bluuebunny/crossref_metadata_2025_split huggingface dataset:
bayroot: Bayesian sampling of HIV-1 integration dates by root-to-tip regression
Authors: Ferreira Roux-Cil , Wong Emmanuel , Poon Art F Y 
Published: December 2022

Abstract
The composition of the latent human immunodeficiency virus 1 (HIV-1) reservoir is shaped by when proviruses integrated into host genomes. These integration dates can be estimated by phylogenetic methods like root-to-tip (RTT) regression. However, RTT does not accommodate variation in the number of mutations over time, uncertainty in estimating the molecular clock, or the position of the root in the tree. To address these limitations, we implemented a Bayesian extension of RTT as an R package (bayroot), which enables the user to incorporate prior information about the time of infection and start of antiretroviral therapy. Taking an unrooted maximum likelihood tree as input, we use a Metropolis–Hastings algorithm to sample from the joint posterior distribution of three parameters (the rate of sequence evolution, i.e., molecular clock; the location of the root; and the time associated with the root). Next, we apply rejection sampling to this posterior sample of model parameters to simulate integration dates for HIV proviral sequences. To validate this method, we use the R package treeswithintrees (twt) to simulate time-scaled trees relating samples of actively and latently infected T cells from a single host. We find that bayroot yields significantly more accurate estimates of integration dates than conventional RTT under a range of model settings.
Topical Cannabidiol in the Treatment of Digital Ulcers in Patients with Scleroderma: Comparative Analysis and Literature Review
Authors: Spinella Amelia , de Pinto Marco , Baraldi Carlo , Galluzzo Claudio , Testoni Sofia , Lumetti Federica , Parenti Luca , Guerzoni Simona , Salvarani Carlo , Giuggioli Dilia 
Published: December 2022

ABSTRACT

OBJECTIVE
To explore the effect of topical cannabidiol (CBD) in treating digital ulcers in patients with systemic sclerosis (SSc).

METHODS
In total, 45 patients with SSc who had digital ulcers were consecutively enrolled between January 2019 and December 2019. Of the participants, 25 were treated with CBD during surgical debridement and 20 were treated with standard local therapy. A numeric rating scale for pain and Health Assessment Questionnaire Disability Index were administered at the baseline and at the end of treatment.

RESULTS
Local treatment with CBD was significantly associated with lower pain scores, higher health assessment scores, and an increase in participants’ total hours of sleep. Patients in the control group more frequently required additional analgesic therapy.

CONCLUSIONS
Topical CBD may be a valuable tool to treat pain related to digital ulcers in patients with SSc.
Wound Infection Detection Using a Rapid Biomarker
Authors: Kordestani Soheila S. , Mohammadi Fahimeh S. , Noordadi Maryam , Rezaee Fatemeh , Fayyazbakhsh Fatemeh 
Published: December 2022

ABSTRACT

OBJECTIVE
To evaluate the performance of a rapid, point-of-care diagnostic biomarker that is sensitive to overexpression of gelatinases, the major expressed biomolecules during wound infection. Wound exudate composition and pH are key determinants of infection, and rapid infection detection has an important role in wound healing.

METHODS
The biomarker was first investigated for cytotoxic effects, and irritation and sensitization tests were carried out. The biomarker was then tested on 198 patients suffering from different types of wounds. Data including age, sex, wound type, depth, site, etiology, and exudate pH were collected. Wound pH was measured to determine if it could be a possible early indicator of infection, and bacterial wound cultures were performed as a control.

RESULTS
Analysis revealed that the biomarker had no cytotoxicity and caused no erythema, edema, or other adverse response. The rapid diagnostic biomarker demonstrated overall clinical sensitivity, specificity, accuracy, positive predictive value, and negative predictive value: 96.84%, 97.5%, 96.96%, 99.35%, and 88.63%, respectively. Moreover, infected wounds had higher pH values according to culture results and nearly 80% of chronic, nonhealing wounds were infected.

