Protein structure similarity from principle component correlation analysis

BACKGROUND: Owing to rapid expansion of protein structure databases in recent years, methods of structure comparison are becoming increasingly effective and important in revealing novel information on functional properties of proteins and their roles in the grand scheme of evolutionary biology. Currently, the structural similarity between two proteins is measured by the root-mean-square-deviation (RMSD) in their best-superimposed atomic coordinates. RMSD is the golden rule of measuring structural similarity when the structures are nearly identical; it, however, fails to detect the higher order topological similarities in proteins evolved into different shapes. We propose new algorithms for extracting geometrical invariants of proteins that can be effectively used to identify homologous protein structures or topologies in order to quantify both close and remote structural similarities. RESULTS: We measure structural similarity between proteins by correlating the principle components of their secondary structure interaction matrix. In our approach, the Principle Component Correlation (PCC) analysis, a symmetric interaction matrix for a protein structure is constructed with relationship parameters between secondary elements that can take the form of distance, orientation, or other relevant structural invariants. When using a distance-based construction in the presence or absence of encoded N to C terminal sense, there are strong correlations between the principle components of interaction matrices of structurally or topologically similar proteins. CONCLUSION: The PCC method is extensively tested for protein structures that belong to the same topological class but are significantly different by RMSD measure. The PCC analysis can also differentiate proteins having similar shapes but different topological arrangements. Additionally, we demonstrate that when using two independently defined interaction matrices, comparison of their maximum eigenvalues can be highly effective in clustering structurally or topologically similar proteins. We believe that the PCC analysis of interaction matrix is highly flexible in adopting various structural parameters for protein structure comparison

Three-Dimensional Magnetic Reconnection With a Spatially Confined X-Line Extent: Implications for Dipolarizing Flux Bundles and the Dawn-Dusk Asymmetry

Using 3‐D particle‐in‐cell simulations, we study magnetic reconnection with the X‐line being spatially confined in the current direction. We include thick current layers to prevent reconnection at two ends of a thin current sheet that has a thickness on an ion inertial (di) scale. The reconnection rate and outflow speed drop significantly when the extent of the thin current sheet in the current direction is urn:x-wiley:jgra:media:jgra54890:jgra54890-math-0001. When the thin current sheet extent is long enough, we find that it consists of two distinct regions; a suppressed reconnecting region (on the ion‐drifting side) exists adjacent to the active region where reconnection proceeds normally as in a 2‐D case with a typical fast rate value ≃0.1. The extent of this suppression region is ≃O(10di), and it suppresses reconnection when the thin current sheet extent is comparable or shorter. The time scale of current sheet thinning toward fast reconnection can be translated into the spatial scale of this suppression region, because electron drifts inside the ion diffusion region transport the reconnected magnetic flux, which drives outflows and furthers the current sheet thinning, away from this region. This is a consequence of the Hall effect in 3‐D. While the existence of this suppression region may explain the shortest possible azimuthal extent of dipolarizing flux bundles at Earth, it may also explain the dawn‐dusk asymmetry observed at the magnetotail of Mercury, which has a global dawn‐dusk extent much shorter than that of Earth.publishedVersio

Seeing Tree Structure from Vibration

Humans recognize object structure from both their appearance and motion; often, motion helps to resolve ambiguities in object structure that arise when we observe object appearance only. There are particular scenarios, however, where neither appearance nor spatial-temporal motion signals are informative: occluding twigs may look connected and have almost identical movements, though they belong to different, possibly disconnected branches. We propose to tackle this problem through spectrum analysis of motion signals, because vibrations of disconnected branches, though visually similar, often have distinctive natural frequencies. We propose a novel formulation of tree structure based on a physics-based link model, and validate its effectiveness by theoretical analysis, numerical simulation, and empirical experiments. With this formulation, we use nonparametric Bayesian inference to reconstruct tree structure from both spectral vibration signals and appearance cues. Our model performs well in recognizing hierarchical tree structure from real-world videos of trees and vessels.Comment: ECCV 2018. The first two authors contributed equally to this work. Project page: http://tree.csail.mit.edu

