Transkingdom Networks: A Systems Biology Approach to Identify Causal Members of Host-Microbiota Interactions

Improvements in sequencing technologies and reduced experimental costs have resulted in a vast number of studies generating high-throughput data. Although the number of methods to analyze these "omics" data has also increased, computational complexity and lack of documentation hinder researchers from analyzing their high-throughput data to its true potential. In this chapter we detail our data-driven, transkingdom network (TransNet) analysis protocol to integrate and interrogate multi-omics data. This systems biology approach has allowed us to successfully identify important causal relationships between different taxonomic kingdoms (e.g. mammals and microbes) using diverse types of data

Sugar sweetened beverage consumption by Australian children: Implications for public health strategy

<p>Abstract</p> <p>Background</p> <p>High consumption of sugar sweetened beverages (SSBs) has been linked to unhealthy weight gain and nutrition related chronic disease. Intake of SSB among children remains high in spite of public health efforts to reduce consumption, including restrictions on marketing to children and limitations on the sale of these products in many schools. Much extant literature on Australian SSB consumption is out-dated and lacks information on several key issues. We sought to address this using a contemporary Australian dataset to examine purchase source, consumption pattern, dietary factors, and demographic profile of SSB consumption in children.</p> <p>Methods</p> <p>Data were from the 2007 Australian National Children's Nutrition and Physical Activity Survey, a representative random sample of 4,834 Australian children aged 2-16 years. Mean SSB intake by type, location and source was calculated and logistic regression models were fitted to determine factors associated with different levels of consumption.</p> <p>Results</p> <p>SSB consumption was high and age-associated differences in patterns of consumption were evident. Over 77% of SSB consumed was purchased via supermarkets and 60% of all SSB was consumed in the home environment. Less than 17% of SSB was sourced from school canteens and fast food establishments. Children whose parents had lower levels of education consumed more SSB on average, while children whose parents had higher education levels were more likely to favour sweetened juices and flavoured milks.</p> <p>Conclusions</p> <p>SSB intake by Australian children remains high and warrants continued public health attention. Evidence based and age-targeted interventions, which also recognise supermarkets as the primary source of SSB, are recommended to reduce SSB consumption among children. Additionally, education of parents and children regarding the health consequences of high consumption of both carbonated and non-carbonated SSBs is required.</p

Can racial disparities in optimal gout treatment be reduced? evidence from a randomized trial

There is a disproportionate burden of gout in African-Americans in the U.S. due to a higher disease prevalence and lower likelihood of receiving urate-lowering therapy (ULT), compared to Caucasians. There is an absence of strong data as to whether the response to ULT differs by race/ethnicity. BMC Musculoskeletal Disorders recently published a secondary analyses of the CONFIRMS trial, a large randomized controlled, double-blind trial of 2,269 gout patients. The authors reported that the likelihood of achieving the primary study efficacy end-point of achieving serum urate < 6 mg/dl was similar between African-Americans and Caucasians, for all three treatment arms (Febuxostat 40 mg and 80 mg and allopurinol 300/200 mg). More importantly, rates were similar in subgroups of patients with mild or moderate renal insufficiency. Adverse event rates were similar, as were the rates of gout flares. These findings constitute a convincing evidence to pursue aggressive ULT in gout patients, regardless of race/ethnicity. This approach will likely help to narrow the documented racial disparities in gout care

Tracking of dietary intakes in early childhood : the Melbourne InFANT program

Background/Objectives: The objectives of the present study were to describe food and nutrient intakes in children aged 9 and 18 months, and to assess tracking of intakes between these two ages.Subjects/Methods: Participants were 177 children of first-time mothers from the control arm of the Melbourne Infant Feeding Activity and Nutrition Trial (InFANT) Program. Dietary intake was collected at 9 and 18 months using three 24&thinsp;h diet recalls. Tracking was assessed for food and nutrient intakes using logistic regression analysis and estimating partial correlation coefficients, respectively.Results: Although overall nutrient intakes estimated in this study did not indicate a particular risk of nutrient deficiency, our findings suggest that consumption of energy-dense, nutrient-poor foods occurred as early as 9 months of age, with some of these foods tracking highly over the weaning period. Intakes of healthier foods such as fruits, vegetables, dairy products, eggs, fish and water were also relatively stable over this transition from infancy to toddlerhood, along with moderate tracking for riboflavin, iodine, fibre, calcium and iron. Tracking was low but close to &rho;=0.3 for zinc, magnesium and potassium intakes.Conclusions: The tracking of energy-dense, nutrient-poor foods has important implications for public health, given the development of early eating behaviours is likely to be modifiable. At this stage of life, dietary intakes are largely influenced by the foods parents provide, parental feeding practices and modelling. This study supports the importance of promoting healthy dietary trajectories from infancy.<br /

