bluuebunny/crossref_metadata_2025_split huggingface dataset:
BEAGLE 3: Improved Performance, Scaling, and Usability for a High-Performance Computing Library for Statistical Phylogenetics
Authors: Ayres Daniel L , Cummings Michael P , Baele Guy , Darling Aaron E , Lewis Paul O , Swofford David L , Huelsenbeck John P , Lemey Philippe , Rambaut Andrew , Suchard Marc A 
Published: April 2019

Abstract
BEAGLE is a high-performance likelihood-calculation library for phylogenetic inference. The BEAGLE library defines a simple, but flexible, application programming interface (API), and includes a collection of efficient implementations for calculation under a variety of evolutionary models on different hardware devices. The library has been integrated into recent versions of popular phylogenetics software packages including BEAST and MrBayes and has been widely used across a diverse range of evolutionary studies. Here, we present BEAGLE 3 with new parallel implementations, increased performance for challenging data sets, improved scalability, and better usability. We have added new OpenCL and central processing unit-threaded implementations to the library, allowing the effective utilization of a wider range of modern hardware. Further, we have extended the API and library to support concurrent computation of independent partial likelihood arrays, for increased performance of nucleotide-model analyses with greater flexibility of data partitioning. For better scalability and usability, we have improved how phylogenetic software packages use BEAGLE in multi-GPU (graphics processing unit) and cluster environments, and introduced an automated method to select the fastest device given the data set, evolutionary model, and hardware. For application developers who wish to integrate the library, we also have developed an online tutorial. To evaluate the effect of the improvements, we ran a variety of benchmarks on state-of-the-art hardware. For a partitioned exemplar analysis, we observe run-time performance improvements as high as 5.9-fold over our previous GPU implementation. BEAGLE 3 is free, open-source software licensed under the Lesser GPL and available at https://beagle-dev.github.io.
Sexual Dichromatism Drives Diversification within a Major Radiation of African Amphibians
Authors: Portik Daniel M , Bell Rayna C , Blackburn David C , Bauer Aaron M , Barratt Christopher D , Branch William R , Burger Marius , Channing Alan , Colston Timothy J , Conradie Werner , Dehling J Maximilian , Drewes Robert C , Ernst Raffael , Greenbaum Eli , Gvoždík Václav , Harvey James , Hillers Annika , Hirschfeld Mareike , Jongsma Gregory F M , Kielgast Jos , Kouete Marcel T , Lawson Lucinda P , Leaché Adam D , Loader Simon P , Lötters Stefan , Meijden Arie Van Der , Menegon Michele , Müller Susanne , Nagy Zoltán T , Ofori-Boateng Caleb , Ohler Annemarie , Papenfuss Theodore J , Rößler Daniela , Sinsch Ulrich , Rödel Mark-Oliver , Veith Michael , Vindum Jens , Zassi-Boulou Ange-Ghislain , McGuire Jimmy A 
Published: April 2019

AbstractTheory predicts that sexually dimorphic traits under strong sexual selection, particularly those involved with intersexual signaling, can accelerate speciation and produce bursts of diversification. Sexual dichromatism (sexual dimorphism in color) is widely used as a proxy for sexual selection and is associated with rapid diversification in several animal groups, yet studies using phylogenetic comparative methods to explicitly test for an association between sexual dichromatism and diversification have produced conflicting results. Sexual dichromatism is rare in frogs, but it is both striking and prevalent in African reed frogs, a major component of the diverse frog radiation termed Afrobatrachia. In contrast to most other vertebrates, reed frogs display female-biased dichromatism in which females undergo color transformation, often resulting in more ornate coloration in females than in males. We produce a robust phylogeny of Afrobatrachia to investigate the evolutionary origins of sexual dichromatism in this radiation and examine whether the presence of dichromatism is associated with increased rates of net diversification. We find that sexual dichromatism evolved once within hyperoliids and was followed by numerous independent reversals to monochromatism. We detect significant diversification rate heterogeneity in Afrobatrachia and find that sexually dichromatic lineages have double the average net diversification rate of monochromatic lineages. By conducting trait simulations on our empirical phylogeny, we demonstrate that our inference of trait-dependent diversification is robust. Although sexual dichromatism in hyperoliid frogs is linked to their rapid diversification and supports macroevolutionary predictions of speciation by sexual selection, the function of dichromatism in reed frogs remains unclear. We propose that reed frogs are a compelling system for studying the roles of natural and sexual selection on the evolution of sexual dichromatism across micro- and macroevolutionary timescales.
Minding the Form That Transforms: Using Kegan’s Model of Adult Development to Understand Personal and Professional Identity Formation in Medicine
Authors: Lewin Linda Orkin , McManamon Alyssa , Stein Michael T.O. , Chen Donna T. 
Published: April 2019

