bluuebunny/crossref_metadata_2025_split huggingface dataset:
Excess Pressure Integral Predicts Long-Term All-Cause Mortality in Stable Heart Failure Patients
Authors: Wang Wei-Ting , Sung Shih-Hsien , Wang Jiun-Jr , Wu Cho-Kai , Lin Lian-Yu , Lee Jia-Chun , Cheng Hao-Min , Chen Chen-Huan 
Published: October 2016

Abstract

BACKGROUND
Excess pressure integral (XSPI) derived from reservoir-excess pressure analysis is proposed as a novel indicator of cardiovascular dysfunction in hypertensives. Our study investigated the prognostic value of XSPI for stable heart failure (HF) patients.

METHODS
In total, 238 subjects (mean age 63 ± 18 years, 111 male), comprising 168 stable HF patients with either reduced (SHF; n = 64) left ventricular (LV) ejection fraction (EF) or isolated diastolic dysfunction (DHF, n = 104), and 70 healthy controls, were enrolled. Tonometry-derived carotid pressure waveforms were analyzed with the reservoir pressure theory. XSPI was calculated by subtracting the reservoir pressure from carotid pressure waveform.

RESULTS
XSPI in SHF and DHF (14.01 ± 5.16 and 13.90 ± 5.05 mm Hg•s) were significantly higher than that in controls (11.01 ± 3.67 mm Hg•s, both P &lt; 0.001). During a median follow-up of 9.9 years, 56 deaths occurred. XSPI was a significant independent predictor of total mortality after adjusting for age, sex, left ventricular ejection fraction (LVEF), glomerular filtration rate (GFR), and N-terminal pro-B-type natriuretic peptide (NT-proBNP) (hazard ratio = 4.37 per 1 SD, 95% confidence interval, 1.31–14.58). In subgroup analysis by different baseline characteristics including age, gender, NT-proBNP, LVEF, and GFR, higher XSPI was consistently associated with greater risk of total mortality.

CONCLUSION
In patients with stable HF, XSPI, a novel maker of cardiovascular dysfunction, was associated with long-term risk of total mortality.
Non-native populations of an invasive tree outperform their native conspecifics
Authors: Hirsch Heidi , Hensen Isabell , Wesche Karsten , Renison Daniel , Wypior Catherina , Hartmann Matthias , von Wehrden Henrik 
Published: October 2016

AbstractIntroduced plants often face new environmental conditions in their non-native ranges. To become invasive, they need to overcome several biotic and abiotic filters that may trigger adaptive changes in life-history traits, like post-germination processes. Such early life cycle traits may play a crucial role in the colonization and establishment success of invasive plants. As a previous study revealed that seeds of non-native populations of the woody Siberian elm, Ulmus pumila, germinated faster than those of native populations, we expected growth performance of seedlings to mirror this finding. Here, we conducted a common garden greenhouse experiment using different temperature and watering treatments to compare the biomass production of U. pumila seedlings derived from 7 native and 13 populations from two non-native ranges. Our results showed that under all treatments, non-native populations were characterized by higher biomass production and enhanced resource allocation to aboveground biomass compared to the native populations. The observed enhanced growth performance of non-native populations might be one of the contributing factors for the invasion success of U. pumila due to competitive advantages during the colonization of new sites.
Uncertainty estimation of predictions of peptides’ chromatographic retention times in shotgun proteomics
Authors: Maboudi Afkham Heydar , Qiu Xuanbin , The Matthew , Käll Lukas 
Published: October 2016

Abstract

Motivation
Liquid chromatography is frequently used as a means to reduce the complexity of peptide-mixtures in shotgun proteomics. For such systems, the time when a peptide is released from a chromatography column and registered in the mass spectrometer is referred to as the peptide’s retention time. Using heuristics or machine learning techniques, previous studies have demonstrated that it is possible to predict the retention time of a peptide from its amino acid sequence. In this paper, we are applying Gaussian Process Regression to the feature representation of a previously described predictor Elude. Using this framework, we demonstrate that it is possible to estimate the uncertainty of the prediction made by the model. Here we show how this uncertainty relates to the actual error of the prediction.

