An adaptive multiscale method for density-driven instabilities

Accurate modeling of flow instabilities requires computational tools able to deal with several interacting scales, from the scale at which fingers are triggered up to the scale at which their effects need to be described. The Multiscale Finite Volume (MsFV) method offers a framework to couple fine-and coarse-scale features by solving a set of localized problems which are used both to define a coarse-scale problem and to reconstruct the fine-scale details of the flow. The MsFV method can be seen as an upscaling-downscaling technique, which is computationally more efficient than standard discretization schemes and more accurate than traditional upscaling techniques. We show that, although the method has proven accurate in modeling density-driven flow under stable conditions, the accuracy of the MsFV method deteriorates in case of unstable flow and an iterative scheme is required to control the localization error. To avoid large computational overhead due to the iterative scheme, we suggest several adaptive strategies both for flow and transport. In particular, the concentration gradient is used to identify a front region where instabilities are triggered and an accurate (iteratively improved) solution is required. Outside the front region the problem is upscaled and both flow and transport are solved only at the coarse scale. This adaptive strategy leads to very accurate solutions at roughly the same computational cost as the non-iterative MsFV method. In many circumstances, however, an accurate description of flow instabilities requires a refinement of the computational grid rather than a coarsening. For these problems, we propose a modified iterative MsFV, which can be used as downscaling method (DMsFV). Compared to other grid refinement techniques the DMsFV clearly separates the computational domain into refined and non-refined regions, which can be treated separately and matched later. This gives great flexibility to employ different physical descriptions in different regions, where different equations could be solved, offering an excellent framework to construct hybrid methods.

The roles of flux- and decompression melting and their respective fractionation lines for continental crust formation: Evidence from the Kohistan arc

Delamination and foundering of the lower continental crust (LCC) into the mantle is part of the crust-forming mechanism. However, knowledge of the composition and mineralogy of the preserved or delaminated LCC over geological timescales remains scarce. We provide a synopsis of recent research within the Kohistan arc (Pakistan) and demonstrate that hydrous and less hydrous liquid lines of descent related to flux assisted and decompression mantle melting, respectively, produce compositionally different lower crustal rocks. The argument refers to two lower crustal sections exposed in Kohistan, the older Southern Plutonic Complex (SPC) and the younger Chilas Complex. The SPC typifies a hydrous, high-pressure fractionation sequence of olivine-pyroxenes-garnet-Fe/Ti-oxide-amphibole-plagioclase. The Chilas Complex illustrates a less hydrous fractionation sequence of olivine-clinopyroxene-orthopyroxene-plagioclase-amphibole. Despite the similarity of the Chilas Complex rocks to proposed lower crust compositions, the less hydrous fractionation results in unrealistically small volumes of silica-rich rocks, precluding the Chilas Complex gabbros to represent the magmatic complement to the upper crust. The composition of the SPC lower crust differs markedly from bulk lower crust estimates, but is complementary to silica-rich rocks exposed along this section and in the Kohistan batholith. These observations inspire a composite model for the formation of continental crust (CC) where the negatively buoyant delaminated and the buoyant preserved lower continental crusts (LCC) differ in genesis, mineralogy, and composition. We propose that the upper, non-sedimentary subsequent removal of the complementary, negatively buoyant garnet-pyroxene-amphibole-plagioclase-rich cumulates. In contrast, the LCC, which is buoyant and preserved over geological timescales, is formed by less hydrous parental mantle melts. We suggest that the bulk continental crust composition is related to mixing of these petrologically not directly related end members. Published by Elsevier B.V.

Stable alpha-synuclein oligomers strongly inhibit chaperone activity of the Hsp70 system by weak interactions with J-domain co-chaperones.

α-Synuclein aggregation and accumulation in Lewy bodies are implicated in progressive loss of dopaminergic neurons in Parkinson disease and related disorders. In neurons, the Hsp70s and their Hsp40-like J-domain co-chaperones are the only known components of chaperone network that can use ATP to convert cytotoxic protein aggregates into harmless natively refolded polypeptides. Here we developed a protocol for preparing a homogeneous population of highly stable β-sheet enriched toroid-shaped α-Syn oligomers with a diameter typical of toxic pore-forming oligomers. These oligomers were partially resistant to in vitro unfolding by the bacterial Hsp70 chaperone system (DnaK, DnaJ, GrpE). Moreover, both bacterial and human Hsp70/Hsp40 unfolding/refolding activities of model chaperone substrates were strongly inhibited by the oligomers but, remarkably, not by unstructured α-Syn monomers even in large excess. The oligomers acted as a specific competitive inhibitor of the J-domain co-chaperones, indicating that J-domain co-chaperones may preferably bind to exposed bulky misfolded structures in misfolded proteins and, thus, complement Hsp70s that bind to extended segments. Together, our findings suggest that inhibition of the Hsp70/Hsp40 chaperone system by α-Syn oligomers may contribute to the disruption of protein homeostasis in dopaminergic neurons, leading to apoptosis and tissue loss in Parkinson disease and related neurodegenerative diseases.

