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Objective: The purpose of this study was to investigate the technical feasibility of integrating the quantitative maps available from SyntheticMR into the head and neck adaptive radiation oncology workflow. While SyntheticMR has been investigated for diagnostic applications, no studies have investigated its feasibility and potential for MR-Simulation or MR-Linac workflow. Demonstrating the feasibility of using this technique will facilitate rapid quantitative biomarker extraction which can be leveraged to guide adaptive radiation therapy decision making. Approach: Two phantoms, two healthy volunteers, and one patient were scanned using SyntheticMR on the MR-Simulation and MR-Linac devices with scan times between four to six minutes. Images in phantoms and volunteers were conducted in a test/retest protocol. The correlation between measured and reference quantitative T1, T2, and PD values were determined across clinical ranges in the phantom. Distortion was also studied. Contours of head and neck organs-at-risk (OAR) were drawn and applied to extract T1, T2, and PD. These values were plotted against each other, clusters were computed, and their separability significance was determined to evaluate SyntheticMR for differentiating tumor and normal tissue. Main Results: The Lin's Concordance Correlation Coefficient between the measured and phantom reference values was above 0.98 for both the MR-Sim and MR-Linac. No significant levels of distortion were measured. The mean bias between the measured and phantom reference values across repeated scans was below 4% for T1, 7% for T2, and 4% for PD for both the MR-Sim and MR-Linac. For T1 vs. T2 and T1 vs. PD, the GTV contour exhibited perfect purity against neighboring OARs while being 0.7 for T2 vs. PD. All cluster significance levels between the GTV and the nearest OAR, the tongue, using the SigClust method was p < 0.001. Significance: The technical feasibility of SyntheticMR was confirmed. Application of this technique to the head and neck adaptive radiation therapy workflow can enrich the current quantitative biomarker landscape.

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Meristic traits are often treated as distinct phenotypes that can be used to differentiate and delineate recently diverged species. For instance, the number of lateral line scales and vertebrae, two traits that vary substantially among Neotropical Heroine cichlid species, have been previously suggested to co-evolve. These meristic traits could co-evolve due to shared adaptive, developmental, or genetic factors. If they were found to be genetically or developmentally non-independent, this might require a more general re-evaluation of their role in evolutionary or taxonomic studies. We expanded a previous analysis of correlated evolution of meristic traits (lateral line scales and vertebrae counts) in these fishes to include a range of phylogenetic reconstructions as well as the analyses of 13 Nicaraguan Midas cichlid species (Amphilophus spp.). Additionally, we performed qualitative traits locus (QTL) mapping in a F2 laboratory-reared hybrid population from two ecologically divergent Midas cichlid fish species to discover and evaluate whether genomic co-segregation might explain the observed patterns of meristic co-evolution. Meristic values for these traits were found to morphologically differentiate some species of the Midas cichlid adaptive radiation. Our QTL analysis pinpointed several genomic regions associated with divergence in these traits and highlighted the potential for genomic co-segregation of the lateral line and vertebrae numbers on two chromosomes. Further, our phylogenetic comparative analyses consistently recovered a significant positive evolutionary correlation between the counts of lateral line scale and vertebrae numbers in Neotropical cichlids. Hence, the findings of genomic co-segregation could partially explain the co-evolution of these two meristic traits in these species. Continuing to unravel the genetic architecture governing meristic divergence helps to better understand both trait correlations and the utility of meristic traits in taxonomic diagnoses and how traits in phenotypes might be expected to co-evolve.

