bluuebunny/crossref_metadata_2025_split huggingface dataset:
ANNOgesic: a Swiss army knife for the RNA-seq based annotation of bacterial/archaeal genomes
Authors: Yu Sung-Huan , Vogel Jörg , Förstner Konrad U 
Published: August 2018

Abstract
To understand the gene regulation of an organism of interest, a comprehensive genome annotation is essential. While some features, such as coding sequences, can be computationally predicted with high accuracy based purely on the genomic sequence, others, such as promoter elements or noncoding RNAs, are harder to detect. RNA sequencing (RNA-seq) has proven to be an efficient method to identify these genomic features and to improve genome annotations. However, processing and integrating RNA-seq data in order to generate high-resolution annotations is challenging, time consuming, and requires numerous steps. We have constructed a powerful and modular tool called ANNOgesic that provides the required analyses and simplifies RNA-seq-based bacterial and archaeal genome annotation. It can integrate data from conventional RNA-seq and differential RNA-seq and predicts and annotates numerous features, including small noncoding RNAs, with high precision. The software is available under an open source license (ISCL) at https://pypi.org/project/ANNOgesic/.
Chronic Pain Self-Management Program for Low-Income Patients: Themes from a Qualitative Inquiry
Authors: Turner Barbara J , Rodriguez Natalia , Bobadilla Raudel , Hernandez Arthur E , Yin Zenong 
Published: August 2018

Abstract

Objective
To examine factors influencing initial engagement, ongoing participation, learned behaviors, and subjective functional outcomes after a trial of the Living Better Beyond Pain (LBBP) chronic pain self-management program.

Design
Qualitative study using the Grounded Theory approach.

Setting
Two 60-minute focus groups and phone interviews in May 2017.

Subjects
Focus groups with 18 participants who completed LBBP and six-month measures; telephone interviews with 17 participants who stopped attending.

Methods
Study coordinators randomly selected program completers for focus groups and conducted phone interviews with noncompleters. Inductive thematic analysis was used to identify patterns in semantic content with a recursive process applied to focus group transcripts and interview transcriptions to codify into themes. Themes were categorized according to the Theory of Planned Behavior.

Results
Focus group and telephone interview participants were primarily Hispanic and unemployed. Attitudes fostering participation in LBBP included dissatisfaction with the status quo, need to reduce pain medication, and lack of training and knowledge about chronic pain. Positive social norms from meeting others with chronic pain and support from the LBBP team encouraged attendance and adoption of behaviors. Transportation, pain, and competing activities were barriers, whereas adapting activities for the disabled was a facilitator. Maintaining behaviors and activities at home was challenging but ultimately rewarding due to improvement in daily function with less pain medication.

Conclusions
This qualitative study complements quantitative results showing clinically significant improvements in function after the LBBP program by adding practical insights into ways to increase participation and outcomes. Participants strongly endorsed the need for chronic pain self-management training.
Predicting Performance of First-Year Residents: Correlations Between Structured Interview, Licensure Exam, and Competency Scores in a Multi-Institutional Study
Authors: Marcus-Blank Brittany , Dahlke Jeffrey A. , Braman Jonathan P. , Borman-Shoap Emily , Tiryaki Ezgi , Chipman Jeffrey , Andrews John S. , Sackett Paul R. , Cullen Michael J. 
Published: August 2018

Purpose
To determine whether scores on structured interview (SI) questions designed to measure noncognitive competencies in physicians (1) predict subsequent first-year resident performance on Accreditation Council for Graduate Medical Education (ACGME) milestones and (2) add incremental validity over United States Medical Licensing Examination (USMLE) Step 1 and Step 2 Clinical Knowledge scores in predicting performance.

Method
The authors developed 18 behavioral description questions to measure key noncognitive competencies (e.g., teamwork). In 2013–2015, 14 programs (13 residency, 1 fellowship) from 6 institutions used subsets of these questions in their selection processes. The authors conducted analyses to determine the validity of SI and USMLE scores in predicting first-year resident milestone performance in the ACGME’s core competency domains and overall.

