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At least 127 records · Page 7Linked to original sources

PubMed1997

Inter- and intrainstitutional evaluation of automated volumetric capillary cytometry for the quantitation of CD4- and CD8-positive T lymphocytes in the peripheral blood of persons infected with human immunodeficiency virus. Site Investigators and the NIAID New CD4 Technologies Focus Group.

Volumetric capillary cytometry (VCC) is a new technology that involves the detection and enumeration of dually fluorochrome-labeled cells in a precise volume. We compared the accuracy and precision of VCC with the accuracy and precision of flow cytometry and hematology (F&H) for the measurement of the absolute numbers of CD4 and CD8 T cells in the whole blood of patients infected with human immunodeficiency virus. Five laboratories, each with a different F&H system and certified by the National institute of Allergy and Infectious Diseases flow cytometry proficiency testing program, were shipped aliquots of the same samples from a central site in addition to procuring samples locally. In general, the VCC technology generated CD4 and CD8 T-cell counts which were lower than those obtained with F&H. Intralaboratory variability of replicate CD4 T-cell determinations was similar for both technologies except in the local samples with CD4 counts less than 200/microliters, where the VCC variability was higher than the F&H variability. Interlaboratory variability on replicate CD4 T-cell counts made by VCC was significantly less than that when counts were made by F&H. The VCC instrument has automated CD4 and CD8 T-cell enumeration in whole blood and has consolidated the process to a single platform. Its performance in this evaluation indicates that it may represent a viable alternative to F&H for obtaining absolute T-cell subset counts.

Analysis of Variance↗

PubMed2000

Evaluation of TruCount absolute-count tubes for determining CD4 and CD8 cell numbers in human immunodeficiency virus-positive adults. Site Investigators and The NIAID DAIDS New Technologies Evaluation Group.

A single-platform technology that uses an internal bead standard and three-color flow cytometry to determine CD4 and CD8 absolute counts was evaluated for reproducibility and agreement. Values obtained using TruCount absolute-count tubes were compared to those obtained using a two-color predicate methodology. Sixty specimens from human immunodeficiency virus type 1-infected donors were shipped to five laboratories. Each site also analyzed replicates of 14 human immunodeficiency virus type 1-infected local specimens at 6 h and again at 24 h. The interlaboratory variability was significantly less with TruCount (median difference in percent coefficient of variation [%CV] between the two methods was -8% and -3% for CD4 and CD8, respectively) than with the predicate method. Intralaboratory variability was smaller, with a median difference in %CV of -1% for both CD4 and CD8 with 6-h samples and -2% and -3% for CD4 and CD8, respectively, with 24-h samples. Use of TruCount for shipped samples resulted in a median CD4 count change of 7 cells (50th estimated percentile) when all laboratories and CD4 strata were combined. For on-site samples, the median CD4 count change was 10 CD4 cells for 6-h samples and 2 CD4 cells for 24-h samples. Individual site biases occurred in both directions and cancelled each other when the data were combined for all laboratories. Thus, the combined data showed a smaller change in median CD4 count than what may have occurred at an individual site. In summary, the use of TruCount decreased both the inter- and intralaboratory variability in determining absolute CD4 and CD8 counts.

Acquired Immunodeficiency Syndrome↗

PubMed1999

Mycobacterium species identification and rifampin resistance testing with high-density DNA probe arrays.

Species identification within the genus Mycobacterium and subsequent antibiotic susceptibility testing still rely on time-consuming, culture-based methods. Despite the recent development of DNA probes, which greatly reduce assay time, there is a need for a single platform assay capable of answering the multitude of diagnostic questions associated with this genus. We describe the use of a DNA probe array based on two sequence databases: one for the species identification of mycobacteria (82 unique 16S rRNA sequences corresponding to 54 phenotypical species) and the other for detecting Mycobacterium tuberculosis rifampin resistance (rpoB alleles). Species identification or rifampin resistance was determined by hybridizing fluorescently labeled, amplified genetic material generated from bacterial colonies to the array. Seventy mycobacterial isolates from 27 different species and 15 rifampin-resistant M. tuberculosis strains were tested. A total of 26 of 27 species were correctly identified as well as all of the rpoB mutants. This parallel testing format opens new perspectives in terms of patient management for bacterial diseases by allowing a number of genetic tests to be simultaneously run.

