bluuebunny/crossref_metadata_2025_split huggingface dataset:
Renal sympathetic denervation prevents the development of pulmonary arterial hypertension and cardiac dysfunction in dogs
Authors: Hu Wei , Yu Sheng‐Bo , Chen Liao , Guo Rui‐Qiang , Zhao Qing‐Yan 
Published: July 2015

AbstractThe renin–angiotensin–aldosterone system is activated in pulmonary arterial hypertension (PAH) patients, and this activation may have long‐term negative effects on the progression of PAH. The purpose of this study was to evaluate the effects of transcatheter renal sympathetic denervation (RSD) on the development of pulmonary arterial hypertension and cardiac dysfunction in dogs using two‐dimensional speckle tracking imaging. Twenty‐two dogs were randomly divided into three groups: control group (n = 7), PAH group (n = 8), and PAH + RSD group (n = 7). All dogs were assessed using two‐dimensional speckle tracking imaging. The ventricular strain, ventricular synchrony, left ventricular (LV) twist, and torsion rate were analyzed to evaluate cardiac function. After 8 weeks, the right ventricular lateral longitudinal strain and the septum longitudinal strain were reduced in the PAH group compared with the control group (p < 0.001). However, these values were significantly restored in the PAH + RSD group compared with the PAH group (p < 0.01). The degree of LV and RV dyssynchrony was significantly higher in the PAH group compared with the control group (p < 0.001), but the degree of LV and RV dyssynchrony was significantly lower in the PAH + RSD group compared to the PAH group (p < 0.01). The LV twist was significantly restored in the PAH + RSD group compared to the PAH group (p < 0.01). Similarly, the rotation rate was markedly decreased in the PAH group, and strikingly improved in the PAH + RSD group (p < 0.01). These results indicate that RSD prevents the development of PAH and cardiac dysfunction in dogs.
Kinematic, Cardiopulmonary, and Metabolic Responses of Overweight Runners While Running at Self‐Selected and Standardized Speeds
Authors: Zdziarski Laura Ann , Chen Cong , Horodyski Marybeth , Vincent Kevin R. , Vincent Heather K. 
Published: July 2015

AbstractObjectiveTo determine the differences in kinematic, cardiopulmonary, and metabolic responses between overweight and healthy weight runners at a self‐selected and standard running speed.DesignComparative descriptive study.SettingTertiary care institution, university‐affiliated research laboratory.ParticipantsOverweight runners (n = 21) were matched with runners of healthy weight (n = 42).MethodsParticipants ran at self‐selected and standardized speeds (13.6 km/h). Sagittal plane joint kinematics were captured simultaneously with cardiopulmonary and metabolic measures using a motion capture system and portable gas analyzer, respectively.Main Outcome MeasurementsSpatiotemporal parameters (cadence, step width and length, center of gravity displacement, stance time) joint kinematics, oxygen cost, heart rate, ventilation and energy expenditure.ResultsAt the self‐selected speed, overweight individuals ran slower (8.5 ± 1.3 versus 10.0 ± 1.6 km/h) and had slower cadence (163 versus 169 steps/min; P < .05). The sagittal plane range of motion (ROM) for flexion‐extension at the ankle, knee, hip, and anterior pelvic tilt were all less in overweight runners compared to healthy weight runners (all P < .05). At self‐selected speed and 13.6 km/h, energy expenditure was higher in the overweight runners compared to their healthy weight counterparts (P < .05). At 13.6 km/h, only the frontal hip and pelvis ROM were higher in the overweight versus the healthy weight runners (P < .05), and energy expenditure, net energy cost, and minute ventilation were higher in the overweight runners compared to the healthy weight runners (P < .05).ConclusionAt self‐selected running speeds, the overweight runners demonstrated gait strategies (less joint ROM, less vertical displacement, and shorter step lengths) that resulted in cardiopulmonary and energetic responses similar to those of healthy weight individuals.
TOX and CDKN2A/B Gene Polymorphisms Are Associated with Type 2 Diabetes in Han Chinese
Authors: Wei Fengjiang , Cai Chunyou , Feng Shuzhi , Lv Jia , Li Shen , Chang Baocheng , Zhang Hong , Shi Wentao , Han Hongling , Ling Chao , Yu Ping , Chen Yongjun , Sun Ning , Tian Jianli , Jiao Hongxiao , Yang Fuhua , Li Mingshan , Wang Yuhua , Zou Lei , Su Long , Li Jingbo , Li Ran , Qiu Huina , Shi Jingmin , Liu Shiying , Chang Mingqin , Lin Jingna , Chen Liming , Li Wei-Dong 
Published: July 2015

