A multi-organ map of the human immune system across age, sex and ethnicity.

Understanding tissue biology's heterogeneity is crucial for advancing precision medicine. Despite the centrality of the immune system in tissue homeostasis, a detailed and comprehensive map of immune cell distribution and interactions across human tissues and demographics remains elusive. To fill this gap, we harmonised data from 12,981 single-cell RNA sequencing samples and curated 29 million cells from 45 anatomical sites to create a comprehensive compositional and transcriptional healthy map of the healthy immune system. We used this resource and a novel multilevel modelling approach to track immune ageing and test differences across sex and ethnicity. We uncovered conserved and tissue-specific immune-ageing programs, resolved sex-dependent differential ageing and identified ethnic diversity in clinically critical immune checkpoints. This study provides a quantitative baseline of the immune system, facilitating advances in precision medicine. By sharing our immune map, we hope to catalyse further breakthroughs in cancer, infectious disease, immunology and precision medicine.

Diet type and changes in food cravings following weight loss: findings from the POUNDS LOST Trial.

Few well-controlled trials have evaluated the effects that macronutrient composition has on changes in food cravings during weight loss treatment. The present study, which was part of the Preventing Overweight Using Novel Dietary Strategies (POUNDS LOST) trial, investigated whether the fat and protein content of four different diets affected changes in specific food cravings in overweight and obese adults. A sample of 811 adults were recruited across two clinical sites, and each participant was randomly assigned to one of four macronutrient prescriptions: 1) low fat (20% of energy), average protein (15% of energy); 2) moderate fat (40%), average protein (15%); 3) low fat (20%), high protein (25%); 4) moderate fat (40%), high protein (25%). With few exceptions, the type of diet that participants were assigned did not differentially affect changes in specific food cravings. Participants assigned to the high-fat diets, however, had reduced cravings for carbohydrates at month 12 (p<0.05) and fruits and vegetables at month 24. Also, participants assigned to high-protein diets had increased cravings for sweets at month 6 and month 12 (ps<0.05). Participants in all four dietary conditions reported significant reductions in food cravings for specific types of foods (i.e., high fat foods, fast food fats, sweets, and carbohydrates/starches; all ps<0.05). Cravings for fruits and vegetables, however, were increased at month 24 (p<0.05). Calorically restricted diets (regardless of their macronutrient composition) yielded significant reductions in cravings for fats, sweets, and starches whereas cravings for fruits and vegetables were increased.

Polymorphic variation in surfactant protein B is associated with COPD exacerbations.

Exacerbations of chronic obstructive pulmonary disease (COPD) reduce quality of life and increase mortality. Genetic variation might explain the substantial variability seen in exacerbation frequency among COPD subjects with similar lung function. Polymorphisms in five candidate genes, previously associated with COPD susceptibility, were analysed in order to determine whether they demonstrated association with COPD exacerbations. A total of 88 single nucleotide polymorphisms (SNPs) in the genes microsomal epoxide hydrolase (EPHX1), transforming growth factor, beta-1 (TGFB1), serpin peptidase inhibitor, clade E (nexin, plasminogen activator inhibitor type 1), member 2 (SERPINE2), glutathione S-transferase pi (GSTP1) and surfactant protein B (SFTPB) were genotyped in 389 non-Hispanic white participants in the National Emphysema Treatment Trial. Exacerbations were defined as COPD-related emergency room visits or hospitalisations using the Centers for Medicare and Medicaid Services claims data. One or more exacerbations were experienced by 216 (56%) subjects during the study period. An SFTPB promoter polymorphism, rs3024791, was associated with COPD exacerbations. Logistic regression models, analysing a binary outcome of presence or absence of exacerbations, confirmed the association of rs3024791 with COPD exacerbations. Negative binomial regression models demonstrated association of multiple SFTPB SNPs (rs2118177, rs2304566, rs1130866 and rs3024791) with exacerbation rates. Polymorphisms in EPHX1, GSTP1, TGFB1 and SERPINE2 did not demonstrate association with COPD exacerbations. In conclusion, genetic variation in surfactant protein B is associated with chronic obstructive pulmonary disease susceptibility and exacerbation frequency.

