bluuebunny/crossref_metadata_2025 huggingface dataset:
Restricted Diffusion in a Thrombosed Anterior Cerebral Artery Aneurysm Mimicking a Dermoid Cyst
Authors: Fifi Johanna T. , Komotar Ricardo , Meyers Philip , Khandji Alexander , Tanji Kurenai , Connolly E. Sander
Published: June 2010

A neurologically intact 37‐year‐old woman presented with an acute severe frontal headache after a month of intermittent headaches. Multimodal radiological examination including computed tomography scan, magnetic resonance imaging, and conventional angiography demonstrated a 1 cm mass in the anterior interhemispheric region with heterogenous calcifications. Of note, MR revealed restricted diffusion within the mass. The presumptive diagnosis of dermoid tumor was made and the patient was scheduled for surgical resection. On operative exploration, a 1 cm thrombosed aneurysm was revealed. Thrombosed aneurysms must be considered in the differential diagnosis for midline cerebral masses with negative angiogram and restricted diffusion. This distinction has implications for the clinical management of the patient.
Computational Biology Approaches to Plant Metabolism and Photosynthesis: Applications for Corals in Times of Climate Change and Environmental Stress
Authors: Crabbe M. James C.
Published: June 2010

Knowledge of factors that are important in reef resilience helps us to understand how reef ecosystems react following major anthropogenic and environmental disturbances. The symbiotic relationship between the photosynthetic zooxanthellae algal cells and corals is that the zooxanthellae provide the coral with carbon, while the coral provides protection and access to enough light for the zooxanthellae to photosynthesise. This article reviews some recent advances in computational biology relevant to photosynthetic organisms, including Beyesian approaches to kinetics, computational methods for flux balances in metabolic processes, and determination of clades of zooxanthallae. Application of these systems will be important in the conservation of coral reefs in times of climate change and environmental stress.
A Novel Pharmacophore Model for the Design of Anthrax Lethal Factor Inhibitors
Authors: Yuan Hongbin , Johnson Sherida L. , Chen Li‐Hsing , Wei Jun , Pellecchia Maurizio
Published: June 2010

This study aims at the identification of novel structural features on the surface of the Zn‐dependant metalloprotease lethal factor (LF) from anthrax onto which to design novel and selective inhibitors. We report that by targeting an unexplored region of LF that exhibits ligand‐induced conformational changes, we could obtain inhibitors with at least 30‐fold LF selectivity compared to two other most related human metalloproteases, MMP‐2 and MMP‐9. Based on these results, we propose a novel pharmacophore model that, together with the preliminarily identified compounds, should help the design of more potent and selective inhibitors against anthrax.
Embryo Stem Cell Research: Ten Years of Controversy
Authors: Robertson John A.
Published: June 2010

Embryonic stem cell (ESC) research has been a source of ethical, legal, and social controversy since the first successful culturing of human ESCs in the laboratory in 1998. The controversy has slowed the pace of stem cell science and shaped many aspects of its subsequent development. This paper assesses the main issues that have bedeviled stem cell progress and identifies the ethical fault lines that are likely to continue.

The time is appropriate for such an assessment because the field is poised for a period of rapid development. President Obama has removed the Bush administration’s restrictions on federal funding. A huge influx of federal research funds is in the offing and presumably a more rapid maturing of the science will take place. Stem cell science is also moving into the clinical realm. In March 2009, the Food and Drug Administration (FDA) approved the first clinical trial with an ESC-derived therapy for spinal cord injuries, an important first step — though by no means a final or a sure one — in moving ESC research out of the laboratory into clinical medicine. Finally, recent work with induced pluripotent stem (IPS) cells suggests that non-embryonic sources of pluripotent stem cells may one day be routinely available. Such a development will lessen the temperature of the ethical debate while raising other issues.
Why Scientific Details are Important When Novel Technologies Encounter Law, Politics, and Ethics
Authors: Goldstein Lawrence
Published: June 2010

Lost at times in the heat of debate about stem cell research, or any controversial advanced technology, is the need for precision in debate and discussion. The details matter a great deal, ranging from the need to use words that have precise definitions, to accurately quote colleagues and adversaries, and to cite scientific and medical results in a way that reflects the quality, rigor, and reliability of the work at issue. Regrettably, considerable inaccuracy has found its way into the debates about stem cells, on all sides, with consequent fogging of the issues.

A key detail that is often overlooked in the debates about the uses of human embryonic stem cells in research comes from the nature of in vitro fertilization (IVF) treatment for infertility. Specifically, there are many frozen human embryos (more precisely called blastocysts) that are in excess of reproductive needs of the couple who generated them, and that must be either frozen indefinitely, donated to another couple, or destroyed.
Political Interventions in U.S. Human Embryo Research: An Ethical Assessment
Authors: Green Ronald M.
Published: June 2010

Although the first human embryonic stem cells (hESCs) were produced in 1998, the direction of U.S. policy on stem cell research was set nearly 20 years earlier when the recommendations of a congressionally established Ethics Advisory Board were ignored by the Reagan administration. Thus began an unprecedented and unparalleled 30-year-long history of political intrusions in an area of scientific and biomedical research that has measurable impacts on the health of Americans. Driving these intrusions were religiously informed public policy positions that have usually escaped critical ethical analysis. Here I record my own encounters with this history of intrusions and the thinking behind them.

