An excursion set model of the cosmic web: The abundance of sheets, filaments and halos

We discuss an analytic approach for modeling structure formation in sheets, filaments and knots. This is accomplished by combining models of triaxial collapse with the excursion set approach: sheets are defined as objects which have collapsed along only one axis, filaments have collapsed along two axes, and halos are objects in which triaxial collapse is complete. In the simplest version of this approach, which we develop here, large scale structure shows a clear hierarchy of morphologies: the mass in large-scale sheets is partitioned up among lower mass filaments, which themselves are made-up of still lower mass halos. Our approach provides analytic estimates of the mass fraction in sheets, filaments and halos, and its evolution, for any background cosmological model and any initial fluctuation spectrum. In the currently popular $\Lambda$CDM model, our analysis suggests that more than 99% of the cosmic mass is in sheets, and 72% in filaments, with mass larger than $10^{10} M_{\odot}$ at the present time. For halos, this number is only 46%. Our approach also provides analytic estimates of how halo abundances at any given time correlate with the morphology of the surrounding large-scale structure, and how halo evolution correlates with the morphology of large scale structure.Comment: 22 pages, 7 figures, Accepted for publication in Ap

Spectral Decomposition of Broad-Line AGNs and Host Galaxies

Using an eigenspectrum decomposition technique, we separate the host galaxy from the broad line active galactic nucleus (AGN) in a set of 4666 spectra from the Sloan Digital Sky Survey (SDSS), from redshifts near zero up to about 0.75. The decomposition technique uses separate sets of galaxy and quasar eigenspectra to efficiently and reliably separate the AGN and host spectroscopic components. The technique accurately reproduces the host galaxy spectrum, its contributing fraction, and its classification. We show how the accuracy of the decomposition depends upon S/N, host galaxy fraction, and the galaxy class. Based on the eigencoefficients, the sample of SDSS broad-line AGN host galaxies spans a wide range of spectral types, but the distribution differs significantly from inactive galaxies. In particular, post-starburst activity appears to be much more common among AGN host galaxies. The luminosities of the hosts are much higher than expected for normal early-type galaxies, and their colors become increasingly bluer than early-type galaxies with increasing host luminosity. Most of the AGNs with detected hosts are emitting at between 1% and 10% of their estimated Eddington luminosities, but the sensitivity of the technique usually does not extend to the Eddington limit. There are mild correlations among the AGN and host galaxy eigencoefficients, possibly indicating a link between recent star formation and the onset of AGN activity. The catalog of spectral reconstruction parameters is available as an electronic table.Comment: 18 pages; accepted for publication in A

Ion Chamber Collection Efficiencies for Proton Spot Scanning Calibration

Charge accumulation was measured under calibration conditions in the spread-out Bragg peak (SOBP) using the calibration bias as well as a range of voltages from 10V to 500V and a Farmer-style ion chamber. Collection efficiency was determined by extrapolating to infinite voltage. Similar measurements were taken in an identical dose distribution with a much shorter spot duration. The impact of each of the three models on calibration was then quantified using the TRS-398 protocol. The collection efficiency for the standard calibration was determined to agree well with the prediction of a continuous beam recombination correction. The standard calibration field was found to persistently agree with a continuous beam recombination correction for much lower operating biases. The collection efficiency result for the short spot duration field did not agree with either the continuous or pulsed-beam correction. Using the incorrect recombination model under the standard calibration conditions resulted in a 0.5% calibration difference. We have determined that our spot scanning system would be most appropriately calibrated using a recombination correction with continuous beam model. Physicists responsible for the calibration of such systems are advised to take measurements described here to correctly identify the applicable recombination model for their clinics.Comment: Submitted December 16, 2015 to Medical Physic

Evaluating Large Language Models on a Highly-specialized Topic, Radiation Oncology Physics

We present the first study to investigate Large Language Models (LLMs) in answering radiation oncology physics questions. Because popular exams like AP Physics, LSAT, and GRE have large test-taker populations and ample test preparation resources in circulation, they may not allow for accurately assessing the true potential of LLMs. This paper proposes evaluating LLMs on a highly-specialized topic, radiation oncology physics, which may be more pertinent to scientific and medical communities in addition to being a valuable benchmark of LLMs. We developed an exam consisting of 100 radiation oncology physics questions based on our expertise at Mayo Clinic. Four LLMs, ChatGPT (GPT-3.5), ChatGPT (GPT-4), Bard (LaMDA), and BLOOMZ, were evaluated against medical physicists and non-experts. ChatGPT (GPT-4) outperformed all other LLMs as well as medical physicists, on average. The performance of ChatGPT (GPT-4) was further improved when prompted to explain first, then answer. ChatGPT (GPT-3.5 and GPT-4) showed a high level of consistency in its answer choices across a number of trials, whether correct or incorrect, a characteristic that was not observed in the human test groups. In evaluating ChatGPTs (GPT-4) deductive reasoning ability using a novel approach (substituting the correct answer with "None of the above choices is the correct answer."), ChatGPT (GPT-4) demonstrated surprising accuracy, suggesting the potential presence of an emergent ability. Finally, although ChatGPT (GPT-4) performed well overall, its intrinsic properties did not allow for further improvement when scoring based on a majority vote across trials. In contrast, a team of medical physicists were able to greatly outperform ChatGPT (GPT-4) using a majority vote. This study suggests a great potential for LLMs to work alongside radiation oncology experts as highly knowledgeable assistants

