bluuebunny/crossref_metadata_2025_split huggingface dataset:
Turning statistical physics models into materials design engines
Authors: Miskin Marc Z. , Khaira Gurdaman , de Pablo Juan J. , Jaeger Heinrich M. 
Published: December 2015

Significance
A fundamental tenet of science is that the properties of a material are intimately linked to the nature of the constituent components. Although there are powerful methods to predict such properties for given components, a key challenge for materials design is the inverse process: identifying the required components and their structural configuration for given target properties. This paper presents a new approach to this challenge. A formalism is introduced that generates algorithms for materials design both under equilibrium and under nonequilibrium conditions and operates without the need for user input beyond a design goal. This formalism is broadly applicable, fast, and robust, and it provides a powerful tool for materials optimization as well as discovery.
Training Opioid Addiction Treatment Providers to Adopt Contingency Management: A Prospective Pilot Trial of a Comprehensive Implementation Science Approach
Authors: Becker Sara J. , Squires Daniel D. , Strong David R. , Barnett Nancy P. , Monti Peter M. , Petry Nancy M. 
Published: December 2015

Background Few prospective studies have evaluated theory-driven approaches to the implementation of evidence-based opioid treatment. This study compared the effectiveness of an implementation model (Science to Service Laboratory; SSL) to training as usual (TAU) in promoting the adoption of contingency management across a multisite opioid addiction treatment program. We also examined whether the SSL affected putative mediators of contingency management adoption (perceived innovation characteristics and organizational readiness to change). Methods Sixty treatment providers (39 SSL, 21 TAU) from 15 geographically diverse satellite clinics (7 SSL, 8 TAU) participated in the 12-month study. Both conditions received didactic contingency management training and those in the predetermined experimental region received 9 months of SSL-enhanced training. Contingency management adoption was monitored biweekly, whereas putative mediators were measured at baseline, 3 months, and 12 months. Results Relative to providers in the TAU region, treatment providers in the SSL region had comparable likelihood of contingency management adoption in the first 20 weeks of the study, and then significantly higher likelihood of adoption (odds ratios = 2.4–13.5) for the remainder of the study. SSL providers also reported higher levels of one perceived innovation characteristic (Observability) and one aspect of organizational readiness to change (Adequacy of Training Resources), although there was no evidence that the SSL affected these putative mediators over time. Conclusions Results of this study indicate that a fully powered randomized trial of the SSL is warranted. Considerations for a future evaluation are discussed.
Clinician Recommendation of 12-Step Meeting Attendance and Discussion regarding Disclosure of Buprenorphine use among Patients in Office-Based Opioid Treatment
Authors: Suzuki Joji , Dodds Tyler 
Published: December 2015

Background Clinicians are encouraged to include 12-step meetings, such as Alcoholics or Narcotics Anonymous (AA/NA), as ancillary services for the treatment for opioid use disorders (OUDs), even though some of these groups may not fully accept individuals receiving buprenorphine. Little is known about whether clinicians actually discuss with patients the issue of disclosure of buprenorphine use at 12-step meetings. Methods An anonymous survey was offered to patients enrolled in office-based opioid treatment with buprenorphine to assess whether their clinicians recommended attendance at 12-step meetings and discussed the issue of disclosing their use of buprenorphine to other members. The patients’ attendance at 12-step meetings was also assessed, as well as beliefs and prior experiences related to disclosure of buprenorphine use at 12-step meetings. Results Thirty patients completed the survey. Twenty-one respondents (75.0%) indicated that they were encouraged to attend meetings, but only 9 (33.3%) reported having any discussion with their clinicians about the issue of disclosing their use of buprenorphine at meetings. The majority (76.7%) reported attending 12-step meetings at least occasionally, and 70% reported finding the meetings helpful. Nearly one third (30%) expressed concerns that other 12-step members would not accept them if their buprenorphine status were known, and a similar proportion (37%) frequently avoided disclosing their use of buprenorphine. Conclusions Clinicians recommended 12-step meetings to most patients but did not routinely discuss issues of disclosure. Despite utilizing 12-step meetings and reporting them to be helpful, many avoided disclosing their use of buprenorphine to others. More research is needed to better understand how clinicians may assist patients to best utilize 12-step meetings.
Primary Care Providers’ Experiences with Urine Toxicology Tests to Manage Prescription Opioid Misuse and Substance use among Chronic Noncancer Pain Patients in Safety Net Health Care Settings
Authors: Ceasar Rachel , Chang Jamie , Zamora Kara , Hurstak Emily , Kushel Margot , Miaskowski Christine , Knight Kelly 
Published: December 2015

