bluuebunny/crossref_metadata_2025 huggingface dataset:
Rail Vehicle Cab Car Collision and Corner Post Designs According to APTA S-034 Requirements
Authors: Mayville Ronald A. , Johnson Kent N. , Tyrell David C. , Stringfellow Richard G.
Published: May 2008

The American Public Transportation Association standard for rail passenger equipment, S-034, includes requirements for the collision and corner posts of cab cars that are consistent with new federal requirements and substantially different than what has been required in the past. This paper describes the development and evaluation of two cab car end frame designs that were generated to investigate the implications on crashworthiness and operations of the new standards. A review was undertaken of prior cab car crashworthiness research and of existing and planned cab car designs for North American operation. The two designs were then generated and both hand and finite element analysis, including analysis for large deformations, was conducted to demonstrate that the designs meet the requirements. Of particular interest is the issue of providing large deformation capacity of the posts and the implications of eliminating the stairwell to meet the strength requirements.
Curving Performance of Newly Trued Wheels of Commuter Rail Passenger Cars
Authors: Kristoff Susan , Schanoes David
Published: May 2008

After a series of derailments in 1996 and 1997, Metro-North Railroad implemented several maintenance procedures in an effort to eliminate future derailments. This included a 300-mile wearing in period for cars with newly trued wheels before they could enter revenue service. Since that time, frequency of derailments has dropped to nearly zero, and Metro-North is evaluating the necessity of each of the derailment prevention policies. The Metro-North Derailment Test Site (MN-DTS) in Grand Central Terminal (GCT) was used to evaluate the curving performance of newly trued wheels and to compare the results with data from cars with worn wheels. The resulting analysis showed no statistical difference in curving performance between the two wheel conditions, giving Metro-North the option to remove the wearing-in period and increase train revenue without sacrificing passenger safety.
Finite Deformation Micromechanical Analysis of Textile-Reinforced Plastics
Authors: Swan Colby C. , Kim HyungJoo
Published: May 2008

Nonlinear elastic stiffness behaviors of plain-weave textile-reinforced composites are considered in this work by modeling finite deformation effects at two scales: (1) at the fiber diameter scale within yarns (~10 microns); (2) at the yarn diameter scale within woven textiles (~1000 microns). To capture the effect of heterogeneous microscale stress and strain fields, symmetric, conjugate, stress and strain measures are first established. A transversely isotropic hyperelasticity model is then presented for modeling finite deformation behaviors of yarns. After the free parameters of this model are estimated using unit cell analysis at the fiber-diameter scale, it is then incorporated into plain-weave textile unit cell model. The textile mode is then subjected to finite strain deformation controlled loading to quantify nonlinearity in stiffness behaviors.
Adaptive FE-Meshfree-Modelling for Impacts of Liquid Filled Vessels on Thin Walled Structures
Authors: Hiermaier Stefan , Sauer Martin
Published: May 2008

A principal approach to simulate the airplane impact and the collapse of World Trade Center North Tower has been shown by Quan and Birnbaum [4]. Using the general purpose hydrocode AUTODYN the impact damage, fire induced strength reduction and progressive collapse were investigated. Both for the fuel propagation after tank break up and the thermodynamic burn processes assumptions have been taken. It is the aim of this paper to focus on the numerical aspects of simulating the fluid propagation after vessel break up. The release of a fluid out of a broken vessel after impact is not easily represented in a numerical simulation as the fluid flow and its interaction with structures can not be modelled using Lagrangian type element formulations. These elements, typically applied for structural analyses, fail under massive deformation and usually need then to be taken out of the simulation. Typical fluid dynamic discretization methods, so called Eulerian grids, would have to cover the whole space potentially being reached by the fluid flow and are therefore inefficient in a large three dimensional simulation. As an alternative method a coupled discretization using Lagrange elements and Lagrange type meshfree methods is proposed here. Meshfree methods have been introduced to structural dynamics more then ten years ago specifically to simulate processes including large deformation [1]. Originally developed as pure meshfree code, the EMI SOPHIA [3] provides now a new form of adaptivity that allows for more efficiency and accuracy. This is achieved by the use of finite elements as long as deformation is capable for the elements. At definable strain or failure thresholds any element can be transformed into one or more meshfree particles. This way, mass and volume of the original elements are conserved. As the particles interact with each other as well as with the remaining elements, all physical processes can be modelled continuously. The purpose of this study was to contribute to numerical simulation of the airplane impacts into the World Trade Center. It includes impact simulations of cylindrical vessels filled with water against thin walled rectangular shaped bars. It shows that coupled discretizations and specifically an adaptive FE-meshfree discretization offer the flexibility needed to gain both accuracy and efficiency in the simulation.
Numerical Simulation of Hydraulically Actuated Natural Gas Compressors
Authors: Hill Philip G. , Hessami Shahin , Gram Anker
Published: May 2008

