Identification of postnatal development dependent genes and proteins in porcine epididymis.

BACKGROUND: The epididymis is a highly regionalized tubular organ possesses vectorial functions of sperm concentration, maturation, transport, and storage. The epididymis-expressed genes and proteins are characterized by regional and developmental dependent pattern. However, a systematic and comprehensive insight into the postnatal development dependent changes in gene and protein expressions of porcine epididymis is still lacking. Here, the RNA and protein of epididymis of Duroc pigs at different postnatal development stages were extracted by using commercial RNeasy Midi kit and extraction buffer (7 M Urea, 2 M thiourea, 3% CHAPS, and 1 mM PMSF) combined with sonication, respectively, which were further subjected to transcriptomic and proteomic profiling. RESULTS: Transcriptome analysis indicated that 198 and 163 differentially expressed genes (DEGs) were continuously up-regulated and down-regulated along with postnatal development stage changes, respectively. Most of the up-regulated DEGs linked to functions of endoplasmic reticulum and lysosome, while the down-regulated DEGs mainly related to molecular process of extracellular matrix. Moreover, the following key genes INSIG1, PGRMC1, NPC2, GBA, MMP2, MMP14, SFRP1, ELN, WNT-2, COL3A1, and SPARC were highlighted. A total of 49 differentially expressed proteins (DEPs) corresponding to postnatal development stages changes were uncovered by the proteome analysis. Several key proteins ACSL3 and ACADM, VDAC1 and VDAC2, and KNG1, SERPINB1, C3, and TF implicated in fatty acid metabolism, voltage-gated ion channel assembly, and apoptotic and immune processes were emphasized. In the integrative network, the key genes and proteins formed different clusters and showed strong interactions. Additionally, NPC2, COL3A1, C3, and VDAC1 are located at the hub position in each cluster. CONCLUSIONS: The identified postnatal development dependent genes and proteins in the present study will pave the way for shedding light on the molecular basis of porcine epididymis functions and are useful for further studies on the specific regulation mechanisms responsible for epididymal sperm maturation.

Identification and validation of hub genes involved in foam cell formation and atherosclerosis development via bioinformatics.

Background: Foam cells play crucial roles in all phases of atherosclerosis. However, until now, the specific mechanisms by which these foam cells contribute to atherosclerosis remain unclear. We aimed to identify novel foam cell biomarkers and interventional targets for atherosclerosis, characterizing their potential mechanisms in the progression of atherosclerosis. Methods: Microarray data of atherosclerosis and foam cells were downloaded from the Gene Expression Omnibus (GEO) database. Differentially expression genes (DEGs) were screened using the "LIMMA" package in R software. The Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analysis and Gene Ontology (GO) annotation were both carried out. Hub genes were found in Cytoscape after a protein-protein interaction (PPI) enrichment analysis was carried out. Validation of important genes in the GSE41571 dataset, cellular assays, and tissue samples. Results: A total of 407 DEGs in atherosclerosis and 219 DEGs in foam cells were identified, and the DEGs in atherosclerosis were mainly involved in cell proliferation and differentiation. CSF1R and PLAUR were identified as common hub genes and validated in GSE41571. In addition, we also found that the expression of CSF1R and PLAUR gradually increased with the accumulation of lipids and disease progression in cell and tissue experiments. Conclusion: CSF1R and PLAUR are key hub genes of foam cells and may play an important role in the biological process of atherosclerosis. These results advance our understanding of the mechanism behind atherosclerosis and potential therapeutic targets for future development.

Lymphatic endothelial transcription factor Tbx1 promotes an immunosuppressive microenvironment to facilitate post-myocardial infarction repair.

The heart is an autoimmune-prone organ. It is crucial for the heart to keep injury-induced autoimmunity in check to avoid autoimmune-mediated inflammatory disease. However, little is known about how injury-induced autoimmunity is constrained in hearts. Here, we reveal an unknown intramyocardial immunosuppressive program driven by Tbx1, a DiGeorge syndrome disease gene that encodes a T-box transcription factor (TF). We found induced profound lymphangiogenic and immunomodulatory gene expression changes in lymphatic endothelial cells (LECs) after myocardial infarction (MI). The activated LECs penetrated the infarcted area and functioned as intramyocardial immune hubs to increase the numbers of tolerogenic dendritic cells (tDCs) and regulatory T (Treg) cells through the chemokine Ccl21 and integrin Icam1, thereby inhibiting the expansion of autoreactive CD8+ T cells and promoting reparative macrophage expansion to facilitate post-MI repair. Mimicking its timing and implementation may be an additional approach to treating autoimmunity-mediated cardiac diseases.

House ammonia exposure causes alterations in microbiota, transcriptome, and metabolome of rabbits.

