Three-dimensional electron beam dose calculations

The MDAH pencil-beam algorithm developed by Hogstrom et al (1981) has been widely used in clinics for electron beam dose calculations for radiotherapy treatment planning. The primary objective of this research was to address several deficiencies of that algorithm and to develop an enhanced version. Two enhancements have been incorporated into the pencil-beam algorithm; one models fluence rather than planar fluence, and the other models the bremsstrahlung dose using measured beam data. Comparisons of the resulting calculated dose distributions with measured dose distributions for several test phantoms have been made. From these results it is concluded (1) that the fluence-based algorithm is more accurate to use for the dose calculation in an inhomogeneous slab phantom, and (2) the fluence-based calculation provides only a limited improvement to the accuracy the calculated dose in the region just downstream of the lateral edge of an inhomogeneity. The source of the latter inaccuracy is believed primarily due to assumptions made in the pencil beam's modeling of the complex phantom or patient geometry.^ A pencil-beam redefinition model was developed for the calculation of electron beam dose distributions in three dimensions. The primary aim of this redefinition model was to solve the dosimetry problem presented by deep inhomogeneities, which was the major deficiency of the enhanced version of the MDAH pencil-beam algorithm. The pencil-beam redefinition model is based on the theory of electron transport by redefining the pencil beams at each layer of the medium. The unique approach of this model is that all the physical parameters of a given pencil beam are characterized for multiple energy bins. Comparisons of the calculated dose distributions with measured dose distributions for a homogeneous water phantom and for phantoms with deep inhomogeneities have been made. From these results it is concluded that the redefinition algorithm is superior to the conventional, fluence-based, pencil-beam algorithm, especially in predicting the dose distribution downstream of a local inhomogeneity. The accuracy of this algorithm appears sufficient for clinical use, and the algorithm is structured for future expansion of the physical model if required for site specific treatment planning problems. ^

Mechanisms for the release of dopamine from turtle retina

The retinal circuitry underlying the release of dopamine was examined in the turtle, Pseudemys scripta elegans, using neurochemical release studies, anatomical techniques, and biochemistry. There was a dose- and calcium-dependent release of dopamine from turtle retinas incubated in $\sp3$H-dopamine after perfusion of the GABA antagonist bicuculline. This indicated that dopamine release was tonically inhibited by GABA. Other putative retinal transmitters were examined. Glutamate antagonists selective for hyperpolarizing bipolar cells, such as 2,3-piperidine dicarboxylic acid (PDA), caused dose- and calcium-dependent release of dopamine from the retina. In contrast, release was not observed after perfusion with 4-aminophosphonobutyric acid, a specific antagonist of depolarizing bipolar cells. This indicated that depolarizing bipolar cells were not involved in retinal circuitry underlying the release of dopamine in the turtle retina. The release produced by PDA was blocked by bicuculline, indicating a polysynaptic mechanism of release. None of the other agents tested, which included carbachol, strychnine, dopamine uptake inhibitors, serotonin, tryptamine, muscimol, melatonin, or dopamine itself produced release.^ The cells capable of the release of dopamine were identified using both uptake autoradiography and immunocytochemical localization with dopamine antisera. The simplest circuitry based on these findings is signal transmission from photoreceptors to hyperpolarizing bipolar cells then to GABAergic cells, and finally to dopaminergic amacrine cells. ^

The physical map of {\it Escherichia coli\/} K-12 strain MG1655: Construction, comparison with other strains and implications for mechanisms controlling oligonucleotide frequency

