uafR: An R package that automates mass spectrometry data processing.

Chemical information has become increasingly ubiquitous and has outstripped the pace of analysis and interpretation. We have developed an R package, uafR, that automates a grueling retrieval process for gas -chromatography coupled mass spectrometry (GC -MS) data and allows anyone interested in chemical comparisons to quickly perform advanced structural similarity matches. Our streamlined cheminformatics workflows allow anyone with basic experience in R to pull out component areas for tentative compound identifications using the best published understanding of molecules across samples (pubchem.gov). Interpretations can now be done at a fraction of the time, cost, and effort it would typically take using a standard chemical ecology data analysis pipeline. The package was tested in two experimental contexts: (1) A dataset of purified internal standards, which showed our algorithms correctly identified the known compounds with R2 values ranging from 0.827-0.999 along concentrations ranging from 1 × 10-5 to 1 × 103 ng/µl, (2) A large, previously published dataset, where the number and types of compounds identified were comparable (or identical) to those identified with the traditional manual peak annotation process, and NMDS analysis of the compounds produced the same pattern of significance as in the original study. Both the speed and accuracy of GC -MS data processing are drastically improved with uafR because it allows users to fluidly interact with their experiment following tentative library identifications [i.e. after the m/z spectra have been matched against an installed chemical fragmentation database (e.g. NIST)]. Use of uafR will allow larger datasets to be collected and systematically interpreted quickly. Furthermore, the functions of uafR could allow backlogs of previously collected and annotated data to be processed by new personnel or students as they are being trained. This is critical as we enter the era of exposomics, metabolomics, volatilomes, and landscape level, high-throughput chemotyping. This package was developed to advance collective understanding of chemical data and is applicable to any research that benefits from GC -MS analysis. It can be downloaded for free along with sample datasets from Github at github.org/castratton/uafR or installed directly from R or RStudio using the developer tools: 'devtools::install_github("castratton/uafR")'.

Development and validation of a HPLC method for the determination of chemical and radiochemical purity of O-(2-[18F]fluoroethyl-l-tyrosine ([18F]FET)), a PET radiotracer for the imaging of brain tumor.

A novel HPLC method was developed and validated to determine radiochemical identity, radiochemical purity and chemical purity for the analysis of O-(2-[18F]fluoroethyl-l-tyrosine ([18F]FET). In this method, an analytical Phenomenex Gemini C18 column was used with an isocratic eluent of 7 % ethanol and 93 % 50 mM potassium phosphate buffer (pH = 6.9). The flow rate was 1.0 mL/min and the injection volume was 10 µL. A photo-diode array detector set at 220 nm was used for UV mass detection and a single channel, high sensitivity radiation detector was used. The method validation assays including specificity, linearity, precision, accuracy, and robustness were evaluated. Results show that the method was suitable for qualitative and quantitative determination of radiochemical and chemical purity of [18F]FET. This system has been routinely used for the analysis of more than 120 batches of [18F]FET with radiochemical yield 23.7 ± 6 % (no decay corrected) and molar activity 593 ± 284 GBq/µmole in our facility to support human use.

Using an Innovative Method for Self-Collection of Capillary Blood for HIV and Syphilis Testing Among Men Who Have Sex With Men Who Use Pre-exposure Prophylaxis in the Netherlands; Limburg4zero.

