Predicting the impact of rare variants on RNA splicing in CAGI6.

Variants which disrupt splicing are a frequent cause of rare disease that have been under-ascertained clinically. Accurate and efficient methods to predict a variant's impact on splicing are needed to interpret the growing number of variants of unknown significance (VUS) identified by exome and genome sequencing. Here, we present the results of the CAGI6 Splicing VUS challenge, which invited predictions of the splicing impact of 56 variants ascertained clinically and functionally validated to determine splicing impact. The performance of 12 prediction methods, along with SpliceAI and CADD, was compared on the 56 functionally validated variants. The maximum accuracy achieved was 82% from two different approaches, one weighting SpliceAI scores by minor allele frequency, and one applying the recently published Splicing Prediction Pipeline (SPiP). SPiP performed optimally in terms of sensitivity, while an ensemble method combining multiple prediction tools and information from databases exceeded all others for specificity. Several challenge methods equalled or exceeded the performance of SpliceAI, with ultimate choice of prediction method likely to depend on experimental or clinical aims. One quarter of the variants were incorrectly predicted by at least 50% of the methods, highlighting the need for further improvements to splicing prediction methods for successful clinical application.

Modeling Mechanochemical Depolymerization of PET in Ball-Mill Reactors Using DEM Simulations.

Developing efficient and sustainable chemical recycling pathways for consumer plastics is critical for mitigating the negative environmental implications associated with their end-of-life management. Mechanochemical depolymerization reactions have recently garnered great attention, as they are recognized as a promising solution for solvent-free transformation of polymers to monomers in the solid state. To this end, physics-based models that accurately describe the phenomena within ball mills are necessary to facilitate the exploration of operating conditions that would lead to optimal performance. Motivated by this, in this paper we develop a mathematical model that couples results from discrete element method (DEM) simulations and experiments to study mechanically-induced depolymerization. The DEM model was calibrated and validated via video experimental data and computer vision algorithms. A systematic study on the influence of the ball-mill operating parameters revealed a direct relationship between the operating conditions of the vibrating milling vessel and the total energy supplied to the system. Moreover, we propose a linear correlation between the high-fidelity DEM simulation results and experimental monomer yield data for poly(ethylene terephthalate) depolymerization, linking mechanical and energetic variables. Finally, we train a reduced-order model to address the high computational cost associated with DEM simulations. The predicted working variables are used as inputs to the proposed mathematical expression which allows for the fast estimation of monomer yields.

Kinetic Phenomena in Mechanochemical Depolymerization of Poly(styrene).

Synthetic polyolefinic plastics comprise one of the largest shares of global plastic waste, which is being targeted for chemical recycling by depolymerization to monomers and small molecules. One promising method of chemical recycling is solid-state depolymerization under ambient conditions in a ball-mill reactor. In this paper, we elucidate kinetic phenomena in the mechanochemical depolymerization of poly(styrene). Styrene is produced in this process at a constant rate and selectivity alongside minor products, including oxygenates like benzaldehyde, via mechanisms analogous to those involved in thermal and oxidative pyrolysis. Continuous monomer removal during reactor operation is critical for avoiding repolymerization, and promoting effects are exhibited by iron surfaces and molecular oxygen. Kinetic independence between depolymerization and molecular weight reduction was observed, despite both processes originating from the same driving force of mechanochemical collisions. Phenomena across multiple length scales are shown to be responsible for differences in reactivity due to differences in grinding parameters and reactant composition.

Dose-Escalated Radiation Therapy as Primary Treatment for Residual Bladder Cancer After Transurethral Resection.

Purpose: The aim of this study was to determine whether escalating the local radiation dose can improve the outcome of residual bladder cancer after transurethral resection of bladder tumor without increasing treatment-related toxicity. Methods and Materials: The treatment plans and medical records of patients with bladder cancer treated with curative-intent radiation therapy between 2008 and 2020 were reviewed. Those who had residual tumors in the computed tomography simulation images were included. A cumulative radiation dose higher than 6600 cGy was defined as dose escalation. The effect of dose escalation on 3-year locoregional control, progression-free survival, and overall survival was evaluated. Results: A total of 149 patients with residual tumors were identified. The median follow-up period was 27.5 months. Among them, 51 patients received an escalated radiation dose, and 98 received a standard dose in the residual tumor area. Patients in the dose-escalation group had higher 3-year locoregional control (65.6% vs 27.8%; P < .001) and progression-free survival (42.6% vs 18.2%; P < .001) than the standard-dose group. Overall survival also showed a trend favoring the dose-escalation group (54.9% vs 36.2%; P = .059). In the multivariate analyses, the differences between the dose-escalation and standard-dose groups were significant in terms of locoregional control (hazard ratio, 0.32; CI, 0.18-0.59; P = <.001) and progression-free survival (hazard ratio, 0.51; CI, 0.32-0.82; P = .005). There was no statistical difference in acute and chronic treatment-related toxicities between the 2 groups. Conclusions: The outcome of residual bladder cancer after transurethral resection of bladder tumor could be improved by dose-escalated radiation therapy.

