bluuebunny/crossref_metadata_2025_split huggingface dataset:
BRAT-nova: fast and accurate mapping of bisulfite-treated reads
Authors: Harris Elena Y. , Ounit Rachid , Lonardi Stefano 
Published: April 2016

Abstract
Summary: In response to increasing amounts of sequencing data, faster and faster aligners need to become available. Here, we introduce BRAT-nova, a completely rewritten and improved implementation of the mapping tool BRAT-BW for bisulfite-treated reads (BS-Seq). BRAT-nova is very fast and accurate. On the human genome, BRAT-nova is 2–7 times faster than state-of-the-art aligners, while maintaining the same percentage of uniquely mapped reads and space usage. On synthetic reads, BRAT-nova is 2–8 times faster than state-of-the-art aligners while maintaining similar mapping accuracy, methylation call accuracy, methylation level accuracy and space efficiency.
Availability and implementation: The software is available in the public domain at http://compbio.cs.ucr.edu/brat/
Contact: elenah@cs.ucr.edu
Supplementary information: Supplementary data are available at Bioinformatics online.
densityCut: an efficient and versatile topological approach for automatic clustering of biological data
Authors: Ding Jiarui , Shah Sohrab , Condon Anne 
Published: April 2016

Abstract
Motivation : Many biological data processing problems can be formalized as clustering problems to partition data points into sensible and biologically interpretable groups.
Results : This article introduces densityCut, a novel density-based clustering algorithm, which is both time- and space-efficient and proceeds as follows: densityCut first roughly estimates the densities of data points from a K -nearest neighbour graph and then refines the densities via a random walk. A cluster consists of points falling into the basin of attraction of an estimated mode of the underlining density function. A post-processing step merges clusters and generates a hierarchical cluster tree. The number of clusters is selected from the most stable clustering in the hierarchical cluster tree. Experimental results on ten synthetic benchmark datasets and two microarray gene expression datasets demonstrate that densityCut performs better than state-of-the-art algorithms for clustering biological datasets. For applications, we focus on the recent cancer mutation clustering and single cell data analyses, namely to cluster variant allele frequencies of somatic mutations to reveal clonal architectures of individual tumours, to cluster single-cell gene expression data to uncover cell population compositions, and to cluster single-cell mass cytometry data to detect communities of cells of the same functional states or types. densityCut performs better than competing algorithms and is scalable to large datasets.
Availability and Implementation : Data and the densityCut R package is available from https://bitbucket.org/jerry00/densitycut_dev .
Contact : condon@cs.ubc.ca or sshah@bccrc.ca or jiaruid@cs.ubc.ca
Supplementary information: Supplementary data are available at Bioinformatics online.
Identifying visual search patterns in eye gaze data; gaining insights into physician visual workflow
Authors: Fong Allan , Hoffman Daniel J , Zachary Hettinger A , Fairbanks Rollin J , Bisantz Ann M 
Published: April 2016

AbstractImportance and Objectives As health information technologies become more prevalent in physician workflow, it is increasingly important to understand how physicians are using and interacting with these systems. This includes understanding how physicians search for information presented through health information technology systems. Eye tracking technologies provide a useful technique to understand how physicians visually search for information. However, analyzing eye tracking data can be challenging and is often done by measuring summative metrics, such as total time looking at a specific area and first-order transitions.Methods In this paper, we propose an algorithmic approach to identify different visual search patterns. We demonstrate this approach by identifying common visual search patterns from physicians using a simulated prototype emergency department patient tracking system.Results and Conclusions We evaluate and compare the visual search pattern results to first-order transition results. We discuss the benefits and limitations of this approach and insights from this initial evaluation.
Development, use, and integration of a nationally-distributed HIV/AIDS electronic health information system
Authors: Milberg John A 
Published: April 2016

AbstractBackground The management of HIV infection requires extensive, longitudinal information record-keeping and coordination to ensure optimal monitoring and outcomes of care and treatment.Objective Agencies funded by The Ryan White HIV/AIDS Treatment Modernization Act are increasingly required to monitor the quality of their HIV care and generate reports for funding agencies. To assist in their data collection and reporting capacity, the HIV/AIDS Bureau in the Health Resources and Services Administration released its first version of a software application called CAREWare in 2000.Methods This report describes the development of the application, the agencies that use it, how it is used, and overall satisfaction. The role of CAREWare in the larger health information technology landscape affecting HIV primary care providers is also discussed.Results and Conclusion CAREWare has evolved significantly in functionality and use, including the capacity to run in a real-time network connecting multiple service providers, generate performance measures, and import data in multiple formats. The application is the source of over half of the Bureau s data, is used regularly by most providers and is installed in nearly every state. Ongoing enhancements will be essential to ensure that CAREWare stays current in a rapidly-changing environment of health information technology and data exchange.
Applying probabilistic temporal and multisite data quality control methods to a public health mortality registry in Spain: a systematic approach to quality control of repositories
Authors: Sáez Carlos , Zurriaga Oscar , Pérez-Panadés Jordi , Melchor Inma , Robles Montserrat , García-Gómez Juan M 
Published: April 2016

