Estimating the causal effects of multiple intermittent treatments with application to COVID-19

To draw real-world evidence about the comparative effectiveness of multiple time-varying treatments on patient survival, we develop a joint marginal structural survival model and a novel weighting strategy to account for time-varying confounding and censoring. Our methods formulate complex longitudinal treatments with multiple start/stop switches as the recurrent events with discontinuous intervals of treatment eligibility. We derive the weights in continuous time to handle a complex longitudinal dataset without the need to discretize or artificially align the measurement times. We further use machine learning models designed for censored survival data with time-varying covariates and the kernel function estimator of the baseline intensity to efficiently estimate the continuous-time weights. Our simulations demonstrate that the proposed methods provide better bias reduction and nominal coverage probability when analyzing observational longitudinal survival data with irregularly spaced time intervals, compared to conventional methods that require aligned measurement time points. We apply the proposed methods to a large-scale COVID-19 dataset to estimate the causal effects of several COVID-19 treatments on the composite of in-hospital mortality and ICU admission.

Microbial Cell-Free DNA Identifies the Causative Pathogen in Infective Endocarditis and Remains Detectable Longer Than Conventional Blood Culture in Patients with Prior Antibiotic Therapy

BACKGROUND

The diagnosis of infective endocarditis (IE) can be difficult, particularly if blood cultures fail to yield a pathogen. This study evaluates the potential utility of microbial cell-free DNA (mcfDNA) as a tool to identify the microbial etiology of IE.

METHODS

Blood samples from patients with suspected IE were serially collected. mcfDNA was extracted from plasma and underwent next-generation sequencing. Reads were aligned against a library containing DNA sequences belonging to >1400 different pathogens. mcfDNA from organisms present above a statistical threshold were reported and quantified in molecules per milliliter (MPM). Additional mcfDNA was collected on each subject every 2-3 days for a total of 7 collections or until discharge.

RESULTS

Of 30 enrolled patients with suspected IE, 23 had definite IE, 2 had possible IE, and IE was rejected in 5 patients by modified Duke Criteria. Only the 23 patients with definite IE were included for analysis. Both mcfDNA and blood cultures achieved a sensitivity of 87%. The median duration of positivity from antibiotic treatment initiation was estimated to be approximately 38.1 days for mcfDNA versus 3.7 days for blood culture (proportional odds, 2.952; P = .02771), using a semiparametric survival analysis. mcfDNA (log10) levels significantly declined (-0.3 MPM log10 units, 95% credible interval -0.45 to -0.14) after surgical source control was performed (pre- vs postprocedure, posterior probability >0.99).

CONCLUSION

mcfDNA accurately identifies the microbial etiology of IE. Sequential mcfDNA levels may ultimately help to individualize therapy by estimating a patient's burden of infection and response to treatment.

Long-read HiFi sequencing of NUDT15: Phased full-gene haplotyping and pharmacogenomic allele discovery

To determine the phase of NUDT15 sequence variants for more comprehensive star (*) allele diplotyping, we developed a novel long-read single-molecule real-time HiFi amplicon sequencing method. A 10.5 kb NUDT15 amplicon assay was validated using reference material positive controls and additional samples for specimen type and blinded accuracy assessment. Triplicate NUDT15 HiFi sequencing of two reference material samples had nonreference genotype concordances of >99.9%, indicating that the assay is robust. Notably, short-read genome sequencing of a subset of samples was unable to determine the phase of star (*) allele-defining NUDT15 variants, resulting in ambiguous diplotype results. In contrast, long-read HiFi sequencing phased all variants across the NUDT15 amplicons, including a *2/*9 diplotype that previously was characterized as *1/*2 in the 1000 Genomes Project v3 data set. Assay throughput was also tested using 8.5 kb amplicons from 100 Ashkenazi Jewish individuals, which identified a novel NUDT15 *1 suballele (c.-121G>A) and a rare likely deleterious coding variant (p.Pro129Arg). Both novel alleles were Sanger confirmed and assigned as *1.007 and *20, respectively, by the PharmVar Consortium. Taken together, NUDT15 HiFi amplicon sequencing is an innovative method for phased full-gene characterization and novel allele discovery, which could improve NUDT15 pharmacogenomic testing and subsequent phenotype prediction.

Upgrade of the helically symmetric experiment Thomson scattering diagnostic suite

The Helically Symmetric eXperiment (HSX) Thomson Scattering (TS) diagnostic is being upgraded to decrease uncertainty in electron temperature and density measurements. Upgrades to the HSX TS diagnostic will consist of a novel redesign of polychromator electronics and digitization of the TS output signal. Here, we also present a study of the benefits of an additional spectral channel that will sample the red-shifted band of the scattered spectrum. To maximize system bandwidth (BW) and gain, while minimizing noise, the existing low-BW polychromator electronics on HSX will be replaced by high-BW, high gain circuitry designed in-house.

928. Clinical Characteristics and Microbiology Testing Patterns Among Transplant Recipients Admitted to Acute Care Hospitals for Suspected Infection

Background

Solid organ transplant (SOT) is a growing option for patients with end-stage organ diseases. Immunosuppressive therapy (IT) is utilized in this population to minimize risk of allograft rejection, which increases infection risk particularly of atypical pathogens that can complicate the infection-related diagnostic journey. The purpose of this analysis was to evaluate baseline clinical characteristics and microbiological testing utilization patterns among a cohort of patients with a history of SOT and IT.

Methods

This retrospective cohort study utilized a US hospital-based, service-level database. Patients were selected from a subsample of database facilities utilizing plasma microbial cell-free DNA diagnostic assays. The study period was 1/1/2017-3/21/2020. Eligible patients were identified by 1^st observation of SOT status and IT. Subsequent inpatient admissions for suspected infection were analyzed.

Results

We identified 749 patients with SOT history and use of IT, 56.4% were male, and the mean age was 52.8 (18.7) years. Kidney was the most prevalent transplant category (49.1%), followed by liver (14.1%), lung (10.9%), and heart (10.3%), and 9.7% were multi-organ. Patients experiencing multiple transplants had the most chronic conditions with a mean Elixhauser comorbidity score of 26.3 (14.7). The median length of stay was 4 [3-7] days. The median number of tests per encounter was 6 [IQR=3-11]. Culture was the most utilized test category (2 [1-4]). Blood culture was the highest utilized culture and overall test at 13.5% of all tests observed, while CMV PCR (7.8%) and multi-panel EIA (2.7%) were the most frequent molecular and antigen tests, respectively. Lung transplant recipients had the greatest utilization of tests overall (9 [3.5-17]) versus other transplant categories (6 [3-10]), consistent with the observed test rate in the 1^st 48 hours of presentation (4 [1-7] vs. 2 [1-5]).

