Theory on quench-induced pattern formation: Application to the isotropic to smectic-A phase transitions

During catastrophic processes of environmental variations of a thermodynamic system, such as rapid temperature decreasing, many novel and complex patterns often form. To understand such phenomena, a general mechanism is proposed based on the competition between heat transfer and conversion of heat to other energy forms. We apply it to the smectic-A filament growth process during quench-induced isotropic to smectic-A phase transition. Analytical forms for the buckling patterns are derived and we find good agreement with experimental observation [Phys. Rev. {\bf E55} (1997) 1655]. The present work strongly indicates that rapid cooling will lead to structural transitions in the smectic-A filament at the molecular level to optimize heat conversion. The force associated with this pattern formation process is estimated to be in the order of $10^{-1}$ piconewton.Comment: 9 pages in RevTex form, with 3 postscript figures. Accepted by PR

Algorithm Selection Framework for Cyber Attack Detection

The number of cyber threats against both wired and wireless computer systems and other components of the Internet of Things continues to increase annually. In this work, an algorithm selection framework is employed on the NSL-KDD data set and a novel paradigm of machine learning taxonomy is presented. The framework uses a combination of user input and meta-features to select the best algorithm to detect cyber attacks on a network. Performance is compared between a rule-of-thumb strategy and a meta-learning strategy. The framework removes the conjecture of the common trial-and-error algorithm selection method. The framework recommends five algorithms from the taxonomy. Both strategies recommend a high-performing algorithm, though not the best performing. The work demonstrates the close connectedness between algorithm selection and the taxonomy for which it is premised.Comment: 6 pages, 7 figures, 1 table, accepted to WiseML '2

Bending and Base-Stacking Interactions in Double-Stranded Semiflexible Polymer

Simple expressions for the bending and the base-stacking energy of double-stranded semiflexible biopolymers (such as DNA and actin) are derived. The distribution of the folding angle between the two strands is obtained by solving a Schr\"{o}dinger equation variationally. Theoretical results based on this model on the extension versus force and extension versus degree of supercoiling relations of DNA chain are in good agreement with the experimental observations of Cluzel {\it et al.} [Science {\bf 271}, 792 (1996)], Smith {\it et al.} [{\it ibid.} {\bf 271}, 795 (1996)], and Strick {\it et al.} [{\it ibid.} {\bf 271}, 1835 (1996)].Comment: 8 pages in Revtex format, with 4 EPS figure

A comparison of repaired, remanufactured and new compressors used in Western Australian small- and medium-sized enterprises in terms of global warming

Repaired compressors are compared with remanufactured and new compressors in terms of economic andenvironmental benefits. A detailed life cycle assessment has been carried out for compressors under threemanufacturing strategies: repaired, remanufactured and new equipment. The life cycle assessment of the globalwarming potential of repaired compressors varies from 4.38 to 119 kg carbon dioxide equivalent (CO2-e),depending on the type of components replaced. While greenhouse gas emissions from the remanufacturedcompressors (110 to 168 kg CO2-e) are relatively higher than those from the repaired ones (4.4 to 119 kg CO2-e), anew compressor has been found to produce a larger amount of greenhouse gas emissions (1,590 kg CO2-e)compared to both repaired and remanufactured compressors. Repairing failed compressors has been found to offerend users both dollar and carbon savings in contrast to remanufactured and new compressors. The research alsofound that extended lifetime is more important than the manufacturing processes in terms of greenhouse gasemissions. Since a remanufactured compressor offers a longer life than a repaired compressor, the replacement ofthe latter with the former can avoid 33% to 66% of the greenhouse gas emissions associated with a newcompressor production with a lifetime of 15 to 25 years

Methods and algorithms for unsupervised learning of morphology

This is an accepted manuscript of a chapter published by Springer in Computational Linguistics and Intelligent Text Processing. CICLing 2014. Lecture Notes in Computer Science, vol 8403 in 2014 available online: https://doi.org/10.1007/978-3-642-54906-9_15 The accepted version of the publication may differ from the final published version.This paper is a survey of methods and algorithms for unsupervised learning of morphology. We provide a description of the methods and algorithms used for morphological segmentation from a computational linguistics point of view. We survey morphological segmentation methods covering methods based on MDL (minimum description length), MLE (maximum likelihood estimation), MAP (maximum a posteriori), parametric and non-parametric Bayesian approaches. A review of the evaluation schemes for unsupervised morphological segmentation is also provided along with a summary of evaluation results on the Morpho Challenge evaluations.Published versio

A hypothetico-deductive approach to assessing the social function of chemical signalling in a non-territorial solitary carnivore

The function of chemical signalling in non-territorial solitary carnivores is still relatively unclear. Studies on territorial solitary and social carnivores have highlighted odour capability and utility, however the social function of chemical signalling in wild carnivore populations operating dominance hierarchy social systems has received little attention. We monitored scent marking and investigatory behaviour of wild brown bears Ursus arctos, to test multiple hypotheses relating to the social function of chemical signalling. Camera traps were stationed facing bear ‘marking trees’ to document behaviour by different age sex classes in different seasons. We found evidence to support the hypothesis that adult males utilise chemical signalling to communicate dominance to other males throughout the non-denning period. Adult females did not appear to utilise marking trees to advertise oestrous state during the breeding season. The function of marking by subadult bears is somewhat unclear, but may be related to the behaviour of adult males. Subadults investigated trees more often than they scent marked during the breeding season, which could be a result of an increased risk from adult males. Females with young showed an increase in marking and investigation of trees outside of the breeding season. We propose the hypothesis that females engage their dependent young with marking trees from a young age, at a relatively ‘safe’ time of year. Memory, experience, and learning at a young age, may all contribute towards odour capabilities in adult bears

