Evaluation of memory B cells among perinatally HIV infected children from Houston Texas

Background: HIV associated B cell exhaustion is a notable characteristic of HIV viremic adults. However, it is not known if such alterations are present in perinatal HIV infected children, whose viral dynamics differs from those seen in adults. In the present study we perform an analysis of B cells subsets and measure antigen-specific memory B cells (MBC) in a pediatric HIV infected cohort. ^ Methods: Peripheral mononuclear cells (PBMC) of perinatal HIV infected individuals are characterized into naïve (CD21hi/CD27−), classic (CD27+), tissue like (CD21lo/CD27 −) and activated MBC (CD27+CD21− ) by FACS. A memory ELISPOT assay is used to detect antibody secreting cells. We measure total IgG and antibodies specific for influenza, HBV, mumps, measles, rubella and VZV. Memory was expressed as spot forming cells (SPC) /million of PBMC. Wilcoxon rank-sum was used to compare unpaired groups and linear regression analysis was used to determine predictors of B cell dysfunction ^ Results: 41 HIV perinatal infected children are included (51.2% females and 65.9% Black). Age at study is median (range) 8.78 years (4.39-11.57). At the time of testing they have a CD4% of 30.9 (23.2-39.4), a viral load (VL) of 1.95 log10 copies/ml (1.68-3.29) and a cumulative VL of 3.4 log10 copy × days (2.7-4.0). Ninety two percent of the children are on cARV for > 6 months. Overall, HIV+ children compared with controls have a significant lower number of IgG and antigen specific SFC. In addition, they have a lower proportion of classical MBC 12.9 (8.09-19.85) vs 29.4 (18.7-39.05); 0.01, but a significant higher proportion of tissue like memory MBC 6.01 (2.79-12.7) vs 0.99 (0.87-1.38); 0.003, compared with controls. Patients are parsed on VL (<400 and ≥ 400 copies/ml) with the objective to evaluate the effect of VL on B cell status. Patients with a VL ≥ 400 copies/ml have a significantly lower IgG, HBV, measles, rubella and VZV SPC compared with those with a VL < 400 copies/ml. There are no significant differences in B cell subpopulations between the groups. A moderate negative correlation was observed between the time of cARV initiation and the frequency of IgG memory B cells, suggesting that early initiation of cARV appears to lead to a better functionality of the IgG memory B cells (P=0.05). A statistically significant positive correlation was observed between the total number of IgG memory cells and the number of antigen-specific memory B cells/SPCs. Suggesting that the progressive recovery of the IgG memory B cell pull goes along with a progressive increase in the number of antigen-specific SPCs. ^ Conclusion: A pediatric cohort in overall good status with respect to HIV infection and on ART has defects in B cell function and numbers (reduced total and antigen specific MBC and increased tissue like and reduced classical MBC).^

Evaluation of the Hosmer -Lemeshow global goodness -of-fit statistic for mixed variable logistic regression models

The performance of the Hosmer-Lemeshow global goodness-of-fit statistic for logistic regression models was explored in a wide variety of conditions not previously fully investigated. Computer simulations, each consisting of 500 regression models, were run to assess the statistic in 23 different situations. The items which varied among the situations included the number of observations used in each regression, the number of covariates, the degree of dependence among the covariates, the combinations of continuous and discrete variables, and the generation of the values of the dependent variable for model fit or lack of fit.^ The study found that the $\rm\ C$g* statistic was adequate in tests of significance for most situations. However, when testing data which deviate from a logistic model, the statistic has low power to detect such deviation. Although grouping of the estimated probabilities into quantiles from 8 to 30 was studied, the deciles of risk approach was generally sufficient. Subdividing the estimated probabilities into more than 10 quantiles when there are many covariates in the model is not necessary, despite theoretical reasons which suggest otherwise. Because it does not follow a X$\sp2$ distribution, the statistic is not recommended for use in models containing only categorical variables with a limited number of covariate patterns.^ The statistic performed adequately when there were at least 10 observations per quantile. Large numbers of observations per quantile did not lead to incorrect conclusions that the model did not fit the data when it actually did. However, the statistic failed to detect lack of fit when it existed and should be supplemented with further tests for the influence of individual observations. Careful examination of the parameter estimates is also essential since the statistic did not perform as desired when there was moderate to severe collinearity among covariates.^ Two methods studied for handling tied values of the estimated probabilities made only a slight difference in conclusions about model fit. Neither method split observations with identical probabilities into different quantiles. Approaches which create equal size groups by separating ties should be avoided. ^

