Metagenomic sequencing unravels gene fragments with phylogenetic signatures of O2-tolerant NiFe membrane-bound hydrogenases in lacustrine sediment

Many promising hydrogen technologies utilising hydrogenase enzymes have been slowed by the fact that most hydrogenases are extremely sensitive to O2. Within the group 1 membrane-bound NiFe hydrogenase, naturally occurring tolerant enzymes do exist, and O2 tolerance has been largely attributed to changes in iron–sulphur clusters coordinated by different numbers of cysteine residues in the enzyme’s small subunit. Indeed, previous work has provided a robust phylogenetic signature of O2 tolerance [1], which when combined with new sequencing technologies makes bio prospecting in nature a far more viable endeavour. However, making sense of such a vast diversity is still challenging and could be simplified if known species with O2-tolerant enzymes were annotated with information on metabolism and natural environments. Here, we utilised a bioinformatics approach to compare O2-tolerant and sensitive membrane-bound NiFe hydrogenases from 177 bacterial species with fully sequenced genomes for differences in their taxonomy, O2 requirements, and natural environment. Following this, we interrogated a metagenome from lacustrine surface sediment for novel hydrogenases via high-throughput shotgun DNA sequencing using the Illumina™ MiSeq platform. We found 44 new NiFe group 1 membrane-bound hydrogenase sequence fragments, five of which segregated with the tolerant group on the phylogenetic tree of the enzyme’s small subunit, and four with the large subunit, indicating de novo O2-tolerant protein sequences that could help engineer more efficient hydrogenases

Residual Weighted Learning for Estimating Individualized Treatment Rules

Personalized medicine has received increasing attention among statisticians, computer scientists, and clinical practitioners. A major component of personalized medicine is the estimation of individualized treatment rules (ITRs). Recently, Zhao et al. (2012) proposed outcome weighted learning (OWL) to construct ITRs that directly optimize the clinical outcome. Although OWL opens the door to introducing machine learning techniques to optimal treatment regimes, it still has some problems in performance. In this article, we propose a general framework, called Residual Weighted Learning (RWL), to improve finite sample performance. Unlike OWL which weights misclassification errors by clinical outcomes, RWL weights these errors by residuals of the outcome from a regression fit on clinical covariates excluding treatment assignment. We utilize the smoothed ramp loss function in RWL, and provide a difference of convex (d.c.) algorithm to solve the corresponding non-convex optimization problem. By estimating residuals with linear models or generalized linear models, RWL can effectively deal with different types of outcomes, such as continuous, binary and count outcomes. We also propose variable selection methods for linear and nonlinear rules, respectively, to further improve the performance. We show that the resulting estimator of the treatment rule is consistent. We further obtain a rate of convergence for the difference between the expected outcome using the estimated ITR and that of the optimal treatment rule. The performance of the proposed RWL methods is illustrated in simulation studies and in an analysis of cystic fibrosis clinical trial data.Comment: 48 pages, 3 figure

Association of Physical Activity with Co-morbid Conditions in Geriatric Population

To find out association of physical activity with co-morbid conditions in geriatric population, a cross-sectional study was conducted in different cties of Pakistan in 2015. A total of 114 participants were inducted by non-probability convenience sampling technique. Data was collected after informed verbal consent by a validated questionnaire that is Rapid Assessment of Physical Activity (RAPA). Participants were categorized into two groups i.e. physically active and physically inactive. Data was entered and analyzed in SPSS version 20. There were 66 (57.9%) males and 48 (42.1%) females with mean age of 57.04±7.348 years. Among hypertensive individuals (n=43, 37.7%) there were 39 (90.7%) physically inactive, among individuals having angina (n=17, 14.9%) there were 15 (88.2%) physically inactive. Out of 37 (32.5%) diabetics, 35 (94.6%) were physically inactive. Among individuals suffering from arthritis (n=40, 35.1%), there were 38 (95%) physically inactive. A significant association was found between physical activity and diabetes and arthritis with p-value of 0.048 and 0.029 respectively. Physical activity is significantly associated with diabetes and arthritis in geriatric population. Adequate physical activity should be performed to reduce the risk of co-morbid conditions and improve the quality of life in geriatric population

Ordering of droplets and light scattering in polymer dispersed liquid crystal films

We study the effects of droplet ordering in initial optical transmittance through polymer dispersed liquid crystal (PDLC) films prepared in the presence of an electrical field. The experimental data are interpreted by using a theoretical approach to light scattering in PDLC films that explicitly relates optical transmittance and the order parameters characterizing both the orientational structures inside bipolar droplets and orientational distribution of the droplets. The theory relies on the Rayleigh-Gans approximation and uses the Percus-Yevick approximation to take into account the effects due to droplet positional correlations.Comment: revtex4, 18 pages, 8 figure

