MaLAdapt Reveals Novel Targets of Adaptive Introgression From Neanderthals and Denisovans in Worldwide Human Populations.

Adaptive introgression (AI) facilitates local adaptation in a wide range of species. Many state-of-the-art methods detect AI with ad-hoc approaches that identify summary statistic outliers or intersect scans for positive selection with scans for introgressed genomic regions. Although widely used, approaches intersecting outliers are vulnerable to a high false-negative rate as the power of different methods varies, especially for complex introgression events. Moreover, population genetic processes unrelated to AI, such as background selection or heterosis, may create similar genomic signals to AI, compromising the reliability of methods that rely on neutral null distributions. In recent years, machine learning (ML) methods have been increasingly applied to population genetic questions. Here, we present a ML-based method called MaLAdapt for identifying AI loci from genome-wide sequencing data. Using an Extra-Trees Classifier algorithm, our method combines information from a large number of biologically meaningful summary statistics to capture a powerful composite signature of AI across the genome. In contrast to existing methods, MaLAdapt is especially well-powered to detect AI with mild beneficial effects, including selection on standing archaic variation, and is robust to non-AI selective sweeps, heterosis from deleterious mutations, and demographic misspecification. Furthermore, MaLAdapt outperforms existing methods for detecting AI based on the analysis of simulated data and the validation of empirical signals through visual inspection of haplotype patterns. We apply MaLAdapt to the 1000 Genomes Project human genomic data and discover novel AI candidate regions in non-African populations, including genes that are enriched in functionally important biological pathways regulating metabolism and immune responses.

A Systematic Review of Partner Satisfaction After Penile Prosthesis with Special Emphasis on LGBTQ + Populations.

PURPOSE OF REVIEW: Despite the current surgical advances and patients' satisfactions after penile prosthesis (PP) implantation, there has been paucity of data on reported partner satisfaction and their quality-of-life (QoL). Our objective was to summarize the current literature on partner satisfaction for both heterosexual and non-heterosexual populations, respectively. We specifically conducted a systematic review according to the Cochrane and Preferred Reporting Items for Systematic Reviews and Meta-Analyses (PRISMA) standards, and stratified studies into three tiers by methodological rigor. RECENT FINDINGS: After an initial search of 172 articles, 33 studies met the inclusion criteria for the final review: 30 for heterosexual partner satisfaction, and 3 for LGBTQ patient satisfaction were included due to lack of published literature on partner satisfaction for LGBTQ patients. For heterosexual partner satisfaction, 10 studies were classified as Tier 1, 11 studies were classified as Tier 2, and 9 studies were classified as Tier 3. From an initial search of 13 records, three studies consisting of 272 patients met the inclusion criteria for our LGBTQ review. Across all the tiers, studies noted satisfaction rates between 50 and 90% and improved satisfaction and sexual QoL metrics compared to pre-surgery rates. That said, partner satisfaction rates were also consistently lower than patient satisfaction rates. Although the range of evidence quality varies, the available literature suggests significant improvements in and relatively high rates of partner satisfaction after PP implantation. Given the diversity of study designs and widespread use of non-validated or non-specific questionnaires in the current literature, future research should focus on prospective studies and/or data collection using validated, PP-specific questionnaires.

Racial discrimination moderates associations between sociopolitical discussions and internalizing problems among racially minoritized college students.

OBJECTIVE: The present study investigated whether associations between sociopolitical discussions and mental health differed by racial discrimination among racially minoritized college students. We also tested whether associations differed between election years-when sociopolitical discussions may be more frequent-and nonelection years. METHOD: In November 2020, racially minoritized college students (N = 225; Mage = 19.84, SD = 1.41; 72.89% female; 52.00% Asian, 22.67% Latino, 16.00% multiracial, 9.33% races including Black and Middle Eastern) reported how often they had experienced racial discrimination, their frequency of sociopolitical discussions with friends and family, and their mental health. RESULTS: Results indicated that participants who had more frequent sociopolitical discussions with friends-but not family-only reported more internalizing problems if they had never or rarely experienced racial discrimination in the past year. To determine whether results were unique to discussions during election years, a second sample (N = 262; Mage = 20.18, SD = 2.30; 82.53% female; 48.86% Asian, 18.56% Latino, 15.42% multiracial, 17.78% races including Black and Middle Eastern) was recruited 1 year later, and racial discrimination did not moderate associations between sociopolitical discussions and internalizing problems. CONCLUSIONS: Sociopolitical discussions with friends during presidential elections may be related to greater internalizing problems for racially minoritized college students who experience racial discrimination less frequently, potentially because they may feel less prepared or less motivated to have these conversations compared to racially minoritized college students who experience racial discrimination more frequently. Future studies should investigate means of promoting sociopolitical discussions on campus while attenuating the association between sociopolitical discussions and internalizing problems. (PsycInfo Database Record (c) 2023 APA, all rights reserved).