Los rasgos merísticos son empleados comúnmente como caracteres fenotípicos que pueden ser utilizados para diferenciar y delimitar especies recientemente divergentes. Por ejemplo, se ha sugerido anteriormente que el número de escamas de la línea lateral, así como el de vértebras, dos rasgos que varían sustancialmente entre las especies de cíclidos Heroine neotropicales, co­evolucionan. Estos rasgos podrían co­evolucionar debido a factores adaptativos, de desarrollo o genéticos compartidos. En el caso de que se descubriera que no son independientes desde el punto de vista genético o del desarrollo, sería necesario reevaluar su función en los estudios evolutivos o taxonómicos. Nosotros hemos ampliado un análisis previo de la evolución correlacionada de los rasgos merísticos (número de escamas de la línea lateral y recuento de vértebras) en estos peces para incluir una serie de reconstrucciones filogenéticas, así como los análisis de las 13 especies de cíclidos nicaragüenses Midas (Amphilophus spp.). Además, realizamos un mapeo QTL en una población híbrida F2 criada en laboratorio de dos especies de cíclidos Midas ecológicamente divergentes para descubrir y evaluar si la co­segregación genómica podría explicar los patrones observados de co­evolución merística. Se observó que los valores merísticos de estos rasgos diferenciaban morfológicamente algunas especies de la radiación adaptativa de los cíclidos Midas. Nuestro análisis QTL identificó varias regiones genómicas asociadas con la divergencia en estos rasgos y destacó la potencial co­segregación genómica de la línea lateral y el número de vértebras en dos cromosomas. Además, nuestros análisis filogenéticos comparativos mostraron una correlación evolutiva positiva y significativa entre el número de escamas de la línea lateral y el número de vértebras en los cíclidos neotropicales. Por lo tanto, los hallazgos de co­segregación genómica podrían explicar parcialmente la co­evolución de estos dos rasgos merísticos en los cíclidos neotropicales. Seguir desentrañando la arquitectura genética que gobierna la divergencia merística ayuda a comprender mejor tanto las correlaciones de rasgos como la utilidad de los rasgos merísticos en los diagnósticos taxonómicos y cómo podría esperarse que co­evolucionen los rasgos en los fenotipos.

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Background and Objective: Magnetic resonance guided radiotherapy (MRgRT) is an emerging technological innovation with more and more institutions gaining clinical experience in this new field of radiation oncology. The ability to better visualize both tumors and healthy tissues due to excellent soft tissue contrast combined with new possibilities regarding motion management and the capability of online adaptive radiotherapy might increase tumor control rates while potentially reducing the risk of radiation-induced toxicities. As conventional computed tomography (CT)-based image guidance methods are insufficient for adaptive workflows in abdominal tumors, MRgRT appears to be an optimal method for this tumor site. The aim of this narrative review is to outline the opportunities and challenges in magnetic resonance guided radiation therapy in gastrointestinal cancers. Methods: We searched for studies, reviews and conceptual articles, including the general technique of MRgRT and the specific utilization in gastrointestinal cancers, focusing on pancreatic cancer, liver metastases and primary liver cancer, rectal cancer and esophageal cancer. Key Content and Findings: This review is highlighting the innovative approach of MRgRT in gastrointestinal cancer and gives an overview of the currently available literature with regard to clinical experiences and theoretical background. Conclusions: MRgRT is a promising new tool in radiation oncology, which can play off several of its beneficial features in the specific field of gastrointestinal cancers. However, clinical data is still scarce. Nevertheless, the available literature points out large potential for improvements regarding dose coverage and escalation as well as the reduction of dose exposure to critical organs at risk (OAR). Further prospective studies are needed to demonstrate the role of this innovative technology in gastrointestinal cancer management, in particular trials that randomly compare MRgRT with conventional CT-based image-guided radiotherapy (IGRT) would be of high value.

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Cone-beam computed tomography (CBCT) is an essential tool in radiotherapy, enhancing patient positioning accuracy and enabling precise treatment delivery by monitoring anatomical changes throughout the treatment process. This case report highlights the significant role of CBCT in managing a patient with lung adenocarcinoma treated with concurrent chemoradiation. The lung mass and lower paratracheal lymph nodes were irradiated with 60 Gy in 30 fractions. During the course of treatment, CBCT allowed us to observe substantial tumor shrinkage, prompting a treatment replanning to ensure optimal targeting of the tumor while minimizing radiation exposure to healthy tissues. This adaptive approach resulted in excellent treatment outcomes with no complications, demonstrating the efficacy of CBCT in modern radiotherapy.

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Cervical cancer is one of the most frequent malignant tumors in females. Concurrent chemoradiotherapy is one of the treatment options for cervical cancer. The treatment time of conventional radiotherapy is long. Moderately hypofractionated radiotherapy (MHRT) offers the advantage of shortening the overall treatment duration and enhancing the radiobiological effects on tumors. MHRT shortens the overall treatment duration while enhancing the radiobiological effects on tumors. Previous studies have reported that MHRT of cervical cancer has relatively high toxicity. Daily online adaptive radiation therapy (oART) showed improvements in dosimetry and a decrease in toxicity. To the best of our knowledge, this case was the first reported case of moderated hypofractionated oART used in a cervical cancer patient to date in a prospective clinical trial (NCT05994300). This case serves as a critical reminder that cervical cancer is a potential tumor that may be in MHRT with iterative cone beam computed tomography-guided oART. Further data are needed to confirm the toxicity and efficacy of this technique.

