Multi-institutional validation of an AI-based sinus CT analytic platform with olfactory assessments.

KEY POINTS: AI-based CT sinus analysis may have advantages over visual based systems, for example, Lund-Mackay score. Here, we show multi-institutional validation of an AI algorithm using novel OMC classification. Significant, robust correlations are seen between algorithm outputs and clinical outcomes.

An eosinophil peroxidase activity assay predicts acute exacerbations in post-operative chronic rhinosinusitis.

KEY POINTS: EPX activity has been correlated with eCRS diagnosis and baseline disease severity. Herein, EPX activity is shown to correlate with post-operative antibiotic and steroid use in CRS. EPX activity has potential to act as a prognostic biomarker of CRS disease severity and control.

VIBES: a workflow for annotating and visualizing viral sequences integrated into bacterial genomes.

Bacteriophages are viruses that infect bacteria. Many bacteriophages integrate their genomes into the bacterial chromosome and become prophages. Prophages may substantially burden or benefit host bacteria fitness, acting in some cases as parasites and in others as mutualists. Some prophages have been demonstrated to increase host virulence. The increasing ease of bacterial genome sequencing provides an opportunity to deeply explore prophage prevalence and insertion sites. Here we present VIBES (Viral Integrations in Bacterial genomES), a workflow intended to automate prophage annotation in complete bacterial genome sequences. VIBES provides additional context to prophage annotations by annotating bacterial genes and viral proteins in user-provided bacterial and viral genomes. The VIBES pipeline is implemented as a Nextflow-driven workflow, providing a simple, unified interface for execution on local, cluster and cloud computing environments. For each step of the pipeline, a container including all necessary software dependencies is provided. VIBES produces results in simple tab-separated format and generates intuitive and interactive visualizations for data exploration. Despite VIBES's primary emphasis on prophage annotation, its generic alignment-based design allows it to be deployed as a general-purpose sequence similarity search manager. We demonstrate the utility of the VIBES prophage annotation workflow by searching for 178 Pf phage genomes across 1072 Pseudomonas spp. genomes.

RNA language models predict mutations that improve RNA function.

Structured RNA lies at the heart of many central biological processes, from gene expression to catalysis. While advances in deep learning enable the prediction of accurate protein structural models, RNA structure prediction is not possible at present due to a lack of abundant high-quality reference data. Furthermore, available sequence data are generally not associated with organismal phenotypes that could inform RNA function. We created GARNET (Gtdb Acquired RNa with Environmental Temperatures), a new database for RNA structural and functional analysis anchored to the Genome Taxonomy Database (GTDB). GARNET links RNA sequences derived from GTDB genomes to experimental and predicted optimal growth temperatures of GTDB reference organisms. This enables construction of deep and diverse RNA sequence alignments to be used for machine learning. Using GARNET, we define the minimal requirements for a sequence- and structure-aware RNA generative model. We also develop a GPT-like language model for RNA in which triplet tokenization provides optimal encoding. Leveraging hyperthermophilic RNAs in GARNET and these RNA generative models, we identified mutations in ribosomal RNA that confer increased thermostability to the Escherichia coli ribosome. The GTDB-derived data and deep learning models presented here provide a foundation for understanding the connections between RNA sequence, structure, and function.

Fecundity decline is male derived following transfluthrin exposures in a field strain of Aedes albopictus (Diptera: Culicidae).

Volatile pyrethroids are effective in reducing mosquito populations and repelling vectors away from hosts. However, many gaps in knowledge exist for the sublethal impacts of volatile pyrethroids on mosquitoes. To that end, transfluthrin exposures were conducted on a field strain of Aedes albopictus (Skuse) held as a laboratory colony. Dose-response analysis was conducted on both sexes at either 1-4 days old or 5-10 days old. Resultant concentration data were used to evaluate the LC20 and LC50 values in various mate pairings of treatments and controls in which either the male or female was from a selectively treated group and mated with a counterpart that was treated independently. Blood feeding proportion, delayed mortality after a 24-h recovery period, egg collection totals, and F1 larval survival were determined following transfluthrin treatment in the F0, but outcomes were not significant. In contrast, sterility was predicated on male treatment, with treated females resulting in higher overall egg viability. Treated males in the mating pair resulted in significantly lower egg viability and accelerated larval hatch in the F1. Additionally, the presence of sperm in female spermathecae was significantly diminished in test groups containing treated male mosquitoes. Male sublethal effects may be a critical determinant of a mixed population's reproductive success.