Partitioning clustering algorithms for protein sequence data sets

<p>Abstract</p> <p>Background</p> <p>Genome-sequencing projects are currently producing an enormous amount of new sequences and cause the rapid increasing of protein sequence databases. The unsupervised classification of these data into functional groups or families, clustering, has become one of the principal research objectives in structural and functional genomics. Computer programs to automatically and accurately classify sequences into families become a necessity. A significant number of methods have addressed the clustering of protein sequences and most of them can be categorized in three major groups: hierarchical, graph-based and partitioning methods. Among the various sequence clustering methods in literature, hierarchical and graph-based approaches have been widely used. Although partitioning clustering techniques are extremely used in other fields, few applications have been found in the field of protein sequence clustering. It is not fully demonstrated if partitioning methods can be applied to protein sequence data and if these methods can be efficient compared to the published clustering methods.</p> <p>Methods</p> <p>We developed four partitioning clustering approaches using Smith-Waterman local-alignment algorithm to determine pair-wise similarities of sequences. Four different sets of protein sequences were used as evaluation data sets for the proposed methods.</p> <p>Results</p> <p>We show that these methods outperform several other published clustering methods in terms of correctly predicting a classifier and especially in terms of the correctness of the provided prediction. The software is available to academic users from the authors upon request.</p

Representing and comparing protein structures as paths in three-dimensional space

BACKGROUND: Most existing formulations of protein structure comparison are based on detailed atomic level descriptions of protein structures and bypass potential insights that arise from a higher-level abstraction. RESULTS: We propose a structure comparison approach based on a simplified representation of proteins that describes its three-dimensional path by local curvature along the generalized backbone of the polypeptide. We have implemented a dynamic programming procedure that aligns curvatures of proteins by optimizing a defined sum turning angle deviation measure. CONCLUSION: Although our procedure does not directly optimize global structural similarity as measured by RMSD, our benchmarking results indicate that it can surprisingly well recover the structural similarity defined by structure classification databases and traditional structure alignment programs. In addition, our program can recognize similarities between structures with extensive conformation changes that are beyond the ability of traditional structure alignment programs. We demonstrate the applications of procedure to several contexts of structure comparison. An implementation of our procedure, CURVE, is available as a public webserver

Antimicrobial resistance among migrants in Europe: a systematic review and meta-analysis

BACKGROUND: Rates of antimicrobial resistance (AMR) are rising globally and there is concern that increased migration is contributing to the burden of antibiotic resistance in Europe. However, the effect of migration on the burden of AMR in Europe has not yet been comprehensively examined. Therefore, we did a systematic review and meta-analysis to identify and synthesise data for AMR carriage or infection in migrants to Europe to examine differences in patterns of AMR across migrant groups and in different settings. METHODS: For this systematic review and meta-analysis, we searched MEDLINE, Embase, PubMed, and Scopus with no language restrictions from Jan 1, 2000, to Jan 18, 2017, for primary data from observational studies reporting antibacterial resistance in common bacterial pathogens among migrants to 21 European Union-15 and European Economic Area countries. To be eligible for inclusion, studies had to report data on carriage or infection with laboratory-confirmed antibiotic-resistant organisms in migrant populations. We extracted data from eligible studies and assessed quality using piloted, standardised forms. We did not examine drug resistance in tuberculosis and excluded articles solely reporting on this parameter. We also excluded articles in which migrant status was determined by ethnicity, country of birth of participants' parents, or was not defined, and articles in which data were not disaggregated by migrant status. Outcomes were carriage of or infection with antibiotic-resistant organisms. We used random-effects models to calculate the pooled prevalence of each outcome. The study protocol is registered with PROSPERO, number CRD42016043681. FINDINGS: We identified 2274 articles, of which 23 observational studies reporting on antibiotic resistance in 2319 migrants were included. The pooled prevalence of any AMR carriage or AMR infection in migrants was 25·4% (95% CI 19·1-31·8; I2 =98%), including meticillin-resistant Staphylococcus aureus (7·8%, 4·8-10·7; I2 =92%) and antibiotic-resistant Gram-negative bacteria (27·2%, 17·6-36·8; I2 =94%). The pooled prevalence of any AMR carriage or infection was higher in refugees and asylum seekers (33·0%, 18·3-47·6; I2 =98%) than in other migrant groups (6·6%, 1·8-11·3; I2 =92%). The pooled prevalence of antibiotic-resistant organisms was slightly higher in high-migrant community settings (33·1%, 11·1-55·1; I2 =96%) than in migrants in hospitals (24·3%, 16·1-32·6; I2 =98%). We did not find evidence of high rates of transmission of AMR from migrant to host populations. INTERPRETATION: Migrants are exposed to conditions favouring the emergence of drug resistance during transit and in host countries in Europe. Increased antibiotic resistance among refugees and asylum seekers and in high-migrant community settings (such as refugee camps and detention facilities) highlights the need for improved living conditions, access to health care, and initiatives to facilitate detection of and appropriate high-quality treatment for antibiotic-resistant infections during transit and in host countries. Protocols for the prevention and control of infection and for antibiotic surveillance need to be integrated in all aspects of health care, which should be accessible for all migrant groups, and should target determinants of AMR before, during, and after migration. FUNDING: UK National Institute for Health Research Imperial Biomedical Research Centre, Imperial College Healthcare Charity, the Wellcome Trust, and UK National Institute for Health Research Health Protection Research Unit in Healthcare-associated Infections and Antimictobial Resistance at Imperial College London

Anatomical heterogeneity of tendon: Fascicular and interfascicular tendon compartments have distinct proteomic composition

This study was funded by the BBSRC (BB/K008412/1)