bluuebunny/crossref_metadata_2025_split huggingface dataset:
Access to Contraception in Local Health Departments, Four Midwest States, 2017–2018
Authors: Satterwhite Catherine Lindsey , French Valerie , Allison Molly , Honderick Tanya , Ramaswamy Megha 
Published: December 2019

(Abstracted from Contraception 2019;99:363–367)
Barriers to contraception use are well known and include education, cost, and access. Successful efforts to expand access for women of reproductive age to a broad range of contraceptive methods focus on intrauterine devices (IUDs) and implants, which are long-acting reversible methods.
Sexual Satisfaction Changes Reported by Men After Their Partners' Robotic-assisted Laparoscopic Sacrocolpopexies
Authors: Culligan Patrick J. , Haughey Sean , Lewis Christa , Priestley Jennifer , Salamon Charbel 
Published: December 2019

(Abstracted from Female Pelvic Med Reconstr Surg 2019;25:365–368)
Most women with symptomatic pelvic organ prolapse (POP) experience improved sexual function after successful POP repair. Little is known about the impact of their reconstructive surgery on their male partners' sexual function and satisfaction.
Neurologic Outcome After Prematurity: Perspectives of Parents and Clinicians
Authors: Lemmon Monica E. , Huffstetler Hanna , Barks Mary Carol , Kirby Christine , Katz Madelaine , Ubel Peter A. , Docherty Sharron L. , Brandon Debra 
Published: December 2019

(Abstracted from Pediatrics 2019;144(1):e20183819)
Clinicians and parents often need to make time-sensitive and high-stakes decisions when caring for premature infants. Yet, little is known about how each group discusses, understands, and makes these decisions.
On Step 1 Mania, USMLE Score Reporting, and Financial Conflict of Interest at the National Board of Medical Examiners
Authors: Carmody J. Bryan , Rajasekaran Senthil K. 
Published: December 2019

Though intended to inform a binary decision on initial medical licensure, the United States Medical Licensing Examination (USMLE) is frequently used for screening candidates for residency positions. Some have argued that reporting results as pass/fail would honor the test’s purpose while preventing inappropriate use. To date, the USMLE’s sponsor organizations have declined to make such a change. In this Perspective, the authors examine the history and mission of the National Board of Medical Examiners (NBME), trace the rise of “Step 1 mania,” and consider the current financial incentives for the NBME in implementing a pass/fail score-reporting policy.
The NBME was founded in 1915 to address the lack of interstate reciprocity in medical licensure examination. With the creation of the USMLE in 1992, a single pathway for licensure was established, and the organization’s original mission was achieved. Yet even after fulfilling its primary purpose, the NBME—classified as a nonprofit organization—has seen its revenues rise dramatically over the past 2 decades. Much of the increased revenue is derived from test products and services not required for medical licensure, with sales driven by the increasing importance of Step 1 scores in residency selection. Revenue from these products and services would likely decline if the NBME reported Step 1 results as pass/fail.
A financial conflict of interest occurs when a judgment concerning a primary interest may be influenced by a secondary interest, such as financial gain. The data presented here demonstrate that the NBME has a conflict of interest in its current score-reporting policy. Possible remedies, such as disclosure, recusal, divestiture, and restructuring, are considered.
The Civil Rights Doctor, Revisited
Authors: Mullan Fitzhugh 
Published: December 2019

The author recalls the summer of 1965, which he spent in Holmes County, Mississippi, as a medical civil rights worker. The poverty, bravery, ignorance, brotherhood, racism, hate, and love he experienced that summer led him to conclude he would become a civil rights doctor. When he returned to medical school in Chicago, the author and his classmates began organizing students around the idea of social justice. They intended to take on society’s big problems even as their medical education ignored them.
More than 50 years later, the author reflects on the sense of mission that attracts many people to medicine. A mission more than the desire to heal. A mission to recognize and address the inequities in the world and, more to the point, in access to health and health care. Medical schools have a unique role or “social mission” in that they are the only institutions that can build doctors for the future. The culture of the medical school is a powerful influence on the values of its graduates and, ultimately, the physicians of the country. The articulated, cerebrated, strategized mission that a medical school selects for itself has an enormous influence on who gets to be a doctor and what the values of that doctor are in the future, and that is why, the author argues, medical schools must incorporate social mission.
To achieve this vision, medical education must move beyond Abraham Flexner’s 20th-century legacy. This is not to disown Flexner, science, or research but to rethink medical education based on the equity challenges that confront our population now. Physicians and the institutions that train them need to see social mission as a living part of the medical skill set rather than an elective perspective exercised by some who are particularly compassionate.
HUMAN AMNIOTIC MEMBRANE TO CLOSE RECURRENT, HIGH MYOPIC MACULAR HOLES IN PATHOLOGIC MYOPIA WITH AXIAL LENGTH OF ≥30 mm
Authors: Caporossi Tomaso , Pacini Bianca , De Angelis Lorenzo , Barca Francesco , Peiretti Enrico , Rizzo Stanislao 
Published: December 2019