Constructing a Stochastic Model of Bumblebee Flights from Experimental Data

PMCID: PMC3592844This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited

Views of new internal medicine faculty of their preparedness and competence in physician-patient communication

BACKGROUND: We sought to assess self-rated importance of the medical interview to clinical practice and competence in physician-patient communication among new internal medicine faculty at an academic medical center. METHODS: Since 2001, new internal medicine faculty at the Mayo Clinic College of Medicine (Rochester, Minnesota) have completed a survey on physician-patient communication. The survey asks the new faculty to rate their overall competence in medical interviewing, the importance of the medical interview to their practice, their confidence and adequacy of previous training in handling eight frequently encountered challenging communication scenarios, and whether they would benefit from additional communication training. RESULTS: Between 2001 and 2004, 75 general internists and internal medicine subspecialists were appointed to the faculty, and of these, 58 (77%) completed the survey. The faculty rated (on a 10-point scale) the importance of the medical interview higher than their competence in interviewing; this difference was significant (average ± SD, 9.4 ± 1.0 vs 7.7 ± 1.2, P < .001). Similar results were obtained by sex, age, specialty, years since residency or fellowship training, and perceived benefit of training. Experienced faculty rated their competence in medical interviewing and the importance of the medical interview higher than recent graduates (ie, less than one year since training). For each challenging communication scenario, the new faculty rated the adequacy of their previous training in handling the scenario relatively low. A majority (57%) said they would benefit from additional communication training. CONCLUSION: Although new internal medicine faculty rate high the importance of the medical interview, they rate their competence and adequacy of previous training in medical interviewing relatively low, and many indicate that they would benefit from additional communication training. These results should encourage academic medical centers to make curricula in physician-patient communication available to their faculty members because many of them not only care for patients, but also teach clinical skills, including communication skills, to trainees

Obstetric anal sphincter injury: a systematic review of information available on the internet.

OBJECTIVE: There is no systematic evaluation of online health information pertaining to obstetric anal sphincter injury. Therefore, we evaluated the accuracy, credibility, reliability, and readability of online information concerning obstetric anal sphincter injury. MATERIALS AND METHODS: Multiple search engines were searched. The first 30 webpages were identified for each keyword and considered eligible if they provided information regarding obstetric anal sphincter injury. Eligible webpages were assessed by two independent researchers for accuracy (prioritised criteria based upon the RCOG Third and Fourth Degree Tear guideline); credibility; reliability; and readability. RESULTS: Fifty-eight webpages were included. Seventeen webpages (30%) had obtained Health On the Net certification, or Information Standard approval and performed better than those without such approvals (p = 0.039). The best overall performing website was http://www.pat.nhs.uk (score of 146.7). A single webpage (1%) fulfilled the entire criteria for accuracy with a score of 18: www.tamesidehospital.nhs.uk . Twenty-nine webpages (50%) were assessed as credible (scores ≥7). A single webpage achieved a maximum credibility score of 10: www.meht.nhs.uk . Over a third (21 out of 58) were rated as poor or very poor. The highest scoring webpage was http://www.royalsurrey.nhs.uk (score 62). No webpage met the recommended Flesch Reading Ease Score above 70. The intra-class coefficient between researchers was 0.98 (95% CI 0.96-0.99) and 0.94 (95% CI 0.89-0.96) for accuracy and reliability assessments. CONCLUSION: Online information concerning obstetric anal sphincter injury often uses language that is inappropriate for a lay audience and lacks sufficient accuracy, credibility, and reliability

Validating child vaccination status in a demographic surveillance system using data from a clinical cohort study: evidence from rural South Africa