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Brachytherapy is a critical component of locally advanced cervical cancer treatment, and patients ineligible for brachytherapy historically have poor outcomes. Delivery of boost with stereotactic body radiation therapy (SBRT) has been studied, though toxicity is a concern. Recent case reports have explored adaptive radiation boost, which can adjust plans for inter-fraction motion using magnetic resonance guidance. Herein, we report the first patient with locally advanced cervical cancer ineligible for brachytherapy who was treated with a cone-beam computed tomography (CBCT)-guided adaptive boost following completion of chemoradiation. A 71-year-old female with locally advanced cervical cancer was treated with chemoradiation and was deemed ineligible for a brachytherapy boost due to tumor size, geometry, and a fistula with a tumor in the bladder. She was prescribed a boost to the primary tumor of 25 Gy in five fractions using CBCT-guided adaptive radiation following the completion of chemoradiation. A simulation was performed using a non-contrast CT fused with a mid-chemoradiation magnetic resonance imaging (MRI) scan to create an initial plan. For each treatment fraction, kilovoltage CBCTs were acquired, contours of organs at risk (OARs) were adjusted to reflect anatomy-of-the-day, and an adapted plan was generated. The initial and adapted plans were compared using dose-volume histogram objectives, and the adapted plan was used if it resolved OAR constraint violations or improved target coverage. The use of the initial treatment plan would have resulted in constraint violations for the rectum, sigmoid, and bladder in all fractions. The adapted plans achieved hard constraints in all fractions for all four critical OARs. The mean total treatment time across all five fractions was 58 minutes. This case demonstrates the feasibility of a CBCT-guided adaptive boost approach and the dosimetric benefits of plan adaptation in this setting. Though larger-scale and longer-term data are needed, CBCT-guided adaptive radiation may present a feasible alternative modality to deliver boost doses for brachytherapy-ineligible patients.

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BACKGROUND: Treatment delivery safety and accuracy are essential to control the disease and protect healthy tissues in radiation therapy. For usual treatment, a phantom-based patient specific quality assurance (PSQA) is performed to verify the delivery prior to the treatment. The emergence of adaptive radiation therapy (ART) adds new complexities to PSQA. In fact, organ at risks and target volume re-contouring as well as plan re-optimization and treatment delivery are performed with the patient immobilized on the treatment couch, making phantom-based pretreatment PSQA impractical. In this case, phantomless PSQA tools based on multileaf collimator (MLC) leaf open times (LOTs) verifications provide alternative approaches for the Radixact® treatment units. However, their validity is compromised by the lack of independent and reliable methods for calculating the LOT performed by the MLC during deliveries. PURPOSE: To provide independent and reliable methods of LOT calculation for the Radixact® treatment units. METHODS: Two methods for calculating the LOTs performed by the MLC during deliveries have been implemented. The first method uses the signal recorded by the build-in detector and the second method uses the signal recorded by optical sensors mounted on the MLC. To calibrate the methods to the ground truth, in-phantom ionization chamber LOT measurements have been conducted on a Radixact® treatment unit. The methods were validated by comparing LOT calculations with in-phantom ionization chamber LOT measurements performed on two Radixact® treatment units. RESULTS: The study shows a good agreement between the two LOT calculation methods and the in-phantom ionization chamber measurements. There are no notable differences between the two methods and the same results were observed on the different treatment units. CONCLUSIONS: The two implemented methods have the potential to be part of a PSQA solution for ART in tomotherapy.

