Molecular dynamics simulation of mechanical behavior of osteopontin-hydroxyapatite interfaces

Bone is characterized with an optimized combination of high stiffness and toughness. The understanding of bone nanomechanics is critical to the development of new artificial biological materials with unique properties. In this work, the mechanical characteristics of the interfaces between osteopontin (OPN, a noncollagenous protein in extrafibrillar protein matrix) and hydroxyapatite (HA, a mineral nanoplatelet in mineralized collagen fibrils) were investigated using molecular dynamics method. We found that the interfacial mechanical behaviour is governed by the electrostatic attraction between acidic amino acid residues in OPN and calcium in HA. Higher energy dissipation is associated with the OPN peptides with a higher number of acidic amino acid residues. When loading in the interface direction, new bonds between some acidic residues and HA surface are formed, resulting in a stick-slip type motion of OPN peptide on the HA surface and high interfacial energy dissipation. The formation of new bonds during loading is considered to be a key mechanism responsible for high fracture resistance observed in bone and other biological materials.

Automated classification of limb fractures from free-text radiology reports using a clinician-informed gazetteer methodology

Background Timely diagnosis and reporting of patient symptoms in hospital emergency departments (ED) is a critical component of health services delivery. However, due to dispersed information resources and a vast amount of manual processing of unstructured information, accurate point-of-care diagnosis is often difficult. Aims The aim of this research is to report initial experimental evaluation of a clinician-informed automated method for the issue of initial misdiagnoses associated with delayed receipt of unstructured radiology reports. Method A method was developed that resembles clinical reasoning for identifying limb abnormalities. The method consists of a gazetteer of keywords related to radiological findings; the method classifies an X-ray report as abnormal if it contains evidence contained in the gazetteer. A set of 99 narrative reports of radiological findings was sourced from a tertiary hospital. Reports were manually assessed by two clinicians and discrepancies were validated by a third expert ED clinician; the final manual classification generated by the expert ED clinician was used as ground truth to empirically evaluate the approach. Results The automated method that attempts to individuate limb abnormalities by searching for keywords expressed by clinicians achieved an F-measure of 0.80 and an accuracy of 0.80. Conclusion While the automated clinician-driven method achieved promising performances, a number of avenues for improvement were identified using advanced natural language processing (NLP) and machine learning techniques.

Nanostructured high strength Mg-5%Al-x%Nd alloys prepared by mechanical alloying

Nanostructured high strength Mg-5%Al-x%Nd alloys were prepared by mechanical alloying. Microstructural characterization reveled average crystalline size to be about 30 nm after mechanical alloying while it increased to about 90 nm after sintering and extrusion. Mechanical properties showed increase in 0.2% yield stress, ultimate tensile strength was attributed to reduction in gain size as well as to the enhanced diffusion after mechanical activation. Although ultra high yield stress was observed from the specimen with 5% Nd, its ductility was reduced to about 1.6%.

Fabrication and microstructure of mechanically alloyed Mg-Al-Nd alloys

In this work, nanocrystalline Mg-Al-Nd alloys were fabricated using mechanical alloying method. Phase structure of the extrided rods was examined using X-ray diffraction (XRD) and the microstructures were observed using transmission electronic microscopy (TEM). High yield strength was obtained in the alloys with a high Nd content due to grain refinement and Nd rich precipitate phase.

Molecular basis for lysine specificity in the yeast ubiquitin-conjugating enzyme Cdc34

Ubiquitin (Ub)-conjugating enzymes (E2s) and ubiquitin ligases (E3s) catalyze the attachment of Ub to lysine residues in substrates and Ub during monoubiquitination and polyubiquitination. Lysine selection is important for the generation of diverse substrate-Ub structures, which provides versatility to this pathway in the targeting of proteins to different fates. The mechanisms of lysine selection remain poorly understood, with previous studies suggesting that the ubiquitination site(s) is selected by the E2/E3-mediated positioning of a lysine(s) toward the E2/E3 active site. By studying the polyubiquitination of Sic1 by the E2 protein Cdc34 and the RING E3 Skp1/Cul1/F-box (SCF) protein, we now demonstrate that in addition to E2/E3-mediated positioning, proximal amino acids surrounding the lysine residues in Sic1 and Ub are critical for ubiquitination. This mechanism is linked to key residues composing the catalytic core of Cdc34 and independent of SCF. Changes to these core residues altered the lysine preference of Cdc34 and specified whether this enzyme monoubiquitinated or polyubiquitinated Sic1. These new findings indicate that compatibility between amino acids surrounding acceptor lysine residues and key amino acids in the catalytic core of ubiquitin-conjugating enzymes is an important mechanism for lysine selection during ubiquitination.

