Expressions for forces and torques in molecular simulations using rigid bodies

Expressions for intermolecular forces and torques, derived from pair potentials between rigid non-spherical units, are presented. The aim is to give compact and clear expressions, which are easily generalised, and which minimise the risk of error in writing molecular dynamics simulation programs. It is anticipated that these expressions will be useful in the simulation of liquid crystalline systems, and in coarse-grained modelling of macromolecules

A summary of the BARREL campaigns: Technique for studying electron precipitation.

BARREL observed electron precipitation over wide range of energy and timescalesPrecipitating electron distribution is determined using spectroscopy for 19 January 2013 eventBARREL timing data has accuracy within sampling interval of 0.05 s

Comparison of 20nm silver nanoparticles synthesized with and without a gold core: Structure, dissolution in cell culture media, and biological impact on macrophages

Widespread use of silver nanoparticles raises questions of environmental and biological impact. Many synthesis approaches are used to produce pure silver and silver-shell gold-core particles optimized for specific applications. Since both nanoparticles and silver dissolved from the particles may impact the biological response, it is important to understand the physicochemical characteristics along with the biological impact of nanoparticles produced by different processes. The authors have examined the structure, dissolution, and impact of particle exposure to macrophage cells of two 20 nm silver particles synthesized in different ways, which have different internal structures. The structures were examined by electron microscopy and dissolution measured in Rosewell Park Memorial Institute media with 10% fetal bovine serum. Cytotoxicity and oxidative stress were used to measure biological impact on RAW 264.7 macrophage cells. The particles were polycrystalline, but 20 nm particles grown on gold seed particles had smaller crystallite size with many high-energy grain boundaries and defects, and an apparent higher solubility than 20 nm pure silver particles. Greater oxidative stress and cytotoxicity were observed for 20 nm particles containing the Au core than for 20 nm pure silver particles. A simple dissolution model described the time variation of particle size and dissolved silver for particle loadings larger than 9 μg/ml for the 24-h period characteristic of many in-vitro studies

Proteomic identification of prognostic tumour biomarkers, using chemotherapy-induced cancer-associated fibroblasts

Cancer cells grow in highly complex stromal microenvironments, which through metabolic remodelling, catabolism, autophagy and inflammation nurture them and are able to facilitate metastasis and resistance to therapy. However, these changes in the metabolic profile of stromal cancer-associated fibroblasts and their impact on cancer initiation, progression and metastasis are not well-known. This is the first study to provide a comprehensive proteomic portrait of the azathioprine and taxol-induced catabolic state on human stromal fibroblasts, which comprises changes in the expression of metabolic enzymes, myofibroblastic differentiation markers, antioxidants, proteins involved in autophagy, senescence, vesicle trafficking and protein degradation, and inducers of inflammation. Interestingly, many of these features are major contributors to the aging process. A catabolic stroma signature, generated with proteins found differentially up-regulated in taxol-treated fibroblasts, strikingly correlates with recurrence, metastasis and poor patient survival in several solid malignancies. We therefore suggest the inhibition of the catabolic state in healthy cells as a novel approach to improve current chemotherapy efficacies and possibly avoid future carcinogenic processes

Using Regular Languages to Explore the Representational Capacity of Recurrent Neural Architectures

The presence of Long Distance Dependencies (LDDs) in sequential data poses significant challenges for computational models. Various recurrent neural architectures have been designed to mitigate this issue. In order to test these state-of-the-art architectures, there is growing need for rich benchmarking datasets. However, one of the drawbacks of existing datasets is the lack of experimental control with regards to the presence and/or degree of LDDs. This lack of control limits the analysis of model performance in relation to the specific challenge posed by LDDs. One way to address this is to use synthetic data having the properties of subregular languages. The degree of LDDs within the generated data can be controlled through the k parameter, length of the generated strings, and by choosing appropriate forbidden strings. In this paper, we explore the capacity of different RNN extensions to model LDDs, by evaluating these models on a sequence of SPk synthesized datasets, where each subsequent dataset exhibits a longer degree of LDD. Even though SPk are simple languages, the presence of LDDs does have significant impact on the performance of recurrent neural architectures, thus making them prime candidate in benchmarking tasks.Comment: International Conference of Artificial Neural Networks (ICANN) 201

A Caenorhabditis elegans model of Yersinia infection: biofilm formation on a biotic surface.

