Changes in use of multiplex respiratory panel testing during the COVID-19 pandemic.

BACKGROUND: COVID-19 changed the epidemiology of community-acquired respiratory viruses. We explored patterns of respiratory viral testing to understand which tests are most clinically useful in the postpandemic era. METHODS: We conducted a retrospective observational study of discharge data from PINC-AI (formerly Premier), a large administrative database. Use of multiplex nucleic acid amplification respiratory panels in acute care, including small (2-5 targets), medium (6-11), and large panels (>11), were compared between the early pandemic (03/2020-10/2020), late pandemic (11/2020-4/2021), and prepandemic respiratory season (11/2019 - 02/2020) using ANOVA. RESULTS: A median of 160.5 facilities contributed testing data per quarter (IQR 155.5-169.5). Prepandemic, facilities averaged 103 respiratory panels monthly (sd 138), including 79 large (sd 126), 7 medium (sd 31), and 16 small panels (sd 73). Relative to prepandemic, utilization decreased during the early pandemic (62 panels monthly/facility; sd 112) but returned to the prepandemic baseline by the late pandemic (107 panels monthly/facility; sd 211). Relative to prepandemic, late pandemic testing involved more small panel use (58 monthly/facility, sd 156) and less large panel use (47 monthly/facility, sd 116). Comparisons among periods demonstrated significant differences in overall testing (P < 0.0001), large panel use (P < 0.0001), and small panel use (P < 0.0001). CONCLUSIONS: Postpandemic, clinical use of respiratory panel testing shifted from predominantly large panels to predominantly small panels. Factors driving this change may include resource availability, costs, and the clinical utility of targeting important pathogenic viruses instead of testing "for everything."

GeneSPIDER2: large scale GRN simulation and benchmarking with perturbed single-cell data.

Single-cell data is increasingly used for gene regulatory network (GRN) inference, and benchmarks for this have been developed based on simulated data. However, existing single-cell simulators cannot model the effects of gene perturbations. A further challenge lies in generating large-scale GRNs that often struggle with computational and stability issues. We present GeneSPIDER2, an update of the GeneSPIDER MATLAB toolbox for GRN benchmarking, inference, and analysis. Several software modules have improved capabilities and performance, and new functionalities have been added. A major improvement is the ability to generate large GRNs with biologically realistic topological properties in terms of scale-free degree distribution and modularity. Another major addition is a simulation of single-cell data, which is becoming increasingly popular as input for GRN inference. Specifically, we introduced the unique feature to generate single-cell data based on genetic perturbations. Finally, the simulated single-cell data was compared to real single-cell Perturb-seq data from two cell lines, showing that the synthetic and real data exhibit similar properties.

Factors affecting community ambulation post-stroke: a mapping review protocol.

Background: Most stroke survivors consider community ambulation an essential but unmet goal of their recovery. Historically, interventions to enhance community ambulation have focused on improving biomechanical impairments of gait; however, recent evidence suggests that biopsychosocial and environmental factors may impact community ambulation, even beyond more obvious physical impairments. The identification of factors that pose as significant facilitators or barriers to community ambulation may serve to guide stakeholders in designing relevant and evidence-based interventions for improving community ambulation post-stroke. Objective: This review aims to map the type and extent of existing evidence on the physical, biopsychosocial, and environmental factors affecting community ambulation post-stroke. Additionally, this review will describe the various methods used to examine the extent to which stroke survivors are restricted to community ambulation. Methods: Nine databases will be searched including CINAHL, PubMed, and Web of Science. We will include studies published in English during or after 2001. Studies that examine physical, biopsychosocial, and/or environmental factors affecting community ambulation in ambulatory adults at least six months post-stroke will be considered for inclusion. Studies that assess general physical activity or community mobility through transportation modes other than walking will be excluded. All identified records will be collated in citation management software, followed by steps of deduplication, title/abstract screening, and full-text reviews by at least two independent reviewers. The bibliographies of the extracted studies will also be reviewed for relevant articles. The extracted studies will be analyzed, critically appraised, and presented in tabular, narrative, and evidence map formats. Discussion: The evidence gained will be used to build a framework for community ambulation, informing stakeholders to develop meaningful interventions to improve community ambulation. The mapped evidence will motivate future studies to develop holistic approaches that specifically focus on the most vital factors that influence post-stroke community ambulation.

