Continuing Progress on a Lattice QCD Software Infrastructure

We report on the progress of the software effort in the QCD Application Area of SciDAC. In particular, we discuss how the software developed under SciDAC enabled the aggressive exploitation of leadership computers, and we report on progress in the area of QCD software for multi-core architectures.Comment: 5 Pages, to appear in the Proceedings of SciDAC 2008 conference, (Seattle, July 13-17, 2008), Conference Poster Presentation Proceeding

Gonzales Gardens public housing community analysis and intervention proposal

This intervention proposal paper focuses on the Gonzales Gardens Housing Area in Columbia, South Carolina. The purpose of this proposal is to fund an on-site program for persons with alcohol related problems specifically adult males who reside at Gonzales Gardens Housing Area. A community analysis was completed assessing the strengths, weaknesses and needs for this community. This analysis revealed the need for an on-site program for persons with alcohol problems. It was found the target population is in need of an on-site program to help them recover from their problems

Inferring the Origin Locations of Tweets with Quantitative Confidence

Social Internet content plays an increasingly critical role in many domains, including public health, disaster management, and politics. However, its utility is limited by missing geographic information; for example, fewer than 1.6% of Twitter messages (tweets) contain a geotag. We propose a scalable, content-based approach to estimate the location of tweets using a novel yet simple variant of gaussian mixture models. Further, because real-world applications depend on quantified uncertainty for such estimates, we propose novel metrics of accuracy, precision, and calibration, and we evaluate our approach accordingly. Experiments on 13 million global, comprehensively multi-lingual tweets show that our approach yields reliable, well-calibrated results competitive with previous computationally intensive methods. We also show that a relatively small number of training data are required for good estimates (roughly 30,000 tweets) and models are quite time-invariant (effective on tweets many weeks newer than the training set). Finally, we show that toponyms and languages with small geographic footprint provide the most useful location signals.Comment: 14 pages, 6 figures. Version 2: Move mathematics to appendix, 2 new references, various other presentation improvements. Version 3: Various presentation improvements, accepted at ACM CSCW 201

Opening the Black Box of Family-Based Treatments: an artificial intelligence Framework to Examine therapeutic alliance and therapist Empathy

The evidence-based treatment (EBT) movement has primarily focused on core intervention content or treatment fidelity and has largely ignored practitioner skills to manage interpersonal process issues that emerge during treatment, especially with difficult-to-treat adolescents (delinquent, substance-using, medical non-adherence) and those of color. A chief complaint of real world practitioners about manualized treatments is the lack of correspondence between following a manual and managing microsocial interpersonal processes (e.g. negative affect) that arise in treating real world clients. Although family-based EBTs share core similarities (e.g. focus on family interactions, emphasis on practitioner engagement, family involvement), most of these treatments do not have an evidence base regarding common implementation and treatment process problems that practitioners experience in delivering particular models, especially in mid-treatment when demands on families to change their behavior is greatest in treatment - a lack that characterizes the field as a whole. Failure to effectively address common interpersonal processes with difficult-to-treat families likely undermines treatment fidelity and sustained use of EBTs, treatment outcome, and contributes to treatment dropout and treatment nonadherence. Recent advancements in wearables, sensing technologies, multivariate time-series analyses, and machine learning allow scientists to make significant advancements in the study of psychotherapy processes by looking under the skin of the provider-client interpersonal interactions that define therapeutic alliance, empathy, and empathic accuracy, along with the predictive validity of these therapy processes (therapeutic alliance, therapist empathy) to treatment outcome. Moreover, assessment of these processes can be extended to develop procedures for training providers to manage difficult interpersonal processes while maintaining a physiological profile that is consistent with astute skills in psychotherapeutic processes. This paper argues for opening the black box of therapy to advance the science of evidence-based psychotherapy by examining the clinical interior of evidence-based treatments to develop the next generation of audit- and feedback- (i.e., systemic review of professional performance) supervision systems

What Sets Physically Active Rural Communities Apart from Less Active Ones? A Comparative Case Study of Three US Counties