Introduction: Pollutant gas emissions in the current production system of the livestock industry have negative influences on environment as well as the health of farm staffs and animals. Although ammonia (NH3) is considered as the primary and harmful gas pollutant in the rabbit farm, less investigation has performed to determine the toxic effects of house ammonia exposure on rabbit in the commercial confined barn. Methods: In this study, we performed multi-omics analysis on rabbits exposed to high and low concentration of house ammonia under similar environmental conditions to unravel the alterations in nasal and colonic microbiota, pulmonary and colonic gene expression, and muscular metabolic profile. Results and discussion: The results showed that house ammonia exposure notably affected microbial structure, composition, and functional capacity in both nasal and colon, which may impact on local immune responses and inflammatory processes. Transcriptome analysis indicated that genes related to cell death (MCL1, TMBIM6, HSPB1, and CD74) and immune response (CDC42, LAMTOR5, VAMP8, and CTSB) were differentially expressed in the lung, and colonic genes associated with redox state (CAT, SELENBP1, GLUD1, and ALDH1A1) were significantly up-regulated. Several key differentially abundant metabolites such as L-glutamic acid, L-glutamine, L-ornithine, oxoglutaric acid, and isocitric acid were identified in muscle metabolome, which could denote house ammonia exposure perturbed amino acids, nucleotides, and energy metabolism. In addition, the widespread and strong inter-system interplay were uncovered in the integrative correlation network, and central features were confirmed by in vitro experiments. Our findings disclose the comprehensive evidence for the deleterious effects of house ammonia exposure on rabbit and provide valuable information for understanding the underlying impairment mechanisms.

Seasonal Variations in Production Performance, Health Status, and Gut Microbiota of Meat Rabbit Reared in Semi-Confined Conditions.

In this study, we investigated the variations in production performance, health status, and gut microbiota of meat rabbits raised in the semi-confined barn during summer and winter. Compared to summer, rabbits reared in winter possessed significantly higher slaughter weight and carcass weight. Rabbits fed in the summer were more vulnerable to different stressors, which led to increased protein levels of HSP90, IL-1α, IL-1ß, IL-2, and concentrations of MDA, but declined GSH and SOD activities. Additionally, significant differences in gut microbial communities were observed. Compared to the winter, rabbits fed in the summer had significantly lower and higher alpha and beta diversity. Both Firmicutes and Verrucomicrobiota were the dominant phyla, and they accounted for greater proportions in the winter than in the summer. At lower microbial taxa levels, several seasonal differentially enriched microbes were identified, such as Akkermansia muciniphila, the Oscillospiraceae NK4A214 group, the Christensenellaceae R-7 group, Alistipes, and Muribaculaceae. Functional capacities linked to microbial proliferation, nutrient metabolism, and environmental adaptive responses exhibited significantly different abundances between summer and winter. Moreover, strong interactions among different indicators were presented. Based on our findings, we not only proposed several potential strategies to ameliorate the undesirable effects of seasonal changes on the productivity and health of meat rabbits but also underscored the directions for future mechanistic studies of adaptation physiology.

Technical Note: Long-term monitoring of diode sensitivity degradation induced by proton irradiation.

PURPOSE: To measure diode sensitivity degradation (DSD) induced by cumulative proton dose delivered to a commercial daily quality assurance (QA) device. METHODS: At our institution, six Daily QA 3 (DQA3, Sun Nuclear Corporation, Melbourne, FL, USA) devices have been used for daily proton pencil beam scanning QA in four proton gantry rooms over a span of 4 years. DQA3 diode counts were cross-calibrated using a homogenous field with a known dose of 1 Gy. The DSD rate (ΔR%/100 Gy) was calculated using linear regression on time-series plots of diode counts and an estimate of cumulative dose per year based on the cross-calibration. The effect of DSD on daily QA spot position measurements was quantified by converting DSD to baseline spot position shift. RESULTS: The average dose delivered to the four inner DQA3 diodes was 104 ± 5 Gy/year, and the rate of DSD was -5.1% ± 1.0/100 Gy with the exception of one DQA3 device that had a significantly higher rate of DSD (-12%/100 Gy). The R2 s of the linear fit to time-series plots were between 0.92 and 0.98. The DSD rates were not constant but decreases with accumulated doses. The four center diodes, which received 40% of the cumulative dose received by inner diodes, had a DSD rate of -7.2% ± 0.9/100 Gy. For our daily QA program, 1 year of DSD was equivalent to a 0.2 mm shift in spot position. CONCLUSIONS: The DSD rate of DQA3 diodes determined by long-term proton daily QA data was about -5%/100 Gy, which is more than 10 times greater than the reported DSD rate from photon irradiation. DQA3 diodes may be used for daily proton QA programs, provided that they are recalibrated at an appropriate frequency that should be determined specifically for different daily QA programs.

Technical Note: Clinical modeling and validation of breast tissue expander metallic ports in a commercial treatment planning system for proton therapy.

