Showing papers in "BMC Research Notes in 2011"

Hand Grip Strength: age and gender stratified normative data in a population-based study

Abstract: The North West Adelaide Health Study is a representative longitudinal cohort study of people originally aged 18 years and over. The aim of this study was to describe normative data for hand grip strength in a community-based Australian population. Secondary aims were to investigate the relationship between body mass index (BMI) and hand grip strength, and to compare Australian data with international hand grip strength norms. The sample was randomly selected and recruited by telephone interview. Overall, 3 206 (81% of those recruited) participants returned to the clinic during the second stage (2004-2006) which specifically focused on the collection of information relating to musculoskeletal conditions. Following the exclusion of 435 participants who had hand pain and/or arthritis, 1366 men and 1312 women participants provided hand grip strength measurement. The study population was relatively young, with 41.5% under 40 years; and their mean BMI was 28.1 kg/m2 (SD 5.5). Higher hand grip strength was weakly related to higher BMI in adults under the age of 30 and over the age of 70, but inversely related to higher BMI between these ages. Australian norms from this sample had amongst the lowest of the hand grip strength of the internationally published norms, except those from underweight populations. This population demonstrated higher BMI and lower grip strength in younger participants than much of the international published, population data. A complete exploration of the relationship between BMI and hand grip strength was not fully explored as there were very few participants with BMI in the underweight range. The age and gender grip strength values are lower in younger adults than those reported in international literature.

Data mining methods in the prediction of Dementia: A real-data comparison of the accuracy, sensitivity and specificity of linear discriminant analysis, logistic regression, neural networks, support vector machines, classification trees and random forests

Abstract: Dementia and cognitive impairment associated with aging are a major medical and social concern. Neuropsychological testing is a key element in the diagnostic procedures of Mild Cognitive Impairment (MCI), but has presently a limited value in the prediction of progression to dementia. We advance the hypothesis that newer statistical classification methods derived from data mining and machine learning methods like Neural Networks, Support Vector Machines and Random Forests can improve accuracy, sensitivity and specificity of predictions obtained from neuropsychological testing. Seven non parametric classifiers derived from data mining methods (Multilayer Perceptrons Neural Networks, Radial Basis Function Neural Networks, Support Vector Machines, CART, CHAID and QUEST Classification Trees and Random Forests) were compared to three traditional classifiers (Linear Discriminant Analysis, Quadratic Discriminant Analysis and Logistic Regression) in terms of overall classification accuracy, specificity, sensitivity, Area under the ROC curve and Press'Q. Model predictors were 10 neuropsychological tests currently used in the diagnosis of dementia. Statistical distributions of classification parameters obtained from a 5-fold cross-validation were compared using the Friedman's nonparametric test. Press' Q test showed that all classifiers performed better than chance alone (p < 0.05). Support Vector Machines showed the larger overall classification accuracy (Median (Me) = 0.76) an area under the ROC (Me = 0.90). However this method showed high specificity (Me = 1.0) but low sensitivity (Me = 0.3). Random Forest ranked second in overall accuracy (Me = 0.73) with high area under the ROC (Me = 0.73) specificity (Me = 0.73) and sensitivity (Me = 0.64). Linear Discriminant Analysis also showed acceptable overall accuracy (Me = 0.66), with acceptable area under the ROC (Me = 0.72) specificity (Me = 0.66) and sensitivity (Me = 0.64). The remaining classifiers showed overall classification accuracy above a median value of 0.63, but for most sensitivity was around or even lower than a median value of 0.5. When taking into account sensitivity, specificity and overall classification accuracy Random Forests and Linear Discriminant analysis rank first among all the classifiers tested in prediction of dementia using several neuropsychological tests. These methods may be used to improve accuracy, sensitivity and specificity of Dementia predictions from neuropsychological testing.

Opening the archives for state of the art tumour genetic research: sample processing for array-CGH using decalcified, formalin-fixed, paraffin-embedded tissue-derived DNA samples.

Abstract: Molecular genetic studies on rare tumour entities, such as bone tumours, often require the use of decalcified, formalin-fixed, paraffin-embedded tissue (dFFPE) samples. Regardless of which decalcification procedure is used, this introduces a vast breakdown of DNA that precludes the possibility of further molecular genetic testing. We set out to establish a robust protocol that would overcome these intrinsic hurdles for bone tumour research. The goal of our study was to establish a protocol, using a modified DNA isolation procedure and quality controls, to select decalcified samples suitable for array-CGH testing. Archival paraffin blocks were obtained from 9 different pathology departments throughout Europe, using different fixation, embedding and decalcification procedures, in order to preclude a bias for certain lab protocols. Isolated DNA samples were subjected to direct chemical labelling and enzymatic labelling systems and were hybridised on a high resolution oligonucleotide chip containing 44,000 reporter elements. Genomic alterations (gains and losses) were readily detected in most of the samples analysed. For example, both homozygous deletions of 0.6 Mb and high level of amplifications of 0.7 Mb were identified. We established a robust protocol for molecular genetic testing of dFFPE derived DNA, irrespective of fixation, decalcification or sample type used. This approach may greatly facilitate further genetic testing on rare tumour entities where archival decalcified, formalin fixed samples are the only source.

Effective implementation of research into practice: an overview of systematic reviews of the health literature.

