Multi-site reproducibility of a human immunophenotyping assay in whole blood and peripheral blood mononuclear cells preparations using CyTOF technology coupled with Maxpar Pathsetter, an automated data analysis system.

High-dimensional mass cytometry data potentially enable a comprehensive characterization of immune cells. In order to positively affect clinical trials and translational clinical research, this advanced technology needs to demonstrate a high reproducibility of results across multiple sites for both peripheral blood mononuclear cells (PBMC) and whole blood preparations. A dry 30-marker broad immunophenotyping panel and customized automated analysis software were recently engineered and are commercially available as the Fluidigm® Maxpar® Direct™ Immune Profiling Assay™. In this study, seven sites received whole blood and six sites received PBMC samples from single donors over a 2-week interval. Each site labeled replicate samples and acquired data on Helios™ instruments using an assay-specific acquisition template. All acquired sample files were then automatically analyzed by Maxpar Pathsetter™ software. A cleanup step eliminated debris, dead cells, aggregates, and normalization beads. The second step automatically enumerated 37 immune cell populations and performed label intensity assessments on all 30 markers. The inter-site reproducibility of the 37 quantified cell populations had consistent population frequencies, with an average %CV of 14.4% for whole blood and 17.7% for PBMC. The dry reagent coupled with automated data analysis is not only convenient but also provides a high degree of reproducibility within and among multiple test sites resulting in a comprehensive yet practical solution for deep immune phenotyping.

Automated Data Cleanup for Mass Cytometry.

Mass cytometry is an emerging technology capable of 40 or more correlated measurements on a single cell. The complexity and volume of data generated by this platform have accelerated the creation of novel methods for high-dimensional data analysis and visualization. A key step in any high-level data analysis is the removal of unwanted events, a process often referred to as data cleanup. Data cleanup as applied to mass cytometry typically focuses on elimination of dead cells, debris, normalization beads, true aggregates, and coincident ion clouds from raw data. We describe a probability state modeling (PSM) method that automatically identifies and removes these elements, resulting in FCS files that contain mostly live and intact events. This approach not only leverages QC measurements such as DNA, live/dead, and event length but also four additional pulse-processing parameters that are available on Fluidigm Helios™ and CyTOF® (Fluidigm, Markham, Canada) 2 instruments with software versions of 6.3 or higher. These extra Gaussian-derived parameters are valuable for detecting well-formed pulses and eliminating coincident positive ion clouds. The automated nature of this new routine avoids the subjectivity of other gating methods and results in unbiased elimination of unwanted events. © 2019 International Society for Advancement of Cytometry.

Sometimes simpler is better: VLog, a general but easy-to-implement log-like transform for cytometry.

The fundamental purpose of log and log-like transforms for cytometry is to make measured population variabilities as uniform as possible. The long-standing success of the log transform was its ability to stabilize linearly increasing gain-dependent uncertainties and the success of the log-like transforms is that they extend this notion to include zero and negative measurement values. This study derives and examines a transform called VLog that stabilizes the three general sources of variability: (1) gain-dependent variability, (2) photo-electron counting error, and (3) signal-independent sources of error. Somewhat surprisingly, this transform has a closed-form solution and therefore is relatively simple to implement. By including some quantitation elements in its formulation, the shape-dependent arguments, α and ß, usually do not require optimization for different datasets. The simplicity and generality of the transform may make it a useful tool for cytometry and possibly other technologies. © 2016 International Society for Advancement of Cytometry.

Probability state modeling theory.