Laryngeal and pharyngeal actinomycosis: a systematic review and report of 3 cases.

INTRODUCTION: Actinomycosis is a granulomatous infection that rarely involves the larynx or pharynx. Three cases of actinomycosis of the larynx or pharynx from our institution were reviewed and a systematic literature review was performed to better define surgical management, antibiotic therapy, risk factors, and incidence of recurrence or complications. MATERIALS AND METHODS: PubMed/Medline, Cochrane, Embase, and Google Scholar were searched on November 30, 2021 using the terms "laryngeal actinomycosis", "pharyngeal actinomycosis", "actinomycosis AND larynx", and "actinomycosis AND pharynx." Articles which did not describe appropriate sites or were non-English were excluded. Results were collected for demographic information, site(s) of infection, comorbidities, lesion characteristics and treatments. RESULTS: Along with three cases reported from our institution, 40 unique cases were reviewed from 37 studies for a total of 43 patients (Table 1). 34 (81.0 %) of the patients were male with the highest incidence of infection in the seventh decade (54.8 %). The most common site for the infection was the larynx (69.0 %) followed by the pharynx (16.7 %). Risk factors included a history of radiation therapy, immunosuppression, inhalational irritant, and diabetes (Table 3). The duration of antibiotic therapy varied greatly, from one month to one year and total follow up ranged from 1 month to 2.5 years (Table 1). CONCLUSIONS: A comprehensive review of the literature on pharyngolaryngeal actinomycosis shows that this infection has increased prevalence within the head and neck cancer patient population. Similar to cervicofacial actinomycosis, these atypical sites have shown favorable responses to extended antibiotic therapy and generally do not require aggressive surgical management.

Normothermia to Decrease Surgical Site Infection Risk: Silver Bullet or Fool's Gold? A Retrospective Cohort Study.

PURPOSE: Surgical site infection (SSI) is the leading cause of nosocomial infections among surgical patients in the United States. Currently, there is compelling evidence suggesting that temperature dysregulation in surgical patients may be a risk factor for the development of SSI. We examined the relationship between perioperative hypothermia (PH) and SSI in a population of surgical patients with diabetes mellitus (DM). METHODS: This retrospective cohort review was conducted on patients with a history of DM undergoing orthopaedic surgery at our institution between May 1, 2018, and April 1, 2022. Inclusion criteria were age older than 15 years, a history of DM or recent hemoglobin A1c concentration of ≥6.5%, and operation of at least 60 minutes under general anesthesia. Perioperative hypothermia was defined as an intraoperative temperature ≤ 35.5°C. Continuous variables were compared using the t-test and Wilcoxon rank-sum test. Categorical variables were compared using the chi-squared test. We constructed a multivariable logistic regression model to estimate SSI risk while controlling for demographic variables. RESULTS: A total of 236 patients were included in the final analysis. The overall incidence of SSI was 5.93%. 99 patients (42%) experienced PH. No difference was observed in the risk of SSI between the normothermic and hypothermic cohorts. Among the 99 patients who experienced PH, increasing HbA1c was associated with increasing risk of SSI (OR = 2.39, 95% CI = 1.12 to 5.32, P-value = 0.0222). The multivariable logistic regression model had good discriminatory ability (c-statistic 0.74, 95% CI: 0.61 to 0.89) and good predictive accuracy (sensitivity 64%, specificity 73%). DISCUSSION: PH is not an independent risk factor of SSI. However, in the presence of elevated HbA1c, PH may more than double the risk of SSI. Perioperative hypothermia may be an additive risk factor in the setting of poor glycemic control and potentially in the setting of other known risk factors.

Testosterone replacement therapy in patients with cachexia: a contemporary review of the literature.

