Impact of high-frequency nonlinear internal waves on plankton dynamics in Massachusetts Bay

Author Posting. © Sears Foundation for Marine Research, 2010. This article is posted here by permission of Sears Foundation for Marine Research for personal use, not for redistribution. The definitive version was published in Journal of Marine Research 68 (2010): 259-281, doi:10.1357/002224010793721415.A simple Nutrient-Phytoplankton-Zooplankton (NPZ) model was coupled with the non-hydrostatic Finite-Volume Coastal Ocean Model (FVCOM-NH) to study the impact of high-frequency nonlinear internal waves on plankton dynamics in Massachusetts Bay (MB) during the stratified summer season. The temporal and spatial variability of phytoplankton concentration follows the vertical isopycnal displacement to the lowest order as the waves are generated by the semidiurnal tidal flow over Stellwagen Bank (SB) and propagate westward across MB. The tidally-averaged distribution of phytoplankton is characterized by three distinct zones of low subsurface concentration: (I) the western flank of Stellwagen Bank; (II) the center of Stellwagen Basin; and (III) the upper western flank of Stellwagen Basin. The result of a model dye experiment suggests that these zones are created by the following physical processes which are dominant in each zone: (I) hydraulic jump; (II) strong internal wave-tidal current nonlinear interaction; and (III) energetic internal wave dissipation and subsequent mixing processes. The nonlinear interaction of the internal waves and offshore tidal currents significantly enhances the vertical velocity, and increases wave dissipation, thus causing an onshore transport of phytoplankton in zone II. Although the phytoplankton patchy structure can be produced using the hydrostatic FVCOM, the resulting phytoplankton concentration is overestimated due to the unrealistic intensification of vertical velocity and thus vertical nutrient flux from the deep water. It suggests that non-hydrostatic dynamics should be considered for certain small-scale biological processes that are driven primarily by the physics.This project is supported by NOAA grants DOC/NOAA/NA04NMF4720332 and DOC/NOAA/NA05NMF4721131, US GLOBEC Northwest Atlantic/Georges Bank Program NSF grants (OCE-0234545; OCE-0227679; OCE-0606928; OCE-0712903; OCE-0732084; OCE- 0726851), and MIT Sea Grant funds (2006-RC-103, 2010-R/RC-116) and NOAA NERACOOS grant NA100558 for the UMassD team, and a NOAA grant (NA-17RJ1223) for R. C. Beardsley. C. Chen’s contribution is also supported by Shanghai Ocean University International Cooperation Program (No. A-2302–10-0003), the Program of Science and Technology Commission of Shanghai Municipality (No. 09320503700), the Leading Academic Discipline Project of Shanghai Municipal Education Commission (Project number: J50702), and Zhi jiang Scholar and 111 project funds of the State Key Laboratory for Estuarine and Coastal Research, East China Normal University (ECNU)

SPA: On-Line Availability Upgrades for Parity-based RAIDs through Supplementary Parity Augmentations

In this paper, we propose a simple but powerful on-line availability upgrade mechanism, Supplementary Parity Augmentations (SPA), to address the availability issue for parity-based RAID systems. The basic idea of SPA is to store and update the supplementary parity units on one or a few newly augmented spare disks for on-line RAID systems in the operational mode, thus achieving the goals of improving the reconstruction performance while tole-rating multiple disk failures and latent sector errors simultaneously. By applying the exclusive OR operations appropriately among supplementary parity, full parity and data units, SPA can reconstruct the data on the failed disks with a fraction of the original overhead that is proportional to the supplementary parity coverage, thus significantly reducing the overhead of data regeneration and decreasing recovery time in parity-based RAID systems. In particular, SPA has two supplementary-parity coverage orientations, SPA Vertical and SPA Diagonal, which cater to user’s different availability needs. The former, which calculates the supplementary parity of a fixed subset of the disks, can tolerate more disk failures and sector errors; whereas, the latter shifts the coverage of supplementary parity by one disk for each stripe to balance the workload and thus maximize the performance of reconstruction during recovery. The SPA with a single supplementary-parity disk can be viewed as a variant of but significantly different from the RAID5+0 architecture in that the former can easily and dynamically upgrade a RAID5 system to a RAID5+0-like system without any change to the data layout of the RAID5 system. Our extensive trace-driven simulation study shows that both SPA orientations can significantly improve the reconstruction performance of the RAID5 system while SPA Diagonal significantly improves the reconstruction performance of RAID5+0, at an acceptable performance overhead imposed in the operational mode. Moreover, our reliability analytical modeling and Sequential Monte-Carlo simulation demonstrate that both SPA orientations consistently more than double the MTTDL of the RAID5 system and improve the reliability of the RAID5+0 system noticeably

Skin transcriptome profiles associated with coat color in sheep

Background Previous molecular genetic studies of physiology and pigmentation of sheep skin have focused primarily on a limited number of genes and proteins. To identify additional genes that may play important roles in coat color regulation, Illumina sequencing technology was used to catalog global gene expression profiles in skin of sheep with white versus black coat color. Results There were 90,006 and 74,533 unigenes assembled from the reads obtained from white and black sheep skin, respectively. Genes encoding for the ribosomal proteins and keratin associated proteins were most highly expressed. A total of 2,235 known genes were differentially expressed in black versus white sheep skin, with 479 genes up-regulated and 1,756 genes down-regulated. A total of 845 novel genes were differentially expressed in black versus white sheep skin, consisting of 107 genes which were up-regulated (including 2 highly expressed genes exclusively expressed in black sheep skin) and 738 genes that were down-regulated. There was also a total of 49 known coat color genes expressed in sheep skin, from which 13 genes showed higher expression in black sheep skin. Many of these up-regulated genes, such as DCT, MATP, TYR and TYRP1, are members of the components of melanosomes and their precursor ontology category. Conclusion The white and black sheep skin transcriptome profiles obtained provide a valuable resource for future research to understand the network of gene expression controlling skin physiology and melanogenesis in sheep