Decreasing Utilization of Vaginal Hysterectomy in the United States: An Analysis by Candidacy for Vaginal Approach.

INTRODUCTION AND HYPOTHESIS: The objective was to assess trends in hysterectomy routes by patients who are likely and unlikely candidates for a vaginal approach. METHODS: We performed a retrospective cohort study of patients who underwent vaginal, abdominal, or laparoscopic/robotics-assisted laparoscopic hysterectomy between 2017 and 2020 using the National Surgical Quality Improvement Program database. Patients undergoing hysterectomy for a primary diagnosis of benign uterine pathology, dysplasia, abnormal uterine bleeding, or pelvic floor disorders were eligible for inclusion. Patients who were parous, had no history of pelvic or abdominal surgery, and had a uterine weight ≤ 280 g on pathology were considered likely candidates for vaginal hysterectomy based on an algorithm developed to guide the surgical approach. Average annual changes in the proportion of likely vaginal hysterectomy candidates and route of hysterectomy were assessed using logistic regression. RESULTS: Of the 77,829 patients meeting the inclusion criteria, 13,738 (17.6%) were likely vaginal hysterectomy candidates. Among likely vaginal hysterectomy candidates, the rate of vaginal hysterectomy was 34.5%, whereas among unlikely vaginal hysterectomy candidates, it was 14.1%. The overall vaginal hysterectomy rate decreased -1.2%/year (p < 0.01). This decreasing trend was nearly twice as rapid among likely vaginal hysterectomy candidates (-1.9%/year, p < .01) compared with unlikely vaginal hysterectomy candidates (-1.1%/year, P < 0.01); the difference in trends was statistically significant (p < 0.01). CONCLUSIONS: The rate of vaginal hysterectomy performed for eligible indications decreased between 2017 and 2020 in a national surgical registry. This negative trend was more pronounced among patients who were likely candidates for vaginal hysterectomy based on favorable parity, surgical history, and uterine weight.

Contact precautions for MRSA and VRE: where are we now? A survey of the Society for Healthcare Epidemiology of America Research Network.

Objective: Contact precautions for methicillin-resistant Staphylococcus aureus (MRSA) and vancomycin-resistant Enterococcus (VRE) have limited data on efficacy and have been associated with patient harm. Still, a 2015 Society for Healthcare Epidemiology of America (SHEA) Research Network (SRN) survey showed only 7% of hospitals discontinued routine MRSA/VRE contact precautions. The study objectives were to identify the current proportion of hospitals that have discontinued routine MRSA/VRE contact precautions and motivations for change. Design: An online survey was conducted of the SRN on current use and views of contact precautions for MRSA/VRE in each facility. An initial survey followed by 2 reminders was sent between 5/18/2021 and 6/9/2021. Participants: SRN facilities. Results: The response rate was 43% (37/87) of facilities surveyed and 35% of respondents were not routinely using contact precautions for MRSA and VRE. The most frequently reported reason for discontinuing contact precautions was research on the safety of discontinuing contact precautions without an increase in healthcare-associated infections (reported for 92% of facilities for MRSA and 100% for VRE). Of those using contact precautions, the most frequently reported reason to continue was a lack of safety data for discontinuation (MRSA 58% and VRE 46%). Most of those continuing contact precautions were interested in using contact precautions differently in their facility (MRSA 63% and VRE 58%). Conclusions: Over one in three healthcare facilities surveyed do not use contact precautions for MRSA or VRE. Most facilities choosing to continue contact precautions are interested in a different implementation strategy.

Impaired Face Feature-to-Location Statistical Learning and Single-Feature Discrimination in Developmental Prosopagnosia.