Results
SI scores predicted midyear and year-end overall performance (r = 0.18 and 0.19, respectively, P < .05) and year-end performance on patient care, interpersonal and communication skills, and professionalism competencies (r = 0.23, r = 0.22, and r = 0.20, respectively, P < .05). SI scores contributed incremental validity over USMLE scores in predicting year-end performance on patient care (ΔR = 0.05), interpersonal and communication skills (ΔR = 0.09), and professionalism (ΔR = 0.09; all P < .05). USMLE scores contributed incremental validity over SI scores in predicting year-end performance overall and on patient care and medical knowledge.

Conclusions
SI scores predict first-year resident year-end performance in the interpersonal and communication skills, patient care, and professionalism competency domains. Future research should investigate whether SIs predict a range of clinically relevant outcomes.
Approaches to Teaching the Physical Exam to Preclerkship Medical Students: Results of a National Survey
Authors: Uchida Toshiko , Park Yoon Soo , Ovitsh Robin K. , Hojsak Joanne , Gowda Deepthiman , Farnan Jeanne M. , Boyle Mary , Blood Angela D. , Achike Francis I. , Silvestri Ronald C. 
Published: August 2018

Purpose
To assess current approaches to teaching the physical exam to preclerkship students at U.S. medical schools.

Method
The Directors of Clinical Skills Courses developed a 49-question survey addressing the approach, pedagogical methods, and assessment methods of preclerkship physical exam curricula. The survey was administered to all 141 Liaison Committee on Medical Education–accredited U.S. medical schools in October 2015. Results were aggregated across schools, and survey weights were used to adjust for response rate and school size.

Results
One hundred six medical schools (75%) responded. Seventy-nine percent of schools (84) began teaching the physical exam within the first two months of medical school. Fifty-six percent of schools (59) employed both a “head-to-toe” comprehensive approach and a clinical reasoning approach. Twenty-three percent (24) taught a portion of the physical exam interprofessionally. Videos, online modules, and simulators were used widely, and 39% of schools (41) used bedside ultrasonography. Schools reported a median of 4 formative assessments and 3 summative assessments, with 16% of schools (17) using criterion-based standard-setting methods for physical exam assessments. Results did not vary significantly by school size.

Conclusions
There was wide variation in how medical schools taught the physical exam to preclerkship students. Common pedagogical approaches included early initiation of physical exam instruction, use of technology, and methods that support clinical reasoning and competency-based medical education. Approaches used by a minority of schools included interprofessional education, ultrasound, and criterion-based standard-setting methods for assessments. Opportunities abound for research into the optimal methods for teaching the physical exam.
Current Basal and Squamous Cell Skin Cancer Management
Authors: Mendez Bernardino M. , Thornton James F. 
Published: August 2018

Learning Objectives:
After studying this article, the participant should be able to: 1. Characterize basal and squamous cell carcinomas as low or high risk based on size, location, histology, and clinical features. 2. Understand appropriate surgical margins in low- and high-risk lesions, and other management options, including Mohs micrographic surgery, electrodissection and curettage, topical agents, cryotherapy, photodynamic therapy, and radiation therapy. 3. Discuss adjuvant therapies for locally advanced and metastatic disease, including radiation therapy, chemotherapy, and targeted therapies such as hedgehog pathway inhibitors. 4. Educate patients on preventive measures such as skin examinations, sun protection, oral retinoids, and oral nicotinamide (vitamin B3). 5. Devise a reconstructive plan once clear oncologic margins are obtained.

Summary:
With the growing incidence of basal and squamous cell carcinoma, there is an increasing demand for appropriate oncologic management and aesthetic reconstruction. The goal of this CME article is to provide a foundation of knowledge to accurately diagnose, stage, and treat nonmelanoma skin cancers. In addition, it provides the practicing plastic surgeon alternate tools for managing these skin lesions, including topical agents, destructive therapies, and radiation therapy. Lastly, reconstructive plans for selected soft-tissue defects are discussed.
Effect of Navigation System on Removal of Foreign Bodies in Head and Neck Surgery
Authors: Ji Yefeng , Jiang Hongbing , Wan Linzhong , Yuan Hua 
Published: August 2018