Complete NotI, SfiI, XbaI and BlnI cleavage maps of Escherichia coli K-12 strain MG1655 were constructed. Techniques used included: CHEF pulsed field gel electrophoresis; transposon mutagenesis; fragment hybridization to the ordered $\lambda$ library of Kohara et al.; fragment and cosmid hybridization to Southern blots; correlation of fragments and cleavage sites with EcoMap, a sequence-modified version of the genomic restriction map of Kohara et al.; and correlation of cleavage sites with DNA sequence databases. In all, 105 restriction sites were mapped and correlated with the EcoMap coordinate system.^ NotI, SfiI, XbaI and BlnI restriction patterns of five commonly used E. coli K-12 strains were compared to those of MG1655. The variability between strains, some of which are separated by numerous steps of mutagenic treatment, is readily detectable by pulsed-field gel electrophoresis. A model is presented to account for the difference between the strains on the basis of simple insertions, deletions, and in one case an inversion. Insertions and deletions ranged in size from 1 kb to 86 kb. Several of the larger features have previously been characterized and some of the smaller rearrangements can potentially account for previously reported genetic features of these strains.^ Some aspects of the frequency and distribution of NotI, SfiI, XbaI and BlnI cleavage sites were analyzed using a method based on Markov chain theory. Overlaps of Dam and Dcm methylase sites with XbaI and SfiI cleavage sites were examined. The one XbaI-Dam overlap in the database is in accord with the expected frequency of this overlap. The occurrence of certain types of SfiI-Dcm overlaps are overrepresented. Of the four subtypes of SfiI-Dcm overlap, only one has a partial inhibitory effect on the activity of SfiI. Recognition sites for all four enzymes are rarer than expected based on oligonucleotide frequency data, with this effect being much stronger for XbaI and BlnI than for NotI and SfiI. The latter two enzyme sites are rare mainly due to apparent negative selection against GGCC (both) and CGGCCG (NotI). The former two enzyme sites are rare mainly due to effects of the VSP repair system on certain di-tri- and tetranucleotides, most notably CTAG. Models are proposed to explain several of the anomalies of oligonucleotide distribution in E. coli, and the biological significance of the systems that produce these anomalies is discussed. ^

In Vitro Testing of a Temporary Catheter-Based Aortic "Parachute" Valve

Recently developed technologies allow aortic valve implantation off-pump in a beating heart. In this procedure, the native, stenotic aortic valve is not removed, but simply crushed by a pressure balloon mounted on a percutaneous catheter. Removal of the native aortic cusps before valve replacement may reduce the incidence of annular or cuspal calcium embolization and late perivalvular leaks and increase implantable valve size. However, a temporary valve system in the ascending aorta may be necessary to maintain hemodynamic stability by reducing acute aortic regurgitation and left ventricular volume overload. This study evaluates the hemodynamic effects of a wire-mounted, monoleaflet, temporary valve apparatus in a mechanical cardiovascular simulator. Aortic flow, systemic pressure and left ventricular pressure were continuously monitored. An intraluminal camera obtained real-time proximal and distal images of the valve in operation. Insertion of the parachute valve in the simulator increased diastolic pressure from 7 to 38 mm Hg. Cardiac output increased from 2.08 to 4.66 L/min and regurgitant volume decreased from 65 to 23 mL. In conclusion, placement of a temporary valve in the ascending aorta may help maintain hemodynamic stability and improve off-pump aortic valve replacement.

Understanding the underlying mechanisms of recent Jatropha curcas L. adoption by smallholders in Kenya: A rural livelihood assessment in Bondo, Kibwezi, and Kwale districts

Between 2004 and 2007, NGOs, community based organisations and private investors promoted jatropha in Kenya with the aim of generating additional income and producing biofuel for rural development. By 2008 it became gradually evident that jatropha plantations (both mono- and intercropping) are uneconomical and risky due to competition for land and labour with food crops. Cultivation of jatropha hedges was found to have better chances of economic success and to present only little risks for the adopting farmers. Still, after 2008 a number of farmers went on adopting jatropha in plots rather than as hedges. It is hypothesised that lack of awareness about the low economic prospects of jatropha plantations was the main reason for continued adoption, and that smallholder farmers with higher resource endowments mainly ventured into its cultivation. In this study we provide an empirical basis for understanding the role of households' capital assets in taking up new livelihood strategies by smallholder farmers in three rural districts in Kenya. For that purpose, we assess the motivation and enabling factors that led to the adoption of jatropha as a new livelihood strategy, as well as the context in which promotion and adoption took place. A household survey was conducted in 2010, using a structured questionnaire, to collect information on household characteristics and capital asset endowment. Data were analysed using descriptive statistics and non-parametric statistical tests. We established that access to additional income and own energy supply were the main motivation for adoption of jatropha, and that financial capital assets do not necessarily have a positive influence on adoption as hypothesised. Further, we found that the main challenges that adopting farmers faced were lack of access to information on good management practices and lack of a reliable market. We conclude that continued adoption of on-farm jatropha after 2008 is a result of lacking awareness about the low economic value of this production type. We recommend abandoning on-farm production of jatropha until improved seed material and locally adapted agronomic knowledge about jatropha cultivation becomes available and its production becomes economically competitive.