Background Guideline recommendations to reduce prescription opioid misuse among patients with chronic noncancer pain include the routine use of urine toxicology tests for high-risk patients. Yet little is known about how the implementation of urine toxicology tests among patients with co-occurring chronic noncancer pain and substance use impacts primary care providers’ management of misuse. Clinicians’ perspectives on the benefits and challenges of implementing urine toxicology tests in the monitoring of opioid misuse and substance use in safety net health care settings are presented in this paper. Methods Twenty-three primary care providers from 6 safety net health care settings whose patients had a diagnosis of co-occurring chronic noncancer pain and substance use were interviewed. Interviews were transcribed, coded, and analyzed using grounded theory methodology. Results The benefits of implementing urine toxicology tests for primary care providers included less reliance on intuition to assess for misuse and the ability to identify unknown opioid misuse and/or substance use. The challenges of implementing urine toxicology tests included insufficient education and training about how to interpret and implement tests, and a lack of clarity on how and when to act on tests that indicated misuse and/or substance use. Conclusions These data suggest that primary care clinicians’ lack of education and training to interpret and implement urine toxicology tests may impact their management of patient opioid misuse and/or substance use. Clinicians may benefit from additional education and training about the clinical implementation and use of urine toxicology tests. Additional research is needed on how primary care providers implementation and use of urine toxicology tests impacts chronic noncancer pain management in primary care and safety net health care settings among patients with co-occurring chronic non cancer pain and substance use.
Barriers to Implementation of Opioid Overdose Prevention Programs in Ohio
Authors: Winstanley Erin L. , Clark Angela , Feinberg Judith , Wilder Christine M. 
Published: December 2015

Background Nationally, overdose fatalities have reached epidemic proportions. Ohio has one of the highest overdose death rates in the country, as well as high rates of prescription opioid trafficking. Methods A cross-sectional self-report survey of opioid overdose prevention programs (OOPPs) in Ohio was conducted between August and October 2014 to characterize programs and ascertain barriers to successful implementation. A 91% response rate was achieved with 18 programs participating in the study. Results The first Ohio OOPP opened in August 2012, a second program opened in 2013, and the remaining programs began in 2014. All of the programs distribute nasal naloxone and provide overdose prevention education, and 89% ( n = 16) provide overdose kits for free. Six OOPPs are funded by the Ohio Department of Health, 3 programs are funded by a local health foundation, and several other public and private funding sources were reported. The OOPPs have funding to distribute a combined total of 8,670 overdose kits and had distributed 1998 kits by October 2014. The OOPPs reported 149 overdose reversals. Fifteen programs (83%) reported implementation barriers that were categorized as stigma-, cost-, staffing-, legal, regulatory, and client-related problems. Legislative changes aimed at removing some of the obstacles to distribution and lay administration of naloxone have recently been enacted in Ohio. Conclusions OOPPs have rapidly expanded in Ohio during the past 3 years. Although recent legislative changes have addressed some of the reported implementation barriers, stigma and the cost of naloxone remain significant problems.
PaxtoolsR: pathway analysis in R using Pathway Commons
Authors: Luna Augustin , Babur Özgün , Aksoy Bülent Arman , Demir Emek , Sander Chris 
Published: December 2015

