Detecting dynamic domains and local fluctuations in complex molecular systems via timelapse neighbors shuffling.

It is known that the behavior of many complex systems is controlled by local dynamic rearrangements or fluctuations occurring within them. Complex molecular systems, composed of many molecules interacting with each other in a Brownian storm, make no exception. Despite the rise of machine learning and of sophisticated structural descriptors, detecting local fluctuations and collective transitions in complex dynamic ensembles remains often difficult. Here, we show a machine learning framework based on a descriptor which we name Local Environments and Neighbors Shuffling (LENS), that allows identifying dynamic domains and detecting local fluctuations in a variety of systems in an abstract and efficient way. By tracking how much the microscopic surrounding of each molecular unit changes over time in terms of neighbor individuals, LENS allows characterizing the global (macroscopic) dynamics of molecular systems in phase transition, phases-coexistence, as well as intrinsically characterized by local fluctuations (e.g., defects). Statistical analysis of the LENS time series data extracted from molecular dynamics trajectories of, for example, liquid-like, solid-like, or dynamically diverse complex molecular systems allows tracking in an efficient way the presence of different dynamic domains and of local fluctuations emerging within them. The approach is found robust, versatile, and applicable independently of the features of the system and simply provided that a trajectory containing information on the relative motion of the interacting units is available. We envisage that "such a LENS" will constitute a precious basis for exploring the dynamic complexity of a variety of systems and, given its abstract definition, not necessarily of molecular ones.

Automatic Optimization of Lipid Models in the Martini Force Field Using SwarmCG.

After two decades of continued development of the Martini coarse-grained force field (CG FF), further refinment of the already rather accurate Martini lipid models has become a demanding task that could benefit from integrative data-driven methods. Automatic approaches are increasingly used in the development of accurate molecular models, but they typically make use of specifically designed interaction potentials that transfer poorly to molecular systems or conditions different than those used for model calibration. As a proof of concept, here, we employ SwarmCG, an automatic multiobjective optimization approach facilitating the development of lipid force fields, to refine specifically the bonded interaction parameters in building blocks of lipid models within the framework of the general Martini CG FF. As targets of the optimization procedure, we employ both experimental observables (top-down references: area per lipid and bilayer thickness) and all-atom molecular dynamics simulations (bottom-up reference), which respectively inform on the supra-molecular structure of the lipid bilayer systems and on their submolecular dynamics. In our training sets, we simulate at different temperatures in the liquid and gel phases up to 11 homogeneous lamellar bilayers composed of phosphatidylcholine lipids spanning various tail lengths and degrees of (un)saturation. We explore different CG representations of the molecules and evaluate improvements a posteriori using additional simulation temperatures and a portion of the phase diagram of a DOPC/DPPC mixture. Successfully optimizing up to ∼80 model parameters within still limited computational budgets, we show that this protocol allows the obtainment of improved transferable Martini lipid models. In particular, the results of this study demonstrate how a fine-tuning of the representation and parameters of the models may improve their accuracy and how automatic approaches, such as SwarmCG, may be very useful to this end.

TimeSOAP: Tracking high-dimensional fluctuations in complex molecular systems via time variations of SOAP spectra.

Many molecular systems and physical phenomena are controlled by local fluctuations and microscopic dynamical rearrangements of the constitutive interacting units that are often difficult to detect. This is the case, for example, of phase transitions, phase equilibria, nucleation events, and defect propagation, to mention a few. A detailed comprehension of local atomic environments and of their dynamic rearrangements is essential to understand such phenomena and also to draw structure-property relationships useful to unveil how to control complex molecular systems. Considerable progress in the development of advanced structural descriptors [e.g., Smooth Overlap of Atomic Position (SOAP), etc.] has certainly enhanced the representation of atomic-scale simulations data. However, despite such efforts, local dynamic environment rearrangements still remain difficult to elucidate. Here, exploiting the structurally rich description of atomic environments of SOAP and building on the concept of time-dependent local variations, we developed a SOAP-based descriptor, TimeSOAP (τSOAP), which essentially tracks time variations in local SOAP environments surrounding each molecule (i.e., each SOAP center) along ensemble trajectories. We demonstrate how analysis of the time-series τSOAP data and of their time derivatives allows us to detect dynamic domains and track instantaneous changes of local atomic arrangements (i.e., local fluctuations) in a variety of molecular systems. The approach is simple and general, and we expect that it will help shed light on a variety of complex dynamical phenomena.