INTRODUCTION: Patients with long-term chronic illnesses frequently present with hypogonadism, which is primarily managed through exogenous testosterone. These same patients also experience a high degree of cachexia, a loss of skeletal muscle and adipose tissue. OBJECTIVE: To perform a contemporary review of the literature to assess the effectiveness of testosterone replacement therapy (TRT) for managing chronic disease-associated cachexia. METHODS: We performed a PubMed literature search using MeSH terms to identify studies from 2000 to 2022 on TRT and the following cachexia-related chronic medical diseases: cancer, COPD, HIV/AIDS, and liver cirrhosis. RESULTS: From the literature, 11 primary studies and 1 meta-analysis were selected. Among these studies, 3 evaluated TRT on cancer-associated cachexia, 3 on chronic obstructive pulmonary disease, 4 on HIV and AIDS, and 2 on liver cirrhosis. TRT showed mixed results favoring clinical improvement on each disease. CONCLUSIONS: Cachexia is commonly observed in chronic disease states. Its occurrence with hypogonadism, alongside the shared symptoms of these 2 conditions, points toward the management of cachexia through the administration of exogenous testosterone. Robust data in the literature support the use of testosterone in increasing lean body mass, improving energy levels, and enhancing the quality of life for patients with chronic disease. However, the data are variable, and further studies are warranted on the long-term efficacy of TRT in patients with cachexia.

Industry Payments to Urologists and Urologic Advanced Practice Providers in 2021.

OBJECTIVE: To compare industry payments from drug and medical device companies to urologists and urologic advanced practice providers (APPs) in 2021. METHODS: We used the 2020 Medicare Data on Provider Practice and Specialty file to identify single-specialty urology practices, defined as those where the majority of physicians were urologists. We then used the Open Payments Program Year 2021 data to summarize the value and number of industry payments to urologists and APPs, including nurse practitioners and physician assistants, in these practices. We calculated the total value and number of payments and median total value and number of payments per provider for urologists and urologic APPs. RESULTS: We identified 4418 urologists and 1099 APPs working in single-specialty urology practices in 2021 (Table 1). Of these, 3646 (87%) urologists received at least one industry payment, totaling $14,755,003 from 116,039 payments, and 954 urologic APPs (87%) received at least one industry payment, including 463 nurse practitioners (85%), totaling $401,283 from 13,035 payments, and 491 physician assistants (89%), totaling $543,429 from 14,626 payments. We observed significantly greater median total value and number of payments per provider for urologists ($620 and 24 payments) compared to urologic APPs ($473 and 21 payments; P < .001 and P = .017, respectively). CONCLUSION: A similar percentage of urologists and urologic APPs received industry payments in 2021. While urologists received a higher total number and total value of payments in 2021, urologic APPs were a common target of industry marketing payments.

Advice and perspectives from navigating the couples match in otolaryngology: A qualitative pilot study.

Introduction: There is a lack of qualitative analysis of the personal experiences within Couples Matching. In this qualitative study, we aim to record personal attitudes, reflections, and advice on experiences with the Couples Match process. Methods: Our survey, consisting of two open-ended questions regarding the experience of Couples Matching, was distributed from January 2022 to March 2022 via email to 106 otolaryngology program directors across the nation. Survey responses were analyzed iteratively using the constructivist grounded theory to construct themes related to pre-match priorities, match-related stressors, and post-match satisfaction. Themes were developed inductively and refined iteratively as the dataset evolved. Results: 18 Couples Match residents responded. In response to the first question: "What was the most difficult part of the process for you and/or your partner?", we identified the following themes: cost and financial burden, increased stress on the relationship, sacrificing top choices, and finalizing the match list. In response to the second question: "Using your experience as a previous applicant, what advice would you give to another couple planning on couples matching?", we identified four common themes: compromise, advocacy, dynamic conversations, and applying broadly. Conclusion: We sought to understand the Couples Match process through the perspective of previous applicants. Analyzing the views and attitudes of Couples Match applicants, our study captures the most challenging aspects of the experience and highlights possible areas to improve advising for couples, including important factors to consider when applying, ranking, and interviewing.

Evaluation of Industry Payments to US Advanced Practice Clinicians in 2021.

