PaPaS: A Portable, Lightweight, and Generic Framework for Parallel Parameter Studies

The current landscape of scientific research is widely based on modeling and simulation, typically with complexity in the simulation's flow of execution and parameterization properties. Execution flows are not necessarily straightforward since they may need multiple processing tasks and iterations. Furthermore, parameter and performance studies are common approaches used to characterize a simulation, often requiring traversal of a large parameter space. High-performance computers offer practical resources at the expense of users handling the setup, submission, and management of jobs. This work presents the design of PaPaS, a portable, lightweight, and generic workflow framework for conducting parallel parameter and performance studies. Workflows are defined using parameter files based on keyword-value pairs syntax, thus removing from the user the overhead of creating complex scripts to manage the workflow. A parameter set consists of any combination of environment variables, files, partial file contents, and command line arguments. PaPaS is being developed in Python 3 with support for distributed parallelization using SSH, batch systems, and C++ MPI. The PaPaS framework will run as user processes, and can be used in single/multi-node and multi-tenant computing systems. An example simulation using the BehaviorSpace tool from NetLogo and a matrix multiply using OpenMP are presented as parameter and performance studies, respectively. The results demonstrate that the PaPaS framework offers a simple method for defining and managing parameter studies, while increasing resource utilization.Comment: 8 pages, 6 figures, PEARC '18: Practice and Experience in Advanced Research Computing, July 22--26, 2018, Pittsburgh, PA, US

Seven Strategies for Successfully Marketing and Stabilizing the Occupancy of Mixed-Income/Mixed-Race Properties - Summary Report

Mixed-Income rental properties that include extremely low-income households (below 30 percent of AMI) are a valuable strategy for community health. They simultaneously address two critical challenges: housing for those most in need and desegregating poverty. Understanding how to operate mixed-income apartments profitably is important to increase the development and underwriting of these properties.With the generous support of the Ford Foundation, NeighborWorks America undertook this study of management and marketing practices of successful mixed-income properties that have served extremely low-income families while maintaining positive cash flow for at least five years.This report describes seven strategies used by these properties to stabilize and maintain high occupancy rates with healthy operating budgets. For each strategy, we provide concrete implementation examples

Construction of a tatA Desulfovibrio vulgaris Hildenborough

Abstract only availabletatA Desulfovibrio vulgaris Hildenborough is a member of the obligately anaerobic bacteria growing by sulfate respiration and involved in environmental biocorrosion of ferrous metals. It also shows potential for bioremediation of toxic metals. Because these important metabolic activities of D. vulgaris are directly linked to electron flow, a better understanding of energy generation is needed. A model for augmenting respiratory energy production through hydrogen cycling has been proposed. This controversial model requires a periplasmic hydrogenase. The genome sequence of D. vulgaris reveals genes for four different periplasmic hydrogenases, the roles of which are currently unclear. There are two primary systems of transport of proteins such as hydrogenases to the periplasm or outer cell membrane. Both the Sec and Tat protein export systems translocate proteins across the cytoplasmic membrane. The Sec pathway exports short unfolded proteins, while the Tat system (Twin Arginine Translocation) translocates longer prefolded proteins. The latter generally contain redox cofactors and share a consensus motif (S/T)-R-R-x-F-L-K recognized for export. The Tat system is found in most prokaryotic plasma membranes. The Tat protein export system is encoded by four genes in E. coli, tatA, tatB, tatC, and tatE. However, only three of these genes, tatA, tatB, and tatC, have been putatively identified in D. vulgaris. Removal of one or more tat genes from E. coli causes deficiency in the transport of proteins by the Tat system. We propose to test the hydrogen cycling model for energy generation by creating a tatA deletion mutant in D. vulgaris that should block the production of all periplasmic hydrogenases. An examination of the deletion mutant should reveal the contribution of the hydrogen cycle to the energy economy of D. vulgaris.Life Sciences Undergraduate Research Opportunity Progra

Probabilistic lower bounds on maximal determinants of binary matrices

Let ${\mathcal D}(n)$ be the maximal determinant for $n \times n$ $\{\pm 1\}$-matrices, and $\mathcal R(n) = {\mathcal D}(n)/n^{n/2}$ be the ratio of ${\mathcal D}(n)$ to the Hadamard upper bound. Using the probabilistic method, we prove new lower bounds on ${\mathcal D}(n)$ and $\mathcal R(n)$ in terms of $d = n-h$, where $h$ is the order of a Hadamard matrix and $h$ is maximal subject to $h \le n$. For example, $\mathcal R(n) > (\pi e/2)^{-d/2}$ if $1 \le d \le 3$, and $\mathcal R(n) > (\pi e/2)^{-d/2}(1 - d^2(\pi/(2h))^{1/2})$ if $d > 3$. By a recent result of Livinskyi, $d^2/h^{1/2} \to 0$ as $n \to \infty$, so the second bound is close to $(\pi e/2)^{-d/2}$ for large $n$. Previous lower bounds tended to zero as $n \to \infty$ with $d$ fixed, except in the cases $d \in \{0,1\}$. For $d \ge 2$, our bounds are better for all sufficiently large $n$. If the Hadamard conjecture is true, then $d \le 3$, so the first bound above shows that $\mathcal R(n)$ is bounded below by a positive constant $(\pi e/2)^{-3/2} > 0.1133$.Comment: 17 pages, 2 tables, 24 references. Shorter version of arXiv:1402.6817v4. Typos corrected in v2 and v3, new Lemma 7 in v4, updated references in v5, added Remark 2.8 and a reference in v6, updated references in v

A qualitative study of patients’ feedback about Outpatient Parenteral Antimicrobial Therapy (OPAT) services in Northern England : implications for service improvement

AbstractObjective Outpatient parenteral antimicrobial therapy (OPAT) provides opportunities for improved cost savings, but in the UK, implementation is patchy and a variety of service models are in use. The slow uptake in the UK and Europe is due to a number of clinical, financial and logistical issues, including concern about patient safety. The measurement of patient experience data is commonly used to inform commissioning decisions, but these focus on functional aspects of services and fail to examine the relational aspects of care. This qualitative study examines patients’ experiences of OPAT.Design In-depth, semistructured interviews.Setting Purposive sample of OPAT patients recruited from four acute National Health Service (NHS) Trusts in Northern England. These NHS Trusts between them represented both well-established and recently set-up services running nurse at home, hospital outpatient and/or self-administration models.Participants We undertook 28 semistructured interviews and one focus group (n=4).Results Despite good patient outcomes, experiences were coloured by patients' personal situation and material circumstances. Many found looking after themselves at home more difficult than they expected, while others continued to work despite their infection. Expensive car parking, late running services and the inconvenience of waiting in for the nurse to arrive frustrated patients, while efficient services, staffed by nurses with the specialist skills needed to manage intravenous treatment had the opposite effect. Many patients felt a local, general practitioner or community health centre based service would resolve many of the practical difficulties that made OPAT inconvenient. Patients could find OPAT anxiety provoking but this could be ameliorated by staff taking the time to reassure patients and provide tailored information.Conclusion Services configurations must accommodate the diversity of the local population. Poor communication can leave patients lacking the confidence needed to be a competent collaborator in their own care and affect their perceptions of the service.This is an Open Access article distributed in accordance with the terms of the Creative Commons Attribution (CC BY 4.0) license, which permits others to distribute, remix, adapt and build upon this work, for commercial use, provided the original work is properly cited. See: http://creativecommons.org/licenses/by/4.0