Purpose:
To assess the effectiveness of the human amniotic membrane plug for recurrent high myopic macular hole (MH) that already underwent pars plana vitrectomy with internal limiting membrane peeling and gas endotamponade.

Methods:
Sixteen eyes of 16 patients with recurrent high myopic MH were enrolled. A 23-gauge pars plana vitrectomy was performed. Human amniotic membrane plugs were implanted under the neuroretina inside the MH. Twenty percent sulfur hexafluoride or air was used as endotamponades. The patients were instructed to maintain facedown position for 5 days after surgery.

Results:
Optical coherence tomography examinations showed that the MHs closed in 15 of the 16 patients (93.75%) 2 weeks after one surgical intervention, and in 100% of patients after second intervention. Mean best-corrected visual acuity improved from 1 logarithm of the minimum angle of resolution (20/200) to 0.67 logarithm of the minimum angle of resolution (20/100) 6 months after surgery. Best-corrected visual acuity remained stable during the 12-month follow-up. One patient had human amniotic membrane plug dislocation after gas absorption that needed a second intervention with new AM plug implantation. No adverse events were reported during the 12-month follow-up.

Conclusion:
The first case series of recurrent high myopic MH was reported, assessing the effectiveness of the human amniotic membrane plug to close recurrent MHs in pathologic myopia. All the cases were successful with encouraging best-corrected visual acuity recovery.
MACULAR HOLE FORMATION ASSOCIATED WITH INTENSE PULSED LIGHT THERAPY
Authors: Maganti Nenita , Kalbag Neil S. , Gill Manjot K. 
Published: December 2019

Purpose:
To describe the first case of macular hole formation following intense pulsed light therapy.

Methods:
This is a retrospective case report. A 68-year-old woman presented with blurry vision that occurred 1 day following intense pulsed light therapy for hair removal.

Results:
A full thickness macular hole, which had not been previously documented was noted on fundus exam. Ocular coherence tomography confirmed a full-thickness macular hole.

Discussion:
Laser treatment for hair removal has been reported to cause ocular injuries including iris atrophy, pupillary distortion, cataracts, and uveitis. Intense pulsed light therapy, a specific type of laser therapy, has been reported to cause iris transillumination defects, anterior uveitis, and pupil abnormalities. Our case is the first to describe a macular hole secondary to intense pulsed light therapy. The etiology of the macular hole is postulated to be secondary to possible thermal injury with absorption of energy at the level of the retinal pigment epithelium. This emphasizes the role and importance of preventative measures, such as protective glasses in reducing the risk of ocular injuries.
Identification of Specific Tumor Markers in Vulvar Carcinoma Through Extensive Human Papillomavirus DNA Characterization Using Next Generation Sequencing Method
Authors: Thomas Jacques , Leufflen Léa , Chesnais Virginie , Diry Ségolène , Demange Jessica , Depardieu Claude , Bani Mohamed Amine , Marchal Frédéric , Charra-Brunaud Claire , Merlin Jean-Louis , Leroux Agnès , Sastre-Garau Xavier , Harlé Alexandre 
Published: December 2019

Objectives
A subset of vulvar carcinomas (VC) are associated with human papillomavirus (HPV) DNA. This trait can be used to identify tumor markers for patient's follow-up. A large diversity of HPV prevalence in VC has been reported, but no data are available concerning the insertional HPV status in this tumor type. Therefore, we have used an innovative next generation sequencing (NGS)-based CaptHPV method able to provide an extensive characterization of HPV DNA in tumors.