Abstract
Purpose: PaxtoolsR package enables access to pathway data represented in the BioPAX format and made available through the Pathway Commons webservice for users of the R language to aid in advanced pathway analyses. Features include the extraction, merging and validation of pathway data represented in the BioPAX format. This package also provides novel pathway datasets and advanced querying features for R users through the Pathway Commons webservice allowing users to query, extract and retrieve data and integrate these data with local BioPAX datasets.
Availability and implementation: The PaxtoolsR package is compatible with versions of R 3.1.1 (and higher) on Windows, Mac OS X and Linux using Bioconductor 3.0 and is available through the Bioconductor R package repository along with source code and a tutorial vignette describing common tasks, such as data visualization and gene set enrichment analysis. Source code and documentation are at http://www.bioconductor.org/packages/paxtoolsr. This plugin is free, open-source and licensed under the LGPL-3.
Contact: paxtools@cbio.mskcc.org or lunaa@cbio.mskcc.org
Hierarchical block matrices as efficient representations of chromosome topologies and their application for 3C data integration
Authors: Shavit Yoli , Walker Barnabas James , Lio’ Pietro 
Published: December 2015

Abstract
Motivation: Recent advancements in molecular methods have made it possible to capture physical contacts between multiple chromatin fragments. The resulting association matrices provide a noisy estimate for average spatial proximity that can be used to gain insights into the genome organization inside the nucleus. However, extracting topological information from these data is challenging and their integration across resolutions is still poorly addressed. Recent findings suggest that a hierarchical approach could be advantageous for addressing these challenges.
Results: We present an algorithmic framework, which is based on hierarchical block matrices (HBMs), for topological analysis and integration of chromosome conformation capture (3C) data. We first describe chromoHBM, an algorithm that compresses high-throughput 3C (HiT-3C) data into topological features that are efficiently summarized with an HBM representation. We suggest that instead of directly combining HiT-3C datasets across resolutions, which is a difficult task, we can integrate their HBM representations, and describe chromoHBM-3C, an algorithm which merges HBMs. Since three-dimensional (3D) reconstruction can also benefit from topological information, we further present chromoHBM-3D, an algorithm which exploits the HBM representation in order to gradually introduce topological constraints to the reconstruction process. We evaluate our approach in light of previous image microscopy findings and epigenetic data, and show that it can relate multiple spatial scales and provide a more complete view of the 3D genome architecture.
Availability and implementation: The presented algorithms are available from: https://github.com/yolish/hbm.
Contact: ys388@cam.ac.uk or pl219@cam.ac.uk
Supplementary information: Supplementary data are available at Bioinformatics online.
FluxModeCalculator: an efficient tool for large-scale flux mode computation
Authors: van Klinken Jan Bert , Willems van Dijk Ko 
Published: December 2015

Abstract
Summary: Elementary flux mode (EFM) analysis is a powerful technique for determining the metabolic capacities and robustness of stoichiometric networks. Recently, several improvements have been made to the algorithm for enumerating the EFMs, making the study of large models possible. However, currently these tools require high performance workstations to perform large-scale EFM computations, thus limiting their applicability. We developed a more time and memory efficient implementation of the algorithm for EFM enumeration in MATLAB, called FluxModeCalculator, which enables large-scale EFM computation on ordinary desktop computers.
Availability and implementation: FluxModeCalculator is open source and freely available under the terms of the GNU General Public License v3.0 at http://www.lumc.nl/jan-bert-van-klinken
Contact: j.b.van_klinken@lumc.nl
Supplementary information: Supplementary data are available at Bioinformatics online.
Fast integration-based prediction bands for ordinary differential equation models
Authors: Hass Helge , Kreutz Clemens , Timmer Jens , Kaschek Daniel 
Published: December 2015

