bluuebunny/crossref_metadata_2025 huggingface dataset:
ALARP Principle and Design
Authors: Trbojevic Vladimir M.
Published: March 2009

The safety framework in most of the industries is based on some kind of goal setting principle, where the safety goals are postulated and not the means of achieving those. This framework has the advantage over the old prescriptive approach to safety, since it not only allows innovation but also encourages more efficient design. The important aspects of goal setting approach is a method (risk criteria) by which the results of a risk analysis can be interpreted in terms of recommendations on the tolerability of the overall facility risk and the optimum design, and the extent to which taking further measures to improve the design and reduce the risk may be justified. In other words, risk criteria should not just drive the risk to the level which is as low as practicable, but should also inspire a designer to seek an optimum design. One such “method” is embodied in the Tolerability Doctrine in the UK in form of the ALARP Principle. This paper sets to explore the ways in which the application of ALARP Principle facilitate search for an optimum design.
A Design Approach for Storage Spar Buoy Platforms in the Concept and Preliminary Design Phases
Authors: Schachter Richard David , Jordani Carlos Gomes , Fernandes Antonio Carlos
Published: March 2009

The objective of this work is to present a design approach for the Concept and Preliminary Design Phases of Storage SPAR Buoy Platforms and to describe how the design method was developed. The influence of a VIV porosity device on the design is taken into consideration. The inherent advantages of Spar concepts for Petrobras’ applications for 1250 m, are discussed and compared with other concepts. The Spar concept was chosen. The design method development was carried out by means of a brainstorming process, using sketches and the creation of interactive flowcharts of the design processes (similar to a design spiral) comprising the main design factors, their sequencing and interrelations, for both the Concept and Preliminary Design phases. The intent of the design approach is to provide the designer with means to define quick and efficiently the optimal hull dimensions for a pre-established scenario. For the Concept Design, the method includes the definition of the main dimensions, the Wellbay, the structural topology and compartmentation, general arrangement, weight control, stability (intact, damaged and flooded), motions and mooring. A discussion on the influence of the VIV porosity device on the dimensioning and mooring of the Spar Platform is provided. A concept design application example is presented.
Hydrogen Absorption in Cathodically Polarized Titanium Alloys
Authors: Seiersten Marion , Eggen Tor Gunnar , Lunde Liv , Rogne Trond
Published: March 2009

Cathodic polarisation may cause hydrogen absorption and embrittlement of titanium alloys. There is no need to protect titanium in seawater, but polarisation is inevitable when titanium components are connected to steel that is cathodically protected. The risk of hydrogen embrittlement of risers and other heavily loaded components rouse a need to quantify the amount of hydrogen that titanium alloys may absorb as a function of alloy composition, polarisation potential, temperature, cold working and time. The test program included Ti-3Al-2.5V and Ti-6Al-4V alloys that are candidate materials for risers. The hydrogen uptake was measured over a 3 years period in natural seawater. The results show that titanium absorbs hydrogen when it is polarised to potentials less than −0.8V vs. Ag/AgCl in seawater, but the absorption rate decreased with time. The maximum hydrogen loading measured after three years exposure at −1.04 V vs. Ag/AgCl was 150 ppm. A calcareous deposit built up on all surfaces and limited the hydrogen evolution and thereby the hydrogen uptake. Ti-3Al-2.5V alloys picked up less hydrogen than Ti-6Al-4V alloys, and palladium or ruthenium enhanced hydrogen uptake to some extent. Welding or cold working did not influence hydrogen uptake of the alloys included in the tests. Temperature had little effect, and thermal gradients in the titanium materials had no measurable influence. The effect of hydrogen on the mechanical properties of the alloys was not studied in detail in these experiments, but most specimens were tensioned C-rings with permanent strain. Neither of these developed cracks or other signs of embrittlement during the tests.
Dynamic Propagation and Arrest of Buckles in Pipe-in-Pipe Systems
Authors: Kyriakides Stelios , Netto Theodoro A.
Published: March 2009

This paper deals with the problem of buckle propagation and arrest in pipe-in-pipe systems. A recent experimental study illustrated that if the geometric integrity of the carrier pipe is compromised, local collapse can result. In a pressure controlled environment such as that encountered in the sea, collapse will propagate dynamically usually collapsing both pipes. A new buckle arrestor consisting of a ring placed inside the annulus between the two pipes has been proposed. A methodology for designing such rings has been developed based on quasi-static buckle propagation and arrest experiments. Here we evaluate experimentally the adequacy of this design methodology under the more realistic case of dynamic buckle propagation. This is achieved by initiating collapse in a constant pressure environment similar to that encountered on the sea floor. The study involves first establishing the effect of the presence of the inner pipe on the velocity of buckles initiated at various external pressures ranging between the propagation pressure of the two-pipe system and the collapse pressure of the carrier pipe. Subsequently, the arresting efficiency of several internal ring buckle arrestors designed by the quasi-static criteria developed is established for buckles travelling at high velocities. Details of the experimental procedures used are presented along with the experimental results and discussion of their implications in practice.
The Effects of Stress Redistribution Due to Member Failure on Structural Reliability of Offshore Steel Jackets
Authors: Nelson A. , Sanderson D. J. , Stacey A.
Published: March 2009

