Basic Selection, Nutrition and Care of Show Poultry

This fact sheet provides tips on selecting chickens for shows, and how to feed and care for show poultry

Emergence of hidden phases of methylammonium lead iodide (CH3NH3PbI3) upon compression

We perform a thorough structural search with the minima hopping method (MHM) to explore low-energy structures of methylammonium lead iodide. By combining the MHM with a forcefield, we efficiently screen vast portions of the configurational space with large simulation cells containing up to 96 atoms. Our search reveals two structures of methylammonium iodide perovskite (MAPI) that are substantially lower in energy than the well-studied experimentally observed low-temperature Pnma orthorhombic phase according to density functional calculations. Both structures have not yet been reported in the literature for MAPI, but our results show that they could emerge as thermodynamically stable phases via compression at low temperatures. In terms of the electronic properties, the two phases exhibit larger band gaps than the standard perovskite-type structures. Hence, the pressure-induced phase selection at technologically achievable pressures (i.e., via thin-film strain) is a viable route towards the synthesis of several MAPI polymorph with variable band gaps

Library of dispersion-corrected atom-centered potentials for generalized gradient approximation functionals: Elements H, C, N, O, He, Ne, Ar, and Kr

Parameters for analytical dispersion-corrected atom-centered potentials (DCACPs) are presented to improve the description of London dispersion forces within the generalized gradient approximation functionals BLYP, BP, and PBE. A library of DCACPs for hydrogen, carbon, nitrogen, oxygen, helium, neon, argon, and krypton was obtained by calibrating against high-level CCSD(T) or configuration interaction references. The performance and transferability of DCACPs were tested on weakly bound complexes and provide excellent results throughout all investigated systems

Experimental library screening demonstrates the successful application of computational protein design to large structural ensembles

The stability, activity, and solubility of a protein sequence are determined by a delicate balance of molecular interactions in a variety of conformational states. Even so, most computational protein design methods model sequences in the context of a single native conformation. Simulations that model the native state as an ensemble have been mostly neglected due to the lack of sufficiently powerful optimization algorithms for multistate design. Here, we have applied our multistate design algorithm to study the potential utility of various forms of input structural data for design. To facilitate a more thorough analysis, we developed new methods for the design and high-throughput stability determination of combinatorial mutation libraries based on protein design calculations. The application of these methods to the core design of a small model system produced many variants with improved thermodynamic stability and showed that multistate design methods can be readily applied to large structural ensembles. We found that exhaustive screening of our designed libraries helped to clarify several sources of simulation error that would have otherwise been difficult to ascertain. Interestingly, the lack of correlation between our simulated and experimentally measured stability values shows clearly that a design procedure need not reproduce experimental data exactly to achieve success. This surprising result suggests potentially fruitful directions for the improvement of computational protein design technology

Ab initio molecular dynamics using density based energy functionals: application to ground state geometries of some small clusters

The ground state geometries of some small clusters have been obtained via ab initio molecular dynamical simulations by employing density based energy functionals. The approximate kinetic energy functionals that have been employed are the standard Thomas-Fermi $(T_{TF})$ along with the Weizsacker correction $T_W$ and a combination $F(N_e)T_{TF} + T_W$. It is shown that the functional involving $F(N_e)$ gives superior charge densities and bondlengths over the standard functional. Apart from dimers and trimers of Na, Mg, Al, Li, Si, equilibrium geometries for $Li_nAl, n=1,8$ and $Al_{13}$ clusters have also been reported. For all the clusters investigated, the method yields the ground state geometries with the correct symmetries with bondlengths within 5\% when compared with the corresponding results obtained via full orbital based Kohn-Sham method. The method is fast and a promising one to study the ground state geometries of large clusters.Comment: 15 pages, 3 PS figure

