Showing papers in "BMC Research Notes in 2013"
TL;DR: The results of this study indicate that MALAT1 complies with key characteristics of diagnostic biomarkers, i.e., minimal invasiveness, high specificity, and robustness.
Abstract: The long noncoding RNA MALAT1 (metastasis-associated lung adenocarcinoma transcript 1) is described as a potential biomarker for NSCLC (non-small cell lung cancer). Diagnostic biomarkers need to be detectable in easily accessible body fluids, should be characterized by high specificity, sufficient sensitivity, and robustness against influencing factors. The aim of this study was to evaluate the performance of MALAT1 as a blood based biomarker for NSCLC. MALAT1 was shown to be detectable in the cellular fraction of peripheral human blood, showing different expression levels between cancer patients and cancer-free controls. For the discrimination of NSCLC patients from cancer-free controls a sensitivity of 56% was calculated conditional on a high specificity of 96%. No impact of tumor stage, age, gender, and smoking status on MALAT1 levels could be observed, but results based on small numbers. The results of this study indicate that MALAT1 complies with key characteristics of diagnostic biomarkers, i.e., minimal invasiveness, high specificity, and robustness. Due to its relatively low sensitivity MALAT1 might not be feasible as a single biomarker for the diagnosis of NSCLC in the cellular fraction of blood. Alternatively, MALAT1 might be applicable as a complementary biomarker within a panel in order to improve the entire diagnostic performance.
170 citations
TL;DR: TXA should be considered for routine use in primary knee and hip arthroplasty to decrease blood loss and no increased incidence of DVT with TXA use in TKA and THA.
Abstract: Tranexamic acid (TXA) is an antifibrinolytic drug used as a blood-sparing technique in many surgical specialties. The principal objective of our meta-analysis was to review randomized, controlled trials (RCT) comparing total blood loss and the number of patients receiving allogeneic blood transfusions with and without the use of TXA for knee (TKA) and hip (THA) arthroplasty. Studies were included if patients underwent primary unilateral TKA or THA; the study involved the comparison of a TXA treatment group to a control group who received either a placebo or no treatment at all; outcome measures included total blood loss TBL, number of patients receiving allogeneic blood transfusions, and/or incidence of thromboembolic complications; the study was a published or unpublished RCT from 1995 – July 2012. Data were tested for publication bias and statistical heterogeneity. Combined weighted mean differences in blood loss favoured TXA over control for TKA and THA patients respectively [ −1.149 (p < 0.001; 95% CI −1.298, -1.000), -0.504 (p < 0.001; 95% CI, -0.672, -0.336)]. Combined odds ratios favoured fewer patients requiring allogeneic transfusions for TKA and THA with the use of TXA respectively [0.145 (p < 0.001; 95% CI, 0.094, 0.223), 0.327 (p < 0.001; 95% CI, 0.208, 0.515)]. Combined odds ratios indicated no increased incidence of DVT with TXA use in TKA and THA respectively [1.030 (p = 0.946; 95% CI, 0.439, 2.420), 1.070 (p = 0.895; 95% CI, 0.393, 2.911)]. TXA should be considered for routine use in primary knee and hip arthroplasty to decrease blood loss.
168 citations
TL;DR: The results suggest that the combined use of the four most stably expressed genes may produce optimal normalization for qRT-PCR in L. decemlineata, and will enable a more accurate and reliable normalization of qRT -PCR data in the future.
Abstract: L. decemlineata is an exotic invasive insect pest, and invaded in Xinjiang Uygur autonomous region in China in the 1990s from Kazakhstan. It is a notorious defoliator of potato throughout most of the northern Xinjiang in current, and often causes extremely large yield losses of potato. The expression stability of nine L. decemlineata house-keeping genes (Actin, ACT1 and ACT2; ADP-ribosylation factor, ARF1 and ARF4; TATA box binding protein, TBP1 and TBP2; ribosomal protein RP4 and RP18; translation elongation factor 1α EF1α) was evaluated by quantitative real-time polymerase chain reaction (qRT-PCR) in seven developmental stages, three larval tissues and two insecticide treatments. The results were analyzed using three software programs: geNorm, NormFinder and BestKeeper. Although there was no consistent ranking observed among the house-keeping genes across the samples, the overall analysis revealed that RP18, RP4, ARF1, and ARF4 were the four most stable house-keeping genes. In contrast, ACT1 and ACT2, two of the most widely used reference genes, had the least stability. Our results suggest that the combined use of the four most stably expressed genes may produce optimal normalization for qRT-PCR. The expression stability of the house-keeping genes varies among different developing stages, in different tissues and under different experimental conditions. Our results will enable a more accurate and reliable normalization of qRT-PCR data in L. decemlineata.
142 citations
TL;DR: In this article, the authors obtained peripheral blood mononuclear cell (PBMC) RNAs from 7 type 1 (T1D), 7 type 2 (T2D), and 6 gestational diabetes (GDM) patients, which were hybridized to Agilent miRNA and mRNA microarrays.