Current practice in providing structural integrity assurance of North Sea Steel Jacket structures relies upon periodic inspection of the sub-structures, with FMD being the preferred method of inspection. The time period between inspections, when employing FMD is dependent upon the structure’s level of redundancy. However, little, if any, consideration is given to the effect a failed member has on the stress distribution within the structure and the probability of a second member failing. A study has been completed that investigated the impact of stress redistribution following failure of a member. The study has considered the impact this has on fatigue lives of adjacent members/joints, and ultimately the impact on structural reliability. The findings from this study suggest that for the type of structures considered, the justification for a given inspection schedule should take due account of the impact of stress redistribution and the possibility that a structure might experience a second member failure during an inspection interval.
Influence of the bias voltage on the structure and mechanical performance of nanoscale multilayer CrAlYN∕CrN physical vapor deposition coatings
Authors: Sáfrán G. , Reinhard C. , Ehiasarian A. P. , Barna P. B. , Székely L. , Geszti O. , Hovsepian P. Eh.
Published: February 2009

The effects of bias voltage on the microstructure and the related tribological properties of CrAlYN∕CrN nanoscale multilayer superlattice coatings were investigated. The coatings were deposited at 450°C substrate temperature by combined high power impulse magnetron sputtering (HIPIMS) and unbalanced magnetron sputtering techniques. The substrates were 304 stainless steel, M2 high speed steel for structural analysis and mechanical testing, as well as cemented carbide substrates end mills for dry high speed milling applications. Substrates were pretreated by HIPIMS etching. The bias voltage Ub was varied between −75 and −150V. The chemical composition was determined by neutral mass spectroscopy. The microstructure was characterized by x-ray diffraction and cross sectional transmission electron microscopy. All coatings had a single phase B1 fcc structure. The chemical composition was not affected by the bias voltage. Local epitaxial or axiotaxial growth attributed to the HIPIMS etching pretreatment was observed on the large surface areas of the substrate crystals. This turned to columnar growth with {110} texture at low bias voltages Ub between −75 and −120V, while at Ub=−150V an equiaxed structure of large crystal sizes developed with {111} texture. At the same time the waviness of the superlattice significantly decreased. An increase in bias voltage resulted in a significant rise in both residual stress levels (from −3.3to−9.5GPa) and plastic hardness (from Hp=34–51GPa), while the coating/substrate adhesion decreased from 61to45N. The friction coefficient increased from 0.43 (at Ub=−75V) to 0.55 (at UB=−120V), while the initial sliding wear rates decreased remarkably (2.6×10−16m3N−1m−1 at UB=−75V to 3.7×10−17m3N−1m−1 at Ub=−150V). The life time of 8mm ball-nosed cemented carbide end mills decreased from 39min at Ub=−75V to 19min when Ub was raised to −150V. These results highlight that the combination of HIPIMS substrate treatment and designed deposition parameters provides good opportunity to tailor coating structures with optimized properties.
Plasma etching of Hf-based high-k thin films. Part III. Modeling the reaction mechanisms
Authors: Martin Ryan M. , Chang Jane P.
Published: February 2009

A generalized etch rate model was formulated to describe metal oxide etching in complex plasma chemistries, based on the understanding gained from detailed plasma characterization and experimental investigation into the metal oxide etching mechanisms. Using a surface site balance-based approach, the correct etch rate dependencies on neutral-to-ion flux ratio, ion energy, competing deposition and etching reaction pathways, and film properties were successfully incorporated into the model. The applicability of the model was assessed by fitting to experimental etch rate data in both Cl2 and BCl3 chemistries. Plasma gas phase analysis as well as etch and deposition rate measurements were used to calculate initial values and appropriate ranges for model parameter variation. Physically meaningful parameter values were extracted from the modeling fitting to the experimental data, thereby demonstrating the applicability of this model in assessing the plasma etching of other complex materials systems.
Growth modes in metal-organic molecular beam epitaxy of TiO2 on r-plane sapphire
Authors: Jalan Bharat , Engel-Herbert Roman , Cagnon Joël , Stemmer Susanne
Published: February 2009

Phase pure, epitaxial (101) rutile TiO2 films were grown on (012) sapphire substrates at temperatures between 485 and 725 °C using metal-organic molecular beam epitaxy with titanium tetraisopropoxide as the Ti source. Growth modes and rates were investigated as a function of substrate temperature using reflection high-energy electron diffraction, x-ray reflectivity, atomic force microscopy, and transmission electron microscopy. Growth rates were as high as 125 nm/h. The influence of additional oxygen supplied from a rf plasma source was investigated. Without oxygen plasma, the growth rate exhibited reaction and flux-limited regimes and layer-by-layer growth was observed in the initial stages of film growth. With oxygen plasma the growth rate became independent of temperature; films grew initially in step-flow mode and were insulating. The mechanisms for the different growth modes as a function of film thickness, temperature, and presence of oxygen are discussed.
Correlation of chemical composition and electrical properties of rf sputtered alumina films
Authors: Voigt M. , Bergmaier A. , Dollinger G. , Sokolowski M.
Published: February 2009

