De Novo Transcriptome Assembly of Cedar (Cedrela odorata L.) and Differential Gene Expression Involved in Herbivore Resistance.

Timber trees are targets of herbivorous attacks. The identification of genes associated with pest resistance can be accomplished through differential expression analysis using transcriptomes. We reported the de novo assembly of cedar (Cedrela odorata L.) transcriptome and the differential expression of genes involved in herbivore resistance. The assembly and annotation of the transcriptome were obtained using RNAseq from healthy cedar plants and those infested with Chrysobothris yucatanensis. A total of 325.6 million reads were obtained, and 127,031 (97.47%) sequences were successfully assembled. A total of 220 herbivory-related genes were detected, of which 170 genes were annotated using GO terms, and 161 genes with 245 functions were identified-165, 75, and 5 were molecular functions, biological processes, and cellular components, respectively. To protect against herbivorous infestation, trees produce toxins and volatile compounds which are modulated by signaling pathways and gene expression related to molecular functions and biological processes. The limited number of genes identified as cellular components suggests that there are minimal alterations in cellular structure in response to borer attack. The chitin recognition protein, jasmonate ZIM-domain (JAZ) motifs, and response regulator receiver domain were found to be overexpressed, whereas the terpene synthase, cytochrome P450, and protein kinase domain gene families were underexpressed. This is the first report of a cedar transcriptome focusing on genes that are overexpressed in healthy plants and underexpressed in infested plants. This method may be a viable option for identifying genes associated with herbivore resistance.

Introducing electron correlation in solid-state calculations for superconducting states.

Analyzing the electronic localization of superconductors has been recently shown to be relevant for understanding their critical temperature [Nature Communications, 12, 5381, (2021)]. However, these relationships have only been shown at the Kohn-Sham density functional theory (DFT) level, where the onset of strong correlation linked to the superconducting state is missing. In this contribution, we approximate the superconducting gap in order to reconstruct the superconducting the one-reduced density matrix (1RDM) from a DFT calculation. This allows us to analyse the electron density and localization in the strong correlation regime. The method is applied to two well-known superconductors. Electron localization features along the electron-phonon coupling directions and hydrogen cluster formations are observed for different solids. However, in both cases we see that the overall localization channels are not affected by the onset of superconductivity, explaining the ability of DFT localization channels to characterize the superconducting ones.

Interactions and reactivity in crystalline intermediates of mechanochemical cyclorhodation reactions.

There is experimental evidence that solid mixtures of the rhodium dimer [Cp*RhCl2]2 and benzo[h] quinoline (BHQ) produce two different polymorphic molecular cocrystals called 4α and 4ß under ball milling conditions. The addition of NaOAc to the mixture leads to the formation of the rhodacycle [Cp*Rh-(BHQ)Cl], where the central Rh atom retains its tetracoordinate character. Isolate 4ß reacts with NaOAc leading to the same rhodacycle while isolate 4α does not under the same conditions. We show that the puzzling difference in reactivity between the two cocrystals can be traced back to fundamental aspects of the intermolecular interactions between the BHQ and [Cp*RhCl2]2 fragments in the crystalline environment. To support this view, we report a number of descriptors of the nature and strength of chemical bonds and intermolecular interactions in the extended solids and in a cluster model. We calculate formal quantum mechanical descriptors based on electronic structure, electron density, and binding and interaction energies including an energy decomposition analysis. Without exception, all descriptors point to 4ß being a transient structure higher in energy than 4α with larger local and global electrophilic and nucleophilic powers, a more favorable spatial and energetic distribution of the frontier orbitals, and a more fragile crystal structure.

Landmark-based auto-contouring of clinical target volumes for radiotherapy of nasopharyngeal cancer.

