96 research outputs found

    Rapid amplification of the RM-Yplex assay

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    A multiplex PCR assay consisting of 13 Rapidly Mutating Y STR loci called RM-Yplex was previously developed. Platinum® Taq DNA polymerase was used to amplify the 13 Y STR loci in a single reaction at an amplification time of approximately 2.5 h. In order to shorten the process with reliable results, two DNA polymerases were tested with the multiplex. Phusion® Flash High Fidelity, TAKARA Z-taqTM, and Platinum® Taq DNA polymerases were investigated for conducting RM-Yplex assay at various PCR cycling conditions. Rapid, robust, and efficient amplification of all the markers within the multiplex were achieved. The amplification time was reduced from 2.5 h to less than 28 min with Phusion® Flash High Fidelity DNA polymerase using Veriti® PCR thermal cycler

    Development, Validation and Applications of a Novel Multiplex Assay RM-Yplex Amplifying 13 Rapidly Mutating Y Chromosome Short Tandem Repeat Regions

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    A polymerase chain reaction (PCR) multiplex assay capable of amplifying 13 rapidly mutating Y chromosome short tandem repeats (RM Y-STRs) simultaneously was developed and optimised. This multiplex assay which was termed RM-Yplex is the first to include all 13 RM Y-STRs including DYF387S1, DYF399S1, DYF403S1a/b, DYF404S1, DYS449, DYS518, DYS526a/b DYS547, DYS570, DYS576, DYS612, DYS626 and DYS627. A developmental validation was performed following the Scientific Working Group for DNA Analysis Methods (SWGDAM) revised guidelines. Robustness and limitations of the assay were demonstrated through a range of studies including reproducibility, sensitivity, specificity, stability and mixture studies. Appropriate controls were used during the studies that included a number of male and female commercial controls including, 2800M, 9948 and Taqman male controls and 9947A female control. An allelic ladder was developed for the assignment of the alleles. This was done by choosing samples with different alleles, amplifying them and then adjusting the volumes of amplified products in a mixture. The developed mixtures were used to balance the composite ladder. Multiple alleles of the various loci included in the ladder were sequenced. Reference haplotypes were developed for the 5 male samples included in the Y chromosome Standard Reference Material 2395 (SRM2395) using RM-Yplex. The International Society of Forensic Genetics (ISFG) recommendations were followed for adopting allele nomenclature. As part of developmental validation, the assay was included in an external proficiency trial which was concluded successfully. An internal validation of RM-Yplex was carried out at the Department of Forensic Sciences and Criminology Laboratory, Dubai where apart from other studies; application of the assay was demonstrated using non-probative forensic casework samples. The value of RM-Yplex was demonstrated for differentiating close male relatives in a case where a previously used Y-STR multiplex assay had shown identical haplotypes for those individuals. 1160 male individual samples were analysed in this study including UAE, other Arabian Peninsula populations as well as two South Asian populations residing in United Arab Emirates. RM-Yplex haplotypes have extremely high power of discrimination. The haplotype diversity for RM-Yplex haplotype is much more than the existing commercial Y-STR assays. Population studies have been carried out for the Arab, Indian and Pakistani populations. AMOVA was conducted for determining the apportionment of diversity and pairwise FST’s were estimated between populations. These have shown a marked homogeneity within the UAE Arab sub-populations. MDS plots of pairwise FST’s indicated that populations were not grouped significantly in accordance with the geographical locations. A network analysis showed the extent of distribution of haplotypes of various populations and their relationships. A highly sensitive and reliable RM-Yplex multiplex assay has been thus developed, which is expected to help genetic populations studies and forensic casework

    Effects Of Neuroscience-Based Thinking (NBT) And Thinking Skills (TS) Strategies On Thinking And Emotion Among Primary Schools Pupils

