Semantic categorization of Chinese eligibility criteria in clinical trials using machine learning methods.

BACKGROUND: Semantic categorization analysis of clinical trials eligibility criteria based on natural language processing technology is crucial for the task of optimizing clinical trials design and building automated patient recruitment system. However, most of related researches focused on English eligibility criteria, and to the best of our knowledge, there are no researches studied the Chinese eligibility criteria. Thus in this study, we aimed to explore the semantic categories of Chinese eligibility criteria. METHODS: We downloaded the clinical trials registration files from the website of Chinese Clinical Trial Registry (ChiCTR) and extracted both the Chinese eligibility criteria and corresponding English eligibility criteria. We represented the criteria sentences based on the Unified Medical Language System semantic types and conducted the hierarchical clustering algorithm for the induction of semantic categories. Furthermore, in order to explore the classification performance of Chinese eligibility criteria with our developed semantic categories, we implemented multiple classification algorithms, include four baseline machine learning algorithms (LR, NB, kNN, SVM), three deep learning algorithms (CNN, RNN, FastText) and two pre-trained language models (BERT, ERNIE). RESULTS: We totally developed 44 types of semantic categories, summarized 8 topic groups, and investigated the average incidence and prevalence in 272 hepatocellular carcinoma related Chinese clinical trials. Compared with the previous proposed categories in English eligibility criteria, 13 novel categories are identified in Chinese eligibility criteria. The classification result shows that most of semantic categories performed quite well, the pre-trained language model ERNIE achieved best performance with macro-average F1 score of 0.7980 and micro-average F1 score of 0.8484. CONCLUSION: As a pilot study of Chinese eligibility criteria analysis, we developed the 44 semantic categories by hierarchical clustering algorithms for the first times, and validated the classification capacity with multiple classification algorithms.

[Artificial intelligence based Chinese clinical trials eligibility criteria classification].

Subject recruitment is a key component that affects the progress and results of clinical trials, and generally conducted with eligibility criteria (includes inclusion criteria and exclusion criteria). The semantic category analysis of eligibility criteria can help optimizing clinical trials design and building automated patient recruitment system. This study explored the automatic semantic categories classification of Chinese eligibility criteria based on artificial intelligence by academic shared task. We totally collected 38 341 annotated eligibility criteria sentences and predefined 44 semantic categories. A total of 75 teams participated in competition, with 27 teams having submitted system outputs. Based on the results, we found out that most teams adopted mixed models. The mainstream resolution was applying pre-trained language models capable of providing rich semantic representation, which were combined with neural network models and used to fine-tune the models with reference to classifier tasks, and finally improved classification performance could be obtained by ensemble modeling. The best-performing system achieved a macro F1 score of 0.81 by using a pre-trained language model, i.e. bidirectional encoder representations from transformers (BERT) and ensemble modeling. With the error analysis we found out that from the point of data processing steps the data pre-processing and post-processing were very important for classification, while from the point of data volume these categories with less data volume showed lower classification performance. Finally, we hope that this study could provide a valuable dataset and state-of-the-art result for the research of Chinese medical short text classification.

Image-guided hypofractionated double-scattering proton therapy in the management of centrally-located early-stage non-small cell lung cancer.