Results
In our experiments, we observe a strong correlation between the estimated uncertainty provided by Gaussian Process Regression and the actual prediction error. This relation provides us with new means for assessment of the predictions. We demonstrate how a subset of the peptides can be selected with lower prediction error compared to the whole set. We also demonstrate how such predicted standard deviations can be used for designing adaptive windowing strategies.

Availability and Implementation
Our software and the data used in our experiments is publicly available and can be downloaded from https://github.com/statisticalbiotechnology/GPTime.
Assocplots: a Python package for static and interactive visualization of multiple-group GWAS results
Authors: Khramtsova Ekaterina A , Stranger Barbara E 
Published: October 2016

Abstract

Summary
Over the last decade, genome-wide association studies (GWAS) have generated vast amounts of analysis results, requiring development of novel tools for data visualization. Quantile–quantile (QQ) plots and Manhattan plots are classical tools which have been utilized to visually summarize GWAS results and identify genetic variants significantly associated with traits of interest. However, static visualizations are limiting in the information that can be shown. Here, we present Assocplots, a Python package for viewing and exploring GWAS results not only using classic static Manhattan and QQ plots, but also through a dynamic extension which allows to interactively visualize the relationships between GWAS results from multiple cohorts or studies.

Availability and Implementation
The Assocplots package is open source and distributed under the MIT license via GitHub (https://github.com/khramts/assocplots) along with examples, documentation and installation instructions.
Visualizing the geography of genetic variants
Authors: Marcus Joseph H , Novembre John 
Published: October 2016

Abstract

Summary
One of the key characteristics of any genetic variant is its geographic distribution. The geographic distribution can shed light on where an allele first arose, what populations it has spread to, and in turn on how migration, genetic drift, and natural selection have acted. The geographic distribution of a genetic variant can also be of great utility for medical/clinical geneticists and collectively many genetic variants can reveal population structure. Here we develop an interactive visualization tool for rapidly displaying the geographic distribution of genetic variants. Through a REST API and dynamic front-end, the Geography of Genetic Variants (GGV) browser (http://popgen.uchicago.edu/ggv/) provides maps of allele frequencies in populations distributed across the globe.

Availability and Implementation
GGV is implemented as a website (http://popgen.uchicago.edu/ggv/) which employs an API to access frequency data (http://popgen.uchicago.edu/freq_api/). Python and javascript source code for the website and the API are available at: http://github.com/NovembreLab/ggv/ and http://github.com/NovembreLab/ggv-api/.

Supplementary information
Supplementary data are available at Bioinformatics online.
iATC-mISF: a multi-label classifier for predicting the classes of anatomical therapeutic chemicals
Authors: Cheng Xiang , Zhao Shu-Guang , Xiao Xuan , Chou Kuo-Chen 
Published: October 2016

Abstract
Motivation: Given a compound, can we predict which anatomical therapeutic chemical (ATC) class/classes it belongs to? It is a challenging problem since the information thus obtained can be used to deduce its possible active ingredients, as well as its therapeutic, pharmacological and chemical properties. And hence the pace of drug development could be substantially expedited. But this problem is by no means an easy one. Particularly, some drugs or compounds may belong to two or more ATC classes.
Results: To address it, a multi-label classifier, called iATC-mISF, was developed by incorporating the information of chemical–chemical interaction, the information of the structural similarity, and the information of the fingerprintal similarity. Rigorous cross-validations showed that the proposed predictor achieved remarkably higher prediction quality than its cohorts for the same purpose, particularly in the absolute true rate, the most important and harsh metrics for the multi-label systems.
Availability and Implementation: The web-server for iATC-mISF is accessible at http://www.jci-bioinfo.cn/iATC-mISF. Furthermore, to maximize the convenience for most experimental scientists, a step-by-step guide was provided, by which users can easily get their desired results without needing to go through the complicated mathematical equations. Their inclusion in this article is just for the integrity of the new method and stimulating more powerful methods to deal with various multi-label systems in biology.
Supplementary information: Supplementary data are available at Bioinformatics online.
CloudPhylo: a fast and scalable tool for phylogeny reconstruction
Authors: Xu Xingjian , Ji Zhaohua , Zhang Zhang 
Published: October 2016