Alumina films were prepared by radio frequency magnetron sputtering from an aluminum oxide target on an indium tin oxide covered glass. The purpose of the study was to test the influence of the sputter parameters on the elemental composition, surface morphology, and electrical insulation properties (breakdown fields and leakage currents). Tested parameters were the sputter gas (Ar) pressure, the sputter rate, the sputter power, the sputter gas composition (Ar:O2), the conditioning of the target, the residual base pressure, and the substrate temperature. The surface morphology of the films was investigated by atomic force microscopy. Depth profiles of the elemental compositions were measured by elastic recoil detection using energetic heavy ions, and the insulation properties were investigated by current voltage measurements and impedance spectroscopy. The main finding is that the leakage currents increase by about five orders of magnitude, if the atomic ratio of O:Al increases from 1.35 to 2.0. In parallel the breakdown fields decrease by a factor of 100, and the character of the breakdowns changes from soft to hard. The highest breakdown fields (2.4MV∕cm) and smallest leakage currents (6.5×10−8A∕cm2 at 2.0MV∕cm) are obtained for slightly Al rich films with small atomic concentrations of H (<0.5at.%). These films were sputtered in pure Ar and under the lowest possible pressure of the residual gas.
Energy scaling of the ion-induced desorption yield for perpendicular collisions of Ar and U with stainless steel in the energy range of 5 and 100MeV∕u
Authors: Kollmus H. , Krämer A. , Bender M. , Bellachioma M. C. , Reich-Sprenger H. , Mahner E. , Hedlund E. , Westerberg L. , Malyshev O. B. , Leandersson M. , Edqvist E.
Published: February 2009

For the GSI future project Facility for Antiproton and Ion Research a beam intensity of 1012U28+ions∕s is planned to be extracted from the GSI heavy ion synchrotron SIS18. Measurements performed in 2001 showed that the beam lifetime of the ions in the synchrotron is decreasing with increasing number of injected particles due to vacuum instabilities caused by ion-induced desorption. The injection energy for the SIS18 is about 10MeV∕u and U28+ ions are accelerated to 200MeV∕u limited by the magnetic rigidity for the low charge state. The aim of this work was to measure the desorption yield as a function of the impact energy from injection to extraction of SIS18 at GSI. Low energy yields at 5.0, 9.7, and 17.7MeV∕u were measured at the Cyclotron of The Svedberg Laboratory in Uppsala. High energy yields at 40, 80, and 100MeV∕u were measured at SIS18 of GSI in a different setup. It was found that the desorption yield scales with the electronic energy loss (dE∕dx)eln, with n between 2 and 3, decreasing for increasing impact energy above the Bragg maximum.
Test particle simulation of the role of ballistic electrons in hybrid dc/rf capacitively coupled CF4 plasmas
Authors: Ventzek P. L. G. , Denpoh K.
Published: February 2009

Hybrid dc/rf plasma sources are an emerging equipment technology in plasma etching for semiconductor manufacturing. In this type of plasma source, ballistic electrons originate as secondary electrons on a dc/rf (i.e., VHF, 60MHz) biased electrode and are then accelerated in the sheath toward an opposite non-dc biased lower electrode. For electropositive (argon) plasmas it has been shown that the primary contribution of ballistic electrons is ionization in the dc sheath and modulation of the discharge properties. Whether applied dc power net increases or decreases the plasma electron density depends on the rf power environment of the opposing substrate electrode. When rf power is applied to a substrate electrode, the rf self-bias creates a potential well that traps the ballistic electrons, the result being that the electron density increases with dc power. In most cases the fraction of high energy electrons that reach the electrode is small. In this article, the authors describe the use of test particle Monte Carlo simulations to describe the behavior of hybrid dc/rf electronegative (CF4) plasmas. In contrast to the behavior in argon, process experiments with electronegative gases such as CF4 indicate that the electron density is independent of dc bias power when no rf power is applied to the wafer. Test particle simulations show that CF4 provides for a “self-confinement” effect caused by large cross sections for vibrational excitation at intermediate to low electron energies, which results in weak dependence of electron density on dc bias voltage when low frequency bias is not applied to the wafer. This emphasizes the important role of gas composition and cross-section structure in the control of dc/rf plasmas. Consistent with experiment, test particle Monte Carlo simulations also show that when rf is applied to the substrate, overall the CF4 plasma’s macroscopic properties are similar manner to argon plasmas. Even so, differences between the argon and CF4 plasmas occur related to the scaling of the fraction of ballistic electrons that reach the wafer as a function of dc and rf power. A regime is identified in which CF4 and argon plasmas have the equivalent ratio of ballistic to thermal electron density adjacent to the surface. The authors explain that the differences are related to different thermalization and ionization mechanisms in these plasmas. In addition, they find the electron attachment constant is zero in the dc sheath and nearly constant value in the bulk as the transit time in the sheath is far less than the mean attachment time. The same simple function to express ionization rate constant as a function of electric field in the dc sheath, developed for argon, can be also applied to CF4.
Elimination of pillar associated with micropipe of SiC in high-rate inductively coupled plasma etching
Authors: Okamoto Naoya
Published: February 2009

