bluuebunny/crossref_metadata_2025_split huggingface dataset:
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

Abstract
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

Abstract
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

Abstract
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 &lt;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

Abstract
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.
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.
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

Abstract:
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.