Diversity and modularity of tyrosine-accepting tRNA-like structures.

Certain positive-sense single-stranded RNA viruses contain elements at their 3' termini that structurally mimic tRNAs. These tRNA-like structures (TLSs) are classified based on which amino acid is covalently added to the 3' end by host aminoacyl-tRNA synthetase. Recently, a cryoEM reconstruction of a representative tyrosine-accepting tRNA-like structure (TLSTyr) from brome mosaic virus (BMV) revealed a unique mode of recognition of the viral anticodon-mimicking domain by tyrosyl-tRNA synthetase. Some viruses in the hordeivirus genus of Virgaviridae are also selectively aminoacylated with tyrosine, yet these TLS RNAs have a different architecture in the 5' domain that comprises the atypical anticodon loop mimic. Herein, we present bioinformatic and biochemical data supporting a distinct secondary structure for the 5' domain of the hordeivirus TLSTyr compared to those in Bromoviridae Despite forming a different secondary structure, the 5' domain is necessary to achieve robust in vitro aminoacylation. Furthermore, a chimeric RNA containing the 5' domain from the BMV TLSTyr and the 3' domain from a hordeivirus TLSTyr are aminoacylated, illustrating modularity in these structured RNA elements. We propose that the structurally distinct 5' domain of the hordeivirus TLSTyrs performs the same role in mimicking the anticodon loop as its counterpart in the BMV TLSTyr Finally, these structurally and phylogenetically divergent types of TLSTyr provide insight into the evolutionary connections between all classes of viral tRNA-like structures.

No Difference in Acute Outcomes for Patients Undergoing Fix and Replace Versus Fixation Alone in the Treatment of Geriatric Acetabular Fractures.

OBJECTIVES: To compare acute outcomes between patients undergoing fix and replace (FaR) versus open-reduction and internal fixation (ORIF) alone in the treatment of geriatric acetabular fractures. DESIGN: Retrospective Cohort Study. SETTING: Single Level 2 Trauma Center. PATIENT SELECTION CRITERIA: Consecutive acetabular fracture patients ≥ 55 years of age treated by two orthopaedic trauma surgeons at one tertiary care center from January 2017 to April 2022 with FaR versus ORIF were identified. Included were those with complete datasets within the 180-day global period. Excluded were patients with previous ORIF of the acetabulum or femur, or revision total hip arthroplasty. OUTCOME MEASURES AND COMPARISONS: The primary outcomes were length of hospital stay (LOS), postoperative weight-bearing status, postoperative disposition, time to postoperative mobilization, and 90-day readmission rates. Secondary outcomes compared included demographic information, injury mechanism, surgical time, complications, revisions, and preoperative and postoperative Hip Disability and Osteoarthritis Outcomes Score for Joint Replacement (HOOS Jr.) scores. These were compared between FaR and ORIF groups. RESULTS: Seventeen FaR patients (average age 74.5 ± 9.0 years) and 11 ORIF patients (average age 69.4 ± 9.6 years) met inclusion criteria. Mean follow-up was 26.4 months (range: 6-75.6 months). More FaR group patients were ordered immediate weight-bearing as tolerated or partial weight-bearing compared with ORIF alone (70% vs. 9.0%, P = 0.03). More patients in the FaR group had pre-existing hip osteoarthritis compared with ORIF alone (71% vs. 27%, P = 0.05). Fracture classification ( P = 0.03) and Charlson Comorbidity Index ( P = 0.02) differed between the 2 groups. There were no other differences in demographics, LOS ( P = 0.99), postoperative disposition ( P = 0.54), time to postoperative mobilization ( P = 0.38), 90-day readmission rates ( P = 0.51), operative time ( P = 0.06), radiographic union ( P = 0.35), time to union ( P = 0.63), pre- ( P = 0.32) or postoperative HOOS Jr. scores ( P = 0.80), delta HOOS Jr. scores ( P = 0.28), or reoperation rates between groups ( P = 0.15). CONCLUSIONS: FaR and ORIF seem to be sound treatment options in the management of geriatric acetabular fractures. Patients in the FaR group achieved immediate or partial weight-bearing earlier than the ORIF group; however, time to postoperative mobilization did not differ between the two groups. The remainder of acute postoperative outcomes (LOS, postoperative disposition, and 90-day readmission rates) did not differ between the two groups. LEVEL OF EVIDENCE: Therapeutic Level III. See Instructions for Authors for a complete description of levels of evidence.

