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Highlights • Real-time respiratory motion management (RRMM) practice, evaluated for 200 centres. • Sixty-eight percent of respondents used RRMM for at least one tumour site. • Across all tumour sites, external marker was the main RRMM signal used. • Overall 71% of respondents wished to implement RRMM for a new treatment site. • The main barriers were human/financial resources and capacity on the machine., Purpose The POP-ART RT study aims to determine to what extent and how intra-fractional real-time respiratory motion management (RRMM) and plan adaptation for inter-fractional anatomical changes (ART), are used in clinical practice and to understand barriers to implementation. Here we report on part I: RRMM. Material and methods A questionnaire was distributed worldwide to assess current clinical practice, wishes for expansion or new implementation and barriers to implementation. RRMM was defined as inspiration/expiration gating in free-breathing or breath-hold, or tracking where the target and the beam are continuously realigned. Results The questionnaire was completed by 200 centres from 41 countries. RRMM was used by 68% of respondents (‘users’) for a median (range) of 2 (1–6) tumour sites. Eighty-one percent of users applied inspiration breath-hold in at least one tumour site (breast: 96%). External marker was used to guide RRMM by 61% of users. KV/MV imaging was frequently used for liver and pancreas (with fiducials) and for lung (with or without fiducials). Tracking was mainly performed on robotic linacs with hybrid internal-external monitoring. For breast and lung, approximately 75% of respondents used or wished to implement RRMM, which was lower for liver (44%) and pancreas (27%). Seventy-one percent of respondents wished to implement RRMM for a new tumour site. Main barriers were human/financial resources and capacity on the machine. Conclusion Sixty-eight percent of respondents used RRMM and 71% wished to implement RRMM for a new tumour site. The main barriers to implementation were human/financial resources and capacity on treatment machines.

RNA polymerase transcribes certain genomic loci with higher errors rates. These transcription error-enriched genomic loci (TEELs) have implications in disease. Current deep-sequencing methods cannot distinguish TEELs from post-transcriptional modifications, stochastic transcription errors, and technical noise, impeding efforts to elucidate the mechanisms linking TEELs to disease. Here, we describe background error model-coupled precision nuclear run-on circular-sequencing (EmPC-seq) to discern genomic regions enriched for transcription misincorporations. EmPC-seq innovatively combines a nuclear run-on assay for capturing nascent RNA before post-transcriptional modifications, a circular-sequencing step that sequences the same nascent RNA molecules multiple times to improve accuracy, and a statistical model for distinguishing error-enriched regions among stochastic polymerase errors. Applying EmPC-seq to the ribosomal RNA transcriptome, we show that TEELs of RNA polymerase I are not randomly distributed but clustered together, with higher error frequencies at nascent transcript 3' ends. Our study establishes a reliable method of identifying TEELs with nucleotide precision, which can help elucidate their molecular origins.

We present detailed comparative analyses to assess population-level differences in patterns of genetic deafness between European/American and Japanese cohorts with non-syndromic hearing loss. One thousand eighty-three audiometric test results (921 European/American and 162 Japanese) from members of 168 families (48 European/American and 120 Japanese) with non-syndromic hearing loss secondary to pathogenic variants in one of three genes (KCNQ4, TECTA, WFS1) were studied. Audioprofile characteristics, specific mutation types, and protein domains were considered in the comparative analyses. Our findings support differences in audioprofiles driven by both mutation type (non-truncating vs. truncating) and ethnic background. The former finding confirms data that ascribe a phenotypic consequence to different mutation types in KCNQ4; the latter finding suggests that there are ethnic-specific effects (genetic and/or environmental) that impact gene-specific audioprofiles for TECTA and WFS1. Identifying the drivers of ethnic differences will refine our understanding of phenotype-genotype relationships and the biology of hearing and deafness.

Cannabinoid receptor interacting protein 1a (CRIP1a) is an important CB1 cannabinoid receptor-associated protein, first identified from a yeast two-hybrid screen to modulate CB1-mediated N-type Ca2+ currents. In this paper we review studies of CRIP1a function and structure based upon in vitro experiments and computational chemistry, which elucidate the specific mechanisms for the interaction of CRIP1a with CB1 receptors. N18TG2 neuronal cells overexpressing or silencing CRIP1a highlighted the ability of CRIP1 to regulate cyclic adenosine 3′,5′monophosphate (cAMP) production and extracellular signal-regulated kinase (ERK1/2) phosphorylation. These studies indicated that CRIP1a attenuates the G protein signaling cascade through modulating which Gi/o subtypes interact with the CB1 receptor. CRIP1a also attenuates CB1 receptor internalization via β-arrestin, suggesting that CRIP1a competes for β-arrestin binding to the CB1 receptor. Predictions of CRIP1a secondary structure suggest that residues 34-110 are minimally necessary for association with key amino acids within the distal C-terminus of the CB1 receptor, as well as the mGlu8a metabotropic glutamate receptor. These interactions are disrupted through phosphorylation of serines and threonines in these regions. Through investigations of the function and structure of CRIP1a, new pharmacotherapies based upon the CRIP-CB1 receptor interaction can be designed to treat diseases such as epilepsy, motor dysfunctions and schizophrenia.

An in-house developed program for real-time reconstruction of motion-induced dose errors, DoseTracker, was extended to handle rotational target motion in addition to the previously implemented translational motion, and applied offline for prostate VMAT treatments. For translational motion, the motion-induced errors of DoseTracker were in good agreement with ground truth dose reconstructions performed in a commercial treatment planning system. For rotational motion, no ground truth was available, but DoseTracker showed that the VMAT dose is highly robust against static interfractional rotations but quite sensitive to dynamic intrafraction rotations due to interplay effects between target motion and machine motion.

PurposeKilovoltage intrafraction monitoring (KIM) is a novel software platform implemented on standard radiation therapy systems and enabling real-time image guided radiation therapy (IGRT). In a multi-institutional prospective trial, we investigated whether real-time IGRT improved the accuracy of the dose patients with prostate cancer received during radiation therapy.Methods and materialsForty-eight patients with prostate cancer were treated with KIM-guided SABR with 36.25 Gy in 5 fractions. During KIM-guided treatment, the prostate motion was corrected for by either beam gating with couch shifts or multileaf collimator tracking. A dose reconstruction method was used to evaluate the dose delivered to the target and organs at risk with and without real-time IGRT. Primary outcome was the effect of real-time IGRT on dose distributions. Secondary outcomes included patient-reported outcomes and toxicity.ResultsMotion correction occurred in ≥1 treatment for 88% of patients (42 of 48) and 51% of treatments (121 of 235). With real-time IGRT, no treatments had prostate clinical target volume (CTV) D98% dose 5% less than planned. Without real-time IGRT, 13 treatments (5.5%) had prostate CTV D98% doses 5% less than planned. The prostate CTV D98% dose with real-time IGRT was closer to the plan by an average of 1.0% (range, -2.8% to 20.3%). Patient outcomes showed no change in the 12-month patient-reported outcomes compared with baseline and no grade ≥3 genitourinary or gastrointestinal toxicities.ConclusionsReal-time IGRT is clinically effective for prostate cancer SABR.