CONCLUSIONS
This biomarker enables caregivers to detect wound infection in a timely manner and treat it efficiently. Wound pH monitoring may potentially be a useful method for indicating the presence or absence of infection.
Effect of a Team Approach to Pressure Injury Management over 5 Years in a Tertiary Hospital
Authors: Kim Min Ji , Jeong Yon Soo , Kim Hee Joung , Hahn Hyung Min , Thai Duy Quang , Lee Il Jae 
Published: December 2022

ABSTRACT

OBJECTIVE
The authors’ facility established a novel integrated wound care team (IWCT), which included the implementation of a strict treatment algorithm by the patients’ attending providers and a specialized wound care team led by a plastic surgeon. Investigators then retrospectively analyzed clinical outcomes of pressure injury (PI) management by the IWCT over 5 years.

METHODS
The authors performed a retrospective chart review and periodic statistical analysis of the data for all patients with PI referred to the IWCT in the authors’ center from May 2015 to April 2019. Data including patients’ demographic information, first and last consultation dates, referring department, PI stage, site of PI, and Braden Scale scores were collected and analyzed.

RESULTS
Patients (N = 15,556) did not differ significantly in age, sex, or Braden Scale score. A preimplementation/postimplementation analysis of PI data before and after establishing the IWCT showed that the incidence of stage 3 or 4 PIs had significantly decreased during the study period (19.1% vs 15.2%, P < .05). Conversely, the incidence of stage 1 PIs significantly increased in the same period (38.0% vs 57.4%, P < .05). The proportion of completely healed PIs also increased, and the median treatment period was significantly shortened (P < .05).

CONCLUSIONS
Implementation of the IWCT in a tertiary hospital setting led to a significant increase in early-stage PI detection and a decrease in severe PIs.
Patient-centered Outcomes for Individuals with a Venous Leg Ulcer: A Scoping Review
Authors: Lazar Michelle , Ershadi Sherry , Bolton Laura , Phillips Tania 
Published: December 2022

ABSTRACT

GENERAL PURPOSE
To summarize randomized clinical trials addressing patient-centered outcomes of individuals with a venous leg ulcer.

TARGET AUDIENCE
This continuing education activity is intended for physicians, physician assistants, nurse practitioners, and nurses with an interest in skin and wound care.

LEARNING OBJECTIVES/OUTCOMES
After participating in this educational activity, the participant will:
1. Summarize the results of the review of randomized controlled trials addressing patient-centered outcomes of individuals with a venous leg ulcer.
2. Identify the limitations of the research analyzed for the review.

OBJECTIVE
To summarize randomized clinical trials addressing patient-centered outcomes of individuals with a venous leg ulcer with a scoping review.

DATA SOURCES
Authors searched PubMed using MESH terms for “venous ulcer” AND “randomized” for randomized clinical trials published from January 2002 to October 2021 that explored content-validated patient-centered outcomes for individuals with a clinically diagnosed venous leg ulcer. Authors also searched Cochrane Reviews from inception to April 15, 2022 for additional references using the same MESH terms.

STUDY SELECTION
Studies in any setting were included if primary or secondary outcomes were venous ulcer-related mobility, pain or analgesic use, healing, infection, quality of life (including odor, social isolation, depression), amputation, or patient-level costs of treatment. Preclinical or nonrandomized clinical studies or those without venous leg ulcers were excluded.

DATA EXTRACTION
Authors tabulated interventions studied, numbers of patients treated per group, risk of delayed ulcer healing, and statistical significance of comparisons of 485 qualifying articles in Google Sheets.

DATA SYNTHESIS
Authors graphically represented and tabulated frequencies of studies addressing patient-centered outcomes of individuals with venous ulcers. Studies mainly reported effects of compression, dressings, topical antimicrobials, or systemic therapy on patient healing or pain outcomes. Related ischemia, ultrasonography, or risk factors for delayed healing were not consistently reported, inflating variability of outcomes and decreasing consistency of differences reported.

CONCLUSIONS
Research is needed on the mobility, amputation risk, infection risk, quality of life, and healthcare costs of patients with venous ulcers. Promising interventions include grafts, exercise, analgesics, electrical modalities, negative pressure, or vascular interventions. Consistently reporting each patient’s baseline ischemia and vascular condition would improve relevance.
Outcomes of a Peer Mentoring Circle: An Innovation to Improve Academic Physician Career Advancement in a Community Hospital Setting
Authors: Kaushik Ruchi , McCallin Tracy , Sedillo Daniel J. , Wolfe Adam D. 
Published: December 2022

Problem
Faculty retention is a prominent topic in academic medicine. Investment in faculty career development supports faculty vitality, advancement, and retention. Academic physicians in community-based settings far from their academic affiliate may find identifying local career advancement mentorship challenging.