To investigate Yersinia pathogenicity and the evolutionary divergence of the genus, the effect of pathogenic yersiniae on the model organism Caenorhabditis elegans was studied. Three strains of Yersinia pestis, including a strain lacking pMT1, caused blockage and death of C. elegans; one strain, lacking the haemin storage (hms) locus, caused no effect. Similarly, 15 strains of Yersinia enterocolitica caused no effect. Strains of Yersinia pseudotuberculosis showed different levels of pathogenicity. The majority of strains (76 %) caused no discernible effect; 5 % caused a weak infection, 9.5 % an intermediate infection, and 9.5 % a severe infection. There was no consistent relationship between serotype and severity of infection; nor was there any relationship between strains causing infection of C. elegans and those able to form a biofilm on an abiotic surface. Electron microscope and cytochemical examination of infected worms indicated that the infection phenotype is a result of biofilm formation on the head of the worm. Seven transposon mutants of Y. pseudotuberculosis strain YPIII pIB1 were completely or partially attenuated; mutated genes included genes encoding proteins involved in haemin storage and lipopolysaccharide biosynthesis. A screen of 15 defined C. elegans mutants identified four where mutation caused (complete) resistance to infection by Y. pseudotuberculosis YPIII pIB1. These mutants, srf-2, srf-3, srf-5 and the dauer pathway gene daf-1, also exhibit altered binding of lectins to the nematode surface. This suggests that biofilm formation on a biotic surface is an interactive process involving both bacterial and invertebrate control mechanisms

From mantle to critical zone: A review of large and giant sized deposits of the rare earth elements

This is the final version. Available from Elsevier via the DOI in this record.The rare earth elements are unusual when defining giant-sized ore deposits, as resources are often quoted as total rare earth oxide, but the importance of a deposit may be related to the grade for individual, or a limited group of the elements. Taking the total REE resource, only one currently known deposit (Bayan Obo) would class as giant (>1.7 × 107 tonnes contained metal), but a range of others classify as large (>1.7 × 106 tonnes). With the exception of unclassified resource estimates from the Olympic Dam IOCG deposit, all of these deposits are related to alkaline igneous activity - either carbonatites or agpaitic nepheline syenites. The total resource in these deposits must relate to the scale of the primary igneous source, but the grade is a complex function of igneous source, magmatic crystallisation, hydrothermal modification and supergene enrichment during weathering. Isotopic data suggest that the sources conducive to the formation of large REE deposits are developed in subcontinental lithospheric mantle, enriched in trace elements either by plume activity, or by previous subduction. The reactivation of such enriched mantle domains in relatively restricted geographical areas may have played a role in the formation of some of the largest deposits (e.g. Bayan Obo). Hydrothermal activity involving fluids from magmatic to meteoric sources may result in the redistribution of the REE and increases in grade, depending on primary mineralogy and the availability of ligands. Weathering and supergene enrichment of carbonatite has played a role in the formation of the highest grade deposits at Mount Weld (Australia) and Tomtor (Russia). For the individual REE with the current highest economic value (Nd and the HREE), the boundaries for the large and giant size classes are two orders of magnitude lower, and deposits enriched in these metals (agpaitic systems, ion absorption deposits) may have significant economic impact in the near future.Natural Environment Research CouncilUniversity of Exete