Abstract
Foreign bodies retained in oral and maxillofacial regions include different types and properties. Road traffic accident is one of the major causes of the maxillofacial trauma. Foreign bodies can cause direct or indirect damage to the body, even life-threatening. It is a demanding procedure to detect the accurate position and implement surgical removal of the embedded fragments in the soft tissue in clinic.
Usually, foreign bodies are close to important structures such as the head and neck region with limited intraoperative visibility and anatomical intricacies. Therefore, the key to remove foreign bodies in head and neck surgery is precise localization and reasonable surgical approaches. The authors reported that the foreign bodies adjacent to large vessels in a case were successfully removed assisted by AccuNavi-A surgical navigation system.
Kidney Transplant Outcomes in Recipients With Cognitive Impairment: A National Registry and Prospective Cohort Study
Authors: Thomas Alvin G. , Ruck Jessica M. , Shaffer Ashton A. , Haugen Christine E. , Ying Hao , Warsame Fatima , Chu Nadia , Carlson Michelle C. , Gross Alden L. , Norman Silas P. , Segev Dorry L. , McAdams-DeMarco Mara 
Published: August 2018

Background.
Cognitive impairment is common in patients with end-stage renal disease and is associated with poor outcomes on dialysis. We hypothesized that cognitive impairment might be associated with an increased risk of all-cause graft loss (ACGL) in kidney transplant (KT) recipients.

Methods.
Using the Modified Mini-Mental State (3MS) examination, we measured global cognitive function at KT hospital admission in a prospective, 2-center cohort of 864 KT candidates (August 2009 to July 2016). We estimated the association between pre-KT cognitive impairment and ACGL using Cox regression, adjusting for recipient, donor, and transplant factors.

Results.
In living donor KT (LDKT) recipients, the prevalence was 3.3% for mild impairment (60 ≤ 3MS < 80) and 3.3% for severe impairment (3MS < 60). In deceased donor KT (DDKT) recipients, the prevalence was 9.8% for mild impairment and 2.6% for severe impairment. The LDKT recipients with cognitive impairment had substantially higher ACGL risk than unimpaired recipients (5-year ACGL: 45.5% vs 10.6%; P < 0.01; adjusted hazard ratio [aHR] any impairment, 5.40 (95% confidence interval [CI], 1.78-16.34; P < 0.01); aHR severe impairment, 5.57 (95% CI, 1.29-24.00; P = 0.02). Similarly, DDKT recipients with severe impairment had higher ACGL risk than recipients without severe impairment (5-year ACGL, 53.0% vs 24.2%; P = 0.04); aHR severe impairment, 2.92 (95% CI, 1.13-7.50; P = 0.03).

Conclusions.
Given the elevated risk of ACGL among KT recipients with cognitive impairment observed in this 2-center cohort, research efforts should explore the mechanisms of graft loss and mortality associated with cognitive impairment and identify potential interventions to improve posttransplant survival.
Incorporation of doxorubicin in different polymer nanoparticles and their anti-cancer activity
Authors: Pieper S. , Onafuye H. , Mulac D. , Cinatl Jindrich , Wass Mark N. , Michaelis M. , Langer K. 
Published: August 2018