Conclusion

This analysis suggests that the infection-related diagnostic journey among patients with a history of SOT involves high utilization of microbiological testing, with greater utilization among lung transplant recipients versus other SOT recipients. Variation in clinical characteristics and microbiological testing patterns were observed across SOT categories.

Disclosures

T Matthew Hill, PharmD, PhD, Karius, Inc (Employee, Shareholder) Erick R. Scott, MD, MHS, Karius, Inc (Employee, Shareholder) Sivan Bercovici, PhD, Karius (Employee)

Microbial Cell-Free DNA Identifies Etiology of Bloodstream Infections, Persists Longer Than Conventional Blood Cultures, and its Duration of Detection is Associated with Metastatic Infection in Patients with Staphylococcus aureus and Gram-Negative Bacteremia

BACKGROUND

Microbial cell-free DNA (mcfDNA) sequencing of plasma can identify presence of a pathogen in a host. This study evaluated the duration of pathogen detection by mcfDNA sequencing vs. conventional blood culture in patients with bacteremia.

METHODS

Blood samples from patients with culture-confirmed bloodstream infection were collected within 24 hours of the index positive blood culture and 48 to 72 hours thereafter. mcfDNA was extracted from plasma and next-generation sequencing (NGS) applied. Reads were aligned against a curated pathogen database. Statistical significance was defined with Bonferroni adjustment for multiple comparisons (p < 0.0033).

RESULTS

A total of 175 patients with Staphylococcus aureus bacteremia (SAB; n=66), Gram-negative bacteremia (GNB; n=74), or non-infected controls (n=35) were enrolled. The overall sensitivity of mcfDNA sequencing compared to index blood culture was 89.3% (125/140) and the specificity was 74.3%. Among patients with bacteremia, pathogen specific mcfDNA remained detectable for significantly longer than conventional blood cultures (median 15 days vs. 2 days; p<0.0001). Each additional day of mcfDNA detection significantly increased the odds of metastatic infection (Odds Ratio [OR]: 2.89; 95% Confidence Interval [CI]: 1.53-5.46; p=0.0011).

CONCLUSIONS

Pathogen mcfDNA identified the bacterial etiology of bloodstream infection for a significantly longer interval than conventional cultures, and its duration of detection was associated with increased risk for metastatic infection. mcfDNA could play a role in the diagnosis of partially treated endovascular infections.

Demonstration of reduced neoclassical energy transport in Wendelstein 7-X

Research on magnetic confinement of high-temperature plasmas has the ultimate goal of harnessing nuclear fusion for the production of electricity. Although the tokamak1 is the leading toroidal magnetic-confinement concept, it is not without shortcomings and the fusion community has therefore also pursued alternative concepts such as the stellarator. Unlike axisymmetric tokamaks, stellarators possess a three-dimensional (3D) magnetic field geometry. The availability of this additional dimension opens up an extensive configuration space for computational optimization of both the field geometry itself and the current-carrying coils that produce it. Such an optimization was undertaken in designing Wendelstein 7-X (W7-X)2, a large helical-axis advanced stellarator (HELIAS), which began operation in 2015 at Greifswald, Germany. A major drawback of 3D magnetic field geometry, however, is that it introduces a strong temperature dependence into the stellarator's non-turbulent 'neoclassical' energy transport. Indeed, such energy losses will become prohibitive in high-temperature reactor plasmas unless a strong reduction of the geometrical factor associated with this transport can be achieved; such a reduction was therefore a principal goal of the design of W7-X. In spite of the modest heating power currently available, W7-X has already been able to achieve high-temperature plasma conditions during its 2017 and 2018 experimental campaigns, producing record values of the fusion triple product for such stellarator plasmas3,4. The triple product of plasma density, ion temperature and energy confinement time is used in fusion research as a figure of merit, as it must attain a certain threshold value before net-energy-producing operation of a reactor becomes possible1,5. Here we demonstrate that such record values provide evidence for reduced neoclassical energy transport in W7-X, as the plasma profiles that produced these results could not have been obtained in stellarators lacking a comparably high level of neoclassical optimization.

Pharmacogenomic education among genetic counseling training programs in North America

The increasing number of genetic counselors participating directly in clinical pharmacogenomic post-test counseling prompted our evaluation of pharmacogenomic education across genetic counseling training programs in North America. Thirty-one program leadership participants from both the United States (U.S.) and Canada responded to a survey assessing pharmacogenomics education and the role of genetic counselors. Eighty-five percent of respondents agreed pharmacogenomics is currently within the scope of genetic counseling practice, and 96.3% indicated their training programs currently provide education on pharmacogenomics, with the majority reporting < 7 hr of education. Lectures on pharmacogenomics were the most common method for didactics; however, some programs also included practical modalities (e.g., case studies, clinical rotations) and online resources. Barriers to expanding pharmacogenomic education included the constrained timeline of training, and lack of resources and local expertise. Moreover, participants suggested that genetic counselors ideally should be able to order pharmacogenomic tests and counsel patients on pharmacogenomics, including result interpretation, as they believe pharmacogenomics does fall within the scope of practice of genetic counseling. Our novel results also confirm that training program leadership support a pharmacogenomic service delivery model that includes a combined effort between genetic counselors and pharmacists to utilize their synergistic expertise. However, this model likely still necessitates expanding pharmacogenomic didactics in genetic counseling training programs through more practical training and/or by leveraging online pharmacogenomic courses dedicated to supporting clinical implementation.