Pillar formation in SiC via holes fabricated by inductively coupled plasma etching at a high etch rate in the order of around 2 μm/min using SF6/O2 was studied by comparing samples etched under different thermal conductivity conditions from wafer to carrier. As a result, it was found that the formation of pillars is attributed to a process in which the origin of micropipes acts as a micromask and is passivated with nonvolatile and difficult-to-etch products of NiSiF, which are generated by a chemical combination of the etched Ni from the metal mask and the formed SiFX species during etching. Furthermore, the optimization of etching conditions to eliminate the pillars in SiC via holes with minimal microtrenches was accomplished at a high etch rate of 2 μm/min and high selectivity over 100 for Ni.
Optimal design of antireflection coating and experimental verification by plasma enhanced chemical vapor deposition in small displays
Authors: Yang S. M. , Hsieh Y. C. , Jeng C. A.
Published: February 2009

Conventional antireflection coating by thin films of quarter-wavelength thickness is limited by material selections and these films’ refractive indices. The optimal design by non-quarter-wavelength thickness is presented in this study. A multilayer thin-film model is developed by the admittance loci to show that the two-layer thin film of SiNx/SiOy at 124/87 nm and three layer of SiNx/SiNy/SiOz at 58/84/83 nm can achieve average transmittances of 94.4% and 94.9%, respectively, on polymer, glass, and silicon substrates. The optimal design is validated by plasma enhanced chemical vapor deposition of N2O/SiH4 and NH3/SiH4 to achieve the desired optical constants. Application of the antireflection coating to a 4 in. liquid crystal display demonstrates that the transmittance is over 94%, the mean luminance can be increased by 25%, and the total reflection angle increased from 41° to 58°.
The direct injection of liquid droplets into low pressure plasmas
Authors: Ogawa D. , Saraf I. , Sra A. , Timmons R. , Goeckner M. , Overzet L.
Published: February 2009

A much greater number of useful precursors for plasma-enhanced chemical vapor deposition (PECVD) can be dispersed in high vapor pressure solvents than can be put into the vapor phase directly. In order to enable the use of such precursors, the authors investigated a method by which one can directly inject these liquids as microdroplets into low pressure PECVD environments. The solvent evaporates first leaving behind the desired precursor in the gas/plasma. The plasma dissociates the vapor and causes the deposition of a composite film (from precursor, solvent, and plasma gas). The authors made preliminary tests using Fe nanoparticles in hexane and were able to incorporate over 4% Fe in the resulting thin films. In addition, the authors simulated the process. The time required for a droplet to fully evaporate is a function of the background pressure, initial liquid temperature, droplet-vapor interactions, and initial droplet size. A typical evaporation time for a 50μm diameter droplet of hexane is ∼3s without plasma at 100mTorr. The presence of plasma can decrease the evaporation time by more than an order of magnitude. In addition, the model predicts that the temperature of the injected droplet first decreases by evaporative cooling (to ∼180K for hexane); however, once the solvent has fully evaporated/sublimated, the plasma heats any remaining solute. As a result the solute temperature can first fall to 180K, then rise to nearly 750K in less than 1s.
Velocity distribution function of sputtered gallium atoms during inductively coupled argon plasma treatment of a GaAs surface
Authors: Despiau-Pujo Emilie , Chabert Pascal , Ramos Raphaël , Cunge Gilles , Sadeghi Nader
Published: February 2009

A GaN laser diode at 403.3nm is used to measure the velocity distribution function (vdf) of Ga atoms sputtered from a radio-frequency biased GaAs substrate in a low pressure inductively coupled plasma (ICP) argon discharge. To investigate both perpendicular (Vz normal to wafer) and longitudinal (Vx parallel to wafer) velocity components, laser induced fluorescence (LIF) measurements are performed in the z direction and atomic absorption spectroscopy (AAS) in the x direction. The longitudinal vdf of Ga sputtered atoms is very close to a Lorentzian function with Vx comprised between 0 and 7500ms−1, while the perpendicular velocities Vz can reach 10000ms−1. Experimental results are compared to molecular dynamics (MD) simulations of Ar+ ion sputtering of GaAs under 200eV bombardment. MD predictions and experiments are in fairly good agreement, which confirms the existence of products sputtered from the surface with kinetic energies larger than 10eV. In etching processes dominated by physical bombardment, these energetic atoms could alter passivation layers on sidewalls and be responsible for defects observed in nanodevices. The best fit of the Doppler-broadened LIF and AAS profiles with the vdfs predicted by sputtering theory allows one to estimate the surface binding energy of Ga atoms in GaAs, Eb, to be around 3eV.
Hydrogen mediated transport of Sn to Ru film surface
Authors: Faradzhev Nadir , Sidorkin Vadim
Published: February 2009

The authors report on the interaction of atomic hydrogen with Sn and thin Ru film at room temperature. The study is done using a combination of photoelectron and low energy ion scattering spectroscopies as well as scanning electron microscopy. The adsorption of hydrogen on a Sn surface leads to the formation of stannane (SnH4), which dissociatively adsorbs on the surface of polycrystalline Ru film. In the range of effective Sn coverages studied (up to 1 ML), the resulting overlayer consists of randomly distributed three-dimensional islands with average size below 40 nm occupying up to several percent of the surface area. Nucleation of Sn is observed presumably at defect sites (e.g., grain boundaries). Ion scattering data are found consistent with Volmer–Weber growth mode: no initial transition wetting layer formation is detected. Oxidation of Sn islands on a Ru surface at room temperature results in the formation of SnO. Neither metallic nor oxidation states of Sn higher than Sn2+ are observed by photoelectron spectroscopy.
Activation and measurement of nonevaporable getter films
Authors: Malyshev O. B. , Middleman K. J. , Colligon J. S. , Valizadeh R.
Published: February 2009