BACKGROUND: The delineation of clinical target volumes (CTVs) for radiotherapy for nasopharyngeal cancer is complex and varies based on the location and extent of disease. PURPOSE: The current study aimed to develop an auto-contouring solution following one protocol guidelines (NRG-HN001) that can be adjusted to meet other guidelines, such as RTOG-0225 and the 2018 International guidelines. METHODS: The study used 2-channel 3-dimensional U-Net and nnU-Net framework to auto-contour 27 normal structures in the head and neck (H&N) region that are used to define CTVs in the protocol. To define the CTV-Expansion (CTV1 and CTV2) and CTV-Overall (the outer envelope of all the CTV contours), we used adjustable morphological geometric landmarks and mimicked physician interpretation of the protocol rules by partially or fully including select anatomic structures. The results were evaluated quantitatively using the dice similarity coefficient (DSC) and mean surface distance (MSD) and qualitatively by independent reviews by two H&N radiation oncologists. RESULTS: The auto-contouring tool showed high accuracy for nasopharyngeal CTVs. Comparison between auto-contours and clinical contours for 19 patients with cancers of various stages showed a DSC of 0.94 ± 0.02 and MSD of 0.4 ± 0.4 mm for CTV-Expansion and a DSC of 0.83 ± 0.02 and MSD of 2.4 ± 0.5 mm for CTV-Overall. Upon independent review, two H&N physicians found the auto-contours to be usable without edits in 85% and 75% of cases. In 15% of cases, minor edits were required by both physicians. Thus, one physician rated 100% of the auto-contours as usable (use as is, or after minor edits), while the other physician rated 90% as usable. The second physician required major edits in 10% of cases. CONCLUSIONS: The study demonstrates the ability of an auto-contouring tool to reliably delineate nasopharyngeal CTVs based on protocol guidelines. The tool was found to be clinically acceptable by two H&N radiation oncology physicians in at least 90% of the cases.

Automatic end-to-end VMAT treatment planning for rectal cancers.

BACKGROUND: The treatment planning process from segmentation to producing a deliverable plan is time-consuming and labor-intensive. Existing solutions automate the segmentation and planning processes individually. The feasibility of combining auto-segmentation and auto-planning for volumetric modulated arc therapy (VMAT) for rectal cancers in an end-to-end process is not clear. PURPOSE: To create and clinically evaluate a complete end-to-end process for auto-segmentation and auto-planning of VMAT for rectal cancer requiring only the gross tumor volume contour and a CT scan as inputs. METHODS: Patient scans and data were retrospectively selected from our institutional records for patients treated for malignant neoplasm of the rectum. We trained, validated, and tested deep learning auto-segmentation models using nnU-Net architecture for clinical target volume (CTV), bowel bag, large bowel, small bowel, total bowel, femurs, bladder, bone marrow, and female and male genitalia. For the CTV, we identified 174 patients with clinically drawn CTVs. We used data for 18 patients for all structures other than the CTV. The structures were contoured under the guidance of and reviewed by a gastrointestinal (GI) radiation oncologist. The predicted results for CTV in 35 patients and organs at risk (OAR) in six patients were scored by the GI radiation oncologist using a five-point Likert scale. For auto-planning, a RapidPlan knowledge-based planning solution was modeled for VMAT delivery with a prescription of 25 Gy in five fractions. The model was trained and tested on 20 and 34 patients, respectively. The resulting plans were scored by two GI radiation oncologists using a five-point Likert scale. Finally, the end-to-end pipeline was evaluated on 16 patients, and the resulting plans were scored by two GI radiation oncologists. RESULTS: In 31 of 35 patients, CTV contours were clinically acceptable without necessary modifications. The CTV achieved a Dice similarity coefficient of 0.85 (±0.05) and 95% Hausdorff distance of 15.25 (±5.59) mm. All OAR contours were clinically acceptable without edits, except for large and small bowel which were challenging to differentiate. However, contours for total, large, and small bowel were clinically acceptable. The two physicians accepted 100% and 91% of the auto-plans. For the end-to-end pipeline, the two physicians accepted 88% and 62% of the auto-plans. CONCLUSIONS: This study demonstrated that the VMAT treatment planning technique for rectal cancer can be automated to generate clinically acceptable and safe plans with minimal human interventions.

Automating the treatment planning process for 3D-conformal pediatric craniospinal irradiation therapy.