BACKGROUND: Home-based sampling could create accessible testing opportunities for men who have sex with men (MSM) who use pre-exposure prophylaxis (PrEP). Blood collection is required for the most reliable laboratory results for HIV and syphilis testing. An innovative blood collection method (Tasso+) creates a vacuum and semi-automatically collects larger volumes of blood from the upper arm. This study aimed to assess acceptability and feasibility of this device among PrEP-using MSM and the performance of blood collection. METHODS: Between August 2022 and January 2023, 47 MSM were recruited during their routine PrEP consultations at a Dutch Centre for Sexual Health. Participants tested the method directly after consultation, and an online questionnaire determined acceptability and feasibility. Blood and residual serum volumes were measured after sampling and after HIV and syphilis testing. RESULTS: Of the participants, 87% had a positive attitude toward use of the device, and 77% would use it again for self-sampling at home. Participants rated the use of the blood collection device as easy (96%). On average, 536 µL whole blood (244 µL serum) was collected. All samples were tested for HIV and syphilis, and most samples had sufficient blood for routine HIV (91%) and syphilis testing (89%). Most samples (85%) had 220 µL residual blood, sufficient for further testing (e.g., confirmation). CONCLUSIONS: Blood self-sampling with a method that creates a vacuum from the upper arm is highly acceptable by users and performs well in blood collection for multiple tests. This method has promising potential for use in home-based sexual health care for PrEP-using MSM.

The Sexual Health Clinic Role in Vaccine and Treatment Access During the 2022 Mpox Outbreak in King County, Washington.

BACKGROUND: Sexual health clinics were frontline providers in the 2022 US mpox public health response, though data on clinic-based mpox vaccine scale-up, diagnoses, and treatment are limited. We describe the role of a public health sexual health clinic (SHC) in King County's mpox response, between 5/23/22-10/31/22. METHODS: In July 2022, the SHC implemented a dedicated vaccine clinic and presumptive tecovirimat treatment (prior to laboratory confirmation) with on-site dispensation. We describe SHC's vaccine scale-up and contribution to clinical care by calculating the weekly number of vaccines administered by SHC and the total number of patients diagnosed and treated for mpox within SHC, and comparing to countywide data. We calculated time from symptom onset to testing and time from testing to treatment, and assessed temporal changes in these metrics using linear regression. RESULTS: The SHC provided ≥1 vaccine doses to 7,442 individuals (10,295 doses), administering 42% of the 24,409 vaccine doses provided countywide, with the greatest contribution in the first week of August (n = 1,562, 58% of countywide vaccinations that week). Of 598 patients evaluated for mpox and tested, 178 (30%) tested positive (37% of countywide cases), and 152 (85% of SHC patients with mpox) received tecovirimat (46% of treatment countywide). Median time from symptom onset to testing decreased from 12 to 6 days (p = 0.045); time from testing to treatment decreased from 4.5 days to 0 days (p < 0.001). CONCLUSION: The SHC was central to mpox vaccination and treatment scale-up, particularly in the first months of the 2022 epidemic.

Histiocytoid Sweet's Syndrome in the Setting of Myelodysplastic Syndrome.

Acute febrile neutrophilic dermatosis, or Sweet's syndrome, is characterized by tender, edematous papules and plaques, favoring the upper extremities and the head and neck regions. The classic variant of Sweet's syndrome involves a predominantly neutrophilic dermal infiltrate on histopathology. However, histiocytoid Sweet's syndrome has been noted to have a primary histiocytoid mononuclear infiltrate and is typically found in patients with malignancies such as myelodysplasia. This case report discusses the treatment of histiocytoid Sweet's syndrome in an immunocompromised patient with a recent history of Mycobacterium avium complex infection and latent tuberculosis in the setting of myelodysplastic syndrome.

Isolation of Primary Porcine Retinal Pigment Epithelial Cells for In Vitro Modeling.

The retinal pigment epithelium (RPE) is a crucial monolayer in the outer retina responsible for supporting photoreceptors. RPE degeneration commonly occurs in diseases marked by progressive vision loss, such as age-related macular degeneration (AMD). Research on AMD often relies on human donor eyes or induced pluripotent stem cells (iPSCs) to represent the RPE. However, these RPE sources require extended differentiation periods and substantial expertise for culturing. Additionally, some research institutions, particularly those in rural areas, lack easy access to donor eyes. While a commercially available immortalized RPE cell line (ARPE-19) exists, it lacks essential in vivo RPE features and is not widely accepted in many ophthalmology research publications. There is a pressing need to obtain representative primary RPE cells from a more readily available and cost-effective source. This protocol elucidates the isolation and subculture of primary RPE cells obtained post-mortem from porcine eyes, which can be sourced locally from commercial or academic suppliers. This protocol necessitates common materials typically found in tissue culture labs. The result is a primary, differentiated, and cost-effective alternative to iPSCs, human donor eyes, and ARPE-19 cells.