Antibiotics, Antitubercular↗

PubMed2026

Decoding glioblastoma evolution and heterogeneity through mechanistic modeling: implications for clinical translation.

Glioblastoma (GBM) is one of the most aggressive and lethal primary brain tumors in adults, characterized by dynamic clonal evolution and extensive genomic, cellular, spatial, and microenvironmental heterogeneity. Multi-omics studies have revealed that GBM follows complex evolutionary trajectories involving genetic, epigenetic, transcriptional, and immune-microenvironmental remodeling as tumors grow, adapt to the brain microenvironment, and acquire therapeutic resistance. Increasing evidence suggests that GBM may originate from aberrant neural stem or progenitor cells, including those residing in the subventricular zone, and that glioblastoma stem cells (GSCs) contribute to tumor propagation, heterogeneity, and recurrence. A key conceptual challenge is to reconcile hierarchical cancer stem cell models, in which GSCs are viewed as relatively stable tumor-propagating subpopulations, with dynamic state plasticity models, in which stem-like properties can be reversibly acquired or lost during transitions among proneural-like, mesenchymal-like, invasive, and therapy-tolerant states. Recent advances in single-cell profiling, spatial transcriptomics, lineage tracing, organoid culture, 3D bioprinting, genetically engineered models, and artificial intelligence (AI)-assisted computational modeling have substantially improved the ability to study these processes. However, no currently available model fully recapitulates human GBM heterogeneity, recurrence, treatment history, and tumor-microenvironment interactions. Therefore, model selection should be guided by clearly defined mechanistic questions rather than by reliance on any single platform. This review summarizes current advances in in vitro, ex vivo, in vivo, and computational models for studying GBM evolution and heterogeneity, and discusses how integrated model pipelines may improve preclinical drug testing, treatment-response prediction, and precision neuro-oncology.

Humans↗

PubMed2003

Efficient storage and transmission of ladar imagery.

We develop novel methods for compressing volumetric imagery that has been generated by single-platform (mobile) range sensors. We exploit the correlation structure inherent in multiple views in order to improve compression efficiency. We show that, for lossless compression, three-dimensional volumes compress more efficiently than two-dimensional (2D) images by a factor of 60%. Furthermore, our error metric for lossy compression suggests that accumulating more than nine range images in one volume before compression yields as much as a 99% improvement in compression performance over 2D compression.

Journal Article↗

PubMed2006

[DNA microarray based rapid drug susceptibility test for Mycobacterium leprae].

Antibiotic susceptibility test of Mycobacterium leprae still relies on the time consuming methods based on the growth of M. leprae in the mouse footpad. Thus, the establishment of a rapid, simple and reliable method for the detection of drug-resistant M. leprae is one of the most urgent subjects in the treatment of leprosy patients. Recently, many data on the mutation of specific genes correlating with drug resistance have been accumulated. Application of these data permit the establishment of new gene diagnostic methods for drug susceptibility test of leprosy. In this paper, the method using the low density oligonucleotide array that enables the detection of base substitutions involved in resistance against anti-leprosy drugs on a single platform was discussed. The low density oligonucleotide array described in this paper will open the new perspectives in terms of patient management for leprosy with low cost requirement.

Animals↗

PubMed2001

An update on the use of flow cytometry in HIV infection and AIDS.