The formation of a physician’s professional identity is a dynamic process shaped by and intertwined with the development of that person’s larger adult identity. Constructive-developmentalist Robert Kegan’s model of adult development describes four mental lenses used for meaning-making and the trajectory through which they transform over time. These lenses determine the way people take in and integrate complex influences into forming their adult identities.
When people use a particular lens to construct meaning, Kegan describes them as being “subject” to that lens: The lens “has them,” and they are unaware of the ways it shapes their world. Transformations occur when individuals are able to take a lens to which they were subject and regard it objectively. Kegan’s lenses that are relevant to medical educators are called instrumental—focused on rules and rewards; socialized—attending to social norms and expectations; self-authoring—seeking to build internal values; and self-transforming—seeing gaps in one’s closely held value systems and being open to those of others.
When individuals have difficulty facing current challenges, they begin to grow a more complex lens. Subsequent lenses bring the ability to deal with more complexity but also bring their own challenges. Familiarity with Kegan’s model can help educators provide more effective support to groups of learners as well as individuals, support learners’ transformational growth through the challenging situations inherent in medical education, and supply a common language for many important areas of medical education, including competencies and entrustable professional activities, remediation, leadership development, and curriculum planning.
Preoperative Chronic Opioid Therapy Negatively Impacts Long-term Outcomes Following Cervical Fusion Surgery
Authors: Kalakoti Piyush , Volkmar Alexander J. , Bedard Nicholas A. , Eisenberg Joshua M. , Hendrickson Nathan R. , Pugely Andrew J. 
Published: April 2019

Study Design.
Retrospective, observational.

Objective.
The aim of this study was to define the impact of preoperative chronic opioid therapy (COT) on outcomes following cervical spine fusions.

Summary of Background Data.
Opioid therapy is a commonly practiced method to control acute postoperative pain. However, concerns exist relating to use of prescription opioids, including inherent risk of abuse, tolerance, and inferior outcomes following major surgery.

Methods.
A commercial dataset was queried from 2007 to 2015 for patients undergoing primary cervical spine arthrodesis [ICD-9 codes 81.01-81.03]. Primary outcome measures were 1-year and 2-year reoperation rates, emergency department (ED) visits, adverse events, and prolonged postoperative opioid use. Secondary outcomes included short-term outcomes including 90-day complications (cardiac, renal, neurologic, infectious, etc.). COT was defined as a history of opioid prescription filling within 3 months before surgery and was the primary exposure variable of interest. Generalized linear models investigated the association of preoperative COT on primary/secondary endpoints following risk-adjustment.

Results.
Overall, 20,730 patients (51.3% female; 85.9% >50 years) underwent primary cervical spine arthrodesis. Of these, 10,539 (n = 50.8%) met criteria for COT. Postoperatively, 75.3% and 29.8% remained on opioids at 3 months and 1 year. Multivariable models identified an association between COT and an increased risk of 90-day ED visit [odds ratio (OR): 1.25; P < 0.001] and wound complications (OR: 1.24; P = 0.036). At 1 year, COT was strongly associated with reoperations (OR: 1.17; P = 0.043), ED visits (OR: 1.31; P < 0.001), and adverse events including wound complications (OR: 1.32; P < 0.001), infections (OR: 1.34; P = 0.042), constipation (OR: 1.11; P = 0.032), neurological complications (OR: 1.44; P = 0.01), acute renal failure (OR: 1.24; P = 0.004), and venous thromboembolism (OR: 1.20; P = 0.008). At 2 years, COT remained a significant risk factor for additional long-term negative outcomes such as reoperations, including adjacent segment disc disease (OR: 1.21; P = 0.005), ED visits (OR: 1.32; P < 0.001), and other adverse events. Preoperative COT was associated with prolonged postoperative narcotic use at 3 months (OR: 1.30; P < 0.001), 1 year (OR: 5.17; P < 0.001), and at 2 years (OR: 5.75; P < 0.001) after cervical arthrodesis.