Abstract

Summary
Phylogeny reconstruction is fundamentally crucial for molecular evolutionary studies but remains computationally challenging. Here we present CloudPhylo, a tool built on Spark that is capable of processing large-scale datasets for phylogeny reconstruction. As testified on empirical data, CloudPhylo is well suited for big data analysis, achieving high efficiency and good scalability on phylogenetic tree inference.

Availability and Implementation
https://github.com/XingjianXu/cloudphylo

Supplementary information
Supplementary data are available at Bioinformatics online.
Pursuit of a moving target with bounded speed on a directed acyclic graph under partial information
Authors: Kalyanam Krishnamoorthy , Casbeer David , Pachter Meir 
Published: October 2016

Abstract
The optimal control of a ‘blind’ airborne pursuer searching for an evader moving on a road network with positive bounded speed toward a set of goal vertices is considered. To aid the pursuer and provide feedback information, certain roads in the network have been instrumented with unattended ground sensors (UGSs) that detect evader motion. When the pursuer arrives at an instrumented node, the UGS therein informs the pursuer if and when the evader visited the node. The pursuer is aware of the bounds on the evader’s speed. Moreover, the embedded graph with the UGSs as vertices and connecting roads as edges is restricted to be a directed acyclic graph (DAG). At time $0$, the evader’s entry into the road network is registered at UGS $1$, the entry node. The pursuer also arrives at the entry node after some delay $d&gt;0$ and is thus informed about the presence of the intruder/evader in the network, whereupon the chase is on. Capture entails the pursuer and evader being co-located at an UGS location. However, if the evader reaches an exit node of the graph without being captured, it is deemed to have escaped. We compute the maximum initial delay $d$ and the ensuing pursuit policy, for which capture is guaranteed.
Anonymization for outputs of population health and health services research conducted via an online data center
Authors: O’Keefe Christine M , Westcott Mark , O’Sullivan Maree , Ickowicz Adrien , Churches Tim 
Published: October 2016

Objective: Online data centers (ODCs) are becoming increasingly popular for making health-related data available for research. Such centers provide good privacy protection during analysis by trusted researchers, but privacy concerns may still remain if the system outputs are not sufficiently anonymized. In this article, we propose a method for anonymizing analysis outputs from ODCs for publication in academic literature.
Methods: We use as a model system the Secure Unified Research Environment, an online computing system that allows researchers to access and analyze linked health-related data for approved studies in Australia. This model system suggests realistic assumptions for an ODC that, together with literature and practice reviews, inform our solution design.
Results: We propose a two-step approach to anonymizing analysis outputs from an ODC. A data preparation stage requires data custodians to apply some basic treatments to the dataset before making it available. A subsequent output anonymization stage requires researchers to use a checklist at the point of downloading analysis output. The checklist assists researchers with highlighting potential privacy concerns, then applying appropriate anonymization treatments.
Conclusion: The checklist can be used more broadly in health care research, not just in ODCs. Ease of online publication as well as encouragement from journals to submit supplementary material are likely to increase both the volume and detail of analysis results publicly available, which in turn will increase the need for approaches such as the one suggested in this paper.
Problems with health information technology and their effects on care delivery and patient outcomes: a systematic review
Authors: Kim Mi Ok , Coiera Enrico , Magrabi Farah 
Published: October 2016

