An analysis pipeline for the processing, annotation, and dissemination of Expressed Sequence Tags.

Due to the complex nature of interactions at the genomic level as well as the large number of proteins present in an organism, understanding the functions of various genes that are expressed is essential. Creating an analysis pipeline for Expressed Sequence Tags (ESTs) is one way to accomplish this, allowing a researcher to quickly take a set of sequences, perform all necessary analysis operations, and publish the data in a database with a graphical user interface (GUI). This pipeline falls into several steps. First, the data must be preprocessed to remove any extraneous sequence data, low-complexity regions, and regions that repeat throughout the genome. Next, it is necessary to combine a large number of ESTs into larger sequences that better describe the underlying mRNA. After larger contiguous sequences have been constructed, putative functions can be assigned to each sequence, whether part of a larger grouping or a singleton. An application of this pipeline using 3906 ESTs generated from trichome tissue of Pelargonium xhotorum (commonly, the geranium plant) resulted in 425 contiguous sequences using the CAP3 program. These sequences, along with the 2208 sequences that are not a part of a contig, were then BLASTed against the non-redundant protein database to assign putative functions to each sequence. Finally, BLAST2GO was run on these BLAST results in order to assign a GO (Gene Ontology) to each sequence. These annotations were then added to the database for later investigation by researchers. In order to aid researchers in the further analysis of the annotated sequences, a mySQL database was used for data storage and a GUI was developed using Java and Java Server Pages. In addition, an applet for viewing the Sanger trace files for each sequence is included to further aid the researcher in determining the validity of the data

Structure prediction of stable sodium germanides at 0 and 10 GPa

In this work we used ab-initio random structure searching (AIRSS) to carry out a systematic search for crystalline Na-Ge materials at both 0 and 10 GPa. The high-throughput structural relaxations were accelerated using a machine-learned interatomic potential (MLIP) fit to density-functional theory (DFT) reference data, allowing ∼1.5 million structures to be relaxed. At ambient conditions we predict three new Zintl phases, Na3Ge2, Na2Ge and Na9Ge4, to be stable and a number of Ge-rich layered structures to lie in close proximity to the convex hull. The known NaδGe34 clathrate and Na4Ge13 host-guest structures are found to be relatively stabilized at higher temperature by vibrational contributions to the free energy. Overall, the low energy phases exhibit exceptional structural diversity, with the expected mixture of covalent and ionic bonding confirmed using the electron-localisation function (ELF). The local Ge structural motifs present at each composition were determined using Smooth Overlap of Atomic Positions (SOAP) descriptors and the Ge-K edge was simulated for representatives of each motif, providing a direct link to experimental x-ray absorption spectroscopy (XAS). Two Ge-rich phases are predicted to be stable at 10 GPa; NaGe3 and NaGe2 have simple kagome and simple hexagonal Ge lattices respectively with Na contained in the pores. NaGe3 is isostructural with the MgB3 and MgSi3 family of kagome superconductors and remains dynamically stable at 0 GPa. Removing the Na from NaGe2 results in the hexagonal lonsdalite Ge allotrope, which has a direct band gap

