Development of novel multiplex microsatellite polymerase chain reactions to enable high-throughput population genetic studies of Schistosoma haematobium

© 2015 Webster et al. 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. The attached file is the published version of the article

Biodynamics of Hepatitis C Virus in Haemodialysis Patients in Pahang

Introduction: HCV infection is frequent in patients undergoing maintenance haemodialysis, with prevalence between 8 and 10%. Hepatitis C has an adverse effect on both patient and graft survival in those who get renal transplants. There are relatively scarce reports on the natural fluctuation in viral load level in patients on chronic haemodialysis. Materials and Methods: This is a longitudinal short-term three months study, where 27 chronic haemodialysis patients infected with known HCV genotypes were recruited from seven haemodialysis centres in Pahang. Serum samples were collected monthly, both pre- and post-haemodialysis sessions, over a period of three months. Viral RNA was extracted from serum using QIAamp Viral RNA Extraction kit (Qiagen). The HCV viral load was measured using one-step reverse transcriptase qPCR (Applied Biosystems) targeting the 5`HCV non-coding region (5’UTR). The serum α-IFN level was measured using commercial ELISA kit (Amersham, UK). Six biochemical liver function tests (AST, ALP, TP, albumin, ALT and TB) were also done for all pre-haemodialysis samples. Results: All patients showed persistent low level viral load that varied significantly over the study period (p = 0.001). HCV genotype 1 viral load was significantly higher than that of genotype 3. Conclusion: No apparent correlation could be recognized between the viral loads and the corresponding interferon-alpha levels which were detectable in only a few patients during the period of study

A Stochastic Approach to Shortcut Bridging in Programmable Matter

In a self-organizing particle system, an abstraction of programmable matter, simple computational elements called particles with limited memory and communication self-organize to solve system-wide problems of movement, coordination, and configuration. In this paper, we consider a stochastic, distributed, local, asynchronous algorithm for "shortcut bridging", in which particles self-assemble bridges over gaps that simultaneously balance minimizing the length and cost of the bridge. Army ants of the genus Eciton have been observed exhibiting a similar behavior in their foraging trails, dynamically adjusting their bridges to satisfy an efficiency trade-off using local interactions. Using techniques from Markov chain analysis, we rigorously analyze our algorithm, show it achieves a near-optimal balance between the competing factors of path length and bridge cost, and prove that it exhibits a dependence on the angle of the gap being "shortcut" similar to that of the ant bridges. We also present simulation results that qualitatively compare our algorithm with the army ant bridging behavior. Our work gives a plausible explanation of how convergence to globally optimal configurations can be achieved via local interactions by simple organisms (e.g., ants) with some limited computational power and access to random bits. The proposed algorithm also demonstrates the robustness of the stochastic approach to algorithms for programmable matter, as it is a surprisingly simple extension of our previous stochastic algorithm for compression.Comment: Published in Proc. of DNA23: DNA Computing and Molecular Programming - 23rd International Conference, 2017. An updated journal version will appear in the DNA23 Special Issue of Natural Computin

Adapted motivational interviewing to improve the uptake of treatment for glaucoma in Nigeria: study protocol for a randomized controlled trial.

BACKGROUND: Glaucoma is a chronic eye disease associated with irreversible visual loss. In Africa, glaucoma patients often present late, with very advanced disease. One-off procedures, such as laser or surgery, are recommended in Africa because of lack of or poor adherence to medical treatment. However, acceptance of surgery is usually extremely low. To prevent blindness, adherence to treatment needs to improve, using acceptable, replicable and cost-effective interventions. After reviewing the literature and interviewing patients in Bauchi (Nigeria) motivational interviewing (MI) was selected as the intervention for this trial, with adaptation for glaucoma (MIG). MI is designed to strengthen personal motivation for, and commitment to a specific goal by eliciting and exploring a person's reasons for change within an atmosphere of acceptance and compassion. The aim of this study is to assess whether MIG increases the uptake of laser or surgery amongst glaucoma patients where this is the recommended treatment. The hypothesis is that MIG increases the uptake of treatment. This will be the first trial of MI in Africa. METHODS: This is a hospital based, single centre, randomized controlled trial of MIG plus an information sheet on glaucoma and its treatment (the latter being "standard care") compared with standard care alone for glaucoma patients where the treatment recommended is surgery or laser.Those eligible for the trial are adults aged 17 years and above who live within 200 km of Bauchi with advanced glaucoma where the examining ophthalmologist recommends surgery or laser. After obtaining written informed consent, participants will be randomly allocated to MIG plus standard care, or standard care alone. Motivational interviewing will be delivered in Hausa or English by one of two MIG trained personnel. One hundred and fifty participants will be recruited to each arm. The primary outcome is the proportion of participants undergoing laser or surgery within two months of the date given to re attend for the procedure. MIG quality will be assessed using the validated MI treatment integrity scale. DISCUSSION: Motivational interviewing may be an important tool to increase the acceptance of treatment for glaucoma. The approach is potentially scalable and may be useful for other chronic conditions in Africa. TRIAL REGISTRATION: ISRCTN79330571 (Controlled-Trials.com)