Development and Analytical Validation of a 29 Gene Clinical Pharmacogenetic Genotyping Panel: Multi-Ethnic Allele and Copy Number Variant Detection

To develop a novel pharmacogenetic genotyping panel, a multidisciplinary team evaluated available evidence and selected 29 genes implicated in interindividual drug response variability, including 130 sequence variants and additional copy number variants (CNVs). Of the 29 genes, 11 had guidelines published by the Clinical Pharmacogenetics Implementation Consortium. Targeted genotyping and CNV interrogation were accomplished by multiplex single‐base extension using the MassARRAY platform (Agena Biosciences) and multiplex ligation‐dependent probe amplification (MRC Holland), respectively. Analytical validation of the panel was accomplished by a strategic combination of > 500 independent tests performed on 170 unique reference material DNA samples, which included sequence variant and CNV accuracy, reproducibility, and specimen (blood, saliva, and buccal swab) controls. Among the accuracy controls were 32 samples from the 1000 Genomes Project that were selected based on their enrichment of sequence variants included in the pharmacogenetic panel (VarCover.org). Coupled with publicly available samples from the Genetic Testing Reference Materials Coordination Program (GeT‐RM), accuracy validation material was available for the majority (77%) of interrogated sequence variants (100% with average allele frequencies > 0.1%), as well as additional structural alleles with unique copy number signatures (e.g., CYP2D6*5, *13, *36, *68; CYP2B6*29; and CYP2C19*36). Accuracy and reproducibility for both genotyping and copy number were > 99.9%, indicating that the optimized panel platforms were precise and robust. Importantly, multi‐ethnic allele frequencies of the interrogated variants indicate that the vast majority of the general population carries at least one of these clinically relevant pharmacogenetic variants, supporting the implementation of this panel for pharmacogenetic research and/or clinical implementation programs.

Charge exchange recombination spectroscopy at Wendelstein 7-X

The Charge Exchange Recombination Spectroscopy (CXRS) diagnostic has become a routine diagnostic on almost all major high temperature fusion experimental devices. For the optimized stellarator Wendelstein 7-X (W7-X), a highly flexible and extensive CXRS diagnostic has been built to provide high-resolution local measurements of several important plasma parameters using the recently commissioned neutral beam heating. This paper outlines the design specifics of the W7-X CXRS system and gives examples of the initial results obtained, including typical ion temperature profiles for several common heating scenarios, toroidal flow and radial electric field derived from velocity measurements, beam attenuation via beam emission spectra, and normalized impurity density profiles under some typical plasma conditions.

Members of the public in the USA, UK, Canada and Australia expressing genetic exceptionalism say they are more willing to donate genomic data

Public acceptance is critical for sharing of genomic data at scale. This paper examines how acceptance of data sharing pertains to the perceived similarities and differences between DNA and other forms of personal data. It explores the perceptions of representative publics from the USA, Canada, the UK and Australia (n = 8967) towards the donation of DNA and health data. Fifty-two percent of this public held ‘exceptionalist’ views about genetics (i.e., believed DNA is different or ‘special’ compared to other types of medical information). This group was more likely to be familiar with or have had personal experience with genomics and to perceive DNA information as having personal as well as clinical and scientific value. Those with personal experience with genetics and genetic exceptionalist views were nearly six times more likely to be willing to donate their anonymous DNA and medical information for research than other respondents. Perceived harms from re-identification did not appear to dissuade publics from being willing to participate in research. The interplay between exceptionalist views about genetics and the personal, scientific and clinical value attributed to data would be a valuable focus for future research.

VarCover: Allele Min-Set Cover Software

To facilitate reference-material selection for clinical genetic testing laboratories, we developed VarCover, open-source software hosted on GitHub, which accepts a file of variants and returns an approximately minimum set (min-set) of samples covering the targeted alleles. VarCover employs the SetCoverPy package, sample weights, and preselection of singleton-possessing samples to efficiently solve the min-set cover problem. As a test case, we attempted to find a min-set of reference samples from the 1000 Genomes Project to cover 237 variants considered putatively pathogenic (of which 12 were classified as pathogenic or likely pathogenic) in the original 56 medically actionable genes recommended by the American College of Medical Genetics and Genomics (ACMG). The number of samples, number of alleles, and processing time were measured in subsets of the 237 target alleles. VarCover identified 140 reference-material samples from the 1000 Genomes Project covering the 237 alleles in the 56 ACMG-recommended genes. Sample weights derived from the minor allele frequency spectrum increased the number of alleles in the solution set. Preselection of samples that possessed singleton target alleles reduced computational processing time when the target set size exceeded 100 alleles. VarCover provides a simple programmatic interface for identifying an approximately min-set of reference samples, thereby reducing clinical laboratory effort and molecular genetic test-validation costs.

On using Rayleigh scattering for in situ spectral calibration of Thomson scattering diagnostics

A new method for in situ spectral calibration of Thomson scattering diagnostics is proposed. The idea of the method is to apply a wavelength tunable optical parametric oscillator for measurements of Rayleigh scattering at different wavelengths, from which relative sensitivities can be calculated. This extends the usual approach where Rayleigh scattering is used only at a single wavelength for the absolute calibration and spectral sensitivities are obtained separately. With the new approach, the full diagnostic setup is spectrally calibrated at once. Such a calibration can be repeated at regular intervals during an experimental campaign since it does not require a break of the vacuum. In this paper, the Rayleigh scattering calibration is tested in a laboratory setup with a sample Wendelstein 7-X (W7-X) polychromator. It is shown that relative sensitivities of spectral channels can be recovered with a sufficient resolution even under conditions of significant stray light. The stray light is overcome by measuring the linear dependence of the scattered signal on the gas pressure. Good results of laboratory tests motivate the installation of the new calibration system for the Thomson scattering diagnostic at W7-X.

The asthma mobile health study, smartphone data collected using ResearchKit

Widespread adoption of smart mobile platforms coupled with a growing ecosystem of sensors including passive location tracking and the ability to leverage external data sources create an opportunity to generate an unprecedented depth of data on individuals. Mobile health technologies could be utilized for chronic disease management as well as research to advance our understanding of common diseases, such as asthma. We conducted a prospective observational asthma study to assess the feasibility of this type of approach, clinical characteristics of cohorts recruited via a mobile platform, the validity of data collected, user retention patterns, and user data sharing preferences. We describe data and descriptive statistics from the Asthma Mobile Health Study, whereby participants engaged with an iPhone application built using Apple's ResearchKit framework. Data from 6346 U.S. participants, who agreed to share their data broadly, have been made available for further research. These resources have the potential to enable the research community to work collaboratively towards improving our understanding of asthma as well as mobile health research best practices.

