Citations

Abstract We are interested in DNA stiffness in vitro and in vivo . Classical approaches for measuring this parameter in vitro involve tedious T4 DNA ligase-mediated cyclization kinetics experiments performed for one DNA fragment length at a time to establish effective local end-end concentrations ( J -factors). Protein-mediated DNA looping is a more relevant biological reaction. An efficient approach to determine length-dependent protein-mediated DNA J - loop values in vitro has been lacking. We describe LOOP-TAG, a massively-parallel method. We leverage intramolecular DNA looping and tagmentation catalyzed by Tn5 transposase (Tnp) tethered to the terminus of a ∼1,000-bp bead-bound duplex DNA. We detected loops terminating with Tnp. Counts of the resulting DNA looping-dependent bead-bound tagmentation products from deep sequencing determine DNA loop length probabilities at single-base pair resolution for all bead-bound fragments. When normalized to DNA fragment length probabilities from tagmentation using known concentrations of free Tnp, length-dependent J - loop values are directly determined. We demonstrate LOOP-TAG for Tnp tethered in two ways and in the presence of DNA-kinking architectural DNA binding protein Nhp6A. Intermediate length J-loop values are consistent with expectations of wormlike chain theory after accounting for strong sequence-dependence of Tnp. DNA loops are shifted to smaller sizes in the presence of Nhp6A, as predicted. (200/200 words)

Abstract Varlilumab is a monoclonal antibody with agonistic activity on CD27. The efficacy of single-agent PD-1 inhibitors on aggressive B-cell non-Hodkin lymphoma is limited. Preclinical and phase 1 data suggest that Varlilumab is safe and may have synergistic activity with PD-1 inhibitors. In the DIAL study, we explored whether dual immunomodulatory therapy with Varlilumab and Nivolumab in patients with relapsed/refractory aggressive B-NHL was safe and effective. We conducted a randomized phase II clinical trial on adult patients with relapsed/refractory aggressive B-NHL. Patients were randomized to receive Nivolumab monotherapy in the control group and Varlilumab combined with Nivolumab in the experimental group. Crossover to the experimental group was allowed upon progression in the control group. The primary endpoint was the overall response rate based on the Lymphoma Response to Immunomodulatory Therapy Criteria (LYRIC). 54 patients underwent randomization, and 51 received assigned intervention and were included in the intention-to-treat analysis. Objective response was observed in 6 out of 51 patients (ORR 12%). There were 4 responders (ORR 16%) in the Nivolumab group and 2 responders (ORR 7.6%) in the Nivolumab and Varlilumab combination group (p = 0.3). None of the 7 patients that crossed over to the experimental group responded to the addition of Varlilumab. The ORR of patients who were previously exposed to CAR-T cell therapy was 13% (5 out of 39) compared to 8.3% (1 out of 12) in the unexposed patients (p > 0.99). The rate of treatment emergent adverse events was similar between groups, and there was no fatal TEAE in the study. The addition of Varlilumab to Nivolumb did not improve outcomes in patients with aggressive B-NHL. Even though this trial was not designed to evaluate immunotherapy as a rescue therapy after CAR-T failure, most patients (76%) had previously received CAR-T therapy, and their outcomes were equally poor.

