bluuebunny/crossref_metadata_2025 huggingface dataset:
Currents in Contemporary Ethics
Authors: Rothstein Mark A.
Published: June 2010

The 2009 pandemic of influenza A (H1N1) was relatively mild, but a subsequent outbreak of pandemic influenza could be much worse. According to projections from the Department of Health and Human Services, the potential health consequences of a severe (1918-like) influenza pandemic in the United States could be literally overwhelming: up to 1.9 million deaths; 90 million people sick; 45 million people needing outpatient care; 9.9 million people hospitalized, of whom 1.485 million would need treatment in an intensive care unit (ICU); and 742,500 patients needing mechanical ventilators. Even a less cataclysmic, moderate pandemic (like 1958 or 1968) would result in 209,000 deaths; 90 million people sick; 45 million people needing outpatient care; 865,000 people hospitalized, of whom 128,750 would need treatment in an ICU; and 64,875 patients needing mechanical ventilators.
Recent Case Developments in Health Law
Authors: Wevers Kate
Published: June 2010

A 2009 decision by a Florida state trial court marks a recent addition to the long line of cases authorizing compelled medical treatment of pregnant women for the benefit of their unborn children. Despite recurring judicial and academic consideration of the issues involved, there is no consensus regarding the correct approach to take in cases that pit a woman's right to refuse medical treatment against the state's interest in protecting fetal health. Burton v. Florida, currently under appeal to Florida's First District Court of Appeals, demonstrates the difficulty of emergency decision-making in this area and the need for robust ex ante consideration of the important interests at stake.

In March 2009, pursuant to a petition by the State of Florida, the Leon County Circuit Court overrode a pregnant woman's informed refusal to consent to medical treatment, and ordered her to remain a hospital inpatient and submit to medical treatment.
Oseltamivir‐resistant influenza A 2009 H1N1 virus in immunocompromised patients
Authors: Couturier Brianne A. , Bender Jeffrey M. , Schwarz Monica A. , Pavia Andrew T. , Hanson Kimberly E. , She Rosemary C.
Published: June 2010

Please cite this paper as: Couturier et al. (2010). Oseltamivir‐resistant influenza A 2009 H1N1 virus in immunocompromised patients. Influenza and Other Respiratory Viruses 4(4), 199–204.

Background  First‐line treatment of influenza A 2009 H1N1 relies on neuraminidase inhibitors such as oseltamivir. Resistance conferred by the H275Y neuraminidase gene mutation is concerning and likely to increase.

Objectives  To characterize oseltamivir resistance in a hospital‐based patient population.

Patients and Methods  All available respiratory specimens positive for influenza A by direct fluorescent antibody, RT‐PCR, or culture from patients at the University of Utah 5/09‐12/09 were collected. Specimens were confirmed as 2009 H1N1 by the Utah Department of Health. RT‐PCR and pyrosequencing were used to test for the H275Y mutation (CDC protocol). PyroMark Q24 AQ software (Qiagen, Valencia, CA, USA) was used to allow for quantitative H275Y mutation analysis. Medical records of patients with resistant virus were reviewed.

Results  We tested 191 influenza A virus‐positive samples from 187 unique patients. Fifty (27%) patients were hospitalized. Four patient specimens (2·1%) were found to carry the H275Y mutation. Three patients were hospitalized, representing 6% of inpatient samples tested. Three patients had undergone hematopoietic stem cell transplant in the past year. Two patients died. Their influenza viruses were confirmed to be oseltamivir‐resistant at an independent reference laboratory and through the Center for Disease Control and Prevention (CDC). One patient reported no history of prior oseltamivir exposure.