Estimating Local Costs Associated With Clostridium difficile Infection Using Machine Learning and Electronic Medical Records

BACKGROUND Reported per-patient costs of Clostridium difficile infection (CDI) vary by 2 orders of magnitude among different hospitals, implying that infection control officers need precise, local analyses to guide rational decision making between interventions. OBJECTIVE We sought to comprehensively estimate changes in length of stay (LOS) attributable to CDI at a single urban tertiary-care facility using only data automatically extractable from the electronic medical record (EMR). METHODS We performed a retrospective cohort study of 171,938 visits spanning a 7-year period. In total, 23,968 variables were extracted from EMR data recorded within 24 hours of admission to train elastic-net regularized logistic regression models for propensity score matching. To address time-dependent bias (reverse causation), we separately stratified comparisons by time of infection, and we fit multistate models. RESULTS The estimated difference in median LOS for propensity-matched cohorts varied from 3.1 days (95% CI, 2.2-3.9) to 10.1 days (95% CI, 7.3-12.2) depending on the case definition; however, dependency of the estimate on time to infection was observed. Stratification by time to first positive toxin assay, excluding probable community-acquired infections, showed a minimum excess LOS of 3.1 days (95% CI, 1.7-4.4). Under the same case definition, the multistate model averaged an excess LOS of 3.3 days (95% CI, 2.6-4.0). CONCLUSIONS In this study, 2 independent time-to-infection adjusted methods converged on similar excess LOS estimates. Changes in LOS can be extrapolated to marginal dollar costs by multiplying by average costs of an inpatient day. Infection control officers can leverage automatically extractable EMR data to estimate costs of CDI at their own institutions. Infect Control Hosp Epidemiol. 2017;38:1478-1486.

Multiplexed analysis of fixed tissue RNA using Ligation in situ Hybridization

Clinical tissues are prepared for histological analysis and long-term storage via formalin fixation and paraffin embedding (FFPE). The FFPE process results in fragmentation and chemical modification of RNA, rendering it less suitable for analysis by techniques that rely on reverse transcription (RT) such as RT-qPCR and RNA-Seq. Here we describe a broadly applicable technique called ‘Ligation in situ Hybridization’ (‘LISH’), which is an alternative methodology for the analysis of FFPE RNA. LISH utilizes the T4 RNA Ligase 2 to efficiently join adjacent chimeric RNA–DNA probe pairs hybridized in situ on fixed RNA target sequences. Subsequent treatment with RNase H releases RNA-templated ligation products into solution for downstream analysis. We demonstrate several unique advantages of LISH-based assays using patient-derived FFPE tissue. These include >100-plex capability, compatibility with common histochemical stains and suitability for analysis of decade-old materials and exceedingly small microdissected tissue fragments. High-throughput DNA sequencing modalities, including single molecule sequencing, can be used to analyze ligation products from complex panels of LISH probes (‘LISH-seq’), which can be amplified efficiently and with negligible bias. LISH analysis of FFPE RNA is a novel methodology with broad applications that range from multiplexed gene expression analysis to the sensitive detection of infectious organisms.

Institutional profile: translational pharmacogenomics at the Icahn School of Medicine at Mount Sinai

For almost 50 years, the Icahn School of Medicine at Mount Sinai has continually invested in genetics and genomics, facilitating a healthy ecosystem that provides widespread support for the ongoing programs in translational pharmacogenomics. These programs can be broadly cataloged into discovery, education, clinical implementation and testing, which are collaboratively accomplished by multiple departments, institutes, laboratories, companies and colleagues. Focus areas have included drug response association studies and allele discovery, multiethnic pharmacogenomics, personalized genotyping and survey-based education programs, pre-emptive clinical testing implementation and novel assay development. This overview summarizes the current state of translational pharmacogenomics at Mount Sinai, including a future outlook on the forthcoming expansions in overall support, research and clinical programs, genomic technology infrastructure and the participating faculty.

METHODS FOR CLUSTERING TIME SERIES DATA ACQUIRED FROM MOBILE HEALTH APPS

In our recent Asthma Mobile Health Study (AMHS), thousands of asthma patients across the country contributed medical data through the iPhone Asthma Health App on a daily basis for an extended period of time. The collected data included daily self-reported asthma symptoms, symptom triggers, and real time geographic location information. The AMHS is just one of many studies occurring in the context of now many thousands of mobile health apps aimed at improving wellness and better managing chronic disease conditions, leveraging the passive and active collection of data from mobile, handheld smart devices. The ability to identify patient groups or patterns of symptoms that might predict adverse outcomes such as asthma exacerbations or hospitalizations from these types of large, prospectively collected data sets, would be of significant general interest. However, conventional clustering methods cannot be applied to these types of longitudinally collected data, especially survey data actively collected from app users, given heterogeneous patterns of missing values due to: 1) varying survey response rates among different users, 2) varying survey response rates over time of each user, and 3) non-overlapping periods of enrollment among different users. To handle such complicated missing data structure, we proposed a probability imputation model to infer missing data. We also employed a consensus clustering strategy in tandem with the multiple imputation procedure. Through simulation studies under a range of scenarios reflecting real data conditions, we identified favorable performance of the proposed method over other strategies that impute the missing value through low-rank matrix completion. When applying the proposed new method to study asthma triggers and symptoms collected as part of the AMHS, we identified several patient groups with distinct phenotype patterns. Further validation of the methods described in this paper might be used to identify clinically important patterns in large data sets with complicated missing data structure, improving the ability to use such data sets to identify at-risk populations for potential intervention.

Sequencing the CYP2D6 gene: from variant allele discovery to clinical pharmacogenetic testing

CYP2D6 is one of the most studied enzymes in the field of pharmacogenetics. The CYP2D6 gene is highly polymorphic with over 100 catalogued star (*) alleles, and clinical CYP2D6 testing is increasingly accessible and supported by practice guidelines. However, the degree of variation at the CYP2D6 locus and homology with its pseudogenes make interrogating CYP2D6 by short-read sequencing challenging. Moreover, accurate prediction of CYP2D6 metabolizer status necessitates analysis of duplicated alleles when an increased copy number is detected. These challenges have recently been overcome by long-read CYP2D6 sequencing; however, such platforms are not widely available. This review highlights the genomic complexities of CYP2D6, current sequencing methods and the evolution of CYP2D6 from allele discovery to clinical pharmacogenetic testing.

Far-infrared tangential interferometer/polarimeter design and installation for NSTX-U

The Far-infrared Tangential Interferometer/Polarimeter (FIReTIP) system has been refurbished and is being reinstalled on the National Spherical Torus Experiment-Upgrade (NSTX-U) to supply real-time line-integrated core electron density measurements for use in the NSTX-U plasma control system (PCS) to facilitate real-time density feedback control of the NSTX-U plasma. Inclusion of a visible light heterodyne interferometer in the FIReTIP system allows for real-time vibration compensation due to movement of an internally mounted retroreflector and the FIReTIP front-end optics. Real-time signal correction is achieved through use of a National Instruments CompactRIO field-programmable gate array.