AbstractTo study associations between type 2 diabetes (T2DM) candidate genes and microvascular complications of diabetes (MVCDs), we performed case-control association studies for both T2DM and MVCDs in Han Chinese subjects. We recruited 1,939 unrelated Han Chinese T2DM patients and 918 individuals with normal blood glucose levels as nondiabetic controls. Among T2DM patients, 1116 have MVCDs, 266 have a history of T2DM of >10 years but never developed MVCDs. Eighty-two single-nucleotide polymorphisms (SNPs) in 54 candidate genes were genotyped. Discrete association studies were performed by the PLINK program for T2DM and MVCDs. Significant associations were found among candidate gene SNPs and T2DM, including rs1526167 of the TOX gene (allele A, P = 2.85 × 10−9, OR = 1.44). The SNP rs10811661 of the CDKN2A/B gene was also associated with T2DM (allele T, P = 4.09 × 10−7, OR = 1.36). When we used control patients with >10 years of T2DM history without MVCD, we found that the G allele of SNP rs1526167 of the TOX gene was associated with MVCD (nominal P = 4.33 × 10−4). In our study, significant associations were found between TOX and CDKN2A/B gene SNPs and T2DM. The TOX polymorphism might account for the higher risk of T2DM and the lower risk of MVCDs in the Han Chinese population.
Impaired mitochondrial energy supply coupled to increased H2O2 emission under energy/redox stress leads to myocardial dysfunction during Type I diabetes
Authors: Tocchetti Carlo G. , Stanley Brian A. , Sivakumaran Vidhya , Bedja Djahida , O'Rourke Brian , Paolocci Nazareno , Cortassa Sonia , Aon Miguel A. 
Published: July 2015

In Type I diabetic (T1DM) patients, both peaks of hyperglycaemia and increased sympathetic tone probably contribute to impair systolic and diastolic function. However, how these stressors eventually alter cardiac function during T1DM is not fully understood. In the present study, we hypothesized that impaired mitochondrial energy supply and excess reactive oxygen species (ROS) emission is centrally involved in T1DM cardiac dysfunction due to metabolic/redox stress and aimed to determine the mitochondrial sites implicated in these alterations. To this end, we used isolated myocytes and mitochondria from Sham and streptozotocin (STZ)-induced T1DM guinea pigs (GPs), untreated or treated with insulin. Relative to controls, T1DM myocytes exhibited higher oxidative stress when challenged with high glucose (HG) combined with β-adrenergic stimulation [via isoprenaline (isoproterenol) (ISO)], leading to contraction/relaxation deficits. T1DM mitochondria had decreased respiration with complex II and IV substrates and markedly lower ADP phosphorylation rates and higher H2O2 emission when challenged with oxidants to mimic the more oxidized redox milieu present in HG + ISO-treated cardiomyocytes. Since in T1DM hearts insulin-sensitivity is preserved and a glucose-to-fatty acid (FA) shift occurs, we next tested whether insulin therapy or acute palmitate (Palm) infusion prevents HG + ISO-induced cardiac dysfunction. We found that insulin rescued proper cardiac redox balance, but not mitochondrial respiration or contractile performance. Conversely, Palm restored redox balance and preserved myocyte function. Thus, stressors such as peaks of HG and adrenergic hyperactivity impair mitochondrial respiration, hampering energy supply while exacerbating ROS emission. Our study suggests that an ideal therapeutic measure to treat metabolically/redox-challenged T1DM hearts should concomitantly correct energetic and redox abnormalities to fully maintain cardiac function.
Gewinnung von Jobcenter-Klienten für die Teilnahme an einem kardiopräventiven Untersuchungsprogramm
Authors: Ulbricht S. , Gürtler D. , Braatz J. , Weymar F. , Meyer C. , Dörr M. , John U. 
Published: July 2015