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This review presents and discusses the ways in which artificial intelligence (AI) tools currently intervene, or could potentially intervene in the future, to enhance the diverse tasks involved in the radiotherapy workflow. The radiotherapy framework is presented on 2 different levels for the personalization of the treatment, distinct in tasks and methodologies. The first level is the clinically well-established anatomy-based workflow, known as adaptive radiation therapy. The second level is referred to as biology-driven workflow, explored in the research literature and recently appearing in some preliminary clinical trials for personalized radiation treatments. A 2-fold role for AI is defined according to these 2 different levels. In the anatomy-based workflow, the role of AI is to streamline and improve the tasks in terms of time and variability reductions compared to conventional methodologies. The biology-driven workflow instead fully relies on AI, which introduces decision-making tools opening uncharted frontiers that were in the past deemed challenging to explore. These methodologies are referred to as radiomics and dosiomics, handling imaging and dosimetric information, or multiomics, when complemented by clinical and biological parameters (ie, biomarkers). The review explicitly highlights the methodologies that are currently incorporated into clinical practice or still in research, with the aim of presenting the AI's growing role in personalized radiotherapy.

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BACKGROUND: High-quality 3D-anatomy of the day is needed for treatment plan adaptation in radiotherapy. For online x-ray-based CBCT workflows, one approach is to create a synthetic CT or to utilize a fan-beam CT with corresponding registrations. The former potentially introduces uncertainties in the dose calculation if deformable image registration is used. The latter can introduce burden and complexity to the process, the facility, and the patient. PURPOSE: Using the CBCT of the day, acquired on the treatment device, for direct dose calculation and plan adaptation can overcome these limitations. This study aims to assess the accuracy of the calculated dose on the CBCT scans acquired on a Halcyon linear accelerator equipped with HyperSight. METHODS: HyperSight's new CBCT reconstruction algorithm includes improvements in scatter correction, HU calibration of the imager, and beam shape adaptation. Furthermore, HyperSight introduced a new x-ray detector. To show the effect of the implemented improvements, gamma comparisons of 2%/2 mm, 2%/1 mm, and 1%/1 mm were made between the dose distribution in phantoms calculated on the CBCT reconstructions and the simulation CT scans, considering this the standard of care. The resulting gamma passing rates were compared to those obtained with the Halcyon 3.0 reconstruction and hardware without HyperSight's technologies. Various anatomical phantoms for dosimetric evaluations on brain, head and neck, lung, breast, and prostate cases have been used in this study. RESULTS: The overall results demonstrated that HyperSight outperformed the Halcyon 3.0 version. Based on the gamma analysis, the calculated dose using HyperSight was closer to the CT scan-based doses than the calculated dose using iCBCT Halcyon 3.0 for most cases. Over all plans and gamma criteria, Halcyon 3.0 achieved an average passing rate of 92.9%, whereas HyperSight achieved 98.1%. CONCLUSION: Using HyperSight CBCT images for direct dose calculation, for example, in (online) plan adaptation, seems feasible for the investigated cases.

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Adaptive radiation involves diversification along multiple trait axes, producing phenotypically diverse, species-rich lineages. Theory generally predicts that multi-trait evolution occurs via a 'stages' model, with some traits saturating early in a lineage's history, and others diversifying later. Despite its multidimensional nature, however, we know surprisingly little about how different suites of traits evolve during adaptive radiation. Here, we investigated the rate, pattern, and timing of morphological and physiological evolution in the anole lizard adaptive radiation from the Caribbean island of Hispaniola. Rates and patterns of morphological and physiological diversity are largely unaligned, corresponding to independent selective pressures associated with structural and thermal niches. Cold tolerance evolution reflects parapatric divergence across elevation, rather than niche partitioning within communities. Heat tolerance evolution and the preferred temperature evolve more slowly than cold tolerance, reflecting behavioral buffering, particularly in edge-habitat species (a pattern associated with the Bogert effect). In contrast to the nearby island of Puerto Rico, closely related anoles on Hispaniola do not sympatrically partition thermal niche space. Instead, allopatric and parapatric separation across biogeographic and environmental boundaries serves to keep morphologically similar close relatives apart. The phenotypic diversity of this island's adaptive radiation accumulated largely as a by-product of time, with surprisingly few exceptional pulses of trait evolution. A better understanding of the processes that guide multidimensional trait evolution (and nuance therein) will prove key in determining whether the stages model should be considered a common theme of adaptive radiation.

