Identification of functional transcription factor binding sites using closely related Saccharomyces species

Comparative genomics provides a rapid means of identifying functional DNA elements by their sequence conservation between species. Transcription factor binding sites (TFBSs) may constitute a significant fraction of these conserved sequences, but the annotation of specific TFBSs is complicated by the fact that these short, degenerate sequences may frequently be conserved by chance rather than functional constraint. To identify intergenic sequences that function as TFBSs, we calculated the probability of binding site conservation between Saccharomyces cerevisiae and its two closest relatives under a neutral model of evolution. We found that this probability is <5% for 134 of 163 transcription factor binding motifs, implying that we can reliably annotate binding sites for the majority of these transcription factors by conservation alone. Although our annotation relies on a number of assumptions, mutations in five of five conserved Ume6 binding sites and three of four conserved Ndt80 binding sites show Ume6- and Ndt80-dependent effects on gene expression. We also found that three of five unconserved Ndt80 binding sites show Ndt80-dependent effects on gene expression. Together these data imply that although sequence conservation can be reliably used to predict functional TFBSs, unconserved sequences might also make a significant contribution to a species' biology

Cloud for Gaming

Cloud for Gaming refers to the use of cloud computing technologies to build large-scale gaming infrastructures, with the goal of improving scalability and responsiveness, improve the user's experience and enable new business models.Comment: Encyclopedia of Computer Graphics and Games. Newton Lee (Editor). Springer International Publishing, 2015, ISBN 978-3-319-08234-

Endogenous circatidal rhythm in the Manila clam Ruditapes philippinarum (Bivalvia: Veneridae)

Manila clams, Ruditapes philippinarum, removed from their natural environment and maintained for 9 weeks in continuously immersed conditions exhibited a clear endogenous circatidal rhythm in oxygen consumption. The clams exhibited a semidiurnal rhythmicity in oxygen consumption after showing a diurnal pattern in the first few days (5 to 7 d) of the experiment. The results of the present study indicate that activity rhythms of clams are controlled not only by exogenous factors, but also by an endogenous circatidal periodicity

Electronic density of states derived from thermodynamic critical field curves for underdoped La-Sr-Cu-O

Thermodynamic critical field curves have been measured for $La_{2-x}Sr_{x}CuO_{4+\delta}$ over the full range of carrier concentrations where superconductivity occurs in order to determine changes in the normal state density of states with carrier concentration. There is a substantial window in the $H-T$ plane where the measurements are possible because the samples are both thermodynamically reversible and the temperature is low enough that vortex fluctuations are not important. In this window, the data fit Hao-Clem rather well, so this model is used to determine $H_c$ and $\kappa_c$ for each temperature and carrier concentration. Using N(0) and the ratio of the energy gap to transition temperature, $\Delta (0)/k_BT_c$, as fitting parameters, the $H_c vs T$ curves give $\Delta (0)/k_BT_c \sim 2.0$ over the whole range of $x$. Values of N(0) remain rather constant in the optimum-doped and overdoped regime, but drops quickly toward zero in the underdoped regime.

Assessing the Geomorphic Evolution and Hydrographic Changes Induced by Winter Storms along the Louisiana Coast

The influence that cold front passages have on Louisiana coastal environments, including land loss and land building processes, has been the primary topic of this multidisciplinary research. This research has combined meteorological, remote sensing, and coastal expertise from the University of Wisconsin (UW) and Louisiana State University (LSU). Analyzed data sets include remotely sensed radiometric data (AVHRR on NOAA-12,13,14, Multispectral Atmospheric Mapping Sensor (MAMS) and MODIS Airborne Simulator (MAS) on NASA ER-2), U.S. Army Corps of Engineers (USACE) water level data, water quality data from the Coastal Studies Institute (CSI) at LSU, USACE river discharge data, National Weather Service (NWS) and CSI wind in sitzi measurements, geomorphic measurements from aerial photography (NASA ER-2 and Learjet), and CSI ground based sediment burial pipes (for monitoring topographic change along the Louisiana coast) and sediment cores. The work reported here-in is a continuation of an initial investigation into coastal Louisiana landform modification by cold front systems. That initial effort demonstrated the importance of cold front winds in the Atchafalaya Bay sediment plume distribution (Moeller et al.), documented the sediment transport and deposition process of the western Louisiana coast (Huh et al.) and developed tools (e.g. water types identification, suspended solids estimation) from multispectral radiometric data for application to the current study. This study has extended that work, developing a Geomorphic Impact Index (GI(sup 2)) for relating atmospheric forcing to coastal response and new tools to measure water motion and sediment transport

How significant is submarine groundwater discharge and its associated dissolved inorganic carbon in a river-dominated shelf system?