Daytime Naps, Motor Memory Consolidation and Regionally Specific Sleep Spindles

BACKGROUND: Increasing evidence demonstrates that motor-skill memories improve across a night of sleep, and that non-rapid eye movement (NREM) sleep commonly plays a role in orchestrating these consolidation enhancements. Here we show the benefit of a daytime nap on motor memory consolidation and its relationship not simply with global sleep-stage measures, but unique characteristics of sleep spindles at regionally specific locations; mapping to the corresponding memory representation. METHODOLOGY/PRINCIPAL FINDINGS: Two groups of subjects trained on a motor-skill task using their left hand – a paradigm known to result in overnight plastic changes in the contralateral, right motor cortex. Both groups trained in the morning and were tested 8 hr later, with one group obtaining a 60–90 minute intervening midday nap, while the other group remained awake. At testing, subjects that did not nap showed no significant performance improvement, yet those that did nap expressed a highly significant consolidation enhancement. Within the nap group, the amount of offline improvement showed a significant correlation with the global measure of stage-2 NREM sleep. However, topographical sleep spindle analysis revealed more precise correlations. Specifically, when spindle activity at the central electrode of the non-learning hemisphere (left) was subtracted from that in the learning hemisphere (right), representing the homeostatic difference following learning, strong positive relationships with offline memory improvement emerged–correlations that were not evident for either hemisphere alone. CONCLUSIONS/SIGNIFICANCE: These results demonstrate that motor memories are dynamically facilitated across daytime naps, enhancements that are uniquely associated with electrophysiological events expressed at local, anatomically discrete locations of the brain

'What did i do wrong?' An empirical evaluation of sample preparation methodologies in matrix-assisted laser desorption/ionization-mass spectrometry imaging

© 2019 MO Rourke. Aim: This guide aims to broaden the uptake of MALDI-MSI biomedical research by removing the initial 'lag phase' associated with empirical determination in sample preparation and data analysis. Methods: Samples from several tissue types were prepared for lipid, protein and peptide MSI analysis. Broadly, samples were cryo sectioned, mounted onto conductive MALDI slides and sublimed with an analyte specific matrix, recrystallised and analyzed in a Bruker UltrafleXtreme MALDI TOF/TOF. Results/conclusion: Here we present a general guide that serves as the first comprehensive, explanatory index for curation and verification of both sample preparation and data generation during the MALDI-MSI process. Lay abstract The field of mass spectrometry tissue imaging is a complex field that is designed to provide a map of the molecules on the surface of tissue sections. It often requires a significant investment of time and resources before useful data can be generated; therefore, this paper provides a visual troubleshooting guide that will act as a reference point for a range of sample preparation mistakes and explanations for unusual or suboptimal data. Elimination of the lag phase associated with the development of new techniques will help to expedite the growth and application of this technology

The influence of oral health status on speech intelligibility, articulation and quality of life of older community-dwelling people

Objective: To investigate the impact of the oral health status on speech intelligibility, articulation and quality of life of older community-dwelling people. Background To our knowledge, there have been no studies on this topic in patients aged 75 years or older. Material and methods: Thirty outpatients of a university dental clinic (median [IQR] age of 77.00 [75-82] years) participated. The OHIP-14, a dental examination, a speech intelligibility study and an articulation examination were conducted. Results: Distortions of rhotacisms and sigmatisms were most common, followed by distortions of labiodentals and apicoalveolars. Seven participants (23%) required dental treatment. Distortions of rhotacisms were lowest in participants with loss of teeth in the posterior part of the maxilla and equal in participants with edentulous maxilla and loss of teeth in the anterior part of the maxilla (P = 0.014). Labiodental distortions were lowest in participants with loss of teeth in the posterior part of the maxilla, but were higher in participants with loss of teeth in the anterior part of the maxilla and highest in participants with an edentulous maxilla (P = 0.035). People with normal mouth opening had lower percentage of labiodental distortions than people with a reduced mouth opening (P = 0.05). The proportion of participants with inadequate denture hygiene and distortions of bilabials was 71.4% compared to 10.5% for participants with adequate denture hygiene (P = 0.005). Conclusion: Dentists must consider the impact of a denture on speech, but also should be aware of other oral health factors that influence the speech and quality of life of elders