As the technology of cytometry matures, there is mounting pressure to address two major issues with data analyses. The first issue is to develop new analysis methods for high-dimensional data that can directly reveal and quantify important characteristics associated with complex cellular biology. The other issue is to replace subjective and inaccurate gating with automated methods that objectively define subpopulations and account for population overlap due to measurement uncertainty. Probability state modeling (PSM) is a technique that addresses both of these issues. The theory and important algorithms associated with PSM are presented along with simple examples and general strategies for autonomous analyses. PSM is leveraged to better understand B-cell ontogeny in bone marrow in a companion Cytometry Part B manuscript. Three short relevant videos are available in the online supporting information for both of these papers. PSM avoids the dimensionality barrier normally associated with high-dimensionality modeling by using broadened quantile functions instead of frequency functions to represent the modulation of cellular epitopes as cells differentiate. Since modeling programs ultimately minimize or maximize one or more objective functions, they are particularly amenable to automation and, therefore, represent a viable alternative to subjective and inaccurate gating approaches.

Iron overload in adults with sickle cell disease who have received intermittent red blood cell transfusions.

OBJECTIVE: To assess the prevalence of iron overload in adults with sickle cell disease (SCD) not on a chronic transfusion protocol. DESIGN: Retrospective chart review. DATA SOURCE: University of South Alabama Comprehensive Sickle Cell Center adult outpatient clinic. RESULTS: There was no significant difference in units transfused across the four genotypes (HbSS, HbSC, HbSß(0)-thalassemia, and HbSß(+)-thalassemia). Only individuals with HbSS (n = 63) met criteria for iron overload with ferritins of ≥1500 ng/mL. Forty-eight had ferritins <1500 ng/mL, eight (13%) had ferritins ≥3000 ng/mL, and seven (11%) had ferritins ≥1500 and <3000 ng/mL. The overall prevalence of iron overload was 9.74% in SCD cohort and 23.8% in the HbSS genotype. CONCLUSIONS: Our data support that patients with HbSS are at a particularly high risk for inadvertent iron overload as compared to HbSC, HbSß(0)-thalassemia, and HbSß(+)-thalassemia. IMPLICATIONS FOR PRACTICE: This study supports the need for healthcare providers to closely monitor the number of red blood cell (RBC) transfusions, RBC units transfused, and serial baseline, steady-state ferritin levels. With closer monitoring, the clinical significance of iron overload in SCD can be established and guide the healthcare provider's management in the prevention of iron overload.

Misclassification of pulmonary hypertension in adults with sickle hemoglobinopathies using Doppler echocardiography.

OBJECTIVE: To compare the diagnostic utility of Doppler echocardiography-derived tricuspid regurgitant jet velocity (TRV) ≥ 2.5 m/s to right heart catheterization (RHC) in defining pulmonary hypertension (PH) in adult patients with sickle cell disease (SCD). METHODS: This is a retrospective chart review of adults with SCD who had a TRV ≥ 2.5 m/s and RHC. A TRV ≥ 2.5 m/s is suggestive of PH. Pulmonary arterial hypertension (PAH) was defined as a mean pulmonary artery pressure (mPAP) ≥ 25 mm Hg and pulmonary capillary wedge pressure ≤ 15 mm Hg. Pulmonary venous hypertension was defined as an mPAP ≥ 25 mm Hg and pulmonary capillary wedge pressure >15 mm Hg. RESULTS: Twenty-five patients with SCD met the inclusion criteria. Nine of the 25 (36%) patients had an mPAP ≥ 25 mm Hg. Of these 9, 3 (33%) had PAH and 6 (66%) had pulmonary venous hypertension. Patients with PH did not have a higher TRV (3.1 ± 0.68 vs 2.70 ± 0.16 m/s; P = 0.12), but they did have higher cardiac outputs (10.4 ± 2.7 vs 7.81 ± 1.85 L/min; P = 0.012. The specificity of TRV equal to 2.51 m/s in diagnosing PH was 18.8%. At a TRV of 2.88 m/s, the specificity increased to 81%. CONCLUSIONS: In adults with SCD, a TRV of 2.5 m/s lacks specificity for use as a screening tool in the diagnosis of PH. Using a TRV of ≥ 2.88 m/s allows the TRV to be used as a screening tool and reduces the false-positive rate and need for unnecessary RHC.

Automated analysis of flow cytometric data for CD34+ stem cell enumeration using a probability state model.

