Microarray Method for the Rapid Detection of Glycosaminoglycan–Protein Interactions

Glycosaminoglycans (GAGs) perform numerous vital functions within the body. As major components of the extracellular matrix, these polysaccharides participate in a diverse array of cell-signaling events. We have developed a simple microarray assay for the evaluation of protein binding to various GAG subclasses. In a single experiment, the binding to all members of the GAG family can be rapidly determined, giving insight into the relative specificity of the interactions and the importance of specific sulfation motifs. The arrays are facile to prepare from commercially available materials

Intra-operative spectroscopic assessment of surgical margins during breast conserving surgery

Background: In over 20% of breast conserving operations, postoperative pathological assessment of the excised tissue reveals positive margins, requiring additional surgery. Current techniques for intra-operative assessment of tumor margins are insufficient in accuracy or resolution to reliably detect small tumors. There is a distinct need for a fast technique to accurately identify tumors smaller than 1 mm2 in large tissue surfaces within 30 min. Methods: Multi-modal spectral histopathology (MSH), a multimodal imaging technique combining tissue auto-fluorescence and Raman spectroscopy was used to detect microscopic residual tumor at the surface of the excised breast tissue. New algorithms were developed to optimally utilize auto-fluorescence images to guide Raman measurements and achieve the required detection accuracy over large tissue surfaces (up to 4 × 6.5 cm2). Algorithms were trained on 91 breast tissue samples from 65 patients. Results: Independent tests on 121 samples from 107 patients - including 51 fresh, whole excision specimens - detected breast carcinoma on the tissue surface with 95% sensitivity and 82% specificity. One surface of each uncut excision specimen was measured in 12–24 min. The combination of high spatial-resolution auto-fluorescence with specific diagnosis by Raman spectroscopy allows reliable detection even for invasive carcinoma or ductal carcinoma in situ smaller than 1 mm2. Conclusions: This study provides evidence that this multimodal approach could provide an objective tool for intra-operative assessment of breast conserving surgery margins, reducing the risk for unnecessary second operations

Modeling Magnification and Anisotropy in the Primate Foveal Confluence

A basic organizational principle of the primate visual system is that it maps the visual environment repeatedly and retinotopically onto cortex. Simple algebraic models can be used to describe the projection from visual space to cortical space not only for V1, but also for the complex of areas V1, V2 and V3. Typically a conformal (angle-preserving) projection ensuring local isotropy is regarded as ideal and primate visual cortex is often regarded as an approximation of this ideal. However, empirical data show systematic deviations from this ideal that are especially relevant in the foveal projection. The aims of this study were to map the nature of anisotropy predicted by existing models, to investigate the optimization targets faced by different types of retino-cortical maps, and finally to propose a novel map that better models empirical data than other candidates. The retino-cortical map can be optimized towards a space-conserving homogenous representation or a quasi-conformal mapping. The latter would require a significantly enlarged representation of specific parts of the cortical maps. In particular it would require significant enlargement of parafoveal V2 and V3 which is not supported by empirical data. Further, the recently published principal layout of the foveal singularity cannot be explained by existing models. We suggest a new model that accurately describes foveal data, minimizing cortical surface area in the periphery but suggesting that local isotropy dominates the most foveal part at the expense of additional cortical surface. The foveal confluence is an important example of the detailed trade-offs between the compromises required for the mapping of environmental space to a complex of neighboring cortical areas. Our models demonstrate that the organization follows clear morphogenetic principles that are essential for our understanding of foveal vision in daily life

Clear cell variant of diffuse large B-cell lymphoma: a case report

<p>Abstract</p> <p>Introduction</p> <p>Diffuse large B-cell lymphoma is a diffuse proliferation of large neoplastic B lymphoid cells with a nuclear size equal to or exceeding the normal macrophage nuclei. We report a case of a clear cell variant of diffuse large B-cell lymphoma involving a lymph node in the neck, which was clinically suspected of being metastatic carcinoma.</p> <p>Case presentation</p> <p>A 39-year-old Caucasian ethnic Albanian man from Kosovo presented with a rapidly enlarging lymph node in his neck, but he also disclosed B symptoms and fatigue. A cytological aspirate of the lymph node revealed pleomorphic features. Our patient underwent a cervical lymph node biopsy (large excision). The mass was homogeneously fish-flesh, pale white tissue replacing almost the whole structure of the lymph node. The lymph node biopsy showed a partial alveolar growth pattern, which raised clinical suspicion that it was an epithelial neoplasm. With regard to morphological and phenotypic features, we discovered large nodules in diffuse areas, comprising large cells with slightly irregular nuclei and clear cytoplasm admixed with a few mononuclear cells. In these areas, there was high mitotic activity, and in some areas there were macrophages with tangible bodies. Staining for cytokeratins was negative. These areas had the following phenotypes: cluster designation marker 20 (CD20) positive, B-cell lymphoma (Bcl)-2-positive, Bcl-6^-, CD5^-, CD3^-, CD21⁺(in alveolar patterns), prostate-specific antigen-negative, human melanoma black marker 45-negative, melanoma marker-negative, cytokeratin-7-negative and multiple myeloma marker 1-positive in about 30% of cells, and exhibited a high proliferation index marker (Ki-67, 80%).</p> <p>Conclusion</p> <p>According to the immunohistochemical findings, we concluded that this patient has a clear cell variant of diffuse large B-cell lymphoma of activated cell type, post-germinal center cell origin. Our patient is undergoing R-CHOP chemotherapy treatment.</p