Heparin-induced thrombocytopenia in lower extremity free tissue transfers.

BACKGROUND: Heparin-induced thrombocytopenia (HIT) an immunologically mediated reaction to heparin products, can lead to severe thrombocytopenia and potentially life-threatening thrombotic events. In microsurgery, a missed or delayed diagnosis of HIT can cause complications requiring revision operations, flap loss, or limb loss. Surgeons must remain vigilant for this uncommon yet potentially devastating condition and keep abreast of management strategies. METHODS: CPT and ICD-10 codes in electronic medical records were used to collect demographic information, clinical courses, and outcomes for patients with a HIT diagnosis who underwent lower extremity free tissue transfer in one institution. RESULTS: The authors' institution performed 415 lower extremity free flaps in 411 patients during the 10-year study period. Flap salvage rate was 71% for compromised lower extremity flaps without HIT, and 25% in those with HIT. Four patients (four flaps) met study inclusion criteria during the study period. Three of the four flaps failed and were later debrided; one was rescued after a takeback for anastomosis revision. Two patients successfully underwent a delayed second free flap procedure after recovery, and one was salvaged with a pedicled muscle flap. CONCLUSIONS: Surgeons should monitor for HIT by establishing coagulation panel and platelet count baselines and trending these values in the early post-operative period for patients treated with heparin products. The 4T score can be used to screen for HIT with high clinical suspicion. Arterial thrombosis or poor flap perfusion despite sound microvascular technique could suggest HIT. Surgical and medical management including strict heparin avoidance can prevent adverse events for these patients.

Characterizing the Suture Pullout Force for Human Small Bowel.

Performing a small bowel anastomosis, or reconnecting small bowel segments, remains a core competency and critical step for the successful surgical management of numerous bowel and urinary conditions. As surgical education and technology moves toward improving patient outcomes through automation and increasing training opportunities, a detailed characterization of the interventional biomechanical properties of the human bowel is important. This is especially true due to the prevalence of anastomotic leakage as a frequent (3.02%) postoperative complication of small bowel anastomoses. This study aims to characterize the forces required for a suture to tear through human small bowel (suture pullout force, SPOF), while analyzing how these forces are affected by tissue orientation, suture material, suture size, and donor demographics. 803 tests were performed on 35 human small bowel specimens. A uni-axial test frame was used to tension sutures looped through 10 × 20 mm rectangular bowel samples to tissue failure. The mean SPOF of the small bowel was 4.62±1.40 N. We found no significant effect of tissue orientation (p = 0.083), suture material (p = 0.681), suture size (p = 0.131), age (p = 0.158), sex (p = .083), or body mass index (BMI) (p = 0.100) on SPOF. To our knowledge, this is the first study reporting human small bowel SPOF. Little research has been published about procedure-specific data on human small bowel. Filling this gap in research will inform the design of more accurate human bowel synthetic models and provide an accurate baseline for training and clinical applications.

Cerebellar Compression by Giant Extracanalicular Osteoma with Central Cholesterol Granuloma.

Temporal bone osteomas comprise 0.1-1% of benign tumors involving the skull, the majority of which arise in the external auditory canal. More rarely, they can arise from the mastoid portion of the temporal bone. These generally present as a slow growing skull base lesion that can cause cosmetic deformity, headache, and/or hearing loss. Here, we report a case of extracanalicular mastoid osteoma uniquely presenting with posterior fossa and cerebellar compression with associated dizziness and imbalance.