My most abrupt encounter with the politics of stem cell research occurred on September 6, 2006, at a hearing of the Senate Subcommittee on Labor, Health and Human Services and Related Agencies, chaired by Senator Arlen Specter. Just a week before, scientists at Advanced Cell Technology (ACT), a small Massachusetts biotech company, had published a paper in the journal Nature in which they described a method for extracting stem cells from early human embryos while leaving the embryos intact and viable. As head of ACT’s Ethics Advisory Board, I had supported this research.
Resolving Ethical Issues in Stem Cell Clinical Trials: The Example of Parkinson Disease
Authors: Lo Bernard , Parham Lindsay
Published: June 2010

Stem cells derived from pluripotent cells offer the hope of new treatments for diseases for which current therapy is inadequate. Clinical trials are essential in developing effective and safe stem cell therapies and fulfilling this promise. However, such clinical trials raise ethical issues that are more complex than those raised in clinical trials using drugs, cord blood stem cells, or adult stem cells. Several clinical trials are now being carried out with stem cells derived from pluripotent cells, and many more can be expected in light of the rapid scientific progress in the field.

Degenerative neurological diseases are desirable targets for stem cell clinical trials. The FDA has approved Phase 1 clinical trials of neural stem cell transplantation for Batten Disease, Pelizaeus-Merzbacher Disease, and spinal cord injury. In Parkinson Disease (PD), stem cell transplantation could correct the primary pathophysiological defect — inadequate levels of the neurotransmitter dopamine. Current treatment is unsatisfactory in late-stage PD.
Will Embryonic Stem Cells Change Health Policy?
Authors: Sage William M.
Published: June 2010

Essays on stem cell policy seem to fall into three categories. Some essays in this collection are about logic and principles. Others are about practices and beliefs. The former group draws lines and defends them, a normative project. The latter group attempts to explain the lines that already exist, a descriptive project that may have important normative goals. Still other essays, by scientists, are about growing stem cell lines instead of drawing them.

The purpose of this essay is to situate the lines being drawn around stem cell science in the larger landscape of health policy. I am interested in the things that cause health policy to take particular directions and the consequences of those directions for cost, access, and quality — all of which are determined in part by biomedical innovations such as those potentially derived from stem cells.
Diagnosing Consciousness: Neuroimaging, Law, and the Vegetative State
Authors: Fisher Carl E. , Appelbaum Paul S.
Published: June 2010

Recent studies indicate that patients who are diagnosed with vegetative states may retain more awareness than their clinical assessments suggest. Disorders of consciousness traditionally have been diagnosed on the basis of outwardly observable behaviors alone, but new functional imaging studies have shown surprising levels of brain activity in some patients, indicating that even higher-level cognitive functions like language processing and visual imagery may be preserved. For example, one recently developed method purports to detect voluntary mental imagery solely on the basis of neural response patterns observed with functional magnetic resonance imaging (fMRI). This line of research has already led to some widely reported cases of patients who were discovered to have more brain activity than expected. In November 2009, Rom Houben, a Belgian man who was thought to be in a coma for 23 years, was diagnosed with locked-in syndrome through the use of neuroimaging; however, that assessment was later overturned by further testing.
Beyond the Cold Hit: Measuring the Impact of the National DNA Data Bank on Public Safety at the City and County Level
Authors: Gabriel Matthew , Boland Cherisse , Holt Cydne
Published: June 2010

Criminalistics laboratories routinely provide cold hits in police investigations by comparing DNA profiles from crime scenes to offenders residing in the Combined DNA Index System (CODIS). Forensic DNA analysis is often glamorized in popular culture, where the perpetrators are identified and crimes solved within a single television episode. In reality forensic DNA hits can identify perpetrators of violent offenses, link multiple crimes committed by the same individual, or exclude suspects and exonerate the falsely accused. Unlike the media portrayals, downstream activities after a DNA identification or cold hit are often more complex. While the Federal Bureau of Investigation (FBI) cites a national Data Bank of more than 7.2 million DNA profiles and 94,000 identifications nationwide, an in-depth analysis of public safety improvements made with CODIS is currently unavailable to forensic practitioners and public policy analysts. A review of case resolutions for 198 DNA database hits in San Francisco created performance metrics to provide a concrete measure of the effectiveness of DNA databasing efforts at the city and county level.
Rotordynamic Stability Predictions for Centrifugal Compressors Using a Bulk-Flow Model to Predict Impeller Shroud Force and Moment Coefficients
Authors: Gupta Manoj K. , Childs Dara W.
Published: June 2010