Individuals with developmental prosopagnosia (DP) experience severe face memory deficits that are often accompanied by impairments in face perception. Images of human facial features are better discriminated between when they are presented in the locations on the visual field that they typically appear in while viewing human faces in daily life, than in locations which they do not typically appear (i.e., better performance for eyes in the upper visual field, and better performance for mouths in the lower visual field). These feature-to-location tuning effects (FLEs) can be explained by a retinotopically organised visual statistical learning mechanism. We had a large group of DP participants (N = 64), a control group (N = 74) and a group of individuals with a mild form of DP (N = 58) complete a single-feature discrimination task to determine whether face perception deficits in DP can be accounted for by an impairment in face feature-to-location tuning. The results showed that individuals with DP did not have significant FLEs, suggesting a marked impairment in the underlying visual statistical learning mechanism. In contrast, the mild DP group showed normal FLE effects which did not differ from the control group. Both DP groups had impaired single-feature processing (SFP) as compared to the control group. We also examined the effects of age on FLEs and SFP.

Diagnostic Stewardship: AJR Podcast Series on Diagnostic Excellence and Error, Episode 3.

In this episode of the AJR Podcast Series on Diagnostic Excellence and Error, Francis Deng, MD, and Daniel Morgan, MD, MS, discuss diagnostic stewardship. They explore how improving diagnostic test ordering, processing, and reporting can reduce error and improve outcomes and address practical strategies and radiologists' role in implementing stewardship.

Pediatric Foot: Development, Variants, and Related Pathology.

Pediatric foot development throughout childhood and adolescence can present a diagnostic dilemma for radiologists because imaging appearances may be confused with pathology. Understanding pediatric foot development and anatomical variants, such as accessory ossification centers, is essential to interpret musculoskeletal imaging in children correctly, particularly because many of these variants are incidental but others can be symptomatic. We first briefly review foot embryology. After describing common accessory ossification centers of the foot, we explain the different patterns of foot maturation with attention to irregular ossification and bone marrow development. Common pediatric foot variants and pathology are described, such as tarsal coalitions and fifth metatarsal base fractures. We also discuss pediatric foot alignment and various childhood foot alignment deformities.

Developing and conducting a language inclusivity assessment on a health science library's website, LibGuides, and signage.

Background: A Diversity, Equity, and Inclusion (DEI) Team at a university health science library created a checklist for inclusive language and conducted an assessment of their library's website, LibGuides, and physical and digital signage. Inclusive language was defined as "language that is free from words, phrases or tones that reflect prejudiced, stereotyped or discriminatory views of particular people or groups". Case Presentation: The 32-item checklist facilitated the identification of gendered language, stereotypes, ableist language, racist language, stigmatizing language, slang, acronyms, and out-of-date terminology regarding physical and mental health conditions. From the library's website, 20 instances were noted for which improvements were necessary. Out of the 130 LibGuides reviewed, 23 LibGuides had no changes needed and 107 had changes identified relating to language inclusivity (14 strongly recommended changes and 116 suggested changes). Regarding the signage, one flyer was removed for reprinting. Conclusion: The checklist enabled the team to implement a number of improvements to the library's website and LibGuides. The checklist has been shared with Library Technology Services and the wider campus libraries' Usability Committee for future use, and has also been added to the DEI Team's LibGuide for use by others outside of the university.

Face Feature Change Detection Ability in Developmental Prosopagnosia and Super-Recognisers.

In non-clinical populations, facial features (eyes, nose, mouth) may vary in their contribution to face identity perception. Changes to whole faces are easier to detect than changes to individual features, and eye changes are typically easier to detect than mouth changes, which in turn are easier to detect than nose changes. However, how this differs for people with face recognition difficulties (developmental prosopagnosia; DP) and for individuals with superior face recognition abilities (super-recognisers; SR) is not clear; although findings from previous studies have suggested differences, the nature of this difference is not understood. The aim of this study was to examine whether differences in the ability to detect feature changes in DPs and SRs were (a) quantitative, meaning that the pattern across feature changes remained the same but there was an overall upwards or downwards shift in performance, or (b) qualitative, meaning that the pattern across feature changes was different. Using a change detection task in which individual face features (eyes, nose, mouth) changed between sequentially presented faces, we found that while prosopagnosics showed a quantitative difference in performance with a downwards shift across all conditions, super-recognisers only showed qualitative differences: they were better able to detect when the face was the same and were marginally (but not non-significantly) worse at detecting when the eyes changed. Further, the only condition which distinguished between the three groups was the ability to identify when the same face was presented, with SRs being better than controls, and controls being better than DPs. Our findings suggest that, in feature-matching tasks, differences for DPs are due to them being overall worse at the task, while SRs use a qualitatively different strategy.

