bluuebunny/crossref_metadata_2025 huggingface dataset:
System Study on Partial Gasification Combined Cycle With CO2 Recovery
Authors: Xu Yujie , Jin Hongguang , Lin Rumou , Han Wei
Published: July 2008

A partial gasification combined cycle with CO2 recovery is proposed in this paper. Partial gasification adopts cascade conversion of the composition of coal. Active composition of coal is simply gasified, while inactive composition, that is char, is burnt in a boiler. Oxy-fuel combustion of syngas produces only CO2 and H2O, so the CO2 can be separated through cooling the working fluid. This decreases the amount of energy consumption to separate CO2 compared with conventional methods. The novel system integrates the above two key technologies by injecting steam from a steam turbine into the combustion chamber of a gas turbine to combine the Rankine cycle with the Brayton cycle. The thermal efficiency of this system will be higher based on the cascade utilization of energy level. Compared with the conventional integrated gasification combined cycle (IGCC), the compressor of the gas turbine, heat recovery steam generator (HRSG) and gasifier are substituted for a pump, reheater, and partial gasifier, so the system is simplified obviously. Furthermore, the novel system is investigated by means of energy-utilization diagram methodology and provides a simple analysis of their economic and environmental performance. As a result, the thermal efficiency of this system may be expected to be 45%, with CO2 recovery of 41.2%, which is 1.5–3.5% higher than that of an IGCC system. At the same time, the total investment cost of the new system is about 16% lower than that of an IGCC. The comparison between the partial gasification technology and the IGCC technology is based on the two representative cases to identify the specific feature of the proposed system. The promising results obtained here with higher thermal efficiency, lower cost, and less environmental impact provide an attractive option for clean-coal utilization technology.
Acoustoelastic Interaction in Combustion Chambers: Modeling and Experiments
Authors: Huls R. A. , van Kampen J. F. , van der Hoogt P. J. M. , Kok J. B. W. , de Boer A.
Published: July 2008

To decrease NOx emissions from combustion systems, lean premixed combustion is used. A disadvantage is the higher sensitivity to combustion instabilities, leading to increased sound pressure levels in the combustor and resulting in an increased excitation of the surrounding structure: the liner. This causes fatigue, which limits the lifetime of the combustor. This paper presents a joint experimental and numerical investigation of this acoustoelastic interaction problem for frequencies up to 1kHz. To study this problem experimentally, a test setup has been built consisting of a single burner, 500kW, 5bar combustion system. The thin structure (liner) is contained in a thick pressure vessel with optical access for a traversing laser vibrometer system to measure the vibration levels of the liner. The acoustic excitation of the liner is measured using pressure sensors measuring the acoustic pressures inside the combustion chamber. For the numerical model, the finite element method with full coupling between structural vibration and acoustics is used. The flame is modeled as an acoustic volume source corresponding to a heat release rate that is frequency independent. The temperature distribution is taken from a Reynolds averaged Navier Stokes (RaNS) computational fluid dynamics (CFD) simulation. Results show very good agreement between predicted and measured acoustic pressure levels. The predicted and measured vibration levels also match fairly well.
An Acoustic-Energy Method for Estimating the Onset of Acoustic Instabilities in Premixed Gas-Turbine Combustors
Authors: Ibrahim Z. M. , Williams F. A. , Buckley S. G. , Twardochleb C. Z.
Published: July 2008

For given acoustic frequencies of premixed gas-turbine combustors, a classical method not currently in use is explored for assessing whether acoustically driven oscillatory combustion will occur. The method involves cataloging linear amplification and attenuation mechanisms and estimating magnitudes of their rates. Linear approximations to nonlinear mechanisms are included in an effort to obtain a reasonably complete description. A stability index is defined such that oscillation is predicted to occur when the value of the index exceeds unity. The method is tested on the basis of new experiments and experimental data available in literature. Moderate success is achieved in rationalizing these experimental results. The objective of the method is to enable quick and inexpensive decisions to be made for a wide variety of potential design configurations and operating conditions, without the complexity of computational fluid dynamics. The approach therefore may complement other approaches already in use.
Results From an Engine Cycle Simulation of Compression Ratio and Expansion Ratio Effects on Engine Performance
Authors: Caton Jerald A.
Published: July 2008

This investigation quantified the effects of compression ratio (CR) and expansion ratio (ER) on performance, efficiency, and second law parameters for an automotive, spark-ignition engine. The well known increase in engine performance for increasing CR and ER is demonstrated. These increases for brake engine performance are modest for CRs greater than about 10 for the conditions studied. The results demonstrated that the increasing friction and heat losses for the higher CRs are of the same order as the thermodynamic gains. Also, the results included the destruction of availability during combustion. For a part load condition, the availability destroyed decreased from about 23% to 21% for CRs of 4 and 10, respectively. In addition, this study examined cases with greater ERs than CRs. The overall cycle for these cases is often called an “Atkinson” cycle. For most cases, the thermal efficiency first increased as ER increased, attained a maximum efficiency, and then decreased. The decrease in efficiency after the maximum value was due to the increased heat losses, increased friction, and ineffective exhaust processes (due to the reduced cylinder pressure at the time of exhaust valve opening). For part load cases, the higher ER provided only modest gains due to the increased pumping losses associated with the constant load requirement. For the wide open throttle cases, however, the higher ERs provided significant gains. For example, for a compression ratio of 10, expansion ratios of 10 and 30 provided brake thermal efficiencies of about 34% and 43%, respectively. Although the net thermodynamic gains are significant, large ERs such as 30 may not be practical in most applications.
Inelastic Behavior in Repeated Shearing of Bovine White Matter
Authors: Cohen Taylor S. , Smith Andrew W. , Massouros Panagiotis G. , Bayly Philip V. , Shen Amy Q. , Genin Guy M.
Published: July 2008

