Deep learning based linear energy transfer calculation for proton therapy

OBJECTIVE

This study aims to address the limitations of traditional methods for calculating linear energy transfer (LET), a critical component in assessing relative biological effectiveness (RBE). Currently, Monte Carlo (MC) simulation, the gold-standard for accuracy, is resource-intensive and slow for dose optimization, while the speedier analytical approximation has compromised accuracy. Our objective was to prototype a deep-learning-based model for calculating dose-averaged LET (LETd) using patient anatomy and dose-to-water (DW) data, facilitating real-time biological dose evaluation and LET optimization within proton treatment planning systems. Approach: 275 4-field prostate proton Stereotactic Body Radiotherapy (SBRT) plans were analyzed, rendering a total of 1100 fields. Those were randomly split into 880, 110, and 110 fields for training, validation, and testing. A 3D Cascaded UNet model, along with data processing and inference pipelines, was developed to generate patient-specific LETd distributions from CT images and DW. The accuracy of the LETd of the test dataset was evaluated against MC-generated ground truth through voxel-based mean absolute error (MAE) and gamma analysis. Main Results: The proposed model accurately inferred LETd distributions for each proton field in the test dataset. A single-field LETd calculation took around 100 ms with trained models running on a NVidia A100 GPU. The selected model yielded an average MAE of 0.94±0.14 MeV/cm and a gamma passing rate of 97.4% ± 1.3% when applied to the test dataset, with the largest discrepancy at the edge of fields where the dose gradient was the largest and counting statistics was the lowest. Significance: This study demonstrates that deep-learning-based models can efficiently calculate LETd with high accuracy as a fast-forward approach. The model shows great potential to be utilized for optimizing the RBE of proton treatment plans. Future efforts will focus on enhancing the model's performance and evaluating its adaptability to different clinical scenarios.

Optimizing Gantry Breakpoint Angles in Proton Therapy: Enhancing Efficiency and Patient Experience

Purpose

The breakpoint for a 360° radiotherapy gantry is typically positioned at 180°. This arbitrary setting has not been systematically evaluated for efficiency and may cause redundant gantry rotation and extended setup times. Our study aimed to identify an optimal gantry breakpoint angle for a full-gantry proton therapy system, with the goal of minimizing gantry movement.

Materials and Methods

We analyzed 70 months of clinically delivered proton therapy plans (9152 plans, 131 883 fractions), categorizing them by treatment site and mapping the fields from a partial-gantry to full-gantry orientation. For each delivered fraction, we computed the minimum total gantry rotation angle as a function of gantry breakpoint position, which was varied between 0° and 360° in 1° steps. This analysis was performed separately within the entire plan cohort and individual treatment sites, both with and without the capability of over-rotating 10° past the breakpoint from either direction (20° overlap). The optimal gantry breakpoint was identified as one which resulted in a low average gantry rotation per fraction.

Results

Considering mechanical constraints, 130° was identified as a reasonable balance between increased gantry-rotation efficiency and practical treatment considerations. With a 20° overlap, this selection reduced the average gantry rotation by 41.4° per fraction when compared to the standard 180° breakpoint. Disease site subgroups showed the following reduction in average gantry rotation: gastrointestinal 192.2°, thoracic 56.3°, pediatric 44.9°, genitourinary 19.9°, central nervous system 10.7°, breast 2.8°, and head and neck 0.1°.

Conclusion

For a full-gantry system, a breakpoint of 130° generally outperforms the conventional 180° breakpoint. This reduction is particularly impactful for gastrointestinal, pediatric, and thoracic sites, which constitute a significant proportion of cases at our center. The adjusted breakpoint could potentially streamline patient delivery, alleviate mechanical wear, and enhance treatment precision by reducing the likelihood of patient movement during delivery.

Rotating Gantries Provide Individualized Beam Arrangements for Charged Particle Therapy

PURPOSE

This study evaluates beam angles used to generate highly individualized proton therapy treatment plans for patients eligible for carbon ion radiotherapy (CIRT).

METHODS AND MATERIALS

We retrospectively evaluated patients treated with pencil beam scanning intensity modulated proton therapy from 2015 to 2020 who had indications for CIRT. Patients were treated with a 190° rotating gantry with a robotic patient positioning system. Treatment plans were individualized to provide maximal prescription dose delivery to the tumor target volume while sparing organs at risk. The utilized beam angles were grouped, and anatomic sites with at least 10 different beam angles were sorted into histograms.

RESULTS

A total of 467 patients with 484 plans and 1196 unique beam angles were evaluated and characterized by anatomic treatment site and the number of beam angles utilized. The most common beam angles used were 0° and 180°. A wide range of beam angles were used in treating almost all anatomic sites. Only esophageal cancers had a predominantly unimodal grouping of beam angles. Pancreas cancers showed a modest grouping of beam angles.

CONCLUSIONS

The wide distribution of beam angles used to treat CIRT-eligible patients suggests that a rotating gantry is optimal to provide highly individualized beam arrangements.

Proton Whole-Lung Irradiation: Initial Report of Outcomes

PURPOSE

Whole-lung irradiation is typically used in pediatric patients to decrease the risk of future lung metastases, but radiation dose to normal tissue is associated with long-term risks. Proton whole-lung irradiation (PWLI) provides an opportunity to decrease radiation dose to normal tissue and potentially decrease late toxicity.

METHODS AND MATERIALS

This retrospective study included patients treated with spot-scanning PWLI at a single institution. Toxicity and oncologic outcomes were reviewed. Intensity modulated radiation therapy (IMRT) plans were created prospectively or retrospectively for dosimetric comparisons. Simple paired t tests were performed to assess differences between IMRT and PWLI dosimetric parameters.

RESULTS

Twelve patients treated with PWLI were included in this study. Median age was 15 years (range, 3-34). Most (75%) had Ewing sarcoma. Most (92%) received 15 Gy in 10 fractions PWLI, and 3 (25%) received a focal pulmonary boost. Median follow-up was 16.5 months (range, 0-40.4 months). At last follow-up, 1 patient died of disease, while 11 were still alive (7 without disease, 4 with ongoing disease). During and immediately after treatment, 5 patients developed fatigue, 2 patients developed cough, and 1 patient developed nausea. Each treatment-related adverse event was Common Terminology Criteria for Adverse Events (version 5.0) grade 1 and resolved within 3 weeks of treatment completion. No patients have experienced clinical or radiographic pneumonitis or evidence of clinically apparent cardiac toxicity. Compared with IMRT plans, PWLI decreased mean dose to the heart, coronary artery, cardiac valve, left ventricle, aorta, breast, esophagus, kidney, liver, pancreas, thyroid, stomach, and spleen (all P < .001), without sacrificing target coverage.