© The Author(s), 2012. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Biogeosciences 9 (2012): 1777-1795, doi:10.5194/bg-9-1777-2012.In order to assess the role of submarine groundwater discharge (SGD) and its impact on the carbonate system on the northern South China Sea (NSCS) shelf, we measured seawater concentrations of four radium isotopes 223,224,226,228Ra along with carbonate system parameters in June–July, 2008. Complementary groundwater sampling was conducted in coastal areas in December 2008 and October 2010 to constrain the groundwater end-members. The distribution of Ra isotopes in the NSCS was largely controlled by the Pearl River plume and coastal upwelling. Long-lived Ra isotopes (228Ra and 226Ra) were enriched in the river plume but low in the offshore surface water and subsurface water/upwelling zone. In contrast, short-lived Ra isotopes (224Ra and 223Ra) were elevated in the subsurface water/upwelling zone as well as in the river plume but depleted in the offshore surface water. In order to quantify SGD, we adopted two independent mathematical approaches. Using a three end-member mixing model with total alkalinity (TAlk) and Ra isotopes, we derived a SGD flux into the NSCS shelf of 2.3–3.7 × 108 m3 day−1. Our second approach involved a simple mass balance of 228Ra and 226Ra and resulted in a first order but consistent SGD flux estimate of 2.2–3.7 × 108 m3 day−1. These fluxes were equivalent to 12–21 % of the Pearl River discharge, but the source of the SGD was mostly recirculated seawater. Despite the relatively small SGD volume flow compared to the river, the associated material fluxes were substantial given their elevated concentrations of dissolved inorganic solutes. In this case, dissolved inorganic carbon (DIC) flux through SGD was 153–347 × 109 mol yr−1, or ~23–53 % of the riverine DIC export flux. Our estimates of the groundwater-derived phosphate flux ranged 3–68 × 107 mol yr−1, which may be responsible for new production on the shelf up to 0.3–6.3 mmol C m−2 d−1. This rate of new production would at most consume 11 % of the DIC contribution delivered by SGD. Hence, SGD may play an important role in the carbon balance over the NSCS shelf.This work was financially supported by the National Basic Research Program of China (973 Program) through grant #2009CB421204 and #2009CB421201, and by the Natural Science Foundation of China (NSFC) through grants #90711005, #41121091 and #41130857. Matthew Charette’s participation was supported by a grant from the U.S. National Science Foundation (#OCE-0751525)

Effects of 3D-printed polycaprolactone/��-tricalcium phosphate membranes on guided bone regeneration

This study was conducted to compare 3D-printed polycaprolactone (PCL) and polycaprolactone/��-tricalcium phosphate (PCL/��-TCP) membranes with a conventional commercial collagen membrane in terms of their abilities to facilitate guided bone regeneration (GBR). Fabricated membranes were tested for dry and wet mechanical properties. Fibroblasts and preosteoblasts were seeded into the membranes and rates and patterns of proliferation were analyzed using a kit-8 assay and by scanning electron microscopy. Osteogenic differentiation was verified by alizarin red S and alkaline phosphatase (ALP) staining. An in vivo experiment was performed using an alveolar bone defect beagle model, in which defects in three dogs were covered with different membranes. CT and histological analyses at eight weeks after surgery revealed that 3D-printed PCL/��-TCP membranes were more effective than 3D-printed PCL, and substantially better than conventional collagen membranes in terms of biocompatibility and bone regeneration and, thus, at facilitating GBR. ? 2017 by the authors. Licensee MDPI, Basel, Switzerland.118Ysciescopu

A stochastic model for a macroscale hybrid renewable energy system

The current supply for electricity generation mostly relies on fossil fuels, which are finite and pose a great threat to the environment. Therefore, energy models that involve clean and renewable energy sources are necessary to ease the concerns about the electricity generation needed to meet the projected demand. Here, we mathematically model a hybrid energy generation and allocation system where the intermittent solar generation is supported by conventional hydropower stations and diesel generation and time variability of the sources are balanced using the water stored in the reservoirs. We develop a two-stage stochastic model to capture the effect of streamflows which present significant inter-annual variability and uncertainty. Using sample case studies from India, we determine the required hydropower generation capacity and storage along with the minimal diesel usage to support 1 GWpeak solar power generation. We compare isolated systems with the connected systems (through inter-regional transmission) to see the effects of geographic diversity on the infrastructure sizing and quantify the benefits of resource-sharing. We develop the optimal sizing relationship between solar and hydropower generation capacities given realistic cost parameters and real data and examine how this relationship would differ as the contribution of diesel is reduced. We also show that if the output of the solar power stations can be controlled (i.e. spill is allowed in our setting), operating them below their maximum energy generation levels may reduce the unit cost of the system. © 2015 Elsevier Ltd

Molecular scale contact line hydrodynamics of immiscible flows

From extensive molecular dynamics simulations on immiscible two-phase flows, we find the relative slipping between the fluids and the solid wall everywhere to follow the generalized Navier boundary condition, in which the amount of slipping is proportional to the sum of tangential viscous stress and the uncompensated Young stress. The latter arises from the deviation of the fluid-fluid interface from its static configuration. We give a continuum formulation of the immiscible flow hydrodynamics, comprising the generalized Navier boundary condition, the Navier-Stokes equation, and the Cahn-Hilliard interfacial free energy. Our hydrodynamic model yields interfacial and velocity profiles matching those from the molecular dynamics simulations at the molecular-scale vicinity of the contact line. In particular, the behavior at high capillary numbers, leading to the breakup of the fluid-fluid interface, is accurately predicted.Comment: 33 pages for text in preprint format, 10 pages for 10 figures with captions, content changed in this resubmissio