Abstract: Regardless the regulatory function of microRNAs (miRNA), their differential expression pattern has been used to define miRNA signatures and to disclose disease biomarkers. To address the question of whether patients presenting the different types of diabetes mellitus could be distinguished on the basis of their miRNA and mRNA expression profiling, we obtained peripheral blood mononuclear cell (PBMC) RNAs from 7 type 1 (T1D), 7 type 2 (T2D), and 6 gestational diabetes (GDM) patients, which were hybridized to Agilent miRNA and mRNA microarrays. Data quantification and quality control were obtained using the Feature Extraction software, and data distribution was normalized using quantile function implemented in the Aroma light package. Differentially expressed miRNAs/mRNAs were identified using Rank products, comparing T1DxGDM, T2DxGDM and T1DxT2D. Hierarchical clustering was performed using the average linkage criterion with Pearson uncentered distance as metrics. The use of the same microarrays platform permitted the identification of sets of shared or specific miRNAs/mRNA interaction for each type of diabetes. Nine miRNAs (hsa-miR-126, hsa-miR-1307, hsa-miR-142-3p, hsa-miR-142-5p, hsa-miR-144, hsa-miR-199a-5p, hsa-miR-27a, hsa-miR-29b, and hsa-miR-342-3p) were shared among T1D, T2D and GDM, and additional specific miRNAs were identified for T1D (20 miRNAs), T2D (14) and GDM (19) patients. ROC curves allowed the identification of specific and relevant (greater AUC values) miRNAs for each type of diabetes, including: i) hsa-miR-1274a, hsa-miR-1274b and hsa-let-7f for T1D; ii) hsa-miR-222, hsa-miR-30e and hsa-miR-140-3p for T2D, and iii) hsa-miR-181a and hsa-miR-1268 for GDM. Many of these miRNAs targeted mRNAs associated with diabetes pathogenesis. These results indicate that PBMC can be used as reporter cells to characterize the miRNA expression profiling disclosed by the different diabetes mellitus manifestations. Shared miRNAs may characterize diabetes as a metabolic and inflammatory disorder, whereas specific miRNAs may represent biological markers for each type of diabetes, deserving further attention.
142 citations
TL;DR: A simple method to remove DSS from colonic RNAs is provided, and it is demonstrated for the first time that DSS can inhibit the activities of both polymerase and reverse transcriptase.
Abstract: Dextran sodium sulfate (DSS) is commonly used in mouse studies to induce a very reproducible colitis that effectively mimics the clinical and histological features of human inflammatory bowel disease (IBD) patients, especially ulcerative colitis. However, the mechanisms of action of DSS remain poorly understood, and observations by our laboratory and other groups indicate that DSS contamination of colonic tissues from DSS-treated mice potently inhibits the quantitative reverse-transcription polymerase chain reaction (qRT-PCR) amplification of mRNA. A prior study used poly-A-mediated mRNA purification to remove DSS from RNA extracts, but we herein report a second efficient and cost-effective approach to counteract this inhibition, using lithium chloride precipitation to entirely remove DSS from RNAs. We also explored how DSS interferes with qRT-PCR process, and we report for the first time that DSS can alter the binding of reverse transcriptase to previously primed RNA and specifically inhibits the enzymatic activities of reverse transcriptase and Taq polymerase in vitro. This likely explains why DSS-treated colonic RNA is not suitable to qRT-PCR amplification without a previous purification step. In summary, we provide a simple method to remove DSS from colonic RNAs, and we demonstrate for the first time that DSS can inhibit the activities of both polymerase and reverse transcriptase. In order to reliably analyze gene expression in the colonic mucosa of DSS-treated mice, the efficiency rate of qRT-PCR must be the same between all the different experimental groups, including the water-treated control group, suggesting that whatever the duration and the percentage of the DSS treatment, RNAs must be purified.
129 citations
TL;DR: Iron was detected in ameloblasts of erupting third molars of 4-week old rats, suggesting iron plays a role in both incisor and molar development, and this is consistent with iron’s role in collagen synthesis.
Abstract: An iron rich layer on the labial surface is characteristic of the enamel of rodent incisors. In order to address a role for iron content in continuously growing incisors during odontogenesis, we studied iron deposition patterns in enamel and dentine using Perls’ blue staining and ferritin heavy chain (Fth) immunolocalization. Fth expression is regulated by iron level; therefore its localization can be used as a sensitive indicator for iron deposition. Sagittal sections of 4-week old rat incisors showed a gradual increase in iron level in the enamel organ from secretory to maturation stages. In addition, iron was detected in ameloblasts of erupting third molars of 4-week old rats, suggesting iron plays a role in both incisor and molar development. In odontoblasts, the presence of iron was demonstrated, and this is consistent with iron’s role in collagen synthesis. Using postnatal 3-, 6-, 9-day old mice, the spatial and temporal expression of Fth in tooth development again indicated the presence of iron in mature ameloblasts and odontoblasts. While these data do not explain what functional role iron has in tooth formation, it does highlight a significant molecular activity associated with the formation of the rodent dentition.
123 citations
TL;DR: The objective of this study was to optimise a protocol for the differentiation of the neuroblastoma cell line, SH-SY5Y that results in a cell population that is both morphologically and biochemically distinct from undifferentiated SH- SY5Y cells and has a distinct adhesion and spreading pattern and display extensive neurite outgrowth.
Abstract: Cell migration is a fundamental biological process and has an important role in the developing brain by regulating a highly specific pattern of connections between nerve cells. Cell migration is required for axonal guidance and neurite outgrowth and involves a series of highly co-ordinated and overlapping signalling pathways. The non-receptor tyrosine kinase, Focal Adhesion Kinase (FAK) has an essential role in development and is the most highly expressed kinase in the developing CNS. FAK activity is essential for neuronal cell adhesion and migration. The objective of this study was to optimise a protocol for the differentiation of the neuroblastoma cell line, SH-SY5Y. We determined the optimal extracellular matrix proteins and growth factor combinations required for the optimal differentiation of SH-SY5Y cells into neuronal-like cells and determined those conditions that induce the expression of FAK. It was confirmed that the cells were morphologically and biochemically differentiated when compared to undifferentiated cells. This is in direct contrast to commonly used differentiation methods that induce morphological differentiation but not biochemical differentiation. We conclude that we have optimised a protocol for the differentiation of SH-SY5Y cells that results in a cell population that is both morphologically and biochemically distinct from undifferentiated SH-SY5Y cells and has a distinct adhesion and spreading pattern and display extensive neurite outgrowth. This protocol will provide a neuronal model system for studying FAK activity during cell adhesion and migration events.
