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Introduction: End-to-end system evaluation was performed to assess dosimetric and targeting characteristics of a novel system dedicated to Stereotactic Ablative Radiotherapy (SAbR). Clinical SAbR capabilities were evaluated in several disease sites. Materials an. Methods: Recently a Vero system (BrainLAB AG, Feldkirchen, Germany) was installed at UT Southwestern. The Vero, optimally designed for SAbR, uses a ring gantry to integrate a beam delivery platform with image guidance systems. The ring is capable of rotating ± 60 degrees about the vertical axis to facilitate the non-coplanar beam arrangements ideal for SAbR delivery. The beam delivery platform consists of a 6 MV C-band linac with a gimbal-mounted MLC that allows the linac and MLC to pivot in two dimensions for tumor tracking. Two orthogonal kV imaging subsystems facilitate both stereoscopic and volumetric (CBCT) image guidance. Specialized head and torso phantoms were constructed (Integrated Medical Technologies, Troy, NY) to assess both localization and dosimetric characteristics. End-to-end evaluation was performed for brain, lung and spine targets. Tissue density targets embedded in lung allowed direct verification of Monte Carlo dose calculations in heterogeneous media. Commissioning was further verified through the use of the Radiological Physics Center thorax and head and neck phantoms. SAbR treatments have subsequently been performed in a number of disease sites. Results: The unique design results in a measured gantry and ring isocenter radius of 0.12 mm and 0.02 mm respectively. 46 independent hidden target evaluations in anthropomorphic phantoms demonstrate excellent end-to-end IGRT localization capabilities, with an average offset of -0.02±0.35 mm, -0.26±0.28 mm and 0.23±0.28 mm in the anterior-posterior, lateral, and superior-inferior directions, respectively. 2D/2D and volumetric (CBCT) localization accuracy are statistically equivalent. Monte Carlo dose calculations demonstrate excellent agreement with dosimetry measurements in lung, while those performed using a pencil beam algorithm overestimate measurement by up to 20%. The Vero non-coplanar beam capabilities provide both compact dose distributions and conformal avoidance. Discussion: The Vero system is ideally suited to the demands for high localization and dosimetric accuracy required of SAbR treatments. Disclosure: No significant relationships. [ABSTRACT FROM AUTHOR]

In this paper, we ask how the written composition of public policies structure an environmental governance system. We answer this question using semi-automated text analyses of 22 state-level policies governing oil and gas development in California between 2007 and 2017. The findings portray an environmental governance system that is both partitioned and connected into different focal areas (called "targeted action situations") through certain actors, issues, and rules. We conclude with substantive insights about California's oil and gas governance system, as well as theoretical and methodological contributions for analyzing the composition of public policy to advance knowledge about hybrid governance., (Copyright © 2021 Elsevier Ltd. All rights reserved.)

Inbreeding poses a real or potential threat to nearly every species of conservation concern. Inbreeding leads to loss of diversity at the individual level, which can cause inbreeding depression, and at the population level, which can hinder ability to respond to a changing environment. In closed populations such as endangered species and ex situ breeding programs, some degree of inbreeding is inevitable. It is therefore vital to understand how different patterns of breeding and inbreeding can affect fitness in real animals. Domestic dogs provide an excellent model, showing dramatic variation in degree of inbreeding and in lifespan, an important aspect of fitness that is known to be impacted by inbreeding in other species. There is a strong negative correlation between body size and lifespan in dogs, but it is unknown whether the higher rate of aging in large dogs is due to body size per se or some other factor associated with large size. We used dense genome-wide SNP array data to calculate average inbreeding for over 100 dog breeds based on autozygous segment length and found that large breeds tend to have higher coefficients of inbreeding than small breeds. We then used data from the Veterinary medical Database and other published sources to estimate life expectancies for pure and mixed breed dogs. When controlling for size, variation in inbreeding was not associated with life expectancy across breeds. When comparing mixed versus purebred dogs, however, mixed breed dogs lived about 1.2 years longer on average than size-matched purebred dogs. Furthermore, individual pedigree coefficients of inbreeding and lifespans for over 9000 golden retrievers showed that inbreeding does negatively impact lifespan at the individual level. Registration data from the American Kennel Club suggest that the molecular inbreeding patterns observed in purebred dogs result from specific breeding practices and/or founder effects and not the current population size. Our results suggest that recent inbreeding, as reflected in variation within a breed, is more likely to affect fitness than historic inbreeding, as reflected in variation among breeds. Our results also indicate that occasional outcrosses, as in mixed breed dogs, can have a substantial positive effect on fitness., Competing Interests: Compliance with ethical standards Conflict of interest Adam Boyko is the co-founder and Chief Science Officer of Embark Veterinary.

