A geomorphic and hydraulic investigation in the context of floodplain revegetation; based on a soil bioengineering application on the Mattole River, Petrolia, California, USA

As fluvial, riparian and floodplain ecosystem functions are recognised for their role supporting fisheries and ecological values, recovery of streamside vegetation is increasingly important in river 'restoration'. Fluvial geomorphology and hydraulic engineering do not yet account well for the role of vegetation in fluvial processes. This research addresses the need for greater understanding of woody riparian vegetation influences on the hydraulics of overbank flow and floodplains sedimentation. Original hypotheses, research design, and data collection were generated by the student to address this gap in knowledge. A soil bioengineering design was constructed on the Mattole River, California, to revegetate the floodplain for better fish rearing habitat. Field data collection was carried out on this unregulated river for two flood events. The sediment samples resulting from a 1.25-year flow permitted the field testing of an hydraulic flume model of vegetation trapping efficiency. From velocity profiles measured during a I5-year storm event, the bed shear stress reduction caused by the vegetation was computed to be approximately 70-90%. A survey conducted in the UK and internationally evaluated from literature, hydraulic researchers and practitioners of river revegetation, the extent of and gaps in knowledge with regard to river bank stabilisation using live vegetation. A flume flow visualisation study simulated the hydraulic behaviour observed on the Mattole floodplain, which enabled characterisation of flow behaviour through a porous filter medium. Results of this research indicate that flexible woody stems have a profound 'calming' effect on overbank flow. These effects are propagated in the downstream direction at least five and as much as ten times the width of the baffle, much further than previously indicated. This research suggests that flexible vegetation is extremely effective in trapping fine (clay) sediments, contrary to general understanding and of importance for fish habitat. For hydraulic reasons, constructed zones of shrubs, such as the siltation baffle, could be spaced further apart than current design practise indicates

Isolation and speciation of genus candida in patients undergoing chemotherapy and radiotherapy for head and neck tumours

Background: Fungal infections occur as a result of defect in the immune system. The use of wide-spectrum antibiotics, immunosuppressive therapy, HIV and an increasing incidence of diabetes are some of the causes that resulted in raising number of immunocompromised individuals, in the global scenario. Opportunistic fungal infections mainly oral candidiasis is common in patients undergoing chemotherapy (CT) or radiotherapy (RT) for Head & Neck tumors. Objectives: Isolation and speciation of Candida with antifungal susceptibility testing in patients undergoing CT and RT for Head and Neck tumors.Methods: Study group comprised of 100 saliva samples collected by oral rinse method, (50 chemotherapy and 50 radiotherapy) from inpatients of King George hospital, Visakhapatnam and 50 normal healthy individuals were taken as control group. Standard mycological tests for the Candida isolation, speciation and antifungal susceptibility were done.Results: In the study group out of the 100 patients, 38% were culture positive for Candida. The most commonly isolated species was C. albicans (60.5%) followed by non albicans species. Most of the candida species showed sensitivity to nystatin, amphotericin B, itraconazole and Ketoconazole. In control group 9 out of 50 samples (18%) were culture positive and all the isolates were Candida albicans.Conclusion: Increase in frequency of oral candidiasis in patients undergoing chemotherapy and radiotherapy was observed. The increase in positivity may be attributed to inadequate nutritional status and poor oral hygiene during chemotherapy and radiotherapy. Culture positivity is more in RT patients than in CT patients. Though C. albicans is the predominant isolate, non albicans species are also emerging. All the Candida species isolated from study group were sensitive to nystatin, amphotericin B, itraconazole and ketoconazole. In the study group all the Candida species were resistant to clotrimazole and fluconazole and in the control group all the C. albicans were sensitive to fluconazole.  

miRNA-mRNA Integrated Analysis Reveals Roles for miRNAs in Primary Breast Tumors

Peer reviewe

Development of multivariable models to predict change in Body Mass Index within a clinical trial population of psychotic individuals

