Comparison of Ba/Ca and d18OWATER as freshwater proxies: a multi-species core-top study on planktonic foraminifera from the vicinity of the Orinoco River mouth

Past river run-off is an important measure for the continental hydrological cycle and the as-sessment of freshwater input into the ocean. However, paleosalinity reconstructions applying different proxies in parallel often show offsets between the respective methods. Here, we compare the established foraminiferal Ba/Ca and d18OWATER salinity proxies for their capability to record the highly seasonal Orinoco freshwater plume in the eastern Caribbean. For this purpose we obtained a data set comprising Ba/Ca and d18OWATER determined on multiple spe-cies of planktonic foraminifera from core tops distributed around the Orinoco river mouth. Our findings indicate that interpretations based on either proxy could lead to different conclu-sions. In particular, Ba/Ca and d18OWATER diverge in their spatial distribution due to different governing factors. Apparently, the Orinoco freshwater plume is best tracked by Ba/Ca ratios of G. ruber (pink and sensu lato morphotypes), while d18OWATER based on the same species is more related to the local precipitation-evaporation balance overprinting the riverine freshwater contribution. Other shallow dwelling species (G. sacculifer, O. universa) show a muted response to the freshwater discharge, most likely due to their ecological and habitat prefer-ences. Extremely high Ba/Ca ratios recorded by G. ruber are attributed to Ba2+-desorption from suspended matter derived from the Orinoco. Samples taken most proximal to the freshwater source do not show pronounced Ba/Ca or d18OWATER anomalies. Here, the suspension loaded freshwater lid developing during maximum discharge suppresses foraminiferal populations. Both proxies are therefore biased towards dry season conditions at these sites, when surface salinity is only minimally reduced.

(Data D1) Annual climate proxy data from the NGRIP ice core, Greenland

The last two abrupt warmings at the onset of our present warm interglacial period, interrupted by the Younger Dryas cooling event, were investigated at high temporal resolution from the North Greenland Ice Core Project ice core. The deuterium excess, a proxy of Greenland precipitation moisture source, switched mode within 1 to 3 years over these transitions and initiated a more gradual change (over 50 years) of the Greenland air temperature, as recorded by stable water isotopes. The onsets of both abrupt Greenland warmings were slightly preceded by decreasing Greenland dust deposition, reflecting the wetting of Asian deserts. A northern shift of the Intertropical Convergence Zone could be the trigger of these abrupt shifts of Northern Hemisphere atmospheric circulation, resulting in changes of 2 to 4 kelvin in Greenland moisture source temperature from one year to the next.

Holocene Mg/Ca, alkenones, and light stable isotope measurements on the outer North Iceland shelf, sediment core MD99-2269

We present new Holocene century to millennial-scale proxies for the well-dated piston core MD99-2269 from Húnaflóadjúp on the North Iceland Shelf. The core is located in 365 mwd and lies close to the fluctuating boundary between Atlantic and Arctic/Polar waters. The proxies are: alkenone-based SST°C, and Mg/Ca SST°C estimates and stable d13C and d18O values on planktonic and benthic foraminifera. The data were converted to 60 yr equi-spaced time-series. Significant trends in the data were extracted using Singular Spectrum Analysis and these accounted for between 50% and 70% of the variance. A comparison between these data with previously published climate proxies from MD99-2269 was carried out on a data set which consisted of 14-variable data set covering the interval 400-9200 cal yr BP at 100 yr time steps. This analysis indicated that the 1st two PC axes accounted for 57% of the variability with high loadings clustering primarily into "nutrient" and "temperature" proxies. Clustering on the 100 yr time-series indicated major changes in environment at ~6350 and ~3450 cal yr BP, which define early, mid- and late Holocene climatic intervals. We argue that a pervasive freshwater cap during the early Holocene resulted in warm SST°s, a stratified water column, and a depleted nutrient supply. The loss of the freshwater layer in the mid-Holocene resulted in high carbonate production, and the late Holocene/neoglacial interval was marked by significantly more variable sea surface conditions.

