Fast Computation of the Fitness Function for Protein Folding Prediction in a 2D Hydrophobic-Hydrophilic Model

Protein Folding Prediction (PFP) is essentially an energy minimization problem formalised by the definition of a fitness function. Several PFP models have been proposed including the Hydrophobic-Hydrophilic (HP) model, which is widely used as a test-bed for evaluating new algorithms. The calculation of the fitness is the major computational task in determining the native conformation of a protein in the HP model and this paper presents a new efficient search algorithm (ESA) for deriving the fitness value requiring only O(n) complexity in contrast to the full search approach, which takes O(n2). The improved efficiency of ESA is achieved by exploiting some intrinsic properties of the HP model, with a resulting reduction of more than 50% in the overall time complexity when compared with the previously reported Caching Approach, with the added benefit that the additional space complexity is linear instead of quadratic

HIV status, breastfeeding modality at 5 months and postpartum maternal weight changes over 24 months in rural South Africa

ObjectiveTo determine the effect of infant feeding practices on postpartum weight change among HIV-infected and -uninfected women in South Africa.MethodsIn a non-randomised intervention cohort study of antiretroviral therapy-naïve women in South Africa, infants were classified as exclusive (EBF), mixed (MF) or non-breastfed (NBF) at each visit. We analysed infant feeding cumulatively from birth to 5 months using 24-hour feeding history (collected weekly for each of the preceding 7 days). Using generalised estimating equation mixed models, allowing for repeated measures, we compared postpartum weight change (kg) from the first maternal postpartum weight within the first 6 weeks (baseline weight) to each subsequent visit through 24 months among 2340 HIV-infected and -uninfected women with live births and at least two postpartum weight measurements.ResultsHIV-infected (?0.2 kg CI: ?1.7 to 1.3 kg; P = 0.81) and -uninfected women (?0.5 kg; 95% CI: ?2.1 to 1.2 kg; P = 0.58) had marginal non-significant weight loss from baseline to 24 months postpartum. Adjusting for HIV status, socio-demographic, pregnancy-related and infant factors, 5-month feeding modality was not significantly associated with postpartum weight change: weight change by 24 months postpartum, compared to the change in the reference EBF group, was 0.03 kg in NBF (95% CI: ?2.5 to +2.5 kg; P = 0.90) and 0.1 kg in MF (95% CI: ?3.0 to +3.2 kg; P = 0.78).ConclusionHIV-infected and -uninfected women experienced similar weight loss over 24 months. Weight change postpartum was not associated with 5-month breastfeeding modality among HIV-infected and -uninfected women.ObjectifDéterminer l'effet des pratiques d'alimentation des nourrissons sur la variation du poids postpartum chez les femmes infectées et non infectées par le VIH en Afrique du Sud.MéthodesDans une étude de cohorte d'intervention non randomisée sur la thérapie aux antirétroviraux, les nourrissons de femmes naïves pour le traitement en Afrique du Sud, ont été classés comme allaités exclusivement au sein (EBF), recevant une alimentation mixte (MF) ou non allaités au sein (NBF), à chaque visite. Nous avons analysé l'alimentation du nourrisson cumulativement de la naissance à cinq mois, en utilisant l'historique de l'alimentation sur 24 heures (recueillies hebdomadairement pour chacun des sept jours précédents). En utilisant l’équation d'estimation des modèles mixtes généralisés, permettant des mesures répétées, nous avons comparé les changements de poids (kg) postpartum de la première mesure du poids postpartum de la mère endéans les six premières semaines (poids de base) au poids à chaque visite subséquente durant 24 mois chez 2340 femmes infectées et non infectées par le VIH, ayant eu des naissances vivantes et au moins deux mesures du poids postpartum.RésultatsLa perte de poids des femmes infectées (-0,2 kg; IC: -1,7 à 1,3 kg; P = 0,81) et non infectées (0,5 kg, IC95%: -2,1 à 1,2 kg; P = 0,58) par le VIH était marginalement non significative de la base à 24 mois postpartum. En ajustant pour le statut VIH et sociodémographique, pour les facteurs liés à la grossesse et infantiles, le mode d'alimentation sur cinq mois n’étaient pas significativement associé à la variation du poids postpartum; la variation de poids sur 24 mois postpartum comparée à celle dans le groupe EBF de référence, était de 0,03 kg chez les NBF (IC95%: -2,5 à 2,5 kg; P = 0,90) et 0,1 kg chez les MF (IC95%: -3,0 à 3,2 kg; P = 0,78).ConclusionLes femmes infectées et non infectées par le VIH connaissent une perte de poids similaire sur 24 mois. La variation du poids postpartum n'a pas été associée au mode d'allaitement à cinq mois chez les femmes infectées et non infectées par le VIH.ObjetivoDeterminar el efecto de las prácticas de alimentación de los bebés en la variación del peso materno postparto entre mujeres infectadas y no infectadas con VIH en Sudáfrica.MétodosEn una intervención en Sudáfrica no aleatorizada, dentro de un estudio de cohortes de mujeres que no habían recibido anteriormente terapia antirretroviral (naive) – los bebés de se clasificaron como recibiendo exclusivamente el pecho (EP), alimentación mixta (AM), o que no eran amamantados (NA) en cada visita. Hemos analizado la alimentación acumulativa del bebé, desde el nacimiento hasta los cinco meses de edad, utilizando un historial de alimentación de 24 horas (recogido semanalmente para los 7 días anteriores). Utilizando modelos mixtos de ecuaciones de estimación generalizadas, permitiendo medidas repetidas, hemos comparado el cambio de peso (kg) durante el postparto - desde la primera pesada dentro de las primeras seis semanas postparto (peso inicial) con cada visita subsiguiente, durante los 24 meses posteriores, para 2340 mujeres - infectadas con VIH y sin infectar – que dieron a luz bebés nacidos vivos y que tenían recogidas al menos dos pesadas postparto.ResultadosLas mujeres infectadas con VIH (-0.2 kg IC: -1.7 – 1.3 kg; P = 0.81) y aquellas no infectadas (-0.5kg; 95% IC: -2.1 – 1.2 kg; P =0.58) tenían una pérdida de peso marginal y no significativa entre el comienzo del estudio hasta los 24 meses después del parto. Ajustando para el estatus de VIH, los factores sociodemográficos y relacionados con el embarazo y el bebé, la modalidad de alimentación del bebé durante sus cinco primeros meses no estaba significativamente asociada con el cambio de peso postparto: el cambio de peso 24 meses después del parto, comparada con el cambio en referencia al grupo EP, era de 0.03 kg en NA (IC 95%: -2.5 – +2.5 kg; P = 0.90) y 0.1 kg en AM (IC 95%: -3.0 – +3.2 kg; P = 0.78).ConclusiónLas mujeres infectadas con VIH y aquellas sin infección experimentaron una pérdida de peso similar en los 24 meses postparto. El cambio de peso no estaba asociado con la modalidad de amamantamiento entre las mujeres VIH positivas y VIH negativas