Conclusions  Widespread oseltamivir resistance among 2009 H1N1 remains a potential threat. Rapid techniques, such as pyrosequencing, which has the additional benefit of identifying mixed mutant populations of virus, may play a key role in identifying at‐risk individuals and potentially unsuspected cases. Targeted surveillance of immunocompromised patients will be critical toward improving future influenza planning and therapy.
Pulmonary mycobacteriosis caused by Mycobacterium intracellulare in a Tasmanian devil (Sarcophilus harrisii)
Authors: Michael SA , Sangster CR
Published: June 2010

The health of captive Tasmanian devils (Sarcophilus harrisii) is currently of increased interest because wild populations are being decimated by the spread of devil facial tumour disease. This report describes the pathology of an aged captive Tasmanian devil that had a pulmonary mycobacterial infection caused by Mycobacterium intracellulare in addition to multiple neoplastic processes.
Caecal intussusceptions in horses: a New Zealand perspective
Authors: Bell RJW , Textor JA
Published: June 2010

Objective To establish the prevalence of intussusceptions involving the caecum in a population of horses admitted to a university hospital for colic.

Design Retrospective clinical study

Methods Medical records of all horses admitted to the Massey University Veterinary Teaching Hospital between 1991 and 2004 were examined for information of those horses diagnosed with an intussusception involving the caecum.

Results A total of 135 horses were admitted for colic surgery during the study period and 61 horses had a diagnosis of ileocaecal (37), caecocaecal (5) or caecocolic intussusception (19) made either at surgery or necropsy. Of the horses with ileocaecal intussusception, 32 had an incomplete hand‐sewn ileocaecostomy without reduction and 29 survived to discharge. All the horses with caecocaecal intussusceptions were diagnosed preoperatively via rectal examination and/or transabdominal ultrasound: 2 were euthanased at surgery and 3 survived to discharge. In the 19 horses with caecocolic intussusceptions, manually reduction at surgery was performed in 6 and 5 of them survived to discharge. A typhlectomy was performed via a colotomy in 6 horses, 3 of which survived to discharge.

Conclusions The high prevalence of intussusceptions involving the caecum seen at this referral centre may indicate a higher prevalence in New Zealand than is reported elsewhere in the world.

Clinical relevance Intussusceptions involving the caecum should be considered as a differential diagnosis in horses presenting with chronic low‐grade colic. Transabdominal ultrasound is useful for identifying caecocaecal and caecocolic intussusceptions. Hand‐sewn side‐to‐side incomplete ileocaecostomy is a quick, effective and safe method of surgical treatment of ileocaecal intussusceptions.
Serovar profiling ofHaemophilus parasuison Australian farms by sampling live pigs
Authors: Turni C , Blackall PJ
Published: June 2010

Objective Investigate the diversity of serovars ofHaemophilus parasuis(Hps) present in Australian pig herds.

Design Nasal swabs were used to obtain multiple isolates of Hps, which were grouped first by genotyping and then by serotyping representative isolates.

Procedure Swabs were taken from the nasal cavity of just‐weaned healthy pigs from multiparous sows on 12 farms and from post‐weaned pigs of multiparous sows on 1 farm. On 5 of the 13 farms, nasal swabs were also obtained from pigs showing clinical signs suggestive of Glässer's disease. On a further 7 farms, nasal swabs were obtained only from pigs with clinical signs suggestive of Glässer's disease.

Results A total of 556 Hps isolates were genotyped, and 150 isolates were serotyped. Hps was detected on 19 of the 20 farms, including 2 farms with a long history of freedom from Glässer's disease. Isolates of Hps belonging to serovars regarded as potentially pathogenic were obtained from healthy pigs at weaning on 8 of the 10 farms with a history of Glässer's disease outbreaks. Sampling 213 sick pigs yielded 115 isolates of Hps, 99 of which belonged to serovars that were either potentially pathogenic or of unknown pathogenicity. Only 16 isolates from these 213 sick pigs were of a serovar known to be non‐pathogenic.