Estimation of sea surface temperature from sediment core PS1768-8

The quantitative diatom analysis of 218 surface sediment samples recovered in the Atlantic and western Indian sector of the Southern Ocean is used to define a base of reference data for paleotemperature estimations from diatom assemblages using the Imbrie and Kipp transfer function method. The criteria which justify the exclusion of samples and species out of the raw data set in order to define a reference database are outlined and discussed. Sensitivity tests with eight data sets were achieved evaluating the effects of overall dominance of single species, different methods of species abundance ranking, and no-analog conditions (e.g., Eucampia Antarctica) on the estimated paleotemperatures. The defined transfer functions were applied on a sediment core from the northern Antarctic zone. Overall dominance of Fragilariopsis kerguelensis in the diatom assemblages resulted in a close affinity between paleotemperature curve and relative abundance pattern of this species downcore. Logarithmic conversion of counting data applied with other ranking methods in order to compensate the dominance of F. kerguelensis revealed the best statistical results. A reliable diatom transfer function for future paleotemperature estimations is presented.

Clay mineral distribution in sediment core AND-2A

Clay mineral assemblages in sediments from ANDRILL drill core AND-2A were used to reconstruct the Neogene palaeoenvironment. For the first time a clay mineral data set can be presented for southern McMurdo Sound, Ross Sea, Antarctica, that covers an expanded and fairly continuous Lower and Middle Miocene section. Although the occurrence of some authigenic smectites, zeolites and opal-CT documents diagenetic processes, the clay mineral assemblages allow a subdivision of the core into three intervals that reflect changes in provenance and volcanic activity. Interval I (1000-440 mbsf, 20.0-16.5 Ma) is characterised by a dominant sediment source in the Transantarctic Mountains. Frequent and short-term changes in the illite and smectite concentrations were caused by the influx of volcanic sediment components from southern McMurdo Sound and by diagenesis. Interval II (440-225 mbsf, 16.5-15.0 Ma) has much more uniform illite and smectite contents. The assemblage is derived from the Transantarctic Mountains. Interval III (225-0 mbsf, 15.0-0 Ma, containing major hiatuses) shows a distinctly enhanced volcanic influence and sediment components that come from the south of McMurdo Sound. The AND-2A clay mineral assemblages indicate persistent physical weathering conditions and do not mirror the Mid-Miocene Climatic Optimum. They indicate that the climatic changes were probably not strong enough to cause a modification in the weathering regime on the Antarctic continent.

(Table 1) Core top Globorotalia truncatulinoides d18O ratios of Atlantic Ocean samples

We investigate whether the oxygen isotope ratio in the test of Globorotalia truncatulinoides can serve as a proxy for intermediate depth (200-500 m) density. Since intermediate depth horizontal density gradients are associated with the vertical shear of upper ocean flows, this proxy could provide a tool for reconstructing past ocean circulation. The spatial pattern of core top Gr. truncatulinoides d18O in the Atlantic Ocean mimics the upper ocean density gradients associated with the major ocean currents. To better constrain the controls on the calcification depth(s) of Gr. truncatulinoides, we attempt to simulate the surface sediment data set using water column temperature and salinity conditions above the core sites. We predicted foraminiferal d18O for each core site assuming (1) the calcification occurs at a single depth and (2) the initial calcification is at the surface and the subsequent calcification is at 800 m water depth. The predicted d18O best resembles measured d18O of Gr. truncatulinoides when using (1) a single depth calcification at 350 m or (2) a two-depth approximation with 30% surface and 70% 800-m calcification. This result gives us confidence in the ability of d18O in Gr. truncatulinoides to proxy lateral density gradients at the intermediate depths associated with upper ocean flow.

Table 1 Core site, fractional abundance of individual isoprenoid GDGTs and TEX86 values

TEXL86 and TEXH86 are organic palaeothermometers based on the lipids of Group 1 Crenarchaeota, recently proposed as a modified version of the original TEX86 index, but with significantly improved geographical coverage. Since few data from the global core top calibration are from the Pacific, this study was carried out to assess whether the global core top calibration is regionally biased or not. The result of principal components analysis of the fractional abundance of GDGTs, an analysis of variance (ANOVA) and the comparison of the residuals of TEXH 86 derived sea surface temperature (SST) estimates of the Pacific subset with that of the global data set suggest that the Pacific subset has a similar TEXH 86-SST relationship with the global data set. However, the regression line through the Pacific data and an ANOVA on the residuals of TEXL 86 derived SST estimates suggest otherwise. The contradictory findings are likely to stem from the large scatter in the Pacific TEXL 86 values in the mid temperature range. While regionality does not seem to exert a strong bias on TEXL 86 and TEXH 86 calibration, it appears that there is a strong need to resolve the large scatter in the global data set, especially in the mid and high latitudes, in order to improve the calibration for a better SST estimation.