Objective: To systematically review studies reporting problems with information technology (IT) in health care and their effects on care delivery and patient outcomes.
Materials and methods: We searched bibliographic databases including Scopus, PubMed, and Science Citation Index Expanded from January 2004 to December 2015 for studies reporting problems with IT and their effects. A framework called the information value chain, which connects technology use to final outcome, was used to assess how IT problems affect user interaction, information receipt, decision-making, care processes, and patient outcomes. The review was conducted in accordance with the Preferred Reporting Items for Systematic Reviews and Meta-Analyses (PRISMA) statement.
Results: Of the 34 studies identified, the majority (n = 14, 41%) were analyses of incidents reported from 6 countries. There were 7 descriptive studies, 9 ethnographic studies, and 4 case reports. The types of IT problems were similar to those described in earlier classifications of safety problems associated with health IT. The frequency, scale, and severity of IT problems were not adequately captured within these studies. Use errors and poor user interfaces interfered with the receipt of information and led to errors of commission when making decisions. Clinical errors involving medications were well characterized. Issues with system functionality, including poor user interfaces and fragmented displays, delayed care delivery. Issues with system access, system configuration, and software updates also delayed care. In 18 studies (53%), IT problems were linked to patient harm and death. Near-miss events were reported in 10 studies (29%).
Discussion and conclusion: The research evidence describing problems with health IT remains largely qualitative, and many opportunities remain to systematically study and quantify risks and benefits with regard to patient safety. The information value chain, when used in conjunction with existing classifications for health IT safety problems, can enhance measurement and should facilitate identification of the most significant risks to patient safety.
From loquacious to reticent: understanding patient health information communication to guide consumer health IT design
Authors: Valdez Rupa S , Guterbock Thomas M , Fitzgibbon Kara , Williams Ishan C , Wellbeloved-Stone Claire A , Bears Jaime E , Menefee Hannah K 
Published: October 2016

AbstractBackground and significance. It is increasingly recognized that some patients self-manage in the context of social networks rather than alone. Consumer health information technology (IT) designed to support socially embedded self-management must be responsive to patients’ everyday communication practices. There is an opportunity to improve consumer health IT design by explicating how patients currently leverage social media to support health information communication.Objective. The objective of this study was to determine types of health information communication patterns that typify Facebook users with chronic health conditions to guide consumer health IT design.Materials and methods. Seven hundred participants with type 2 diabetes were recruited through a commercial survey access panel. Cluster analysis was used to identify distinct approaches to health information communication both on and off Facebook. Analysis of variance (ANOVA) methods were used to identify demographic and behavioral differences among profiles. Secondary analysis of qualitative interviews (n = 25) and analysis of open-ended survey questions were conducted to understand participant rationales for each profile.Results. Our analysis yielded 7 distinct health information communication profiles. Five of 7 profiles had consistent patterns both on and off Facebook, while the remaining 2 demonstrated distinct practices, with no health information communication on Facebook but some off Facebook. One profile was distinct from all others in both health information communication practices and demographic composition. Rationales for following specific health information communication practices were categorized under 6 themes: altruism, instrumental support, social support, privacy and stigma, convenience, and Facebook knowledge.Conclusion. Facebook has been widely adopted for health information communication; This study demonstrates that Facebook has been widely adopted for health information communication. It also shows that the ways in which patients communicate health information on and off Facebook are diverse.
Prospective Longitudinal Analysis of Immune Responses in Pediatric Subjects After Pharyngeal Acquisition of Group A Streptococci
Authors: Hysmith Nicholas D. , Kaplan Edward L. , Cleary P. Patrick , Johnson Dwight R. , Penfound Thomas A. , Dale James B. 
Published: October 2016