CONCLUSIONS

PWLI is feasible to deliver, decreases dose to normal tissue compared with IMRT, and appears to be well-tolerated. PWLI provides potential for decreased late toxicity and merits further investigation.

New school technology meets old school technique: Intensity modulated proton therapy and laparoscopic pelvic sling facilitate safe and efficacious treatment of pelvic sarcoma

Purpose

Small bowel tolerance may be dose-limiting in the management of some pelvic and abdominal malignancies with curative-intent radiation therapy. Multiple techniques previously have been attempted to exclude the small bowel from the radiation field, including the surgical insertion of an absorbable mesh to serve as a temporary pelvic sling. This case highlights a clinically meaningful application of this technique with modern radiation therapy.

Methods and Materials

A patient with locally invasive, unresectable high-grade sarcoma of the right pelvic vasculature was evaluated for definitive radiation therapy. The tumor immediately abutted the small bowel. The patient underwent laparoscopic placement of a mesh sling to retract the abutting small bowel and subsequently completed intensity modulated proton therapy.

Results

The patient tolerated the mesh insertion procedure and radiation therapy well with no significant toxic effects. The combination approach achieved excellent dose metrics, and the patient has no evidence of progression 14 months out from treatment.

Conclusions

The combination of mesh as a pelvic sling and proton radiation therapy enabled the application of a curative dose of radiation therapy and should be considered for patients in need of curative-intent radiation when the bowel is in close proximity to the target.

Nuclear Fragmentation Imaging for Carbon-Ion Radiation Therapy Monitoring: an In Silico Study

Purpose

This article presents an in vivo imaging technique based on nuclear fragmentation of carbon ions in irradiated tissues for potential real-time monitoring of carbon-ion radiation therapy (CIRT) treatment delivery and quality assurance purposes in clinical settings.

Materials and Methods

A proof-of-concept imaging and monitoring system (IMS) was devised to implement the technique. Monte Carlo simulations were performed for a prospective pencil-beam scanning CIRT nozzle. The development IMS benchmark considered a 5×5-cm² pixelated charged-particle detector stack positioned downstream from a target phantom and list-mode data acquisition. The abundance and production origins, that is, vertices, of the detected fragments were studied. Fragment trajectories were approximated by straight lines and a beam back-projection algorithm was built to reconstruct the vertices. The spatial distribution of the vertices was then used to determine plan relevant markers.

Results

The IMS technique was applied for a simulated CIRT case, a primary brain tumor. Four treatment plan monitoring markers were conclusively recovered: a depth dose distribution correlated profile, ion beam range, treatment target boundaries, and the beam spot position. Promising millimeter-scale (3-mm, ≤10% uncertainty) beam range and submillimeter (≤0.6-mm precision for shifts <3 cm) beam spot position verification accuracies were obtained for typical therapeutic energies between 150 and 290 MeV/u.

Conclusions

This work demonstrated a viable online monitoring technique for CIRT treatment delivery. The method's strong advantage is that it requires few signal inputs (position and timing), which can be simultaneously acquired with readily available technology. Future investigations will probe the technique's applicability to motion-sensitive organ sites and patient tissue heterogeneities. In-beam measurements with candidate detector-acquisition systems are ultimately essential to validate the IMS benchmark performance and subsequent deployment in the clinic.

Intensity Modulated Proton Therapy for Hepatocellular Carcinoma: Initial Clinical Experience

Purpose

Our purpose was to assess the safety and efficacy of intensity modulated proton therapy (IMPT) for the treatment of hepatocellular carcinoma (HCC).

Methods and Materials

A retrospective review was conducted on all patients who were treated with IMPT for HCC with curative intent from June 2015 to December 2018. All patients had fiducials placed before treatment. Inverse treatment planning used robust optimization with 2 to 3 beams. The majority of patients were treated in 15 fractions (n = 30, 81%, 52.5-67.5 Gy, relative biological effectiveness), whereas the remainder were treated in 5 fractions (n = 7, 19%, 37.5-50 Gy, relative biological effectiveness). Daily image guidance consisted of orthogonal kilovoltage x-rays and use of a 6° of freedom robotic couch. Outcomes (local control, progression free survival, and overall survival) were determined using Kaplan-Meier methods.

Results

Thirty-seven patients were included. The median follow-up for living patients was 21 months (Q1-Q3, 17-30 months). Pretreatment Child-Pugh score was A5-6 in 70% of patients and B7-9 in 30% of patients. Nineteen patients had prior liver directed therapy for HCC before IMPT. Eight patients (22%) required a replan during treatment, most commonly due to inadequate clinical target volume coverage. One patient (3%) experienced a grade 3 acute toxicity (pain) with no recorded grade 4 or 5 toxicities. An increase in Child-Pugh score by ≥ 2 within 3 months of treatment was observed in 6 patients (16%). At 1 year, local control was 94%, intrahepatic control was 54%, progression free survival was 35%, and overall survival was 78%.

Conclusions

IMPT is safe and feasible for treatment of HCC.

The role of Cytochrome b6f in the control of steady-state photosynthesis: a conceptual and quantitative model

Here, we present a conceptual and quantitative model to describe the role of the Cytochrome [Formula: see text] complex in controlling steady-state electron transport in [Formula: see text] leaves. The model is based on new experimental methods to diagnose the maximum activity of Cyt [Formula: see text] in vivo, and to identify conditions under which photosynthetic control of Cyt [Formula: see text] is active or relaxed. With these approaches, we demonstrate that Cyt [Formula: see text] controls the trade-off between the speed and efficiency of electron transport under limiting light, and functions as a metabolic switch that transfers control to carbon metabolism under saturating light. We also present evidence that the onset of photosynthetic control of Cyt [Formula: see text] occurs within milliseconds of exposure to saturating light, much more quickly than the induction of non-photochemical quenching. We propose that photosynthetic control is the primary means of photoprotection and functions to manage excitation pressure, whereas non-photochemical quenching functions to manage excitation balance. We use these findings to extend the Farquhar et al. (Planta 149:78-90, 1980) model of [Formula: see text] photosynthesis to include a mechanistic description of the electron transport system. This framework relates the light captured by PS I and PS II to the energy and mass fluxes linking the photoacts with Cyt [Formula: see text], the ATP synthase, and Rubisco. It enables quantitative interpretation of pulse-amplitude modulated fluorometry and gas-exchange measurements, providing a new basis for analyzing how the electron transport system coordinates the supply of Fd, NADPH, and ATP with the dynamic demands of carbon metabolism, how efficient use of light is achieved under limiting light, and how photoprotection is achieved under saturating light. The model is designed to support forward as well as inverse applications. It can either be used in a stand-alone mode at the leaf-level or coupled to other models that resolve finer-scale or coarser-scale phenomena.

