TP53_PROF: a machine learning model to predict impact of missense mutations in TP53.

Correctly identifying the true driver mutations in a patient's tumor is a major challenge in precision oncology. Most efforts address frequent mutations, leaving medium- and low-frequency variants mostly unaddressed. For TP53, this identification is crucial for both somatic and germline mutations, with the latter associated with the Li-Fraumeni syndrome (LFS), a multiorgan cancer predisposition. We present TP53_PROF (prediction of functionality), a gene specific machine learning model to predict the functional consequences of every possible missense mutation in TP53, integrating human cell- and yeast-based functional assays scores along with computational scores. Variants were labeled for the training set using well-defined criteria of prevalence in four cancer genomics databases. The model's predictions provided accuracy of 96.5%. They were validated experimentally, and were compared to population data, LFS datasets, ClinVar annotations and to TCGA survival data. Very high accuracy was shown through all methods of validation. TP53_PROF allows accurate classification of TP53 missense mutations applicable for clinical practice. Our gene specific approach integrated machine learning, highly reliable features and biological knowledge, to create an unprecedented, thoroughly validated and clinically oriented classification model. This approach currently addresses TP53 mutations and will be applied in the future to other important cancer genes.

AAPM medical physics practice guideline 13.a: HDR brachytherapy, part A.

The American Association of Physicists in Medicine (AAPM) is a nonprofit professional society whose primary purposes are to advance the science, education, and professional practice of medical physics. The AAPM has more than 8000 members and is the principal organization of medical physicists in the United States. The AAPM will periodically define new practice guidelines for medical physics practice to help advance the science of medical physics and to improve the quality of service to patients throughout the United States. Existing medical physics practice guidelines (MPPGs) will be reviewed for the purpose of revision or renewal, as appropriate, on their fifth anniversary or sooner. Each medical physics practice guideline represents a policy statement by the AAPM, has undergone a thorough consensus process in which it has been subjected to extensive review, and requires the approval of the Professional Council. The medical physics practice guidelines recognize that the safe and effective use of diagnostic and therapeutic radiology requires specific training, skills, and techniques, as described in each document. Reproduction or modification of the published practice guidelines and technical standards by those entities not providing these services is not authorized. The following terms are used in the AAPM practice guidelines: (1) Must and must not: Used to indicate that adherence to the recommendation is considered necessary to conform to this practice guideline. (2) Should and should not: Used to indicate a prudent practice to which exceptions may occasionally be made in appropriate circumstances. Approved by AAPM's Executive Committee April 28, 2022.

Salvage resection plus cesium-131 brachytherapy durably controls post-SRS recurrent brain metastases.

BACKGROUND: Salvage of recurrent previously irradiated brain metastases (rBrM) is a significant challenge. Resection without adjuvant re-irradiation is associated with a high local failure rate, while reirradiation only partially reduces failure but is associated with greater radiation necrosis risk. Salvage resection plus Cs131 brachytherapy may offer dosimetric and biologic advantages including improved local control versus observation, with reduced normal brain dose versus re-irradiation, however data are limited. METHODS: A prospective registry of consecutive patients with post-stereotactic radiosurgery (SRS) rBrM undergoing resection plus implantation of collagen-matrix embedded Cs131 seeds (GammaTile, GT Medical Technologies) prescribed to 60 Gy at 5 mm from the cavity was analyzed. RESULTS: Twenty patients underwent 24 operations with Cs131 implantation in 25 tumor cavities. Median maximum preoperative diameter was 3.0 cm (range 1.1-6.3). Gross- or near-total resection was achieved in 80% of lesions. A median of 16 Cs131 seeds (range 6-30), with a median air-kerma strength of 3.5 U/seed were implanted. There was one postoperative wound dehiscence. With median follow-up of 1.6 years for survivors, two tumors recurred (one in-field, one marginal) resulting in 8.4% 1-year progression incidence (95%CI = 0.0-19.9). Radiographic seed settling was identified in 7/25 cavities (28%) 1.9-11.7 months post-implantation, with 1 case of distant migration (4%), without clinical sequelae. There were 8 cases of radiation necrosis, of which 4 were symptomatic. CONCLUSIONS: With > 1.5 years of follow-up, intraoperative brachytherapy with commercially available Cs131 implants was associated with favorable local control and toxicity profiles. Weak correlation between preoperative tumor geometry and implanted tiles highlights a need to optimize planning criteria.