Conclusion.
Preoperative COT is a modifiable risk factor that is strongly associated with prolonged postoperative opioid use. In addition, COT was associated with inferior short-term and long-term outcomes after cervical spine fusion.

Level of Evidence: 3
The Conundrum of Diagnosing Cutaneous Composite Lymphoma in the Molecular Age
Authors: Ahmed Aadil , Aragao Alessa P. , Mudaliar Kumaran , Wilcox Rebecca , Vardiman James , Anastasi John , Mirza Kamran 
Published: April 2019

Introduction:
Cutaneous composite lymphoma (CCL) is extremely rare. When 2 potentially distinct lymphoid lesions occur at one skin site, distinguishing between one neoplastic clone and a secondary reactionary lymphoid response versus a second neoplasm is difficult. In this study, we describe a unique case of CCL along with a review of reported cases in literature to identify clues and discuss issues that are relevant to the diagnosis of CCL.

Design:
Review of a CCL case from our institution and a systematic review of reported cases of CCL in the literature.

Results:
A total of 18 studies describing 22 cases and a case report from our institution are included. The mean age at diagnosis was 68 years. Most cases herein presented with multiple skin lesions (67%) and reported a history of immune suppression (76%). Nineteen cases (83%) had a combination of T-cell and B-cell neoplasms, whereas the remaining cases had 2 distinct B-cell clones. Clonal differentiation was confirmed based on morphology and immunohistochemistry in all cases, and by polymerase chain reaction studies in 19 cases. Complete remission was achieved in only one quarter of reported cases.

Conclusion:
Diagnosing CCL can be challenging because accurate differentiation of 2 or more clonal populations at 1 site is tedious. A stepwise approach and integration of clinical, morphologic, immunohistochemistry, and molecular data along with an understanding of the prognosis of the lymphomas in question is essential for an accurate diagnosis and necessary because of therapeutic and prognostic implications.
Assessing the outcome of organ allocation: choosing metrics
Authors: Schold Jesse D. 
Published: April 2019

Purpose of review
Organ allocation is a highly complex process with significant impact on outcomes of donor organs and end-stage organ disease patients. Policies governing allocation must incorporate numerous factors to meet stated objective. There have been significant alterations and ongoing discussion about changes in allocation policy for all solid organs in the United States. As with any policy change, rigorous evaluation of the impact of changes is important.

Recent findings
This manuscript discusses metrics to consider to evaluate the impact of organ allocation policy that may be monitored on an ongoing basis including examples of research evaluating current policies. Potential metrics to evaluate allocation policy include the effectiveness, efficiency, equity, costs, donor rates, and transparency associated with the system.

Summary
Ultimately, policies will often need to adapt to secular changes in donor and patient characteristics, clinical and technological advances, and overarching healthcare polices. Providing objective empirical evaluation of the impact of policies is a critical component for assessing quality of the allocation system and informing the effect of changes. The foundation of organ transplantation is built upon public trust and the dependence on the gift of donor organs, as such the importance of the most appropriate organ allocation policies cannot be overstated.
Psychological Outcomes and Quality of Life in Relation to Pancreatectomy
Authors: Lounis Léna , Aurran-Schleinitz Thérèse , Turrini Olivier , Delpero Jean-Robert , Bréjard Vincent 
Published: April 2019

