Whole-genome sequencing of ocular Chlamydia trachomatis isolates from Gadarif State, Sudan

Background: Trachoma, caused by ocular Chlamydia trachomatis, is the leading infectious cause of blindness worldwide. Sudan first reported trachoma in the 1930s and has since been consistently endemic. Ocular C. trachomatis previously isolated from trachoma patients in Sudan in 1963 was antigenically identical to an isolate from Saudi Arabia (A/SA1). No contemporary ocular C. trachomatis whole genome sequences have been reported from Sudan. Methods: This study sequenced twenty ocular C. trachomatis isolates to improve understanding of pathogen diversity in North-East Africa and examine for genomic variation specific to Sudan, possibly related to the persistence of trachoma in surveyed communities. High quality, whole genome sequences were obtained from 12/20 isolates. Results: All isolates were serovar A and had tarP and trpA sequences typical of classical, ocular C. trachomatis isolates. The Sudanese isolates formed a closely related subclade within the T2-trachoma clade of C. trachomatis phylogeny distinct from geographically disparate ocular isolates, with little intra-population diversity. We found 333 SNPs that were conserved in Sudanese ocular isolates but rare compared to other ocular C. trachomatis populations, which were focused in two genomic loci (CTA0172-CTA0173 and CTA0482). Conclusions: Limited intra-population diversity and geographical clustering of ocular C. trachomatis suggests minimal transmission between and slow diversification within trachoma-endemic communities. However, diversity may have been higher pre-treatment in these communities. Over-representation of Sudan-specific SNPs in three genes suggests they may have an impact on C. trachomatis growth and transmission in this population

Integration Concept of Injection, Forming and Foaming: A Practical Approach to Manufacture Hybrid Structures

Motivated by the concept of the integrative production systems, the hybrid process of polymer injection molding and sheet metal forming, known as polymer injection forming (PIF), has been introduced to manufacture sheet metal-polymer components in a single operation. Despite the wide potential application of this technology, its implementation in actual industrial production has been hindered due to several challenges; a thick layer of polymer where there is deep deformation, non-uniform deformation due to pressure loss and the opposite phenomena of shrinkage and springback. To mitigate these practical issues, the novel idea of integrating supercritical fluid (Sc.F.) technology with the PIF process is introduced in this work. As the proposed technology is a manufacturing innovation, with no available information in the literature correlating to this concept, two sets of experiments are designed to investigate the feasibility of this integration. In the first set, the effect of blank material and shot volume as design variables were investigated over a range of Sc.F. weight percentage. To improve the cell morphology in experiments with the low-strength sheet material, several other processing scenarios are explored in the second set of experiments. The results of this study clearly demonstrate the capabilities of this concept manufacturing process in terms of initiating the foaming process within the simultaneous injection/forming process, ensuring weight reduction (of up to 16%) and complete elimination of issues related to shrinkage

Modeling of groundwater potential using cloud computing platform: A case study from nineveh plain, Northern Iraq

Knowledge of the groundwater potential, especially in an arid region, can play a major role in planning the sustainable management of groundwater resources. In this study, nine machine learning (ML) algorithms—namely, Artificial Neural Network (ANN), Decision Jungle (DJ), Aver-aged Perceptron (AP), Bayes Point Machine (BPM), Decision Forest (DF), Locally-Deep Support Vector Machine (LD-SVM), Boosted Decision Tree (BDT), Logistic Regression (LG), and Support Vector Machine (SVM)—were run on the Microsoft Azure cloud computing platform to model the groundwater potential. We investigated the relationship between 512 operating boreholes with a specified specific capacity and 14 groundwater-influencing occurrence factors. The unconfined aquifer in the Nineveh plain, Mosul Governorate, northern Iraq, was used as a case study. The groundwater-influencing factors used included elevation, slope, curvature, topographic wetness index, stream power index, soil, land use/land cover (LULC), geology, drainage density, aquifer saturated thickness, aquifer hydraulic conductivity, aquifer specific yield, depth to groundwater, distance to faults, and fault density. Analysis of the contribution of these factors in groundwater potential using information gain ratio indicated that aquifer saturated thickness, rainfall, hydraulic conductivity, depth to groundwater, specific yield, and elevation were the most important factors (average merit > 0.1), followed by geology, fault density, drainage density, soil, LULC, and distance to faults (average merit < 0.1). The average merits for the remaining factors were zero, and thus, these factors were removed from the analysis. When the selected ML classifiers were used to esti-mate groundwater potential in the Azure cloud computing environment, the DJ and BDT models performed the best in terms of all statistical error measures used (accuracy, precision, recall, F-score, and area under the receiver operating characteristics curve), followed by DF and LD-SVM. The probability of groundwater potential from these algorithms was mapped and visualized into five groundwater potential zones: very low, low, moderate, high, and very high, which correspond to the northern (very low to low), southern (moderate), and middle (high to very high) portions of the study area. Using a cloud computing service provides an improved platform for quickly and cheaply running and testing different algorithms for predicting groundwater potential