AbstractBackground.Despite the significant burden of disease associated with infection by group A streptococcus (GAS), little is known about the human immune response to GAS antigens after natural infection.Methods.We evaluated 195 serum samples obtained prospectively over a consecutive 24-month period from 41 pediatric subjects who experienced a new pharyngeal GAS acquisition. An enzyme-linked immunoassay was used to determine the kinetics and antigen specificity of antibodies against 13 shared GAS antigens and 18 type-specific M peptides. The majority of the antigens tested are currently being considered as vaccine candidates.Results.Twelve M types of GAS were recovered from 41 subjects who experienced 51 new GAS acquisitions that elicited antibody responses against at least 1 of the 31 antigens tested (immunologically significant new GAS acquisitions). The immune responses to the 13 shared antigens were highly variable. Increases in antibody levels were detected against a mean of 3.5 shared antigens (range, 1–8). Antibody responses to the homologous M peptide were observed in 32 (63%) of the 51 episodes. Seven subjects acquired more than 1 M type of GAS. There were no new immunologically significant acquisitions of an M type against which the subject had preexisting antibodies to the homologous M peptide. Of the subjects with new GAS acquisition, 65% were asymptomatic, yet immune responses were detected against 1 or more GAS antigens. Immune responses to streptolysin O and/or deoxyribonuclease B were observed after 67% of the new GAS acquisitions. Persistently positive (&gt;12 weeks) throat culture results were returned for 20% of the 41 subjects despite immune responses to homologous M peptides and/or shared antigens.Conclusions.The availability of throat culture results, GAS isolates, and serial serum samples collected prospectively over a 2-year period of observation provided a unique opportunity for us to assess the serologic status of pediatric subjects before and after new pharyngeal acquisitions of GAS. With the exception of antibody responses to the homologous M peptides, no clear pattern of immune responses against the remaining GAS antigens was seen. There were no new immunologically significant acquisitions ofemm types of GAS against which the subjects had preexisting elevated levels of antibodies against the homologous M peptide. The observation that 65% of new GAS acquisitions caused no symptoms yet were immunologically significant suggests that the majority of infections are not detected, which would result in missed opportunities for primary prevention of rheumatic fever and rheumatic heart disease with appropriate antimicrobial therapy.
Implementation of Feeding Guidelines Hastens the Time to Initiation of Enteral Feeds and Improves Growth Velocity in Very Low Birth-Weight Infants
Authors: Culpepper Christine , Hendrickson Kendra , Marshall Susan , Benes Jessica , Grover Theresa R. 
Published: October 2016

Background:
Growth and nutrition are critical in neonatal care. Whether feeding guidelines improve growth and nutrition and reduce morbidity is unknown.

Purpose:
Feeding guidelines for very low birth-weight (VLBW) infants were implemented in our neonatal intensive care unit (NICU) to start and achieve full enteral feeds sooner, and increase weight gain over the first month.

Methods:
Feeding guidelines for VLBW infants were implemented in January 2014, stratified by birth weight (<750, 750-1000, and 1000-1500 g). After trophic feedings, enteral feedings were advanced by 20 to 30 mL/kg/d.
Data were analyzed for 2 years prior (baseline) and 6 months after (guideline) guidelines were implemented and included days to initiation of enteral feeds, days on total parenteral nutrition (TPN), and weight gain over the first month. Potential concomitant factors that could affect feeding tolerance were examined including indomethacin or dopamine treatment, delivery room cardiopulmonary resuscitation, and growth restriction.

Results:
A total of 95 infants with a birth weight of less than 1500 g were included (59 baseline and 36 guideline). Days to start enteral feeds decreased by 47% (P < .01) and days on TPN decreased by 25% (16 days vs 11 days; P < .01). Weight gain over the first month of life increased by 15% (p < .05). Dopamine and indomethacin use decreased during the study period, and small for gestational age infants were overrepresented in the guideline group.

Implications for Practice/Research:
Establishment of feeding guidelines for VLBW infants in our NICU reduced the days to start feeds and days on TPN while increasing weight gain over the first month. Improving growth and nutrition and reducing need for TPN in this vulnerable population may ultimately prevent infection and improve neurodevelopmental outcomes.