Crustal processes sustain Arctic abiotic gas hydrate and fluid flow systems

The Svyatogor Ridge and surroundings, located on the sediment-covered western flank of the Northern Knipovich Ridge, host extensive gas hydrate and related fluid flow systems. The fluid flow system here manifests in the upper sedimentary sequence as gas hydrates and free gas, indicated by bottom simulating reflections (BSRs) and amplitude anomalies. Using 2D seismic lines and bathymetric data, we map tectonic features such as faults, crustal highs, and indicators of fluid flow processes. Results indicate a strong correlation between crustal faults, crustal highs and fluid accumulations in the overlying sediments, as well as an increase in geothermal gradient over crustal faults. We conclude here that gas generated during the serpentinization of exhumed mantle rocks drive the extensive occurrence of gas hydrate and fluid flow systems in the region and transform faults act as an additional major pathway for fluid circulation.

Optimization of motion management parameters in a synchrotron-based spot scanning system

PURPOSE

To quantify the effects of combining layer-based repainting and respiratory gating as a strategy to mitigate the dosimetric degradation caused by the interplay effect between a moving target and dynamic spot-scanning proton delivery.

METHODS

An analytic routine modeled three-dimensional dose distributions of pencil-beam proton plans delivered to a moving target. Spot positions and weights were established for a single field to deliver 100 cGy to a static, 15-cm deep, 3-cm radius spherical clinical target volume with a 1-cm isotropic internal target volume expansion. The interplay effect was studied by modeling proton delivery from a clinical synchrotron-based spot scanning system and respiratory target motion, patterned from surrogate patient breathing traces. Motion both parallel and orthogonal to the beam scanning direction was investigated. Repainting was modeled using a layer-based technique. For each of 13 patient breathing traces, the dose from 20 distinct delivery schemes (combinations of four gate window amplitudes and five repainting techniques) was computed. Delivery strategies were inter-compared based on target coverage, dose homogeneity, high dose spillage, and delivery time.

RESULTS

Notable degradation and variability in plan quality were observed for ungated delivery. Decreasing the gate window reduced this variability and improved plan quality at the expense of longer delivery times. Dose deviations were substantially greater for motion orthogonal to the scan direction when compared with parallel motion. Repainting coupled with gating was effective at partially restoring dosimetric coverage at only a fraction of the delivery time increase associated with very small gate windows alone. Trends for orthogonal motion were similar, but more complicated, due to the increased severity of the interplay.

CONCLUSIONS

Layer-based repainting helps suppress the interplay effect from intra-gate motion, with only a modest penalty in delivery time. The magnitude of the improvement in target coverage is strongly influenced by individual patient breathing patterns and the tumor motion trajectory.

Clinical implementation of respiratory-gated spot-scanning proton therapy: An efficiency analysis of active motion management

Purpose

The aim of this work is to describe the clinical implementation of respiratory‐gated spot‐scanning proton therapy (SSPT) for the treatment of thoracic and abdominal moving targets. The experience of our institution is summarized, from initial acceptance and commissioning tests to the development of standard clinical operating procedures for simulation, motion assessment, motion mitigation, treatment planning, and gated SSPT treatment delivery.

Materials and methods

A custom respiratory gating interface incorporating the Real‐Time Position Management System (RPM, Varian Medical Systems, Inc., Palo Alto, CA, USA) was developed in‐house for our synchrotron‐based delivery system. To assess gating performance, a motion phantom and radiochromic films were used to compare gated vs nongated delivery. Site‐specific treatment planning protocols and conservative motion cutoffs were developed, allowing for free‐breathing (FB), breath‐holding (BH), or phase‐gating (Ph‐G). Room usage efficiency of BH and Ph‐G treatments was retrospectively evaluated using beam delivery data retrieved from our record and verify system and DICOM files from patient‐specific quality assurance (QA) procedures.

Results

More than 70 patients were treated using active motion management between the launch of our motion mitigation program in October 2015 and the end date of data collection of this study in January 2018. During acceptance procedures, we found that overall system latency is clinically‐suitable for Ph‐G. Regarding room usage efficiency, the average number of energy layers delivered per minute was <10 for Ph‐G, 10‐15 for BH and ≥15 for FB, making Ph‐G the slowest treatment modality. When comparing to continuous delivery measured during pretreatment QA procedures, the median values of BH treatment time were extended from 6.6 to 9.3 min (+48%). Ph‐G treatments were extended from 7.3 to 13.0 min (+82%).

Conclusions

Active motion management has been crucial to the overall success of our SSPT program. Nevertheless, our conservative approach has come with an efficiency cost that is more noticeable in Ph‐G treatments and should be considered in decision‐making.

Automation of routine elements for spot-scanning proton patient-specific quality assurance

PURPOSE

At our institution, all proton patient plans undergo patient-specific quality assurance (PSQA) prior to treatment delivery. For intensity-modulated proton beam therapy, quality assurance is complex and time consuming, and it may involve multiple measurements per field. We reviewed our PSQA workflow and identified the steps that could be automated and developed solutions to improve efficiency.

METHODS

We used the treatment planning system's (TPS) capability to support C# scripts to develop an Eclipse scripting application programming interface (ESAPI) script and automate the preparation of the verification phantom plan for measurements. A local area network (LAN) connection between our measurement equipment and shared database was established to facilitate equipment control, measurement data transfer, and storage. To improve the analysis of the measurement data, a Python script was developed to automatically perform a 2D-3D γ-index analysis comparing measurements in the plane of a two-dimensional detector array with TPS predictions in a water phantom for each acquired measurement.

RESULTS

Device connection via LAN granted immediate access to the plan and measurement information for downstream analysis using an online software suite. Automated scripts applied to verification plans reduced time from preparation steps by at least 50%; time reduction from automating γ-index analysis was even more pronounced, dropping by a factor of 10. On average, we observed an overall time savings of 55% in completion of the PSQA per patient plan.

CONCLUSIONS

The automation of the routine tasks in the PSQA workflow significantly reduced the time required per patient, reduced user fatigue, and frees up system users from routine and repetitive workflow steps allowing increased focus on evaluating key quality metrics.

A Monte-Carlo-based and GPU-accelerated 4D-dose calculator for a pencil beam scanning proton therapy system

PURPOSE

The presence of respiratory motion during radiation treatment leads to degradation of the expected dose distribution, both for target coverage and healthy tissue sparing, particularly for techniques like pencil beam scanning proton therapy which have dynamic delivery systems. While tools exist to estimate this degraded four-dimensional (4D) dose, they typically have one or more deficiencies such as not including the particular effects from a dynamic delivery, using analytical dose calculations, and/or using nonphysical dose-accumulation methods. This work presents a clinically useful 4D-dose calculator that addresses each of these shortcomings.

