ParaMonte: An Efficient Serial/Parallel MCMC Library

The scientific inference is a multistep process requiring observational data from which a model/hypothesis is derived. The parameters of this physical model then have to be tuned to more accurately represent data in a process known as model calibration. This calibrated model is then validated and is finally used to predict different quantities of interest. The most fundamental tool for model calibration and uncertainty quantification is the Markov Chain Monte Carlo (MCMC). While existing packages achieve many of the goals of the MCMC simulations, none currently addresses all critical aspects of an MCMC simulation. For instance, packages are frequently limited to only one programming language environment, perform serial or parallel simulations, or lack restart functionality. We present ParaMonte, a generic user-friendly, high- performance Monte Carlo simulation toolbox for serial and parallel Monte Carlo simulations accessible from multiple programming languages. ParaMonte features automatically-enabled restart functionality of all simulations in serial or parallel and comprehensive post-processing and visualization of the simulation results. This package is available to the public under the MIT license from its permanent repository: https://github.com/cdslaborg/paramont

The Grizzly, September 28, 2016

Campus Safety Takes Safety Initiatives • Poet Comes to UC • ESL Program Promotes Community Between Students and Staff • New Club Aims to Get Money Out of Politics • Shakespeare in the Summer of Love • Family Day Branches Out • Opinions: Let\u27s (Finally) Talk About Sex Addiction; Frank Ocean\u27s Blonde was Worth Waiting For • Ursinus Men\u27s and Women\u27s Cross Country Team Off to a Hot Start • Rare Breed: The Two-Sport Athletehttps://digitalcommons.ursinus.edu/grizzlynews/1650/thumbnail.jp

Predicting the environmental suitability for onchocerciasis in Africa as an aid to elimination planning

Recent evidence suggests that, in some foci, elimination of onchocerciasis from Africa may be feasible with mass drug administration (MDA) of ivermectin. To achieve continental elimination of transmission, mapping surveys will need to be conducted across all implementation units (IUs) for which endemicity status is currently unknown. Using boosted regression tree models with optimised hyperparameter selection, we estimated environmental suitability for onchocerciasis at the 5 × 5-km resolution across Africa. In order to classify IUs that include locations that are environmentally suitable, we used receiver operating characteristic (ROC) analysis to identify an optimal threshold for suitability concordant with locations where onchocerciasis has been previously detected. This threshold value was then used to classify IUs (more suitable or less suitable) based on the location within the IU with the largest mean prediction. Mean estimates of environmental suitability suggest large areas across West and Central Africa, as well as focal areas of East Africa, are suitable for onchocerciasis transmission, consistent with the presence of current control and elimination of transmission efforts. The ROC analysis identified a mean environmental suitability index of 0·71 as a threshold to classify based on the location with the largest mean prediction within the IU. Of the IUs considered for mapping surveys, 50·2% exceed this threshold for suitability in at least one 5 × 5-km location. The formidable scale of data collection required to map onchocerciasis endemicity across the African continent presents an opportunity to use spatial data to identify areas likely to be suitable for onchocerciasis transmission. National onchocerciasis elimination programmes may wish to consider prioritising these IUs for mapping surveys as human resources, laboratory capacity, and programmatic schedules may constrain survey implementation, and possibly delaying MDA initiation in areas that would ultimately qualify

Active RNA Polymerases: Mobile or Immobile Molecular Machines?

Although it is widely assumed that active RNA polymerase tracks along its template, we find that DNA, not the polymerase, moves, suggesting that polymerase works by reeling in the template

Credibility in Policy Expertise: The Function of Boundaries Between Research and Policy

As science becomes an increasingly crucial resource for addressing complex challenges in society, extensive demands are placed upon the researchers who produce it. Creating valuable expert knowledge that intervenes in policy or practice requires knowledge brokers to facilitate interactions at the boundary between research and policy. Yet, existing research lacks a compelling account of the ways in which brokerage is performed to gain credibility. Drawing on mixed-method analysis of twelve policy research settings, I outline a novel set of strategies for attaining symbolic power, whereby policy experts position themselves and others via conceptual distances drawn between the ‘world of ideas’ and the ‘world of policy and practice’. Disciplinary distance works to situate research as either disciplinary or undisciplinary, epistemic distance creates a boundary between complex specialist research and direct digestible outputs, temporal distance represents the separation of slow rigorous research and agile responsive analysis, and economic distance situates research as either pure and intrinsic or marketable and fundable. I develop a theoretical account that unpacks the boundaries between research communities and shows how these boundaries permit policy research actors to achieve various strategic aims.ESRC Future Research Leaders ES/N016319/1 Commonwealth Scholarship Commissio

Home Range and Ranging Behaviour of Bornean Elephant (Elephas maximus borneensis) Females

BACKGROUND: Home range is defined as the extent and location of the area covered annually by a wild animal in its natural habitat. Studies of African and Indian elephants in landscapes of largely open habitats have indicated that the sizes of the home range are determined not only by the food supplies and seasonal changes, but also by numerous other factors including availability of water sources, habitat loss and the existence of man-made barriers. The home range size for the Bornean elephant had never been investigated before. METHODOLOGY/PRINCIPAL FINDINGS: The first satellite tracking program to investigate the movement of wild Bornean elephants in Sabah was initiated in 2005. Five adult female elephants were immobilized and neck collars were fitted with tracking devices. The sizes of their home range and movement patterns were determined using location data gathered from a satellite tracking system and analyzed by using the Minimum Convex Polygon and Harmonic Mean methods. Home range size was estimated to be 250 to 400 km(2) in a non-fragmented forest and 600 km(2) in a fragmented forest. The ranging behavior was influenced by the size of the natural forest habitat and the availability of permanent water sources. The movement pattern was influenced by human disturbance and the need to move from one feeding site to another. CONCLUSIONS/SIGNIFICANCE: Home range and movement rate were influenced by the degree of habitat fragmentation. Once habitat was cleared or converted, the availability of food plants and water sources were reduced, forcing the elephants to travel to adjacent forest areas. Therefore movement rate in fragmented forest was higher than in the non-fragmented forest. Finally, in fragmented habitat human and elephant conflict occurrences were likely to be higher, due to increased movement bringing elephants into contact more often with humans

Microarray Analysis Reveals Distinct Gene Expression Profiles Among Different Tumor Histology, Stage and Disease Outcomes in Endometrial Adenocarcinoma

Endometrial cancer is the most common gynecologic malignancy in developed countries and little is known about the underlying mechanism of stage and disease outcomes. The goal of this study was to identify differentially expressed genes (DEG) between late vs. early stage endometrioid adenocarcinoma (EAC) and uterine serous carcinoma (USC), as well as between disease outcomes in each of the two histological subtypes.Gene expression profiles of 20 cancer samples were analyzed (EAC = 10, USC = 10) using the human genome wide illumina bead microarrays. There was little overlap in the DEG sets between late vs. early stages in EAC and USC, and there was an insignificant overlap in DEG sets between good and poor prognosis in EAC and USC. Remarkably, there was no overlap between the stage-derived DEGs and the prognosis-derived DEGs for each of the two histological subtypes. Further functional annotation of differentially expressed genes showed that the composition of enriched function terms were different among different DEG sets. Gene expression differences for selected genes of various stages and outcomes were confirmed by qRT-PCR with a high validation rate.This data, although preliminary, suggests that there might be involvement of distinct groups of genes in tumor progression (late vs. early stage) in each of the EAC and USC. It also suggests that these genes are different from those involved in tumor outcome (good vs. poor prognosis). These involved genes, once clinically verified, may be important for predicting tumor progression and tumor outcome