Understanding the brain’s response to multiple loadings requires knowledge of how straining changes the mechanical response of brain tissue. We studied the inelastic behavior of bovine white matter and found that when this tissue is stretched beyond a critical strain threshold, its reloading stiffness drops. An upper bound for this strain threshold was characterized, and was found to be strain rate dependent at low strain rates and strain rate independent at higher strain rates. Results suggest that permanent changes to tissue mechanics can occur at strains below those believed to cause physiological disruption or rupture of axons. Such behavior is characteristic of disentanglement in fibrous-networked solids, in which strain-induced mechanical changes may result from fiber realignment rather than fiber breakage.
Interaction Between the Interstitial Fluid and the Extracellular Matrix in Confined Indentation
Authors: Lu Yiling , Wang Wen
Published: July 2008

The Movement of the interstitial fluid in extracellular matrices not only affects the mechanical properties of soft tissues, but also facilitates the transport of nutrients and the removal of waste products. In this study, we aim to quantify interstitial fluid movement and fluid-matrix interaction in a new loading configuration—confined tissue indentation, using a poroelastic theory. The tissue sample sits in a cylindrical chamber and loading is applied on the top central surface of the specimen by a porous indenter that is fixed on the specimen. The interaction between the solid and the fluid is examined using a finite element method under ramp and cyclic loads. Typical compression-relaxation responses of the specimen are observed in a ramp load. Under a cyclic load, the system reaches a dynamic equilibrium after a number of loading cycles. Fluid circulation, with opposite directions in the loading and unloading phases in the extracellular matrix, is observed. The most significant variation in the fluid pressure locates just beneath the indenter. Fluid pressurization arrives at equilibrium much faster than the solid matrix deformation. As the loading frequency increases, the location of the peak pressure oscillation moves closer to the indenter and the magnitude of the pressure oscillation increases. Concomitantly, the axial stress variation of the solid matrix is reduced. It is found that interstitial fluid movement helps to alleviate severe strain of the solid matrix beneath the indenter. This study quantifies the interaction between the interstitial fluid and the extracellular matrix by decomposing the loading response of the specimen into the “transient” and “dynamic equilibrium” phases. Confined indentation in this manuscript gives a better representation of some in vitro and in vivo loading configurations where the indenter covers part of the top surface of the tissue.
The 12cc Penn State Pulsatile Pediatric Ventricular Assist Device: Fluid Dynamics Associated With Valve Selection
Authors: Cooper Benjamin T. , Roszelle Breigh N. , Long Tobias C. , Deutsch Steven , Manning Keefe B.
Published: July 2008

The mortality rate for infants awaiting a heart transplant is 40% because of the extremely limited number of donor organs. Ventricular assist devices (VADs), a common bridge-to-transplant solution in adults, are becoming a viable option for pediatric patients. A major obstacle faced by VAD designers is thromboembolism. Previous studies have shown that the interrelated flow characteristics necessary for the prevention of thrombosis in a pulsatile VAD are a strong inlet jet, a late diastolic recirculating flow, and a wall shear rate greater than 500s−1. Particle image velocimetry was used to compare the flow fields in the chamber of the 12cc Penn State pediatric pulsatile VAD using two mechanical heart valves: Björk–Shiley monostrut (BSM) tilting disk valves and CarboMedics (CM) bileaflet valves. In conjunction with the flow evaluation, wall shear data were calculated and analyzed to help quantify wall washing. The major orifice inlet jet of the device containing BSM valves was more intense, which led to better recirculation and wall washing than the three jets produced by the CM valves. Regurgitation through the CM valve served as a significant hindrance to the development of the rotational flow.
P188 Reduces Cell Death and IGF-I Reduces GAG Release Following Single-Impact Loading of Articular Cartilage
Authors: Natoli Roman M. , Athanasiou Kyriacos A.
Published: July 2008

