Clustering with shallow trees

We propose a new method for hierarchical clustering based on the optimisation of a cost function over trees of limited depth, and we derive a message--passing method that allows to solve it efficiently. The method and algorithm can be interpreted as a natural interpolation between two well-known approaches, namely single linkage and the recently presented Affinity Propagation. We analyze with this general scheme three biological/medical structured datasets (human population based on genetic information, proteins based on sequences and verbal autopsies) and show that the interpolation technique provides new insight.Comment: 11 pages, 7 figure

Glacial cycles promote greater dispersal, which can help explain larger clutch sizes, in north temperate birds

Earth’s glacial history and patterns in the life history traits of the planet’s avifauna suggest the following interpretations of how recent geological history has affected these key characteristics of the biota: 1) Increased colonizing ability has been an important advantage of increased dispersal, and life history strategies are better categorized by dispersive colonizing ability than by their intrinsic growth rates; 2) Birds of the North Temperate Zone show a greater tendency to disperse, and they disperse farther, than tropical or south temperate birds; 3) Habitat changes associated with glacial advance and retreat selected for high dispersal ability, particularly in the North; and 4) Selection for greater dispersal throughout the unstable Pleistocene has also resulted in other well-recognized life history contrasts, especially larger clutch sizes in birds of North Temperate areas

Self-guided mindfulness and cognitive behavioural practices reduce anxiety in autistic adults: A pilot 8-month waitlist-controlled trial of widely available online tools

Anxiety in autism is an important treatment target because of its consequences for quality of life and wellbeing. Growing evidence suggests that Cognitive Behaviour Therapies (CBT) and Mindfulness-Based Therapies (MBT) can ameliorate anxiety in autism but cost-effective delivery remains a challenge. This pilot randomized controlled trial examined whether online CBT and MBT self-help programmes could help reduce anxiety in 54 autistic adults who were randomly allocated to either an online CBT (n=16) or MBT (n=19) programme or a waitlist control group (WL; n=19). Primary outcome measures of anxiety, secondary outcome measures of broader wellbeing, and potential process of change variables were collected at baseline, after programme completion, and then 3 and 6 months post-completion. Baseline data confirmed that intolerance of uncertainty and emotional acceptance accounted for up to 61% of self-reported anxiety across all participants. The 23 participants who were retained in the active conditions (14 MBT, 9 CBT) showed significant decreases in anxiety that were maintained over 3, and to some extent also 6 months. Overall, results suggest that online self-help CBT and MBT tools may provide a cost-effective method for delivering mental health support to those autistic adults who can engage effectively with online support tools

Scalable high-resolution forecasting of sparse spatiotemporal events with kernel methods: a winning solution to the NIJ "Real-Time Crime Forecasting Challenge"

We propose a generic spatiotemporal event forecasting method, which we developed for the National Institute of Justice’s (NIJ) RealTime Crime Forecasting Challenge (National Institute of Justice, 2017). Our method is a spatiotemporal forecasting model combining scalable randomized Reproducing Kernel Hilbert Space (RKHS) methods for approximating Gaussian processes with autoregressive smoothing kernels in a regularized supervised learning framework. While the smoothing kernels capture the two main approaches in current use in the field of crime forecasting, kernel density estimation (KDE) and self-exciting point process (SEPP) models, the RKHS component of the model can be understood as an approximation to the popular log-Gaussian Cox Process model. For inference, we discretize the spatiotemporal point pattern and learn a log-intensity function using the Poisson likelihood and highly efficient gradientbased optimization methods. Model hyperparameters including quality of RKHS approximation, spatial and temporal kernel lengthscales, number of autoregressive lags, bandwidths for smoothing kernels, as well as cell shape, size, and rotation, were learned using crossvalidation. Resulting predictions significantly exceeded baseline KDE estimates and SEPP models for sparse events

Combat and Warfare in the Early Paleolithic and Medically Unexplained Musculo-Facial Pain in the 21st Century War Veterns and Active-Duty Military Personnel