Whole-Genome Sequencing of a Healthy Aging Cohort

Studies of long-lived individuals have revealed few genetic mechanisms for protection against age-associated disease. Therefore, we pursued genome sequencing of a related phenotype-healthy aging-to understand the genetics of disease-free aging without medical intervention. In contrast with studies of exceptional longevity, usually focused on centenarians, healthy aging is not associated with known longevity variants, but is associated with reduced genetic susceptibility to Alzheimer and coronary artery disease. Additionally, healthy aging is not associated with a decreased rate of rare pathogenic variants, potentially indicating the presence of disease-resistance factors. In keeping with this possibility, we identify suggestive common and rare variant genetic associations implying that protection against cognitive decline is a genetic component of healthy aging. These findings, based on a relatively small cohort, require independent replication. Overall, our results suggest healthy aging is an overlapping but distinct phenotype from exceptional longevity that may be enriched with disease-protective genetic factors. VIDEO ABSTRACT.

An Examination of the Relationship between Lipid Levels and Associated Genetic Markers across Racial/Ethnic Populations in the Multi-Ethnic Study of Atherosclerosis

Large genome-wide association studies have reported hundreds of genetic markers associated with lipid levels. However, the discovery and estimated effect of variants at these loci, derived from samples of exclusively European descent, may not generalize to the majority of the world populations. We examined the collective strength of association among these loci in a diverse set of U.S. populations from the Multi-Ethnic Study of Atherosclerosis. We constructed a genetic risk score for each lipid outcome based on previously identified lipid-associated genetic markers, and examined the relationship between the genetic risk scores and corresponding outcomes. We discover this relationship was often moderated by race/ethnicity. Our findings provide insight into the generalizability and predictive utility of large sample size meta-analyses results when leveraging data from a single population. We hope these findings will encourage researchers to investigate genetic susceptibility in more diverse populations and explore the source of such discrepancies. Until then, we caution clinicians, genetic counselors, and genetic testing consumers when interpreting genetic data on complex traits.

A genome sequencing program for novel undiagnosed diseases

PURPOSE

The Scripps Idiopathic Diseases of Man (IDIOM) study aims to discover novel gene-disease relationships and provide molecular genetic diagnosis and treatment guidance for individuals with novel diseases using genome sequencing integrated with clinical assessment and multidisciplinary case review. Here we describe the operational protocol and initial results of the IDIOM study.

METHODS

A total of 121 cases underwent first-tier review by the principal investigators to determine whether the primary inclusion criteria were satisfied, 59 (48.8%) underwent second-tier review by our clinician-scientist review panel, and 17 patients (14.0%) and their family members were enrolled.

RESULTS

60% of cases resulted in a plausible molecular diagnosis, and 18% of cases resulted in a confirmed molecular diagnosis. Two of three confirmed cases led to the identification of novel gene-disease relationships. In the third confirmed case a previously described but unrecognized disease was revealed. In all three confirmed cases a new clinical management strategy was initiated based on the genetic findings.

CONCLUSION

Genome sequencing provides tangible clinical benefit for individuals with idiopathic genetic disease, not only in the context of molecular genetic diagnosis of known rare conditions but also in cases where prior clinical information regarding a new genetic disorder is lacking.

Sensitive, multiplex and direct quantification of RNA sequences using a modified RASL assay

A sensitive and highly multiplex method to directly measure RNA sequence abundance without requiring reverse transcription would be of value for a number of biomedical applications, including high throughput small molecule screening, pathogen transcript detection and quantification of short/degraded RNAs.

R NA A

nnealing, S: election and L: igation (RASL) assays, which are based on RNA template-dependent oligonucleotide probe ligation, have been developed to meet this need, but technical limitations have impeded their adoption. Whereas DNA ligase-based RASL assays suffer from extremely low and sequence-dependent ligation efficiencies that compromise assay robustness, Rnl2 can join a fully DNA donor probe to a 3'-diribonucleotide-terminated acceptor probe with high efficiency on an RNA template strand. Rnl2-based RASL exhibits sub-femtomolar transcript detection sensitivity, and permits the rational tuning of probe signals for optimal analysis by massively parallel DNA sequencing (RASL-seq). A streamlined Rnl2-based RASL-seq protocol was assessed in a small molecule screen using 77 probe sets designed to monitor complex human B cell phenotypes during antibody class switch recombination. Our data demonstrate the robustness, cost-efficiency and broad applicability of Rnl2-based RASL assays.

Gain-of-function ADCY5 mutations in familial dyskinesia with facial myokymia

OBJECTIVE

To identify the cause of childhood onset involuntary paroxysmal choreiform and dystonic movements in 2 unrelated sporadic cases and to investigate the functional effect of missense mutations in adenylyl cyclase 5 (ADCY5) in sporadic and inherited cases of autosomal dominant familial dyskinesia with facial myokymia (FDFM).

METHODS

Whole exome sequencing was performed on 2 parent-child trios. The effect of mutations in ADCY5 was studied by measurement of cyclic adenosine monophosphate (cAMP) accumulation under stimulatory and inhibitory conditions.

RESULTS

The same de novo mutation (c.1252C>T, p.R418W) in ADCY5 was found in both studied cases. An inherited missense mutation (c.2176G>A, p.A726T) in ADCY5 was previously reported in a family with FDFM. The significant phenotypic overlap with FDFM was recognized in both cases only after discovery of the molecular link. The inherited mutation in the FDFM family and the recurrent de novo mutation affect residues in different protein domains, the first cytoplasmic domain and the first membrane-spanning domain, respectively. Functional studies revealed a statistically significant increase in β-receptor agonist-stimulated intracellular cAMP consistent with an increase in adenylyl cyclase activity for both mutants relative to wild-type protein, indicative of a gain-of-function effect.

INTERPRETATION

FDFM is likely caused by gain-of-function mutations in different domains of ADCY5-the first definitive link between adenylyl cyclase mutation and human disease. We have illustrated the power of hypothesis-free exome sequencing in establishing diagnoses in rare disorders with complex and variable phenotype. Mutations in ADCY5 should be considered in patients with undiagnosed complex movement disorders even in the absence of a family history.