BACKGROUND: Flow Cytometry is widely used for enumeration of hematopoietic stem cell (SC) levels in bone marrow, cord blood, peripheral blood, and apheresis products. The ISHAGE single-platform gating method is considered by many to be the standard for CD34+ SC enumeration. However, attempts at uniform application of this ISHAGE method have met with only partial success. We propose an automated, multivariate classification approach for SC analysis based on Probability State Modeling™ (PSM). In this study, we compare the results from automated PSM analysis with manual ISHAGE gating analysis as performed by a trained analyst. METHODS: A total of 258 samples were assayed on BD FACSCanto II flow cytometers using a stain-lyse-no-wash technique. Populations were defined using CD34, CD45, 7-AAD, and light scatter. BD TruCount™ bead tubes were used for absolute SC concentrations. A PSM was designed to classify events into beads, debris, intact-dead cells, and intact-live SC; run unattended and record results. RESULTS: The ISHAGE and PSM methods show excellent agreement in estimating the concentration of #SC/µL: slope = 1.009, r² = 0.999. Bland-Altman Analysis for the SC concentration has an average difference (bias) of 2.018 SC/µL. The 95% confidence interval is from -59.350 to 63.380 SC/µL. The operator-to-operator agreement using PSM is perfect: r² = 1.000. CONCLUSIONS: Automated PSM analysis of SC listmode data produces results that agree strongly with ISHAGE gate-based results. The PSM approach provides higher reproducibility, objectivity, and speed with accuracy at least equivalent to the ISHAGE method.

Severe human metapneumovirus infection in hospitalized children.

Human metapneumovirus is a recently discovered pathogen that causes upper and lower respiratory tract disease in children. This study describes the course of illness in hospitalized children with this infection. During a 6-month period, 11 children were diagnosed with human metapneumovirus infection by reverse transcription-polymerase chain reaction. Oxygen supplementation was required for 82% of patients. Severe disease developed in 45%, and mechanical ventilation was required. An apparent life-threatening event was the indication for hospitalization of 27% of patients infected with human metapneumovirus. Children with underlying asthma or neuromuscular disease had a prolonged hospitalization.

Comparison of hospital laboratory serum alcohol levels obtained by an enzymatic method with whole blood levels forensically determined by gas chromatography.

Estimating the equivalent whole blood ethanol level from a serum or plasma determination has been addressed by numerous articles in both the clinical and forensic literature. All previous studies have either involved sample sizes insufficient for adequate statistical evaluation or have utilized gas chromatography for both serum and whole blood analysis. In this study, based on samples from 212 consecutive patients admitted to a hospital trauma center, serum was assayed for ethanol using an enzymatic oxidation method, and the results were compared to whole blood samples taken simultaneously and analyzed by headspace gas chromatography in a forensic toxicology laboratory. Contrary to previously published conclusions, it was found that the serum/whole blood alcohol ratio (SAC/BAC) is concentration-dependent, with average values ranging from around 1.12 to as high as around 1.18, depending on SAC, thus precluding a generally applicable SAC/BAC conversion factor. However, a linear regression model was found to provide adequate prediction intervals at any desired level of confidence for whole blood alcohol from serum alcohol levels up to 300 mg/dL. For example, at a confidence level of 95%, an SAC of 103 mg/dL corresponds to a BAC of at least 0.080 g/dL.

Physicians' attitude and practices in sickle cell disease pain management.

Many physicians believe that patients with sickle cell disease (SCD) are more likely to become addicted to pain medication than are other patient populations. This study hypothesizes that physicians' attitudes towards addiction in patients with SCD affects pain management practices. The Physician Attitudes Survey was sent to 286 physicians at seven National Institutes of Health-funded university-based comprehensive sickle cell centres. The survey assessed demographic information; and physician's attitudes toward and knowledge of pain, pain treatment, and drug addiction and abuse. Significant Pearson product-moment correlations were found between attitudes towards pain and beliefs regarding addiction to prescribed opioids. Physicians reported varied pain management strategies, however, many believe that attitudes toward addiction and to patients in pain crises may result in undertreatment of pain. These results indicate that physicians might benefit from additional education regarding sickle cell disease, addiction to pain medication, the pharmacology of opioids, and the assessment and treatment of pain.