Flow cytometry has played an invaluable role in recent advances made against HIV and AIDS, and there is every reason to expect it will continue to do so. Newer-generation machines, using three- and four-color panels, make measurements of lymphocyte subsets ever more accurate and potentially cost-effective. Similarly, recent single-platform techniques promise even more efficiencies, freeing CD4 enumeration from parallel determination of the CBC. In other developments, quantitative reporting of immunophenotype may well change the way subsets traditionally defined by qualitative determinations are viewed. The most promising initial candidates for such changes are surrogates of immune activation, such as CD38 expression on CD8 cells. But technical demonstration of reproducibility and reliability, and clinical trial evidence of utility--especially as measured against such established laboratory parameters as CD4 cell and HIV RNA determinations--are needed before a change from qualitative to quantitative immunophenotype measurement can be widely accepted. Although too soon to tell if they will emerge from the research arena into the clinical arena, tetramer binding, intracellular cytokine detection, and assays of cell division are rapidly advancing understanding of HIV-disease, and indeed understanding of all of human immunology. Some of these assays provide often subtly different information, and together they will help determine the most important surrogate measures of clinical immunity. Identifying such surrogates is critical to developing a rational HIV vaccine. The power of flow cytometry is its ability simultaneously to analyze data in four, five, six, or more dimensions. For longitudinal experiments, time adds yet another dimension. Humans struggle to think past three dimensions; interpreting results from experimental permutations and combinations that expand geometrically with each additional parameter studied requires considerable effort. Ultimately computer programs might come to our aid, but for now we have to live with the information overload if we hope to gain insight into the workings of complex biologic systems. In a world of limited resources, and with limited capacity to conceptualize in multiple dimensions, insight, inspiration, and perhaps a little luck are needed to ask the right questions and use the right assays if the recent string of advances against AIDS is to continue.

Acquired Immunodeficiency Syndrome↗

PubMed2002

Picture archiving and computing systems: the key to enterprise digital imaging.

The utopian view of the electronic medical record includes the digital transformation of all aspects of patient information. Historically, imagery from the radiology, cardiology, ophthalmology, and pathology departments, as well as the emergency room, has been a morass of paper, film, and other media, isolated within each department's system architecture. In answer to this dilemma, picture archiving and computing systems have become the focal point of efforts to create a single platform for the collection, storage, and distribution of clinical imagery throughout the health care enterprise.

Decision Making, Organizational↗

PubMed2003

Clinical utility of the absolute number of circulating CD34-positive cells in patients with chronic myeloproliferative disorders.

BACKGROUND AND OBJECTIVES: Flow cytometry enumeration of peripheral blood CD34-positive cells provides reliable measurements of circulating hematopoietic progenitors in humans. Since the absolute number of circulating CD34-positive cells has been previously found to be elevated in myelofibrosis with myeloid metaplasia (MMM), we prospectively studied the clinical utility of this parameter in the work-up of patients with chronic myeloproliferative disorders. DESIGN AND METHODS: Of the 248 consecutive patients enrolled in this study, 106 had polycythemia vera (PV), 90 essential thrombocythemia (ET), and 52 myelofibrosis with myeloid metaplasia (MMM). The study population included both newly diagnosed and established cases, and of these latter some patients were on cytoreductive treatment while others were chemotherapy naive. Both cross-sectional and longitudinal investigations were carried out. Flow cytometry enumeration of CD34-positive cells was performed using a single-platform assay. RESULTS: Median numbers and ranges of circulating CD34-positive cells were 2.3x10(6)/L (0-5) in 20 control subjects, 2.2x10(6)/L (0-14) in those with PV, 2.4x10(6)/L (0-14) in those with ET, and 114x10(6)/L (6-2,520) in MMM patients. Analysis of variance demonstrated that values were markedly higher in MMM patients than in the remaining groups, and counts did not appear to fluctuate over short periods of follow-up. In both cross-sectional and longitudinal investigations on patients at clinical onset and/or out of cytoreductive treatment, a CD34-positive count of > or = 15x10(6)/L was always associated with MMM, clearly indicating a disease-related specificity. INTERPRETATION AND CONCLUSIONS: The absolute number of circulating CD34-positive cells is normal or anyhow lower than 15x10(6)/L in patients with uncomplicated PV or ET, whereas it is equal or above this cut-off in those with MMM, likely reflecting abnormal hematopoietic progenitor cell trafficking. Thus, enumeration of circulating CD34-positive cells may be useful in the work-up of patients with myeloproliferative disorders.

Adolescent↗

PubMed2004

Strategies to control costs and quality: a focus on outcomes research for disease management.