BACKGROUND: The treatment of centrally-located early-stage non-small cell lung cancer (NSCLC) with image-guided stereotactic body radiotherapy (SBRT) is challenging due to the proximity of critical normal structures to the tumor target. The purpose of this study was to report the results of our experience in treating centrally-located early-stage NSCLC with hypofractionated proton therapy (PT). MATERIAL AND METHODS: Between 2009 and 2018, 23 patients with T1-T2N0M0 NSCLC (T1, 46%; T2, 54%) were treated with image-guided hypofractionated double-scattering PT. The median age at the time of treatment was 74 years (range, 58-88). Patients underwent 4-dimensional computed tomography (CT) simulation following fiducial marker placement, and daily image guidance was performed. All patients were treated with 60 GyRBE in 10 fractions. Patients were assessed for CTCAEv4 toxicities weekly during treatment, and at regular follow-up intervals with CT imaging for tumor assessment. Overall survival, cause-specific survival, local control, regional control, and metastases-free survival were evaluated using cumulative incidence with competing risks. RESULTS: Median follow-up for all patients was 3.2 years (range, 0.2-9.2 years). Overall survival rates at 3 and 5 years were 81% and 50% (95% CI, 27-79%), respectively. Cause-specific survival rates at 3 and 5 years were 81% and 71% (95% CI, 46-92%). The 3-year local, regional, and distant control rates were 90%, 81%, and 87%, respectively. Three patients (13%) experienced local recurrences as their first recurrence, at a median time of 28 months from completion of radiation (range, 18-61 months). Two patients (9%) experienced late grade 3 toxicities, including 1 patient who developed a bronchial stricture that required stent placement. CONCLUSION: Image-guided hypofractionated PT for centrally-located early-stage NSCLC provides excellent local control with low rates of grade ≥3 toxicities. For tumors in sensitive locations, PT may provide safer treatment than photon-based treatments due to its dosimetric advantages.

Serum Testosterone 60 Months after Passive-Scatter Proton Therapy for Localized Prostate Cancer.

Studies demonstrate a decline of ∼10% in serum testosterone (ST) level after X-ray radiotherapy for prostate cancer. We evaluated changes in ST for patients with low- and intermediate-risk prostate cancer receiving 70-82Gy(RBE) using passive-scatter proton therapy (PT). ST was checked at baseline (n = 358) and at 60+ months after PT (n = 166). The median baseline ST was 363.3 ng/dl (range, 82.0-974.0). The median ST 5 years after PT was 391.5 ng/dl (range, 108.0-1061.0). The difference was not statistically significant (p = 0.9341). Passive-scatter PT was not associated with testosterone suppression at 5 years, suggesting that protons may cause less out-of-field scatter radiation than X-rays.

Radiation doses to brain substructures associated with cognition in radiotherapy of pediatric brain tumors.

Background: Several brain substructures associated with cognition (BSCs) are located close to typical pediatric brain tumors. Pediatric patients therefore have considerable risks of neurocognitive impairment after brain radiotherapy. In this study, we investigated the radiation doses received by BSCs for three common locations of pediatric brain tumor entities. Material and methods: For ten patients in each group [posterior fossa ependymoma (PFE), craniopharyngioma (CP), and hemispheric ependymoma (HE)], the cumulative fraction of BSCs volumes receiving various dose levels were analyzed. We subsequently explored the differences in dose pattern between the three groups and used available dose response models from the literature to estimate treatment-induced intelligence quotient (IQ) decline. Results: Doses to BSCs were found to differ considerably between the groups, depending on their position relative to the tumor. Large inter-patient variations were observed in the ipsilateral structures of the HE groups, and at low doses for all three groups. IQ decline estimates differed depending on the model applied, presenting larger variations in the HE group. Conclusion: While there were notable differences in the dose patterns between the groups, the extent of estimated IQ decline depended more on the model applied. This inter-model variability should be considered in dose-effect assessments on cognitive outcomes of pediatric patients.

Impact of intrafraction prostate motion on clinical target coverage in proton therapy: A simulation study of dosimetric differences in two delivery techniques.

PURPOSE: To investigate the dosimetric impact of prostate intrafraction motion on proton double-scattering (DS) and uniform scanning (US) treatments using electromagnetic transponder-based prostate tracking data in simulated treatment deliveries. METHODS: In proton DS delivery, the spread-out Bragg peak (SOBP) is created almost instantaneously by the constant rotation of the range modulator. US, however, delivers each entire energy layer of the SOBP sequentially from distal to proximal direction in time, which can interplay with prostate intrafraction motion. This spatiotemporal interplay during proton treatment was simulated to evaluate its dosimetric impact. Prostate clinical target volume (CTV) dose was obtained by moving CTV through dose matrices of the energy layers according to prostate-motion traces. Fourteen prostate intrafraction motion traces of each of 17 prostate patients were used in the simulated treatment deliveries. Both single fraction dose-volume histograms (DVHs) and fraction-cumulative DVHs were obtained for both 2 Gy per fraction and 7.25 Gy per fraction stereotactic body radiotherapy (SBRT). RESULTS: The simulation results indicated that CTV dose degradation depends on the magnitude and direction of prostate intrafraction motion and is patient specific. For some individual fractions, prescription dose coverage decreased in both US and DS treatments, and hot and cold spots inside the CTV were observed in the US results. However, fraction-cumulative CTV dose coverage showed much reduced dose degradation for both DS and US treatments for both 2 Gy per fraction and SBRT simulations. CONCLUSIONS: This study indicated that CTV dose inhomogeneity may exist for some patients with severe prostate intrafraction motion during US treatments. However, there are no statistically significant dose differences between DS and US treatment simulations. Cumulative dose of multiple-fractions significantly reduced dose uncertainties.