Male elephant management in AZA institutions: Current status and priorities for the future.

Asian elephant (Elephas maximus) and African savanna elephant (Loxodonta africana) populations collectively managed by ex-situ facilities accredited by the Association of Zoos and Aquariums (AZA) face sustainability challenges. Among the priorities to strengthen animal wellbeing and population sustainability is male elephant management. We conducted a survey of AZA facilities currently housing male elephants to assess the status, challenges, and priorities in three areas of male elephant management: musth, socialization, and semen collection. Surveys were administered to elephant care teams at AZA-accredited institutions between November 2022 and February 2023, and we received responses from 34 institutions (91.9% of AZA-accredited facilities holding adult male elephants), housing 32 adult male Asians and 26 adult male Africans. Most facilities prioritized breeding and male socialization over musth management and semen collection (although most facilities acknowledged that all these efforts are important), citing leadership support and staffing as most important to achieve male management goals. Behaviors most commonly accompanying musth included reduced appetite, difficulty training or shifting, human-directed aggression, and interest in females. Musth timing was variable between males and facilities. Most males were well-socialized with females and/or other males, though elephant compatibility and facility design were limiting factors in managing socialization. Although 60.6% of facilities collected semen or were training for semen collection, very few male elephants could reliably provide viable semen samples, challenging assisted reproductive efforts that could bolster population sustainability in both species. Together, our results provide a better understanding of the state of male elephant management, offering specific areas deserving of research and development to enhance wellbeing and sustainability.

In vitro activity of gepotidacin and comparator antimicrobials against isolates of nontuberculous mycobacteria (NTM).

Novel antimicrobials are needed to treat rising nontuberculous mycobacteria (NTM) infections. Using standard broth microdilution methods, 68 NTM isolates were tested against gepotidacin, a new, first-in-class, oral triazaacenaphthylene bacterial topoisomerase inhibitor. MICs varied (0.25 to >64 µg/mL) with the lowest being M. fortuitum complex (0.25-8 µg/mL), M. mucogenicum complex (1-2 µg/mL), M. kansasii (0.25-8 µg/mL), and M. marinum (4-16 µg/mL). Testing greater numbers of some species is suggested to better understand gepotidacin activity against NTM.

A randomized trial to compare smooth monofilament suture vs. barbed suture using the three-layer continuous closure technique in canine ovariohysterectomy in a high-quality high-volume spay/neuter clinic.

The primary objective of this study was to compare time efficiency and complication rates between smooth monofilament suture (SMS) and barbed suture (BS) using the three-layer continuous incisional closure pattern after ovariohysterectomy in a high-quality high-volume spay/neuter clinic. The study was designed as a randomized controlled trial enrolling 71 adult female dogs. Dogs were randomly assigned to SMS or BS treatments. The effect of closure with BS or SMS on closure time was tested through multilevel, multivariable linear regression in a generalized linear mixed model. Body condition score, weight, and pre-closure incision length were tested as covariates. Surgeon was included in the model as a random effect. Pre-closure incision length (p = 0.01) and method (p ≤ 0.0001) were associated with closure time. Adjusting for pre-closure incision length, the average time for closure with SMS was 6.5 min (range 3.70-10.31 min), and the average time for closure with BS was 4.91 min (range 3.05-8.05 min). Accounting for the closure method, the closure time increased by 39 s for each additional centimeter of incision length. BS was more efficient than SMS when performing the three-layer continuous suture pattern. No short-term telemedicine-assessed complications were noted with either treatment method. BS can improve efficiency in surgical closures, especially considering large volumes of animals, and appears to have a similar short-term, telemedicine-assessed complication rate when compared to SMS.

Vegfc-expressing cells form heterotopic bone after musculoskeletal injury.