A numerical simulation has been developed to assist in design of low-speed hydraulically actuated compressors delivering natural gas at overall pressure ratios of 90: 1. The model has been used to estimate the effect of heat transfer during compression, the effects of reduced inter-stage volume, and the effects of departures from ideal gas behavior during the last stage of compression. It estimates overall compression efficiency, volumetric efficiency and cylinder pressures as a function of time. The model is capable of estimating dynamic behavior in intercooler passages when inter-stage volumes are small, and has been adapted to two or three stages.
Modeling of Blade Tip Geometries in an Axial Compressor Stage
Authors: Stockhaus Carsten , Volgmann Werner , Stoff Horst
Published: May 2008

The purpose of this paper is to investigate numerically the tip leakage flow for different blade tip geometries in an axial compressor stage under design and off-design conditions. Using flat tips, suction and pressure side squealers in combination with knife tips, a comparison of the rotor performance in terms of pressure and efficiency gain is reported. Detailed flow characteristics within the tip clearance gap, interaction of the leakage flow with the main flow and resultant turning effects at the exit of the row have been investigated. The CFD method is based on a commercially available compressible Navier-Stokes solver (STAR-CD), using a turbulent compressible high Reynolds number k-ε model. Accurate numerical comparison of different blade tip geometries is achieved by using the same grid for the various shapes. The blocking strategy with O-grid structure is presented. The numerical results show clearly the beneficial effect of cutting away material from the pressure side. The higher surface curvature of the suction side squealer affects the pressure blade loading and increases the lift in the same way. This effect is increased by increasing the squealer height and results in a lower efficiency gain near the surge line. The best modification of the blade tip shows a maximum reduction of the tip discharge coefficient of 20 %. This leads to an improved total pressure ratio of 0.29% and an improved total polytropic efficiency of 0.40% under design condition. The influences of favourable squealer geometries on stage characteristics are described along an operating line. With a simulation of IGV-setting from Δα = −15° to Δα = +20° different operating points have been investigated in a swirl performance map. The beneficial effect of the suction side squealer found for the rotor row could assign to the stator row and results in an improved static pressure gain. Furthermore, design indications are presented which help to keep the efficiency gain under surge condition as high as possible.
Nonlinear and Chaotic Vibration-Based Damage Detection
Authors: Epureanu Bogdan I.
Published: May 2008

The dynamics of an aeroelastic system composed of a panel forced by unsteady buffeting aerodynamic loads is investigated numerically. The focus is on detecting parametric changes in the system. The upstream end point of the panel is considered supported by a spring of variable stiffness. Changes of in the stiffness of the spring are detected by exploring the chaotic dynamics of the panel.
Enhancement of Optical Transmission Through Planar Nano-Apertures in a Metal Film
Authors: Jin Eric X. , Xu Xianfan
Published: May 2008

In this work, we investigate transmission enhancement through ridged-apertures of nanometer size in a metal film in the optical frequency range. It is demonstrated that the fundamental propagation TE10 mode concentrated in the gap between the two ridges of the aperture provides transmission efficiency higher than unity, and the size of the gap between the two ridges determines the sub-wavelength resolution. Fabry-Perot-like resonance with respect to the thickness of the aperture and the red-shift phenomena with respect to the wavelength of the incident light are observed. As a comparison, transmission through regular apertures is also computed, and is found much lower. Localized surface plasmon (LSP) is excited on the edges of the aperture in a silver film but plays a negative role with respect to the field concentration and signal contrast. With optimized geometries, the ridged apertures are capable of achieving sub-wavelength resolution in the near field with transmission efficiency above unity and high contrast.
Molecular Dynamics Study of Mechanism of Ablation Induced by a Femtosecond Laser Pulse
Authors: Cheng Changrui , Xu Xianfan
Published: May 2008

In this work, molecular dynamics (MD) simulations are carried out to study femtosecond laser ablation of a metal, with an emphasis on the understanding of the mechanism of laser ablation. Theoretically, it has been shown that under intense femtosecond laser irradiation, the material can undergo a volumetric phase change process; its temperature can be close to or even above the critical point. MD simulations allow us to determine the transient temperature of the irradiated material as well as the transient thermodynamic state, which explain the mechanisms of femtosecond laser ablation.
Using Parametric Simulation to Optimize Suspension Design
Authors: Rosenberger G. Walter , Klauser Peter E. , Binns George P. , Wolf Gary P.
Published: May 2008

A project to design and implement suspension improvements to Amtrak’s F-40 Non-Powered Control Unit (NPCU) cars is described. The cars, built from former F-40 locomotives, had a history of poor ride quality. Rail Sciences Inc. (RSI) inspected one of the cab cars and measured its ride quality. Peter Klauser modeled the vehicle in NUCARS™ and validated the model against the test data. The vehicle response was primarily in pitch and bounce modes. To optimize the suspension, Klauser simulated vehicle response for a range of four suspension parameters: primary stiffness and damping, and secondary stiffness and damping. Nearly 2600 suspension combinations were considered. Simulation file setup and data analysis were performed automatically using parameter analysis software interacting with NUCARS™. The result was a five-dimensional response contour for each output variable, such as the engineer’s seat vertical and lateral accelerations, and car body acceleration. The most cost effective stiffness and damping parameters were selected from the response contour and translated into component specifications. RSI then provided Amtrak with new axle box springs and dampers, and re-tested the vehicle. The test result closely followed the predicted results from the simulation. Engineer’s seat vertical and cab lateral accelerations improved by 42% and 32% respectively for the worst-case conditions in the test territory.
Heat and Mass Transfer Design of a Silicon Carbide Micro-Channel Heat Exchanger
Authors: Wilson Merrill A. , Bullough Michele , Brooks Kriston , Recknagle Kurt
Published: May 2008