Conclusion Healthy pigs contain a range of Hps serovars, even on farms free of Glässer's disease. Nasal swabbing of both healthy and sick pigs seems a useful method of serovar profiling of farms.
Photo‐oxidation of 6‐Thioguanine by UVA: The Formation of Addition Products with Low Molecular Weight Thiol Compounds
Authors: Ren Xiaolin , Xu Yao‐Zhong , Karran Peter
Published: June 2010

The thiopurine, 6‐thioguanine (6‐TG) is present in the DNA of patients treated with the immunosuppressant and anticancer drugs azathioprine or mercaptopurine. The skin of these patients is selectively sensitive to UVA radiation—which comprises >90% of the UV light in incident sunlight—and they suffer high rates of skin cancer. UVA irradiation of DNA 6‐TG produces DNA lesions that may contribute to the development of cancer. Antioxidants can protect 6‐TG against UVA but 6‐TG oxidation products may undergo further reactions. We characterize some of these reactions and show that addition products are formed between UVA‐irradiated 6‐TG and N‐acetylcysteine and other low molecular weight thiol compounds including β‐mercaptoethanol, cysteine and the cysteine‐containing tripeptide glutathione (GSH). GSH is also adducted to 6‐TG‐containing oligodeoxynucleotides in an oxygen‐ and UVA‐dependent nucleophilic displacement reaction that involves an intermediate oxidized 6‐TG, guanine sulfonate (GSO3). These photochemical reactions of 6‐TG, particularly the formation of a covalent oligodeoxynucleotide–GSH complex, suggest that crosslinking of proteins or low molecular weight thiol compounds to DNA may be a previously unrecognized hazard in sunlight‐exposed cells of thiopurine‐treated patients.
The ‘LipoYeasts’ project: using the oleaginous yeast Yarrowia lipolytica in combination with specific bacterial genes for the bioconversion of lipids, fats and oils into high‐value products
Authors: Sabirova Julia S. , Haddouche R. , Van Bogaert I. N. , Mulaa F. , Verstraete W. , Timmis K. N. , Schmidt‐Dannert C. , Nicaud J. M. , Soetaert W.
Published: June 2010

The oleochemical industry is currently still dominated by conventional chemistry, with biotechnology only starting to play a more prominent role, primarily with respect to the biosurfactants or lipases, e.g. as detergents, or for biofuel production. A major bottleneck for all further biotechnological applications is the problem of the initial mobilization of cheap and vastly available lipid and oil substrates, which are then to be transformed into high‐value biotechnological, nutritional or pharmacological products. Under the EU‐sponsored LipoYeasts project we are developing the oleaginous yeast Yarrowia lipolytica into a versatile and high‐throughput microbial factory that, by use of specific enzymatic pathways from hydrocarbonoclastic bacteria, efficiently mobilizes lipids by directing its versatile lipid metabolism towards the production of industrially valuable lipid‐derived compounds like wax esters (WE), isoprenoid‐derived compounds (carotenoids, polyenic carotenoid ester), polyhydroxyalkanoates (PHAs) and free hydroxylated fatty acids (HFAs). Different lipid stocks (petroleum, alkane, vegetable oil, fatty acid) and combinations thereof are being assessed as substrates in combination with different mutant and recombinant strains of Y. lipolytica, in order to modulate the composition and yields of the produced added‐value products.
Rituximab in intractable ocular lesions of Behcet’s disease; randomized single‐blind control study (pilot study)
Authors: DAVATCHI Fereydoun , SHAMS Hormoz , REZAIPOOR Mozhgan , SADEGHI‐ABDOLLAHI Bahar , SHAHRAM Farhad , NADJI Abdolhadi , CHAMS‐DAVATCHI Cheyda , AKHLAGHI Massoomeh , FAEZI Tahereh , NADERI Nasim
Published: June 2010

Background:  Ocular lesions, the main morbidity of Behcet’s disease (BD), are the most difficult to treat. The aim of this study was to evaluate the efficacy of rituximab.