Heterotopic ossification (HO) is a challenging condition that occurs after musculoskeletal injury and is characterized by the formation of bone in non-skeletal tissues. While the effect of HO on blood vessels is well established, little is known about its impact on lymphatic vessels. Here, we use a mouse model of traumatic HO to investigate the relationship between HO and lymphatic vessels. We show that injury triggers lymphangiogenesis at the injury site, which is associated with elevated vascular endothelial growth factor C (VEGF-C) levels. Through single-cell transcriptomic analyses, we identify mesenchymal progenitor cells and tenocytes as sources of Vegfc. We demonstrate by lineage tracing that Vegfc-expressing cells undergo osteochondral differentiation and contribute to the formation of HO. Last, we show that Vegfc haploinsufficiency results in a nearly 50% reduction in lymphangiogenesis and HO formation. These findings shed light on the complex mechanisms underlying HO formation and its impact on lymphatic vessels.

BioVDB: biological vector database for high-throughput gene expression meta-analysis.

High-throughput sequencing has created an exponential increase in the amount of gene expression data, much of which is freely, publicly available in repositories such as NCBI's Gene Expression Omnibus (GEO). Querying this data for patterns such as similarity and distance, however, becomes increasingly challenging as the total amount of data increases. Furthermore, vectorization of the data is commonly required in Artificial Intelligence and Machine Learning (AI/ML) approaches. We present BioVDB, a vector database for storage and analysis of gene expression data, which enhances the potential for integrating biological studies with AI/ML tools. We used a previously developed approach called Automatic Label Extraction (ALE) to extract sample labels from metadata, including age, sex, and tissue/cell-line. BioVDB stores 438,562 samples from eight microarray GEO platforms. We show that it allows for efficient querying of data using similarity search, which can also be useful for identifying and inferring missing labels of samples, and for rapid similarity analysis.

Intersections of Fibrodysplasia Ossificans Progressiva and Traumatic Heterotopic Ossification.

Heterotopic ossification (HO) is a debilitating pathology where ectopic bone develops in areas of soft tissue. HO can develop as a consequence of traumatic insult or as a result of dysregulated osteogenic signaling, as in the case of the orphan disease fibrodysplasia ossificans progressiva (FOP). Traumatic HO (tHO) formation is mediated by the complex interplay of signaling between progenitor, inflammatory, and nerve cells, among others, making it a challenging process to understand. Research into the pathogenesis of genetically mediated HO (gHO) in FOP has established a pathway involving uninhibited activin-like kinase 2 receptor (ALK2) signaling that leads to downstream osteogenesis. Current methods of diagnosis and treatment lag behind pre-mature HO detection and progressive HO accumulation, resulting in irreversible decreases in range of motion and chronic pain for patients. As such, it is necessary to draw on advancements made in the study of tHO and gHO to better diagnose, comprehend, prevent, and treat both.

Association of Tecovirimat Therapy With Mpox Symptom Improvement: A Cross-sectional Study-King County, Washington, May-October 2022.

Background: Data on tecovirimat effectiveness for human mpox are limited. We conducted a retrospective cross-sectional interview-based study to identify associations between tecovirimat treatment and the mpox clinical course. Methods: Using public health surveillance data from King County, Washington, we recruited and interviewed persons diagnosed with mpox during May-October 2022. We calculated descriptive statistics on demographics, vaccination status, comorbidities, and symptoms including 3 self-reported dates (symptom onset, first date of symptom improvement, and illness resolution). We used multivariable linear regression, stratified by illness severity, to evaluate the association of tecovirimat treatment with time to symptom improvement and time to illness resolution. We compared individuals who did not receive tecovirimat to participants who started tecovirimat early (≤5 days from symptom onset) and late (>5 days and ≤28 days from symptom onset) in their illness. Results: Of 465 individuals diagnosed with mpox, 115 (25%) participated in this study. Eighty participants (70%) received tecovirimat and 43 (37%) initiated tecovirimat early. Sixty-eight (59%) reported severe symptoms during their illness, including proctitis (n = 38 [33%]), rectal bleeding (n = 27 [24%]), or severe pain (n = 24 [21%]). In the multivariable analysis, early tecovirimat was associated with shorter time to symptom improvement (-5.5 days, P = .04) among participants with severe illness but not among those with nonsevere illness (0.9 day, P = .66). Early tecovirimat was not associated with faster illness resolution, regardless of severity. Conclusions: Our small study suggests that early tecovirimat initiation may hasten subjective symptomatic improvement in people with severe mpox. Larger randomized trials are needed to evaluate this finding.