Geochemistry and stratigraphy on sediment cores from Leg198 and Leg 208

The first complete cyclic sedimentary successions for the early Paleogene from drilling multiple holes have been retrieved during two ODP expeditions: Leg 198 (Shatsky Rise, NW Pacific Ocean) and Leg 208 (Walvis Ridge, SE Atlantic Ocean). These new records allow us to construct a comprehensive astronomically calibrated stratigraphic framework with an unprecedented accuracy for both the Atlantic and the Pacific Oceans covering the entire Paleocene epoch based on the identification of the stable long-eccentricity cycle (405-kyr). High resolution X-ray fluorescence (XRF) core scanner and non-destructive core logging data from Sites 1209 through1211 (Leg 198) and Sites 1262, 1267 (Leg 208) are the basis for such a robust chronostratigraphy. Former investigated marine (ODP Sites 1001 and 1051) and land-based (e.g., Zumaia) sections have been integrated as well. The high-fidelity chronology is the prerequisite for deciphering mechanisms in relation to prominent transient climatic events as well as completely new insights into Greenhouse climate variability in the early Paleogene. We demonstrate that the Paleocene epoch covers 24 long eccentricity cycles. We also show that no definite absolute age datums for the K/Pg boundary or the Paleocene - Eocene Thermal Maximum (PETM) can be provided by now, because of still existing uncertainties in orbital solutions and radiometric dating. However, we provide two options for tuning of the Paleocene which are only offset by 405-kyr. Our orbitally calibrated integrated Leg 208 magnetostratigraphy is used to revise the Geomagnetic Polarity Time Scale (GPTS) for Chron C29 to C25. We established a high-resolution calcareous nannofossil biostratigraphy for the South Atlantic which allows a much more detailed relative scaling of stages with biozones. The re-evaluation of the South Atlantic spreading rate model features higher frequent oscillations in spreading rates for magnetochron C28r, C27n, and C26n.

X-ray fluorescence (XRF) scannings and grain size analysis at sites in the Gulf of Cádiz

Contourites in the Gulf of Cádiz preserve a unique archive of Mediterranean Outflow Water (MOW) variability over the past 5.3 Ma. In our study we investigate the potential of geochemical data obtained by XRF scanning to decipher bottom current processes and paleoclimatic evolution at two different sites drilled through contourite deposits in the northern Gulf of Cadiz: Site U1387, which is bathed by the upper MOW core, and Site U1389, located more proximal to the Straits of Gibraltar. The lack of major downslope transport at both locations during the Pleistocene makes them ideal locations for the purpose of our study. The results indicate that the Zr/Al ratio, representing the relative enrichment of heavy minerals (zircon) over less dense alumosilicates under strong bottom current flow, is the most useful indicator for a semi-quantitative assessment of current strength. While most elements are biased by current-related processes, the bromine record, representing organic content, preserves the most pristine climate signal rather independent of grain size changes. Hence, Br can be used for chronostratigraphy and site-to-site correlation in addition to stable isotope stratigraphy. Based on these findings we reconstructed MOW variability for Marine Isotope Stages 1-5 using the Zr/Al ratio from Site U1387. The results reveal abrupt, millennial-scale variations of MOW strength during Greenland Stadials (GS) and Interstadials (GI) with strong MOW during GS and glacial Terminations and a complex behavior during Heinrich Stadials. Millennial-scale variability persisting during periods of poorly expressed GS/GI cyclicities implies a strong internal oscillation of the Mediterranean/North Atlantic climate system.

Evaluation of long chain 1,14-alkyl diols in marine sediments as indicators for upwelling and temperature