Methods:  Inclusion criteria were retinal vasculitis and edema, resistant to cytotoxic drugs. Twenty patients were randomized to a rituximab group (RG) or cytotoxic combination therapy group (CCTG). Rituximab was given in two 1000‐mg courses (15‐day interval). Subjects received methotrexate (15 mg/weekly) with prednisolone (0.5 mg/kg per day). The CCTG received pulse cyclophosphamide (1000 mg/monthly), azathioprine (2–3 mg/kg per day) and prednisolone (0.5 mg/kg per day). The primary endpoint was the overall state of patients’ eyes and the Total Adjusted Disease Activity Index (TADAI). Secondary endpoints were: visual acuity (VA), posterior uveitis (PU), and retinal vasculitis (RV). The baseline data were compared at 6 months by paired sample t‐test and analysis of variance.

Results:  TADAI improved significantly in the RG (t = 3.340, P = 0.009), but not in the CCTG (t = 2.241, P = 0.052). For secondary endpoints (RG/CCTG), the mean VA improved in two patients versus three (2/3), remained unchanged in 1/1, and worsened in 7/6 patients. The mean PU improved significantly in the RG (t = 3.943, P = 0.001), not in the CCTG (t = 2.371, P = 0.028). RV improved, but not statistically (t = 2.027, P = 0.057 vs. t = 1.045, P = 0.31). Edema of retina, disc and macula improved significantly in both, but much better for the RG (t = 2.781, P = 0.012 vs. t = 2.707, P = 0.014).

Conclusion:  Rituximab was efficient in severe ocular manifestations of BD, TADAI improved significantly after 6 months with rituximab, but not with CCT.
Nonparametric Stochastic Modeling of Uncertainty in Rotordynamics—Part I: Formulation
Authors: Murthy Raghavendra , Mignolet Marc P. , El-Shafei Aly
Published: June 2010

A systematic and rational approach is presented for the consideration of uncertainty in rotordynamics systems, i.e., in rotor mass and gyroscopic matrices, stiffness matrix, and bearing coefficients. The approach is based on the nonparametric stochastic modeling technique, which permits the consideration of both data and modeling uncertainty. The former is induced by a lack of exact knowledge of properties such as density, Young’s modulus, etc. The latter occurs in the generation of the computational model from the physical structure as some of its features are invariably ignored, e.g., small anisotropies, or approximately represented, e.g., detailed meshing of gears. The nonparametric stochastic modeling approach, which is briefly reviewed first, introduces uncertainty in reduced order models through the randomization of their system matrices (e.g., stiffness, mass, and damping matrices of nonrotating structural dynamic systems). Here, this methodology is extended to permit the consideration of uncertainty in symmetric and asymmetric rotor dynamic systems. More specifically, uncertainties on the rotor stiffness (stiffness matrix) and/or mass properties (mass and gyroscopic matrices) are first introduced that maintain the symmetry of the rotor. The generalization of these concepts to uncertainty in the bearing coefficients is achieved next. Finally, the consideration of uncertainty in asymmetric rotors is described in detail.
Nonparametric Stochastic Modeling of Uncertainty in Rotordynamics—Part II: Applications
Authors: Murthy Raghavendra , Mignolet Marc P. , El-Shafei Aly
Published: June 2010

In the first part of this series, a comprehensive methodology was proposed for the consideration of uncertainty in rotordynamic systems. This second part focuses on the application of this approach to a simple, yet representative, symmetric rotor supported by two journal bearings exhibiting linear, asymmetric properties. The effects of uncertainty in rotor properties (i.e., mass, gyroscopic, and stiffness matrices) that maintain the symmetry of the rotor are first considered. The parameter λ that specifies the level of uncertainty in the simulation of stiffness and mass uncertain properties (the latter with algorithm I) is obtained by imposing a standard deviation of the first nonzero natural frequency of the free nonrotating rotor. Then, the effects of these uncertainties on the Campbell diagram, eigenvalues and eigenvectors of the rotating rotor on its bearings, forced unbalance response, and oil whip instability threshold are predicted and discussed. A similar effort is also carried out for uncertainties in the bearing stiffness and damping matrices. Next, uncertainties that violate the asymmetry of the present rotor are considered to exemplify the simulation of uncertain asymmetric rotors. A comparison of the effects of symmetric and asymmetric uncertainties on the eigenvalues and eigenvectors of the rotating rotor on symmetric bearings is finally performed to provide a first perspective on the importance of uncertainty-born asymmetry in the response of rotordynamic systems.
Analysis of Thermal Effects in a Cavitating Orifice Using Rayleigh Equation and Experiments
Authors: De Giorgi Maria Grazia , Bello Daniela , Ficarella Antonio
Published: June 2010

