ALBERT

Beschreibung: Transformation of refractory cratonic mantle into more fertile lithologies is the key to the fate of cratonic lithosphere. This process has been extensively studied in the eastern North China Craton (NCC) while that of its western part is still poorly constrained. A comprehensive study of newly-found pyroxenite xenoliths from the Langshan area, in the northwestern part of this craton is integrated with a regional synthesis of pyroxenite and peridotite xenoliths to constrain the petrogenesis of the pyroxenites and provide an overview of the processes involved in the modification of the deep lithosphere. The Langshan pyroxenites are of two types, high-Mg# [Mg2+/(Mg2++Fe2+)*100 = ∼ 90, atomic ratios] olivine-bearing websterites with high equilibration temperatures (880 ∼ 970 oC), and low-Mg# (70 ∼ 80) plagioclase-bearing websterites with low equilibration temperatures (550 ∼ 835 oC). The high-Mg# pyroxenites show trade-off abundances of olivine and orthopyroxene, highly depleted bulk Sr-Nd (ƐNd = +11.41, 87Sr/86Sr = ∼0.7034) and low clinopyroxene Sr isotopic ratios (mean 87Sr/86Sr = ∼0.703). They are considered to reflect the reaction of mantle peridotites with silica-rich silicate melts derived from the convective mantle. Their depletion in fusible components (e.g., FeO, TiO2 and Na2O) and progressive exhaustion of incompatible elements suggest melt extraction after their formation. The low-Mg# pyroxenites display layered structures, convex-upward rare earth element patterns, moderately enriched bulk Sr-Nd isotopic ratios (ƐNd = -14.20 ∼ -16.74, 87Sr/86Sr = 0.7070 ∼ 0.7078) and variable clinopyroxene Sr-isotope ratios (87Sr/86Sr = 0.706-0.711). They are interpreted to be crustal cumulates from hypersthene-normative melts generated by interaction between the asthenosphere and heterogeneous lithospheric mantle. Combined with studies on regional peridotite xenoliths, it is shown that the thinning and refertilization of the lithospheric mantle was accompanied by crustal rejuvenation and that such processes occurred ubiquitously in the northwestern part of the NCC. A geodynamic model is proposed for the evolution of the deep lithosphere, which includes long-term mass transfer through a mantle wedge into the deep crust from the Paleozoic to the Cenozoic, triggered by subduction of the Paleo-Asian ocean and the Late Mesozoic lithospheric extension of eastern Asia.

Beschreibung: The orogenic development after the continental collision between Laurussia and Gondwana, led to two contrasting associations of mantle-derived magmatic rocks on the territory of the Bohemian Massif: (i) a 340–310 Ma lamprophyre-lamproite orogenic association and (ii) a 300–275 Ma lamprophyre association of anorogenic affinity. Major types of potassic mantle-derived magmatic rocks recognised in the orogenic and anorogenic associations include: (i) calc-alkaline to alkaline lamprophyres, (ii) alkaline “orthopyroxene minettes” (and geochemically related rocks), and (iii) peralkaline lamproites. These three types significantly differ with respect to mineral, whole-rock and Sr–Nd–Pb–Li isotope composition, and spatial distribution. The calc-alkaline lamprophyres occur throughout the entire Saxo-Thuringian and Moldanubian zones, whereas the different types of malte-derived potassic rocks are spatially restricted to particular zones. Rocks of the Carboniferous lamprophyre-lamproite orogenic association are characterised by variable negative εNd(i) and variably radiogenic Sr(i), whereas the rocks of the Permian lamprophyre association of anorogenic affinity are characterised by positive εNd(i) and relatively young depleted-mantle Nd-model ages reflecting increasing input from upwelling asthenospheric mantle. The small variation in the Pb isotopic composition of post-collisional potassic mantle-derived magmatic rocks (of both the orogenic and anorogenic series) implies that the Pb budget of the mantle beneath the Bohemian Massif is dominated by the same crust-derived material, which itself may include material derived from several sources. The source rocks of “orthopyroxene minettes” are characterised by isotopically light (“eclogitic”) Li and strongly radiogenic (crustal) Sr and may have been metasomatised by high-pressure fluids along the edge of a subduction zone. In contrast, the strongly Al2O3 and CaO depleted mantle source of the lamproites is characterised by isotopically heavy Li and high SiO2 and extreme K2O contents. This mantle source may have been metasomatised predominantly by melts. The mantle source of the lamprophyres may have undergone metasomatism by both fluids and melts.