AbstractNanoparticles are under investigation as carrier systems for anti-cancer drugs. They have been shown to accumulate in cancer tissues through the enhanced permeability and retention (EPR) effect, to reduce toxicity to non-target tissues, and to protect drugs from preliminary inactivation. However, nanoparticle preparations are not commonly compared for their anti-cancer effects at the cellular level. Here, we prepared doxorubicin-loaded nanoparticles based on poly(lactic-co-glycolic acid) (PLGA), polylactic acid (PLA), and PEGylated PLGA (PLGA-PEG) by solvent displacement and emulsion diffusion approaches. The resulting nanoparticles covered a size range between 73 and 246 nm. PLGA-PEG nanoparticle preparation by solvent displacement resulted in the smallest nanoparticles. In PLGA nanoparticles, the drug load could be optimised using solvent displacement at pH7 reaching 53 µg doxorubicin/mg nanoparticle. In addition, these PLGA nanoparticles displayed sustained doxorubicin release kinetics compared to the more burst-like kinetics of the other preparations. In neuroblastoma cells, doxorubicin-loaded PLGA-PEG nanoparticles (presumably due to their small size) and PLGA nanoparticles prepared by solvent displacement at pH7 (presumably due to their high drug load and superior drug release kinetics) exerted the strongest anti-cancer effects. In conclusion, doxorubicin-loaded nanoparticles made by different methods from different materials displayed substantial discrepancies in their anti-cancer activity at the cellular level. Optimised preparation methods resulted in PLGA nanoparticles characterised by increased drug load, controlled drug release, and high anti-cancer efficacy. The design of drug-loaded nanoparticles with optimised anti-cancer activity at the cellular level is an important step in the development of improved nanoparticle preparations for anti-cancer therapy.
Evidence for minimal cardiogenic potential of Sca-1 positive cells in the adult mouse heart
Authors: Neidig Lauren E. , Weinberger Florian , Palpant Nathan J. , Mignone John , Martinson Amy M. , Sorensen Daniel W. , Bender Ingrid , Nemoto Natsumi , Reinecke Hans , Pabon Lil , Molkentin Jeffery D. , Murry Charles E. , van Berlo Jop H. 
Published: August 2018

ABSTRACTBackgroundDespite modern pharmacotherapy, heart failure remains a major medical burden. The heart has a limited regenerative capacity, and bolstering regeneration might represent new therapeutic approaches for heart failure patients. Various progenitor cells in the heart have been proposed to have cardiomyogenic properties, but this evidence is based mostly on cell culture and transplantation studies. One population of interest is characterized by the expression of Stem Cell Antigen-1 (Sca-1). Here we tested the hypothesis that Sca-1+cells are endogenous progenitors for cardiomyocytes in the adult heart.MethodsWe evaluated the innate cardiogenic potential of Sca-1+cellsin vivoby generating a novel mouse model to genetically lineage-trace the fate of Sca-1 expressing cells. This was accomplished by introducing a tamoxifen-inducible Cre-recombinase into the Sca-1 locus (Sca-1mCm/+). Crossing this mouse line to a Cre-dependent tdTomato reporter line allowed for genetic lineage-tracing of endogenous Sca-1+cells (Sca-1mCmR26tdTomato). The frequency of Sca-1+cardiomyocytes was quantified from dispersed cell preparations and confirmed by in situ histology.ResultsWe validated the genetic lineage tracing mouse model in bone marrow and heart. Unlike previous publications suggesting significant cardiogenic potential, we found that less than 0.02% of cardiomyocytes per year were derived from Sca-1+cells in the adult heart under homeostatic conditions. At six months after myocardial infarction, we found less than 0.01% of cardiomyocytes were derived from Sca-1+cells.ConclusionOur results show that Sca-1+cells in the adult heart have minimal cardiogenic potential under homeostatic conditions or in response to myocardial infarction.
HIV-1 Protease Uses Bi-Specific S2/S2’ Subsites To Optimize Cleavage of Two Classes of Target Sites
Authors: Potempa Marc , Lee Sook-Kyung , KurtYilmaz Nese , Nalivaika Ellen A. , Rogers Amy , Spielvogel Ean , Carter Charles W. , Schiffer Celia A. , Swanstrom Ronald 
Published: August 2018

AbstractRetroviral proteases (PR) have a unique specificity that allows cleavage of sites with or without a P1’ proline. A P1’ proline is required at the MA/CA cleavage site due to its role in a post-cleavage conformational change in the capsid protein. However, the HIV-1 PR prefers to have large hydrophobic amino acids flanking the scissile bond, suggesting PR recognizes two different classes of substrate sequences. We analyzed the cleavage rate of over 150 iterations of six different HIV-1 cleavage sites to explore rate determinants of cleavage. We found that cleavage rates are strongly influenced by the two amino acids flanking the amino acids at the scissile bond (P2-P1/P1’-P2’), with two complementary sets of rules. When P1’ is proline, the P2 side chain interacts with a polar region in the S2 subsite of the PR, while the P2’ amino acid interacts with a hydrophobic region of the S2’ subsite. When P1’ is not proline, the orientations of the P2 and P2’ side chains with respect to the scissile bond are reversed; P2 residues interact with a hydrophobic face of the S2 subsite while the P2’ amino acid usually engages hydrophilic amino acids in the S2’ subsite. These results reveal that the HIV-1 PR has evolved bi-functional S2 and S2’ subsites to accommodate the steric effects imposed by a P1’ proline on the orientation of P2 and P2’ substrate side chains. These results also suggest a new strategy for inhibitor design to engage the multiple specificities in these subsites.
Bayesian-estimated hierarchical HMMs enable robust analysis of single-molecule kinetic heterogeneity
Authors: Hon Jason , Gonzalez Ruben L. 
Published: August 2018