Stable isotope and Mg/Ca ratios of Globigerinoides ruber from core-top sediment samples

Seasonal changes in surface ocean temperature are increasingly recognized as an important parameter of the climate system. Here we assess the potential of analyzing single-specimen planktonic foraminifera as proxy for the seasonal temperature contrast (seasonality). Oxygen isotopes and Mg/Ca ratios were measured on single specimens of Globigerinoides ruber, extracted from surface sediment samples of the Mediterranean Sea and the adjacent Atlantic Ocean. Variability in d18O and Mg/Ca was then compared to established modern seasonal changes in temperature and salinity for both regions. The results show that (1) average d18O-derived temperatures correlate with modern annual average temperatures for most sites, (2) the range in d18O- and Mg/Ca-derived temperature estimates from single-specimen analysis resembles the range in seasonal temperature values at the sea surface (0-50 m) in the Mediterranean Sea and the Atlantic Ocean, and (3) there is no strong correlation between Mg/Ca- and d18O-derived temperatures from the same specimens in the current data set, indicating that other parameters (salinity, carbonate ion concentration, symbiont activity, ontogenesis, and natural variability) potentially affect these proxies.

Nd/Ca ratios in plankton-towed and core top foraminifera

Planktic foraminifera have been used as recorders of the neodymium (Nd) isotopic composition of seawater, although there is still controversy over the precise provenance of the Nd signal. We present an extensive, multispecific plankton tow Nd/Ca data set from several geographic locations (SE Atlantic, NE Atlantic, Norwegian Sea, and western Mediterranean), together with core top samples from the Mediterranean region. The range of Nd/Ca ratios in plankton-towed foraminifera, cleaned only of organic material, from all regions (0.01-0.7 µmol/mol), is similar to previously published analyses of sedimentary foraminifera cleaned using both oxidative and reductive steps, with distribution coefficients (Kd) ranging between 4 and 302. For the Mediterranean, where core top and plankton tow data are both available, the range for plankton tows (0.05-0.7 µmol/mol) is essentially identical to that for the core tops (0.1-0.5 µmol/mol). Readsorption of Nd during cleaning is ruled out by the fact that the plankton tow samples underwent only an oxidative cleaning process. We find a relationship between manganese (Mn) and Nd in plankton tow samples that is mirrored by a similar correlation in core top samples. This relationship suggests that Fe-Mn coatings are of negligible importance to the Nd budgets of foraminifera as the Nd/Mn ratio it implies is over an order of magnitude greater than that seen in other Fe-Mn oxide phases. Rather, since both plankton tows and core tops present a similar behavior, the Nd/Mn relationship must originate in the upper water column. The data are consistent with the acquisition of Nd and Mn from the water column by binding to organic material and the fact that intratest organic material is shielded from both aggressive cleaning and diagenetic processes. Collectively, the results help to explain two abiding puzzles about Nd in sedimentary planktic foraminifera: their high REE contents and the fact that they record a surface water Nd isotopic signal, regardless of the cleaning procedure used.

(Table 1) Age control points and of sediment core MD01-2444

The marine isotopic stage 3 (MIS3) at Ocean Drilling Program (ODP) Site 1060 (Gulf Stream) shows both sharp onset and end of interstadials, the existence of very short lived warm events during stadials, and points to differences in detail between the sea surface temperature (SST) record from the western North Atlantic and the atmospheric temperature record inferred from d18O in Greenland ice. Investigating MIS3 and obtaining comparable data from other locations appears crucial. The eastern Atlantic provides well-documented records of climate changes. We have selected a core from off Portugal and use it to examine Dansgaard/Oeschger events (D/O) at centennial-scale resolution (139 years on average between two data points). We have obtained a faunal data set for core MD01-2444, 37°N, 10°W, 2600 m water depth and use a group of species (Globigerina bulloides + Globigerinita glutinata) as a proxy of upwelling intensity driven by trade winds intensity changes. We tentatively relate the variation of this group to a North Atlantic Oscillation-like phenomenon (NAO) off Portugal. We observe that it resembles the rainfall index in the Caribbean as recorded at ODP Site 1002 (Cariaco Basin) which traces the Intertropical Convergence Zone (ITCZ) location through changes of terrigenous inputs. The driest intervals (ITZC to the south) at Site 1002 correspond to intervals of increased upwelling in MD01-2444 as well as the driest periods identified during stadials on similar cores in the area. Because the ITZC to the south is consistent with an El Niño-Southern Oscillation (ENSO+) situation, our study suggests a positive correlation between ENSO-like conditions and NAO-like conditions at a millennial timescale. During interstadial intervals when increased wetness over Cariaco is recorded (ITCZ to the north) and the upwelling in MD01-2444 is decreased, we see from both SSTs and faunal tropical indicators that MD01-2444 site is warm. In addition, interstadials are equally warm through each so-called Bond cycle. This contrasts with the Greenland Ice Core Project (GRIP) record where interstadial peaks are successively cooler through each Bond cycle. This record confirms a link between tropical climate linked to ITCZ position and the climate of southern Europe at millennial timescales, in spite of showing a very good correlation with polar latitudes (GRIP) through d18O on Globigerina bulloides. In addition, because the warmest SSTs and the d18O on G. bulloides are so remarkably different, our work points to changes in seasonality as a strong control over the climatic pattern of the North Atlantic area and the marked influence of winter conditions.