Medical therapy for mycotic aortic aneurysms (MAA) is almost universally fatal, while surgical and endovascular repair carry high morbidity and mortality. The purpose of this study was to compare outcomes between patients receiving treatment for MAA. Records were obtained and patients with MAA were stratified by intervention: endovascular repair, open surgery, and medical therapy. Primary outcomes were aneurysm-related mortality and survival. Risk-adjusted associations with mortality were assessed using time-to-event analysis. Thirty-eight patients were identified (median age, 67). Twenty-one underwent endovascular repair,10 had open surgery and 7 received medical therapy alone. Overall mortality was 47% (n = 18), with 94% aneurysm related. Median survival was significantly longer in the endovascular group (747.0 [161-1249]) vs open surgery and medical therapy (507.5 [34-806] and 66 [13-146] days, respectively; P = .02). The endovascular group had significantly fewer perioperative complications (43% vs 80%, P < .01). However, 4 endovascular patients experienced reinfection versus no open surgery patients. Mortality risk factors included medical therapy (hazard ratio [HR]: 5.3, P < .01) and aneurysm size (HR: 1.4 per 1-cm increase in diameter, P = .03). Endovascular repair of MAA was associated with the best long-term survival and lowest perioperative complication rate, although it is associated with greater reinfection. These tradeoffs should be considered when selecting which procedure is best for a patient.

Bordetella bacteria are respiratory pathogens of humans, birds, and livestock. Bordetella pertussis the causative agent of whopping cough remains a significant health issue. The transcriptional regulator, BpsR, represses a number of Bordetella genes relating to virulence, cell adhesion, cell motility, and nicotinic acid metabolism. DNA binding of BpsR is allosterically regulated by interaction with 6-hydroxynicotinic acid (6HNA), the first product in the nicotinic acid degradation pathway. To understand the mechanism of this regulation, we have determined the crystal structures of BpsR and BpsR in complex with 6HNA. The structures reveal that BpsR binding of 6HNA induces a conformational change in the protein to prevent DNA binding. We have also identified homologs of BpsR in other Gram negative bacteria in which the amino acids involved in recognition of 6HNA are conserved, suggesting a similar mechanism for regulating nicotinic acid degradation.

BACKGROUND AND PURPOSE: To test the hypothesis that 4DCT and 4DCBCT-measured target motion ranges predict target motion ranges during lung cancer SABR. MATERIALS AND METHODS: Ten lung SABR patients were implanted with Calypso beacons. 4DCBCT was reconstructed for 29 fractions (1-4fx/patient) from a 1 min CBCT scan. The beacon centroid motion segmented for all 4DCT and 4DCBCT bins was compared with the real-time imaging and treatment beacon centroid ("target") motion range (4SDs) for each fraction. We tested the hypotheses that (1) 4DCT and 4CBCT predict treatment motion range and (2) there is no difference between 4DCT and 4DCBCT for predicting treatment motion range. Phase-wise root-mean-square errors (RMSEs) between imaging and treatment motion and reconstructed motion (4DCT, 4DCBCT) were calculated. Relationships between motion ranges in 4DCT and 4DCBCT and imaging and treatment motion ranges were investigated for the superior-inferior (SI), left-right (LR) and anterior-posterior (AP) directions. Baseline drifts and amplitude variability were investigated as potential factors leading to motion misrepresentation. RESULTS: SI 4DCT, 4DCBCT, imaging and treatment motion ranges were 6.3 ± 3.6 mm, 7.1 ± 4.5 mm, 11.1 ± 7.5 mm and 10.9 ± 6.9 mm, respectively. Similar 4DCT and 4DCBCT under-predictions were observed in the LR and AP directions. Hypothesis (1) was rejected (p

Background Liver tumors are subject to motion with respiration, which is typically accounted for by increasing the target volume. The prescription dose is often reduced to keep the mean liver dose under a threshold level to limit the probability of radiation induced liver toxicity. A retrospective planning study was performed to determine the potential clinical gains of removal of respiratory motion from liver SABR treatment volumes, which may be achieved with gating or tumor tracking. Methods Twenty consecutive liver SABR patients were analysed. The treated PTV included the GTV in all phases of respiration (ITV) with a 5 mm margin. The goal prescription was 50Gy/5# (BED 100 Gy10) but was reduced by 2.5 Gy increments to meet liver dose constraints. Elimination of motion was modelled by contouring the GTV in the expiration phase only, with a 5 mm PTV margin. All patients were replanned using the no-motion PTV and tumor dose was escalated to higher prescription levels where feasible given organ-at-risk constraints. For the cohort of patients with metastatic disease, BED gains were correlated to increases in tumour control probability (TCP). The effect of the gradient of the TCP curve on the magnitude of TCP increase was evaluated by repeating the study for an additional prescription structure, 54Gy/3# (BED 151 Gy10). Results Correlation between PTV size and prescribed dose exists; PTVs encompassing

© 2019 Institute of Physics and Engineering in Medicine. In this study we develop and characterise a six degree-of-freedom (6 DoF) robotic motion system for quality assurance of real-time image-guided radiotherapy techniques. The system consists of a commercially available robotic arm, an acrylic phantom with embedded Calypso markers, a custom base plate to mount the robot to the treatment couch, and control software implementing the appropriate sequence of transformations to reproduce measured tumour motion traces. The robotic motion system was evaluated in terms of the set-up and motion trace repeatability, static localization accuracy and dynamic localization accuracy. Four prostate, two liver and three lung motion traces, representing a range of tumor motion trajectories recorded in real patient treatments, were executed using the robotic motion system and compared with motion measurements from the clinical Calypso motion tracking system. System set-up and motion trace repeatability was better than 0.5 deg and 0.3 mm for rotation and translation, respectively. The static localization accuracy of the robotic motion system in the LR, SI and AP directions was 0.09 mm, 0.08 mm and 0.02 mm for translations, respectively, and 0.2°, 0.06° and 0.06° for rotations, respectively. The dynamic localization accuracy of the robotic motion system was

© 2019 American Association of Physicists in Medicine Purpose: Kilovoltage intrafraction monitoring (KIM) allows for real-time image guidance for tracking tumor motion in six-degrees-of-freedom (6DoF) on a standard linear accelerator. This study assessed the geometric accuracy and precision of KIM used to guide patient treatments in the TROG 15.01 multi-institutional Stereotactic Prostate Ablative Radiotherapy with KIM trial and investigated factors affecting accuracy and precision. Methods: Fractions from 44 patients with prostate cancer treated using KIM-guided SBRT were analyzed across four institutions, on two different linear accelerator models and two different beam models (6 MV and 10 MV FFF). The geometric accuracy and precision of KIM was assessed from over 33 000 images (translation) and over 9000 images (rotation) by comparing the real-time measured motion to retrospective kV/MV triangulation. Factors potentially affecting accuracy, including contrast-to-noise ratio (CNR) of kV images and incorrect marker segmentation, were also investigated. Results: The geometric accuracy and precision did not depend on treatment institution, beam model or motion magnitude, but was correlated with gantry angle. The centroid geometric accuracy and precision of the KIM system for SABR prostate treatments was 0.0 ± 0.5, 0.0 ± 0.4 and 0.1 ± 0.3 mm for translation, and −0.1 ± 0.6°, −0.1 ± 1.4° and −0.1 ± 1.0° for rotation in the AP, LR and SI directions respectively. Centroid geometric error exceeded 2 mm for 0.05% of this dataset. No significant relationship was found between large geometric error and CNR or marker segmentation correlation. Conclusions: This study demonstrated the ability of KIM to locate the prostate with accuracy below other uncertainties in radiotherapy treatments, and the feasibility for KIM to be implemented across multiple institutions.

