bluuebunny/crossref_metadata_2025 huggingface dataset:
An algorithm for computing the gene tree probability under the multispecies coalescent and its application in the inference of population tree
Authors: Wu Yufeng
Published: June 2016

Motivation: Gene tree represents the evolutionary history of gene lineages that originate from multiple related populations. Under the multispecies coalescent model, lineages may coalesce outside the species (population) boundary. Given a species tree (with branch lengths), the gene tree probability is the probability of observing a specific gene tree topology under the multispecies coalescent model. There are two existing algorithms for computing the exact gene tree probability. The first algorithm is due to Degnan and Salter, where they enumerate all the so-called coalescent histories for the given species tree and the gene tree topology. Their algorithm runs in exponential time in the number of gene lineages in general. The second algorithm is the STELLS algorithm (2012), which is usually faster but also runs in exponential time in almost all the cases.

Results: In this article, we present a new algorithm, called CompactCH, for computing the exact gene tree probability. This new algorithm is based on the notion of compact coalescent histories: multiple coalescent histories are represented by a single compact coalescent history. The key advantage of our new algorithm is that it runs in polynomial time in the number of gene lineages if the number of populations is fixed to be a constant. The new algorithm is more efficient than the STELLS algorithm both in theory and in practice when the number of populations is small and there are multiple gene lineages from each population. As an application, we show that CompactCH can be applied in the inference of population tree (i.e. the population divergence history) from population haplotypes. Simulation results show that the CompactCH algorithm enables efficient and accurate inference of population trees with much more haplotypes than a previous approach.

Availability: The CompactCH algorithm is implemented in the STELLS software package, which is available for download at http://www.engr.uconn.edu/ywu/STELLS.html.

Contact:  ywu@engr.uconn.edu

Supplementary information:  Supplementary data are available at Bioinformatics online.
An integer programming framework for inferring disease complexes from network data
Authors: Mazza Arnon , Klockmeier Konrad , Wanker Erich , Sharan Roded
Published: June 2016

Motivation: Unraveling the molecular mechanisms that underlie disease calls for methods that go beyond the identification of single causal genes to inferring larger protein assemblies that take part in the disease process.

Results: Here, we develop an exact, integer-programming-based method for associating protein complexes with disease. Our approach scores proteins based on their proximity in a protein–protein interaction network to a prior set that is known to be relevant for the studied disease. These scores are combined with interaction information to infer densely interacting protein complexes that are potentially disease-associated. We show that our method outperforms previous ones and leads to predictions that are well supported by current experimental data and literature knowledge.

Availability and Implementation: The datasets we used, the executables and the results are available at www.cs.tau.ac.il/roded/disease_complexes.zip

Contact:  roded@post.tau.ac.il
Structure-based prediction of transcription factor binding specificity using an integrative energy function
Authors: Farrel Alvin , Murphy Jonathan , Guo Jun-tao
Published: June 2016

Transcription factors (TFs) regulate gene expression through binding to specific target DNA sites. Accurate annotation of transcription factor binding sites (TFBSs) at genome scale represents an essential step toward our understanding of gene regulation networks. In this article, we present a structure-based method for computational prediction of TFBSs using a novel, integrative energy (IE) function. The new energy function combines a multibody (MB) knowledge-based potential and two atomic energy terms (hydrogen bond and π interaction) that might not be accurately captured by the knowledge-based potential owing to the mean force nature and low count problem. We applied the new energy function to the TFBS prediction using a non-redundant dataset that consists of TFs from 12 different families. Our results show that the new IE function improves the prediction accuracy over the knowledge-based, statistical potentials, especially for homeodomain TFs, the second largest TF family in mammals.

Contact:  jguo4@uncc.edu

Supplementary information:  Supplementary data are available at Bioinformatics online.
Genome assembly from synthetic long read clouds
Authors: Kuleshov Volodymyr , Snyder Michael P. , Batzoglou Serafim
Published: June 2016

Motivation: Despite rapid progress in sequencing technology, assembling de novo the genomes of new species as well as reconstructing complex metagenomes remains major technological challenges. New synthetic long read (SLR) technologies promise significant advances towards these goals; however, their applicability is limited by high sequencing requirements and the inability of current assembly paradigms to cope with combinations of short and long reads.

Results: Here, we introduce Architect, a new de novo scaffolder aimed at SLR technologies. Unlike previous assembly strategies, Architect does not require a costly subassembly step; instead it assembles genomes directly from the SLR’s underlying short reads, which we refer to as read clouds . This enables a 4- to 20-fold reduction in sequencing requirements and a 5-fold increase in assembly contiguity on both genomic and metagenomic datasets relative to state-of-the-art assembly strategies aimed directly at fully subassembled long reads.

Availability and Implementation: Our source code is freely available at https://github.com/kuleshov/architect .