Abstract
Motivation: To gain a deeper understanding of biological processes and their relevance in disease, mathematical models are built upon experimental data. Uncertainty in the data leads to uncertainties of the model’s parameters and in turn to uncertainties of predictions. Mechanistic dynamic models of biochemical networks are frequently based on nonlinear differential equation systems and feature a large number of parameters, sparse observations of the model components and lack of information in the available data. Due to the curse of dimensionality, classical and sampling approaches propagating parameter uncertainties to predictions are hardly feasible and insufficient. However, for experimental design and to discriminate between competing models, prediction and confidence bands are essential. To circumvent the hurdles of the former methods, an approach to calculate a profile likelihood on arbitrary observations for a specific time point has been introduced, which provides accurate confidence and prediction intervals for nonlinear models and is computationally feasible for high-dimensional models.
Results: In this article, reliable and smooth point-wise prediction and confidence bands to assess the model’s uncertainty on the whole time-course are achieved via explicit integration with elaborate correction mechanisms. The corresponding system of ordinary differential equations is derived and tested on three established models for cellular signalling. An efficiency analysis is performed to illustrate the computational benefit compared with repeated profile likelihood calculations at multiple time points.
Availability and implementation: The integration framework and the examples used in this article are provided with the software package Data2Dynamics, which is based on MATLAB and freely available at http://www.data2dynamics.org.
Contact: helge.hass@fdm.uni-freiburg.de
Supplementary information: Supplementary data are available at Bioinformatics online.
MSAcquisitionSimulator: data-dependent acquisition simulator for LC-MS shotgun proteomics
Authors: Goldfarb Dennis , Wang Wei , Major Michael B. 
Published: December 2015

Abstract
Summary: Data-dependent acquisition (DDA) is the most common method used to control the acquisition process of shotgun proteomics experiments. While novel DDA approaches have been proposed, their evaluation is made difficult by the need of programmatic control of a mass spectrometer. An alternative is in silico analysis, for which suitable software has been unavailable. To meet this need, we have developed MSAcquisitionSimulator—a collection of C ++ programs for simulating ground truth LC-MS data and the subsequent application of custom DDA algorithms. It provides an opportunity for researchers to test, refine and evaluate novel DDA algorithms prior to implementation on a mass spectrometer.
Availability and implementation: The software is freely available from its Github repository http://www.github.com/DennisGoldfarb/MSAcquisitionSimulator/ which contains further documentation and usage instructions.
Contact: weiwang@cs.ucla.edu or ben_major@med.unc.edu
Supplementary information: Supplementary data are available at Bioinformatics online.
Impact of high pCO2 and warmer temperatures on the process of silica biomineralization in the sponge Mycale grandis
Authors: Vicente Jan , Silbiger Nyssa J. , Beckley Billie A. , Raczkowski Charles W. , Hill Russell T. 
Published: December 2015

Abstract
Siliceous sponges have survived pre-historical mass extinction events caused by ocean acidification and recent studies suggest that siliceous sponges will continue to resist predicted increases in ocean acidity. In this study, we monitored silica biomineralization in the Hawaiian sponge Mycale grandis under predicted pCO2 and sea surface temperature scenarios for 2100. Our goal was to determine if spicule biomineralization was enhanced or repressed by ocean acidification and thermal stress by monitoring silica uptake rates during short-term (48 h) experiments and comparing biomineralized tissue ratios before and after a long-term (26 d) experiment. In the short-term experiment, we found that silica uptake rates were not impacted by high pCO2 (1050 µatm), warmer temperatures (27°C), or combined high pCO2 with warmer temperature (1119 µatm; 27°C) treatments. The long-term exposure experiments revealed no effect on survival or growth rates of M. grandis to high pCO2 (1198 µatm), warmer temperatures (25.6°C), or combined high pCO2 with warmer temperature (1225 µatm, 25.7°C) treatments, indicating that M. grandis will continue to prosper under predicted increases in pCO2 and sea surface temperature. However, ash-free dry weight to dry weight ratios, subtylostyle lengths, and silicified weight to dry weight ratios decreased under conditions of high pCO2 and combined pCO2 warmer temperature treatments. Our results show that rising ocean acidity and temperature have marginal negative effects on spicule biomineralization and will not affect sponge survival rates of M. grandis.
Effects of spatial heterogeneity in growth and fishing effort on yield-per-recruit models: an application to the US Atlantic sea scallop fishery
Authors: Truesdell Samuel B. , Hart Deborah R. , Chen Yong 
Published: December 2015