Abstract
This review aimed to inventory and analyze previous studies regarding quality of life (QoL) and psychological outcomes in relation to pancreatectomy. PubMed and PsycInfo databases were reviewed using the Preferred Reporting Items for Systematic review and Meta-Analysis guidelines. Thirteen studies were selected, 9 of which focused on the QoL after surgery. Quality of life significantly improved 3 to 6 months after surgery. Regarding the postoperative experience, one study reported high fear of recurrence of cancer, whereas another emphasized various expressions of patient needs. One study explained how strategy and ability to adapt are not related to the type, the cause, nor the physical condition, but are mainly influenced by the age and the subjective experience of the patients. A last study showed that depression did not affect survival rate after surgery. Our systematic review found only few studies regarding the psychological condition after pancreatectomy and highlights the need to describe and characterize the patients' psychological characteristics in this setting.
Measurement and Validation of Primary Care Nursing Indicators Based on a Wound Care Tracer Condition
Authors: Dufour Émilie , Duhoux Arnaud , Contandriopoulos Damien 
Published: April 2019

Background:
Access to both valid and reliable nursing-sensitive indicators is currently limited in primary care.

Purpose:
The objectives were to (1) measure primary care nursing indicators using a wound care tracer condition and (2) study the associations between process and outcome indicators.

Methods:
We conducted a longitudinal study in an ambulatory care clinic in Quebec, Canada. The sample included 482 episodes of care. We studied 5 indicators related to processes and 3 to outcomes.

Results:
Performance levels were moderately high for indicators of initial assessment and duration and low for those of continuity and education. Associations between nursing follow-up and continuity indicators and 3 outcome indicators were highly significant.

Conclusion:
Continuity and nursing follow-up are associated with improved outcomes. Increasing these indicators' performance level can improve both nursing processes and patient outcomes.
Pulmonary Alveolar Proteinosis
Authors: Feld Lance , Jennings John , Fiorino Elizabeth K. , Harris Matthew 
Published: April 2019

Abstract
The profoundly hypoxemic child presents an interesting set of diagnostic and management challenges in the pediatric emergency department. While common pathologies including pneumonia, asthma, bronchiolitis, and pneumothoraces are managed using evidence-based algorithms, more enigmatic pathologies may present the treating physician with less diagnostic and therapeutic clarity. We present the case of a profoundly hypoxemic 16-year-old girl who presented in minimal distress, with oxyhemoglobin saturation of 63% on room air.
Current US Guidelines for Prescribing HIV Pre-exposure Prophylaxis (PrEP) Disqualify Many Women Who Are at Risk and Motivated to Use PrEP
Authors: Calabrese Sarah K. , Willie Tiara C. , Galvao Rachel W. , Tekeste Mehrit , Dovidio John F. , Safon Cara B. , Blackstock Oni , Taggart Tamara , Kaplan Clair , Caldwell Abigail , Kershaw Trace S. 
Published: April 2019

Background:
US Centers for Disease Control and Prevention clinical guidelines for HIV pre-exposure prophylaxis (PrEP) are widely used to assess patients' PrEP eligibility. The guidelines include 2 versions of criteria—guidance summary criteria and recommended indications criteria—that diverge in a potentially critical way for heterosexually active women: Both require women's knowledge of their own risk behavior, but the recommended indications also require women's knowledge of their partners' HIV risk or recognition of a potentially asymptomatic sexually transmitted infection. This study examined women's PrEP eligibility according to these 2 different versions of criteria across risk and motivation categories.

Setting/Methods:
HIV-negative women (n = 679) recently engaged in care at Connecticut Planned Parenthood centers were surveyed online in 2017. The survey assessed PrEP eligibility by both versions of Centers for Disease Control and Prevention criteria, HIV risk indicators, PrEP motivation indicators, and sociodemographic characteristics.