Abstract: Background: The gap between research findings and clinical practice is well documented and a range of interventions has been developed to increase the implementation of research into clinical practice. Findings: A review of systematic reviews of the effectiveness of interventions designed to increase the use of research in clinical practice. A search for relevant systematic reviews was conducted of Medline and the Cochrane Database of Reviews 1998-2009. 13 systematic reviews containing 313 primary studies were included. Four strategy types are identified: audit and feedback; computerised decision support; opinion leaders; and multifaceted interventions. Nine of the reviews reported on multifaceted interventions. This review highlights the small effects of single interventions such as audit and feedback, computerised decision support and opinion leaders. Systematic reviews of multifaceted interventions claim an improvement in effectiveness over single interventions, with effect sizes ranging from small to moderate. This review found that a number of published systematic reviews fail to state whether the recommended practice change is based on the best available research evidence. Conclusions: This overview of systematic reviews updates the body of knowledge relating to the effectiveness of key mechanisms for improving clinical practice and service development. Multifaceted interventions are more likely to improve practice than single interventions such as audit and feedback. This review identified a small literature focusing explicitly on getting research evidence into clinical practice. It emphasizes the importance of ensuring that primary studies and systematic reviews are precise about the extent to which the reported interventions focus on changing practice based on research evidence (as opposed to other information codified in guidelines and education materials).

An RNA isolation system for plant tissues rich in secondary metabolites.

Abstract: Secondary metabolites are reported to interfere with the isolation of RNA particularly with the recipes that use guanidinium-based salt. Such interference was observed in isolation of RNA with medicinal plants rheum (Rheum australe) and arnebia (Arnebia euchroma). A rapid and less cumbersome system for isolation of RNA was essential to facilitate any study related to gene expression. An RNA isolation system free of guanidinium salt was developed that successfully isolated RNA from rheum and arnebia. The method took about 45 min and was successfully evaluated on twenty one tissues with varied secondary metabolites. The A260/280 ratio ranged between 1.8 - 2.0 with distinct 28 S and 18 S rRNA bands visible on a formaldehyde-agarose gel. The present manuscript describes a rapid protocol for isolation of RNA, which works well with all the tissues examined so far. The remarkable feature was the success in isolation of RNA with those tissues, wherein the most commonly used methods failed. Isolated RNA was amenable to downstream applications such as reverse transcription-polymerase chain reaction (RT-PCR), differential display (DD), suppression subtractive hybridization (SSH) library construction, and northern hybridization.

The BrainMap strategy for standardization, sharing, and meta-analysis of neuroimaging data

Abstract: Background: Neuroimaging researchers have developed rigorous community data and metadata standards that encourage meta-analysis as a method for establishing robust and meaningful convergence of knowledge of human brain structure and function. Capitalizing on these standards, the BrainMap project offers databases, software applications, and other associated tools for supporting and promoting quantitative coordinate-based meta-analysis of the structural and functional neuroimaging literature. Findings: In this report, we describe recent technical updates to the project and provide an educational description for performing meta-analyses in the BrainMap environment. Conclusions: The BrainMap project will continue to evolve in response to the meta-analytic needs of biomedical researchers in the structural and functional neuroimaging communities. Future work on the BrainMap project regarding software and hardware advances are also discussed.

The physical activity patterns of children with autism

Abstract: Although motor deficits are gaining attention in autism research much less attention has been paid to the physical activity patterns in this group of children. The participants in this study were a group of children with autism spectrum disorder (N = 72) between the ages of 9-18 years. This cross-sectional study explored the physical activity patterns of seventy-two children with autism spectrum disorder as they aged. Results indicated significant differences between the mean time spent in moderate to vigorous physical activity and the mean time spent in sedentary activity. Older children with autism spectrum disorder are significantly more physically inactive, compared to younger children. Physical activity programs and interventions need to address this deficit, in physical activity. Children with autism have a similar trend in physical activity patterns compared to their peers without autism; associated benefits and future research will be discussed.

The Netherlands study of depression in older persons (NESDO); a prospective cohort study

Abstract: Background: To study late-life depression and its unfavourable course and co morbidities in The Netherlands. Methods: We designed the Netherlands Study of Depression in Older Persons (NESDO), a multi-site naturalistic prospective cohort study which makes it possible to examine the determinants, the course and the consequences of depressive disorders in older persons over a period of six years, and to compare these with those of depression earlier in adulthood. Results: From 2007 until 2010, the NESDO consortium has recruited 510 depressed and non depressed older persons (≥ 60 years) at 5 locations throughout the Netherlands. Depressed persons were recruited from both mental health care institutes and general practices in order to include persons with late-life depression in various developmental and severity stages. Non-depressed persons were recruited from general practices. The baseline assessment included written questionnaires, interviews, a medical examination, cognitive tests and collection of blood and saliva samples. Information was gathered about mental health outcomes and demographic, psychosocial, biological, cognitive and genetic determinants. The baseline NESDO sample consists of 378 depressed (according to DSM-IV criteria) and 132 non-depressed persons aged 60 through 93 years. 95% had a major depression and 26.5% had dysthymia. Mean age of onset of the depressive disorder was around 49 year. For 33.1% of the depressed persons it was their first episode. 41.0% of the depressed persons had a co morbid anxiety disorder. Follow up assessments are currently going on with 6 monthly written questionnaires and face-to-face interviews after 2 and 6 years. Conclusions: The NESDO sample offers the opportunity to study the neurobiological, psychosocial and physical determinants of depression and its long-term course in older persons. Since largely similar measures were used as in the Netherlands Study of Depression and Anxiety (NESDA; age range 18-65 years), data can be pooled thus creating a large longitudinal database of clinically depressed persons with adequate power and a large set of neurobiological, psychosocial and physical variables from both younger and older depressed persons.