Prior joint injury predisposes an individual to developing post-traumatic osteoarthritis, for which there is presently no disease modifying treatment. In this condition, articular cartilage degenerates due to cell death and matrix breakdown, resulting in tissue with diminished biomechanical function. P188, a nonionic surfactant, and the growth factor IGF-I have been shown to decrease cell death. Additionally, IGF-I is known to have beneficial effects on cartilage matrix. The objective of this study was to determine the efficacy of P188, IGF-I, and their combination following articular cartilage impact injury with two energy levels, 1.1J (“low”) and 2.8J (“high”), at 24h and 1week. Bovine articular cartilage with attached underlying bone was impacted at the low or high level. Impact sites were explanted and examined immediately, or cultured for 24h or 1week in serum-free media supplemented with P188 (8mg∕ml), IGF-I (100ng∕ml), or their combination. Gross morphology, cell viability, GAG release to the media, and tissue mechanical properties were assessed. Immediately postimpact, high level impacted tissue had significantly increased gross morphology scores, indicating tissue damage, which were maintained over 1week. Gross scores following low impact were initially similar to nonimpacted controls, but, at 24h and 1week, low impact gross scores significantly increased compared to nonimpacted controls. Additionally, at 24h, high impact resulted in increased cell death, and both low and high impacts had increased GAG release compared to nonimpacted controls. Furthermore, high impact caused decreased tissue stiffness at 24h that appeared to worsen over 1week, evident by the percent decrease from nonimpacted controls increasing from 16% to 26%. No treatment type studied mitigated this loss. The combination did not perform better than either individual treatment; however, following low impact at 1week, P188 reduced cell death by 75% compared to no treatment and IGF-I decreased GAG release from the tissue by 49%. In conclusion, high impact resulted in immediate tissue changes that worsened over 1week. Though not causing immediate changes, low impact also resulted in tissue degeneration evident by 24h. No treatment studied was effective at 24h, but by 1week P188 and IGF-I ameliorated established detrimental changes occurring in articular cartilage postimpact. However, further work is needed to optimize treatment strategies to prevent and/or reverse cell death and matrix destruction in a way that maintains tissue mechanical properties, and hence its functionality.
Modeling of Nociceptor Transduction in Skin Thermal Pain Sensation
Authors: Xu F. , Wen T. , Lu T. J. , Seffen K. A.
Published: July 2008

All biological bodies live in a thermal environment with the human body as no exception, where skin is the interface with protecting function. When the temperature moves out of normal physiological range, skin fails to protect and pain sensation is evocated. Skin thermal pain is one of the most common problems for humans in everyday life as well as in thermal therapeutic treatments. Nocicetors (special receptor for pain) in skin play an important role in this process, converting the energy from external noxious thermal stimulus into electrical energy via nerve impulses. However, the underlying mechanisms of nociceptors are poorly understood and there have been limited efforts to model the transduction process. In this paper, a model of nociceptor transduction in skin thermal pain is developed in order to build direct relationship between stimuli and neural response, which incorporates a skin thermomechanical model for the calculation of temperature, damage and thermal stress at the location of nociceptor and a revised Hodgkin–Huxley form model for frequency modulation. The model qualitatively reproduces measured relationship between spike rate and temperature. With the addition of chemical and mechanical components, the model can reproduce the continuing perception of pain after temperature has returned to normal. The model can also predict differences in nociceptor activity as a function of nociceptor depth in skin tissue.
Dynamic Elastic-Plastic Buckling of Structural Elements: A Review
Authors: Karagiozova D. , Alves Marcílio
Published: July 2008

Structural elements, which deform inelastically, are often used in energy-absorbing devices due to their simple design and the high efficiency achieved by several buckling deformation mechanisms. The application of light ductile materials in transportation systems and increased loading intensity requires studies on the influence of the rate of loading and material characteristics on dynamic buckling behavior. The present review article is focused on summarizing the state of the art related to the inelastic dynamic stability and postbuckling behavior of various basic structural members. In particular, studies on the dynamic response of axially loaded idealized elastic-plastic models, rods, shells with circular and square cross sections, and long tubes are discussed with consideration given to the influence of the geometric and material characteristics as well as the loading conditions on the buckling phenomena observed in these structural elements. The findings from the theoretical and experimental investigations on the phenomenon of dynamic inelastic buckling reported in this review article are based on 118 references.
Effect of Upper and Lower Extremity Control Strategies on Predicted Injury Risk During Simulated Forward Falls: A Study in Healthy Young Adults
Authors: Lo JiaHsuan , Ashton-Miller James A.
Published: July 2008

Fall-related wrist fractures are common at any age. We used a seven-link, sagittally symmetric, biomechanical model to test the hypothesis that systematically alterations in the configuration of the body during a forward fall from standing height can significantly influence the impact force on the wrists. Movement of each joint was accomplished by a pair of agonist and antagonist joint muscle torque actuators with assigned torque-angle, torque-velocity, and neuromuscular latency properties. Proportional-derivative joint controllers were used to achieve desired target body segment configurations in the pre- and∕or postground contact phases of the fall. Outcome measures included wrist impact forces and whole-body kinetic energy at impact in the best, and worst, case impact injury risk scenarios. The results showed that peak wrist impact force ranged from less than 1kN to more than 2.5kN, reflecting a fourfold difference in whole-body kinetic energy at impact (from less than 40J to more than 160J) over the range of precontact hip and knee joint angles used at impact. A reduction in the whole-body kinetic energy at impact was primarily associated with increasing negative work associated with hip flexion. Altering upper extremity configuration prior to impact significantly reduced the peak wrist impact force by up to 58% (from 919Nto2212N). Increased peak wrist impact forces associated greater shoulder flexion and less elbow flexion. Increasing postcontact arm retraction can reduce the peak wrist impact force by 28% (from 1491Nto1078N), but postcontact hip and knee rotations had a relatively small effect on the peak wrist impact force (8% reduction; from 1411Nto1303N). In summary, the choice of the joint control strategy during a forward fall can significantly affect the risk of wrist injury. The most effective strategy was to increase the negative work during hip flexion in order to dissipate kinetic energy thereby reducing the loss in potential energy prior to first impact. Extended hip or elbow configurations should be avoided in order to reduce forearm impact forces.
A Nonlinear Anisotropic Viscoelastic Model for the Tensile Behavior of the Corneal Stroma
Authors: Nguyen T. D. , Jones R. E. , Boyce B. L.
Published: July 2008

