The diagnostic value of 18F-FDG PET and MRI in paediatric histiocytosis.

PURPOSE: To analyse the diagnostic value of (18)F-FDG PET and MRI for the evaluation of active lesions in paediatric Langerhans cell histiocytosis. METHODS: We compared 21 (18)F-FDG PET scans with 21 MRI scans (mean time interval 17 days) in 15 patients (11 male, 4 female, age range 4 months to 19 years) with biopsy-proven histiocytosis. Primary criteria for the lesion-based analysis were signs of vital histiocyte infiltrates (bone marrow oedema and contrast enhancement for MRI; SUV greater than the mean SUV of the right liver lobe for PET). PET and MR images were analysed separately and side-by-side. The results were validated by biopsy or follow-up scans after more than 6 months. RESULTS: Of 53 lesions evaluated, 13 were confirmed by histology and 40 on follow-up investigations. The sensitivity and specificity of PET were 67 % and 76 % and of MRI were 81 % and 47 %, respectively. MRI showed seven false-positive bone lesions after successful chemotherapy. PET showed five false-negative small bone lesions, one false-negative lesion of the skull and three false-negative findings for intracerebral involvement. PET showed one false-positive lesion in the lymphoid tissue of the head and neck region and two false-positive bone lesions after treatment. Combined PET/MR analysis decreased the number of false-negative findings on primary staging, whereas no advantage over PET alone was seen in terms of false-positive or false-negative results on follow-up. CONCLUSION: Our retrospective analysis suggests a pivotal role of (18)F-FDG PET in lesion follow-up due to a lower number of false-positive findings after chemotherapy. MRI showed a higher sensitivity and is indispensable for primary staging, evaluation of brain involvement and biopsy planning. Combined MRI/PET analysis improved sensitivity by decreasing the false-negative rate during primary staging indicating a future role of simultaneous whole-body PET/MRI for primary investigation of paediatric histiocytosis.

Nuclear medicine and multimodality imaging of pediatric neuroblastoma.

Neuroblastoma is an embryonic tumor of the peripheral sympathetic nervous system and is metastatic or high risk for relapse in nearly 50% of cases. Therefore, exact staging with radiological and nuclear medicine imaging methods is crucial for defining the adequate therapeutic choice. Tumor cells express the norepinephrine transporter, which makes metaiodobenzylguanidine (MIBG), an analogue of norepinephrine, an ideal tumor specific agent for imaging. MIBG imaging has several disadvantages, such as limited spatial resolution, limited sensitivity in small lesions and the need for two or even more acquisition sessions. Most of these limitations can be overcome with positron emission tomography (PET) using [F-18]2-fluoro-2-deoxyglucose [FDG]. Furthermore, new tracers, such as fluorodopa or somatostatin receptor agonists, have been tested for imaging neuroblastoma recently. However, MIBG scintigraphy and PET alone are not sufficient for operative or biopsy planning. In this regard, a combination with morphological imaging is indispensable. This article will discuss strategies for primary and follow-up diagnosis in neuroblastoma using different nuclear medicine and radiological imaging methods as well as multimodality imaging.

Decentralised system for demand-oriented collection of food waste - Assessment of biomethane potential, pathogen development and microbial community structure.

Enormous amounts of food waste (FW) are produced worldwide, requiring efficient disposal strategies, both economically and ecologically. Anaerobic digestion to produce biomethane is among the most promising strategies, but requires proper solutions for storage and delivery of the waste material. Here, a decentralized system for demand-oriented FW storage and its practical usability was assessed. FW was stored under batch and fed-batch strategies at 5 °C, 20 °C and 30 °C for 28 days. The results showed that FW can be stored without cooling since bacterially produced lactic acid rapidly stabilized the material and inactivated pathogens. While FW storage worked well under all storage conditions and strategies, 16S analysis revealed a distinct microbiota, which was highly characteristic for each storage temperature. Moreover, FW storage had no negative impact on methane yield and stored FW contained readily degradable substances for demand-oriented biogas production.

High-Throughput Phenotypic Screening and Machine Learning Methods Enabled the Selection of Broad-Spectrum Low-Toxicity Antitrypanosomatidic Agents.