Feature selection using Haar wavelet power spectrum

BACKGROUND: Feature selection is an approach to overcome the 'curse of dimensionality' in complex researches like disease classification using microarrays. Statistical methods are utilized more in this domain. Most of them do not fit for a wide range of datasets. The transform oriented signal processing domains are not probed much when other fields like image and video processing utilize them well. Wavelets, one of such techniques, have the potential to be utilized in feature selection method. The aim of this paper is to assess the capability of Haar wavelet power spectrum in the problem of clustering and gene selection based on expression data in the context of disease classification and to propose a method based on Haar wavelet power spectrum. RESULTS: Haar wavelet power spectra of genes were analysed and it was observed to be different in different diagnostic categories. This difference in trend and magnitude of the spectrum may be utilized in gene selection. Most of the genes selected by earlier complex methods were selected by the very simple present method. Each earlier works proved only few genes are quite enough to approach the classification problem [1]. Hence the present method may be tried in conjunction with other classification methods. The technique was applied without removing the noise in data to validate the robustness of the method against the noise or outliers in the data. No special softwares or complex implementation is needed. The qualities of the genes selected by the present method were analysed through their gene expression data. Most of them were observed to be related to solve the classification issue since they were dominant in the diagnostic category of the dataset for which they were selected as features. CONCLUSION: In the present paper, the problem of feature selection of microarray gene expression data was considered. We analyzed the wavelet power spectrum of genes and proposed a clustering and feature selection method useful for classification based on Haar wavelet power spectrum. Application of this technique in this area is novel, simple, and faster than other methods, fit for a wide range of data types. The results are encouraging and throw light into the possibility of using this technique for problem domains like disease classification, gene network identification and personalized drug design

Health workforce development planning in the Sultanate of Oman: a case study

<p>Abstract</p> <p>Introduction</p> <p>Oman's recent experience in health workforce development may be viewed against the backdrop of the situation just three or four decades ago, when it had just a few physicians and nurses (mostly expatriate). All workforce categories in Oman have grown substantially over the last two decades. Increased self-reliance was achieved despite substantial growth in workforce stocks. Stocks of physicians and nurses grew significantly during 1985–2007. This development was the outcome of well-considered national policies and plans. This case outlines how Oman is continuing to turn around its excessive dependence on expatriate workforce through strategic workforce development planning.</p> <p>Case description</p> <p>The Sultanate's early development initiatives focused on building a strong health care infrastructure by importing workforce. However, the policy-makers stressed national workforce development for a sustainable future. Beginning with the formulation of a strategic health workforce development plan in 1991, the stage was set for adopting workforce planning as an essential strategy for sustainable health development and workforce self-reliance. Oman continued to develop its educational infrastructure, and began to produce as much workforce as possible, in order to meet health care demands and achieve workforce self-reliance.</p> <p>Other policy initiatives with a beneficial impact on Oman's workforce development scenario were: regionalization of nursing institutes, active collaboration with universities and overseas specialty boards, qualitative improvement of the education system, development of a strong continuing professional development system, efforts to improve workforce management, planned change management and needs-based micro/macro-level studies. Strong political will and bold policy initiatives, dedicated workforce planning and educational endeavours have all contributed to help Oman to develop its health workforce stocks and gain self-reliance.</p> <p>Discussion and evaluation</p> <p>Oman has successfully innovated workforce planning within a favorable policy environment. Its intensive and extensive workforce planning efforts, with the close involvement of policy-makers, educators and workforce managers, have ensured adequacy of suitable workforce in health institutions and its increased self-reliance in the health workforce.</p> <p>Conclusion</p> <p>Oman's experience in workforce planning and development presents an illustration of a country benefiting from successful application of workforce planning concepts and tools. Instead of being complacent about its achievements so far, every country needs to improve or sustain its planning efforts in this way, in order to circumvent the current workforce deficiencies and to further increase self-reliance and improve workforce efficiency and effectiveness.</p

Metal-Free ALS Variants of Dimeric Human Cu,Zn-Superoxide Dismutase Have Enhanced Populations of Monomeric Species

