Theory of phase segregation in DNA assemblies containing two different base pair sequence types

Spontaneous pairing of homologous DNA sequences – a challenging subject in molecular biophysics, often referred to as ‘homology recognition’ – ha s been observed in vitro for several DNA system s a . One of th e se experiments involved liquid crystalline quasi - columnar phases formed by a mixture of two kinds of oligo mer of double stranded DNA . Both oligomer types were of the same length and identical stoichiometric base - pair composition , but the base - pairs followed a different order . Phase segregation of the two DNA types was observed in the experiments , wit h the formation of boundaries between domai ns rich in molecules of one type (order) of base pair sequence . We formulate here a modified ‘ X - Y model ’ for phase segregation in such assemblies , obtain approximate solutions of the model , compare analytical results to Monte Carlo simulations, and rationalize past experimental observations . This study, furthermore , reveals the factors that affect the degree of segregat ion . Such information c ould be used in planning new versions of similar segregation experiments , needed for deepen i ng our understanding of forces that might be involved , e.g., in gene - gene recognition

Evaluating e-Government services from a citizens' prespective: A reference process model

Evaluating and optimizing e-government services is imperative for governments especially due to the capacity of e-services to transform public administrations and assist the interactions of governments with citizens, businesses and other government agencies. Existing widely applied evaluation approaches neglect to incorporate citizens’ satisfaction measures. Several citizen satisfaction models and indicators have been suggested in academia; however a reference process model that can assist practitioners to apply these performance measures is missing. In this paper we draw upon the evaluation approach proposed by the EU funded project CEES and propose a reference process model that captures re-usable practices for e-government evaluation from a citizens’ perspective. The novelty of the proposed approach is that using DEA for evaluating the e-services the assessment results in suggestions for strategic improvement of the e-services.EU FP7 Marie Curie People Project “CEES - Citizen oriented Evaluation of E-Government Systems” (reference IAPP-2008-230658

Predicting protein-ligand affinity with a random matrix framework

Rapid determination of whether a candidate compound will bind to a particular target receptor remains a stumbling block in drug discovery. We use an approach inspired by random matrix theory to decompose the known ligand set of a target in terms of orthogonal "signals" of salient chemical features, and distinguish these from the much larger set of ligand chemical features that are not relevant for binding to that particular target receptor. After removing the noise caused by finite sampling, we show that the similarity of an unknown ligand to the remaining, cleaned chemical features is a robust predictor of ligand-target affinity, performing as well or better than any algorithm in the published literature. We interpret our algorithm as deriving a model for the binding energy between a target receptor and the set of known ligands, where the underlying binding energy model is related to the classic Ising model in statistical physics.This research was funded by a grant from Roche Pharmaceuticals. A.A.L. acknowledges the support of a Fulbright Fellowship. L.J.C. was supported by a Next Generation Fellowship, and a Marie Curie Career Integration Grant (Evo-Couplings, Grant 631609). M.P.B. is an investigator of the Simons Foundation, and also acknowledges support from the National Science Foundation through DMS-1411694

Finite-size scaling considerations on the ground state microcanonical temperature in entropic sampling simulations

In this work we discuss the behavior of the microcanonical temperature $\frac{\partial S(E)}{\partial E}$ obtained by means of numerical entropic sampling studies. It is observed that in almost all cases the slope of the logarithm of the density of states $S(E)$ is not infinite in the ground state, since as expected it should be directly related to the inverse temperature $\frac{1}{T}$. Here we show that these finite slopes are in fact due to finite-size effects and we propose an analytic expression $a\ln(bL)$ for the behavior of $\frac{\varDelta S}{\varDelta E}$ when $L\rightarrow\infty$. To test this idea we use three distinct two-dimensional square lattice models presenting second-order phase transitions. We calculated by exact means the parameters $a$ and $b$ for the two-states Ising model and for the $q=3$ and $4$ states Potts model and compared with the results obtained by entropic sampling simulations. We found an excellent agreement between exact and numerical values. We argue that this new set of parameters $a$ and $b$ represents an interesting novel issue of investigation in entropic sampling studies for different models

Optimizing hardware function evaluation

Published versio

Associations between active travel and weight, blood pressure and diabetes in six middle income countries: a cross-sectional study in older adults

BACKGROUND: There is little published data on the potential health benefits of active travel in low and middle-income countries. This is despite increasing levels of adiposity being linked to increases in physical inactivity and non-communicable diseases. This study will examine: (1) socio-demographic correlates of using active travel (walking or cycling for transport) among older adults in six populous middle-income countries (2) whether use of active travel is associated with adiposity, systolic blood pressure and self-reported diabetes in these countries. METHODS: Data are from the WHO Study on Global Ageing and Adult Health (SAGE) of China, India, Mexico, Ghana, Russia and South Africa with a total sample size of 40,477. Correlates of active travel (≥150 min/week) were examined using logistic regression. Logistic and linear regression analyses were used to examine health related outcomes according to three groups of active travel use per week. RESULTS: 46.4% of the sample undertook ≥150 min of active travel per week (range South Africa: 21.9% Ghana: 57.8%). In pooled analyses those in wealthier households were less likely to meet this level of active travel (Adjusted Risk Ratio (ARR) 0.77, 95% Confidence Intervals 0.67; 0.88 wealthiest fifth vs. poorest). Older people and women were also less likely to use active travel for ≥150 min per week (ARR 0.71, 0.62; 0.80 those aged 70+ years vs. 18-29 years old, ARR 0.82, 0.74; 0.91 women vs. men). In pooled fully adjusted analyses, high use of active travel was associated with lower risk of overweight (ARR 0.71, 0.59; 0.86), high waist-to-hip ratio (ARR 0.71, 0.61; 0.84) and lower BMI (-0.54 kg/m(2), -0.98;- 0.11). Moderate (31-209 min/week) and high use (≥210 min/week) of active travel was associated with lower waist circumference (-1.52 cm (-2.40; -0.65) and -2.16 cm (3.07; -1.26)), and lower systolic blood pressure (-1.63 mm/Hg (-3.19; -0.06) and -2.33 mm/Hg (-3.98; -0.69)). CONCLUSIONS: In middle-income countries use of active travel for ≥150 min per week is more common in lower socio-economic groups and appears to confer similar health benefits to those identified in high-income settings. Efforts to increase active travel levels should be integral to strategies to maintain healthy weight and reduce disease burden in these settings