An analysis is developed for a compressible bulk-flow model of the leakage path between a centrifugal-compressor impeller’s shroud and its housing along the impeller’s front and back sides. This development is an extension of analyses performed first by Childs (1989, ASME J. Vib. Acoust., Stress, Reliab. Des., 111, pp. 216–225) for pump impellers. The bulk-flow model is used to predict reaction force and moment coefficients for the impeller shroud. A labyrinth seal code developed by Childs and Scharrer ( 1986, ASME Trans. J. Eng. Gas Turbines Power, 108, pp. 325–331) is used to calculate the rotordynamic coefficients developed by the labyrinth seals in the compressor stage and also provides a boundary condition for the shroud calculations. Comparisons between the measured shroud moment coefficients by Yoshida et al. (1996, Proceedings of the 6th International Symposium on Transport Phenomena and Dynamics of Rotating Machinery, 2, pp. 151–160) and model predictions show reasonable agreements for the clearance flow and reaction moments. For the conditions considered, low Mach number flow existed in the shroud clearance areas and compressible-flow and incompressible-flow models produced similar predictions. Childs’ model predictions for the direct damping and cross-coupled stiffness coefficients of a pump impeller produced reasonable agreement; hence the present model was validated to the extent possible. A rotor model consisting of an overhung impeller stage supported by a nominally cantilevered rotor was analyzed for stability using the present bulk-flow model and an API standard Wachel–von Nimitz formula model (1981, J. Petrol. Technol., pp. 2252–2260). The bulk-flow model predicted significantly higher onset speeds of instability. Given that some compressors have been predicted to be comfortably stable using API standard Wachel–von Nimitz formula but have been unstable on the test stand, these results suggest that unidentified destabilizing forces and or moments are present in compressors. Seal rub conditions that arise from surge events and increase the seal clearances are simulated, showing that enlarged clearances increase the preswirl at the seals, thus increasing these seal’s destabilizing forces and reducing stability margins. These results are consistent with field experience. Predictions concerning the back shroud indicate that shunt-hole injection mainly acts to enhance stability by changing the flow field of the division wall or balance piston seals, not by influencing the back-shroud’s forces or moments. Effective swirl brakes at these seals also serve this purpose.
A Detailed and Reduced Reaction Mechanism of Biomass-Based Syngas Fuels
Authors: Braun-Unkhoff Marina , Slavinskaya Nadezhda , Aigner Manfred
Published: June 2010

In the present work, the elaboration of a reduced kinetic reaction mechanism is described, which predicts reliably fundamental characteristic combustion properties of two biogenic gas mixtures consisting mainly of hydrogen, methane, and carbon monoxide, with small amounts of higher hydrocarbons (ethane and propane) in different proportions. From the in-house detailed chemical kinetic reaction mechanism with about 55 species and 460 reactions, a reduced kinetic reaction mechanism was constructed consisting of 27 species and 130 reactions. Their predictive capability concerning laminar flame speed (measured at T0=323 K, 373 K, and 453 K, at p=1 bar, 3 bars, and 6 bars for equivalence ratios φ between 0.6 and 2.2) and auto ignition data (measured in a shock tube between 1035 K and 1365 K at pressures around 16 bars for φ=0.5 and 1.0) are discussed in detail. Good agreement was found between experimental and calculated values within the investigated parameter range.
Determination of Contact Stiffness of Rod-Fastened Rotors Based on Modal Test and Finite Element Analysis
Authors: Zhang Yanchun , Du Zhaogang , Shi Liming , Liu Shaoquan
Published: June 2010

A series of simplified rod-fastened rotors, which have different surface contact roughness are manufactured and their modal parameters under different pretightening force, are measured in free-free state. The concept of surface contact stiffness is introduced to simulate the influence of pretightening force on modal parameters of these simplified rod-fastened rotors using finite element method. The experiment measured results are compared and fitted to the finite element analysis results and the relationship between contact stiffness and contact stress is established in which the contact stress is defined by the pretightening force. The relationship is then applied on the modal analysis of a real gas turbine rotor, and its modal test results and finite element analysis results are consistent with each other, proving that the relationship and the described determination method of contact stiffness based on modal test and finite element analysis are effective.
Tri-Axial Force Measurements on the Cylinder of a Motored SI Engine Operated on Lubricants of Differing Viscosity
Authors: O’Rourke Bryan , Radford Donald , Stanglmaier Rudolf
Published: June 2010

Friction is a determining factor in the efficiency and performance of internal combustion engines. Losses in the form of friction work typically account for 10–20% of an engine’s output. Improvements in the friction characteristics of the power cylinder assembly are essential for reducing total engine friction and improving the mechanical efficiency of internal combustion engines. This paper describes the development and implementation of a new concept of the “floating liner” engine at Colorado State University that allows 0.5 crank angle deg resolved measurement of the forces on the cylinder along three axes—in the axial direction, the thrust direction, and along the wrist pin. Three different lubricants with differing properties were tested to observe the friction characteristics of each. The experimental results showed that the floating liner engine was able to resolve changes in friction characteristics coinciding with changes in lubricant viscosity and temperature. The axial force increases at TDC and BDC were observed as lubricant viscosity was decreased and larger amounts of mixed and boundary lubrication began to occur. For each test the axial friction force data was used to calculate total cycle friction work. The thrust and off-axis (wrist pin direction) forces are discussed under the same circumstances.
Ethanol-Hydrocarbon Blend Vapor Prediction
Authors: Privat Romain , Jaubert Jean-Noël , Garcia Freddy , Molière Michel
Published: June 2010