PURPOSE: To validate breast tissue expander metallic port (MP) models in a commercial treatment planning system (TPS) in proton pencil beam scanning (PBS) treatments for breast cancer patients with breast tissue expanders. METHODS AND MATERIALS: Three types of MPs taken out of a Mentor CPX4, a Natrelle 133, and a PMT Integra breast tissue expanders and a 650 cc saline filled Mentor CPX4 expander were placed on top of acrylic slabs, and scanned using a Siemens Somatom Definition AS Open RT CT scanner. Structure templates for each of the MPs were designed within Eclipse TPS. The CT numbers for the metallic parts were overridden to reflect measured or calculated relative proton stopping powers (RPSPs). Mock targets were contoured in acrylic to represent postmastectomy chest-wall radiation therapy (PMRT) targets. Plans with different beam incident angles were optimized using the Eclipse TPS to deliver uniform prescription dose to the target using Hitachi Probeat-V PBS beams. Eclipse calculated doses and an in-house Monte Carlo (MC) code calculated doses were compared to the measured Gafchromic EBT3 film doses in acrylic. RESULTS: TPS/MC and film dose comparison results showed that (1) 3%/2 mm/10% threshold Gamma pass rates were better than 90.8% in the acrylic target region for all plans; (2) comparing TPS and film doses for the individual beam plans in the MP dose shadow areas, the area with dose difference above 5% ([ΔA] 5%) ranged from 1.1 to 5.0 cm2 , and the maximum dose difference ([ΔD] 0.01 cm2 ) ranged from 12.5% to 25.0%; (3) comparing MC and film doses for the individual beam plans in the MP dose shadow areas, the (ΔA) 5% varied from 1.1 to 2.9 cm2 and (ΔD) 0.01 cm2 varied from 8.5% to 24.2%; (4) for a plan composed of three individual beams treating through the Mentor CPX4 expander, the TPS (ΔA) 5% was less than 0.13 cm2 , and the (ΔD) 0.01 cm2 was less than 6% in the MP dose shadow areas. CONCLUSIONS: It is feasible to treat patients with tissue expanders using multiple PBS beams using a structure template with CT number overridden to represent the measured/calculated RPSP for MPs for PBS treatment planning. MC dose was more accurate than analytical dose in the areas with high dose gradient caused by the density heterogeneity of the breast tissue expander MPs.

Technical Note: Multiple energy extraction techniques for synchrotron-based proton delivery systems may exacerbate motion interplay effects in lung cancer treatments.

PURPOSE: The multiple energy extraction (MEE) delivery technique for synchrotron-based proton delivery systems reduces beam delivery time by decelerating the beam multiple times during one accelerator spill, but this might cause additional plan quality degradation due to intrafractional motion. We seek to determine whether MEE causes significantly different plan quality degradation compared to single energy extraction (SEE) for lung cancer treatments due to the interplay effect. METHODS: Ten lung cancer patients treated with IMPT at our institution were nonrandomly sampled based on a representative range of tumor motion amplitudes, tumor volumes, and respiratory periods. Dose-volume histogram (DVH) indices from single-fraction SEE and MEE four-dimensional (4D) dynamic dose distributions were compared using the Wilcoxon signed-rank test. Distributions of monitor units (MU) to breathing phases were investigated for features associated with plan quality degradation. SEE and MEE DVH indices were compared in fractionated deliveries of the worst-case patient treatment scenario to evaluate the impact of fractionation. RESULTS: There were no clinically significant differences in target mean dose, target dose conformity, or dose to organs-at-risk between SEE and MEE in single-fraction delivery. Three patients had significantly worse dose homogeneity with MEE compared to SEE (single-fraction mean D5% -D95% increased by up to 9.6% of prescription dose), and plots of MU distribution to breathing phases showed synchronization patterns with MEE but not SEE. However, after 30 fractions the patient in the worst-case scenario had clinically acceptable target dose homogeneity and coverage with MEE (mean D5% -D95% increased by 1% compared to SEE). CONCLUSIONS: For some patients with breathing periods close to the mean spill duration, MEE resulted in significantly worse single-fraction target dose homogeneity compared to SEE due to the interplay effect. However, this was mitigated by fractionation, and target dose homogeneity and coverage were clinically acceptable after 30 fractions with MEE.

Feasibility of using megavoltage computed tomography to reduce proton range uncertainty: A simulation study.

PURPOSE: To demonstrate that variation in chemical composition has a negligible effect on the mapping curve from relative electron density (RED) to proton stopping power ratio (SPR), and to establish the theoretical framework of using Megavoltage (MV) computed tomography (CT), instead of kilovoltage (kV) dual energy CT, to accurately estimate proton SPR. METHODS: A simulation study was performed to evaluate the effect of chemical composition variation on kVCT number and proton SPR. The simulation study involved both reference and simulated human tissues. The reference human tissues, together with their physical densities and chemical compositions, came from the ICRP publication 23. The simulated human tissues were created from the reference human tissues assuming that elemental percentage weight followed a Gaussian distribution. For all tissues, kVCT number and proton SPR were obtained through (a) theoretical calculation from tissue's physical density and chemical composition which served as the ground truth, and (b) estimation from RED using the calibration curves established from the stoichiometric method. Deviations of the estimated values from the calculated values were quantified as errors in using RED to estimate kVCT number and proton SPR. RESULTS: Given a chemical composition variation of 5% (1σ) of the nominal percentage weights, the total estimation error of using RED to estimate kVCT number was 0.34%, 0.62%, and 0.77% and the total estimation error of using RED to estimate proton SPR was 0.30%, 0.22%, and 0.16% for fat tissues, non-fat soft tissues and bone tissues, respectively. CONCLUSION: Chemical composition had a negligible effect on the method of using RED to determine proton SPR. RED itself is sufficient to accurately determine proton SPR. MVCT number maintains a superb linear relationship with RED because it is highly dominated by Compton scattering. Therefore, MVCT has great potential in reducing the proton range uncertainty.

