Abundant but short second‐generation sequencing reads make assembly difficult, leading to fragmented genomes and gene annotations. Gene structure information from RNA sequences can be used to improve the completeness and contiguity of an assembly, but bioinformatics methods have been lacking. Rascaf is a highly efficient tool leveraging long‐range continuity information from intron spanning RNA sequencing (RNA‐seq) read pairs to detect new contig connections. It determines a heaviest path in an exon block graph that simultaneously represents a gene and the underlying contig relationships. Rascaf is more accurate than its competitors, highly precise, and finds thousands of new verifiable connections in several draft Rosaceae genomes. Lightweight and practical, it can be readily incorporated into sequencing pipelines to improve an assembly and its gene annotations.

The purpose of our study was to examine the impact that an increased body mass index (BMI) has on arthroscopic rotator cuff repair (aRCR) outcomes. We identified a sample of 313 patients who underwent aRCR at our institution from 2017 to 2020. Patients were classified into cohorts by BMI: normal BMI (<25), overweight (25-30), and obese (≥30). Patient-Reported Outcomes Measurement Information System (PROMIS) scores (Pain Interference, Pain Intensity, and Upper Extremity) and Clinical Global Impressions scale rating of pain and functional improvement after surgery were obtained at 1 year postoperatively. The significance of the BMI category as a predictor for outcomes was evaluated using multiple linear and multivariable logistic regressions. Receiver operating characteristic curve analysis with Youden’s J-statistic was used to determine optimal BMI cutoff for predicting likelihood of achieving minimum clinically important difference (MCID) and substantial clinical benefit (SCB) on the Clinical Global Impressions scales. Obesity was a significant predictor of reduced preoperative-to-postoperative improvement in the PROMIS Upper Extremity score (P = .04). However, BMI was not predictive of other preoperative-to-postoperative differences in outcome scores or the size and number of cuff tendons torn (P > .05). Optimal BMI cutoffs were determined for pain MCID (40.8), pain SCB (26.8), function MCID (27.4), and function SCB (26.8), but all cutoffs had low correct classification rates (≤13%). Obesity was not found to be an independent risk factor for increased rotator cuff tear size or tendon involvement but was nonetheless associated with worse upper extremity function and pain after aRCR.

Background: Single-stage medial meniscus allograft transplantation (MAT) with concomitant anterior cruciate ligament reconstruction (ACLR) is a technically challenging procedure for management of knee pain and instability in younger patients, but clinical and functional outcomes data are sparse. The purpose of this study was to assess surgical and patient-reported outcomes following concomitant ACLR and medial MAT. Methods: We conducted a retrospective case series of patients who underwent medial MAT with concomitant primary or revision ACLR at our institution from 2010 to 2021 and had minimum 12-month follow-up. Complications, reoperations, visual analog scale (VAS) pain, satisfaction, Lysholm score, return to sport, and return to work outcomes were assessed. Patient-Reported Outcomes Measurement Information System (PROMIS) Pain Interference, Pain Intensity, and Physical Function Scores were used to measure patients’ functional status relative to the US population. P-values < 0.05 were considered significant. Results: The cohort consisted of 17 knees of 16 individual patients. The cohort was majority male (82.4%) with mean age of 31.9 years (range 19–49 years) and mean body mass index (BMI) of 27.9 kg/m² (range 22.5–53.3 kg/m²). Mean follow-up time was 56.8 months (range 13–106 months). Most patients underwent revision ACLR (64.7%). The 1-year reoperation rate was high (23.5%), with two patients (11.8%) tearing their meniscus graft. Patient-reported outcomes indicated low VAS pain (mean 2.2), high satisfaction (mean 77.9%), and fair Lysholm score (mean 81.1). Return to work rate was high (92.9%), while return to sport rate was low (42.9%). Postoperative PROMIS scores were comparable or superior to the national average and correlated significantly with patient satisfaction (p < 0.05). Conclusions: The concomitant ACLR and MAT procedure is associated with excellent knee pain and functional outcomes and high rate of return to work after surgery, though the 1-year reoperation rate is high and rate of return to sport is low. Level of evidence: IV.

The purpose of this study was to identify prognostic factors that are associated with improvements in patient-reported outcomes measures (PROMs) related to upper extremity function and pain in those suffering from idiopathic adhesive capsulitis. All patients treated conservatively for primary idiopathic adhesive capsulitis were identified from our institutional database between 2019 and 2021. Exclusion criteria included any patients treated surgically, follow-up less than one year, or incomplete survey results. PROMs including Patient-Reported Outcomes Measurement Information System (PROMIS) Upper Extremity Computer Adaptive Test Version 2.0 (P-UE), Pain Interference (P-Interference), Pain Intensity (P-Intensity), and visual analog scale (VAS) pain scores. They were obtained at initial consultation and at one year to assess patient-perceived impact of their condition. Multiple linear and multivariable logistic regressions were performed to identify factors associated with improvement in patient-perceived pain and shoulder function using final PROM scores and difference in PROM scores from initial consultation. An independent t-test was used to compare baseline and one-year minimum follow-up PROMs. Odds ratios and their 95% confidence intervals were calculated for each factor; a P value of < .05 was considered statistically significant. A total of 56 patients (40 females and 16 males) were enrolled in the study with an average age of 54.7 ± 7.7 years. A significant improvement (P < .001) was demonstrated at one-year minimum outcomes for P-UE, P-Interference, P-Intensity, and VAS scores. With respect to comorbid conditions, hypothyroidism [P-UE (β: 9.57, P = .006)] was associated with greater improvements in PROMs, while hyperlipidemia [P-UE (β: -4.13, P = .01) and P-Intensity (β: 2.40, P = .02)] and anxiety [P-UE (β: -4.13, P = .03)] were associated with poorer reported changes in PROMs. Female sex [P-UE (β: 4.03, P = .007) and P-Interference (β: -2.65, P = .04)] and employment in manual labor professions [P-Interference (β: -3.07, P = .01), P-Intensity (β: -2.92, P = .006), and VAS (β: -0.66, P = .03)] were associated with significantly better patient-perceived outcomes. Hispanic heritage was associated with higher reported changes of P-Intensity (β: 8.45, P = .004) and VAS (β: 2.65, P = .002). Patient-perceived improvements in PROMIS score during the natural history of adhesive capsulitis are likely multifactorial, with anxiety, hyperlipidemia, increased body mass index, and Hispanic heritage associated with reduced improvement in PROMIS scores.