Tensile strip experiments of bovine corneas have shown that the tissue exhibits a nonlinear rate-dependent stress-strain response and a highly nonlinear creep response that depends on the applied hold stress. In this paper, we present a constitutive model for the finite deformation, anisotropic, nonlinear viscoelastic behavior of the corneal stroma. The model formulates the elastic and viscous response of the stroma as the average of the elastic and viscous response of the individual lamellae weighted by a probability density function of the preferred in-plane lamellar orientations. The result is a microstructure-based model that incorporates the viscoelastic properties of the matrix and lamellae and the lamellar architecture in the response of the stroma. In addition, the model includes a fully nonlinear description of the viscoelastic response of the lamellar(fiber) level. This is in contrast to previous microstructure-based models of fibrous soft tissues, which relied on quasilinear viscoelastic formulations of the fiber viscoelasticity. Simulations of recent tensile strip experiments show that the model is able to predict, well within the bounds of experimental error and natural variations, the cyclic stress-strain behavior and nonlinear creep behavior observed in uniaxial tensile experiments of excised strips of bovine cornea.
Chondrocyte Damage and Contact Pressures Following Impact on the Rabbit Tibiofemoral Joint
Authors: Isaac Daniel I. , Meyer Eric G. , Haut Roger C.
Published: July 2008

Epidemiological studies show that tibial plateau fractures comprise about 10% of all below-knee injuries in car crashes. Studies from this laboratory document that impacts to the tibiofemoral (TF) joint at 50% of the energy producing gross fracture can generate cartilage damage and microcracks at the interface between calcified cartilage and underlying subchondral bone in the tibial plateau. These injuries are suggestive of the initiation for a long term chronic disease, such as osteoarthritis. The disease process may be further encouraged by acute damage to chondrocytes in the cartilage overlying areas of occult microcracking. The hypothesis of the current study was that significant damage to chondrocytes in tibial plateau cartilage could be generated in areas of high contact pressure by a single impact delivered to the rabbit TF joint, without a gross fracture of bone. Three rabbits received a single, 13J of energy blunt insult to the TF joint, while another three animals were used as controls. Cell viability analyses compared chondrocyte damage in impacted versus control cartilage. Two additional rabbits were impacted to document contact pressures generated in the TF joint. The study showed high contact pressures in uncovered areas of the plateau, with a trend for higher pressures in the lateral versus medial facets. A significantly higher percentage of damaged chondrocytes existed in impacted versus the opposite, nonimpacted limbs. Additionally, more chondrocyte damage was documented in the superficial zone (top 20% of cartilage thickness) of the cartilage compared to middle (middle 50% of thickness) and deep (bottom 30% of thickness) zones. This study showed that a single blunt insult to the in situ rabbit TF joint, generating large areas of contact pressure exceeding 20MPa, produces significant chondrocyte damage in the tibial articular cartilage, especially in the superficial zone, without gross fracture of bone. Future studies will be needed to investigate the long term, chronic outcome of this blunt force joint trauma.
Response to Comment on "Genetically Determined Differences in Learning from Errors"
Authors: Klein Tilmann A. , Reuter Martin , von Cramon D. Yves , Ullsperger Markus
Published: July 2008

Since the publication of our findings, further genetic and pharmacological studies have bolstered our conclusion that dopamine D2 receptors are essential for performance monitoring and learning. Although the functionally complex dopamine D2 receptor gene polymorphism DRD2-TAQ-IA may also affect cellular signaling components, the accumulated evidence supports the notion that our findings were mediated by differential D2 receptor density.
The High-Affinity
E. coli
Methionine ABC Transporter: Structure and Allosteric Regulation
Authors: Kadaba Neena S. , Kaiser Jens T. , Johnson Eric , Lee Allen , Rees Douglas C.
Published: July 2008

The crystal structure of the high-affinity
Escherichia coli
MetNI methionine uptake transporter, a member of the adenosine triphosphate (ATP)–binding cassette (ABC) family, has been solved to 3.7 angstrom resolution. The overall architecture of MetNI reveals two copies of the adenosine triphosphatase (ATPase) MetN in complex with two copies of the transmembrane domain MetI, with the transporter adopting an inward-facing conformation exhibiting widely separated nucleotide binding domains. Each MetI subunit is organized around a core of five transmembrane helices that correspond to a subset of the helices observed in the larger membrane-spanning subunits of the molybdate (ModBC) and maltose (MalFGK) ABC transporters. In addition to the conserved nucleotide binding domain of the ABC family, MetN contains a carboxyl-terminal extension with a ferredoxin-like fold previously assigned to a conserved family of regulatory ligand-binding domains. These domains separate the nucleotide binding domains and would interfere with their association required for ATP binding and hydrolysis. Methionine binds to the dimerized carboxyl-terminal domain and is shown to inhibit ATPase activity. These observations are consistent with an allosteric regulatory mechanism operating at the level of transport activity, where increased intracellular levels of the transported ligand stabilize an inward-facing, ATPase-inactive state of MetNI to inhibit further ligand translocation into the cell.
Structural Basis for Specific Substrate Recognition by the Chloroplast Signal Recognition Particle Protein cpSRP43
Authors: Stengel Katharina F. , Holdermann Iris , Cain Peter , Robinson Colin , Wild Klemens , Sinning Irmgard
Published: July 2008