Importance: Advanced practice clinicians (APCs) are a growing part of the US health care system, and their financial relationships with pharmaceutical and medical device companies have not been well studied. Objectives: To examine the value, frequency, and types of payments made to APCs and the association of state scope-of-practice laws with these payments. Design, Setting, and Participants: This cross-sectional study used 2021 Open Payments Program data to analyze payments from pharmaceutical or medical device companies to physicians or APCs between January 1 and December 31, 2021. Doctors of medicine and osteopathy were categorized as physicians, and nurse practitioners, physician assistants, clinical nurse specialists, certified registered nurse anesthetists, certified nurse midwives, and anesthesiologist assistants as APCs. Main Outcomes and Measures: The total value and total number of payments were calculated in aggregate and per clinician for each type of APC, all APCs, and physicians. These calculations were repeated by submitting manufacturer, form of payment, nature of payment, and state scope-of-practice law for nurse practitioners, physician assistants, and physicians. Results: A total of 412 000 physicians and 232 000 APCs collectively received $1.99 billion in payments from industry in 2021, of which APCs received $121 million (6.1%). The median total value of payments per clinician for physicians was $167 (IQR, $45-$712) and for APCs was $117 (IQR, $33-$357). The median total number of payments per clinician was equal for physicians and APCs (n = 4). The most common payments to APCs included food and beverage ($69 million [57.6%]), compensation for services other than consulting ($32 million [26.4%]), and consulting fees ($8 million [6.6%]). Advanced practice clinicians in states with the most restrictive scope-of-practice laws received 15.9% lower total value of payments than those in the least restrictive states (P = .002). Physician assistants received 7.6% (P = .005) higher value and 18.1% (P < .001) greater number of payments than nurse practitioners. Conclusions and Relevance: In this cross-sectional study, 232 000 APCs collectively received $121 million in industry payments in 2021. The frequency of industry interactions with APCs was similar to that for physicians, but the average value was lower. The greater value of payments to APCs who practice in states with the least restrictive scope-of-practice laws suggests that industry payments may be related to clinician autonomy.

Growth of for-profit involvement in emergency medicine graduate medical education and association between for-profit affiliation and resident salary.

Background: Following projections of an emergency medicine (EM) physician oversupply, the growth of EM residency programs affiliated with for-profit hospitals has been subject to increased attention and speculation. However, essentially no literature exists regarding these programs. Resident pay is one area where these programs could differ from nonprofit-affiliated programs, as investor obligations could make for-profit corporations more likely to reduce resident salaries to increase profit margins. Here, we aim to quantify the growth of EM for-profit affiliated residency programs from 2001-2021 and determine if PGY1 salaries differ between these program types. Methods: Medicare and ACGME accreditation data were used to determine the profit status of hospitals affiliated with EM residency programs. ACGME new accreditation data from 2001-2021 were used to quantify the growth of both for-profit and nonprofit affiliated programs over this period. We searched program websites and called programs to determine 2021-2022 PGY1 salary. Multiple regression was used to model the relationship between profit status and salary using program characteristic covariates to control for confounding variables. Results: The number of EM programs increased from 117 to 276 from 2001-2021 while the number of for-profit affiliated EM residency programs increased from 1 to 29 during this period. Most (85.7%, [24/29]) for-profit affiliated programs were accredited from 2016-2021. Mean for-profit affiliated program salary ($55,658, n  = 24) was $3840 lower than mean nonprofit affiliated program salary ($59,498, n  = 203). For-profit affiliation was a significant predictor of lower 2021-2022 PGY1 salary after controlling for other program characteristics using multiple regression ( ß  = -1919.88, P = 0.010). Conclusions: We found a substantial growth of newly ACGME accredited for-profit affiliated EM residency programs from 2016-2021. We also found for-profit affiliated programs pay lower PGY1 salaries than nonprofit-affiliated programs after controlling for potential confounding variables, which suggests more oversight over the salary determination process could be necessary to prevent resident underpayment.

Advanced Practice Providers and Wait Times in Urology Offices: A Secret Shopper Study.

INTRODUCTION: Advanced practice providers (APPs), such as nurse practitioners and physician assistants, are a growing part of urology practices. However, the impact of APPs on improving new patient access in urology is unknown. We examined the impact of APPs on new patient wait times in a real-world sample of urology offices. METHODS: Research assistants posing as caretakers called urology offices in the Chicago metropolitan area and attempted to schedule a new patient appointment for an elderly grandparent with gross hematuria. Appointments were requested with any available provider: physician or APP. Descriptive measurements of clinic characteristics were reported and differences in appointment wait times were determined using negative binomial regressions. RESULTS: Of the 86 offices with which we scheduled appointments, 55 (64%) employed at least 1 APP but only 18 (21%) allowed for new patient appointments with APPs. When requested for the earliest appointment regardless of provider type, offices with APPs could offer shorter wait times compared to physician-only offices (10 vs 18 days; p=0.09). Initial appointments with an APP were available with a significantly shorter wait than those with a physician (5 days vs 15 days; p=0.04). CONCLUSIONS: Urology offices are commonly employing APPs but giving them a limited role in new patient visits. This suggests that offices with APPs may have an unrealized opportunity to improve new patient access. Further work is needed to better elucidate the role of APPs in these offices and how they might best be deployed.

Association between Industry Payments and Published Position on Use of Devices for the Treatment of Lower Urinary Tract Symptoms.

