, California was greater than the proportion of juveniles in the lagoon's winter population. This is evidence that raptor predation may be one of the factors contributing to the age differences in annual mortality rates of shorebirds. We suggest that the greater vulnerability of juveniles to predation by the Merlin may be caused by age-related differences in Dunlin flocking behavior.
Growth Energetics of Nestling Northern Gannets (Sula bassanus)
Authors: Montevecchi W. A. , Ricklefs R. E. , Kirkham I. R. , Gabaldon D.
Published: September 2019

We describe the energetics of postnatal growth and development of wild and captive Northern Gannet chicks. For 14 chicks 0-9 weeks old, a 24-week immature, and a breeding female, we determined water, lipid, and nonlipid content. During the 13-week nestling period, mass increased over 40-fold. Accumulation of lipid caused the energy density of chicks to increase steadily through 9 weeks. Lipid eventually accounted for about 60% of energy in tissues. Two captive chicks grew at rates comparable to wild young and consumed, on average, about 24 kg of fish containing 190,000 kJ during the nestling period. The energy density of chick guano was 13.3 Â± 0.8 kJ/g. Estimated metabolizable energy (ME) rose rapidly from 952 kJ during week 1 to 19,318 kJ during week 6, after which ME fluctuated between about 9,000 and 16,400 kJ/week. During week 1, the growth increment (GI) was 801 kJ; GI increased sharply to 9,667 kJ during week 4 and peaked at 12,711 kJ in week 7. Net growth efficiency was 49% to 8 weeks of age and 33% to fledging at 13 weeks. The food requirement of the gannet population of Newfoundland is estimated.
Flight Speed and Directional Responses to Wind by Migrating Canada Geese
Authors: Wege Michael L. , Raveling Dennis G.
Published: September 2019

We monitored headings, flight speeds, and time of flight of nine transmittertagged giant Canada geese (Branta canadensis maxima) during 10 different autumn migration flights during which data on wind directions and speeds were also available. Destination of these individuals was known because of previous observations of the same birds. This enabled us to evaluate their headings with respect to wind drift. As the magnitude of the following component of the wind increased, air speeds of migrating geese declined while ground speeds were not significantly changed. Therefore, the cost of transport over the ground, and probably metabolic rate, were minimized. Headings of migrant geese varied systematically and significantly with wind direction, but track directions did not deviate significantly from the goal direction. Thus, the geese compensated for wind drift. Visual reference to landmarks may have been the cue used to correct for drift, as weather conditions were such that geese could see the ground.
Why Does Intensity of Avian Nest Defense Increase During the Nesting Cycle?
Authors: Knight Richard L. , Temple Stanley A.
Published: September 2019

Theoretical models predict that intensity of avian nest defense should increase with age of the offspring. Empirical observations conforming with this prediction have been taken as support for these models. We here present a new explanation for the observed correlations between offspring age and level of nest defense. We propose that increased intensity of nest-defense behavior is largely a result of the methods used by the researchers who made the observations. We suggest that when an observer repeatedly visits or brings a potential nest predator to a nest, nest-defense behavior of parents is modified by positive reinforcement and loss of fear. We tested this hypothesis by measuring nest-defense behavior of female American Robins (Turdus migratorius) and male and female Red-winged Blackbirds (Agelaius phoeniceus). The tests were performed at nests visited only once during different stages of the nesting cycle and at a group of nests visited repeatedly from initiation of incubation to fledging. Nest-defense intensity (as measured by call rates, closest approach to the predator, and numbers of dives and strikes) of robins and blackbirds at nests visited once, in most cases, did not increase through the nesting cycle. At nests visited repeatedly through the nesting cycle, intensity of nest defense by both robins and blackbirds, in many cases, increased significantly. In addition to intensity of nest defense increasing at multiple-visit nests, we observed higher proportions of birds at these nests performing nest-defense behaviors than at single-visit nests.
Body Size and Condition, Timing of Breeding, and Aspects of Egg Production in Eastern Kingbirds
Authors: Murphy Michael T.
Published: September 2019

Variation in timing of breeding in Eastern Kingbirds (Tyrannus tyrannus) was correlated only weakly with external morphological characters, but was correlated positively and significantly with estimates of body size based on measurements of skeletons and muscle weights. Small females apparently held a reproductive advantage in being able to mobilize resources for reproduction before large females. Egg weight was independent of all measures of female size, but was directly and significantly (P = 0.03) correlated with standard flight muscle weight, a relative index of body condition. Egg size was thus a function more of female body condition than size.