Long chain alkyl diols form a group of lipids occurring widely in marine environments. Recent studies have suggested several palaeoclimatological applications for proxies based on their distributions, but also revealed uncertainties about their applicability. Here we evaluate the use of long chain 1,14-alkyl diol indices for reconstruction of temperature and upwelling conditions by comparing index values, obtained from a comprehensive set of marine surface sediments, with environmental factors like sea surface temperature (SST), salinity and nutrient concentrations. Previous cultivation efforts indicated a strong effect of temperature on the degree of saturation and the chain length distribution of long chain 1,14-alkyl diols in Proboscia spp., quantified in the diol saturation index (DSI) and diol chain length index (DCI), respectively. However, values of these indices in surface sediments show no relationship with annual mean SST of the overlying water. It remains unknown what determines the DSI, although our data suggests that it may be affected by diagenesis, while the relationship between temperature and DCI may be different for different Proboscia species. In addition, contributions of algae other than Proboscia diatoms may affect both indices, although our data provide no direct evidence for additional long chain 1,14-alkyl diol sources. Two other indices using the abundance of 1,14-diols vs. 1,13-diols and C30 1,15-diols have previously been applied as indicators for upwelling intensity at different locations. The geographical distribution of their values supports the use of 1,14 diols vs. 1,13 diols [C28 + C30 1,14-diols]/[(C28 + C30 1,13-diols) + (C28 + C30 1,14-diols)] as a general indicator for high nutrient or upwelling conditions.

Compilation of scientific results of the OASIS project

Seamounts are of great interest to science, industry and conservation because of their potential role as 'stirring rods' of the oceans, their enhanced productivity, their high local biodiversity, and the growing exploitation of their natural resources. This is accompanied by rising concern about the threats to seamount ecosystems, e.g. through over-fishing and the impact of trawling. OASIS described the functioning characteristics of seamount ecosystems. OASIS' integrated hydrographic, biogeochemical and biological information. Based on two case studies. The scientific results, condensed in conceptual and mass balanced ecosystem models, were applied to outline a model management plan as well as site-specific management plans for the seamounts investigated. OASIS addressed five main objectives: Objective 1: To identify and describe the physical forcing mechanisms effecting seamount systems Objective 2: To assess the origin, quality and dynamics of particulate organic material within the water column and surface sediment at seamounts. Objective 3: To describe aspects of the biodiversity and the ecology of seamount biota, to assess their dynamics and the maintenance of their production. Objective 4: Modelling the trophic ecology of seamount ecosystems. Objective 5: Application of scientific knowledge to practical conservation.

Nd, Sr and Pb isotopic composition of eolian dust deposited in the central North Pacific

The silicate fractions of recent pelagic sediments in the central north Pacific Ocean are dominated by eolian dust derived from central Asia. An 11 Myr sedimentary record at ODP Sites 885/886 at 44.7°N, 168.3°W allows the evaluation of how such dust and its sources have changed in response to late Cenozoic climate and tectonics. The extracted eolian fraction contains variable amounts (>70%) of clay minerals with subordinate quartz and plagioclase. Uniform Nd isotopic compositions (epsilon-Nd =38.6 to 310.5) and Sm/Nd ratios (0.170-0.192) for most of the 11 Myr record demonstrate a well-mixed provenance in the basins north of the Tibetan Plateau and the Gobi Desert that was a source of dust long before the oldest preserved Asian loess formed. epsilon-Nd values of up to 36.5 for samples 62.9 Ma indicate <=35 wt% admixture of a young, Kamchatka-like volcanic arc component. The coherence of Pb and Nd in the erosional cycle allows us to constrain the Pb isotopic composition of Asian loess devoid of anthropogenic contamination to 206Pb/204Pb =18.97 +/- 0.06, 207Pb/204Pb =15.67 +/- 0.02, 208Pb/204Pb =39.19 +/- 0.11. 87Sr/86Sr (0.711-0.721) and Rb/Sr ratios (0.39-1.1) vary with dust mineralogy and provide an age indication of ~250 Ma. 40Ar/39Ar ages of six dust samples are uniform around 200 Ma and match the K-Ar ages of modern dust deposited on Hawaii. These data reflect the weighted age average of illite formation. Changes from illite- smectite with significant kaolinite to illite- and chlorite-rich, kaolinite-free assemblages since the late Pliocene document changes in the intensity of chemical weathering in the source region. Such weathering evidently did not disturb the K-Ar systematics, and only induced scatter in the Rb-Sr data. We propose that when smectite forms at the expense of illite, K and Ar are quantitatively lost from what becomes smectite, but are quantitatively retained in adjacent illite layers. 40Ar/39Ar age data, therefore, are insensitive to smectite formation during chemical weathering but date the diagenetic growth of illite, the major K-bearing phase in the dust. Over the past 12 Myr, the dust flux to the north Pacific increased by more than an order of magnitude, documenting a substantial drying of central Asia. This climatic change, however, did not alter the ultimate source of the dust, and neoformational products of chemical weathering always remained subordinate to assemblages reworked by mechanical erosion in dust deposited in eastern Asia and the Pacific Ocean.