Efficiency and emissions of advanced gas turbine power cycles can be improved by incorporating high-temperature ceramic heat exchangers. In cooperation with the DOE, a highly effective microchannel ceramic recuperator for a microturbine is under development. In this recuperator, the use of microchannel architecture will improve heat transfer and provide a more uniform temperature distribution. This will result in overall higher productivity per unit volume compared to conventional hardware. The use of ceramic for the recuperator will allow higher temperature operation than available in conventional microturbines. Based on a model for a typical microturbine, these changes may improve the overall system efficiency from about 27% to over 40%.
Cavity Specific Control of Melt Flow During Injection Molding Processes
Authors: Coulter John P.
Published: May 2008

The competitive global marketplace of the new century requires that industrial organizations develop capabilities to rapidly produce increasingly complex products with improved quality at lower cost. To do so successfully, significant innovations in manufacturing process technology need to be developed and implemented. The present paper describes a new research concept targeted at the development of “intelligent” or “adaptive” injection molding technology. More specifically, the effort is focused on the establishment of a capability to improve injection molding processing by monitoring shot to shot product quality and controlling the filling of multi-cavity molds in real time. During the first phase of the research, a target product having features and dimensional characteristics matching anticipated future requirements was selected. A two-cavity mold with which to manufacture the target product was then designed and fabricated. Candidate methodologies through which to implement control and assure proper filling of all product cavities at the individual cavity level were identified and evaluated. Based on this analysis, several types of mechanical valves for inclusion in runner systems were designed and fabricated. The resultant valve systems were tested on the prototype two-cavity mold, with important process as well as product quality variables monitored and/or measured during testing. All initial testing was performed using a liquid crystal polymer (LCP) material from Hoechst Celanese. The results of the testing trials were analyzed to both validate the concept of individual cavity filling modification and identify an optimal valve type through which this can be accomplished. It was concluded that the flow control concept developed was experimentally validated, and that a custom characterized valve type appears most promising for future utilization at industrial manufacturing facilities. The future directions for the continuing project are also discussed.
FE Approach to the Sensitivity of Load on a Hopper to the Filling Method and Process With Granular Material
Authors: Ding Songxiong , Enstad Gisle G.
Published: May 2008

An analysis (ABAQUS) has been carried out to investigate the development of loads exerted on the wall of a hopper when it is being filled with granular material in a method of either distributed-filling or concentric-filling. A finite element program was created to model the hopper, the granular material and the interaction between them. To simulate a filling process, a partition technique was applied to the granular material to divide it into layers; the meshes, the gravity loading and the interaction were all suspended first. They were then reactivated in a designated sequence layer by layer. Such an operation of reactivation was regarded as an approach to a process of filling. There were two geometries designed for the granular material, the distributed-filling or concentric-filling methods were also thought to be obtained. The sensitivity of loads to the method of filling and to the process of filling was addressed.
Design and Preliminary Testing of a Prototype Thermophotovoltaic System
Authors: Astle Chris J. , Kovacik Gary J. , Heidrick Ted R.
Published: May 2008

Thermophotovoltaics (TPV) is technology similar to conventional solar photovoltaics, which have been in existence for over 50 years. The main difference between traditional solar photovoltaics and TPV is that, instead of the sun, an “emitter” is used to produce light, which is then converted into electricity by the TPV system. This emitter is heated via combustion or some other method until photons are ejected. Although the light utilized in the TPV system is not as energetic as that from the sun, the fact that the TPV cells can be placed in close proximity to the source (compared with the distance to the sun) increases the intensity of the light received by the cells. This results in a higher power production density than is possible with traditional solar photovoltaic systems. One estimate of maximum achievable output power density for TPV systems is 5W/cm2, approximately 500 times that of a traditional solar PV system. Researchers in this field have already demonstrated power densities of 1.5W/cm2. Other attractions of TPV systems include fuel versatility, compact size, silent sun-independent operation, and low maintenance costs. A TPV test station has been assembled at the Alberta Research Council in Canada. A general overview of the background technology and system components will be presented, as well as preliminary experimental results. Areas that require additional improvement in order to increase system efficiency will also be addressed.
Safety and Field Testing of a New Generation AC Module
Authors: Islam Saiful , Woyte Achim , Belmans Ronnie
Published: May 2008

Safety and quality requirements for a new type of AC module have been identified and its performance has been evaluated for two prototypes. The laboratory tests have to show whether the so-called PV2go inverter can comply with the expectations and where improvements are still necessary. Afterwards, the AC modules have been tested under typical European field conditions.
Nonlinear Vibrations of Circular Cylindrical Panels: Theory and Experiments
Authors: Amabili M. , Pellegrini M.
Published: May 2008

