GATE: a simulation toolkit for PET and SPECT

Monte Carlo simulation is an essential tool in emission tomography that can assist in the design of new medical imaging devices, the optimization of acquisition protocols and the development or assessment of image reconstruction algorithms and correction techniques. GATE, the Geant4 Application for Tomographic Emission, encapsulates the Geant4 libraries to achieve a modular, versatile, scripted simulation toolkit adapted to the field of nuclear medicine. In particular, GATE allows the description of time-dependent phenomena such as source or detector movement, and source decay kinetics. This feature makes it possible to simulate time curves under realistic acquisition conditions and to test dynamic reconstruction algorithms. This paper gives a detailed description of the design and development of GATE by the OpenGATE collaboration, whose continuing objective is to improve, document and validate GATE by simulating commercially available imaging systems for PET and SPECT. Large effort is also invested in the ability and the flexibility to model novel detection systems or systems still under design. A public release of GATE licensed under the GNU Lesser General Public License can be downloaded at http:/www-lphe.epfl.ch/GATE/. Two benchmarks developed for PET and SPECT to test the installation of GATE and to serve as a tutorial for the users are presented. Extensive validation of the GATE simulation platform has been started, comparing simulations and measurements on commercially available acquisition systems. References to those results are listed. The future prospects towards the gridification of GATE and its extension to other domains such as dosimetry are also discussed.

Stress and hippocampal abnormalities in psychiatric disorders

The hippocampus plays a main role in regulating stress response in humans, but is itself highly sensitive to neurotoxic effects of repeated stressful episodes. Hippocampal atrophy related to experimental stress has been reported in laboratory studies in animals. Several controlled brain imaging studies have also shown hippocampal abnormalities in psychiatric disorders, including posttraumatic stress disorder (PTSD), major depressive disorder (MDD), and borderline personality disorder (BPD). This paper reviews the physiological role of the hippocampus in stress circuitry and the effects of stress on cognitive functions mediated by the hippocampus. We also review brain imaging studies investigating hippocampus in PTSD, MDD, and BPD. This literature suggests that individuals with PTSD, MDD, and BPD may suffer hippocampal atrophy as a result of stressors associated with these disorders. Prospective, longitudinal studies will be needed in high-risk offspring and first-episode subjects to explore the relationship between stress and hippocampal atrophy in these neuropsychiatric illnesses.

Documentation of subtype C HIV Type 1 strains in Argentina, Paraguay, and Uruguay

HIV subtypes B, F, and BF recombinants have been previously reported in South America. This report describes the presence of HIV-1 subtype C infection in the countries of Argentina, Uruguay, and Paraguay dating back to at least 1999. Surveillance for uncommon non-B/non-F subtype viruses circulating in South America has been conducted in samples obtained from nine countries. Peripheral blood mononuclear cells (PBMC), dried filter paper (FP), and fresh blood (FB) samples were collected from HIV-positive patients from Ecuador, Colombia, Venezuela, Peru, Chile, Bolivia, Argentina, Uruguay, and Paraguay. From a total of 2962 HIV seropositive samples examined during a 9-year period (1995-2003), only 11 (0.4%) were found to be infected with non-B/non-F HIV variants. Eight of these 11 strains were determined to be subtype C by heteroduplex mobility assay (HMA). Five of these 8 strains were further characterized by sequencing and phylogenetic analysis of the protease (Pro) and reverse transcriptase (RT) region of the genome and two were sequenced full length. One of the strains was found to be a unique BC recombinant. The spread of a third subtype of HIV, subtype C, should raise the question of its potential future role in the HIV epidemic in this region.

Results from the multi-species benchmark problem (BM3) using one-dimensional models

The IWA's Biofilm Modeling Task Group created a multi-species benchmark problem in which heterotrophic bacteria, nitrifying bacteria, and inert biomass coexist in a biofilm. Members of the Task Group submitted solutions from nine different one-dimensional models. The most important distinctions among the models were (1) whether the model required a full numerical solution or was solved with a spreadsheet, and (2) the way the biomass types were distributed in the biofilm. The models that protected the slow-growing species by having them accumulate away from the outer surface always had the largest surface coverage by nitrifiers and inerts, but the heterotroph coverage declined to compensate. Coverage by heterotrophs and removal of substrate COD were most strongly affected by dilution from nitrifiers and inerts near the outer surface. Models that did not allow the nitrifiers and inerts to dilute the heterotrophs significantly in the outer layer predicted more removal of COD than did the other models. The choice of the model to use depends on the user's needs and the relative importance of including protection of slow-growing species and/or dilution of fast-growing species.