Applications of various range shifters for proton pencil beam scanning radiotherapy

Background A range pull-back device, such as a machine-related range shifter (MRS) or a universal patient-related range shifter (UPRS), is needed in pencil beam scanning technique to treat shallow tumors. Methods Three UPRS made by QFix (Avondale, PA, USA) allow treating targets across the body: U-shaped bolus (UB), anterior lateral bolus (ALB), and couch top bolus. Head-and-neck (HN) patients who used the UPRS were tested. The in-air spot sizes were measured and compared in this study at air gaps: 6 cm, 16 cm, and 26 cm. Measurements were performed in a solid water phantom using a single-field optimization pencil beam scanning field with the ALB placed at 0, 10, and 20 cm air gaps. The two-dimensional dose maps at the middle of the spread-out Bragg peak were measured using ion chamber array MatriXX PT (IBA-Dosimetry, Schwarzenbruck, Germany) located at isocenter and compared with the treatment planning system. Results A UPRS can be consistently placed close to the patient and maintains a relatively small spot size resulting in improved dose distributions. However, when a UPRS is non-removable (e.g. thick couch top), the quality of volumetric imaging is degraded due to their high Z material construction, hindering the value of Image-Guided Radiation Therapy (IGRT). Limitations of using UPRS with small air gaps include reduced couch weight limit, potential collision with patient or immobilization devices, and challenges using non-coplanar fields with certain UPRS. Our experience showed the combination of a U-shaped bolus exclusively for an HN target and an MRS as the complimentary device for head-and-neck targets as well as for all other treatment sites may be ideal to preserve the dosimetric advantages of pencil beam scanning proton treatments across the body. Conclusion We have described how to implement UPRS and MRS for various clinical indications using the PBS technique, and comprehensively reviewed the advantage and disadvantages of UPRS and MRS. We recommend the removable UB only to be employed for the brain and HN treatments while an automated MRS is used for all proton beams that require RS but not convenient or feasible to use UB

Study of linear energy transfer effect on rib fracture in breast patients receiving pencil-beam-scanning proton therapy

Purpose: To study the effect of proton linear energy transfer (LET) on rib fracture in breast cancer patients treated with pencil-beam scanning proton therapy (PBS) using a novel tool of dose-LET volume histogram (DLVH). Methods: From a prospective registry of patients treated with post-mastectomy proton therapy to the chest wall and regional lymph nodes for breast cancer between 2015 and 2020, we retrospectively identified rib fracture cases detected after completing treatment. Contemporaneously treated control patients that did not develop rib fracture were matched to patients 2:1 considering prescription dose, boost location, reconstruction status, laterality, chest wall thickness, and treatment year. The DLVH index, V(d, l), defined as volume(V) of the structure with at least dose(d) and LET(l), was calculated. DLVH plots between the fracture and control group were compared. Conditional logistic regression (CLR) model was used to establish the relation of V(d, l) and the observed fracture at each combination of d and l. The p-value derived from CLR model shows the statistical difference between fracture patients and the matched control group. Using the 2D p-value map, the DLVH features associated with the patient outcomes were extracted. Results: Seven rib fracture patients were identified, and fourteen matched patients were selected for the control group. The median time from the completion of proton therapy to rib fracture diagnosis was 12 months (range 5 to 14 months). Two patients had grade 2 symptomatic rib fracture while the remaining 5 were grade 1 incidentally detected on imaging. The derived p-value map demonstrated larger V(0-36 Gy[RBE], 4.0-5.0 keV/um) in patients experiencing fracture (p<0.1). Conclusions: In breast cancer patients receiving PBS, a larger volume of chest wall receiving moderate dose and high LET may result in increased risk of rib fracture.Comment: 1 Table and 3 Figure

Modelling small block aperture in an in-house developed GPU-accelerated Monte Carlo-based dose engine for pencil beam scanning proton therapy