119 citations
TL;DR: The results indicate high correlation and regression between phenolic contents and antioxidant potentials of the extracts, hence the Tut plant could serve as effective free radical inhibitor or scavenger which may be a good candidate for pharmaceutical plant-based products.
Abstract: Antioxidants play an important role to protect damage caused by oxidative stress (OS). Plants having phenolic contents are reported to possess antioxidant properties. The present study was designed to investigate the antioxidant properties and phenolic contents (total phenols, flavonoids, flavonols and proanthrocyanidins) of methanolic extracts from Morus alba (locally named as Tut and commonly known as white mulberry) stem barks (TSB), root bark (TRB), leaves (TL) and fruits (TF) to make a statistical correlation between phenolic contents and antioxidant potential. The antioxidant activities and phenolic contents of methanolic extractives were evaluated by in vitro standard method using spectrophotometer. The antioxidant activities were determined by total antioxidant capacity, DPPH (1,1-diphenyl-2-picrylhydrazine) radical scavenging assay, hydroxyl radical scavenging assay, ferrous reducing antioxidant capacity and lipid peroxidation inhibition assay methods. Among the extracts, TSB showed the highest antioxidant activity followed by TRB, TF and TL. Based on DPPH and hydroxyl radical scavenging activity, the TSB extract was the most effective one with IC50 37.75 and 58.90 μg/mL, followed by TRB, TF and TL with IC50 40.20 and 102.03; 175.01 and 114.63 and 220.23 and 234.63 μg/mL, respectively. The TSB extract had the most potent inhibitory activity against lipid peroxidation with IC50 145.31 μg/mL. In addition, the reducing capacity on ferrous ion was in the following order: TSB > TRB > TL > TF. The content of phenolics, flavonoids, flavonols and proanthocyanidins of TSB was found to be higher than other extractives. The results indicate high correlation and regression (p-value <0 .001) between phenolic contents and antioxidant potentials of the extracts, hence the Tut plant could serve as effective free radical inhibitor or scavenger which may be a good candidate for pharmaceutical plant-based products. However, further exploration is necessary for effective use in both modern and traditional system of medicines.
119 citations
TL;DR: Many pregnant women have poor knowledge about obesity, GWG, their consequences and management strategies, and Bridging this knowledge gap is an important step towards improving perinatal outcomes for all pregnant women, especially those who enter pregnancy overweight or obese.
Abstract: Obesity is increasingly common in the obstetric population. Maternal obesity and excess gestational weight gain (GWG) are associated with increased perinatal risk. There is limited published data demonstrating the level of pregnant women’s knowledge regarding these problems, their consequences and management strategies. We aimed to assess the level of knowledge of pregnant women regarding: (i) their own weight and body mass index (BMI) category, (ii) awareness of guidelines for GWG, (iii) concordance of women’s own expectations with guidelines, (iv) knowledge of complications associated with excess GWG, and (v) knowledge of safe weight management strategies in pregnancy. 364 pregnant women from a single center university hospital antenatal clinic were interviewed by an obstetric registrar. The women in this convenience sample were asked to identify their weight category, their understanding of the complications of obesity and excessive GWG in pregnancy and safe and/or effective weight management strategies in pregnancy. Nearly half (47.8%) of the study population were overweight or obese. 74% of obese women underestimated their BMI category. 64% of obese women and 40% of overweight women overestimated their recommended GWG. Women’s knowledge of the specific risks associated with excess GWG or maternal obesity was poor. Women also reported many incorrect beliefs about safe weight management in pregnancy. Many pregnant women have poor knowledge about obesity, GWG, their consequences and management strategies. Bridging this knowledge gap is an important step towards improving perinatal outcomes for all pregnant women, especially those who enter pregnancy overweight or obese.
109 citations
TL;DR: UTI was high among pregnant women in the presence of associated risk factor such as anaemia, low income level, past history of UTI and sexual activity, and multiparity, history of catheterization, genitourinary abnormality, maternal age, gestational age and educational status were not significantly associated with UTI.
Abstract: Urinary tract infections (UTIs) are among the most common bacterial infections in humans, both in the community and hospital settings. It is a serious health problem affecting millions of people each year and is the leading cause of Gram-negative bacteremia. We previously conducted a study on “Urinary Bacterial Profile and Antibiotic Susceptibility Pattern of UTI among Pregnant Women in North West Ethiopia” but the study did not address risk factors associated with urinary tract infection so the aim of the study was to assess associated risk factors of UTI among pregnant women in Felege Hiwot Referral Hospital, Bahir Dar, North West Ethiopia. A total of 367 pregnant women with and without symptoms of urinary tract infection(UTI) were included as a study subject from January 2011 to April 2011. Midstream urine samples were collected and processed following standard bacteriological tests. Data concerning associated risk factors were collected using structured questionnaires and were processed and analyzed using Statistical Package for Social Science (SPSS version 16). Bivarait analysis of socio-demographic characteristics and associated risk factors of UTI showed that family income level (family monthly income level ≤ 500 birr($37.85); P = 0.006, OR = 5.581, CI = 1.658, 18.793 and 501–1000 birr ($37.93-$75.70), P = 0.039, OR = 3.429, CI = 1.065, 11.034), anaemia (P = 0.003, OR = 4.388, CI = 1.776, 10.839), sexual activity (P = 0.032, OR = 3.520, CI = 1.197,10.363) and past history of UTI (P = 0.000, OR = 3.397, CI = 1.672, 6.902) were found to be factors significantly associated with increase prevalence of UTI. In contrast multiparity, history of catheterization, genitourinary abnormality, maternal age, gestational age and educational status were not significantly associated with UTI among pregnant women. In this study UTI was high among pregnant women in the presence of associated risk factor such as anaemia, low income level, past history of UTI and sexual activity.