In the volatile fuel price environment of today, the quest for alternative fuels has become a heavy and long term trend in power generation worldwide. Incorporating alternative fuels in gas turbine installations raises multiple engineering questions relating to combustion, emissions, on-base and auxiliary hardware capability, safety, etc. In 2008, GE carried out a field test aimed at characterizing the combustion of ethanol in a naphtha fuelled gas turbine plant. The testing strategy has been to locally prepare and burn ethanol-naphtha blends with a fraction of ethanol increasing from 0% to nearly 100%. During the engineering phase prior to this field test, it appeared necessary to develop a sufficient knowledge on the behavior of ethanol-hydrocarbon blends in order to establish the safety analysis and address in particular the risks of (i) potential uncontrolled ignition event in the air blanket of fuel tanks and (ii) flash vaporization of potential fuel pond in a confined environment. Although some results exist in the car engine literature for ethanol-gasoline blends, it was necessary to take into account the specificities of gas turbine applications, namely, (i) the much greater potential ethanol concentration range (from 0% to 100%) and (ii) the vast composition spectrum of naphtha likely to generate a much larger Reid vapor pressure envelope as compared with automotive applications. In order to fulfill the safety needs of this field test, the “Laboratoire de Thermodynamique des Milieux Polyphasés” of Nancy, France has developed a thermodynamic model to approach the vaporization equilibria of ethanol-hydrocarbons mixtures with variable ethanol strength and naphtha composition. This model, named PPR78, is based on the 1978 Peng–Robinson equation of state and allows the estimation of the thermodynamic properties of a multicomponent mixture made of ethanol and naphtha compounds by using the group contribution concept. The saturation equilibrium partial pressure of such fluids in the various situations of relevance for the safety analysis can thus be calculated. The paper reports the elaboration of this model and illustrates the results obtained when using it in different safety configurations.
Properties of Humid Air for Calculating Power Cycles
Authors: Herrmann Sebastian , Kretzschmar Hans-Joachim , Teske Viola , Vogel Eckhard , Ulbig Peter , Span Roland , Gatley Donald P.
Published: June 2010

Accurate calculation algorithms for the thermodynamic and transport properties of humid air are required for modeling compressed air energy-storage power cycles and designing their individual components. The development of such algorithms was part of the Advanced Adiabatic Compressed Air Energy Storage (AA-CAES) project, which had been supported by the European Commission. To obtain the statements of this paper, all available experimental data and new experimental data generated within the AA-CAES project were used as basis for comparisons between the different models for thermodynamic and transport properties. As a result, one model for calculating thermodynamic and one model for transport properties of humid air in AA-CAES cycle design and operation is recommended. Their application is possible for wide ranges of temperature from 243 K up to 2000 K, total pressure from 0.611 kPa up to 100 MPa, and water content up to 10% mass fraction with some restrictions concerning the calculation of viscosity η and thermal conductivity λ (up to 1000 K for both and up to 40 MPa for λ). These models have been implemented into a property library, which meets the requirements of programs for calculating compressed air energy-storage cycles. The developed property library can be used for the daily work of an engineer who calculates such cycles. The results summarized in this paper have been used for preparing Section 6, “Real Gas” of the ASME Report No. STP-TS-012, “Thermophysical Properties of Gases used in Working Gas Turbine Applications.”
Growth Kinetics ofHyphomicrobiumandThiobacillusspp. in Mixed Cultures Degrading Dimethyl Sulfide and Methanol
Authors: Hayes Alexander C. , Liss Steven N. , Allen D. Grant
Published: June 2010

The growth kinetics ofHyphomicrobiumspp. andThiobacillusspp. on dimethyl sulfide (DMS) and methanol (in the case ofHyphomicrobiumspp.) in an enrichment culture created from a biofilter cotreating DMS and methanol were studied. Specific growth rates of 0.099 h−1and 0.11 h−1were determined forHyphomicrobiumspp. andThiobacillusspp., respectively, growing on DMS at pH 7. These specific growth rates are double the highest maximum specific growth rate for bacterial growth on DMS reported to date in the literature. When the pH of the medium was decreased from pH 7 to pH 5, the specific growth rate ofHyphomicrobiumspp. decreased by 85%, with a near 100-fold decline in the yield ofHyphomicrobium16S rRNA gene copies in the mixed culture. Through the same pH shift, the specific growth rate and 16S rRNA gene yield ofThiobacillusspp. remained similar. When methanol was used as a substrate, the specific growth rate ofHyphomicrobiumspp. declined much less over the same pH range (up to 30%) while the yield of 16S rRNA gene copies declined by only 50%. Switching from an NH4+-N-based source to a NO3−-N-based source resulted in the same trends for the specific growth rate of these microorganisms with respect to pH. This suggests that pH has far more impact on the growth kinetics of these microorganisms than the nitrogen source. The results of these mixed-culture batch experiments indicate that the increased DMS removal rates observed in previous studies of biofilters cotreating DMS and methanol are due to the proliferation of DMS-degradingHyphomicrobiumspp. on methanol at pH levels not conducive to high growth rates on DMS alone.
Novel Bifunctional α-l-Arabinofuranosidase/Xylobiohydrolase (ABF3) fromPenicillium purpurogenum
Authors: Ravanal María Cristina , Callegari Eduardo , Eyzaguirre Jaime
Published: June 2010