miRPlant : an integrated tool for identification of plant miRNA from RNA sequencing data

Background Small RNA sequencing is commonly used to identify novel miRNAs and to determine their expression levels in plants. There are several miRNA identification tools for animals such as miRDeep, miRDeep2 and miRDeep*. miRDeep-P was developed to identify plant miRNA using miRDeep’s probabilistic model of miRNA biogenesis, but it depends on several third party tools and lacks a user-friendly interface. The objective of our miRPlant program is to predict novel plant miRNA, while providing a user-friendly interface with improved accuracy of prediction. Result We have developed a user-friendly plant miRNA prediction tool called miRPlant. We show using 16 plant miRNA datasets from four different plant species that miRPlant has at least a 10% improvement in accuracy compared to miRDeep-P, which is the most popular plant miRNA prediction tool. Furthermore, miRPlant uses a Graphical User Interface for data input and output, and identified miRNA are shown with all RNAseq reads in a hairpin diagram. Conclusions We have developed miRPlant which extends miRDeep* to various plant species by adopting suitable strategies to identify hairpin excision regions and hairpin structure filtering for plants. miRPlant does not require any third party tools such as mapping or RNA secondary structure prediction tools. miRPlant is also the first plant miRNA prediction tool that dynamically plots miRNA hairpin structure with small reads for identified novel miRNAs. This feature will enable biologists to visualize novel pre-miRNA structure and the location of small RNA reads relative to the hairpin. Moreover, miRPlant can be easily used by biologists with limited bioinformatics skills.

Speckle-type POZ protein mutations interrupt tumor suppressor function of speckle-type POZ protein in prostate cancer by affecting androgen receptor degradation

Large scale exome sequencing studies have revealed regions of the genome, which contribute to the castrate resistant prostate cancer (CRPC) phenotype. [1],[2],[3] Such studies have identified mutations in genes, which may have diagnostic/prognostic potential, or which may be targeted therapeutically. Two of these genes include the androgen receptor (AR) and speckle-type POZ protein (SPOP) genes. However, the findings from these exome sequencing studies can only be translated therapeutically once the functional consequences of these mutations have been determined. Here, we highlight the recent study by An et al. [4] which investigated the functional effects of mutations in the SPOP gene that were identified in the aforementioned exome sequencing studies, particularly in the context of SPOP-mediated degradation of the AR.

Numerical investigation of deformation and failure mechanisms of osteopontin-hydroxyapatite interfaces and mineralized collagen fibril arrays

This thesis is a comprehensive study of deformation and failure mechanisms in bone at nano- and micro-scale levels. It explores the mechanical behaviour of osteopontin-hydroxyapatite interfaces and mineralized collagen fibril arrays, through atomistic molecular dynamics and finite element simulations. This thesis shows some main factors contributing to the excellent material properties of bone and provides some guidelines for development of new artificial biological materials and medical implants.

J-Circos : an interactive Circos plotter

Circos plots are graphical outputs that display three dimensional chromosomal interactions and fusion transcripts. However, the Circos plot tool is not an interactive visualization tool, but rather a figure generator. For example, it does not enable data to be added dynamically, nor does it provide information for specific data points interactively. Recently, an R-based Circos tool (RCircos) has been developed to integrate Circos to R, but similarly, Rcircos can only be used to generate plots. Thus, we have developed a Circos plot tool (J-Circos) that is an interactive visualization tool that can plot Circos figures, as well as being able to dynamically add data to the figure, and providing information for specific data points using mouse hover display and zoom in/out functions. J-Circos uses the Java computer language to enable it to be used on most operating systems (Windows, MacOS, Linux). Users can input data into JCircos using flat data formats, as well as from the GUI. J-Circos will enable biologists to better study more complex chromosomal interactions and fusion transcripts that are otherwise difficult to visualize from next-generation sequencing data.

