An immobilized cell bioreactor for the malolactic fermentation of wine : a thesis submitted in partial fulfilment of the requirements for the degree of Master of Technology in Biotechnology at Massey University

Malolactic fermentation using immobilized cells of Leuconostoc oenos was investigated in order to improve this fermentation at an industrial-scale. Three strains of bacteria were investigated in some detail, and one was chosen for further work. A satisfactory growth medium for the strain of bacteria used was found to be an apple juice broth. The effect, on both the growth and malic acid bioconversion for Leuconostoc oenos strain 1070, of having 6% v/v ethanol in the growth media was tested and found to cause a longer lag phase, and be slightly beneficial, respectively. Oak chips were decided on as the immobilization media, in preference to bone char, and a synthetic, apple-juice based wine was used to determine operation parameters for a continuous culture bioreactor. Temperature, pH, ethanol concentration, SO2, malic acid concentrations, anaerobic conditions and dilution rate were investigated and it was shown that lower malic acid concentrations, and also an interaction between low pH, high temperature and high ethanol concentration affected the malic acid bioconversion adversely. Increasing the dilution rate above 0.35 h·1 caused a 30% drop in the bioconversion rate. The pH level had no effect on bioconversion if the temperature was kept at 21°C or lower. Decreasing the temperature, increasing the ethanol concentration above 10% v/v and increasing SO2 levels all caused a slight drop in bioconversion rates while strict anaerobic growth and bioconversion conditions caused an increase. The bioconversion rates ranged between 20 and 100 mg malic acid consumed/lO0ml oak chips/hour. An industrial prototype bioreactor was built and used at Villa Maria Wineries, Auckland, during the 1991 vintage and successfully processed 200 litres of Chardonnay-style wine in 2 days. The bioconversion rate was between 25 and 30 mg malic acid consumed/l00ml oak chips/hour. Informal taste tests showed satisfactory malolactic characteristics in the treated wine

Effects of Self-explaining on Learning and Transfer of Critical Thinking Skills

Critical thinking is considered to be an important competence for students and graduates of higher education. Yet, it is largely unclear which teaching methods are most effective in supporting the acquisition of critical thinking skills, especially regarding one important aspect of critical thinking: avoiding biased reasoning. The present study examined whether creating desirable difficulties in instruction by prompting students to generate explanations of a problem-solution to themselves (i.e., self-expl

Elevated Risk for HIV-1 Infection in Adolescents and Young Adults in São Paulo, Brazil

Background. Recent studies have sought to describe HIV infection and transmission characteristics around the world. Identification of early HIV-1 infection is essential to proper surveillance and description of regional transmission trends. In this study we compare people recently infected (RI) with HIV-1, as defined by Serologic Testing Algorithm for Recent HIV Seroconversion (STARHS), to those with chronic infection. Methodology/Principal Findings Subjects were identified from 2002-2004 at four testing sites in São Paulo. Of 485 HIV-1-positive subjects, 57 (12%) were defined as RI. Of the participants, 165 (34.0%) were aware of their serostatus at the time of HIV-1 testing. This proportion was statistically larger (p<0.001) among the individuals without recent infection (n = 158, 95.8%) compared to 7 individuals (4.2%) with recently acquired HIV-1 infection. In the univariate analysis, RI was more frequent in <25 and >59 years-old age strata (p<0.001). The majority of study participants were male (78.4%), 25 to 45 years-old (65.8%), white (63.2%), single (61.7%), with family income of four or more times the minimum wage (41.0%), but with an equally distributed educational level. Of those individuals infected with HIV-1, the predominant route of infection was sexual contact (89.4%), with both hetero (47.5%) and homosexual (34.5%) exposure. Regarding sexual activity in these individuals, 43.9% reported possible HIV-1 exposure through a seropositive partner, and 49.4% reported multiple partners, with 47% having 2 to 10 partners and 37.4% 11 or more; 53.4% of infected individuals reported condom use sometimes; 34.2% reported non-injecting, recreational drug use and 23.6% were reactive for syphilis by VDRL. Subjects younger than 25 years of age were most vulnerable according to the multivariate analysis. ) Conclusions/Significance In this study, we evaluated RI individuals and discovered that HIV-1 has been spreading among younger individuals in São Paulo and preventive approaches should, therefore, target this age stratu

Prevalence and correlates of adherence to the Global Total Physical Activity Guideline based on step counting among 3- to 4-year-olds : evidence from SUNRISE pilot studies from 17 countries