Desmethylclomipramine triggers mitochondrial damage and death in TGF-ß-induced mesenchymal type of A549 cells.

Lung cancer is the leading cause of cancer deaths, where the metastasis often causes chemodrug resistance and leads to recurrence after treatment. Desmethylclomipramine (DCMI), a bioactive metabolite of clomipramine, shows the therapeutic efficacy with antidepressive agency as well as potential cytostatic effects on lung cancer cells. Here, we demonstrated that DCMI effectively caused transforming growth factor (TGF)-ß1-mediated mesenchymal type of A549 cells to undergo mitochondrial death via myeloid cell leukemia-1 (Mcl-1) suppression and activation of truncated Bid (tBid). TGF-ß1 induced epithelial mesenchymal transition in A549 cells with the increase of fibronectin and decrease of E-cadherin, the activation of Akt/glycogen synthase kinase-3ß (GSK-ß)/Mcl-1 axis, and the hypo-responsiveness to cisplatin. DCMI initiated a dose-dependent cytotoxicity on TGF-ß1-mediated mesenchymal type of A549 cells through inactivating Akt/GSK-ß/Mcl-1 axis, in which mitochondria instability and caspase-9/3 activation also occurred concurrently. Pharmacological inhibition of caspase-8 and cathepsin B partly reversed tBid expression and mitochondrial damage to further attenuate DCMI-mediated cytotoxicity. Additionally, DCMI presented partial therapeutic effects in treating mesenchymal type of A549 tumor bearing nude mice through an acceleration of cancer cell death. Taken together, DCMI exerts antitumor effects via initiating the mechanisms of Akt/GSK-ß/Mcl-1 inactivation and cathepsin B/caspase-8-regulated mitochondrial death, which suggests its potential role in mesenchymal type of cancer cell therapy.

Transaxillary Capsulorrhaphy with Reimplantation to Correct Bottoming-Out Deformity in Breast Mycobacterial Periprosthetic Infection: A Case Report with Literature Review.

Augmentation mammoplasty is one of the most popular cosmetic surgeries, but there is a high reoperation rate (29.7%) commonly due to capsular contracture, implant malpositioning, infection, and unsatisfactory size. Although infection only accounts for 2% of cases, its management is very challenging, especially with nontuberculous mycobacteria (NTM) infection. Breast prosthetic NTM infection is a rare but is a disastrous condition with an incidence of approximately 0.013%. Immediate salvage reimplantation is usually not suggested, and most studies recommend a gap of 3 to 6 months after combination antibiotics therapy before reimplantation. However, delayed reimplantation often leads to great psychological stress and struggle between the doctor and patient. We present the case report of successful reimplantation in treating prosthetic NTM infections in a 28-year-old female. We discuss a novel technique "transaxillary capsulorrhaphy" to correct the bottoming-out deformity. One year after the combination of antibiotics and surgery, the follow-up computed tomography scan showed complete remission of NTM without recurrence. We discuss the surgical technique in detail. The 1-year follow-up assessment (photos and dynamic video) revealed good cosmesis and reliable correction using the new technique. This report is the first formal description and discussion of one-stage reimplantation following NTM infections. Transaxillary capsulorrhaphy allows for a successful salvage operation when an implant is displaced. This approach provides highly favorable result in eastern women undergoing revision augmentation mammoplasty. This study reflects level of evidence V, considering opinions of respected authorities based on clinical experience, descriptive studies, or reports of expert committees.

Structural and Adsorption Properties of ZIF-8-7 Hybrid Materials Synthesized by Acid Gas-Assisted and De Novo Routes.

The tuning of micropore environments in zeolitic imidazolate frameworks (ZIFs) by mixed-linker synthesis has the potential for enabling new molecular separation properties. However, de novo synthesis of mixed-linker (hybrid) ZIFs is often challenging due to the disparate chemical properties of the different linkers. Here, we elucidate the structure and properties of an unconventional ZIF-8-7 hybrid material synthesized via a controlled-acid-gas-assisted degradation and reconstruction (solvent-assisted crystal redemption, SACRed) strategy. Selective insertion of benzimidazole (ZIF-7 linker) into ZIF-8 using SACRed is used as a facile method to generate a ZIF-8-7 hybrid material that is otherwise difficult to synthesize by de novo methods. Detailed crystal structure and textural characterizations clarify the significant differences in the microstructure of the SACRed-derived ZIF-8-7 hybrid material relative to a de novo synthesized hybrid of the same overall linker composition as well as the parent ZIF-8 material. Unary and binary adsorption measurements reveal the tunability of adsorption characteristics as well as the prevalence of nonideal cooperative mixture adsorption effects that lead to large deviations from predictions made with ideal adsorbed solution theory.