Community wide interventions for increasing physical activity

Background Multi-strategic community wide interventions for physical activity are increasingly popular but their ability to achieve population level improvements is unknown. Objectives To evaluate the effects of community wide, multi-strategic interventions upon population levels of physical activity. Search methods We searched the Cochrane Public Health Group Segment of the Cochrane Register of Studies,The Cochrane Library, MEDLINE, MEDLINE in Process, EMBASE, CINAHL, LILACS, PsycINFO, ASSIA, the British Nursing Index, Chinese CNKI databases, EPPI Centre (DoPHER, TRoPHI), ERIC, HMIC, Sociological Abstracts, SPORTDiscus, Transport Database and Web of Science (Science Citation Index, Social Sciences Citation Index, Conference Proceedings Citation Index). We also scanned websites of the EU Platform on Diet, Physical Activity and Health; Health-Evidence.org; the International Union for Health Promotion and Education; the NIHR Coordinating Centre for Health Technology (NCCHTA); the US Centre for Disease Control and Prevention (CDC) and NICE and SIGN guidelines. Reference lists of all relevant systematic reviews, guidelines and primary studies were searched and we contacted experts in the field. The searches were updated to 16 January 2014, unrestricted by language or publication status. Selection criteria Cluster randomised controlled trials, randomised controlled trials, quasi-experimental designs which used a control population for comparison, interrupted time-series studies, and prospective controlled cohort studies were included. Only studies with a minimum six-month follow up from the start of the intervention to measurement of outcomes were included. Community wide interventions had to comprise at least two broad strategies aimed at physical activity for the whole population. Studies which randomised individuals from the same community were excluded. Data collection and analysis At least two review authors independently extracted the data and assessed the risk of bias. Each study was assessed for the setting, the number of included components and their intensity. The primary outcome measures were grouped according to whether they were dichotomous (per cent physically active, per cent physically active during leisure time, and per cent physically inactive) or continuous (leisure time physical activity time (time spent)), walking (time spent), energy expenditure (as metabolic equivalents or METS)). For dichotomous measures we calculated the unadjusted and adjusted risk difference, and the unadjusted and adjusted relative risk. For continuous measures we calculated percentage change from baseline, unadjusted and adjusted. Main results After the selection process had been completed, 33 studies were included. A total of 267 communities were included in the review (populations between 500 and 1.9 million). Of the included studies, 25 were set in high income countries and eight were in low income countries. The interventions varied by the number of strategies included and their intensity. Almost all of the interventions included a component of building partnerships with local governments or non-governmental organisations (NGOs) (29 studies). None of the studies provided results by socio-economic disadvantage or other markers of equity. However, of those included studies undertaken in high income countries, 14 studies were described as being provided to deprived, disadvantaged or low socio-economic communities. Nineteen studies were identified as having a high risk of bias, 10 studies were unclear, and four studies had a low risk of bias. Selection bias was a major concern with these studies, with only five studies using randomisation to allocate communities. Four studies were judged as being at low risk of selection bias although 19 studies were considered to have an unclear risk of bias. Twelve studies had a high risk of detection bias, 13 an unclear risk and four a low risk of bias. Generally, the better designed studies showed no improvement in the primary outcome measure of physical activity at a population level. All four of the newly included, and judged to be at low risk of bias, studies (conducted in Japan, United Kingdom and USA) used randomisation to allocate the intervention to the communities. Three studies used a cluster randomised design and one study used a stepped wedge design. The approach to measuring the primary outcome of physical activity was better in these four studies than in many of the earlier studies. One study obtained objective population representative measurements of physical activity by accelerometers, while the remaining three low-risk studies used validated self-reported measures. The study using accelerometry, conducted in low income, high crime communities of USA, emphasised social marketing, partnership with police and environmental improvements. No change in the seven-day average daily minutes of moderate to vigorous physical activity was observed during the two years of operation. Some program level effect was observed with more people walking in the intervention community, however this result was not evident in the whole community. Similarly, the two studies conducted in the United Kingdom (one in rural villages and the other in urban London; both using communication, partnership and environmental strategies) found no improvement in the mean levels of energy expenditure per person per week, measured from one to four years from baseline. None of the three low risk studies reporting a dichotomous outcome of physical activity found improvements associated with the intervention. Overall, there was a noticeable absence of reporting of benefit in physical activity for community wide interventions in the included studies. However, as a group, the interventions undertaken in China appeared to have the greatest possibility of success with high participation rates reported. Reporting bias was evident with two studies failing to report physical activity measured at follow up. No adverse events were reported.The data pertaining to cost and sustainability of the interventions were limited and varied. Authors' conclusions Although numerous studies have been undertaken, there is a noticeable inconsistency of the findings in the available studies and this is confounded by serious methodological issues within the included studies. The body of evidence in this review does not support the hypothesis that the multi-component community wide interventions studied effectively increased physical activity for the population, although some studies with environmental components observed more people walking. Plain language summary Community wide interventions for increasing physical activity Not having enough physical activity leads to poorer health. Regular physical activity can reduce the risk of chronic disease and improve one's health and wellbeing. The lack of physical activity is a common and in some cases a growing health problem. To address this, 33 studies have used improvement activities directed at communities, using more than one approach in a single program. When we first looked at the available research in 2011 we observed that there was a lack of good studies which could show whether this approach was beneficial or not. Some studies claimed that community wide programs improved physical activities and other studies did not. In this update we found four new studies that were of good quality; however none of these four studies increased physical activity levels for the population. Some studies reported program level effects such as observing more people walking, however the population level of physical activity had not increased. This review found that community wide interventions are very difficult to undertake, and it appears that they usually fail to provide a measurable benefit in physical activity for a population. It is apparent that many of the interventions failed to reach a substantial portion of the community, and we speculate that some single strategies included in the combination may lack individual effectiveness. Laički sažetak Intervencije u zajednici za povećanje tjelesne aktivnosti Nedostatna tjelesna aktivnost povezana je s lošijim zdravljem.Redovita tjelesna aktivnost može umanjiti rizik od kroničnih bolesti te poboljšati zdravlje i kvalitetu života pojedinca.Manjak tjelesne aktivnosti čest je problem, a učestalost tog problema se povećava.Cochrane sustavni pregled je analizirao 33 studije koje su istražile programe za povećanje tjelesne aktivnosti u zajednici, u kojima se koristilo više od jednog pristupa.Kad su prvi put pregledani dokazi iz istraživanja koja su bila dostupna 2011. godine, utvrđeno je da nema dovoljno dobrih studija koje bi mogle pokazati je li takav pristup koristan ili ne.Primjerice, neke studije tvrde da programi za povećanje tjelesne aktivnosti u zajednici poboljšavaju tjelesnu aktivnost pojedinaca u zajednici, a druge studije tvrde suprotno.U ovom obnovljenom sustavnom pregledu pronađene su 4 nove studije koje su bile visoke kvalitete, ail nijedna od tih studija nije pokazala da je istraživana intervencija dovela do povećanja tjelesne aktivnosti u zajednici.Neke su studije opisale učinak na način da je opisano da je uočeno da više ljudi u zajednici hoda, međutim, ukupna razina tjelesne aktivnosti u promatranoj populaciji nije se povećala.Ovaj sustavni pregled je utvrdio da je intervencije za povećanje tjelesne aktivnosti u zajednici teško provesti i čini se da one obično ne uspijevaju u svojoj namjeri da na mjerljiv način povećaju tjelesnu aktivnost u populaciji.Čini se da mnoge intervencije nisu uspjele doseći veći broj stanovnika u zajednici pa se može smatrati da neke od strategija uključene u analizirane kombinacije nisu zasebno učinkovite.