Large-amplitude (geometrically nonlinear) vibrations of circular cylindrical panels subjected to radial harmonic excitation in the spectral neighborhood of the lowest resonances are investigated. The Donnell’s nonlinear thin-shell theory is used to calculate the elastic strain energy. The formulations is also valid for orthotropic and symmetric cross-ply laminated composite shells; geometric imperfections are taken into account. Comparison of calculations to numerical results available in the literature is also performed. The nonlinear equations of motion are studied by using a code based on arclength continuation method that allows bifurcation analysis. Vibration response of three thin circular cylindrical panels of different materials (stainless steel, copper and composite) to harmonic excitation in the neighborhood of the first three natural frequencies has been measured for different force levels. The experimental boundary conditions approximate (i) on the curved edges: zero radial, axial and circumferential displacements; all rotations were allowed; (ii) on the straight edges: zero radial and axial displacements; all rotations and circumferential displacements were allowed. The different levels of excitation permitted to reconstruct the relatively strong, softening type nonlinearity of the panels.
On the Optimisation of Hot Workability in Austenitic Stainless Steels Using Dynamic Material Model and a Novel Methodology for the Control of Microstructure During Hot Working
Authors: Venugopal S. , Mannan S. L.
Published: May 2008

The constitutive flow behaviour of austenitic stainless steels type AISI 304L, 316L, and 304 in the warm and hot working regions has been evaluated. The technique adopted for the study of constitutive behaviour is through establishing processing maps and instability maps, and interpreting them on the basis of dynamic materials model (DMM). The “safe” processing regime predicted by processing maps have been further refined using the values of apparent activation energy during deformation. The validity and the merit of this refining procedure have been demonstrated with an example of press forging trials on stainless steel 316L.
Application of Time Series Analysis and Neural Networks to the Modeling and Analysis of Forced Vibrating Mechanical Systems
Authors: Zolock John , Greif Robert
Published: May 2008

A theoretical and mathematical based methodogy is discussed that utilizes time series analysis techniques and neural networks to model forced vibrating mechanical systems using measured input-output data. A technique in nonlinear time series analysis known as phase space reconstruction may be used to extend our understanding of the active dynamics recorded in a single time series measurement. Using a recorded output (response) measurement phase space reconstruction parameters are calculated; the embedding dimension is estimated using the method of false nearest neighbor, and the time delay is estimated from the first minimum of the mutual information. The phase space reconstruction characteristics are then used to fully shape the architecture of a time delayed neural network model for the dynamical system. The modeling methodology is applied to several forced vibrating systems common to many fields of engineering. The neural models are then used to analyze new input, demonstrating the usefulness and importance of the methodology.
An Innovative Fuel Cell Theory, Testing and Manufacturing Course
Authors: Rogers Brad , Tamizhmani Govindasamy , Sundararajan Rajiswari , Danielson Scott
Published: May 2008

A unique course in the theory, testing and manufacturing of fuel cells has been developed at Arizona State University in the College of Technology and Applied Sciences. The course is designed for the engineering technology graduate students, but is also accessible to advanced undergraduates. The interdisciplinary nature of the course necessitates a team-teaching approach, and faculty with backgrounds in electrochemistry, electrical engineering and mechanical engineering deliver portions of the course. The course includes a theoretical portion, but also contains a comprehensive practical portion in which the students build a membrane electrode assembly and assemble, test and characterize this assembly as a single stage proton exchange membrane fuel cell. Feedback from the students indicates a great deal of excitement over the course, and has resulted in several students deciding to concentrate their graduate work in the fuel cell area. The paper describes the first course offering in the spring of 2003.
Nano-Scale Heat Transfer Education at Carnegie Mellon University: Programs for Mechanical Engineering and High School Students
Authors: Sadeghipour Sadegh M. , Asheghi Mehdi
Published: May 2008

The evolving high technology industries of recent years have created a growing need for mechanical engineers with nano-scale heat transfer expertise to aid analysis, design, and fabrication of micro devices such as transistors, sensors, actuators, etc. The trends and predictions for activities in this field are even more promising for the next decade. Therefore, the new generation of mechanical engineers should have a reasonable knowledge of the subject to meet the growing demands of the job market. This has created need for inclusion of nano-scale heat transfer topics and experiments in the mechanical engineering curriculum. To meet this demand, we have started a few programs in the mechanical engineering department of the Carnegie Mellon University. We have added nano-scale heat transfer topics, including lab experiments, to some of the existing courses also have developed and offered new specialized courses on the subject. In addition, we have started a summer program for interested high school students entitled “The Exciting World of Thermal Engineering”. The purpose of the latter program has been to expose the student to the subject, and to create/promote enthusiasm for pursuing a thermal engineering career. In this paper we are going to explain the program and to share our observations and experiences.
The Effect of Mercury in the Micro-Dynamics of Injection Pipettes
Authors: Ediz Kerem , Olgac Nejat
Published: May 2008

“Microinjection” is becoming increasingly important in molecular biology. These operations include the micromanipulation of cellular subjects, such as piercing procedure through the zona pellucida and the membrane in ICSI (intracytoplasmic sperm injection).
Design of High Precision High Bandwidth and Reliable Nanopositioning Systems
Authors: Salapaka Srinivasa , Sebastian Abu
Published: May 2008

