bluuebunny/crossref_metadata_2025 huggingface dataset:
Conceptual Design of Net Zero Energy Campus Residence
Authors: Mertz George A. , Raffio Gregory S. , Kissock Kelly , Hallinan Kevin P.
Published: October 2008

In response to both global and local challenges, the University of Dayton is committed to building a net-zero energy student residence, called the Eco-house. A unique aspect of the Eco-house is the degree of student involvement; in accordance with UD’s mission, interdisciplinary student teams from mechanical engineering, civil engineering and the humanities are leading the design effort. This paper discusses the conceptual design of a net-zero energy use campus residence, and the analysis completed thus far. Energy use of current student houses is analyzed to provide a baseline and to identify energy saving opportunities. The use of the whole-system inside-out approach to guide the overall design is described. Using the inside-out method as a guide, the energy impacts of occupant behavior, appliances and lights, building envelope, energy distribution systems and primary energy conversion equipment are discussed. The design of solar thermal and solar photovoltaic systems to meet the hot water and electricity requirements of the house is described. Eco-house energy use is simulated and compared to the energy use of the existing houses. The analysis shows the total source energy requirements of the Eco-house could be reduced by about 340 mmBtu per year over older baseline houses, resulting in CO2 emission reductions of about 54,000 lb per year and utility cost savings of about $3,000 per year. Detailed cost analysis and cost optimization have not been performed but are critical aspects of the UD Eco-house project, which will be performed in the future.
Sensitivity Analysis of Optimal Building Thermal Mass Control
Authors: Henze Gregor P. , Le Thoi H. , Florita Anthony R.
Published: October 2008

In order to avoid high utility demand charges from cooling during the summer and to level a building’s electrical demand-profile, precooling of the building’s massive structure can be applied to shift cooling-related thermal loads in response to utility pricing signals. Several previous simulation and experimental studies have shown that proper precooling can attain considerable reduction of operating cost in buildings. This paper systematically evaluates the merits of the passive building thermal capacitance to minimize energy cost using optimal control. The evaluation is conducted by means of a sensitivity analysis utilizing a dynamic building energy simulation program coupled to a popular technical computing environment. The optimal controller predicts the required extent of precooling (zone temperature setpoint depression) depending on utility rate structure, occupancy and on-peak period duration and onset, internal gains, building mass, occupancy period temperature setpoint range, and weather as characterized by diurnal temperature and relative humidity swings. In addition to quantifying the building response, energy consumption, and utility cost, this paper extracts the dominant features of the optimal precooling strategies for each of the investigated cases so that guidelines for near-optimal building thermal mass savings can be developed in the future. These will offer guidance to HVAC system operators and practitioners on how to adapt existing or design new building thermal mass control strategies in order to save operating cost or energy.
Study on the Performance of a Fluidized Air Dehumidifier
Authors: Hamed Ahmed M. , Abd El Ramadan Walaa R. , El-Eman S. H.
Published: October 2008

Transient adsorption/desorption characteristics of solid desiccant particles in fluidized bed have been presented. The system operates in batch mode and the atmospheric air with controlled inlet humidity and temperature is dehumidified by the applied desiccant. Also, heated air is used for regeneration purposes. A simplified analytical solution, with isothermal adsorption assumption, is demonstrated. In the experimental study, spherical particles of silica gel about 3 mm in diameter are used as the working desiccant in the fluidized bed. The experimental system is equipped with the necessary control valves to facilitate operation in adsorption and desorption modes, respectively. To control the humidity of inlet air, a humidifier is designed and fitted in a proper location in the system. Also, the system is well instrumented to measure the inlet and outlet air parameters as well as bed temperatures during the operation modes. Transient values of the mass of adsorbed water in the bed, rate of adsorption and water content in silica gel particles are evaluated from the experimental measurements. Also, numerical values of the volumetric mass transfer coefficient are plotted and discussed for different operating conditions. Model output, which shows the dependence of the dimensionless value of water content in the bed [(w*i − w)/(w*i − wo)] on the dimensionless time, is compared with the experimental results. Good agreement is found at the first period of adsorption, when the adsorption is nearly isothermal. Successive increase in bed temperature, due to the heat of adsorption, results in increase in discrepancy between the model and the experimental data. Accordingly, the isothermal model could be applied with reasonable degree of reality for systems with shorter adsorption/desorption cycles. The effect of air inlet humidity on the system operation has been highlighted. The drop in air humidity is highly affected by its inlet value. It is found that, the maximum decrease in air humidity occurs at the beginning of adsorption for the different inlet values. Also, the rate of water vapor adsorption increases with the increase in the inlet humidity.
Evaluation of a High-Performance Solar Home in Loveland, Colorado
Authors: Hendron Robert , Eastment Mark , Hancock Ed , Barker Greg , Reeves Paul
Published: October 2008