Beschreibung: The Lu–Hf isotope system and Sr–Nd–Hf–Os isotope systematics of mantle rocks are capable of unravelling the early processes in collision belts, especially in a hot subduction context where the Sm–Nd and U–Pb systems in crustal rocks are prone to resetting owing to high temperatures and interaction with melts during exhumation. To improve models of the Devonian–Carboniferous evolution of the Bohemian Massif, we investigated in detail mafic and ultramafic rocks (eclogite, pyroxenite, and peridotite) from the ultrahigh-pressure and ultrahigh-temperature Kutná Hora Crystalline Complex (KHCC: Úhrov, Bečváry, Doubrava, and Spačice localities). Petrography, multiphase solid inclusions, major and trace element compositions of rocks and minerals, and radiogenic isotopic data document contrasting sources and protoliths as well as effects of subduction-related processes for these rocks. The Úhrov peridotite has a depleted composition corresponding to the suboceanic asthenospheric mantle, whereas Bečváry and Doubrava peridotites represent lithospheric mantle that underwent melt refertilization by basaltic and SiO2-undersaturated melts, respectively. Multiphase solid inclusions enclosed in garnet from Úhrov and Bečváry peridotites represent trapped H2O ± CO2-bearing metasomatizing agents and Fe–Ti-rich melts. The KHCC eclogites either formed by high-pressure crystal accumulation from mantle-derived basaltic melts (Úhrov) or represent a fragment of mid-ocean ridge basalt-like gabbroic cumulate (Spačice) and crustal-derived material (Doubrava) both metamorphosed at high P–T conditions. The Lu–Hf age of 395 ± 23 Ma obtained for the Úhrov peridotite reflects garnet growth related to burial of the asthenospheric mantle during subduction of the oceanic slab. By contrast, Spačice and Doubrava eclogites yield younger Lu–Hf ages of ∼350 and 330 Ma, respectively, representing mixed ages as demonstrated by the strong granulite-facies overprint and trace element zoning in garnet grains. We propose a refined model for the Early Variscan evolution of the Bohemian Massif starting with the subduction of the oceanic crust (Saxothuringian ocean) and associated oceanic asthenospheric mantle (Úhrov) beneath the Teplá–Barrandian at ≥380 Ma, which was responsible for melt refertilization of the associated mantle wedge (Bečváry, Doubrava). This was followed by continental subduction (∼370–360 Ma?) accompanied by the oceanic slab break-off and incorporation of the upwelling asthenospheric mantle into the Moldanubian lithospheric mantle and subsequent coeval exhumation of mantle and crustal rocks at ∼350–330 Ma.