Since the inception of the National Institute for Health Research (NIHR) in 2006, the landscape for the delivery of clinical research within the National Health Service (NHS) has been transformed. Clinical radiology has benefitted from funding opportunities for primary imaging research as well as improvements to the supporting research infrastructure to provide imaging for many clinical trials; however, in an increasingly challenging NHS environment, the NIHR and clinical radiology have to evolve an effective working partnership to ensure imaging research is sustainable and will make an impact. A number of initiatives have arisen from discussions between the NIHR, the Royal College of Radiologists (RCR), and stakeholders that will be discussed in this article. It is hoped that these initiatives will be embraced by the imaging community and create a more dynamic sustainable imaging workforce, driving and supporting research and innovation towards future sustainability.

Purpose. To compare the accuracies of the AAA and AcurosXB dose calculation algorithms and to predict the change in the down-stream and lateral dose deposition of high energy photons in the presence of material with densities higher that commonly found in the body. Method. Metal rods of titanium (d = 4.5 g cm−3), stainless steel (d = 8 g cm−3) and tungsten (d = 19.25 g cm−3) were positioned in a phantom. Film was position behind and laterally to the rods to measure the dose distribution for a 6 MV, 18 MV and 10 FFF photon beams. A DOSXYZnrc Monte Carlo simulation of the experimental setup was performed. The AAA and AcurosXB dose calculation algorithms were used to predict the dose distributions. The dose from film and DOSXYZnrc were compared with the dose predicted by AAA and AcurosXB. Results. AAA overestimated the dose behind the rods by 15%–25% and underestimated the dose laterally to the rods by 5%–15% depending on the range of materials and energies investigated. AcurosXB overestimated the dose behind the rods by 1%–18% and underestimated the dose laterally to the rods by up to 5% depending on the range of material and energies investigated. Conclusion. AAA cannot deliver clinically acceptable dose calculation results at a distance less than 10 mm from metals, for a single field treatment. Acuros XB is able to handle metals of low atomic numbers (Z ≤ 26), but not tungsten (Z = 74). This can be due to the restriction of the CT-density table in EclipseTM TPS, which has an upper HU limit of 10501.

Global sea turtle populations are threatened by rising atmospheric temperatures which result in higher incubation temperatures. Increased incubation temperatures affect embryo survival, hatchling sex ratio and hatchling locomotor performance. This study aimed to determine the effectiveness of natural and artificial shade on reducing green turtle (Chelonia mydas) incubation temperature at Chagar Hutang beach, Redang Island, Malaysia. To achieve this objective, clutches were incubated using three treatments: unshaded control, artificial shade, and natural tree shade. Estimated hatchling sex ratios, hatching success and locomotor performance were compared across the shade treatments. Clutches incubated in the shaded hatchery were on average 1.3 °C cooler than the unshaded control group, but remained above 30.5 °C and were predicted to produce 100% female hatchlings. In contrast, natural shade from the fringing forest reduced incubation temperatures by 2.7 °C relative to the unshaded clutches, and were predicted to produce up to 85% male hatchlings. Hatching success was similar across treatments and little effect of treatment was observed on hatchling locomotor performance. We recommend relocating nests at high risk of inundation or predation to natural tree shade as a viable solution for ensuring at least some male hatchling production at Chagar Hutang beach.

Purpose Our purpose was to report outcomes of a novel palliative radiation therapy protocol that omits computed tomography simulation and prospectively collects electronic patient-reported outcomes (ePROs). Methods and Materials Patients receiving extracranial, nonstereotactic, linear accelerator-based palliative radiation therapy who met inclusion criteria (no mask-based immobilization and a diagnostic computed tomography within 4 weeks) were eligible. Global pain was scored with the 11-point numerical pain rating scale (NPRS). Patients were coded as having osseous or soft tissue metastases and no/mild versus severe baseline pain (NPRS ≥ 5). Pain response at 4 weeks was measured according to the international consensus (no analgesia adjustment). Transition to ePRO questionnaires was completed in 3 phases. Initially, pain assessments were collected on paper for 11 months, then pilot ePROs for 1 month and then, after adjustments, revised ePROs from 1 year onwards. ePRO feasibility criteria were established with reference to the paper-based process and published evidence. Results Between May 2018 and November 2019, 542 consecutive patients were screened, of whom 163 were eligible (30%), and 160 patients were successfully treated. The proportion of patients eligible for the study improved from approximately 20% to 50% by study end. Routine care pain monitoring via ePROs was feasible. One hundred twenty-seven patients had a baseline NPRS recording. Ninety-five patients had osseous (61% severe pain) and 32 had soft tissue (25% severe pain) metastases. Eighty-four patients (66%) were assessable for pain response at 4 weeks. In the 41 patients with severe osseous pain, overall and complete pain response was 78% and 22%, respectively. Conclusions By study completion, 50% of patients receiving palliative extracranial radiation therapy avoided simulation, streamlining the treatment process and maximizing patient convenience. Pain response for patients with severe pain from osseous lesions was equivalent to published evidence.

Ocean wastewater dischargers in southern California maintain extensive water quality monitoring programs to assess their effects on coastal receiving waters, but there is no shared protocol to analyze these measurements for compliance with California Ocean Plan standards. Here we present an assessment methodology that we apply regionally to determine discharge effects on dissolved oxygen (DO). The methodology was developed using an optimization algorithm to determine the following: (1) the most appropriate number of reference sites to capture natural variability among sites without moving so far from the potentially affected site to confound the comparison with natural latitudinal and offshore gradients; (2) the thickness of depth slices for comparing profiles between reference and potentially affected sites that minimizes false positives from natural vertical variability while not being so large as to average out plume-caused deviations; and (3) an allowable difference from the reference mean associated with variability among reference profiles. The algorithm was based on maximizing the chance of detecting DO outranges in the effluent plume, while simultaneously minimizing the chance to falsely identify outranges at reference sites outside of the plume zone. The assessment methodology also differentiates DO outranges resulting from physical upward entrainment of deep, low-oxygen water by rising of lower density plume water, as opposed to outranges resulting from low-oxygen and oxygen demanding properties of the effluent, using temperature-oxygen relationships as a tracer of water masses. When the algorithm was applied to a ten year monitoring record from four discharge monitoring programs along the southern California coast, 11% of effluent sites were found to contain DO outranges, with about half of them resulting from deep water entrainment.

