Salient Frame Detection for Molecular Dynamics Simulations

Recent advances in sophisticated computational techniques have facilitated simulation of incrediblydetailed time-varying trajectories and in the process have generated vast quantities of simulation data. The current tools to analyze and comprehend large-scale time-varying data, however, lag far behind our ability to produce such simulation data. Saliency-based analysis can be applied to time-varying 3D datasets for the purpose of summarization, abstraction, and motion analysis. As the sizes of time-varying datasets continue to grow, it becomes more and more difficult to comprehend vast amounts of data and information in a short period of time. In this paper, we use eigenanalysis to generate orthogonal basis functions over sliding windows to characterize regions of unusual deviations and significant trends. Our results show that motion subspaces provide an effective technique for summarization of large molecular dynamics trajectories

Lateral Gene Expression in Drosophila Early Embryos Is Supported by Grainyhead-Mediated Activation and Tiers of Dorsally-Localized Repression

The general consensus in the field is that limiting amounts of the transcription factor Dorsal establish dorsal boundaries of genes expressed along the dorsal-ventral (DV) axis of early Drosophila embryos, while repressors establish ventral boundaries. Yet recent studies have provided evidence that repressors act to specify the dorsal boundary of intermediate neuroblasts defective (ind), a gene expressed in a stripe along the DV axis in lateral regions of the embryo. Here we show that a short 12 base pair sequence (“the A-box”) present twice within the ind CRM is both necessary and sufficient to support transcriptional repression in dorsal regions of embryos. To identify binding factors, we conducted affinity chromatography using the A-box element and found a number of DNA-binding proteins and chromatin-associated factors using mass spectroscopy. Only Grainyhead (Grh), a CP2 transcription factor with a unique DNA-binding domain, was found to bind the A-box sequence. Our results suggest that Grh acts as an activator to support expression of ind, which was surprising as we identified this factor using an element that mediates dorsally-localized repression. Grh and Dorsal both contribute to ind transcriptional activation. However, another recent study found that the repressor Capicua (Cic) also binds to the A-box sequence. While Cic was not identified through our A-box affinity chromatography, utilization of the same site, the A-box, by both factors Grh (activator) and Cic (repressor) may also support a “switch-like” response that helps to sharpen the ind dorsal boundary. Furthermore, our results also demonstrate that TGF-β signaling acts to refine ind CRM expression in an A-box independent manner in dorsal-most regions, suggesting that tiers of repression act in dorsal regions of the embryo

Graphene-protected copper and silver plasmonics.

Plasmonics has established itself as a branch of physics which promises to revolutionize data processing, improve photovoltaics, and increase sensitivity of bio-detection. A widespread use of plasmonic devices is notably hindered by high losses and the absence of stable and inexpensive metal films suitable for plasmonic applications. To this end, there has been a continuous search for alternative plasmonic materials that are also compatible with complementary metal oxide semiconductor technology. Here we show that copper and silver protected by graphene are viable candidates. Copper films covered with one to a few graphene layers show excellent plasmonic characteristics. They can be used to fabricate plasmonic devices and survive for at least a year, even in wet and corroding conditions. As a proof of concept, we use the graphene-protected copper to demonstrate dielectric loaded plasmonic waveguides and test sensitivity of surface plasmon resonances. Our results are likely to initiate wide use of graphene-protected plasmonics.SAIT GRO Program and EPSRC grant EP/K011022/1. Y.-J. Kim was supported by the Global Research Laboratory Program (2011-0021972) of the Ministry of Education, Science and Technology, Korea. The support of the Graphene Flagship project is acknowledged

Listen to genes : dealing with microarray data in the frequency domain

Background: We present a novel and systematic approach to analyze temporal microarray data. The approach includes normalization, clustering and network analysis of genes. Methodology: Genes are normalized using an error model based uniform normalization method aimed at identifying and estimating the sources of variations. The model minimizes the correlation among error terms across replicates. The normalized gene expressions are then clustered in terms of their power spectrum density. The method of complex Granger causality is introduced to reveal interactions between sets of genes. Complex Granger causality along with partial Granger causality is applied in both time and frequency domains to selected as well as all the genes to reveal the interesting networks of interactions. The approach is successfully applied to Arabidopsis leaf microarray data generated from 31,000 genes observed over 22 time points over 22 days. Three circuits: a circadian gene circuit, an ethylene circuit and a new global circuit showing a hierarchical structure to determine the initiators of leaf senescence are analyzed in detail. Conclusions: We use a totally data-driven approach to form biological hypothesis. Clustering using the power-spectrum analysis helps us identify genes of potential interest. Their dynamics can be captured accurately in the time and frequency domain using the methods of complex and partial Granger causality. With the rise in availability of temporal microarray data, such methods can be useful tools in uncovering the hidden biological interactions. We show our method in a step by step manner with help of toy models as well as a real biological dataset. We also analyse three distinct gene circuits of potential interest to Arabidopsis researchers