Abstract Objective To evaluate whether systemic hormone replacement therapy (HRT) influences recurrence outcomes in postmenopausal patients with idiopathic subglottic stenosis (iSGS). Study Design Retrospective cohort study. Setting Tertiary academic medical center. Methods Postmenopausal women (≥50 years) with iSGS who underwent laser‐wedge excision between 2002 and 2024 were included. Patients were categorized by systemic HRT exposure (oral estrogen, progesterone, combined estrogen‐progesterone, or transdermal estrogen) at or before their first surgery. Overdispersion was assessed for all Poisson models; given significant overdispersion, negative binomial regression with a log‐offset for follow‐up time was used as the primary model. Surgery‐free intervals were analyzed using linear mixed models, and time to first recurrence using Cox regression. Models were adjusted for age, body mass index (BMI), parity, oophorectomy, follow‐up length, surgery type, and serial intralesional steroid injections (SILSI) use. Results Among 125 patients, 96 had never used HRT (Never HRT) and 29 used HRT, including 19 actively using HRT at presentation (Current HRT), 5 past users, and 5 subsequent users. The HRT versus Never‐HRT recurrence rate comparison was not significant (adjusted incidence rate ratio [IRR] = 0.81, 95% CI: 0.48‐1.37, P = .422). However, Current HRT use was associated with a 53% lower adjusted recurrence rate versus Never‐HRT use (adjusted IRR = 0.47, 95% CI: 0.25, 0.89, P = .0203). Surgery‐free intervals and time to first recurrence trended longer in Current HRT users but were not statistically significant. Conclusion Current HRT use at presentation was associated with significantly fewer recurrences in postmenopausal iSGS patients. These findings may inform individualized, shared decision‐making regarding HRT use in this population. Level of Evidence 3.

Purpose To compare short‐term outcomes of intratunnel anchor fixation versus transtibial pull‐through repair for meniscus root tears with a minimum of 12‐month follow‐up. Methods Patients who underwent primary meniscus root repair between 2011 and 2024 at a single institution were retrospectively reviewed. Inclusion criteria consisted of primary medial or lateral meniscus root repair using either intratunnel anchor fixation or transtibial pull‐through repair, availability of preoperative radiographs, and completion of postoperative patient‐reported outcome measures with a minimum of 12‐month follow‐up. The groups were propensity‐matched by age, sex, body mass index, operative side, root laterality, and concomitant procedures. Baseline radiographic characteristics (hip‐knee‐ankle angle and posterior tibial slope) were measured. Outcomes included Lysholm score, International Knee Documentation Committee score, Tegner activity score (preoperative and postoperative), Visual Analog Scale for pain at rest and with activity, satisfaction, subjective surgical outcome, and reoperations. Results Fifty patients who underwent intratunnel anchor fixation (mean age, 44 years) were propensity‐matched to 100 patients who underwent transtibial pull‐through repair (mean age, 41 years). Mean follow‐up was 1.5 years (range, 1.0‐2.3) in the intratunnel anchor group and 6.1 years (range, 2.7‐13.7) in the transtibial pull‐through group. Reoperation rates were 8% and 14%, respectively ( P = .43), with repair failure occurring in 4% and 6% ( P > .99). Preoperative and postoperative Tegner scores were similar between groups. Tegner minimal clinical important difference was 0.8, and 26.5% of intratunnel anchor patients achieved this compared with 0% of transtibial pull‐through patients. Patients in the intratunnel anchor cohort reported slightly lower Visual Analog Scale pain with activity (1.8 vs 2.5, P = .02). Postoperative Lysholm (87 vs 83, P = .05) and International Knee Documentation Committee scores (79 vs 76, P = .09) were comparable between groups. A greater proportion of intratunnel anchor patients achieved Patient Acceptable Symptomatic State compared with transtibial pull‐through patients for Visual Analog Scale with activity (74% vs 56%, P = .03) and Lysholm (66% vs 47%, P = .01). Most patients in both cohorts rated their outcome as “much better” or “slightly better” ( P = .49), and satisfaction scores were high. Conclusions At short‐term follow‐up, both the intratunnel anchor and transtibial pull‐through techniques showed high patient satisfaction and comparable overall clinical outcomes. There were no differences in reoperation rates between techniques. Level of Evidence Level III, retrospective comparative case series.