The genus Cladonia is widely distributed around the world. Since the section Cladonia contains species complexes that are difficult to distinguish, the distributions of species within these complexes are even less well-known than others. The cup-forming species, Cladonia magyarica, is morphologically similar to C. pyxidata and C. pocillum; and C. humilis is morphologically similar to C. conista and C. chlorophaea. Both species, C. magyarica and C. humilis, have not been previously reported for Manitoba, but their distribution ranges fall very close to the province, and they grow in habitats that are present in southern Manitoba. The goal of this paper was to report the presence of C. magyarica and C. humilis in Manitoba representing range extensions for both species, and to show morphological differences among them and their close allies present in the same geographic locations. The morphological differences between C. magyarica and C. pyxidata include squamules inside the cup and a significantly taller podetium and wider cup diameter in C. magyarica than C. pyxidata. Cladonia magyarica also differs from C. pyxidata in possessing atranorin in addition to fumarprotocetraric acid, in every specimen we collected. Atranorin and fumarprotocetraric acid were also shown to be present in C. humilis, but C. humilis has soredia covering the podetium, which is not present in the aforementioned taxa.

Development of dental faculty members is paramount to providing outstanding education and role modeling for students. With the large number of second career educators in dental schools, an efficient method of acquiring teaching skills is important for new faculty members. Knowing the skill progression and learning experiences identified by dental educators of varying rank may lead to more efficient, effective faculty development. The aims of this study were to identify the perceptions of a group of faculty members about the knowledge, skills, attitudes, and learning experiences that contribute to developing teaching expertise and to compare and contrast the perceptions of new and more senior faculty members on these subjects. The Dreyfus skill acquisition continuum of novice to expert performance was used as a construct reference. The study used a mixed-methods approach in which qualitative and quantitative data were collected concurrently in an electronic survey of faculty members at one U.S. dental school. Of the 492 total faculty members, 80 survey responses were received, for a 16% response rate. Open coding and analysis of responses revealed some common themes. Building rich content knowledge and learning varied methodologies for teaching and assessment, supported by an awareness of peer role models, were perceived to be features of early growth. Content prioritization, clarity, and customization appropriate for the learner characterized mid growth. As theorized in the Dreyfus model, more experienced faculty members described a fluid, less structured teaching process, increased reflection, and appreciation of the strength of the educational community. The results of this study may help increase dental educators' understanding of teaching skill acquisition and inform faculty development and support.

The individual and social protective factors that help break the cycle of violence are examined. Specifically, this study investigates (a) the individual and social protective factors that reduce violent offending among previously victimized children, and (b) whether certain protective factors are more or less important depending on the type and frequency of childhood victimization experienced. Data on young adults from Wave III of the National Longitudinal Study of Adolescent to Adult Health are used ( N = 13,116). Negative binomial regression models are estimated to examine the protective factors that promote resiliency to violent offending among individuals who reported being physically and sexually victimized as children. Results indicate that a number of individual and social protective factors reduce violent offending in young adulthood. With a few exceptions, these factors are specific to the type, frequency, and comorbidity of abuse experienced. The results suggest a number of promising approaches to break the cycle of violence among previously victimized children. Future research should move beyond explaining the cycle of violence to examine how the cycle may be broken.

Complex regulation of gene expression in mammals has evolved from simpler eukaryotic systems, yet the mechanistic features of this evolution remain elusive. Here, we compared the transcriptional landscapes of the distantly related budding and fission yeast. We adapted the Precision Run-On sequencing (PRO-seq) approach to map the positions of RNA polymerase active sites genome-wide in Schizosaccharomyces pombe and Saccharomyces cerevisiae. Additionally, we mapped preferred sites of transcription initiation in each organism using PRO-cap. Unexpectedly, we identify a pause in early elongation, specific to S. pombe, that requires the conserved elongation factor subunit Spt4 and resembles promoter-proximal pausing in metazoans. PRO-seq profiles in strains lacking Spt4 reveal globally elevated levels of transcribing RNA Polymerase II (Pol II) within genes in both species. Messenger RNA abundance, however, does not reflect the increases in Pol II density, indicating a global reduction in elongation rate. Together, our results provide the first base-pair resolution map of transcription elongation in S. pombe and identify divergent roles for Spt4 in controlling elongation in budding and fission yeast.

PURPOSE: Kilovoltage intrafraction monitoring (KIM) is a new real-time 3-dimensional image guidance method. Unlike previous real-time image guidance methods, KIM uses a standard linear accelerator without any additional equipment needed. The first prospective clinical trial of KIM is underway for prostate cancer radiation therapy. In this paper we report on the measured motion accuracy and precision using real-time KIM-guided gating. METHODS AND MATERIALS: Imaging and motion information from the first 200 fractions from 6 patient prostate cancer radiation therapy volumetric modulated arc therapy treatments were analyzed. A 3-mm/5-second action threshold was used to trigger a gating event where the beam is paused and the couch position adjusted to realign the prostate to the treatment isocenter. To quantify the in vivo accuracy and precision, KIM was compared with simultaneously acquired kV/MV triangulation for 187 fractions. RESULTS: KIM was successfully used in 197 of 200 fractions. Gating events occurred in 29 fractions (14.5%). In these 29 fractions, the percentage of beam-on time, the prostate displacement was >3 mm from the isocenter position, reduced from 73% without KIM to 24% with KIM-guided gating. Displacements >5 mm were reduced from 16% without KIM to 0% with KIM. The KIM accuracy was measured at

Hearing loss is the most common sensory deficit in humans, affecting 1 in 500 newborns. Due to its genetic heterogeneity, comprehensive diagnostic testing has not previously been completed in a large multiethnic cohort. To determine the aggregate contribution inheritance makes to non-syndromic hearing loss, we performed comprehensive clinical genetic testing with targeted genomic enrichment and massively parallel sequencing on 1119 sequentially accrued patients. No patient was excluded based on phenotype, inheritance or previous testing. Testing resulted in identification of the underlying genetic cause for hearing loss in 440 patients (39 %). Pathogenic variants were found in 49 genes and included missense variants (49 %), large copy number changes (18 %), small insertions and deletions (18 %), nonsense variants (8 %), splice-site alterations (6 %), and promoter variants (

Background Parents who experience relational trauma may inadvertently create contexts of care that undermine secure beginnings to life for their young children. Universal health services such as Maternal and Child Health (MCH) services offer a unique whole-of-population platform for prevention through early detection and intervention. To date however, relevant workforce training has been minimal. Objectives We report on an evaluation of state-wide workforce training to support MCH nurses to identify and respond to early relational trauma within parent-child dyads. Design Process and learning evaluation data were obtained at baseline (N = 1450), exit (n = 734) and follow-up (n = 651). Settings and participants Specialist training was developed and delivered to 1513 MCH staff in Victoria, Australia, via a 20-hour program of online learning and clinical skills workshops. Results At baseline, across eight measures of confidence in recognizing and responding to relational trauma, 30–49% of nurses rated their confidence as low. Significant increases in all areas of self-rated learning were found post-training. Three months post-training, gains in confidence and capability were sustained, with no significant variations by participant role or setting. Overall program satisfaction was >90%. Continuing concerns at follow-up focused on pragmatic concerns about inadequacy of referral networks and appropriate intervention pathways. Conclusions In this evaluation of a state-wide training program for nurses working with early relational trauma, we found excellent uptake and program satisfaction, and results support learning impact and retention. Findings are discussed with regard to translation potential across early childhood settings.