Molecular analysis of the role of the group A streptococcal cysteine protease, hyaluronic acid capsule, and M protein in a murine model of human invasive soft-tissue infection.

Human invasive soft-tissue infections caused by group A Streptococcus are associated with significant morbidity and mortality. To investigate the pathogenesis of these serious infections, we characterized the host response to bacterial challenge with an M-type 3 isolate recovered from a patient with necrotizing fasciitis, or with isogenic gene replacement mutants deficient in cysteine protease, hyaluronic acid capsule, or M protein in a murine model of human invasive soft-tissue infection. Animals challenged with the wild-type or cysteine protease-deficient strain developed spreading tissue necrosis at the site of inoculation, became bacteremic, and subsequently died. Histopathologic examination of the necrotic lesion revealed bacteria throughout inflamed subcutaneous tissue. Arterioles and venules in the subcutaneous layer were thrombosed and the overlying tissue was infarcted. In contrast, animals challenged with either an acapsular or M protein-deficient mutant developed a focal area of tissue swelling at the site of inoculation without necrosis or subsequent systemic disease. Histopathologic examination of the soft-tissue lesion demonstrated bacteria confined within a well-formed subcutaneous abscess. We conclude that the group A streptococcal hyaluronic acid capsule and M protein, but not the cysteine protease, are critical for the development of tissue necrosis, secondary bacteremia, and lethal infection in a murine model of human necrotizing fasciitis.

Immune response to type III group B streptococcal polysaccharide-tetanus toxoid conjugate vaccine.

Group B Streptococcus (GBS) is an important perinatal pathogen. Because transplacentally acquired maternal antibodies to the GBS capsular polysaccharides (CPS) confer protection, prevention of infant disease may be possible after immunization of women. Unfortunately, the purified CPS of GBS are only variably immunogenic in adults; therefore to enhance immunogenicity we have designed and developed a CPS-protein conjugate vaccine. The lability of a conformationally dependent epitope on the III CPS containing a critical sialic acid residue was important to consider in vaccine design. 100 women were randomized to receive GBS type III CPS-tetanus toxoid conjugate (III-TT) vaccine at one of three doses; unconjugated GBS type III CPS; or saline. Serum samples were obtained before immunization and 2, 4, 8, and 26 wk thereafter, and specific antibody to type III CPS was measured. Vaccines were well tolerated. In sera from recipients of the highest dose of III-TT, CPS-specific IgG levels rose from a geometric mean of 0.09 microg/ml before immunization to 4.53 microg/ml 8 wk later, whereas levels in recipients of unconjugated type III CPS rose from 0.21 microg/ml to 1.41 microg/ml. Lower doses resulted in lower antibody levels. A > or = 4-fold rise in antibody concentration was achieved in 90% of recipients of III-TT compared with 50% of those that received III CPS (P = 0.0015). Antibodies evoked by the conjugate vaccine recognized a conformationally dependent epitope of the III-CPS, promoted opsonophagocytosis and killing of GBS, and, after maternal immunization, protected neonatal mice from lethal challenge with type III GBS. We conclude that directed coupling of type III GBS polysaccharide to a carrier protein yielded a conjugate vaccine with preserved expression of a highly labile conformational epitope involving sialic acid and enhanced immunogenicity compared with uncoupled CPS.

Deregulated expression of fat and muscle genes in B-cell chronic lymphocytic leukemia with high lipoprotein lipase expression.

Lipoprotein lipase (LPL) is a prognostic marker in B-cell chronic lymphocytic leukemia (B-CLL) related to immunoglobulin V(H) gene (IgV(H))mutational status. We determined gene expression profiles using Affymetrix U133A GeneChips in two groups of B-CLLs selected for either high ('LPL+', n=10) or low ('LPL-', n=10) LPL mRNA expression. Selected genes were verified by real-time PCR in an extended patient cohort (n=42). A total of 111 genes discriminated LPL+ from LPL- B-CLLs. Of these, the top three genes associated with time to first treatment were Septin10, DMD and Gravin (P

Pediatric AIDS prognosis using somatic growth velocity.

