Anatomical and biomechanical traits of broiler chickens across ontogeny. Part II. Body segment inertial properties and muscle architecture of the pelvic limb

In broiler chickens, genetic success for desired production traits is often shadowed by welfare concerns related to musculoskeletal health. Whilst these concerns are clear, a viable solution is still elusive. Part of the solution lies in knowing how anatomical changes in afflicted body systems that occur across ontogeny influence standing and moving. Here, to demonstrate these changes we quantify the segment inertial properties of the whole body, trunk (legs removed) and the right pelvic limb segments of five broilers at three different age groups across development. We also consider how muscle architecture (mass, fascicle length and other properties related to mechanics) changes for selected muscles of the pelvic limb. All broilers used had no observed lameness, but we document the limb pathologies identified post mortem, since these two factors do not always correlate, as shown here. The most common leg disorders, including bacterial chondronecrosis with osteomyelitis and rotational and angular deformities of the lower limb, were observed in chickens at all developmental stages. Whole limb morphology is not uniform relative to body size, with broilers obtaining large thighs and feet between four and six weeks of age. This implies that the energetic cost of swinging the limbs is markedly increased across this growth period, perhaps contributing to reduced activity levels. Hindlimb bone length does not change during this period, which may be advantageous for increased stability despite the increased energetic costs. Increased pectoral muscle growth appears to move the centre of mass cranio-dorsally in the last two weeks of growth. This has direct consequences for locomotion (potentially greater limb muscle stresses during standing and moving). Our study is the first to measure these changes in the musculoskeletal system across growth in chickens, and reveals how artificially selected changes of the morphology of the pectoral apparatus may cause deficits in locomotion

Windows .NET Network Distributed Basic Local Alignment Search Toolkit (W.ND-BLAST)

BACKGROUND: BLAST is one of the most common and useful tools for Genetic Research. This paper describes a software application we have termed Windows .NET Distributed Basic Local Alignment Search Toolkit (W.ND-BLAST), which enhances the BLAST utility by improving usability, fault recovery, and scalability in a Windows desktop environment. Our goal was to develop an easy to use, fault tolerant, high-throughput BLAST solution that incorporates a comprehensive BLAST result viewer with curation and annotation functionality. RESULTS: W.ND-BLAST is a comprehensive Windows-based software toolkit that targets researchers, including those with minimal computer skills, and provides the ability increase the performance of BLAST by distributing BLAST queries to any number of Windows based machines across local area networks (LAN). W.ND-BLAST provides intuitive Graphic User Interfaces (GUI) for BLAST database creation, BLAST execution, BLAST output evaluation and BLAST result exportation. This software also provides several layers of fault tolerance and fault recovery to prevent loss of data if nodes or master machines fail. This paper lays out the functionality of W.ND-BLAST. W.ND-BLAST displays close to 100% performance efficiency when distributing tasks to 12 remote computers of the same performance class. A high throughput BLAST job which took 662.68 minutes (11 hours) on one average machine was completed in 44.97 minutes when distributed to 17 nodes, which included lower performance class machines. Finally, there is a comprehensive high-throughput BLAST Output Viewer (BOV) and Annotation Engine components, which provides comprehensive exportation of BLAST hits to text files, annotated fasta files, tables, or association files. CONCLUSION: W.ND-BLAST provides an interactive tool that allows scientists to easily utilizing their available computing resources for high throughput and comprehensive sequence analyses. The install package for W.ND-BLAST is freely downloadable from . With registration the software is free, installation, networking, and usage instructions are provided as well as a support forum

Ordinal Probit Functional Regression Models with Application to Computer-Use Behavior in Rhesus Monkeys

Research in functional regression has made great strides in expanding to non-Gaussian functional outcomes, however the exploration of ordinal functional outcomes remains limited. Motivated by a study of computer-use behavior in rhesus macaques (\emph{Macaca mulatta}), we introduce the Ordinal Probit Functional Regression Model or OPFRM to perform ordinal function-on-scalar regression. The OPFRM is flexibly formulated to allow for the choice of different basis functions including penalized B-splines, wavelets, and O'Sullivan splines. We demonstrate the operating characteristics of the model in simulation using a variety of underlying covariance patterns showing the model performs reasonably well in estimation under multiple basis functions. We also present and compare two approaches for conducting posterior inference showing that joint credible intervals tend to out perform point-wise credible. Finally, in application, we determine demographic factors associated with the monkeys' computer use over the course of a year and provide a brief analysis of the findings

Phoretic Motion of Spheroidal Particles Due To Self-Generated Solute Gradients

We study theoretically the phoretic motion of a spheroidal particle, which generates solute gradients in the surrounding unbounded solvent via chemical reactions active on its surface in a cap-like region centered at one of the poles of the particle. We derive, within the constraints of the mapping to classical diffusio-phoresis, an analytical expression for the phoretic velocity of such an object. This allows us to analyze in detail the dependence of the velocity on the aspect ratio of the polar and the equatorial diameters of the particle and on the fraction of the particle surface contributing to the chemical reaction. The particular cases of a sphere and of an approximation for a needle-like particle, which are the most common shapes employed in experimental realizations of such self-propelled objects, are obtained from the general solution in the limits that the aspect ratio approaches one or becomes very large, respectively.Comment: 18 pages, 5 figures, to appear in European Physical Journal

Status and distribution of colonial waterbirds in coastal Virginia: 2018 breeding season