Background: Rural US communities experience health disparities, including a lower prevalence of physical activity (PA). However, “Positive Deviants”—rural communities with greater PA than their peers—exist. The purpose of this study was to identify the factors that help create physically active rural US communities. Methods: Stakeholder interviews, on-site intercept interviews, and in-person observations were used to form a comparative case study of two rural counties with high PA prevalence (HPAs) and one with low PA prevalence (LPA) from a southern US state, selected based on rurality and adult PA prevalence. Interview transcripts were inductively coded by three readers, resulting in a thematic structure that aligned with a Community Capital Framework, which was then used for deductive coding and analysis. Results: Fifteen stakeholder interviews, nine intercept interviews, and on-site observations were conducted. Human and Organizational Capital differed between the HPAs and LPA, manifesting as Social, Built, Financial, and Political Capital differences and a possible “spiraling-up” or cyclical effect through increasing PA and health (Human Capital), highlighting a potential causal model for future study. Conclusions: Multi-organizational PA coalitions may hold promise for rural PA by directly influencing Human and Organizational Capital in the short term and the other forms of capital in the long term

Land beneficiaries as game farmers: conservation, land reform and the invention of the 'community game farm' in KwaZulu-Natal

Scholarship on post-apartheid land reform includes research on land claims made to formal protected areas, such as national parks and state game reserves. Little attention has however, been paid to the question of land restitution claims on private lands, on which a range of nominally ‘conservation-friendly’ land-uses (including commercial hunting) have taken place. This article traces the emergence of the ‘community game farm’ as a product of land reform processes affecting freehold land in the midlands of KwaZulu-Natal province, South Africa. Two groups of land beneficiaries who were granted title to former privately owned game farms used for leisure hunting are studied in detail. The article shows that a range of state and private actors, as well as traditional authorities, have worked to ensure the continuation of the land under conservation or game farming after transfer. The central argument is that in this process, a generic narrative is imposed which works to conflate or deny the distinct historical identities of the beneficiary groups. The article raises questions about the real efficacy of land restitution in this context, as well as the appropriateness of a community-based conservation narrative when applied in the context of small farms such as those considered here.International Bibliography of Social Science

Human topoisomerase IIα uses a two-metal-ion mechanism for DNA cleavage

The DNA cleavage reaction of human topoisomerase IIα is critical to all of the physiological and pharmacological functions of the protein. While it has long been known that the type II enzyme requires a divalent metal ion in order to cleave DNA, the role of the cation in this process is not known. To resolve this fundamental issue, the present study utilized a series of divalent metal ions with varying thiophilicities in conjunction with DNA cleavage substrates that replaced the 3′-bridging oxygen of the scissile bond with a sulfur atom (i.e. 3′-bridging phosphorothiolates). Rates and levels of DNA scission were greatly enhanced when thiophilic metal ions were included in reactions that utilized sulfur-containing substrates. Based on these results and those of reactions that employed divalent cation mixtures, we propose that topoisomerase IIα mediates DNA cleavage via a two-metal-ion mechanism. In this model, one of the metal ions makes a critical interaction with the 3′-bridging atom of the scissile phosphate. This interaction greatly accelerates rates of enzyme-mediated DNA cleavage, and most likely is needed to stabilize the leaving 3′-oxygen

Modeling Conformational Ensembles of Slow Functional Motions in Pin1-WW

Protein-protein interactions are often mediated by flexible loops that experience conformational dynamics on the microsecond to millisecond time scales. NMR relaxation studies can map these dynamics. However, defining the network of inter-converting conformers that underlie the relaxation data remains generally challenging. Here, we combine NMR relaxation experiments with simulation to visualize networks of inter-converting conformers. We demonstrate our approach with the apo Pin1-WW domain, for which NMR has revealed conformational dynamics of a flexible loop in the millisecond range. We sample and cluster the free energy landscape using Markov State Models (MSM) with major and minor exchange states with high correlation with the NMR relaxation data and low NOE violations. These MSM are hierarchical ensembles of slowly interconverting, metastable macrostates and rapidly interconverting microstates. We found a low population state that consists primarily of holo-like conformations and is a “hub” visited by most pathways between macrostates. These results suggest that conformational equilibria between holo-like and alternative conformers pre-exist in the intrinsic dynamics of apo Pin1-WW. Analysis using MutInf, a mutual information method for quantifying correlated motions, reveals that WW dynamics not only play a role in substrate recognition, but also may help couple the substrate binding site on the WW domain to the one on the catalytic domain. Our work represents an important step towards building networks of inter-converting conformational states and is generally applicable