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AbstractAdaptive radiations highlight the mechanisms by which species and traits diversify and the extent to which these patterns are predictable. We used 1,110 high-speed videos of suction feeding to study functional and morphological diversification in 300 cichlid species from three African Great Lake radiations of varying ages (Victoria, Malawi, and Tanganyika) and an older, spatially dispersed continental radiation in the Neotropics. Among African radiations, standing diversity was reflective of time. Morphological and functional variance in Lake Victoria, the youngest radiation, was a subset of that within Lake Malawi, which itself was nested within the older Tanganyikan radiation. However, functional diversity in Neotropical cichlids was often lower than that in Lake Tanganyika, despite being much older. These two radiations broadly overlapped, but each diversified into novel trait spaces not found in the youngest lake radiations. Evolutionary rates across radiations were inversely related to age, suggesting extremely rapid trait evolution at early stages, particularly in lake radiations. Despite this support for early bursts, other patterns of trait diversity were inconsistent with expectations of adaptive radiations. This work suggests that cichlid functional evolution has played out in strikingly similar fashion in different radiations, with contingencies eventually resulting in lineage-specific novelties.

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Radiation therapy (RT) is a highly digitized field relying heavily on computational methods and, as such, has a high affinity for the automation potential afforded by modern artificial intelligence (AI). This is particularly relevant where imaging is concerned and is especially so during image-guided RT (IGRT). With the advent of online adaptive RT (ART) workflows at magnetic resonance (MR) linear accelerators (linacs) and at cone-beam computed tomography (CBCT) linacs, the need for automation is further increased. AI as applied to modern IGRT is thus one area of RT where we can expect important developments in the near future. In this review article, after outlining modern IGRT and online ART workflows, we cover the role of AI in CBCT and MRI correction for dose calculation, auto-segmentation on IGRT imaging, motion management, and response assessment based on in-room imaging.

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BACKGROUND: Stereotactic MR-guided Adaptive Radiation Therapy (SMART) dose painting for hypoxia has potential to improve treatment outcomes, but clinical implementation on low-field MR-Linac faces substantial challenges due to dramatically lower signal-to-noise ratio (SNR) characteristics. While quantitative MRI and T1 mapping of hypoxia biomarkers show promise, T1-to-noise ratio (T1NR) optimization at low fields is paramount, particularly for the clinical implementation of oxygen-enhanced (OE)-MRI. The 3D Magnetization Prepared (2) Rapid Gradient Echo (MP2RAGE) sequence stands out for its ability to acquire homogeneous T1-weighted contrast images with simultaneous T1 mapping. PURPOSE: To optimize MP2RAGE for low-field T1 mapping; conduct experimental validation in a ground-truth phantom; establish feasibility and reproducibility of low-field MP2RAGE acquisition and T1 mapping in healthy volunteers. METHODS: The MP2RAGE optimization was performed to maximize the contrast-to-noise ratio (CNR) of T1 values in white matter (WM) and gray matter (GM) brain tissues at 0.35T. Low-field MP2RAGE images were acquired on a 0.35T MR-Linac (ViewRay MRIdian) using a multi-channel head coil. Validation of T1 mapping was performed with a ground-truth Eurospin phantom, containing inserts of known T1 values (400-850 ms), with one and two average (1A and 2A) MP2RAGE scans across four acquisition sessions, resulting in eight T1 maps. Mean (± SD) T1 relative error, T1NR, and intersession coefficient of variation (CV) were determined. Whole-brain MP2RAGE scans were acquired in 5 healthy volunteers across two sessions (A and B) and T1 maps were generated. Mean (± SD) T1 values for WM and GM were determined. Whole-brain T1 histogram analysis was performed, and reproducibility was determined with the CV between sessions. Voxel-by-voxel T1 difference maps were generated to evaluate 3D spatial variation. RESULTS: Low-field MP2RAGE optimization resulted in parameters: MP2RAGETR of 3250 ms, inversion times (TI1/TI2) of 500/1200 ms, and flip angles (α1/α2) of 7/5°. Eurospin T1 maps exhibited a mean (± SD) relative error of 3.45% ± 1.30%, T1NR of 20.13 ± 5.31, and CV of 2.22% ± 0.67% across all inserts. Whole-brain MP2RAGE images showed high anatomical quality with clear tissue differentiation, resulting in mean (± SD) T1 values: 435.36 ± 10.01 ms for WM and 623.29 ± 14.64 ms for GM across subjects, showing excellent concordance with literature. Whole-brain T1 histograms showed high intrapatient and intersession reproducibility with characteristic intensity peaks consistent with voxel-level WM and GM T1 values. Reproducibility analysis revealed a CV of 0.46% ± 0.31% and 0.35% ± 0.18% for WM and GM, respectively. Voxel-by-voxel T1 difference maps show a normal 3D spatial distribution of noise in WM and GM. CONCLUSIONS: Low-field MP2RAGE proved effective in generating accurate, reliable, and reproducible T1 maps with high T1NR in phantom studies and in vivo feasibility established in healthy volunteers. While current work is focused on refining the MP2RAGE protocol to enable clinically efficient OE-MRI, this study establishes a foundation for TOLD T1 mapping for hypoxia biomarkers. This advancement holds the potential to facilitate a paradigm shift toward MR-guided biological adaptation and dose painting by leveraging 3D hypoxic spatial distributions and improving outcomes in conventionally challenging-to-treat cancers.