In this paper, we present a paradigm which prescribes a procedure for a systematic design, analysis and development of nanopositioning devices. In this effort, we have used many tools from modern control theory to model devices, to quantify device resolution, bandwidth, range, and robustness, and to tackle undesirable nonlinear effects such as hysteresis and creep. The implementation of this procedure for the simultaneous achievement of robustness, high precision, and high bandwidth objectives is presented. The merits of the paradigm are demonstrated through experimental results.
The Influence of Bone Mineral Density on Pelvic Fracture Load and Compression in Lateral Impact
Authors: Etheridge Brandon S. , Beason David P. , Lopez Robert R. , Alonso Jorge E. , Eberhardt Alan W.
Published: May 2008

Pelvic injuries due to lateral motor vehicle crashes continue to be a source of morbidity and mortality for accident victims as well as a serious problem for trauma surgeons and automotive safety engineers. In the present study, we sought to further explore the relationship between bone mineral density (BMD) measurements in the hip and pelvic fracture load and compression. We conducted experimental side impacts on intact lower torsos of female cadavers, building upon our previous work conducted on isolated bone-ligament structures. Significant linear relationships between pelvic fracture load/compression and total hip BMD emerged as further evidence that total hip bone mineral density may be a useful predictor of pelvic fracture risk. The presence of soft tissues increased resulting pelvic fracture loads as compared to those found in our previous isolated pelvic impacts.
Turbulence and Magnetic Fields in the Large-Scale Structure of the Universe
Authors: Ryu Dongsu , Kang Hyesung , Cho Jungyeon , Das Santabrata
Published: May 2008

The nature and origin of turbulence and magnetic fields in the intergalactic space are important problems that are yet to be understood. We propose a scenario in which turbulent-flow motions are induced via the cascade of the vorticity generated at cosmological shocks during the formation of the large-scale structure. The turbulence in turn amplifies weak seed magnetic fields of any origin. Supercomputer simulations show that the turbulence is subsonic inside clusters and groups of galaxies, whereas it is transonic or mildly supersonic in filaments. Based on a turbulence dynamo model, we then estimated that the average magnetic field strength would be a few microgauss (μG) inside clusters and groups, approximately 0.1 μG around clusters and groups, and approximately 10 nanogauss in filaments. Our model presents a physical mechanism that transfers the gravitational energy to the turbulence and magnetic field energies in the large-scale structure of the universe.
Ultrafast Probing of Core Hole Localization in N
2
Authors: Schöffler M. S. , Titze J. , Petridis N. , Jahnke T. , Cole K. , Schmidt L. Ph. H. , Czasch A. , Akoury D. , Jagutzki O. , Williams J. B. , Cherepkov N. A. , Semenov S. K. , McCurdy C. W. , Rescigno T. N. , Cocke C. L. , Osipov T. , Lee S. , Prior M. H. , Belkacem A. , Landers A. L. , Schmidt-Böcking H. , Weber Th. , Dörner R.
Published: May 2008

Although valence electrons are clearly delocalized in molecular bonding frameworks, chemists and physicists have long debated the question of whether the core vacancy created in a homonuclear diatomic molecule by absorption of a single x-ray photon is localized on one atom or delocalized over both. We have been able to clarify this question with an experiment that uses Auger electron angular emission patterns from molecular nitrogen after inner-shell ionization as an ultrafast probe of hole localization. The experiment, along with the accompanying theory, shows that observation of symmetry breaking (localization) or preservation (delocalization) depends on how the quantum entangled Bell state created by Auger decay is detected by the measurement.
Early Forebrain Wiring: Genetic Dissection Using Conditional
Celsr3
Mutant Mice
Authors: Zhou Libing , Bar Isabelle , Achouri Younès , Campbell Kenneth , De Backer Olivier , Hebert Jean M. , Jones Kevin , Kessaris Nicoletta , de Rouvroit Catherine Lambert , O'Leary Dennis , Richardson William D. , Goffinet Andre M. , Tissir Fadel
Published: May 2008

Development of axonal tracts requires interactions between growth cones and the environment. Tracts such as the anterior commissure and internal capsule are defective in mice with null mutation of
Celsr3
. We generated a conditional
Celsr3
allele, allowing regional inactivation. Inactivation in telencephalon, ventral forebrain, or cortex demonstrated essential roles for Celsr3 in neurons that project axons to the anterior commissure and subcerebral targets, as well as in cells that guide axons through the internal capsule. When Celsr3 was inactivated in cortex, subcerebral projections failed to grow, yet corticothalamic axons developed normally, indicating that besides guidepost cells, additional Celsr3-independent cues can assist their progression. These observations provide in vivo evidence that Celsr3-mediated interactions between axons and guidepost cells govern axonal tract formation in mammals.
The Energetic Cost of Climbing in Primates
Authors: Hanna Jandy B. , Schmitt Daniel , Griffin Timothy M.
Published: May 2008

Primates are exceptional among mammals for their climbing abilities and arboreal lifestyles. Here we show that small primates (less than 0.5 kilogram) consume the same amount of mass-specific energy (COTTOT) whether climbing or walking a given distance. COTTOT decreases with increasing body size for walking but does not change for climbing. This divergence of COTTOT is likely due to fundamental differences in the biomechanical determinants of the costs of climbing versus walking. These results have important implications for understanding the origins of primates, suggesting that small early primates may have been able to move into a novel arboreal niche without increasing metabolic costs.
Activation of the Cellular DNA Damage Response in the Absence of DNA Lesions
Authors: Soutoglou Evi , Misteli Tom
Published: May 2008