A comprehensive dosimetric study of Monte Carlo and pencil-beam algorithms on intensity-modulated proton therapy for breast cancer.

PB algorithms are commonly used for proton therapy. Previously reported limitations of the PB algorithm for proton therapy are mainly focused on high-density gradients and small-field dosimetry, the effect of PB algorithms on intensity-modulated proton therapy (IMPT) for breast cancer has yet to be illuminated. In this study, we examined 20 patients with breast cancer and systematically investigated the dosimetric impact of MC and PB algorithms on IMPT. Four plans were generated for each patient: (a) a PB plan that optimized and computed the final dose using a PB algorithm; (b) a MC-recomputed plan that recomputed the final dose of the PB plan using a MC algorithm; (c) a MC-renormalized plan that renormalized the MC-recomputed plan to restore the target coverage; and (d) a MC-optimized plan that optimized and computed the final dose using a MC algorithm. The DVH on CTVs and on organ-at-risks (OARs) from each plan were studied. The Mann-Whitney U-test was used for testing the differences between any two types of plans. We found that PB algorithms significantly overestimated the target dose in breast IMPT plans. The median value of the CTV D99% , D95% , and Dmean dropped by 3.7%, 3.4%, and 2.1%, respectively, of the prescription dose in the MC-recomputed plans compared with the PB plans. The magnitude of the target dose overestimation by the PB algorithm was higher for the breast CTV than for the chest wall CTV. In the MC-renormalized plans, the target dose coverage was comparable with the original PB plans, but renormalization led to a significant increase in target hot spots as well as skin dose. The MC-optimized plans led to sufficient target dose coverage, acceptable target hot spots, and good sparing of skin and other OARs. Utilizing the MC algorithm for both plan optimization and final dose computation in breast IMPT treatment planning is therefore desirable.

Long-term outcomes following proton therapy for prostate cancer in young men with a focus on sexual health.

BACKGROUND: We investigated long-term outcomes for men ≤60 years old treated with proton therapy (PT). METHODS: Of 254 men ≤60 years old were treated with proton therapy alone for prostate cancer. Risk stratification included 56% with low-, 42% with intermediate- and 2% with high-risk disease. Patients received 76-82 Gy at 2 Gy/fraction or 70-72.5 Gy at 2.5 Gy/fraction. Before treatment and every 6-12 months for 5 years, patients were evaluated by a physician, answered health-related quality of life surveys, including the EPIC, IIEF and IPSS, and had PSA evaluated. RESULTS: Median follow-up for the cohort was 7.1 years; 7-year biochemical-free survival was 97.8%. Eight men (one high-risk; five intermediate-risk and two low-risk) experienced biochemical progression, including one who died of disease 9 years after treatment. Potency (erections firm enough for sexual intercourse) was 90% at baseline and declined to 72% at the first-year follow-up, but declined to only 67% at 5 years. Only 2% of patients developed urinary incontinence requiring pads. The bowel habits mean score declined from a baseline of 96 to 88 at 1 year, which improved over the following years to 93 at 5 years. CONCLUSIONS: Young men with prostate cancer continue to have excellent results with respect to 7-year biochemical control and 5-year erectile function, without clinically significant urinary incontinence 5 years after proton therapy. Comparative effectiveness studies of proton therapy with surgery and IMRT are needed.

Five-year outcomes from a prospective trial of image-guided accelerated hypofractionated proton therapy for prostate cancer.