Secretory and membrane proteins carry amino-terminal signal sequences that, in cotranslational targeting, are recognized by the signal recognition particle protein SRP54 without sequence specificity. The most abundant membrane proteins on Earth are the light-harvesting chlorophyll a/b binding proteins (LHCPs). They are synthesized in the cytoplasm, imported into the chloroplast, and posttranslationally targeted to the thylakoid membrane by cpSRP, a heterodimer formed by cpSRP54 and cpSRP43. We present the 1.5 angstrom crystal structure of cpSRP43 characterized by a unique arrangement of chromodomains and ankyrin repeats. The overall shape and charge distribution of cpSRP43 resembles the SRP RNA, which is absent in chloroplasts. The complex with the internal signal sequence of LHCPs reveals that cpSRP43 specifically recognizes a DPLG peptide motif. We describe how cpSPR43 adapts the universally conserved SRP system to posttranslational targeting and insertion of the LHCP family of membrane proteins.
Optical Pumping and Vibrational Cooling of Molecules
Authors: Viteau Matthieu , Chotia Amodsen , Allegrini Maria , Bouloufa Nadia , Dulieu Olivier , Comparat Daniel , Pillet Pierre
Published: July 2008

The methods producing cold molecules from cold atoms tend to leave molecular ensembles with substantial residual internal energy. For instance, cesium molecules initially formed via photoassociation of cold cesium atoms are in several vibrational levels ν of the electronic ground state. We applied a broadband femtosecond laser that redistributes the vibrational population in the ground state via a few electronic excitation/spontaneous emission cycles. The laser pulses are shaped to remove the excitation frequency band of the ν = 0 level, preventing re-excitation from that state. We observed a fast and efficient accumulation (∼70% of the initially detected molecules) in the lowest vibrational level, ν = 0, of the singlet electronic state. The validity of this incoherent depopulation pumping method is very general and opens exciting prospects for laser cooling and manipulation of molecules.
Genetic Determinants of Self Identity and Social Recognition in Bacteria
Authors: Gibbs Karine A. , Urbanowski Mark L. , Greenberg E. Peter
Published: July 2008

The bacterium
Proteus mirabilis
is capable of movement on solid surfaces by a type of motility called swarming. Boundaries form between swarming colonies of different
P. mirabilis
strains but not between colonies of a single strain. A fundamental requirement for boundary formation is the ability to discriminate between self and nonself. We have isolated mutants that form boundaries with their parent. The mutations map within a six-gene locus that we term
ids
for identification of self. Five of the genes in the
ids
locus are required for recognition of the parent strain as self. Three of the
ids
genes are interchangeable between strains, and two encode specific molecular identifiers.
Comparison of Conventional, Nested, and Real-Time PCR Assays for Rapid and Accurate Detection of
Vibrio vulnificus
Authors: Kim Hyong Sun , Kim Dong-Min , Neupane Ganesh Prasad , Lee Yu-mi , Yang Nam-Woong , Jang Sook Jin , Jung Sook-In , Park Kyung-Hwa , Park Hae-Ryoung , Lee Chang Seop , Lee Sun Hee
Published: July 2008

We conducted a prospective study to target
toxR
in the blood of patients with skin and soft tissue infections who were admitted to four tertiary hospitals to assess the clinical usefulness of real-time quantitative PCR (Q-PCR) as a diagnostic technique. We performed conventional PCR (C-PCR), nested PCR (N-PCR), and Q-PCR assays and compared the results to those obtained using the “gold standard” of microbiological culture. The lower detection limit for the Q-PCR assay was 5 × 10
0
copies/μl. By use of blood samples of patients with skin and soft tissue infections, the sensitivities of the C-PCR and N-PCR assays against the target
toxR
gene of
V. vulnificus
as diagnostic tools were determined to be 45% and 86%, respectively. The C-PCR and N-PCR assays had specificities of 100% and 73%, respectively. When we adopted a crossing-point (cp) cutoff value of <38 cp as a positive result, the Q-PCR assay had 100% sensitivity and specificity. Q-PCR to detect
V. vulnificus
-specific genes is not only the most sensitive and specific of the techniques but also the most rapid diagnostic method. Therefore, the appropriate application of the Q-PCR assay using blood is useful for the rapid diagnosis and subsequent treatment of
V. vulnificus
sepsis.
Comprehensive Study of Strains Previously DesignatedStreptococcus bovisConsecutively Isolated from Human Blood Cultures and Emended Description ofStreptococcus gallolyticusandStreptococcus infantariussubsp.coli
Authors: Beck Marcella , Frodl Reinhard , Funke Guido
Published: July 2008