Background: There is limited evidence from globally diverse samples on the prevalence and correlates of meeting the global guideline of 180 minutes per day of total physical activity (TPA) among 3- to 4-year-olds. Methods: Cross-sectional study involving 797 (49.2% girls) 3- to 4-year-olds from 17 middle- and high-income countries who participated in the pilot phases 1 and 2 of the SUNRISE International Study of Movement Behaviours in the Early Years. Daily step count was measured using thigh-worn activPAL accelerometers. Children wore the accelerometers for at least one 24-hour period. Children were categorized as meeting the TPA guideline based on achieving ≥11,500 steps per day. Descriptive analyses were conducted to describe the proportion of meeting the TPA guideline for the overall sample and each of the sociodemographic variables, and 95% CIs were calculated. Multivariable logistic regression was used to determine the sociodemographic correlates of meeting the TPA guideline. Results: Mean daily step count was 10,295 steps per day (SD = 4084). Approximately one-third of the sample (30.9%, 95% CI, 27.6–34.2) met the TPA guideline. The proportion meeting the guideline was significantly lower among girls (adjusted OR [aOR] = 0.70, 95% CI, 0.51–0.96) and 4-year-olds (aOR = 0.50, 95% CI, 0.34–0.75) and higher among rural residents (aOR = 1.78, 95% CI, 1.27–2.49) and those from lower middle-income countries (aOR = 1.35, 95% CI, 0.89–2.04). Conclusions: The findings suggest that a minority of children might meet the TPA guideline globally, and the risk of not meeting the guideline differed by sociodemographic indicators. These findings suggest the need for more surveillance of TPA in young children globally and, possibly, interventions to improve childhood health and development

Pan-cancer Alterations of the MYC Oncogene and Its Proximal Network across the Cancer Genome Atlas

Although theMYConcogene has been implicated incancer, a systematic assessment of alterations ofMYC, related transcription factors, and co-regulatoryproteins, forming the proximal MYC network (PMN),across human cancers is lacking. Using computa-tional approaches, we define genomic and proteo-mic features associated with MYC and the PMNacross the 33 cancers of The Cancer Genome Atlas.Pan-cancer, 28% of all samples had at least one ofthe MYC paralogs amplified. In contrast, the MYCantagonists MGA and MNT were the most frequentlymutated or deleted members, proposing a roleas tumor suppressors.MYCalterations were mutu-ally exclusive withPIK3CA,PTEN,APC,orBRAFalterations, suggesting that MYC is a distinct onco-genic driver. Expression analysis revealed MYC-associated pathways in tumor subtypes, such asimmune response and growth factor signaling; chro-matin, translation, and DNA replication/repair wereconserved pan-cancer. This analysis reveals insightsinto MYC biology and is a reference for biomarkersand therapeutics for cancers with alterations ofMYC or the PMN

Pan-Cancer Analysis of lncRNA Regulation Supports Their Targeting of Cancer Genes in Each Tumor Context

Long noncoding RNAs (lncRNAs) are commonly dys-regulated in tumors, but only a handful are known toplay pathophysiological roles in cancer. We inferredlncRNAs that dysregulate cancer pathways, onco-genes, and tumor suppressors (cancer genes) bymodeling their effects on the activity of transcriptionfactors, RNA-binding proteins, and microRNAs in5,185 TCGA tumors and 1,019 ENCODE assays.Our predictions included hundreds of candidateonco- and tumor-suppressor lncRNAs (cancerlncRNAs) whose somatic alterations account for thedysregulation of dozens of cancer genes and path-ways in each of 14 tumor contexts. To demonstrateproof of concept, we showed that perturbations tar-geting OIP5-AS1 (an inferred tumor suppressor) andTUG1 and WT1-AS (inferred onco-lncRNAs) dysre-gulated cancer genes and altered proliferation ofbreast and gynecologic cancer cells. Our analysis in-dicates that, although most lncRNAs are dysregu-lated in a tumor-specific manner, some, includingOIP5-AS1, TUG1, NEAT1, MEG3, and TSIX, synergis-tically dysregulate cancer pathways in multiple tumorcontexts

Genomic, Pathway Network, and Immunologic Features Distinguishing Squamous Carcinomas

This integrated, multiplatform PanCancer Atlas study co-mapped and identified distinguishing molecular features of squamous cell carcinomas (SCCs) from five sites associated with smokin

Spatial Organization and Molecular Correlation of Tumor-Infiltrating Lymphocytes Using Deep Learning on Pathology Images