OBJECTIVE: To describe the natural history of somatic growth in HIV infection by constructing age-specific growth velocity norms and to assess specific prognostic information available using these norms. DESIGN: Observations on 1338 HIV-infected children aged 3 months to 15 years who participated in one of four US clinical trials of pediatric anti-HIV therapies were pooled; baseline growth velocity data were obtained using the first 6 months of observation for each child. METHODS: Distributions of physical growth velocities in HIV-infected children in the Pediatric AIDS Clinical Trials Group were computed. Statistical smoothing of growth histories was employed to derive velocity estimates, and quantile regression analysis of growth velocities was performed to allow comparisons of growth rates in age- and gender-heterogeneous cohorts in the context of HIV infection. The quantile regressions provide corrected z-scores for growth velocity that appropriately compare HIV-infected children with one another for the purpose of distinguishing more from less favorable prognoses. RESULTS: Consistent deficits in growth velocity amongst HIV-infected children were revealed when compared with the Fels Institute velocity standards. Approximately 33% of height (and 20% of weight) age- and sex-corrected velocity measurements obtained in the first 6 months of clinical trial participation lay beneath the corresponding third percentiles of the Fels reference distributions, which are commonly regarded as critical indicators of growth failure. Proportional hazards regression tests indicated that both weight and height velocity contributed significant information on the risk of death among children with AIDS after adjusting for antiretroviral therapy received, CD4 cell counts, and age at trial enrollment. Comparing subjects who differ in initial weight velocity by one age- and sex-corrected SD, the relative hazard of death was 0.63 (95% confidence interval, 0.55-0.72; P < or = 0.0001) in favor of the child with greater weight velocity, controlling for antiretroviral therapy received, age and CD4 cell count at baseline. The analogous hazard ratio for height velocity was 0.68 (95% confidence interval, 0.57-0.79; P < or = 0.0001). CONCLUSIONS: Suitably normalized growth velocities are informative and inexpensive criteria for pediatric AIDS prognosis; the growth velocity distributions presented will be useful for comparing growth effects of new therapeutic strategies to those of single and combination antiretrovirals employed for maintenance of pediatric HIV infection in the mid-1990s.

Race, socioeconomic factors, and area of residence are associated with asthma prevalence.

Asthma prevalence in the United States has been reported to be higher in minority groups such as Blacks and Hispanics. Because a disproportionate number of individuals from such minority groups are of low socioeconomic status (SES), it is unclear how much of the racial/ethnic differences in asthma prevalence is related to low SES. We investigated the effect of SES on the relationship between race/ethnicity and asthma prevalence in a cohort of families with a history of asthma or allergies from the Boston, Massachusetts area. From 499 families, a cohort of 998 parents and 307 children was identified. We used total yearly family income (<$50,000 vs. > or = $50, 000), highest level of education (< or = high school vs. > or = college), and residence in high-poverty areas vs. low-poverty areas as measures of SES. Yearly family income <$50,000, < or = high school education, and residence in high poverty areas were all associated with increased risks for asthma in both cohorts. In the parental cohort, Blacks and Hispanics (OR = 2.1, 95% CI = 1.5, 2.8; and OR = 2.2, 95% CI = 1.5, 3.2, respectively) were at greater risk for asthma than Whites. In the cohort of children, Black and Hispanic children (OR = 2.9, 95% CI = 1.0, 8.0; and OR = 5.3, 95% CI = 1.6, 17.5, respectively) were also at increased risk for asthma. When the three measures of SES were included in the multivariable models, the risks associated with Blacks and Hispanics decreased in both cohorts: OR = 1.4, 95% CI = 0.9, 2.0; and OR = 1.6, 95% CI = 1.0, 2. 6, respectively, for the parents; and OR = 0.8, 95% CI = 0.2, 3.0; and 2.5, 95% CI = 0.5, 11.7, respectively, for the children. We conclude that a large proportion of the racial/ethnic differences in asthma prevalence in our study is explained by factors related to income, area of residence, and level of education.

Results of physical inspection before races and race-related characteristics and their association with musculoskeletal injuries in Thoroughbreds during races.