Modern taxonomy has delineatedStreptococcus gallolyticussubsp.gallolyticus,S. gallolyticussubsp.pasteurianus,Streptococcus infantariussubsp.coli, andS. infantariussubsp.infantariuswithin the heterogenous group of previously designated clinicalStreptococcus bovisbacteria. In the present study, 58 consecutive blood culture isolates initially designatedS. boviswere further characterized by applying phenotypic and molecular genetic methods, and possible disease associations were investigated by studying the patients' records. Published phenotypic characteristics ofS. gallolyticusandS. infantariuswere not unequivocal and did not allow an unambiguous phenotypic differentiation of the 58 clinical isolates. However, full-length 16S rRNA gene sequences clearly assigned the strains toS. gallolyticussubsp.gallolyticus(n= 29),S. gallolyticussubsp.pasteurianus(n= 12), andS. infantariussubsp.coli(n= 17). Only 28% of the patients with available records presented with endocarditis and 7% presented with colon carcinoma, whereas 37% of the patients had altered liver parenchyma and 28% had gall bladder disease as underlying diseases. Detailed antimicrobial susceptibility data on bothS. gallolyticussubspecies andS. infantariussubsp.coliare given for the first time. As a result of the extensive characterization of the largest number ofS. gallolyticusandS. infantariushuman clinical isolates published so far, emended species descriptions are given. It is recommended that both clinical microbiologists and infectious disease specialists avoid the designationS. bovisfor trueS. gallolyticusandS. infantariusstrains in the future in order to get a clearer picture of the possible disease associations of these species.
Diminished Human Immunodeficiency Virus Type 1 DNA Yield from Dried Blood Spots after Storage in a Humid Incubator at 37°C Compared to −20°C
Authors: Mitchell Caroline , Jennings Cheryl , Brambilla Donald , Aldrovandi Grace , Amedee Angela Martin , Beck Ingrid , Bremer James W. , Coombs Robert , Decker Don , Fiscus Susan , Fitzgibbon Joseph , Luzuriaga Katherine , Moye John , Palumbo Paul , Reichelderfer Patricia , Somasundaran Mohan , Stevens Wendy , Frenkel Lisa
Published: July 2008

Collecting whole blood on filter paper simplifies the processing, transport, and storage of specimens used for the diagnosis of human immunodeficiency virus type 1 (HIV-1) and other tests. Specimens may be collected in tropical or rural areas with minimal facilities for handling specimens. To compare simulated tropical conditions with freezer storage, we examined the stability of HIV-1 DNA in dried blood spots (DBS) stored in humid heat and at −20°C. DBS were created by spotting 50-μl aliquots of whole blood on 903 filter paper. DNA was extracted from DBS at baseline and after 2, 6, or 12 months of storage at −20°C or at 37°C with ∼85% humidity. The DNA was tested undiluted or diluted using the Amplicor HIV-1 DNA PCR (Roche), version 1.5. Each reaction was scored positive, negative, or indeterminate based on optical density. Results were compared between storage conditions and over time. A total of 1,832 reactions from 916 DBS were analyzed, including 100 DBS at baseline, 418 stored at −20°C, and 398 stored at 37°C. A chi-square test showed fewer positive reactions for DBS stored at 37°C (55%) than for those stored at −20°C (78%) (
P
< 0.0001). Samples stored at −20°C showed little change in the probability of detection of HIV-1 DNA over time; the odds ratio (OR) was 0.93 after storage for 1 year. Samples stored at 37°C demonstrated a significant change in detection at 1 year (OR, 0.29). We conclude that exposure of DBS to 37°C and high humidity impaired the recovery of HIV-1 DNA from DBS, whereas DNA recovery was preserved when DBS were stored frozen.
Contamination of the Hospital Environment with Gastroenteric Viruses: Comparison of Two Pediatric Wards over a Winter Season
Authors: Gallimore Chris I. , Taylor Clive , Gennery Andrew R. , Cant Andrew J. , Galloway Angela , Xerry Jacqueline , Adigwe Juliet , Gray Jim J.
Published: July 2008

The aims of this study were to examine the extent of gastroenteric virus contamination in a pediatric primary immunodeficiency (PPI) ward and a general pediatric ward over a winter season and to determine whether changes to hospital infection control interventions would have an impact on environmental contamination levels within pediatric units. Environmental swabs were collected weekly from 11 sites in both wards from 15 December 2005 to 3 March 2006 and examined for the presence of norovirus (NoV), astrovirus, and rotavirus (RV) by reverse transcriptase PCR. Viruses were detected in 17% and 19% of swabs from both wards. Virus contamination for NoV and RV decreased from 20% to 6% and 15% to 10% of swabs, respectively, in the PPI ward from the 2004 study by Gallimore et al. (C. I. Gallimore, C. Taylor, A. R. Gennery, A. J. Cant, A. Galloway, M. Iturriza-Gomara, and J. J. Gray, J. Clin. Microbiol. 44:395-399, 2006). Overall, changes to cleaning protocols were deemed to have reduced the level of environmental contamination with gastroenteric viruses, but contamination still occurred due to a breakdown in infection control procedures indicated by contamination in areas frequented by parents but used only occasionally by staff.
Utility of New 24-Locus Variable-Number Tandem-Repeat Typing for Discriminating
Mycobacterium tuberculosis
Clinical Isolates Collected in Bulgaria
Authors: Valcheva Violeta , Mokrousov Igor , Narvskaya Olga , Rastogi Nalin , Markova Nadya
Published: July 2008