Contact:  kuleshov@stanford.edu
Faster and more accurate graphical model identification of tandem mass spectra using trellises
Authors: Wang Shengjie , Halloran John T. , Bilmes Jeff A. , Noble William S.
Published: June 2016

Tandem mass spectrometry (MS/MS) is the dominant high throughput technology for identifying and quantifying proteins in complex biological samples. Analysis of the tens of thousands of fragmentation spectra produced by an MS/MS experiment begins by assigning to each observed spectrum the peptide that is hypothesized to be responsible for generating the spectrum. This assignment is typically done by searching each spectrum against a database of peptides. To our knowledge, all existing MS/MS search engines compute scores individually between a given observed spectrum and each possible candidate peptide from the database. In this work, we use a trellis , a data structure capable of jointly representing a large set of candidate peptides, to avoid redundantly recomputing common sub-computations among different candidates. We show how trellises may be used to significantly speed up existing scoring algorithms, and we theoretically quantify the expected speedup afforded by trellises. Furthermore, we demonstrate that compact trellis representations of whole sets of peptides enables efficient discriminative learning of a dynamic Bayesian network for spectrum identification, leading to greatly improved spectrum identification accuracy.

Contact:  bilmes@uw.edu or william-noble@uw.edu

Supplementary information:  Supplementary data are available at Bioinformatics online.
A network-driven approach for genome-wide association mapping
Authors: Lee Seunghak , Kong Soonho , Xing Eric P.
Published: June 2016

Motivation : It remains a challenge to detect associations between genotypes and phenotypes because of insufficient sample sizes and complex underlying mechanisms involved in associations. Fortunately, it is becoming more feasible to obtain gene expression data in addition to genotypes and phenotypes, giving us new opportunities to detect true genotype–phenotype associations while unveiling their association mechanisms.

Results : In this article, we propose a novel method, NETAM, that accurately detects associations between SNPs and phenotypes, as well as gene traits involved in such associations. We take a network-driven approach: NETAM first constructs an association network, where nodes represent SNPs, gene traits or phenotypes, and edges represent the strength of association between two nodes. NETAM assigns a score to each path from an SNP to a phenotype, and then identifies significant paths based on the scores. In our simulation study, we show that NETAM finds significantly more phenotype-associated SNPs than traditional genotype–phenotype association analysis under false positive control, taking advantage of gene expression data. Furthermore, we applied NETAM on late-onset Alzheimer’s disease data and identified 477 significant path associations, among which we analyzed paths related to beta-amyloid, estrogen, and nicotine pathways. We also provide hypothetical biological pathways to explain our findings.

Availability and implementation : Software is available at http://www.sailing.cs.cmu.edu/ .

Contact : epxing@cs.cmu.edu
SHARAKU: an algorithm for aligning and clustering read mapping profiles of deep sequencing in non-coding RNA processing
Authors: Tsuchiya Mariko , Amano Kojiro , Abe Masaya , Seki Misato , Hase Sumitaka , Sato Kengo , Sakakibara Yasubumi
Published: June 2016

Motivation: Deep sequencing of the transcripts of regulatory non-coding RNA generates footprints of post-transcriptional processes. After obtaining sequence reads, the short reads are mapped to a reference genome, and specific mapping patterns can be detected called read mapping profiles, which are distinct from random non-functional degradation patterns. These patterns reflect the maturation processes that lead to the production of shorter RNA sequences. Recent next-generation sequencing studies have revealed not only the typical maturation process of miRNAs but also the various processing mechanisms of small RNAs derived from tRNAs and snoRNAs.

Results: We developed an algorithm termed SHARAKU to align two read mapping profiles of next-generation sequencing outputs for non-coding RNAs. In contrast with previous work, SHARAKU incorporates the primary and secondary sequence structures into an alignment of read mapping profiles to allow for the detection of common processing patterns. Using a benchmark simulated dataset, SHARAKU exhibited superior performance to previous methods for correctly clustering the read mapping profiles with respect to 5′-end processing and 3′-end processing from degradation patterns and in detecting similar processing patterns in deriving the shorter RNAs. Further, using experimental data of small RNA sequencing for the common marmoset brain, SHARAKU succeeded in identifying the significant clusters of read mapping profiles for similar processing patterns of small derived RNA families expressed in the brain.

Availability and Implementation: The source code of our program SHARAKU is available at http://www.dna.bio.keio.ac.jp/sharaku/ , and the simulated dataset used in this work is available at the same link. Accession code: The sequence data from the whole RNA transcripts in the hippocampus of the left brain used in this work is available from the DNA DataBank of Japan (DDBJ) Sequence Read Archive (DRA) under the accession number DRA004502.