Rapid adoption of disease management has outpaced systematic evaluation of its net value in improving health outcomes and mitigating healthcare cost. This article identifies areas in which outcomes research in disease management is needed to demonstrate its value or to enhance its performance. Patient identification for disease management relies on administrative database queries but the trade-offs in sensitivity, specificity, and predictive value of alternative queries are not well known. Large-scale deployment, rapid patient engagement, and repeated interactions between patients and nurses could be important attributes for attaining measurable improvements in quality and cost reduction over short periods of time, but these hypothesis need to be tested. There is a trend toward integration of multiple chronic disease management programs onto a single platform. To support this trend, there is a need for a corresponding set of integrated clinical guidelines or "meta-guidelines" that combine the contents of individual practice guidelines. The relative contribution of various disease management interventions in improving clinical results, lowering costs, and their respective ease of implementation is not known. Research leading to a better understanding of tradeoffs could lead to more rational resource allocation and better overall outcomes. Coordination between disease management programs and physician practices is lacking. Research aimed at defining operational and technical interfaces and cultural and behavioral professional adjustments necessary to achieve integration and coordination is needed. The lack of a consistent analytical framework for evaluating clinical and financial outcomes has made comparisons of reported results impossible and has rendered many reports unreliable. Theoretical work on a standard methodology that integrates clinical and financial outcomes and empiric validation is needed.

Aged↗

PubMed2003

Acute leukemia: subtype discovery and prediction of outcome by gene expression profiling.

Contemporary treatment of acute leukemia requires the accurate assignment of patients at diagnosis to specific risk groups. To determine whether gene expression profiling could enhance risk assignment, we used oligonucleotide microarrays to analyze the pattern of genes expressed in leukemic blasts from 360 pediatric ALL patients and 130 pediatric AML patients. Our analysis demonstrates that the single platform of gene expression profiling can accurately identify the known prognostically important genetic subtypes of ALL, including T-ALL, E2A-PBX1, TEL-AML1, MLL rearrangements, BCR-abl, and hyperdiploid >50 chromosomes, and AML, including t(15;17)[PML-RARalpha], t(8;21)[AML1-ETO], inv(16)[CBFbeta-MYH11], MLL gene rearrangement, and cases with FAB-M7 morphology. In addition, within ALL, a novel subgroup was identified based on its unique expression profile. Examination of the gene expression signatures for the different genetic subtypes of acute leukemia provided important insights into the molecular pathology of these leukemias.

Acute Disease↗

PubMed1998

Impact of unified procedures as implemented in the Canadian Quality Assurance Program for T lymphocyte subset enumeration. Participating Flow Cytometry Laboratories of the Canadian Clinical Trials Network for HIV/AIDS Therapies.

The objective of the Canadian Quality Assurance Program (CQAP) is to provide the most reproducible and accurate T-cell subset enumeration for individuals living with HIV who are enrolled in the Canadian Clinical Trial Network for Human Immunodeficiency Virus (HIV) and Acquired Immune Deficiency Syndrome (AIDS) Therapies (abbreviated as CTN). The Canadian National Laboratory for Analytical Cytology, within the Laboratory Centre for Disease Control, is part of the Health Protection Branch of Health Canada. For the past eight years, the Laboratory for Analytical Cytology has been responsible for delivering a bilingual quality assurance program for CD4 T-cell enumeration. This federal program, which integrates biotechnology transfer with quality assessment, was achieved through the organization of workshops focused on technology transfer and essential skill-building techniques. Two training sessions were conducted for the CTN flow cytometer operators. The first introduced the concept of window of analysis, to demonstrate the practical benefits of unified quantitative fluorescent measurement. As a follow-up to the first workshop, participants performed a series of quantitative assays that monitored the expression of CD69, an early activation marker. This quantitative fluorescence protocol was performed with acceptable inter-laboratory variation using modified commercial kits. The second workshop focused on a absolute count method based on a single platform. Four preserved whole-blood preparations were tested with this approach. The combined effort reduced inter-laboratory variation. The direct impact was monitored as related to the frequency of participation. Over the years, the standard deviation of average accumulated variation decreased dramatically with increased frequency of participation, from 10% to <4%.

Canada↗

PubMedDate not supplied

Comparison of single- and dual-platform approaches to enumerate CD34(+) cells in bone marrow and mobilized peripheral blood stem cells.

