Citations

Abstract Accurate taxonomic profiling of human microbiomes is essential for advancing research and understanding the complex role microbial communities play in human health. When using shotgun metagenomics, the sequencing data is analyzed through metagenomic pipelines, which incorporate various open-source tools and classify microbes based on matched paired-end DNA reads. However, differences in sequencing and computational approaches can produce substantially different microbiome profiles from the same sample, making validation critical. One approach for validation is benchmarking with realistic mock communities, but this remains relatively rare. Additionally, existing benchmarks often overlook microbiome variability across life stages and body sites, limiting their clinical and research utility. Here, we developed age- and body site-stratified synthetic metagenomes, enabling context-aware benchmarking of microbiome pipelines. Using novelty-based sampling to prioritize microbial diversity and minimize redundancy among selected samples, we selected 300 representative, real biological samples spanning six categories: adult, child, toddler, and infant (>6 months and <6 months) gut samples, as well as adult vaginal samples. We validated three pipelines, Tiny Health’s proprietary Metagenomic Classifier v2 (THMCv2), MetaPhlAn4, and Kraken2+Bracken, using precision, recall, F1 score, and area under the precision-recall curve (AUPR) across age groups and sample types. THMCv2 demonstrated higher recall and F1 scores, detecting more taxa across sample types and ages, while MetaPhlAn4 achieved the highest precision. THMCv2 also achieved the highest area under the precision-recall curve, reflecting peak performance across both abundant and rare species. When analyses were weighted by abundance, THMCv2 and MetaPhlAn4 each characterized the mock community nearly perfectly. Errors for THMCv2 were largely restricted to very low-abundance taxa (<0.001%), whereas MetaPhlAn4 occasionally produced false positives for higher-abundance taxa. Species-level analyses of clinically relevant microbes confirmed these patterns, with THMCv2 demonstrating higher sensitivity, MetaPhlAn4 higher specificity, and Kraken2 lower overall performance. These results demonstrate clear precision-recall trade-offs in metagenomic profiling. This benchmarking framework provides a reproducible approach for evaluating pipeline performance across diverse microbiome contexts and life stages.

Cercospora leaf spot (CLS) is a destructive disease of sugar beet (Beta vulgaris ssp. vulgaris L.) for which resistance conferred by the gene BvCR4 has been introgressed from sea beet (B. vulgaris ssp. maritima). BvCR4-mediated resistance has been broadly deployed to manage CLS globally in sugar beet; however, continuous implementation exerts strong selection pressure, increasing the risk of disease outbreaks due to resistance-breaking C. beticola populations. This study aimed to identify BvCR4 variants in public B. vulgaris spp. germplasm to assess their genetic and structural diversity. Polymerase chain reaction screening of 589 public B. vulgaris spp. germplasm detected BvCR4 homologs in 32 accessions with diverse responses to CLS including historically relevant sugar beet lines represented in breeding programs and Mediterranean sea beet populations of diverse genetic backgrounds. Analysis of the genomic sequences revealed higher diversity in sea beet compared to sugar beet. Additionally, population genetic analysis indicated that BvCR4 homologs in sugar beet likely originated from sea beet populations in Italy and Greece. We identified historical cultivated materials carrying full proteins encoded by BvCR4 alleles and delineated geographic regions where sea beet populations harbor BvCR4 homologs that may be useful in breeding programs. Structural variation was largely circumscribed within leucine-rich repeat domains, although CLS resistance phenotyping was not associated with specific polymorphisms, suggesting BvCR4-mediated resistance may rely on interactions with other co-receptors. This study provides resources for sugar beet improvement by enabling the identification of BvCR4 homologs in diverse germplasm and disclosing materials with potentially novel resistance.

