Understanding consumer liking of beef using hierarchical cluster analysis and external preference mapping

Background This study was conducted to assess if there are differences in consumer liking of beef. Samples were collected from different groups and analyses were conducted, including quantitative descriptive analysis, consumer panels and instrumental analyses. Palatability traits, such as aroma liking (AL), tenderness (TE), juiciness (JU), flavour liking (FL) and overall liking (OL) were rated by consumers. Results Warner Bratzler shear force was negatively associated with tender mouthfeel and consumer tenderness score. Cluster analysis identified 4 groups of clusters, which were described as “easily‐pleased”, “bull beef liker”, “tender beef liker” and “fastidious” consumers. Cluster group 2 awarded higher score for bulls and located in a separate region on external preference map. Conclusion External preference mapping showed the association between consumer liking of beef and sensory attributes

From affect programs to dynamical discrete emotions

According to Discrete Emotion Theory, a number of emotions are distinguishable on the basis of neural, physiological, behavioral and expressive features. Critics of this view emphasize the variability and context-sensitivity of emotions. This paper discusses some of these criticisms, and argues that they do not undermine the claim that emotions are discrete. This paper also presents some works in dynamical affective science, and argues that to conceive of discrete emotions as self-organizing and softly assembled patterns of various processes accounts more naturally than traditional Discrete Emotion Theory for the variability and context-sensitivity of emotions

Evidence, Content and Corroboration and the Tree of Life

We examine three critical aspects of Popper’s formulation of the ‘Logic of Scientific Discovery’—evidence, content and degree of corroboration—and place these concepts in the context of the Tree of Life (ToL) problem with particular reference to molecular systematics. Content, in the sense discussed by Popper, refers to the breadth and scope of existence that a hypothesis purports to explain. Content, in conjunction with the amount of available and relevant evidence, determines the testability, or potential degree of corroboration, of a statement; content distinguishes scientific hypotheses from metaphysical assertions. Degree of corroboration refers to the relative and tentative confidence assigned to one hypothesis over another, based upon the performance of each under critical tests. Here we suggest that systematists attempt to maximize content and evidence to increase the potential degree of corroboration in all phylogenetic endeavors. Discussion of this “total evidence” approach leads to several interesting conclusions about generating ToL hypotheses

Phylogenetic comparative assembly

Husemann P, Stoye J. Phylogenetic Comparative Assembly. Algorithms for Molecular Biology. 2010;5(1): 3.BACKGROUND:Recent high throughput sequencing technologies are capable of generating a huge amount of data for bacterial genome sequencing projects. Although current sequence assemblers successfully merge the overlapping reads, often several contigs remain which cannot be assembled any further. It is still costly and time consuming to close all the gaps in order to acquire the whole genomic sequence. RESULTS:Here we propose an algorithm that takes several related genomes and their phylogenetic relationships into account to create a graph that contains the likelihood for each pair of contigs to be adjacent. Subsequently, this graph can be used to compute a layout graph that shows the most promising contig adjacencies in order to aid biologists in finishing the complete genomic sequence. The layout graph shows unique contig orderings where possible, and the best alternatives where necessary. CONCLUSIONS:Our new algorithm for contig ordering uses sequence similarity as well as phylogenetic information to estimate adjacencies of contigs. An evaluation of our implementation shows that it performs better than recent approaches while being much faster at the same tim

Global kidney health 2017 and beyond: a roadmap for closing gaps in care, research, and policy

The global nephrology community recognises the need for a cohesive plan to address the problem of chronic kidney disease (CKD). In July, 2016, the International Society of Nephrology hosted a CKD summit of more than 85 people with diverse expertise and professional backgrounds from around the globe. The purpose was to identify and prioritise key activities for the next 5-10 years in the domains of clinical care, research, and advocacy and to create an action plan and performance framework based on ten themes: strengthen CKD surveillance; tackle major risk factors for CKD; reduce acute kidney injury-a special risk factor for CKD; enhance understanding of the genetic causes of CKD; establish better diagnostic methods in CKD; improve understanding of the natural course of CKD; assess and implement established treatment options in patients with CKD; improve management of symptoms and complications of CKD; develop novel therapeutic interventions to slow CKD progression and reduce CKD complications; and increase the quantity and quality of clinical trials in CKD. Each group produced a prioritised list of goals, activities, and a set of key deliverable objectives for each of the themes. The intended users of this action plan are clinicians, patients, scientists, industry partners, governments, and advocacy organisations. Implementation of this integrated comprehensive plan will benefit people who are at risk for or affected by CKD worldwide

Towards a realistic interpretation of quantum mechanics providing a model of the physical world