Chronic administration of cannabinoid agonists ACEA (CB1), AM1241 (CB2), and CP55,940 (mixed CB1/CB2) induce sex-specific differences in tolerance and sex hormone changes in a chemotherapy-induced peripheral neuropathy.

Chemotherapy-induced peripheral neuropathy (CIPN) is a common side effect of chemotherapy treatment, routinely manifesting as increased pain sensitivity (allodynia) in distal extremities. Despite its prevalence, effective treatment options are limited. Cannabinoids are increasingly being evaluated for their ability to treat chronic pain conditions, including CIPN. While previous studies have revealed sex differences in cannabinoid-mediated antinociception in acute and chronic pain models, there is a paucity of studies addressing potential sex differences in the response of CIPN to cannabinoid treatment. Therefore, we evaluated the long-term anti-allodynic efficacy of CB1-selective (ACEA), CB2-selective (AM1241), and CB1/CB2 mixed (CP55,940) agonists in the cisplatin CIPN model, using both male and female mice. CB1 selective agonism was observed to have sex differences in the development of tolerance to anti-allodynic effects, with females developing tolerance more rapidly than males, while the anti-allodynic effects of selective CB2 agonism lacked tolerance development. Compound-specific changes to the female estrous cycle and female plasma estradiol levels were noted, with CB1 selective agonism decreasing plasma estradiol while CB2 selective agonism increased plasma estradiol. Chronic administration of a mixed CB1/CB2 agonist resulted in increased mRNA expression of proinflammatory cytokines and endocannabinoid regulatory enzymes in female spinal cord tissue. Ovarian tissue was noted to have proinflammatory cytokine mRNA expression following administration of a CB2 acting compound while selective CB1 agonism resulted in decreased proinflammatory cytokines and endocannabinoid regulatory enzymes in testes. These results support the need for further investigation into the role of sex and sex hormones signaling in pain and cannabinoid-mediated antinociceptive effects. Significance Statement CIPN is a common side effect of chemotherapy. We have found that both CB1 and CB2 receptor agonism produce antinociceptive effects in a cisplatin CIPN model. We observed that tolerance to CB1-mediated antinociception developed faster in females and did not develop for CB¬2-mediated antinociception. Additionally, we found contrasting roles for CB1/CB¬2 receptors in the regulation of plasma estradiol in females, with CB1 agonism attenuating estradiol and CB¬2 agonism enhancing estradiol. These findings support the exploration of cannabinoid agonists for CIPN.

Psychological Constructs From the Fear Avoidance Model and Beyond as Predictors for Persisting Symptoms After Concussion: An Integrative Review.

OBJECTIVES: To identify the range of evidence for relationships between psychological factors using the Fear Avoidance Model (FAM) as a guiding framework and relevant clinical outcomes in adult patients with persisting symptoms after concussion (PSaC), develop a comprehensive understanding of psychological factors that have been identified as predictors of clinical outcomes for PSaC, and contribute to the theoretical framework of the FAM for PSaC. DATA SOURCES: Six databases (CINAHL, Embase, PsycINFO, PubMed, SportDiscus, and Web of Science) were searched by a librarian for empirical and theoretical publications and experimental and quasi-experimental study designs. The literature search was not limited by publication date restrictions. Gray literature, with the exception of doctoral dissertations, was excluded. STUDY SELECTION: We included studies in the English language consisting of human participants aged ≥18 years. Articles must have included both outcomes pertaining to PSaC (≥3mo after injury) and psychological constructs. DATA EXTRACTION: One reviewer extracted data from the resulting studies using a standardized data extraction form designed for this review. Two reviewers independently assessed risk of bias using the Quality in Prognosis Studies tool. DATA SYNTHESIS: This review found numerous psychological constructs, some directly linked to the FAM, that have potential prognostic relationships with PSaC. However, research remains limited and some psychological factors central to FAM were only identified in a small number of studies (catastrophizing, cogniphobia, and avoidance), whereas other psychological factors were studied more extensively (anxiety and depression). CONCLUSIONS: There is the need for additional evidence, and this integrative review provides an adaptation of the FAM for PSaC to be used as a guiding preliminary framework for future research. Future research should aim to include psychological factors proposed in this modified FAM to fully understand PSaC.