How Do Tor Users Interact With Onion Services?

Onion services are anonymous network services that are exposed over the Tor network. In contrast to conventional Internet services, onion services are private, generally not indexed by search engines, and use self-certifying domain names that are long and difficult for humans to read. In this paper, we study how people perceive, understand, and use onion services based on data from 17 semi-structured interviews and an online survey of 517 users. We find that users have an incomplete mental model of onion services, use these services for anonymity and have varying trust in onion services in general. Users also have difficulty discovering and tracking onion sites and authenticating them. Finally, users want technical improvements to onion services and better information on how to use them. Our findings suggest various improvements for the security and usability of Tor onion services, including ways to automatically detect phishing of onion services, more clear security indicators, and ways to manage onion domain names that are difficult to remember.Comment: Appeared in USENIX Security Symposium 201

Over-The-Air Deramping For Multistatic Perimeter Surveillance

This paper explores the use of an over-the-air deramping (OTAD) system as a solution for perimeter surveillance. Over-the-air deramping is a technique for wirelessly synchronising distributed passive FMCW radar nodes to a dual-frequency master FMCW transmitter node. Such a system allows simultaneous monostatic and multistatic measurements for improved clutter resilience, and multiple looks at a target for reduced susceptibility to signal fading due to target scintillation. To prove the latter, a simultaneous monostatic and OTAD bistatic node were set up with a 5 m baseline and a walking person was measured. The results show that signal fading occurs in both the monostatic and the bistatic node, but rarely at the same time. Hence, combining the measurements from the two nodes gives a consistent response from the target. This demonstrates OTAD as a compelling system for a robust perimeter surveillance system