Closing the gap between T-cell life span estimates from stable isotope-labeling studies in mice and humans.

Quantitative knowledge of the turnover of different leukocyte populations is a key to our understanding of immune function in health and disease. Much progress has been made thanks to the introduction of stable isotope labeling, the state-of-the-art technique for in vivo quantification of cellular life spans. Yet, even leukocyte life span estimates on the basis of stable isotope labeling can vary up to 10-fold among laboratories. We investigated whether these differences could be the result of variances in the length of the labeling period among studies. To this end, we performed deuterated water-labeling experiments in mice, in which only the length of label administration was varied. The resulting life span estimates were indeed dependent on the length of the labeling period when the data were analyzed using a commonly used single-exponential model. We show that multiexponential models provide the necessary tool to obtain life span estimates that are independent of the length of the labeling period. Use of a multiexponential model enabled us to reduce the gap between human T-cell life span estimates from 2 previously published labeling studies. This provides an important step toward unambiguous understanding of leukocyte turnover in health and disease.

Hsp70 chaperones accelerate protein translocation and the unfolding of stable protein aggregates by entropic pulling.

Hsp70s are highly conserved ATPase molecular chaperones mediating the correct folding of de novo synthesized proteins, the translocation of proteins across membranes, the disassembly of some native protein oligomers, and the active unfolding and disassembly of stress-induced protein aggregates. Here, we bring thermodynamic arguments and biochemical evidences for a unifying mechanism named entropic pulling, based on entropy loss due to excluded-volume effects, by which Hsp70 molecules can convert the energy of ATP hydrolysis into a force capable of accelerating the local unfolding of various protein substrates and, thus, perform disparate cellular functions. By means of entropic pulling, individual Hsp70 molecules can accelerate unfolding and pulling of translocating polypeptides into mitochondria in the absence of a molecular fulcrum, thus settling former contradictions between the power-stroke and the Brownian ratchet models for Hsp70-mediated protein translocation across membranes. Moreover, in a very different context devoid of membrane and components of the import pore, the same physical principles apply to the forceful unfolding, solubilization, and assisted native refolding of stable protein aggregates by individual Hsp70 molecules, thus providing a mechanism for Hsp70-mediated protein disaggregation.

Shallow-platform palaeoenvironmental conditions recorded in deep-shelf sediments: C and stable isotopes in Upper Jurassic sections of southern Germany (Oxfordian-Kimmeridgian)

A high-resolution carbon and oxygen isotope analysis of Late Oxfordian-Early Kimmeridgian deep-shelf sediments of southern Germany is combined with investigation of nannofossil assemblage composition and sedimentological interpretations in order to evaluate the impact of regional palaeoenvironmental conditions on isotopic composition of carbonates. This study suggests that carbonate mud was essentially derived from the Jura shallow platform environments and also that the isotopic signature of carbonates deposited in the Swabian Alb deep shelf indirectly expresses the palaeoenvironmental evolution of the platform. Short-term fluctuations in delta(13) C and delta(18)O are probably controlled by changes in salinity (fresh-water input versus evaporation) in platform environments. Long-term fluctuations in carbon and oxygen isotope record throughout the Late Oxfordian-Early Kimmeridgian result from the interplay of increasing temperature and decreasing humidity, which both control the trophic level. Changes from mesotrophic to oligotrophic conditions in platform environments and in the deep-shelf surface waters are inferred. During the Late Oxfordian (Bimammatum Subzone to Planula Zone), the delta(13)C curve displays a positive shift of about 1 parts per thousand, which is comparable in intensity to global perturbations of the carbon cycle. This evident isotopic shift has not been documented yet in other basinal settings. It can be reasonably explained by local palaeoenvironmental changes on the Jura platform (salinity, temperature, and nutrient availability) that controlled platform carbonate production, and the geochemistry of overlying waters. However, increasing carbonate production on the Jura platform and related positive delta(13)C shifts recorded in the Swabian Alb deep shelf are the regional signatures of climatic changes affecting other palaeogeographical domains of Europe in which the carbonate production increased throughout the Late Oxfordian. (C) 2002 Elsevier Science B.V. All rights reserved.

Regions of mouse mammary tumor virus superantigen involved in interaction with the major histocompatibility complex class II I-A molecule.

To study the major histocompatibility complex class II I-E dependence of mouse mammary tumor virus (MMTV) superantigens, we constructed hybrids between the I-E-dependent MMTV(GR) and the I-E-independent mtv-7 superantigens and tested them in vivo. Our results suggest that, although the C-terminal third mediates I-A interaction, additional binding sites are located elsewhere in the superantigen.