The soft rot fungusPenicillium purpurogenumgrows on a variety of natural substrates and secretes various isoforms of xylanolytic enzymes, including three arabinofuranosidases. This work describes the biochemical properties as well as the nucleotide and amino acid sequences of arabinofuranosidase 3 (ABF3). This enzyme has been purified to homogeneity. It is a glycosylated monomer with a molecular weight of 50,700 and can bind cellulose. The enzyme is active withp-nitrophenyl α-l-arabinofuranoside andp-nitrophenyl β-d-xylopyranoside with aKmof 0.65 mM and 12 mM, respectively. The enzyme is active on xylooligosaccharides, yielding products of shorter length, including xylose. However, it does not hydrolyze arabinooligosaccharides. When assayed with polymeric substrates, little arabinose is liberated from arabinan and debranched arabinan; however, it hydrolyzes arabinose and releases xylooligosaccharides from arabinoxylan. Sequencing both ABF3 cDNA and genomic DNA reveals that this gene does not contain introns and that the open reading frame is 1,380 nucleotides in length. The deduced mature protein is composed of 433 amino acids residues and has a calculated molecular weight of 47,305. The deduced amino acid sequence has been validated by mass spectrometry analysis of peptides from purified ABF3. A total of 482 bp of the promoter were sequenced; putative binding sites for transcription factors such as CreA (four), XlnR (one), and AreA (three) and two CCAAT boxes were found. The enzyme has two domains, one similar to proteins of glycosyl hydrolase family 43 at the amino-terminal end and a family 6 carbohydrate binding module at the carboxyl end. ABF3 is the first described modular family 43 enzyme from a fungal source, having both α-l-arabinofuranosidase and xylobiohydrolase functionalities.
Molecular Analysis of Two Bacterioferritin Genes,
bfr
α and
bfr
β, in the Model Rhizobacterium
Pseudomonas putida
KT2440
Authors: Chen Shicheng , Bleam William F. , Hickey William J.
Published: June 2010

The model rhizobacterium
Pseudomonas putida
KT2440 and other fluorescent pseudomonads possess two bacterioferritins, Bfrα and Bfrβ. However, the regulatory systems controlling the expression of these genes and the roles of these proteins in iron homeostasis are ill defined. Our studies show that both
bfr
α and
bfr
β were monocistronic: promoter motifs and transcriptional start sites were identified, and Fur boxes and σ
S
-dependent regulatory motifs were absent. The expressions of
bfr
α and
bfr
β were enhanced by iron exposure and were maximal in cells rapidly growing in a high-iron environment. Both
bfr
α and
bfr
β were positively regulated by Fur, and both were expressed independently of adjoining, functionally related genes. The loss of Bfrα or Bfrβ individually resulted in a significant reduction (ca. 17%) in cellular iron levels, and the deletion of both
bfr
α and
bfr
β reduced cellular iron levels by 38% relative to those of the wild type. The mutants varied in their abilities to grow in low-iron medium; while growths (rate and final cell density) of single mutants and the wild type were similar, that of the double mutant was reduced significantly. Mutants lacking Bfrα and/or Bfrβ showed no change relative to the wild type in sensitivity to reactive oxygen species toxicity. Collectively, the data show that while Bfrα and Bfrβ could function independently of each other, an interaction-dependent function cannot be ruled out. Furthermore, regardless of the mechanism, a primary benefit of the bacterioferritins to
P. putida
KT2440 appears to be the enhancement of its survival in the environment by strengthening its tolerance to iron starvation.
Metatranscriptome Analysis of the Human Fecal Microbiota Reveals Subject-Specific Expression Profiles, with Genes Encoding Proteins Involved in Carbohydrate Metabolism Being Dominantly Expressed
Authors: Booijink Carien C. G. M. , Boekhorst Jos , Zoetendal Erwin G. , Smidt Hauke , Kleerebezem Michiel , de Vos Willem M.
Published: June 2010

The human gastrointestinal (GI) tract provides home to a complex microbial community, collectively termed microbiota. Although major efforts have been made to describe the diversity and stability of the microbiota, functional studies have been largely restricted to intestinal isolates and include few community studies. The aim of this study was to explore the
in situ
gene expression of the fecal microbiota and to evaluate the RNA fingerprinting method cDNA-AFLP (cDNA amplified fragment length polymorphism) for this purpose. To this end, cDNA-AFLP analysis of enriched mRNA revealed that two healthy subjects showed highly divergent expression profiles with considerable fluctuations in time. Subsequent excision and sequence determination of bands from the mRNA-enriched profiles resulted in 122 identifiable sequences (transcripts and rRNAs). The classification of retrieved transcripts into functional clusters based on COG (cluster of orthologous genes) annotation showed that most assigned transcripts belonged to the metabolism cluster (26% of all sequences), underlining that even at the very end of the intestinal tract the microbiota is still very active. This study furthermore revealed that cDNA-AFLP is a useful tool to compare gene expression profiles in time in complex microbial communities.
Novel High-Throughput Detection Method To Assess Bacterial Surfactant Production
Authors: Burch Adrien Y. , Shimada Briana K. , Browne Patrick J. , Lindow Steven E.
Published: June 2010

A novel biosurfactant detection assay was developed for the observation of surfactants on agar plates. By using an airbrush to apply a fine mist of oil droplets, surfactants can be observed instantaneously as halos around biosurfactant-producing colonies. This atomized oil assay can detect a wide range of different synthetic and bacterially produced surfactants. This method could detect much lower concentrations of many surfactants than a commonly used water drop collapse method. It is semiquantitative and therefore has broad applicability for uses such as high-throughput mutagenesis screens of biosurfactant-producing bacterial strains. The atomized oil assay was used to screen for mutants of the plant pathogenPseudomonas syringaepv. syringae B728a that were altered in the production of biosurfactants. Transposon mutants displaying significantly altered surfactant halos were identified and further analyzed. All mutants identified displayed altered swarming motility, as would be expected of surfactant mutants. Additionally, measurements of the transcription of the syringafactin biosynthetic cluster in the mutants, the principal biosurfactant known to be produced by B728a, revealed novel regulators of this pathway.
Transcriptomic Responses ofSalmonella entericaSerovars Enteritidis and Typhimurium to Chlorine-Based Oxidative Stress
Authors: Wang Siyun , Phillippy Adam M. , Deng Kaiping , Rui Xiaoqian , Li Zengxin , Tortorello Mary Lou , Zhang Wei
Published: June 2010