Self medication with antibiotics in Yogyakarta City Indonesia: a cross sectional population-based survey

Abstract: Background Self medication with antibiotics has become an important factor driving antibiotic resistance. This study investigated the period prevalence, patterns of use, and socio-demographic factors associated with self medication with antibiotics in Yogyakarta City Indonesia. This cross-sectional population-based survey used a pre-tested questionnaire which was self-administered to randomly selected respondents (over 18 years old) in Yogyakarta City Indonesia in 2010 (N = 625). Descriptive statistics, chi-square and logistic regression were applied.

Psychometric assessment of the Wagnild and Young's resilience scale in Kano, Nigeria

Abstract: Resilience seemed to lie at the core of the recent promotion of positive mental health and wellbeing. This concept has been well studied in western countries and less in developing countries, particularly Nigeria. The aim of the study is therefore, to demonstrate the internal consistency and concurrent validity of the Resilience Scale (RS) and its 14-item short version (RS-14) in a Nigerian sample. The RS, RS-14, the Hospital Anxiety Depression Scale (HADS) and two screening questions on experience of recent and upcoming distress were administered to 70 clinical students who consented to participate after a major professional examination. Internal consistency and convergent validity were assessed. The participants mean age was 22.50 years (SD = 0.60). The mean score of RS and RS-14 were 130.23 (SD = 17.08) and 74.17 (SD = 10.14) respectively. Cronbach's alpha coefficient for the RS was 0.87 and that of the RS-14 was 0.81. The mean RS score by gender was 132.04 (SD = 19.08) and 126.52 (SD = 11.50) for males and females respectively and the difference was significant (t = 2.50; p = 0.012). The correlation of RS with RS-14 (r = 0.97; p = 0.000), the HADS depression (r = -0.28; p = 0.017) and anxiety (r = -0.26; p = 0.028) subscales, were significant. The corresponding t-test values for the means of RS and RS-14 scores for both cases and non-cases as determined by HADS, were significant at p < 0.05 and p < 0.01 for the depression and anxiety subscales respectively. The difference between RS means of those who experienced distress (38/125.69) to those that did not (32/134.05) from the recent clinical examination was also significant (t = 2.01; p = 0.045). The study confirms that the RS and RS-14 may be potentially useful instruments to measure resilience in Nigerians.

Internal control genes for quantitative RT-PCR expression analysis in mouse osteoblasts, osteoclasts and macrophages

Abstract: Real-time quantitative RT-PCR (qPCR) is a powerful technique capable of accurately quantitating mRNA expression levels over a large dynamic range. This makes qPCR the most widely used method for studying quantitative gene expression. An important aspect of qPCR is selecting appropriate controls or normalization factors to account for any differences in starting cDNA quantities between samples during expression studies. Here, we report on the selection of a concise set of housekeeper genes for the accurate normalization of quantitative gene expression data in differentiating osteoblasts, osteoclasts and macrophages. We implemented the use of geNorm, an algorithm that determines the suitability of genes to function as housekeepers by assessing expression stabilities. We evaluated the expression stabilities of 18S, ACTB, B2M, GAPDH, HMBS and HPRT1 genes. Our analyses revealed that 18S and GAPDH were regulated during osteoblast differentiation and are not suitable for use as reference genes. The most stably expressed genes in osteoblasts were ACTB, HMBS and HPRT1 and their geometric average constitutes a suitable normalization factor upon which gene expression data can be normalized. In macrophages, 18S and GAPDH were the most variable genes while HMBS and B2M were the most stably expressed genes. The geometric average of HMBS and B2M expression levels forms a suitable normalization factor to account for potential differences in starting cDNA quantities during gene expression analysis in macrophages. The expression stabilities of the six candidate reference genes in osteoclasts were, on average, more variable than that observed in macrophages but slightly less variable than those seen in osteoblasts. The two most stably expressed genes in osteoclasts were HMBS and B2M and the genes displaying the greatest levels of variability were 18S and GAPDH. Notably, 18S and GAPDH were the two most variably expressed control genes in all three cell types. The geometric average of HMBS, B2M and ACTB creates an appropriate normalization factor for gene expression studies in osteoclasts. We have identified concise sets of genes suitable to use as normalization factors for quantitative real-time RT-PCR gene expression studies in osteoblasts, osteoclasts and macrophages.

Assessment of severity and frequency of self-reported hypoglycemia on quality of life in patients with type 2 diabetes treated with oral antihyperglycemic agents: A survey study