100 citations
TL;DR: Preliminary evidence is provided that exercise has the potential to reduce stress and prevent the development of a deeper depression among burnout patients, which has important health implications given that burnout is considered an antecedent of depressive disorders.
Abstract: Background
Occupational burnout is associated with severe negative health effects. While stress management programs proved to have a positive influence on the well-being of patients suffering from burnout, it remains unclear whether aerobic exercise alleviates burnout severity and other parameters related to occupational burnout. Therefore, the main purpose of this study was to pilot-test the potential outcomes of a 12-week exercise training to generate hypotheses for future larger scale studies.
TL;DR: In the present study most of the pathogens isolated from blood culture showed high rate of resistance to most commonly used antibiotics used to treat bacterial infections, and rational use of antibiotics should be practiced.
Abstract: Bacterial blood stream infection constitutes a significant public health problem and it is an important cause of morbidity and mortality in hospitalized patients The aim of this study was to assess the prevalence of bacterial isolates from septicemia suspected patients and their antimicrobial susceptibility pattern in Gondar University Hospital This laboratory based retrospective study of 390 blood culture and susceptibility tests was conducted in Bacteriology Laboratory of the University of Gondar Teaching Hospital The samples were collected and processed following standard microbiological techniques as part of the routine clinical management of the patient Antibiotic susceptibility testing was done on pure culture isolates employing disc-diffusion method for the commonly used antibiotics The data were analyzed by using SPSS version 16 and the results were summarized by using tables and graphs Out of 390 blood culture results, 71 (182%) were culture positive The predominant bacteria isolated from blood culture were Coagulase negative staphylococci 30 (423%), followed by S aureus 17 (239%) and Klebiesella spp 9 (129%), E coli 5 (70%), Pseudomonas aeroginosa 4 (56%) and Salmonella spp 3 (42%) The gram positive and gram negative bacteria constituted 49 (69%) and 22 (31%) of the culture isolates; respectively The isolates showed high rates of resistance to most antibiotics tested The range of resistance for Gram positive and Gram negative were from 235% – 588%, and 20%– 100% respectively In the present study most of the pathogens isolated from blood culture showed high rate of resistance to most commonly used antibiotics used to treat bacterial infections Therefore, rational use of antibiotics should be practiced
TL;DR: A 58-year-old white male presented with shortness of breath, dry cough, fatigue and weight loss for two months, but there was an unfavorable response and the patient was subsequently referred for lung transplant.
Abstract: Background
The diagnosis of idiopathic pulmonary fibrosis can be quite challenging, even after careful clinical evaluation, imaging and pathological tests. This case report intends to demonstrate and discuss these difficulties, especially those concerning the differential diagnosis with chronic hypersensitivity pneumonitis.
TL;DR: Isolation of MRSA and ESBL-producing Enterobacteriaceae in higher proportions than previously reported calls for laboratory guided SSIs- therapy and strengthening of infection control surveillance in this setting are presented.
Abstract: Surgical site infections (SSIs) are difficult to treat and are associated with substantially longer hospital stay, higher treatment cost, morbidity and mortality, particularly when the etiological agent is multidrug-resistant (MDR). To address the limited data in Uganda on SSIs, we present the spectrum of bacteria isolated from hospitalized patients, the magnitude and impact of MDR bacterial isolates among patients with SSIs. A descriptive cross sectional study was conducted from September 2011 through April 2012 involving 314 patients with SSIs in the obstetrics & gynecology, general surgery and orthopedic wards at Mulago National Hospital in Kampala, Uganda. Wound swabs were taken and processed using standard microbiological methods. Clinico-demographic characteristics of patients were obtained using structured questionnaires and patients’ files. Of the 314 enrolled patients with SSIs (mean age 29.7 ±13.14 years), 239 (76.1%) were female. More than half of the patients were from obstetrics and gynecology (62.1%, 195/314). Of 314 wound swabs taken, 68.8% (216/314) were culture positive aerobically, yielding 304 bacterial isolates; of which 23.7% (72/304) were Escherichia coli and 21.1% (64/304) were Staphylococcus aureus. More than three quarters of Enterobacteriaceae were found to be extended spectrum beta lactamase (ESBL) producers and 37.5% of S. aureus were Methicillin resistant S. aureus (MRSA). MDR occurred in 78.3% (238/304) of the isolates; these were more among Gram-negative bacteria (78.6%, 187/238) compared to Gram-positive bacteria (21.4%, 51/238), (p-value < 0.0001, χ2 = 49.219). Amikacin and imepenem for ESBL-producing Enterobacteriacea and vancomycin for MRSA showed excellent performance except that they remain expensive drugs in Uganda. Most SSIs at Mulago National Hospital are due to MDR bacteria. Isolation of MRSA and ESBL-producing Enterobacteriaceae in higher proportions than previously reported calls for laboratory guided SSIs- therapy and strengthening of infection control surveillance in this setting.
TL;DR: The study results indicate that medical school authorities should take measures to prevent MSP due to factors related to medical school and students should make aware of importance of weight reduction to reduce MSP.