Background: Large language models (LLMs) are increasingly used in patient-facing clinical applications, creating a need for scalable methods to evaluate the accuracy, safety, and appropriateness of their responses. Although physician review remains the reference standard, it is resource-intensive and difficult to scale. Objective: To develop and clinically validate an LLM-as-a-judge framework for evaluating responses to patients’ periprocedural questions. Methods: We retrospectively evaluated 1285 patient–AIVA interactions from 112 patients across two Mayo Clinic sites and multiple surgical specialties. Physician reviewers classified interactions using a predefined true-positive (TP), false-negative (FN), true-negative (TN), and false-positive (FP) framework. The finalized LLM judge independently evaluated the same interactions. Agreement was assessed using four-class and category-specific agreement, Cohen’s kappa, and a secondary binary analysis of response correctness. Results: Overall, four-class agreement was 93.1% (95% CI, 91.7–94.5%), with Cohen’s κ = 0.852 (95% CI, 0.823–0.882). Category-specific agreement was 94.1% for TP, 90.7% for FN, 95.5% for TN, and 84.9% for FP classifications. In the binary correctness analysis, accuracy was 93.4% (95% CI, 92.0–94.7%), sensitivity 94.6%, specificity 90.2%, precision 96.2%, and F1-score 0.954. McNemar’s test demonstrated no significant asymmetry between paired classifications (p = 0.11). Conclusions: A clinically grounded LLM judge closely approximated physician evaluation of patient-facing AI responses. These findings support its potential as a scalable assistive monitoring tool while preserving physician oversight for uncertain or safety-sensitive interactions.

BACKGROUND Acral lentiginous melanoma (ALM) is a biologically distinct, inherently aggressive, and understudied melanoma subtype without a unified surgical approach. OBJECTIVE To provide an updated review of ALM and offer practical, surgeon-focused guidance on diagnosis, biopsy, margin-controlled excision, and Mohs micrographic surgery (MMS)-based management of ALM. METHODS & MATERIALS A PubMed/MEDLINE search of ALM, with an emphasis on articles published after 2015. RESULTS ALM demonstrates inherent biological aggressiveness characterized by extensive subclinical spread, delayed diagnosis, and higher stage-adjusted recurrence compared with nonacral cutaneous melanomas. Anatomic constraints additionally necessitate specialized surgical approaches, although current management is extrapolated from nonacral melanoma data. Retrospective data support MMS and margin-controlled excision and tissue preservation in ALM, with the benefit of digit-sparing surgery and functional preservation. No randomized trials have included ALM, highlighting a key evidence gap. CONCLUSION Margin-controlled approaches such as MMS may improve local control and tissue preservation in select ALM patients. Prospective ALM-specific research and standardized diagnostic and surgical protocols are strongly needed.

Objective To evaluate the efficacy of cytokine‐directed therapies in VEXAS (vacuoles, E1 enzyme, X‐linked, autoinflammatory somatic) syndrome using previously proposed treatment response criteria. Methods All patients with genetically confirmed VEXAS syndrome who received targeted therapies with JAK inhibitors (JAKi), tumor necrosis factor α inhibitors (TNFαi), or interleukin‐1 (IL‐1) or IL‐6 inhibitors were identified. Clinical and biochemical data were recorded for patients at time of targeted therapy initiation, and at 3‐, 6‐, and 12‐month follow‐up time points. Treatment response was labeled as complete response (CR; normalization of C‐reactive protein [CRP], prednisone <10 mg/day, and resolution of disease activity), partial response (PR; >50% improvement in CRP, >50% prednisone dose reduction, improvement or resolution of disease features), treatment failure (TF; worsening CRP, increasing prednisone, worsening of disease features), or no response (not meeting criteria for CR, PR, or TF). Results Overall, 52 patients received an IL‐1i, IL‐6i, or JAKi therapy. At six‐month follow‐up, 3 of 19 IL‐6i patients experienced CR, 4 of 19 experienced PR, and 7 of 19 experienced TF. 2 of 17 patients receiving JAKi experienced CR, 3 of 17 experienced PR, and 6 of 17 experienced TF. No patients receiving IL‐1i or TNFαi experienced CR, and only 1 of 5 IL‐1i patients experienced PR. Among those still receiving biologic therapy at 12 months, only 1 of 11 receiving IL‐6i and 0 of 7 receiving JAKi experienced CR. Conclusion IL‐6i and JAKi therapies demonstrated limited, unsustained efficacy for management of VEXAS syndrome. IL‐1i and TNFαi therapies were not efficacious. Useful application of previously reported treatment response criteria was demonstrated, but future incorporation of hematologic parameters may be beneficial.