The distinct features of microbial 'dysbiosis' of Crohn's disease do not occur to the same extent in their unaffected, genetically linked kindred

Background/Aims: Studying the gut microbiota in unaffected relatives of people with Crohn’s disease (CD) may advance our understanding of the role of bacteria in disease aetiology. Methods: Faecal microbiota composition (16S rRNA gene sequencing), genetic functional capacity (shotgun metagenomics) and faecal short chain fatty acids (SCFA) were compared in unaffected adult relatives of CD children (CDR, n = 17) and adult healthy controls, unrelated to CD patients (HUC, n = 14). The microbiota characteristics of 19 CD children were used as a benchmark of CD ‘dysbiosis’. Results: The CDR microbiota was less diverse (p = 0.044) than that of the HUC group. Local contribution of β-diversity analysis showed no difference in community structure between the CDR and HUC groups. Twenty one of 1,243 (1.8%) operational taxonomic units discriminated CDR from HUC. The metagenomic functional capacity (p = 0.207) and SCFA concentration or pattern were similar between CDR and HUC (p>0.05 for all SCFA). None of the KEGG metabolic pathways were different between these two groups. Both of these groups (HUC and CDR) had a higher microbiota α-diversity (CDR, p = 0.026 and HUC, p<0.001) with a community structure (β-diversity) distinct from that of children with CD. Conclusions: While some alterations were observed, a distinct microbial ‘dysbiosis’, characteristic of CD patients, was not observed in their unaffected, genetically linked kindred

Behavior of thin-walled tubes with combined cross-sectional geometries under oblique loading

Hollow tubes are the most important part of any structure because of their load-bearing capacity, lightweight and inexpensive manufacturing cost. One of the methods for improving the performance under quasi-static loading is to vary the cross-sectional shapes. In the real case, structures are seldom subjected to pure axial or pure bending rather they are subjected to a combination of two load cases i.e. oblique loading. In this paper, the circular cross-section was combined with four different polygonal cross-sections namely tetragon, hexagon, octagon and decagon and a total of 13 geometries were obtained. The buckling behavior of each tube was investigated numerically at various angles of inclination. Each tube was modeled in SOLIDWORKS and then was analyzed in ANSYS. Linear buckling code was used for finding the critical load at various angles ranging from 0° to 14°. The overall result was then compared and it was found that the proposed geometry can be a good alternative over conventional circular tubes in terms of load-bearing capacity at angular load

Uncovering the burden of intentional injuries among children and adolescents in the emergency department

Introduction: In low- and middle-income countries, injuries are a leading cause of mortality in children. Much work has been done in the context of unintentional injuries but there is limited knowledge about intentional injuries among children. The objective of this paper was to understand the characteristics of children with intentional injuries presenting to emergency departments in Pakistan.Methods: The data was from the Pakistan National Emergency Departments Surveillance (Pak-NEDS), conducted from November 2010 to March 2011 in seven major emergency departments of Pakistan. Data on 30,937 children under 18 years of age was collected. This paper reports frequency of intentional injuries and compares patient demographics, nature of injury, and discharge outcome for two categories of intentional injuries: assault and self-inflicted injuries.Results:Intentional injuries presenting to the emergency departments (EDs) accounted for 8.2% (2551/30,937) amongst all other causes for under 18 years. The boy to girl ratio was 1:0.35. Intentional injuries included assault (n = 1679, 65.8%) and self-inflicted injuries (n = 872, 34.2%). Soft tissue injuries were most commonly seen in assault injuries in boys and girls but fractures were more common in self-inflicted injuries in both genders. Conclusion: Intentional injury is one of the reasons for seeking emergency treatment amongst children and a contributor to morbidity in EDs of Pakistan. Moreover, such injuries may be underestimated due to lack of reporting and investigative resources. Early identification may be the first step leading to prevention

Finite element Analysis of Honeycomb filled Metallic Tubes Subjected to Axial Loading

A comprehensive study of buckling behavior of polygonal tubes with honeycomb filler under axial loading is presented in this paper. Honeycomb filled tubes have got a lot more attention due to their strong and stiff behavior with enhanced energy absorption capacity. For simulating the buckling behavior events of finite element models eigen value buckling code was used using the Abaqus/Explicit. This paper firstly investigates the buckling behavior of polygonal tubes without honeycomb filler and then the antipodal with honeycomb filler. The calculated buckling response of polygonal tubes is shown to better resembled when honeycomb filler is used