In a series of recent articles, we suggest that family dentists, military dentists and psychiatrists with expertise in posttraumatic stress disorder (especially in the Veterans Health Administration) are likely to see an increased number of patients with symptomatic jaw-clenching and early stages of tooth- grinding (Bracha et al., 2005). Returning warfighters and other returnees from military deployment may be especially at risk for high rates of clenching- induced masticatory muscle disorders at early stages of incisor grinding. The literature we have recently reviewed strongly supports the conclusion that clenching and grinding may primarily be a manifestation of experiencing extreme fear or severe chronic distress (respectively). We have recently reviewed the clinical and paleoanthropological literature and have noted that ancestral warfare and ancestral combat, in the early Paleolithic Environment of Evolutionary Adaptedness (EEA) may be a neglected factor explaining the conservation of the archaic trait of bite-muscle strengthening. We have hypothesized that among ancestral warriors, jaw clenching may have rapidly strengthened the two primary muscles involved in biting, the masseter muscles and the much larger temporalis muscles. The strengthening of these muscles may have served the purpose of enabling a stronger, deeper, and therefore more lethal, defensive bite for early Paleolithic humans. The neuroevolutionary perspective presented here may be novel to many dentists. However, it may be useful in patient education and in preventing progression from jaw-clenching to chronic facial pain

Inferring HIV incidence trends and transmission dynamics with a spatio-temporal HIV epidemic model

Reliable estimation of spatio-temporal trends in population-level HIV incidence is becoming an increasingly critical component of HIV prevention policy-making. However, direct measurement is nearly impossible. Current, widely used models infer incidence from survey and surveillance seroprevalence data, but they require unrealistic assumptions about spatial independence across spatial units. In this study, we present an epidemic model of HIV that explicitly simulates the spatial dynamics of HIV over many small, interacting areal units. By integrating all available population-level data, we are able to infer not only spatio-temporally varying incidence, but also ART initiation rates and patient counts. Our study illustrates the feasibility of applying compartmental models to larger inferential problems than those to which they are typically applied, as well as the value of data fusion approaches to infectious disease modeling.Comment: 28 pages, 9 figures, submitted to Epidemics

'Feel the Feeling': Psychological practitioners' experience of acceptance and commitment therapy well-being training in the workplace.

This empirical study investigates psychological practitioners' experience of worksite training in acceptance and commitment therapy using an interpretative phenomenological analysis methodology. Semi-structured interviews were conducted with eight participants, and three themes emerged from the interpretative phenomenological analysis data analysis: influence of previous experiences, self and others and impact and application. The significance of the experiential nature of the acceptance and commitment therapy training is explored as well as the dual aspects of developing participants' self-care while also considering their own clinical practice. Consistencies and inconsistencies across acceptance and commitment therapy processes are considered as well as clinical implications, study limitations and future research suggestions

Increasing Our Ability to Predict Contemporary Evolution

Classic debates concerning the extent to which scientists can predict evolution have gained new urgency as environmental changes force species to adapt or risk extinction. We highlight how our ability to predict evolution can be constrained by data limitations that cause poor understanding of deterministic natural selection. We then emphasize how such data limits can be reduced with feasible empirical effort involving a combination of approaches

EFFECTS OF METHOTREXATE ON PROLIFERATION OF HUMAN KERATINOCYTES IN VITRO

Normal human keratinocytes, propagated as epithelial outgrowths in vitro, were exposed to different concentrations of methotrexate (MTX) for different periods of time. After a 1-hr exposure, DNA synthesis was inhibited in a reversible manner. No change in the mitotic index was observed. After a 6-hr exposure, both DNA synthesis and mitosis were inhibited, again in a reversible fashion. Prolonged exposure (24 hr) resulted in irreversible mitotic inhibition even when followed by recovery periods of 168 hr. The effective concentrations of MTX in vitro were similar to those described previously in vivo