Oktoberfest: Open-source spectral library generation and rescoring pipeline based on Prosit.

Machine learning (ML) and deep learning (DL) models for peptide property prediction such as Prosit have enabled the creation of high quality in silico reference libraries. These libraries are used in various applications, ranging from data-independent acquisition (DIA) data analysis to data-driven rescoring of search engine results. Here, we present Oktoberfest, an open source Python package of our spectral library generation and rescoring pipeline originally only available online via ProteomicsDB. Oktoberfest is largely search engine agnostic and provides access to online peptide property predictions, promoting the adoption of state-of-the-art ML/DL models in proteomics analysis pipelines. We demonstrate its ability to reproduce and even improve our results from previously published rescoring analyses on two distinct use cases. Oktoberfest is freely available on GitHub (https://github.com/wilhelm-lab/oktoberfest) and can easily be installed locally through the cross-platform PyPI Python package.

Clinical and Radiological Evaluation of Onlay Mesh Abdominoplasty in Obese Multiparous Patients with Moderate-to-Severe Rectus Diastasis.

BACKGROUND: Women with multiple pregnancies often experience abdominal protrusion and/or a lax abdominal wall. Various open surgical techniques have been developed to address rectus diastasis in abdominoplasty, ranging from suture plication to mesh reinforcement. This study aims to compare the clinical and radiological changes between traditional abdominal plication and the addition of non-absorbable mesh for rectus muscle (RM) diastasis repair in terms of function, postoperative outcome, and recurrence. PATIENTS AND METHOD: This prospective retrospective study involved 63 women who underwent cosmetic tummy tuck surgery and met certain eligibility criteria. Patients with only mild diastasis recti, midline hernia, contraindications for major surgery, recent smoking history, or refusal of mesh augmentation were excluded. Clinical examination for abdominal protrusion or bulging and CT imaging was performed to check for recurrence of diastasis recti. The study included 33 patients who underwent mesh repair and 30 who underwent traditional abdominal plication. Follow-up was conducted after 1 year using CT and a questionnaire to assess various factors compared to preoperative measurements, with overall satisfaction rated on a 10-point Likert scale. RESULTS: There was no significant difference in demographic data between the two groups. Patients who underwent mesh repair had a slightly longer hospital stay and drain duration. The average waist circumference decreased in both groups without any statistically significant difference. Objective CT showed significant reductions in both groups in inter-rectus distance, RM width and circumference, and intra-abdominal circumference compared to preoperative values. All patients expressed satisfaction with scar quality and umbilicus aesthetics, and no recurrence was detected either clinically or radiologically during the follow-up period. CONCLUSION: Comprehensive preoperative assessment and imaging techniques like ultrasound and CT scans allow surgeons to detect postpartum changes in the abdominal wall. Mesh reinforcement may be indicated for diastasis above 4 cm in obese multiparous females. Thorough preoperative evaluation permits customized surgical plans to optimally restore abdominal wall anatomy and function. LEVEL OF EVIDENCE IV: This journal requires that authors assign a level of evidence to each article. For a full description of these Evidence-Based Medicine ratings, please refer to the Table of Contents or the online Instructions to Authors at www.springer.com/00266 .

Prosit-TMT: Deep Learning Boosts Identification of TMT-Labeled Peptides.

The prediction of fragment ion intensities and retention time of peptides has gained significant attention over the past few years. However, the progress shown in the accurate prediction of such properties focused primarily on unlabeled peptides. Tandem mass tags (TMT) are chemical peptide labels that are coupled to free amine groups usually after protein digestion to enable the multiplexed analysis of multiple samples in bottom-up mass spectrometry. It is a standard workflow in proteomics ranging from single-cell to high-throughput proteomics. Particularly for TMT, increasing the number of confidently identified spectra is highly desirable as it provides identification and quantification information with every spectrum. Here, we report on the generation of an extensive resource of synthetic TMT-labeled peptides as part of the ProteomeTools project and present the extension of the deep learning model Prosit to accurately predict the retention time and fragment ion intensities of TMT-labeled peptides with high accuracy. Prosit-TMT supports CID and HCD fragmentation and ion trap and Orbitrap mass analyzers in a single model. Reanalysis of published TMT data sets show that this single model extracts substantial additional information. Applying Prosit-TMT, we discovered that the expression of many proteins in human breast milk follows a distinct daily cycle which may prime the newborn for nutritional or environmental cues.