PURPOSE: To report 5-year outcomes of a prospective trial of image-guided accelerated hypofractionated proton therapy (AHPT) for prostate cancer. PATIENTS AND METHODS: 215 prostate cancer patients accrued to a prospective institutional review board-approved trial of 70Gy(RBE) in 28 fractions for low-risk disease (n = 120) and 72.5Gy(RBE) in 29 fractions for intermediate-risk disease (n = 95). This trial excluded patients with prostate volumes of ≥60 cm3 or International Prostate Symptom Scores (IPSS) of ≥15, patients on anticoagulants or alpha-blockers, and patients in whom dose-constraint goals for organs at risk (OAR) could not be met. Toxicities were graded prospectively according to Common Terminology Criteria for Adverse Events (CTCAE), version 3.0. This trial can be found on ClinicalTrials.gov (NCT00693238). RESULTS: Median follow-up was 5.2 years. Five-year rates of freedom from biochemical and clinical disease progression were 95.9%, 98.3%, and 92.7% in the overall group and the low- and intermediate-risk subsets, respectively. Actuarial 5-year rates of late radiation-related CTCAE v3.0 grade 3 or higher gastrointestinal and urologic toxicities were 0.5% and 1.7%, respectively. Median IPSS before treatment and at 4+ years after treatment were 6 and 5 for low-risk patients and 4 and 6 for intermediate-risk patients. CONCLUSIONS: Image-guided AHPT 5-year outcomes show high efficacy and minimal physician-assessed toxicity in selected patients. These results are comparable to the 5-year results of our prospective trials of standard fractionated proton therapy for patients with low-risk and intermediate-risk prostate cancer. Longer follow-up and a larger cohort are necessary to confirm these findings.

Biological dose and complication probabilities for the rectum and bladder based on linear energy transfer distributions in spot scanning proton therapy of prostate cancer.

BACKGROUND: The increased linear energy transfer (LET) at the end of the Bragg peak causes concern for an elevated and spatially varying relative biological effectiveness (RBE) of proton therapy (PT), often in or close to dose-limiting normal tissues. In this study, we investigated dose-averaged LET (LETd) distributions for spot scanning PT of prostate cancer patients using different beam angle configurations. In addition, we derived RBE-weighted (RBEw) dose distributions and related normal tissue complication probabilities (NTCPs) for the rectum and bladder. MATERIAL AND METHODS: A total of 21 spot scanning proton plans were created for each of six patients using a prescription dose of 78 Gy(RBE1.1), with each plan using two 'mirrored' beams with gantry angles from 110°/250° to 70°/290°, in steps of 2°. Physical dose and LETd distributions were calculated as well as RBEw dose distributions using either RBE = 1.1 or three different variable RBE models. The resulting biological dose distributions were used as input to NTCP models for the rectum and bladder. RESULTS: For anterior oblique (AO) configurations, the rectum LETd volume and RBEw dose increased with increasing angles off the lateral opposing axis, with the RBEw rectum dose being higher than for all posterior oblique (PO) configurations. For PO configurations, the corresponding trend was seen for the bladder. Using variable RBE models, the rectum NTCPs were highest for the AO configurations with up to 3% for the 80°/280° configuration while the bladder NTCPs were highest for the PO configurations with up to 32% for the 100°/260°. The rectum D1cm3 constraint was fulfilled for most patients/configurations when using uniform RBE but not for any patient/configuration with variable RBE models. CONCLUSIONS: Compared to using constant RBE, the variable RBE models predicted increased biological doses to the rectum, bladder and prostate, which in turn lead to substantially higher estimated rectum and bladder NTCPs.

Sperm preservation and neutron contamination following proton therapy for prostate cancer study.