METHODS

To quickly compute the 4D dose, the three main tasks of the calculator were run on graphics processing units (GPUs). These tasks were (a) simulating the delivery of the plan using measured delivery parameters to distribute the plan amongst 4DCT phases characterizing the patient breathing, (b) using an in-house Monte Carlo simulation (MC) dose calculator to determine the dose delivered to each breathing phase, and (c) accumulating the doses from the various breathing phases onto a single phase for evaluation. The accumulation was performed by individually transferring the energy and mass of dose-grid subvoxels, a technique that models the transfer of dose in a more physically realistic manner. The calculator was run on three test cases, with lung, esophagus, and liver targets, respectively, to assess the various uncertainties in the beam delivery simulation as well as to characterize the dose-accumulation technique.

RESULTS

Four-dimensional doses were successfully computed for the three test cases with computation times ranging from 4-6 min on a server with eight NVIDIA Titan X graphics cards; the most time-consuming component was the MC dose engine. The subvoxel-based dose-accumulation technique produced stable 4D-dose distributions at subvoxel scales of 0.5-1.0 mm without impairing the total computation time. The uncertainties in the beam delivery simulation led to moderate variations of the dose-volume histograms for these cases; the variations were reduced by implementing repainting or phase-gating motion mitigation techniques in the calculator.

CONCLUSIONS

A MC-based and GPU-accelerated 4D-dose calculator was developed to estimate the effects of respiratory motion on pencil beam scanning proton therapy treatments. After future validation, the calculator could be used to assess treatment plans and its quick runtime would make it easily usable in a future 4D-robust optimization system.

Gas hydrate dissociation off Svalbard induced by isostatic rebound rather than global warming

Methane seepage from the upper continental slopes of Western Svalbard has previously been attributed to gas hydrate dissociation induced by anthropogenic warming of ambient bottom waters. Here we show that sediment cores drilled off Prins Karls Foreland contain freshwater from dissociating hydrates. However, our modeling indicates that the observed pore water freshening began around 8 ka BP when the rate of isostatic uplift outpaced eustatic sea-level rise. The resultant local shallowing and lowering of hydrostatic pressure forced gas hydrate dissociation and dissolved chloride depletions consistent with our geochemical analysis. Hence, we propose that hydrate dissociation was triggered by postglacial isostatic rebound rather than anthropogenic warming. Furthermore, we show that methane fluxes from dissociating hydrates were considerably smaller than present methane seepage rates implying that gas hydrates were not a major source of methane to the oceans, but rather acted as a dynamic seal, regulating methane release from deep geological reservoirs.

Methane seepage from continental slopes has been attributed to gas hydrate dissociation induced by anthropogenic bottom water warming. Here, the authors show that hydrates dissociated before the Anthropocene when the isostatic rebound induced by deglaciation of the Arctic ice sheet outpaced eustatic sea-level rise.

Performance of induction module cavity ring-down spectroscopy (IM-CRDS) for measuring δ18 O and δ2 H values of soil, stem, and leaf waters

RATIONALE

Induction module cavity ring-down spectroscopy (IM-CRDS) has been proposed as a rapid and cost-effective alternative to cryogenic vacuum distillation (CVD) and isotope ratio mass spectrometry (IRMS) for the measurement of δ¹⁸ O and δ² H values in matrix-bound waters. In the current study, we characterized the performance of IM-CRDS relative to CVD and IRMS and investigated the mechanisms responsible for differences between the methods.

METHODS

We collected a set of 75 soil, stem, and leaf water samples, and measured the δ¹⁸ O and δ² H values of each sample with four techniques: CVD and IRMS, CVD and CRDS, CVD and IM-CRDS, and IM-CRDS alone. We then calculated the isotopic errors for each of the three CRDS methods relative to CVD and IRMS, and analyzed the relationships among these errors and suites of diagnostic spectral parameters that are indicative of organic contamination.

RESULTS

The IM-CRDS technique accurately assessed the δ¹⁸ O and δ² H values of pure waters, but exhibited progressively increasing errors for soil waters, stem waters, and leaf waters. For soils, the errors were attributable to subsampling of isotopically heterogeneous source material, whereas for stems and leaves, they were attributable to spectral interference. Unexpectedly, the magnitude of spectral interference was higher for the solid samples analyzed directly via IM-CRDS than for those originally extracted via CVD and then analyzed by IM-CRDS.

CONCLUSIONS

There are many types of matrix-bound water samples for which IM-CRDS measurements include significant errors from spectral interference. As a result, spectral analysis and validation should be incorporated into IM-CRDS post-processing procedures. In the future, IM-CRDS performance could be improved through: (i) identification of the compounds that cause spectral interference, and either (ii) modification of the combustion step to completely oxidize these compounds to CO₂ , and/or (iii) incorporation of corrections for these compounds into the spectral fitting models used by the CRDS analyzers. Copyright © 2016 John Wiley & Sons, Ltd.

Investigating the dosimetric impact of seed location uncertainties in Collaborative Ocular Melanoma Study-based eye plaques

PURPOSE

To quantify the dosimetric effects of random and systematic seed position uncertainties in Collaborative Ocular Melanoma Study-based eye plaques.

METHODS AND MATERIALS

An eye plaque dose calculation routine was created using Task Group 43 formalism. A variety of clinical configurations were simulated, including two seed models: (125)I and (103)Pd, three eye plaque sizes, and eight plaque/eye orientations. Dose was calculated at four ocular anatomic sites and three central axis plaque depths. Random seed positional uncertainty was modeled by adding Gaussian random displacements, in one of three seed-motion degrees of freedom, to each seed's nominal coordinate. Distributions of dosimetric outcomes were obtained and fitted after 10(6) randomizations. Similar analysis was performed for deterministic, systematic shifts of the plaque along the eye surface and radially from the globe center.

RESULTS

Random seed placement uncertainties of 0.2-mm root mean square (RMS) (amplitude) produce dose changes that are typically <4% for each degree of freedom (95% confidence interval). Systematic seed placement uncertainties are generally greater than random uncertainty 95% confidence intervals (factor of 0.72-2.15), with the relative magnitudes depending on plaque size and location of interest. Eye plaque dosimetry is most sensitive to seed movement toward the center of the eye. Dosimetric uncertainty also increases with increasing dose gradients, which are typically greatest near the inner sclera, with smaller plaques, and with lower energy radionuclides (e.g., (103)Pd).

CONCLUSIONS

Dosimetric uncertainties due to the random seed positional displacements anticipated in the clinic are expected to be <4% for each degree of freedom in most circumstances.

Stereotactic body radiotherapy for primary and metastatic liver tumors - the Mayo Clinic experience

INTRODUCTION

To better understand the efficacy of liver SBRT we reviewed our prospectively collected institutional SBRT database.