The present study evaluated new markers for molecular typing of
Mycobacterium tuberculosis
with a collection of strains circulating in Bulgaria. A study sample included 133 strains from epidemiologically unlinked patients from different regions of the country. Spoligotyping was used as a primary typing tool; it subdivided these strains into 37 types, including 15 clusters and 22 singletons. Traditional IS
6110
-restriction fragment length polymorphism (RFLP) typing and novel 24-locus variable number tandem-repeat (VNTR) typing methods were applied to the selection of 73 strains. Discriminatory power (Hunter-Gaston index [HGI]) of these methods was found to be 0.983 and 0.997, respectively. The 73 strains were subdivided into 66 types by a 24-locus mycobacterial interspersed repetitive unit (MIRU)-VNTR scheme, 62 types by a classical 12-locus MIRU-VNTR scheme, 51 types by IS
6110
-RFLP typing, and 31 types by spoligotyping. A combination of the five most polymorphic loci (MIRU40, Mtub04, Mtub21, QUB-11b, and QUB-26) was shown to achieve a high discrimination (HGI = 0.984). To conclude, a complete 24-locus scheme excellently differentiated strains in our study, whereas a reduced 5-locus set provided a sufficiently high differentiation and may be preliminarily suggested for the first-line typing of
M. tuberculosis
isolates in Bulgaria.
Evaluation of Three Real-Time PCR Assays for Detection of
Mycoplasma pneumoniae
in an Outbreak Investigation
Authors: Winchell Jonas M. , Thurman Kathleen A. , Mitchell Stephanie L. , Thacker W. Lanier , Fields Barry S.
Published: July 2008

We compared the performances of three recently optimized real-time PCR assays derived from distinct genomic regions of
Mycoplasma pneumoniae
during an outbreak. Comprehensive evaluation established that a newly described toxin gene represents a superior target for detecting
M. pneumoniae
DNA in clinical specimens, although use of multiple targets may increase testing confidence.
Molecular Epidemiology of Methicillin-Resistant and Methicillin-Susceptible
Staphylococcus aureus
Isolates from Global Clinical Trials
Authors: Goering Richard V. , Shawar Ribhi M. , Scangarella Nicole E. , O'Hara F. Patrick , Amrine-Madsen Heather , West Joshua M. , Dalessandro Marybeth , Becker Julie A. , Walsh Stacey L. , Miller Linda A. , van Horn Stephanie F. , Thomas Elizabeth S. , Twynholm Monique E.
Published: July 2008

Determining the genetic characteristics of
Staphylococcus aureus
is important for better understanding of the global and dynamic epidemiology of this organism as we witness the emergence and spread of virulent and antibiotic-resistant clones. We genotyped 292
S. aureus
isolates (105 methicillin resistant and 187 methicillin susceptible) using a combination of pulsed-field gel electrophoresis, multilocus sequence typing, and SCC
mec
typing. In addition,
S. aureus
isolates were tested for the presence of the Panton-Valentine leukocidin (PVL) genes. Isolates were recovered from patients with uncomplicated skin infections in 10 different countries during five phase III global clinical trials of retapamulin, a new topical antibiotic agent. The most common methicillin-resistant clone had multilocus sequence type 8, pulsed-field type USA300, and SCC
mec
type IV and possessed the PVL genes. This clone was isolated exclusively in the United States. The most common PVL-positive, methicillin-susceptible clone had multilocus sequence type 121 and pulsed-field type USA1200. This clone was found primarily in South Africa and the Russian Federation. Other clones were found at lower frequencies and were limited in their geographic distribution. Overall, considerable genetic diversity was observed within multilocus sequence type clonal complexes and pulsed-field types.
Rapid Detection of
bla
KPC
Carbapenemase Genes by Real-Time PCR
Authors: Hindiyeh Musa , Smollen Gill , Grossman Zehava , Ram Daniela , Davidson Yehudit , Mileguir Fernando , Vax Marina , Ben David Debbie , Tal Ilana , Rahav Galia , Shamiss Ari , Mendelson Ella , Keller Nathan
Published: July 2008

Carbapenem resistance among
Enterobacteriaceae
is an emerging problem worldwide.
Klebsiella pneumoniae
carbapenemase (
bla
KPC
) enzymes are among the most common β-lactamases described. In this study, we report the development and validation of a real-time PCR (q-PCR) assay for the detection of
bla
KPC
genes using TaqMan chemistry. The q-PCR amplification of
bla
KPC
DNA was linear over 7 log dilutions (
r
2
= 0.999; slope, 3.54), and the amplification efficiency was 91.6%. The q-PCR detection limit was 1 CFU, and there was no cross-reaction with DNA extracted from several multidrug-resistant bacteria. Perianal/rectal swabs (
n
= 187) collected in duplicate from 128 patients admitted to Sheba Medical Center surgical intensive care units were evaluated for the presence of carbapenem-resistant bacteria by culturing on MacConkey agar-plus-carbapenem disks and for
bla
KPC
genes by q-PCR. Carbapenem-resistant organisms, all
K. pneumoniae
, were isolated from 47 (25.1%) of the 187 samples collected, while
bla
KPC
genes were detected in 54 (28.9%) of the patient samples extracted by the NucliSENS easyMAG system. Of these, seven samples were positive for
bla
KPC
genes by q-PCR but negative for carbapenem resistance by culture, while all samples in which no carbapenem-resistant bacteria were detected by culture also tested negative by q-PCR. Thus, the sensitivity and specificity of the q-PCR assay after extraction by the NucliSENS easyMAG system were 100% and 95%, respectively. Similar values were obtained after DNA extraction by the Roche MagNA Pure LC instrument: 97.9% sensitivity and 96.4% specificity. Overall, the
bla
KPC
q-PCR assay appears to be highly sensitive and specific. The utilization of q-PCR will shorten the time to bla
KPC
detection from 24 h to 4 h and will help in rapidly isolating colonized or infected patients and assigning them to cohorts.
Changing Patterns in Frequency of Recovery of Five Methicillin-Resistant
Staphylococcus aureus
Clones in Portuguese Hospitals: Surveillance over a 16-Year Period
Authors: Aires-de-Sousa Marta , Correia Bruno , de Lencastre Hermínia
Published: July 2008