Contact:  yasu@bio.keio.ac.jp

Supplementary information:  Supplementary data are available at Bioinformatics online.
A cross-species bi-clustering approach to identifying conserved co-regulated genes
Authors: Sun Jiangwen , Jiang Zongliang , Tian Xiuchun , Bi Jinbo
Published: June 2016

Motivation: A growing number of studies have explored the process of pre-implantation embryonic development of multiple mammalian species. However, the conservation and variation among different species in their developmental programming are poorly defined due to the lack of effective computational methods for detecting co-regularized genes that are conserved across species. The most sophisticated method to date for identifying conserved co-regulated genes is a two-step approach. This approach first identifies gene clusters for each species by a cluster analysis of gene expression data, and subsequently computes the overlaps of clusters identified from different species to reveal common subgroups. This approach is ineffective to deal with the noise in the expression data introduced by the complicated procedures in quantifying gene expression. Furthermore, due to the sequential nature of the approach, the gene clusters identified in the first step may have little overlap among different species in the second step, thus difficult to detect conserved co-regulated genes.

Results: We propose a cross-species bi-clustering approach which first denoises the gene expression data of each species into a data matrix. The rows of the data matrices of different species represent the same set of genes that are characterized by their expression patterns over the developmental stages of each species as columns. A novel bi-clustering method is then developed to cluster genes into subgroups by a joint sparse rank-one factorization of all the data matrices. This method decomposes a data matrix into a product of a column vector and a row vector where the column vector is a consistent indicator across the matrices (species) to identify the same gene cluster and the row vector specifies for each species the developmental stages that the clustered genes co-regulate. Efficient optimization algorithm has been developed with convergence analysis. This approach was first validated on synthetic data and compared to the two-step method and several recent joint clustering methods. We then applied this approach to two real world datasets of gene expression during the pre-implantation embryonic development of the human and mouse. Co-regulated genes consistent between the human and mouse were identified, offering insights into conserved functions, as well as similarities and differences in genome activation timing between the human and mouse embryos.

Availability and Implementation: The R package containing the implementation of the proposed method in C ++ is available at: https://github.com/JavonSun/mvbc.git and also at the R platform https://www.r-project.org/ .

Contact:  jinbo@engr.uconn.edu
DFLpred: High-throughput prediction of disordered flexible linker regions in protein sequences
Authors: Meng Fanchi , Kurgan Lukasz
Published: June 2016

Motivation: Disordered flexible linkers (DFLs) are disordered regions that serve as flexible linkers/spacers in multi-domain proteins or between structured constituents in domains. They are different from flexible linkers/residues because they are disordered and longer. Availability of experimentally annotated DFLs provides an opportunity to build high-throughput computational predictors of these regions from protein sequences. To date, there are no computational methods that directly predict DFLs and they can be found only indirectly by filtering predicted flexible residues with predictions of disorder.

Results: We conceptualized, developed and empirically assessed a first-of-its-kind sequence-based predictor of DFLs, DFLpred. This method outputs propensity to form DFLs for each residue in the input sequence. DFLpred uses a small set of empirically selected features that quantify propensities to form certain secondary structures, disordered regions and structured regions, which are processed by a fast linear model. Our high-throughput predictor can be used on the whole-proteome scale; it needs <1 h to predict entire proteome on a single CPU. When assessed on an independent test dataset with low sequence-identity proteins, it secures area under the receiver operating characteristic curve equal 0.715 and outperforms existing alternatives that include methods for the prediction of flexible linkers, flexible residues, intrinsically disordered residues and various combinations of these methods. Prediction on the complete human proteome reveals that about 10% of proteins have a large content of over 30% DFL residues. We also estimate that about 6000 DFL regions are long with ≥30 consecutive residues.

Availability and implementation:  http://biomine.ece.ualberta.ca/DFLpred/ .

Contact:  lkurgan@vcu.edu

Supplementary information:  Supplementary data are available at Bioinformatics online.
DeepMeSH: deep semantic representation for improving large-scale MeSH indexing
Authors: Peng Shengwen , You Ronghui , Wang Hongning , Zhai Chengxiang , Mamitsuka Hiroshi , Zhu Shanfeng
Published: June 2016

Motivation: Medical Subject Headings (MeSH) indexing, which is to assign a set of MeSH main headings to citations, is crucial for many important tasks in biomedical text mining and information retrieval. Large-scale MeSH indexing has two challenging aspects: the citation side and MeSH side. For the citation side, all existing methods, including Medical Text Indexer (MTI) by National Library of Medicine and the state-of-the-art method, MeSHLabeler, deal with text by bag-of-words, which cannot capture semantic and context-dependent information well.

Methods: We propose DeepMeSH that incorporates deep semantic information for large-scale MeSH indexing. It addresses the two challenges in both citation and MeSH sides. The citation side challenge is solved by a new deep semantic representation, D2V-TFIDF, which concatenates both sparse and dense semantic representations. The MeSH side challenge is solved by using the ‘learning to rank’ framework of MeSHLabeler, which integrates various types of evidence generated from the new semantic representation.

Results: DeepMeSH achieved a Micro F-measure of 0.6323, 2% higher than 0.6218 of MeSHLabeler and 12% higher than 0.5637 of MTI, for BioASQ3 challenge data with 6000 citations.