Salmonella entericaserovars Enteritidis and Typhimurium are the leading causative agents of salmonellosis in the United States.S.Enteritidis is predominantly associated with contamination of shell eggs and egg products, whereasS.Typhimurium is frequently linked to tainted poultry meats, fresh produce, and recently, peanut-based products. Chlorine is an oxidative disinfectant commonly used in the food industry to sanitize the surfaces of foods and food processing facilities (e.g., shell eggs and poultry meats). However, chlorine disinfection is not always effective, as someS. entericastrains may resist and survive the disinfection process. To date, little is known about the underlying mechanisms of howS. entericaresponds to chlorine-based oxidative stress. In this study, we designed a custom bigenome microarray that consists of 385,000 60-mer oligonucleotide probes and targets 4,793 unique gene features in the genomes ofS.Enteritidis strain PT4 andS.Typhimurium strain LT2. We explored the transcriptomic responses of both strains to two different chlorine treatments (130 ppm of chlorine for 30 min and 390 ppm of chlorine for 10 min) in brain heart infusion broth. We identified 209S. entericacore genes associated with Fe-S cluster assembly, cysteine biosynthesis, stress response, ribosome formation, biofilm formation, and energy metabolism that were differentially expressed (>1.5-fold;P< 0.05). In addition, we found that serovars Enteriditis and Typhimurium differed in the responses of 33 stress-related genes and 19 virulence-associated genes to the chlorine stress. Findings from this study suggest that the oxidative-stress response may renderS. entericaresistant or susceptible to certain types of environmental stresses, which in turn promotes the development of more effective hurdle interventions to reduce the risk ofS. entericacontamination in the food supply.
Inhibition of
Salmonella
Host Cell Invasion by Dimethyl Sulfide
Authors: Antunes L. Caetano M. , Buckner Michelle M. C. , Auweter Sigrid D. , Ferreira Rosana B. R. , Lolić Petra , Finlay B. Brett
Published: June 2010

We show that dimethyl sulfoxide (DMSO) inhibits
Salmonella hilA
expression and that this inhibition is stronger under anaerobiosis. Because DMSO can be reduced to dimethyl sulfide (DMS) during anaerobic growth, we hypothesized that DMS was responsible for
hilA
inhibition. Indeed, DMS strongly inhibited the expression of
hilA
and multiple
Salmonella
pathogenicity island 1 (SPI-1)-associated genes as well as the invasion of cultured epithelial cells. Because DMSO and DMS are widespread in nature, we hypothesize that this phenomenon may contribute to environmental sensing by
Salmonella
.
Rapid Method for Isolation of Desiccation-Tolerant Strains and Xeroprotectants
Authors: Narváez-Reinaldo J. J. , Barba I. , González-López J. , Tunnacliffe A. , Manzanera M.
Published: June 2010

A novel biotechnological process has been developed for the isolation of desiccation-tolerant microorganisms and their xeroprotectants, i.e., compatible solutes involved in long-term stability of biomolecules in the dry state. Following exposure of soil samples to chloroform, we isolated a collection of desiccation-tolerant microorganisms. This collection was screened for the production of xeroprotectants by a variation of the bacterial milking (osmotic downshock) procedure and by a novel air-drying/rehydration (“dry milking”) incubation method. The resultant solutes were shown to protect both proteins and living cells against desiccation damage, thereby validating them as xeroprotectants. Nuclear magnetic resonance (NMR) analytical studies were performed to identify the xeroprotectants; synthetic mixtures of these compounds were shown to perform similarly to natural isolates in drying experiments with proteins and cells. This new approach has biotechnological and environmental implications for the identification of new xeroprotectants of commercial and therapeutic value.
The LysR-Type Virulence Activator AphB Regulates the Expression of Genes in
Vibrio cholerae
in Response to Low pH and Anaerobiosis
Authors: Kovacikova Gabriela , Lin Wei , Skorupski Karen
Published: June 2010

AphB is a LysR-type activator that initiates the expression of the virulence cascade in
Vibrio cholerae
by cooperating with the quorum-sensing-regulated activator AphA at the
tcpPH
promoter on the
Vibrio
pathogenicity island (VPI). To identify the ancestral chromosomal genes in
V. cholerae
regulated by AphB, we carried out a microarray analysis and show here that AphB influences the expression of a number of genes that are not associated with the VPI. One gene strongly activated by AphB is
cadC
, which encodes the ToxR-like transcriptional activator responsible for activating the expression of lysine decarboxylase, which plays an important role in survival at low pH. Other genes activated by AphB encode a Na
+
/H
+
antiporter, a carbonic anhydrase, a member of the ClC family of chloride channels, and a member of the Gpr1/Fun34/YaaH family. AphB influences each of these genes directly by recognizing a conserved binding site within their promoters, as determined by gel mobility shift assays. Transcriptional
lacZ
fusions indicate that AphB activates the expression of these genes under aerobic conditions in response to low pH and also under anaerobic conditions at neutral pH. Further experiments show that the regulation of
cadC
by AphB in response to low pH and anaerobiosis is mirrored in the heterologous organism
Escherichia coli
, is independent of the global regulators Fnr and ArcAB, and depends upon the region of the promoter that contains the AphB binding site. These results raise the possibility that the activity of AphB is influenced by the pH and oxygen tension of the environment.
Target Immunity of the Tn
3
-Family Transposon Tn
4430
Requires Specific Interactions between the Transposase and the Terminal Inverted Repeats of the Transposon
Authors: Nicolas Emilien , Lambin Michaël , Hallet Bernard
Published: June 2010