Biophysical characterization of two different stable misfolded monomeric polypeptides that are chaperone-amenable substrates.

Misfolded polypeptide monomers may be regarded as the initial species of many protein aggregation pathways, which could accordingly serve as primary targets for molecular chaperones. It is therefore of paramount importance to study the cellular mechanisms that can prevent misfolded monomers from entering the toxic aggregation pathway and moreover rehabilitate them into active proteins. Here, we produced two stable misfolded monomers of luciferase and rhodanese, which we found to be differently processed by the Hsp70 chaperone machinery and whose conformational properties were investigated by biophysical approaches. In spite of their monomeric nature, they displayed enhanced thioflavin T fluorescence, non-native β-sheets, and tertiary structures with surface-accessible hydrophobic patches, but differed in their conformational stability and aggregation propensity. Interestingly, minor structural differences between the two misfolded species could account for their markedly different behavior in chaperone-mediated unfolding/refolding assays. Indeed, only a single DnaK molecule was sufficient to unfold by direct clamping a misfolded luciferase monomer, while, by contrast, several DnaK molecules were necessary to unfold the more resistant misfolded rhodanese monomer by a combination of direct clamping and cooperative entropic pulling.

Stable isotope geochemistry and phase-equilibria of coesite-bearing whiteschists, Dora Maira massif, Western Alps

Peak metamorphic temperatures for the coesite-pyrope-bearing whiteschists from the Dora Maira Massif, western Alps were determined with oxygen isotope thermometry. The deltaO-18(SMOW) values of the quartz (after coesite) (delta O-18 = 8.1 to 8.6 parts per thousand, n = 6), phengite (6.2 to 6.4 parts per thousand, n = 3), kyanite (6.1 parts per thousand, n = 2), garnet (5.5 to 5.8 parts per thousand, n = 9), ellenbergerite (6.3 parts per thousand, n = 1) and rutile (3.3. to 3.6 parts per thousand, n = 3) reflect isotopic equilibrium. Temperature estimates based on quartz-garnet-rutile fractionation are 700-750-degrees-C. Minimum pressures are 31-32 kb based on the pressure-sensitive reaction pyrope + coesite = kyanite + enstatite. In order to stabilize pyrope and coesite by the temperature-sensitive dehydration reaction talc + kyanite = pyrope + coesite + H2O, the a(H2O) must be reduced to 0.4-0.75 at 700 750-degrees-C. The reduced a(H2O) cannot be due to dilution by CO2, as pyrope is not stable at X (CO2) > 0.02 (T = 750-degrees-C; P = 30 kb). In the absence of a more exotic fluid diluent (e.g. CH4 or N2), a melt phase is required. Granite solidus temperatures are approximately 680-degrees-C/30 kb at a(H2O) = 1.0 and are calculated to be approximately 70-degrees-C higher at a(H2O) = 0.7, consistent with this hypothesis. Kyanite-jadeite-quartz bands may represent a relict melt phase. Peak P-T-f(H2O) estimates for the whiteschist are 34 +/- 2 kb, 700-750-degrees-C and 0.4-0.75. The oxygen isotope fractionation between quartz (deltaO-18 = 11.6%.) and garnet (deltaO-18 = 8.7 parts per thousand) in the surrounding orthognesiss is identical to that in the coesite-bearing unit, suggesting that the two units shared a common, final metamorphic history. Hydrogen isotope measurements were made on primary talc and phengite (deltaD(smow) = -27 to -32 parts per thousand), on secondary talc and chlorite after pyrope (deltaD = - 39 to - 44 parts per thousand) and on the surrounding biotite (deltaD = -64 parts per thousand) and phengite (deltaD = -44 parts per thousand) gneiss. All phases appear to be in near-equilibrium. The very high deltaD values for the primary hydrous phases is consistent with an initial oceanic-derived/connate fluid source. The fluid source for the retrograde talc + chlorite after pyrope may be fluids evolved locally during retrograde melt crystallization. The similar deltaD, but dissimilar deltaO-18 values of the coesite-bearing whiteschists and hosting orthogneiss suggest that the two were in hydrogen isotope equilibrium, but not oxygen isotope equilibrium. The unusual hydrogen and oxygen isotope compositions of the coesite-bearing unit can be explained as the result of metasomatism from slab-derived fluids at depth.

MGMT methylation analysis of glioblastoma on the Infinium methylation BeadChip identifies two distinct CpG regions associated with gene silencing and outcome, yielding a prediction model for comparisons across datasets, tumor grades, and CIMP-status.