In 77 African painted dog (Lycaon pictus) litters born in North American zoos since 1998, pup mortality at 30 days was 53% (n = 478). More alarmingly, 52% of those 77 litters had zero pups surviving at 30 days. Many variables may have the potential to affect pup mortality in captivity, including kinship, maternal age, prior maternal breeding experience, and numerous social and husbandry factors. Data on these variables were obtained from the North American Regional Studbook, with supplemental information compiled from a survey sent to painted dog breeding facilities in North America. Survival curve analysis revealed significant effects for maternal age and kinship, with kinship being most significant (χ 2 , df = 19.71, 1; P < 0.0001). Pups born to unrelated parents had a median age at death two orders of magnitude higher than pups born to parents who were related to each other. Pup mortality was also lower for experienced mothers and for females under 2.5 years or between 4.5 and 6.5 years old. Follow-up analyses of these findings indicated that among first-time mothers, the youngest females achieved the lowest juvenile mortality, while juvenile mortality for experienced mothers was relatively low in all age classes until 6.5 years old. Regression analysis indicated that chances of survival are improved for pups born to younger mothers, unrelated parents, and in packs of >2 individuals. Enclosure size and area per animal may also be important factors. Our findings indicate that specific characteristics can be used to predict and potentially reduce pup mortality in captive African painted dogs. Zoo Biol. 35:367-377, 2016. © Wiley Periodicals, Inc., (© 2016 Wiley Periodicals, Inc.)

Driver mutations propel oncogenesis and occur much less frequently than passenger mutations. The need for automatic and accurate identification of driver mutations has increased dramatically with the exponential growth of mutation data. Current computational solutions to identify driver mutations rely on sequence homology. Here we construct a machine learning-based framework that does not rely on sequence homology or domain knowledge to predict driver missense mutations. A windowing approach to represent the local environment of the sequence around the mutation point as a mutation sample is applied, followed by extraction of three sequence-level features from each sample. After selecting the most significant features, the support vector machine and multimodal fusion strategies are employed to give final predictions. The proposed framework achieves relatively high performance and outperforms current state-of-the-art algorithms. The ease of deploying the proposed framework and the relatively accurate performance make this solution applicable to large-scale mutation data analyses.

The health of many Florida manatees (Trichechus manatus latirostris) is adversely affected by exposure to blooms of the toxic dinoflagellate, Karenia brevis. K. brevis blooms are common in manatee habitats of Florida's southwestern coast and produce a group of cyclic polyether toxins collectively referred to as red tide toxins, or brevetoxins. Although a large number of manatees exposed to significant levels of red tide toxins die, several manatees are rescued from sublethal exposure and are successfully treated and returned to the wild. Sublethal brevetoxin exposure may potentially impact the manatee immune system. Lymphocyte proliferative responses and a suite of immune function parameters in the plasma were used to evaluate effects of brevetoxin exposure on health of manatees rescued from natural exposure to red tide toxins in their habitat. Blood samples were collected from rescued manatees at Lowry Park Zoo in Tampa, FL and from healthy, unexposed manatees in Crystal River, FL. Peripheral blood leukocytes (PBL) isolated from whole blood were stimulated with T-cell mitogens, ConA and PHA. A suite of plasma parameters, including plasma protein electrophoresis profiles, lysozyme activity, superoxide dismutase (SOD) activity, and reactive oxygen/nitrogen (ROS/RNS) species, was also used to assess manatee health. Significant decreases (p<0.05) in lymphocyte proliferation were observed in ConA and PHA stimulated lymphocytes from rescued animals compared to non-exposed animals. Significant correlations were observed between oxidative stress markers (SOD, ROS/RNS) and plasma brevetoxin concentrations. Sublethal exposure to brevetoxins in the wild impacts some immune function components, and thus, overall health, in the Florida manatee., (Copyright © 2015 Elsevier B.V. All rights reserved.)