Availability and Implementation: The software is available upon request.

Contact:  zhusf@fudan.edu.cn

Supplementary information:  Supplementary data are available at Bioinformatics online.
Health information exchange policies of 11 diverse health systems and the associated impact on volume of exchange
Authors: Downing N Lance , Adler-Milstein Julia , Palma Jonathan P , Lane Steven , Eisenberg Matthew , Sharp Christopher ,   Northern California HIE Collaborative, Longhurst Christopher A
Published: June 2016

Background: Provider organizations increasingly have the ability to exchange patient health information electronically. Organizational health information exchange (HIE) policy decisions can impact the extent to which external information is readily available to providers, but this relationship has not been well studied.

Objective: Our objective was to examine the relationship between electronic exchange of patient health information across organizations and organizational HIE policy decisions. We focused on 2 key decisions: whether to automatically search for information from other organizations and whether to require HIE-specific patient consent.

Methods: We conducted a retrospective time series analysis of the effect of automatic querying and the patient consent requirement on the monthly volume of clinical summaries exchanged. We could not assess degree of use or usefulness of summaries, organizational decision-making processes, or generalizability to other vendors.

Results: Between 2013 and 2015, clinical summary exchange volume increased by 1349% across 11 organizations. Nine of the 11 systems were set up to enable auto-querying, and auto-querying was associated with a significant increase in the monthly rate of exchange (P = .006 for change in trend). Seven of the 11 organizations did not require patient consent specifically for HIE, and these organizations experienced a greater increase in volume of exchange over time compared to organizations that required consent.

Conclusions: Automatic querying and limited consent requirements are organizational HIE policy decisions that impact the volume of exchange, and ultimately the information available to providers to support optimal care. Future efforts to ensure effective HIE may need to explicitly address these factors.
Using an inpatient portal to engage families in pediatric hospital care
Authors: Kelly Michelle M , Hoonakker Peter L T , Dean Shannon M
Published: June 2016

Objective: Assess parent use and perceptions of an inpatient portal application on a tablet computer that provides information about a child’s hospital stay.

Methods: This cross-sectional study was conducted with parents of children hospitalized on a medical/surgical unit at a tertiary children’s hospital. From December 2014 to June 2015, parents were provisioned a tablet portal application to use throughout the hospitalization. The portal includes real-time hospital vitals, medications, schedules, lab results, education, health care team pictures/roles, and request and messaging functionalities. Portal use information was gathered from tablet metadata. Parents completed discharge surveys on portal satisfaction, use, and impact on their information needs, engagement, communication, error detection, and care safety and quality. Data were analyzed using descriptive statistics and qualitative content analysis.

Results: Over 6 months, 296 parents used the portal, sending 176 requests and 36 messages. No tablets were lost or damaged. The most used and liked features included vitals, medication list, health care team information, and schedules. Overall, parent survey respondents (90) were satisfied with the portal (90%), reporting that it was easy to use (98%), improved care (94%), and gave them access to information that helped them monitor, understand, make decisions, and care for their child. Many parents reported that portal use improved health care team communication (60%). Most perceived that portal use reduced errors in care (89%), with 8% finding errors in their child’s medication list.

Conclusions: Overall, parents were satisfied with the inpatient portal. Portals may engage parents in hospital care, facilitate parent recognition of medication errors, and improve perceptions of safety and quality.
Women in Academic Medicine
Authors: Thibault George E.
Published: June 2016

More than a decade ago, women achieved parity with men in the number of matriculants to medical school, nearly one-third of the faculty of medical schools were women, and there were some women deans and department chairs. These trends were promising, but today there are still significant differences in pay, academic rank, and leadership positions for women compared with men in academic medicine. Though there has been progress in many areas, the progress is too slow to achieve previously recommended goals, such as 50% women department chairs by 2025 and 50% women deans by 2030.

The author points to the findings presented in the articles from the Research Partnership on Women in Biomedical Careers in this issue, as well as research being published elsewhere, as an evidence base for the ongoing discussion of gender equity in academic medicine. More attention to culture and the working environment will be needed to achieve true parity for women in academic medical careers.
Advancement of Women in the Biomedical Workforce: Insights for Success
Authors: Barfield Whitney L. , Plank-Bazinet Jennifer L. , Austin Clayton Janine
Published: June 2016

Women continue to face unique barriers in the biomedical workforce that affect their advancement and retention in this field. The National Institutes of Health (NIH) formed the Working Group on Women in Biomedical Careers to address these issues. Through the efforts of the working group, the NIH funded 14 research grants to identify barriers or to develop and/or test interventions to support women in the biomedical workforce. The grantees that were funded through this endeavor later established the grassroots Research Partnership on Women in Biomedical Careers, and they continue to conduct research and disseminate information on the state of women in academic medicine. This Commentary explores the themes introduced in a collection of articles organized by the research partnership and published in this issue of Academic Medicine. The authors highlight the role that government plays in the advancement of women in academic medicine and highlight the findings put forward in this collection.
Gender, Race/Ethnicity, and National Institutes of Health R01 Research Awards: Is There Evidence of a Double Bind for Women of Color?
Authors: Ginther Donna K. , Kahn Shulamit , Schaffer Walter T.
Published: June 2016

Purpose

To analyze the relationship between gender, race/ethnicity, and the probability of being awarded an R01 grant from the National Institutes of Health (NIH).