The cavitation phenomenon interests a wide range of machines, from internal combustion engines to turbines and pumps of all sizes. It affects negatively the hydraulic machines’ performance and may cause materials’ erosion. The cavitation, in most cases, is a phenomenon that develops at a constant temperature, and only a relatively small amount of heat is required for the formation of a significant volume of vapor, and the flow is assumed isothermal. However, in some cases, such as thermosensible fluids and cryogenic liquid, the heat transfer needed for the vaporization is such that phase change occurs at a temperature lower than the ambient liquid temperature. The focus of this research is the experimental and analytical studies of the cavitation phenomena in internal flows in the presence of thermal effects. Experiments have been done on water and nitrogen cavitating flows in orifices at different operating conditions. Transient growth process of the cloud cavitation induced by flow through the throat is observed using high-speed video images and analyzed by pressure signals. The experiments show different cavitating behaviors at different temperatures and different fluids; this is related to the bubble dynamics inside the flow. So to investigate possible explanations for the influence of fluid temperature and of heat transfer during the phase change, initially, a steady, quasi-one-dimensional model has been implemented to study an internal cavitating flow. The nonlinear dynamics of the bubbles has been modeled by Rayleigh–Plesset equation. In the case of nitrogen, thermal effects in the Rayleigh equation are taken into account by considering the vapor pressure at the actual bubble temperature, which is different from the liquid temperature far from the bubble. A convective approach has been used to estimate the bubble temperature. The quasisteady one-dimensional model can be extensively used to conduct parametric studies useful for fast estimation of the overall performance of any geometric design. For complex geometry, three-dimensional computational fluid dynamic (CFD) codes are necessary. In the present work good agreements have been found between numerical predictions by the CFD FLUENT code, in which a simplified form of the Rayleigh equation taking into account thermal effects has been implemented by external user routines and some experimental observations.
Effects of Pilot Fuel and Liner Cooling on the Flame Structure in a Full Scale Swirl-Stabilized Combustion Setup
Authors: Färber Jens , Koch Rainer , Bauer Hans-Jörg , Hase Matthias , Krebs Werner
Published: June 2010

The flame structure and the limits of operation of a lean premixed swirl flame were experimentally investigated under piloted and nonpiloted conditions. Flame stabilization and blow out limits are discussed with respect to pilot fuel injection and combustor liner cooling for lean operating conditions. Two distinctly different flow patterns are found to develop depending on piloting and liner cooling parameters. These flow patterns are characterized with respect to flame stability, blow out limits, combustion noise, and emissions. The combustion system explored consists of a single burner similar to the burners used in Siemens annular combustion systems. The burner feeds a distinctively nonadiabatic combustion chamber operated with natural gas under atmospheric pressure. Liner cooling is mimicked by purely convective cooling and an additional flow of “leakage air” injected into the combustion chamber. Both additional air flow and the pilot fuel ratio were found to have a strong influence on the flow structure and stability of the flame close to the lean blow off (LBO) limit. It is shown by laser Doppler velocimetry that the angle of the swirl cone is strongly affected by pilot fuel injection. Two distinct types of flow patterns are observed close to LBO in this large scale setup: While nonpiloted flames exhibit tight cone angles and small inner recirculation zones (IRZs), sufficient piloting results in a wide cone angle and a large IRZ. Only in the latter case, the main flow becomes attached to the combustor liner. Flame structures deduced from flow fields and CH-chemiluminescence images depend on both the pilot fuel injection and liner cooling.
Tuning of the Acoustic Boundary Conditions of Combustion Test Rigs With Active Control: Extension to Actuators With Nonlinear Response
Authors: Bothien Mirko R. , Paschereit Christian Oliver
Published: June 2010