In vivo imaging characterization of basal cell carcinoma and cutaneous response to high-dose ionizing radiation therapy: A prospective study of reflectance confocal microscopy, dermoscopy, and ultrasonography.

BACKGROUND: Radiation therapy (RT) is a treatment option for select skin cancers. The histologic effects of RT on normal skin or skin cancers are not well characterized. Dermoscopy, high-frequency ultrasonography (HFUS), and reflectance confocal microscopy (RCM) are noninvasive imaging modalities that may help characterize RT response. OBJECTIVES: To describe changes in the tumor and surrounding skin of patients with basal cell carcinoma (BCC) treated with RT. METHODS: The study was conducted between 2014 and 2018. Patients with biopsy-proven BCCs were treated with 42 Gy in 6 fractions using a commercially available brachytherapy device. Dermoscopy, HFUS, and RCM were performed before treatment and at 6 weeks, 3 months, and 12 months after RT. RESULTS: A total of 137 imaging assessments (RCM + dermoscopy + HFUS) were performed in 12 patients. BCC-specific features were present in 81.8%, 91%, and 17% of patients imaged with dermoscopy, RCM, and HFUS at baseline, respectively, before treatment. After treatment, the resolution of these features was noted in 33.4%, 91.7%, and 100% of patients imaged with the respective modalities. No recurrences were seen after a mean of 31.7 months of follow-up. LIMITATIONS: Small sample size and no histopathologic correlation. CONCLUSION: Dermoscopy and HFUS were not as reliable as RCM at characterizing BCC RT response.

The Information Conveyed in a SPAC's Offering.

The popularity of SPACs (Special Purpose Acquisition Companies) has grown dramatically in recent years as a substitute for the traditional IPO (Initial Public Offer). We modeled the average annual return for SPAC investors and found that this financial tool produced an annual return of 17.3%. We then constructed an information model that examined a SPAC's excess returns during the 60 days after a potential merger or acquisition had been announced. We found that the announcement had a major impact on the SPAC's share price over the 60 days, delivering on average 0.69% daily excess returns over the IPO portfolio and 31.6% cumulative excess returns for the entire period. Relative to IPOs, the cumulative excess returns of SPACs rose dramatically in the next few days after the potential merger or acquisition announcement until the 26th day. They then declined but rose again until the 48th day after the announcement. Finally, the SPAC's structure reduced the investors' risk. Thus, if investors buy a SPAC stock immediately after a potential merger or acquisition has been announced and hold it for 48 days, they can reap substantial short-term returns.

Dynamics and Properties of the Cohesive Zone in Rapid Fracture and Friction.

The cohesive zone is the elusive region in which material fracture takes place. Here, the putatively singular stresses at a crack's tip are regularized. We present experiments, performed on PMMA, in which we visualize the cohesive zone of frictional ruptures as they propagate. Identical to shear cracks, these ruptures range from slow velocities to nearly the limiting speeds of cracks. We reveal that the cohesive zone is a dynamic quantity; its spatial form undergoes a sharp transition between distinct phases at a critical velocity. The structure of these phases provides an important window into material properties under the extreme conditions that occur during fracture.

How Fast Cracks in Brittle Solids Choose Their Path.

While we fundamentally understand the dynamics of simple cracks propagating in brittle solids within perfect (homogeneous) materials, we do not understand how paths of moving cracks are determined. We experimentally study strongly perturbed cracks that propagate between 10% and 95% of their limiting velocity within a brittle material. These cracks are deflected by either interaction with sparsely implanted defects or via an intrinsic oscillatory instability in defect-free media. Dense high-speed measurements of the strain fields surrounding the crack tips reveal that crack paths are governed by the direction of maximal strain energy density, even when the near-tip singular fields are highly disrupted. This fundamentally important result may be utilized to either direct or guide running cracks.

Forecasting Bitcoin Trends Using Algorithmic Learning Systems.