Method

The authors used data from the NIH Information for Management, Planning, Analysis, and Coordination grants management database for the years 2000–2006 to examine gender differences and race/ethnicity-specific gender differences in the probability of receiving an R01 Type 1 award. The authors used descriptive statistics and probit models to determine the relationship between gender, race/ethnicity, degree, investigator experience, and R01 award probability, controlling for a large set of observable characteristics.

Results

White women PhDs and MDs were as likely as white men to receive an R01 award. Compared with white women, Asian and black women PhDs and black women MDs were significantly less likely to receive funding. Women submitted fewer grant applications, and blacks and women who were new investigators were more likely to submit only one application between 2000 and 2006.

Conclusions

Differences by race/ethnicity explain the NIH funding gap for women of color, as white women have a slight advantage over men in receiving Type 1 awards. Findings of a lower submission rate for women and an increased likelihood that they will submit only one proposal are consistent with research showing that women avoid competition. Policies designed to address the racial and ethnic diversity of the biomedical workforce have the potential to improve funding outcomes for women of color.
Women in Academic Medicine Leadership: Has Anything Changed in 25 Years?
Authors: Rochon Paula A. , Davidoff Frank , Levinson Wendy
Published: June 2016

Over the past 25 years, the number of women graduating from medical schools in the United States and Canada has increased dramatically to the point where roughly equal numbers of men and women are graduating each year. Despite this growth, women continue to face challenges in moving into academic leadership positions. In this Commentary, the authors share lessons learned from their own careers relevant to women’s careers in academic medicine, including aspects of leadership, recruitment, editorship, promotion, and work–life balance. They provide brief synopses of current literature on the personal and social forces that affect women’s participation in academic leadership roles. They are persuaded that a deeper understanding of these realities can help create an environment in academic medicine that is generally more supportive of women’s participation, and that specifically encourages women in medicine to take on academic leadership positions.
Human papillomavirus immunization uptake among girls with a refugee background compared with Danish-born girls: a national register-based cohort study
Authors: Møller Sanne P. , Kristiansen Maria , Norredam Marie
Published: June 2016

Refugee children and their families may experience impaired access to healthcare; therefore, we aimed to uncover human papillomavirus (HPV) immunization patterns among a large group of refugee girls compared with Danish-born girls. We also examined possible predictors of uptake among refugee girls. We used a register-based cohort design where refugee girls (n=3264) who, between 1 January 1994 and 31 December 2010, obtained residency permits in Denmark, were included and matched on age and sex with Danish-born girls (n=19 584). Personal identification numbers were cross-linked to the National Danish Health Service Register, identifying all contacts for HPV-immunization in both the ordinary HPV-immunization program and in a catch-up program. We applied logistic regression to estimate the odds ratios (OR) of uptake. We found that refugee girls had significantly lower HPV immunization uptake compared with Danish-born girls in the ordinary immunization program (OR=0.44; 95% confidence interval: 0.37–0.51) and the catch-up program (OR=0.61; 95% confidence interval: 0.54–0.69). The difference in odds decreased after adjusting by family income, but remained significant for the ordinary immunization program. We also identified that region of origin, duration of residence, and income were predictors of uptake among refugee girls. The lower uptake of HPV immunization among refugee girls raises questions about the coverage of this immunization program across increasingly ethnic diverse societies. More efforts to secure equal uptake are needed.
Adaptation and Validation of the Spanish Version of the Nomophobia Questionnaire in Nursing Studies
Authors: Gutiérrez-Puertas Lorena , Márquez-Hernández Verónica V. , Aguilera-Manrique Gabriel
Published: June 2016

Nomophobia is the uncontrollable fear of leaving your house without your mobile phone and is currently having a significant impact on the younger population. The aim of this study was first to translate the original version (written in English) of the Nomophobia questionnaire, culturally adapting it to the Spanish sociolinguistic context, and subsequently to analyze the psychometric properties of the Spanish version with a sample of nursing students. In the first stage, a process of translation-back translation was carried out, following standardized recommendations. In order to validate the content, the adapted and agreed version of the Nomophobia questionnaire, consisting of 20 items, was submitted to a panel of 20 experts. After the content analysis and subsequent debate, a third version of the scale was obtained. The results confirmed a four-dimensional structure, the same as the original questionnaire, with a Cronbach’s α value of .928 for the questionnaire as a whole, thus showing good internal consistency. The results of this study mean a suitable tool can be offered to nursing professionals with the aim of facilitating the diagnosis of addictive behaviors in relation to mobile phone use.
Cutaneous Collision Tumor Associated With Porocarcinomatous and Angiosarcomatous Components: A Potential Diagnostic Pitfall
Authors: Parra-Medina Rafael , Melo-Uribe Mario A. , Messa-Botero Oscar , Morales Samuel D.
Published: June 2016