In the design process, new burners are generally tested in combustion test rigs. With these experiments, as well as with computational fluid dynamics, finite element calculations, and low-order network models, the burner’s performance in the full-scale engine is sought to be predicted. Especially, information about the thermoacoustic behavior and the emissions is very important. As the thermoacoustics strongly depend on the acoustic boundary conditions of the system, it is obvious that test rig conditions should match or be close to those of the full-scale engine. This is, however, generally not the case. Hence, if the combustion process in the test rig is stable at certain operating conditions, it may show unfavorable dynamics at the same conditions in the engine. In previous works, the authors introduced an active control scheme, which is able to mimic almost arbitrary acoustic boundary conditions. Thus, the test rig properties can be tuned to correspond to those of the full-scale engine. The acoustic boundary conditions were manipulated using woofers. In the present study, an actuator with higher control authority is investigated, which could be used to apply the control scheme in industrial test rigs. The actuator modulates an air mass flow to generate an acoustic excitation. However, in contrast to the woofers, it exhibits a strong nonlinear response regarding amplitude and frequency. Thus, the control scheme is further developed to account for these nonlinear transfer characteristics. This modified control scheme is then applied to change the acoustic boundary conditions of an atmospheric swirl-stabilized combustion test rig. Excellent results were obtained in terms of changing the reflection coefficient to different levels. By manipulating its phase, different resonance frequencies could be imposed without any hardware changes. The nonlinear control approach is not restricted to the actuator used in this study and might therefore be of use for other actuators as well.
High-Resolution Scalar and Velocity Measurements in an Internal Combustion Engine
Authors: Petersen B. R. , Heim D. M. , Ghandhi J. B.
Published: June 2010

High-resolution planar laser-induced fluorescence and particle image velocimetry (PIV) measurements were acquired during the intake stroke in a motored engine to investigate the mixing behavior of in-cylinder flows. The data were analyzed to determine the scalar energy and kinetic energy spectra, which were used to find the corresponding dissipation spectra. The results were compared with a model turbulent spectrum. The scalar energy and scalar dissipation spectra were shown to be resolved through the full dissipation range, enabling the determination of the Batchelor/Kolmogorov length scale and agreed well with the model turbulent spectrum at all but the highest wavenumbers where the effects of random noise were present. The 2% point in the scalar dissipation spectra was used to estimate the Batchelor scale, which was found to be approximately 32 μm. The PIV data, which had a 675 μm interrogation region, were used to calculate a one-dimensional kinetic energy spectrum. The kinetic energy spectrum agreed well with the scalar energy spectrum and the model spectrum up to wavenumbers corresponding to approximately two times the PIV interrogation region size. For the present measurements, this meant that the PIV data were not able to resolve the peak in the dissipation spectrum, i.e., the full high-wavenumber part of the inertial subrange.
Transient Control of Combustion Phasing and Lambda in a Six-Cylinder Port-Injected Natural-Gas Engine
Authors: Kaiadi Mehrzad , Lewander Magnus , Borgqvist Patrick , Tunestal Per , Johansson Bengt
Published: June 2010

Fuel economy and emissions are the two central parameters in heavy duty engines. High exhaust gas recirculation rates combined with turbocharging has been identified as a promising way to increase the maximum load and efficiency of heavy duty spark ignition engines. With stoichiometric conditions, a three way catalyst can be used, which keeps the regulated emissions at very low levels. The Lambda window, which results in very low emissions, is very narrow. This issue is more complex with transient operation, resulting in losing brake efficiency and also catalyst converting efficiency. This paper presents different control strategies to maximize the reliability for maintaining efficiency and emissions levels under transient conditions. Different controllers are developed and tested successfully on a heavy duty six-cylinder port injected natural gas engine. Model predictive control was used to control lambda, which was modeled using system identification. Furthermore, a proportional integral regulator combined with a feedforward map for obtaining maximum brake torque timing was applied. The results show that excellent steady-state and transient performance can be achieved.
Analytical Model to Predict Thermomechanical Relaxation of Shot Peening Induced Residual Stresses
Authors: Huang Min , Potdar Yogesh K. , Akkaram Srikanth
Published: June 2010