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Purpose/Objectives: Retrospective analysis suggests that dose escalation to a biologically effective dose of more than 70 Gy may improve overall survival in patients with pancreatic ductal adenocarcinoma (PDAC), but such treatments in practice are limited by proximity of organs at risk (OARs). We hypothesized that CT-guided online adaptive radiotherapy (OART) can account for interfraction movement of OARs and allow for safe delivery of ablative doses. Materials/Methods: This is a single institution retrospective analysis of patients with PDAC treated with OART on the Ethos platform (Varian Medical Systems, a Siemens Healthineers Company, Palo Alto). All patients were treated to 40 Gy in 5 fractions. PTV overlapping with a 5 mm planning risk volume expansion on the stomach, duodenum and bowel received 25 Gy. Initial treatment plans were created conventionally. For each fraction, PTV and OAR volumes were recontoured with AI assistance after initial cone beam CT (CBCT). The adapted plan was calculated, underwent QA, and then compared to the scheduled plan. A second CBCT was obtained prior to delivery of the selected plan. Total treatment time (first CBCT to end of radiation delivery) and active physician time (first to second CBCT) were recorded. PTV_4000 V95 %, PTV_2500 V9 5%, and D0.03 cc to stomach, duodenum and bowel were reported for scheduled (S) and adapted (A) plans. CTCAEv5.0 toxicities were recorded. Statistical analysis was performed using a two-sided T test and α of 0.05. Results: 21 patients with unresectable or locally-recurrent PDAC were analyzed, with a total of 105 fractions. Average total time was 29 min and 16 s (16:36-49:40) and average active physician time was 19:41 min (9:25-39:34). All fractions were treated with adapted plans. 97 % of adapted plans met PTV_4000 V95.0 % >95.0 % coverage goal and 100 % of adapted plans met OAR dose constraints. Median follow up was 6.6 months. Only 1 patient experienced acute grade 3+ toxicity directly attributable to radiation. Only 1 patient experienced late grade 3+ toxicity directly attributable to radiation. Conclusions: Daily CT-based OART was associated with significantly reduced dose OARs while achieving superior PTV coverage. Given the relatively quick total treatment time, radiation delivery was generally well tolerated and easily incorporated into the clinic workflow. Our initial clinical experience demonstrates OART allows for safe dose escalation in the treatment of PDAC.

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Constraint is a fundamental concept in evolutionary theory. Morphology and ecology both are limited by functional, historical and developmental factors to a subset of the theoretical range species could occupy. Cat-like carnivorans (Feliformia) offer a unique opportunity to investigate phenotypic constraint, as several feliform clades are purported to be limited to generalized ecomorphological roles, while others possess extremely specialized durophagous (bone-crushing) and sabretooth morphology. We investigated the evolutionary history of feliforms by considering their phylogeny, morphological disparity and rates of evolution. We recover results that show a mosaic pattern exists in the degree of morphological disparity per anatomical region per clade and ecology. Non-hypercarnivores, such as viverrids (civets and genets), Malagasy euplerids and lophocyonids (extinct hypocarnivores), have the greatest dental disparity, while hypercarnivores (felids, nimravids, many hyaenids) have the lowest dental disparity but highest cranial and mandibular disparity (excluding dentition). However, high disparity is not necessarily associated with high rates of evolution, but instead with ecological radiations. We reveal that relationships between specialization and disparity are not as simple as past research has concluded. Instead, morphological disparity results from an anatomical mosaic of evolution, where different ecologies correlate with and likely channel unique patterns/combinations of disparity per anatomical partition.