Building America (BA) partner McStain Neighborhoods built the Discovery House in Loveland, Colorado, with an extensive package of energy-efficient features, including a high-performance envelope, efficient mechanical systems, a solar water heater integrated with the space-heating system, a heat-recovery ventilator (HRV), and ENERGY STAR™ appliances. The National Renewable Energy Laboratory (NREL) and Building Science Consortium (BSC) conducted short-term field-testing and building energy simulations to evaluate the performance of the house. These evaluations are utilized by BA to improve future prototype designs and to identify critical research needs. The Discovery House building envelope and ducts were very tight under normal operating conditions. The HRV provided fresh air at a rate of about 75 cfm (35 l/s), consistent with the recommendations of ASHRAE Standard 62.2. The solar hot water system is expected to meet the bulk of the domestic hot water (DHW) load (>83%), but only about 12% of the space-heating load. DOE-2.2 simulations predict whole-house source energy savings of 54% compared to the BA Benchmark [1]. The largest contributors to energy savings beyond McStain’s standard practice are the solar water heater, HRV, improved air distribution, high-efficiency boiler, and compact fluorescent lighting package.
Thermal Energy Storage Technology for Industrial Process Heat Applications
Authors: Tamme Rainer , Steinmann Wolf-Dieter , Laing Doerte
Published: October 2008

This paper deals with the assessment of different thermal energy storage technologies for solar process heat application. Three different storage concepts are discussed in detail: sensible solid media storage, steam accumulators, and phase change energy storage. The first two systems are sensible storage systems and the latter one is using solid-liquid phase change of salts for isothermal heat storage. All three concepts are superior to commercially available pressurized water storage units. For the assessment of the different concepts a reference case was defined consisting of a solar system providing saturated steam for an industrial process demanding heat at 140 °C. The temperature difference between operation temperature of the solar system and the industrial process has significant influence on the assessment of the different storage technologies. A small temperature difference of 20K or even less shows significant advantage of the PCM storage approach. Values in the order of 60K lead to an adjustment of the cost of the different concepts. In this case a more detailed evaluation is required to identify the most economic technology.
Microelectrode Design in MEMS-Based DEP Cell Filtration Devices
Authors: Ahamed Mohammed J. , Rahman Mohammad A.
Published: October 2008

This paper presents the design of a MEMS-based active DEP (dielectrophoresis) cell filtration microchip for manipulating and separating biological cells. Depending on the dielectric constant and polarizability, biological cells are either attracted to or repelled from the electrodes inside a microfluidic channel. Through the optimization of electrode geometries using the finite element method (FEM), it was found that circular electrodes are capable of producing a more uniform and larger gradient of the squared electric field intensity compared to electrodes of other shapes, such as square, diamond, or triangle, FEM numerical simulation results were also used to determine 50μm as the optimal circular electrode diameter and 25μm as the optimal gap between electrodes.
Mechanical Testing of Freestanding Nano-Films Using a Novel Finite Diameter Tip MEMS-Based Testing Machine
Authors: Leseman Zayd C. , Sheikh Zuhaib , Mackin Thomas J. , Begley Matthew
Published: October 2008

We present a new experimental method for measuring the mechanical properties of nanoscale-thick materials using the free-standing membrane test. Freestanding circular membranes are centrally deflected using a spherical indenter attached to a microfabricated fixed-fixed beam device. Experiments of this type allow us to extract mechanical properties of the thin films without the complicating effects of the substrate, enabling accurate study of length scale effects. These experiments differ from previous work by testing freestanding films and by including the finite contact size of the indenter tip.
Molecular Scale Imaging With a Mutlilayer Superlens
Authors: Chaturvedi P. , Fang N.
Published: October 2008

Recent theory [1] suggested a thin negative index film should function as a “superlens”, providing image detail with resolution beyond the diffraction limit—a limitation to which all positive index optics are subject. The superlens allows the recovery of evanescent waves in the image via the excitation of surface plasmons. It has been demonstrated experimentally [2] that a silver superlens allows to resolve features well below the working wavelength. Resolution as high as 60 nanometer (λ/6) half-pitch has been achieved. This unique class of superlens will enable parallel imaging and nanofabrication in a single snapshot, a feat that are not yet available with other nanoscale imaging techniques such as atomic force microscope or scanning electron microscope. In this paper, we explore the possibility of further refining the image resolution using a multilayer superlens [3]. Using a stable transfer matrix scheme, our numerical calculations show an ultimate imaging resolution of λ/24. This is made possible using alternating stacks of alumina (Al2O3) and silver (Ag) layers to enhance a broad spectrum of evanescent waves via surface plasmon modes. Furthermore, we present the effect of alterations in number of layers and thickness to the image transfer function. With optimized design of multilayer superlens (working wavelength of 387.5nm), our study indicates the feasibility of resolving features of 16nm and below. Moreover, our tolerance analysis indicates that a 380 nm commercial light source would degrade slightly the imaging resolution to about 20nm. Preliminary experiments are ongoing to demonstrate the molecular scale imaging resolution. The development of potential low-loss and high resolution superlens opens the door to exciting applications in nanoscale optical metrology and nanomanufacturing.
Surface-Plasmons-Assisted Nanoscale Photolithography
Authors: Shao Dongbing , Chen Shaochen
Published: October 2008

Photolithography has remained a useful micro-fabrication technology because of its high throughput, low cost, simplicity, and reproducibility over the past several decades. However its resolution is limited at a sub-wavelength scale due to optical diffraction. Among all different approaches to overcoming this problem, such as electron-beam lithography, imprint lithography and scanning probe lithography, near-field optical lithography inherits many merits of the traditional photolithography method. Major drawbacks of this approach include low contrast, low transmission and low density.
Thermal Characterization of Silicon Nanowires
Authors: Liu Wenjun , Yang Yizhang , Asheghi Mehdi
Published: October 2008

