Fast, Linear Time Hierarchical Clustering using the Baire Metric

The Baire metric induces an ultrametric on a dataset and is of linear computational complexity, contrasted with the standard quadratic time agglomerative hierarchical clustering algorithm. In this work we evaluate empirically this new approach to hierarchical clustering. We compare hierarchical clustering based on the Baire metric with (i) agglomerative hierarchical clustering, in terms of algorithm properties; (ii) generalized ultrametrics, in terms of definition; and (iii) fast clustering through k-means partititioning, in terms of quality of results. For the latter, we carry out an in depth astronomical study. We apply the Baire distance to spectrometric and photometric redshifts from the Sloan Digital Sky Survey using, in this work, about half a million astronomical objects. We want to know how well the (more costly to determine) spectrometric redshifts can predict the (more easily obtained) photometric redshifts, i.e. we seek to regress the spectrometric on the photometric redshifts, and we use clusterwise regression for this.Comment: 27 pages, 6 tables, 10 figure

Clinical research without consent in adults in the emergency setting: a review of patient and public views

<p>Abstract</p> <p>Background</p> <p>In emergency research, obtaining informed consent can be problematic. Research to develop and improve treatments for patients admitted to hospital with life-threatening and debilitating conditions is much needed yet the issue of research without consent (RWC) raises concerns about unethical practices and the loss of individual autonomy. Consistent with the policy and practice turn towards greater patient and public involvement in health care decisions, in the US, Canada and EU, guidelines and legislation implemented to protect patients and facilitate acute research with adults who are unable to give consent have been developed with little involvement of the lay public. This paper reviews research examining public opinion regarding RWC for research in emergency situations, and whether the rules and regulations permitting research of this kind are in accordance with the views of those who ultimately may be the most affected.</p> <p>Methods</p> <p>Seven electronic databases were searched: Medline, Embase, CINAHL, Cochrane Database of Systematic Reviews, Philosopher's Index, Age Info, PsychInfo, Sociological Abstracts and Web of Science. Only those articles pertaining to the views of the public in the US, Canada and EU member states were included. Opinion pieces and those not published in English were excluded.</p> <p>Results</p> <p>Considering the wealth of literature on the perspectives of professionals, there was relatively little information about public attitudes. Twelve studies employing a range of research methods were identified. In five of the six questionnaire surveys around half the sample did <it>not </it>agree generally with RWC, though paradoxically, a higher percentage would <it>personally </it>take part in such a study. Unfortunately most of the studies were not designed to investigate individuals' views in any depth. There also appears to be a level of mistrust of medical research and some patients were more likely to accept an experimental treatment 'outside' of a research protocol.</p> <p>Conclusion</p> <p>There are too few data to evaluate whether the rules and regulations permitting RWC protects – or is acceptable to – the public. However, any attempts to engage the public should take place in the context of findings from further basic research to attend to the apparently paradoxical findings of some of the current surveys.</p

Walk with Me: a protocol for a pilot RCT of a peer-led walking programme to increase physical activity in inactive older adults

Background: Levels of physical activity decline with age. Some of the most disadvantaged individuals in society, such as those from lower socio-economic position, are also the most inactive. Increasing physical activity levels, particularly among those most inactive, is a public health priority. Peer-led physical activity interventions may offer a model to increase physical activity in the older adult population. This study aims to test the feasibility of a peer-led, multicomponent physical activity intervention in socio-economically disadvantaged community dwelling older adults. Methods: The Medical Research Council framework for developing and evaluating complex interventions will be used to design and test the feasibility of a randomised controlled trial (RCT) of a multicomponent peer-led physical activity intervention. Data will be collected at baseline, immediately after the intervention (12 weeks) and 6 months after baseline measures. The pilot RCT will provide information on recruitment of peer mentors and participants and attrition rates, intervention fidelity, and data on the variability of the primary outcome (minutes of moderate to vigorous physical activity measured with an accelerometer). The pilot trail will also assess the acceptability of the intervention and identify potential resources needed to undertake a definitive study. Data analyses will be descriptive and include an evaluation of eligibility, recruitment, and retention rates. The findings will be used to estimate the sample size required for a definitive trial. A detailed process evaluation using qualitative and quantitative methods will be conducted with a variety of stakeholders to identify areas of success and necessary improvements. Discussion: This paper describes the protocol for the ‘Walk with Me’ pilot RCT which will provide the information necessary to inform the design and delivery of a fully powered trial should the Walk with Me intervention prove feasible