Abstract: Some oral antihyperglycemic agents may increase risk of hypoglycemia and thereby reduce patient quality of life. Our objective was to assess the impact of the severity and frequency of self-reported hypoglycemia on health-related quality of life (HRQoL) among patients with type 2 diabetes treated with oral antihyperglycemic agents. A follow-up survey was conducted in participants with self-reported type 2 diabetes treated with oral antihyperglycemic agents from the US National Health and Wellness Survey 2007. Data were collected on the severity and frequency of hypoglycemic episodes in the 6 months prior to the survey, with severity defined as mild (no interruption of activities), moderate (some interruption of activities), severe (needed assistance of others), or very severe (needed medical attention). HRQoL was assessed using the EuroQol-5D Questionnaire (EQ-5D) US weighted summary score (utility) and Worry subscale of the Hypoglycemia Fear Survey (HFS). Of the participants who completed the survey (N = 1,984), mean age was 58 years, 57% were male, 72% reported an HbA1c <7.0%, and 50% reported treatment with a sulfonylurea-containing regimen. Hypoglycemic episodes were reported by 63% of patients (46% mild, 37% moderate, 13% severe and 4% very severe). For patients reporting hypoglycemia, mean utility score was significantly lower (0.78 versus 0.86, p < 0.0001) and mean HFS score was significantly higher (17.5 versus 6.2, p < 0.0001) compared to patients not reporting hypoglycemia. Differences in mean scores between those with and without hypoglycemia increased with the level of severity (mild, moderate, severe, very severe) for utility (0.03, 0.09, 0.18, 0.23) and HFS (6.1, 13.9, 20.1, 25.6), respectively. After adjusting for age, gender, weight gain, HbA1c, microvascular complications, and selected cardiovascular conditions, the utility decrement was 0.045 (by level of severity: 0.009, 0.055, 0.131, 0.208), and the HFS increase was 9.6 (by severity: 5.3, 12.4, 17.6, 23.2). HRQoL further decreased with greater frequency of hypoglycemic episodes. Self-reported hypoglycemia is independently associated with lower HRQoL, and the magnitude of this reduction increases with both severity and frequency of episodes in patients with type 2 diabetes treated with oral antihyperglycemic agents.

CloudAligner: A fast and full-featured MapReduce based tool for sequence mapping

Abstract: Research in genetics has developed rapidly recently due to the aid of next generation sequencing (NGS) However, massively-parallel NGS produces enormous amounts of data, which leads to storage, compatibility, scalability, and performance issues The Cloud Computing and MapReduce framework, which utilizes hundreds or thousands of shared computers to map sequencing reads quickly and efficiently to reference genome sequences, appears to be a very promising solution for these issues Consequently, it has been adopted by many organizations recently, and the initial results are very promising However, since these are only initial steps toward this trend, the developed software does not provide adequate primary functions like bisulfite, pair-end mapping, etc, in on-site software such as RMAP or BS Seeker In addition, existing MapReduce-based applications were not designed to process the long reads produced by the most recent second-generation and third-generation NGS instruments and, therefore, are inefficient Last, it is difficult for a majority of biologists untrained in programming skills to use these tools because most were developed on Linux with a command line interface To urge the trend of using Cloud technologies in genomics and prepare for advances in second- and third-generation DNA sequencing, we have built a Hadoop MapReduce-based application, CloudAligner, which achieves higher performance, covers most primary features, is more accurate, and has a user-friendly interface It was also designed to be able to deal with long sequences The performance gain of CloudAligner over Cloud-based counterparts (35 to 80%) mainly comes from the omission of the reduce phase In comparison to local-based approaches, the performance gain of CloudAligner is from the partition and parallel processing of the huge reference genome as well as the reads The source code of CloudAligner is available at http://cloudalignersourceforgenet/ and its web version is at http://minecswayneedu:8080/CloudAligner/ Our results show that CloudAligner is faster than CloudBurst, provides more accurate results than RMAP, and supports various input as well as output formats In addition, with the web-based interface, it is easier to use than its counterparts

Severe anaemia is associated with a higher risk for preeclampsia and poor perinatal outcomes in Kassala hospital, eastern Sudan

Abstract: Anaemia during pregnancy is major health problem. There is conflicting literature regarding the association between anaemia and its severity and maternal and perinatal outcomes. This is a retrospective case-control study conducted at Kassala hospital, eastern Sudan. Medical files of pregnant women with severe anaemia (haemoglobin (Hb) 11 g/dl, n = 303). Logistic regression analysis was performed separately for each of the outcome measures: preeclampsia, eclampsia, preterm birth, low birth weight (LBW) and stillbirth. There were 9578 deliveries at Kassala hospital, 4012 (41.8%) women had anaemia and 303 (3.2%) had severe anaemia. The corrected risk for preeclampsia increased only in severe anaemia (OR = 3.6, 95% CI: 1.4-9.1, P = 0.007). Compared with women with no anaemia, the risk of LBW was 2.5 times higher in women with mild/moderate anaemia (95% CI: 1.1-5.7), and 8.0 times higher in women with severe anaemia (95% CI: 3.8-16.0). The risk of preterm delivery increased significantly with the severity of anaemia (OR = 3.2 for women with mild/moderate anaemia and OR = 6.6 for women with severe anaemia, compared with women with no anaemia). The corrected risk for stillbirth increased only in severe anaemia (OR = 4.3, 95% CI: 1.9-9.1, P < 0.001). The greater the severity of the anaemia during pregnancy, the greater the risk of preeclampsia, preterm delivery, LBW and stillbirth. Preventive measures should be undertaken to decrease the prevalence of anaemia in pregnancy.