Neonatal Heart Responds to Pressure Overload With Differential Alterations in Various Cardiomyocyte Maturation Programs That Accommodate Simultaneous Hypertrophy and Hyperplasia.

Pressure overload is one of the pathophysiological conditions commonly associated with right-sided congenital heart disease (CHD). Patients suffer from this condition right after birth. However, little is known about how neonatal heart reacts to it. We have previously established a pulmonary artery banding (PAB) model in neonatal rat. Here we show that PAB accelerated transition of mononuclear cardiomyocytes into multinucleated cells to promote hypertrophic growth in neonatal heart. The elevated afterload significantly increased the mitotic activities of neonatal cardiomyocytes. Consistent with the proliferative potential, the elevated pressure overload also increased cytokinetic marker counts of cardiomyocytes. Using cardiomyocyte-specific lineage tracing, we noticed a clonal expansion of rare unlabeled cardiomyocytes in the PAB group, revealing a subgroup of cardiomyocytes with a strong capability of proliferation. In addition, PAB hearts at post-banding day 7 didn't have the accumulation of macrophages, which is an immune response essential for neonatal heart regeneration in injury models. Transcriptomic analyses revealed that neonatal PAB induced an expression profile featuring both cardiomyocyte hypertrophy, such as highly activated translation, oxidative phosphorylation, and mitochondrial biogenesis programs etc., and immature cardiomyocyte, such as enhanced cell cycle activities and glycolytic metabolism, down-regulated cytoskeleton and ion channel gene expression, and maintenance of fetal-specific sarcomeric isoforms etc. It indicates that pressure overload has differential impacts on various cardiomyocyte maturation (CM) programs that may contribute to the concurrent cardiomyocyte hypertrophy and hyperplasia. The bivalent status of transcriptional profile highlights the plasticity of neonatal cardiomyocytes that can be exploited to adapt the postnatal environment.

Technical Note: Integrating an open source Monte Carlo code "MCsquare" for clinical use in intensity-modulated proton therapy.

PURPOSE: To commission an open source Monte Carlo (MC) dose engine, "MCsquare" for a synchrotron-based proton machine, integrate it into our in-house C++-based I/O user interface and our web-based software platform, expand its functionalities, and improve calculation efficiency for intensity-modulated proton therapy (IMPT). METHODS: We commissioned MCsquare using a double Gaussian beam model based on in-air lateral profiles, integrated depth dose of 97 beam energies, and measurements of various spread-out Bragg peaks (SOBPs). Then we integrated MCsquare into our C++-based dose calculation code and web-based second check platform "DOSeCHECK." We validated the commissioned MCsquare based on 12 different patient geometries and compared the dose calculation with a well-benchmarked GPU-accelerated MC (gMC) dose engine. We further improved the MCsquare efficiency by employing the computed tomography (CT) resampling approach. We also expanded its functionality by adding a linear energy transfer (LET)-related model-dependent biological dose calculation. RESULTS: Differences between MCsquare calculations and SOBP measurements were <2.5% (<1.5% for ~85% of measurements) in water. The dose distributions calculated using MCsquare agreed well with the results calculated using gMC in patient geometries. The average 3D gamma analysis (2%/2 mm) passing rates comparing MCsquare and gMC calculations in the 12 patient geometries were 98.0 ± 1.0%. The computation time to calculate one IMPT plan in patients' geometries using an inexpensive CPU workstation (Intel Xeon E5-2680 2.50 GHz) was 2.3 ± 1.8 min after the variable resolution technique was adopted. All calculations except for one craniospinal patient were finished within 3.5 min. CONCLUSIONS: MCsquare was successfully commissioned for a synchrotron-based proton beam therapy delivery system and integrated into our web-based second check platform. After adopting CT resampling and implementing LET model-dependent biological dose calculation capabilities, MCsquare will be sufficiently efficient and powerful to achieve Monte Carlo-based and LET-guided robust optimization in IMPT, which will be done in the future studies.

Robust Optimization for Intensity Modulated Proton Therapy to Redistribute High Linear Energy Transfer from Nearby Critical Organs to Tumors in Head and Neck Cancer.