BACKGROUND: The present study investigates the impact of scatter dose radiation to the testis on ejaculate and sperm counts from treatment of prostate cancer with passive-scatter proton therapy. MATERIAL AND METHODS: From March 2010 to November 2014, 20 men with low- or intermediate-risk prostate cancer enrolled in an IRB-approved protocol and provided a semen sample prior to passive-scatter proton therapy and 6-12 months following treatment. Men were excluded if they had high-risk prostate cancer, received androgen deprivation therapy, were on alpha blockers (due to retrograde ejaculation) prior to treatment, had baseline sperm count <1 million, or were unable to produce a pre-treatment sample or could not provide a follow-up specimen. Sperm counts of 0 were considered azoospermia and <15 million/ml were classified as oligospermia. RESULTS: Four patients were unable to provide a sufficient quantity of semen for analysis. Among the 16 remaining patients, only one was found to have oligospermia (7 million/ml). There was a statistically significant reduction in semen volume (median, 0.5 ml) and increase in pH (median 0.5). Although not statistically significant, there appeared to be a decline in sperm concentration (median, 16 million/ml), total sperm count (median, 98.5 million), normal morphology (median, 9%), and rapid progressive motility (median, 9.5%). DISCUSSION: Men did not have azoospermia 6-12 months following passive-scatter proton therapy indicating minimal scatter radiation to the testis during treatment. Changes in semen quantity and consistency may occur due to prostate irradiation, which could impact future fertility and/or sexual activity.

Linear energy transfer distributions in the brainstem depending on tumour location in intensity-modulated proton therapy of paediatric cancer.

BACKGROUND: For tumours near organs at risk, there is concern about unintended increase in biological dose from elevated linear energy transfer (LET) at the distal end of treatment fields. The objective of this study was therefore to investigate how different paediatric posterior fossa tumour locations impact LET and biological dose to the brainstem during intensity-modulated proton therapy (IMPT). MATERIAL AND METHODS: Multiple IMPT plans were generated for four different simulated tumour locations relative to the brainstem for a five-year-old male patient. A prescribed dose of 59.4 Gy(RBE) was applied to the planning target volumes (PTVs). Plans with two lateral and one posterior non-coplanar fields were created, along with plans with modified field arrangements. The dose-averaged LET (LETd) and the physical dose × RBELET (D × RBELET), where RBELET=1+c × LETd, were calculated using the FLUKA Monte Carlo code. A scaling parameter c was applied to make the RBELET represent variations in the biological effect due to LET. RESULTS: High LETd values surrounded parts of the PTV and encompassed portions of the brainstem. Mean LETd values in the brainstem were 3.2-6.6 keV/µm. The highest absolute brainstem LETd values were seen with the tumour located most distant from the brainstem, whereas lower and more homogeneous LETd values were seen when the tumour invaded the brainstem. In contrast, the highest mean D × RBELET values were found in the latter case (54.0 Gy(RBE)), while the case with largest distance between tumour and brainstem had a mean D × RBELET of 1.8 Gy(RBE). CONCLUSIONS: Using IMPT to treat posterior fossa tumours may result in high LETd values within the brainstem, particularly if the tumour volume is separated from the brainstem. However, the D × RBELET was greater for tumours that approached or invaded the brainstem. Changing field angles showed a reduction of LETd and D × RBELET in the brainstem.

Complement-related proteins control the flavivirus infection of Aedes aegypti by inducing antimicrobial peptides.

The complement system functions during the early phase of infection and directly mediates pathogen elimination. The recent identification of complement-like factors in arthropods indicates that this system shares common ancestry in vertebrates and invertebrates as an immune defense mechanism. Thioester (TE)-containing proteins (TEPs), which show high similarity to mammalian complement C3, are thought to play a key role in innate immunity in arthropods. Herein, we report that a viral recognition cascade composed of two complement-related proteins limits the flaviviral infection of Aedes aegypti. An A. aegypti macroglobulin complement-related factor (AaMCR), belonging to the insect TEP family, is a crucial effector in opposing the flaviviral infection of A. aegypti. However, AaMCR does not directly interact with DENV, and its antiviral effect requires an A. aegypti homologue of scavenger receptor-C (AaSR-C), which interacts with DENV and AaMCR simultaneously in vitro and in vivo. Furthermore, recognition of DENV by the AaSR-C/AaMCR axis regulates the expression of antimicrobial peptides (AMPs), which exerts potent anti-DENV activity. Our results both demonstrate the existence of a viral recognition pathway that controls the flaviviral infection by inducing AMPs and offer insights into a previously unappreciated antiviral function of the complement-like system in arthropods.

