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1.  Dicoogle, a Pacs Featuring Profiled Content Based Image Retrieval 
PLoS ONE  2013;8(5):e61888.
Content-based image retrieval (CBIR) has been heralded as a mechanism to cope with the increasingly larger volumes of information present in medical imaging repositories. However, generic, extensible CBIR frameworks that work natively with Picture Archive and Communication Systems (PACS) are scarce. In this article we propose a methodology for parametric CBIR based on similarity profiles. The architecture and implementation of a profiled CBIR system, based on query by example, atop Dicoogle, an open-source, full-fletched PACS is also presented and discussed. In this solution, CBIR profiles allow the specification of both a distance function to be applied and the feature set that must be present for that function to operate. The presented framework provides the basis for a CBIR expansion mechanism and the solution developed integrates with DICOM based PACS networks where it provides CBIR functionality in a seamless manner.
doi:10.1371/journal.pone.0061888
PMCID: PMC3646026  PMID: 23671578
2.  Dicoogle - an Open Source Peer-to-Peer PACS 
Journal of Digital Imaging  2010;24(5):848-856.
Picture Archiving and Communication Systems (PACS) have been widely deployed in healthcare institutions, and they now constitute a normal commodity for practitioners. However, its installation, maintenance, and utilization are still a burden due to their heavy structures, typically supported by centralized computational solutions. In this paper, we present Dicoogle, a PACS archive supported by a document-based indexing system and by peer-to-peer (P2P) protocols. Replacing the traditional database storage (RDBMS) by a documental organization permits gathering and indexing data from file-based repositories, which allows searching the archive through free text queries. As a direct result of this strategy, more information can be extracted from medical imaging repositories, which clearly increases flexibility when compared with current query and retrieval DICOM services. The inclusion of P2P features allows PACS internetworking without the need for a central management framework. Moreover, Dicoogle is easy to install, manage, and use, and it maintains full interoperability with standard DICOM services.
doi:10.1007/s10278-010-9347-9
PMCID: PMC3180530  PMID: 20981467
PACS; Digital Imaging and Communications in Medicine (DICOM); Medical imaging; Peer-to-peer; Computer communication networks; Open source; PACS implementation; Information storage and retrieval
3.  Live Imaging of Mouse Endogenous Neural Progenitors Migrating in Response to an Induced Tumor 
PLoS ONE  2012;7(9):e44466.
Adult neurogenesis is restricted to specific brain regions. Although involved in the continuous supply of interneurons for the olfactory function, the role of neural precursors in brain damage-repair remains an open question. Aiming to in vivo identify endogenous neural precursor cells migrating towards a brain damage site, the monoclonal antibody Nilo2 recognizing cell surface antigens on neuroblasts, was coupled to magnetic glyconanoparticles (mGNPs). The Nilo2-mGNP complexes allowed, by magnetic resonance imaging in living animals, the in vivo identification of endogenous neural precursors at their niche, as well as their migration to a lesion site (induced brain tumor), which was fast (within hours) and orderly. Interestingly, the rapid migration of neuroblasts towards a damage site is a characteristic that might be exploited to precisely localize early damage events in neurodegenerative diseases. In addition, it might facilitate the study of regenerative mechanisms through the activation of endogenous neural cell precursors. A similar approach, combining magnetic glyconanoparticles linked to appropriate antibodies could be applied to flag other small cell subpopulations within the organism, track their migration, localize stem cell niches, cancer stem cells or even track metastatic cells.
doi:10.1371/journal.pone.0044466
PMCID: PMC3434138  PMID: 22957072
4.  Image Denoising Methods for Tumor Discrimination in High-Resolution Computed Tomography 
Journal of Digital Imaging  2010;24(3):464-469.
Pixel accuracy in images from high-resolution computed tomography (HRCT) is ultimately limited by reconstruction error and noise. While for visual analysis this may not be relevant, for computer-aided quantitative analysis in either densitometric, or shape studies aiming at accurate results, the impact of pixel uncertainty must be taken into consideration. In this work, we study several denoising methods: geometric mean filter, Wiener filtering, and wavelet denoising. The performance of each method was assessed through visual inspection, profile region intensity analysis, and global figures of merit, using images from brain and thoracic phantoms, as well as several real thoracic HRCT images.
doi:10.1007/s10278-010-9305-6
PMCID: PMC3092045  PMID: 20503063
Denoising methods; tomographic reconstruction; Poisson noise; computed tomography
5.  The emergence and current performance of a health research system: lessons from Guinea Bissau 
Background
Little is known about how health research systems (HRS) in low-income countries emerge and evolve over time, and how this process relates to their performance. Understanding how HRSs emerge is important for the development of well functioning National Health Research Systems (NHRS). The aim of this study was to assess how the HRS in Guinea Bissau has emerged and evolved over time and how the present system functions.