PURPOSE: Pediatric patients with medulloblastoma in low- and middle-income countries (LMICs) are most treated with 3D-conformal photon craniospinal irradiation (CSI), a time-consuming, complex treatment to plan, especially in resource-constrained settings. Therefore, we developed and tested a 3D-conformal CSI autoplanning tool for varying patient lengths. METHODS AND MATERIALS: Autocontours were generated with a deep learning model trained:tested (80:20 ratio) on 143 pediatric medulloblastoma CT scans (patient ages: 2-19 years, median = 7 years). Using the verified autocontours, the autoplanning tool generated two lateral brain fields matched to a single spine field, an extended single spine field, or two matched spine fields. Additional spine subfields were added to optimize the corresponding dose distribution. Feathering was implemented (yielding nine to 12 fields) to give a composite plan. Each planning approach was tested on six patients (ages 3-10 years). A pediatric radiation oncologist assessed clinical acceptability of each autoplan. RESULTS: The autocontoured structures' average Dice similarity coefficient ranged from .65 to .98. The average V95 for the brain/spinal canal for single, extended, and multi-field spine configurations was 99.9% ± 0.06%/99.9% ± 0.10%, 99.9% ± 0.07%/99.4% ± 0.30%, and 99.9% ± 0.06%/99.4% ± 0.40%, respectively. The average maximum dose across all field configurations to the brainstem, eyes (L/R), lenses (L/R), and spinal cord were 23.7 ± 0.08, 24.1 ± 0.28, 13.3 ± 5.27, and 25.5 ± 0.34 Gy, respectively (prescription = 23.4 Gy/13 fractions). Of the 18 plans tested, all were scored as clinically acceptable as-is or clinically acceptable with minor, time-efficient edits preferred or required. No plans were scored as clinically unacceptable. CONCLUSION: The autoplanning tool successfully generated pediatric CSI plans for varying patient lengths in 3.50 ± 0.4 minutes on average, indicating potential for an efficient planning aid in a resource-constrained settings.

In silico design of bio-marker detection fluorescent probes.

Fluorescent probes capable of sensing the biological medium are of utmost importance in medical diagnostics. However, the optical spectrum of such probes needs to be tuned with care for compatibility with living tissues. More specifically, fluorescent bioprobes must be adjusted so as to avoid light interference with pigments (e.g. hemoglobin), tissue photodamage, scattering of the emitted light, and autofluorescence. This leads to two important conditions on the optical spectrum of the probes. On the one hand, the emission wavelength must be in an optical window of 650 to 950 nm. On the other hand, the Stokes shift must be large, ideally greater than 150 nm. In this paper, we showcase the in-silico design of potential fluorescent biomarkers fulfilling these two conditions by means of heteroatomic substitution and conjugation on a 1,2,4-triazole core initially far away from biological standards.

Calculation of the ELF in the excited state with single-determinant methods.

Since its first definition, back in 1990, the electron localization function (ELF) has settled as one of the most commonly employed techniques to characterize the nature of the chemical bond in real space. Although most of the work using the ELF has focused on the study of ground-state chemical reactivity, a growing interest has blossomed to apply these techniques to the nearly unexplored realm of excited states and photochemistry. Since accurate excited electronic states usually require to account appropriately for electron correlation, the standard single-determinant ELF formulation cannot be blindly applied to them, and it is necessary to turn to correlated ELF descriptions based on the two-particle density matrix (2-PDM). The latter requires costly wavefunction approaches, unaffordable for most of the systems of current photochemical interest. Here, we compare the exact, 2-PDM-based ELF results with those of approximate 2-PDM reconstructions taken from reduced density matrix functional theory. Our approach is put to the test in a wide variety of representative scenarios, such as those provided by the lowest-lying excited electronic states of simple diatomic and polyatomic molecules. Altogether, our results suggest that even approximate 2-PDMs are able to accurately reproduce, on a general basis, the topological and statistical features of the ELF scalar field, paving the way toward the application of cost-effective methodologies, such as time-dependent-Hartree-Fock or time-dependent density functional theory, in the accurate description of the chemical bonding in excited states of photochemical relevance.

Do we need patient-specific QA for adaptively generated plans? Retrospective evaluation of delivered online adaptive treatment plans on Varian Ethos.