Atlas-based Segmentation of Tumor-bearing Brain Images

In diagnostic neuroradiology as well as in radiation oncology and neurosurgery, there is an increasing demand for accurate segmentation of tumor-bearing brain images. Atlas-based segmentation is an appealing automatic technique thanks to its robustness and versatility. However, atlas-based segmentation of tumor-bearing brain images is challenging due to the confounding effects of the tumor in the patient image. In this article, we provide a brief background on brain tumor imaging and introduce the clinical perspective, before we categorize and review the state of the art in the current literature on atlas-based segmentation for tumor-bearing brain images. We also present selected methods and results from our own research in more detail. Finally, we conclude with a short summary and look at new developments in the field, including requirements for future routine clinical use.

Measurement of the neutrino velocity with the OPERA detector in the CNGS beam using the 2012 dedicated data

In spring 2012 CERN provided two weeks of a short bunch proton beam dedicated to the neutrino velocity measurement over a distance of 730 km. The OPERA neutrino experiment at the underground Gran Sasso Laboratory used an upgraded setup compared to the 2011 measurements, improving the measurement time accuracy. An independent timing system based on the Resistive Plate Chambers was exploited providing a time accuracy of ∼1 ns. Neutrino and anti-neutrino contributions were separated using the information provided by the OPERA magnetic spectrometers. The new analysis profited from the precision geodesy measurements of the neutrino baseline and of the CNGS/LNGS clock synchronization. The neutrino arrival time with respect to the one computed assuming the speed of light in vacuum is found to be δtν≡TOFc−TOFν=(0.6±0.4 (stat.)±3.0 (syst.)) ns and δtν¯≡TOFc−TOFν¯=(1.7±1.4 (stat.)±3.1 (syst.)) ns for νμ and ν¯μ, respectively. This corresponds to a limit on the muon neutrino velocity with respect to the speed of light of −1.8×10−6<(vν−c)/c<2.3×10−6 at 90% C.L. This new measurement confirms with higher accuracy the revised OPERA result.

Search for νμ→νe oscillations with the OPERA experiment in the CNGS beam

A first result of the search for nu(mu)->nu(e) oscillations in the OPERA experiment, located at the Gran Sasso Underground Laboratory, is presented. The experiment looked for the appearance of nu(e) in the CNGS neutrino beam using the data collected in 2008 and 2009. Data are compatible with the non-oscillation hypothesis in the three-flavour mixing model. A further analysis of the same data constrains the non-standard oscillation parameters theta(new) and Delta m(new)(2) suggested by the LSND and MiniBooNE experiments. For large Delta m(new)(2) values (>0.1 eV(2)), the OPERA 90% C.L. upper limit on sin(2)(2 theta(new)) based on a Bayesian statistical method reaches the value 7.2 x 10(-3).

Characterisation and mitigation of beam-induced backgrounds observed in the ATLAS detector during the 2011 proton-proton run

This paper presents a summary of beam-induced backgrounds observed in the ATLAS detector and discusses methods to tag and remove background contaminated events in data. Trigger-rate based monitoring of beam-related backgrounds is presented. The correlations of backgrounds with machine conditions, such as residual pressure in the beam-pipe, are discussed. Results from dedicated beam-background simulations are shown, and their qualitative agreement with data is evaluated. Data taken during the passage of unpaired, i.e. non-colliding, proton bunches is used to obtain background-enriched data samples. These are used to identify characteristic features of beam-induced backgrounds, which then are exploited to develop dedicated background tagging tools. These tools, based on observables in the Pixel detector, the muon spectrometer and the calorimeters, are described in detail and their efficiencies are evaluated. Finally an example of an application of these techniques to a monojet analysis is given, which demonstrates the importance of such event cleaning techniques for some new physics searches.

The new bern PET cyclotron, its research beam line, and the development of an innovative beam monitor detector

The new Bern cyclotron laboratory aims at industrial radioisotope production for PET diagnostics and multidisciplinary research by means of a specifically conceived beam transfer line, terminated in a separate bunker. In this framework, an innovative beam monitor detector based on doped silica and optical fibres has been designed, constructed, and tested. Scintillation light produced by Ce and Sb doped silica fibres moving across the beam is measured, giving information on beam position, shape, and intensity. The doped fibres are coupled to commercial optical fibres, allowing the read-out of the signal far away from the radiation source. This general-purpose device can be easily adapted for any accelerator used in medical applications and is suitable either for low currents used in hadrontherapy or for currents up to a few μA for radioisotope production, as well as for both pulsed and continuous beams.