Risk Compensation After Initiation of Daily Oral Pre-exposure Prophylaxis Among Sexual and Gender Minorities in Nigeria.

Pre-exposure prophylaxis (PrEP) use may be associated with risk compensation. We enrolled and provided PreP to sexual and gender minorities (SGM) in Abuja, Nigeria between April 2018 and May 2019. Behavioral information and samples for urogenital and anorectal Chlamydia trachomatis and Neisseria gonorrhoeae sexually transmitted infections (STIs) were collected at baseline. Blood samples for PrEP assay and self-reported adherence were collected at three-monthly follow-up visits. STIs were detected using Aptima Combo2 assay. We estimated the odds ratios (ORs) of PCR-diagnosed bacterial STIs and self-reported behavioral outcomes (condomless anal intercourse [CAI] and concurrent sexual relationships) with conditional logistic regression. Of 400 SGM who initiated PrEP, 206 were eligible for analysis, and had a median age of 24 years (IQR 22-27). In multivariable analysis, participants in the PrEP period had decreased odds of CAI (adjusted OR: 0.49, 95% CI 0.28, 0.84). PrEP use was not associated with risk compensation.

Diagnostic Stewardship for Urine Cultures.

Urinary tract infections are among the most common infectious diagnoses in health care, but most urinary tract infections are diagnosed inappropriately in patients without signs or symptoms of infection. Asymptomatic bacteriuria leads to inappropriate antibiotic prescribing and negative downstream effects, including antimicrobial resistance, health care-associated infections, and adverse drug events. Diagnostic stewardship is the process of modifying the ordering, performing, or reporting of test results to improve clinical care. Diagnostic stewardship impacts the diagnostic pathway to decrease inappropriate detection and treatment of asymptomatic bacteriuria. This article reviews diagnostic stewardship methods and closes with a case study illustrating these principles in practice.

The importance of pharmacist engagement in diagnostic stewardship.

Diagnostic stewardship is increasingly recognized as a powerful tool to improve patient safety. Given the close relationship between diagnostic testing and antimicrobial misuse, antimicrobial stewardship (AMS) pharmacists should be key members of the diagnostic team. Pharmacists practicing in AMS already frequently engage with clinicians to improve the diagnostic process and have many skills needed for the implementation of diagnostic stewardship initiatives. As diagnostic stewardship becomes more broadly used, all infectious disease clinicians, including pharmacists, must collaborate to optimize patient care.

MetaQuad: shared informative variants discovery in metagenomic samples.

Motivation: Strain-level analysis of metagenomic data has garnered significant interest in recent years. Microbial single nucleotide polymorphisms (SNPs) are genomic variants that can reflect strain-level differences within a microbial species. The diversity and emergence of SNPs in microbial genomes may reveal evolutionary history and environmental adaptation in microbial populations. However, efficient discovery of shared polymorphic variants in a large collection metagenomic samples remains a computational challenge. Results: MetaQuad utilizes a density-based clustering technique to effectively distinguish between shared variants and non-polymorphic sites using shotgun metagenomic data. Empirical comparisons with other state-of-the-art methods show that MetaQuad significantly reduces the number of false positive SNPs without greatly affecting the true positive rate. We used MetaQuad to identify antibiotic-associated variants in patients who underwent Helicobacter pylori eradication therapy. MetaQuad detected 7591 variants across 529 antibiotic resistance genes. The nucleotide diversity of some genes is increased 6 weeks after antibiotic treatment, potentially indicating the role of these genes in specific antibiotic treatments. Availability and implementation: MetaQuad is an open-source Python package available via https://github.com/holab-hku/MetaQuad.