SYTO dyes and EvaGreen outperform SYBR Green in real-time PCR

Abstract: Real-time PCR can be carried out using either probes or DNA dyes. SYBR Green has been used the most, but it suffers from several drawbacks. Numerous other DNA dyes are commercially available, but with limited structural information. Dye behavior in real time PCR is difficult to predict, so empirical data are needed. In the work described here, a panel of 23 different DNA dyes--including green, orange, and red SYTO dyes, EvaGreen, and SYBR Green--were evaluated with respect to their performance in real time PCR. Data were analyzed for reaction inhibition, effects on amplicon melting temperature, fluorescent signal strength, and reaction efficiency. This is the first report of reaction efficiency using alternatives to SYBR Green. Results indicated substantial variation in performance even within the SYTO dye family. EvaGreen and the SYTO dyes 13, 16, 80, and 82 performed better than SYBR Green in general, and high reaction efficiencies can be achieved using these dyes. Empirical data were generated for 23 DNA dyes. This paper confirms and extends previous findings that among commercially available DNA dyes, EvaGreen and certain SYTO dyes are the most desirable alternatives to the commonly used SYBR Green in real-time PCR.

Biofilm formation at the solid-liquid and air-liquid interfaces by Acinetobacter species.

Abstract: The members of the genus Acinetobacter are Gram-negative cocobacilli that are frequently found in the environment but also in the hospital setting where they have been associated with outbreaks of nosocomial infections. Among them, Acinetobacter baumannii has emerged as the most common pathogenic species involved in hospital-acquired infections. One reason for this emergence may be its persistence in the hospital wards, in particular in the intensive care unit; this persistence could be partially explained by the capacity of these microorganisms to form biofilm. Therefore, our main objective was to study the prevalence of the two main types of biofilm formed by the most relevant Acinetobacter species, comparing biofilm formation between the different species. Biofilm formation at the air-liquid and solid-liquid interfaces was investigated in different Acinetobacter spp. and it appeared to be generally more important at 25°C than at 37°C. The biofilm formation at the solid-liquid interface by the members of the ACB-complex was at least 3 times higher than the other species (80-91% versus 5-24%). In addition, only the isolates belonging to this complex were able to form biofilm at the air-liquid interface; between 9% and 36% of the tested isolates formed this type of pellicle. Finally, within the ACB-complex, the biofilm formed at the air-liquid interface was almost 4 times higher for A. baumannii and Acinetobacter G13TU than for Acinetobacter G3 (36%, 27% & 9% respectively). Overall, this study has shown the capacity of the Acinetobacter spp to form two different types of biofilm: solid-liquid and air-liquid interfaces. This ability was generally higher at 25°C which might contribute to their persistence in the inanimate hospital environment. Our work has also demonstrated for the first time the ability of the members of the ACB-complex to form biofilm at the air-liquid interface, a feature that was not observed in other Acinetobacter species.

Modern management of pyogenic hepatic abscess: a case series and review of the literature.

Abstract: Background: Pyogenic hepatic abscesses are relatively rare, though untreated are uniformly fatal. A recent paradigm shift in the management of liver abscesses, facilitated by advances in diagnostic and interventional radiology, has decreased mortality rates. The aim of this study was to review our experience in managing pyogenic liver abscess, review the literature in this field, and propose guidelines to aid in the current management of this complex disease. Methods: Demographic and clinical details of all patients admitted to a single institution with liver abscess over a 5 year period were reviewed. Clinical presentation, aetiology, diagnostic work-up, treatment, morbidity and mortality data were collated. Results: Over a 5 year period 11 patients presented to a single institution with pyogenic hepatic abscess (55% males, mean age 60.3 years). Common clinical features at presentation were non-specific constitutional symptoms and signs. Aetiology was predominantly gallstones (45%) or diverticular disease (27%). In addition to empiric antimicrobial therapy, all patients underwent radiologically guided percutaneous drainage of the liver abscess at diagnosis and only 2 patients required surgical intervention, including one 16-year old female who underwent hemi-hepatectomy for a complex and rare Actinomycotic abscess. There were no mortalities after minimum followup of one year. Conclusions: Pyogenic liver abscesses are uncommon, and mortality has decreased over the last two decades. Antimicrobial therapy and radiological intervention form the mainstay of modern treatment. Surgical intervention should be considered for patients with large, complex, septated or multiple abscesses, underlying disease or in whom percutaneous drainage has failed.

Determinants of fatigue and stress

Abstract: Fatigue can be triggered by previous perceived stress which may lead to impairment of performance and function. The purpose of the study was to investigate the relationship between fatigue and perceived stress.

Selection of reliable reference genes for quantitative real-time PCR in human T cells and neutrophils

Abstract: The choice of reliable reference genes is a prerequisite for valid results when analyzing gene expression with real-time quantitative PCR (qPCR). This method is frequently applied to study gene expression patterns in immune cells, yet a thorough validation of potential reference genes is still lacking for most leukocyte subtypes and most models of their in vitro stimulation. In the current study, we evaluated the expression stability of common reference genes in two widely used cell culture models-anti-CD3/CD28 activated T cells and lipopolysaccharide stimulated neutrophils-as well as in unselected untreated leukocytes. The mRNA expression of 17 (T cells), 7 (neutrophils) or 8 (unselected leukocytes) potential reference genes was quantified by reverse transcription qPCR, and a ranking of the preselected candidate genes according to their expression stability was calculated using the programs NormFinder, geNorm and BestKeeper. IPO8, RPL13A, TBP and SDHA were identified as suitable reference genes in T cells. TBP, ACTB and SDHA were stably expressed in neutrophils. TBP and SDHA were also the most stable genes in untreated total blood leukocytes. The critical impact of reference gene selection on the estimated target gene expression is demonstrated for IL-2 and FIH expression in T cells. The study provides a shortlist of suitable reference genes for normalization of gene expression data in unstimulated and stimulated T cells, unstimulated and stimulated neutrophils and in unselected leukocytes.