An experimental setup for studying the pumping and capacity properties of nonevaporable getter (NEG)-coated films has been designed and built in the ASTeC Vacuum Science Laboratory at Daresbury Laboratory. The measurement system is based on the dynamic expansion method with a gas injection system that is capable of injecting the residual gases present in a typical UHV system, such as H2, CO, CO2, and CH4. The test particle Monte Carlo model was used for accurate evaluation of NEG film sticking probability from the pressure reading during gas injection. The experimental measurements with NEG-coated samples have shown that the NEG film can be poisoned during the NEG film activation (and/or regeneration) by molecules of CO and CO2 desorbed from uncoated parts of the vacuum chamber. The effect of NEG film poisoning was reduced by lowering the temperature of the uncoated parts of the vacuum chamber during the NEG film activation and, as a result, a new activation procedure was developed for vacuum systems containing NEG-coated parts.
Oxygen incorporation and charge donor activation via subplantation during growth of indium tin oxide films
Authors: Amassian A. , Dudek M. , Zabeida O. , Gujrathi S. C. , Klemberg-Sapieha J. E. , Martinu L.
Published: February 2009

The use of plasma assistance is shown to enhance the optoelectronic properties (i.e., transparency, free carrier density, and conductivity) of indium tin oxide (ITO) deposited by reactive magnetron sputtering by promoting the incorporation of oxygen in substoichiometric oxide films during magnetron sputtering. The authors demonstrate that subplantation of oxygen ions (O2+ and O+), i.e., their implantation to depths of several nanometers below the growth surface, is the primary pathway by which radio frequency plasma assistance at the substrate surface enhances oxygen incorporation during reactive magnetron sputtering of ITO. These conclusions are supported independently by elastic recoil detection measurements of ITO films in the time-of-flight regime and Monte Carlo TRIDYN simulations of oxygen ion bombardment in the reactive low-pressure plasma environment. The findings indicate that subplantation plays a crucial role in improving the optoelectronic properties of O-deficient ITO films.
Vacuum outgassing of high density polyethylene
Authors: Dinh L. N. , Sze J. , Schildbach M. A. , Chinn S. C. , Maxwell R. S. , Raboin P. , McLean W.
Published: February 2009

A combination of thermogravimetric analysis and temperature programmed decomposition was employed to identify the outgassing species, the total amount of outgassing, and the outgassing kinetics of high density polyethylene (HDPE) in a vacuum environment. The isoconversional kinetic analysis was then used to analyze the outgassing kinetics and to predict the long-term outgassing of HDPE in vacuum applications at ambient temperature. H2O and CnHx, with n as high as 9 and x centering around 2n, are the major outgassing species from solid HDPE, but the quantities evolved can be significantly reduced by vacuum baking at 368K for a few hours prior to device assembly.
Mixing-layer kinetics model for plasma etching and the cellular realization in three-dimensional profile simulator
Authors: Guo Wei , Bai Bo , Sawin Herbert H.
Published: February 2009

In this article the major kinetics models for plasma-surface interactions were reviewed highlighting their strengths and limitations. As a subset of reactive-site modeling, mixing-layer kinetics model was developed based upon the assumption of random atomic mixing in the top surface layer. The translation of the layer enabled the modeling of both etching and deposition. A statistical concept, nearest-neighbor bonding probability, was defined to express the concentration of any surface moieties with the surface elemental composition. A lumped set of reactions was adopted to carry on the overall physichemical processes including ion incorporation, neutral adsorption, physical sputtering, ion-enhanced etching, dangling bond generation and annihilation, and spontaneous etching. The rate coefficients were fitted to the experimental etching yields at various beam etching conditions. The good match between the kinetics modeling and the experimental results verified the capability of the mixing-layer model of predicting the poly-Si etching in chlorine plasma at various operating conditions. Then the kinetics model was incorporated into the three-dimensional Monte Carlo profile simulator. The concept of the mixing layer was simulated by a cellular-based model through composition averaging among neighboring cells. The reactions were sorted out in terms of ion initiated and neutral initiated, respectively, as discrete events. The reaction rates were calculated based upon the cellular composition and used as probabilities to remove particles from the cell. Results showed that the profile simulation combined with the kinetics, the numeric kinetics model, and the experimental etching yields are in quantitative agreement, which demonstrated the accuracy of kinetics after incorporation into the profile simulation. The simulation was compared to the published research work comprehensively including the etching yields, surface compositions, and dominant product distributions.
Effect of a competing instrument on melodic contour identification by cochlear implant users
Authors: Galvin John J. , Fu Qian-Jie , Oba Sandra I.
Published: March 2009

Cochlear implant (CI) users have limited access to fundamental frequency (F0) and timbre cues, which are needed to segregate competing voices and/or musical instruments. In the present study, CI users’ melodic contour identification was measured for three target instruments in the presence of a masker instrument; the F0 of the masker was varied relative to the target instruments. Mean CI performance significantly declined in the presence of the masker, while mean normal-hearing performance was largely unaffected. However, the most musically experienced CI users were able to make use of timbre and F0 differences between instruments.
Quantifying sound-field diffuseness in small rooms using multifractals
Authors: Loutridis S. J.
Published: March 2009