PurposeProper interpretation of genomic variants is critical to successful medical decision making based on genetic testing results. A fundamental prerequisite to accurate variant interpretation is the clear understanding of the clinical validity of gene-disease relationships. The Clinical Genome Resource (ClinGen) has developed a semi-quantitative framework to assign clinical validity to gene-disease relationships.MethodsThe ClinGen Hearing Loss Gene Curation Expert Panel (HL GCEP) uses this framework to perform evidence-based curations of genes present on testing panels from 17 clinical laboratories in the Genetic Testing Registry. The HL GCEP curated and reviewed 142 genes and 164 gene-disease pairs, including 105 nonsyndromic and 59 syndromic forms of hearing loss.ResultsThe final outcome included 82 Definitive (50%), 12 Strong (7%), 25 Moderate (15%), 32 Limited (20%), 10 Disputed (6%), and 3 Refuted (2%) classifications. The summary of each curation is date stamped with the HL GCEP approval, is live, and will be kept up-to-date on the ClinGen website (https://search.clinicalgenome.org/kb/gene-validity).ConclusionThis gene curation approach serves to optimize the clinical sensitivity of genetic testing while reducing the rate of uncertain or ambiguous test results caused by the interrogation of genes with insufficient evidence of a disease link.

Previous formulations of the FlexyDos3D dosimeter have shown significant changes in the dose-response over time. In this study, various formulations of the dosimeter were created and tested to see if this stability could be improved. A dosimeter that was stable over a three-day period was found. Rapid manufacture of this dosimeter for patient-specific validation of radiotherapy treatments is desirable. The use of 3D printing manufacturing techniques for thermosetting polymers require high temperatures to cure the polymer within a reasonable time. The effect of different curing temperatures and times were investigated for the FlexyDos3D radiation dosimeter for its effect on stability. No significant difference in the dose-response was found for dosimeters cured for different curing times beyond an hour. A significant dose-response offset was found between dosimeters cured at different temperatures, but the dose-response sensitivity was the same.

Purpose: Multileaf collimator (MLC) tracking is being clinically pioneered to continuously compensate for thoracic and pelvic motion during radiotherapy. The purpose of this work was to characterize the performance of two MLC leaf-fitting algorithms, direct optimization and piecewise optimization, for real-time motion compensation with different plan complexity and tumor trajectories. Methods: To test the algorithms, both in silico and phantom experiments were performed. The phantom experiments were performed on a Trilogy Varian linac and a HexaMotion programmable motion platform. High and low modulation VMAT plans for lung and prostate cancer cases were used along with eight patient-measured organ-specific trajectories. For both MLC leaf-fitting algorithms, the plans were run with their corresponding patient trajectories. To compare algorithms, the average exposure errors, i.e., the difference in shape between ideal and fitted MLC leaves by the algorithm, plan complexity and system latency of each experiment were calculated. Results: Comparison of exposure errors for the in silico and phantom experiments showed minor differences between the two algorithms. The average exposure errors for in silico experiments with low/high plan complexity were 0.66/0.88 cm 2 for direct optimization and 0.66/0.88 cm 2 for piecewise optimization, respectively. The average exposure errors for the phantom experiments with low/high plan complexity were 0.73/1.02 cm 2 for direct and 0.73/1.02 cm 2 for piecewise optimization, respectively. The measured latency for the direct optimization was 226 ± 10 ms and for the piecewise algorithm was 228 ± 10 ms. In silico and phantom exposure errors quantified for each treatment plan demonstrated that the exposure errors from the high plan complexity (0.96 cm 2 mean, 2.88 cm 2 95% percentile) were all significantly different from the low plan complexity (0.70 cm 2 mean, 2.18 cm 2 95% percentile) (P

© 2019 American Association of Physicists in Medicine Purpose: Real-time image-guided adaptive radiation therapy (IGART) requires accurate marker segmentation to resolve three-dimensional (3D) motion based on two-dimensional (2D) fluoroscopic images. Most common marker segmentation methods require prior knowledge of marker properties to construct a template. If marker properties are not known, an additional learning period is required to build the template which exposes the patient to an additional imaging dose. This work investigates a deep learning-based fiducial marker classifier for use in real-time IGART that requires no prior patient-specific data or additional learning periods. The proposed tracking system uses convolutional neural network (CNN) models to segment cylindrical and arbitrarily shaped fiducial markers. Methods: The tracking system uses a tracking window approach to perform sliding window classification of each implanted marker. Three cylindrical marker training datasets were generated from phantom kilovoltage (kV) and patient intrafraction images with increasing levels of megavoltage (MV) scatter. The cylindrical shaped marker CNNs were validated on unseen kV fluoroscopic images from 12 fractions of 10 prostate cancer patients with implanted gold fiducials. For the training and validation of the arbitrarily shaped marker CNNs, cone beam computed tomography (CBCT) projection images from ten fractions of seven lung cancer patients with implanted coiled markers were used. The arbitrarily shaped marker CNNs were trained using three patients and the other four unseen patients were used for validation. The effects of full training using a compact CNN (four layers with learnable weights) and transfer learning using a pretrained CNN (AlexNet, eight layers with learnable weights) were analyzed. Each CNN was evaluated using a Precision-Recall curve (PRC), the area under the PRC plot (AUC), and by the calculation of sensitivity and specificity. The tracking system was assessed using the validation data and the accuracy was quantified by calculating the mean error, root-mean-square error (RMSE) and the 1st and 99th percentiles of the error. Results: The fully trained CNN on the dataset with moderate noise levels had a sensitivity of 99.00% and specificity of 98.92%. Transfer learning of AlexNet resulted in a sensitivity and specificity of 99.42% and 98.13%, respectively, for the same datasets. For the arbitrarily shaped marker CNNs, the sensitivity was 98.58% and specificity was 98.97% for the fully trained CNN. The transfer learning CNN had a sensitivity and specificity of 98.49% and 99.56%, respectively. The CNNs were successfully incorporated into a multiple object tracking system for both cylindrical and arbitrarily shaped markers. The cylindrical shaped marker tracking had a mean RMSE of 1.6 ± 0.2 pixels and 1.3 ± 0.4 pixels in the x- and y-directions, respectively. The arbitrarily shaped marker tracking had a mean RMSE of 3.0 ± 0.5 pixels and 2.2 ± 0.4 pixels in the x- and y-directions, respectively. Conclusion: With deep learning CNNs, high classification performances on unseen patient images were achieved for both cylindrical and arbitrarily shaped markers. Furthermore, the application of CNN models to intrafraction monitoring was demonstrated using a simple tracking system. The results demonstrate that CNN models can be used to track markers without prior knowledge of the marker properties or an additional learning period.