Results:
Participants were mostly non-Hispanic white (33.9%) or black (35.8%) and had low income (<$30,000/year; 58.3%). Overall, 82.3% were eligible for PrEP by guidance summary criteria vs. 1.5% by recommended indications criteria. Women disqualified by recommended indications criteria included those reporting condomless sex with HIV-positive or serostatus-unknown male partners (n = 27, 11.1% eligible); 1 or more recent sexually transmitted infection(s) (n = 53, 3.8% eligible); multiple sex partners (n = 168, 3.0% eligible); intended PrEP use (n = 211, 2.8% eligible); and high self-perceived risk (n = 5, 0.0% eligible).

Conclusion:
Current guidelines disqualify many women who could benefit from PrEP and may lead to discrepant assessments of eligibility. Guideline reform is needed to improve clarity and increase women's PrEP access and consequent HIV protection.
Flexor Tendon Reconstruction
Authors: Al-Qattan Mohammad M. 
Published: April 2019

Purpose
In the first stage of flexor tendon reconstruction, a silicon rod is fixed distally to the remnant of the flexor tendon at the distal phalanx. The proximal end of the rod is left free (unsutured) in the distal forearm. Hence, the rod insertion is not expected to result in any active flexion of the finger. The author reports on a case series in which adhesions have occurred between the rod and the adjacent flexor tendons in the distal forearm.

Methods
A retrospective study of 110 patients who underwent 2-stage flexor tendon reconstruction by the author revealed 5 patients in which the fingers were actively moving good enough after the insertion of the silicone rod to the extent that patients refused to undergo the second grafting procedure. Complications, range of motion, strength, and patient satisfaction were documented.

Results
There were no complications related to the surgery or the presence of the rod for several years. Using the Strickland criteria, all patients qualified for a good outcome. Grip strength of the affected hand averaged 85% of the contralateral normal hand, and the pinch strength of the affected finger against the thumb averaged 68% compared with the contralateral side. All patients/parents were satisfied. Ultrasound imaging confirmed the presence of adhesions between the proximal end of the silicone rod and the adjacent flexor tendons.

Conclusions
Our series documents a very unusual “desirable” event following the first-stage flexor tendon reconstruction. The study also documents the lack of silicone rod–related complications on long-term follow-up. The results may also encourage the use of permanent implants in flexor tendon reconstruction.
Surgical Site Infection Risk Factor Analysis in Postbariatric Patients Undergoing Body Contouring Surgery
Authors: Wiser Itay , Plonski Lori , Shimon Nitai , Friedman Tali , Heller Lior 
Published: April 2019

Background
Surgical site infections (SSIs) following body-contouring plastic surgery pose a significant burden on patients and caregivers, possibly leading to undesired surgical outcomes. Surgical site infection incidence following body-contouring plastic surgery ranges from 2% to 7%, but is estimated much higher among postbariatric massive weight loss (MWL) patients.

Objective
The aim of this study was to evaluate SSI rate, risk and protective factors among postbariatric MWL patients following body-contouring plastic surgery.

Methods
This was a nested case-control study of MWL patients who underwent body-contouring plastic surgery at the Department of Plastic Surgery at Assaf Harofeh Medical Center, between 2007 and 2014. Data were obtained from medical records. Surgical site infection was defined according to the Centers for Disease Control and Prevention criteria. Logistic regression was conducted to assess independent risk factors for SSIs.

Results
From a cohort of 172 patients, 86 were included in the study. Surgical site infection rate was 20% (n = 17). Significant SSI risk factors included lifetime maximal weight and lifetime maximal body mass index (P = 0.039 and P = 0.002, respectively), body mass index loss prior to surgery (P = 0.032), estimated blood loss during surgery (P = 0.002), and gynecomastia repair procedure (P = 0.038). Independent SSI-associated factors included thigh lift procedure (odds ratio, 4.66; 95% confidence interval, 1.13–19.28) and preoperative antimicrobial prophylaxis (odds ratio, 0.04; 95% confidence interval, 0.03–0.61).

Conclusions
Although not required by current guidelines for body-contouring plastic surgery, preoperative antimicrobial prophylaxis in our study demonstrated a significant protective effect against SSIs. Further research may reveal its true contribution to SSI prevention in body-contouring plastic surgery.