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    The aim of this study is to investigate the effects of Neuroscience-Based Thinking (NBT) strategy and Thinking Skills (TS) strategy on creative thinking and the performance of science tasks (thinking and emotion) among Malaysian pupils in primary schools. This study used quasi-experimental research design with one control group and two experimental groups. Ninety eight pupils enrolled in standard five during the 2010 educational year formed the sample. The two experimental groups were named NBT and TS while prevalent strategy (P) as the control group. The instruction was carried out by three different science teachers. These three groups were measured twice (pretest and posttest) of three different instruments: the Test of Creative Thinking (TCT), Science Task of Thinking (STT) and of Emotion (STE). The instruments' reliabilities are good as showed by Cronbach alpha and Pearson correlation. Inferential statistics, namely two ways ANCOVA and MANCOVA tests, and LSD post hoc method were used at α .05 level to determine statistically significant differences between study groups. The results showed that there were significant differences between groups. The result of the test of creative thinking in science and its sub-skills (fluency, flexibility and originality) indicated that the pupils in NBT group scored higher as compared to TS and P groups in all but one sub-skill (fluency) where TS group has better score. Likewise, the TS pupils are higher than P pupils except in originality where both were similar. Similarly, the results of thinking and emotion of science tasks revealed that the pupils of NBT scored higher than TS and P groups in their thinking and emotion. Furthermore, the results revealed that there were no significant differences in posttest between gender in all groups. Similarly, there were no significant in interaction effects in post-test between all groups and both gender on all variables yet the female pupils of TS group have high scores in fluency. Therefore, the study recommends that educators should work to enhance learning and creativity among pupils by employing neuroscience principles in teaching and learning process by integrating them into curriculum

    Mobile phones of paediatric hospital staff are never cleaned and commonly used in toilets with implications for healthcare nosocomial diseases

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    An ever-increasing number of medical staff use mobile phones as a work aid, yet this may pose nosocomial diseases. To assess and report via a survey the handling practices and the use of phones by paediatric wards healthcare workers. 165 paediatric healthcare workers and staff filled in a questionnaire consisting of 14 questions (including categorical, ordinal and numerical data). Analysis of categorical data used non-parametric techniques such as the Chi-squared test. Although 98% of respondents (165 in total) report that their phones may be contaminated, 56% have never cleaned their devices. Of the respondents that clean their devices, 10% (17/165) had done so with alcohol swabs or disinfectant within that day or week; and an additional 12% respondents (20/165) within that month. Of concern, 52% (86/165) of the respondents use their phones in the bathroom, emphasising the unhygienic environments in which mobile phones/smartphones are constantly used. Disinfecting phones is a practice that only a minority of healthcare workers undertake appropriately. Mobile phones, present in billions globally, are therefore Trojan Horses if contaminated with microbes and potentially contributing to the spread and propagation of micro-organisms as per the rapid spread of SARS-CoV-2 virus in the world

    Study Protocol for "MOVEdiabetes":A Trial to Promote Physical Activity for Adults with Type 2 Diabetes in Primary Health Care in Oman

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    Abstract Background Benefits of physical activity in the management of diabetes are well documented. However, evidence on the effectiveness of interventions integrating physical activity in diabetes care is sparse especially in the countries of the Gulf Cooperation Council. The results from this study will increase our understanding of the use of multi-component interventions aimed at increasing physical activity levels in inactive adults with type 2 diabetes in primary health care in Oman. Methods/design The study is a one year 1:1 cluster randomized controlled trial of the MOVEdiabetes programme (intervention) versus usual care in eight primary health care centres in Oman. The MOVEdiabetes programme utilizes face to face physical activity consultations promoting 150 min of moderate to vigorous physical activity per week (≥600MET-mins/week), pedometers to self-monitor step counts and monthly telephone WhatsApp messages for follow up support. Inactive adults with type 2 diabetes and no contraindication to physical activity will be recruited over a two months period, and followed up for 12 months. To demonstrate a 50% between group difference in physical activity levels (MET-mins/week) over 12 months, (at a power of 80%, and significance level of 5%), 128 participants would be required to complete the study (64 in each arm). Based on a drop-out rate of 20%, 154 participants would require to be recruited (77 in each arm). Assuming a recruitment rate of 70%, 220 potential eligible participants would need to be approached. The primary outcome is change in levels of physical activity measured by the Global Physical Activity Questionnaire. In addition, accelerometers will be used in a sub group to objectively assess physical activity. Secondary outcomes include changes in metabolic and cardiovascular biomarkers, change in self-reported health, social support, self-efficacy for physical activity, and perceived acceptability of the program. All intervention delivery and support costs will be monitored. Discussion This study will contribute to the evidence on the feasibility, cultural acceptability and efficacy of interventional approaches for increasing physical activity in primary care for persons with type 2 diabetes in Oman. Trial registration International Standard Randomised Controlled Trials No: ISRCTN14425284 . Registered 12 April 2016

