Pre- and post-processing for Cosmic/NASTRAN on personal computers and mainframes

An interface between Cosmic/NASTRAN and GIFTS has recently been released, combining the powerful pre- and post-processing capabilities of GIFTS with Cosmic/NASTRAN's analysis capabilities. The interface operates on a wide range of computers, even linking Cosmic/NASTRAN and GIFTS when the two are on different computers. GIFTS offers a wide range of elements for use in model construction, each translated by the interface into the nearest Cosmic/NASTRAN equivalent; and the options of automatic or interactive modelling and loading in GIFTS make pre-processing easy and effective. The interface itself includes the programs GFTCOS, which creates the Cosmic/NASTRAN input deck (and, if desired, control deck) from the GIFTS Unified Data Base, COSGFT, which translates the displacements from the Cosmic/NASTRAN analysis back into GIFTS; and HOSTR, which handles stress computations for a few higher-order elements available in the interface, but not supported by the GIFTS processor STRESS. Finally, the versatile display options in GIFTS post-processing allow the user to examine the analysis results through an especially wide range of capabilities, including such possibilities as creating composite loading cases, plotting in color and animating the analysis

Breeding latitude predicts timing but not rate of spring migration in a widespread migratory bird in South America

Identifying the processes that determine avian migratory strategies in different environmental contexts is imperative to understanding the constraints to survival and reproduction faced by migratory birds across the planet. We compared the spring migration strategies of Fork‐tailed Flycatchers (Tyrannus s. savana) that breed at south‐temperate latitudes (i.e., austral migrants) vs. tropical latitudes (i.e., intratropical migrants) in South America. We hypothesized that austral migrant flycatchers are more time‐selected than intratropical migrants during spring migration. As such, we predicted that austral migrants, which migrate further than intratropical migrants, will migrate at a faster rate and that the rate of migration for austral migrants will be positively correlated with the onset of spring migration. We attached light‐level geolocators to Fork‐tailed Flycatchers at two tropical breeding sites in Brazil and at two south‐temperate breeding sites in Argentina and tracked their movements until the following breeding season. Of 286 geolocators that were deployed, 37 were recovered ~1 year later, of which 28 provided useable data. Rate of spring migration did not differ significantly between the two groups, and only at one site was there a significantly positive relationship between date of initiation of spring migration and arrival date. This represents the first comparison of individual migratory strategies among conspecific passerines breeding at tropical vs. temperate latitudes and suggests that austral migrant Fork‐tailed Flycatchers in South America are not more time‐selected on spring migration than intratropical migrant conspecifics. Low sample sizes could have diminished our power to detect differences (e.g., between sexes), such that further research into the mechanisms underpinning migratory strategies in this poorly understood system is necessary.Fil: Jahn, Alex. Universidade Estadual Paulista Julio de Mesquita Filho; BrasilFil: Cereghetti, Joaquín. Universidad Nacional de La Pampa; ArgentinaFil: Cueto, Víctor. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Patagonia Norte. Centro de Investigación Esquel de Montaña y Estepa Patagóica. Universidad Nacional de la Patagonia "San Juan Bosco". Facultad de Ciencias Naturales - Sede Esquel. Centro de Investigación Esquel de Montaña y Estepa Patagónica; ArgentinaFil: Hallworth, Michael T.. Smithsonian Conservation Biology Institute; Estados UnidosFil: Levey, Douglas J.. National Science Foundation; Estados UnidosFil: Marini, Miguel Â.. Universidade do Brasília; BrasilFil: Masson, Diego. Universidad Nacional de La Plata. Facultad de Ciencias Naturales y Museo; ArgentinaFil: Pizo, Marco A.. Universidade Estadual Paulista Julio de Mesquita Filho; BrasilFil: Sarasola, José Hernán. Consejo Nacional de Investigaciones Científicas y Técnicas. Instituto de Ciencias de la Tierra y Ambientales de La Pampa. Universidad Nacional de La Pampa. Facultad de Ciencias Exactas y Naturales. Instituto de Ciencias de la Tierra y Ambientales de La Pampa; ArgentinaFil: Tuero, Diego Tomas. Consejo Nacional de Investigaciones Científicas y Técnicas. Oficina de Coordinación Administrativa Ciudad Universitaria. Instituto de Ecología, Genética y Evolución de Buenos Aires. Universidad de Buenos Aires. Facultad de Ciencias Exactas y Naturales. Instituto de Ecología, Genética y Evolución de Buenos Aires; Argentin