BACKGROUND: The clinical introduction of dedicated treatment units for online adaptive radiation therapy (OART) has led to widespread adoption of daily adaptive radiotherapy. OART allows for rapid generation of treatment plans using daily patient anatomy, potentially leading to reduction of treatment margins and increased normal tissue sparing. However, the OART workflow does not allow for measurement of patient-specific quality assurance (PSQA) during treatment delivery sessions and instead relies on secondary dose calculations for verification of adapted plans. It remains unknown if independent dose verification is a sufficient surrogate for PSQA measurements. PURPOSE: To evaluate the plan quality of previously treated adaptive plans through multiple standard PSQA measurements. METHODS: This IRB-approved retrospective study included sixteen patients previously treated with OART at our institution. PSQA measurements were performed for each patient's scheduled and adaptive plans: five adaptive plans were randomly selected to perform ion chamber measurements and two adaptive plans were randomly selected for ArcCHECK measurements. The same ArcCHECK 3D dose distribution was also sent to Mobius3D to evaluate the second-check dosimetry system. RESULTS: All (n = 96) ion chamber measurements agreed with the planned dose within 3% with a mean of 1.4% (± 0.7%). All (n = 48) plans passed ArcCHECK measurements using a 95% gamma passing threshold and 3%/2 mm criteria with a mean of 99.1% (± 0.7%). All (n = 48) plans passed Mobius3D second-check performed with 95% gamma passing threshold and 5%/3 mm criteria with a mean of 99.0% (± 0.2%). CONCLUSION: Plan measurement for PSQA may not be necessary for every online-adaptive treatment verification. We recommend the establishment of a periodic PSQA check to better understand trends in passing rates for delivered adaptive treatments.

Parametric delineation uncertainties contouring (PDUC) modeling on CT scans of prostate cancer patients.

PURPOSE: Variability in contouring contributes to large variations in radiation therapy planning and treatment outcomes. The development and testing of tools to automatically detect contouring errors require a source of contours that includes well-understood and realistic errors. The purpose of this work was to develop a simulation algorithm that intentionally injects errors of varying magnitudes into clinically accepted contours and produces realistic contours with different levels of variability. METHODS: We used a dataset of CT scans from 14 prostate cancer patients with clinician-drawn contours of the regions of interest (ROI) of the prostate, bladder, and rectum. Using our newly developed Parametric Delineation Uncertainties Contouring (PDUC) model, we automatically generated alternative, realistic contours. The PDUC model consists of the contrast-based DU generator and a 3D smoothing layer. The DU generator transforms contours (deformation, contraction, and/or expansion) as a function of image contrast. The generated contours undergo 3D smoothing to obtain a realistic look. After model building, the first batch of auto-generated contours was reviewed. Editing feedback from the reviews was then used in a filtering model for the auto-selection of clinically acceptable (minor-editing) DU contours. RESULTS: Overall, C values of 5 and 50 consistently produced high proportions of minor-editing contours across all ROI compared to the other C values (0.936 ± $ \pm \;$ 0.111 and 0.552 ± $ \pm \;$ 0.228, respectively). The model performed best on the bladder, which had the highest proportion of minor-editing contours (0.606) of the three ROI. In addition, the classification AUC for the filtering model across all three ROI is 0.724 ± $ \pm \;$ 0.109. DISCUSSION: The proposed methodology and subsequent results are promising and could have a great impact on treatment planning by generating mathematically simulated alternative structures that are clinically relevant and realistic enough (i.e., similar to clinician-drawn contours) to be used in quality control of radiation therapy.

Evaluation and correlation of patient movement during online adaptive radiotherapy with CBCT and a surface imaging system.