Development and validation of multivariable machine learning algorithms to predict risk of cancer in symptomatic patients referred urgently from primary care: a diagnostic accuracy study

Objectives To develop and validate tests to assess the risk of any cancer for patients referred to the NHS Urgent Suspected Cancer (2-week wait, 2WW) clinical pathways. Setting Primary and secondary care, one participating regional centre. Participants Retrospective analysis of data from 371 799 consecutive 2WW referrals in the Leeds region from 2011 to 2019. The development cohort was composed of 224 669 consecutive patients with an urgent suspected cancer referral in Leeds between January 2011 and December 2016. The diagnostic algorithms developed were then externally validated on a similar consecutive sample of 147 130 patients (between January 2017 and December 2019). All such patients over the age of 18 with a minimum set of blood counts and biochemistry measurements available were included in the cohort. Primary and secondary outcome measures sensitivity, specificity, negative predictive value, positive predictive value, Receiver Operating Characteristic (ROC) curve Area Under Curve (AUC), calibration curves Results We present results for two clinical use-cases. In use-case 1, the algorithms identify 20% of patients who do not have cancer and may not need an urgent 2WW referral. In use-case 2, they identify 90% of cancer cases with a high probability of cancer that could be prioritised for review. Conclusions Combining a panel of widely available blood markers produces effective blood tests for cancer for NHS 2WW patients. The tests are affordable, and can be deployed rapidly to any NHS pathology laboratory with no additional hardware requirements

Ataxin-1 Fusion Partners Alter PolyQ Lethality and Aggregation

Intranuclear inclusion bodies (IBs) are the histopathologic markers of multiple protein folding diseases. IB formation has been extensively studied using fluorescent fusion products of pathogenic polyglutamine (polyQ) expressing proteins. These studies have been informative in determining the cellular targets of expanded polyQ protein as well as the methods by which cells rid themselves of IBs. The experimental thrust has been to intervene in the process of polyQ aggregation in an attempt to alleviate cytotoxicity. However new data argues against the notion that polyQ aggregation and cytotoxicity are inextricably linked processes. We reasoned that changing the protein context of a disease causing polyQ protein could accelerate its precipitation as an IB, potentially reducing its cytotoxicity. Our experimental strategy simply exploited the fact that conjoined proteins influence each others folding and aggregation properties. We fused a full-length pathogenic ataxin-1 construct to fluorescent tags (GFP and DsRed1-E5) that exist at different oligomeric states. The spectral properties of the DsRed1-E5-ataxin-1 transfectants had the additional advantage of allowing us to correlate fluorochrome maturation with cytotoxicity. Each fusion protein expressed a distinct cytotoxicity and IB morphology. Flow cytometric analyses of transfectants expressing the greatest fluorescent signals revealed that the DsRed1-E5-ataxin-1 fusion was more toxic than GFP fused ataxin-1 (31.8±4.5% cell death versus 12.85±3%), although co-transfection with the GFP fusion inhibited maturation of the DsRed1-E5 fluorochrome and diminished the toxicity of the DsRed1-E5-ataxin-1 fusion. These data show that polyQ driven aggregation can be influenced by fusion partners to generate species with different toxic properties and provide new opportunities to study IB aggregation, maturation and lethality

Feasibility of an incentive scheme to promote active travel to school: a pilot cluster randomised trial