Improving primary palliative care in Scotland:lessons from a mixed methods study

BACKGROUND: Since 2012, all GP practices across Scotland have been supported to take a systematic approach to end-of-life care, by helping them to identify more patients for palliative care through a Palliative Care Directed Enhanced Service (DES). We aimed to understand the impact of this initiative. METHODS: Routine quantitative data from the 2012/13, and 2013/14 DES were collected from regional health boards, analysed and discussed. Qualitative data were collected from a sample of 2012/13 DES returns and analysed using Thematic Analysis. RESULTS: Data were received from 512 practices in nine Scottish Health boards for the 2012-13 DES and 638 practices in 11 Health boards for 2013-14. A sample of 90 of the returns for 2012-13 was selected for qualitative analysis. In 2012-13, 72 % of patients who died of cancer were listed on the palliative care register (PCR) before death while 27 % of patients who died as a result of non-malignant conditions were listed on the PCR. In 2013-14, cancer identification remained the same but identification of people dying with other long-term conditions had improved to 32.5 %. We identified several key issues needed to improve palliative care in the community. The need for training to identify patients with palliative care needs (particularly non-cancer); communication skills training; improvements in sharing information across the NHS; under-resource of and lack of coordination with district nurses; improvements in information technology; and tools for working with enlarged palliative care registers. CONCLUSIONS: The DES helped more patients with long-term conditions (LTC) receive generalist palliative care. Approaching generalist palliative care as anticipatory care could facilitate communication between GPs and patients/families and remove some barriers to early identification of palliative care needs. Improvement of information technology and use of identification tools like the SPICT™ may improve professionals’ communication with each other and help may make identification and management of patients easier. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (doi:10.1186/s12875-015-0391-x) contains supplementary material, which is available to authorized users

Genetic variation in the odorant receptors family 13 and the mhc loci influence mate selection in a multiple sclerosis dataset

<p>Abstract</p> <p>Background</p> <p>When selecting mates, many vertebrate species seek partners with major histocompatibility complex (MHC) genes different from their own, presumably in response to selective pressure against inbreeding and towards MHC diversity. Attempts at replication of these genetic results in human studies, however, have reached conflicting conclusions.</p> <p>Results</p> <p>Using a multi-analytical strategy, we report validated genome-wide relationships between genetic identity and human mate choice in 930 couples of European ancestry. We found significant similarity between spouses in the MHC at class I region in chromosome 6p21, and at the odorant receptor family 13 locus in chromosome 9. Conversely, there was significant dissimilarity in the MHC class II region, near the <it>HLA-DQA1 </it>and -<it>DQB1 </it>genes. We also found that genomic regions with significant similarity between spouses show excessive homozygosity in the general population (assessed in the HapMap CEU dataset). Conversely, loci that were significantly dissimilar among spouses were more likely to show excessive heterozygosity in the general population.</p> <p>Conclusions</p> <p>This study highlights complex patterns of genomic identity among partners in unrelated couples, consistent with a multi-faceted role for genetic factors in mate choice behavior in human populations.</p

Universal Artifacts Affect the Branching of Phylogenetic Trees, Not Universal Scaling Laws

The superficial resemblance of phylogenetic trees to other branching structures allows searching for macroevolutionary patterns. However, such trees are just statistical inferences of particular historical events. Recent meta-analyses report finding regularities in the branching pattern of phylogenetic trees. But is this supported by evidence, or are such regularities just methodological artifacts? If so, is there any signal in a phylogeny?In order to evaluate the impact of polytomies and imbalance on tree shape, the distribution of all binary and polytomic trees of up to 7 taxa was assessed in tree-shape space. The relationship between the proportion of outgroups and the amount of imbalance introduced with them was assessed applying four different tree-building methods to 100 combinations from a set of 10 ingroup and 9 outgroup species, and performing covariance analyses. The relevance of this analysis was explored taking 61 published phylogenies, based on nucleic acid sequences and involving various taxa, taxonomic levels, and tree-building methods.All methods of phylogenetic inference are quite sensitive to the artifacts introduced by outgroups. However, published phylogenies appear to be subject to a rather effective, albeit rather intuitive control against such artifacts. The data and methods used to build phylogenetic trees are varied, so any meta-analysis is subject to pitfalls due to their uneven intrinsic merits, which translate into artifacts in tree shape. The binary branching pattern is an imposition of methods, and seldom reflects true relationships in intraspecific analyses, yielding artifactual polytomies in short trees. Above the species level, the departure of real trees from simplistic random models is caused at least by two natural factors--uneven speciation and extinction rates; and artifacts such as choice of taxa included in the analysis, and imbalance introduced by outgroups and basal paraphyletic taxa. This artifactual imbalance accounts for tree shape convergence of large trees.There is no evidence for any universal scaling in the tree of life. Instead, there is a need for improved methods of tree analysis that can be used to discriminate the noise due to outgroups from the phylogenetic signal within the taxon of interest, and to evaluate realistic models of evolution, correcting the retrospective perspective and explicitly recognizing extinction as a driving force. Artifacts are pervasive, and can only be overcome through understanding the structure and biological meaning of phylogenetic trees. Catalan Abstract in Translation S1

Incorporating Neighborhood Reduction for the Solution of the Planar p-Median Problem

Two efficient neighbourhood reduction schemes are proposed for the solution of the p-Median problem on the plane. Their integration into a local search significantly reduces the run time with an insignificant deterioration in the quality of the solution. For completeness this fast local search is also embedded into one of the most powerful meta-heuristic algorithms recently developed for this continuous location problem. Excellent results for instances with up to 1060 demand points with various values of p are reported. Eight new best known solutions for ten instances of a large problem with 3,038 demand points and up to 500 facilities are also found