Evidence for Alteration of Gene Regulatory Networks through MicroRNAs of the HIV-infected brain: novel analysis of retrospective cases

HIV infection disturbs the central nervous system (CNS) through inflammation and glial activation. Evidence suggests roles for microRNA (miRNA) in host defense and neuronal homeostasis, though little is known about miRNAs' role in HIV CNS infection. MiRNAs are non-coding RNAs that regulate gene translation through post-transcriptional mechanisms. Messenger-RNA profiling alone is insufficient to elucidate the dynamic dance of molecular expression of the genome. We sought to clarify RNA alterations in the frontal cortex (FC) of HIV-infected individuals and those concurrently infected and diagnosed with major depressive disorder (MDD). This report is the first published study of large-scale miRNA profiling from human HIV-infected FC. The goals of this study were to: 1. Identify changes in miRNA expression that occurred in the frontal cortex (FC) of HIV individuals, 2. Determine whether miRNA expression profiles of the FC could differentiate HIV from HIV/MDD, and 3. Adapt a method to meaningfully integrate gene expression data and miRNA expression data in clinical samples. We isolated RNA from the FC (n = 3) of three separate groups (uninfected controls, HIV, and HIV/MDD) and then pooled the RNA within each group for use in large-scale miRNA profiling. RNA from HIV and HIV/MDD patients (n = 4 per group) were also used for non-pooled mRNA analysis on Affymetrix U133 Plus 2.0 arrays. We then utilized a method for integrating the two datasets in a Target Bias Analysis. We found miRNAs of three types: A) Those with many dysregulated mRNA targets of less stringent statistical significance, B) Fewer dysregulated target-genes of highly stringent statistical significance, and C) unclear bias. In HIV/MDD, more miRNAs were downregulated than in HIV alone. Specific miRNA families at targeted chromosomal loci were dysregulated. The dysregulated miRNAs clustered on Chromosomes 14, 17, 19, and X. A small subset of dysregulated genes had many 3′ untranslated region (3′UTR) target-sites for dysregulated miRNAs. We provide evidence that certain miRNAs serve as key elements in gene regulatory networks in HIV-infected FC and may be implicated in neurobehavioral disorder. Finally, our data indicates that some genes may serve as hubs of miRNA activity.

Scanning electrochemical microscopy of iontophoretic transport in hairless mouse skin. Analysis of the relative contributions of diffusion, migration, and electroosmosis to transport in hair follicles

Scanning electrochemical microscopy (SECM) is used to measure spatially localized diffusive and iontophoretic transport rates in hairless mouse skin. Molecular fluxes within individual hair follicles are quantified by measuring the rate at which redox-active probe molecules emerge from the follicle. The influence of an applied current on the flux of an anion (ascorbate), a cation (ferrocenylmethyltrimethylammonium), and a neutral molecule (acetaminophen) is used to determine the contributions of diffusion, migration, and electroosmosis to iontophoretic transport. The direction of electroosmotic transport is consistent with hair follicles possessing a net negative charge at neutral pH. Electroosmosis results in a modest increase in the transport rate of the neutral molecule (a factor of approximately 2.4x at an iontophoretic current density of 0.1 mA/cm(2)). Larger enhancements in the flux of the electrically charged species are associated with migration. The electroosmotic flow velocity within hair follicles is established to be 0.5 (+/-0.1) microm/s at 0.1 mA/cm(2), independent of the electrical charge of permeant. The net volume flow rate across skin resulting from electroosmosis in hair follicles is estimated to be 0.3 microL/cm(2)h. The results suggest that hair follicles are a significant pathway for electroosmotic solution flow during iontophoresis. The radius of the hair follicle openings in hairless mouse skin is measured to be 21 +/- 5 microm.

Visualization and analysis of electroosmotic flow in hairless mouse skin

PURPOSE

To identify the physiological structures in hairless mouse skin responsible for the generation of electroosmotic flow during iontophoresis. Also, to determine the effects of changing the pH of the contacting solution on the magnitude of electroosmotic flow in these structures.

METHODS

Localized diffusive and iontophoretic fluxes of a neutral molecule, hydroquinone (HQ), across hairless mouse skin were quantified using scanning electrochemical microscopy (SECM). The iontophoretic flux was determined as a function of the direction of the applied current and pH of the contacting solution.

RESULTS

SECM images of HQ transport recorded during iontophoresis at moderate current densities (+/-0.1 mA/cm2) demonstrate that electroosmotic flow is localized to hair follicles. The direction of flow is from anode to cathode at pH > 3.5 and from cathode to anode at pH <3.5.

CONCLUSIONS

Electroosmotic flow through hair follicles is an efficient and controllable means of transporting small, electrically neutral molecules across hairless mouse skin. Transport through the appendages is sensitive to the pH of the solution in contact with the skin. The isoelectric point of hair follicles, pI, is estimated to be 3.5 from the dependence of electroosmotic flow on the solution pH.

Electrically facilitated molecular transport. Analysis of the relative contributions of diffusion, migration, and electroosmosis to solute transport in an ion-exchange membrane

Electrically facilitated molecular transport in an ion-exchange membrane (Nafion, 1100 equiv wt) has been studied using a scanning electrochemical microscope. The transport rates of ferrocenylmethyltrimethylammonium (a cation), acetaminophen (a neutral molecule), and ascorbate (an anion) through approximately 120-micron-thick membranes were measured as a function of the iontophoretic current passed across the membrane (-1.0 to +1.0 A/cm2). Transport rates were analyzed by employing the Nernst-Planck equation, modified to account for electric field-driven convective transport. Excellent agreement between experimental and theoretical values of the molecular flux was obtained using a single fitting parameter for each molecule (electroosmotic drag coefficient). The electroosmotic velocity of the neutral molecule, acetaminophen, was shown to be a factor of approximately 500 larger than that of the cation ferrocenylmethyltrimethylammonium, a consequence of the electrostatic interaction of the cation with the negatively charged pore walls of the ion-exchange membrane. Electroosmotic transport of ascorbate occurred at a negligible rate due to repulsion of the anion by the cation-selective membrane. These results suggest that electroosmotic velocities of solute molecules are determined by specific chemical interactions of the permeant and membrane and may be very different from the average solution velocity. The efficiency of electroosmotic transport was also shown to be a function of the membrane thickness, in addition to membrane/solute interactions.