Polarized light field under dynamic ocean surfaces: Numerical modeling compared with measurements

As part of the Radiance in a Dynamic Ocean (RaDyO) program, we have developed a numerical model for efficiently simulating the polarized light field under highly dynamic ocean surfaces. Combining the advantages of the three-dimensional Monte Carlo and matrix operator methods, this hybrid model has proven to be computationally effective for simulations involving a dynamic air-sea interface. Given water optical properties and ocean surface wave slopes obtained from RaDyO field measurements, model-simulated radiance and polarization fields under a dynamic surface are found to be qualitatively comparable to their counterparts from field measurements and should be quantitatively comparable if the light field measurement and the wave slope/water optical property measurements are appropriately collocated and synchronized. This model serves as a bridge to connect field measurements of water optical properties, wave slopes and polarized light fields. It can also be used as a powerful yet convenient tool to predict the temporal underwater polarized radiance in a real-world situation. When appropriate surface measurements are available, model simulation is shown to reveal more dynamic features in the underwater light field than direct measurements

A quasi-experimental study to mobilize rural low-income communities to assess and improve the ecological environment to prevent childhood obesity

Citation: Peters, P., Gold, A., Abbott, A., Contreras, D., Keim, A., Oscarson, R., . . . Mobley, A. R. (2016). A quasi-experimental study to mobilize rural low-income communities to assess and improve the ecological environment to prevent childhood obesity. Bmc Public Health, 16, 7. doi:10.1186/s12889-016-3047-4Background: The Ecological Model of Childhood Overweight focuses on characteristics that could affect a child's weight status in relation to the multiple environments surrounding that child. A community coaching approach allows community groups to identify their own strengths, priorities and identity. Little to no research currently exists related to community-based efforts inclusive of community coaching in creating environmental change to prevent childhood obesity particularly in rural communities. Methods: A quasi-experimental study will be conducted with low-income, rural communities (n = 14) in the North Central region of the United States to mobilize capacity in communities to create and sustain an environment of healthy eating and physical activity to prevent childhood obesity. Two rural communities within seven Midwestern states (IN, KS, MI, OH, ND, SD, WI) will be randomly assigned to serve as an intervention or comparison community. Coalitions will complete assessments of their communities, choose from evidence-based approaches, and implement nutrition and physical activity interventions each year to prevent childhood obesity with emphasis on policy, system or environmental changes over four years. Only intervention coalitions will receive community coaching from a trained coach. Outcomes will be assessed at baseline, annually and project end using previously validated instruments and include coalition self-assessments, parental perceptions regarding the built environment, community, neighborhood, and early childhood environments, self-reflections from coaches and project staff, ripple effect mapping with coalitions and, final interviews of key stakeholders and coaches. A mixed-methods analysis approach will be used to evaluate if Community Coaching enhances community capacity to create and sustain an environment to support healthy eating and physical activity for young children. ANOVA or corresponding non-parametric tests will be used to analyze quantitative data relating to environmental change with significance set at P < .05. Dominant emergent themes from the qualitative data will be weaved together with quantitative data to develop a theoretical model representing how communities were impacted by the project. Discussion: This project will yield data and best practices that could become a model for community development based approaches to preventing childhood obesity in rural communities

Diode laser based light sources for biomedical applications

Diode lasers are by far the most efficient lasers currently available. With the ever-continuing improvement in diode laser technology, this type of laser has become increasingly attractive for a wide range of biomedical applications. Compared to the characteristics of competing laser systems, diode lasers simultaneously offer tunability, high-power emission and compact size at fairly low cost. Therefore, diode lasers are increasingly preferred in important applications, such as photocoagulation, optical coherence tomography, diffuse optical imaging, fluorescence lifetime imaging, and terahertz imaging. This review provides an overview of the latest development of diode laser technology and systems and their use within selected biomedical applications