Structure-Function Analysis of Diacylglycerol Acyltransferase Sequences from 70 Organisms

Abstract: Diacylglycerol acyltransferase families (DGATs) catalyze the final and rate-limiting step of triacylglycerol (TAG) biosynthesis in eukaryotic organisms. Understanding the roles of DGATs will help to create transgenic plants with value-added properties and provide clues for therapeutic intervention for obesity and related diseases. The objective of this analysis was to identify conserved sequence motifs and amino acid residues for better understanding of the structure-function relationship of these important enzymes. 117 DGAT sequences from 70 organisms including plants, animals, fungi and human are obtained from database search using tung tree DGATs. Phylogenetic analysis separates these proteins into DGAT1 and DGAT2 subfamilies. These DGATs are integral membrane proteins with more than 40% of the total amino acid residues being hydrophobic. They have similar properties and amino acid composition except that DGAT1s are approximately 20 kDa larger than DGAT2s. DGAT1s and DGAT2s have 41 and 16 completely conserved amino acid residues, respectively, although only two of them are shared by all DGATs. These residues are distributed in 7 and 6 sequence blocks for DGAT1s and DGAT2s, respectively, and located at the carboxyl termini, suggesting the location of the catalytic domains. These conserved sequence blocks do not contain the putative neutral lipid-binding domain, mitochondrial targeting signal, or ER retrieval motif. The importance of conserved residues has been demonstrated by site-directed and natural mutants. This study has identified conserved sequence motifs and amino acid residues in all 117 DGATs and the two subfamilies. None of the completely conserved residues in DGAT1s and DGAT2s is present in recently reported isoforms in the multiple sequences alignment, raising an important question how proteins with completely different amino acid sequences could perform the same biochemical reaction. The sequence analysis should facilitate studying the structure-function relationship of DGATs with the ultimate goal to identify critical amino acid residues for engineering superb enzymes in metabolic engineering and selecting enzyme inhibitors in therapeutic application for obesity and related diseases.

Detection of macrolide and disinfectant resistance genes in clinical Staphylococcus aureus and coagulase-negative staphylococci

Abstract: Staphylococcus aureus and Coagulase-negative staphylococci (CoNS) are a major source of infections associated with indwelling medical devices. Many antiseptic agents are used in hygienic handwash to prevent nosocomial infections by Staphylococci. Our aim was to determine the antibiotic susceptibility and resistance to quaternary ammonium compound of 46 S. aureus strains and 71 CoNS. S. aureus (n = 46) isolated from auricular infection and CoNS (n = 71), 22 of the strains isolated from dialysis fluids and 49 of the strains isolated from needles cultures were investigated. Erythromycin resistance genes (erm A, erm B, erm C, msr A and mef) were analysed by multiplex PCR and disinfectant-resistant genes (qac A, qac B, and qac C) were studied by PCR-RFLP. The frequency of erythromycin resistance genes in S. aureus was: erm A+ 7.7%, erm B+ 13.7%, erm C+ 6% and msr A+ 10.2%. In addition, the number of positive isolates in CoNS was respectively erm A+ (9.4%), erm B+ (11.1%), erm C+ (27.4%), and msr A+ (41%). The MIC analyses revealed that 88 isolates (74%) were resistant to quaternary ammonium compound-based disinfectant benzalkonium chloride (BC). 56% of the BC-resistant staphylococcus isolates have at least one of the three resistant disinfectants genes (qac A, qac B and qac C). Nine strains (7.7%) among the CoNS species and two S. aureus strains (2%) harboured the three-qac genes. In addition, the qac C were detected in 41 strains. Multi-resistant strains towards macrolide and disinfectant were recorded. The investigation of antibiotics and antiseptic-resistant CoNS may provide crucial information on the control of nosocomial infections.

Dengue epidemic in Malaysia: Not a predominantly urban disease anymore

Abstract: Background Dengue infection has been an important and serious public health concern in Malaysia ever since its first reported case here in 1902. Nevertheless, to our knowledge, no nationwide investigation has been carried out to determine the actual magnitude of dengue endemicity in the Malaysian population. In this study, we describe a cross sectional seroepidemiology study of dengue IgG seroprevalence in the Malaysian adult population.

Medication prescribing errors in a pediatric inpatient tertiary care setting in Saudi Arabia

Abstract: Background: Medication errors (MEs) are among the most common types of medical errors and one of the most common and preventable causes of iatrogenic injuries. The aims of the present study were; (i) to determine the incidence and types of medication prescribing errors (MPEs), and (ii) to identify some potential risk factors in a pediatric inpatient tertiary care setting in Saudi Arabia. Findings: A five-week retrospective cohort study identified medication errors in the general pediatric ward and pediatric intensive care unit (PICU) at King Abdulaziz Medical City (KAMC) through the physical inspection of physician medication orders and reviews of patients’ files. Out of the 2,380 orders examined, the overall error rate was 56 per 100 medication orders (95% CI: 54.2%, 57.8%). Dose errors were the most prevalent (22.1%). These were followed by route errors (12.0%), errors in clarity (11.4%) and frequency errors (5.4%). Other types of errors were incompatibility (1.9%), incorrect drug selection (1.7%) and duplicate therapy (1%). The majority of orders (81.8%) had one or more abbreviations. Error rates were highest in prescriptions for electrolytes (17.17%), antibiotics (13.72%) and bronchodilators (12.97%). Medication prescription errors occurred more frequently in males (64.5%), infants (44.5%) and for medications with an intravenous route of administration (50.2%). Approximately one third of the errors occurred in the PICU (33.9%). Conclusions: The incidence of MPEs was significantly high. Large-scale prospective studies are recommended to determine the extent and outcome of medication errors in pediatric hospitals in Saudi Arabia.

