Plio-Quaternary exhumation history of the central Nepalese Himalaya: 1. Apatite and zircon fission track and apatite [U-Th]/He analyses

New apatite and zircon fission track and (U-Th)/He analyses serve to document the bedrock cooling history of the central Nepalese Himalaya near the Annapurna Range. We have obtained 82 apatite fission track (AFT), 7 zircon fission track (ZFT), and 7 apatite (U-Th)/He (AHe) ages from samples collected along the Marsyandi drainage, including eight vertical relief profiles from ridges on either side of the river averaging more than 2 km in elevation range. In addition, three profiles were sampled along ridge crests that also lie ∼2 km above the adjacent valleys, and a transect of >20 valley bottom samples spans from the Lesser Himalaya across the Greater Himalaya and into the Tethyan strata. As a consequence, these data provide one of the more comprehensive low-temperature thermochronologic studies within the Himalaya. Conversely, the youthfulness of this orogen is pushing the limits of these dating techniques. AFT ages range from >3.8 to 0 Ma, ZFT ages from 1.9 to 0.8 Ma, and AHe ages from 0.9 to 0.3 Ma. Most ridges have maximum ages of 1.3–0.8 Ma at 2 km above the valley bottom. Only one ridge crest (in the south central zone of the field area) yielded significantly older ZFT and AFT ages of ∼2 Ma; we infer that a splay of the Main Central Thrust separates this ridge from the rest of the Greater Himalaya. ZFT and AFT ages from a vertical transect along this ridge indicate exhumation rates of ∼1.5 km Myr−1 (r2 > 0.7) from ∼2 to 0.6–0.8 Ma, whereas AHe ages indicate a faster exhumation rate of ∼2.6 km Myr−1 (r2 = 0.9) over the last 0.8 Myr. Exhumation rates calculated for six of the remaining seven vertical profiles ranged from 1.5 to 12 km Myr−1 (all with low r2 values of <0.6) for the time period from ∼1.2 to 0.3 Ma, with no discernible patterns in south to north exhumation rates evident. The absence of a trend in exhumation rates, despite a strong spatial gradient in rainfall, argues against a correlation of long-term exhumation rates with modern patterns of rainfall. AFT ages in the Tethyan strata are, on average, older than in the Greater Himalaya and may be a response to a drier climate, slip on the South Tibetan Detachment, or a gentler dip of the underlying thrust ramp. These data are further evaluated with thermokinematic modeling in the companion paper by Whipp et al

Evolving Spatially Aggregated Features from Satellite Imagery for Regional Modeling

Satellite imagery and remote sensing provide explanatory variables at relatively high resolutions for modeling geospatial phenomena, yet regional summaries are often desirable for analysis and actionable insight. In this paper, we propose a novel method of inducing spatial aggregations as a component of the machine learning process, yielding regional model features whose construction is driven by model prediction performance rather than prior assumptions. Our results demonstrate that Genetic Programming is particularly well suited to this type of feature construction because it can automatically synthesize appropriate aggregations, as well as better incorporate them into predictive models compared to other regression methods we tested. In our experiments we consider a specific problem instance and real-world dataset relevant to predicting snow properties in high-mountain Asia

Prognostic gene network modules in breast cancer hold promise

A substantial proportion of lymph node-negative patients who receive adjuvant chemotherapy do not derive any benefit from this aggressive and potentially toxic treatment. However, standard histopathological indices cannot reliably detect patients at low risk of relapse or distant metastasis. In the past few years several prognostic gene expression signatures have been developed and shown to potentially outperform histopathological factors in identifying low-risk patients in specific breast cancer subgroups with predictive values of around 90%, and therefore hold promise for clinical application. We envisage that further improvements and insights may come from integrative expression pathway analyses that dissect prognostic signatures into modules related to cancer hallmarks