Beschreibung: The Changning–Menglian orogenic belt (CMOB) in the southeastern Tibetan Plateau is an important link between the Longmu Co–Shuanghu suture (LCSS) in the northern Tibetan Plateau and the Chiang Mai–Inthanon and Bentong–Raub sutures in Thailand and Peninsular Malaysia. These belts and sutures are generally regarded as containing the remnants of the oceanic crust of the Palaeo-Tethys that formed by seafloor spreading as a result of the separation of Gondwana- and Eurasia-derived blocks during the Middle Cambrian. In this paper we report the first discovery of abundant unaltered and retrograde eclogites that occur as irregular lenses and blocks in metasedimentary rocks of the CMOB, and these eclogites form an elongate and almost north–south-trending high-pressure (HP)–ultrahigh-pressure (UHP) metamorphic belt that is ∼200 km long and ∼50 km wide. The newly discovered phengite/talc/epidote–glaucophane eclogites, lawsonite–talc–phengite eclogites, dolomite/magnesite–kyanite eclogites and phengite–kyanite-bearing retrograde eclogites have enriched (E-) and normal mid-ocean ridge basalt (N-MORB)-like affinities and mainly positive as well as some negative whole-rock εNd values (–4·34 to +7·89), which suggest an enriched and depleted oceanic lithosphere source for their protoliths. Magmatic zircons separated from the epidote–glaucophane, magnesite–kyanite and (phengite–kyanite-bearing) retrograde eclogites gave protolith ages of 317–250 Ma, which fit well within the time frame of the opening of the Palaeo-Tethys during the Middle Cambrian and its closure during the Triassic. Abundant metamorphic zircons in the eclogites indicate a Triassic metamorphic event related to the subduction of the Palaeo-Tethys oceanic crust from 235 to 227 Ma. Taking into account previous isotopic age data, we now establish the periods of Early–Middle Triassic (246–227 Ma) and Late Triassic (222–209 Ma) as the ages of subduction and exhumation of the Palaeo-Tethyan oceanic crust, respectively. Thermodynamic modelling revealed that the eclogites record distinct HP–UHP peak metamorphic conditions of 23·0–25·5 kbar and 582–610 °C for the phengite–glaucophane eclogites, 24·0–25·5 kbar and 570–586 °C for the talc–glaucophane eclogites, 29·0–31·0 kbar and 675–712 °C for the dolomite–kyanite eclogites, and 30·0–32·0 kbar and 717–754 °C for the magnesite–kyanite eclogites. These P–T estimates and geochronological data indicate that the Palaeo-Tethys oceanic slab was subducted to different mantle depths from 75 km down to 95 km, forming distinct types of eclogite with a variety of peak eclogite-facies mineral assemblages. The eclogites consistently record clockwise metamorphic P–T–t paths characterized by a heating–compression prograde loop under a low geothermal gradient of 5–10 °C km–1, indicating the rapid subduction of cold oceanic crust at a rate of 4·5–6·0 km Ma–1, followed by isothermal or cooling–decompressive retrogression and exhumation at an average rate of 3·2–4·2 km Ma–1. The newly discovered eclogites of the CMOB with their signatures of ocean-crust subduction are petrologically, geochemically and geochronologically comparable with those of the LCSS, providing powerful support for the idea that a nearly 2000 km long HP–UHP eclogite belt extends from the northern Tibetan Plateau to the southeastern Tibetan Plateau, and that it represents the main boundary suture of the Palaeo-Tethyan domain. These results have far-reaching implications for the tectonic framework and complex metamorphic evolution of the Palaeo-Tethyan domain.

Beschreibung: Replacive symplectites (vermicular intergrowths of two or more minerals) are an important feature of layered igneous intrusions, recording evidence of late-stage reactions between interstitial liquid and crystals. They are common throughout the Layered Series of the 564 Ma Sept Iles layered intrusion in Quebec, Canada, and fall into three types: oxy-symplectites, ‘Type I’ symplectites, and ‘Type II’ symplectites. Oxy-symplectites are comprised of magnetite and orthopyroxene, nucleate on olivine primocrysts, and form via the reaction Olivine + O2 → Orthopyroxene + Magnetite; Type I symplectites (of which there are 3 distinct categories) are comprised of anorthitic plagioclase with pyroxene, amphibole, or olivine vermicules, grow from primocryst oxide grains, and replace primary plagioclase; and Type II symplectites (of which there are 2 distinct categories) are comprised of anorthitic plagioclase with orthopyroxene ± amphibole vermicules, grow from primocryst olivine grains, and replace primocryst plagioclase. Rare symplectites composed of biotite and plagioclase are also present. Symplectite growth occurred at 700-1030 °C with pressure constraints of 1-2 kbar. We propose that Type I symplectites, and some Type II symplectites, formed from interaction of primocrysts with residual Fe-rich liquid as a consequence of differential loss of an immiscible Si-rich liquid conjugate from the crystal mush. However, redistribution and concentration of hydrous fluids in incompletely solidified rock, or an increase in water activity of the interstitial melt, may be more plausible processes responsible for the formation of replacive symplectites comprising abundant hydrous mineral assemblages.