Proton Therapy for Pediatric Hodgkin Lymphoma.

BACKGROUND: Compared to X-ray radiation therapy, proton therapy (PT) reduces the radiation dose to organs at risk, which is expected to translate into fewer second cancers and less cardiac morbidity decades after treatment. The Children's Oncology Group high-risk pediatric Hodgkin lymphoma (PHL) protocol, AHOD1331, allows the use of PT, yet limited data exist on the use of PT in PHL. PROCEDURE: Between 2010 and 2014, 22 pediatric patients were treated with PT for PHL at our institution: 7 intermediate-risk patients, 11 high-risk patients, and 4 relapsed patients. The patients' age ranged from 6 to 18 years old. Median follow-up was 36 months. All patients received chemotherapy before PT. RESULTS: The 2-year and 3-year overall survival rates were both 94%, and the progression-free survival rate was 86%. Recurrences occurred in three high-risk patients: one isolated in-field cervical lymph node and two in-field and out-of-field. All recurrences occurred within 5 months of completing PT. No PT-related grade 3 or higher acute or late complications were observed. CONCLUSION: PT for PHL showed no short-term severe toxicity and yields similar short-term control to recently published large multi-institutional clinical trials.

Pharmacotherapies for Posttraumatic Stress Disorder: A Meta-Analysis.

The purpose of this study was to assess the acceptability and efficacy of all types of pharmacotherapeutic agents in reducing the symptoms of posttraumatic stress disorder (PTSD). In this systematic meta-analysis, the dropout and response rates of various pharmacotherapy and placebo treatments reported by randomized clinical trials were compared. A total of 34 reports that described the acceptability and efficacy of PTSD pharmacotherapies were retrieved and analyzed. Of them, 30 trials examined the dropout rate as an index of acceptability and revealed the superiority of the PTSD pharmacotherapy to placebos (odds ratio, 0.75; 95% confidence interval, 0.66-0.86; n = 4313). The response rate was determined in 20 trials as an index of efficacy, showing that the PTSD pharmacotherapies were superior to the placebos (odds ratio, 1.47; 95% confidence interval, 1.34-1.62; n = 2166). Pharmacotherapy is an important component of the care of patients with PTSD.

A neural network-based 2D/3D image registration quality evaluator for pediatric patient setup in external beam radiotherapy.

Our purpose was to develop a neural network-based registration quality evaluator (RQE) that can improve the 2D/3D image registration robustness for pediatric patient setup in external beam radiotherapy. Orthogonal daily setup X-ray images of six pediatric patients with brain tumors receiving proton therapy treatments were retrospectively registered with their treatment planning computed tomography (CT) images. A neural network-based pattern classifier was used to determine whether a registration solution was successful based on geometric features of the similarity measure values near the point-of-solution. Supervised training and test datasets were generated by rigidly registering a pair of orthogonal daily setup X-ray images to the treatment planning CT. The best solution for each registration task was selected from 50 optimizing attempts that differed only by the randomly generated initial transformation parameters. The distance from each individual solution to the best solution in the normalized parametrical space was compared to a user-defined error tolerance to determine whether that solution was acceptable. A supervised training was then used to train the RQE. Performance of the RQE was evaluated using test dataset consisting of registration results that were not used in training. The RQE was integrated with our in-house 2D/3D registration system and its performance was evaluated using the same patient dataset. With an optimized sampling step size (i.e., 5 mm) in the feature space, the RQE has the sensitivity and the specificity in the ranges of 0.865-0.964 and 0.797-0.990, respectively, when used to detect registration error with mean voxel displacement (MVD) greater than 1 mm. The trial-to-acceptance ratio of the integrated 2D/3D registration system, for all patients, is equal to 1.48. The final acceptance ratio is 92.4%. The proposed RQE can potentially be used in a 2D/3D rigid image registration system to improve the overall robustness by rejecting unsuccessful registration solutions. The RQE is not patient-specific, so a single RQE can be constructed and used for a particular application (e.g., the registration for images acquired on the same anatomical site). Implementation of the RQE in a 2D/3D registration system is clinically feasible.

Evaluation of the range shifter model for proton pencil-beam scanning for the Eclipse v.11 treatment planning system.