ABSTRACTSingle-molecule kinetic experiments allow the reaction trajectories of individual biomolecules to be directly observed, eliminating the effects of population averaging and providing a powerful approach for elucidating the kinetic mechanisms of biomolecular processes. A major challenge to the analysis and interpretation of these experiments, however, is the kinetic heterogeneity that almost universally complicates the recorded single-molecule signal versus time trajectories (i.e., signal trajectories). Such heterogeneity manifests as changes and/or differences in the transition rates that are observed within individual signal trajectories or across a population of signal trajectories. Although characterizing kinetic heterogeneity can provide critical mechanistic information, there are currently no computational methods available that effectively and/or comprehensively enable such analysis. To address this gap, we have developed a computational algorithm and software program, hFRET, that uses the variational approximation for Bayesian inference to estimate the parameters of a hierarchical hidden Markov model, thereby enabling robust identification and characterization of kinetic heterogeneity. Using simulated signal trajectories, we demonstrate the ability of hFRET to accurately and precisely characterize kinetic heterogeneity. In addition, we use hFRET to analyze experimentally recorded signal trajectories reporting on the conformational dynamics of ribosomal pre-translocation (PRE) complexes. The results of our analyses demonstrate that PRE complexes exhibit kinetic heterogeneity, reveal the physical origins of this heterogeneity, and allow us to expand the current model of PRE complex dynamics. The methods described here can be applied to signal trajectories generated using any type of signal and can be easily extended to the analysis of signal trajectories exhibiting more complex kinetic behaviors. Moreover, variations of our approach can be easily developed to integrate kinetic data obtained from different experimental constructs and/or from molecular dynamics simulations of a biomolecule of interest. The hFRET source code, graphical user interface, and user manual can be downloaded as freeware at https://github.com/GonzalezBiophysicsLab/hFRET.
Towards excellence in managing the public-sector project cycle: a TQM context
Authors: Gomes Carlos F. , Small Michael H. , Yasin Mahmoud M. 
Published: August 2018

Purpose
The purpose of this paper is to assess the management of public-sector projects in Portugal paying particular attention to the extent to which total quality management (TQM) principles are being utilized in such projects.

Design/methodology/approach
Based on an extensive review of the literature, nine propositions are advanced about the interrelationships among seven factors that were identified, in a previous study, as having some influence on the management process in the planning and implementation of public-sector projects in Portugal. Structural equation modeling was used to investigate these propositions using data obtained from 211 respondents to a survey of project managers from municipalities across Portugal.

Findings
The results of the structural equation model indicate that the TQM components working in tandem with project-management-specific variables provide a systematic means of managing the planning and implementation stages of projects, with technical items being critical in the planning stage and softer management items becoming important in the implementation stage.

Research limitations/implications
Readers should be careful not to generalize the findings in a global context or for private sector projects. However, researchers are encouraged to extend this study by including other planning and implementation variables with a view to discerning what particular characteristics of a project make it more amenable to TQM solutions.

Practical implications
The findings are presented to show how the key components of TQM, customer focus, employee involvement and continuous involvement, can be applied during the planning and implementation stages of projects.

Originality/value
The sample size of 211 is representative of the underlying population of project managers in municipalities across Portugal and is comparatively large in relation to other empirical project management studies from Portugal, lending credence to the generalizability of these finding to public-sector projects in Portugal.