This research has examined the ability of two forecasting methods to forecast Bitcoin's price trends. The research is based on Bitcoin-USA dollar prices from the beginning of 2012 until the end of March 2020. Such a long period of time that includes volatile periods with strong up and downtrends introduces challenges to any forecasting system. We use particle swarm optimization to find the best forecasting combinations of setups. Results show that Bitcoin's price changes do not follow the "Random Walk" efficient market hypothesis and that both Darvas Box and Linear Regression techniques can help traders to predict the bitcoin's price trends. We also find that both methodologies work better predicting an uptrend than a downtrend. The best setup for the Darvas Box strategy is six days of formation. A Darvas box uptrend signal was found efficient predicting four sequential daily returns while a downtrend signal faded after two days on average. The best setup for the Linear Regression model is 42 days with 1 standard deviation.

Topological defects govern crack front motion and facet formation on broken surfaces.

Cracks develop intricate patterns on the surfaces that they create. As faceted fracture surfaces are commonly formed by slow tensile cracks in both crystalline and amorphous materials, facet formation and structure cannot reflect microscopic order. Although fracture mechanics predict that slow crack fronts should be straight and form mirror-like surfaces, facet-forming fronts propagate simultaneously within different planes separated by steps. Here we show that these steps are topological defects of crack fronts and that crack front separation into disconnected overlapping segments provides the condition for step stability. Real-time imaging of propagating crack fronts combined with surface measurements shows that crack dynamics are governed by localized steps that drift at a constant angle to the local front propagation direction while their increased dissipation couples to long-ranged elasticity to determine front shapes. We study how three-dimensional topology couples to two-dimensional fracture dynamics to provide a fundamental picture of how patterned surfaces are generated.

Frictional Resistance within the Wake of Frictional Rupture Fronts.

Frictional resistance to slip, τ, is determined by the real area of contact, A, and the shear strength of the contacts forming the frictional interface. We perform simultaneous high-speed local measurements of τ and A at the tail of propagating rupture fronts. Rate dependence is investigated over 2 orders of magnitude of local slip velocities which reach up to ∼1 m/s. A critical slip velocity is observed that signifies a transition in the frictional behavior: enhanced velocity weakening of A and τ. These measurements enable us to infer the contact shear strength, an otherwise elusive quantity, and show that the contact shear strength persistently increases with slip rate. This, surprisingly, contrasts with expected contact softening at the high temperatures induced by rapid sliding.

Brittle Fracture Theory Predicts the Equation of Motion of Frictional Rupture Fronts.

We study rupture fronts propagating along the interface separating two bodies at the onset of frictional motion via high-temporal-resolution measurements of the real contact area and strain fields. The strain measurements provide the energy flux and dissipation at the rupture tips. We show that the classical equation of motion for brittle shear cracks, derived by balancing these quantities, well describes the velocity evolution of frictional ruptures. Our results demonstrate the extensive applicability of the dynamic brittle fracture theory to friction.

Crack front dynamics: the interplay of singular geometry and crack instabilities.

When fast cracks become unstable to microscopic branching (microbranching), fracture no longer occurs in an effective 2D medium. We follow in-plane crack front dynamics via real-time measurements in brittle gels as microbranching unfolds and progresses. We first show that spatially local energy balance quantitatively describes crack dynamics, even when translational invariance is badly broken. Furthermore, our results explain microbranch dynamics; why microbranches form along spatially localized chains and how finite-time formation of cusps along the crack front leads to their death.

Origin of the microbranching instability in rapid cracks.

The origin of the microbranching instability is a long-standing unresolved issue in the fracture of brittle amorphous materials. We investigate the onset of this instability by measuring the real-time dynamics and symmetries of the strain fields produced by rapid tensile cracks in brittle gels. We find that once a simple tensile crack is subjected to shear perturbations, cracks undergo the microbranching instability above a finite velocity-dependent threshold. We further reveal a distinct relation between the microbranching and the oscillatory instabilities of rapid cracks.

Impact of Dietary Fat and Oral Delivery System on Cannabigerol Pharmacokinetics in Adults.