Abstract: The main purpose of the study was to assess the prevalence, body distributions and factors associated with musculoskeletal pain (MSP) among medical students in a private Malaysian medical college. This cross-sectional study was conducted among 232 medical students in a private medical college using an online questionnaire. The questionnaire was a modified Standardized Nordic Questionnaire focused on neck, shoulder and low back pain in the past week and the past year. Two hundred and thirty two medical students responded to the questionnaire out of 642. Mean age was 20.7 ± 2.1 years. The majority were female (62.9%), Malay (80.6%) and in the preclinical years (72%). One hundred and six (45.7%) of all students had at least one site of MSP in the past week and 151 (65.1%) had at least one site of MSP in the past year. MSP in the past week was associated significantly with the academic year, (OR 2.0, 95% CI 1.15-3.67, P = 0.015), history of trauma (OR 2.6, 95% CI 1.2-5.3, P = 0.011), family history of MSP (OR 2.1, 95% CI 1.1-3.9, P = 0.023) and Body Mass Index (BMI) (P = 0.028). MSP in the past year was significantly associated with computer use (P = 0.027), daily hours of computer use (median ± IQR (5.0 ±3.0), history of trauma (OR 7.5, 95% CI 2.24-2.56, P < 0.01) and family history of MSP (OR 2.5, 95% CI 1.31-4.90, P = 0.006). On multivariate analysis, factors associated with MSP during the past week were a family history of MSP (p = 0.029) and BMI (p = 0.03). Factors associated with MSP during the past year were being in clinical years (p = 0.002, computer use (p = 0.038), and a history of trauma (p = 0.030). MSP among medical students was relatively high, thus, further clinical assessment is needed in depth study of ergonomics. The study results indicate that medical school authorities should take measures to prevent MSP due to factors related to medical school. Students should make aware of importance of weight reduction to reduce MSP.
TL;DR: Nigerian mothers demonstrated good knowledge and positive attitude towards breastfeeding, and most of the mothers practiced advisable breastfeeding postures, preferred sitting on a chair to breastfeed and utilized cross-cradle hold and baby-to-breast latch-on.
Abstract: Background
Mothers’ poor knowledge and negative attitude towards breastfeeding may influence practices and constitute barriers to optimizing the benefits of the baby-friendly initiative. This study assessed breastfeeding knowledge, attitude and techniques of postures, positioning, hold practice and latch-on among Nigerian mothers from a Semi-Urban community.
TL;DR: 18s rRNA, Cyclophilin and APRT have been found to be appropriate for the normalization of real-time PCR data for gene expression studies in eggplant.
Abstract: Analysis of gene expression patterns leads to functional understanding of biological processes. Quantitative real-time PCR has become the most commonly used technique for in-depth studies of gene expression. To quantify variation in specific gene expression, accurate and reliable normalization across different samples and tissues is necessary. This can be achieved by selecting one or more suitable reference genes to compare the target mRNA transcript levels. In the present work, we illustrate the first evaluation of potential internal control or reference genes across different developmental stages of eggplant for reliable quantification of transcripts by real-time PCR. We have evaluated the stability in expression of six candidate reference genes (18s rRNA, APRT, GAPDH, Cyclophilin, Actin, and RuBP) in a set of tissues representing six developmental stages of eggplant. The candidate genes were cloned from cDNA and analysed by real-time PCR. The expression data analyzed by three statistical methods (geNorm, NormFinder and BestKeeper) identified 18s rRNA, Cyclophilin and APRT as the most stable and suitable reference genes in eggplant. This was further confirmed in four different varieties, two representative lines of transgenic eggplant as well as in nematode infected eggplant. 18s rRNA, Cyclophilin and APRT have been found to be appropriate for the normalization of real-time PCR data for gene expression studies in eggplant.
TL;DR: The snoRNA orthological gene database (snOPY) is introduced, which provides comprehensive information about the small nucleolar RNAs and their orthologues and will help users to study RNA modifications and sno RNA gene evolution.
Abstract: Background
Small nucleolar RNAs (snoRNAs) are a class of non-coding RNAs that guide the modification of specific nucleotides in ribosomal RNAs (rRNAs) and small nuclear RNAs (snRNAs). Although most non-coding RNAs undergo post-transcriptional modifications prior to maturation, the functional significance of these modifications remains unknown. Here, we introduce the snoRNA orthological gene database (snOPY) as a tool for studying RNA modifications.
TL;DR: The above evidences suggest that APE of A. procera leaf is a potential source of natural antioxidant and can be used to prevent diseases associated with free radicals.
Abstract: Research on natural products has gained a wide popularity due to the potential of discovering active compounds. The antioxidant properties contained in plants have been proposed as one of the mechanisms for the observed beneficial effect. Therefore, the present study investigated the antioxidant activity and total phenolic contents of various solvent extracts of Albizia procera leaves. Antioxidant activity of the methanol extract and its derived fractions petroleum ether (APP), carbon tetrachloride (APC), dichloromethane (APD), ethyl acetate (APE), and residual aqueous fraction (APA) of the leaves of Albizia procera was performed by in vitro chemical analyses. Total phenolic content of the APM and other five fractions were also determined. APM and its derived fractions were also subjected to preliminary phytochemical screening test for various constituents. Phytochemical screening revealed the presence of saponins, steroids, tannins, glycosides and flavonoids in the extracts. Amongst the extracts, APE showed the highest total phenolic content (449.18 ± 18.41mg of gallic acid equivalent/g of extract). In DPPH (1,1-diphenyl-2-picrylhydrazyl) radical scavenging test, the IC50 value of APM, APP, APC, APD, APE and APA was 43.43, 63.60, 166.18, 41.15, 11.79, and 63.06 μg/mL, respectively. Therefore, among the APM and its derived fractions, APE showed the highest antioxidant activity which is comparable to that of standard ascorbic acid (AA) (IC50 10.12 μg/mL). The total antioxidant capacity was found to be varied in different fractions. The reducing activity on ferrous ion was ranked as APE > APD > APM > APA > APC. The above evidences suggest that APE of A. procera leaf is a potential source of natural antioxidant and can be used to prevent diseases associated with free radicals.
TL;DR: An emerging and moderately high prevalence of ESBL-producing E.coli and K. pneumoniae in urinary isolates at a centrally located major tertiary care hospital in Kathmandu valley, Nepal was observed and confirmed in the urinary isolate investigated.