OBJECTIVE: To determine the impact of industry payments to authors of opinion articles on the Urolift and Rezum devices. We also examined the extent to which authors omitted acknowledgements of financial conflicts-of-interest. METHODS: We searched Google Scholar for all articles that cite either of the respective pivotal trials for these devices. 2 blinded urologists coded the articles as favorable or neutral. A separate blinded researcher recorded industry payments from the manufacturers using the Open Payments Program database. RESULTS: We identified 29 articles written by 27 unique authors from an initial screening list of 235 articles. Of these articles, 15 (52%) were coded as positive and 14 (48%) were coded as neutral. 20 (74%) authors have accepted payments from the manufacturer of the device. Since 2014, these authors have collectively received $270,000 from NeoTract and $314,000 from Boston Scientific. Of the 20 authors with payments, 9 (45%) received more than $10,000 from either manufacturer. Of authors with payments, 65% (13/20) contributed to only positive articles. Authors who received payments had more than 4 times the number of article contributions than did authors without payments (42 vs 10). Authors of at least one favorable article were more likely to have received payments from the device manufacturers than authors of neutral articles (P = .014, Chi-squared test). Most (80%, 16/20) authors with payments did not report a relevant conflict-of-interest within any of their articles. CONCLUSION: These data suggest a relationship between payments from a manufacturer and positive published position on that company's device. There may be a critical lack of published editorial pieces by authors without financial conflicts of interest.

A Historical and Contemporary Review of Questionnaires Used in the Management of Post-Radical Prostatectomy Patients.

INTRODUCTION: Patients undergoing radical prostatectomy (RP) face obstacles to recovery spanning the domains of erectile and sexual function; urinary function; and health-related quality of life (HRQoL). Numerous patient-directed questionnaires exist that serve to assist in the care of these men. AIM: To describe patient-directed questionnaires of historical and contemporary relevance involving the evaluation and treatment of men after radical prostatectomy. METHODS: A comprehensive review of peer-reviewed publications on the topic was performed. Using PubMed, the search terms used were: "radical prostatectomy; erectile function; lower urinary tract symptoms; sexual dysfunction; urinary incontinence; and health-related quality of life. MAIN OUTCOME MEASURE: We aimed to summarize questionnaires and survey devices of historical and contemporary importance for the care of men after RP. RESULTS: Many questionnaires have been developed specifically for, or conscripted for use in, the care of men after RP. Some of the oldest questionnaires relating to sexual function, urinary function, and general and cancer-specific QoL are important and still utilized in the routine clinical care of post-RP patients. However, recent devices that may offer clinicians a more comprehensive understanding to aid in the evaluation and care of these men. CONCLUSIONS: Post-RP patients face numerous challenges that require a thoughtful approach, one that is broad enough to identify a variety of potential physical and emotional disturbances, yet granular enough to identify appropriate areas for intervention. While there is not a "best" questionnaire for this population, having an appropriate understanding of the current available instruments and what information they provide may help clinicians more thoroughly assess and treat these men. Castillo O, Chen IK, Amini E, et al. Male Sexual Health Related Complications Among Combat Veterans. Sex Med Rev 2022;10:681-690.

A Historical and Contemporary Review of Questionnaires Used in the Management of Post-Radical Prostatectomy Patients.

INTRODUCTION: Patients undergoing radical prostatectomy (RP) face obstacles to recovery spanning the domains of erectile and sexual function; urinary function; and health-related quality of life (HRQoL). Numerous patient-directed questionnaires exist that serve to assist in the care of these men. AIM: To describe patient-directed questionnaires of historical and contemporary relevance involving the evaluation and treatment of men after radical prostatectomy. METHODS: A comprehensive review of peer-reviewed publications on the topic was performed. Using PubMed, the search terms used were: "radical prostatectomy; erectile function; lower urinary tract symptoms; sexual dysfunction; urinary incontinence; and health-related quality of life. Main Outcome Measure: We aimed to summarize questionnaires and survey devices of historical and contemporary importance for the care of men after RP. RESULTS: Many questionnaires have been developed specifically for, or conscripted for use in, the care of men after RP. Some of the oldest questionnaires relating to sexual function, urinary function, and general and cancer-specific QoL are important and still utilized in the routine clinical care of post-RP patients. However, recent devices that may offer clinicians a more comprehensive understanding to aid in the evaluation and care of these men. CONCLUSIONS: Post-RP patients face numerous challenges that require a thoughtful approach, one that is broad enough to identify a variety of potential physical and emotional disturbances, yet granular enough to identify appropriate areas for intervention. While there is not a "best" questionnaire for this population, having an appropriate understanding of the current available instruments and what information they provide may help clinicians more thoroughly assess and treat these men.