OBJECTIVE: To estimate the relative risk of injury among horses deemed to be at increased risk of injury on the basis of prerace physical inspection findings and to examine the association of injury during races with race-related characteristics. DESIGN: Cohort study. ANIMALS: 2,187 Thoroughbred horses that started 3,227 races in Kentucky. PROCEDURE: All race starts for which a horse was deemed to be at increased risk of injury on the basis of prerace physical inspection findings and a random sample of race starts for which horses were not deemed at increased risk of injury were included in the study. Findings of prerace physical inspection, race-related characteristics, and outcome of the race (race results and whether the horse incurred an injury) were recorded for each race start. Race starts in which a horse incurred an injury during a race were compared with race starts in which injuries were not incurred to identify factors associated with injury during races. RESULTS: Abnormality of the suspensory ligament of the forelimbs detected during prerace physical inspection, racetrack, class of race (claiming race < or = $25,000 vs other classes), and distance of race (< 7 furlongs vs other distances) were significantly associated with increased risk of injury. CONCLUSIONS AND CLINICAL RELEVANCE: Prerace physical inspection findings, particularly abnormalities of the suspensory ligament, may be used to identify horses at increased risk of injury during races. Rate of injury differed among racetracks, and horses in certain types of races (lower-priced claiming races and races of shorter distance) may be at increased risk of injury during races.

Interpreting genetics of gene expression: integrative architecture in Bioconductor.

Several influential studies of genotypic determinants of gene expression in humans have now been published based on various populations including HapMap cohorts. The magnitude of the analytic task (transcriptome vs. SNP-genome) is a hindrance to dissemination of efficient, thorough, and auditable inference methods for this project. We describe the structure and use of Bioconductor facilities for inference in genetics of gene expression, with simultaneous application to multiple HapMap cohorts. Tools distributed for this purpose are readily adapted for the structure and analysis of privately-generated data in expression genetics.

SGDI: system for genomic data integration.

This paper describes a framework for collecting, annotating, and archiving high-throughput assays from multiple experiments conducted on one or more series of samples. Specific applications include support for large-scale surveys of related transcriptional profiling studies, for investigations of the genetics of gene expression and for joint analysis of copy number variation and mRNA abundance. Our approach consists of data capture and modeling processes rooted in R/Bioconductor, sample annotation and sequence constituent ontology management based in R, secure data archiving in PostgreSQL, and browser-based workspace creation and management rooted in Zope. This effort has generated a completely transparent, extensible, and customizable interface to large archives of high-throughput assays. Sources and prototype interfaces are accessible at www.sgdi.org/software.

Distribution of four capsular serotypes of Enterococcus faecalis among clinical isolates from different geographical origins and infection sites.

BACKGROUND: Enterococci possess capsular polysaccharide antigens that are the targets of opsonic antibodies. These antibodies are potential candidates for development as immunotherapy. MATERIAL AND METHODS: The present study analyzes the distribution of four capsular serotypes within a collection of 157 isolates of Enterococcus faecalis from four countries with different sites of clinical infection. RESULTS: By using a capsular polysaccharide-specific ELISA, 42% of the isolates were grouped into one of four serogroups, and another 9% showed cross-reactivity between two serotype-specific sera. Heterogeneity of serotype distribution by both geographical origin and infection site was observed. CONCLUSION: Half of the strain collection could be typed with four serotype-specific sera. No serotype from a given country or infection site clearly predominated.

Using hypertext and the Internet for structure and management of observational studies.

The evolution of computer and communications systems in the past decade brings new opportunities for increased efficiency and accuracy of observational studies. In ongoing, large scale research studies, the problem of bridging organizational and analytical methods of the past to modern methods of data structure and control can consume considerable effort. A model for information flow in an observational study is sketched, and the flow is found inherently complex. This complexity and corresponding managerial demands are compounded by database file proliferation and by evolution of system hardware and software. Interactive, network-based database mapping and documentation tools are described as currently implemented in an SAS-based system for the management and analysis of several large epidemiologic studies.

Analysis of longitudinally observed irregularly timed multivariate outcomes: regression with focus on cross-component correlation.