Physician views of artificial intelligence in otolaryngology and rhinology: A mixed methods study.

Objective: The study aimed to investigate otolaryngologists' knowledge, trust, acceptance, and concerns with clinical applications of artificial intelligence (AI). Methods: This study used mixed methods with survey and semistructured interviews. Survey was e-mailed to American Rhinologic Society members, of which a volunteer sample of 86 members responded. Nineteen otolaryngologists were purposefully recruited and interviewed until thematic saturation was achieved. Results: Seventy-six respondents (10% response rate) completed the majority of the survey: 49% worked in academic settings and 43% completed residency 10 or fewer years ago. Of 19 interviewees, 58% worked in academic settings, and 47% completed residency 10 or fewer years ago. Familiarity: Only 8% of survey respondents reported having AI training in residency, although 72% had familiarity with general AI concepts; 0 interviewees had personal experience with AI in clinical settings. Expected uses: Of the surveyed otolaryngologists, 82% would use an AI-based clinical decision aid and 74% were comfortable with AI proposing treatment recommendations. However, only 44% of participants would trust AI to identify malignancy and 53% to interpret radiographic images. Interviewees trusted AI for simple tasks, such as labeling septal deviation, more than complex ones, such as identifying tumors. Factors influencing AI adoption: 89% of survey participants would use AI if it improved patient satisfaction, 78% would be willing to use AI if experts and studies validated the technologies, and 73% would only use AI if it increased efficiency. Sixty-one percent of survey respondents expected AI incorporation into clinical practice within 5 years. Interviewees emphasized that AI adoption depends on its similarity to their clinical judgment and to expert opinion. Concerns included nuanced or complex cases, poor design or accuracy, and the personal nature of physician-patient relationships. Conclusion: Few physicians have experience with AI technologies but expect rapid adoption in the clinic, highlighting the urgent need for clinical education and research. Otolaryngologists are most receptive to AI "augmenting" physician expertise and administrative capacity, with respect for physician autonomy and maintaining relationships with patients. Level of Evidence: Level VI, descriptive or qualitative study.

A generalizable scaffold-based approach for structure determination of RNAs by cryo-EM.

Single-particle cryo-electron microscopy (cryo-EM) can reveal the structures of large and often dynamic molecules, but smaller biomolecules (≤50 kDa) remain challenging targets due to their intrinsic low signal to noise ratio. Methods to help resolve small proteins have been applied but development of similar approaches to aid in structural determination of small, structured RNA elements have lagged. Here, we present a scaffold-based approach that we used to recover maps of sub-25 kDa RNA domains to 4.5-5.0 Å. While lacking the detail of true high-resolution maps, these maps are suitable for model building and preliminary structure determination. We demonstrate this method helped faithfully recover the structure of several RNA elements of known structure, and that it promises to be generalized to other RNAs without disturbing their native fold. This approach may streamline the sample preparation process and reduce the optimization required for data collection. This first-generation scaffold approach provides a robust system to aid in RNA structure determination by cryo-EM and lays the groundwork for further scaffold optimization to achieve higher resolution.

ACAA2 is a novel molecular indicator for cancers with neuroendocrine phenotype.

BACKGROUND: Neuroendocrine phenotype is commonly associated with therapy resistance and poor prognoses in small-cell neuroendocrine cancers (SCNCs), such as neuroendocrine prostate cancer (NEPC) and small-cell lung cancer (SCLC). Expression levels of current neuroendocrine markers exhibit high case-by-case variability, so multiple markers are used in combination to identify SCNCs. Here, we report that ACAA2 is elevated in SCNCs and is a potential molecular indicator for SCNCs. METHODS: ACAA2 expressions in tumour xenografts, tissue microarrays (TMAs), and patient tissues from prostate and lung cancers were analysed via immunohistochemistry. ACAA2 mRNA levels in lung and prostate cancer (PC) patients were assessed in published datasets. RESULTS: ACAA2 protein and mRNA levels were elevated in SCNCs relative to non-SCNCs. Medium/high ACAA2 intensity was observed in 78% of NEPC PDXs samples (N = 27) relative to 33% of adeno-CRPC (N = 86), 2% of localised PC (N = 50), and 0% of benign prostate specimens (N = 101). ACAA2 was also elevated in lung cancer patient tissues with neuroendocrine phenotype. 83% of lung carcinoid tissues (N = 12) and 90% of SCLC tissues (N = 10) exhibited medium/high intensity relative to 40% of lung adenocarcinoma (N = 15). CONCLUSION: ACAA2 expression is elevated in aggressive SCNCs such as NEPC and SCLC, suggesting it is a potential molecular indicator for SCNCs.