METHODS

Between May 2008 and March 2013, 80 patients with 104 liver lesions received SBRT. The Kaplan-Meier method estimated local control (LC), overall survival (OS). Cox proportional hazards regression models identified factors associated with LC and OS.

RESULTS

The median follow-up for living patients was 38.6 months. Patients had primary (n=17) or metastatic (n=63) tumors. The median tumor size was 2.7 cm (range, 0.6-14.0). The 1 and 4 year rates of LC were 89.4% and 88%, respectively. Colorectal (CRC) metastasis was associated with lower rates of LC (p=0.013). OS at 1 and 4 years was 78% and 25%, respectively. Patients with CRC metastases had higher rates of OS (p=0.03). The occurrence of severe acute and late toxicity was 3.8% and 6.3%, respectively.

CONCLUSIONS

SBRT should be studied in prospective clinical trials compared with other liver-directed treatment modalities.

Heralded state preparation in a superconducting qubit

We demonstrate high-fidelity, quantum nondemolition, single-shot readout of a superconducting flux qubit in which the pointer state distributions can be resolved to below one part in 1000. In the weak excitation regime, continuous measurement permits the use of heralding to ensure initialization to a fiducial state, such as the ground state. This procedure boosts readout fidelity to 93.9% by suppressing errors due to spurious thermal population. Furthermore, heralding potentially enables a simple, fast qubit reset protocol without changing the system parameters to induce Purcell relaxation.

Genomic and functional analysis of Vibrio phage SIO-2 reveals novel insights into ecology and evolution of marine siphoviruses

We report on a genomic and functional analysis of a novel marine siphovirus, the Vibrio phage SIO-2. This phage is lytic for related Vibrio species of great ecological interest including the broadly antagonistic bacterium Vibrio sp. SWAT3 as well as notable members of the Harveyi clade (V.harveyi ATTC BAA-1116 and V.campbellii ATCC 25920). Vibrio phage SIO-2 has a circularly permuted genome of 80598 bp, which displays unusual features. This genome is larger than that of most known siphoviruses and only 38 of the 116 predicted proteins had homologues in databases. Another divergence is manifest by the origin of core genes, most of which share robust similarities with unrelated viruses and bacteria spanning a wide range of phyla. These core genes are arranged in the same order as in most bacteriophages but they are unusually interspaced at two places with insertions of DNA comprising a high density of uncharacterized genes. The acquisition of these DNA inserts is associated with morphological variation of SIO-2 capsid, which assembles as a large (80 nm) shell with a novel T=12 symmetry. These atypical structural features confer on SIO-2 a remarkable stability to a variety of physical, chemical and environmental factors. Given this high level of functional and genomic novelty, SIO-2 emerges as a model of considerable interest in ecological and evolutionary studies.

Quantitative methods for analysing cumulative effects on fish migration success: a review

It is often recognized, but seldom addressed, that a quantitative assessment of the cumulative effects, both additive and non-additive, of multiple stressors on fish survival would provide a more realistic representation of the factors that influence fish migration. This review presents a compilation of analytical methods applied to a well-studied fish migration, a more general review of quantitative multivariable methods, and a synthesis on how to apply new analytical techniques in fish migration studies. A compilation of adult migration papers from Fraser River sockeye salmon Oncorhynchus nerka revealed a limited number of multivariable methods being applied and the sub-optimal reliance on univariable methods for multivariable problems. The literature review of fisheries science, general biology and medicine identified a large number of alternative methods for dealing with cumulative effects, with a limited number of techniques being used in fish migration studies. An evaluation of the different methods revealed that certain classes of multivariable analyses will probably prove useful in future assessments of cumulative effects on fish migration. This overview and evaluation of quantitative methods gathered from the disparate fields should serve as a primer for anyone seeking to quantify cumulative effects on fish migration survival.

Motoneuron programmed cell death in response to proBDNF

Motoneurons (MN) as well as most neuronal populations undergo a temporally and spatially specific period of programmed cell death (PCD). Several factors have been considered to regulate the survival of MNs during this period, including availability of muscle-derived trophic support and activity. The possibility that target-derived factors may also negatively regulate MN survival has been considered, but not pursued. Neurotrophin precursors, through their interaction with p75(NTR) and sortilin receptors have been shown to induce cell death during development and following injury in the CNS. In this study, we find that muscle cells produce and secrete proBDNF. ProBDNF through its interaction with p75(NTR) and sortilin, promotes a caspase-dependent death of MNs in culture. We also provide data to suggest that proBDNF regulates MN PCD during development in vivo.

Soil warming alters nitrogen cycling in a New England forest: implications for ecosystem function and structure

Global climate change is expected to affect terrestrial ecosystems in a variety of ways. Some of the more well-studied effects include the biogeochemical feedbacks to the climate system that can either increase or decrease the atmospheric load of greenhouse gases such as carbon dioxide and nitrous oxide. Less well-studied are the effects of climate change on the linkages between soil and plant processes. Here, we report the effects of soil warming on these linkages observed in a large field manipulation of a deciduous forest in southern New England, USA, where soil was continuously warmed 5°C above ambient for 7 years. Over this period, we have observed significant changes to the nitrogen cycle that have the potential to affect tree species composition in the long term. Since the start of the experiment, we have documented a 45% average annual increase in net nitrogen mineralization and a three-fold increase in nitrification such that in years 5 through 7, 25% of the nitrogen mineralized is then nitrified. The warming-induced increase of available nitrogen resulted in increases in the foliar nitrogen content and the relative growth rate of trees in the warmed area. Acer rubrum (red maple) trees have responded the most after 7 years of warming, with the greatest increases in both foliar nitrogen content and relative growth rates. Our study suggests that considering species-specific responses to increases in nitrogen availability and changes in nitrogen form is important in predicting future forest composition and feedbacks to the climate system.

STUDIES ON THE PATHOGENESIS OF STAPHYLOCOCCAL INFECTION : I. THE EFFECT OF REPEATED SKIN INFECTIONS

The influence of repeated staphylococcal infection of rabbit skin upon the characteristics of the experimentally induced lesion was studied. It was found that the repeated infection was associated with the development of delayed hypersensitivity unaccompanied by the appearance of demonstrable serum antibody. The delayed hypersensitivity to the staphylococcus resulted in an increased infectivity of the organism in skin of the sensitized animal, characterized by intensification of the lesions seen with large bacterial inocula and the induction of abscesses with inocula incapable of producing any lesion in normal rabbit skin. Similarly, the severity of experimentally induced pyoarthrosis was greater in sensitized than in normal rabbits. Induction of delayed hypersensitivity by vaccination of rabbits with washed heat-killed staphylococci resulted in the same increased severity of the infection and an increase in infectivity of the microorganism. In contrast to the observations of cutaneous and joint infection, the sensitized animals appeared to be less susceptible to severe infection of the anterior chamber of the eye. The role of immunity and hypersensitivity in staphylococcal infection is discussed and the possibility that non-specific inflammation may influence staphylococcal infection in the same way as specific hypersensitivity is indicated. Studies to further elucidate this are presented in the following pages.