Abstract: Background
Escherichia coli and Klebsiella pneumoniae are the major bacterial pathogens being isolated and reported from mid stream urine (MSU) specimens, globally. These uropathogens are mostly implicated as the major extended spectrum beta-lactamase (ESBL) producers, severely limiting the therapeutic management in cases of urinary tract infections. Limited studies had been reported from Nepal investigating the ESBL producers among uropathogens. This study was designed to assess the prevalence of ESBL producing E.coli and K. pneumoniae in urinary isolates at a centrally located major tertiary care hospital in Kathmandu valley, Nepal.
TL;DR: A seeding density of not less than 10,000 cells per cm2 is proposed for regular passage of primary human corneal endothelial cells to elucidate an optimal seedingdensity for their extended expansion in vitro whilst maintaining their unique cellular morphology.
Abstract: Global shortage of donor corneas greatly restricts the numbers of corneal transplantations performed yearly. Limited ex vivo expansion of primary human corneal endothelial cells is possible, and a considerable clinical interest exists for development of tissue-engineered constructs using cultivated corneal endothelial cells. The objective of this study was to investigate the density-dependent growth of human corneal endothelial cells isolated from paired donor corneas and to elucidate an optimal seeding density for their extended expansion in vitro whilst maintaining their unique cellular morphology. Established primary human corneal endothelial cells were propagated to the second passage (P2) before they were utilized for this study. Confluent P2 cells were dissociated and seeded at four seeding densities: 2,500 cells per cm2 (‘LOW’); 5,000 cells per cm2 (‘MID’); 10,000 cells per cm2 (‘HIGH’); and 20,000 cells per cm2 (‘HIGH×2’), and subsequently analyzed for their propensity to proliferate. They were also subjected to morphometric analyses comparing cell sizes, coefficient of variance, as well as cell circularity when each culture became confluent. At the two lower densities, proliferation rates were higher than cells seeded at higher densities, though not statistically significant. However, corneal endothelial cells seeded at lower densities were significantly larger in size, heterogeneous in shape and less circular (fibroblastic-like), and remained hypertrophic after one month in culture. Comparatively, cells seeded at higher densities were significantly homogeneous, compact and circular at confluence. Potentially, at an optimal seeding density of 10,000 cells per cm2, it is possible to obtain between 10 million to 25 million cells at the third passage. More importantly, these expanded human corneal endothelial cells retained their unique cellular morphology. Our results demonstrated a density dependency in the culture of primary human corneal endothelial cells. Sub-optimal seeding density results in a decrease in cell saturation density, as well as a loss in their proliferative potential. As such, we propose a seeding density of not less than 10,000 cells per cm2 for regular passage of primary human corneal endothelial cells.
TL;DR: Improving participation rates in epidemiological studies may require different recruitment strategies for men and women in order to address sex-specific concerns about participating in research, as investigated in the Geelong Osteoporosis Study.
Abstract: Background: Understanding reasons for non-participation in health studies can help guide recruitment strategies and inform researchers about potential sources of bias in their study sample. Whilst there is a paucity of literature regarding this issue, it remains highly plausible that men and women may have varied reasons for declining an invitation to participate in research. We aimed to investigate sex-differences in the reasons for non-participation at baseline of the Geelong Osteoporosis Study (GOS). Methods: The GOS, a prospective cohort study, randomly recruited men and women aged 20 years and over from a region in south-eastern Australia using Commonwealth electoral rolls (2001–06 and 1993–97, respectively). Reasons for non-participation (n=1,200) were documented during the two recruitment periods. We used the Pearson’s chi squared test to explore differences in the reasons for non-participation between men and women. Results: Non-participation in the male cohort was greater than in the female cohort (32.9% vs. 22.9%; p<0.001). Overall, there were sex-differences in the reasons provided for non-participation (p<0.001); apparent differences related to time constraints (men 26.3% vs. women 10.4%), frailty/inability to cope with or understand the study (men 18.7% vs. women 30.6%), and reluctance over medical testing (men 1.1% vs women 9.9%). No sex-differences were observed for non-participation related to personal reason/disinterest, and language- or travel-related reasons. Conclusions: Improving participation rates in epidemiological studies may require different recruitment strategies for men and women in order to address sex-specific concerns about participating in research.
TL;DR: Exposure of HUVECs to leptin up-regulated Ob-Ra expression and elevated ERK1/2 phosphorylation and NFkB activation, and increased TNF-alpha secretion was exposed, and these effects strongly suppressed by quercetin.
Abstract: High concentrations of plasma leptin and the release of pro-inflammatory cytokines in leptin-resistance in obesity have been reported to trigger endothelial dysfunction. The objective of this study was to elucidate the role of quercetin in modulating leptin-induced inflammation as assessed by the levels of Ob-Ra expression, ERK1/2 phosphorylation, NF-kappa B activation and TNF-alpha secretion in umbilical vein endothelial cells (HUVECs) in vitro. HUVECs were exposed to either control levels (0 ng/ml) or 500 ng/mL leptin (L) for 48 hours, followed by control or 125 uM quercetin (Q) for another 6 h. The experimental groups were as follows: L0Q0, L0Q125, L500Q0, L500Q125. The presence of the short chain leptin receptor isoform Ob-Ra in HUVECs was determined by Western blot and immunocytochemistry analyses. Ob-Ra expression, ERK1/2 phosphorylation, NF-kappa B activation and TNF-alpha secretion were quantified by ELISA, and NF-kappa B activationby immunofluorescence staining. Our results showed that Ob-Ra expression, ERK1/2 phosphorylation and NF-kappa B activation increased significantly after 500 ng/mL leptin exposure (1.8x, 1.5x, 6.2x for Ob-Ra, ERK1/2 and NF-kappa B, respectively), but were reduced by addition of 125 uM quercetin (0.7x, 0.3x and 0.4x for Ob-Ra, ERK1/2 and NF-kappa B, respectively), and that quercetin could also partially suppress leptin-induced TNF-alpha secretion (3.8x) by 0.8x. Exposure of HUVECs to leptin up-regulated Ob-Ra expression and elevated ERK1/2 phosphorylation and NFkB activation, and increased TNF-alpha secretion. These effects strongly suppressed by quercetin, with the exception of TNF-alpha which was partially suppressed. The findings might be of clinical significance, as endothelial dysfunction that could lead to cardiovascular disease is preventable, and quercetin is a natural compound found in various plants and fruits.