On Budget-Feasible Mechanism Design for Symmetric Submodular Objectives

We study a class of procurement auctions with a budget constraint, where an auctioneer is interested in buying resources or services from a set of agents. Ideally, the auctioneer would like to select a subset of the resources so as to maximize his valuation function, without exceeding a given budget. As the resources are owned by strategic agents however, our overall goal is to design mechanisms that are truthful, budget-feasible, and obtain a good approximation to the optimal value. Budget-feasibility creates additional challenges, making several approaches inapplicable in this setting. Previous results on budget-feasible mechanisms have considered mostly monotone valuation functions. In this work, we mainly focus on symmetric submodular valuations, a prominent class of non-monotone submodular functions that includes cut functions. We begin first with a purely algorithmic result, obtaining a $\frac{2e}{e-1}$-approximation for maximizing symmetric submodular functions under a budget constraint. We view this as a standalone result of independent interest, as it is the best known factor achieved by a deterministic algorithm. We then proceed to propose truthful, budget feasible mechanisms (both deterministic and randomized), paying particular attention on the Budgeted Max Cut problem. Our results significantly improve the known approximation ratios for these objectives, while establishing polynomial running time for cases where only exponential mechanisms were known. At the heart of our approach lies an appropriate combination of local search algorithms with results for monotone submodular valuations, applied to the derived local optima.Comment: A conference version appears in WINE 201

Evaluating citizen satisfaction and prioritizing their needs based on citizens' complaint data

© 2019 by the authors. Citizen Relationship Management (CiRM) is one of the important matters in citizen-centric e-government. In fact, the most important purpose of e-government is to satisfy citizens. The '137 system' is one of the most important ones based on the citizen-centric that is a municipality phone based request/response system. The aim of this research is a data-mining of a '137 system' (citizens' complaint system) of the first district of Bojnourd municipality in Iran, to prioritize the urban needs and to estimate citizens' satisfaction. To reach this, the K-means and Bees Algorithms (BA) were used. Each of these two algorithms was executed using two different methods. In the first method, prioritization and estimation of satisfaction were done separately, whereas in the second method, prioritization and estimation of satisfaction were done simultaneously. To compare the clustering results in the two methods, an index was presented quantitatively. The results showed the superiority of the second method. The index of the second method for the first needs in K-means was 0.299 more than the first method and it was the same in two methods in BA. Also, the results of the BA clustering were better at it because of the S (silhouette) and CH (Calinski-Harabasz) indexes. Considering the final prioritization done by the two algorithms in two methods, the primary needs included asphalt, so specific schemes should be considered

Rural, urban and migrant differences in noncommunicable disease risk-factors in middle income countries: a cross-sectional study of WHO-SAGE Data

Understanding how urbanisation and rural-urban migration influence risk-factors for non-communicable disease (NCD) is crucial for developing effective preventative strategies globally. This study compares NCD risk-factor prevalence in urban, rural and migrant populations in China, Ghana, India, Mexico, Russia and South Africa.Study participants were 39,436 adults within the WHO Study on global AGEing and adult health (SAGE), surveyed 2007-2010. Risk ratios (RR) for each risk-factor were calculated using logistic regression in country-specific and all country pooled analyses, adjusted for age, sex and survey design. Fully adjusted models included income quintile, marital status and education.Regular alcohol consumption was lower in migrant and urban groups than in rural groups (pooled RR and 95%CI: 0.47 (0.31-0.68); 0.58, (0.46-0.72), respectively). Occupational physical activity was lower (0.86 (0.72-0.98); 0.76 (0.65-0.85)) while active travel and recreational physical activity were higher (pooled RRs for urban groups; 1.05 (1.00-1.09), 2.36 (1.95-2.83), respectively; for migrant groups: 1.07 (1.0 -1.12), 1.71 (1.11-2.53), respectively). Overweight, raised waist circumference and diagnosed diabetes were higher in urban groups (1.19 (1.04-1.35), 1.24 (1.07-1.42), 1.69 (1.15-2.47), respectively). Exceptions to these trends exist: obesity indicators were higher in rural Russia; active travel was lower in urban groups in Ghana and India; and in South Africa, urban groups had the highest alcohol consumption.Migrants and urban dwellers had similar NCD risk-factor profiles. These were not consistently worse than those seen in rural dwellers. The variable impact of urbanisation on NCD risk must be considered in the design and evaluation of strategies to reduce the growing burden of NCDs globally

Implications of sperm banking for health-related quality of life up to 1 year after cancer diagnosis.

Sperm banking is recommended for all men diagnosed with cancer where treatment is associated with risk of long-term gonadatoxicity, to offer the opportunity of fatherhood and improved quality of life. However, uptake of sperm banking is lower than expected and little is known about why men refuse. Our aims were to determine: (i) demographic and medical variables associated with decisions about banking and (ii) differences in quality of life between bankers and non-bankers at diagnosis (Time 1 (T1)) and 1 year later (Time 2 (T2))