Material and Methods
Tumor tissue specimens from 55 patients with VC were analyzed using p16 immunohistochemistry, in situ hybridization, polymerase chain reaction, and CaptHPV-NGS assays.

Results
Our analyses showed that 8 (14.5%) of 55 cases were associated with HPV 16 DNA. No other HPV genotypes were identified. The HPV genome was in a free episomal state only in one case and both episomal and integrated into the tumor cell genome in 7. There was a single insertion in 5 cases and multiple sites, scattered at different chromosomal loci in two. ISH data suggest that some of these might reflect tumor heterogeneity. Viral integration targeted cellular genes among which were TP63, CCDC148, LOC100133091, PKP1, and POLA2. Viral integration at the PKP1 locus was associated with partial gene deletion, and no PKP1 protein was detected in tumor tissue.

Conclusions
Using the NGS-based innovative capture-HPV approach, we established a cartography of HPV 16 DNA in 8 VC cases and identified novel genes targeted by integration that may be used as specific tumor markers. In addition, we established a rationale strategy for optimal characterization of HPV status in VC.
18F-FDG-PET/CT in measuring volume and global metabolic activity of thigh muscles: a novel CT-based tissue segmentation methodology
Authors: Kothekar Esha , Yellanki Dani , Borja Austin J. , Al-zaghal Abdullah , Werner Thomas J. , Revheim Mona-Elisabeth , Gerke Oke , Saboury Babak , Gholamrezanezad Ali , Høilund-Carlsen Poul F. , Alavi Abass 
Published: December 2019

PurposeWe present a novel computed tomography-based tissue segmentation methodology for determining volume and global uptake of FDG of the thigh muscles and correlate these parameters with age.Materials and methodsA total of 71 subjects from a prospective clinical trial (NCT01724749) were included. PET/CT scans were acquired 180 minutes after intravenous injection of FDG. A 3D growing region algorithm with neighborhood Hounsfield unit threshold between one and 150 was used to highlight the muscle. FDG uptake was expressed as the average mean standardized uptake value normalized for lean body mass (average SULmean). Femur volume was used to normalize thigh muscle volume to calculate normalized volume and correlate with age.ResultsWe found a significant negative correlation between normalized volume and age (left side r = −0.262,P= 0.02; right side r = −0.286,P= 0.01). No statistically significant difference was found between SUL and age or between SUL and BMI. There was no statistically significant difference in muscle volume on the two sides. Statistically significant difference was noted in the global metabolic activity (SUL) between the two sides (left 0.39 ± 0.06, right 0.42 ± 0.08,P< 0.001), with 56/71 (78.8%) subjects having higher uptake on the right side.ConclusionFDG-PET/CT using CT-based segmentation is a novel imaging modality assessing the volume and global metabolic activity of the thigh muscles. It could be possible to utilize this methodology for the research and understanding of lower limb muscle pathophysiology.
Establishing Meaningful Learning in Online Nursing Postconferences
Authors: Petrovic Kristin A. , Hack Regan , Perry Beth 
Published: December 2019

Background
Effective teaching and learning strategies in online postconference can assist students to find meaning within clinical experiences.

Purpose
To explore this, we completed a literature review about meaningful learning in online clinical postconferencing in prelicensure nursing education.

Methods
Articles that were peer-reviewed, published within the last 10 years, written in English, and addressed online learning in clinical postconferences in prelicensure nursing programs were included.

Results
Analysis revealed the following themes: connecting theory to practice, reflective practice, impact on future practice, peer and instructor support, mentoring and leadership development, giving and receiving feedback effectively, critical thinking, and engagement of active learners. Gaps were evident with minimal evidence-based practice described related to postconferences in general. Additionally, there is limited discussion of online postconferencing.