With the aim of quantifying sound-field uniformity in spaces of relatively low volume, four different configurations in terms of acoustic treatment and sound-field diffuseness were constructed and tested. In a diffuse sound field, reflections are not strongly correlated both to the original sound and to earlier reflections. The degree of correlation is embedded in the impulse response structure, but is not trivial to identify. The room impulse responses exhibit self-similarity and therefore may be treated as multifractal signals characterized by a singularity spectrum. The singularity spectrum contains a wealth of information about the acoustic field established in the room. The width of the singularity spectrum, in particular, is directly related to the complexity of the impulse response structure. The uniformity of the sound field in the room can be evaluated by examining the variation of the singularity spectra with position. A new definition for sound field diffuseness is given that is not based on the concept of the energy density. The proposed method is simple to apply, statistically robust, and provides a measure of diffusion independent of the room reverberation.
Multisensory integration enhances phonemic restoration
Authors: Shahin Antoine J. , Miller Lee M.
Published: March 2009

Phonemic restoration occurs when speech is perceived to be continuous through noisy interruptions, even when the speech signal is artificially removed from the interrupted epochs. This temporal filling-in illusion helps maintain robust comprehension in adverse environments and illustrates how contextual knowledge through the auditory modality (e.g., lexical) can improve perception. This study investigated how one important form of context, visual speech, affects phonemic restoration. The hypothesis was that audio-visual integration of speech should improve phonemic restoration, allowing the perceived continuity to span longer temporal gaps. Subjects listened to tri-syllabic words with a portion of each word replaced by white noise while watching lip-movement that was either congruent, temporally reversed (incongruent), or static. For each word, subjects judged whether the utterance sounded continuous or interrupted, where a “continuous” response indicated an illusory percept. Results showed that illusory filling-in of longer white noise durations (longer missing segments) occurred when the mouth movement was congruent with the spoken word compared to the other conditions, with no differences occurring between the static and incongruent conditions. Thus, phonemic restoration is enhanced when applying contextual knowledge through multisensory integration.
DNA as an Adhesin:
Bacillus cereus
Requires Extracellular DNA To Form Biofilms
Authors: Vilain Sébastien , Pretorius Jakobus M. , Theron Jacques , Brözel Volker S.
Published: February 2009

The soil saprophyte
Bacillus cereus
forms biofilms at solid-liquid interfaces. The composition of the extracellular polymeric matrix is not known, but biofilms of other bacteria are encased in polysaccharides, protein, and also extracellular DNA (eDNA). A Tn
917
screen for strains impaired in biofilm formation at a solid-liquid interface yielded several mutants. Three mutants deficient in the purine biosynthesis genes
purA
,
purC
, and
purL
were biofilm impaired, but they grew planktonically like the wild type in Luria-Bertani broth. Biofilm populations had higher
purA
,
purC
, and
purL
transcript ratios than planktonic cultures, as measured by real-time PCR. Laser scanning confocal microscopy (LSCM) of BacLight-stained samples indicated that there were nucleic acids in the cell-associated matrix. This eDNA could be mobilized off the biofilm into an agarose gel matrix through electrophoresis, and it was a substrate for DNase. Glass surfaces exposed to exponentially growing populations acquired a DNA-containing conditioning film, as indicated by LSCM. Planktonic exponential-phase cells released DNA into an agarose gel matrix through electrophoresis, while stationary-phase populations did not do this. DNase treatment of planktonic exponential-phase populations rendered cells more susceptible than control populations to the DNA-interacting antibiotic actinomycin D. Exponential-phase
purA
cells did not contain detectable eDNA, nor did they convey a DNA-containing conditioning film to the glass surface. These results indicate that exponential-phase cells of
B. cereus
ATCC 14579 are decorated with eDNA and that biofilm formation requires DNA as part of the extracellular polymeric matrix.
Effect of Freezing on PCR Amplification of 16S rRNA Genes from Microbes Associated with Black Band Disease of Corals
Authors: Sekar Raju , Kaczmarsky Longin T. , Richardson Laurie L.
Published: February 2009

Molecular analysis of black band disease of corals revealed that samples frozen immediately after collection yielded more proteobacterial 16S rRNA sequences, while unfrozen samples produced more cyanobacterial and sulfur-oxidizing bacterial sequences. These results suggest the need to use multiple approaches for preparation of samples to characterize this complex polymicrobial disease.
Mutagenesis of the Bacterial RNA Polymerase Alpha Subunit for Improvement of Complex Phenotypes
Authors: Klein-Marcuschamer Daniel , Santos Christine Nicole S. , Yu Huimin , Stephanopoulos Gregory
Published: February 2009