AbstractConventional yield-per-recruit (Y/R) and spawning-stock biomass-per-recruit (SSB/R) models make no allowance for spatial heterogeneity in fishing mortality, natural mortality, or growth across the stock area, although variability in these processes can affect model results. For example, areas with higher growth and/or lower natural mortality rates should be fished at a lower rate to maximize Y/R; however, these areas may be especially attractive to fishers and are often fished harder. Here, Y/R and SSB/R models are developed that simultaneously account for spatial heterogeneity in growth and fishing effort. These models are applied to the US Atlantic sea scallop (Placopecten magellanicus) fishery. The spatial variability in growth uses depth-integrated models from the literature and variability in effort is based on, alternatively, uniform, observed, and relative-optimal spatial harvesting distributions. The observed effort patterns are derived from vessel monitoring system positions, and illustrate one application for these widely collected but underutilized spatial data. In this example, the distribution of observed fishing effort reduces Y/R compared with the relative-optimal, or the uniform effort distribution implicitly assumed by conventional Y/R analysis. SSB/R was in some cases considerably higher under the relative-optimal distribution of effort than when calculated using observed or uniform effort patterns. Such more realistic spatially integrated Y/R and SSB/R models can help to evaluate the impact of effort patterns on fishery yield and stock egg production. These models demonstrate that the spatial distribution of effort can be as important as the overall average fishing mortality when managing fisheries to optimize Y/R, SSB/R, and yield.
Dynamics of European eel landings and stocks in the coastal waters of Estonia
Authors: Bernotas P. , Vetemaa M. , Saks L. , Eschbaum R. , Verliin A. , Järvalt A. 
Published: December 2015

AbstractEuropean eel stocks are in a decline all over Europe. In Estonia, we analysed three different dataseries (commercial landings 1969–2014, scientific eel monitoring 1998–2014, and recreational catches 2005–2012). In the commercial fishery, the biggest drop in landings occurred in the 1980s, with a small recovery in the end of the 1990s. We also interviewed fishers to evaluate the quality of the official catch figures. In the monitoring dataseries, gathered by the use of special eel fykenets, the steepest cpue decline occurred in the last 5 years. Finally, recreational eel fishery has almost stopped: in 2012, catches were only 3% of that in 2005. In conclusion, both professional and recreational eel catches have declined in all the coastal areas of Estonia. The number of professional and recreational fishers specialized to eel fishing has decreased and the number of licences for eel-specific fishing gear has been reduced.
A Meta-Analysis Examining Differences in Short-Term Outcomes between Sutureless and Conventional Aortic Valve Prostheses
Authors: Hurley Eoghan T. , O'Sullivan Katie E. , Segurado Ricardo , Hurley John P. 
Published: December 2015

Objective Sutureless aortic valve prostheses are anchored by radial force in a mechanism similar to that of transcatheter aortic valve implantation. Transcatheter aortic valve implantation is associated with an increased permanent pacemaker (PPM) requirement in a significant proportion of patients. We undertook a meta-analysis to examine the incidence of PPM insertion associated with sutureless compared with conventional surgical aortic valve replacement. Methods A systematic review was conducted in accordance with the Prisma guidelines.1 All searches were performed on August 10, 2014. Studies between 2007 and 2014 were included in the search. Results A total of 832 patients were included in the sutureless group and 3,740 in the conventional group. Aortic cross-clamp (39.8 vs 62.4 minutes; P < 0.001) and cardiopulmonary bypass (64.9 vs 86.7 minutes; P = 0.002) times were shorter in the sutureless group. Permanent pacemaker implantation rate was higher in the sutureless cohort (9.1% vs 2.4%; P = 0.025). Conclusions Sutureless aortic valve prostheses are associated with significantly shorter cardiopulmonary bypass and aortic cross-clamp times and a higher incidence of PPM insertion than conventional. Further investigation of the prognostic significance is required.