Approach
In June 2018, a career advancement in-service day at The Children’s Hospital of San Antonio and Baylor College of Medicine in Houston was convened to design a peer mentoring circle (PMC). Using self-determination theory, this program aimed to help PMC members develop goals; schedule and attend regular meetings; format, review, and critique member curricula vitae and portfolios; and hold one another accountable to submitting award and promotion applications.

Outcomes
Eleven inaugural PMC cohort members attended regular monthly meetings from July 2018 to June 2019 (median, 6 members per meeting). All members were competent in accessing the PMC repository of materials. Statistically significant improvement (P < .01) was seen in self-reported knowledge and skills relevant to award or academic promotion support and resources. Compared with no patient care or teaching awards and 1 academic promotion among non-PMC faculty, 5 PMC members (45.5%) earned a patient care award, 4 (36.4%) earned a teaching award, and 5 of 10 faculty members (50.0%) achieved academic promotion (P < .001 for all). On the retrospective pre–post survey, members endorsed several PMC strengths, including personal and emotional support, professional support, and accountability.

Next Steps
Next steps include establishing a local faculty development office, convening a second cohort, revising evaluation methods, expanding membership, and offering 1-on-1 career counseling. Community-based academicians who aim to replicate this program should organize a career advancement and faculty development in-service day, identify local faculty members to manage meetings, retain a repository of resources, set deadlines and hold one another accountable to them, and celebrate achievements and support one another in failure.
Respiratory Effects of Biased Ligand Oliceridine in Older Volunteers: A Pharmacokinetic–Pharmacodynamic Comparison with Morphine
Authors: Simons Pieter , van der Schrier Rutger , van Lemmen Maarten , Jansen Simone , Kuijpers Kiki W.K. , van Velzen Monique , Sarton Elise , Nicklas Todd , Michalsky Cathy , Demitrack Mark A. , Fossler Michael , Olofsen Erik , Niesters Marieke , Dahan Albert 
Published: December 2022

Background
Oliceridine is a G protein–biased µ-opioid, a drug class that is associated with less respiratory depression than nonbiased opioids, such as morphine. The authors quantified the respiratory effects of oliceridine and morphine in elderly volunteers. The authors hypothesized that these opioids differ in their pharmacodynamic behavior, measured as effect on ventilation at an extrapolated end-tidal Pco
2 at 55 mmHg, V̇E55.

Methods
This four-arm double-blind, randomized, crossover study examined the respiratory effects of intravenous 0.5 or 2 mg oliceridine and 2 or 8 mg morphine in 18 healthy male and female volunteers, aged 55 to 89 yr, on four separate occasions. Participants’ CYP2D6 genotypes were determined, hypercapnic ventilatory responses were obtained, and arterial blood samples were collected before and for 6 h after treatment. A population pharmacokinetic–pharmacodynamic analysis was performed on V̇E55, the primary endpoint; values reported are median ± standard error of the estimate.

Results
Oliceridine at low dose was devoid of significant respiratory effects. High-dose oliceridine and both morphine doses caused a rapid onset of respiratory depression with peak effects occurring at 0.5 to 1 h after opioid dosing. After peak effect, compared with morphine, respiratory depression induced by oliceridine returned faster to baseline. The effect-site concentrations causing a 50% depression of V̇E55 were 29.9 ± 3.5 ng/ml (oliceridine) and 21.5 ± 4.6 ng/ml (morphine), the blood effect-site equilibration half-lives differed by a factor of 5: oliceridine 44.3 ± 6.1 min and morphine 214 ± 27 min. Three poor CYP2D6 oliceridine metabolizers exhibited a significant difference in oliceridine clearance by about 50%, causing higher oliceridine plasma concentrations after both low- and high-dose oliceridine, compared with the other participants.

Conclusions
Oliceridine and morphine differ in their respiratory pharmacodynamics with a more rapid onset and offset of respiratory depression for oliceridine and a smaller magnitude of respiratory depression over time.