BACKGROUND: Different flow cytometric methods have been developed to derive absolute CD34(+) cells in predicting transplant outcome. Two techniques for preparing cells for quantification of CD34(+) cells were compared. METHODS: Enumeration of CD34(+) cells in 16 samples of bone marrow (BM) and in 29 samples of mobilized peripheral blood stem cells (PBSC) obtained by leukapheresis was assessed simultaneously by single-platform (ProCOUNT kit) and dual-platform (Milan protocol) approaches within the first 3 h of collection. RESULTS: Absolute number of CD34(+) cells obtained in PBSC and BM using single- and dual-platform methods showed high determination coefficients as follows: for PBSC, slope = 1.0515 +/- 0.048, y-intercept = 88.638 +/- 52.45, and r(2) = 0.941, and for BM, slope = 1.0203 +/- 0.093, y-intercept = 122.25 +/- 20.65, and r(2) = 0.878. There were no statistically significant differences in absolute number of CD34(+) cells from PBSC between single-platform (mean 575/microL, range 70-3683/microL) and dual-platform (786/microL, range 51-3804/microL) assays. In contrast, absolute number of CD34(+) cells from BM was significantly lower (p = 0.0002) when enumerated by ProCount kit (135/microL, 14-758/microL) than with dual-platform method (260/microL, 74-889/microL). CONCLUSIONS: Both approaches can be used indistinctly to estimate absolute number of CD34(+) cells in PBSC but not in BM.

Antigens, CD34↗

PubMed2005

Thermoplastic microfluidic platform for single-molecule detection, cell culture, and actuation.

We have developed a multipurpose microfluidic platform that allows for sensitive fluorescence detection on inexpensive disposable chips. The fabrication scheme involves rapid injection molding of thermoplastics, followed by silica deposition and covalent attachment of an unstructured flexible lid. This combines the virtues of elastomer technology with high-throughput compact disk injection molding. Using this technique, the time to produce 100 chips using a single master can be lowered from more than 1 week by standard PDMS technologies to only a couple hours. The optical properties of the fabricated chips were evaluated by studying individual fluorescence-labeled DNA molecules in a microchannel. Concatemeric DNA molecules were generated through rolling circle replication of circular DNA molecules, which were labeled by hybridization of fluorescence-tagged oligonucleotides. Rolling circle products (RCPs) were detected after as little as 5 min of DNA polymerization, and the RCPs in solution showed no tendency for aggregation. To illustrate the versatility of the platform, we demonstrate two additional applications: The flexible property of the lid was used to create a peristaltic pump generating a flow rate of 9 nL/s. Biocompatibility of the platform was illustrated by culturing Chinese hamster ovary cells for 7 days in the microfluidic channels.

Animals↗

PubMed1999

Single- versus dual-platform assays for human CD34+ cell enumeration.

We comparatively assessed CD34+ cell quantification by two of the recently available single platform assays, the IMAGN 2000 STELLer (Immucor, Lisbon, Portugal) microvolume fluorimetry and the ProCOUNT (BD-ENZIfarma, Lisbon, Portugal) flow cytometry, with our "in-house" dual-platform flow cytometric assay. The performance of the methods was evaluated by linearity and reproducibility tests. The linearity study, over a range of 0-1,200 CD34+ cell/microl, gave a good linear relationship for the three methods, with R(2) > 0.99. Precision tested at three different concentrations gave coefficients of variation ranging from 3.6-26.4% for the STELLertrade mark, 2.4-13.8% for the ProCOUNT, and 3.2-6.4% for flow cytometry. CD34+ cells were quantified in umbilical cord blood (UCB), UCB enriched-leukocyte buffy-coat (BC), mobilized peripheral blood (PB) and mobilized peripheral blood progenitor cells (PBPC) collected by leucapheresis, from a total of 72 samples. Flow cytometric results showed good linear correlation to the absolute counts obtained by the STELLer and ProCOUNT for all samples (R > 0.90 for all methods), with no differences when compared by paired tests (P > 0.05). Linear correlations between methods were also found when individually looking at the different cell sources: UCB or PB, BC, and PBPC, with low, intermediate and high CD34+ cell concentrations, respectively. Furthermore, with the exception of a significant difference between the ProCOUNT and STELLer results for UCB (P < 0.05), no other difference between methods was found for each of the individual populations (P > 0.05). To our knowledge, this is the first report in which the results are presented and analyzed according to each source of CD34+ cells. Our results show that the STELLer and the ProCOUNT are equally efficient for the dual-platform flow cytometric assay in CD34+ cell quantification.