When crystalline solids are confined to the nanometer range, phonon transport within them can be significantly altered due to various effects, namely (i) increased boundary scattering; (ii) changes in phonon dispersion relation; and (iii) quantization of phonon transport. For example, theoretical studies (e.g., Chung et al., 2000) have suggested that, as the diameter of a silicon nanowire (NW) becomes smaller than 20 nm, the phonon dispersion relation, and therefore its density of states, could be modified due to phonon confinement. This in turn impacts the phonon group velocities and scattering rates that can further reduce the thermal conductivity of confined structures.
Pump-Probe Experimental Study of Phonon Reflectivity at an Interface and Phonon Relaxation Time
Authors: Yang Ronggui , Chen Xiaoyuan , Schmidt Aaron , Chen Gang
Published: October 2008

Heat transfer in nanostructures differs significantly from that in macrostructures because of classical and quantum size effects on energy carriers, i.e., phonons, electrons, and photons [1–3]. Understanding thermal transport in nanostructures is of fundamental importance to a variety of technologies, including thermal management of nanoelectronics and optoelectronics, energy conversion, nanofabrication, and sensor development. A better understanding of the energy transport at nanoscale calls for both simulations and experimental techniques on thermal transport in nanostructures.
High-Yield Plasma Synthesis of Luminescent Silicon Quantum Dots
Authors: Mangolini Lorenzo , Thimsen Elijah , Kortshagen Uwe
Published: October 2008

Crystalline silicon quantum dots are of interest for a variety of applications from solid state lighting, to optoelectronic devices, to use as fluorescent tagging agents. Compared to other quantum dot materials, silicon’s appeal lies in its low toxicity and environmental hazard, and its compatibility with silicon technology used for microelectronics.
Direct Measurement of Slip Velocities Using Three-Dimensional Total Internal Reflection Velocimetry
Authors: Huang Peter , Guasto Jeffrey , Breuer Kenneth
Published: October 2008

The possible existence of slip of liquids in close proximity to a smooth surface is studied experimentally via the dynamics of small particles suspended in a shear flow. Sub-micron fluorescent particles suspended in water are imaged and analyzed using Total Internal Reflection Velocimetry (TIRV). For water flowing over a hydrophilic surface, the measurements are in agreement with previous experiments and indicate that slip, if present, is minimal at low shear rates, but increases slightly as the shear rate increases. Furthermore, surface hydrophobicity can be attributed for additional shear-rate dependent boundary slip. Issues associated with the experimental technique and the interpretation of results are also discussed.
Flipping Carbon Nanotubes to Continuously Produce Strong, Transparent, Multifunctional Sheets
Authors: Zhang Mei , Fang Shaoli , Zakhidov Anvar A. , Lee Sergey B. , Aliev Ali E. , Williams Christopher D. , Atkinson Ken R. , Baughman Ray H.
Published: October 2008

We demonstrate carbon nanotube assembly by cooperatively rotating carbon nanotubes in vertically-oriented nanotube arrays (forests) and make 5-centimeter-wide, meter-long transparent sheets. These self-supporting nanotube sheets are initially formed as a highly anisotropic electronically conducting aerogel that can be densified into strong sheets that are as thin as 50 nanometers. The measured gravimetric strength of orthogonally oriented sheet arrays exceeds that of high strength steel sheet.
Preliminary Results Related to the Design of Virtual Probes for Use in a Nano-Manipulation Test-Bed
Authors: Trivedi Anant , Cecil J.
Published: October 2008

This paper discusses the design of virtual probe tip models for use in a nano-manipulation research test-bed (NMRT). The proposed NMRT would help study the feasibility of a given manipulation technique in a virtual environment before physical experiments. For example, NMRT would be able to help users determine if a specific kind of probe tip can be used to pull out a nano-particle from a given substrate. A virtual probe tip model (for instance) would consider the given geometry and material of probe tip and simulate its behavior in a manipulation application in a physics based virtual reality environment. Such a virtual analysis and overall approach would result in considerable saving in time and financial resources with substantial application potential in medical and biotechnology fields where nanoparticle manipulation is useful. Expandability of the NMRT is made possible by designing an ‘information oriented’ or ‘information intensive’ model for a target set of nano-manipulation activities, which maps in detail various attributes related to a target nano-manipulation process [1]. In this approach, information models based on “engineering Enterprise Modeling Language” (eEML) are used. For example, consider an existing information model for interaction of a probe tip with a spherical particle; a user can use an existing information model, or modify it quickly to study the impact of two approaches (eg. manipulation strategy-A versus strategy-B, which may apply a different probe-tip for gripping). For a target nano-manipulation process (for example, the assembly of nano particles using an Atomic Force Microscope probe as a gripper), an information model can represent the core attributes influencing the target process; influencing criteria including constraints, information inputs, and physical inputs can be modeled explicitly and used to drive a target analysis or simulation activity.
Higher-Order Cellular Information Processing with Synthetic RNA Devices
Authors: Win Maung Nyan , Smolke Christina D.
Published: October 2008