Editor’s Perspective

What We Already Know about This Topic

What This Article Tells Us That Is New
Extended-age Out-of-sample Validation of Risk Stratification Index 3.0 Models Using Commercial All-payer Claims
Authors: Greenwald Scott , Chamoun George F. , Chamoun Nassib G. , Clain David , Hong Zhenyu , Jordan Richard , Manberg Paul J. , Maheshwari Kamal , Sessler Daniel I. 
Published: December 2022

Background
The authors previously reported a broad suite of individualized Risk Stratification Index 3.0 (Health Data Analytics Institute, Inc., USA) models for various meaningful outcomes in patients admitted to a hospital for medical or surgical reasons. The models used International Classification of Diseases, Tenth Revision, trajectories and were restricted to information available at hospital admission, including coding history in the previous year. The models were developed and validated in Medicare patients, mostly age 65 yr or older. The authors sought to determine how well their models predict utilization outcomes and adverse events in younger and healthier populations.

Methods
The authors’ analysis was based on All Payer Claims for surgical and medical hospital admissions from Utah and Oregon. Endpoints included unplanned hospital admissions, in-hospital mortality, acute kidney injury, sepsis, pneumonia, respiratory failure, and a composite of major cardiac complications. They prospectively applied previously developed Risk Stratification Index 3.0 models to the younger and healthier 2017 Utah and Oregon state populations and compared the results to their previous out-of-sample Medicare validation analysis.

Results
In the Utah dataset, there were 55,109 All Payer Claims admissions across 40,710 patients. In the Oregon dataset, there were 21,213 admissions from 16,951 patients. Model performance on the two state datasets was similar or better than in Medicare patients, with an average area under the curve of 0.83 (0.71 to 0.91). Model calibration was reasonable with an R
2 of 0.93 (0.84 to 0.97) for Utah and 0.85 (0.71 to 0.91) for Oregon. The mean sensitivity for the highest 5% risk population was 28% (17 to 44) for Utah and 37% (20 to 56) for Oregon.

Conclusions
Predictive analytical modeling based on administrative claims history provides individualized risk profiles at hospital admission that may help guide patient management. Similar predictive performance in Medicare and in younger and healthier populations indicates that Risk Stratification Index 3.0 models are valid across a broad range of adult hospital admissions.

Editor’s Perspective

What We Already Know about This Topic

What This Article Tells Us That Is New
Prevalence of Unhealthy Substance Use and Associated Characteristics Among Patients Presenting for Surgery
Authors: Fernandez Anne C. , Waljee Jennifer F. , Gunaseelan Vidhya , Brummett Chad M. , Englesbe Michael J. , Bicket Mark C. 
Published: December 2022

Objective:
To assess the prevalence of and identify characteristics associated with unhealthy use before surgery.

Background:
Although the escalation in US drug overdose deaths is apparent, the unhealthy use of substances among patients presenting for surgery is unclear.

Methods:
We conducted a retrospective study of patients presenting for elective surgical procedures between December 2018 and July 2021 and prospectively recruited to 1 of 2 clinical research studies (Michigan Genomics Initiative, Prevention of Iatrogenic Opioid Dependence after Surgery Study). The primary outcome was unhealthy substance use in the past 12 months as determined using the Tobacco, Alcohol, Prescription medication, and other Substance use tool.

Results:
Among 1912 patients, unhealthy substance use was reported in 768 (40.2%). The most common substances with unhealthy use were illicit drugs [385 (20.1%)], followed by alcohol 358 (18.7%)], tobacco [262 (13.7%)], and prescription medications [86 (4.5%)]. Patients reporting unhealthy substance use were significantly more likely to be younger, male [aOR: 1.95 (95% CI, 1.58–2.42)], and have higher scores for pain [aOR: 1.07 (95% CI, 1.02–1.13)], and anxiety [aOR: 1.03 (95% CI, 1.01–1.04)]. Unhealthy substance use was more common among surgical procedures of the forearm, wrist, and hand [aOR: 2.58 (95% CI, 1.01–6.55)].