Retromer binds the FANSHY sorting motif in SorLA to regulate amyloid precursor protein sorting and processing

sorLA is a sorting receptor for amyloid precursor protein (APP) genetically linked to Alzheimer's disease (AD). Retromer, an adaptor complex in the endosome-to-Golgi retrieval pathway, has been implicated in APP transport because retromer deficiency leads to aberrant APP sorting and processing and levels of retromer proteins are altered in AD. Here we report that sorLA and retromer functionally interact in neurons to control trafficking and amyloidogenic processing of APP. We have identified a sequence (FANSHY) in the cytoplasmic domain of sorLA that is recognized by the VPS26 subunit of the retromer complex. Accordingly, we characterized the interaction between the retromer complex and sorLA and determined the role of retromer on sorLA-dependent sorting and processing of APP. Mutations in the VPS26 binding site resulted in receptor redistribution to the endosomal network, similar to the situation seen in cells with VPS26 knockdown. The sorLA mutant retained APP-binding activity but, as opposed to the wild-type receptor, misdirected APP into a distinct non-Golgi compartment, resulting in increased amyloid processing. In conclusion, our data provide a molecular link between reduced retromer expression and increased amyloidogenesis as seen in patients with sporadic AD

Актуальність впровадження систем газового обліку в сучасних умовах

Free energy calculation has long been an important goal for molecular dynamics simulation and force field development, but historically it has been challenged by limited performance, accuracy, and creation of topologies for arbitrary small molecules. This has made it difficult to systematically compare different sets of parameters to improve existing force fields, but in the past few years several authors have developed increasingly automated procedures to generate parameters for force fields such as Amber, CHARMM, and OPLS. Here, we present a new framework that enables fully automated generation of GROMACS topologies for any of these force fields and an automated setup for parallel adaptive optimization of high-throughput free energy calculation by adjusting lambda point placement on the fly. As a small example of this automated pipeline, we have calculated solvation free energies of 50 different small molecules using the GAFF, OPLS-AA, and CGenFF force fields and four different water models, and by including the often neglected polarization costs, we show that the common charge models are somewhat underpolarized.QC 20150505</p

Insights into Ligand–Protein Binding from Local Mechanical Response

Computational studies of ligand–protein binding are crucial for properly designing novel compounds of potential pharmacological interest. In this respect, researchers are increasingly interested in steered molecular dynamics for ligand–protein binding and unbinding studies. In particular, it has been suggested that analyzing the work profiles along the ligand–protein undocking paths could be fruitful. Here, we propose that small portions of work profiles, termed “local mechanical responses” of the system to a steering force, could serve as a universal measure for capturing relevant information about the system under investigation. Specifically, we first collected a high number of steering trajectories using two biological systems of increasing complexity (i.e., alanine dipeptide and (R)-roscovitine/CDK5 complex). Then, we devised a novel postprocessing tool to be applied to the local mechanical responses, to extract structural information related to the biological processes under investigation. Despite the out-of-equilibrium character of the trajectories, the analysis carried out on the work profiles provided pivotal information about the investigated biological processes. This could eventually be applied to drug design

NGF effects on developing forebrain cholinergic neurons are regionally specific

Nerve growth factor (NGF) has been shown to have an effect on neurons in the central nervous system (CNS). A number of observations suggest that NGF acts as a trophic factor for cholinergic neurons of the basal forebrain and the caudate-putamen. We sought to further characterize the CNS actions of NGF by examining its effect on choline acetyltransferase (ChAT) activity in the cell bodies and fibers of developing neurons of the septum and caudate-putamen. ChAT activity was increased after even a single NGF injection. Interestingly, the magnitude of the effect of multiple NGF injections suggested that repeated treatments may augment NGF actions on these neurons. The time-course of the response to NGF was followed after a single injection on postnatal day (PD) 2. NGF treatment produced long-lasting increases in ChAT activity in septum, hippocampus and caudate-putamen. The response in cell body regions (septum, caudate-putamen) was characterized by an initial lag period of approximately 24 hr, a rapid rise to maximum values, a plateau phase and a return to baseline. The response in hippocampus was delayed by 48 hr relative to that in septum, indicating that NGF actions on ChAT were first registered in septal cell bodies. Finally, developmental events were shown to have a regionally specific influence on the response of neurons to NGF. For though the septal response to a single NGF injection was undiminished well into the third postnatal week, little or no response was detected in caudate-putamen at that time. In highlighting the potency and regional specificity of NGF effects, these observations provide additional, support for the hypothesis that NGF is a trophic factor for CNS cholinergic neurons.Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/45403/1/11064_2004_Article_BF00970927.pd