Background and Aims: Cannabigerol (CBG) is a nonintoxicating cannabinoid synthesized in the Cannabis sativa plant that is incorporated into dietary supplements. This study investigated the influence of dietary fat and an emulsified delivery vehicle on CBG pharmacokinetics (PKs) after oral ingestion by adults. Materials and Methods: Consented participants were enrolled in a double-crossover pilot study and were blinded to the delivery vehicle type (isolate or emulsification) and isocaloric meal condition (low-fat=<5 g fat/meal or high-fat [HF]=>30 g fat/meal). The concentration of CBG in human plasma was measured after a single 25 mg dose of CBG using liquid chromatography-tandem mass spectrometry (LC-MS/MS). PK parameters were calculated using noncompartmental analysis. Results: The PKs of the two delivery systems (emulsified vs. non-emulsified) were significantly impacted by the HF meal condition. Participants in the HF meal group exhibited significantly higher area under the plasma concentration time curve from time 0 to last quantifiable value, maximum concentration, and terminal half-life. Participants in the HF meal group also had a significantly lower terminal elimination rate constant and time to maximum concentration (Tmax), in addition to decreased Tmax variation. The threshold for bioequivalence between conditions was not met. An exploratory aim correlated anthropometric measures and previous day's dietary intake on PK parameters which yielded inconsistent results across dietary fat conditions. Conclusions: In aggregate, dietary fat had a greater effect on CBG PKs than the emulsified delivery vehicle. This supports accounting for dietary intake in development of therapeutics and administration guidelines for orally delivered CBG.

Cancer mutational signatures identification in clinical assays using neural embedding-based representations.

While mutational signatures provide a plethora of prognostic and therapeutic insights, their application in clinical-setting, targeted gene panels is extremely limited. We develop a mutational representation model (which learns and embeds specific mutation signature connections) that enables prediction of dominant signatures with only a few mutations. We predict the dominant signatures across more than 60,000 tumors with gene panels, delineating their landscape across different cancers. Dominant signature predictions in gene panels are of clinical importance. These included UV, tobacco, and apolipoprotein B mRNA editing enzyme, catalytic polypeptide (APOBEC) signatures that are associated with better survival, independently from mutational burden. Further analyses reveal gene and mutation associations with signatures, such as SBS5 with TP53 and APOBEC with FGFR3S249C. In a clinical use case, APOBEC signature is a robust and specific predictor for resistance to epidermal growth factor receptor-tyrosine kinase inhibitors (EGFR-TKIs). Our model provides an easy-to-use way to detect signatures in clinical setting assays with many possible clinical implications for an unprecedented number of cancer patients.

Commissioning considerations for the Bravos high-dose-rate afterloader: Towards improving treatment delivery accuracy.

BACKGROUND AND PURPOSE: The upgrade of major equipment can be disruptive to clinical operations and introduce risk as policy and procedures need to adapt to new technical possibilities and constraints. We describe here the transition from GammaMedPlus-iX to Bravos in a busy brachytherapy clinic, involving four afterloaders across two sites. MATERIAL AND METHODS: Our clinic employs three high-dose-rate remote afterloaders in four dedicated treatment vaults at the main site and a fourth afterloader at a regional location. Of more than 600 new HDR treatment plans performed annually, most are planned and treated intraoperatively. Most treatments are for prostate cancer, followed by GYN, intraoperative brachytherapy, GI, and other sites. Applicators used include vendor-provided applicators as well as third party applicators and in-house 3D-printed devices to provide interstitial, intracavitary, intraluminal, and surface treatments. All applicators were commissioned according to recommended guidelines. The choice of tolerances and the design of new procedures were informed by current guidelines and leveraged new HDR afterloader functionalities. A review of clinical operations in the 4 months postupgrade was conducted to evaluate the feasibility of new tolerances and the effectiveness of new procedures. RESULTS: The procedures outlined improved and standardized afterloader QA and treatment protocols with clear actionable steps for staff to follow to ensure treatments are delivered as planned. Re-commissioning of applicators yielded results similar to those previously reported by other investigators. A review of initial treatment data revealed that in one case, due to the implementation of tight tolerances, obstruction near the tip of the channel was detected and corrected prior to treatment. It confirms that the implementation of the tolerances adopted is feasible and effective in flagging treatment deviations. CONCLUSION: Enhanced procedures and QA processes were implemented successfully. We established clear actionable steps to follow by staff to ensure that treatments are delivered accurately.

AAPM Task Group 334: A guidance document to using radiotherapy immobilization devices and accessories in an MR environment.