Multiparameter flow cytometry of fluorescent protein reporters.

Reporters based on the green fluorescent protein (GFP) from the jellyfish Aequorea victoria and GFP-like proteins from other marine organisms provide valuable tools to monitor gene transfer and expression noninvasively in living cells. Stable cell lines were generated from the Sp2/0-Ag14 hybridoma that express up to three spectral enhanced versions of GFP, the enhanced cyan fluorescent protein (ECFP), the enhanced green fluorescent protein (EGFP), and the enhanced yellow fluorescent protein (EYFP), and/or a variant of the Discosoma coral red fluorescent protein (DsRed). The panel of lines was used to demonstrate a flow cytometric procedure for simultaneous analysis of all four fluorescent proteins that utilizes dual-laser excitation at 488 nm and 407 nm. Additional schemes for simultaneous detection of two, three or four of these fluorescent proteins are also presented.

Melatonin increases survival and inhibits oxidative and amyloid pathology in a transgenic model of Alzheimer's disease.

Increased levels of a 40-42 amino-acid peptide called the amyloid beta protein (A beta) and evidence of oxidative damage are early neuropathological markers of Alzheimer's disease (AD). Previous investigations have demonstrated that melatonin is decreased during the aging process and that patients with AD have more profound reductions of this hormone. It has also been recently shown that melatonin protects neuronal cells from A beta-mediated oxidative damage and inhibits the formation of amyloid fibrils in vitro. However, a direct relationship between melatonin and the biochemical pathology of AD had not been demonstrated. We used a transgenic mouse model of Alzheimer's amyloidosis and monitored over time the effects of administering melatonin on brain levels of A beta, abnormal protein nitration, and survival of the mice. We report here that administration of melatonin partially inhibited the expected time-dependent elevation of beta-amyloid, reduced abnormal nitration of proteins, and increased survival in the treated transgenic mice. These findings may bear relevance to the pathogenesis and therapy of AD.

Are we doing any good by doing really well? (Where's the Bacon?).

Francis Bacon, who with Rene Decartes laid the intellectual foundations for Western science in the seventeenth century, asserted that the purpose of all knowledge is "action in the production of works for ... the relief of man's estate." We assess briefly several aspects of a few of the current efforts directed to the production of such "works" with respect to such "relief" as they may provide: cancer mortality, the medical literature, evidence-based medicine, clinical trials, observational databases and criteria for the promotion and tenure of the medical faculty. We suggest why each of these efforts appears to have failed to some degree and then propose some measures that may possibly serve as correctives.

Methodological issues in radiation dose-volume outcome analyses: summary of a joint AAPM/NIH workshop.

This report represents a summary of presentations at a joint workshop of the National Institutes of Health and the American Association of Physicists in Medicine (AAPM). Current methodological issues in dose-volume modeling are addressed here from several different perspectives. Areas of emphasis include (a) basic modeling issues including the equivalent uniform dose framework and the bootstrap method, (b) issues in the valid use of statistics, including the need for meta-analysis, (c) issues in dealing with organ deformation and its effects on treatment response, (d) evidence for volume effects for rectal complications, (e) the use of volume effect data in liver and lung as a basis for dose escalation studies, and (f) implications of uncertainties in volume effect knowledge on optimized treatment planning. Taken together, these approaches to studying volume effects describe many implications for the development and use of this information in radiation oncology practice. Areas of significant interest for further research include the meta-analysis of clinical data; interinstitutional pooled data analyses of volume effects; analyses of the uncertainties in outcome prediction models, minimal parameter number outcome models for ranking treatment plans (e.g., equivalent uniform dose); incorporation of the effect of motion in the outcome prediction; dose-escalation/isorisk protocols based on outcome models; the use of functional imaging to study radioresponse; and the need for further small animal tumor control probability/normal tissue complication probability studies.