Pseudonocardians A–C, New Diazaanthraquinone Derivatives from a Deap-Sea Actinomycete Pseudonocardia sp. SCSIO 01299

Pseudonocardians A–C (2–4), three new diazaanthraquinone derivatives, along with a previously synthesized compound deoxynyboquinone (1), were produced by the strain SCSIO 01299, a marine actinomycete member of the genus Pseudonocardia, isolated from deep-sea sediment of the South China Sea. The structures of compounds 1–4 were determined by mass spectrometry and NMR experiments (1H, 13C, HSQC, and HMBC). The structure of compound 1, which was obtained for the first time from a natural source, was confirmed by X-ray analysis. Compounds 1–3 exhibited potent cytotoxic activities against three tumor cell lines of SF-268, MCF-7 and NCI-H460 with IC50 values between 0.01 and 0.21 μm, and also showed antibacterial activities on Staphylococcus aureus ATCC 29213, Enterococcus faecalis ATCC 29212 and Bacillus thuringensis SCSIO BT01, with MIC values of 1–4 μg mL−1

Promoting Effect of Layered Titanium Phosphate on the Electrochemical and Photovoltaic Performance of Dye-Sensitized Solar Cells

We reported a composite electrolyte prepared by incorporating layered α-titanium phosphate (α-TiP) into an iodide-based electrolyte using 1-ethyl-3-methylimidazolium tetrafluoroborate(EmimBF4) ionic liquid as solvent. The obtained composite electrolyte exhibited excellent electrochemical and photovoltaic properties compared to pure ionic liquid electrolyte. Both the diffusion coefficient of triiodide (I3−) in the electrolyte and the charge-transfer reaction at the electrode/electrolyte interface were improved markedly. The mechanism for the enhanced electrochemical properties of the composite electrolyte was discussed. The highest conversion efficiency of dye-sensitized solar cell (DSSC) was obtained for the composite electrolyte containing 1wt% α-TiP, with an improvement of 58% in the conversion efficiency than the blank one, which offered a broad prospect for the fabrication of stable DSSCs with a high conversion efficiency

GP88 (PC-Cell Derived Growth Factor, progranulin) stimulates proliferation and confers letrozole resistance to aromatase overexpressing breast cancer cells

<p>Abstract</p> <p>Background</p> <p>Aromatase inhibitors (AI) that inhibit breast cancer cell growth by blocking estrogen synthesis have become the treatment of choice for post-menopausal women with estrogen receptor positive (ER⁺) breast cancer. However, some patients display de novo or acquired resistance to AI. Interactions between estrogen and growth factor signaling pathways have been identified in estrogen-responsive cells as one possible reason for acquisition of resistance. Our laboratory has characterized an autocrine growth factor overexpressed in invasive ductal carcinoma named PC-Cell Derived Growth Factor (GP88), also known as progranulin. In the present study, we investigated the role GP88 on the acquisition of resistance to letrozole in ER⁺breast cancer cells</p> <p>Methods</p> <p>We used two aromatase overexpressing human breast cancer cell lines MCF-7-CA cells and AC1 cells and their letrozole resistant counterparts as study models. Effect of stimulating or inhibiting GP88 expression on proliferation, anchorage-independent growth, survival and letrozole responsiveness was examined.</p> <p>Results</p> <p>GP88 induced cell proliferation and conferred letrozole resistance in a time- and dose-dependent fashion. Conversely, naturally letrozole resistant breast cancer cells displayed a 10-fold increase in GP88 expression when compared to letrozole sensitive cells. GP88 overexpression, or exogenous addition blocked the inhibitory effect of letrozole on proliferation, and stimulated survival and soft agar colony formation. In letrozole resistant cells, silencing GP88 by siRNA inhibited cell proliferation and restored their sensitivity to letrozole.</p> <p>Conclusion</p> <p>Our findings provide information on the role of an alternate growth and survival factor on the acquisition of aromatase inhibitor resistance in ER⁺breast cancer.</p

Minimum Information about a Biosynthetic Gene cluster

A wide variety of enzymatic pathways that produce specialized metabolites in bacteria, fungi and plants are known to be encoded in biosynthetic gene clusters. Information about these clusters, pathways and metabolites is currently dispersed throughout the literature, making it difficult to exploit. To facilitate consistent and systematic deposition and retrieval of data on biosynthetic gene clusters, we propose the Minimum Information about a Biosynthetic Gene cluster (MIBiG) data standard.Chemistry and Chemical Biolog

Fast and robust short video clip search using an index structure

In this paper, we present an index structure-based method to fast and robustly search short video clips in large video collections. First we temporally segment a given long video stream into overlapped matching windows, then map extracted features from the windows into points in a high dimensional feature space, and construct index structures for these feature points for querying process. Different from linear-scan similarity matching methods, querying process can be accelerated by spatial pruning brought by an index structure. A multi-resolution kd-tree (mrkd-tree) is employed to complete exact K-NN Query and range query with the aim of fast and precisely searching out all short video segments having the same contents as the query. In terms of feature representation, rather than selecting representative key frames, we develop a set of spatial-temporal features in order to globally capture the pattern of a short video clip (e.g. a commercial clip, a lead in/out clip) and combine it with the color range feature to form video signatures. Our experiments have shown the efficiency and effectiveness of the proposed method that the very first instance of a given 10-sec query clip can be identified from a 10.5hour video collection in tens of milliseconds. The proposed method has been also compared with the fast sequential search algorithm