Components of repeatedly observed multivariate outcomes (for example, the two components of blood pressure measures (SBP(it), DBP(it)), obtained on subject i at arbitrarily spaced times t) are often analysed separately. We present a unified approach to regression analysis of such irregularly timed multivariate longitudinal data, with particular attention to assessment of the magnitude and durability of cross-component correlation. Maximum likelihood estimates are presented for component-specific regression parameters and autocorrelation and cross-correlation functions. The component-specific autocorrelation function has the 'damped exponential' form [see text], which generalizes the AR(1), MA(1) and random intercept models for univariate longitudinal outcomes. The cross-component correlation function (CCCF) has an analogous form, allowing damped-exponential decay of cross-component correlation as time between repeated measures elapses. Finite sample performance is assessed through simulation studies. The methods are illustrated through blood pressure modelling and construction of multivariate prediction regions.

Bayesian inference on protective antibody levels using case-control data.

In the study of immune responses to infectious pathogens, the minimum protective antibody concentration (MPAC) is a quantity of great interest. We use case-control data to estimate the posterior distribution of the conditional risk of disease given a lower bound on antibody concentration in an at-risk subject. The concentration bound beyond which there is high credibility that infection risk is zero or nearly so is a candidate for the MPAC. A very simple Gibbs sampling procedure that permits inference on the risk of disease given antibody level is presented. In problems involving small numbers of patients, the procedure is shown to have favorable accuracy and robustness to choice/misspecification of priors. Frequentist evaluation indicates good coverage probabilities of credibility intervals for antibody-dependent risk, and rules for estimation of the MPAC are illustrated with epidemiological data.

Estimation of design effects and diarrhea clustering within households and villages.

The degree to which diarrheal disease clustered within households and within villages among preschool age children was examined using data from four population-based prevalence surveys undertaken in Malawi, Zambia, Indonesia, and Nepal over the past decade. The design effect for each cluster survey was calculated using the diarrhea prevalence, the cluster sizes, and the magnitude of diarrhea clustering within the sampling unit (villages). A recently developed statistical method, alternating logistic regression, was used to estimate disease associations within households of up to nine preschool age children residing within villages of up to 589 such children. Pairwise odds ratios estimating diarrhea clustering within villages ranged from 1.03 (95% confidence interval (CI) 1.01-1.07) in Zambia to 2.19 (95% CI 1.73-2.78) in Indonesia. The design effects ranged from 2.07 (95% CI 1.26-3.19) in Zambia to 7.93 (95% CI 5.16-11.52) in Indonesia. Design effects were strongly dependent on cluster size. The design effects for clusters of size 50 would have ranged from 1.38 to 4.73. Pairwise odds ratios for diarrhea clustering within households ranged from 1.88 (95% CI 1.61-2.19) in Nepal to 10.05 (95% CI 8.46-11.94) in Indonesia. Household odds ratios were always larger than village odds ratios. The village and household pairwise odds ratios adjusted for age, the type of latrine used by the household, and presence of a market in the village were slightly higher than the unadjusted odds ratios. Alternating logistic regression provided useful estimates of disease clustering within villages and household while allowing for covariate adjustment.

Growth velocity assessment in paediatric AIDS: smoothing, penalized quantile regression and the definition of growth failure.

The analysis of growth records in paediatric anti-HIV clinical trials plays an important role in trial evaluation. Growth failure may be a manifestation of progressive disease or treatment toxicity, and is commonly specified as a major trial outcome event indicating poor treatment performance. Despite new therapeutic advances against HIV proliferation in infected patients, accurate monitoring and interpretation of somatic growth in paediatric AIDS remains clinically important, in light of uncertainties regarding relationship between viral load reductions and achievement of favourable somatic growth profiles. Our aim in this paper is to construct a criterion for growth failure that discriminates patients whose risk of death subsequent to growth failure is elevated to a clinically significant degree. To construct the criterion, individual growth curves and velocities are modelled using loess smoothing, penalized likelihood quantile regressions are fit to model age-specific growth velocity distributions for gender-stratified cohorts, and proportional hazards model selection is conducted to identify features of velocity series that are informative on the survival distribution. The resulting growth-failure criterion is expected to be useful for disease staging in resource-limited medical environments where T-cell counts and viral load measures are unavailable.