Incidental findings on cone beam computed tomography scans in cleft lip and palate patients.

OBJECTIVES Cone beam computed tomography (CBCT) is frequently used in treatment planning for alveolar bone grafting (ABG) and orthognathic surgery in patients with cleft lip and palate (CLP). CBCT images may depict coincident findings. The aim of this study was to assess the prevalence of incidental findings on CBCT scans in CLP patients. SUBJECTS AND METHODS Initial CBCTs taken from consecutive patients (n = 187; mean age 11.7 years, range 6.9-45) with a non-syndromic orofacial cleft from January 2006 until June 2012 were systematically evaluated. Twenty-eight patients (mean age 19.3 years, range 13.2-30.9) had been subjected to ABG before their first CBCT was taken; 61 patients had a CBCT before and after ABG. Sinuses, nasopharynx, oropharynx, throat, skull, vertebrae, temporomandibular joint (TMJ), maxilla and mandible were checked for incidental findings. RESULTS On 95.1 % of the CBCTs, incidental findings were found. The most prevalent were airway/sinus findings (56.1 %), followed by dental problems, e.g. missing teeth (52 %), nasal septum deviation (34 %), middle ear and mastoid opacification, suggestive for otitis media (10 %) and (chronic) mastoiditis (9 %), abnormal TMJ anatomy (4.9 %) and abnormal vertebral anatomy (1.6 %). In the 28 patients whose first CBCT was taken at least 2 years after ABG, bone was still present in the reconstructed cleft area except in 2 out of 12 patients with a bilateral CLP. The ABG donor site (all bone grafts were taken from the chin area) was still recognizable in over 50 % of the patients. Based on the CBCT findings, 10 % of the patients were referred for further diagnosis and 9 % for further treatment related to dental problems. CONCLUSION Incidental findings are common on CBCTs. Compared with the literature, CLP patients have more dental, nasal and ear problems. Thus, whenever a CBCT is available, this scan should be reviewed by all specialists in the CLP team focusing on their specific background knowledge concerning symptoms and treatment of these patients. CLINICAL RELEVANCE The high number of findings indicates that CBCT imaging is a helpful tool in the treatment of CLP patients not only related to alveolar bone grafting and orthognathic surgery but it also provides diagnostic information for almost all specialties involved in CLP treatment.

An image-based method to automatically propagate bony landmarks: application to computational spine biomechanics.

In attempts to elucidate the underlying mechanisms of spinal injuries and spinal deformities, several experimental and numerical studies have been conducted to understand the biomechanical behavior of the spine. However, numerical biomechanical studies suffer from uncertainties associated with hard- and soft-tissue anatomies. Currently, these parameters are identified manually on each mesh model prior to simulations. The determination of soft connective tissues on finite element meshes can be a tedious procedure, which limits the number of models used in the numerical studies to a few instances. In order to address these limitations, an image-based method for automatic morphing of soft connective tissues has been proposed. Results showed that the proposed method is capable to accurately determine the spatial locations of predetermined bony landmarks. The present method can be used to automatically generate patient-specific models, which may be helpful in designing studies involving a large number of instances and to understand the mechanical behavior of biomechanical structures across a given population.

Coherence and phase locking in the scalp EEG and between LORETA model sources, and microstates as putative mechanisms of brain temporo-spatial functional organization

Brain electric mechanisms of temporary, functional binding between brain regions are studied using computation of scalp EEG coherence and phase locking, sensitive to time differences of few milliseconds. However, such results if computed from scalp data are ambiguous since electric sources are spatially oriented. Non-ambiguous results can be obtained using calculated time series of strength of intracerebral model sources. This is illustrated applying LORETA modeling to EEG during resting and meditation. During meditation, time series of LORETA model sources revealed a tendency to decreased left-right intracerebral coherence in the delta band, and to increased anterior-posterior intracerebral coherence in the theta band. An alternate conceptualization of functional binding is based on the observation that brain electric activity is discontinuous, i.e., that it occurs in chunks of up to about 100 ms duration that are detectable as quasi-stable scalp field configurations of brain electric activity, called microstates. Their functional significance is illustrated in spontaneous and event-related paradigms, where microstates associated with imagery- versus abstract-type mentation, or while reading positive versus negative emotion words showed clearly different regions of cortical activation in LORETA tomography. These data support the concept that complete brain functions of higher order such as a momentary thought might be incorporated in temporal chunks of processing in the range of tens to about 100 ms as quasi-stable brain states; during these time windows, subprocesses would be accepted as members of the ongoing chunk of processing.