Shot peening is widely used to improve the fatigue life of engine blades and rotors by inducing compressive residual stress on component surfaces. However, the residual stresses can relax due to exposure at high service temperature and mechanical loading. A physics-motivated analytical solution is developed to predict the residual stress relaxation at high temperature and under mechanical loading. In this thermomechanical relaxation model, the plastic strains in the shot peening layer and the substrate are obtained analytically by using linear kinematic hardening material law, and the plastic strain evolution at high temperature is modeled by using a recovery strain term. The final residual stress as a function of time, temperature, and mechanical loading is obtained analytically by combining this recovery strain with equilibrium and compatibility conditions. The whole method can be implemented into Microsoft Excel, and is easy to use and validate. As a special case, an analytical closed-form solution to predict the pure thermal relaxation of a shot peening residual stress is developed. The model predictions agree satisfactorily with published experimental measurements.
Numerical analysis of the Poiseuille flow and the thermal transpiration of a rarefied gas through a pipe with a rectangular cross section based on the linearized Boltzmann equation for a hard sphere molecular gas
Authors: Doi Toshiyuki
Published: June 2010

Poiseuille flow and the thermal transpiration of a rarefied gas through a long straight pipe with a rectangular cross section are analyzed numerically based on the linearized Boltzmann equation for a hard sphere molecular gas. A deterministic numerical analysis based on the finite difference is carried out, where the collision integral is evaluated with the aid of the numerical kernel method [Y. Sone et al., Phys. Fluids A 1, 363 (1989)]. The numerical solution, the mass flow rate as well as the macroscopic variables, is presented and discussed for a wide range of the Knudsen number and various aspect ratios of the cross section.
Distribution in Tissue and Seasonal Variation of Norovirus Genogroup I and II Ligands in Oysters
Authors: Maalouf Haifa , Zakhour Maha , Le Pendu Jacques , Le Saux Jean-Claude , Atmar Robert L. , Le Guyader Françoise S.
Published: June 2010

Bivalve molluscan shellfish, such as oysters, filter large volumes of water as part of their feeding activities and are able to accumulate and concentrate different types of pathogens, particularly noroviruses, from fecal human pollution. Based on our previous observation of a specific binding of the Norwalk strain (prototype norovirus genogroup I) to the oyster digestive tract through an A-like carbohydrate structure indistinguishable from human blood group A antigen and on the large diversity between strains in terms of carbohydrate-binding specificities, we evaluated the different ligands implicated in attachment to oysters tissues of strains representative of two main genogroups of human norovirus. The GI.1 and GII.4 strains differed in that the latter recognized a sialic acid-containing ligand, present in all tissues, in addition to the A-like ligand of the digestive tract shared with the GI.1 strain. Furthermore, bioaccumulation experiments using wild-type or mutant GI.1 Viruslike particles showed accumulation in hemocytes largely, but not exclusively, based on interaction with the A-like ligand. Moreover, a seasonal effect on the expression of these ligands was detected, most visibly for the GI.1 strain, with a peak in late winter and spring, a period when GI strains are regularly involved in oyster-related outbreaks. These observations may explain some of the distinct epidemiological features of strains from different genogroups.
Influence of Temperature and Predation on Survival ofSalmonella entericaSerovar Typhimurium and Expression ofinvAin Soil and Manure-Amended Soil
Authors: García R. , Bælum J. , Fredslund L. , Santorum P. , Jacobsen C. S.
Published: June 2010