TL;DR: There are significant variations in the policies and recommendations around mask and respirator use for protection against influenza, SARS and TB and these differences may reflect the scarcity of level-one evidence available to inform policy development.
Abstract: Currently there is an ongoing debate and limited evidence on the use of masks and respirators for the prevention of respiratory infections in health care workers (HCWs). This study aimed to examine available policies and guidelines around the use of masks and respirators in HCWs and to describe areas of consistency between guidelines, as well as gaps in the recommendations, with reference to the WHO and the CDC guidelines. Policies and guidelines related to mask and respirator use for the prevention of influenza, SARS and TB were examined. Guidelines from the World Health Organization (WHO), the Center for Disease Control and Prevention (CDC), three high-income countries and six low/middle-income countries were selected. Uniform recommendations are made by the WHO and the CDC in regards to protecting HCWs against seasonal influenza (a mask for low risk situations and a respirator for high risk situations) and TB (use of a respirator). However, for pandemic influenza and SARS, the WHO recommends mask use in low risk and respirators in high risk situations, whereas, the CDC recommends respirators in both low and high risk situations. Amongst the nine countries reviewed, there are variations in the recommendations for all three diseases. While, some countries align with the WHO recommendations, others align with those made by the CDC. The choice of respirator and the level of filtering ability vary amongst the guidelines and the different diseases. Lastly, none of the policies discuss reuse, extended use or the use of cloth masks. Currently, there are significant variations in the policies and recommendations around mask and respirator use for protection against influenza, SARS and TB. These differences may reflect the scarcity of level-one evidence available to inform policy development. The lack of any guidelines on the use of cloth masks, despite widespread use in many low and middle-income countries, remains a policy gap. Health organizations and countries should jointly evaluate the available evidence, prioritize research to inform evidence gaps, and develop consistent policy on masks and respirator use in the health care setting.
TL;DR: A feeding protocol for infants ≤ 1250 g BW providing an exclusive human milk-based diet with early and rapid advancement of fortification leads to growth meeting targeted standards with a low rate of extrauterine growth restriction.
Abstract: Despite current nutritional strategies, premature infants remain at high risk for extrauterine growth restriction. The use of an exclusive human milk-based diet is associated with decreased incidence of necrotizing enterocolitis (NEC), but concerns exist about infants achieving adequate growth. The objective of this study was to evaluate growth velocities and incidence of extrauterine growth restriction in infants ≤ 1250 grams (g) birth weight (BW) receiving an exclusive human milk-based diet with early and rapid advancement of fortification using a donor human milk derived fortifier. In a single center, prospective observational cohort study, preterm infants weighing ≤ 1250 g BW were fed an exclusive human milk-based diet until 34 weeks postmenstrual age. Human milk fortification with donor human milk derived fortifier was started at 60 mL/kg/d and advanced to provide 6 to 8 additional kilocalories per ounce (or 0.21 to 0.28 kilocalories per gram). Data for growth were compared to historical growth standards and previous human milk-fed cohorts. We consecutively evaluated 104 infants with mean gestational age of 27.6 ± 2.0 weeks and BW of 913 ± 181 g (mean ± standard deviation). Weight gain was 24.8 ± 5.4 g/kg/day with length 0.99 ± 0.23 cm/week and head circumference 0.72 ± 0.14 cm/week. There were 3 medical NEC cases and 1 surgical NEC case. 22 infants (21%) were small for gestational age at birth. Overall, 45 infants (43%) had extrauterine growth restriction. Weight velocity was affected by day of fortification (p = 0.005) and day of full feeds (p = 0.02). Our cohort had significantly greater growth in weight and length compared to previous entirely human milk-fed cohorts. A feeding protocol for infants ≤ 1250 g BW providing an exclusive human milk-based diet with early and rapid advancement of fortification leads to growth meeting targeted standards with a low rate of extrauterine growth restriction. Consistent nutritional policies using this approach may be considered for this population.
TL;DR: In this article, the accuracy of infrared tympanic thermometers in comparison to mercury thermometers was compared in the measurement of body temperature in Omdurman Hospital, Sudan during the month of October 2012, and the mean difference between the two readings was - 0.093 (−0.20; 0.02) °C.
Abstract: During investigation and diagnosis of patients, accurate temperature measurement is of great importance. The advantages of tympanic membrane thermometry are speed (temperature reading available within seconds), safety, and ease of use. The aim of this study was to compare the accuracy of infrared tympanic thermometers in comparison to mercury thermometers in measurement of body temperature. Axillary and tympanic temperature was measured simultaneously in consecutive patients using mercury glass and infrared tympanic thermometers at Omdurman Hospital, Sudan during October 2012. In total, temperature was measured in 174 patients, 95 of whom (54.6%) were male. The mean (SD) patient age and weight was 33.18 (25.07) years and 52.13 (69.85) kg. There was no significant difference in mean (SD) temperature measurement between mercury and infrared tympanic membrane thermometers, 37.29°C (0.91) versus 37.38°C (0.95), P = 0.373, respectively. There was a significant positive correlation between axillary and tympanic body temperature measurements (r = 0.697, P < 0.001). The mean difference between the two readings (with limits of agreements) was - 0.093 (−0.20; 0.02) °C. In this study, tympanic membrane thermometry is as reliable and accurate as axillary mercury glass thermometry. Thus, tympanic thermometry can be used in clinical practice, especially in the emergency setting, where ease of use and speed of obtaining the temperature reading are important.