The engineering of biological systems is anticipated to provide effective solutions to challenges that include energy and food production, environmental quality, and health and medicine. Our ability to transmit information to and from living systems, and to process and act on information inside cells, is critical to advancing the scale and complexity at which we can engineer, manipulate, and probe biological systems. We developed a general approach for assembling RNA devices that can execute higher-order cellular information processing operations from standard components. The engineered devices can function as logic gates (AND, NOR, NAND, or OR gates) and signal filters, and exhibit cooperativity. RNA devices process and transmit molecular inputs to targeted protein outputs, linking computation to gene expression and thus the potential to control cellular function.
Feedback Loops Shape Cellular Signals in Space and Time
Authors: Brandman Onn , Meyer Tobias
Published: October 2008

Positive and negative feedback loops are common regulatory elements in biological signaling systems. We discuss core feedback motifs that have distinct roles in shaping signaling responses in space and time. We also discuss approaches to experimentally investigate feedback loops in signaling systems.
Accurate Temperature Imaging Based on Intermolecular Coherences in Magnetic Resonance
Authors: Galiana Gigi , Branca Rosa T. , Jenista Elizabeth R. , Warren Warren S.
Published: October 2008

Conventional magnetic resonance methods that provide interior temperature profiles, which find use in clinical applications such as hyperthermic therapy, can develop inaccuracies caused by the inherently inhomogeneous magnetic field within tissues or by probe dynamics, and work poorly in important applications such as fatty tissues. We present a magnetic resonance method that is suitable for imaging temperature in a wide range of environments. It uses the inherently sharp resonances of intermolecular zero-quantum coherences, in this case flipping up a water spin while flipping down a nearby fat spin. We show that this method can rapidly and accurately assign temperatures in vivo on an absolute scale.
Molecular Layering of Fluorinated Ionic Liquids at a Charged Sapphire (0001) Surface
Authors: Mezger Markus , Schröder Heiko , Reichert Harald , Schramm Sebastian , Okasinski John S. , Schöder Sebastian , Honkimäki Veijo , Deutsch Moshe , Ocko Benjamin M. , Ralston John , Rohwerder Michael , Stratmann Martin , Dosch Helmut
Published: October 2008

Room-temperature ionic liquids (RTILs) are promising candidates for a broad range of “green” applications, for which their interaction with solid surfaces plays a crucial role. In this high-energy x-ray reflectivity study, the temperature-dependent structures of three ionic liquids with the tris(pentafluoroethyl)trifluorophosphate anion in contact with a charged sapphire substrate were investigated with submolecular resolution. All three RTILs show strong interfacial layering, starting with a cation layer at the substrate and decaying exponentially into the bulk liquid. The observed decay length and layering period point to an interfacial ordering mechanism, akin to the charge inversion effect, which is suggested to originate from strong correlations between the unscreened ions. The observed layering is expected to be a generic feature of RTILs at charged interfaces.
From Signals to Patterns: Space, Time, and Mathematics in Developmental Biology
Authors: Lewis Julian
Published: October 2008

We now have a wealth of information about the molecular signals that act on cells in embryos, but how do the control systems based on these signals generate pattern and govern the timing of developmental events? Here, I discuss four examples to show how mathematical modeling and quantitative experimentation can give some useful answers. The examples concern the Bicoid gradient in the early
Drosophila
embryo, the dorsoventral patterning of a frog embryo by bone morphogenetic protein signals, the auxin-mediated patterning of plant meristems, and the Notch-dependent somite segmentation clock.
Evaluation of a Multilocus Variable-Number Tandem-Repeat Analysis Scheme for Typing Human
Brucella
Isolates in a Region of Brucellosis Endemicity
Authors: Kattar Mireille M. , Jaafar Rola F. , Araj George F. , Le Flèche Philippe , Matar Ghassan M. , Abi Rached Roland , Khalife Simon , Vergnaud Gilles
Published: October 2008

Brucellosis remains an important anthropozoonosis worldwide.
Brucella
species are genetically homogeneous, and thus, the typing of
Brucella
species for epidemiological purposes by conventional molecular typing methods has remained elusive. Although many methods could segregate isolates into the phylogenetically recognized taxa, limited within-species genetic diversity has been identified. Recently, multilocus variable-number tandem-repeat analysis (MLVA) was found to have a high degree of resolution when it was applied to collections of
Brucella
isolates from geographically widespread locations, and an assay comprising 16 such loci (MLVA-16) was proposed. This scheme includes eight minisatellite loci (panel 1) and eight microsatellites (panel 2, which is subdivided into panels 2A and 2B). The utility of MLVA-16 for the subtyping of human
Brucella
isolates from geographically restricted regions needs to be further evaluated, and genotyping databases with worldwide coverage must be progressively established. In the present study, MLVA-16 was applied to the typing of 42 human
Brucella
isolates obtained from 41 patients recovered from 2002 to 2006 at a tertiary-care center in Lebanon. All isolates were identified as
Brucella melitensis
by MLVA-16 and were found to be closely related to
B. melitensis
isolates from neighboring countries in the Middle East when their genotypes were queried against those in the web-based Brucella2007 MLVA database (
http://mlva.u-psud.fr/
). Panel 2B, which comprised the most variable loci, displayed a very high discriminatory power, while panels 1 and 2A showed limited diversity. The most frequent genotype comprised seven isolates obtained over 7 weeks in 2002, demonstrating an outbreak from a common source. Two isolates obtained from one patient 5 months apart comprised another genotype, indicating relapsing disease. These findings confirm that MLVA-16 has a good discriminatory power for species determination, typing of
B. melitensis
isolates, and inferring their geographical origin. Abbreviated panel 2B could be used as a short-term epidemiological tool in a small region of endemicity.
Detection of Bacterial and Yeast Species with the Bactec 9120 Automated System with Routine Use of Aerobic, Anaerobic, and Fungal Media
Authors: Chiarini Alfredo , Palmeri Angelo , Amato Teresa , Immordino Rita , Distefano Salvatore , Giammanco Anna
Published: October 2008