The cellular DNA damage response (DDR) is initiated by the rapid recruitment of repair factors to the site of DNA damage to form a multiprotein repair complex. How the repair complex senses damaged DNA and then activates the DDR is not well understood. We show that prolonged binding of DNA repair factors to chromatin can elicit the DDR in an ATM (ataxia telangiectasia mutated)– and DNAPK (DNA-dependent protein kinase)–dependent manner in the absence of DNA damage. Targeting of single repair factors to chromatin revealed a hierarchy of protein interactions within the repair complex and suggests amplification of the damage signal. We conclude that activation of the DDR does not require DNA damage and stable association of repair factors with chromatin is likely a critical step in triggering, amplifying, and maintaining the DDR signal.
Localized Gene Expression in
Pseudomonas aeruginosa
Biofilms
Authors: Lenz Ailyn P. , Williamson Kerry S. , Pitts Betsey , Stewart Philip S. , Franklin Michael J.
Published: May 2008

Gene expression in biofilms is dependent on bacterial responses to the local environmental conditions. Most techniques for studying bacterial gene expression in biofilms characterize average values across the entire population. Here, we describe the use of laser capture microdissection microscopy (LCMM) combined with multiplex quantitative real-time reverse transcriptase PCR (qRT-PCR) to isolate and quantify RNA transcripts from small groups of cells at spatially resolved sites within biofilms. The approach was first tested and analytical parameters were determined for
Pseudomonas aeruginosa
containing an isopropyl-β-
d
-thiogalactopyranoside-inducible gene for the green fluorescent protein (
gfp
). The results show that the amounts of
gfp
mRNA were greatest in the top zones of the biofilms, and that
gfp
mRNA levels correlated with the zone of active green fluorescent protein fluorescence. The method then was used to quantify transcripts from wild-type
P. aeruginosa
biofilms for a housekeeping gene,
acpP
; the 16S rRNA; and two genes regulated by quorum sensing,
phzA1
and
aprA
. The results demonstrated that the amount of
acpP
mRNA was greatest in the top 30 μm of the biofilm, with little or no mRNA for this gene at the base of the biofilms. In contrast, 16S rRNA amounts were relatively uniform throughout biofilm strata. Using this strategy, the RNA amounts of individual genes were determined, and therefore the results are dependent on both gene expression and the half-life of the transcripts. Therefore, the uniform amount of rRNA throughout the biofilms likely is due to the stability of the rRNA within ribosomes. The levels of
aprA
mRNA showed stratification, with the largest amounts in the upper 30-μm zone of these biofilms. The results demonstrate that mRNA levels for individual genes are not uniformly distributed throughout biofilms but may vary by orders of magnitude over small distances. The LCMM/qRT-PCR technique can be used to resolve and quantify this RNA variability at high spatial resolution.
Diversity of Human Vaginal Bacterial Communities and Associations with Clinically Defined Bacterial Vaginosis
Authors: Oakley Brian B. , Fiedler Tina L. , Marrazzo Jeanne M. , Fredricks David N.
Published: May 2008

Bacterial vaginosis (BV) is a common syndrome associated with numerous adverse health outcomes in women. Despite its medical importance, the etiology and microbial ecology of BV remain poorly understood. We used broad-range PCR to census the community structure of the healthy and BV-affected vaginal microbial ecosystems and synthesized current publicly available bacterial 16S rRNA gene sequence data from this environment. The community of vaginal bacteria detected in subjects with BV was much more taxon rich and diverse than in subjects without BV. At a 97% sequence similarity cutoff, the number of operational taxonomic units (OTUs) per patient in 28 subjects with BV was nearly three times greater than in 13 subjects without BV: 14.8 ± 0.7 versus 5.2 ± 0.75 (mean ± standard error). OTU-based analyses revealed previously hidden diversity for many vaginal bacteria that are currently poorly represented in GenBank. Our sequencing efforts yielded many novel phylotypes (123 of our sequences represented 38 OTUs not previously found in the vaginal ecosystem), including several novel BV-associated OTUs, such as those belonging to the
Prevotella
species complex, which remain severely underrepresented in the current NCBI database. Community composition was highly variable among subjects at a fine taxonomic scale, but at the phylum level,
Actinobacteria
and
Bacteroidetes
were strongly associated with BV. Our data describe a previously unrecognized extent of bacterial diversity in the vaginal ecosystem. The human vagina hosts many bacteria that are only distantly related to known species, and subjects with BV harbor particularly taxon-rich and diverse bacterial communities.
Hos2p/Set3p Deacetylase Complex Signals Secretory Stress through the Mpk1p Cell Integrity Pathway
Authors: Cohen T. J. , Mallory M. J. , Strich R. , Yao T.-P.
Published: May 2008