Sarcomatoid eccrine porocarcinoma (SEP) is a very rare malignancy including epithelial and mesenchymal components exhibiting pleomorphic cells, nuclear hyperchromasia, and high mitotic activity in both elements. To date, only 6 cases of this uncommon neoplasm have been reported, corresponding to women over 70 years of age with ulcerated skin lesions. The authors describe the first sarcomatoid eccrine porocarcinoma in a 75-year-old male patient with a right hallux lesion, presenting a collision tumor with a mixed population of epithelial cells and a spindle cell angiosarcomatous mesenchymal component each expressing distinct and nonoverlapping morphologic and immunohistochemical features of epithelial and mesenchymal differentiation.
Geography of community health information organization activity in the United States
Authors: Vest Joshua R.
Published: June 2016

Background:

The United States has invested nearly a billion dollars in creating community health information organizations (HIOs) to foster health information exchange. Community HIOs provide exchange services to health care organizations within a distinct geographic area. While geography is a key organizing principle for community HIOs, it is unclear if geography is an effective method for organization or what challenges are created by a geography-based approach to health information exchange.

Purpose:

This study describes the extent of reported community HIO coverage in the United States and explores the practical and policy implications of overlaps and gaps in HIO service areas. Furthermore, because self-reported service areas may not accurately reflect the true extent of HIOs activities, this study maps the actual markets for health services included in each HIO.

Methodology:

An inventory of operational community HIOs that included self-reported geographic markets and participating organizations was face-validated using a crowd-sourcing approach. Aggregation of the participating hospitals’ individual health care markets provided the total geographic market served by each community HIO. Mapping and overlay analyses using geographic information system methods described the extent of community HIO activity in the United States.

Findings:

Evidence suggests that community HIOs may be inefficiently distributed. Parts of the United States have multiple, overlapping HIOs, while others do not have any providing health information exchange services. In markets served by multiple community HIOs, 45% of hospitals were participants of only one HIO.

Practice implications:

The current geography of community HIO activity does not provide comprehensive patient information to providers, nor community-wide information for public health agencies. The discord between the self-reported and market geography of community HIOs raises concerns about the potential effectiveness of health information exchange, illustrates the limitations of geography as an organizing principle, and indicates operational challenges facing those leading and working with community HIOs.
The strategic nature of individual change behavior: How physicians and their staff implement medical home care
Authors: Hoff Timothy , Scott Sarah
Published: June 2016

Background:

The patient-centered medical home (PCMH) model of care is central to primary care system success and transformation. Less is known about which PCMH activities primary care workers most frequently perform, if or why they might view that work more favorably, and how such work may function strategically to advance individual and organizational adaptation to new demands, as well as deliver good patient care.

Purpose:

Understanding better how primary care physicians and staff perceive, experience, and use certain types of PCMH work for adapting to new demands looms a key imperative for gaining insights into PCMH implementation at the workplace level.

Methods:

Using a worker adaptation perspective that emphasizes the role of social learning and individual agency, this study explores the strategic nature of PCMH implementation through 51 in-depth interviews with physicians and staff in six accredited PCMHs.

Findings:

Select medical home activities were identified, in which primary care physicians and staff most engaged on a daily basis, and they fell into five distinct PCMH work domains labeled team care, medical home responsibilities, care management, access, and medication management. These activities had common features such as high levels of familiarity, simplicity, and camaraderie. In addition, through their experiences performing these activities, physicians and staff appeared to gain strategic benefits for themselves and the larger organization including enhanced self-efficacy and readiness for change.

Conclusions:

The findings show that particular forms of PCMH work not only advance patient care in favorable ways but also enhance individual and organizational capacity for adapting to this innovative model and its demands. This knowledge adds to our understanding of how to implement PCMH care in ways that are good for workers, primary care organizations, and patients and offers practical guidance as to which forms of PCMH work should be encouraged, incented, and rewarded.
Nursing Home Administrator Quality Improvement Self-Efficacy Scale
Authors: Siegel Elena O. , Zisberg Anna , Bakerjian Debra , Zysberg Leehu
Published: June 2016

Background:

Nursing home (NH) quality improvement (QI) is challenging. The critical role of NH leaders in successful QI is well established; however, current options for assessing the QI capabilities of leaders such as the licensed NH administrator are limited.

Purpose:

This article presents the development and preliminary validation of an instrument to measure NH administrator self-efficacy in QI.