Automatic multi-objective optimization of coarse-grained lipid force fields using SwarmCG.

The development of coarse-grained (CG) molecular models typically requires a time-consuming iterative tuning of parameters in order to have the approximated CG models behave correctly and consistently with, e.g., available higher-resolution simulation data and/or experimental observables. Automatic data-driven approaches are increasingly used to develop accurate models for molecular dynamics simulations. However, the parameters obtained via such automatic methods often make use of specifically designed interaction potentials and are typically poorly transferable to molecular systems or conditions other than those used for training them. Using a multi-objective approach in combination with an automatic optimization engine (SwarmCG), here, we show that it is possible to optimize CG models that are also transferable, obtaining optimized CG force fields (FFs). As a proof of concept, here, we use lipids for which we can avail reference experimental data (area per lipid and bilayer thickness) and reliable atomistic simulations to guide the optimization. Once the resolution of the CG models (mapping) is set as an input, SwarmCG optimizes the parameters of the CG lipid models iteratively and simultaneously against higher-resolution simulations (bottom-up) and experimental data (top-down references). Including different types of lipid bilayers in the training set in a parallel optimization guarantees the transferability of the optimized lipid FF parameters. We demonstrate that SwarmCG can reach satisfactory agreement with experimental data for different resolution CG FFs. We also obtain stimulating insights into the precision-resolution balance of the FFs. The approach is general and can be effectively used to develop new FFs and to improve the existing ones.

A Diamond-Based Dose-per-Pulse X-ray Detector for Radiation Therapy.

One of the goals of modern dynamic radiotherapy treatments is to deliver high-dose values in the shortest irradiation time possible. In such a context, fast X-ray detectors and reliable front-end readout electronics for beam diagnostics are crucial to meet the necessary quality assurance requirements of care plans. This work describes a diamond-based detection system able to acquire and process the dose delivered by every single pulse sourced by a linear accelerator (LINAC) generating 6-MV X-ray beams. The proposed system is able to measure the intensity of X-ray pulses in a limited integration period around each pulse, thus reducing the inaccuracy induced by unnecessarily long acquisition times. Detector sensitivity under 6-MV X-photons in the 0.1-10 Gy dose range was measured to be 302.2 nC/Gy at a bias voltage of 10 V. Pulse-by-pulse measurements returned a charge-per-pulse value of 84.68 pC, in excellent agreement with the value estimated (but not directly measured) with a commercial electrometer operating in a continuous integration mode. Significantly, by intrinsically holding the acquired signal, the proposed system enables signal processing even in the millisecond period between two consecutive pulses, thus allowing for effective real-time dose-per-pulse monitoring.

Alveolar epithelial cell type II as main target of SARS-CoV-2 virus and COVID-19 development via NF-Kb pathway deregulation: A physio-pathological theory.

The Corona Virus Disease (COVID-19) pandemic caused by Severe Acute Respiratory Syndrome Corona Virus 2 (SARS-CoV-2) requires a rapid solution and global collaborative efforts in order to define preventive and treatment strategies. One of the major challenges of this disease is the high number of patients needing advanced respiratory support due to the Acute Respiratory Distress Syndrome (ARDS) as the lung is the major - although not exclusive - target of the virus. The molecular mechanisms, pathogenic drivers and the target cell type(s) in SARS-CoV-2 infection are still poorly understood, but the development of a "hyperactive" immune response is proposed to play a role in the evolution of the disease and it is envisioned as a major cause of morbidity and mortality. Here we propose a theory by which the main targets for SARS-CoV-2 are the Type II Alveolar Epithelial Cells and the clinical manifestations of the syndrome are a direct consequence of their involvement. We propose the existence of a vicious cycle by which once alveolar damage starts in AEC II cells, the inflammatory state is supported by macrophage pro-inflammatory polarization (M1), cytokines release and by the activation of the NF-κB pathway. If this theory is confirmed, future therapeutic efforts can be directed to target Type 2 alveolar cells and the molecular pathogenic drivers associated with their dysfunction with currently available therapeutic strategies.

Long-Term Outcomes of Once-Daily Accelerated Partial-Breast Irradiation With Tomotherapy: Results of a Phase 2 Trial.