Dual compressible hybrid quantum secret sharing schemes based on extended unitary operations

A crucial issue with hybrid quantum secret sharing schemes is the amount of data that is allocated to the participants. The smaller the amount of allocated data, the better the performance of a scheme. Moreover, quantum data is very hard and expensive to deal with, therefore, it is desirable to use as little quantum data as possible. To achieve this goal, we first construct extended unitary operations by the tensor product of n, n ≥ 2, basic unitary operations, and then by using those extended operations, we design two quantum secret sharing schemes. The resulting dual compressible hybrid quantum secret sharing schemes, in which classical data play a complementary role to quantum data, range from threshold to access structure. Compared with the existing hybrid quantum secret sharing schemes, our proposed schemes not only reduce the number of quantum participants, but also the number of particles and the size of classical shares. To be exact, the number of particles that are used to carry quantum data is reduced to 1 while the size of classical secret shares also is also reduced to l−2 m−1 based on ((m+1, n′)) threshold and to l−2 r2 (where r2 is the number of maximal unqualified sets) based on adversary structure. Consequently, our proposed schemes can greatly reduce the cost and difficulty of generating and storing EPR pairs and lower the risk of transmitting encoded particles.

The epidemiology of Plasmodium vivax and Plasmodium falciparum malaria in China, 2004–2012 : from intensified control to elimination

Background In China, the national malaria elimination programme has been operating since 2010. This study aimed to explore the epidemiological changes in patterns of malaria in China from intensified control to elimination stages. Methods Data on nationwide malaria cases from 2004 to 2012 were extracted from the Chinese national malaria surveillance system. The secular trend, gender and age features, seasonality, and spatial distribution by Plasmodium species were analysed. Results In total, 238,443 malaria cases were reported, and the proportion of Plasmodium falciparum increased drastically from <10% before 2010 to 55.2% in 2012. From 2004 to 2006, malaria showed a significantly increasing trend and with the highest incidence peak in 2006 (4.6/100,000), while from 2007 onwards, malaria decreased sharply to only 0.18/100,000 in 2012. Males and young age groups became the predominantly affected population. The areas affected by Plasmodium vivax malaria shrunk, while areas affected by P. falciparum malaria expanded from 294 counties in 2004 to 600 counties in 2012. Conclusions This study demonstrated that malaria has decreased dramatically in the last five years, especially since the Chinese government launched a malaria elimination programme in 2010, and areas with reported falciparum malaria cases have expanded over recent years. These findings suggest that elimination efforts should be improved to meet these changes, so as to achieve the nationwide malaria elimination goal in China in 2020.