The HIF-1α/PLOD2 axis integrates extracellular matrix organization and cell metabolism leading to aberrant musculoskeletal repair.

While hypoxic signaling has been shown to play a role in many cellular processes, its role in metabolism-linked extracellular matrix (ECM) organization and downstream processes of cell fate after musculoskeletal injury remains to be determined. Heterotopic ossification (HO) is a debilitating condition where abnormal bone formation occurs within extra-skeletal tissues. Hypoxia and hypoxia-inducible factor 1α (HIF-1α) activation have been shown to promote HO. However, the underlying molecular mechanisms by which the HIF-1α pathway in mesenchymal progenitor cells (MPCs) contributes to pathologic bone formation remain to be elucidated. Here, we used a proven mouse injury-induced HO model to investigate the role of HIF-1α on aberrant cell fate. Using single-cell RNA sequencing (scRNA-seq) and spatial transcriptomics analyses of the HO site, we found that collagen ECM organization is the most highly up-regulated biological process in MPCs. Zeugopod mesenchymal cell-specific deletion of Hif1α (Hoxa11-CreERT2; Hif1afl/fl) significantly mitigated HO in vivo. ScRNA-seq analysis of these Hoxa11-CreERT2; Hif1afl/fl mice identified the PLOD2/LOX pathway for collagen cross-linking as downstream of the HIF-1α regulation of HO. Importantly, our scRNA-seq data and mechanistic studies further uncovered that glucose metabolism in MPCs is most highly impacted by HIF-1α deletion. From a translational aspect, a pan-LOX inhibitor significantly decreased HO. A newly screened compound revealed that the inhibition of PLOD2 activity in MPCs significantly decreased osteogenic differentiation and glycolytic metabolism. This suggests that the HIF-1α/PLOD2/LOX axis linked to metabolism regulates HO-forming MPC fate. These results suggest that the HIF-1α/PLOD2/LOX pathway represents a promising strategy to mitigate HO formation.

Increasing access to behavioral health care: Examples of task shifting in two U.S. government health care systems.

INTRODUCTION: Addressing U.S. health disparities in behavioral health care requires innovative solutions to expand access beyond the traditional specialty behavioral health (BH) service model. One evidence-based strategy to increase access is task shifting, whereby tasks usually reserved for licensed clinicians are delegated to less specialized but uniquely capable health workers. Health care systems in the United States have been slow to adopt this approach, despite the widespread success of task shifting in other countries. However, two large government health care systems have employed unique task-shifting models for decades, integrating nonclinician health workers into BH settings: the Defense Health Agency (behavioral health technicians) and the Veterans Health Administration (peer specialists). METHOD: This conceptual article provides overviews of these successful approaches. Challenges and opportunities, and the potential for other U.S. health care systems to adopt task shifting for behavioral health care with paraprofessionals such as community health workers (CHWs), are discussed. RESULTS: CHWs and other paraprofessionals are ideally situated to increase access to behavioral health care, but barriers must be overcome. Recommendations are provided based on lessons from these federal system approaches to task shifting. DISCUSSION: Expanding task-shifting paradigms as the Defense Health Agency and Veterans Health Administration have done may be vital to reaching more people who could benefit from BH intervention and prevention strategies. (PsycInfo Database Record (c) 2024 APA, all rights reserved).

Developing a Text Messaging Intervention to Prevent Binge and Heavy Drinking in a Military Population: Mixed Methods Development Study.