Methods
We used a qualitative case-study methodology to explore the emergence and current performance of the HRS, using the NHRS framework. We reviewed documents and carried out 39 in-depth interviews, ranging from health research to policy and practice stakeholders. Using an iterative approach, we undertook a thematic analysis of the data.
Results
The research practices in Guinea Bissau led to the emergence of a HRS with both local and international links and strong dependencies on international partners and donors. The post-colonial, volatile and resource-dependent context, changes in donor policies, training of local researchers and nature of the research findings influenced how the HRS evolved. Research priorities have mostly been set by 'expatriate' researchers and focused on understanding and reducing child mortality. Research funding is almost exclusively provided by foreign donors and international agencies. The training of Guinean researchers started in the mid-nineties and has since reinforced the links with the health system, broadened the research agenda and enhanced local use of research. While some studies have made an important contribution to global health, the use of research within Guinea Bissau has been constrained by the weak and donor dependent health system, volatile government, top-down policies of international agencies, and the controversial nature of some of the research findings.
Conclusions
In Guinea Bissau a de facto 'system' of research has emerged through research practices and co-evolving national and international research and development dynamics. If the aim of research is to contribute to local decision making, it is essential to modulate the emerged system by setting national research priorities, aligning funding, building national research capacity and linking research to decision making processes. Donors and international agencies can contribute to this process by coordinating their efforts and aligning to national priorities.
doi:10.1186/1478-4505-10-5
PMCID: PMC3295730  PMID: 22321566
6.  Population densities and genetic diversity of actinomycetes associated to the rhizosphere of Theobroma cacao 
Brazilian Journal of Microbiology  2008;39(3):464-470.
In spite of the acknowledged importance of growth-promoting bacteria, only a reduced number of studies were conducted with these microorganisms on Theobroma cacao. The objectives of this work were to study the population densities and genetic diversity of actinomycetes associated with the rhizosphere of cacao as a first step in their application in plant growth promotion and biological control. The populations densities of actinomycetes in soil and cacao roots were similar, with mean values of 1,0 x 106 CFU/g and 9,6 x 105 CFU/g, respectively. All isolates selected and used in this study were identified through sequencing analyses of a fragment of the rpoB gene that encodes the β-subunit of the RNA polymerase as species of the genus Streptomyces. In vitro cellulolytic, xilanolytic and chitinolytic activity, indolacetic acid production and phosphate solubilization activities were observed in most of the isolates tested. The data obtained in this study demonstrate that actinomycetes account for a higher percentage of the total population of culturable bacteria in soil than on cacao roots. Additionally, actinomycetes from the cacao rhizosphere are genetically diverse and have potential applications as agents of growth promotion.
doi:10.1590/S1517-838220080003000010
PMCID: PMC3768440  PMID: 24031247
cacao; rpoB sequence analyses; Streptomyces spp.
7.  Src Family Kinases Are Required for Prolactin Induction of Cell Proliferation 
Molecular Biology of the Cell  2001;12(7):2171-2183.
Prolactin (PRL) is a pleiotropic cytokine promoting cellular proliferation and differentiation. Because PRL activates the Src family of tyrosine kinases (SFK), we have studied the role of these kinases in PRL cell proliferation signaling. PRL induced [3H]thymidine incorporation upon transient transfection of BaF-3 cells with the PRL receptor. This effect was inhibited by cotransfection with the dominant negative mutant of c-Src (K>A295/Y>F527, SrcDM). The role of SFK in PRL-induced proliferation was confirmed in the BaF-3 PRL receptor-stable transfectant, W53 cells, where PRL induced Fyn and Lyn activation. The SFK-selective inhibitors PP1/PP2 and herbimycin A blocked PRL-dependent cell proliferation by arresting the W53 cells in G1, with no evident apoptosis. In parallel, PP1/PP2 inhibited PRL induction of cell growth-related genes c-fos, c-jun, c-myc, and odc. These inhibitors have no effect on PRL-mediated activation of Ras/Mapk and Jak/Start pathways. In contrast, they inhibited the PRL-dependent stimulation of the SFKs substrate Sam68, the phosphorylation of the tyrosine phosphatase Shp2, and the PI3K-dependent Akt and p70S6k serine kinases. Consistently, transient expression of SrcDM in W53 cells also blocked PRL activation of Akt. These results demonstrate that activation of SFKs is required for cell proliferation induced by PRL.
PMCID: PMC55670  PMID: 11452011

Results 1-7 (7)