PURPOSE: With the clinical implementation of kV-CBCT-based daily online-adaptive radiotherapy, the ability to monitor, quantify, and correct patient movement during adaptive sessions is paramount. With sessions lasting between 20-45 min, the ability to detect and correct for small movements without restarting the entire session is critical to the adaptive workflow and dosimetric outcome. The purpose of this study was to quantify and evaluate the correlation of observed patient movement with machine logs and a surface imaging (SI) system during adaptive radiation therapy. METHODS: Treatment machine logs and SGRT registration data log files for 1972 individual sessions were exported and analyzed. For each session, the calculated shifts from a pre-delivery position verification CBCT were extracted from the machine logs and compared to the SGRT registration data log files captured during motion monitoring. The SGRT calculated shifts were compared to the reported shifts of the machine logs for comparison for all patients and eight disease site categories. RESULTS: The average (±STD) net displacement of the SGRT shifts were 2.6 ± 3.4 mm, 2.6 ± 3.5 mm, and 3.0 ± 3.2 in the lateral, longitudinal, and vertical directions, respectively. For the treatment machine logs, the average net displacements in the lateral, longitudinal, and vertical directions were 2.7 ± 3.7 mm, 2.6 ± 3.7 mm, and 3.2 ± 3.6 mm. The average difference (Machine-SGRT) was -0.1 ± 1.8 mm, 0.2 ± 2.1 mm, and -0.5 ± 2.5 mm for the lateral, longitudinal, and vertical directions. On average, a movement of 5.8 ± 5.6 mm and 5.3 ± 4.9 mm was calculated prior to delivery for the CBCT and SGRT systems, respectively. The Pearson correlation coefficient between CBCT and SGRT shifts was r = 0.88. The mean and median difference between the treatment machine logs and SGRT log files was less than 1 mm for all sites. CONCLUSION: Surface imaging should be used to monitor and quantify patient movement during adaptive radiotherapy.

Automated evaluation for rapid implementation of knowledge-based radiotherapy planning models.

PURPOSE: Knowledge-based planning (KBP) offers the ability to predict dose-volume metrics based on information extracted from previous plans, reducing plan variability and improving plan quality. As clinical integration of KBP is increasing there is a growing need for quantitative evaluation of KBP models. A .NET-based application, RapidCompare, was created for automated plan creation and analysis of Varian RapidPlan models. METHODS: RapidCompare was designed to read calculation parameters and a list of reference plans. The tool copies the reference plan field geometry and structure set, applies the RapidPlan model, optimizes the KBP plan, and generates data for quantitative evaluation of dose-volume metrics. A cohort of 85 patients, divided into training (50), testing (10), and validation (25) groups, was used to demonstrate the utility of RapidCompare. After training and tuning, the KBP model was paired with three different optimization templates to compare various planning strategies in the validation cohort. All templates used the same set of constraints for the planning target volume (PTV). For organs-at-risk, the optimization template provided constraints using the whole dose-volume histogram (DVH), fixed-dose/volume points, or generalized equivalent uniform dose (gEUD). The resulting plans from each optimization approach were compared using DVH metrics. RESULTS: RapidCompare allowed for the automated generation of 75 total plans for comparison with limited manual intervention. In comparing optimization techniques, the Dose/Volume and Lines optimization templates generated plans with similar DVH metrics, with a slight preference for the Lines technique with reductions in heart V30Gy and spinal cord max dose. The gEUD model produced high target heterogeneity. CONCLUSION: Automated evaluation allowed for the exploration of multiple optimization templates in a larger validation cohort than would have been feasible using a manual approach. A final KBP model using line optimization objectives produced the highest quality plans without human intervention.

Automated field-in-field whole brain radiotherapy planning.

PURPOSE: We developed and tested an automatic field-in-field (FIF) solution for whole-brain radiotherapy (WBRT) planning that creates a homogeneous dose distribution by minimizing hotspots, resulting in clinically acceptable plans. METHODS: A configurable auto-planning algorithm was developed to automatically generate FIF WBRT plans independent of the treatment planning system. Configurable parameters include the definition of hotspots, target volume, maximum number of subfields, and minimum number of monitor units per field. This algorithm iteratively identifies a hotspot, creates two opposing subfields, calculates the dose, and optimizes the beam weight based on user-configured constraints of dose-volume histogram coverage and least-squared cost functions. The algorithm was retrospectively tested on 17 whole-brain patients. First, an in-house landmark-based automated beam aperture technique was used to generate the treatment fields and initial plans. Second, the FIF algorithm was employed to optimize the plans using physician-defined goals of 99.9% of the brain volume receiving 100% of the prescription dose (30 Gy in 10 fractions) and a target hotspot definition of 107% of the prescription dose. The final auto-optimized plans were assessed for clinical acceptability by an experienced radiation oncologist using a five-point scale. RESULTS: The FIF algorithm reduced the mean (± SD) plan hotspot percentage dose from 35.0 Gy (116.6%) ± 0.6 Gy (2.0%) to 32.6 Gy (108.8%) ± 0.4 Gy (1.2%). Also, it decreased the mean (± SD) hotspot V107% [cm3 ] from 959 ± 498 cm3 to 145 ± 224 cm3 . On average, plans were produced in 16 min without any user intervention. Furthermore, 76.5% of the auto-plans were clinically acceptable (needing no or minor stylistic edits), and all of them were clinically acceptable after minor clinically necessary edits. CONCLUSIONS: This algorithm successfully produced high-quality WBRT plans and can improve treatment planning efficiency when incorporated into an automatic planning workflow.