The epidemiology of injuries across the weight-training sports

Background: Weight-training sports, including weightlifting, powerlifting, bodybuilding, strongman, Highland Games, and CrossFit, are weight-training sports that have separate divisions for males and females of a variety of ages, competitive standards, and bodyweight classes. These sports may be considered dangerous because of the heavy loads commonly used in training and competition. Objectives: Our objective was to systematically review the injury epidemiology of these weight-training sports, and, where possible, gain some insight into whether this may be affected by age, sex, competitive standard, and bodyweight class. Methods: We performed an electronic search using PubMed, SPORTDiscus, CINAHL, and Embase for injury epidemiology studies involving competitive athletes in these weight-training sports. Eligible studies included peer-reviewed journal articles only, with no limit placed on date or language of publication. We assessed the risk of bias in all studies using an adaption of the musculoskeletal injury review method. Results: Only five of the 20 eligible studies had a risk of bias score ≥75 %, meaning the risk of bias in these five studies was considered low. While 14 of the studies had sample sizes >100 participants, only four studies utilized a prospective design. Bodybuilding had the lowest injury rates (0.12–0.7 injuries per lifter per year; 0.24–1 injury per 1000 h), with strongman (4.5–6.1 injuries per 1000 h) and Highland Games (7.5 injuries per 1000 h) reporting the highest rates. The shoulder, lower back, knee, elbow, and wrist/hand were generally the most commonly injured anatomical locations; strains, tendinitis, and sprains were the most common injury type. Very few significant differences in any of the injury outcomes were observed as a function of age, sex, competitive standard, or bodyweight class. Conclusion: While the majority of the research we reviewed utilized retrospective designs, the weight-training sports appear to have relatively low rates of injury compared with common team sports. Future weight-training sport injury epidemiology research needs to be improved, particularly in terms of the use of prospective designs, diagnosis of injury, and changes in risk exposure

Ultra High Energy Cosmic Rays

The current status of Ultra High Energy Cosmic Rays (UHECR) is reviewed, with emphasis given to theoretical interpretation of the observed events. The galactic and extragalactic origin, in case of astrophysical sources of UHE particles, have the problems either with acceleration to the observed energies or with the fluxes and spectra. Topological defects can naturally produce particles with energies as observed and much higher, but in most cases fail to produce the observed fluxes. Cosmic necklaces and monopole-antimonopole pairs are identified as most plausible sources, which can provide the observed flux and spectrum. The relic superheavy particles are shown to be clustering in the Galactic halo, producing UHECR without Greisen-Zatsepin-Kuzmin cutoff. The Lightest Supersymmetric Particles are discussed as UHE carriers in the Universe.Comment: 10 pages text, 6 ps figures, 1 jpeg figure. Invited talk at TAUP-9

Ferromagnetic transition metal implanted ZnO: a diluted magnetic semiconductor?

Recently theoretical works predict that some semiconductors (e.g. ZnO) doped with magnetic ions are diluted magnetic semiconductors (DMS). In DMS magnetic ions substitute cation sites of the host semiconductor and are coupled by free carriers resulting in ferromagnetism. One of the main obstacles in creating DMS materials is the formation of secondary phases because of the solid-solubility limit of magnetic ions in semiconductor host. In our study transition metal ions were implanted into ZnO single crystals with the peak concentrations of 0.5-10 at.%. We established a correlation between structural and magnetic properties. By synchrotron radiation X-ray diffraction (XRD) secondary phases (Fe, Ni, Co and ferrite nanocrystals) were observed and have been identified as the source for ferromagnetism. Due to their different crystallographic orientation with respect to the host crystal these nanocrystals in some cases are very difficult to be detected by a simple Bragg-Brentano scan. This results in the pitfall of using XRD to exclude secondary phase formation in DMS materials. For comparison, the solubility of Co diluted in ZnO films ranges between 10 and 40 at.% using different growth conditions pulsed laser deposition. Such diluted, Co-doped ZnO films show paramagnetic behaviour. However, only the magnetoresistance of Co-doped ZnO films reveals possible s-d exchange interaction as compared to Co-implanted ZnO single crystals.Comment: 27 pages, 8 figure

Different genes interact with particulate matter and tobacco smoke exposure in affecting lung function decline in the general population