Combinatorial or random methods for strain engineering have been extensively used for the improvement of multigenic phenotypes and other traits for which the underlying mechanism is not fully understood. Although the preferred method has traditionally been mutagenesis and selection, our laboratory has successfully used mutant transcription factors, which direct the RNA polymerase (RNAP) during transcription, to engineer complex phenotypes in microbial cells. Here, we show that it is also possible to impart new phenotypes by altering the RNAP core enzyme itself, in particular through mutagenesis of the alpha subunit of the bacterial polymerase. We present the use of this tool for improving tolerance of
Escherichia coli
to butanol and other solvents and for increasing the titers of two commercially relevant products,
l
-tyrosine and hyaluronic acid. In addition, we explore the underlying physiological changes that give rise to the solvent-tolerant mutant.
Evaluation of Single-Nucleotide Primer Extension for Detection and Typing of Phylogenetic Markers Used for Investigation of Microbial Communities
Authors: Nikolausz Marcell , Chatzinotas Antonis , Táncsics András , Imfeld Gwenaël , Kästner Matthias
Published: February 2009

Single-nucleotide primer extension (SNuPE) is an emerging tool for parallel detection of DNA sequences of different target microorganisms. The specificity and sensitivity of the SNuPE method were assessed by performing single and multiplex reactions using defined template mixtures of 16S rRNA gene PCR products obtained from pure bacterial cultures. The mismatch discrimination potential of primer extension was investigated by introducing different single and multiple primer-target mismatches. The type and position of the mismatch had significant effects on the specificity of the assay. While a 3′-terminal mismatch has a considerable effect on the fidelity of the extension reaction, the internal mismatches influenced hybridization mostly by destabilizing the hybrid duplex. Thus, carefully choosing primer-mismatch positions should result in a high signal-to-noise ratio and prevent any nonspecific extension. Cyclic fluorescent labeling of the hybridized primers via extension also resulted in a significant increase in the detection sensitivity of the PCR. In multiplex reactions, the signal ratios detected after specific primer extension correlated with the original template ratios. In addition, reverse-transcribed 16S rRNA was successfully used as a nonamplified template to prove the applicability of SNuPE in a PCR-independent manner. In conclusion, this study demonstrates the great potential of SNuPE for simultaneous detection and typing of various nucleic acid sequences from both environmental and engineered samples.
Succession of Selected Strains of
Acetobacter pasteurianus
and Other Acetic Acid Bacteria in Traditional Balsamic Vinegar
Authors: Gullo Maria , De Vero Luciana , Giudici Paolo
Published: February 2009

The application of a selected
Acetobacter pasteurianus
strain for traditional balsamic vinegar production was assessed. Genomic DNA was extracted from biofilms after enrichment cultures on GYC medium (10% glucose, 1.0% yeast extract, 2.0% calcium carbonate) and used for PCR/denaturing gradient gel electrophoresis, 16S rRNA gene sequencing, and enterobacterial repetitive intergenic consensus/PCR sequencing. Results suggested that double-culture fermentation is suitable for traditional balsamic vinegar acetification.
Fermentative Production of Thymidine by a Metabolically Engineered
Escherichia coli
Strain
Authors: Lee Hyeon Cheol , Kim Jin Ha , Kim Jin Sook , Jang Wonhee , Kim Sang Yong
Published: February 2009

Thymidine is an important precursor in the production of various antiviral drugs, including azidothymidine for the treatment of AIDS. Since thymidine-containing nucleotides are synthesized only by the de novo pathway during DNA synthesis, it is not easy to produce a large amount of thymidine biologically. In order to develop a host strain to produce thymidine, thymidine phosphorylase, thymidine kinase, and uridine phosphorylase genes were deleted from an
Escherichia coli
BL21 strain to develop BLdtu. Since the genes coding for the enzymes related to the nucleotide salvage pathway were disrupted, BLdtu was unable to utilize thymidine or thymine, and thymidine degradation activity was completely abrogated. We additionally expressed T4 thymidylate synthase, T4 nucleotide diphosphate reductase, bacteriophage PBS2 TMP phosphohydrolase,
E. coli
dCTP deaminase, and
E. coli
uridine kinase in the BLdtu strain to develop a thymidine-producing strain (BLdtu24). BLdtu24 produced 649.3 mg liter
−1
of thymidine in a 7-liter batch fermenter for 24 h, and neither thymine nor uridine was detected. However, the dUTP/dTTP ratio was increased in BLdtu24, which could lead to increased double-strand breakages and eventually to cell deaths during fermentation. To enhance thymidine production and to prevent cell deaths during fermentation, we disrupted a gene (encoding uracil-DNA
N
-glycosylase) involved in DNA excision repair to suppress the consumption of dTTP and developed BLdtug24. Compared with the thymidine production in BLdtu24, the thymidine production in BLdtug24 was increased by ∼1.2-fold (740.3 mg liter
−1
). Here, we show that a thymidine-producing strain with a relatively high yield can be developed using a metabolic engineering approach.
Heterologous Expression of Tulip Petal Plasma Membrane Aquaporins in
Pichia pastoris
for Water Channel Analysis
Authors: Azad Abul Kalam , Sawa Yoshihiro , Ishikawa Takahiro , Shibata Hitoshi
Published: February 2009