PURPOSE: We propose linear energy transfer (LET)-guided robust optimization in intensity modulated proton therapy for head and neck cancer. This method simultaneously considers LET and physical dose distributions of tumors and organs at risk (OARs) with uncertainties. METHODS AND MATERIALS: Fourteen patients with head and neck cancer were included in this retrospective study. Cord, brain stem, brain, and oral cavity were considered. Two algorithms, voxel-wise worst-case robust optimization and LET-guided robust optimization (LETRO), were used to generate intensity modulated proton therapy plans for each patient. The latter method directly optimized LET distributions rather than indirectly as in previous methods. LET-volume histograms (LETVHs) were generated, and high LET was redistributed from nearby OARs to tumors in a user-defined way via LET-volume constraints. Dose-volume histogram indices, such as clinical target volume (CTV) D98% and D2%-D98%, cord Dmax, brain stem Dmax, brain Dmax, and oral cavity Dmean, were calculated. Plan robustness was quantified using the worst-case analysis method. LETVH indices analogous to dose-volume histogram indices were used to characterize LET distributions. The Wilcoxon signed rank test was performed to measure statistical significance. RESULTS: In the nominal scenario, LETRO provided higher LET distributions in the CTV (unit: keV/µm; CTV LET98%: 1.18 vs 1.08, LETRO vs RO, P = .0031) while preserving comparable physical dose and plan robustness. LETRO achieved significantly reduced LET distributions in the cord, brain stem, and oral cavity compared with RO (cord LETmax: 7.20 vs 8.20, P = .0010; brain stem LETmax: 10.95 vs 12.05, P = .0007; oral cavity LETmean: 2.11 vs 3.12, P = .0052) and had comparable physical dose and plan robustness in all OARs. In the worst-case scenario, LETRO achieved significantly higher LETmean in the CTV, reduced LETmax in the brain, and was comparable to other LETVH indices (CTV LETmean: 3.26 vs 3.35, P = .0012; brain LETmax: 24.80 vs 22.00, P = .0016). CONCLUSIONS: LETRO robustly optimized LET and physical dose distributions simultaneously. It redistributed high LET from OARs to targets with slightly modified physical dose and plan robustness.

Hybrid 3D analytical linear energy transfer calculation algorithm based on precalculated data from Monte Carlo simulations.

PURPOSE: The dose-averaged linear energy transfer (LETd ) for intensity-modulated proton therapy (IMPT) calculated by one-dimensional (1D) analytical models deviates from more accurate but time-consuming Monte Carlo (MC) simulations. We developed a fast hybrid three-dimensional (3D) analytical LETd calculation that is more accurate than 1D analytical model. METHODS: We used the Geant4 MC code to generate 3D LETd distributions of monoenergetic proton beams in water for all energies and used a customized error function to fit the LETd lateral profiles at various depths to the MC simulation. The 3D LETd calculation kernel was a lookup table of these fitted coefficients, and LETd was determined directly from spot energies and voxel coordinates during analytical dose calculations. We validated our new method by comparing the calculated LETd distributions to MC results using 3D Gamma index analysis with 3%/2 mm criteria in 12 patient geometries. The significance of the improvement in Gamma index analysis passing rates over the 1D analytical model was determined using the Wilcoxon rank-sum test. RESULTS: The passing rate of 3D Gamma analysis comparing LETd distributions from the hybrid 3D method and the 1D method to MC simulations was significantly improved from 94.0% ± 2.5% to 98.0% ± 1.0% (P = 0.0003). The typical time to calculate dose and LETd simultaneously using an Intel Xeon E5-2680 2.50 GHz workstation was approximately 2.5 min. CONCLUSIONS: Our new method significantly improved the LETd calculation accuracy compared to the 1D method while maintaining significantly shorter calculation time even comparing with the GPU-based fast MC code.

Clinical Validation of a Ray-Casting Analytical Dose Engine for Spot Scanning Proton Delivery Systems.

PURPOSE: To describe and validate the dose calculation algorithm of an independent second-dose check software for spot scanning proton delivery systems with full width at half maximum between 5 and 14 mm and with a negligible spray component. METHODS: The analytical dose engine of our independent second-dose check software employs an altered pencil beam algorithm with 3 lateral Gaussian components. It was commissioned using Geant4 and validated by comparison to point dose measurements at several depths within spread-out Bragg peaks of varying ranges, modulations, and field sizes. Water equivalent distance was used to compensate for inhomogeneous geometry. Twelve patients representing different disease sites were selected for validation. Dose calculation results in water were compared to a fast Monte Carlo code and ionization chamber array measurements using dose planes and dose profiles as well as 2-dimensional-3-dimensional and 3-dimensional-3-dimensional γ-index analysis. Results in patient geometry were compared to Monte Carlo simulation using dose-volume histogram indices, 3-dimensional-3-dimensional γ-index analysis, and inpatient dose profiles. RESULTS: Dose engine model parameters were tuned to achieve 1.5% agreement with measured point doses. The in-water γ-index passing rates for the 12 patients using 3%/2 mm criteria were 99.5% ± 0.5% compared to Monte Carlo. The average inpatient γ-index analysis passing rate compared to Monte Carlo was 95.8% ± 2.9%. The average difference in mean dose to the clinical target volume between the dose engine and Monte Carlo was -0.4% ± 1.0%. For a typical plan, dose calculation time was 2 minutes on an inexpensive workstation. CONCLUSIONS: Following our commissioning process, the analytical dose engine was validated for all treatment sites except for the lung or for calculating dose-volume histogram indices involving point doses or critical structures immediately distal to target volumes. Monte Carlo simulations are recommended for these scenarios.