Modelling a spatially heterogeneous biofilm and the bulk fluid: selected results from benchmark problem 2 (BM2)

The numerical simulation of mass transfer and conversion in spatially heterogeneous biofilms on the meso-scale requires an accurate description of the hydrodynamics in the biofilm systems and of spatial effects. This leads to systems of three-dimensional nonlinear partial differential equations that are numerically very expensive to solve and to data requirements that are not easy to meet. In this paper several modeling approaches to reduce the physical complexity and, hence, accelerate the computation are compared. They range from a mere reduction of dimensionality by lumping the problem along a secondary flow direction to global mass balances or empirical correlations, at the core of which a one-dimensional boundary value problem must be solved. It is found that even strongly simplified models can describe the qualitative behaviour of the model with regard to variations in the geometrical and hydrodynamic model parameters quite well. In order to obtain also quantitatively reliable results the hydrodynamics must be considered in an appropriate manner.

Painful vascular compression syndrome of the sciatic nerve caused by gluteal varicosities

The authors report three patients with chronic sciatic pain without focal neurologic deficit. Sitting or lying on the affected side provoked pain, and standing and walking relieved it. MRI revealed varicotic gluteal vessels compressing the sciatic nerve. Decompression of the nerve resulted in complete and permanent pain relief. Sciatic or buttock pain in patients with varicosities and pain provocation in the sitting or lying position suggests this neurovascular compression syndrome.

GABAergic dysfunction in mood disorders

The authors review the available literature on the preclinical and clinical studies involving GABAergic neurotransmission in mood disorders. Gamma-aminobutyric acid (GABA) is an inhibitory neurotransmitter present almost exclusively in the central nervous system (CNS), distributed across almost all brain regions, and expressed in interneurons modulating local circuits. The role of GABAergic dysfunction in mood disorders was first proposed 20 years ago. Preclinical studies have suggested that GABA levels may be decreased in animal models of depression, and clinical studies reported low plasma and CSF GABA levels in mood disorder patients. Also, antidepressants, mood stabilizers, electroconvulsive therapy, and GABA agonists have been shown to reverse the depression-like behavior in animal models and to be effective in unipolar and bipolar patients by increasing brain GABAergic activity. The hypothesis of reduced GABAergic activity in mood disorders may complement the monoaminergic and serotonergic theories, proposing that the balance between multiple neurotransmitter systems may be altered in these disorders. However, low GABAergic cortical function may probably be a feature of a subset of mood disorder patients, representing a genetic susceptibility. In this paper, we discuss the status of GABAergic hypothesis of mood disorders and suggest possible directions for future preclinical and clinical research in this area.

Paracoccidioidomycosis and larynx carcinoma

Report of a case of paracoccidioidomycosis associated with a carcinoma: both located in the larynx in a patient whose therapeutic response to antifungal treatment produced a recovery of physical conditions. This case shows the importance of taking into account the diagnosis of paracoccidioidomycosis in all patients with problems in the larynx, especially those who inhabit or inhabited endemic areas of Paracoccidioides brasiliensis.

Distribution patterns of entomopathogenic nematodes applied through drip irrigation systems

The distribution of entomopathogenic nematodes applied by drip irrigation was evaluated by injecting small volumes of Steinernema carpocapsae (Weiser) All strain, Steinernema feltiae (Filipjev) SN strain, Steinernema glaseri Steiner, and Heterorhabditis bacteriophora HP 88 strain Poinar suspensions into drip irrigation lines. Additionally, Steinernema riobrave Cabanillas, Poinar, & Raulston, and S. carpocapsae were injected in a 10-liter volume of water with an injection pump. Overall, the nematodes were evenly distributed along the drip lines. The total number of nematodes recovered from drip emitters was variable ranging from 42 to 92%. However, drip irrigation lines have potential to deliver entomopathogenic nematodes efficiently into pest habitats.

Circulating recombinant form CRF02_AG in South America

With the objective of monitoring the distribution of HIV-1 subtypes and circulating recombinant forms (CRFs)in South America, population-based surveillance studies were performed in seven countries. Peripheral blood mononuclear cell, filter paper, fresh blood, and cocultivation samples were collected from HIV-positive patients from Colombia, Ecuador, Peru, Bolivia, Chile, Argentina, and Uruguay, during a 7-year period(1995-2001). DNA was prepared and HIV envelope subtypes were determined by heteroduplex mobility as-say and DNA sequencing from 1289 HIV-positive samples. While subtypes B and F were the most commonly observed subtypes, two CRF02_AG strains were detected, in Ecuador. This is the first report of the existence of this CRF in South America.

Interspecific barriers between salmonids when hybridisation is due to sneak mating

Male sneaking behaviour can lead to interspecific hybridisation if sneakers attempt to fertilise ova in heterospecific mating, contributing to break down of interspecific barriers. In south European rivers, sneaking Atlantic salmon males fertilise an important proportion of ova from adult females in heterospecific crosses, up to 65%. In a south French flow-controlled stream, we found that they were able to naturally fertilise brown trout ova in absence of brown trout males. Aggressiveness of brown trout males towards sneaking salmon males and low survival of hybrids issued from salmon sneakers are found to be interspecific barriers.