Customizable landmark-based field aperture design for automated whole-brain radiotherapy treatment planning.

PURPOSE: To develop and evaluate an automated whole-brain radiotherapy (WBRT) treatment planning pipeline with a deep learning-based auto-contouring and customizable landmark-based field aperture design. METHODS: The pipeline consisted of the following steps: (1) Auto-contour normal structures on computed tomography scans and digitally reconstructed radiographs using deep learning techniques, (2) locate the landmark structures using the beam's-eye-view, (3) generate field apertures based on eight different landmark rules addressing different clinical purposes and physician preferences. Two parallel approaches for generating field apertures were developed for quality control. The performance of the generated field shapes and dose distributions were compared with the original clinical plans. The clinical acceptability of the plans was assessed by five radiation oncologists from four hospitals. RESULTS: The performance of the generated field apertures was evaluated by the Hausdorff distance (HD) and mean surface distance (MSD) from 182 patients' field apertures used in the clinic. The average HD and MSD for the generated field apertures were 16 ± 7 and 7 ± 3 mm for the first approach, respectively, and 17 ± 7 and 7 ± 3 mm, respectively, for the second approach. The differences regarding HD and MSD between the first and the second approaches were 1 ± 2 and 1 ± 3 mm, respectively. A clinical review of the field aperture design, conducted using 30 patients, achieved a 100% acceptance rate for both the first and second approaches, and the plan review achieved a 100% acceptance rate for the first approach and a 93% acceptance rate for the second approach. The average acceptance rate for meeting lens dosimetric recommendations was 80% (left lens) and 77% (right lens) for the first approach, and 70% (both left and right lenses) for the second approach, compared with 50% (left lens) and 53% (right lens) for the clinical plans. CONCLUSION: This study provided an automated pipeline with two field aperture generation approaches to automatically generate WBRT treatment plans. Both quantitative and qualitative evaluations demonstrated that our novel pipeline was comparable with the original clinical plans.

Resection cavity auto-contouring for patients with pediatric medulloblastoma using only CT information.

PURPOSE: Target delineation for radiation therapy is a time-consuming and complex task. Autocontouring gross tumor volumes (GTVs) has been shown to increase efficiency. However, there is limited literature on post-operative target delineation, particularly for CT-based studies. To this end, we trained a CT-based autocontouring model to contour the post-operative GTV of pediatric patients with medulloblastoma. METHODS: One hundred four retrospective pediatric CT scans were used to train a GTV auto-contouring model. Eighty patients were then preselected for contour visibility, continuity, and location to train an additional model. Each GTV was manually annotated with a visibility score based on the number of slices with a visible GTV (1 = < 25%, 2 = 25-50%, 3 = > 50-75%, and 4 = > 75-100%). Contrast and the contrast-to-noise ratio (CNR) were calculated for the GTV contour with respect to a cropped background image. Both models were tested on the original and pre-selected testing sets. The resulting surface and overlap metrics were calculated comparing the clinical and autocontoured GTVs and the corresponding clinical target volumes (CTVs). RESULTS: Eighty patients were pre-selected to have a continuous GTV within the posterior fossa. Of these, 7, 41, 21, and 11 were visibly scored as 4, 3, 2, and 1, respectively. The contrast and CNR removed an additional 11 and 20 patients from the dataset, respectively. The Dice similarity coefficients (DSC) were 0.61 ± 0.29 and 0.67 ± 0.22 on the models without pre-selected training data and 0.55 ± 13.01 and 0.83 ± 0.17 on the models with pre-selected data, respectively. The DSC on the CTV expansions were 0.90 ± 0.13. CONCLUSION: We successfully automatically contoured continuous GTVs within the posterior fossa on scans that had contrast > ± 10 HU. CT-Based auto-contouring algorithms have potential to positively impact centers with limited MRI access.

