A theorem proving approach for automatically synthesizing visualizations of flow cytometry data.

Background: Polychromatic flow cytometry is a popular technique that has wide usage in the medical sciences, especially for studying phenotypic properties of cells. The high-dimensionality of data generated by flow cytometry usually makes it difficult to visualize. The naive solution of simply plotting two-dimensional graphs for every combination of observables becomes impractical as the number of dimensions increases.

Simultaneous hepatosplenic T-cell lymphoma and myelofibrosis.

Hepatosplenic T-cell lymphoma (HSTL) is a rare T-cell neoplasm of the lymphoid system. This type of lymphoma is characterized by sinusoidal infiltration of spleen, liver, bone marrow and lymph nodes by neoplastic lymphocytes. Here, we discuss a patient who had a left axillary lymph node biopsy with characteristic histological and immunohistochemical features of HSTL.

Characterization of p38 MAPK isoforms for drug resistance study using systems biology approach.

Motivation: p38 mitogen-activated protein kinase activation plays an important role in resistance to chemotherapeutic cytotoxic drugs in treating multiple myeloma (MM). However, how the p38 mitogen-activated protein kinase signaling pathway is involved in drug resistance, in particular the roles that the various p38 isoforms play, remains largely unknown.

Method: To explore the underlying mechanisms, we developed a novel systems biology approach by integrating liquid chromatography-mass spectrometry and reverse phase protein array data from human MM cell lines with computational pathway models in which the unknown parameters were inferred using a proposed novel algorithm called modularized factor graph.

Modeling cell-cell interactions in regulating multiple myeloma initiating cell fate.

Cancer initiating cells have been documented in multiple myeloma and believed to be a key factor that initiates and drives tumor growth, differentiation,metastasis, and recurrence of the diseases. Although myeloma initiating cells (MICs) are likely to share many properties of normal stem cells, the underlying mechanisms regulating the fate of MICs are largely unknown. Studies designed to explore such communication are urgently needed to enhance our ability to predict the fate decisions of ICs (self-renewal, differentiation, and proliferation).

FusionQ: a novel approach for gene fusion detection and quantification from paired-end RNA-Seq.

Background: Gene fusions, which result from abnormal chromosome rearrangements, are a pathogenic factor in cancer development. The emerging RNA-Seq technology enables us to detect gene fusions and profile their features.

Results: In this paper, we proposed a novel fusion detection tool, FusionQ, based on paired-end RNA-Seq data.

Cancer stem cells: a review of potential clinical applications.

Context: Cancer stem cells (CSCs) comprise a minor cell population in a tumor; however, they possess self-renewal capacity and are responsible for tumor recurrence and the emerging issue of tumor resistance. Despite recent advances in the study of pathogenesis and mechanisms of CSC-mediated disease recurrence and multidrug resistance, many questions remain unanswered.

Objectives: To provide an overview of CSC theory and to describe major methods of CSC detection and isolation, with the emphasis on those techniques that are potentially relevant in clinical laboratory practice.

Differentiating between Burkitt lymphoma and CD10+ diffuse large B-cell lymphoma: the role of commonly used flow cytometry cell markers and the application of a multiparameter scoring system.

The goal of this study was to evaluate routine flow cytometric (FC) immunophenotypic markers in differentiating between Burkitt lymphoma (BL) and CD10+ diffuse large B-cell lymphoma (DLBCL). We performed retrospective analysis of FC data from 55 patients. We evaluated 9 FC parameters: forward and side scatter (FSC and SSC); mean fluorescent intensity (MFI) for CD20, CD10, CD38, CD79b, CD43, and CD71; and the percentage of neoplastic cells positive for CD71 (%CD71).

p38 Mitogen-activated protein kinase and hematologic malignancies.

Context: p38 mitogen-activated protein kinase (MAPK) signaling has been implicated in responses ranging from apoptosis to cell cycle, induction of expression of cytokine genes, and differentiation. This plethora of activators conveys the complexity of the p38 pathway. This complexity is further complicated by the observation that the downstream effects of p38 MAPK activation may be different depending on types of stimuli, cell types, and various p38 MAPK isoforms involved.

Intraocular lymphoma: diagnostic approach and immunophenotypic findings in vitrectomy specimens.

Context: Diagnosis and classification of primary intraocular lymphoma can be challenging because of the sparse cellularity of the vitreous specimens.

Objective: To classify and clinically correlate intraocular lymphoma according to the World Health Organization (WHO) classification by using vitrectomy specimens.

Design: Clinical history, cytologic preparations, flow cytometry reports, and outcome of 16 patients diagnosed with intraocular lymphoma were reviewed.

Polymorphisms in TGFbeta and TNFalpha are associated with the myelodysplastic syndrome phenotype.

Context: Myelodysplastic syndromes (MDSs) are characterized by ineffective hematopoiesis, excessive apoptosis, and the aberrant expression of a number of cytokines. The genes encoding these cytokines are significantly polymorphic. It is unknown whether these cytokine polymorphisms are associated with, and may therefore be playing a role in the pathogenesis of, MDS.

Histiocytic sarcoma - a case with evenly distributed multinucleated giant cells.

Histiocytic sarcoma is an uncommon neoplasm of mature histiocytes with a poor clinical outcome. We report a case of a true histiocytic sarcoma with prominent and evenly distributed multinucleated giant cells that mimics a giant cell tumor of soft tissue. The tumor was located between the appendix, right ovary, and the terminal ileum with severe adhesion.

Chronic idiopathic myelofibrosis: clinicopathologic features, pathogenesis, and prognosis.

Context: Chronic idiopathic myelofibrosis (CIMF) is a clonal myeloproliferative disease characterized by panmyelosis with intact maturation, progressive bone marrow fibrosis, and multiorgan extramedullary hematopoiesis.

Objective: This review article aims to summarize the recent updates regarding the clinicopathologic features, molecular pathogenesis, cytogenetic abnormalities, diagnostic criteria, new diagnostic ancillary tests, and prognostic factors of CIMF.

Data Sources: Important relevant articles indexed in PubMed/MEDLINE (National Library of Medicine) through the end of 2005 and referenced medical texts.