Technical Note: Comprehensive evaluation and implementation of two independent methods for beam monitor calibration for proton scanning beam.

PURPOSE: To clinically implement and comprehensively evaluate two independent methods for beam monitor calibration of scanning proton beam. METHODS: Seven proton energies that represent the lowest to highest energy proton beams were selected. Single energy layer circular fields of diameter 15 cm with 2.5 mm spot spacing and 10 times of repainting (FS15cm ) were designed for all energies. The effective measurement points of Bragg peak chamber (BPC), advanced Markus chamber (AMC) and farmer chamber (FC) were all aligned to 2 cm depth in water using SSD setup. The BPC and AMC were cross-calibrated with farmer chamber (FC) using the field FS15cm . In order to evaluate BPC's lateral response uniformity, a collimated narrow proton beam (5.8 mm diameter) was delivered to the active area and edge of the BPC. The dose area product (DAP) was measured using two methods by two BPCs, one AMC and one FC. For method 1, a single spot proton beam was delivered to the geometric center of the BPC. For method 2, the fields FS15cm were delivered to FC and AMC, respectively. Accumulated charges by these chambers were converted to DAPs, and the quantitative difference of DAPs between both methods was calculated. The causes of the uncertainties were discussed, and the advantages of the two methods were compared. RESULTS: The two BPCs showed different lateral response uniformity. BPC1 has a uniform response from the center up to a radius of 3.5 cm. BPC2 has a uniform response only to 2 cm and the response dropped 1% to 2% at 3.5 cm from center. BPC2 also has significant over-response compared to BPC1. A 2.2% systematic error would be transferred to DAP if the over-response from BPC2 was not considered. The DAPs measured by method 1 with two BPCs and by method 2 with FC and AMC were consistent to 0.5%. The major uncertainty component of method 1 is from the cross-calibration of the BPC. CONCLUSIONS: The two independent methods for DAP were shown to give consistent results, given the sources of uncertainties were carefully addressed in the measurements. Direct measurement of DAP with BPC is very efficient, but it may be subject to more than 2% systematic error if the BPC lateral response is not carefully evaluated.

Technical Note: Treatment planning system (TPS) approximations matter - comparing intensity-modulated proton therapy (IMPT) plan quality and robustness between a commercial and an in-house developed TPS for nonsmall cell lung cancer (NSCLC).

PURPOSE: Approximate dose calculation methods were used in the nominal dose distribution and the perturbed dose distributions due to uncertainties in a commercial treatment planning system (CTPS) for robust optimization in intensity-modulated proton therapy (IMPT). We aimed to investigate whether the approximations influence plan quality, robustness, and interplay effect of the resulting IMPT plans for the treatment of locally advanced lung cancer patients. MATERIALS AND METHODS: Ten consecutively treated locally advanced nonsmall cell lung cancer (NSCLC) patients were selected. Two IMPT plans were created for each patient using our in-house developed TPS, named "Solo," and also the CTPS, EclipseTM (Varian Medical Systems, Palo Alto, CA, USA), respectively. The plans were designed to deliver prescription doses to internal target volumes (ITV) drawn by a physician on averaged four-dimensional computed tomography (4D-CT). Solo plans were imported back to CTPS, and recalculated in CTPS for fair comparison. Both plans were further verified for each patient by recalculating doses in the inhalation and exhalation phases to ensure that all plans met clinical requirements. Plan robustness was quantified on all phases using dose-volume-histograms (DVH) indices in the worst-case scenario. The interplay effect was evaluated for every plan using an in-house developed software, which randomized starting phases of each field per fraction and accumulated dose in the exhalation phase based on the patient's breathing motion pattern and the proton spot delivery in a time-dependent fashion. DVH indices were compared using Wilcoxon rank-sum test. RESULTS: Compared to the plans generated using CTPS on the averaged CT, Solo plans had significantly better target dose coverage and homogeneity (normalized by the prescription dose) in the worst-case scenario [ITV D95% : 98.04% vs 96.28%, Solo vs CTPS, P = 0.020; ITV D5% -D95% : 7.20% vs 9.03%, P = 0.049] while all DVH indices were comparable in the nominal scenario. On the inhalation phase, Solo plans had better target dose coverage and cord Dmax in the nominal scenario [ITV D95% : 99.36% vs 98.45%, Solo vs CTPS, P = 0.014; cord Dmax : 20.07 vs 23.71 Gy(RBE), P = 0.027] with better target coverage and cord Dmax in the worst-case scenario [ITV D95% : 97.89% vs 96.47%, Solo vs CTPS, P = 0.037; cord Dmax : 24.57 vs 28.14 Gy(RBE), P = 0.037]. On the exhalation phase, similar phenomena were observed in the nominal scenario [ITV D95% : 99.63% vs 98.87%, Solo vs CTPS, P = 0.037; cord Dmax : 19.67 vs 23.66 Gy(RBE), P = 0.039] and in the worst-case scenario [ITV D95% : 98.20% vs 96.74%, Solo vs CTPS, P = 0.027; cord Dmax : 23.47 vs 27.93 Gy(RBE), P = 0.027]. In terms of interplay effect, plans generated by Solo had significantly better target dose coverage and homogeneity, less hot spots, and lower esophageal Dmean , and cord Dmax [ITV D95% : 101.81% vs 98.68%, Solo vs CTPS, P = 0.002; ITV D5% -D95% : 2.94% vs 7.51%, P = 0.002; cord Dmax : 18.87 vs 22.29 Gy(RBE), P = 0.014]. CONCLUSIONS: Solo-generated IMPT plans provide improved cord sparing, better target robustness in all considered phases, and reduced interplay effect compared with CTPS. Consequently, the approximation methods currently used in commercial TPS programs may have space for improvement in generating optimal IMPT plans for patient cases with locally advanced lung cancer.