During the period 2006 and 2007, all blood cultures required by four units at high infective risk and most of those required by other units of the University Hospital of Palermo, Palermo, Italy were performed using a Bactec 9120 automated blood culture system with a complete set of Plus Aerobic/F, Plus Anaerobic/F, and Mycosis IC/F bottles. The aim of the study was to enable the authors to gain firsthand experience of the culture potentialities of the three different media, to obtain information regarding the overall and specific recovery of bacteria and yeasts from blood cultures in the hospital, and to reach a decision as to whether and when to utilize anaerobic and fungal bottles. Although very few bloodstream infections (1.8%) were associated with obligate anaerobes, the traditional routine use of anaerobic bottles was confirmed because of their usefulness, not only in the detection of anaerobes, but also in that of gram-positive cocci and fermentative gram-negative bacilli. In this study, Mycosis IC/F bottles detected 77.4% of all the yeast isolates, 87.0% of yeasts belonging to the species
Candida albicans
, and 45.7% of nonfermentative gram-negative bacilli resistant to chloramphenicol and tobramycin. In order to improve the diagnosis of fungemia in high-risk patients, the additional routine use of fungal bottles was suggested when, as occurred in the intensive-care unit and in the hematology unit of the University Hospital of Palermo, high percentages of bloodstream infections are associated with yeasts, and/or antibiotic-resistant bacteria and/or multiple bacterial isolates capable of inhibiting yeast growth in aerobic bottles.
Rapid Multiplex PCR and Real-Time TaqMan PCR Assays for Detection of
Salmonella enterica
and the Highly Virulent Serovars Choleraesuis and Paratyphi C
Authors: Woods David F. , Reen F. Jerry , Gilroy Deirdre , Buckley Jim , Frye Jonathan G. , Boyd E. Fidelma
Published: October 2008

Salmonella enterica
is a human pathogen with over 2,500 serovars characterized.
S. enterica
serovars Choleraesuis and Paratyphi C are two globally distributed serovars. We have developed a rapid molecular-typing method to detect serovars Choleraesuis and Paratyphi C in food samples by using a comparative-genomics approach to identify regions unique to each serovar from the sequenced genomes. A
Salmonella
-specific primer pair based on
oriC
was designed as an internal control to establish accuracy, sensitivity, and reproducibility. Serovar-specific primer sets based on regions of difference between serovars Choleraesuis and Paratyphi C were designed for real-time PCR assays. Three primer sets were used to screen a collection of over 100
Salmonella
strains, and both serovars Choleraesuis and Paratyphi C gave unique amplification patterns. To develop the technique for practical use, its sensitivity for detection of
Salmonella
spp. in a food matrix was determined by spiking experiments. The technique was also adapted for a real-time PCR rapid-detection assay for both serovars Choleraesuis and Paratyphi C that complements the current procedures for
Salmonella
sp. isolation and serotyping.
Escherichia coli
O125ac:H6 Encompasses Atypical Enteropathogenic
E. coli
Strains That Display the Aggregative Adherence Pattern
Authors: Barros Samar F. , Abe Cecilia M. , Rocha Sérgio P. D. , Ruiz Renato M. , Beutin Lothar , Trabulsi Luiz R. , Elias Waldir P.
Published: October 2008

O125 is an enteropathogenic
Escherichia coli
(EPEC) serogroup, which includes the O125ac:H6 serotype, defined as atypical EPEC. Strains of this serotype displayed the aggregative adherence (AA) pattern with HEp-2, Caco-2, T84, and HT-29 cells, possessed all the LEE region genes, and expressed intimin, Tir, and EspABD, although the attaching-effacing lesion was not detected in vitro. These results confirm that
E. coli
O125ac:H6 is atypical EPEC that displays the AA pattern and indicate the necessity of testing for EPEC genes combined with the determination of the adherence pattern for atypical EPEC identification.
Combined Multilocus Short-Sequence-Repeat and Mycobacterial Interspersed Repetitive Unit-Variable-Number Tandem-Repeat Typing ofMycobacterium aviumsubsp.paratuberculosisIsolates
Authors: Thibault Virginie C. , Grayon Maggy , Boschiroli Maria Laura , Willery Eve , Allix-Béguec Caroline , Stevenson Karen , Biet Franck , Supply Philip
Published: October 2008

Short-sequence-repeat (SSR) sequencing was applied to 127Mycobacterium aviumsubsp.paratuberculosisisolates typed by mycobacterial interspersed repetitive unit-variable-number tandem repeats (MIRU-VNTR) and IS900restriction fragment length polymorphism (RFLP). Combined MIRU-VNTR and SSR typing followed by secondary IS900RFLP typing is an improved approach to high-resolution genotyping of this pathogen.
Long-Term Follow-Up of Methicillin-Resistant
Staphylococcus aureus
Molecular Epidemiology after Emergence of Clone USA300 in San Francisco Jail Populations
Authors: Tattevin Pierre , Diep Binh An , Jula Michael , Perdreau-Remington Françoise
Published: October 2008