Phage typing or CRISPR typing for epidemiological surveillance of Salmonella Typhimurium?

Objective: Salmonella Typhimurium is the most dominant Salmonella serovar around the world. It is associated with foodborne gastroenteritis outbreaks but has recently been associated with invasive illness and deaths. Characterization of S. Typhimurium is therefore very crucial for epidemiological surveillance. Phage typing has been used for decades for subtyping of S. Typhimurium to determine the epidemiological relation among isolates. Recent studies however have suggested that high throughput clustered regular interspaced short palindromic repeats (CRISPR) typing has the potential to replace phage typing. This study aimed to determine the efficacy of highthroughput CRISPR typing over conventional phage typing in epidemiological surveillance and outbreak investigation of S. Typhimurium. Results: In silico analysis of whole genome sequences (WGS) of well-documented phage types of S. Typhimurium reveals the presence of different CRISPR type among strains belong to the same phage type. Furthermore, different phage types of S. Typhimurium share identical CRISPR type. Interestingly, identical spacers were detected among outbreak and non-outbreak associated DT8 strains of S. Typhimurium. Therefore, CRISPR typing is not useful for the epidemiological surveillance and outbreak investigation of S. Typhimurium and phage typing, until it is replaced by WGS, is still the gold standard method for epidemiological surveillance of S. Typhimurium

Performance of Some Durum Wheat Varieties at Kadawa, Kano State of Nigeria

A two-year trial was conducted during the 2001/02 and 2002/03 dry seasons at Kadawa (lat. 110 39'N, long. 080 27'E and 500 m above sea level) to evaluate the performance of twelve durum wheat varieties. The varieties were laid out in Randomized Complete Block Design with three replications. The results revealed that plant height of wheat was influenced by variety in 2002/03 season only while number of tillers/plant, number of grains/spike, grain weight/spike/ 1000-grain weight and grain yield were significantly affected in both seasons. Variety Tody-6 and Anser-8 outyielded the other varieties in 2001/02 and 2002/03, respectively. Thus, the two varieties could be selected for higher yields of durum wheat in the study area. Keywords: Durum wheat, Grain yield, Kadawa, Sudan savanna, Nigeria

In-situ upgrading of Napier grass pyrolysis vapour over microporous and hierarchical mesoporous zeolites

This study presents in-situ upgrading of pyrolysis vapour derived from Napier grass over microporous and mesoporous ZSM-5 catalysts. It evaluates effect of process variables such catalyst–biomass ratio and catalyst type in a vertical fixed bed pyrolysis system at 600 °C, 50 °C/min under 5 L/min nitrogen flow. Increasing catalyst–biomass ratio during the catalytic process with microporous structure reduced production of organic phase bio-oil by approximately 7.0 wt%. Using mesoporous catalyst promoted nearly 4.0 wt% higher organic yield relative to microporous catalyst, which translate to only about 3.0 wt% reduction in organic phase compared to the yield of organic phase from non-catalytic process. GC–MS analysis of bio-oil organic phase revealed maximum degree of deoxygenation of about 36.9% with microporous catalyst compared to the mesoporous catalysts, which had between 39 and 43%. Mesoporous catalysts promoted production olefins and alkanes, normal phenol, monoaromatic hydrocarbons while microporous catalyst favoured the production of alkenes and polyaromatic hydrocarbons. There was no significant increase in the production of normal phenols over microporous catalyst due to its inability to transform the methoxyphenols and methoxy aromatics. This study demonstrated that upgrading of Napier grass pyrolysis vapour over mesoporous ZSM-5 produced bio-oil with improved physicochemical properties

Immunohistochemical evaluation of human epidermal growth factor receptor 2 and estrogen and progesterone receptors in breast carcinoma in Jordan