(Abridged) We describe here the most ambitious survey currently planned in the optical, the Large Synoptic Survey Telescope (LSST). A vast array of science will be enabled by a single wide-deep-fast sky survey, and LSST will have unique survey capability in the faint time domain. The LSST design is driven by four main science themes: probing dark energy and dark matter, taking an inventory of the Solar System, exploring the transient optical sky, and mapping the Milky Way. LSST will be a wide-field ground-based system sited at Cerro Pach\'{o}n in northern Chile. The telescope will have an 8.4 m (6.5 m effective) primary mirror, a 9.6 deg$^2$ field of view, and a 3.2 Gigapixel camera. The standard observing sequence will consist of pairs of 15-second exposures in a given field, with two such visits in each pointing in a given night. With these repeats, the LSST system is capable of imaging about 10,000 square degrees of sky in a single filter in three nights. The typical 5$\sigma$ point-source depth in a single visit in $r$ will be $\sim 24.5$ (AB). The project is in the construction phase and will begin regular survey operations by 2022. The survey area will be contained within 30,000 deg$^2$ with $\delta, Comment: 57 pages, 32 color figures, version with high-resolution figures available from https://www.lsst.org/overview

It is not always apparent when the optimal IMRT/VMAT plan for post-prostatectomy radiotherapy (PPRT) has been achieved. Individual variation in patient anatomy is a key contributor. This study aimed to create a model to determine the probability of rectum and/or bladder doses exceeding planning goals based on individual patient anatomy prior to planning.The IMRT/VMAT PPRT plans from 200 men were randomly and evenly allocated into the Training Cohort and the Validation Cohort. Univariate and multivariate analysis of the Training Cohort identified variables which impacted bladder and rectal doses. Significant variables were included in a Classification and Regression Tree (CART) analysis. The resultant algorithm was then applied to the Validation Cohort.On multivariate analysis, prescription dose; bladder and rectal volume; lymph node treatment; and percentage of bladder and rectal overlap with the PTV were significant variables. Following CART analysis, the overlap volume (OV) for both rectum (rectum overlap 20%) and bladder (bladder overlap 20%) were the key drivers of meeting planning goals. Treatment of pelvic lymph nodes was included as the secondary driving factor for bladder (but not rectal) dose. On application to the Validation Cohort, CART analysis predicted 95% and 87% of patients who would meet bladder and rectal planning goals respectively.A simple algorithm was developed to predict plan quality by using the OV of the bladder and rectum with the PTV. This algorithm may be used a priori to assess the planning process in the context of variable anatomy, and to optimise planning quality and efficiency.

Promoter-proximal pausing and divergent transcription at promoters and enhancers, which are prominent features in animals, have been reported to be absent in plants based on a study of Arabidopsis thaliana. Here, our PRO-Seq analysis in cassava (Manihot esculenta) identified peaks of transcriptionally-engaged RNA polymerase II (Pol2) at both 5’ and 3’ ends of genes, consistent with paused or slowly-moving Pol2, and divergent transcription at potential intragenic enhancers. A full genome search for bi-directional transcription using an algorithm for enhancer detection developed in mammals (dREG) identified many enhancer candidates. These sites show distinct patterns of methylation and nucleotide variation based on genomic evolutionary rate profiling characteristic of active enhancers. Maize GRO-Seq data showed RNA polymerase occupancy at promoters and enhancers consistent with cassava but not Arabidopsis. Furthermore, putative enhancers in maize identified by dREG significantly overlapped with sites previously identified on the basis of open chromatin, histone marks, and methylation. We show that SNPs within these divergently transcribed intergenic regions predict significantly more variation in fitness and root composition than SNPs in chromosomal segments randomly ascertained from the same intergenic distribution, suggesting a functional importance of these sites on cassava. The findings shed new light on plant transcription regulation and its impact on development and plasticity.

PURPOSE: To report on the primary and secondary outcomes of a prospective clinical trial of electromagnetic-guided multileaf collimator (MLC) tracking radiation therapy for prostate cancer.METHODS AND MATERIALS: Twenty-eight men with prostate cancer were treated with electromagnetic-guided MLC tracking with volumetric modulated arc therapy. A total of 858 fractions were delivered, with the dose per fraction ranging from 2 to 13.75 Gy. The primary outcome was feasibility, with success determined if >95% of fractions were successfully delivered. The secondary outcomes were (1) the improvement in beam-target geometric alignment, (2) the improvement in dosimetric coverage of the prostate and avoidance of critical structures, and (3) no acute grade ≥3 genitourinary or gastrointestinal toxicity.RESULTS: All 858 planned fractions were successfully delivered with MLC tracking, demonstrating the primary outcome of feasibility (P < .001). MLC tracking improved the beam-target geometric alignment from 1.4 to 0.90 mm (root-mean-square error). MLC tracking improved the dosimetric coverage of the prostate and reduced the daily variation in dose to critical structures. No acute grade ≥3 genitourinary or gastrointestinal toxicity was observed.CONCLUSIONS: Electromagnetic-guided MLC tracking radiation therapy for prostate cancer is feasible. The patients received improved geometric targeting and delivered dose distributions that were closer to those planned than they would have received without electromagnetic-guided MLC tracking. No significant acute toxicity was observed.

Purpose: The aim of this study was to determine the genetic cause of autosomal dominant non-syndromic hearing loss segregating in a multi-generational family. Methods: Clinical examination, genome-wide linkage analysis, and exome sequencing were carried out on the family. Results: Affected individuals presented with early-onset progressive mild hearing impairment with a fairly flat, gently downsloping or U-shaped audiogram configuration. Detailed clinical examination excluded any additional symptoms. Linkage analysis detected an interval on chromosome 1p21 with a LOD score of 8.29: designated locus DFNA37. Exome sequencing identified a novel canonical acceptor splice-site variant c.652–2A>C in the COL11A1 gene within the DFNA37 locus. Genotyping of all 48 family members confirmed segregation of this variant with the deafness phenotype in the extended family. The c.652–2A>C variant is novel, highly conserved, and confirmed in vitro to alter RNA-splicing. Conclusion: We have identified COL11A1 as the gene responsible for deafness at the DFNA37 locus. Previously, COL11A1 was solely associated with Marshall and Stickler syndromes. This study expands its phenotypic spectrum to include non-syndromic deafness. The implications of this discovery are valuable in the clinical diagnosis, prognosis, and treatment of patients with COL11A1 pathogenic variants.