Origin of carbonate-magnetite-sulfide assemblages in Martian meteorite ALH84001

A review of the mineralogical, isotopic, and chemical properties of the carbonates and associated submicrometer iron oxides and sulfides in Martian meteorite ALH84001 provides minimal evidence for microbial activity. Some magnetites resemble those formed by magnetotactic microorganisms but cubic crystals <50 nm in size and elongated grains <25 nm long are too small to be single-domain magnets and are probably abiogenic. Magnetites with shapes that are clearly unique to magnetotactic bacteria appear to be absent in ALH84001. Magnetosomes have not been reported in plutonic rocks and are unlikely to have been transported in fluids through fractures and uniformly deposited where abiogenic magnetite was forming epitaxially on carbonate. Submicrometer sulfides and magnetites probably formed during shock heating. Carbonates have correlated variations in Ca, Mg, and 18O/16O, magnetite-rich rims, and they appear to be embedded in pyroxene and plagiociase glass. Carbonates with these features have not been identified in carbonaceous chondrites and terrestrial rocks, suggesting that the ALH84001 carbonates have a unique origin. Carbonates and hydrated minerals in ALH84001, like secondary phases in other Martian meteorites, have O and H isotopic ratios favoring formation from fluids that exchanged with the Martian atmosphere. I propose that carbonates originally formed in ALH84001 from aqueous fluids and were subsequently shock heated and vaporized. The original carbonates were probably dolomite-magnesite-siderite assemblages that formed in pores at interstitial sites with minor sulfate, chloride, and phyllosilicates. These phases, like many other volatile-rich phases in Martian meteorites, may have formed as evaporate deposits from intermittent floods.

53Mn-53Cr dating of fayalite formation in the CV3 chondrite Mokoia: evidence for asteroidal alteration

Fayalite grains in chondrules in the oxidized, aqueously altered CV3 chondrite Mokoia have large excesses of radiogenic chromium-53. These excesses indicate the in situ decay of short-lived manganese-53 (half-life = 3.7 million years) and define an initial 53Mn/55Mn ratio of 2.32 (+/-0.18) x 10(-6). This ratio is comparable to values for carbonates in CI and CM chondrites and for several classes of differentiated meteorites. Mokoia fayalites formed 7 to 16 million years after Allende calcium-aluminum-rich inclusions, during hydrothermal activity on a geologically active asteroid after chondritic components had ceased forming in the solar nebula.

Carbonates in fractures of Martian meteorite Allan Hills 84001: petrologic evidence for impact origin

Carbonates in Martian meteorite Allan Hills 84001 occur as grains on pyroxene grain boundaries, in crushed zones, and as disks, veins, and irregularly shaped grains in healed pyroxene fractures. Some carbonate disks have tapered Mg-rich edges and are accompanied by smaller, thinner and relatively homogeneous, magnesite microdisks. Except for the microdisks, all types of carbonate grains show the same unique chemical zoning pattern on MgCO3-FeCO3-CaCO3 plots. This chemical characteristic and the close spatial association of diverse carbonate types show that all carbonates formed by a similar process. The heterogeneous distribution of carbonates in fractures, tapered shapes of some disks, and the localized occurrence of Mg-rich microdisks appear to be incompatible with growth from an externally derived CO2-rich fluid that changed in composition over time. These features suggest instead that the fractures were closed as carbonates grew from an internally derived fluid and that the microdisks formed from a residual Mg-rich fluid that was squeezed along fractures. Carbonate in pyroxene fractures is most abundant near grains of plagioclase glass that are located on pyroxene grain boundaries and commonly contain major or minor amounts of carbonate. We infer that carbonates in fractures formed from grain boundary carbonates associated with plagiociase that were melted by impact and dispersed into the surrounding fractured pyroxene. Carbonates in fractures, which include those studied by McKay et al. (1996), could not have formed at low temperatures and preserved mineralogical evidence for Martian organisms.

Petrological evidence for shock melting of carbonates in the martian meteorite ALH84001

The meteorite ALH84001--a shocked igneous rock of probable martian origin-contains chemically and isotopically heterogeneous carbonate globules, associated with which are organic and inorganic structures that have been interpreted as possible fossil remains of ancient martian biota. A critical assumption underlying this suggestion is that the carbonates formed from low-temperature fluids penetrating the cracks and voids of the host rock. Here we report petrological studies of ALH84001 which investigate the effects of shock on the various mineralogical components of the rock. We find that carbonate, plagioclase and silica were melted and partly redistributed by the same shock event responsible for the intense local crushing of pyroxene in the meteorite. Texture and compositional data show that, during the period of shock decompression, monomineralic melts were injected into pyroxene fractures that were subsequently cooled and resealed within seconds. Our results therefore suggest that the carbonates in ALH84001 could not have formed at low temperatures, but instead crystallized from shock-melted material; this conclusion weakens significantly the arguments that these carbonates could host the fossilized remnants of biogenic activity.

Visualization of iontophoretic transport paths in cultured and animal skin models

Physiological structures associated with iontophoretic paths in hairless mouse skin and two cultured skin models ("EpiDerm" by Mattek, Corp., and "SKIN2" by Advanced Tissue Sciences, Inc.) are reported. Visualization of ionic paths at current densities between 20 and 100 microA/ cm2 is accomplished by the counterdirectional transport of Fe(CN)6(4-) and Fe3+, resulting in the controlled precipitation of colloidal Prussian blue, Fe4[Fe(CN)6]3, at sites of high ionic conductivity. Examination of the Fe4[Fe(CN)6]3-stained tissues using optical microscopy allows unequivocal assignment of iontophoretic paths to physiological structures in the stratum corneum. Deposition of Fe4[Fe(CN)6]3 occurs exclusively at hair follicles in hairless mouse skin, indicating that these appendages provide highly conductive porous paths during iontophoresis. In contrast, the counterdirectional transport of Fe(CN)6(4-) and Fe3+ across cultured skin models, which lack appendages, results in the deposition of Fe4-[Fe(CN)6]3 along the boundaries of corneocytes. This observation suggests that paracellular iontophoretic transport through lipid bilayer regions is the predominant transport path in the absence of low-resistance pores.