Promoting independence, health and well-being for older people: : a feasibility study of computer-aided health and social risk appraisal system in primary care

© The Author(s). 2017 Open Access This article is distributed under the terms of the Creative Commons Attribution 4.0 International License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution, and reproduction in any medium, provided you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated. Walters et al, BMC Family Practice (2017), 18:47, DOI: 10.1186/s12875-017-0620-6Abstract Background: With population ageing, research is needed into new low-cost, scalable methods of effective promotion of health and wellbeing for older people. We aimed to assess feasibility, reach and costs of implementing a new tailored computer-aided health and social risk appraisal system in primary care. Methods: Design: Feasibility study. Setting: Five General Practices in London (Ealing) and Hertfordshire, United Kingdom (UK) Participants: Random sample of patients aged 65+years. Intervention: The Multi-dimensional Risk Appraisal for Older people (MRA-O) system includes: 1) Postal questionnaire including health, lifestyle, social and environmental domains; 2) Software system generating a personalised feedback report with advice on health and wellbeing; 3) Follow-up of people with new concerning or complex needs by GPs or practice nurses. Evaluation: Feasibility of implementation; participant wellbeing, functional ability and quality of life; social needs, health risks, potential lifestyle changes; and costs of implementation. Results: Response rates to initial postal invitations were low (526/1550, 34%). Of these, 454/526 (86%) completed MRA-O assessments. Compared to local UK Census data on older people, participants were younger, more were owner-occupiers and fewer were from ethnic minority groups than expected. A range of problems was identified by participants, including pain in last week (269/438, 61.4%), low physical activity (173/453, 38.2%), sedentary lifestyle (174/447, 38.3%), falls (117/439, 26.7%), incontinence (111/441 25.2%), impaired vision 116/451 (25.7%), impaired hearing (145/431, 33.6%), depressed mood (71/451, 15.7%), impaired memory (44/444 9.9%), social isolation (46/449, 10.2%) and loneliness (31/442, 7.0%). Self-rated health was good/excellent in 312/437 (71.4%), and quality of life and well-being were slightly above age-specific population norms. Implementation costs were low. Practices reviewed medical records of 143/454 (31.5%) of participants as a consequence of their responses, and actively followed up 110/454 (24.2%) of their patients. Conclusions: A computer-aided risk appraisal system was feasible for General Practices to implement, yields useful information about health and social problems, and identifies individual needs. Participation rates were however low, particularly for the oldest old, the poorest, and ethnic minority groups, and this type of intervention may increase inequalities in access. Widespread implementation of this approach would require work to address potential inequalities.Peer reviewedFinal Published versio

The Nucleus Accumbens: A Switchboard for Goal-Directed Behaviors

Reward intake optimization requires a balance between exploiting known sources of rewards and exploring for new sources. The prefrontal cortex (PFC) and associated basal ganglia circuits are likely candidates as neural structures responsible for such balance, while the hippocampus may be responsible for spatial/contextual information. Although studies have assessed interactions between hippocampus and PFC, and between hippocampus and the nucleus accumbens (NA), it is not known whether 3-way interactions among these structures vary under different behavioral conditions. Here, we investigated these interactions with multichannel recordings while rats explored an operant chamber and while they performed a learned lever-pressing task for reward in the same chamber shortly afterward. Neural firing and local field potentials in the NA core synchronized with hippocampal activity during spatial exploration, but during lever pressing they instead synchronized more strongly with the PFC. The latter is likely due to transient drive of NA neurons by bursting prefrontal activation, as in vivo intracellular recordings in anesthetized rats revealed that NA up states can transiently synchronize with spontaneous PFC activity and PFC stimulation with a bursting pattern reliably evoked up states in NA neurons. Thus, the ability to switch synchronization in a task-dependent manner indicates that the NA core can dynamically select its inputs to suit environmental demands, thereby contributing to decision-making, a function that was thought to primarily depend on the PFC