Alar Base Augmentation Using Vomerine Bone Graft in Patients With Cleft Lip Nasal Deformity.

BACKGROUND: Although many trials have been made to augment the unilateral alar base depression, the ultimate aesthetic satisfaction has proven difficult to achieve. In our study, we present a novel submucosal dissection technique to harvest the vomer bone and use it as an onlay graft to correct the alar base depression. METHODS: We collected a prospective cohort study of 11 patients with unilateral cleft lip nasal deformity. Using CorelDRAW X7 software, we obtained perioperative clinical photographs to analyze the nostril and lateral lip morphometric measurements on the cleft side. Computed tomography scans were used to assess the required graft's volume and to detect resorption. We performed vomerine ostectomy and placed and fixed the bone graft in with a lag screw over the alar base depression. RESULTS: The nostril width showed a significant increase, in addition to the height/width ratio. The columellar angle with the lateral lip height increased remarkably, with a general improvement in the nasal tip aesthetics. CONCLUSIONS: The vomer bone graft has been shown to correct the lateral and inferior disorientation of the alar base and improve the nostril and nasal tip aesthetic measurements. The vomer bone is therefore a sufficient bone source for grafting with high viability and no resorption.

Uses of Smartphone Thermal Imaging in Perforator Flaps as a Versatile Intraoperative Tool: The Microsurgeon's Third Eye.

Introduction: In this study, we evaluate the versatility of smartphone thermal imaging technology as a valuable intraoperative modality in different stages of perforator flap surgery aiming to minimize the complications and achieve the best postoperative outcome. Patients and methods: Thermography was performed in 20 perforator flaps in 20 patients at different surgical stages in three different ways to identify the most dominant perforator: first, by measuring the surface temperature of the skin; second, by using the dynamic infrared thermography technique; and third, by assessing the perfusion pattern when the flap was supplied by each perforator separately. Thermography was used to help in discarding the least perfused area of the flap. After microvascular anastomosis, the flap reheating pattern was evaluated. Results: Seventeen free and three pedicled perforator flaps were included. Intraoperatively, each of the selected perforators had a corresponding hotspot. The perforator with the hottest hotpot, best rewarming, and provision of best flap perfusion on thermography was found clinically dominant. After microvascular anastomosis in free flaps, rapid rewarming was recorded in 15 cases. In two deep inferior epigastric perforator flaps, no rapid rewarming was observed. The pedicle was kinked in one case and there was a venous insufficiency in another case that required a cephalic turndown. All flaps showed good perfusion on thermography after inset. Conclusion: Smartphone thermography has proven to be a valuable, cheap, rapidly employed, and objective tool not only for the design of perforator flaps, but also for the decision making intraoperatively to achieve the best surgical outcome.

Postbariatric Abdominal Contouring: Technical Approach and Quality of Life.

BACKGROUND: Abdominal contouring is a common procedure after bariatric surgery, but few studies on its outcomes have been conducted. The authors measured surgical and functional outcomes after postbariatric abdominal contouring and their effects on quality of life. METHODS: Thirty patients, male and female, of different age groups, underwent postbariatric abdominal contouring using traditional abdominoplasty, fleur-de-lis abdominoplasty, or belt lipectomy. The technical approach was decided according to each patient's presentation regarding the amount and extent of skin redundancy. All patients were given a booklet containing simplified questionnaires to assess quality of life and appearance to fill out both before and 6 months after the procedure. Data were collected face-to-face at the outpatient clinic during follow-up, by e-mail, or by messaging. RESULTS: The authors performed traditional abdominoplasty (seven cases), fleur-de-lis abdominoplasty (eight cases), or belt lipectomy (15 cases). Surgical outcomes (operative time, resection weight, blood transfusion, postoperative hemoglobin level, postoperative albumin level, hospital stay, drain period, and complications) were influenced significantly by the procedure type ( p ≤ 0.01). Health-related quality-of-life and appearance scale scores changed significantly from the precontouring stage to the postcontouring stage. This significant change in functional outcome was not correlated to the technical approach. CONCLUSION: Abdominal contouring surgery improves quality of life after bariatric surgery irrespective of the procedure type. . CLINICAL QUESTION/LEVEL OF EVIDENCE: Therapeutic, IV.