Conclusions
Understanding the nuances of meaningful learning in online postconference is critical to facilitating students' ability to connect theory to practice.
Patient Preferences for Attributes of Primary Surgical Debulking Versus Neoadjuvant Chemotherapy for Treatment of Newly Diagnosed Ovarian Cancer
Authors: Havrilesky Laura J. , Yang Jui-Chen , Lee Paula S. , Secord Angeles Alvarez , Ehrisman Jessie A. , Davidson Brittany , Berchuck Andrew , Darcy Kathleen M. , Maxwell G. Larry , Reed Shelby D. 
Published: December 2019

(Abstracted from Cancer 2019;125:4399–4406)
Retrospective analyses have found that optimal tumor debulking after a new diagnosis of ovarian cancer results in significantly greater progression-free survival (PFS) and overall survival (OS) compared with those who are suboptimally debulked. Primary debulking surgery (PDS) has become a common first line of therapy in patients with ovarian cancer.
Two-Dose Versus Single-Dose Methotrexate for Treatment of Ectopic Pregnancy: A Meta-analysis
Authors: Alur-Gupta Snigdha , Cooney Laura G. , Senapati Suneeta , Sammel Mary D. , Barnhart Kurt T. 
Published: December 2019

(Abstracted from Am J Obstet Gynecol 2019;221:95–108.e2)
A number of studies have demonstrated comparable efficacy of medical and surgical management for treatment of stable ectopic pregnancies. Methotrexate, a folate antagonist, has been the mainstay of medical management.
A Review of CONSORT Guidelines About Comparison Groups With a Focused Discussion on Implications for Rehabilitation Clinical Trials
Authors: Levack William M. M. , Engkasan Julia P. , Heinemann Allen W. , Negrini Stefano 
Published: December 2019

Objective
We examined and appraised the Consolidated Standards of Reporting Trials (CONSORT) 2010 Statement and its extension from the perspective of the reporting of comparison groups (ie, interventions or control conditions against which an experimental intervention is compared) in clinical trials on rehabilitation topics.

Design
We downloaded the CONSORT 2010 Statement and all endorsed and unofficial extensions reported on the CONSORT and EQUATOR Web sites. We extracted all statements on the selection, design, delivery, or interpretation of data from comparison groups in clinical trials. We discussed preliminary findings during the Cochrane Rehabilitation Methodology Meeting in Kobe and then further by email before finalizing results.

Results
We identified 23 standards reported across the CONSORT 2010 Statement and 10 extensions. Overall, these standards address many, but not all, issues related to reporting of comparison groups in rehabilitation trials.

Conclusions
We recommend that additional standards be created for the selection of types of comparisons, choices around reporting of “usual care,” reporting of intended “mechanisms of control,” and reporting a rationale for the hypothesized superiority of one intervention over another when superiority trial design are used. Rehabilitation research would benefit from development of a specific checklist and guidelines to help researchers make best use of existing extensions.
Resilience After Spinal Cord Injury
Authors: McDonald Scott D. , Pugh Mickeal , Mickens Melody N. 
Published: December 2019

Abstract
Rehabilitation medicine has recently embraced resilience, and research in this area has surged within the past decade. Several systematic reviews of resilience research have been conducted in traumatic brain injury, chronic diseases, and stroke populations. A decade into research into the role of resilience in the lives of individuals with spinal cord injury, a review of the current state of the research literature is needed to identify trends and knowledge gaps. The aims of this scoping review were (a) to classify study methods and designs used for resilience research in spinal cord injury to date, (b) to describe how researchers have defined “resilience,” and (c) to identify knowledge gaps and suggest future directions for research. Literature searches were conducted to identify English-language, peer-reviewed articles on resilience and spinal cord injury. Most of the 40 studies reviewed were correlational using cross-sectional data, although descriptive, longitudinal, qualitative, test development, and intervention studies and review articles were found as well. As is the case outside of rehabilitation medicine, there is considerable definitional and conceptual heterogeneity that limits our ability to apply resilience research to clinical practice. Moving forward, the field needs model-driven, longitudinal research that offers clear, conceptual distinctions between risk and protective factors, processes, and outcomes.
Characterization of 100 extended major histocompatibility complex haplotypes in Indonesian cynomolgus macaques
Authors: Shortreed Cecilia G. , Wiseman Roger W. , Karl Julie A. , Bussan Hailey E. , Baker David A. , Prall Trent M. , Haj Amelia K. , Moreno Gage K. , Penedo Maria Cecilia T. , O’Connor David H. 
Published: December 2019