Specificity of the Tn
4430
target immunity signal was examined by fusing the transposase TnpA to the LacI repressor of
Escherichia coli
. The resulting chimeric proteins failed to impose immunity to DNA targets carrying copies of the
lacO
operator, though they were proficient in
lacO
binding
in vivo
and remained responsive to wild-type immunity conferred by the Tn
4430
inverted repeat end. Intriguingly, the presence of
lacO
repeats within the target was found to strongly influence target site selection by Tn
4430
, but in a LacI-independent manner.
HIGH-FREQUENCY DIELECTRIC BEHAVIOR OF INDIUM AND CHROMIUM SUBSTITUTED Mg–Mn FERRITES
Authors: LAKSHMAN A. , SUBBA RAO P. S. V. , RAO K. H.
Published: June 2010

Dielectric properties such as DC resistivity (ρ), dielectric constant (ε) and dielectric loss factor ( tan δ) have been measured for Mg 0.9 Mn 0.1 In x Fe 2-x O 4 and Mg 0.9 Mn 0.1 Cr y Fe 2-y O 4 at room temperature. The composition dependence of ρ, ε and tan δ and the frequency dependence of ε and tan δ are presented in this paper. The resistivity increases while the dielectric constant decreases with increasing concentrations of indium and chromium ions. The dielectric loss factor at 100 kHz increases with composition for the samples 0.1 ≤ x ≤ 0.9 and 0.1 ≤ y ≤ 0.7. The dielectric constant for a given sample decreases with increasing frequency showing the normal dielectric behavior. The values of dielectric loss factor have been found to increase with frequency for the samples corresponding to x or y = 0.1 to 0.5; while other samples showed abnormal dielectric behavior. The observed variations in ρ are explained by Verwey's hopping mechanism while the variations in ε and tan δ with composition and frequency are explained by space charge polarization using Koop's theory. Higher values of DC resistivity and low dielectric losses suggest that the prepared materials have great potential for microwave and high-frequency applications.
Unusual Band-Edge Photoluminescence Intensity Emitted by Cu-Diffused Silicon Crystals
Authors: Nakamura Minoru , Murakami Susumu
Published: June 2010

Band-edge photoluminescence (BDE-PL) intensities of Czochralski (Cz) and float-zone (FZ)-grown silicon crystals diffused with Cu were observed from room temperature (RT) to 4.2 K. In contrast to the behavior of ordinary transition metals, unexpected enhancements of the BDE-PL intensities of both Cz and FZ samples were observed at RT in an appropriate Cu concentration range. For the observation temperature of 77 K, however, while the BDE-PL intensity of the Cz sample increased following the same trend as that observed at RT, the intensity of the FZ sample abruptly decreased given the same Cu concentration range as that of the Cz sample. The marked difference in the BDE-PL intensities between Cz and FZ samples was also observed with the change in the diffusion temperature of Cu. These unusual BDE-PL intensities were well explained on the basis of two competitive actions of Cu: the intensity enhancement due to surface passivation by Cu and the intensity reduction caused by a deep-level Cu center formed in the bulk.
Investigation for (100)-/(001)-Oriented Pb(Zr,Ti)O3 Films Using Platinum Nanofacets and PbTiO3 Seeding Layer
Authors: Matsuo Hirokazu , Kawai Yusuke , Tanaka Shuji , Esashi Masayoshi
Published: June 2010

The (100)-/(001)-oriented Pb(Zr,Ti)O3 films using Pt nanofacets and PbTiO3 seeding layer were invesigated. The Ti/Pt electrodes were deposited using a sputtering system. Pb(Zr,Ti)O3 and PbTiO3 seeding layer were deposited using a semi-homemade metal organic chemical vapor deposition (MOCVD) apparatus. The Pt nanofacets on hillocks caused by Ti diffusion and compressive stress can be prepared by preannealing of the electrode on the substrate. The most highly (100)-/(001)-oriented Pb(Zr,Ti)O3 films were obtained with the same thickness deposition of the PbTiO3 seeding layer as the half value of maximum roughness (Rz) of the Pt surface, which is approximately 3.5–4.0 nm. A simple (100)/(001) orientation method was developed without any special oxide metal electrodes or single-crystal substrates for orientation using commonly unpreferable hillocks, which cause the problems. This simple method is suitable for commercial applications in the future.
Observation of Complex Optical Processes in ZnSe under Extreme Optical Excitation from a Kilojoule-Class Nd:Glass Laser
Authors: Nakazato Tomoharu , Furukawa Yusuke , Shimizu Toshihiko , Cadatal-Raduban Marilou , Estacio Elmer , Sarukura Nobuhiko , Shiroshita Akiyuki , Otani Kazuto , Kadono Toshihiko , Shigemori Keisuke , Azechi Hiroshi
Published: June 2010