Purpose: To enhance an in-house graphic-processing-unit (GPU) accelerated virtual particle (VP)-based Monte Carlo (MC) proton dose engine (VPMC) to model aperture blocks in both dose calculation and optimization for pencil beam scanning proton therapy (PBSPT)-based stereotactic radiosurgery (SRS). Methods and Materials: A block aperture module was integrated into VPMC. VPMC was validated by an opensource code, MCsquare, in eight water phantom simulations with 3cm thick brass apertures: four were with aperture openings of 1, 2, 3, and 4cm without a range shifter, while the other four were with same aperture opening configurations with a range shifter of 45mm water equivalent thickness. VPMC was benchmarked with MCsquare and RayStation MC for 10 patients with small targets (average volume 8.4 cc). Finally, 3 patients were selected for robust optimization with aperture blocks using VPMC. Results: In the water phantoms, 3D gamma passing rate (2%/2mm/10%) between VPMC and MCsquare were 99.71$\pm$0.23%. In the patient geometries, 3D gamma passing rates (3%/2mm/10%) between VPMC/MCsquare and RayStation MC were 97.79$\pm$2.21%/97.78$\pm$1.97%, respectively. The calculation time was greatly decreased from 112.45$\pm$114.08 seconds (MCsquare) to 8.20$\pm$6.42 seconds (VPMC), both having statistical uncertainties of about 0.5%. The robustly optimized plans met all the dose-volume-constraints (DVCs) for the targets and OARs per our institutional protocols. The mean calculation time for 13 influence matrices in robust optimization by VPMC was 41.6 seconds. Conclusion: VPMC has been successfully enhanced to model aperture blocks in dose calculation and optimization for the PBSPT-based SRS.Comment: 3 tables, 3 figure

Beam mask and sliding window-facilitated deep learning-based accurate and efficient dose prediction for pencil beam scanning proton therapy

Purpose: To develop a DL-based PBSPT dose prediction workflow with high accuracy and balanced complexity to support on-line adaptive proton therapy clinical decision and subsequent replanning. Methods: PBSPT plans of 103 prostate cancer patients and 83 lung cancer patients previously treated at our institution were included in the study, each with CTs, structure sets, and plan doses calculated by the in-house developed Monte-Carlo dose engine. For the ablation study, we designed three experiments corresponding to the following three methods: 1) Experiment 1, the conventional region of interest (ROI) method. 2) Experiment 2, the beam mask (generated by raytracing of proton beams) method to improve proton dose prediction. 3) Experiment 3, the sliding window method for the model to focus on local details to further improve proton dose prediction. A fully connected 3D-Unet was adopted as the backbone. Dose volume histogram (DVH) indices, 3D Gamma passing rates, and dice coefficients for the structures enclosed by the iso-dose lines between the predicted and the ground truth doses were used as the evaluation metrics. The calculation time for each proton dose prediction was recorded to evaluate the method's efficiency. Results: Compared to the conventional ROI method, the beam mask method improved the agreement of DVH indices for both targets and OARs and the sliding window method further improved the agreement of the DVH indices. For the 3D Gamma passing rates in the target, OARs, and BODY (outside target and OARs), the beam mask method can improve the passing rates in these regions and the sliding window method further improved them. A similar trend was also observed for the dice coefficients. In fact, this trend was especially remarkable for relatively low prescription isodose lines. The dose predictions for all the testing cases were completed within 0.25s

The Black Hole-Bulge Relationship in Luminous Broad-Line Active Galactic Nuclei and Host Galaxies

We have measured the stellar velocity dispersions (\sigma_*) and estimated the central black hole (BH) masses for over 900 broad-line active galactic nuclei (AGNs) observed with the Sloan Digital Sky Survey. The sample includes objects which have redshifts up to z=0.452, high quality spectra, and host galaxy spectra dominated by an early-type (bulge) component. The AGN and host galaxy spectral components were decomposed using an eigenspectrum technique. The BH masses (M_BH) were estimated from the AGN broad-line widths, and the velocity dispersions were measured from the stellar absorption spectra of the host galaxies. The range of black hole masses covered by the sample is approximately 10^6 < M_BH < 10^9 M_Sun. The host galaxy luminosity-velocity dispersion relationship follows the well-known Faber-Jackson relation for early-type galaxies, with a power-law slope 4.33+-0.21. The estimated BH masses are correlated with both the host luminosities (L_{H}) and the stellar velocity dispersions (\sigma_*), similar to the relationships found for low-redshift, bulge-dominated galaxies. The intrinsic scatter in the correlations are large (~0.4 dex), but the very large sample size allows tight constraints to be placed on the mean relationships: M_BH ~ L_H^{0.73+-0.05} and M_BH ~ \sigma_*^{3.34+-0.24}. The amplitude of the M_BH-\sigma_* relation depends on the estimated Eddington ratio, such that objects with larger Eddington ratios have smaller black hole masses than expected at a given velocity dispersion.Comment: Accepted for publication in A