AbstractMany medical advancements – including improvements to anti-rejection therapies in transplantation and vaccine development – rely on pre-clinical studies conducted in cynomolgus macaques (Macaca fascicularis). Major histocompatibility complex (MHC) class I and class II genes of cynomolgus macaques are orthologous to human leukocyte antigen complex (HLA) class I and class II genes, respectively. Both encode cell-surface proteins involved in cell recognition and rejection of non-host tissues. MHC class I and class II genes are highly polymorphic, so comprehensive genotyping requires the development of complete databases of allelic variants. Our group used PacBio circular consensus sequencing of full-length cDNA amplicons to characterize MHC class I and class II transcript sequences for a cohort of 295 Indonesian cynomolgus macaques (ICM) in a large, pedigreed breeding colony. These studies allowed us to expand the existing database ofMacaca fascicularis(Mafa) alleles by identifying an additional 141 MHC class I and 61 class II transcript sequences. In addition, we defined co-segregating combinations of allelic variants as regional haplotypes for 70 Mafa-A, 78 Mafa-B and 45 Mafa-DRB gene clusters. Finally, we defined class I and class II transcripts that are associated with 100 extended MHC haplotypes in this breeding colony by combining our genotyping analyses with short tandem repeat (STR) patterns across the MHC region. Our sequencing analyses and haplotype definitions improve the utility of these ICM for transplantation studies as well as infectious disease and vaccine research.
Accurate and simultaneous identification of differential expression and splicing using hierarchical Bayesian analysis
Authors: Karlebach Guy , Hansen Peter , Veiga Diogo F.T. , Steinhaus Robin , Danis Daniel , Li Sheng , Anczukow Olga , Robinson Peter N. 
Published: December 2019

AbstractThe regulation of mRNA controls both overall gene expression as well as the distribution of mRNA isoforms encoded by the gene. Current algorithmic approaches focus on characterization of significant differential expression or alternative splicing events or isoform distribution without integrating both events. Here, we present Hierarchical Bayesian Analysis of Differential Expression and ALternative SPlicing (HBA-DEALS), which simultaneously characterizes differential expression and splicing in cohorts. HBA-DEALS attains state of the art or better performance for both expression and splicing, and allows genes to be characterized as having differential gene expression (DGE), differential alternative splicing (DAST), both, or neither. Based on an analysis of Genotype-Tissue Expression (GTEx) data we demonstrate the existence of sets of genes that show predominant DGE or DAST across a comparison of 20 tissue types, and show that these sets have pervasive differences with respect to gene structure, function, membership in protein complexes, and promoter architecture.
EPIGENE: genome wide transcription unit annotation using a multivariate probabilistic model of histone modifications
Authors: Sahu Anshupa , Li Na , Dunkel Ilona , Chung Ho-Ryun 
Published: December 2019

AbstractBackgroundUnderstanding transcriptome is critical for explaining functional as well as regulatory roles of genomic regions. Current methods for the identification of transcription unit (TU) uses RNA-seq which, however, requires large quantities of mRNA limiting the identification of inherently unstable TUs e.g. for miRNA precursors. This problem can be resolved by chromatin based approaches due to a correlation between histone modifications and transcription.ResultsHere we introduce EPIGENE, a novel chromatin segmentation method for the identification of active TUs using transcription associated histone modifications. Unlike existing chromatin segmentation approaches, EPIGENE uses a constrained, semi-supervised multivariate hidden markov model (HMM) that models the observed combination of histone modifications using a product of independent Bernoulli random variables, to identify active TUs. Our results show that EPIGENE can identify genome-wide TUs unbiasedly. EPIGENE predicted TUs showed an enrichment of RNA Polymerase II in transcription start site and gene body indicating that they have been transcribed. Comprehensive validation with existing annotations revealed that 93% of EPIGENE TUs can be explained by existing gene annotations and 5% of EPIGENE TUs in HepG2 can be explained by microRNA annotations. EPIGENE outperforms existing RNA-Seq based approaches in TU prediction precision across human cell lines. Finally, we identify 381 novel TUs in K562 and 43 novel cell-specific TUs all of which are supported by RNA Polymerase II data.ConclusionsWe demonstrate the applicability of HMM to identify genome-wide active TUs and provides valuable information about unannotated TUs. EPIGENE is an open-source method and is freely available at:https://github.com/imbeLab/EPIGENE.