PURPOSE: We report long-term outcomes of phase 2 trial on patients with invasive breast cancer treated with accelerated partial-breast irradiation (APBI) using tomotherapy after breast conservative surgery. METHODS AND MATERIALS: From December 2010 to December 2018, we treated 338 women with APBI-tomotherapy: 38.5 Gy in 10 once-daily fractions. Patients selected were age ≥50 years old, with ≤3 cm in size unifocal tumor and at least 2 mm of clear margins. Disease outcomes were analyzed by clinicopathologic characteristics, molecular phenotypes, and American Society for Radiation Oncology (ASTRO) 2017 updated consensus groupings. RESULTS: The median age was 65 years (range, 50-86). The invasive ductal (87.5%) and the luminal A-like molecular phenotype (70%) were the most common tumors. Overall 242 patients (71.6%) were considered "suitable" for enrollment in APBI according to the eligibility criteria of the ASTRO-2017 consensus statement. With a median follow-up of 76 months (range, 17-113), 2 patients (0.6%) had an invasive ipsilateral breast tumor recurrence (IBTR), and 2 patients (0.6%) had an axillary ipsilateral failure. The rate of local control in terms of free of IBTR was 99.4% and locoregional control (no recurrence in ipsilateral breast as well as in regional nodes) was 98.8%. Progression-free survival was 98.4% and 92% at 5 and 10 years, respectively. Acute and late skin toxicity, graded according to the Common Terminology Criteria for Adverse Events, were 7.7% (G1) and 0.6% (G2) and 4.4% (G1) and 1.1% (G2), respectively. There were no grade 3/4 toxicities, however. Very few patients (2%) or physicians (2%) assessed cosmetic outcome as fair or poor at the 2-year follow-up. CONCLUSIONS: This phase 2 trial on APBI-tomotherapy shows excellent long-term results. Once-daily fractionation schedule was well tolerated with a low rate of adverse events and worse cosmetic outcome. In this series, even among those deemed cautionary or unsuitable for APBI by ASTRO criteria, we demonstrated a low rate of IBTR.

Once Daily Accelerated Partial Breast Irradiation: Preliminary Results with Helical Tomotherapy®.

BACKGROUND: Accelerated partial breast irradiation (APBI) is becoming an option for patients with low-risk breast cancer. The current practice is 38.5 Gy in 10 fractions b.i.d. over 5 days. This fractionation has a higher bioequivalent dose compared to the standard schedule. We report on preliminary results of once-daily APBI in patients treated with TomoTherapy®. PATIENTS AND METHODS: Patients with unifocal-breast disease who underwent breast-conserving surgery were enrolled in the study. Treatment was administered with TomoTherapy, by contouring in accordance with the NSABP B-39/RTOG 0413 APBI protocol. Treatment schedule was 38.5 Gy in 10 once-daily fractions. EORTC Cosmetic Rating System was adopted for cosmetic outcome. RESULTS: From 2010 to 2013, 111 patients were treated. With a median follow-up of 34 months, no ipsilateral breast recurrence was observed. Very few patients (1-4%) assessed their cosmetic outcome as fair or poor during follow-up. CONCLUSION: Once-daily APBI with TomoTherapy yielded good cosmetic results without compromising local control efficacy.

Management of radiation therapy patients with cardiac defibrillator or pacemaker.

The increasing growth of population with cardiac implantable electronic devices (CIEDs) such as Pacemaker (PM) and Implantable Cardiac Defibrillators (ICD), requires particular attention in management of patients needing radiation treatment. This paper updates and summarizes some recommendations from different international guidelines. Ionizing radiation and/or electromagnetic interferences could cause device failure. Current approaches to treatment in patients who have these devices vary among radiation oncology centres. We refer to the German Society of Radiation Oncology and Cardiology guidelines (ed. 2015); to the Society of Cardiology Australia and New Zealand Statement (ed. 2015); to the guidelines in force in the Netherlands (ed. 2012) and to the Italian Association of Radiation Oncology recommendations (ed. 2013) as reported in the guidelines for the treatment of breast cancer in patients with CIED. Although there is not a clear cut-off point, risk of device failure increases with increasing doses. Cumulative dose and pacing dependency have been combined to categorize patients into low-, medium- and high-risk groups. Measures to secure patient safety are described for each category. The use of energy ≤6MV is preferable and it's strongly recommended not to exceed a total dose of 2 Gy to the PM and 1 Gy for ICD. Given the dangers of device malfunction, radiation oncology departments should adopt all the measures designed to minimize the risk to patients. For this reason, a close collaboration between cardiologist, radiotherapist and physicist is necessary.