Tandem repeat deletion in the alpha C protein of group B streptococcus is recA independent.

Group B streptococci (GBS) contain a family of protective surface proteins characterized by variable numbers of repeating units within the proteins. The prototype alpha C protein of GBS from the type Ia/C strain A909 contains a series of nine identical 246-bp tandem repeat units. We have previously shown that deletions in the tandem repeat region of the alpha C protein affect both the immunogenicity and protective efficacy of the protein in animal models, and these deletions may serve as a virulence mechanism in GBS. The molecular mechanism of tandem repeat deletion is unknown. To determine whether RecA-mediated homologous recombination is involved in this process, we identified, cloned, and sequenced the recA gene homologue from GBS. A strain of GBS with recA deleted, A909DeltarecA, was constructed by insertional inactivation in the recA locus. A909DeltarecA demonstrated significant sensitivity to UV light, and the 50% lethal dose of the mutant strain in a mouse intraperitoneal model of sepsis was 20-fold higher than that of the parent strain. The spontaneous rate of tandem repeat deletion in the alpha C protein in vitro, as well as in our mouse model of immune infection, was studied using A909DeltarecA. We report that tandem repeat deletion in the alpha C protein does occur in the absence of a functional recA gene both in vitro and in vivo, indicating that tandem repeat deletion in GBS occurs by a recA-independent recombinatorial pathway.

Tracking of markers and onset of disease among HIV-1 seroconverters.

Repeated measurements on persons infected with HIV-1 indicate that infection has a dynamic impact on several markers of immune suppression and activation. The objectives of this report are: (a) to provide a statistical model for the correlation structure of serial measurements of immunological markers, and (b) to identify features of marker profiles associated with the timing of AIDS diagnoses. We analyse data obtained from 328 seroconverters participating in the Multicenter AIDS Cohort Study on whom the date of HIV-1 seroconversion is known within +/- 4.5 months. Immunological markers considered here are CD4 cell counts, serum beta 2-microglobulin and serum neopterin. The statistical model for HIV-related changes in markers consists of (1) a piecewise linear regression model for the trajectories of markers over time and (2) a two-parameter autocorrelation function that generalizes Markovian and simple random effects autocorrelation structures. Application of this model for marker measurements revealed a high degree of tracking, as the estimated autocorrelation function exhibited sub-exponential decay over time. Though current marker levels are most informative on future values, there is substantial information (memory) in previous measurements. A feature suggested by the analysis of groups formed according to the length of the AIDS-free period, is the sequential divergence of the CD4 trajectories where steeper declines occurred with a two-year lag prior to AIDS onset. For AIDS cases diagnosed 3-5 and 5-7 years after seroconversion, the rates of decline compared with those free of AIDS for at least 4 years were steeper by 95 and 46 per cent respectively at two years prior to AIDS.

Passive respiratory mechanics in healthy infants. Effects of growth, gender, and smoking.

This investigation characterizes the normal growth, variability, and effects of gender and smoking on passive respiratory mechanics in healthy infants. Passive respiratory mechanics were assessed at 193 test sessions on 127 infants (55 boys, 72 girls) between 2 wk and 18 mo of age using the single-occlusion passive flow-volume technique. Respiratory compliance (Crs) increased significantly with increasing infant length, whereas respiratory resistance (Rrs) declined. No significant gender differences were apparent for Crs, although there was a tendency for this measure to be both lower at birth and increase at a slower rate in girls than in boys. Rrs was significantly higher at birth in infant boys than in infant girls, but the rate of the normal decline in Rrs during the first 18 mo also occurred at a significantly greater rate in boys. The passive respiratory time constant (Trs) overall showed little change over this age range, but it was both lower near birth and increased at a significantly greater rate versus infant length in girls than in boys. Maternal smoking during pregnancy was associated with lower levels of Rrs at birth, as well as with significantly slower growth of Crs and natural decline of Rrs in the first 18 mo of life. These data suggest that infant girls may have more mature respiratory mechanics at birth, but that postnatal growth/maturation may be faster in boys.