Identifying the optimal deep learning architecture and parameters for automatic beam aperture definition in 3D radiotherapy.

PURPOSE: Two-dimensional radiotherapy is often used to treat cervical cancer in low- and middle-income countries, but treatment planning can be challenging and time-consuming. Neural networks offer the potential to greatly decrease planning time through automation, but the impact of the wide range of hyperparameters to be set during training on model accuracy has not been exhaustively investigated. In the current study, we evaluated the effect of several convolutional neural network architectures and hyperparameters on 2D radiotherapy treatment field delineation. METHODS: Six commonly used deep learning architectures were trained to delineate four-field box apertures on digitally reconstructed radiographs for cervical cancer radiotherapy. A comprehensive search of optimal hyperparameters for all models was conducted by varying the initial learning rate, image normalization methods, and (when appropriate) convolutional kernel size, the number of learnable parameters via network depth and the number of feature maps per convolution, and nonlinear activation functions. This yielded over 1700 unique models, which were all trained until performance converged and then tested on a separate dataset. RESULTS: Of all hyperparameters, the choice of initial learning rate was most consistently significant for improved performance on the test set, with all top-performing models using learning rates of 0.0001. The optimal image normalization was not consistent across architectures. High overlap (mean Dice similarity coefficient = 0.98) and surface distance agreement (mean surface distance < 2 mm) were achieved between the treatment field apertures for all architectures using the identified best hyperparameters. Overlap Dice similarity coefficient (DSC) and distance metrics (mean surface distance and Hausdorff distance) indicated that DeepLabv3+ and D-LinkNet architectures were least sensitive to initial hyperparameter selection. CONCLUSION: DeepLabv3+ and D-LinkNet are most robust to initial hyperparameter selection. Learning rate, nonlinear activation function, and kernel size are also important hyperparameters for improving performance.

A roadmap for implementation of kV-CBCT online adaptive radiation therapy and initial first year experiences.

PURPOSE: Online Adaptive Radiation Therapy (oART) follows a different treatment paradigm than conventional radiotherapy, and because of this, the resources, implementation, and workflows needed are unique. The purpose of this report is to outline our institution's experience establishing, organizing, and implementing an oART program using the Ethos therapy system. METHODS: We include resources used, operational models utilized, program creation timelines, and our institutional experiences with the implementation and operation of an oART program. Additionally, we provide a detailed summary of our first year's clinical experience where we delivered over 1000 daily adaptive fractions. For all treatments, the different stages of online adaption, primary patient set-up, initial kV-CBCT acquisition, contouring review and edit of influencer structures, target review and edits, plan evaluation and selection, Mobius3D 2nd check and adaptive QA, 2nd kV-CBCT for positional verification, treatment delivery, and patient leaving the room, were analyzed. RESULTS: We retrospectively analyzed data from 97 patients treated from August 2021-August 2022. One thousand six hundred seventy seven individual fractions were treated and analyzed, 632(38%) were non-adaptive and 1045(62%) were adaptive. Seventy four of the 97 patients (76%) were treated with standard fractionation and 23 (24%) received stereotactic treatments. For the adaptive treatments, the generated adaptive plan was selected in 92% of treatments. On average(±std), adaptive sessions took 34.52 ± 11.42 min from start to finish. The entire adaptive process (from start of contour generation to verification CBCT), performed by the physicist (and physician on select days), was 19.84 ± 8.21 min. CONCLUSION: We present our institution's experience commissioning an oART program using the Ethos therapy system. It took us 12 months from project inception to the treatment of our first patient and 12 months to treat 1000 adaptive fractions. Retrospective analysis of delivered fractions showed that the average overall treatment time was approximately 35 min and the average time for the adaptive component of treatment was approximately 20 min.

