Hyperdimensional Analysis of Amino Acid Pair Distributions in Proteins

Our manuscript presents a novel approach to protein structure analyses. We have organized an 8-dimensional data cube with protein 3D-structural information from 8706 high-resolution non-redundant protein-chains with the aim of identifying packing rules at the amino acid pair level. The cube contains information about amino acid type, solvent accessibility, spatial and sequence distance, secondary structure and sequence length. We are able to pose structural queries to the data cube using program ProPack. The response is a 1, 2 or 3D graph. Whereas the response is of a statistical nature, the user can obtain an instant list of all PDB-structures where such pair is found. The user may select a particular structure, which is displayed highlighting the pair in question. The user may pose millions of different queries and for each one he will receive the answer in a few seconds. In order to demonstrate the capabilities of the data cube as well as the programs, we have selected well known structural features, disulphide bridges and salt bridges, where we illustrate how the queries are posed, and how answers are given. Motifs involving cysteines such as disulphide bridges, zinc-fingers and iron-sulfur clusters are clearly identified and differentiated. ProPack also reveals that whereas pairs of Lys residues virtually never appear in close spatial proximity, pairs of Arg are abundant and appear at close spatial distance, contrasting the belief that electrostatic repulsion would prevent this juxtaposition and that Arg-Lys is perceived as a conservative mutation. The presented programs can find and visualize novel packing preferences in proteins structures allowing the user to unravel correlations between pairs of amino acids. The new tools allow the user to view statistical information and visualize instantly the structures that underpin the statistical information, which is far from trivial with most other SW tools for protein structure analysis

Material Density Distribution of a Radial Symmetric Product from a Single X-Ray Radiograph

X-ray digital tomographic methods may be classified according to the number of projections and the angular coverage required to obtain the density distribution of the object under study. At one extremity stands computerized tomography which employs multiple projections and wide angular coverage (± π). At the other extremity stand reconstruction methods employing a single projection. As the number of projections decreases, the information provided for the reconstruction becomes more incomplete. The decrease in the information content may sometimes be compensated by the use of a priori knowledge about the product and thus alleviate to some extent the ill-posedness of the problem [l–4]

Do you really follow them? Automatic detection of credulous Twitter users

Online Social Media represent a pervasive source of information able to reach a huge audience. Sadly, recent studies show how online social bots (automated, often malicious accounts, populating social networks and mimicking genuine users) are able to amplify the dissemination of (fake) information by orders of magnitude. Using Twitter as a benchmark, in this work we focus on what we define credulous users, i.e., human-operated accounts with a high percentage of bots among their followings. Being more exposed to the harmful activities of social bots, credulous users may run the risk of being more influenced than other users; even worse, although unknowingly, they could become spreaders of misleading information (e.g., by retweeting bots). We design and develop a supervised classifier to automatically recognize credulous users. The best tested configuration achieves an accuracy of 93.27% and AUC-ROC of 0.93, thus leading to positive and encouraging results.Comment: 8 pages, 2 tables. Accepted for publication at IDEAL 2019 (20th International Conference on Intelligent Data Engineering and Automated Learning, Manchester, UK, 14-16 November, 2019). The present version is the accepted version, and it is not the final published versio

Adaptive Subspace Sampling for Class Imbalance Processing-Some clarifications, algorithm, and further investigation including applications to Brain Computer Interface

© 2020 IEEE. Kohonen's Adaptive Subspace Self-Organizing Map (ASSOM) learns several subspaces of the data where each subspace represents some invariant characteristics of the data. To deal with the imbalance classification problem, earlier we have proposed a method for oversampling the minority class using Kohonen's ASSOM. This investigation extends that study, clarifies some issues related to our earlier work, provides the algorithm for generation of the oversamples, applies the method on several benchmark data sets, and makes an application to a Brain Computer Interface (BCI) problem. First we compare the performance of our method using some benchmark data sets with several state-of-The-Art methods. Finally, we apply the ASSOM-based technique to analyze a BCI based application using electroencephalogram (EEG) datasets. Our results demonstrate the effectiveness of the ASSOM-based method in dealing with imbalance classification problem