It is argued that a realistic interpretation of quantum mechanics is possible and useful. Current interpretations, from Copenhagen to many worlds are critically revisited. The difficulties for intuitive models of quantum physics are pointed out and possible solutions proposed. In particular the existence of discrete states, the quantum jumps, the alleged lack of objective properties, measurement theory, the probabilistic character of quantum physics, the wave-particle du- ality and the Bell inequalities are analyzed. The sketch of a realistic picture of the quantum world is presented. It rests upon the assump- tion that quantum mechanics is a stochastic theory whose randomness derives from the existence of vacuum fields. They correspond to the vacuum fluctuations of quantum field theory, but taken as real rather than virtual.Comment: 43 pages, paper throughout revised and somewhat enlarged, sections on the Bell inequalities and on the sketch of a picture of the quantum world rewritten, new references adde

Clinical audit of core podiatry treatment in the NHS

<p>Abstract</p> <p>Background</p> <p>Core podiatry involves treatment of the nails, corns and callus and also giving footwear and foot health advice. Though it is an integral part of current podiatric practice little evidence is available to support its efficacy in terms of research and audit data. This information is important in order to support the current NHS commissioning process where services are expected to provide data on standards including outcomes. This study aimed to increase the evidence base for this area of practice by conducting a multi-centre audit in 8 NHS podiatry departments over a 1-year period.</p> <p>Methods</p> <p>The outcome measure used in this audit was the Podiatry Health Questionnaire which is a self completed short measure of foot health including a pain visual analogue scale and a section for the podiatrist to rate an individual's foot health based on their podiatric problems. The patient questionnaire was completed by individuals prior to receiving podiatry care and then 2 weeks after treatment to assess the effect of core podiatry in terms of pain and foot health.</p> <p>Results</p> <p>1047 patients completed both questionnaires, with an age range from 26–95 years and a mean age of 72.9 years. The podiatrists clinical rating at baseline showed 75% of patients had either slight or moderate podiatric problems. The differences in questionnaire and visual analogue scores before and after treatment were determined according to three categories – <it>better, same, worse </it>and 75% of patients' scores either remained the same or improved after core podiatry treatment. A student t-test showed a statistical significant difference in pre and post treatment scores where P < 0.001, though the confidence interval indicated that the improvement was relatively small.</p> <p>Conclusion</p> <p>Core podiatry has been shown to sustain or improve foot health and pain in 75% of the patients taking part in the audit. Simple outcome measures including pain scales should be used routinely in podiatric practice to assess the affect of different aspects of treatments and improve the evidence base for podiatry.</p

Cluster analysis of protein array results via similarity of Gene Ontology annotation

BACKGROUND: With the advent of high-throughput proteomic experiments such as arrays of purified proteins comes the need to analyse sets of proteins as an ensemble, as opposed to the traditional one-protein-at-a-time approach. Although there are several publicly available tools that facilitate the analysis of protein sets, they do not display integrated results in an easily-interpreted image or do not allow the user to specify the proteins to be analysed. RESULTS: We developed a novel computational approach to analyse the annotation of sets of molecules. As proof of principle, we analysed two sets of proteins identified in published protein array screens. The distance between any two proteins was measured as the graph similarity between their Gene Ontology (GO) annotations. These distances were then clustered to highlight subsets of proteins sharing related GO annotation. In the first set of proteins found to bind small molecule inhibitors of rapamycin, we identified three subsets containing four or five proteins each that may help to elucidate how rapamycin affects cell growth whereas the original authors chose only one novel protein from the array results for further study. In a set of phosphoinositide-binding proteins, we identified subsets of proteins associated with different intracellular structures that were not highlighted by the analysis performed in the original publication. CONCLUSION: By determining the distances between annotations, our methodology reveals trends and enrichment of proteins of particular functions within high-throughput datasets at a higher sensitivity than perusal of end-point annotations. In an era of increasingly complex datasets, such tools will help in the formulation of new, testable hypotheses from high-throughput experimental data

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

TISs-ST: a web server to evaluate polymorphic translation initiation sites and their reflections on the secretory targets

<p>Abstract</p> <p>Background</p> <p>The nucleotide sequence flanking the translation initiation codon (start codon context) affects the translational efficiency of eukaryotic mRNAs, and may indicate the presence of an alternative translation initiation site (TIS) to produce proteins with different properties. Multi-targeting may reflect the translational variability of these other protein forms. In this paper we present a web server that performs computations to investigate the usage of alternative translation initiation sites for the synthesis of new protein variants that might have different functions.</p> <p>Results</p> <p>An efficient web-based tool entitled TISs-ST (Translation Initiation Sites and Secretory Targets) evaluates putative translation initiation sites and indicates the prediction of a signal peptide of the protein encoded from this site. The TISs-ST web server is freely available to both academic and commercial users and can be accessed at <url>http://ipe.cbmeg.unicamp.br/pub/TISs-ST</url>.</p> <p>Conclusion</p> <p>The program can be used to evaluate alternative translation initiation site consensus with user-specified sequences, based on their composition or on many position weight matrix models. TISs-ST provides analytical and visualization tools for evaluating the periodic frequency, the consensus pattern and the total information content of a sequence data set. A search option allows for the identification of signal peptides from predicted proteins using the PrediSi software.</p