Increased entropy of signal transduction in the cancer metastasis phenotype

Studies into the statistical properties of biological networks have led to important biological insights, such as the presence of hubs and hierarchical modularity. There is also a growing interest in studying the statistical properties of networks in the context of cancer genomics. However, relatively little is known as to what network features differ between the cancer and normal cell physiologies, or between different cancer cell phenotypes. Based on the observation that frequent genomic alterations underlie a more aggressive cancer phenotype, we asked if such an effect could be detectable as an increase in the randomness of local gene expression patterns. Using a breast cancer gene expression data set and a model network of protein interactions we derive constrained weighted networks defined by a stochastic information flux matrix reflecting expression correlations between interacting proteins. Based on this stochastic matrix we propose and compute an entropy measure that quantifies the degree of randomness in the local pattern of information flux around single genes. By comparing the local entropies in the non-metastatic versus metastatic breast cancer networks, we here show that breast cancers that metastasize are characterised by a small yet significant increase in the degree of randomness of local expression patterns. We validate this result in three additional breast cancer expression data sets and demonstrate that local entropy better characterises the metastatic phenotype than other non-entropy based measures. We show that increases in entropy can be used to identify genes and signalling pathways implicated in breast cancer metastasis. Further exploration of such integrated cancer expression and protein interaction networks will therefore be a fruitful endeavour.Comment: 5 figures, 2 Supplementary Figures and Table

A New Method of Probing the Phonon Mechanism in Superconductors including MgB2_{2}

Weak localization has a strong influence on both the normal and superconducting properties of metals. In particular, since weak localization leads to the decoupling of electrons and phonons, the temperature dependence of resistance (i.e., $\lambda_{tr}$) is decreasing with increasing disorder, as manifested by Mooij's empirical rule. In addition, Testardi's universal correlation of $T_{c}$ (i.e., $\lambda$) and the resistance ratio (i.e., $\lambda_{tr}$) follows. This understanding provides a new means to probe the phonon mechanism in superconductors including MgB$_{2}$. The merits of this method are its applicability to any superconductors and its reliability because the McMillan's electron-phonon coupling constant $\lambda$ and $\lambda_{tr}$ change in a broad range, from finite values to zero, due to weak localization. Karkin et al's preliminary data of irradiated MgB$_{2}$ show the Testardi correlation, indicating that the dominant pairing mechanism in MgB$_{2}$ is the phonon-mediated interaction.Comment: 9 pages, latex, 3 figure

Modeled and Observed Volcanic Aerosol Control on Stratospheric NOy and Cly

Decreases in stratospheric NOx associated with enhanced aerosol have been observed after large volcanic eruptions, for example, after the eruption of Mount Pinatubo in 1991. While the 1991 Mount Pinatubo eruption was the last large explosive eruption, recent studies have shed light on the impacts of moderate-sized eruptions since the year 2000 on the global stratospheric aerosol budget. We use an ensemble of simulations from a coupled climate-chemistry model to quantify and analyze changes in NO and NO2 (NOx), N2O5, HNO3, ClO, and ClONO2 during periods of increased stratospheric volcanic aerosol concentrations since 2000. By using an ensemble approach, we are able to distinguish forced responses from internal variability. We also compare the model ensemble results to satellite measurements of these changes in atmospheric composition, including measurements from the Optical Spectrograph and Infrared Imaging Spectrometer on the Odin satellite and the Aura Microwave Limb Sounder. We find decreases in stratospheric NOx concentrations up to 20 hPa, consistent with increases in stratospheric HNO3 concentrations. The HNO3 perturbations also extend higher, up to 5 hPa, associated with periods of increased volcanic aerosol concentrations in both model simulations and observations, though correlations with volcanic aerosol are considerably higher in the model simulations. The model simulates increases in ClO at altitudes and magnitudes similar to the NOx reductions, but this response is below the detectable limit in the available observations (100 pptv). We also demonstrate the value of accounting for transport-related anomalies of atmospheric trace gases by regression onto N2O anomalies

Angiogenic gene expression and vascular density are reflected in ultrasonographic features of synovitis in early Rheumatoid Arthritis: an observational study.