Planktic foraminiferal distribution and stable isotope ratios of sediment core MSM05/5_712-1 from the Arctic Ocean

The Arctic is responding more rapidly to global warming than most other areas on our planet. Northward flowing Atlantic Water is the major means of heat advection towards the Arctic and strongly affects the sea ice distribution. Records of its natural variability are critical for the understanding of feedback mechanisms and the future of the Arctic climate system, but continuous historical records reach back only ~150 years. Here, we present a multidecadal scale record of ocean temperature variations during the last 2000 years, derived from marine sediments off Western Svalbard (79°N). We find that early-21st-century temperatures of Atlantic Water entering the Arctic Ocean are unprecedented over the past 2000 years and are presumably linked to the Arctic Amplification of global warming.

Pre-processing for noise detection in gene expression classification data

Due to the imprecise nature of biological experiments, biological data is often characterized by the presence of redundant and noisy data. This may be due to errors that occurred during data collection, such as contaminations in laboratorial samples. It is the case of gene expression data, where the equipments and tools currently used frequently produce noisy biological data. Machine Learning algorithms have been successfully used in gene expression data analysis. Although many Machine Learning algorithms can deal with noise, detecting and removing noisy instances from the training data set can help the induction of the target hypothesis. This paper evaluates the use of distance-based pre-processing techniques for noise detection in gene expression data classification problems. This evaluation analyzes the effectiveness of the techniques investigated in removing noisy data, measured by the accuracy obtained by different Machine Learning classifiers over the pre-processed data.

Assessing influence in survival data with a cure fraction and covariates

Diagnostic methods have been an important tool in regression analysis to detect anomalies, such as departures from error assumptions and the presence of outliers and influential observations with the fitted models. Assuming censored data, we considered a classical analysis and Bayesian analysis assuming no informative priors for the parameters of the model with a cure fraction. A Bayesian approach was considered by using Markov Chain Monte Carlo Methods with Metropolis-Hasting algorithms steps to obtain the posterior summaries of interest. Some influence methods, such as the local influence, total local influence of an individual, local influence on predictions and generalized leverage were derived, analyzed and discussed in survival data with a cure fraction and covariates. The relevance of the approach was illustrated with a real data set, where it is shown that, by removing the most influential observations, the decision about which model best fits the data is changed.

Purification, crystallization and preliminary crystallographic analysis of the catalytic domain of the extracellular cellulase CBHI from Trichoderma harzianum

The filamentous fungus Trichoderma harzianum has a considerable cellulolytic activity that is mediated by a complex of enzymes which are essential for the hydrolysis of microcrystalline cellulose. These enzymes were produced by the induction of T. harzianum with microcrystalline cellulose (Avicel) under submerged fermentation in a bioreactor. The catalytic core domain (CCD) of cellobiohydrolase I (CBHI) was purified from the extracellular extracts and submitted to robotic crystallization. Diffraction-quality CBHI CCD crystals were grown and an X-ray diffraction data set was collected under cryogenic conditions using a synchrotron-radiation source.

Different Approaches for Modeling Grouped Survival Data: A Mango Tree Study

Interval-censored survival data, in which the event of interest is not observed exactly but is only known to occur within some time interval, occur very frequently. In some situations, event times might be censored into different, possibly overlapping intervals of variable widths; however, in other situations, information is available for all units at the same observed visit time. In the latter cases, interval-censored data are termed grouped survival data. Here we present alternative approaches for analyzing interval-censored data. We illustrate these techniques using a survival data set involving mango tree lifetimes. This study is an example of grouped survival data.