VIBES: A Workflow for Annotating and Visualizing Viral Sequences Integrated into Bacterial Genomes.

Bacteriophages are viruses that infect bacteria. Many bacteriophages integrate their genomes into the bacterial chromosome and become prophages. Prophages may substantially burden or benefit host bacteria fitness, acting in some cases as parasites and in others as mutualists, and have been demonstrated to increase host virulence. The increasing ease of bacterial genome sequencing provides an opportunity to deeply explore prophage prevalence and insertion sites. Here we present VIBES, a workflow intended to automate prophage annotation in complete bacterial genome sequences. VIBES provides additional context to prophage annotations by annotating bacterial genes and viral proteins in user-provided bacterial and viral genomes. The VIBES pipeline is implemented as a Nextflow-driven workflow, providing a simple, unified interface for execution on local, cluster, and cloud computing environments. For each step of the pipeline, a container including all necessary software dependencies is provided. VIBES produces results in simple tab separated format and generates intuitive and interactive visualizations for data exploration. Despite VIBES' primary emphasis on prophage annotation, its generic alignment-based design allows it to be deployed as a general-purpose sequence similarity search manager. We demonstrate the utility of the VIBES prophage annotation workflow by searching for 178 Pf phage genomes across 1,072 Pseudomonas spp. genomes. VIBES software is available at https://github.com/TravisWheelerLab/VIBES.

A conserved class of viral RNA structures regulate translation reinitiation through dynamic ribosome interactions.

Certain viral RNAs encode proteins downstream of the main protein coding region, expressed through "termination-reinitiation" events, dependent on RNA structure. RNA elements located upstream of the first stop codon within these viral mRNAs bind the ribosome, preventing ribosome recycling and inducing reinitiation. We used bioinformatic methods to identify new examples of viral reinitiation-stimulating RNAs and experimentally verified their secondary structure and function. We determined the structure of a representative viral RNA-ribosome complex using cryoEM. 3D classification and variability analyses reveal that the viral RNA structure can sample a range of conformations while remaining tethered to the ribosome, which enabling the ribosome to find a reinitiation start site within a limited range of mRNA sequence. Evaluating the conserved features and constraints of this entire RNA class in the context of the cryoEM reconstruction provides insight into mechanisms enabling reinitiation, a translation regulation strategy employed by many other viral and eukaryotic systems.

Potato Non-Specific Lipid Transfer Protein StnsLTPI.33 Is Associated with the Production of Reactive Oxygen Species, Plant Growth, and Susceptibility to Alternaria solani.

Plant non-specific lipid transfer proteins (nsLTPs) are small proteins capable of transferring phospholipids between membranes and binding non-specifically fatty acids in vitro. They constitute large gene families in plants, e.g., 83 in potato (Solanum tuberosum). Despite their recognition decades ago, very few have been functionally characterized. Here, we set out to better understand the function of one of the potato members, StnsLTPI.33. Using quantitative polymerase chain reaction, we show that StnsLTPI.33 is expressed throughout the potato plant, but at relatively higher levels in roots and leaves compared to petals, anthers, and the ovary. We also show that ectopically-expressed StnsLTPI.33 fused to green fluorescent protein colocalized with an apoplastic marker in Nicotiana benthamiana leaves, indicating that StnsLTPI.33 is targeted to the apoplast. Constitutive overexpression of the StnsLTPI.33 gene in potato led to increased levels of superoxide anions and reduced plant growth, particularly under salt stress conditions, and enhanced susceptibility to Alternaria solani. In addition, StnsLTPI.33-overexpressing plants had a depleted leaf pool of pipecolic acid, threonic acid, and glycine, while they accumulated putrescine. To our knowledge, this is the first report of an nsLTP that is associated with enhanced susceptibility to a pathogen in potato.