Antigens, CD34↗

PubMed2026

SeqUIaSCOPE: multi-omics data integration platform for single-patient clinical oncology pathway exploration.

SUMMARY: SeqUIaSCOPE is an open-source platform designed for routine clinical oncology diagnostics through case-centric integration and visualization of genomic variants, fusion events, and expression profiles. The platform combines molecular-level validation via embedded genome browsing with systems-level interpretation through dynamic pathway visualization, enabling geneticists to assess how alterations converge across biological networks. Flexible reporting with customizable templates accommodates diverse institutional requirements, while secure cluster-based or local deployment ensures compliance with data protection policies, making advanced multi-omics diagnostics accessible to academic and clinical institutions. AVAILABILITY AND IMPLEMENTATION: SeqUIaSCOPE is freely available on GitHub at https://github.com/BioIT-CEITEC/sequiascope under the MIT license and archived at Zenodo (https://zenodo.org/records/21338445). Due to the sensitive nature of patient data, the repository provides simulated datasets that mimic the structure of real clinical data for testing and exploration. Documentation and a live demo accompany these datasets, allowing users to explore the application without any prior setup. The repository also includes a Helm chart for Kubernetes deployment and Docker containers for local deployment, ensuring compatibility across Linux, macOS, and Windows. No user registration is required, and all data remains on local or institutional infrastructure.

Humans↗

PubMed2026

Standardizing stem cell enumeration: A methodological comparison of single and dual flow cytometry platforms.

Two flow cytometry methods are used for stem cell (CD34+) enumeration; single platform (SP) and dual platform (DP). While several studies reported comparable results, others suggested superiority of the SP method. This study evaluated variations between both methods using a modified workflow. A total of 54 fresh and thawed specimens, including mobilized peripheral blood, apheresis products, and umbilical cord blood, were analyzed using both methods. High concordance between SP and DP methods was observed for absolute viable CD34+ counts in fresh and thawed specimens (p = 0.088 and 0.427, respectively), as well as for CD34+ viability (p = 0.085 and 0.801). Absolute viable WBC counts were comparable between methods in thawed specimens (p = 0.124), whereas a modest statistical variation was observed in fresh specimen group (p = 0.039), largely influenced by umbilical cord blood samples. Variation in absolute viable CD34+ counts remained within clinically acceptable limits, with median variations of 2.4 for fresh and 1.4 for thawed samples. SP and DP methods demonstrated high concordance for absolute viable CD34+ enumeration and CD34+ viability in fresh and thawed specimens. Although a modest variation in viable WBC counts was observed in fresh samples, this did not affect CD34+ enumeration and remained clinically acceptable. While SP provides a standardized approach, the DP method offered greater gating flexibility, with fewer technical resources required, and was approximately 70% more cost-effective, supporting its use as a practical alternative in appropriate laboratory settings.

Humans↗

PubMed2004

Three-dimensional microarray platform applied to single nucleotide polymorphism analysis.

Bio-Strand, Inc., has developed a novel DNA microarray platform utilizing a three-dimensional (3D) DNA format. DNA probes or polymerase chain reaction (PCR) products are spotted onto a thread-like scaffold, which is then wound onto a cylindrical core. By wrapping the thread around the core, high efficiencies are achieved in sample analysis. Using allele-specific oligo (ASO) competitive hybridization (with Cy5 fluorescently labeled sequences), hybridized arrays are visualized using a helium-neon (HeNe) laser and quantitated/scored. The method can readily detect single nucleotide differences. We demonstrate the use of this Bio-Strand 3D array in the analysis of a single nucleotide polymorphism (SNP).

Carbocyanines↗