    A novel multiplex assay for simultaneously analysing 13 rapidly mutating Y-STRs

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    A multiplex polymerase chain reaction (PCR) assay (RM-Yplex) was developed which is capable of simultaneously amplifying 13 recently introduced rapidly mutating Y-STR markers (RM Y-STRs). This multiplex assay is expected to aid human identity testing in forensic and other applications to improve differentiating unrelated males and allow separating related males. The 13 RM Y-STR markers included in the multiplex are: DYF387S1, DYF399S1, DYF403S1ab, DYF404S1, DYS449, DYS518, DYS526ab, DYS547, DYS570, DYS576, DYS612, DYS626 and DYS627. This study reflects the proof of concept to analyse all currently known RM Y-STRs simultaneously and describes the optimization of the multiplex assay. The RM-Yplex assay generated complete RM Y-STR profiles down to 62.5 pg of male template DNA, and from male–female DNA mixtures at all ratios tested. We herewith introduce and make available for widespread use in forensic and anthropological studies, an effective and sensitive single multiplex assay for simultaneous genotyping of 13 RM Y-STRs

    Perceived barriers to leisure time physical activity in adults with type 2 diabetes attending primary healthcare in Oman:a cross-sectional survey

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    Objectives: Physical activity is fundamental in diabetes management for good metabolic control. This study aimed to identify barriers to performing leisure time physical activity and explore differences based on gender, age, marital status, employment, education, income and perceived stages of change in physical activity in adults with type 2 diabetes in Oman.Design: Cross-sectional study using an Arabic version of the “Barriers to Being Active” 27 item questionnaire.Setting: Seventeen primary health centres randomly selected in Muscat.Participants: Individuals >18 years with type 2 diabetes, attending diabetes clinic for > 2 years and with no contraindications to performing physical activity.Primary and secondary outcome measures: Participants were asked to rate how far different factors influenced their physical activity, under the following categories: fear of injury, lack of time, social support, energy, willpower, skills, resources, religion and environment. On a scale of 0-9, barriers were considered important if scored ≥5.Results: A total of 305 questionnaires were collected. Most (96%) reported at least one barrier to performing leisure time physical activity. Lack of willpower (44.4%), lack of resources (30.5%) and lack of social support (29.2%) were the most frequently reported barriers. Using chi-square test, lack of willpower was significantly different in individuals with low vs high income (54.2% vs 40%, P=0.002) and in those reporting inactive vs active stages of change for physical activity (50.7% vs 34.7%, P=0.029), lack of resources was significantly different in those with low vs high income (40% vs 24.3%, P=0.004) and married vs unmarried (33.8% vs 18.5%, P=0.018). Lack of social support was significant in females vs males (35.4% vs 20.8%, P=0.005).Conclusions: The findings can inform the design on physical activity intervention studies by testing the impact of strategies which incorporate ways to address reported barriers including approaches that enhance self-efficacy and social support

    A pilot metagenomic study reveals that community derived mobile phones are reservoirs of viable pathogenic microbes

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    There is increasing attention focussed on the risks associated with mobile phones possibly serving as ‘Trojan Horse’ fomites for microbial transmission in healthcare settings. However, little is reported on the presence of microbes on community derived mobile phones which in 2021, numbered in the billions in circulation with majority being used on a daily basis. Identify viable microbial organisms swabbed from smartphones on a university campus. Entire surfaces of 5 mobile phones were swabbed and examined for their microbial content using pre-agar-based growths followed by downstream DNA metagenomic next-generation sequencing analysis. All phones were contaminated with viable microbes. 173 bacteria, 8 fungi, 8 protists, 53 bacteriophages, 317 virulence factor genes and 41 distinct antibiotic resistant genes were identified. While this research represents a pilot study, the snapshot metagenomic analysis of samples collected from the surface of mobile phones has revealed the presence of a large population of viable microbes and an array of antimicrobial resistant factors. With billions of phones in circulation, these devices might be responsible for the rise of community acquired infections. These pilot results highlight the importance of public health authorities considering mobile phones as ‘Trojan Horse’ devices for microbial transmission and ensure appropriate decontamination campaigns are implemented
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