Zusammenfassung
Ziel: Über die Teilnehmergewinnung für Präventionsmaßnahmen in Bevölkerungen mit niedrigerem Sozialstatus ist wenig bekannt. Ergebnisse proaktiver Kontaktierung für ein 2-stufiges kardiopräventives Untersuchungsprogramm (KUP) in 2 Jobcentern einer norddeutschen Region werden dargestellt.
Methode: Über jeweils 10 Wochen erhielten Jobcenter-Klienten im Alter zwischen 40 und 65 Jahren das Angebot, am KUP teilzunehmen. Dieses umfasste einen ersten Abschnitt im Jobcenter und einen zweiten in einem kardiovaskulären Untersuchungszentrum. Abschnitt 1 beinhaltete eine EDV-gestützte Befragung, und bei Anwesenheit einer medizinischen Fachkraft, eine Blutdruckmessung und/oder Blutentnahme. Teilnehmer ohne kardiovaskuläre Vorerkrankungen, interventionelle/operative Gefäßeingriffe, Diabetes mellitus und einem Body-Maß Index≤35 kg/m2 erhielten das Angebot der Teilnahme an Abschnitt 2. Mittels logistischer Regressionsanalysen wurden für beide Abschnitte Prädiktoren der Teilnahme analysiert. Dazu zählten Lebensalter und Geschlecht, für die Teilnahme an Abschnitt 2 die Entfernung zwischen Wohnadresse und Untersuchungszentrum, kardiovaskuläre Risikofaktoren, subjektive Gesundheit und weitere soziodemografische Merkmale.
Ergebnisse: In Abschnitt 1 nahmen 344 der 1 046 eingeladenen Personen an der Befragung teil. Dabei handelte es sich um überzufällig mehr Frauen als Männer. Von diesen erhielten 253 das Angebot der Blutdruckmessung, der Blutentnahme sowie der postalischen Zusendung der Laborergebnisse. Die Teilnahme von 209 Personen war positiv mit dem Lebensalter assoziiert. An Abschnitt 2 nahmen 138 Personen teil. Je weiter vom Untersuchungszentrum entfernt die Personen wohnten, desto weniger nahmen sie dieses Angebot wahr. Von Tabakrauchern, Personen mit Hauptschulbildung bzw. solche mit nicht erhöhten Blutfetten nahmen ebenfalls weniger teil.
Schlussfolgerungen: Blutdruckmessung und Blutentnahme im Jobcenter treffen auf hohe Akzeptanz. Anforderungen zusätzlicher Wege für präventive kardiovaskuläre Untersuchungsangebote sind gering zu halten.
al3c: high-performance software for parameter inference using Approximate Bayesian Computation
Authors: Stram Alexander H. , Marjoram Paul , Chen Gary K. 
Published: July 2015

Abstract
Motivation: The development of Approximate Bayesian Computation (ABC) algorithms for parameter inference which are both computationally efficient and scalable in parallel computing environments is an important area of research. Monte Carlo rejection sampling, a fundamental component of ABC algorithms, is trivial to distribute over multiple processors but is inherently inefficient. While development of algorithms such as ABC Sequential Monte Carlo (ABC-SMC) help address the inherent inefficiencies of rejection sampling, such approaches are not as easily scaled on multiple processors. As a result, current Bayesian inference software offerings that use ABC-SMC lack the ability to scale in parallel computing environments.
Results: We present al3c, a C++ framework for implementing ABC-SMC in parallel. By requiring only that users define essential functions such as the simulation model and prior distribution function, al3c abstracts the user from both the complexities of parallel programming and the details of the ABC-SMC algorithm. By using the al3c framework, the user is able to scale the ABC-SMC algorithm in parallel computing environments for his or her specific application, with minimal programming overhead.
Availability and implementation: al3c is offered as a static binary for Linux and OS-X computing environments. The user completes an XML configuration file and C++ plug-in template for the specific application, which are used by al3c to obtain the desired results. Users can download the static binaries, source code, reference documentation and examples (including those in this article) by visiting https://github.com/ahstram/al3c.
Contact: astram@usc.edu
Supplementary information: Supplementary data are available at Bioinformatics online.
JASSA: a comprehensive tool for prediction of SUMOylation sites and SIMs
Authors: Beauclair Guillaume , Bridier-Nahmias Antoine , Zagury Jean-François , Saïb Ali , Zamborlini Alessia 
Published: July 2015