STUDIES ON THE PATHOGENESIS OF STAPHYLOCOCCAL INFECTION : III. THE EFFECT OF TISSUE NECROSIS AND ANTITOXIC IMMUNITY

Necrosis of rabbit skin produced by thermal injury was found to result in a striking increase in local infectivity of staphylococci that were coagulase-positive and hemolytic, but no local increase in the infectivity of non-pathogenic staphylococci. Infection produced in necrotic burns extended beyond the area of burn and was characterized by hemorrhage, edema, and necrosis of contiguous normal skin. Such infections, however, never resulted in bacteriemia or metastatic abscesses, and there was no effect of the necrotic burn upon the infectivity of staphylococci injected into normal skin of the burned animal. Recovery of rabbits from severe burn infections was associated with the development of high titers of serum antibody to the alpha hemolysin or dermonecrotoxin of the staphylococcus. Thirty to 100 days after the initial burn infection, it was found that rabbits could no longer be infected in a necrotic burn, although infection induced in normal skin of these resistant animals was no different from that in normal rabbits. Immunity to infection by pathogenic staphylococci in necrotic burns could be induced by vaccination with potent alpha hemolysin toxoid, and this immunity was passively transferable with rabbit antiserum. No strain specificity was detected for this immunity in that immunization with toxoid prepared from bacteriophage type 52/42B/80/81 staphylococci protected animals against infection in a necrotic burn by other typable and non-typable staphylococci. Histopathological study of infected necrotic burns in normal rabbits showed extensive necrosis, hemorrhage, edema, and many masses of bacteria but leucocytic infiltration was observed only at the margin of the infection. In contrast, the infected necrotic burns in animals immunized with alpha hemolysin toxoid showed few bacteria and marked leucocytic infiltration throughout the burn. These experiments have, therefore, demonstrated a significant immunity to infection by pathogenic staphylococci in necrotic tissue but not in normal skin, associated with serum antibody to the alpha hemolysin or dermonecrotoxin of the bacteria. The implications of these findings are discussed.

Muscle imbalance and reduced ankle joint motion in people with hammer toe deformity

BACKGROUND

Multiple factors may contribute to hammer toe deformity at the metatarsophalangeal joint. The purposes of this study were to (1) compare the ratio of toe extensor/flexor muscle strength in toes 2-4 among groups with and without hammer toe deformity, (2) to determine correlations between the ratio of toe extensor/flexor muscle strength in toes 2-4, and metatarsophalangeal joint deformity (3) to determine if other clinical measures differ between groups and if these measures are correlated with metatarsophalangeal joint angle.

METHODS

Twenty-seven feet with visible hammer toe deformity and 31 age matched feet without hammer toe deformity were tested. Toe muscle strength was measured using a dynamometer and the ratio of toe extensor muscle strength to flexor muscle strength was calculated. Metatarsophalangeal joint angle was measured from a computerized tomography image. Ankle and subtalar joint range of motion, and tibial torsion were measured using goniometry.

FINDINGS

Extensor/flexor toe muscle strength ratio was 2.3-3.0 times higher in the hammer toe group compared to the non-hammer toe group, in toes 2-4. The ratios of extensor/flexor toe muscle strength for toes 2-4 and metatarsophalangeal joint angle were highly correlated (r=0.69-0.80). Ankle dorsiflexion and metatarsophalangeal joint angle were negatively correlated for toes 2-4 (r=-0.38 to -0.56) as were eversion and metatarsophalangeal joint angle.

INTERPRETATION

These results provide insight into potential risk factors for the development of hammer toe deformity. Additional research is needed to determine the causal relationship between hammer toe deformity and the ratio of toe extensor/flexor muscle strength in toes 2-4.

A strategic framework for responding to coral bleaching events in a changing climate

The frequency and severity of mass coral bleaching events are predicted to increase as sea temperatures continue to warm under a global regime of rising ocean temperatures. Bleaching events can be disastrous for coral reef ecosystems and, given the number of other stressors to reefs that result from human activities, there is widespread concern about their future. This article provides a strategic framework from the Great Barrier Reef to prepare for and respond to mass bleaching events. The framework presented has two main inter-related components: an early warning system and assessment and monitoring. Both include the need to proactively and consistently communicate information on environmental conditions and the level of bleaching severity to senior decision-makers, stakeholders, and the public. Managers, being the most timely and credible source of information on bleaching events, can facilitate the implementation of strategies that can give reefs the best chance to recover from bleaching and to withstand future disturbances. The proposed framework is readily transferable to other coral reef regions, and can easily be adapted by managers to local financial, technical, and human resources.

Neurotrophic factors and neuronal death

The well-documented physiological role of nerve growth factor (NGF) in peripheral sympathetic and neural-crest-derived sensory neurons in vivo has its exact counterpart in vitro. This provided the conceptual basis for developing in vitro analytical procedures for the purification of new neurotrophic molecules. The experimental approaches used are discussed in the context of the purification of new neurotrophic factors, brain-derived neurotrophic factor (BDNF) and ciliary neurotrophic factor (CNTF). The importance of the modulatory role played by extracellular matrix molecules, in particular laminin, on both NGF-mediated and BDNF-mediated survival effects is also delineated. BDNF is a very basic (pI approximately 10) molecule of about 12 kDa, having physico-chemical characteristics close to those of the monomer of NGF. However, the spectrum of its biological actions is distinctly different from that of NGF. In particular, BDNF supports the survival of retinal ganglion cells and placode-derived peripheral sensory neurons which are not supported by NGF. The trophic supply of primary sensory neurons projecting to both the central nervous system and the periphery is discussed. It is hypothesized that sensory neurons receive limited quantities of neurotrophic molecules from both peripheral and central axons, a mechanism ensuring the survival of neurons adequately connected with both peripheral and central targets.

Lisfranc injury in a national hockey league player: a case report

Tarsometatarsal joint dislocations and fracture-dislocations are uncommon injuries most frequently resulting from high-energy trauma as encountered in crush injuries, falls, and motor vehicle accidents. Although less common in athletes, this injury is being recognized with greater frequency and may carry a poor prognosis for return to high levels of competition. These injuries present a considerable challenge to orthopedic surgeons caring for athletes because of the prolonged period of recovery often required [ 1,2,5,6,12]. The literature contains descriptions of this injury in football players, gymnasts, tennis players, and track and field athletes [2,5,9]. To our knowledge, no report of such a Lisfranc injury to a hockey player has been described. This is a case report of a National Hockey League player that sustained a Lisfranc injury requiring surgical stabilization, but was able to return to elite hockey play.