Impact of planned dose reporting methods on Gamma pass rates for IROC lung and liver motion phantoms treated with pencil beam scanning protons.

PURPOSE: The purpose of this study is to evaluate the impact of two methods of reporting planned dose distributions on the Gamma analysis pass rates for comparison with measured 2D film dose and simulated delivered 3D dose for proton pencil beam scanning treatment of the Imaging and Radiation Oncology Core (IROC) proton lung and liver mobile phantoms. METHODS AND MATERIALS: Four-dimensional (4D) computed-tomography (CT) image sets were acquired for IROC proton lung and liver mobile phantoms, which include dosimetry inserts that contains targets, thermoluminescent dosimeters and EBT2 films for plan dose verification. 4DCT measured fixed motion magnitudes were 1.3 and 1.0 cm for the lung and liver phantoms, respectively. To study the effects of motion magnitude on the Gamma analysis pass rate, three motion magnitudes for each phantom were simulated by creating virtual 4DCT image sets with motion magnitudes scaled from the scanned phantom motion by 50, 100, and 200%. The internal target volumes were contoured on the maximum intensity projection CTs of the 4DCTs for the lung phantom and on the minimum intensity projection CTs of the 4DCTs for the liver phantom. Treatment plans were optimized on the average intensity projection (AVE) CTs of the 4DCTs using the RayStation treatment planning system. Plan doses were calculated on the AVE CTs, which was defined as the planned AVE dose (method one). Plan doses were also calculated on all 10 phase CTs of the 4DCTs and were registered using target alignment to and equal-weight-summed on the 50% phase (T50) CT, which was defined as the planned 4D dose (method two). The planned AVE doses and 4D doses for phantom treatment were reported to IROC, and the 2D-2D Gamma analysis pass rates for measured film dose relative to the planned AVE and 4D doses were compared. To evaluate motion interplay effects, simulated delivered doses were calculated for each plan by sorting spots into corresponding respiratory phases using spot delivery time recorded in the log files by the beam delivery system to calculate each phase dose and accumulate dose to the T50 CTs. Ten random beam starting phases were used for each beam to obtain the range of the simulated delivered dose distributions. 3D-3D Gamma analyses were performed to compare the planned 4D/AVE doses with simulated delivered doses. RESULTS: The planned 4D dose matched better with the measured 2D film dose and simulated delivered 3D dose than the planned AVE dose. Using planned 4D dose as institution reported planned dose to IROC improved IROC film dose 2D-2D Gamma analysis pass rate from 92 to 96% on average for three films for the lung phantom (7% 5 mm), and from 92 to 94% in the sagittal plane for the liver phantom (7% 4 mm), respectively, compared with using the planned AVE dose. The 3D-3D Gamma analysis (3% 3 mm) pass rate showed that the simulated delivered doses for lung and liver phantoms using 10 random beam starting phases for each delivered beam matched the planned 4D dose significantly better than the planned AVE dose for phantom motions larger than 1 cm (p ≤ 0.04). CONCLUSIONS: It is recommended to use the planned 4D dose as the institution reported planned dose to IROC to compare with the measured film dose for proton mobile phantoms to improve film Gamma analysis pass rate in the IROC credentialing process.

Dosimetric comparison of distal esophageal carcinoma plans for patients treated with small-spot intensity-modulated proton versus volumetric-modulated arc therapies.