Abstract
Motivation: Post-translational modification by the Small Ubiquitin-like Modifier (SUMO) proteins, a process termed SUMOylation, is involved in many fundamental cellular processes. SUMO proteins are conjugated to a protein substrate, creating an interface for the recruitment of cofactors harboring SUMO-interacting motifs (SIMs). Mapping both SUMO-conjugation sites and SIMs is required to study the functional consequence of SUMOylation. To define the best candidate sites for experimental validation we designed JASSA, a Joint Analyzer of SUMOylation site and SIMs.
Results: JASSA is a predictor that uses a scoring system based on a Position Frequency Matrix derived from the alignment of experimental SUMOylation sites or SIMs. Compared with existing web-tools, JASSA displays on par or better performances. Novel features were implemented towards a better evaluation of the prediction, including identification of database hits matching the query sequence and representation of candidate sites within the secondary structural elements and/or the 3D fold of the protein of interest, retrievable from deposited PDB files.
Availability and Implementation: JASSA is freely accessible at http://www.jassa.fr/. Website is implemented in PHP and MySQL, with all major browsers supported.
Contact: guillaume.beauclair@inserm.fr
Supplementary information: Supplementary data are available at Bioinformatics online.
Nsite, NsiteH and NsiteM computer tools for studying transcription regulatory elements
Authors: Shahmuradov Ilham A. , Solovyev Victor V. 
Published: July 2015

Abstract
Summary: Gene transcription is mostly conducted through interactions of various transcription factors and their binding sites on DNA (regulatory elements, REs). Today, we are still far from understanding the real regulatory content of promoter regions. Computer methods for identification of REs remain a widely used tool for studying and understanding transcriptional regulation mechanisms. The Nsite, NsiteH and NsiteM programs perform searches for statistically significant (non-random) motifs of known human, animal and plant one-box and composite REs in a single genomic sequence, in a pair of aligned homologous sequences and in a set of functionally related sequences, respectively.
Availability and implementation: Pre-compiled executables built under commonly used operating systems are available for download by visiting http://www.molquest.kaust.edu.sa and http://www.softberry.com.
Contact: solovictor@gmail.com
Supplementary information: Supplementary data are available at Bioinformatics online.
Data2Dynamics: a modeling environment tailored to parameter estimation in dynamical systems
Authors: Raue A. , Steiert B. , Schelker M. , Kreutz C. , Maiwald T. , Hass H. , Vanlier J. , Tönsing C. , Adlung L. , Engesser R. , Mader W. , Heinemann T. , Hasenauer J. , Schilling M. , Höfer T. , Klipp E. , Theis F. , Klingmüller U. , Schöberl B. , Timmer J. 
Published: July 2015

Abstract
Summary: Modeling of dynamical systems using ordinary differential equations is a popular approach in the field of systems biology. Two of the most critical steps in this approach are to construct dynamical models of biochemical reaction networks for large datasets and complex experimental conditions and to perform efficient and reliable parameter estimation for model fitting. We present a modeling environment for MATLAB that pioneers these challenges. The numerically expensive parts of the calculations such as the solving of the differential equations and of the associated sensitivity system are parallelized and automatically compiled into efficient C code. A variety of parameter estimation algorithms as well as frequentist and Bayesian methods for uncertainty analysis have been implemented and used on a range of applications that lead to publications.
Availability and implementation: The Data2Dynamics modeling environment is MATLAB based, open source and freely available at http://www.data2dynamics.org.
Contact: andreas.raue@fdm.uni-freiburg.de
Supplementary information: Supplementary data are available at Bioinformatics online.
A system to build distributed multivariate models and manage disparate data sharing policies: implementation in the scalable national network for effectiveness research
Authors: Meeker Daniella , Jiang Xiaoqian , Matheny Michael E , Farcas Claudiu , D’Arcy Michel , Pearlman Laura , Nookala Lavanya , Day Michele E , Kim Katherine K , Kim Hyeoneui , Boxwala Aziz , El-Kareh Robert , Kuo Grace M , Resnic Frederic S , Kesselman Carl , Ohno-Machado Lucila 
Published: July 2015