Conclusions:
As many as 2 in 5 patients in the preoperative period may present with unhealthy substance use before elective surgery. Given the potential impact of substance use on surgical outcomes, increased recognition of the problem by screening patients is a critical next step for surgeons and perioperative care teams.
Characterizing the Impact of Procedure Funding on the Covid-19 Generated Procedure Gap in Ontario: A Population-Based Analysis
Authors: Gomez David , de Mestral Charles , Stukel Therese A. , Irish Jonathan , Simpson Andrea N. , Wilton Andrew S. , Rotstein Ori D. , Campbell Robert J. , Eskander Antoine , Urbach David R. , Baxter Nancy N. 
Published: December 2022

Background:
Surgical procedures in Canada were historically funded through global hospital budgets. Activity-based funding models were developed to improve access, equity, timeliness, and value of care for priority areas. COVID-19 upended health priorities and resulted in unprecedented disruptions to surgical care, which created a significant procedure gap. We hypothesized that activity-based funding models influenced the magnitude and trajectory of this procedure gap.

Methods:
Population-based analysis of procedure rates comparing the pandemic (March 1, 2020–December 31, 2021) to a prepandemic baseline (January 1, 2017–February 29, 2020) in Ontario, Canada. Poisson generalized estimating equation models were used to predict expected rates in the pandemic based on the prepandemic baseline. Analyses were stratified by procedure type (outpatient, inpatient), body region, and funding category (activity-based funding programs vs. global budget).

Results:
In all, 281,328 fewer scheduled procedures were performed during the COVID-19 period compared with the prepandemic baseline (Rate Ratio 0.78; 95% CI 0.77–0.80). Inpatient procedures saw a larger reduction (24.8%) in volume compared with outpatient procedures (20.5%). An increase in the proportion of procedures funded through activity-based programs was seen during the pandemic (52%) relative to the prepandemic baseline (50%). Body systems funded predominantly through global hospital budgets (eg, gynecology, otologic surgery) saw the least months at or above baseline volumes, whereas those with multiple activity-based funding options (eg, musculoskeletal, abdominal) saw the most months at or above baseline volumes.

Conclusions:
Those needing procedures funded through global hospital budgets may have been disproportionately disadvantaged by pandemic-related health care disruptions.
Evaluation of Triglyceride-Glucose Index as a Marker for Severity in New Onset Diabetes in Patients of COVID-19 Pneumonia- a Single Center Study
Authors: Ashraf Faiza , Mehmood Majid , Aurang Zeb Mohammad , Rehman Jehanzeb ur , Siddiqui Fariha Masood 
Published: December 2022

IntroductionSevere Acute Respiratory Syndrome Coronavirus-2 (SARS CoV 2) Covid-19 is responsible for the pandemic affecting the world population since 2019. Starting from Wuhan, China enveloped the globe within a few months. It affected the healthy population, but played havoc in terms of mortality and morbidity for old and diseased populations. Diabetes is a known condition putting patients at high risk of complications, resulting from metabolic syndrome-derived impaired immune responses. The world is still grappling with the challenge of managing diabetic patients with covid pneumonia and newly added Diabetics resulting from post covid complications driven by Covid-19-induced damage to pancreatic beta cells. Resulting in worsening of existing Diabetic control and new onset Diabetes (NOD) in susceptible individuals. The TYG (Triglyceride-Glucose Index) may serve as a marker to identify patients at risk of developing a serious illnessHypothesisTriglyceride Glucose Index is a marker for severity of Covid-19 and new onset of diabetes.Aim To evaluate role of TYG index in prediction of new onset of Diabetes mellitus in Covid-19 patients and as a marker for disease severity in diabetic Covid-19 patients.MethodologyThis cross-sectional study was carried out in Combined Military Hospital (CMH) Rawalakot. Covid-19 patients' diagnosis was confirmed by RT-PCR. Glycosylated hemoglobin (HBA1c), fasting glucose and Triglycerides (TG) were performed at the biochemistry lab using SELECTRA chemical analyzer. TYG index was calculated and related with clinical symptoms of patients.ResultsA total of 2974 samples has been tested by RT-PCR. Three hundred and ninety-three (13%) were positive for COVID-19 infection. Twenty-one patients (5%) developed new-onset Diabetes (NOD) during the COVID infection. A TYG index of 43 people affected with COVID-19 (21 NOD and 22 non-diabetic individuals (control group) was calculated as a marker of severity index. It was found that the higher TYG was associated with severity and mortality in patients with COVID-19 diabetes. ConclusionCovid-19 infection is associated with worsening disease in preexisting diabetic patients and is responsible for new-onset Diabetes in patients. TYG index correlates directly with the severity of Covid-19. TYG index can be used as a predictor marker for mortality and morbidity in Covid-19.