Antisense oligonucleotides (ASOs) represent a promising therapeutic modality for RNA-based disease mechanisms, but identifying high-efficacy candidates from large sequence spaces remains a major bottleneck in drug development. Here, we present ASOFormer, a novel Transformer-based neural network that predicts the inhibition efficiency of RNase H-mediated ASOs from sequence, predicted secondary structure, and chemical modification features. ASOFormer was trained on a knockdown efficacy dataset spanning over 170,000 ASO-target pairs compiled largely from published patents. Ablation analysis confirmed that the addition of chemical modification features to the primary sequence drove the largest performance gains, with predicted secondary structure providing complementary benefit when combined with modification information. Further analysis highlighted the importance of the wings of gapmer ASOs and other features. As independent validation, ASOFormer was applied to ASOs targeting seven genes that were not in the training dataset gene list. For four out of the seven genes, the ground truth ASO inhibition efficiency was obtained from a public dataset, whereas the others were measured in-house via qPCR. Compared to two published state-of-the-art methods, ASOFormer achieved the best overall accuracy and prioritized the strongest inhibitors. Crucially, only ASOFormer consistently exceeded random expectation for top-candidate recovery across all seven test genes.

Abstract Introduction Quantitative interpretation of pediatric brain [ 18 F]-FDG PET is limited by the lack of age-matched normative reference databases, despite substantial developmental variation in cerebral glucose metabolism. This study aimed to construct a large-scale normative pediatric [ 18 F]-FDG PET database and develop an age-specific z-score mapping framework for quantitative evaluation of pediatric epilepsy. Method Pediatric brain PET data were retrospectively derived from clinically acquired whole-body or dedicated [ 18 F]-FDG PET examinations in participants 0–19 years of age without neurologic disease or visible brain abnormalities. A total of 417 PET scans from 341 participants were stratified into five developmental age groups: infancy, early childhood, middle childhood/school age, adolescence, and late adolescence. SUVR maps were generated using whole-brain atlas and brainstem reference regions. Voxel-wise t-test analyses were performed to characterize age- and sex-related metabolic differences. Age-specific voxel-wise mean and standard deviation maps were generated from the normative cohort and used to calculate age-matched hypometabolic z-score maps in 14 pediatric patients with epilepsy. The resulting abnormalities were qualitatively evaluated for concordance with epileptogenic findings identified on clinical MRI and/or PET by expert image review. Results Voxel-wise analyses demonstrated prominent age-dependent SUVR differences, particularly between infancy and older age groups. With whole-brain atlas normalization, older children showed progressively higher relative SUVR in cortical and cerebellar gray matter regions, whereas infancy showed relatively higher SUVR in the occipital cortex, white matter, thalamus, and brainstem. Brainstem normalization produced distinct developmental patterns, emphasizing higher white matter SUVR in infancy and broader gray matter differences in older groups. Sex-related differences were limited and regionally specific. Whole-brain atlas normalization showed lower variability than brainstem normalization and was selected for z-score mapping. In representative epilepsy cases, age-matched z-score maps identified focal or regional hypometabolism corresponding to malformations of cortical development, focal cortical dysplasia, mesial temporal sclerosis, nonlesional MRI cases, remote insult, tumor-related abnormalities, and Sturge-Weber syndrome. Discussion A large-scale normative pediatric [18F]-FDG PET database can support developmentally appropriate quantitative interpretation of pediatric brain PET. Age-matched z-score mapping may complement visual assessment by highlighting abnormal cerebral glucose metabolism in pediatric epilepsy, although findings should be interpreted with MRI, EEG, seizure semiology, and other presurgical data.