Direct imaging of molecular transport through skin

Scanning electrochemical microscopy (SECM) was used to image spatial variations in the molecular flux of Fe(CN)6(-4) across excised hairless and nude mouse skin. The SECM response is specific to electroactive molecules, allowing selective imaging of the flux of Fe(CN)6(-4) in multicomponent ionic solutions. Quantitative SECM image analysis demonstrated that 40% to 60% of the total Fe(CN)6(-4) flux occurred through appendages in the skin. SECM analysis of skin samples exposed to a known transport enhancer, sodium dodecylsulfate, indicated that the increase in the ion transport rate occurred exclusively in nonporous skin tissue.

Transport of ionic species in skin: contribution of pores to the overall skin conductance

Two methods are reported that allow visualization of high conductance paths in skin at current densities typically used during clinical iontophoretic drug delivery (10-200 microA/cm2). In the first method, the counter-directional iontophoretic transport of Fe(CN)6(4-) and Fe3+ across skin results in the precipitation of colloidal prussian blue, Fe4[Fe(CN)6]3, at sites of high iontophoretic flux. The appearance of localized deposits of Fe4[Fe(CN)6]3 is recorded by video microscopy and used to document the activation of low-resistance paths. In the second method, the ionic flux of Fe(CN)6(4-) through pores is directly imaged by scanning electrochemical microscopy (SECM). Both methods demonstrate that the iontophoretic flux across skin is highly localized. Activation of low-resistance pores in hairless mouse skin is shown to occur during iontophoresis. The spatial density of current carrying pores increases from 0 to 100-600 pores/cm2 during the first 30-60 min of iontophoresis. At longer times, the active pore density approaches a quasi-steady-state value that is proportional to the applied current density. The total conductance of the skin is proportional to the number of pores, consistent with a model of conduction in skin that is comprised of low-resistivity pores in parallel with a high-resistivity bulk phase. The contribution of pores to the total skin conductance during iontophoresis increases from an initial value of 0-5% to a quasi-steady-state value of 50-95%.

Iontophoretic transport through porous membranes using scanning electrochemical microscopy: application to in vitro studies of ion fluxes through skin

Scanning electrochemical microscopy (SECM) is used to map localized iontophoretic fluxes of electroactive species through porous membranes. A method is described that allows both the rate of transport of species from a microscopic pore and the pore's diameter to be measured. SECM images and analyses of synthetic porous membranes (track-etched polycarbonate and mica membranes) and hairless mouse skin are reported. Preliminary analysis of SECM images of the mouse skin indicates that a significant percentage of the iontophoretic flux occurs through pores associated with hair follicles.

Comparison of lymphocyte immunophenotypes obtained simultaneously from two different data acquisition and analysis systems on the same flow cytometer

Immunophenotyping of different lymphocyte populations was carried out in parallel on 113 consecutively received specimens of human peripheral blood using 2 different data acquisition and analysis systems (EPICS C and 4Cyte-Acmecyte) on the same flow cytometer (EPICS C). The phenotypes analyzed were CD3+, CD4+, CD8+ CD56+ CD16+ CD3-, TCR-gamma delta+ CD8-, and TCR-gamma delta+ CD8+. Both HIV- and HIV+ specimens were used for this study, including some with CD4 levels as low as 2% of all lymphocytes. Despite differences in gating procedures and shapes of bitmap (rectilinear vs. "amorphous"), the 2 methods agreed to within 2% positive cells in 97% of the cases. Although some statistically significant biases in the methods were observed, these were small and not biologically important. We conclude that both methods of data acquisition and analysis, as employed by experienced operators on the EPICS C flow cytometer, gave essentially equivalent results for lymphocyte sub-populations in peripheral blood preparations.

Flow cytometric analysis of gamma delta T cells and natural killer cells in HIV-1 infection

We have previously shown that HIV-1 seropositivity is associated with an increase in the difference between the number of CD3+ lymphocytes and the total number of CD4+ and CD8+ lymphocytes [CD3 - (CD4 + CD8)] among peripheral blood lymphocytes (PBL). To investigate the cellular basis of this increase, PBL from seronegative (SN) and AIDS-free seropositive (SP) homosexual men and intravenous drug users were analyzed by two-color flow cytometry. Results showed that SP compared to SN manifested the expected elevation in calculated [CD3 - (CD4 + CD8)] cells (87 vs 28 cells/mm3; P less than 0.001). Only small differences in lymphocyte populations that could contribute to this increase were observed, namely lymphocytes expressing the CD3+CD4-CD8-phenotype (67 vs 56 cells/mm3; P greater than 0.10) or the CD8dim phenotype (135 vs 142 cells/mm3; P greater than 0.10). However, SP had significantly lower numbers of cells expressing the CD56+CD3- phenotype characteristic of natural killer cells (81 vs 170 cells/mm3; P less than 0.001) and significantly higher numbers of T cells expressing the gamma delta T cell receptor (TCR) (81 vs 62 cells/mm3; P = 0.10). The latter difference was primarily due to higher numbers of cells coexpressing gamma delta-TCR and low levels of CD8 (27 vs 15 cells/mm3; P = 0.009). These data suggest that HIV-1 seropositivity is associated with low numbers of natural killer cells and high numbers of CD8+ gamma delta-TCR lymphocytes. Changes in these populations may reflect altered host defense against HIV-1 or altered T cell kinetics in the presence of HIV-1 infection.

Flow cytometric quantitation of T cell phenotypes in cerebrospinal fluid and peripheral blood of homosexual men with and without antibodies to human immunodeficiency virus, type I

Two-color flow cytometry was used to analyze T cell subsets (total (CD3), helper-inducer (CD4), and suppressor-cytotoxic (CD8] in paired specimens of cerebrospinal fluid (CSF) and peripheral blood of 66 homosexual men, including 62 with antibodies to human immunodeficiency virus, type 1 (HIV-1). With the exception of one traumatic specimen, all of the CSF specimens, 52 of which had less than or equal to 5 lymphocytes/mm3, were evaluated fully, with the number of lymphocytes counted for each antibody ranging from 200 to 2933 (mean = 1129). Proportions of CD3, CD4, and CD8 lymphocytes in CSF were very highly correlated with the proportions of these cells in the peripheral blood (r = 0.87, 0.96, and 0.94, respectively), as was the CD4/CD8 ratio (r = 0.98). These strong correlations were present in each of seven subgroups of study subjects defined on the basis of detailed neurologic examination, neuropsychological testing, and the presence or absence of antibodies to HIV-1. In the population studied, T cell phenotypes in CSF as analyzed by two-color flow cytometry were largely determined by the corresponding proportions in the peripheral blood.