Perturbations in secretory function activate stress response pathways critical for yeast survival. Here we report the identification of the Hos2p/Set3p deacetylase complex (SET3C) as an essential component of the secretory stress response. Strains lacking core components of the Hos2p/Set3p complex exhibit hypersensitivity to secretory stress. Although not required for the unfolded protein response (UPR) and ribosomal gene repression, the Hos2p complex is required for proper activation of the Mpk1p/Slt2p cell integrity kinase cascade. Disruption of the Hos2p complex results in abrogated Mpk1p phosphorylation, whereas constitutive activation of the Mpk1p pathway rescues the
hos2
Δ mutant growth defect in response to secretory stress. Furthermore, Hos2p activity is required for the Mpk1p-mediated activation of stress-responsive transcription factor Rlm1p, but not for the stress-induced degradation of the C-type cyclin Ssn8p. Our results identify the Hos2p complex as a critical component of the secretory stress response and support the existence a coordinated stress response consisting of the UPR, ribosomal gene repression, and mitogen-activated protein kinase signaling in response to defects in secretory function.
AinS Quorum Sensing Regulates theVibrio fischeriAcetate Switch
Authors: Studer Sarah V. , Mandel Mark J. , Ruby Edward G.
Published: May 2008

The marine bacteriumVibrio fischeriuses two acyl-homoserine lactone (acyl-HSL) quorum-sensing systems. The earlier signal, octanoyl-HSL, produced by AinS, is required for normal colonization of the squidEuprymna scolopesand, in culture, is necessary for a normal growth yield. In examining the latter requirement, we found that during growth in a glycerol/tryptone-based medium, wild-typeV. fischericells initially excrete acetate but, in a metabolic shift termed the acetate switch, they subsequently utilize the acetate, removing it from the medium. In contrast, anainSmutant strain grown in this medium does not remove the excreted acetate, which accumulates to lethal levels. The acetate switch is characterized by the induction ofacs, the gene encoding acetyl coenzyme A (acetyl-CoA) synthetase, leading to uptake of the excreted acetate. Wild-type cells induce anacstranscriptional reporter 25-fold, coincident with the disappearance of the extracellular acetate; in contrast, theainSmutant did not display significant induction of theacsreporter. Supplementation of the medium of anainSmutant with octanoyl-HSL restored normal levels ofacsinduction and acetate uptake. Additional mutant analyses indicated thatacsregulation was accomplished through the regulator LitR but was independent of the LuxIR quorum-signaling pathway. Importantly, theacsmutant ofV. fischerihas a competitive defect when colonizing the squid, indicating the importance of proper control of acetate metabolism in the light of organ symbiosis. This is the first report of quorum-sensing control of the acetate switch, and it indicates a metabolic connection between acetate utilization and cell density.
mgtAExpression Is Induced by Rob Overexpression and Mediates aSalmonella entericaResistance Phenotype
Authors: Barchiesi Julieta , Castelli María E. , Soncini Fernando C. , Véscovi Eleonora García
Published: May 2008

Rob is a member of the Sox/Mar subfamily of AraC/XylS-type transcriptional regulators implicated in bacterial multidrug, heavy metal, superoxide, and organic solvent resistance phenotypes. We demonstrate that, inSalmonella enterica, Rob overexpression upregulates the transcription ofmgtA, which codes for the MgtA Mg2+transporter.mgtAwas previously characterized as a member of the Mg2+-modulated PhoPQ regulon. Here we demonstrate that Rob (but not its paralog protein SoxS or MarA) is able to inducemgtAtranscription in a PhoP-independent fashion by binding to a conserved Mar/Sox/Rob motif localized downstream of the PhoP-box and overlapping the PhoP-dependent transcriptional start site. We found that Rob-inducedmgtAexpression confers low-level cyclohexane resistance onSalmonella. BecausemgtAintactness is required for Rob-induced cyclohexane resistance, provided the AcrAB multidrug efflux pump can be expressed, we postulate that MgtA is involved in the AcrAB-mediated cyclohexane detoxification mechanism promoted by Rob inSalmonella.
Role of the Global Transcriptional Regulator PrrA inRhodobacter sphaeroides2.4.1: Combined Transcriptome and Proteome Analysis
Authors: Eraso Jesus M. , Roh Jung Hyeob , Zeng Xiaohua , Callister Stephen J. , Lipton Mary S. , Kaplan Samuel
Published: May 2008