GO Trimming: Systematically reducing redundancy in large Gene Ontology datasets

Abstract: The increased accessibility of gene expression tools has enabled a wide variety of experiments utilizing transcriptomic analyses. As these tools increase in prevalence, the need for improved standardization in processing and presentation of data increases, as does the need to guard against interpretation bias. Gene Ontology (GO) analysis is a powerful method of interpreting and summarizing biological functions. However, while there are many tools available to investigate GO enrichment, there remains a need for methods that directly remove redundant terms from enriched GO lists that often provide little, if any, additional information. Here we present a simple yet novel method called GO Trimming that utilizes an algorithm designed to reduce redundancy in lists of enriched GO categories. Depending on the needs of the user, this method can be performed with variable stringency. In the example presented here, an initial list of 90 terms was reduced to 54, eliminating 36 largely redundant terms. We also compare this method to existing methods and find that GO Trimming, while simple, performs well to eliminate redundant terms in a large dataset throughout the depth of the GO hierarchy. The GO Trimming method provides an alternative to other procedures, some of which involve removing large numbers of terms prior to enrichment analysis. This method should free up the researcher from analyzing overly large, redundant lists, and instead enable the concise presentation of manageable, informative GO lists. The implementation of this tool is freely available at: http://lucy.ceh.uvic.ca/go_trimming/cbr_go_trimming.py

Identification of superior reference genes for data normalisation of expression studies via quantitative PCR in hybrid roses ( Rosa hybrida )

Abstract: Background Gene expression studies are a prerequisite for understanding the biological function of genes. Because of its high sensitivity and easy use, quantitative PCR (qPCR) has become the gold standard for gene expression quantification. To normalise qPCR measurements between samples, the most prominent technique is the use of stably expressed endogenous control genes, the so called reference genes. However, recent studies show there is no universal reference gene for all biological questions. Roses are important ornamental plants for which there has been no evaluation of useful reference genes for gene expression studies.

Characterization of barley (Hordeum vulgare L.) NAC transcription factors suggests conserved functions compared to both monocots and dicots.

Abstract: The NAC transcription factor family is involved in the regulation of traits in both monocots and dicots of high agronomic importance. Understanding the precise functions of the NAC genes can be of utmost importance for the improvement of cereal crop plants through plant breeding. For the cereal crop plant barley (Hordeum vulgare L.) only a few NAC genes have so far been investigated. Through searches in publicly available barley sequence databases we have obtained a list of 48 barley NAC genes (HvNACs) with 43 of them representing full-length coding sequences. Phylogenetic comparisons to Brachypodium, rice, and Arabidopsis NAC proteins indicate that the barley NAC family includes members from all of the eight NAC subfamilies, although by comparison to these species a number of HvNACs still remains to be identified. Using qRT-PCR we investigated the expression profiles of 46 HvNACs across eight barley tissues (young flag leaf, senescing flag leaf, young ear, old ear, milk grain, late dough grain, roots, and developing stem) and two hormone treatments (abscisic acid and methyl jasmonate). Comparisons of expression profiles of selected barley NAC genes with the published functions of closely related NAC genes from other plant species, including both monocots and dicots, suggest conserved functions in the areas of secondary cell wall biosynthesis, leaf senescence, root development, seed development, and hormone regulated stress responses.

Assessment of knowledge, attitude and risk behaviors towards HIV/AIDS and other sexual transmitted infection among preparatory students of Gondar town, north west Ethiopia

Abstract: The first case of HIV in Ethiopia was reported in 1984. Since then, HIV/AIDS has become a major public health concern in the country, leading the Government of Ethiopia to declare a public health emergency in 2002. Although the epidemic is currently stable, HIV/AIDS remains a major development challenge for Ethiopia. The spread of HIV in any community is in part determined by the knowledge of attitude towards sexuality of its members and by their actual sexual practices. The aim of the study was to assess students' knowledge, attitudes and practices regarding HIV/AIDS and STDs in Gondar, North West Ethiopia. A cross sectional study was conducted between February 1 to March 1, 2009 in preparatory high school students. Pre-tested questioner was used to generate the data and analysis was made by SPSS version 15. Chi -square value was calculated and p-value < 0.05 was considered statistically significant. All the students had heard about AIDS before the interview. Knowledge on some aspect of the disease was quite low in the study group. Only half of the students knew that at present, AIDs is incurable and that HIV infection can be acquired through sexual contact with a 'familiar' person. Knowledge about STI was also quite low, 39% knew that pus in the urine is a symptom of STI and 45.4% knew that acquisition of other STIs is increases the chance of HIV transmission following unsafe sex with known cases. 25% of the study group had previous sexual intercourse and exposed at least one risk behavior. About 34% of the respondents had negative attitude towards AIDS and STDs. Awareness about STDs and methods of prevention of HIV and STDs was low. More risk behavior was observed in male and those with alcohol and drugs of abuse.