Structure prediction of stable sodium germanides at 0 and 10 GPa

In this work we used $\textit{ab-initio}$ random structure searching (AIRSS) to carry out a systematic search for crystalline Na-Ge materials at both 0 and 10 GPa. The high-throughput structural relaxations were accelerated using a machine-learned interatomic potential (MLIP) fit to density-functional theory (DFT) reference data, allowing $\sim$1.5 million structures to be relaxed. At ambient conditions we predict three new Zintl phases, Na$_3$Ge$_2$, Na$_2$Ge and Na$_9$Ge$_4$, to be stable and a number of Ge-rich layered structures to lie in close proximity to the convex hull. The known Na$_\delta$Ge$_{34}$ clathrate and Na$_4$Ge$_{13}$ host-guest structures are found to be relatively stabilized at higher temperature by vibrational contributions to the free energy. Overall, the low energy phases exhibit exceptional structural diversity, with the expected mixture of covalent and ionic bonding confirmed using the electron-localisation function (ELF). The local Ge structural motifs present at each composition were determined using Smooth Overlap of Atomic Positions (SOAP) descriptors and the Ge-K edge was simulated for representatives of each motif, providing a direct link to experimental x-ray absorption spectroscopy (XAS). Two Ge-rich phases are predicted to be stable at 10 GPa; NaGe$_3$ and NaGe$_2$ have simple kagome and simple hexagonal Ge lattices respectively with Na contained in the pores. NaGe$_3$ is isostructural with the MgB$_3$ and MgSi$_3$ family of kagome superconductors and remains dynamically stable at 0 GPa. Removing the Na from NaGe$_2$ results in the hexagonal lonsdalite Ge allotrope, which has a direct band gap.Comment: 11 pages, 8 figure

Kinetic desorption models for the release of nanosilver from an experimental nanosilver coating on polystyrene food packaging

To predict the kinetic desorption of silver from an experimental nanosilver coated polystyrene food packaging material into food simulants (0, 1, 2 and 3% acetic acid (HAc) in distilled water (dH2O)) at 4 temperatures (10, 20, 40 and 70 °C), 5 sorption models were examined for their performance. A pseudo-second order kinetic sorption model was found to provide the best prediction of an unseen desorption validation dataset with R2 = 0.90 and RMSE = 3.21. Poor predictions were witnessed for desorption at 70 °C, potentially due to re-adsorption of the silver back onto the polystyrene substrate, as shown in the kinetic migration experiments. Similarly, the temperature dependence of the desorption rate constant was satisfactorily described using the Arrhenius equation with the exception of the 70 °C scenario. The use of sorption models identified scenarios that may limit human exposure to nanosilver migrating from this experimental nanocoating, i.e. low temperature applications. Industrial relevance: The use of antimicrobial packaging has the potential to reduce food spoilage and risk from pathogenic microorganisms while reducing food waste by extending the shelf life of food products. Coating of antimicrobial silver nanoparticles (AgNPs) to polymer surfaces is a highly advantageous technology as microbial contamination predominantly occurs on the surface of fresh and processed food products. However, uncertainty related to the potential release of nanoparticles from food packaging materials, subsequent potential human exposure and toxicology is a barrier to the uptake of these novel materials. In the European Union, where the safety assessment of these materials is stringent, mathematical models used to predict the worst case migration of nanoparticles from food packaging materials have supported the acceptance of some nanomaterials for use in food packaging. The performance of a number of desorption models was evaluated to predict the release of AgNPs from AgNP coated polystyrene. The model identified factors that influenced migration and possible industrial applications for the developed material to minimise human exposure. The study highlights the potential benefits of using predictive models to assess migration of NPs from polymers into food simulants instead of time consuming and expensive migration studies

Association of computed tomographic leg muscle characteristics with lower limb and cardiovascular events in patients with peripheral artery disease

Background Poor lower extremity physical performance is an independent predictor of unfavorable outcome in patients with peripheral artery disease (PAD); however, few studies have assessed muscle characteristics on imaging directly. Method and Results A novel 3‐dimensional semi‐automated protocol was developed to estimate leg muscle volume and density (mean attenuation) from computed tomography images. Patients with PAD who underwent a lower extremity computed tomography scan at a tertiary vascular surgery center were included, and were followed up using hospital records and linked data as part of a retrospective cohort study. The primary outcomes were lower limb events (major amputation or peripheral revascularization) and cardiovascular events (myocardial infarction, stroke, or cardiovascular death). Two hundred and twenty‐three patients with PAD were included (median age 69.0 years; 73% men) and followed for a median of 4.9 [2.6–7.0] years. During this time there were 99 index lower limb events and 97 cardiovascular events. Low leg muscle density was associated with increased risk of lower limb (rate ratio 1.41 [1.11–1.80] per SD reduction) and cardiovascular events (rate ratio 1.60 [1.29–1.99] per SD reduction). Low muscle density remained an independent predictor of cardiovascular (but not lower limb) events, after adjusting for age, sex, traditional cardiovascular risk factors, and angiographic PAD severity (rate ratio 1.39 [1.09–1.77] per lower SD). In contrast, leg muscle volume was not associated with outcomes after adjusting for risk factors and PAD severity. Conclusions Low leg muscle density, but not volume, is a strong, independent predictor of major cardiovascular events among people with PAD. Further research is needed to understand the mechanisms underlying these associations