Methodology/Approach:

We used a mixed-methods cross-sectional design to develop and test the measure. For item generation, 39 NH leaders participated in qualitative interviews. Item reduction and content validity were established with a sample of eight subject matter experts. A random sample of 211 administrators from NHs with the lowest and highest Centers for Medicare and Medicaid Services Five-Star Quality ratings completed the measure. We conducted exploratory and confirmatory factor analyses and tested the measure for internal reliability and convergent, discriminant, and known group validity.

Findings:

The final measure included five subscales and 32 items. Confirmatory factor analysis reaffirmed the factorial structure with good fit indices. The new measure’s subscales correlated with valid measures of self-efficacy and locus of control, supporting the measure’s convergent and discriminant validity. Significant differences in most of the subscales were found between the objective (Centers for Medicare and Medicaid Services Five-Star Quality rating) and subjective (Self-Rated Facility QI Index) quality outcomes, supporting the measure’s known group validity.

Practice Implications:

The instrument has usefulness to both NH organizations and individual NH administrators as a diagnostic tool to identify administrators with higher/lower chances of successfully implementing QI. Organizations and individuals can use this diagnostic to identify the administrator’s professional development needs for QI, in general, and specific to the instrument’s five subscales, informing directions for in-house training, mentoring, and outside professional development. Attending to NH administrators’ QI professional development needs prior to implementing QI holds promise to enhance the chances for successful implementation of QI, which is urgently needed in many NHs.
Insider versus outsider executive succession: The relationship to hospital efficiency
Authors: Ford Eric W. , Lowe Kevin B. , Silvera Geoffrey B. , Babik Dmytro , Huerta Timothy R.
Published: June 2016

Background:

The relationship between Chief Executive Officer (CEO) succession and hospitals’ competitive performance is an area of interest for health services researchers. Of particular interest is the impact on overall strategic direction and health system performance that results from selecting a CEO from inside the firm as opposed to seeking outside leadership. Empirical work-to-date has yielded mixed results. Much of this variability has been attributed to design flaws; however, in the absence of a clear message from the evidence, the preference for hiring “outsiders” continues to grow.

Purpose:

This paper investigates on the extent to which insider CEO succession versus outsider succession impacts hospitals’ competitive advantage vis-à-vis a sample of organizations that compete in the same sector.

Methods:

A hospital matching protocol based on propensity scores is used to control for endogeneity and makes comparisons of productivity across organizations through the use of stochastic frontier estimation.

Findings:

Succession negatively impacts hospitals’ productivity, and firms with outsider CEO succession events closed the gap toward the competitive advantage frontier faster than comparable firms with insider successions.

Practice Implications:

More research needs to be done on succession planning and its impact on CEO turnover.
Integrating
Authors: Kerrissey Michaela , Satterstrom Patricia , Leydon Nicholas , Schiff Gordon , Singer Sara
Published: June 2016

Background:

How some organizations improve while others remain stagnant is a key question in health care research. Studies identifying how organizations can implement improvement despite barriers are needed, particularly in primary care.

Purposes:

This inductive qualitative study examines primary care clinics implementing improvement efforts in order to identify mechanisms that enable implementation despite common barriers, such as lack of time and fragmentation across stakeholder groups.

Methodology:

Using an embedded multiple case study design, we leverage a longitudinal data set of field notes, meeting minutes, and interviews from 16 primary care clinics implementing improvement over 15 months. We segment clinics into those that implemented more versus those that implemented less, comparing similarities and differences. We identify interpersonal mechanisms promoting implementation, develop a conceptual model of our key findings, and test the relationship with performance using patient surveys conducted pre-/post-implementation.

Findings:

Nine clinics implemented more successfully over the study period, whereas seven implemented less. Successfully implementing clinics exhibited the managerial practice of integrating, which we define as achieving unity of effort among stakeholder groups in the pursuit of a shared and mutually developed goal. We theorize that integrating is critical in improvement implementation because of the fragmentation observed in health care settings, and we extend theory about clinic managers’ role in implementation. We identify four integrating mechanisms that clinic managers enacted: engaging groups, bridging communication, sensemaking, and negotiating. The mean patient survey results for integrating clinics improved by 0.07 units over time, whereas the other clinics’ survey scores declined by 0.08 units on a scale of 5 (p = .02).

Practice Implications:

Our research explores an understudied element of how clinics can implement improvement despite barriers: integrating stakeholders within and outside the clinic into the process. It provides clinic managers with an actionable path for implementing improvement.
Simultaneous Catheter and Epicardial Ablations Enable a Comprehensive Atrial Fibrillation Procedure
Authors: Kiser Andy C. , Landers Mark D. , Boyce Ker , šinkovec Matjaž , Pernat Andrej , Geršak Borut
Published: June 2016

Objective

Transmural and contiguous ablations and a comprehensive lesion pattern are difficult to create from the surface of a beating heart but are critical to the successful treatment of persistent, isolated atrial fibrillation. A codisciplinary simultaneous epicardial (surgical) and endocardial (catheter) procedure (Convergent procedure) addresses these issues.