ABSTRACT Clinical pharmacists are increasingly recognized as vital contributors to acute stroke care, yet their role remains inconsistently defined and underutilized across health care systems. This consensus statement explores the expanding presence of clinical pharmacists within interdisciplinary stroke teams, particularly in the management of both acute ischemic stroke ( AIS ) and hemorrhagic stroke. This consensus statement panel was composed of clinical pharmacists, emergency medicine physicians, and a vascular neurologist. The Grading of Recommendations, Assessment, Development, and Evaluation ( GRADE ) approach was used to assess the level of certainty and strength of recommendations. We focused on two questions regarding the clinical pharmacist's role in caring for adult patients presenting to the emergency department ( ED ) with AIS or hemorrhagic stroke. Despite the very low level of evidence, a consensus was reached for the following recommendations: (1) clinical pharmacist involvement in AIS care for adult patients presenting to the ED and (2) clinical pharmacist involvement in hemorrhagic stroke care for adult patients presenting to the ED . Based on the available literature, we believe optimizing the clinical pharmacist role is a critical factor in improving time‐sensitive treatment and equity in care delivery.

Abstract While the launch of the da Vinci Surgical System catalyzed the expansion of robotic surgery across disciplines, adoption in plastic surgery remains modest. To explore this disconnect, this study surveys plastic surgeons to gauge interest, utilization, and perceived barriers to robotic surgery adoption. A 15-question survey on training, access, interest, and barriers to robotic procedures was developed on Qualtrics and distributed via email to members of the American Society of Plastic Surgeons (ASPS) in May 2024. Descriptive statistics were used to summarize responses. About 123 responses were collected among 3,512 survey recipients. Among respondents, 84.6% reported having access to a surgical robot; however, only 13.8% had training on robotic systems during residency, and only 12.2% utilized the technology for plastic surgery procedures. Interest in robotics was noted among 47.9% of respondents, particularly for deep inferior epigastric perforator (DIEP) flap procedures (65.5%), rectus/Vertical Rectus Abdominis Myocutaneous (VRAM) flap (58.2%), and hernia repairs (27.3%). Key barriers to adoption included training requirements (63.9%), lack of demand (60.2%), increased operative time (54.6%), and financial concerns (26.9%). Additional obstacles cited were credentialing difficulties and skepticism about the necessity of robotics in plastic surgery. The present survey identified inadequate training, high costs, and limited demand as key barriers to the adoption of robotics in plastic surgery, reflecting the current lack of robotic integration into residency curricula, as well as the substantial investment and maintenance costs associated with robotic systems. Nevertheless, the strong interest in robotics highlights the need for expanded training programs, promotion of clinical benefits, and research quantifying potential downstream savings to overcome these barriers.

Abstract Gangliosides are structurally complex glycosphingolipids that regulate cellular signaling via interactions with extracellular binding partners and by influencing protein function within the membrane. Their comprehensive analysis remains analytically challenging, in part due to low endogenous abundance, extensive structural diversity, and the frequent occurrence of isomeric species arising from both glycan and ceramide moieties. Here, we present a hydrophilic interaction liquid chromatography (HILIC) nanoelectrospray ionization tandem mass spectrometry (nanoESI-MS/MS) method specifically designed to achieve isomer-resolved analysis and molecular species-level quantification of gangliosides. To improve characterization of low-abundance fatty acyl fragments, the workflow was extended by combining nanoESI with online fraction collection and subsequent direct infusion. The method demonstrated stable chromatographic performance, high sensitivity, and reproducible quantitative results across ten mouse tissues. Application of the workflow enabled quantification of 80 ganglioside molecular species belonging to 18 subclasses and revealed pronounced tissue-specific differences in subclass distribution and ceramide composition. Overall, this study establishes a robust and sensitive platform for comprehensive ganglioside analysis, providing new opportunities to investigate ganglioside diversity, regulation, and function in complex biological systems.