Changing Agendas on Sleep, Treatment and Learning in Epilepsy (CASTLE) Sleep-E: A protocol for a randomised controlled trial comparing an online behavioural sleep intervention with standard care in children with Rolandic epilepsy

This is the final version. Available from BMJ Publishing Group via the DOI in this record. INTRODUCTION: Sleep and epilepsy have an established bidirectional relationship yet only one randomised controlled clinical trial has assessed the effectiveness of behavioural sleep interventions for children with epilepsy. The intervention was successful, but was delivered via face-to-face educational sessions with parents, which are costly and non-scalable to population level. The Changing Agendas on Sleep, Treatment and Learning in Epilepsy (CASTLE) Sleep-E trial addresses this problem by comparing clinical and cost-effectiveness in children with Rolandic epilepsy between standard care (SC) and SC augmented with a novel, tailored parent-led CASTLE Online Sleep Intervention (COSI) that incorporates evidence-based behavioural components. METHODS AND ANALYSES: CASTLE Sleep-E is a UK-based, multicentre, open-label, active concurrent control, randomised, parallel-group, pragmatic superiority trial. A total of 110 children with Rolandic epilepsy will be recruited in outpatient clinics and allocated 1:1 to SC or SC augmented with COSI (SC+COSI). Primary clinical outcome is parent-reported sleep problem score (Children's Sleep Habits Questionnaire). Primary health economic outcome is the incremental cost-effectiveness ratio (National Health Service and Personal Social Services perspective, Child Health Utility 9D Instrument). Parents and children (≥7 years) can opt into qualitative interviews and activities to share their experiences and perceptions of trial participation and managing sleep with Rolandic epilepsy. ETHICS AND DISSEMINATION: The CASTLE Sleep-E protocol was approved by the Health Research Authority East Midlands (HRA)-Nottingham 1 Research Ethics Committee (reference: 21/EM/0205). Trial results will be disseminated to scientific audiences, families, professional groups, managers, commissioners and policymakers. Pseudo-anonymised individual patient data will be made available after dissemination on reasonable request. TRIAL REGISTRATION NUMBER: ISRCTN13202325.National Institute for Health and Care Research (NIHR)National Health and Medical Research Council (NHMRC, Australia)Victorian Government’s Operational Infrastructure Support Progra

The impact of measurement errors in the identification of regulatory networks

<p>Abstract</p> <p>Background</p> <p>There are several studies in the literature depicting measurement error in gene expression data and also, several others about regulatory network models. However, only a little fraction describes a combination of measurement error in mathematical regulatory networks and shows how to identify these networks under different rates of noise.</p> <p>Results</p> <p>This article investigates the effects of measurement error on the estimation of the parameters in regulatory networks. Simulation studies indicate that, in both time series (dependent) and non-time series (independent) data, the measurement error strongly affects the estimated parameters of the regulatory network models, biasing them as predicted by the theory. Moreover, when testing the parameters of the regulatory network models, p-values computed by ignoring the measurement error are not reliable, since the rate of false positives are not controlled under the null hypothesis. In order to overcome these problems, we present an improved version of the Ordinary Least Square estimator in independent (regression models) and dependent (autoregressive models) data when the variables are subject to noises. Moreover, measurement error estimation procedures for microarrays are also described. Simulation results also show that both corrected methods perform better than the standard ones (i.e., ignoring measurement error). The proposed methodologies are illustrated using microarray data from lung cancer patients and mouse liver time series data.</p> <p>Conclusions</p> <p>Measurement error dangerously affects the identification of regulatory network models, thus, they must be reduced or taken into account in order to avoid erroneous conclusions. This could be one of the reasons for high biological false positive rates identified in actual regulatory network models.</p

Late cardiac events after childhood cancer: Methodological aspects of the pan-european study pancaresurfup