On the Prediction of Lattice Energy with the Fukui Potential: Some Supports on Hardness Maximization in Inorganic Solids.

Using perturbation theory within the framework of conceptual density functional theory, we derive a lower bound for the lattice energy of the ionic solids. The main element of the lower bound is the Fukui potential in the nuclei of the molecule corresponding to the unit formula of the solid. Thus, we propose a model to calculate the lattice energy in terms of the Fukui potential. Our method, which is extremely simple, performs well as other methods using the crystal structure information of alkali halide solids. The method proposed here correlates surprisingly well with the experimental data on the lattice energy of a diverse series of solids having even a non-negligible covalent characteristic. Finally, the validity of the maximum hardness principle (MHP) is assessed, showing that in this case, the MHP is limited.

Bi-based photocatalysts for bacterial inactivation in water: Inactivation mechanisms, challenges, and strategies to improve the photocatalytic activity.

Bi-based photocatalysts have been considered suitable materials for water disinfection under natural solar light due to their outstanding optical and electronic properties. However, until now, there are not extensive reviews about the development of Bi-based materials and their application in bacterial inactivation in aqueous solutions. For this reason, this work has focused on summarizing the state of the art related to the inactivation of Gram- and Gram + pathogenic bacteria under visible light irradiation using different Bi-based micro and nano structures. In this sense, the photocatalytic bacterial inactivation mechanisms are analyzed, considering several modifications. The factors that can affect the photocatalytic performance of these materials in real conditions and at a large scale (e.g., water characteristics, pH, light intensity, photocatalyst dosage, and bacteria level) have been studied. Furthermore, current alternatives for improving the photocatalytic antibacterial activity and reuse of Bi-based materials (e.g., surface engineering, crystal facet engineering, doping, noble metal coupling, heterojunctions, Z-scheme junctions, coupling with graphene derivatives, magnetic composites, immobilization) have been explored. According to several reports, inactivation rate values higher than 90% can be achieved by using the modified Bi-based micro/nano structures, which become them excellent candidates for photocatalytic water disinfection. However, these innovative photocatalytic materials bring a variety of future difficulties and opportunities in water disinfection.

Knowledge-based planning for the radiation therapy treatment plan quality assurance for patients with head and neck cancer.

This study aimed to investigate the feasibility of using a knowledge-based planning technique to detect poor quality VMAT plans for patients with head and neck cancer. We created two dose-volume histogram (DVH) prediction models using a commercial knowledge-based planning system (RapidPlan, Varian Medical Systems, Palo Alto, CA) from plans generated by manual planning (MP) and automated planning (AP) approaches. DVHs were predicted for evaluation cohort 1 (EC1) of 25 patients and compared with achieved DVHs of MP and AP plans to evaluate prediction accuracy. Additionally, we predicted DVHs for evaluation cohort 2 (EC2) of 25 patients for which we intentionally generated plans with suboptimal normal tissue sparing while satisfying dose-volume limits of standard practice. Three radiation oncologists reviewed these plans without seeing the DVH predictions. We found that predicted DVH ranges (upper-lower predictions) were consistently wider for the MP model than for the AP model for all normal structures. The average ranges of mean dose predictions among all structures was 9.7 Gy (MP model) and 3.4 Gy (AP model) for EC1 patients. RapidPlan models identified 7 MP plans as outliers according to mean dose or D1% for at least one structure, while none of AP plans were flagged. For EC2 patients, 22 suboptimal plans were identified by prediction. While re-generated AP plans validated that these suboptimal plans could be improved, 40 out of 45 structures with predicted poor sparing were also identified by oncologist reviews as requiring additional planning to improve sparing in the clinical setting. Our study shows that knowledge-based DVH prediction models can be sufficiently accurate for plan quality assurance purposes. A prediction model built by a small cohort automatically-generated plans was effective in detecting suboptimal plans. Such tools have potential to assist the plan quality assurance workflow for individual patients in the clinic.