Abstract
Objective To assess the variability in data distributions among data sources and over time through a case study of a large multisite repository as a systematic approach to data quality (DQ).
Materials and Methods Novel probabilistic DQ control methods based on information theory and geometry are applied to the Public Health Mortality Registry of the Region of Valencia, Spain, with 512 143 entries from 2000 to 2012, disaggregated into 24 health departments. The methods provide DQ metrics and exploratory visualizations for (1) assessing the variability among multiple sources and (2) monitoring and exploring changes with time. The methods are suited to big data and multitype, multivariate, and multimodal data.
Results The repository was partitioned into 2 probabilistically separated temporal subgroups following a change in the Spanish National Death Certificate in 2009. Punctual temporal anomalies were noticed due to a punctual increment in the missing data, along with outlying and clustered health departments due to differences in populations or in practices.
Discussion Changes in protocols, differences in populations, biased practices, or other systematic DQ problems affected data variability. Even if semantic and integration aspects are addressed in data sharing infrastructures, probabilistic variability may still be present. Solutions include fixing or excluding data and analyzing different sites or time periods separately. A systematic approach to assessing temporal and multisite variability is proposed.
Conclusion Multisite and temporal variability in data distributions affects DQ, hindering data reuse, and an assessment of such variability should be a part of systematic DQ procedures.
Electronic medical record phenotyping using the anchor and learn framework
Authors: Halpern Yoni , Horng Steven , Choi Youngduck , Sontag David 
Published: April 2016

ABSTRACTBackground Electronic medical records (EMRs) hold a tremendous amount of information about patients that is relevant to determining the optimal approach to patient care. As medicine becomes increasingly precise, a patient’s electronic medical record phenotype will play an important role in triggering clinical decision support systems that can deliver personalized recommendations in real time. Learning with anchors presents a method of efficiently learning statistically driven phenotypes with minimal manual intervention.Materials and Methods We developed a phenotype library that uses both structured and unstructured data from the EMR to represent patients for real-time clinical decision support. Eight of the phenotypes were evaluated using retrospective EMR data on emergency department patients using a set of prospectively gathered gold standard labels.Results We built a phenotype library with 42 publicly available phenotype definitions. Using information from triage time, the phenotype classifiers have an area under the ROC curve (AUC) of infection 0.89, cancer 0.88, immunosuppressed 0.85, septic shock 0.93, nursing home 0.87, anticoagulated 0.83, cardiac etiology 0.89, and pneumonia 0.90. Using information available at the time of disposition from the emergency department, the AUC values are infection 0.91, cancer 0.95, immunosuppressed 0.90, septic shock 0.97, nursing home 0.91, anticoagulated 0.94, cardiac etiology 0.92, and pneumonia 0.97.Discussion The resulting phenotypes are interpretable and fast to build, and perform comparably to statistically learned phenotypes developed with 5000 manually labeled patients.Conclusion Learning with anchors is an attractive option for building a large public repository of phenotype definitions that can be used for a range of health IT applications, including real-time decision support.
Public preferences for electronic health data storage, access, and sharing — evidence from a pan-European survey
Authors: Patil Sunil , Lu Hui , Saunders Catherine L , Potoglou Dimitris , Robinson Neil 
Published: April 2016

Abstract
Objective To assess the public’s preferences regarding potential privacy threats from devices or services storing health-related personal data.
Materials and Methods A pan-European survey based on a stated-preference experiment for assessing preferences for electronic health data storage, access, and sharing.
Results We obtained 20 882 survey responses (94 606 preferences) from 27 EU member countries. Respondents recognized the benefits of storing electronic health information, with 75.5%, 63.9%, and 58.9% agreeing that storage was important for improving treatment quality, preventing epidemics, and reducing delays, respectively. Concerns about different levels of access by third parties were expressed by 48.9% to 60.6% of respondents.
On average, compared to devices or systems that only store basic health status information, respondents preferred devices that also store identification data (coefficient/relative preference 95% CI = 0.04 [0.00-0.08], P = 0.034) and information on lifelong health conditions (coefficient = 0.13 [0.08 to 0.18], P &lt; 0.001), but there was no evidence of this for devices with information on sensitive health conditions such as mental and sexual health and addictions (coefficient = −0.03 [−0.09 to 0.02], P = 0.24). Respondents were averse to their immediate family (coefficient = −0.05 [−0.05 to −0.01], P = 0.011) and home care nurses (coefficient = −0.06 [−0.11 to −0.02], P = 0.004) viewing this data, and strongly averse to health insurance companies (coefficient = −0.43 [−0.52 to 0.34], P &lt; 0.001), private sector pharmaceutical companies (coefficient = −0.82 [−0.99 to −0.64], P &lt; 0.001), and academic researchers (coefficient = −0.53 [−0.66 to −0.40], P &lt; 0.001) viewing the data.
Conclusions Storing more detailed electronic health data was generally preferred, but respondents were averse to wider access to and sharing of this information. When developing frameworks for the use of electronic health data, policy makers should consider approaches that both highlight the benefits to the individual and minimize the perception of privacy risks.
Health information exchange in the wild: the association between organizational capability and perceived utility of clinical event notifications in ambulatory and community care
Authors: Vest Joshua R , Ancker Jessica S 
Published: April 2016