A New Multistatic FMCW Radar Architecture by Over-the-Air Deramping

© 2015 IEEE. Frequency modulated continuous wave (FMCW) radar is widely adopted solution for low-cost, short to medium range sensing applications. However, a multistatic FMCW architecture suitable for meeting the low-cost requirement has yet to be developed. This paper introduces a new FMCW radar architecture that implements a novel technique of synchronizing nodes in a multistatic system, known as over-the-air deramping (OTAD). The architecture uses a dual-frequency design to simultaneously broadcast an FMCW waveform on a lower frequency channel directly to a receiver as a reference synchronization signal, and a higher frequency channel to illuminate the measurement scene. The target echo is deramped in hardware with the synchronization signal. OTAD allows for low-cost multistatic systems with fine range-resolution, and low peak power and sampling rate requirements. Furthermore, the approach avoids problems with direct signal interference. OTAD is shown to be a compelling solution for low-cost multistatic radar systems through the experimental measurements using a newly developed OTAD radar system

A review of hyperspectral remote sensing and its application in vegetation and water resource studies

Multispectral imagery has been used as the data source for water and land observational remote sensing from airborne and satellite systems since the early 1960s. Over the past two decades, advances in sensor technology have made it possible for the collection of several hundred spectral bands. This is commonly referred to as hyperspectral imagery. This review details the differences between multispectral and hyperspectral data; spatial and spectral resolutions and focuses on the application of hyperspectral imagery in water resource studies and, in particular the classification and mapping of land uses and vegetation

Relationship of serum adiponectin and resistin to glucose intolerance and fat topography in south-Asians

Objectives South-Asians have lower adiponectin levels compared to Caucasians. It was not clear however, if this intrinsic feature is related to aspects of glucose metabolism. This study aims to determine the relationship between body fat distribution and adipocytokine in South-Asian subjects by measuring serum adipocytokines, adiposity, insulinemia, and glucose tolerance levels. Methods In this cross-sectional study, 150 South-Asians (80 males, 70 females) were included, 60 had NGT (Control group, Age 51.33 ± 11.5, BMI 27 ± 2.3), 60 had IGT (Age 57.7 ± 12.5, BMI 27.2 ± 2.7), 30 had type 2 DM (Age 49.5 ± 10.9, BMI 28 ± 1.7). Measures of adiposity, adipocytokines and other metabolic parameters were determined. Parameters were measured using the following: a) Plasma glucose by glucose oxidase method b) CRP by immunoturbidimetric method (Roche/Hitachi analyser) c) insulin by Medgenix INS-ELISA immunoenzymetric assay by Biosource (Belgium) d) Leptin, Adiponectin by radioimmunoassay kits by Linco Research (St. Charles MO) e) Resistin by immunoassay kits by Phoenix Pharmaceuticals INC (530 Harbor Boulevard, Belmont CA 94002, USA). Results Adiponectin concentrations were highest in NGT, decreased in IGT and lowest in DMT2, (both p < 0.01). Leptin was significantly higher in DMT2 than IGT and NGT p = 0.02 and 0.04 respectively. There was a significant positive relationships between log adiponectin and 2-hr insulin values, p = 0.028 and history of hypertensions and a ischemic heart disease p = 0.008 with R = 0.65. There was a significant inverse correlation between log adiponectin and resistin, p < 0.01. Conclusion Resistin levels had an inverse correlation with adiponectin levels, indicating an inverse relationship between pro-inflammatory cytokines and adiponectin. Adiponectin levels were related to glucose tolerance

Osteoporosis-pseudoglioma syndrome in South Africa

The osteoporosis-pseudoglioma syndrome (MIM 259770) is a rare autosomal recessive disorder in which bone fragility and frequent fractures are associated with serious ocular changes. The skeletal manifestations resemble those of osteogenesis imperfecta while hyperplasia of the vitreous, eye and corneal opacities often mimics the appearance of intraocular glioma. This disorder was previously reported in a South African family of Indian stock as 'the ocular form of osteogenesis imperfecta'. Terminological discussion followed and it was suggested that these individuals had osteoporosis-pseudoglioma syndrome. This article describes and depicts the manifestations of the disorder and discusses the nosology.DHE