Evaluation of a dual-arm Archimedean spiral array for microwave hyperthermia

PURPOSE

This effort describes a third-party performance evaluation of a novel, commercial, dual-armed Archimedean spiral array hyperthermia applicator. The applicator is analysed for its ability to couple efficiently into muscle equivalent phantom loads, operate over a broad bandwidth to help accommodate variable tissue properties and generate predictable and repeatable SAR contours that are adaptable to clinically probable disease shapes.

MATERIALS AND METHODS

Characterization of the applicator includes E-field and return-loss measurements in liquid muscle tissue-equivalent phantom, as well as comparison of 'treatment-planning' simulations of several possible array SAR patterns with measured SAR from non-coherently driven spiral array antennae.

RESULTS

The applicator demonstrates a reasonably low return loss over a large bandwidth and the ability to generate a very uniform heating pattern. Ability to adjust SAR contours spatially to fit specific shapes is also demonstrated.

CONCLUSIONS

This device should prove a welcome addition to a currently limited set of superficial heating applicators to provide controllable heating of superficial tissue disease.

Preliminary x-ray characterization of authentic providence virus and attempts to express its coat protein gene in recombinant baculovirus

Providence Virus (PrV) is a non-envoloped, T = 4 icosahedral beta-tetravirus that undergoes autocatalytic cleavage of its coat protein precursor after capsid assembly. This is also a well characterized function of Nudaurelia capensis omega virus (NomegaV), a member of the related omegatetraviruses, whose x-ray structure has been determined. Virus-like particle (VLP) production of PrV in a recombinant baculovirus expression system was attempted to obtain high VLP yields for comparison of structural and autocatalytic active site properties between these virus groups. This resulted in insoluble aggregates of PrV coat protein even though NomegaV VLPs have been successfully produced in the same system. Betatetraviruses may be more dependent on compartmentalization and availability of their full-length genome for proper folding and assembly. However, crystals were grown of limited quantities of authentic PrV produced in cell culture and a partial X-ray data set collected to 3.8 A resolution. The virus particle position and orientation in the unit cell was determined by space group consideration and rotation function analysis. A phasing model, based on NomegaV, was developed to initiate the structure solution of PrV.

Preoperative evaluation of live renal donors using multislice CT angiography

AIM

To determine the accuracy of multidetector row CT renal angiography in the preoperative evaluation of live kidney donors, and to identify potential pitfalls when reporting.

METHODS

Between July 1998 and June 2003, 74 consecutive live renal donors underwent contrast-enhanced multidetector row CT renal angiography before donor nephrectomy. The operative notes and radiological reports of all cases were reviewed retrospectively. Where a significant discrepancy was identified, the archived images were reviewed by two radiologists in the light of the intraoperative findings.

RESULTS

A total of 12 discrepancies were identified in 11 of the 74 cases (15%). In the preoperative CT angiography reports, 4 accessory arteries, 6 early-branching renal arteries, 1 duplicated renal vein and 1 accessory ureter were not identified; 9 of these were evident on review, but were not detected at the time of reporting. In 3 cases (1 accessory artery, the duplicated renal vein and the accessory ureter), the anomaly was not visible on review of the CT angiographic data, even with the benefit of hindsight. Surgical feedback during the study period resulted in modifications to CT technique and improved performance.

CONCLUSION

In the majority of cases, there was good correlation between preoperative CT renal angiography and operative findings. Most discrepancies were due either to an oversight by the reporting radiologist, or failure to fully appreciate the potential surgical significance of certain findings. Regular surgical feedback plays a valuable role in improving reporting accuracy and maintaining imaging standards.

BK and JC polyomaviruses are not associated with idiopathic pulmonary fibrosis

We sought to determine if the BK and JC polyomaviruses were associated with idiopathic pulmonary fibrosis (IPF). We did not detect the BK or JC polyomaviruses in lung tissue extracts from 33 patients with IPF by using real-time PCR, which suggests that an etiologic association is unlikely.

Tendon Achilles lengthening for the treatment of neuropathic ulcers causes a temporary reduction in forefoot pressure associated with changes in plantar flexor power rather than ankle motion during gait

The purposes of this study were to determine the effects of tendon Achilles lengthening (TAL) on ambulatory plantar pressures and ankle range of motion, moment, and power, and to determine whether changes in forefoot pressure after treatment of a neuropathic ulcer are related to changes in ankle dorsiflexion range of motion (DFROM) or plantar flexor (PF) power during gait. Pressure and gait tests were performed before treatment, and at 3 weeks and 8 months after treatment in two randomly assigned groups of subjects with diabetes, equinus deformity, and a neuropathic forefoot ulcer treated with TAL and total contact casting (TAL group, n=14), or total contact casting alone (TCC group, n=14). The TAL group had an initial decrease in forefoot peak pressure (PP) (27%), forefoot pressure-time integral (PTI) (42%), PF moment (53%), and PF power (65%), along with an initial increase in rear foot PP (34%), rear foot PTI (48%), and DFROM (74%). Post-surgical changes in rear foot pressure and DFROM were maintained up to 8 months after treatment with TAL, whereas forefoot pressure and PF moment and power increased significantly. Changes in forefoot pressure after treatment in either group were correlated with changes in PF power (r=0.45-0.60), but not with changes in DFROM during gait (r=-0.02-0.08). Results suggest TAL causes a temporary reduction in forefoot pressure primarily by reducing PF power during gait. The initial decrease in forefoot pressure, followed by progressive reloading of forefoot tissues as PF muscles regain strength after TAL, may help reduce the risk of ulcer recurrence in patients with diabetes.