Use of magnetic resonance (MR) imaging in radiation therapy has increased substantially in recent years as more radiotherapy centers are having MR simulators installed, requesting more time on clinical diagnostic MR systems, or even treating with combination MR linear accelerator (MR-linac) systems. With this increased use, to ensure the most accurate integration of images into radiotherapy (RT), RT immobilization devices and accessories must be able to be used safely in the MR environment and produce minimal perturbations. The determination of the safety profile and considerations often falls to the medical physicist or other support staff members who at a minimum should be a Level 2 personnel as per the ACR. The purpose of this guidance document will be to help guide the user in making determinations on MR Safety labeling (i.e., MR Safe, Conditional, or Unsafe) including standard testing, and verification of image quality, when using RT immobilization devices and accessories in an MR environment.

Extended Follow-Up Outcomes from Pooled Prospective Studies Evaluating Efficacy of Interstitial Alpha Radionuclide Treatment for Skin and Head and Neck Cancers.

The initial favorable efficacy and safety profile for Alpha DaRT have been demonstrated (NCT04377360); however, the longer-term safety and durability of the treatment are unknown. This pooled analysis of four prospective trials evaluated the long-term safety and efficacy of Alpha DaRT for the treatment of head and neck or skin tumors. A total of 81 lesions in 71 patients were treated across six international institutions, with a median follow-up of 14.1 months (range: 2-51 months). Alpha DaRT sources were delivered via a percutaneous interstitial technique and placed to irradiate the tumor volume with the margin. The sources were removed two to three weeks following implantation. A complete response was observed in 89% of treated lesions (n = 72) and a partial response in 10% (n = 8). The two-year actuarial local recurrence-free survival was 77% [95% CI 63-87]. Variables, including recurrent versus non-recurrent lesions, baseline tumor size, or histology, did not impact long-term outcomes. Twenty-seven percent of patients developed related acute grade 2 or higher toxicities, which resolved with conservative measures. No grade 2 or higher late toxicities were observed. These data support the favorable safety profile of Alpha DaRT, which is currently being explored in a pivotal US trial.

Favourable long-term outcomes with brachytherapy-based regimens in men ≤60 years with clinically localized prostate cancer.

OBJECTIVE: To report long-term outcomes of men ≤60 years treated with brachytherapy (BT) for low- and intermediate-risk prostate cancer. PATIENTS AND METHODS: Of 1655 patients treated with BT for clinically localized prostate cancer between January 1998 and May 2008 at Memorial Sloan-Kettering Cancer Center, 236 patients with National Comprehensive Cancer Network low- (n = 178) or intermediate-risk (n = 58) prostate cancer were ≤60 years old with a 3-year minimum follow-up, and represent the subjects of this report. Brachytherapy was given either as monotherapy (n = 169) or with external beam radiation therapy (EBRT; n = 67). Forty-four patients (19%) received neoadjuvant cytoreductive hormone therapy. The 'nadir+2' definition was used for prostate-specific antigen (PSA) recurrence. Common Terminology Criteria for Acute Events (CTCAE) v 3.0 was used to grade genitourinary (GU) and gastrointestinal (GI) toxicity. Potency was defined as the ability to obtain an erection suitable for intercourse or an International Index of Erectile Function score ≥ 22. The Kaplan-Meier method and Cox regression were used for statistical analysis. The median follow-up was 83 months. RESULTS: The 8-year PSA relapse-free survival (RFS), cancer-specific and overall survival rates for the entire cohort were 96, 99 and 96%, respectively. For patients with low-risk disease, the 8-year PSA RFS rate was 97% and for intermediate-risk patients it was 94% (P = 0.34). There was no difference in PSA RFS between BT alone and combined therapy (P = 0.17). Late grade ≥ 2 GU and GI toxicity was 14 and 3%, respectively. Of 150 patients potent before treatment, 76 (51%) were potent at last follow-up, with 50/76 (66%) using no medication. There was no significant difference in post-treatment potency between BT alone and BT with EBRT (P = 0.74). CONCLUSIONS: Brachytherapy provides patients aged ≤ 60 years with low- and intermediate-risk prostate cancer with excellent outcomes and has a low risk of significant long-term GU or GI morbidity. Erectile function is preserved in >50% of patients and the majority do not require erectile dysfunction medication.