Many antipsychotics promote weight gain, which can lead to non-compliance and relapse of psychosis. By developing models that accurately identify individuals at greater risk of weight gain, clinicians can make informed treatment decisions and target intervention measures. We examined clinical, genetic and expression data for 284 individuals with psychosis derived from a previously published randomised controlled trial (IMPACT). These data were used to develop regression and classification models predicting change in Body Mass Index (BMI) over one year. Clinical predictors included demographics, anthropometrics, cardiac and blood measures, diet and exercise, physical and mental health, medication and BMI outcome measures. We included genetic polygenic risk scores (PRS) for schizophrenia, bipolar disorder, BMI, waist-hip-ratio, insulin resistance and height, as well as gene co-expression modules generated by Weighted Gene Co-expression Network Analysis (WGCNA). The best performing predictive models for BMI and BMI gain after one year used clinical data only, which suggests expression and genetic data do not improve prediction in this cohort

Individual and combined effects of DNA methylation and copy number alterations on miRNA expression in breast tumors

Peer reviewe

Gene x dietary pattern interactions in obesity : analysis of up to 68 317 adults of European ancestry

Obesity is highly heritable. Genetic variants showing robust associationswith obesity traits have been identified through genome wide association studies. We investigated whether a composite score representing healthy diet modifies associations of these variants with obesity traits. Totally, 32 body mass index (BMI)- and 14 waist-hip ratio (WHR)-associated single nucleotide polymorphismswere genotyped, and genetic risk scores (GRS) were calculated in 18 cohorts of European ancestry (n = 68 317). Diet score was calculated based on self-reported intakes of whole grains, fish, fruits, vegetables, nuts/seeds (favorable) and red/processed meats, sweets, sugar-sweetened beverages and fried potatoes (unfavorable). Multivariable adjusted, linear regression within each cohort followed by inverse variance-weighted, fixed-effects meta-analysis was used to characterize: (a) associations of each GRS with BMI and BMI-adjustedWHR and (b) diet score modification of genetic associations with BMI and BMI-adjusted WHR. Nominally significant interactions (P = 0.006-0.04) were observed between the diet score and WHR-GRS (but not BMI-GRS), two WHR loci (GRB14 rs10195252; LYPLAL1 rs4846567) and two BMI loci (LRRN6C rs10968576; MTIF3 rs4771122), for the respective BMI-adjustedWHR or BMI outcomes. Although the magnitudes of these select interactions were small, our data indicated that associations between genetic predisposition and obesity traits were stronger with a healthier diet. Our findings generate interesting hypotheses; however, experimental and functional studies are needed to determine their clinical relevance.Peer reviewe

Habitual coffee consumption and cognitive function: a Mendelian randomization meta-analysis in up to 415,530 participants

Coffee's long-term effect on cognitive function remains unclear with studies suggesting both benefits and adverse effects. We used Mendelian randomization to investigate the causal relationship between habitual coffee consumption and cognitive function in mid-to later life. This included up to 415,530 participants and 300,760 coffee drinkers from 10 meta-analysed European ancestry cohorts. In each cohort, composite cognitive scores that capture global cognition and memory were computed using available tests. A genetic score derived using CYP1A1/2 (rs2472297) and AHR (rs6968865) was chosen as a proxy for habitual coffee consumption. Null associations were observed when examining the associations of the genetic score with global and memory cognition (beta = -0.0007, 95% C.I. -0.009 to 0.008, P = 0.87; beta = -0.001, 95% C.I. -0.005 to 0.002, P = 0.51, respectively), with high consistency between studies (P-heterogeneity > 0.4 for both). Domain specific analyses using available cognitive measures in the UK Biobank also did not support effects by habitual coffee intake for reaction time, pairs matching, reasoning or prospective memory (P >= 0.05 for all). Despite the power to detect very small effects, our meta-analysis provided no evidence for causal long-term effects of habitual coffee consumption on global cognition or memory