A total of 629 nonduplicate methicillin-resistant
Staphylococcus aureus
MRSA isolates were recovered between June and November 2006 from 11 hospitals located in different areas of Portugal. Selected isolates (
n
= 271, 43%) were typed by pulsed-field gel electrophoresis (PFGE), representatives of which were additionally characterized by
spa
typing, multilocus sequence typing, staphylococcal cassette chromosome
mec
(SCC
mec
) typing, and the presence of Panton-Valentine leukocidin (PVL). The 271 isolates were classified into 13 different clonal types. Three pandemic clones included the majority (
n
= 241, 88%) of the isolates and were observed in several hospitals: (i) EMRSA-15 (54%)—PFGE type A, ST22,
spa
type t022, SCC
mec
IV—was found in the 11 hospitals studied and was identified as the major clone in seven of them; (ii) the New York/Japan clone (17%)—PFGE B, ST5,
spa
type t067, SCC
mec
II—was identified in nine hospitals and represented the major clone in four; and (iii) the Brazilian MRSA (17%)—PFGE C, ST239,
spa
type t037, SCC
mec
IIIA—was also detected in nine hospitals but never as the main clone. All isolates tested were PVL negative. Clone EMRSA-15 is currently the predominant MRSA clonal type circulating in Portuguese hospitals, but a new wave of MRSA has emerged in the country with the recent introduction and spread of the New York/Japan clone. The Brazilian MRSA that was the leading clone in Portugal in the late 1990s is declining and being progressively replaced by the two former clones. We report the first isolate SCC
mec
type V (ST45) in Portugal.
New
Erwinia
-Like Organism Causing Cervical Lymphadenitis
Authors: Shin Sang Yop , Lee Mi Young , Song Jae-Hoon , Ko Kwan Soo
Published: July 2008

The first case of cervical lymphadenitis due to infection by a new
Erwinia
-like organism is reported. The organism was identified initially as
Pantoea
sp. by a Vitek 2-based assessment but was finally identified as a member of the genus
Erwinia
by 16S rRNA gene sequence analysis. The isolate displayed 98.9% 16S rRNA gene sequence similarity to that of
E. tasmaniensis
and showed phenotypic characteristics that were different from other
Erwinia
species.
Kocuria rhizophilaAdds to the Emerging Spectrum of Micrococcal Species Involved in Human Infections
Authors: Becker Karsten , Rutsch Frank , Uekötter Andreas , Kipp Frank , König Jens , Marquardt Thorsten , Peters Georg , von Eiff Christof
Published: July 2008

We describe the first case of aKocuria rhizophilainfection in a boy with methylmalonic aciduria. A single clone was isolated from blood samples drawn through a port system and from peripheral veins during septic episodes within a 2-year period.K. rhizophilaexpands the emerging number of “micrococci” considered to be etiologically relevant.
Sensitivities of Nasal and Rectal Swabs for Detection of Methicillin-Resistant
Staphylococcus aureus
Colonization in an Active Surveillance Program
Authors: Currie Andrea , Davis Linda , Odrobina Ewa , Waldman Suzanne , White Diane , Tomassi Joanne , Katz Kevin C.
Published: July 2008

All medical and high-risk surgical patients were screened for methicillin-resistant
Staphylococcus aureus
colonization over 3.5 years. The sensitivities of nasal and rectal swabs were 68% and 62%, respectively. Naris and open-skin-site swabs detected 467 (74%) of 627 adult carriers identified. Rectal swabs detected an additional 160 (26%) carriers.
Countrywide Molecular Survey of Methicillin-Resistant
Staphylococcus aureus
Strains in Poland
Authors: Łuczak-Kadłubowska Agnieszka , Sulikowska Agnieszka , Empel Joanna , Piasecka Anna , Orczykowska Monika , Kozinska Aleksandra , Hryniewicz Waleria
Published: July 2008

The present investigation was undertaken to assess the proportion of methicillin-resistant
Staphylococcus aureus
(MRSA) strains among hospital-acquired isolates and to determine the clones of MRSA currently circulating in Poland by using a number of molecular techniques. Between January and May 2005, methicillin resistance was investigated among a total of 915
S. aureus
isolates collected from 39 hospitals. A total of 208 (22.7%) isolates were positive for the
mecA
gene by PCR. The molecular characterization of MRSA isolates was carried out by the multiple-locus variable-number tandem repeat fingerprinting, pulsed-field gel electrophoresis, multilocus sequence typing, and staphylococcal chromosomal cassette
mec
(SCC
mec
) typing methods. The Hungarian (PFGE B; ST239, SCC
mec
type III [ST239-III]), Iberian (ST247-I), and Berlin (ST45-IV) clones were predominant, representing approximately 52.9, 11.5, and 10.0% of the MRSA isolates, respectively. A decline in the proportion of earlier MRSA clones, such as ST5-IV (a Pediatric clone), ST80-IV) (a Mediterranean clone), ST239-III (a Polish and Brazilian clone), and ST30-IV (a southwest Pacific clone) was observed. Additionally, the emergence of an MRSA clone with SCC
mec
type V, possibly representing a community-acquired strain, was observed in two hospitals during this study.