A two-stage approach to relaxation in billiard systems of locally confined hard spheres

We consider the three-dimensional dynamics of systems of many interacting hard spheres, each individually confined to a dispersive environment, and show that the macroscopic limit of such systems is characterized by a coefficient of heat conduction whose value reduces to a dimensional formula in the limit of vanishingly small rate of interaction. It is argued that this limit arises from an effective loss of memory. Similarities with the diffusion of a tagged particle in binary mixtures are emphasized.Comment: Submitted to Chaos, special issue "Statistical Mechanics and Billiard-Type Dynamical Systems

Introducing the microbiome into Precision Medicine

© The Author(s), 2016. This is the author's version of the work and is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Trends in Pharmacological Sciences 38 (2017): 81-91, doi:10.1016/j.tips.2016.10.001.Understanding how individual people respond to medical therapy is a key facet of improving the odds ratio that interventions will have a positive impact. Reducing the non-responder rate for an intervention or reducing complications associated with a particular treatment or surgery is the next stage of medical advance. The Precision Medicine Initiative, launched in January 2015, set the stage for enhanced collaboration between researchers and medical professionals to develop next-generation techniques to aid patient treatment and recovery, and increased the opportunities for impactful pre-emptive care. The microbiome plays a crucial role in health and disease, as it influences endocrinology, physiology, and even neurology, altering the outcome of many different disease states, and it augments drug responses and tolerance. We review the implications of the microbiome on precision health initiatives and highlight excellent examples, whereby precision microbiome health has been implemented.2017-11-0

A question of trust: can we build an evidence base to gain trust in systematic review automation technologies?

Background Although many aspects of systematic reviews use computational tools, systematic reviewers have been reluctant to adopt machine learning tools. Discussion We discuss that the potential reason for the slow adoption of machine learning tools into systematic reviews is multifactorial. We focus on the current absence of trust in automation and set-up challenges as major barriers to adoption. It is important that reviews produced using automation tools are considered non-inferior or superior to current practice. However, this standard will likely not be sufficient to lead to widespread adoption. As with many technologies, it is important that reviewers see “others” in the review community using automation tools. Adoption will also be slow if the automation tools are not compatible with workflows and tasks currently used to produce reviews. Many automation tools being developed for systematic reviews mimic classification problems. Therefore, the evidence that these automation tools are non-inferior or superior can be presented using methods similar to diagnostic test evaluations, i.e., precision and recall compared to a human reviewer. However, the assessment of automation tools does present unique challenges for investigators and systematic reviewers, including the need to clarify which metrics are of interest to the systematic review community and the unique documentation challenges for reproducible software experiments. Conclusion We discuss adoption barriers with the goal of providing tool developers with guidance as to how to design and report such evaluations and for end users to assess their validity. Further, we discuss approaches to formatting and announcing publicly available datasets suitable for assessment of automation technologies and tools. Making these resources available will increase trust that tools are non-inferior or superior to current practice. Finally, we identify that, even with evidence that automation tools are non-inferior or superior to current practice, substantial set-up challenges remain for main stream integration of automation into the systematic review process

iDNA from terrestrial haematophagous leeches as a wildlife surveying and monitoring tool - prospects, pitfalls and avenues to be developed

Invertebrate-derived DNA (iDNA) from terrestrial haematophagous leeches has recently been proposed as a powerful non-invasive tool with which to detect vertebrate species and thus to survey their populations. However, to date little attention has been given to whether and how this, or indeed any other iDNA-derived data, can be combined with state-of-the-art analytical tools to estimate wildlife abundances, population dynamics and distributions. In this review, we discuss the challenges that face the application of existing analytical methods such as site-occupancy and spatial capture-recapture (SCR) models to terrestrial leech iDNA, in particular, possible violations of key assumptions arising from factors intrinsic to invertebrate parasite biology. Specifically, we review the advantages and disadvantages of terrestrial leeches as a source of iDNA and summarize the utility of leeches for presence, occupancy, and spatial capture-recapture models. The main source of uncertainty that attends species detections derived from leech gut contents is attributable to uncertainty about the spatio-temporal sampling frame, since leeches retain host-blood for months and can move after feeding. Subsequently, we briefly address how the analytical challenges associated with leeches may apply to other sources of iDNA. Our review highlights that despite the considerable potential of leech (and indeed any) iDNA as a new survey tool, further pilot studies are needed to assess how analytical methods can overcome or not the potential biases and assumption violations of the new field of iDNA. Specifically we argue that studies to compare iDNA sampling with standard survey methods such as camera trapping, and those to improve our knowledge on leech (and other invertebrate parasite) physiology, taxonomy, and ecology will be of immense future value

Neighborhood Social Conditions Mediate the Association Between Physical Deterioration and Mental Health

This study investigates how neighborhood deterioration is associated with stress and depressive symptoms and the mediating effects of perceived neighborhood social conditions. Data come from a community survey of 801 respondents geocoded and linked to a systematic on‐site assessment of the physical characteristics of nearly all residential and commercial structures around respondents' homes. Structural equation models controlling for demographic effects indicate that the association between neighborhood deterioration and well‐being appear to be mediated through social contact, social capital, and perceptions of crime, but not through neighborhood satisfaction. Specifically, residential deterioration was mediated by social contact, then, social capital and fear of crime. Commercial deterioration, on the other hand, was mediated only through fear of crime. Additionally, data indicate that the functional definition of a “neighborhood” depends on the characteristics measured. These findings suggest that upstream interventions designed to improve neighborhood conditions as well as proximal interventions focused on social relationships, may promote well‐being.Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/117109/1/ajcp9139.pd

DNA Extraction from Dry Museum Beetles without Conferring External Morphological Damage

BACKGROUND: A large number of dry-preserved insect specimens exist in collections around the world that might be useful for genetic analyses. However, until now, the recovery of nucleic acids from such specimens has involved at least the partial destruction of the specimen. This is clearly undesirable when dealing with rare species or otherwise important specimens, such as type specimens. METHODOLOGY: We describe a method for the extraction of PCR-amplifiable mitochondrial and nuclear DNA from dry insects without causing external morphological damage. Using PCR to amplify ≈220 bp of the mitochondrial gene cytochrome c oxidase I, and 250–345 bp fragments of the multi-copy, nuclear 28s ribosomal DNA gene, we demonstrate the efficacy of this method on beetles collected up to 50 years ago. CONCLUSIONS: This method offers a means of obtaining useful genetic information from rare insects without conferring external morphological damage