The purpose of this work is to develop an automated landmark-guided deformable image registration (LDIR) algorithm between the planning CT and daily cone-beam CT (CBCT) with low image quality. This method uses an automated landmark generation algorithm in conjunction with a local small volume gradient matching search engine to map corresponding landmarks between the CBCT and the planning CT. The landmarks act as stabilizing control points in the following Demons deformable image registration. LDIR is implemented on graphics processing units (GPUs) for parallel computation to achieve ultra fast calculation. The accuracy of the LDIR algorithm has been evaluated on a synthetic case in the presence of different noise levels and data of six head and neck cancer patients. The results indicate that LDIR performed better than rigid registration, Demons, and intensity corrected Demons for all similarity metrics used. In conclusion, LDIR achieves high accuracy in the presence of multimodality intensity mismatch and CBCT noise contamination, while simultaneously preserving high computational efficiency.

The purpose of this study is to describe the comprehensive commissioning process and initial clinical performance of the Vero linear accelerator, a new radiotherapy device recently installed at UT Southwestern Medical Center specifically developed for delivery of image-guided stereotactic ablative radiotherapy (SABR). The Vero system utilizes a ring gantry to integrate a beam delivery platform with image guidance systems. The ring is capable of rotating ± 60° about the vertical axis to facilitate noncoplanar beam arrangements ideal for SABR delivery. The beam delivery platform consists of a 6 MV C-band linac with a 60 leaf MLC projecting a maximum field size of 15 × 15 cm² at isocenter. The Vero planning and delivery systems support a range of treatment techniques, including fixed beam conformal, dynamic conformal arcs, fixed gantry IMRT in either SMLC (step-and-shoot) or DMLC (dynamic) delivery, and hybrid arcs, which combines dynamic conformal arcs and fixed beam IMRT delivery. The accelerator and treatment head are mounted on a gimbal mechanism that allows the linac and MLC to pivot in two dimensions for tumor tracking. Two orthogonal kV imaging subsystems built into the ring facilitate both stereoscopic and volumetric (CBCT) image guidance. The system is also equipped with an always-active electronic portal imaging device (EPID). We present our commissioning process and initial clinical experience focusing on SABR applications with the Vero, including: (1) beam data acquisition; (2) dosimetric commissioning of the treatment planning system, including evaluation of a Monte Carlo algorithm in a specially-designed anthropomorphic thorax phantom; (3) validation using the Radiological Physics Center thorax, head and neck (IMRT), and spine credentialing phantoms; (4) end-to-end evaluation of IGRT localization accuracy; (5) ongoing system performance, including isocenter stability; and (6) clinical SABR applications.

The p53-binding protein 1 (53BP1) is a well-known DNA damage response (DDR) factor, which is recruited to nuclear structures at the site of DNA damage and forms readily visualized ionizing radiation (IR) induced foci. Depletion of 53BP1 results in cell cycle arrest in G2/M phase as well as genomic instability in human as well as mouse cells. Within the DNA damage response mechanism, 53BP1 is classified as an adaptor/mediator, required for processing of the DNA damage response signal and as a platform for recruitment of other repair factors. More recently, specific 53BP1 contributions to DSB repair pathway choice have been recognized and are being characterized. In this review, we have summarized recent advances in understanding the role of 53BP1 in regulating DNA DSBs repair pathway choice, variable diversity joining [V(D)J] recombination and class-switch recombination (CSR).