Risky driving behaviors for road traffic accident among drivers in Mekele city, Northern Ethiopia

Abstract: Due to its perception as a disease of development, road traffic accident and related injuries tend to be under recognized as a major health problem in developing countries. However, majority of the world's fatalities on the roads occur in low income and middle income countries. Since the main cause of road traffic accident is attributed to human risky behaviors, it is important to identify significant factors for risky behaviors of drivers. A quantitative cross-sectional study with a sample size of 350 drivers was conducted in April 2011. The study was conducted among Taxi, Bajaj (three tire vehicles) and private owned car drivers. After proportion to size allocation for Taxi (75), Baja (103) and private owned car (172) drivers, we used systematic random sampling method to identify illegible study subjects. Data was collected with face to face interview using a pretested questioner. Univariate, bivariate and multivariate analysis was done using SPSS version 16. The mean age of the respondents was 28.7 (SD 9.9). Majority were 339 (96.9%) males. Significant number of the study subjects 233 (66.6%) had risky driving behaviors. More than a quarter 100 (28.6%) had less knowledge about basic traffic signs. Majority of drivers 181 (51.7%) had negative attitude towards risky driving behaviors. Significant percent of them 148 (42.3%) had a habit of using mobile phone while driving vehicle and 28 (9.7%) had experience of driving after drinking alcohol. All the Bajaj, 97(62.6%) house car and 58(37.4%) taxi unfasten their seat belt while driving. Majority 303 (86.6%) followed the recommended speed limit of driving. About 66 (18.9%) of them had experience of punishment or warning by traffic polices in the previous 1 year and 77 (22%) ever had car accident while driving. Drivers of secondary education and with high average monthly income were more likely to have risky driving behavior. Having supportive attitude towards risky driving behaviors and not getting advice about risky driving from significant others increases the likelihood of developing risky driving behavior. Interventions targeted at developing negative attitude towards risky driving behaviors on drivers and significant others should be implemented to bring positive behavior change. The interventions need to be segmented with educational status and income.

Cook It Up! A community-based cooking program for at-risk youth: overview of a food literacy intervention.

Abstract: In Canada, there are limited occasions for youth, and especially at-risk youth, to participate in cooking programs. The paucity of these programs creates an opportunity for youth-focused cooking programs to be developed, implemented, and evaluated with the goal of providing invaluable life skills and food literacy to this potentially vulnerable group. Thus, an 18-month community-based cooking program for at-risk youth was planned and implemented to improve the development and progression of cooking skills and food literacy. This paper provides an overview of the rationale for and implementation of a cooking skills intervention for at-risk youth. The manuscript provides information about the process of planning and implementing the intervention as well as the evaluation plan. Results of the intervention will be presented elsewhere. Objectives of the intervention included the provision of applied food literacy and cooking skills education taught by local chefs and a Registered Dietitian, and augmented with fieldtrips to community farms to foster an appreciation and understanding of food, from 'gate to plate'. Eight at-risk youth (five girls and three boys, mean age = 14.6) completed the intervention as of November 2010. Pre-test cooking skills assessments were completed for all participants and post-test cooking skills assessments were completed for five of eight participants. Post intervention, five of eight participants completed in-depth interviews about their experience. The Cook It Up! program can provide an effective template for other agencies and researchers to utilize for enhancing existing programs or to create new applied cooking programs for relevant vulnerable populations. There is also a continued need for applied research in this area to reverse the erosion of cooking skills in Canadian society.

Transcriptome characterization of the South African abalone Haliotis midae using sequencing-by-synthesis

Abstract: Background: Worldwide, the genus Haliotis is represented by 56 extant species and several of these are commercially cultured. Among the six abalone species found in South Africa, Haliotis midae is the only aquacultured species. Despite its economic importance, genomic sequence resources for H. midae, and for abalone in general, are still scarce. Next generation sequencing technologies provide a fast and efficient tool to generate large sequence collections that can be used to characterize the transcriptome and identify expressed genes associated with economically important traits like growth and disease resistance. Results: More than 25 million short reads generated by the Illumina Genome Analyzer were de novo assembled in 22,761 contigs with an average size of 260 bp. With a stringent E-value threshold of 10 -10 , 3,841 contigs (16.8%) had a BLAST homologous match against the Genbank non-redundant (NR) protein database. Most of these sequences were annotated using the gene ontology (GO) and eukaryotic orthologous groups of proteins (KOG) databases and assigned to various functional categories. According to annotation results, many gene families involved in immune response were identified. Thousands of simple sequence repeats (SSR) and single nucleotide polymorphisms (SNP) were detected. Setting stringent parameters to ensure a high probability of amplification, 420 primer pairs in 181 contigs containing SSR loci were designed. Conclusion: This data represents the most comprehensive genomic resource for the South African abalone H. midae to date. The amount of assembled sequences demonstrated the utility of the Illumina sequencing technology in the transcriptome characterization of a non-model species. It allowed the development of several markers and the identification of promising candidate genes for future studies on population and functional genomics in H. midae and in other abalone species. Background Abalones (Haliotis spp., Haliotidae) are important fishery resources worldwide, with high commercial value. Because of their sedentary lifestyle along shallow rocky coastlines [1], these gastropods are vulnerable to capture. The subsequent over-exploitation resulted in a substantial decrease of wild populations. To compensate for the high demand of abalone, farming by means of aquaculture has been developed for several Haliotis species in different regions of their distribution area. Currently, abalone aquaculture is practiced on 12 species in 16 different countries [2].