BACKGROUND: Oxidative stress related genes modify the effects of ambient air pollution or tobacco smoking on lung function decline. The impact of interactions might be substantial, but previous studies mostly focused on main effects of single genes. OBJECTIVES: We studied the interaction of both exposures with a broad set of oxidative-stress related candidate genes and pathways on lung function decline and contrasted interactions between exposures. METHODS: For 12679 single nucleotide polymorphisms (SNPs), change in forced expiratory volume in one second (FEV(1)), FEV(1) over forced vital capacity (FEV(1)/FVC), and mean forced expiratory flow between 25 and 75% of the FVC (FEF(25-75)) was regressed on interval exposure to particulate matter >10 microm in diameter (PM10) or packyears smoked (a), additive SNP effects (b), and interaction terms between (a) and (b) in 669 adults with GWAS data. Interaction p-values for 152 genes and 14 pathways were calculated by the adaptive rank truncation product (ARTP) method, and compared between exposures. Interaction effect sizes were contrasted for the strongest SNPs of nominally significant genes (p(interaction)>0.05). Replication was attempted for SNPs with MAF<10% in 3320 SAPALDIA participants without GWAS. RESULTS: On the SNP-level, rs2035268 in gene SNCA accelerated FEV(1)/FVC decline by 3.8% (p(interaction) = 2.5x10(-6)), and rs12190800 in PARK2 attenuated FEV1 decline by 95.1 ml p(interaction) = 9.7x10(-8)) over 11 years, while interacting with PM10. Genes and pathways nominally interacting with PM10 and packyears exposure differed substantially. Gene CRISP2 presented a significant interaction with PM10 (p(interaction) = 3.0x10(-4)) on FEV(1)/FVC decline. Pathway interactions were weak. Replications for the strongest SNPs in PARK2 and CRISP2 were not successful. CONCLUSIONS: Consistent with a stratified response to increasing oxidative stress, different genes and pathways potentially mediate PM10 and tobac smoke effects on lung function decline. Ignoring environmental exposures would miss these patterns, but achieving sufficient sample size and comparability across study samples is challengin

Conservative management for postprostatectomy urinary incontinence

BACKGROUND: Urinary incontinence is common after radical prostatectomy and can also occur in some circumstances after transurethral resection of the prostate (TURP). Conservative management includes pelvic floor muscle training with or without biofeedback, electrical stimulation, extra-corporeal magnetic innervation (ExMI), compression devices (penile clamps), lifestyle changes, or a combination of methods.   OBJECTIVES: To determine the effectiveness of conservative management for urinary incontinence up to 12 months after transurethral, suprapubic, laparoscopic, radical retropubic or perineal prostatectomy, including any single conservative therapy or any combination of conservative therapies.  SEARCH METHODS: We searched the Cochrane Incontinence Group Specialised Register (5 February 2014), CENTRAL (2014, Issue 1), EMBASE (January 2010 to Week 3 2014), CINAHL (January 1982 to 18 January 2014), ClinicalTrials.gov and World Health Organization (WHO) International Clinical Trials Registry Platform (ICTRP) (both searched 29 January 2014), and the reference lists of relevant articles.  SELECTION CRITERIA: Randomised or quasi-randomised controlled trials evaluating conservative interventions for urinary continence in men after prostatectomy.  DATA COLLECTION AND ANALYSIS: Two or more review authors assessed the methodological quality of the trials and abstracted data. We tried to contact several authors of included studies to obtain extra information.  MAIN RESULTS: Fifty trials met the inclusion criteria, 45 in men after radical prostatectomy, four trials after TURP and one trial after either operation. The trials included 4717 men of whom 2736 had an active conservative intervention. There was considerable variation in the interventions, populations and outcome measures. Data were not available for many of the pre-stated outcomes. Men's symptoms improved over time irrespective of management.There was no evidence from eight trials that pelvic floor muscle training with or without biofeedback was better than control for men who had urinary incontinence up to 12 months after radical prostatectomy; the quality of the evidence was judged to be moderate (for example 57% with urinary incontinence in the intervention group versus 62% in the control group, risk ratio (RR) for incontinence after 12 months 0.85, 95% confidence interval (CI) 0.60 to 1.22). One large multi-centre trial of one-to-one therapy showed no difference in any urinary or quality of life outcome measures and had narrow CIs. It seems unlikely that men benefit from one-to-one PFMT therapy after TURP. Individual small trials provided data to suggest that electrical stimulation, external magnetic innervation, or combinations of treatments might be beneficial but the evidence was limited. Amongst trials of conservative treatment for all men after radical prostatectomy, aimed at both treatment and prevention, there was moderate evidence of an overall benefit from pelvic floor muscle training versus control management in terms of reduction of urinary incontinence (for example 10% with urinary incontinence after one year in the intervention groups versus 32% in the control groups, RR for urinary incontinence 0.32, 95% CI 0.20 to 0.51). However, this finding was not supported by other data from pad tests. The findings should be treated with caution because the risk of bias assessment showed methodological limitations. Men in one trial were more satisfied with one type of external compression device, which had the lowest urine loss, compared to two others or no treatment. The effect of other conservative interventions such as lifestyle changes remained undetermined as no trials involving these interventions were identified.  AUTHORS' CONCLUSIONS: The value of the various approaches to conservative management of postprostatectomy incontinence after radical prostatectomy remains uncertain. The evidence is conflicting and therefore rigorous, adequately powered randomised controlled trials (RCTs) which abide by the principles and recommendations of the CONSORT statement are still needed to obtain a definitive answer. The trials should be robustly designed to answer specific well constructed research questions and include outcomes which are important from the patient's perspective in decision making and are also relevant to the healthcare professionals. Long-term incontinence may be managed by an external penile clamp, but there are safety problems