BACKGROUND: Esophageal carcinoma is the eighth most common cancer in the world. Volumetric-modulated arc therapy (VMAT) is widely used to treat distal esophageal carcinoma due to high conformality to the target and good sparing of organs at risk (OAR). It is not clear if small-spot intensity-modulated proton therapy (IMPT) demonstrates a dosimetric advantage over VMAT. In this study, we compared dosimetric performance of VMAT and small-spot IMPT for distal esophageal carcinoma in terms of plan quality, plan robustness, and interplay effects. METHODS: 35 distal esophageal carcinoma patients were retrospectively reviewed; 19 patients received small-spot IMPT and the remaining 16 of them received VMAT. Both plans were generated by delivering prescription doses to clinical target volumes (CTVs) on phase-averaged 4D-CT's. The dose-volume-histogram (DVH) band method was used to quantify plan robustness. Software was developed to evaluate interplay effects with randomized starting phases for each field per fraction. DVH indices were compared using Wilcoxon rank-sum test. For fair comparison, all the treatment plans were normalized to have the same CTVhigh D95% in the nominal scenario relative to the prescription dose. RESULTS: In the nominal scenario, small-spot IMPT delivered statistically significantly lower liver Dmean and V30Gy[RBE] , lung Dmean , heart Dmean compared with VMAT. CTVhigh dose homogeneity and protection of other OARs were comparable between the two treatments. In terms of plan robustness, the IMPT and VMAT plans were comparable for kidney V18Gy[RBE] , liver V30Gy[RBE] , stomach V45Gy[RBE] , lung Dmean , V5Gy[RBE] , and V20Gy[RBE] , cord Dmax and D 0.03 c m 3 , liver Dmean , heart V20Gy[RBE] , and V30Gy[RBE] , but IMPT was significantly worse for CTVhigh D95% , D 2 c m 3 , and D5% -D95% , CTVlow D95% , heart Dmean , and V40Gy[RBE] , requiring careful and experienced adjustments during the planning process and robustness considerations. The small-spot IMPT plans still met the standard clinical requirements after interplay effects were considered. CONCLUSIONS: Small-spot IMPT decreases doses to heart, liver, and total lung compared to VMAT as well as achieves clinically acceptable plan robustness. Our study supports the use of small-spot IMPT for the treatment of distal esophageal carcinoma.

Small-spot intensity-modulated proton therapy and volumetric-modulated arc therapies for patients with locally advanced non-small-cell lung cancer: A dosimetric comparative study.

PURPOSE: To compare dosimetric performance of volumetric-modulated arc therapy (VMAT) and small-spot intensity-modulated proton therapy for stage III non-small-cell lung cancer (NSCLC). METHODS AND MATERIALS: A total of 24 NSCLC patients were retrospectively reviewed; 12 patients received intensity-modulated proton therapy (IMPT) and the remaining 12 received VMAT. Both plans were generated by delivering prescription doses to clinical target volumes (CTV) on averaged 4D-CTs. The dose-volume-histograms (DVH) band method was used to quantify plan robustness. Software was developed to evaluate interplay effects with randomized starting phases of each field per fraction. DVH indices were compared using Wilcoxon rank sum test. RESULTS: Compared with VMAT, IMPT delivered significantly lower cord Dmax , heart Dmean , and lung V5 Gy[ RBE ] with comparable CTV dose homogeneity, and protection of other OARs. In terms of plan robustness, the IMPT plans were statistically better than VMAT plans in heart Dmean , but were statistically worse in CTV dose coverage, cord Dmax , lung Dmean , and V5 Gy[ RBE ] . Other DVH indices were comparable. The IMPT plans still met the standard clinical requirements with interplay effects considered. CONCLUSIONS: Small-spot IMPT improves cord, heart, and lung sparing compared to VMAT and achieves clinically acceptable plan robustness at least for the patients included in this study with motion amplitude less than 11 mm. Our study supports the usage of IMPT to treat some lung cancer patients.

Multiple energy extraction reduces beam delivery time for a synchrotron-based proton spot-scanning system.

PURPOSE: Multiple energy extraction (MEE) is a technology that was recently introduced by Hitachi for its spot-scanning proton treatment system, which allows multiple energies to be delivered in a single synchrotron spill. The purpose of this paper is to investigate how much beam delivery time (BDT) can be reduced with MEE compared with single energy extraction (SEE), in which one energy is delivered per spill. METHODS AND MATERIALS: A recently developed model based on BDT measurements of our synchrotron's delivery performance was used to compute BDT. The total BDT for 2694 beam deliveries in a cohort of 79 patients treated at our institution was computed in both SEE and 9 MEE configurations to determine BDT reduction. The cohort BDT reduction was also calculated for hypothetical accelerators with increased deliverable charge and compared with the results of our current delivery system. RESULTS: A vendor-provided MEE configuration with 4 energy layers per spill reduced the total BDT on average by 35% (41 seconds) compared with SEE, with up to 65% BDT reduction for individual fields. Adding an MEE layer reduced the total BDT by <1% of SEE BDT. However, improving charge recapture efficiency increased BDT savings by up to 42% of SEE BDT. CONCLUSIONS: The MEE delivery technique reduced the total BDT by 35%. Increasing the charge per spill and charge recapture efficiency is necessary to further reduce BDT and thereby take full advantage of our MEE system's potential to improve treatment delivery efficiency and operational throughput.