Existing proton therapy pencil-beam scanning (PBS) systems have limitations on the minimum range to which a patient can be treated. This limitation arises from practical considerations, such as beam current intensity, layer spacing, and delivery time. The range shifter (RS) - a slab of stopping material inserted between the nozzle and the patient - is used to reduce the residual range of the incident beam so that the treatment ranges can be extended to shallow depths. Accurate modeling of the RS allows one to calculate the beam spot size entering the patient, given the proton energy, for arbitrary positions and thicknesses of the RS in the beam path. The Eclipse version 11 (v11) treatment planning system (TPS) models RS-induced beam widening by incorporating the scattering properties of the RS material into the V-parameter. Monte Carlo simulations with Geant4 code and analytical calculations using the Fermi-Eyges (FE) theory with Highland approximation of multiple Coulomb scattering (MCS) were employed to calculate proton beam widening due to scattering in the RS. We demonstrated that both methods achieved consistent results and could be used as a benchmark for evaluating the Eclipse V-parameter model. In most cases, the V-parameter model correctly predicted the beam spot size after traversing the RS. However, Eclipse did not enforce the constraint for a nonnegative covariance matrix when fitting the spot sizes to derive the phase space parameters, which resulted in incorrect calculations under specific conditions. In addition, Eclipse v11 incorrectly imposed limits on the individual values of the phase space parameters, which could lead to incorrect spot size values in the air calculated for beams with spot sigmas <3.8 mm. Notably, the TPS supplier (Varian) and hardware vendor (Ion Beam Applications) inconsistently refer to the RS position, which may result in improper spot size calculations.

A Web application for the management of clinical workflow in image-guided and adaptive proton therapy for prostate cancer treatments.

Image-guided radiotherapy (IGRT), based on radiopaque markers placed in the prostate gland, was used for proton therapy of prostate patients. Orthogonal X-rays and the IBA Digital Image Positioning System (DIPS) were used for setup correction prior to treatment and were repeated after treatment delivery. Following a rationale for margin estimates similar to that of van Herk,(1) the daily post-treatment DIPS data were analyzed to determine if an adaptive radiotherapy plan was necessary. A Web application using ASP.NET MVC5, Entity Framework, and an SQL database was designed to automate this process. The designed features included state-of-the-art Web technologies, a domain model closely matching the workflow, a database-supporting concurrency and data mining, access to the DIPS database, secured user access and roles management, and graphing and analysis tools. The Model-View-Controller (MVC) paradigm allowed clean domain logic, unit testing, and extensibility. Client-side technologies, such as jQuery, jQuery Plug-ins, and Ajax, were adopted to achieve a rich user environment and fast response. Data models included patients, staff, treatment fields and records, correction vectors, DIPS images, and association logics. Data entry, analysis, workflow logics, and notifications were implemented. The system effectively modeled the clinical workflow and IGRT process.

Resistance of Bacillus subtilis spore DNA to lethal ionizing radiation damage relies primarily on spore core components and DNA repair, with minor effects of oxygen radical detoxification.

The roles of various core components, including α/ß/γ-type small acid-soluble spore proteins (SASP), dipicolinic acid (DPA), core water content, and DNA repair by apurinic/apyrimidinic (AP) endonucleases or nonhomologous end joining (NHEJ), in Bacillus subtilis spore resistance to different types of ionizing radiation including X rays, protons, and high-energy charged iron ions have been studied. Spores deficient in DNA repair by NHEJ or AP endonucleases, the oxidative stress response, or protection by major α/ß-type SASP, DPA, and decreased core water content were significantly more sensitive to ionizing radiation than wild-type spores, with highest sensitivity to high-energy-charged iron ions. DNA repair via NHEJ and AP endonucleases appears to be the most important mechanism for spore resistance to ionizing radiation, whereas oxygen radical detoxification via the MrgA-mediated oxidative stress response or KatX catalase activity plays only a very minor role. Synergistic radioprotective effects of α/ß-type but not γ-type SASP were also identified, indicating that α/ß-type SASP's binding to spore DNA is important in preventing DNA damage due to reactive oxygen species generated by ionizing radiation.