AbstractBackground Centralized and federated models for sharing data in research networks currently exist. To build multivariate data analysis for centralized networks, transfer of patient-level data to a central computation resource is necessary. The authors implemented distributed multivariate models for federated networks in which patient-level data is kept at each site and data exchange policies are managed in a study-centric manner.Objective The objective was to implement infrastructure that supports the functionality of some existing research networks (e.g., cohort discovery, workflow management, and estimation of multivariate analytic models on centralized data) while adding additional important new features, such as algorithms for distributed iterative multivariate models, a graphical interface for multivariate model specification, synchronous and asynchronous response to network queries, investigator-initiated studies, and study-based control of staff, protocols, and data sharing policies.Materials and Methods Based on the requirements gathered from statisticians, administrators, and investigators from multiple institutions, the authors developed infrastructure and tools to support multisite comparative effectiveness studies using web services for multivariate statistical estimation in the SCANNER federated network.Results The authors implemented massively parallel (map-reduce) computation methods and a new policy management system to enable each study initiated by network participants to define the ways in which data may be processed, managed, queried, and shared. The authors illustrated the use of these systems among institutions with highly different policies and operating under different state laws.Discussion and Conclusion Federated research networks need not limit distributed query functionality to count queries, cohort discovery, or independently estimated analytic models. Multivariate analyses can be efficiently and securely conducted without patient-level data transport, allowing institutions with strict local data storage requirements to participate in sophisticated analyses based on federated research networks.
CSER and eMERGE: current and potential state of the display of genetic information in the electronic health record
Authors: Shirts Brian H , Salama Joseph S , Aronson Samuel J , Chung Wendy K , Gray Stacy W , Hindorff Lucia A , Jarvik Gail P , Plon Sharon E , Stoffel Elena M , Tarczy-Hornoch Peter Z , Van Allen Eliezer M , Weck Karen E , Chute Christopher G , Freimuth Robert R , Grundmeier Robert W , Hartzler Andrea L , Li Rongling , Peissig Peggy L , Peterson Josh F , Rasmussen Luke V , Starren Justin B , Williams Marc S , Overby Casey L 
Published: July 2015

Abstract
Objective Clinicians’ ability to use and interpret genetic information depends upon how those data are displayed in electronic health records (EHRs). There is a critical need to develop systems to effectively display genetic information in EHRs and augment clinical decision support (CDS).
Materials and Methods The National Institutes of Health (NIH)-sponsored Clinical Sequencing Exploratory Research and Electronic Medical Records & Genomics EHR Working Groups conducted a multiphase, iterative process involving working group discussions and 2 surveys in order to determine how genetic and genomic information are currently displayed in EHRs, envision optimal uses for different types of genetic or genomic information, and prioritize areas for EHR improvement.
Results There is substantial heterogeneity in how genetic information enters and is documented in EHR systems. Most institutions indicated that genetic information was displayed in multiple locations in their EHRs. Among surveyed institutions, genetic information enters the EHR through multiple laboratory sources and through clinician notes. For laboratory-based data, the source laboratory was the main determinant of the location of genetic information in the EHR. The highest priority recommendation was to address the need to implement CDS mechanisms and content for decision support for medically actionable genetic information.
Conclusion Heterogeneity of genetic information flow and importance of source laboratory, rather than clinical content, as a determinant of information representation are major barriers to using genetic information optimally in patient care. Greater effort to develop interoperable systems to receive and consistently display genetic and/or genomic information and alert clinicians to genomic-dependent improvements to clinical care is recommended.
Assessing payer perspectives on health information exchange
Authors: Cross Dori A , Lin Sunny C , Adler-Milstein Julia 
Published: July 2015

AbstractObjective To identify factors that impede payer engagement in a health information exchange (HIE), along with organizational and policy strategies that might effectively address the impediments.Materials and Methods Qualitative analysis of semi-structured interviews with leaders from 17 varied payer organizations from across the country (e.g., large, national payers; state Blues plans; local Medicaid managed care plans).Results We found a large gap between payers’ vision of what optimal HIE should be and the current approach to HIE in the United States. Notably, payers sought to be active participants in HIE efforts – both providing claims data and accessing clinical data to support payer HIE use cases. Instead, payers were often asked by HIE efforts only to provide financial support without the option to participate in data exchange, or, when given the option, their data needs were secondary to those of providers.Discussion Efforts to engage payers in pursuit of more robust and sustainable HIE need to better align their value proposition with payer HIE use cases. This will require addressing provider concerns about payer access to clinical data. Policymakers should focus on creating the conditions for broader payer engagement by removing common obstacles, such as low provider engagement in HIE.Conclusion Despite variation in the extent to which payers engaged with current HIE efforts, there was agreement on the vision of optimal HIE and the facilitators of greater payer engagement. Specific actions by those leading HIE efforts, complemented by policy efforts nationally, could greatly increase payer engagement and enhance HIE sustainability.