Dominance status modulates activity in medial amygdala cells with projections to the bed nucleus of the stria terminalis.

The medial amygdala (MeA) controls several types of social behavior via its projections to other limbic regions. Cells in the posterior dorsal and posterior ventral medial amygdala (MePD and MePV, respectively) project to the bed nucleus of the stria terminalis (BNST) and these pathways respond to chemosensory cues and regulate aggressive and defensive behavior. Because the BNST is also essential for the display of stress-induced anxiety, a MePD/MePV-BNST pathway may modulate both aggression and responses to stress. In this study we tested the hypothesis that dominant animals would show greater neural activity than subordinates in BNST-projecting MePD and MePV cells after winning a dominance encounter as well as after losing a social defeat encounter. We created dominance relationships in male and female Syrian hamsters (Mesocricetus auratus), used cholera toxin b (CTB) as a retrograde tracer to label BNST-projecting cells, and collected brains for c-Fos staining in the MePD and MePV. We found that c-Fos immunoreactivity in the MePD and MePV was positively associated with aggression in males, but not in females. Also, dominant males showed a greater proportion of c-Fos+ /CTB+ double-labeled cells compared to their same-sex subordinate counterparts. Another set of animals received social defeat stress after acquiring a dominant or subordinate social status and we stained for stress-induced c-Fos expression in the MePD and MePV. We found that dominant males showed a greater proportion of c-Fos+ /CTB+ double-labeled cells in the MePD after social defeat stress compared to subordinates. Also, dominants showed a longer latency to submit during social defeat than subordinates. Further, in males, latency to submit was positively associated with the proportion of c-Fos+ /CTB+ double-labeled cells in the MePD and MePV. These findings indicate that social dominance increases neural activity in BNST-projecting MePD and MePV cells and activity in this pathway is also associated with proactive responses during social defeat stress. In sum, activity in a MePD/MePV-BNST pathway contributes to status-dependent differences in stress coping responses and may underlie experience-dependent changes in stress resilience.

Postpolymerization Modification by Nucleophilic Addition to Styrenic Carbodiimides.

Carbodiimides are electrophilic functional groups that react with select nucleophiles under mild conditions. However, their potential as platforms for postpolymerization modification has been relatively underexplored. We describe the synthesis and radical polymerization of a styrenic carbodiimide which undergoes rapid nucleophilic addition with primary and secondary alkyl amines under ambient conditions, even in the presence of other protic nucleophiles. The monomer is amenable to both free and controlled radical (co)polymerization, and we further demonstrate the utility of this approach by preparing covalent adaptable networks through guanylation of the styrenic carbodiimide with difunctional amines. These materials exhibit a variation in relaxation times according to both the guanidine structure and concentration, providing a facile means for tuning dynamic behavior.

A Generalizable Scaffold-Based Approach for Structure Determination of RNAs by Cryo-EM.

Single-particle cryo-electron microscopy (cryo-EM) can reveal the structures of large and often dynamic molecules, but smaller biomolecules remain challenging targets due to their intrinsic low signal to noise ratio. Methods to resolve small proteins have been applied but development of similar approaches for small structured RNA elements have lagged. Here, we present a scaffold-based approach that we used to recover maps of sub-25 kDa RNA domains to 4.5 - 5.0 Å. While lacking the detail of true high-resolution maps, these are suitable for model building and preliminary structure determination. We demonstrate this method faithfully recovers the structure of several RNA elements of known structure, and it promises to be generalized to other RNAs without disturbing their native fold. This approach may streamline the sample preparation process and reduce the optimization required for data collection. This first-generation scaffold approach provides a system for RNA structure determination by cryo-EM and lays the groundwork for further scaffold optimization to achieve higher resolution.