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Phenotypic covariation among suites of traits may constrain or promote diversification both within and between species, yet few studies have empirically tested this relationship. In this study, we investigate whether phenotypic covariation of craniofacial traits is associated with diversification in an adaptive radiation of pupfishes found only on San Salvador Island, Bahamas (SSI). The radiation includes generalist, durophagous, and lepidophagous species. We compared phenotypic variation and covariation (i.e., the P matrix) between (1) allopatric populations of generalist pupfish from neighboring islands and estuaries in the Caribbean, (2) SSI pupfish allopatric lake populations with only generalist pupfish, and (3) SSI lake populations containing the full radiation in sympatry. Additionally, we examine patterns observed in the P matrices of two independent lab-reared F2 hybrid crosses of the two most morphologically distinct members of the radiation to make inferences about the underlying mechanisms contributing to the variation in craniofacial traits in SSI pupfishes. We found that the P matrix of SSI allopatric generalist populations exhibited higher levels of mean trait correlation, constraints, and integration with simultaneously lower levels of flexibility compared to allopatric generalist populations on other Caribbean islands and sympatric populations of all three species on SSI. We also document that while many craniofacial traits appear to result from additive genetic effects, variation in key traits such as head depth, maxilla length, and lower jaw length may be produced via non-additive genetic mechanisms. Ultimately, this study suggests that differences in phenotypic covariation significantly contribute to producing and maintaining organismal diversity.

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The physical interactions between organisms and their environment ultimately shape diversification rates, but the contributions of biomechanics to evolutionary divergence are frequently overlooked. Here, we estimated a performance landscape for biting in an adaptive radiation of Cyprinodon pupfishes, including scale-biting and molluscivore specialists, and compared performance peaks with previous estimates of the fitness landscape in this system. We used high-speed video to film feeding strikes on gelatin cubes by scale eater, molluscivore, generalist and hybrid pupfishes and measured bite dimensions. We then measured five kinematic variables from 227 strikes using the SLEAP machine-learning model. We found a complex performance landscape with two distinct peaks best predicted gel-biting performance, corresponding to a significant non-linear interaction between peak gape and peak jaw protrusion. Only scale eaters and their hybrids were able to perform strikes within the highest performance peak, characterized by larger peak gapes and greater jaw protrusion. A performance valley separated this peak from a lower performance peak accessible to all species, characterized by smaller peak gapes and less jaw protrusion. However, most individuals exhibited substantial variation in strike kinematics and species could not be reliably distinguished by their strikes, indicating many-to-many mapping of morphology to performance. The two performance peaks observed in the lab were partially consistent with estimates of a two-peak fitness landscape measured in the wild, with the exception of the new performance peak for scale eaters. We thus reveal a new bimodal non-linear biomechanical model that connects morphology to performance to fitness in a sympatric radiation of trophic niche specialists.

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With 289 known species in 51 genera, the ophidiiform family Ophidiidae together with their relatives from the Carapidae (36 species in eight genera) of the same suborder Ophidioidei dominate the deep sea, but some occur also in shallow water habitats. Despite their high species diversity in the deep sea and wide bathymetric distributions, their phylogenetic relationships and evolution remain unexplored due in part to sampling difficulties. Thanks to the biodiversity exploratory program entitled "Tropical Deep-Sea Benthos" and joint efforts between Taiwan and French teams for sampling from different localities across the Indo-West Pacific over the last two decades, we are able to compile comprehensive datasets for investigations. In this study, 59 samples representing 36 of 59 known ophidioid genera are selected and used to construct a multi-gene dataset to infer the phylogenetic relationships of ophidioid fishes and their relatives. Our results reveal that the Ophidiidae forms a paraphyletic group with respect to the Carapidae. The four main clades of Ophidioidei resolved are the (1) clade comprising species from the subfamily Brotulinae; (2) clade that includes species in the genera Acanthonus and Xyelacyba; (3) clade grouping Hypopleuron caninum with species from the family Carapidae; and (4) clade containing the species in the subfamily Brotulotaenilinae, Neobythitinae (in part), and Ophidiinae. Accordingly, we suggest the following new revisions based on our results and proposed morphological diagnoses. The subfamily Brotulinae should be elevated to the family level. The genera Xyelacyba and probably Tauredophidium (unsampled in this study) should be included in the newly established family Acanthonidae with Acanthonus. The families Carapidae and Ophidiidae are re-defined. Our time-calibrated phylogenetic and ancestral depth reconstructions enable us to clarify the evolutionary history of ophidiiform fishes and infer past patterns of species distributions at different depths. While Ophidiiformes is inferred to have originated in shallow waters around 96.25 million years ago (Mya), the common ancestor to the Ophidioidei is inferred to have invaded the deep sea around 90.22 Mya, the dates coinciding with the global anoxic event of the OAE2. The observed bathymetric distribution patterns in Ophidioidei most likely point to the mesopelagic zone as the center of origin and diversification. This was followed by multiple events of depth transitions or range expansions towards either shallower waters or greater depth zones, which were likely triggered by past climate changes during the Paleogene-Neogene.