Large-angle convergent-beam setup for femtosecond X-ray crystallography

It is demonstrated how femtosecond plasma X-ray sources can be used to record X-ray diffraction images with many simultaneous reflections. A convergent-beam geometry was implemented and tested with a crystal of a small molecule [Fe-py3(tren)] as well as with a crystal of the protein lysozyme. The results pave the way for femtosecond X-ray crystallography.

BPTI liquid-liquid phase separation monitored by light and small angle X-ray scattering

In the field of protein crystallization, a better knowledge of the nucleation process is essential to control the nucleation rate, the growth and therefore the size and the quality of crystals. With that aim, it becomes clear that the important stage is the determination of the protein phase diagram. We highlighted and investigated the bovine pancreatic trypsin inhibitor (BPTI) binary liquid-liquid phase separation in 350 mM KSCN solutions as a function of temperature. We measured the low concentration part of the binodal curve using light scattering and optical microscopy. We show, from small angle X-ray scattering experiments, that the high concentrated phase sediments in the bottom of the capillary and we analysed the low concentrated phase in terms of monomers/decamers equilibrium.

Immunohistochemical characterization of tumor cells and inflammatory infiltrate associated with cutaneous melanocytic tumors of Duroc and Iberian swine

The immunophenotype of tumor cells and inflammatory infiltrate associated with cutaneous melanocytic lesions (29 melanocytomas, two malignant melanomas, and 23 residual lesions) from 54 adult Iberian and Iberian x Duroc pigs were examined using a panel of nine antibodies. All neoplastic cells were vimentin+, cytokeratin-, and alpha-1-antitrypsin- and the majority were S100+, whereas all pigmented macrophages were vimentin+, cytokeratin-, and S100- and most expressed alpha-1-antitrypsin. Regressing tumors were characterized by zones with low density of neoplastic cells accompanied by heavy infiltration of CD3+ T lymphocytes, whereas zones with high density of neoplastic cells showed very low numbers of CD3+ T lymphocytes. The infiltrate of CD79a+ B cells and IgG, IgM, and IgA plasma cells was low. The majority of lymphocytes of the peri- and intratumoral infiltrate were major histocompatibility complex class II+, but neoplastic cells did not express class II antigen. The 17 residual lesions examined were composed of macrophages containing abundant melanin pigment and low to moderate numbers of CD3+ T lymphocytes. The results of the present study suggest that the local cellular immune response plays a crucial role in the host response that induces regression of cutaneous melanomas and melanocytomas of the Iberian and crossbred Iberian x Duroc pigs.

[Rhabdoid meningioma. A new malignant subtype]

Of the numerous morphological variants of meningiomas only few, and among these the rhabdoid meningioma, have prognostic importance. Rhabdoid meningiomas were described for the first time in 1998 as an unusual variant with increased proliferative activity. In 2000 they have been included in the revised WHO classification of tumours of the CNS as a subtype of meningiomas with increased risk of recurrence and more aggressive growth, corresponding to WHO grade III. We report the case of a rhabdoid meningioma in a 21-year-old woman presenting as a intracerebral tumour mimicking an oligodendroglioma. The tumour showed features of a meningioma and a rhabdoid morphology with angiomatous components and was considered to be a rhabdoid meningioma. After surgery a small residual tumour remained. The patient received postoperative radiotherapy resulting in regression of the residual tumour in control examinations after 4 and 8 months. Using the presented case we discuss the differential diagnosis and prognostic significance of recognition of a rhabdoid meningioma.

Peroneal nerve palsy caused by thrombosis of crural veins

Acute palsies of the peroneal nerve may have a variety of causes. In many patients, the cause remains undetermined. The authors report a patient with a thrombosis of a crural vein causing an acute peroneal nerve palsy. If the clinical history of patients with an acute peroneal nerve lesion is suggestive of venous thrombosis an appropriate diagnostic workup should be considered.

cAMP signaling pathway in depressed patients with psychotic features

Abnormalities in protein kinase A (PKA) and Rap1 have recently been reported in depressed patients. The aim of the present study was to investigate the levels of these proteins in platelets from untreated unipolar and bipolar depressed patients with psychotic features. The levels PKA and Rap1 were assessed by Western blot analysis and immunostaining in 37 drug-free patients and 29 healthy subjects. Both unipolar and bipolar patients with psychotic depression have significantly lower levels of platelet regulatory type I and higher levels of catalytic subunits of PKA than controls, whereas the levels of regulatory type II were higher only in psychotic unipolar patients. No significant differences were found in the immunolabeling of both Rap1 and actin among groups. These findings support the idea that besides nonpsychotic depression, abnormalities of PKA could be linked, albeit in a somewhat different way, with psychotic depression.