Broad-spectrum anti-infective chemotherapy agents with activity against Trypanosomes, Leishmania, and Mycobacterium tuberculosis species were identified from a high-throughput phenotypic screening program of the 456 compounds belonging to the Ty-Box, an in-house industry database. Compound characterization using machine learning approaches enabled the identification and synthesis of 44 compounds with broad-spectrum antiparasitic activity and minimal toxicity against Trypanosoma brucei, Leishmania Infantum, and Trypanosoma cruzi. In vitro studies confirmed the predictive models identified in compound 40 which emerged as a new lead, featured by an innovative N-(5-pyrimidinyl)benzenesulfonamide scaffold and promising low micromolar activity against two parasites and low toxicity. Given the volume and complexity of data generated by the diverse high-throughput screening assays performed on the compounds of the Ty-Box library, the chemoinformatic and machine learning tools enabled the selection of compounds eligible for further evaluation of their biological and toxicological activities and aided in the decision-making process toward the design and optimization of the identified lead.

RightField: embedding ontology annotation in spreadsheets.

MOTIVATION: In the Life Sciences, guidelines, checklists and ontologies describing what metadata is required for the interpretation and reuse of experimental data are emerging. Data producers, however, may have little experience in the use of such standards and require tools to support this form of data annotation. RESULTS: RightField is an open source application that provides a mechanism for embedding ontology annotation support for Life Science data in Excel spreadsheets. Individual cells, columns or rows can be restricted to particular ranges of allowed classes or instances from chosen ontologies. The RightField-enabled spreadsheet presents selected ontology terms to the users as a simple drop-down list, enabling scientists to consistently annotate their data. The result is 'semantic annotation by stealth', with an annotation process that is less error-prone, more efficient, and more consistent with community standards. AVAILABILITY AND IMPLEMENTATION: RightField is open source under a BSD license and freely available from http://www.rightfield.org.uk

Diagnostic value of combined ¹8F-FDG PET/MRI for staging and restaging in paediatric oncology.

PURPOSE: The present study compares the diagnostic value of (18)F-fluorodeoxyglucose (FDG) positron emission tomography (PET) and MRI to combined/registered (18)F-FDG PET/MRI for staging and restaging in paediatric oncology. METHODS: Over 8 years and 2 months, 270 (18)F-FDG PET and 270 MRI examinations (mean interval 5 days) were performed in 132 patients with proven (n = 117) or suspected (n = 15) malignant disease: solid tumours (n = 64), systemic malignancy (n = 53) and benign disease (n = 15). A total of 259 suspected tumour lesions were analysed retrospectively during primary diagnosis and 554 lesions during follow-up. Image analysis was performed separately on each modality, followed by analysis of combined and registered (18)F-FDG PET/MRI imaging. RESULTS: A total of 813 lesions were evaluated and confirmed by histopathology (n = 158) and/or imaging follow-up (n = 655) after 6 months. In the separate analysis of (18)F-FDG PET and MRI, sensitivity was 86 %/94 % and specificity 85 %/38 %. Combined/registered (18)F-FDG PET/MRI led to a sensitivity of 97 %/97 % and specificity of 81 %/82 %. False-positive results ((18)F-FDG PET n = 69, MRI n = 281, combined (18)F-FDG PET/MRI n = 85, registered (18)F-FDG PET/MRI n = 80) were due to physiological uptake or post-therapeutic changes. False-negative results ((18)F-FDG PET n = 50, MRI n = 20, combined (18)F-FDG PET/MRI n = 11, registered (18)F-FDG PET/MRI n = 11) were based on low uptake or minimal morphological changes. Examination-based evaluation during follow-up showed a sensitivity/specificity of 91 %/81 % for (18)F-FDG PET, 93 %/30 % for MRI and 96 %/72 % for combined (18)F-FDG PET/MRI. CONCLUSION: For the detection of single tumour lesions, registered (18)F-FDG PET/MRI proved to be the methodology of choice for adequate tumour staging. In the examination-based evaluation, MRI alone performed better than (18)F-FDG PET and combined/registered imaging during primary diagnosis. At follow-up, however, the examination-based evaluation demonstrated a superiority of (18)F-FDG PET alone.

CD103 is a hallmark of tumor-infiltrating regulatory T cells.