Objective: Event notifications are real-time, electronic, automatic alerts to providers of their patients’ health care encounters at other facilities. Our objective was to examine the effects of organizational capability and related social/organizational issues upon users’ perceptions of the impact of event notifications on quality, efficiency, and satisfaction.
Materials and methods: We surveyed representatives (n = 49) of 10 organizations subscribing to the Bronx Regional Health Information Organization’s event notification services about organizational capabilities, notification information quality, perceived usage, perceived impact, and organizational and respondent characteristics. The response rate was 89%. Average item scores were used to create an individual domain summary score. The association between the impact of event notifications and organizational characteristics was modeled using random-intercept logistic regression models.
Results: Respondents estimated that organizations followed up on the majority (83%) of event notifications. Supportive organizational policies were associated with the perception that event notifications improved quality of care (odds ratio [OR] = 2.12; 95% CI, = 1.05, 4.45), efficiency (OR = 2.06; 95% CI = 1.00, 4.21), and patient satisfaction (OR = 2.56; 95% CI = 1.13, 5.81). Higher quality of event notification information was also associated with a perceived positive impact on quality of care (OR = 2.84; 95% CI = 1.31, 6.12), efficiency (OR = 3.04; 95% CI = 1.38, 6.69), and patient satisfaction (OR = 2.96; 95% CI = 1.25, 7.03).
Conclusions: Health care organizations with appropriate processes, workflows, and staff may be better positioned to use event notifications. Additionally, information quality remains critical in users’ assessments and perceptions.
A national report of nursing home information technology: year 1 results
Authors: Alexander Gregory L , Madsen Richard W , Miller Erin L , Schaumberg Melissa K , Holm Allison E , Alexander Rachel L , Wise Keely K , Dougherty Michelle L , Gugerty Brian 
Published: April 2016

Abstract

Objective
To provide a report on year 1 results of a national study investigating nursing home information technology (IT) adoption, called IT sophistication.

Methods
A reliable and valid survey was used to measure IT sophistication. The target goal was 10% from each state in the United States, 1570 nursing homes. A random sample of homes from each state was recruited from Nursing Home Compare.

Results
The team reached 2627 nursing home administrators, among whom 1799 administrators agreed to participate and were sent a survey. A total of 815 surveys were completed (45.3% response rate), which was below the goal. Facilities in the participating sample have similar demographic characteristics (ownership, total population in a location, and bed size) to the remaining homes not participating. There are greater IT capabilities in resident care and administrative activities, less in clinical support. The extent of use of these capabilities appears to be highest in administrative activities and lowest in clinical support. IT in resident care appears to be the most integrated with internal and external stakeholders. IT capabilities appear to be greater than IT extent of use in all health domains, with the greatest difference in resident care.

Discussion
National evaluations of nursing home IT are rare. Measuring trends in IT adoption in a nationally representative sample provides meaningful analytics that could be more useful for policy makers and nursing home leaders in the future.

Conclusion
Discovering national baseline assessments is a first step toward recognizing nursing home trends in IT adoption.
Mass constraint for a planet in a protoplanetary disk from the gap width
Authors: Kanagawa Kazuhiro D. , Muto Takayuki , Tanaka Hidekazu , Tanigawa Takayuki , Takeuchi Taku , Tsukagoshi Takashi , Momose Munetake 
Published: April 2016

Abstract
A giant planet creates a gap in a protoplanetary disk, which might explain the observed gaps in protoplanetary disks. The width and depth of the gaps depend on the planet mass and disk properties. We have performed two-dimensional hydrodynamic simulations for various planet masses, disk aspect ratios, and viscosities, to obtain an empirical formula for the gap width. The gap width is proportional to the square root of the planet mass, −3/4 the power of the disk aspect ratio and −1/4 the power of the viscosity. This empirical formula enables us to estimate the mass of a planet embedded in the disk from the width of an observed gap. We have applied the empirical formula for the gap width to the disk around HL Tau, assuming that each gap observed by the Atacama Large Millimeter/submillimeter Array (ALMA) observations is produced by planets, and discussed the planet masses within the gaps. The estimate of planet masses from the gap widths is less affected by the observational resolution and dust filtration than that by the gap depth.
Possible identification of massive and evolved galaxies at z ≳ 5
Authors: Mawatari Ken , Yamada Toru , Fazio Giovanni G. , Huang Jia-Sheng , Ashby Matthew L. N. 
Published: April 2016