Water channels formed by aquaporins (AQPs) play an important role in the control of water homeostasis in individual cells and in multicellular organisms. Plasma membrane intrinsic proteins (PIPs) constitute a subclass of plant AQPs. TgPIP2;1 and TgPIP2;2 from tulip petals are members of the PIP family. In this study, we overexpressed TgPIP2;1 and TgPIP2;2 in
Pichia pastoris
and monitored their water channel activity (WCA) either by an in vivo spheroplast-bursting assay performed after hypo-osmotic shock or by growth assay. Osmolarity, pH, and inhibitors of AQPs, protein kinases (PKs), and protein phosphatases (PPs) affect the WCA of heterologous AQPs in this expression system. The WCA of TgPIP2;2-expressing spheroplasts was affected by inhibitors of PKs and PPs, which indicates that the water channel of this homologue is regulated by phosphorylation in
P. pastoris
. From the results reported herein, we suggest that
P. pastoris
can be employed as a heterologous expression system to assay the WCA of PIPs and to monitor the AQP-mediated channel gating mechanism, and it can be developed to screen inhibitors/effectors of PIPs.
Changes in Biochemical and Phenotypic Properties of
Streptococcus mutans
during Growth with Aeration
Authors: Ahn Sug-Joon , Ahn Sang-Joon , Browngardt Christopher M. , Burne Robert A.
Published: February 2009

Oxygen has a potent influence on the expression of genes and the activity of physiological and biochemical pathways in bacteria. We have found that oxygen significantly altered virulence-related phenotypic properties of
Streptococcus mutans
, the primary etiological agent of human dental caries. Transport of glucose, fructose, or mannose by the sugar:phosphotransferase system was significantly enhanced by growth under aerobic conditions, whereas aeration caused an extended lag phase and slower growth of
S. mutans
in medium containing glucose, fructose, or mannose as the carbohydrate source. Aeration resulted in a decrease in the glycolytic rate and enhanced the production of intracellular storage polysaccharides. Although aeration decreased the acid tolerance of
S. mutans
, aerobically grown cells had higher F-ATPase activity. Aeration altered biofilm architecture but did not change the ability of
S. mutans
to interact with salivary agglutinin. Growth in air resulted in enhanced cell-associated glucosyltransferase (Gtf) activity at the expense of cell-free Gtf activity. These results demonstrate that
S. mutans
can dramatically alter its pathogenic potential in response to exposure to oxygen, suggesting that the phenotype of the organism may be highly variable in the human oral cavity depending on the maturity of the dental plaque biofilm.
Heterologous Production of Methionine-γ-Lyase from
Brevibacterium linens
in
Lactococcus lactis
and Formation of Volatile Sulfur Compounds
Authors: Hanniffy Sean B. , Philo Mark , Peláez Carmen , Gasson Michael J. , Requena Teresa , Martínez-Cuesta M. C.
Published: February 2009

The conversion of methionine to volatile sulfur compounds (VSCs) is of great importance in flavor formation during cheese ripening and is the focus of biotechnological approaches toward flavor improvement. A synthetic
mgl
gene encoding methionine-γ-lyase (MGL) from
Brevibacterium linens
BL2 was cloned into a
Lactococcus lactis
expression plasmid under the control of the nisin-inducible promoter P
nisA
. When expressed in
L. lactis
and purified as a recombinant protein, MGL was shown to degrade
l
-methionine as well as other sulfur-containing compounds such as
l
-cysteine,
l
-cystathionine, and
l
-cystine. Overproduction of MGL in recombinant
L. lactis
also resulted in an increase in the degradation of these compounds compared to the wild-type strain. Importantly, gas chromatography-mass spectrometry analysis identified considerably higher formation of methanethiol (and its oxidized derivatives dimethyl disulfide and dimethyl trisulfide) in reactions containing either purified protein, whole cells, or cell extracts from the heterologous
L. lactis
strain. This is the first report of production of MGL from
B. linens
in
L. lactis
. Given their significance in cheese flavor development, the use of lactic acid bacteria with enhanced VSC-producing abilities could be an efficient way to enhance cheese flavor development.
Temperature-Dependent Phage Resistance of
Listeria monocytogenes
Epidemic Clone II
Authors: Kim Jae-Won , Kathariou Sophia
Published: February 2009

Listeria monocytogenes
epidemic clone II (ECII) has been responsible for two multistate outbreaks in the United States in 1998-1999 and in 2002, in which contaminated ready-to-eat meat products (hot dogs and turkey deli meats, respectively) were implicated. However, ecological adaptations of ECII strains in the food-processing plant environment remain unidentified. In this study, we found that broad-host-range phages, including phages isolated from the processing plant environment, produced plaques on ECII strains grown at 37°C but not when the bacteria were grown at lower temperatures (30°C or below). ECII strains grown at lower temperatures were resistant to phage regardless of the temperature during infection and subsequent incubation. In contrast, the phage susceptibility of all other tested strains of serotype 4b (including epidemic clone I) and of strains of other serotypes and
Listeria
species was independent of the growth temperature of the bacteria. This temperature-dependent phage susceptibility of ECII bacteria was consistently observed with all surveyed ECII strains from outbreaks or from processing plants, regardless of the presence or absence of cadmium resistance plasmids. Phages adsorbed similarly on ECII bacteria grown at 25°C and at 37°C, suggesting that resistance of ECII strains grown at 25°C was not due to failure of the phage to adsorb. Even though the underlying mechanisms remain to be elucidated, temperature-dependent phage resistance may represent an important ecological adaptation of
L. monocytogenes
ECII in processed, cold-stored foods and in the processing plant environment, where relatively low temperatures prevail.