© 2018 American Association of Physicists in Medicine Purpose: Fixed beam radiotherapy systems utilize couch movement and rotation instead of gantry rotation in order to simplify linear accelerator design. We investigate the ability to deliver fixed beam treatments with the same level of clinical accuracy as conventional (rotating beam) treatments using real-time image guidance to maintain this accuracy in the presence of rigid target motion. Methods: A prototype fixed beam radiotherapy system was built using a standard linac with the beam fixed in the vertical position and a computer controlled rotation stage that rotated a rigid phantom about the superior–inferior axis. Kilovoltage Intrafraction Monitoring (KIM) and real-time beam adaptation with MLC tracking was applied to a five-field IMRT treatment plan with motion introduced to the phantom. The same IMRT treatment was also delivered with real-time adaptation using the conventional rotating beam geometry. Film dosimetry was used to measure the dose delivered with a fixed beam compared to a rotating beam, as well as to compare treatments delivered with and without real-time adaptation. Results: The dose distributions were found to be equivalent between the fixed beam and rotating beam geometry for real-time adaptive radiotherapy using KIM and MLC tracking beam adaptation. Gamma analysis on the films showed agreement >98% using a 2%/2 mm criteria with adaptation for static shifts and periodic motion. Conclusions: Fixed beam treatments with real-time beam adaptation are dosimetrically equivalent to conventional treatments with a rotating beam, even in the presence of rigid target motion. This suggests that, for a rigid target, the high clinical accuracy of real-time adaptive radiotherapy can be achieved with simpler beam geometry.

Purpose As the predominant driver of respiratory motion, the diaphragm represents a key surrogate for motion management during the irradiation of thoracic cancers. Existing approaches to diaphragm tracking often produce phase-based estimates, suffer from lateral side failures or are not executable in real-time. In this paper, we present an algorithm that continuously produces real-time estimates of three-dimensional (3D) diaphragm position using kV images acquired on a standard linear accelerator. Methods Patient-specific 3D diaphragm models were generated via automatic segmentation on end-exhale four-dimensional-computed tomography (4D-CT) images. The estimated trajectory of diaphragmatic motion, referred to as the principal motion vector, was obtained by registering end-exhale to end-inhale 4D-CT images. Two-dimensional (2D) diaphragm masks were generated by forward-projecting 3D models over the complement of angles spanned during kV image acquisition. For each kV image, diaphragm position was determined by shifting angle-matched 2D masks along the principal motion vector and selecting the position of highest contrast on a vertical difference image. Retrospective analysis was performed using 22 cone beam CT (CBCT) image sequences for six lung cancer patients across two datasets. Given the current lack of objective ground truth for diaphragm position, our algorithm was evaluated by examining its ability to track implanted markers. Simple linear regression was used to construct 3D marker motion models and estimation errors were computed as the difference between estimated and ground truth marker positions. Additionally, Pearson correlation coefficients were used to characterize diaphragm-marker correlation. Results The mean ± standard deviation of the estimation errors across all image sequences was -0.1 ± 0.7 mm, -0.1 ± 1.8 mm and 0.2 ± 1.4 mm in the LR, SI, and AP directions respectively. The 95th percentile of the absolute errors ranged over 0.5-3.1 mm, 1.6-6.7 mm, and 1.2-4.0 mm in the LR, SI, and AP directions, respectively. The mean ± standard deviation of diaphragm-marker correlations over all image sequences was -0.07 ± 0.57, 0.67 ± 0.49, and 0.29 ± 0.52 in the LR, SI, and AP directions, respectively. Diaphragm-marker correlation was observed to be highly dependent on marker position. Mean correlation along the SI axis ranged over 0.91-0.93 for markers situated in the lower lobes of the lung, while correlations ranging over -0.51-0.79 were observed for markers situated in the upper and middle lobes. Conclusion This work advances a new approach to real-time direct diaphragm tracking in realistic treatment scenarios. By achieving continuous estimates of diaphragmatic motion, the proposed method has applications for both markerless tumor tracking and respiratory binning in 4D-CBCT.

© 2018 Elsevier B.V. Purpose: Until now, real-time image guided adaptive radiation therapy (IGART) has been the domain of dedicated cancer radiotherapy systems. The purpose of this study was to clinically implement and investigate real-time IGART using a standard linear accelerator. Materials/methods: We developed and implemented two real-time technologies for standard linear accelerators: (1) Kilovoltage Intrafraction Monitoring (KIM) that finds the target and (2) multileaf collimator (MLC) tracking that aligns the radiation beam to the target. Eight prostate SABR patients were treated with this real-time IGART technology. The feasibility, geometric accuracy and the dosimetric fidelity were measured. Results: Thirty-nine out of forty fractions with real-time IGART were successful (95% confidence interval 87–100%). The geometric accuracy of the KIM system was −0.1 ± 0.4, 0.2 ± 0.2 and −0.1 ± 0.6 mm in the LR, SI and AP directions, respectively. The dose reconstruction showed that real-time IGART more closely reproduced the planned dose than that without IGART. For the largest motion fraction, with real-time IGART 100% of the CTV received the prescribed dose; without real-time IGART only 95% of the CTV would have received the prescribed dose. Conclusion: The clinical implementation of real-time image-guided adaptive radiotherapy on a standard linear accelerator using KIM and MLC tracking is feasible. This achievement paves the way for real-time IGART to be a mainstream treatment option.

Hatchling turtles typically emerge from underground nests in groups, so the nest escape process may represent another example of animals sharing a task (in this case, digging out of a nest) to save on individual energy expenditure. Previous studies have reported the energetic cost of embryonic development across chelonian taxa, but none has quantified the extra amount of energy needed to escape the nest. Brisbane river turtle (Emydura macquarii signata) hatchlings were found to fuel this activity by using approximately 50 % of their residual yolk energy content. An open-flow respirometry system was used to quantify the effect of clutch size on an individual’s energetic cost while digging out of the nest. The energetic cost of nest escaping 15 cm upward in the fine moist sand was calculated to be between 0.34 and 2.32 kJ per individual depending upon the number of hatchlings digging together. The energetic cost decreased as the number of individuals digging together increased and thus supports the ‘social facilitation’ hypothesis which suggests hatchlings cooperate to share the workload of digging out of the nest amongst clutch mates to reduce individual energy expenditure. The reduced energetic cost associated with large cohorts was chiefly caused by the shorter time taken to dig out of the nest by larger numbers of individuals. We conclude that synchronous digging activity of many individuals during nest escape evolved not only to facilitate quicker nest emergence but also reduce the energetic cost to individuals.

Temperature is arguably the most important abiotic factor influencing the life history of ectotherms. It limits survival and affects all physiological and metabolic processes, including energy and nutrient procurement and processing, development and growth rates, locomotion ability and ultimately reproductive success. However, the influence of temperature on the energetic cost of development has not been thoroughly investigated. We show that in the diamondback moth [Plutella xylostellaL. (Lepidoptera: Plutellidae)] rearing temperature (range10–30°C) affected growth and development rates, the energetic cost of development and fecundity. Rearing at lower temperatures increased development times and slowed growth rate, but resulted in larger adult mass. Fecundity was lowest at 10°C, highest at 15°C and intermediate at temperatures of 20°C and above. At a given rearing temperature fecundity was correlated with pupal mass and most eggs were laid on the first day of oviposition, there was no correlation between total eggs laid and adult longevity. The highest production cost was incurred at 10°C; this decreased with increasing temperature, was minimized in the range 20–25°C, and then increased again at 30°C. These minimized production costs occurred at temperatures close to the intrinsic optimum temperature for this species and may reflect the rearing temperature for optimal fitness. Thus at sub-optimal temperatures greater food resources are required during the development period. Predicted increased temperatures at the margins of the current core distribution ofP. xylostellacould ameliorate current seasonal effects on fecundity, thereby increasing the probability of winter survival leading to more resilient range expansion and an increased probability of pest outbreaks.