TL;DR: Overall, this study suggests that MSD are a reasonably common problem for Australian dental hygienists, and that they often need to seek medical treatment for these problems.
Abstract: Recent literature has identified that musculoskeletal disorders (MSD) are a significant occupational health issue for both dentists and dental hygienists. Research on the occupational health of dental hygienists is lacking in Australia, which is of particular concern given that it is a rapidly growing field in this country. The aims of this research are to investigate the prevalence of MSD and correlating regions of pain among Australian dental hygienists. A self-reporting questionnaire was distributed to all registered dental hygienists in Australia. The questionnaire was a modified version of a validated tool, used previously among health practitioners and students. A total of 624 dental hygienists responded to the questionnaire, achieving a response rate of 42%. MSD were frequently reported by dental hygienists in the neck (85%), shoulder (70%), and lower back (68%). Of those reporting pain, over two thirds reported that the pain lasted for longer than two days, for all body regions. Logistic regression analysis revealed that there is a correlation between reports of MSD in the neck, shoulder and lower back regions. Overall, this study suggests that MSD are a reasonably common problem for Australian dental hygienists, and that they often need to seek medical treatment for these problems. It is concerning that there is a correlation between reports of MSD in the neck, shoulder and lower back regions; further studies are needed to establish the epidemiological patterns of MSD in this profession.
TL;DR: Though, low levels of co-infection with all three viruses were reported, there could be higher prevalence rates than reported here especially among high risk populations.
Abstract: Hepatitis B virus (HBV) and Hepatitis C virus (HCV) co-infections among HIV-1 infected individuals are growing worldwide health problems characterized by lack of effective vaccines, need for expensive treatment, chronicity of morbidity and associated mortality. Their prevalence and distribution patterns continue to vary across geographical locations with high prevalence being detected among high risk populations. To determine the prevalence of HBV and HCV among HIV-1 infected individuals, blood samples were collected from consenting study subjects visiting comprehensive HIV clinics in Nairobi during the period between October and December 2009. Blood samples from volunteers were screened with ELISA tests for detecting HIV, HBV surface antigen (HBsAg) and anti-HCV antibodies. In a total of three (300) hundred infected individuals consisting of 129 (43%) males and 171 (57%) females 15.3% (46/300) were HIV-1 co-infected with either HBV or HCV or both, 10.3% (31/300) with HIV-1 and HCV and 6% (18/300) with HIV-1 and HBV infections. However, only three individuals (1%) were coinfected with the three viruses (HIV/HBV/HCV). Though, low levels of co-infection with all three viruses were reported, there could be higher prevalence rates than reported here especially among high risk populations.
TL;DR: With the number of genomes sequenced increasing daily and interest in determining phylogenetic relationships, CoreGenes3.5 provides a user-friendly web interface for wet-bench biologists to process multiple small genomes for core gene determinations.
Abstract: Background: CoreGenes3.5 is a webserver that determines sets of core genes from viral and small bacterial genomes as an automated batch process. Previous versions of CoreGenes have been used to classify bacteriophage genomes and mine data from pathogen genomes. Findings: CoreGenes3.5 accepts as input GenBank accession numbers of genomes and performs iterative BLASTP analyses to output a set of core genes. After completion of the program run, the results can be either displayed in a new window for one pair of reference and query genomes or emailed to the user for multiple pairs of small genomes in tabular format. Conclusions: With the number of genomes sequenced increasing daily and interest in determining phylogenetic relationships, CoreGenes3.5 provides a user-friendly web interface for wet-bench biologists to process multiple small genomes for core gene determinations. CoreGenes3.5 is available at http://binf.gmu.edu:8080/CoreGenes3.5.
TL;DR: A de novo probabilistic measure of assembly quality which allows for an objective comparison of multiple assemblies generated from the same set of reads and highlights the application of the score to optimize assembly parameters used in genome assemblers, which enables better assemblies to be produced, even without prior knowledge of the genome being assembled.
Abstract: The current revolution in genomics has been made possible by software tools called genome assemblers, which stitch together DNA fragments “read” by sequencing machines into complete or nearly complete genome sequences. Despite decades of research in this field and the development of dozens of genome assemblers, assessing and comparing the quality of assembled genome sequences still relies on the availability of independently determined standards, such as manually curated genome sequences, or independently produced mapping data. These “gold standards” can be expensive to produce and may only cover a small fraction of the genome, which limits their applicability to newly generated genome sequences. Here we introduce a de novo probabilistic measure of assembly quality which allows for an objective comparison of multiple assemblies generated from the same set of reads. We define the quality of a sequence produced by an assembler as the conditional probability of observing the sequenced reads from the assembled sequence. A key property of our metric is that the true genome sequence maximizes the score, unlike other commonly used metrics. We demonstrate that our de novo score can be computed quickly and accurately in a practical setting even for large datasets, by estimating the score from a relatively small sample of the reads. To demonstrate the benefits of our score, we measure the quality of the assemblies generated in the GAGE and Assemblathon 1 assembly “bake-offs” with our metric. Even without knowledge of the true reference sequence, our de novo metric closely matches the reference-based evaluation metrics used in the studies and outperforms other de novo metrics traditionally used to measure assembly quality (such as N50). Finally, we highlight the application of our score to optimize assembly parameters used in genome assemblers, which enables better assemblies to be produced, even without prior knowledge of the genome being assembled. Likelihood-based measures, such as ours proposed here, will become the new standard for de novo assembly evaluation.