Moderately Escalated Hypofractionated (Chemo) Radiotherapy Delivered with Helical Intensity-Modulated Technique in Stage III Unresectable Non-Small Cell Lung Cancer.

PURPOSE: To assess clinical outcomes and toxicities in patients with stage III unresectable non-small cell lung cancer (NSCLC) treated with a moderately escalated hypofractionated radiotherapy delivered with Helical Intensity-Modulated Technique in combination with sequential or concurrent chemotherapy. MATERIALS AND METHODS: Sixty-one consecutive patients considered non-progressive after two cycles of induction chemotherapy were treated with a moderately escalated hypofractionated radiation course of 30 daily fractions of 2.25-2.28 Gy each administered in 6 weeks up to a total dose of 67.5-68.4 Gy (range, 64.5-71.3 Gy). Thirty-two received sequential RT after two more cycles (total = 4 cycles) of chemotherapy, while 29 were treated with concurrent chemo-radiation. The target was considered the gross tumor volume and the clinically proven nodal regions, without elective nodal irradiation. RESULTS: With a median follow up of 27 months (range 6-40), 1-year and 2-year OS rate for all patients was 77 and 53%, respectively, with a median survival duration of 18.6 months in the sequential group and 24.1 months in the concomitant group. No Grade ≥4 acute and late toxicity was reported. Acute Grade 3 treatment-related pneumonitis was detected in 10% of patients. Two patients, both receiving the concurrent schedule, developed a Grade 3 acute esophagitis. The overall incidence of late Grade 3 lung toxicity was 5%. No patients experienced a Grade 3 late esophageal toxicity. CONCLUSION: A moderately hypofractionated radiation course delivered with a Helical Intensity-Modulated Technique is a feasible treatment option for patients with unresectable locally advanced NSCLC receiving chemotherapy (sequentially or concurrently). Hypofractionated radiotherapy with a dedicated technique allows safely dose escalation, minimizing the effect of tumor repopulation that may occur with prolonged treatment time.

Radiation therapy in the treatment of HIV-related Kaposi's sarcoma.

BACKGROUND: Kaposi's sarcoma (KS) is the most frequent neoplasm occurring in patients with HIV-related AIDS and very often exhibits multifocal distribution so that a systemic approach is needed. KS is considered a radiosensitive tumor and (RT) has always played an important role in the therapeutic strategy of its various forms. RT is a valuable means of pain relief, bleeding control and edema palliation, but it is also an effective treatment modality for local control of skin and mucosal lesions in KS. The purpose of the present article is to report the results obtained by the Radiotherapy Unit of S. Camillo-Forlanini Hospital in Rome in the management of 38 AIDS-associated KS lesions and to assess the efficacy of RT in the treatment and local control of KS. PATIENTS AND METHODS: Eighteen patients histologically-diagnosed with HIV-related KS underwent RT in the period between January 2002 and January 2012 at the Radiotherapy Unit of S. Camillo-Forlanini Hospital in Rome. In all cases, the lesions caused pain or discomfort and a thorough careful clinical evaluation had indicated a radiation treatment. A total of 38 lesions were treated with radiotherapy. Fifteen patients received systemic chemotherapy. Eight patients with multiple cutaneous lesions on their legs and arms were treated with a radiation schedule prescribing extended cutaneous irradiation using 6-18 MeV electron beam energy, 200 cGy per fraction and a total dose between 24-30 Gy, according to the depth of lesions. One of these patients had also a cutaneous lesion on an eyelid that was treated with a radiation schedule using 6 MeV electron beam energy and bolus of 1 cm, 200 cGy per fraction and a total dose of 30 Gy. Seven patients with single cutaneous lesions on the legs and arms were treated using a photon regimen of 6 Mv energy, 200 cGy per fraction and a total dose between 20 and 36 Gy. Two patients had oral mucosa lesions and they were treated with a radiation schedule prescribing irradiation using 6 Mev photon regimen and personal mask, 200 cGy per fraction and a total dose of 24 and 30 Gy, respectively. A patient with a single bone lesion on the spinal column was treated with irradiation using 6 Mev photon regimen, 300 cGy per fraction and a total dose of 30 Gy. RESULTS: At the time of reporting, 14 patients were alive and four patients had died. One patient died due to complications from HIV infection. The follow-up from the end of the treatment ranged from four to 124 months (mean=51.17 months). The overall survival for the group was 88.8% at one year. The mean overall survival was 57.4 months. A complete response was achieved for 31 lesions (83.8 %); a partial response with a tumor regression was observed for six lesions (16.2 %). No relapses were observed during the period of follow-up, but we observed new lesions in one patient. According to the Radiation Therapy Oncology Group scale we observed erythematic and dry desquamation (grade 1) in eight sites (21%); in only one patient (2.6%) did stomatitis occur (grade 1). Good cosmetic results were described for 25 (65.7%) out of 31 lesions. Effective palliative action was obtained for all lesions except for two (5.2%) located in a vertebra and hard palate. CONCLUSION: RT will be a mainstay of cure for this group of patients especially when of young age and the will to preserve the cosmetic appearance is a primary need.