We performed a longitudinal analysis of 502 unique methicillin-resistant
Staphylococcus aureus
(MRSA) clinical isolates originating from San Francisco jail inmates between 2000 and 2007. Strain USA300, first encountered in 2001, accounted for 82.1% (412/502) of MRSA infections. Non-USA300 MRSA strains were rarely found after 2005 (one isolate in 2006, three in 2007).
Human Cytomegalovirus Protein pp71 Displaces the Chromatin-Associated Factor ATRX from Nuclear Domain 10 at Early Stages of Infection
Authors: Lukashchuk Vera , McFarlane Steven , Everett Roger D. , Preston Chris M.
Published: October 2008

The human cytomegalovirus (HCMV) tegument protein pp71, encoded by gene UL82, stimulates viral immediate-early (IE) transcription. pp71 interacts with the cellular protein hDaxx at nuclear domain 10 (ND10) sites, resulting in the reversal of hDaxx-mediated repression of viral transcription. We demonstrate that pp71 displaces an hDaxx-binding protein, ATRX, from ND10 prior to any detectable effects on hDaxx itself and that this event contributes to the role of pp71 in alleviating repression. Introduction of pp71 into cells by transfection, infection with a pp71-expressing herpes simplex virus type 1 vector, or by generation of transformed cell lines promoted the rapid relocation of ATRX from ND10 to the nucleoplasm without alteration of hDaxx levels or localization. A pp71 mutant protein unable to interact with hDaxx did not affect the intranuclear distribution of ATRX. Infection with HCMV at a high multiplicity of infection resulted in rapid displacement of ATRX from ND10, the effect being observed maximally by 2 h after adsorption, whereas infection with the UL82-null HCMV mutant ADsubUL82 did not affect ATRX localization even at 7 h postinfection. Cell lines depleted of ATRX by transduction with shRNA-expressing lentiviruses supported increased IE gene expression and virus replication after infection with ADsubUL82, demonstrating that ATRX has a role in repressing IE transcription. The results show that ATRX, in addition to hDaxx, is a component of cellular intrinsic defenses that limit HCMV IE transcription and that displacement of ATRX from ND10 by pp71 is important for the efficient initiation of viral gene expression.
Measles Virus V Protein Is a Decoy Substrate for IκB Kinase α and Prevents Toll-Like Receptor 7/9-Mediated Interferon Induction
Authors: Pfaller Christian K. , Conzelmann Karl-Klaus
Published: October 2008

The central role of plasmacytoid dendritic cells (pDC) in activating host immune responses stems from their high capacity to express alpha interferon (IFN-α) after stimulation of Toll-like receptors 7 and 9 (TLR7 and -9). This involves the adapter MyD88 and the kinases interleukin-1 receptor-associated kinase 1 (IRAK1), IRAK4, and IκB kinase α (IKKα), which activates IFN regulatory factor 7 (IRF7) and is independent of the canonical kinases TBK1 and IKKε. We have recently shown that the immunosuppressive measles virus (MV) abolishes TLR7/9/MyD88-dependent IFN induction in human pDC (Schlender et al., J. Virol.
79:
5507-5515, 2005), but the molecular mechanisms remained elusive. Here, we have reconstituted the pathway in cell lines and identified IKKα and IRF7 as specific targets of the MV V protein (MV-V). Binding of MV-V to IKKα resulted in phosphorylation of V on the expense of IRF7 phosphorylation by IKKα in vitro and in living cells. This corroborates the role of IKKα as the kinase phosphorylating IRF7. MV-V in addition bound to IRF7 and to phosphomimetic IRF7 and inhibited IRF7 transcriptional activity. Binding to both IKKα and IRF7 required the 68-amino-acid unique C-terminal domain of V. Inhibition of TLR/MyD88-dependent IFN induction by MV-V is unique among paramyxovirus V proteins and should contribute to the unique immunosuppressive phenotype of measles. The mechanisms employed by MV-V inspire strategies to interfere with immunopathological TLR/MyD88 signaling.
Simian Virus 40 Large T Antigen Disrupts Genome Integrity and Activates a DNA Damage Response via Bub1 Binding
Authors: Hein Jennifer , Boichuk Sergei , Wu Jiaping , Cheng Yuan , Freire Raimundo , Jat Parmjit S. , Roberts Thomas M. , Gjoerup Ole V.
Published: October 2008

Simian virus 40 (SV40) large T antigen (LT) is a multifunctional protein that is important for viral replication and oncogenic transformation. Previously, infection of monkey or human cells with SV40 was shown to lead to the induction of DNA damage response signaling, which is required for efficient viral replication. However, it was not clear if LT is sufficient to induce the damage response and, if so, what the genetic requirements and functional consequences might be. Here, we show that the expression of LT alone, without a replication origin, can induce key DNA damage response markers including the accumulation of γ-H2AX and 53BP1 in nuclear foci. Other DNA damage-signaling components downstream of ATM/ATR kinases were induced, including chk1 and chk2. LT also bound the Claspin mediator protein, which normally facilitates the ATR activation of chk1 and monitors cellular replication origins. Stimulation of the damage response by LT depends mainly on binding to Bub1 rather than to the retinoblastoma protein. LT has long been known to stabilize p53 despite functionally inactivating it. We show that the activation of a DNA damage response by LT via Bub1 appears to play a major role in p53 stabilization by promoting the phosphorylation of p53 at Ser15. Accompanying the DNA damage response, LT induces tetraploidy, which is also dependent on Bub1 binding. Taken together, our data suggest that LT, via Bub1 binding, breaches genome integrity mechanisms, leading to DNA damage responses, p53 stabilization, and tetraploidy.
Antiviral Activity of the Zinc Ionophores Pyrithione and Hinokitiol against Picornavirus Infections
Authors: Krenn B. M. , Gaudernak E. , Holzer B. , Lanke K. , Van Kuppeveld F. J. M. , Seipelt J.
Published: October 2008