Colonial waterbirds are highly visible components of coastal avifaunas that share the unusual characteristic of nesting in dense assemblages. One consequence of having large portions of populations nesting in few locations is that even restricted disturbance may have profound consequences on a population level. Development of conservation strategies for these sensitive species requires current status and distribution information. In the fall of 1992, a consortium of agencies and individuals agreed that a comprehensive monitoring program for the Virginia colonial waterbird community was needed and that assessments should be made on regular (initially every 10 years but reduced to 5 years in 2003) intervals for trend analyses. Systematic surveys have been conducted during the breeding seasons of 1993, 2003, 2008 and 2013. The 2018 survey reported here is the fifth in the time series. These surveys have covered colonial waterbird populations (24 species – Great Blue Herons were not included in 2008 and 2018 due to budgetary constraints) throughout the Coastal Plain province of Virginia. We surveyed 270 waterbird colonies during the breeding season of 2018. Colonies supported an estimated 43,159 breeding pairs of 23 species. Gulls were the most abundant group with more than 19,700 breeding pairs. Terns and waders accounted for 7,129 and 6,386 pairs respectively. Although they have declined dramatically, Laughing Gulls continue to be the most abundant species and were three times more abundant than any other species, accounting for nearly 40% of the total waterbird community. The barrier island/lagoon system of the Eastern Shore was the most important region for the majority of colonial species encountered. In 2018, this region supported 22 of the 23 species evaluated. The Eastern Shore accounted for 50.5% and 46.6% of all breeding pairs and colonies respectively. For 17 of the 23 species, the region supported more than 50% of the known coastal population. The colonial waterbird community as a whole in coastal Virginia has declined dramatically since 1993 (2018 survey did not include Great Blue Herons or all Great Egrets). Population estimates for 15 (68%) of the 22 species assessed declined between 1993 and 2018. Declines varied considerably between species with 14 species declining more than 40% and 9 species declining more than 60%. Cattle Egrets showed the highest loss rate (-96.7%), declining from an estimated 1,459 to only 48 pairs. Little Blue Herons declined by 83% from 374 to only 64 pairs. Seven species increased between 1993 and 2018. Dramatic expansions were documented for White Ibis, Double-crested Cormorant, and Brown Pelican. Over the past 25 years, two major forces appear to be shaping the colonial waterbird community in Virginia. These include 1) regional shifts in population centers that are driving population increases in Virginia and 2) habitat degradation related to sea-level rise. With the exception of Great Egrets, all species that have increased over the past 20 years have experienced ongoing range expansions and are riding a population wave that is progressing through Virginia. This includes Great Black-backed Gull, Double-crested Cormorant, Brown Pelican, and White Ibis. Most of the decline in medium-sized waders is being driven by habitat loss related to erosion of islands. This erosion results from sea-level rise, is ongoing and represents a significant threat to these populations. Several ground-nesting seabirds are likely more directly impacted by the loss of viable habitat and demographic impacts related to frequent flooding. The most notable example is the Laughing Gull that has experienced a catastrophic decline in both population and distribution

Generalized stacking fault energetics and dislocation properties: compact vs. spread unit dislocation structures in TiAl and CuAu

We present a general scheme for analyzing the structure and mobility of dislocations based on solutions of the Peierls-Nabarro model with a two component displacement field and restoring forces determined from the ab-initio generalized stacking fault energetics (ie., the so-called $\gamma$-surface). The approach is used to investigate dislocations in L1$_{0}$ TiAl and CuAu; predicted differences in the unit dislocation properties are explicitly related with features of the $\gamma$-surface geometry. A unified description of compact, spread and split dislocation cores is provided with an important characteristic "dissociation path" revealed by this highly tractable scheme.Comment: 7 two columns pages, 2 eps figures. Phys. Rev. B. accepted November 199

Generic theory of colloidal transport

We discuss the motion of colloidal particles relative to a two component fluid consisting of solvent and solute. Particle motion can result from (i) net body forces on the particle due to external fields such as gravity; (ii) slip velocities on the particle surface due to surface dissipative phenomena. The perturbations of the hydrodynamic flow field exhibits characteristic differences in cases (i) and (ii) which reflect different patterns of momentum flux corresponding to the existence of net forces, force dipoles or force quadrupoles. In the absence of external fields, gradients of concentration or pressure do not generate net forces on a colloidal particle. Such gradients can nevertheless induce relative motion between particle and fluid. We present a generic description of surface dissipative phenomena based on the linear response of surface fluxes driven by conjugate surface forces. In this framework we discuss different transport scenarios including self-propulsion via surface slip that is induced by active processes on the particle surface. We clarify the nature of force balances in such situations.Comment: 22 pages, 1 figur

A tight binding model for water

We demonstrate for the first time a tight binding model for water incorporating polarizable anions. A novel aspect is that we adopt a "ground up" approach in that properties of the monomer and dimer only are fitted. Subsequently we make predictions of the structure and properties of hexamer clusters, ice-XI and liquid water. A particular feature, missing in current tight binding and semiempirical hamiltonians, is that we reproduce the almost two-fold increase in molecular dipole moment as clusters are built up towards the limit of bulk liquid. We concentrate on properties of liquid water which are very well rendered in comparison with experiment and published density functional calculations. Finally we comment on the question of the contrasting densities of water and ice which is central to an understanding of the subtleties of the hydrogen bond