INTRODUCTION: Although breast carcinoma (BC) is the most common malignancy affecting Jordanian females and the affected population in Jordan is younger than that in the West, no information is available on its biological characteristics. Our aims in this study are to evaluate the expression of estrogen receptor (ER) and progesterone receptor (PR) and Her-2/neu overexpression in BC in Jordan, and to compare the expression of these with other prognostic parameters for BC such as histological type, histological grade, tumor size, patients' age, and number of lymph node metastases. METHOD: This is a retrospective study conducted in the Department of Pathology at Jordan University of Science and Technology. A confirmed 91 cases of BC diagnosed in the period 1995 to 1998 were reviewed and graded. We used immunohistochemistry to evaluate the expression of ER, PR, and Her-2. Immunohistochemical findings were correlated with age, tumor size, grade and axillary lymph node status. RESULTS: Her-2 was overexpressed in 24% of the cases. The mean age of Her-2 positive cases was 42 years as opposed to 53 years among Her-2 negative cases (p = 0.0001). Her-2 expression was inversely related to ER and PR expression. Her-2 positive tumors tended to be larger than Her-2 negative tumors with 35% overexpression among T3 tumors as opposed to 22% among T2 tumors (p = 0.13). Her-2 positive cases tended to have higher rates of axillary metastases, but this did not reach statistical significance. ER and PR positive cases were seen in older patients with smaller tumor sizes. CONCLUSION: Her-2 overexpression was seen in 24% of BC affecting Jordanian females. Her-2 overexpression was associated with young age at presentation, larger tumor size, and was inversely related to ER and PR expression. One-fifth of the carcinomas were Her-2 positive and ER negative. This group appears to represent an aggressive form of BC presenting at a young age with large primary tumors and a high rate of four or more axillary lymph node metastases

Prevalence of Depression among Sudanese Patients with type-2 Diabetes Mellitus

Background: Both diabetes mellitus and depression are common disorders, and when coexist; they lead to poor glycemic control that may ultimately increase the risk of both micro and macrovascular complications. In Sudan, few data are available regarding prevalence of depression among subjects with type -2 diabetes mellitus.Objectives: The aim of the study is to determine the prevalence of depression among Sudanese patients with type-2 diabetes mellitus.Materials and Methods: A cross-sectional descriptive study, carried out among Sudanese patients with type-2 diabetes mellitus who attended medical insurance clinic in Omdurman. The patients gave consent and HADS questionnaire was filled.Results: The study enrolled 400 patients with type 2 diabetes mellitus, 176 (44%) of them had depression. Among those with depression, 52.3% had mild depression, 29.5% and 18.2% of them, had severe and moderate depression, respectively. Sixty three percent of the study group were female. Their ages range from 30-79 years with a mean of 56.6 ±13.The average duration of diabetes was 10.3 years. 76% of patients were physically inactive and 16 (4%) of them were smokers. Fifty six (14%) had family history of psychiatric disorders, 170 (42.5%) of them showed lack of enjoyment, 77 (19.3%) of them lacked laughing, 81(20.3%) of them lost sensation of happiness, 68(17%) of them lost energy, 238 (59.5%) of them neglected their external appearance, 76 (19%) of them showed no enjoyment, and 62 (15.5%) of them lost enjoying reading or watching television.Conclusion: Depression is common among Sudanese patients with type -2 diabetes mellitus, therefore screening for depression should be part of routine clinical evaluation of these patients.Key words: Sudan, diabetes mellitus, depression

Elongation, rooting and acclimatization of micropropagated shoots from mature material of hybrid larch

Factors were defined for elongation, rooting and acclimatization of micropropagated shoots of Larix x eurolepis Henry initiated from short shoot buds of plagiotropic stecklings serially propagated for 9 years from an 8-year-old tree. Initiation and multiplication were on Schenk and Hildebrandt (SH) medium supplemented with 5 μM 6-benzyladenine (BA) and 1 μM indole-butyric acid (IBA). Stem elongation was obtained in 36% of the shoots on SH medium containing 0.5 μM BA and 63% of the remaining non-elongated shoots initiated stem elongation after transfer on SH medium devoid of growth regulators. Rooting involved 2 steps: root induction on Campbell and Durzan mineral salts and Murashige and Skoog organic elements, both half-strength (CD-MS/2), supplemented with 1 μM of both naphthaleneacetic acid (NAA) and IBA, and root elongation following transfer to CD-MS/2 medium devoid of growth regulators. Repeating this 2-step sequence yielded up to 67% rooted shoots. Acclimatization of plantlets ranged from 83% to 100%. Over 300 plants were transferred to the greenhouse; some showed plagiotropic growth