Forecasting the Impacts of Silver and Bighead Carp on the Lake Erie Food Web

Nonindigenous bigheaded carps (Bighead Carp Hypophthalmichthys nobilis and Silver Carp H. molitrix; hereafter, “Asian carps” [AC]) threaten to invade and disrupt food webs and fisheries in the Laurentian Great Lakes through their high consumption of plankton. To quantify the potential effects of AC on the food web in Lake Erie, we developed an Ecopath with Ecosim (EwE) food web model and simulated four AC diet composition scenarios (high, low, and no detritus and low detritus with Walleye Sander vitreus and Yellow Perch Perca flavescens larvae) and two nutrient load scenarios (the 1999 baseline load and 2× the baseline [HP]). We quantified the uncertainty of the potential AC effects by coupling the EwE model with estimates of parameter uncertainty in AC production, consumption, and predator diets obtained using structured expert judgment. Our model projected mean ± SD AC equilibrium biomass ranging from 52 ± 34 to 104 ± 75 kg/ha under the different scenarios. Relative to baseline simulations without AC, AC invasion under all detrital diet scenarios decreased the biomass of most fish and zooplankton groups. The effects of AC in the HP scenario were similar to those in the detrital diet scenarios except that the biomasses of most Walleye and Yellow Perch groups were greater under HP because these fishes were buffered from competition with AC by increased productivity at lower trophic levels. Asian carp predation on Walleye and Yellow Perch larvae caused biomass declines among all Walleye and Yellow Perch groups. Large food web impacts of AC occurred in only 2% of the simulations, where AC biomass exceeded 200 kg/ha, resulting in biomass declines of zooplankton and planktivorous fish near the levels observed in the Illinois River. Our findings suggest that AC would affect Lake Erie's food web by competing with other planktivorous fishes and by providing additional prey for piscivores. Our methods provide a novel approach for including uncertainty into forecasts of invasive species' impacts on aquatic food webs. Received December 6, 2014; accepted July 15, 201

Vibrational signatures for low-energy intermediate-sized Si clusters

We report low-energy locally stable structures for the clusters Si20 and Si21. The structures were obtained by performing geometry optimizations within the local density approximation. Our calculated binding energies for these clusters are larger than any previously reported for this size regime. To aid in the experimental identification of the structures, we have computed the full vibrational spectra of the clusters, along with the Raman and IR activities of the various modes using a recently developed first-principles technique. These represent, to our knowledge, the first calculations of Raman and IR spectra for Si clusters of this size

Four small puzzles that Rosetta doesn't solve

A complete macromolecule modeling package must be able to solve the simplest structure prediction problems. Despite recent successes in high resolution structure modeling and design, the Rosetta software suite fares poorly on deceptively small protein and RNA puzzles, some as small as four residues. To illustrate these problems, this manuscript presents extensive Rosetta results for four well-defined test cases: the 20-residue mini-protein Trp cage, an even smaller disulfide-stabilized conotoxin, the reactive loop of a serine protease inhibitor, and a UUCG RNA tetraloop. In contrast to previous Rosetta studies, several lines of evidence indicate that conformational sampling is not the major bottleneck in modeling these small systems. Instead, approximations and omissions in the Rosetta all-atom energy function currently preclude discriminating experimentally observed conformations from de novo models at atomic resolution. These molecular "puzzles" should serve as useful model systems for developers wishing to make foundational improvements to this powerful modeling suite.Comment: Published in PLoS One as a manuscript for the RosettaCon 2010 Special Collectio

Endovascular equipoise shift in a phase III randomized clinical trial of sonothrombolysis for acute ischemic stroke

Background: Results of our recently published phase III randomized clinical trial of ultrasound-enhanced thrombolysis (sonothrombolysis) using an operator-independent, high frequency ultrasound device revealed heterogeneity of patient recruitment among centers. Methods: We performed a post hoc analysis after excluding subjects that were recruited at centers reporting a decline in the balance of randomization between sonothrombolysis and concurrent endovascular trials. Results: From a total of 676 participants randomized in the CLOTBUST-ER trial we identified 52 patients from 7 centers with perceived equipoise shift in favor of endovascular treatment. Post hoc sensitivity analysis in the intention-to-treat population adjusted for age, National Institutes of Health Scale score at baseline, time from stroke onset to tPA bolus and baseline serum glucose showed a significant (p < 0.01) interaction of perceived endovascular equipoise shift on the association between sonothrombolysis and 3 month functional outcome [adjusted common odds ratio (cOR) in centers with perceived endovascular equipoise shift: 0.22, 95% CI 0.06–0.75; p = 0.02; adjusted cOR for centers without endovascular equipoise shift: 1.20, 95% CI 0.89–1.62; p = 0.24)]. After excluding centers with perceived endovascular equipoise shift, patients randomized to sonothrombolysis had higher odds of 3 month functional independence (mRS scores 0–2) compared with patients treated with tPA only (adjusted OR: 1.53; 95% CI 1.01–2.31; p = 0.04). Conclusion: Our experience in CLOTBUST-ER indicates that increasing implementation of endovascular therapies across major academic stroke centers raises significant challenges for clinical trials aiming to test noninterventional or adjuvant reperfusion strategies