We have discovered two metal ion binding compounds, pyrithione (PT) and hinokitiol (HK), that efficiently inhibit human rhinovirus, coxsackievirus, and mengovirus multiplication. Early stages of virus infection are unaffected by these compounds. However, the cleavage of the cellular eukaryotic translation initiation factor eIF4GI by the rhinoviral 2A protease was abolished in the presence of PT and HK. We further show that these compounds inhibit picornavirus replication by interfering with proper processing of the viral polyprotein. In addition, we provide evidence that these structurally unrelated compounds lead to a rapid import of extracellular zinc ions into cells. Imported Zn2+was found to be localized in punctate structures, as well as in mitochondria. The observed elevated level of zinc ions was reversible when the compounds were removed. As the antiviral activity of these compounds requires the continuous presence of the zinc ionophore PT, HK, or pyrrolidine-dithiocarbamate, the requirement for zinc ions for the antiviral activity is further substantiated. Therefore, an increase in intracellular zinc levels provides the basis for a new antipicornavirus mechanism.
OPERATOR-SUM REPRESENTATION OF DENSITY OPERATORS AS SOLUTIONS TO MASTER EQUATIONS OBTAINED VIA THE ENTANGLED STATE APPROACH
Authors: FAN HONG-YI , HU LI-YUN
Published: October 2008

We solve various master equations to obtain density operators' infinite operator-sum representation via a new approach, i.e., by virtue of the thermo-entangled state representation that has a fictitious mode as a counterpart mode of the system mode. The corresponding Kraus operators from the point of view of quantum channel are derived, whose normalization conditions are proved. Miscellaneous characters possessed by different quantum channels, such as decoherence, phase diffusion, damping, and amplification, can be shown explicitly in the entangled state representation of the density operators. Squeezing transformation is applied to the density operator for decoherence to generate a master equation for describing the phase sensitive process. Partial trace method for deriving new density operators is also introduced. Throughout our discussion, the technique of integration within an ordered product (IWOP) of operators is fully used.
THE PROBABILITY OF THE CREATION OF EXTRA DIMENSIONS IN NUCLEAR COLLISIONS
Authors: NAZARENKO A. V.
Published: October 2008

The minisuperspace model in 3+d spatial dimensions with matter described by the bag model is considered with the aim of estimating the probability of creation of compactified extra dimensions in nuclear collisions. The amplitude of transition from three- to (3+d)-dimensional space has been calculated both in the case of completely confined matter, when the contribution of radiation is ignored, and in the case of radiation domination, when the bag constant is negligible. It turns out that the number of additional dimensions is limited in the first regime, while it is infinite in the second one. It is shown that the probability of creation of extra dimensions is finite in the both regimes.
Two-stage erosion and deposition in a continental margin setting: an
40
Ar/
39
Ar laserprobe study of offshore detrital white micas in the Norwegian Sea
Authors: SHERLOCK SARAH C.
Published: October 2008

Detrital white micas from a restricted region of the Norwegian Sea have been analysed by the
40
Ar/
39
Ar laserprobe. Examining the ages of individual white mica grains from offshore Triassic, Jurassic and Cretaceous sandstones reveals a narrow range of detrital white mica ages (369–424 Ma). Moreover, there is an inverse relationship between sediment age and detrital white mica age, with the Triassic sands containing a larger proportion of younger white micas, and the Cretaceous sands containing the oldest white micas. In addition, residence times of the detritus, which is the age of the sediment subtracted from the age of the detrital white mica, range from
c.
150 to
c.
300 Ma (for the Triassic and Cretaceous sands respectively). The inverse age relationships combined with the large residence times for these stratigraphic levels can best be explained by an erosion-deposition model involving at least two stages. Taking into account previous provenance studies in the Lofoten region of the Norwegian Sea, these new data suggest that detritus shed initially from the exhuming Caledonian nappes of NW Norway in late Silurian-early Devonian times was deposited in intramontane basins that were themselves, subsequently unroofed and re-eroded from Permo-Triassic times. This caused the recycling of the Caledonian detritus from the Devono-Carboniferous basins and led to the inverted detrital age distribution ovserved in the Triassic-Cretaceous sediments examined in this study. While sedimentary recycling is not a surprising feature for Mesozoic basins in the North and Norwegian Seas, this study documents a previously untapped method,
40
Ar/
39
Ar laserprobe provenance studies, by which to identify its effect and extent.
The role of crustal and mantle sources in the genesis of granitoids of the Antarctic Peninsula and adjacent crustal blocks
Authors: MILLAR I. L. , WILLAN R. C. R. , WAREHAM C. D. , BOYCE A. J.
Published: October 2008