Regulatory T cells (Treg) mediate tolerance towards self-antigens by suppression of innate and adaptive immunity. In cancer patients, tumor-infiltrating FoxP3+ Treg suppress local anti-tumor immune responses and are often associated with poor prognosis. Markers that are selectively expressed on tumor-infiltrating Treg may serve as targets for immunotherapy of cancer. Here we show that CD103, an integrin mediating lymphocyte retention in epithelial tissues, is expressed at high levels on tumor-infiltrating FoxP3+ Treg in several types of murine cancer. In the CT26 model of colon cancer up to 90% of the intratumoral FoxP3+ cells expressed CD103 compared to less than 20% in lymphoid organs. CD103+ Treg suppressed T effector cell activation more strongly than CD103(neg) Treg. Expression of CD103 on Treg closely correlated with intratumoral levels of transforming growth factor ß (TGF-ß) and could be induced in a TGF-ß-dependent manner by tumor cell lines. In vivo, gene silencing of TGF-ß reduced the frequency of CD103+ Treg, demonstrating that CD103 expression on tumor-infiltrating Treg is driven by intratumoral TGF-ß. Functional blockade of CD103 using a monoclonal antibody did however not reduce the number of intratumoral Treg, indicating that CD103 is not involved in homing or retention of FoxP3+ cells in the tumor tissue. In conclusion, expression of CD103 is a hallmark of Treg that infiltrate TGF-ß-secreting tumors. CD103 thus represents an interesting target for selective depletion of tumor-infiltrating Treg, a strategy that may help to improve anti-cancer therapy.

Physarum polymalic acid hydrolase: Recombinant expression and enzyme activation.

As a platform for syntheses of nanoconjugates in antitumor drug delivery, polymalic acid together with its tailoring specific exohydrolase is purified from plasmodium cultures of the slime mold Physarum polycephalum, a member of the phylum myxomycota. Polymalic acid hydrolase is expressed in an inactive form that functions as a molecular adapter for polymalic acid trafficking within the plasmodium and is activated only during secretion. Activation follows specific protein tyrosine phosphorylation and dissociation from plasma membranes. Purified inactive Physarum polymalic acid hydrolase, recombinantly expressed in yeast Saccharomyces, is activated on a preparative basis by the addition of plasma membrane fragments from plasmodia of P. polycephalum. Activation of polymalic acid hydrolase and inhibition of polymalic acid synthesis by protein tyrosine phosphorylation are complementary events and could indicate a joint signal response to plasma membrane damage.

The 5-HT3 receptor antagonist tropisetron inhibits T cell activation by targeting the calcineurin pathway.

Tropisetron, an antagonist of serotonin type 3 receptor, has been investigated in chronic inflammatory joint process. Since T cells play a key role in the onset of several inflammatory diseases, we have evaluated the immunosuppressive activity of tropisetron in human T cells, discovering that this compound is a potent inhibitor of early and late events in TCR-mediated T cell activation. Moreover, we found that tropisetron specifically inhibited both IL-2 gene transcription and IL-2 synthesis in stimulated T cells. To further characterize the inhibitory mechanisms of tropisetron at the transcriptional level, we examined the DNA binding and transcriptional activities of NF-(kappa)B, NFAT and AP-1 transcription factors in Jurkat T cells. We found that tropisetron inhibited both the binding to DNA and the transcriptional activity of NFAT and AP-1. We also observed that tropisetron is a potent inhibitor of PMA plus ionomycin-induced NF-(kappa)B activation but in contrast TNF(alpha)-mediated NF-(kappa)B activation was not affected by this antagonist. Finally, overexpression of a constitutively active form of calcineurin indicated that this phosphatase may represent one of the main targets for the inhibitory activity of tropisetron. These findings provide new mechanistic insights into the anti-inflammatory activities of tropisetron, which are probably independent of serotonin receptor signalling and highlight their potential to design novel therapeutic strategies to manage inflammatory diseases.

SEEK: a systems biology data and model management platform.