BACKGROUND: Alcohol misuse is the fourth leading cause of death in the United States and a significant problem in the US military. Brief alcohol interventions can reduce negative alcohol outcomes in civilian and military populations, but additional scalable interventions are needed to reduce binge and heavy drinking. SMS text messaging interventions could address this need, but to date, no programs exist for military populations. OBJECTIVE: We aimed to develop an SMS text messaging intervention to address binge and heavy drinking among Airmen in Technical Training in the US Air Force. METHODS: We implemented a 2-phase, mixed methods study to develop the SMS text messaging intervention. In phase 1, a total of 149 respondents provided feedback about the persuasiveness of 49 expert-developed messages, preferences regarding message frequency, timing and days to receive messages, and suggested messages, which were qualitatively coded. In phase 2, a total of 283 respondents provided feedback about the persuasiveness of 77 new messages, including those developed through the refinement of messages from phase 1, which were coded and assessed based on the Behavior Change Technique Taxonomy (BCTT). For both phases, mean persuasiveness scores (range 1-5) were calculated and compared according to age (aged <21 or ≥21 years) and gender. Top-ranking messages from phase 2 were considered for inclusion in the final message library. RESULTS: In phase 1, top-rated message themes were about warnings about adverse outcomes (eg, impaired judgment and financial costs), recommendations to reduce drinking, and invoking values and goals. Through qualitative coding of suggested messages, we identified themes related to warnings about adverse outcomes, recommendations, prioritizing long-term goals, team and belonging, and invoking values and goals. Respondents preferred to receive 1 to 3 messages per week (124/137, 90.5%) and to be sent messages on Friday, Saturday, and Sunday (65/142, 45.8%). In phase 2, mean scores for messages in the final message library ranged from 3.31 (SD 1.29) to 4.21 (SD 0.90). Of the top 5 highest-rated messages, 4 were categorized into 2 behavior change techniques (BCTs): valued self-identity and information about health consequences. The final message library includes 28 BCTT-informed messages across 13 BCTs, with messages having similar scores across genders. More than one-fourth (8/28, 29%) of the final messages were informed by the suggested messages from phase 1. As Airmen aged <21 years face harsher disciplinary action for alcohol consumption, the program is tailored based on the US legal drinking age. CONCLUSIONS: This study involved members from the target population throughout 2 formative stages of intervention development to design a BCTT-informed SMS text messaging intervention to reduce binge and heavy drinking, which is now being tested in an efficacy trial. The results will determine the impact of the intervention on binge drinking and alcohol consumption in the US Air Force.

Management of Refractory Post-operative Osteomyelitis and Discitis: A Case Report.

Vertebral osteomyelitis/discitis is a relatively rare disease but is a known potential complication of spinal surgical intervention. In general, the first-line treatment for this condition is targeted antibiotic therapy with surgical intervention only utilized in refractory cases with evidence of extensive damage, structural instability, or abscess formation. However, surgical best practices have not been established for osteomyelitis, including indications for anterior lateral interbody fusion (ALIF), posterior lateral interbody fusion (PLIF), or direct lateral interbody fusion (DLIF). This case provides a discussion of the indications that led to a direct lateral approach in the setting of refractory osteomyelitis/discitis, supporting factors that led to its success, and the efficacy of utilizing intraoperative neuromonitoring in cases of infection.

On The Horizon: Novel Approaches to Sexually Transmitted Infection Prevention.

Rates of sexually transmitted infections (STIs), especially cases of infectious and congenital syphilis, are increasing in the United States. Novel strategies for STI prevention are being explored and include doxycycline post-exposure prophylaxis and the potential utility of vaccines against gonorrhea. Self-collection of samples and point of care testing for STI are increasingly being employed in a variety of settings. Both can improve uptake of screening and lead to earlier detection and treatment of incident STI in target populations. Overcoming existing regulatory issues and optimizing implementation of current evidence-based strategies will be key to maximizing future STI prevention efforts. Here we provide an update for primary care providers on selected new strategies for STI prevention either currently available or under development for possible future use.