Abstract:
Magmatic rocks from the Antarctic Peninsula show marked variations in isotope composition, which reflect changes in the geodynamic evolution of the peninsula through time. Most Antarctic Peninsula granitoids formed as a result of subduction: they fall on well‐defined trends on plots of
ϵ
Nd,
207
Pb/
204
Pb and
δ
18
O against
87
Sr/
86
Sr
i
, between a component derived from subduction‐modified mantle or juvenile basaltic underplate (
ϵ
Ndi>6,
207
Pb/
204
Pb=15.61,
δ
18
O=5.5‰,
87
Sr/
86
Sr<0.704) and an end‐member interpreted as a melt of Proterozoic lower crust (
ϵ
Nd=−7,
207
Pb/
204
Pb=15.67,
δ
18
O=10‰,
87
Sr/
86
Sr=0.709). A small group of granitoids, emplaced before or during Gondwana break‐up, plot on distinct trends towards high
87
Sr/
86
Sr
i
compositions, reflecting mixing between melts derived from Proterozoic lower crust and melts of middle–upper crustal rocks (
ϵ
Ndi=−9,
207
Pb/
204
Pb=15.64,
δ
18
O=10‰,
87
Sr/
86
Sr=0.726), with little or no input of new material derived from the mantle or from juvenile basaltic underplate. These granitoids are thought to have formed as a result of crustal attenuation during the initial rifting phase of Gondwana break‐up. Similar trends are shown by data from granitoids of the adjacent crustal blocks of West Antarctica. The isotope data suggest that an enriched Ferrar/Karoo‐type lithosphere was not involved in the genesis of granitoids of the Antarctic Peninsula or of the Ellsworth–Whitmore Mountains crustal block.
How U–Pb detrital monazite ages contribute to the interpretation of the Pennine Basin infill
Authors: EVANS J. A. , CHISHOLM J. I. , LENG M. J.
Published: October 2008

New U–Pb ages on detrital monazite from the Carboniferous of central England show a clear difference between populations from northerly and southeasterly derived sandstones. The northern source was responsible for most of the detritus that entered the basin during Namurian times and is dominated by monazites of Scandian age with normally distributed
235
U/
207
Pb ages averaging 420 ± 7 Ma (2
σ
). One older grain gives a Proterozoic age of 2040 ± 1.4 Ma (2
σ
). The data suggest a source region within the Scandian orogen. Southeasterly derived sediments are more heterogeneous and show a range of Variscan, Acadian, Ordovician and Sveconorwegian ages. Variscan uplifting of terranes of central Europe would provide a suitable source for this assemblage.
Environmental Issues in Russia
Authors: Henry Laura A. , Douhovnikoff Vladimir
Published: October 2008

This review examines the literature available on the state of the environment and environmental protection in the Russian Federation. As the largest country on Earth, rich in natural resources and biodiversity, Russia's problems and policies have global consequences. Environmental quality and management are influenced by the legacy of Soviet economic planning and authoritarian governance, as well as by Russia's post-Soviet economic recession and current strategies of economic development. Russia achieved a reduction in some pollutants owing to the collapse of industrial production in the 1990s, but many environmental indicators suggest growing degradation. Russia has signed on to a number of international environmental agreements, but its record on implementation is mixed, and it discourages environmental activism. Scholarship on the Russian environment is a limited, but growing, field, constrained by challenges of data availability, yet it offers great potential for testing scientific and social scientific hypotheses.
Neutrino Masses and Mixings: Status and Prospects
Authors: Camilleri Leslie , Lisi Eligio , Wilkerson John F.
Published: October 2008

Neutrino oscillations have been found in experiments observing solar and atmospheric neutrinos. They were confirmed by experiments using neutrinos produced by reactors and accelerators. These observations imply that neutrinos have nonzero masses and that the flavor states are superpositions of mass states through a mixing matrix. Indeed, the observed oscillations have revealed two distinct mass differences and two large mixing angles. In this article we discuss these discoveries, the emerging neutrino standard model, the present knowledge of the neutrino masses and mixing parameters, and the prospects for improving upon this knowledge.
Mechanosensing machinery for cells under low substratum rigidity
Authors: Wei Wei-Chun , Lin Hsi-Hui , Shen Meng-Ru , Tang Ming-Jer
Published: October 2008

Mechanical stimuli are essential during development and tumorigenesis. However, how cells sense their physical environment under low rigidity is still unknown. Here we show that low rigidity of collagen gel downregulates β1-integrin activation, clustering, and focal adhesion kinase (FAK) Y397 phosphorylation, which is mediated by delayed raft formation. Moreover, overexpression of autoclustered β1-integrin (V737N), but not constitutively active β1-integrin (G429N), rescues FAKY397 phosphorylation level suppressed by low substratum rigidity. Using fluorescence resonance energy transfer to assess β1-integrin clustering, we have found that substratum rigidity between 58 and 386 Pa triggers β1-integrin clustering in a dose-dependent manner, which is highly dependent on actin filaments but not microtubules. Furthermore, augmentation of β1-integrin clustering enhances the interaction between β1-integrin, FAK, and talin. Our results indicate that contact with collagen fibrils is not sufficient for integrin activation. However, substratum rigidity is required for integrin clustering and activation. Together, our findings provide new insight into the mechanosensing machinery and the mode of action for epithelial cells in response to their physical environment under low rigidity.