Evaluation of helical tomotherapy in the treatment of high-grade gliomas near critical structures.

BACKGROUND: Our purpose was to investigate the role of helical tomotherapy using a simultaneous integrated boost technique for the treatment of high-grade gliomas near intracranial critical structures. METHODS AND MATERIALS: Of 27 patients treated with helical tomotherapy, 11 were eligible. Only patients whose tumors were within 0.5 cm of the optic chiasm, the optic nerve or the brainstem were included. The therapeutic approach was a simultaneous integrated boost, prescribing 66 and 60 Gy to the PTV1 and PTV2, respectively, in 30 fractions. All patients received concomitant temozolomide at a dose of 75 mg/m2 daily during radiation therapy. RESULTS: Of the 11 patients considered, 3 patients (27%) died after 4 months from the completion of the combined treatment. Three patients (27%) presented local progression, and the median time to disease progression was 6 months (range, 1-12). Five patients (45%), at the time of this evaluation, did not have signs or symptoms of recurrence or progression of the disease. Acute toxicity, evaluated during radiochemotherapy, was minimal, with all patients experiencing RTOG grade 0 and grade 1 toxicity. CONCLUSIONS: . Helical tomotherapy proved to be an effective and safe treatment modality, with an improvement of accuracy in delivery of high-dose radiotherapy despite the presence of nearby critical structures.

Radiotherapy for inoperable non-small cell lung cancer using helical tomotherapy.

AIM: To investigate the impact of tomotherapy on the dose delivered to the lungs and other normal tissues. MATERIAL AND METHODS: From February 2008 to May 2009, 35 patients with stage IIIA/IIIB non-small cell lung cancer were treated with helical tomotherapy at the S. Camillo-Forlanini Hospital. For our study we selected 20 patients who underwent chemotherapy followed by sequential radiotherapy. The planning target volume was delineated using planning CT scan and FDG-PET. The mean prescribed radiation dose was 67.5 Gy delivered in 30 fractions at a dose of 2.25 Gy per fraction. RESULTS: Median follow-up was 12.3 months. All patients developed acute esophageal toxicity, 15 of RTOG grade 1 and 5 of RTOG grade 2. At first follow-up 15 patients presented stable disease or partial response, 4 patients presented complete response, and 1 patient presented disease progression. CONCLUSIONS: Helical tomotherapy is useful to achieve dose-per-fraction escalation without increasing the treatment-related morbidity. Our results applying dose escalation were encouraging considering that we delivered doses that may be difficult to achieve with 3-dimensional treatments with no excessive complication rates.

Adjuvant radiotherapy and radiochemotherapy in the management of esophageal cancer: a review of the literature.

Surgical resection remains the mainstay treatment for esophageal cancer and the failure of surgery alone is attributed to the systemic nature of the disease at the time of presentation. In an effort to improve local control of the disease that should correspond to a benefit in survival, postoperative adjuvant schemes of treatment have been explored. Current standard treatment, and future implications in light of the new knowledge are analyzed, based on the present literature. The possibility of different treatments in relation to different histology findings, is stressed.