Development of active, nanoparticle, antimicrobial technologies for muscle-based packaging applications

Fresh and processed muscle-based foods are highly perishable food products and packaging plays a crucial role in providing containment so that the full effect of preservation can be achieved through the provision of shelf-life extension. Conventional packaging materials and systems have served the industry well, however, greater demands are being placed upon industrial packaging formats owing to the movement of muscle-based products to increasingly distant markets, as well as increased customer demands for longer product shelf-life and storage capability. Consequently, conventional packaging materials and systems will have to evolve to meet these challenges. This review presents some of the new strategies that have been developed by employing novel nanotechnological concepts which have demonstrated some promise in significantly extending the shelf-life of muscle-based foods by providing commercially-applicable, antimicrobially-active, smart packaging solutions. The primary focus of this paper is applied to subject aspects, such as; material chemistries employed, forming methods utilised, interactions of the packaging functionalities including nanomaterials employed with polymer substrates and how such materials ultimately affect microbes. In order that such materials become industrially feasible, it is important that safe, stable and commercially-viable packaging materials are shown to be producible and effective in order to gain public acceptance, legislative approval and industrial adoption

Circumstellar Structure around Evolved Stars in the Cygnus-X Star Formation Region

We present observations of newly discovered 24 micron circumstellar structures detected with the Multiband Imaging Photometer for Spitzer (MIPS) around three evolved stars in the Cygnus-X star forming region. One of the objects, BD+43 3710, has a bipolar nebula, possibly due to an outflow or a torus of material. A second, HBHA 4202-22, a Wolf-Rayet candidate, shows a circular shell of 24 micron emission suggestive of either a limb-brightened shell or disk seen face-on. No diffuse emission was detected around either of these two objects in the Spitzer 3.6-8 micron Infrared Array Camera (IRAC) bands. The third object is the luminous blue variable candidate G79.29+0.46. We resolved the previously known inner ring in all four IRAC bands. The 24 micron emission from the inner ring extends ~1.2 arcmin beyond the shorter wavelength emission, well beyond what can be attributed to the difference in resolutions between MIPS and IRAC. Additionally, we have discovered an outer ring of 24 micron emission, possibly due to an earlier episode of mass loss. For the two shell stars, we present the results of radiative transfer models, constraining the stellar and dust shell parameters. The shells are composed of amorphous carbon grains, plus polycyclic aromatic hydrocarbons in the case of G79.29+0.46. Both G79.29+0.46 and HBHA 4202-22 lie behind the main Cygnus-X cloud. Although G79.29+0.46 may simply be on the far side of the cloud, HBHA 4202-22 is unrelated to the Cygnus-X star formation region.Comment: Accepted by A

Status Characteristics and Social Interaction

The authors review literature on effects of status differences on interaction and formulate general principles of status generalization to explain them. Next they conduct direct tests of the explanation in an experimental study of 180 Air Force Sergeants in the standard experimental situation developed by Berger (Berger 2007). Sergeants paired with a commissioned officer formed low self-expectations and Sergeants paired with an Airman formed high self-expectations, as predicted

Status Characteristics and Expectation States

This is the first statement of the theory of status characteristics and expectation states and a form of the manuscipt was published by the authors (1966). The theory generalizes the theory of performance expectations first presented in TR#1. The theory was generalized two more times. Webster and Driskell (1978) describe the development in successive formulations of this theor