Background and Aim Childhood cancer survivors are at high risk of long-Termadverse effects of cancer and its treatment, including cardiac events. The pan-European PanCareSurFup study determined the incidence and risk factors for cardiac events among childhood cancer survivors. The aim of this article is to describe the methodology of the cardiac cohort and nested case-control study within PanCareSurFup. Methods Eight data providers in Europe participating in PanCareSurFup identified and validated symptomatic cardiac events in their cohorts of childhood cancer survivors. Data onsymptomatic heart failure, ischemia, pericarditis, valvular disease and arrhythmia were collected and graded according to the Criteria for Adverse Events. Detailed treatment data, data on potential confounders, lifestyle related risk factors and general health problems were collected. Results The PanCareSurFup cardiac cohort consisted of 59,915 5-year childhood cancer survivors with malignancies diagnosed between 1940 and 2009 and classified according to the International Classification of Childhood Cancer 3. Different strategies were used to identify cardiac events such as record linkage to population/ hospital or regional based databases, and patient-And general practitioner-based questionnaires. Conclusion The cardiac study of the European collaborative research project PanCareSurFup will provide the largest cohort of 5-year childhood cancer survivors with systematically ascertained and validated data on symptomatic cardiac events. The result of this study can provide information to minimize the burden of cardiac events in childhood cancer survivors by tailoring the follow-up of childhood cancer survivors at high risk of cardiac adverse events, transferring this knowledge into evidence-based clinical practice guidelines and providing a platformfor future research studies in childhood cancer patients. © 2016 Feijen et al. This 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

A typhoid fever outbreak in a slum of South Dumdum municipality, West Bengal, India, 2007: Evidence for foodborne and waterborne transmission

<p>Abstract</p> <p>Background</p> <p>In April 2007, a slum of South Dumdum municipality, West Bengal reported an increase in fever cases. We investigated to identify the agent, the source and to propose recommendations.</p> <p>Methods</p> <p>We defined a suspected case of typhoid fever as occurrence of fever for ≥ one week among residents of ward 1 of South Dumdum during February – May 2007. We searched for suspected cases in health care facilities and collected blood specimens. We described the outbreak by time, place and person. We compared probable cases (Widal positive >= 1:80) with neighbourhood-matched controls. We assessed the environment and collected water specimens.</p> <p>Results</p> <p>We identified 103 suspected cases (Attack rate: 74/10,000, highest among 5–14 years old group, no deaths). Salmonella (enterica) Typhi was isolated from one of four blood specimens and 65 of 103 sera were >= 1:80 Widal positive. The outbreak started on 13 February, peaked twice during the last week of March and second week of April and lasted till 27 April. Suspected cases clustered around three public taps. Among 65 probable cases and 65 controls, eating milk products from a sweet shop (Matched odds ratio [MOR]: 6.2, 95% confidence interval [CI]: 2.4–16, population attributable fraction [PAF]: 53%) and drinking piped water (MOR: 7.3, 95% CI: 2.5–21, PAF-52%) were associated with illness. The sweet shop food handler suffered from typhoid in January. The pipelines of intermittent non-chlorinated water supply ran next to an open drain connected with sewerage system and water specimens showed faecal contamination.</p> <p>Conclusion</p> <p>The investigation suggested that an initial foodborne outbreak of typhoid led to the contamination of the water supply resulting in a secondary, waterborne wave. We educated the food handler, repaired the pipelines and ensured chlorination of the water.</p

Search for CP violation in D+→ϕπ+ and D+s→K0Sπ+ decays

A search for CP violation in D + → ϕπ + decays is performed using data collected in 2011 by the LHCb experiment corresponding to an integrated luminosity of 1.0 fb−1 at a centre of mass energy of 7 TeV. The CP -violating asymmetry is measured to be (−0.04 ± 0.14 ± 0.14)% for candidates with K − K + mass within 20 MeV/c 2 of the ϕ meson mass. A search for a CP -violating asymmetry that varies across the ϕ mass region of the D + → K − K + π + Dalitz plot is also performed, and no evidence for CP violation is found. In addition, the CP asymmetry in the D+s→K0Sπ+ decay is measured to be (0.61 ± 0.83 ± 0.14)%