On average, shell, yolk, and albumen comprised 5.6%, 21.9%, and 72.5%, respectively, of fresh egg weight. Dry albumen and dry shell increased proportionately with fresh egg weight, but dry yolk did not. Total protein, lipid, and energy of fresh eggs all increased proportionately with weight. Comparison of egg composition and standard flight muscle weight of laying females indicated moderate positive, although nonsignificant, correlations between body condition and measures of egg quality, especially lipid content. Based on post-egg-laying body composition and nutrient requirements for the production of one egg, it appeared that most females probably could have laid an additional egg almost solely from body reserves. Clutch size thus appears to be independent of body condition.
Olfactory Sensitivity of the Turkey Vulture (Cathartes aura) to Three Carrion-associated Odorants
Authors: Smith Steven A. , Paselk Richard A.
Published: September 2019

The Turkey Vulture (Cathartes aura) is generally thought to rely on olfactory cues to locate carrion. Because vertically rising odorants are dispersed rapidly by wind turbulence, we predict that Turkey Vultures should be highly sensitive to these chemicals to detect them at foraging altitudes.

Olfactory thresholds to three by-products of animal decomposition (1× 10-6 M for butanoic acid and ethanethiol, and 1× 10-5-5 M for trimethylamine) were determined from heart-rate responses. These relatively high thresholds indicate that these odorants are probably not cues for foraging Turkey Vultures. Odorant thresholds, food habits of Turkey Vultures, and the theoretical properties of odorant dispersion cast some doubt on the general importance of olfaction in food location by this species.
Extensive Protein Similarity of the Hybridizing Chickadees Parus atricapillus and P. carolinensis
Authors: Braun Michael J. , Robbins Mark B.
Published: September 2019

Starch gel electrophoresis of proteins was used to assess genetic differentiation and introgression across a contact zone between Parus atricapillus and P. carolinensis. Little or no differentiation was found at 35 presumed genetic loci, even between distantly allopatric population samples. Nei's (1978) genetic distance (D) was ≤0.001 for all comparisons. In contrast, Parus gambeli, another chickadee known to hybridize with atricapillus, was well differentiated at 3 loci (D ≈ 0.065). While the data suggest that atricapillus and carolinensis are closely related, they do not allow conclusions on the extent of introgression across the contact zone. The implications of these data are discussed in the light of the emerging pattern of isozyme variation in birds.
Reidentification of “Phalacrocorax” Subvolans Brodkorb as the Earliest Record of Anhingidae
Authors: Becker Jonathan J.
Published: September 2019

The putative cormorant Phalacrocorax subvolans Brodkorb 1956, from the early Miocene of Florida, is moved from the Phalacrocoracidae to the Anhingidae and should be known as Anhinga subvolans (Brodkorb 1956). This species is the earliest known anhinga and demonstrates that the family Anhingidae has been present in North America for at least 18 million years. It has been at least 30 million years since the Anhingidae and the Phalacrocoracidae shared a common ancestor.
Interseasonal and Intersexual Resource Partitioning in Hairy and White-Headed Woodpeckers
Authors: Morrison Michael L. , With Kimberly A.
Published: September 2019

Foraging behavior in the closely related Hairy (Picoides villosus) and White-headed (P. albolarvatus) woodpeckers was examined in an area of sympatry to evaluate interseasonal and intersexual resource use. Similar foraging heights were observed for each species-sex sample during summer, but significant differences were evident during winter. Male and female White-heads maintained similar relative foraging heights between seasons, whereas male and female Hairies foraged relatively higher during winter. Use of tree species differed significantly for each class between seasons, except for male Hairies. Differences in foraging substrates and tree health also were noted interseasonally. All foraged at similar times of day during summer, but negative relationships occurred between times of foraging during winter; foraging times were significantly different between male Hairies and White-heads.

A general trend toward decreased overlap in foraging behaviors during winter was a reflection of concentration of foraging activities on live incense cedar (Calocedrus decurrens), especially by female White-heads. This change apparently was due to the presence of an abundant and accessible prey (incense cedar scale, Xylococculus macrocarpae) on cedar. Behavioral shifts in foraging activities may be related to the differential ability to extract prey as a function of bill morphology; such an idea can be extended to intersexual as well as interseasonal considerations. Thus, segregation of foraging activities in these two woodpecker species may be attributed to morphological differences and habitat complexity rather than to competitive interactions dictated by resource limititions.
Why Are Waxwings “Waxy”? Delayed Plumage Maturation in the Cedar Waxwing
Authors: Mountjoy D. James , Robertson Raleigh J.
Published: September 2019