The PrrBA two-component regulatory system is a major global regulator inRhodobacter sphaeroides2.4.1. Here we have compared the transcriptome and proteome profiles of the wild-type (WT) and mutant PrrA2 cells grown anaerobically in the dark with dimethyl sulfoxide as an electron acceptor. Approximately 25% of the genes present in the PrrA2 genome are regulated by PrrA at the transcriptional level, either directly or indirectly, by twofold or more relative to the WT. The genes affected are widespread throughout all COG (cluster of orthologous group) functional categories, with previously unsuspected “metabolic” genes affected in PrrA2 cells. PrrA was found to act as both an activator and a repressor of transcription, with more genes being repressed in the presence of PrrA (9:5 ratio). An analysis of the genes encoding the 1,536 peptides detected through our chromatographic study, which corresponds to 36% coverage of the genome, revealed that approximately 20% of the genes encoding these proteins were positively regulated, whereas approximately 32% were negatively regulated by PrrA, which is in excellent agreement with the percentages obtained for the whole-genome transcriptome profile. In addition, comparison of the transcriptome and proteome mean parameter values for WT and PrrA2 cells showed good qualitative agreement, indicating that transcript regulation paralleled the corresponding protein abundance, although not one for one. The microarray analysis was validated by direct mRNA measurement of randomly selected genes that were both positively and negatively regulated.lacZtranscriptional andkantranslational fusions enabled us to map putative PrrA binding sites and revealed potential gene targets for indirect regulation by PrrA.
Impact of Aeration and Heme-Activated Respiration on
Lactococcus lactis
Gene Expression: Identification of a Heme-Responsive Operon
Authors: Pedersen Martin Bastian , Garrigues Christel , Tuphile Karine , Brun Célia , Vido Karin , Bennedsen Mads , Møllgaard Henrik , Gaudu Philippe , Gruss Alexandra
Published: May 2008

Lactococcus lactis
is a widely used food bacterium mainly characterized for its fermentation metabolism. However, this species undergoes a metabolic shift to respiration when heme is added to an aerobic medium. Respiration results in markedly improved biomass and survival compared to fermentation. Whole-genome microarrays were used to assess changes in
L. lactis
expression under aerobic and respiratory conditions compared to static growth, i.e., nonaerated. We observed the following. (i) Stress response genes were affected mainly by aerobic fermentation. This result underscores the differences between aerobic fermentation and respiration environments and confirms that respiration growth alleviates oxidative stress. (ii) Functions essential for respiratory metabolism, e.g., genes encoding cytochrome
bd
oxidase, menaquinone biosynthesis, and heme uptake, are similarly expressed under the three conditions. This indicates that cells are prepared for respiration once O
2
and heme become available. (iii) Expression of only 11 genes distinguishes respiration from both aerobic and static fermentation cultures. Among them, the genes comprising the putative
ygfCBA
operon are strongly induced by heme regardless of respiration, thus identifying the first heme-responsive operon in lactococci. We give experimental evidence that the
ygfCBA
genes are involved in heme homeostasis.
Impact of Individual Mutations on Increased Fitness in Adaptively Evolved Strains of
Escherichia coli
Authors: Applebee M. Kenyon , Herrgård Markus J. , Palsson Bernhard Ø.
Published: May 2008

We measured the relative fitness among a set of experimentally evolved
Escherichia coli
strains differing by a small number of adaptive mutations by directly measuring allelic frequencies in head-to-head competitions using a mass spectrometry-based method. We compared the relative effects of mutations to the same or similar genes acquired in multiple strains when expressed in allele replacement strains. We found that the strongest determinant of fitness among the evolved strains was the impact of beneficial mutations to the RNA polymerase β and β′ subunit genes. We also identified several examples of epistatic interactions between
rpoB/C
and
glpK
mutations and identified two other mutations that are beneficial only in the presence of previously acquired mutations but that have little or no adaptive benefit to the wild-type strain. Allele frequency estimation is shown to be a highly sensitive method for measuring selection rates during competitions between strains differing by as little as a single-nucleotide polymorphism and may be of great use for investigating epistatic interactions.
Incidence and risk factors of running-related injuries during preparation for a 4-mile recreational running event
Authors: Buist I , Bredeweg S W , Bessem B , van Mechelen W , Lemmink K A P M , Diercks R L
Published: May 2008

Objective

In this study, the incidence and the sex-specific predictors of running-related injury (RRI) among a group of recreational runners training for a 4-mile running event were determined and identified, respectively.

Design

Prospective cohort study.

Methods

Several potential risk factors were prospectively measured in 629 novice and recreational runners. They were observed during an 8-week training period for any running-related musculoskeletal injuries of the lower limbs and back. A running-related injury was defined as any musculoskeletal pain of the lower limb or back causing a restriction of running for at least 1 day.

Results

At least one RRI was reported by 25.9% of the runners during the 8-week observation period. The incidence of RRI was 30.1 (95% CI 25.4 to 34.7) per 1000 h of running exposure. Multivariate Cox regression showed that male participants were more prone to sustain a RRI than female participants (HR 1.4; 95% CI 1.0 to 2.0). No previous running experience was the most important risk factor in male (HR 2.6; 95% CI 1.2 to 5.5) and female (HR 2.1; 95% CI 1.2 to 3.7) participants.

Conclusions

The incidence of running-related injuries in recreational runners preparing for a 4-mile running event is substantially high. Male and female participants have different risk profiles. Furthermore, the findings suggest that novice runners may benefit the most out of preventive interventions for RRI.
STUDIES ON THE MECHANISM OF FUNGICIDAL ACTION OF DISODIUM ETHYLENE BISDITHIOCARBAMATE (NABAM)
Authors: Ludwig R. A. , Thorn G. D. , Miller D. M.
Published: May 2008

A crude aeration precipitate of nabam was found to possess a relatively high order of fungicidal activity. Evidence is presented to show that this activity can be attributed to ethylene thiuram nonosulphide, both monomer and polymer. This substance was demonstrated on the foliage of plants sprayed with nabam and could account for its protective fungicidal action.