Methods

Patients with symptomatic atrial fibrillation who failed medical treatment were evaluated. Using only pericardioscopy, the surgeon performed near-complete epicardial isolation of the pulmonary veins and a “box” lesion on the posterior left atrium using unipolar radiofrequency ablation. Simultaneous endocardial catheter radiofrequency ablation completed pulmonary vein isolation, performed a mitral annular and cavotricuspid isthmus line of block, and debulked the coronary sinus. Twelve-month results for the Convergent procedure were compared with 12-month results for concomitant and pericardioscopic (stand-alone transdiaphragmatic/thoracoscopic) atrial fibrillation procedures using unipolar radiofrequency ablation.

Results

Sixty-five patients underwent the Convergent procedure (mean age, 62 y; mean body surface area, 2.17 m2; mean atrial fibrillation duration, 4.8 y; mean left atrial size, 5.2 cm). Ninety-two percent were in persistent or long-standing persistent atrial fibrillation. At 12 months, evaluation with 24-hour Holter monitors found 82% of patients in sinus rhythm, while only 47% of pericardioscopic and 77% of concomitant patients treated with unipolar radiofrequency ablation were in sinus rhythm.

Conclusions

Simultaneous epicardial and endocardial ablation improves outcomes for patients with persistent or longstanding persistent atrial fibrillation. This successful collaboration between cardiac surgeon and electrophysiologist is an important treatment option for patients with large left atriums and chronic atrial fibrillation.
Lacrimal Sac Smooth Muscle Tumor of Uncertain Malignant Potential
Authors: Grumbine F. Lawson , DeParis Sarah W. , Vagefi M. Reza , Bloomer Michelle , Kersten Robert C.
Published: June 2016

A 13-year-old male presented with recurrent left nasolacrimal duct obstruction following endoscopic dacryocystorhinostomy 4 years prior at an outside institution. The past medical history was significant for stage IV neuroblastoma, diagnosed at age 2, requiring surgical resection, induction chemotherapy, autologous bone marrow transplantation and radiation, currently in remission. Preoperative CT scan demonstrated a 2 cm ovoid mass centered in the left lacrimal fossa, consistent with dacryocystocele; however, a solid tumor could not be ruled out. Subsequent surgical exploration of the lacrimal sac revealed a friable, solid mass filling the lacrimal sac, and extending into the duct. The mass was grossly resected with preservation of the lacrimal drainage system and placement of indwelling silicone stents. Histopathology confirmed the diagnosis of smooth muscle tumor of uncertain malignant potential. The patient remained free of epiphora and showed no clinical or radiographic evidence of recurrence at 6 months of follow up.
Pediatric Orbital Osteoradionecrosis
Authors: Skippen Brent , Rossi Andrea , Nozza Paolo , Bernardini Francesco P.
Published: June 2016

Orbital osteoradionecrosis is a rare complication of orbital radiotherapy. It can occur in children, associated with orbital radiotherapy treatment, mimicking recurrence of malignancy and infection. In children, it is most likely to be associated with orbital malignancies treated with higher doses of radiotherapy, such as recurrent orbital rhabdomyosarcoma.
Coping Styles Mediate the Relationship Between Self-esteem, Health Locus of Control, and Health-Promoting Behavior in Chinese Patients With Coronary Heart Disease
Authors: Zou Huijing , Tian Qian , Chen Yuxia , Cheng Cheng , Fan Xiuzhen
Published: June 2016

Background:

Health-promoting behavior plays an important role in reducing the burden of coronary heart disease. Self-esteem and health locus of control may contribute to health-promoting behavior, and coping styles may mediate these associations.

Objective:

The aims of our study were to examine whether self-esteem and health locus of control are associated with health-promoting behavior and examine the possible mediating effect of coping styles in patients with coronary heart disease.

Methods:

Health-promoting behavior, self-esteem, health locus of control, and coping styles were assessed in 272 hospitalized patients (60 ± 12 years, 61% male) with coronary heart disease. Hierarchical regression analysis was conducted to analyze the relationships between health-promoting behavior and other variables. Mediation effect was examined according to the methods of Baron and Kenny.

Results:

The mean score for health-promoting behavior was 2.57 ± 0.51; 38.2% of patients (n = 104) scored lower than 2.5. Self-esteem (β = .139, P < .05), confrontation coping style (β = .491, P < .001), disease duration (≥6 months, β = .147, P < .05), and monthly income (≥1000 RMB [approximately US$154], β = .111, P < .05) were positively associated with health-promoting behavior, accounting for 47.5% of its variance (F = 19.828). Confrontation partly mediated the association between self-esteem and health-promoting behavior and completely mediated the relationship between internal health locus of control and health-promoting behavior.

Conclusions:

Confrontation plays a mediating role in the association among self-esteem, internal health locus of control, and health-promoting behavior. Strategies should be undertaken to encourage the use of confrontation coping style, which will facilitate health-promoting behavior.