In adaptive radiotherapy, deformable image registration is often conducted between the planning CT and treatment CT (or cone beam CT) to generate a deformation vector field (DVF) for dose accumulation and contour propagation. The auto-propagated contours on the treatment CT may contain relatively large errors, especially in low-contrast regions. A clinician's inspection and editing of the propagated contours are frequently needed. The edited contours are able to meet the clinical requirement for adaptive therapy; however, the DVF is still inaccurate and inconsistent with the edited contours. The purpose of this work is to develop a contour-guided deformable image registration (CG-DIR) algorithm to improve the accuracy and consistency of the DVF for adaptive radiotherapy. Incorporation of the edited contours into the registration algorithm is realized by regularizing the objective function of the original demons algorithm with a term of intensity matching between the delineated structures set pairs. The CG-DIR algorithm is implemented on computer graphics processing units (GPUs) by following the original GPU-based demons algorithm computation framework (Gu et al 2010 Phys Med Biol. 55 207-219). The performance of CG-DIR is evaluated on five clinical head-and-neck and one pelvic cancer patient data. It is found that compared with the original demons, CG-DIR improves the accuracy and consistency of the DVF, while retaining similar high computational efficiency.

Unlabelled: Small cell lung cancer (SCLC) is an aggressive malignancy distinct from non-small cell lung cancer (NSCLC) in its metastatic potential and treatment response. Using an integrative proteomic and transcriptomic analysis, we investigated molecular differences contributing to the distinct clinical behavior of SCLCs and NSCLCs. SCLCs showed lower levels of several receptor tyrosine kinases and decreased activation of phosphoinositide 3-kinase (PI3K) and Ras/mitogen-activated protein (MAP)/extracellular signal-regulated kinase (ERK) kinase (MEK) pathways but significantly increased levels of E2F1-regulated factors including enhancer of zeste homolog 2 (EZH2), thymidylate synthase, apoptosis mediators, and DNA repair proteins. In addition, PARP1, a DNA repair protein and E2F1 co-activator, was highly expressed at the mRNA and protein levels in SCLCs. SCLC growth was inhibited by PARP1 and EZH2 knockdown. Furthermore, SCLC was significantly more sensitive to PARP inhibitors than were NSCLCs, and PARP inhibition downregulated key components of the DNA repair machinery and enhanced the efficacy of chemotherapy., Significance: SCLC is a highly lethal cancer with a 5-year survival rate of less than 10%. To date, no molecularly targeted agents have prolonged survival in patients with SCLCs. As a step toward identifying new targets, we systematically profiled SCLCs with a focus on therapeutically relevant signaling pathways. Our data reveal fundamental differences in the patterns of pathway activation in SCLCs and NSCLCs and identify several potential therapeutic targets for SCLCs, including PARP1 and EZH2. On the basis of these results, clinical studies evaluating PARP and EZH2 inhibition, together with chemotherapy or other agents, warrant further investigation.

Persistent organic pollutants (POPs) including legacy POPs (PCBs, chlordanes, mirex, DDTs, HCB, and dieldrin) and polybrominated diphenyl ether (PBDE) flame retardants were determined in 300 blubber biopsy samples from coastal and near shore/estuarine male bottlenose dolphins (Tursiops truncatus) sampled along the U.S. East and Gulf of Mexico coasts and Bermuda. Samples were from 14 locations including urban and rural estuaries and near a Superfund site (Brunswick, Georgia) contaminated with the PCB formulation Aroclor 1268. All classes of legacy POPs in estuarine stocks varied significantly (p < 0.05) among sampling locations. POP profiles in blubber varied by location with the most characteristic profile observed in bottlenose dolphins sampled near the Brunswick and Sapelo estuaries along the Georgia coast which differed significantly (p < 0.001) from other sites. Here and in Sapelo, PCB congeners from Aroclor 1268 dominated indicating widespread food web contamination by this PCB mixture. PCB 153, which is associated with non-Aroclor 1268 PCB formulations, correlated significantly to human population indicating contamination from a general urban PCB source. Factors influencing regional differences of other POPs were less clear and warrant further study. This work puts into geographical context POP contamination in dolphins to help prioritize efforts examining health effects from POP exposure in bottlenose dolphins.