BACKGROUND: Systems biology research typically involves the integration and analysis of heterogeneous data types in order to model and predict biological processes. Researchers therefore require tools and resources to facilitate the sharing and integration of data, and for linking of data to systems biology models. There are a large number of public repositories for storing biological data of a particular type, for example transcriptomics or proteomics, and there are several model repositories. However, this silo-type storage of data and models is not conducive to systems biology investigations. Interdependencies between multiple omics datasets and between datasets and models are essential. Researchers require an environment that will allow the management and sharing of heterogeneous data and models in the context of the experiments which created them. RESULTS: The SEEK is a suite of tools to support the management, sharing and exploration of data and models in systems biology. The SEEK platform provides an access-controlled, web-based environment for scientists to share and exchange data and models for day-to-day collaboration and for public dissemination. A plug-in architecture allows the linking of experiments, their protocols, data, models and results in a configurable system that is available 'off the shelf'. Tools to run model simulations, plot experimental data and assist with data annotation and standardisation combine to produce a collection of resources that support analysis as well as sharing. Underlying semantic web resources additionally extract and serve SEEK metadata in RDF (Resource Description Format). SEEK RDF enables rich semantic queries, both within SEEK and between related resources in the web of Linked Open Data. CONCLUSION: The SEEK platform has been adopted by many systems biology consortia across Europe. It is a data management environment that has a low barrier of uptake and provides rich resources for collaboration. This paper provides an update on the functions and features of the SEEK software, and describes the use of the SEEK in the SysMO consortium (Systems biology for Micro-organisms), and the VLN (virtual Liver Network), two large systems biology initiatives with different research aims and different scientific communities.

The SEEK: a platform for sharing data and models in systems biology.

Systems biology research is typically performed by multidisciplinary groups of scientists, often in large consortia and in distributed locations. The data generated in these projects tend to be heterogeneous and often involves high-throughput "omics" analyses. Models are developed iteratively from data generated in the projects and from the literature. Consequently, there is a growing requirement for exchanging experimental data, mathematical models, and scientific protocols between consortium members and a necessity to record and share the outcomes of experiments and the links between data and models. The overall output of a research consortium is also a valuable commodity in its own right. The research and associated data and models should eventually be available to the whole community for reuse and future analysis. The SEEK is an open-source, Web-based platform designed for the management and exchange of systems biology data and models. The SEEK was originally developed for the SysMO (systems biology of microorganisms) consortia, but the principles and objectives are applicable to any systems biology project. The SEEK provides an index of consortium resources and acts as gateway to other tools and services commonly used in the community. For example, the model simulation tool, JWS Online, has been integrated into the SEEK, and a plug-in to PubMed allows publications to be linked to supporting data and author profiles in the SEEK. The SEEK is a pragmatic solution to data management which encourages, but does not force, researchers to share and disseminate their data to community standard formats. It provides tools to assist with management and annotation as well as incentives and added value for following these recommendations. Data exchange and reuse rely on sufficient annotation, consistent metadata descriptions, and the use of standard exchange formats for models, data, and the experiments they are derived from. In this chapter, we present the SEEK platform, its functionalities, and the methods employed for lowering the barriers to adoption of standard formats. As the production of biological data continues to grow, in systems biology and in the life sciences in general, the need to record, manage, and exploit this wealth of information in the future is increasing. We promote the SEEK as a data and model management tool that can be adapted to the specific needs of a particular systems biology project.

Radiosensitivity and repair kinetics of gamma-irradiated leukocytes from sporadic prostate cancer patients and healthy individuals assessed by alkaline comet assay.

BACKGROUND: Impaired DNA repair mechanism is one of the main causes of tumor genesis. Study of intrinsic radiosensitivity of cancer patients in a non-target tissue (e.g. peripheral blood) might show the extent of DNA repair deficiency of cells in affected individuals and might be used a predictor of cancer predisposition. METHODS: Initial radiation-induced DNA damage (ratio of Tail DNA/Head DNA), dose-response curves and kinetics of DNA repair in leukocytes from healthy volunteers and prostate cancer patients were assessed using alkaline comet assay after exposure to 60Co gamma rays. RESULTS: Results showed that higher levels of baseline and gamma rays induced DNA damage in leukocytes of prostate cancer cases than in controls. A similar dose response was obtained for both groups. After a repair time of 24 h following in vitro irradiation, samples from the healthy individuals showed no residual DNA damage in their leukocytes, whereas prostate cancer patients revealed more than 20 percent. Although similar initial radiosensitivity was observed for both groups, the repair kinetics of radiation induced DNA damage of leukocytes from prostate cancer cases and healthy subjects were statistically different. CONCLUSION: These results support the hypothesis that men affected by prostate cancer may have a constitutional genomic instability.