In this paper, we report on three-photon fluorescence and the possible observation of other complex optical processes in a ZnSe crystal for a kilojoule-class, 100 ps pulse, Nd:glass laser excitation. The emission properties of the ZnSe crystal and its excitation energy dependence were investigated under low and high-energy excitations. A 15 to 10 nm full width at half maximum (FWHM) spectral collapse, a 5 nm blue shift, and a shortened lifetime of fluorescence under high-energy excitation could indicate an amplified spontaneous emission. These findings present the feasibility of investigating the dynamics and spectral properties of three-photon fluorescence and other complex nonlinear optical processes in ZnSe at an extremely high excitation energy.
Characterization of Electronic Charged States of Impurity Doped Si Quantum Dots Using Atomic Force Microsope/Kelvin Probe Technique
Authors: Makihara Katsunori , Miyazaki Seiichi
Published: June 2010

Boron and phosphorous were doped into Si quantum dots (Si-QDs) by pulse injection of 1% B2H6 and PH3 diluted with He, respectively, during the self-assembling formation of Si-QDs from the thermal decomposition of pure SiH4 on a ∼4.2-nm-thick SiO2 layer thermally grown on a n+-Si(100) substrate. Electron charging and discharging of both the B- and P-doped Si-QDs were investigated to characterize their charged states by a Kelvin probe technique with a Rh-coated atomic force microscope (AFM) tip. Potential changes due to the extraction of one electron from the B- and P-doped Si-QDs were observed in applying the AFM tip biases of +2.0 and +0.2 V, respectively. At a tip bias of ∼1.0 V, potential changes observed in the case of undoped Si-QDs, whose size is almost the same as that of doped Si-QDs, were almost the same as those observed in the case of doped Si-QDs. Changes in the tip bias required for the electron extraction from Si-QDs by doping of B and P atoms are attributable to the difference in the electron emission process such that the emissions of a localized electron from an ionized B acceptor and a conduction electron caused by an ionized P donor need higher and lower tip biases than for the case of emission of a valence electron from undoped Si-QDs, respectively.
Micro- and Nano-Scale Fabrication of Fluorinated Polymers by Direct Etching Using Focused Ion Beam
Authors: Fukutake Naoyuki , Miyoshi Nozomi , Takasawa Yuya , Urakawa Tatsuya , Gowa Tomoko , Okamoto Kazumasa , Oshima Akihiro , Tagawa Seiichi , Washio Masakazu
Published: June 2010

Micro- and nano-scale fabrications of various fluorinated polymers were demonstrated by direct maskless etching using a focused ion beam (FIB). The etching rates of perfluorinated polymers, such as poly(tetrafluoroethylene) (PTFE), poly(tetrafluoroethylene-co-hexafluoropropylene) (FEP), poly(tetrafluoroethylene-co-perfluoroalkoxyvinylether) (PFA), were about 500–1000 times higher than those of partially fluorinated polymers, such as poly(tetrafluoroethylene-co-ethylene) (ETFE) and poly(vinilydene–fluoride) (PVdF). Controlled high quality and high aspect-ratio nanostructures of spin-coated cross-linked PTFE were obtained without solid debris. The height and diameter of the fibers were about 1.5 µm and 90 nm, respectively. Their aspect ratio was about 17.
Immersion-Specific Defects of High-Receding-Angle Topcoat
Authors: Terai Mamoru , Kumada Teruhiko , Hagiwara Takuya , Hanawa Tetsuro , Ando Tomoyuki , Matsunobe Takeshi , Okada Kazuyuki , Muraji Yuichi , Yoshikawa Kazuhiro , Man Naoki
Published: June 2010

Dynamic receding contact angle (RCA) is a well-known parameter for estimating the degree of immersion-specific defects that have mainly circular and bridge shapes. In general, these defects decrease in number with increasing RCA of the topcoat (TC). However, we found the occurrence of circular defects despite using the TC with a large RCA. In this study, we analyzed the relationship between the physical properties of TC to reduce the number of defects. The result shows that the number of defects depends not only on a large RCA but also on a small amount of water uptake of TC. To understand well the degree of defects, the effective hysteresis (EH) is defined in terms of the RCA, the advancing contact angle (ACA) and the water absorption of TC. EH will be a useful way of explaining the circular defects. The characteristics of the defects are also discussed with a focus on the structure of the polymer attached to water.
Reconstruction of Latent Images from Dose-Pitch Matrices of Line Width and Edge Roughness of Chemically Amplified Resist for Extreme Ultraviolet Lithography
Authors: Kozawa Takahiro , Oizumi Hiroaki , Itani Toshiro , Tagawa Seiichi
Published: June 2010

The line width and line edge roughness (LER) of resist patterns are related to the concentration and its gradient of chemical compounds that determine the solubility of the resist, respectively. Therefore, latent images can be obtained from the line width and LER of resist patterns. In this study, two-dimensional (exposure dose and half-pitch) matrices of resist line width and LER were analyzed on the basis of the sensitization mechanisms of chemically amplified resists used for extreme ultraviolet (EUV) lithography. In the reconstruction of latent images, the effective reaction radius for catalytic chain reaction is an important parameter. The probable range of effective reaction radius was from 0.05 to 0.2 nm. In this range, latent images were successfully reconstructed. The finding that the effective reaction radius is smaller than the typical size of a counteranion suggests that the resist performance can be improved by increasing the effective reaction radius.