Virus stability and protein-nucleic acid interaction as studied by high-pressure effects on nodaviruses

In this work, we evaluate the stability, dynamics and protein-nucleic acid interaction in Flock House virus (FHV). FHV is an RNA insect virus, non-enveloped, member of the family Nodaviridae. It is composed of a bipartite single-stranded RNA genome packaged in an icosahedral capsid of 180 copies of an identical protein (alpha protein). A fundamental property of many animal viruses is the post-assembly maturation required for infectivity. FHV is constructed as a provirion, which matures to an infectious virion by cleavage of alpha protein into beta and gamma subunits. We used high pressure, temperature and chemical denaturing agents to promote perturbation of the viral capsid. These effects were monitored by spectroscopy measurements (fluorescence, light scattering and CD) and size-exclusion chromatography. The data showed that FHV was stable to pressures up to 310 MPa at room temperature. The fluorescence emission and light scattering values showed small changes that were reversible after decompression. When we combined pressure and sub-denaturing urea concentrations (1 M), the changes were more drastic, suggesting dissociation of the capsid. However, these changes were reversible after pressure release. The complete dissociation of FHV could be observed only under high urea concentrations (10 M). There were no significant changes in emission spectra up to 5 M urea. FHV also was stable when we used temperature treatments (high and low). We also compared the effects of urea and pressure on FHV wild type and cleavage-defective mutant VLPs (virus-like particles). The VLPs and authentic particles are distinguishable by protein-RNA interactions, since VLPs pack cellular RNA and native particles contain viral RNA. Our results demonstrated that native particles are more stable than VLPs to physical and chemical treatments. Our data point to the specificity of the interaction between the capsid protein and the viral RNA. This specificity is crucial to the stability of the particle, which makes this interaction an excellent target for drug development.

An empirical study of the impact of complexity on participation in horserace betting

The aim of the research reported in this paper was to explore empirically whether levels of participation in horserace betting are affected by the complexity of the betting task. The study employed a systematic random sample of 1161 betting decisions made in UK offcourse betting offices during 1987. The research was conducted in a naturalistic setting where it was possible to grade complexity and to measure levels of participation. Complexity was defined in terms of both the number of alternatives in the decision-maker's choice set (number of horses in a race) and the complexity of the attributes set for each horserace (handicap vs. non-handicap races). Results indicated that bettors are not inhibited by alternative-based complexity, but may be inhibited to some extent by attribute-defined complexity.

Sediment microbes of deep-sea bioherms on the northwest shelf of Australia

The northwest shelf of Australia is a region with known petroleum reserves. Recent geological investigations have revealed carbonate knolls postulated to be of biological origin. Sediment microbial populations at three sites on the northwest shelf, Pee Shoal, Mermaid Reef, and Scott Reef, were investigated for the presence of hydrocarbon-degrading bacteria. From two sampling trips, 246 bacterial strains were purified, and 182 of these strains displayed preferential growth on hydrocarbon-selective media. Strains were tested for nutrient specificity using single hydrocarbon fermentations. Metabolic profiles were constructed using biochemical testing, fatty acid analysis, and metabolic rate experiments. 16S rRNA gene sequence analysis of four strains identified these strains as members of the genera Sphingomonas, Bacillus, and Microbacterium, and one strain as a member of the alpha-Proteobacteria. The potential of these strains as bioindicators of hydrocarbon pollutants or for bioremediation in marine environments is discussed.

Cowpea mosaic virus: from the presentation of antigenic peptides to the display of active biomaterials

The potential of cowpea mosaic virus (CPMV), a plant icosahedral virus, for the presentation of foreign peptides and proteins is reported. The most prominent feature at the virus surface is a region of the smaller of the two coat proteins (S) which has been extensively used for the insertion of foreign peptides. Given the availability of the three-dimensional structure of the native virus and the amenability of foreign peptide-expressing CPMV chimeras to crystallisation, immunological data can be correlated with the conformational state of the foreign insert. The latter is influenced by proteolysis which occurs within the foreign inserts. In an effort to offer an alternative context for peptide expression, extensive exploration of a second region of the S protein is reported with respect to tolerance to small insertions. Moreover, to make CPMV suitable for a wider spectrum of presentation, a technique was developed to allow surface coupling of a peptide which can serve as the anchoring point for a range of proteins. This new approach is also widely applicable for the direct chemical cross-linking of peptides and full-length protein domains to the viral capsid.

Bilevel multidisciplinary discharge planning and length of stay

As health care funding gets more and more tenuous, leaders in all institutions are called upon to find innovative ways to reduce costs while maintaining quality. It is possible to realize undreamed-of savings by reengineering certain processes, but such an undertaking demands that wholesale changes in the corporate culture and substantial effort at all levels. This paper reports a long-term project at a large, urban, tertiary care institution, the redesign of discharge planning to improve patient care and reduce lengths of stay and related expenses.

Evolutionary and taxonomic implications of conserved structural motifs between picornaviruses and insect picorna-like viruses

A comparison of the recently determined structure of an insect picorna-like virus, Cricket paralysis virus (CrPV), with that of the mammalian picornaviruses shows that several structural features are highly conserved between these viruses. These conserved features include the topology of the coat proteins, the conformation of most loops, and the general arrangement of the internally located N-terminal arms of the coat proteins. The conformational conservation of the N-termini of the three major coat proteins between CrPV and the picornaviruses suggests a putative ancestral T = 3 virus. Comparisons of the genome structure and amino-acid sequence of the coat proteins of CrPV with a number of other insect picorna-like viruses show that most of them belong to a novel group, recently given the interim name Cricket paralysis-like viruses. Two other insect picorna-like viruses, Infectious flacherie virus (IFV) and Sacbrood virus (SBV), for which the genome sequences have recently been determined, have very different coat protein sequences and a genome organization more like the picornaviruses. However, the position of the small VP4 protein in the structural protein polyprotein as well as the mechanism for its cleavage from VP3 upon assembly strongly suggests an evolutionary link to the "Cricket paralysis-like viruses". We propose that the picornaviruses, Cricket paralysis-like viruses and IFV/SBV group are a natural assemblage. The ancestor for this assemblage had a structure based upon the CrPV/picornavirus paradigm and a genome encoding a single major coat protein; gene duplication and rearrangements have subsequently produced the viruses that we observe today. We also discuss the possible relatives of the proposed assemblage and the likely implications of future structural studies that may be carried out on the putative relatives.

Obstructive jaundice secondary to lymphoma in childhood

In children, biliary obstruction secondary to lymphoma is rare. Previous reports in adults and children suggest that these lymphomas are associated with a poor prognosis. The authors reviewed the medical records and imaging studies of 4 children treated for pancreaticobiliary lymphoma at our children's hospital over the past 10 years. All 4 presented with jaundice. Abdominal ultrasound scan and computed tomography (CT) scans were helpful in defining the anatomy of the obstruction. In the cases of involvement of the porta hepatis, the diagnosis was made by biopsy. In one child a mass was in the head of the pancreas, and evaluation of frozen section biopsy results were not diagnostic for lymphoma, and a major resection was performed. All the lymphomas were of nonHodgkin's B-cell type and one was a Burkitt's lymphoma. All responded promptly to chemotherapy. One child had a testicular relapse and currently is receiving additional therapy. Pancreaticobiliary lymphomas are an unusual cause of obstructive jaundice in children. Biopsy alone without resection or biliary drainage is recommended surgical therapy. Long-term survival rate in children with this disorder appears to be more promising than previously reported. J Pediatr Surg 36:1792-1795.