The methylation status of the O(6)-methylguanine-DNA methyltransferase (MGMT) gene is an important predictive biomarker for benefit from alkylating agent therapy in glioblastoma. Recent studies in anaplastic glioma suggest a prognostic value for MGMT methylation. Investigation of pathogenetic and epigenetic features of this intriguingly distinct behavior requires accurate MGMT classification to assess high throughput molecular databases. Promoter methylation-mediated gene silencing is strongly dependent on the location of the methylated CpGs, complicating classification. Using the HumanMethylation450 (HM-450K) BeadChip interrogating 176 CpGs annotated for the MGMT gene, with 14 located in the promoter, two distinct regions in the CpG island of the promoter were identified with high importance for gene silencing and outcome prediction. A logistic regression model (MGMT-STP27) comprising probes cg1243587 and cg12981137 provided good classification properties and prognostic value (kappa = 0.85; log-rank p < 0.001) using a training-set of 63 glioblastomas from homogenously treated patients, for whom MGMT methylation was previously shown to be predictive for outcome based on classification by methylation-specific PCR. MGMT-STP27 was successfully validated in an independent cohort of chemo-radiotherapy-treated glioblastoma patients (n = 50; kappa = 0.88; outcome, log-rank p < 0.001). Lower prevalence of MGMT methylation among CpG island methylator phenotype (CIMP) positive tumors was found in glioblastomas from The Cancer Genome Atlas than in low grade and anaplastic glioma cohorts, while in CIMP-negative gliomas MGMT was classified as methylated in approximately 50 % regardless of tumor grade. The proposed MGMT-STP27 prediction model allows mining of datasets derived on the HM-450K or HM-27K BeadChip to explore effects of distinct epigenetic context of MGMT methylation suspected to modulate treatment resistance in different tumor types.

Physical activity in free-living, overweight white and black women: divergent responses by race to diet-induced weight loss.

BACKGROUND: Black women are at greater risk of obesity than are white women, perhaps because of their lower levels of physical activity. OBJECTIVE: We compared free-living activity energy expenditure (AEE) in sedentary white and black women (in overweight and normal-weight states) and in never-overweight control subjects. DESIGN: Subjects included 46 women (23 white, 23 black) studied while overweight and after reaching a normal weight and 38 female control subjects (23 white, 15 black). Diet, without exercise training, resulted in a mean weight loss of 13 kg and a body mass index (in kg/m(2)) < 25. Body composition, sleeping energy expenditure, free-living total energy expenditure, and the energy cost of activity and aerobic capacity were assessed before and after weight loss under 4-wk, diet-controlled, weight-stable conditions and in the control subjects. AEE was defined as above-sleep energy expenditure. RESULTS: No significant racial differences in body composition, before or after weight loss, were found. After weight loss, AEE and aerobic capacity increased in the white women and decreased in the black women (P < 0.05 and P < 0.02, respectively). After weight loss, but not before, the white women had a significantly higher mean AEE than did the black women (2448 +/- 979 and 1728 +/- 1373 kJ/d, respectively; P < 0.05), approximating AEEs in the white (2314 +/- 1105) and black (2310 +/- 1251) control subjects. CONCLUSIONS: Relative to the responses of the white women to diet-induced weight loss, the black women became less fit and less physically active. Induction of a normal body weight in overweight black women appeared to produce a more obesity-prone state, favoring weight relapse.

Advanced geostatistical and machine-learning models for spatial data analysis of radioactively contaminated regions

Radioactive soil-contamination mapping and risk assessment is a vital issue for decision makers. Traditional approaches for mapping the spatial concentration of radionuclides employ various regression-based models, which usually provide a single-value prediction realization accompanied (in some cases) by estimation error. Such approaches do not provide the capability for rigorous uncertainty quantification or probabilistic mapping. Machine learning is a recent and fast-developing approach based on learning patterns and information from data. Artificial neural networks for prediction mapping have been especially powerful in combination with spatial statistics. A data-driven approach provides the opportunity to integrate additional relevant information about spatial phenomena into a prediction model for more accurate spatial estimates and associated uncertainty. Machine-learning algorithms can also be used for a wider spectrum of problems than before: classification, probability density estimation, and so forth. Stochastic simulations are used to model spatial variability and uncertainty. Unlike regression models, they provide multiple realizations of a particular spatial pattern that allow uncertainty and risk quantification. This paper reviews the most recent methods of spatial data analysis, prediction, and risk mapping, based on machine learning and stochastic simulations in comparison with more traditional regression models. The radioactive fallout from the Chernobyl Nuclear Power Plant accident is used to illustrate the application of the models for prediction and classification problems. This fallout is a unique case study that provides the challenging task of analyzing huge amounts of data ('hard' direct measurements, as well as supplementary information and expert estimates) and solving particular decision-oriented problems.