A community-based geological reconstruction of Antarctic Ice Sheet deglaciation since the Last Glacial Maximum

A robust understanding of Antarctic Ice Sheet deglacial history since the Last Glacial Maximum is important in order to constrain ice sheet and glacial-isostatic adjustment models, and to explore the forcing mechanisms responsible for ice sheet retreat. Such understanding can be derived from a broad range of geological and glaciological datasets and recent decades have seen an upsurge in such data gathering around the continent and Sub-Antarctic islands. Here, we report a new synthesis of those datasets, based on an accompanying series of reviews of the geological data, organised by sector. We present a series of timeslice maps for 20 ka, 15 ka, 10 ka and 5 ka, including grounding line position and ice sheet thickness changes, along with a clear assessment of levels of confidence. The reconstruction shows that the Antarctic Ice sheet did not everywhere reach the continental shelf edge at its maximum, that initial retreat was asynchronous, and that the spatial pattern of deglaciation was highly variable, particularly on the inner shelf. The deglacial reconstruction is consistent with a moderate overall excess ice volume and with a relatively small Antarctic contribution to meltwater pulse 1a. We discuss key areas of uncertainty both around the continent and by time interval, and we highlight potential priorities for future work. The synthesis is intended to be a resource for the modelling and glacial geological community.

Beamlet based direct aperture optimization for MERT using a photon MLC

PURPOSE A beamlet based direct aperture optimization (DAO) for modulated electron radiotherapy (MERT) using photon multileaf collimator (pMLC) shaped electron fields is developed and investigated. METHODS The Swiss Monte Carlo Plan (SMCP) allows the calculation of dose distributions for pMLC shaped electron beams. SMCP is interfaced with the Eclipse TPS (Varian Medical Systems, Palo Alto, CA) which can thus be included into the inverse treatment planning process for MERT. This process starts with the import of a CT-scan into Eclipse, the contouring of the target and the organs at risk (OARs), and the choice of the initial electron beam directions. For each electron beam, the number of apertures, their energy, and initial shape are defined. Furthermore, the DAO requires dose-volume constraints for the structures contoured. In order to carry out the DAO efficiently, the initial electron beams are divided into a grid of beamlets. For each of those, the dose distribution is precalculated using a modified electron beam model, resulting in a dose list for each beamlet and energy. Then the DAO is carried out, leading to a set of optimal apertures and corresponding weights. These optimal apertures are now converted into pMLC shaped segments and the dose calculation for each segment is performed. For these dose distributions, a weight optimization process is launched in order to minimize the differences between the dose distribution using the optimal apertures and the pMLC segments. Finally, a deliverable dose distribution for the MERT plan is obtained and loaded back into Eclipse for evaluation. For an idealized water phantom geometry, a MERT treatment plan is created and compared to the plan obtained using a previously developed forward planning strategy. Further, MERT treatment plans for three clinical situations (breast, chest wall, and parotid metastasis of a squamous cell skin carcinoma) are created using the developed inverse planning strategy. The MERT plans are compared to clinical standard treatment plans using photon beams and the differences between the optimal and the deliverable dose distributions are determined. RESULTS For the idealized water phantom geometry, the inversely optimized MERT plan is able to obtain the same PTV coverage, but with an improved OAR sparing compared to the forwardly optimized plan. Regarding the right-sided breast case, the MERT plan is able to reduce the lung volume receiving more than 30% of the prescribed dose and the mean lung dose compared to the standard plan. However, the standard plan leads to a better homogeneity within the CTV. The results for the left-sided thorax wall are similar but also the dose to the heart is reduced comparing MERT to the standard treatment plan. For the parotid case, MERT leads to lower doses for almost all OARs but to a less homogeneous dose distribution for the PTV when compared to a standard plan. For all cases, the weight optimization successfully minimized the differences between the optimal and the deliverable dose distribution. CONCLUSIONS A beamlet based DAO using multiple beam angles is implemented and successfully tested for an idealized water phantom geometry and clinical situations.