Abstract
We report on the identification of the old stellar population galaxy candidates at z ≳ 5. We developed a new infrared color selection scheme to isolate galaxies with the strong Balmer breaks at z ≳ 5, and applied it to the ultra-deep and wide infrared survey data from the Spitzer Extended Deep Survey (SEDS) and the UKIRT Infrared Deep Sky Survey. The eight objects satisfying K − [3.6] &gt; 1.3 and K − [3.6] &gt; 2.4([3.6] − [4.5]) + 0.6 are selected in the 0.34 deg2 SEDS Ultra Deep Survey field. Rich multi-wavelength imaging data from optical to far-infrared are also used to reject blending sources and strong nebular line emitters, and we finally obtained the three most likely evolved galaxies at z ≳ 5. Their stacked spectral energy distribution is fitted well with the old stellar population template with M* = (7.5 ± 1.5) × 1010 M⊙, star formation rate = 0.9 ± 0.2 M⊙ yr−1, dust AV &lt; 1, and age =0.7 ± 0.4 Gyr at z = 5.7 ± 0.6, where the dusty star-forming galaxies at z ∼ 2.8 are disfavored because of the faintness in the 24 μm. The stellar mass density of these evolved galaxy candidates, (6 ± 4) × 104 M⊙ Mpc−3, is much lower than that of star-forming galaxies, but the non-zero fraction suggests that initial star-formation and quenching have been completed by z ∼ 6.
Activated Ras/JNK driven Dilp8 in imaginal discs adversely affects organismal homeostasis during early pupal stage inDrosophila, a new checkpoint for development
Authors: Ray Mukulika , Lakhotia Subhash C. 
Published: April 2016

AbstractBackgroundDilp8-mediated inhibition of ecdysone synthesis and pupation in holometabolous insects maintains developmental homeostasis through stringent control of timing and strength of moulting signals. We examined reasons for normal pupation but early pupal death observed in certain cases.ResultsOver-expression of activated Ras in developing eye/wing discs inhibited Ptth expression in brain via up-regulated JNK signaling mediated Dilp8 secretion from imaginal discs, which inhibited ecdysone synthesis in prothoracic glandafterpupariation, leading to death of ~25-30 Hr old pupae. Inhibition of elevated Ras signaling completely rescued early pupal death while post-pupation administration of ecdysone to organisms with elevated Ras signaling in eye discs partially rescued their early pupal death. Unlike the earlier known Dilp8 action in delaying pupation, hyperactivated Ras mediated elevation of pJNK signaling in imaginal discs caused Dilp8 secretionafterpupariation. Ectopic expression of certain other transgene causing pupal lethality similarly enhanced pJNK and early pupal Dilp8. Sub-optimal ecdysone levels after 8 Hr of pupation prevented the early pupal metamorphic changes and caused organismal death.ConclusionsOur results reveal early pupal stage as a novel Dilp8 mediated post-pupariation checkpoint and provide further evidence for inter-organ signaling during development, wherein a peripheral tissue influences the CNS driven endocrine function.
Radical amino acid mutations persist longer in the absence of sex
Authors: Sharbrough Joel , Luse Meagan , Boore Jeffrey L. , Logsdon John M. , Neiman Maurine 
Published: April 2016

ABSTRACTHarmful mutations are ubiquitous and inevitable, and the rate at which these mutations are removed from populations is a critical determinant of evolutionary fate. Closely related sexual and asexual taxa provide a particularly powerful setting to study deleterious mutation elimination because sexual reproduction should facilitate mutational clearance by reducing selective interference between sites and by allowing the production of offspring with different mutational complements than their parents. Here, we compared the rate of removal of conservative (i.e., similar biochemical properties) and radical (i.e., distinct biochemical properties) nonsynonymous mutations from mitochondrial genomes of sexualvs. asexualPotamopyrgus antipodarum, a New Zealand freshwater snail characterized by coexisting and ecologically similar sexual and asexual lineages. Our analyses revealed that radical nonsynonymous mutations are cleared at higher rates than conservative changes and that sexual lineages eliminate radical changes more rapidly than asexual counterparts. These results are consistent with reduced efficacy of purifying selection in asexual lineages allowing harmful mutations to remain polymorphic longer than in sexual lineages. Together, these data illuminate some of the population-level processes contributing to mitochondrial mutation accumulation and suggest that mutation accumulation could influence the outcome of competition between sexual and asexual lineages.