INTRODUCTION: Neovascularization contributes to the development of sustained synovial inflammation in the early stages of Rheumatoid Arthritis. Ultrasound (US) provides an indirect method of assessing synovial blood flow and has been shown to correlate with clinical disease activity in patients with Rheumatoid Arthritis. This study examines the relationship of US determined synovitis with synovial vascularity, angiogenic/lymphangiogenic factors and cellular mediators of inflammation in a cohort of patients with early Rheumatoid Arthritis (RA) patients prior to therapeutic intervention with disease modifying therapy or corticosteroids. METHODS: An ultrasound guided synovial biopsy of the supra-patella pouch was performed in 12 patients with early RA prior to treatment. Clinical, US and biochemical assessments were undertaken prior to the procedure. Ultrasound images and histological samples were obtained from the supra-patella pouch. Histological samples were stained for Factor VIII and a-SMA (a-smooth muscle actin). Using digital imaging analysis a vascular area score was recorded. QT-PCR (quantitative-PCR) of samples provided quantification of angiogenic and lymphangiogenic gene expression and immunohistochemistry stained tissue was scored for macrophage, T cell and B cell infiltration using an existing semi-quantitative score. RESULTS: Power Doppler showed a good correlation with histological vascular area (Spearman r--0.73) and angiogenic factors such as vascular endothelial growth factor-A (VEGF-A), Angiopoietin 2 and Tie-2. In addition, lymphangiogenic factors such as VEGF-C and VEGF-R3 correlated well with US assessment of synovitis. A significant correlation was also found between power Doppler and synovial thickness, pro-inflammatory cytokines and sub-lining macrophage infiltrate. Within the supra-patella pouch there was no significant difference in US findings, gene expression or inflammatory cell infiltrate between any regions of synovium biopsied. CONCLUSION: Ultrasound assessment of synovial tissue faithfully reflects synovial vascularity. Both grey scale and power Doppler synovitis in early RA patients correlate with a pro-angiogenic and lymphangiogenic gene expression profile. In early RA both grey scale and power Doppler synovitis are associated with a pro-inflammatory cellular and cytokine profile providing considerable validity in its use as an objective assessment of synovial inflammation in clinical practice

In the dark in a large urban park: DNA barcodes illuminate cryptic and introduced moth species

Abstract To facilitate future assessments of diversity following disturbance events, we conducted a first level inventory of nocturnal Lepidoptera in Stanley Park, Vancouver, Canada. To aid the considerable task, we employed high-throughput DNA barcoding for the rough sorting of all material and for tentative species identifications, where possible. We report the preliminary species list of 190, the detection of four new exotic species (Argyresthia pruniella, Dichelia histrionana, Paraswammerdamia lutarea, and Prays fraxinella), and the potential discovery of two cryptic species. We describe the magnitude of assistance that barcoding presents for faunal inventories, from reducing specialist time to facilitating the detection of native and exotic species at low density

Chilean Bromeliaceae: diversity, distribution and evaluation of conservation status

Abstract Chile is home to 23 species of Bromeliaceae, including 2 subspecies and 4 varieties. Twenty species are endemic to the country. We examined 883 herbarium specimens from 27 herbaria for our treatment of the Bromeliaceae for the &apos;&apos;Flora de Chile&apos;&apos;. These data and field observations resulted in a comprehensive database that we used to generate distribution maps for each species. We applied ecological niche modelling to reveal distribution areas and centers of Bromeliaceae diversity. We further analysed the collecting dates of the herbarium specimens to assess possible changes in species abundance. In this study we assess the conservation status of the bromeliad species in Chile. IUCN categories were assigned to the 27 bromeliad taxa as follows: Critically endangered: 4, Endangered: 6, Vulnerable: 11, Near threatened: 2, Least concern: 4. No species has become &apos;&apos;Extinct&apos;&apos; up to now. We also put forth a hypothesis about their biogeographic history

Searching for network modules

When analyzing complex networks a key target is to uncover their modular structure, which means searching for a family of modules, namely node subsets spanning each a subnetwork more densely connected than the average. This work proposes a novel type of objective function for graph clustering, in the form of a multilinear polynomial whose coefficients are determined by network topology. It may be thought of as a potential function, to be maximized, taking its values on fuzzy clusterings or families of fuzzy subsets of nodes over which every node distributes a unit membership. When suitably parametrized, this potential is shown to attain its maximum when every node concentrates its all unit membership on some module. The output thus is a partition, while the original discrete optimization problem is turned into a continuous version allowing to conceive alternative search strategies. The instance of the problem being a pseudo-Boolean function assigning real-valued cluster scores to node subsets, modularity maximization is employed to exemplify a so-called quadratic form, in that the scores of singletons and pairs also fully determine the scores of larger clusters, while the resulting multilinear polynomial potential function has degree 2. After considering further quadratic instances, different from modularity and obtained by interpreting network topology in alternative manners, a greedy local-search strategy for the continuous framework is analytically compared with an existing greedy agglomerative procedure for the discrete case. Overlapping is finally discussed in terms of multiple runs, i.e. several local searches with different initializations.Comment: 10 page