Amino acid replacements at dozens of positions in the dimeric protein human, Cu,Zn superoxide dismutase (SOD1) can cause amyotrophic lateral sclerosis (ALS). Although it has long been hypothesized that these mutations might enhance the populations of marginally-stable aggregation-prone species responsible for cellular toxicity, there has been little quantitative evidence to support this notion. Perturbations of the folding free energy landscapes of metal-free versions of five ALS-inducing variants, A4V, L38V, G93A, L106V and S134N SOD1, were determined with a global analysis of kinetic and thermodynamic folding data for dimeric and stable monomeric versions of these variants. Utilizing this global analysis approach, the perturbations on the global stability in response to mutation can be partitioned between the monomer folding and association steps, and the effects of mutation on the populations of the folded and unfolded monomeric states can be determined. The 2- to 10-fold increase in the population of the folded monomeric state for A4V, L38V and L106V and the 80- to 480-fold increase in the population of the unfolded monomeric states for all but S134N would dramatically increase their propensity for aggregation through high-order nucleation reactions. The wild-type-like populations of these states for the metal-binding region S134N variant suggest that even wild-type SOD1 may also be prone to aggregation in the absence of metals

First-line high-dose sequential chemotherapy with rG-CSF and repeated blood stem cell transplantation in untreated inflammatory breast cancer: toxicity and response (PEGASE 02 trial)

Despite the generalization of induction chemotherapy and a better outcome for chemosensitive diseases, the prognosis of inflammatory breast cancer (IBC) is still poor. In this work, we evaluate response and toxicity of high-dose sequential chemotherapy with repeated blood stem cell (BSC) transplantation administered as initial treatment in 100 women with non-metastatic IBC. Ninety-five patients (five patients were evaluated as non-eligible) of median age 46 years (range 26–56) received four cycles of chemotherapy associating: cyclophosphamide (C) 6 g m−2 – doxorubicin (D) 75 mg m−2 cycle 1, C: 3 g m−2 – D: 75 mg m−2 cycle 2, C: 3 g m−2 – D: 75 mg m−2 – 5 FU 2500 mg m−2 cycle 3 and 4. BSC were collected after cycle 1 or 2 and reinfused after cycle 3 and 4. rG-CSF was administered after the four cycles. Mastectomy and radiotherapy were planned after chemotherapy completion. Pathological response was considered as the first end point of this trial. A total of 366 cycles of chemotherapy were administered. Eighty-seven patients completed the four cycles and relative dose intensity was respectively 0.97 (range 0.4–1.04) and 0.96 (range 0.25–1.05) for C and D. Main toxicity was haematological with febrile neutropenia ranging from 26% to 51% of cycles; one death occurred during aplasia. Clinical response rate was 90% ± 6%. Eighty-six patients underwent mastectomy in a median of 3.5 months (range 3–9) after the first cycle of chemotherapy; pathological complete response rate in breast was 32% ± 10%. All patients were eligible to receive additional radiotherapy. High-dose chemotherapy with repeated BSC transplantation is feasible with acceptable toxicity in IBC. Pathological response rate is encouraging but has to be confirmed by final outcome. © 1999 Cancer Research Campaig

Chondroitin sulfates and their binding molecules in the central nervous system

Chondroitin sulfate (CS) is the most abundant glycosaminoglycan (GAG) in the central nervous system (CNS) matrix. Its sulfation and epimerization patterns give rise to different forms of CS, which enables it to interact specifically and with a significant affinity with various signalling molecules in the matrix including growth factors, receptors and guidance molecules. These interactions control numerous biological and pathological processes, during development and in adulthood. In this review, we describe the specific interactions of different families of proteins involved in various physiological and cognitive mechanisms with CSs in CNS matrix. A better understanding of these interactions could promote a development of inhibitors to treat neurodegenerative diseases

Raman spectroscopy: techniques and applications in the life sciences

Raman spectroscopy is an increasingly popular technique in many areas including biology and medicine. It is based on Raman scattering, a phenomenon in which incident photons lose or gain energy via interactions with vibrating molecules in a sample. These energy shifts can be used to obtain information regarding molecular composition of the sample with very high accuracy. Applications of Raman spectroscopy in the life sciences have included quantification of biomolecules, hyperspectral molecular imaging of cells and tissue, medical diagnosis, and others. This review briefly presents the physical origin of Raman scattering explaining the key classical and quantum mechanical concepts. Variations of the Raman effect will also be considered, including resonance, coherent, and enhanced Raman scattering. We discuss the molecular origins of prominent bands often found in the Raman spectra of biological samples. Finally, we examine several variations of Raman spectroscopy techniques in practice, looking at their applications, strengths, and challenges. This review is intended to be a starting resource for scientists new to Raman spectroscopy, providing theoretical background and practical examples as the foundation for further study and exploration