&lt;p&gt;&lt;b&gt;Background:&lt;/b&gt; Childhood vaccination coverage can be estimated from a range of sources. This study aims to validate vaccination data from a longitudinal population-based demographic surveillance system (DSS) against data from a clinical cohort study.&lt;/p&gt; &lt;p&gt;&lt;b&gt;Methods:&lt;/b&gt; The sample includes 821 children in the Vertical Transmission cohort Study (VTS), who were born between December 2001 and April 2005, and were matched to the Africa Centre DSS, in northern KwaZulu-Natal. Vaccination information in the surveillance was collected retrospectively, using standardized questionnaires during bi-annual household visits, when the child was 12 to 23 months of age. DSS vaccination information was based on extraction from a vaccination card or, if the card was not available, on maternal recall. In the VTS, vaccination data was collected at scheduled maternal and child clinic visits when a study nurse administered child vaccinations. We estimated the sensitivity of the surveillance in detecting vaccinations conducted as part of the VTS during these clinic visits.&lt;/p&gt; &lt;p&gt;&lt;b&gt;Results:&lt;/b&gt; Vaccination data in matched children in the DSS was based on the vaccination card in about two-thirds of the cases and on maternal recall in about one-third. The sensitivity of the vaccination variables in the surveillance was high for all vaccines based on either information from a South African Road-to-Health (RTH) card (0.94-0.97) or maternal recall (0.94-0.98). Addition of maternal recall to the RTH card information had little effect on the sensitivity of the surveillance variable (0.95-0.97). The estimates of sensitivity did not vary significantly, when we stratified the analyses by maternal antenatal HIV status. Addition of maternal recall of vaccination status of the child to the RTH card information significantly increased the proportion of children known to be vaccinated across all vaccines in the DSS.&lt;/p&gt; &lt;p&gt;&lt;b&gt;Conclusion:&lt;/b&gt; Maternal recall performs well in identifying vaccinated children aged 12-23 months (both in HIV-infected and HIV-uninfected mothers), with sensitivity similar to information extracted from vaccination cards. Information based on both maternal recall and vaccination cards should be used if the aim is to use surveillance data to identify children who received a vaccination.&lt;/p&gt

The effectiveness of neuromuscular warm-up strategies, that require no additional equipment, for preventing lower limb injuries during sports participation: a systematic review

PMCID: PMC3408383The electronic version of this article is the complete one and can be found online at: http://www.biomedcentral.com/1741-7015/10/75. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited

Segregation discovery in a social network of companies

We introduce a framework for a data-driven analysis of segregation of minority groups in social networks, and challenge it on a complex scenario. The framework builds on quantitative measures of segregation, called segregation indexes, proposed in the social science literature. The segregation discovery problem consists of searching sub-graphs and sub-groups for which a reference segregation index is above a minimum threshold. A search algorithm is devised that solves the segregation problem. The framework is challenged on the analysis of segregation of social groups in the boards of directors of the real and large network of Italian companies connected through shared directors

Shift Work Is Not Associated with High Blood Pressure or Prevalence of Hypertension

Background: Working mostly at night has been suggested to be associated with upset of chronobiological rhythms and high blood pressure, but the evidence from epidemiological studies is weak. Methods: In a cross-sectional survey, we evaluated the association between shift work and blood pressure, pre-hypertension and hypertension. In total, 493 nurses, nurse technicians and assistants, were selected at random in a large general hospital setting. Hypertension was diagnosed by the mean of four automatic blood pressure readings $140/ 90 mmHg or use of blood pressure lowering agents, and pre-hypertension by systolic blood pressure$120–139 or diastolic blood pressure $80–89 mmHg. Risk factors for hypertension were evaluated by a standardized questionnaire and anthropometric measurements. The association between the shift of work and blood pressure, pre-hypertension and hypertension was explored using univariate and multivariate analyses that controlled for risk factors for hypertension by covariance analysis and modified Poisson regression. Results: The mean age of the participants was 34.369.4 years and 88.2 % were women. Night shift workers were older, more frequently married or divorced, and less educated. The prevalence of hypertension in the whole sample was 16%, and 28% had pre-hypertension. Blood pressure (after adjustment for confounding) was not different in day and night shift workers. The prevalence of hypertension and pre-hypertension by shift work was not different in the univariate analysis and afte