Abstract INTRODUCTION We integrate visual and quantitative metrics in white matter and medial temporal lobe to examine relationships with neuropathology in a community cohort. METHODS Postmortem in situ MRI (T1, T2, DWI) was performed in 25 human brains, followed by visual ratings (Fazekas, MTA, ERICA, Koedam). Neuropathology included ADNC, LATE-NC, hippocampal sclerosis, PART, ARTAG, Lewy pathology, and CAA. RESULTS Increased Fazekas score was linked to aging, lower education, hypertension, higher basilar artery wall thickness, and greater Braak NFT stage. WMH volume also correlated with lacunes, Thal phase, and CERAD score that was not observed using Fazekas. Hippocampal volumes were lower in elderly, less educated people and were associated with higher atrophy scores and higher Braak NFT stage. Higher amygdala volume was only associated with higher CERAD score. DISCUSSION Quantitative MRI may detect neuropathologic associations more sensitively than visual ratings. Tau pathology is a key predictor of WMH burden and hippocampal atrophy.

Purpose of review Photon-counting detector computed tomography (PCD-CT) represents a major technological advancement in computed tomography, offering improved spatial resolution, reduced image noise, and increased dose efficiency compared with conventional energy-integrating detector CT (EID-CT). Because many clinically relevant structures within the temporal bone are submillimeter in size, the temporal bone represents an ideal region for determining whether these technical improvements translate into meaningful clinical benefits. This review evaluates the emerging literature on PCD-CT in temporal bone imaging and examines whether higher spatial resolution meaningfully impacts clinical decision-making. Recent findings Recent studies demonstrate improved visualization of middle ear anatomy, ossicular prostheses, cochlear implant electrode arrays, and superior semicircular canal dehiscence with PCD-CT compared with conventional CT. Improved spatial resolution and reduced metal artifact have been shown to enhance assessment of prosthesis positioning, cochlear duct measurements, and differentiation of true versus near semicircular canal dehiscence. However, given the recent availability of PCD-CT, most studies to date have focused on cadaveric studies, phantom studies, or patient studies evaluating image quality rather than diagnostic accuracy or clinical outcomes. Summary PCD-CT provides substantially improved visualization of submillimeter temporal bone structures and may improve diagnostic confidence in select clinical scenarios. Nevertheless, evidence demonstrating improved clinical outcomes remains limited, and further clinical studies are needed to define the role of PCD-CT in routine temporal bone imaging.

Background. Chronic kidney disease (CKD) is a common complication of nonrenal transplantation, influencing recipients’ morbidity and mortality. The incidence of CKD varies depending on the transplanted organ. Recipients of vascularized composite allotransplantation (VCA) need lifelong immunosuppression similar to that of solid organ transplantation. This study investigated renal function in VCA recipients. Methods. We studied 70 recipients from 17 centers (median follow-up: 8 y): 59 upper extremity, 10 face, and 1 penis transplant. Pretransplant and posttransplant clinical data and sera were collected to calculate the estimated glomerular filtration rate (eGFR) using the CKD Epidemiology collaboration 2021 formula. Results. Pretransplantation, the median eGFR was 105.36 mL/min (range, 71.39–155.39 mL/min). By 3 mo posttransplant, the eGFR had significantly decreased to 78.42 mL/min (range, 32.49–130.74 mL/min; P = 0.001) before stabilizing. Despite higher tacrolimus levels at 3 mo, no correlation with eGFR was found. During follow-up, 17.1% of patients experienced a ≥50% eGFR decline, 10.9% progressed to CKD, and 4.7% developed end-stage kidney disease. Some risk factors were identified, but their responsibility could not be established with certainty because of the low number of severe renal outcomes. Conclusions. Renal function declines in the majority of VCA recipients, but the function loss is lower compared with nonrenal solid organ transplantation recipients. Although no statistically significant correlation could be established between tacrolimus exposure and renal function decline, strategies aiming at minimizing calcineurin inhibitor exposure and avoiding other nephrotoxic causes are recommended to preserve long-term kidney function.