Background Countries with culturally accepted consanguinity provide a unique resource for the study of rare recessively inherited genetic diseases. Although hereditary hearing loss (HHL) is not uncommon, it is genetically heterogeneous, with over 85 genes causally implicated in non-syndromic hearing loss (NSHL). This heterogeneity makes many gene-specific types of NSHL exceedingly rare. We sought to define the spectrum of autosomal recessive HHL in Iran by investigating both common and rarely diagnosed deafness-causing genes. Design Using a custom targeted genomic enrichment (TGE) panel, we simultaneously interrogated all known genetic causes of NSHL in a cohort of 302 GJB2 -negative Iranian families. Results We established a genetic diagnosis for 67% of probands and their families, with over half of all diagnoses attributable to variants in five genes: SLC26A4 , MYO15A , MYO7A , CDH23 and PCDH15 . As a reflection of the power of consanguinity mapping, 26 genes were identified as causative for NSHL in the Iranian population for the first time. In total, 179 deafness-causing variants were identified in 40 genes in 201 probands, including 110 novel single nucleotide or small insertion–deletion variants and three novel CNV. Several variants represent founder mutations. Conclusion This study attests to the power of TGE and massively parallel sequencing as a diagnostic tool for the evaluation of hearing loss in Iran, and expands on our understanding of the genetics of HHL in this country. Families negative for variants in the genes represented on this panel represent an excellent cohort for novel gene discovery.

Recent advances in targeted genomic enrichment with massively parallel sequencing (TGE+MPS) have made comprehensive genetic testing for non-syndromic hearing loss (NSHL) possible. After excluding NSHL subjects with causative mutations in GJB2 and the MT-RNR1 (1555A>G) variant by Sanger sequencing, we completed TGE+MPS on 194 probands with presumed NSHL identified across Japan. We used both publicly available minor allele frequency (MAF) datasets and ethnic-specific MAF filtering against an in-house database of 200 normal-hearing Japanese controls. Ethnic-specific MAF filtering allowed us to re-categorize as common 203 variants otherwise annotated as rare or novel in non-Japanese ethnicities. This step minimizes false-positive results and improves the annotation of identified variants. Causative variants were identified in 27% of probands with solve rates of 35%, 35% and 19% for dominant, recessive and sporadic NSHL, respectively. Mutations in MYO15A and CDH23 follow GJB2 as the frequent causes of recessive NSHL; copy number variations in STRC are a major cause of mild-to-moderate NSHL. Ethnic-specific filtering by allele frequency is essential to optimize the interpretation of genetic data.

Deafness is the most frequent sensory disorder. With over 90 genes and 110 loci causally implicated in non-syndromic hearing loss, it is phenotypically and genetically heterogeneous. Here, we investigate the genetic etiology of deafness in four families of Iranian origin segregating autosomal recessive non-syndromic hearing loss (ARNSHL). We used a combination of linkage analysis, homozygosity mapping, and a targeted genomic enrichment platform to simultaneously screen 90 known deafness-causing genes for pathogenic variants. Variant segregation was confirmed by Sanger sequencing. Linkage analysis and homozygosity mapping showed segregation with the DFNB57 locus on chromosome 10 in two families. Targeted genomic enrichment with massively parallel sequencing identified causal variants in PDZD7: a homozygous missense variant (p.Gly103Arg) in one family and compound heterozygosity for missense (p.Met285Arg) and nonsense (p.Tyr500Ter) variants in the second family. Screening of two additional families identified two more variants: (p.Gly228Arg) and (p.Gln526Ter). Variant segregation with the hearing loss phenotype was confirmed in all families by Sanger sequencing. The missense variants are predicted to be deleterious, and the two nonsense mutations produce null alleles. This report is the first to show that mutations in PDZD7 cause ARNSHL, a finding that offers addition insight into the USH2 interactome. We also describe a novel likely disease-causing mutation in CIB2 and illustrate the complexity associated with gene identification in diseases that exhibit large genetic and phenotypic heterogeneity.

Purpose: The purpose of this study was 2-fold. One purpose was to develop an automated, streamlined quality assurance (QA) program for use by multiple centers. The second purpose was to evaluate machine performance over time for multiple centers using linear accelerator (Linac) log files and electronic portal images. The authors sought to evaluate variations in Linac performance to establish as a reference for other centers. Methods: The authors developed analytical software tools for a QA program using both log files and electronic portal imaging device (EPID) measurements. The first tool is a general analysis tool which can read and visually represent data in the log file. This tool, which can be used to automatically analyze patient treatment or QA log files, examines the files for Linac deviations which exceed thresholds. The second set of tools consists of a test suite of QA fields, a standard phantom, and software to collect information from the log files on deviations from the expected values. The test suite was designed to focus on the mechanical tests of the Linac to include jaw, MLC, and collimator positions during static, IMRT, and volumetric modulated arc therapy delivery. A consortium of eight institutions delivered the test suitemore » at monthly or weekly intervals on each Linac using a standard phantom. The behavior of various components was analyzed for eight TrueBeam Linacs. Results: For the EPID and trajectory log file analysis, all observed deviations which exceeded established thresholds for Linac behavior resulted in a beam hold off. In the absence of an interlock-triggering event, the maximum observed log file deviations between the expected and actual component positions (such as MLC leaves) varied from less than 1% to 26% of published tolerance thresholds. The maximum and standard deviations of the variations due to gantry sag, collimator angle, jaw position, and MLC positions are presented. Gantry sag among Linacs was 0.336 ± 0.072 mm. The standard deviation in MLC position, as determined by EPID measurements, across the consortium was 0.33 mm for IMRT fields. With respect to the log files, the deviations between expected and actual positions for parameters were small (

How tiny insects respond to prevailing rainfall events to protect themselves from water droplets is poorly known. If such insects could anticipate impending rainfall and take shelter to avoid being hit by rain drops their chances of surviving such events would be increased. Some insect species can detect atmospheric pressure changes associated with rainfall events and respond accordingly. Laboratory experiments were conducted on the flower thrips Frankliniella schultzei to discern whether they adjust their behavior in response to atmospheric pressure change. F. schultzei mating frequency and shelter seeking behaviors were assessed under a range of different atmospheric pressure regimes including, a rapid change in atmospheric pressure (50 hPa/h), designed to simulate atmospheric changes associated with cyclonic conditions, and a slower rate of change (20 hPa/h), that is commonly associated with rainfall. The mating frequency of the thrips was significantly reduced in response to rapid changes in atmospheric pressure, whereas the slower rate had no such effect. These results indicate that F. schultzei is capable of detecting atmospheric pressure changes. The shelter seeking behaviors of each sex were assessed under the same two atmospheric pressure regimes. The thrips did not seek shelter significantly more or less under either pressure regime. Field experiments are now required to clarify if the ability to detect pressure is used by these thrips to protect themselves before the onset of rainfall events.