Cedar Waxwings (Bombycilla cedrorum) often have their secondaries tipped with red waxlike appendages, but a plausible hypothesis for the function of these tips has not been presented. Both males and females may have such tips, but second-year birds normally have none or only a few. This appears to be the first described instance of a passerine species to show distinctive delayed plumage maturation in both sexes. We found that waxwings mated assortatively with respect to the number of tips on the secondaries of the birds. Pairs of older birds (with high tip index scores) tended to nest earlier than younger (low tip index) birds. Older birds also had larger clutch/brood sizes and fledged more young. We suggest that the waxlike tips function as signals of age and status and that some combination of mate choice and competition for mates results in the observed assortative mating. Of the hypotheses proposed to explain the adaptive significance of delayed plumage maturation, two (the female-mimicry and cryptic hypotheses) are not confirmed in the case of the Cedar Waxwing, while the status-signaling hypothesis appears to offer the best explanation for the occurrence of delayed plumage maturation in this species.
Natal and Breeding Dispersal in House Wrens (Troglodytes aedon)
Authors: Drilling Nancy E. , Thompson Charles F.
Published: September 2019

We studied the natal and breeding dispersal of yearling and adult House Wrens (Troglodytes aedon) for 7 yr in central Illinois. The forested study areas contained 910 identical nest boxes placed in a grid pattern. On average 38.1% (n = 643) of the adult males and 23.3% (n = 1,468) of the adult females present in one year returned the next; 2.8% (n = 6,299) of the nestlings that survived to leave the nest returned each year. Adult male (median distance = 67 m) and adult female (median = 134 m) breeding dispersal was less than yearling male (median = 607.5 m) and yearling female (median = 674 m) natal dispersal. Females that returned had produced more offspring the previous season than had nonreturning females, and females that successfully produced at least one chick in their last nesting attempt of the previous season moved shorter distances than did unsuccessful females. There were, however, no consistent differences between returning and nonreturning females in two other measures of reproductive success. Females that were unsuccessful in their last breeding attempt of the previous year were more likely to be successful in their next attempt if they moved two or more territories than if they did not move. Reproductive success did not affect the likelihood that a male would return nor the distance that he moved. The success of subsequent nesting attempts by males was also not related to the distance moved.

Inbreeding avoidance may explain differences between breeding and natal dispersal, but it does not explain the lack of difference in dispersal of yearling females and males. Differences between adult and yearling dispersal are best explained by advantages accruing to adults that remain near former breeding sites and by the necessity for yearlings to move farther because of their late return from the wintering grounds. The advantages for adults to reoccupy previous breeding sites are counterbalanced, especially in females, by advantages associated with moving after breeding failure.
Song Similarity between Neighboring American Redstarts (Setophaga ruticilla): A Statistical Analysis
Authors: Shackell N. L. , Lemon R. E. , Roff D.
Published: September 2019

We examined the hypothesis that territorial American Redstart (Setophaga ruticilla) males are geographically randomly distributed with respect to structure of the single song used predominantly before nesting. Present methods to assess the degree of similarity of song between neighboring birds are often inadequate because they do not give the level of statistical significance. We present a computer method to generate the appropriate null distribution from which the level of significance can be determined. We found statistically significant correlations between neighbors primarily in the last and penultimate discrete vocal items (phones) of the song. There were also important differences between the 2 samples.
VikNGS: a C++ variant integration kit for next generation sequencing association analysis
Authors: Baskurt Zeynep , Mastromatteo Scott , Gong Jiafen , Wintle Richard F , Scherer Stephen W , Strug Lisa J
Published: September 2019

Integration of next generation sequencing data (NGS) across different research studies can improve the power of genetic association testing by increasing sample size and can obviate the need for sequencing controls. If differential genotype uncertainty across studies is not accounted for, combining datasets can produce spurious association results. We developed the Variant Integration Kit for NGS (VikNGS), a fast cross-platform software package, to enable aggregation of several datasets for rare and common variant genetic association analysis of quantitative and binary traits with covariate adjustment. VikNGS also includes a graphical user interface, power simulation functionality and data visualization tools.

Availability and implementation

The VikNGS package can be downloaded at http://www.tcag.ca/tools/index.html.

Supplementary information

Supplementary data are available at Bioinformatics online.
MitoTrack, a user-friendly semi-automatic software for lineage tracking in living embryos
Authors: Trullo A , Dufourt J , Lagha M
Published: September 2019

Motivation

During development, progenitor cells undergo multiple rounds of cellular divisions during which transcriptional programs must be faithfully propagated. Investigating the timing of transcriptional activation, which is a highly stochastic phenomenon, requires the analysis of large amounts of data. In order to perform automatic image analysis of transcriptional activation, we developed a software that segments and tracks both small and large objects, leading the user from raw data up to the results in their final form.

Results

MitoTrack is a user-friendly open-access integrated software that performs the specific dual task of reporting the precise timing of transcriptional activation while keeping lineage tree history for each nucleus of a living developing embryo. The software works automatically but provides the possibility to easily supervise, correct and validate each step.

Availability and implementation

MitoTrack is an open source Python software, embedded within a graphical user interface (download here).

Supplementary information

Supplementary data are available at Bioinformatics online.