Beschreibung: : As sequencing becomes cheaper and more widely available, there is a greater need to quickly and effectively analyze large-scale genomic data. While the functionality of AVIA v1.0, whose implementation was based on ANNOVAR, was comparable with other annotation web servers, AVIA v2.0 represents an enhanced web-based server that extends genomic annotations to cell-specific transcripts and protein-level functional annotations. With AVIA’s improved interface, users can better visualize their data, perform comprehensive searches and categorize both coding and non-coding variants. Availability and implementation : AVIA is freely available through the web at http://avia.abcc.ncifcrf.gov . Contact : Hue.Vuong@fnlcr.nih.gov Supplementary information: Supplementary data are available at Bioinformatics online.

Beschreibung: : As new methods for multivariate analysis of genome wide association studies become available, it is important to be able to combine results from different cohorts in a meta-analysis. The R package MultiMeta provides an implementation of the inverse-variance-based method for meta-analysis, generalized to an n -dimensional setting. Availability and implementation: The R package MultiMeta can be downloaded from CRAN. Contact: dragana.vuckovic@burlo.trieste.it ; vi1@sanger.ac.uk Supplementary information: Supplementary data are available at Bioinformatics online.

Beschreibung: Motivation: Stem cell differentiation is largely guided by master transcriptional regulators, but it also depends on the expression of other types of genes, such as cell cycle genes, signaling genes, metabolic genes, trafficking genes, etc. Traditional approaches to understanding gene expression patterns across multiple conditions, such as principal components analysis or K-means clustering, can group cell types based on gene expression, but they do so without knowledge of the differentiation hierarchy. Hierarchical clustering can organize cell types into a tree, but in general this tree is different from the differentiation hierarchy itself. Methods: Given the differentiation hierarchy and gene expression data at each node, we construct a weighted Euclidean distance metric such that the minimum spanning tree with respect to that metric is precisely the given differentiation hierarchy. We provide a set of linear constraints that are provably sufficient for the desired construction and a linear programming approach to identify sparse sets of weights, effectively identifying genes that are most relevant for discriminating different parts of the tree. Results: We apply our method to microarray gene expression data describing 38 cell types in the hematopoiesis hierarchy, constructing a weighted Euclidean metric that uses just 175 genes. However, we find that there are many alternative sets of weights that satisfy the linear constraints. Thus, in the style of random-forest training, we also construct metrics based on random subsets of the genes and compare them to the metric of 175 genes. We then report on the selected genes and their biological functions. Our approach offers a new way to identify genes that may have important roles in stem cell differentiation. Contact: tperkins@ohri.ca Supplementary information: Supplementary data are available at Bioinformatics online.

Beschreibung: Motivation: Principal component analysis (PCA) is a basic tool often used in bioinformatics for visualization and dimension reduction. However, it is known that PCA may not consistently estimate the true direction of maximal variability in high-dimensional, low sample size settings, which are typical for molecular data. Assuming that the underlying signal is sparse, i.e. that only a fraction of features contribute to a principal component (PC), this estimation consistency can be retained. Most existing sparse PCA methods use L1-penalization, i.e. the lasso , to perform feature selection. But, the lasso is known to lack variable selection consistency in high dimensions and therefore a subsequent interpretation of selected features can give misleading results. Results: We present S4VDPCA, a sparse PCA method that incorporates a subsampling approach, namely stability selection. S4VDPCA can consistently select the truly relevant variables contributing to a sparse PC while also consistently estimate the direction of maximal variability. The performance of the S4VDPCA is assessed in a simulation study and compared to other PCA approaches, as well as to a hypothetical oracle PCA that ‘knows’ the truly relevant features in advance and thus finds optimal, unbiased sparse PCs. S4VDPCA is computationally efficient and performs best in simulations regarding parameter estimation consistency and feature selection consistency. Furthermore, S4VDPCA is applied to a publicly available gene expression data set of medulloblastoma brain tumors. Features contributing to the first two estimated sparse PCs represent genes significantly over-represented in pathways typically deregulated between molecular subgroups of medulloblastoma. Availability and implementation: Software is available at https://github.com/mwsill/s4vdpca . Contact: m.sill@dkfz.de Supplementary information: Supplementary data are available at Bioinformatics online.