An increasing number of studies use blood obtained noninvasively to monitor organohalogen contaminants; however, blood can be difficult to analyze because of its aqueous nature and high protein content. We compared five methods for extracting polychlorinated biphenyls (PCBs), polybrominated diphenyl ethers (PBDEs), organochlorine pesticides, and lipids from serum using National Institute of Standards and Technology Standard Reference Material 1589a PCBs, Pesticides, PBDEs, and Dioxins/Furans in Human Serum. Liquid:liquid (LLE), cavity-dispersed microwave-assisted (MAE), focused microwave-assisted (FME), solid-phase (SPE), and pressurized fluid (PFE) extraction techniques were compared. FME extraction yielded the optimal recovery of internal standards (IS). All methods resulted in similar contaminant concentrations that also agreed with the certified values for SRM 1589a, except for only a few compounds measured by methods other than FME. Based on these findings, the FME method was determined to be the best overall extraction method. One procedural factor was found to affect contaminant concentrations; use of IS carrier solvents that were immiscible with serum (or when the serum was not directly physically mixed with IS) resulted in a 30% underestimation of organohalogen concentrations. This study offers valid, novel extraction alternatives beyond traditional methods (e.g., LLE) for blood contaminant measurements.

Cellular responses to environmental stimuli are controlled by a series of signaling cascades that transduce extracellular signals from ligand-activated cell surface receptors to the nucleus. Although most pathways were initially thought to be linear, it has become apparent that there is a dynamic interplay between signaling pathways that result in the complex pattern of cell-type specific responses required for proliferation, differentiation and survival. One group of nuclear effectors of these signaling pathways are the Ets family of transcription factors, directing cytoplasmic signals to the control of gene expression. This family is defined by a highly conserved DNA binding domain that binds the core consensus sequence GGAA/T. Signaling pathways such as the MAP kinases, Erk1 and 2, p38 and JNK, the PI3 kinases and Ca2+-specific signals activated by growth factors or cellular stresses, converge on the Ets family of factors, controlling their activity, protein partnerships and specification of downstream target genes. Interestingly, Ets family members can act as both upstream and downstream effectors of signaling pathways. As downstream effectors their activities are directly controlled by specific phosphorylations, resulting in their ability to activate or repress specific target genes. As upstream effectors they are responsible for the spacial and temporal expression or numerous growth factor receptors. This review provides a brief survey of what is known to date about how this family of transcription factors is regulated by cellular signaling with a special focus on Ras responsive elements (RREs), the MAP kinases (Erks, p38 and JNK) and Ca2+-specific pathways and includes a description of the multiple roles of Ets family members in the lymphoid system. Finally, we will discuss other potential mechanisms and pathways involved in the regulation of this important family of transcription factors.

This paper reviews the use of extracorporeal immunoadsorption with immobilized Staphylococcal Protein A in attempts to lower the inhibitor titer in 22 patients with either congenital hemophilia or with acquired inhibitors. Eighty-five immunoadsorption procedures were performed at 13 locations in the United States between June, 1987 and February, 1990. In general, immunoadsorption was shown to efficiently remove IgG and, in eight congenital hemophilia patients, it also produced a clinically significant lowering of inhibitors allowing effective conventional factor replacement therapy. Three of thirteen congenital hemophilia patients treated received factor concentrate prior to immunoadsorption and were anamnestic at the time of treatment. Although they experienced substantial lowering of their inhibitor titers, it was not sufficient to allow effective factor replacement. The effectiveness of immunoadsorption therapy in the 9 patients with acquired inhibitors was more difficult to evaluate due to the wide variety of concomitant medications which were employed, although in several patients serious bleeding episodes were substantially improved (or halted) following immunoadsorption. Side effects associated with immunoadsorption were slight. These findings suggest that immunoadsorption can be a significant benefit to patients with inhibitors, particularly if it is instituted prior to factor administration.