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Speciation generates biodiversity and the mechanisms involved are thought to vary across the tree of life and across environments. For example, well-studied adaptive radiations are thought to be fuelled by divergent ecological selection, but additionally are influenced heavily by biogeographic, genomic and demographic factors. Mechanisms of non-adaptive radiations, producing ecologically cryptic taxa, have been less well-studied but should likewise be influenced by these latter factors. Comparing among contexts can help pinpoint universal mechanisms and outcomes, especially if we integrate biogeographic, ecological and evolutionary processes. We investigate population divergence in the swordtail cricket Laupala cerasina, a wide-spread endemic on Hawai'i Island and one of 38 ecologically cryptic Laupala species. The nine sampled populations show striking population genetic structure at small spatio-temporal scales. The rapid differentiation among populations and species of Laupala shows that neither a specific geographical context nor ecological opportunity are pre-requisites for rapid divergence. Spatio-temporal patterns in population divergence, population size change, and gene flow are aligned with the chronosequence of the four volcanoes on which L. cerasina occurs and reveal the composite effects of geological dynamics and Quaternary climate change on population dynamics. Spatio-temporal patterns in genetic variation along the genome reveal the interplay of genetic and genomic architecture in shaping population divergence. In early phases of divergence, we find elevated differentiation in genomic regions harbouring mating song loci. In later stages of divergence, we find a signature of linked selection that interacts with recombination rate variation. Comparing our findings with recent work on complementary systems supports the conclusion that mostly universal factors influence the speciation process.

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Background: Adaptive radiotherapy (ART) can compensate for the dosimetric impact of anatomic change during radiotherapy of head neck cancer (HNC) patients. However, implementing ART universally poses challenges in clinical workflow and resource allocation, given the variability in patient response and the constraints of available resources. Therefore, early identification of head and neck cancer (HNC) patients who would experience significant anatomical change during radiotherapy (RT) is of importance to optimize patient clinical benefit and treatment resources. Purpose: The purpose of this study is to assess the feasibility of using a vision-transformer (ViT) based neural network to predict radiotherapy induced anatomic change of HNC patients. Methods: We retrospectively included 121 HNC patients treated with definitive RT/CRT. We collected the planning CT (pCT), planned dose, CBCTs acquired at the initial treatment (CBCT01) and fraction 21 (CBCT21), and primary tumor volume (GTVp) and involved nodal volume (GTVn) delineated on both pCT and CBCTs for model construction and evaluation. A UNet-style ViT network was designed to learn the spatial correspondence and contextual information from embedded image patches of CT, dose, CBCT01, GTVp, and GTVn. The deformation vector field between CBCT01 and CBCT21 was estimated by the model as the prediction of anatomic change, and deformed CBCT01 was used as the prediction of CBCT21. We also generated binary masks of GTVp, GTVn and patient body for volumetric change evaluation. We used data from 100 patients for training and validation, and the remaining 21 patients for testing. Image and volumetric similarity metrics including mean square error (MSE), structural similarity index (SSIM), dice coefficient, and average surface distance were used to measure the similarity between the target image and predicted CBCT. Results: The predicted image from the proposed method yielded the best similarity to the real image (CBCT21) over pCT, CBCT01, and predicted CBCTs from other comparison models. The average MSE and SSIM between the normalized predicted CBCT to CBCT21 are 0.009 and 0.933, while the average dice coefficient between body mask, GTVp mask, and GTVn mask are 0.972, 0.792, and 0.821 respectively. Conclusions: The proposed method showed promising performance for predicting radiotherapy induced anatomic change, which has the potential to assist in the decision making of HNC Adaptive RT.