Abstract Background In Great Britain, 19% of trips to primary school within 1 mile, and 62% within 1–2 miles, are by car. Active travel to school (ATS) offers a potential source of moderate-to-vigorous physical activity (MVPA). This study tested the feasibility of an intervention to promote ATS in 9–10 year olds and associated trial procedures. Methods A parallel cluster randomised pilot trial was conducted over 9 weeks in two schools from a low-income area in northeast England. Measures included daily parental ATS reports (optionally by SMS) and child ATS reports, as well as accelerometry (ActiGraph GT3X+). At baseline, all children were asked to wear the accelerometer for the same week; in the post-randomisation phase, small subsamples were monitored each week. In the 2 weeks when a child wore the accelerometer, parents also reported the start and finish times of the journey to school. The intervention consisted of a lottery-based incentive scheme; every ATS day reported by the parent, whether by paper or SMS, corresponded to one ticket entered into a weekly £5 voucher draw. Before each draw session, the researcher prepared the tickets and placed them into an opaque bag, from which one was randomly picked by the teacher at the draw session. Results Four schools replied positively (3.3%, N = 123) and 29 participants were recruited in the two schools selected (33.0%, N = 88). Participant retention was 93.1%. Most materials were returned on time: accelerometers (81.9%), parental reports (82.1%) and child reports (97.9%). Draw sessions lasted on average 15.9 min (IQR 10–20) and overall session attendance was 94.5%. Parent-child report agreement regarding ATS was moderate (k = 0.53, CI 95% 0.45; 0.60). Differences in minutes of accelerometer-assessed MVPA between parent-reported ATS and non-ATS trips were assessed during two timeframes: during the journey to school based on the times reported by the parent (U = 390.5, p < 0.05, 2.46 (n = 99) vs 0.76 (n = 13)) and in the hour before classes (U = 665.5, p < 0.05, 4.99 (n = 104) vs 2.55 (n = 19)). Differences in MVPA minutes between child-reported ATS and non-ATS trips were also significant for each of the timeframes considered (U = 596.5, p < 0.05, 2.40 (n = 128) vs 0.81 (n = 15) and U = 955.0, p < 0.05, 4.99 (n = 146) vs 2.59 (n = 20), respectively). Conclusions Data suggest the feasibility of an ATS incentive scheme and of most trial procedures. School recruitment stood out as requiring further piloting. Trial registration ClinicalTrials.gov: NCT02282631 . Registered 5th September 2014

Does General Parenting Context Modify Adolescents' Appraisals and Coping with a Situation of Parental Regulation? The Case of Autonomy-Supportive Parenting

Theory and research suggest that adolescents differ in their appraisals and coping reactions in response to parental regulation. Less is known, however, about factors that determine these differences in adolescents’ responses. In this study, we examined whether adolescents' appraisals and coping reactions depend upon parents’ situation-specific autonomy-supportive or controlling communication style (i.e., the situation) in interaction with adolescents’ past experiences with general autonomy-supportive parenting (i.e., the parenting context). Whereas in Study 1 (N = 176) adolescents’ perceived general autonomy-supportive parenting context was assessed at one point in time, in Study 2 (N = 126) it was assessed multiple times across a 6-year period, allowing for an estimation of trajectories of perceived autonomy-supportive parenting context. In each study, adolescents read a vignette-based scenario depicting a situation of maternal regulation (i.e., a request to study more), which was communicated in either an autonomy-supportive or a controlling way. Following this scenario, they reported upon their appraisals and their anticipated coping reactions. Results of each study indicated that both the autonomy-supportive (relative to the controlling) situation and the perceived autonomy-supportive parenting context generally related to more positive appraisals (i.e., more autonomy need satisfaction, less autonomy need frustration), as well as to more constructive coping responses (i.e., less oppositional defiance and submission, more negotiation and accommodation). In addition, situation × context interactions were found, whereby adolescents growing up in a more autonomy-supportive context seemed to derive greater benefits from the exposure to an autonomy-supportive situation and reacted more constructively to a controlling situation

A multi-disciplinary education process related to the discharging of children from hospital when the child has been diagnosed with type 1 diabetes - a qualitative study

<p>Abstract</p> <p>Background</p> <p>Worldwide, insulin-dependent type 1 diabetes is one of the most frequently diagnosed long-term endocrine disorders found in children and the incidences of this diseased is still increasing. In Sweden the routines are, according to national guidelines, when the child is diagnosed with type 1 diabetes, the child and its family remains at the hospital for about two weeks. There is limited knowledge about how a diabetes team handles a child and its family from admission to discharge, therefore the purpose of this study was to seek a deeper understanding of how the diabetes team's parent/child education process works, from admission to discharge, among families with a child newly diagnosed with type 1 diabetes.</p> <p>Methods</p> <p>Qualitative data collection was used. Four focus-group interviews, with a sample of three diabetes teams from different paediatric hospitals in the south western part of Sweden, were conducted and the data recorded on tape and then analysed using qualitative content analysis.</p> <p>Results</p> <p>The results indicate that achieving a status of self-care on the part of the patient is the goal of the diabetes education programme. Part of the programme is aimed at guiding the child and its parents towards self-help through the means of providing them with knowledge of the disease and its treatment to enable the whole family to understand the need for cooperation in the process. To do this requires an understanding, by the diabetes team, of the individualities of the family in order to gain an overall picture.</p> <p>Conclusion</p> <p>The results of this study show that the diabetes education programme is specifically designed for each family using the internationally recommended clinical practice guidelines with its specific aims and objectives. Achieving the families' willingness to assist in the self-care of the child care is the goal of the parent education process. To achieve this, the paediatric diabetes specialist nurse and the diabetes specialist paediatrician immediately and deliberately start the process of educating the family using a programme designed to give them the necessary knowledge and skills they will need to manage their child's type 1 diabetes at home.</p