Beyond sample curation and basic pathologic characterization, the digitized H&E-stained images of TCGA samples remain underutilized. To highlight this resource, we present mappings of tumorinfiltrating lymphocytes (TILs) based on H&E images from 13 TCGA tumor types. These TIL maps are derived through computational staining using a convolutional neural network trained to classify patches of images. Affinity propagation revealed local spatial structure in TIL patterns and correlation with overall survival. TIL map structural patterns were grouped using standard histopathological parameters. These patterns are enriched in particular T cell subpopulations derived from molecular measures. TIL densities and spatial structure were differentially enriched among tumor types, immune subtypes, and tumor molecular subtypes, implying that spatial infiltrate state could reflect particular tumor cell aberration states. Obtaining spatial lymphocytic patterns linked to the rich genomic characterization of TCGA samples demonstrates one use for the TCGA image archives with insights into the tumor-immune microenvironment

Validity of low-cost measures for global surveillance of physical activity in pre-school children : the SUNRISE validation study

Objective: To validate parent-reported child's habitual total physical activity (TPA) against accelerometry and three existing step-count thresholds for classifying 3 h/day of TPA in pre-schoolers from 13 culturally and geographically diverse countries. Design: Cross-sectional validation study. Methods: We used data involving 3- and 4-year-olds from 13 middle- and high-income countries who participated in the SUNRISE study. We used Spearman's rank-order correlation, Bland-Altman plots, and Kappa statistics to assess correlation and classification ability of parent-reported child's habitual TPA against activPAL™-measured TPA over 3 days. Additionally, we used Receiver Operating Characteristic Area Under the Curve (ROC-AUC) analysis to validate three existing step-count thresholds (Gabel, Vale, and De Craemer) for accurately classifying achievement of the WHO guideline of at least 3 h/day TPA using step-counts derived from activPAL™. Results: Of the 352 pre-schoolers, 49.1 % were girls. There was a very weak but significant positive correlation and slight agreement between parent-reported and accelerometer-measured TPA (r: 0.140; p = 0.009; Kappa: 0.030). Parents over-estimated their child's TPA compared to accelerometer data (mean bias: 69 min/day; standard deviation: 126; 95 % limits of agreement: −179, 316). Of the three step-count thresholds tested, the De Craemer step-count threshold of 11,500 steps/day provided excellent classification of meeting the TPA guideline as measured by accelerometry (AUC: 0.945; 95 % CI: 0.928, 0.961; Sensitivity: 100.0 %; Specificity: 88.9 %). Conclusions: Parent reports may have limited validity for assessing pre-schooler's level of TPA. Step-counting is a promising alternative – low-cost global surveillance initiatives could potentially use pedometers for assessing compliance with the physical activity guideline in early childhood

Cross-sectional examination of 24-hour movement behaviours among 3-and 4-year-old children in urban and rural settings in low-income, middle-income and high-income countries : the SUNRISE study protocol

Introduction 24-hour movement behaviours (physical activity, sedentary behaviour and sleep) during the early years are associated with health and developmental outcomes, prompting the WHO to develop Global guidelines for physical activity, sedentary behaviour and sleep for children under 5 years of age. Prevalence data on 24-hour movement behaviours is lacking, particularly in low-income and middle-income countries (LMICs). This paper describes the development of the SUNRISE International Study of Movement Behaviours in the Early Years protocol, designed to address this gap. Methods and analysis SUNRISE is the first international cross-sectional study that aims to determine the proportion of 3- and 4-year-old children who meet the WHO Global guidelines. The study will assess if proportions differ by gender, urban/rural location and/or socioeconomic status. Executive function, motor skills and adiposity will be assessed and potential correlates of 24-hour movement behaviours examined. Pilot research from 24 countries (14 LMICs) informed the study design and protocol. Data are collected locally by research staff from partnering institutions who are trained throughout the research process. Piloting of all measures to determine protocol acceptability and feasibility was interrupted by COVID-19 but is nearing completion. At the time of publication 41 countries are participating in the SUNRISE study. Ethics and dissemination The SUNRISE protocol has received ethics approved from the University of Wollongong, Australia, and in each country by the applicable ethics committees. Approval is also sought from any relevant government departments or organisations. The results will inform global efforts to prevent childhood obesity and ensure young children reach their health and developmental potential. Findings on the correlates of movement behaviours can guide future interventions to improve the movement behaviours in culturally specific ways. Study findings will be disseminated via publications, conference presentations and may contribute to the development of local guidelines and public health interventions.Peer reviewe