Renal function in HIV-infected children and adolescents treated with tenofovir disoproxil fumarate and protease inhibitors

<p>Abstract</p> <p>Background</p> <p>Kidney disease is an important complication in HIV infected people, and this may be related to infection or antiretroviral therapy (ART). Our aim is to assess renal function in HIV infected paediatric patients, who may be particularly affected and are likely to take ART for longer than adults, and investigate the long term role of Tenofovir Disoproxil Fumarate (TDF) alone or co-administered with Ritonavir-boosted Protease Inhibitors (PI).</p> <p>Methods</p> <p>Serum creatinine, phosphate and potassium levels, with estimated Glomerular Filtration Rate (eGFR), had been prospectively evaluated for 2 years in a cohort of HIV infected children and adolescents (age 9-18) on ART, and data analyzed according to the exposure to TDF or simultaneous TDF and PI.</p> <p>Results</p> <p>Forty-nine patients were studied (57% female, mean age 14). Sixty-three percent were treated with ART containing TDF (Group A), and 37% without TDF (Group B); 47% with concomitant use of TDF and PI (Group C) and 53% without this combination (Group D). The groups didn't differ for age, gender or ethnicity. The median creatinine increased in the entire cohort and in all the groups analyzed; eGFR decreased from 143.6 mL/min/1.73 m²at baseline to 128.9 after 2 years (<it>p </it>= 0.006) in the entire cohort. Three patients presented a mild eGFR reduction, all were on TDF+PI. Phosphatemia decreased significantly in the entire cohort (<it>p </it>= 0.0003) and in TDF+PI group (<it>p </it>= 0.0128) after 2 years. Five patients (10%) developed hypophosphatemia (Division of Acquired Immune Deficiency AE grade 1 or 2), and four of them were on TDF+PI.</p> <p>Conclusions</p> <p>Renal function decrease and hypophosphatemia occur over time in HIV infected children and adolescents on ART. The association with co-administration of TDF and PI appears weak, and further studies are warranted.</p

A meta-analysis of long-term effects of conservation agriculture on maize grain yield under rain-fed conditions

Conservation agriculture involves reduced tillage, permanent soil cover and crop rotations to enhance soil fertility and to supply food from a dwindling land resource. Recently, conservation agriculture has been promoted in Southern Africa, mainly for maize-based farming systems. However, maize yields under rain-fed conditions are often variable. There is therefore a need to identify factors that influence crop yield under conservation agriculture and rain-fed conditions. Here, we studied maize grain yield data from experiments lasting 5 years and more under rain-fed conditions. We assessed the effect of long-term tillage and residue retention on maize grain yield under contrasting soil textures, nitrogen input and climate. Yield variability was measured by stability analysis. Our results show an increase in maize yield over time with conservation agriculture practices that include rotation and high input use in low rainfall areas. But we observed no difference in system stability under those conditions. We observed a strong relationship between maize grain yield and annual rainfall. Our meta-analysis gave the following findings: (1) 92% of the data show that mulch cover in high rainfall areas leads to lower yields due to waterlogging; (2) 85% of data show that soil texture is important in the temporal development of conservation agriculture effects, improved yields are likely on well-drained soils; (3) 73% of the data show that conservation agriculture practices require high inputs especially N for improved yield; (4) 63% of data show that increased yields are obtained with rotation but calculations often do not include the variations in rainfall within and between seasons; (5) 56% of the data show that reduced tillage with no mulch cover leads to lower yields in semi-arid areas; and (6) when adequate fertiliser is available, rainfall is the most important determinant of yield in southern Africa. It is clear from our results that conservation agriculture needs to be targeted and adapted to specific biophysical conditions for improved impact