The effects of three temperatures (5, 15, and 25°C) on the survival ofSalmonella entericaserovar Typhimurium in topsoil were investigated in small microcosms by three different techniques: plate counting,invAgene quantification, andinvAmRNA quantification. Differences in survival were related to the effect of protozoan predation. Tetracycline-resistantSalmonellaserovar Typhimurium was inoculated into soil and manure-amended soil at 1.5 × 108cells g soil−1. Population densities were determined by plate counting and by molecular methods and monitored for 42 days. Simultaneous extraction of RNA and DNA, followed by quantitative PCR, was used to investigateinvAgene levels and expression. Analysis by these three techniques showed thatSalmonellaserovar Typhimurium survived better at 5°C. Comparing DNA and CFU levels, significantly higher values were determined by DNA-based techniques.invAmRNA levels showed a fast decrease in activity, with no detectable mRNA after an incubation period of less than 4 days in any of the soil scenarios. A negative correlation was found betweenSalmonella serovar Typhimurium CFU levels and protozoan most probable numbers, and we propose the role of the predator-prey interaction as a factor to explain the die-off of the introduced strain by both culture- and DNA quantification-based methods. The results indicate that temperature, manure, and protozoan predation are important factors influencing the survival ofSalmonellaserovar Typhimurium in soil.
Microbial Community Development in a Dynamic Gut Model Is Reproducible, Colon Region Specific, and Selective forBacteroidetesandClostridiumCluster IX
Authors: Van den Abbeele Pieter , Grootaert Charlotte , Marzorati Massimo , Possemiers Sam , Verstraete Willy , Gérard Philippe , Rabot Sylvie , Bruneau Aurélia , El Aidy Sahar , Derrien Muriel , Zoetendal Erwin , Kleerebezem Michiel , Smidt Hauke , Van de Wiele Tom
Published: June 2010

Dynamic, multicompartmentin vitrogastrointestinal simulators are often used to monitor gut microbial dynamics and activity. These reactors need to harbor a microbial community that is stable upon inoculation, colon region specific, and relevant toin vivoconditions. Together with the reproducibility of the colonization process, these criteria are often overlooked when the modulatory properties from different treatments are compared. We therefore investigated the microbial colonization process in two identical simulators of the human intestinal microbial ecosystem (SHIME), simultaneously inoculated with the same human fecal microbiota with a high-resolution phylogenetic microarray: the human intestinal tract chip (HITChip). Following inoculation of thein vitrocolon compartments, microbial community composition reached steady state after 2 weeks, whereas 3 weeks were required to reach functional stability. This dynamic colonization process was reproducible in both SHIME units and resulted in highly diverse microbial communities which were colon region specific, with the proximal regions harboring saccharolytic microbes (e.g.,Bacteroidesspp. andEubacteriumspp.) and the distal regions harboring mucin-degrading microbes (e.g.,Akkermansiaspp.). Importantly, the shift from anin vivoto anin vitroenvironment resulted in an increasedBacteroidetes/Firmicutesratio, whereasClostridiumcluster IX (propionate producers) was enriched compared to clusters IV and XIVa (butyrate producers). This was supported by proportionally higherin vitropropionate concentrations. In conclusion, high-resolution analysis ofin vitro-cultured gut microbiota offers new insight on the microbial colonization process and indicates the importance of digestive parameters that may be crucial in the development of newin vitromodels.
Metatranscriptomic Analysis of the Response of River Biofilms to Pharmaceutical Products, Using Anonymous DNA Microarrays
Authors: Yergeau Etienne , Lawrence John R. , Waiser Marley J. , Korber Darren R. , Greer Charles W.
Published: June 2010

Pharmaceutical products are released at low concentrations into aquatic environments following domestic wastewater treatment. Such low concentrations have been shown to induce transcriptional responses in microorganisms, which could have consequences on aquatic ecosystem dynamics. In order to test if these transcriptional responses could also be observed in complex river microbial communities, biofilm reactors were inoculated with water from two rivers of differing trophic statuses and subsequently treated with environmentally relevant doses (ng/liter to μg/liter range) of four pharmaceuticals (erythromycin [ER], gemfibrozil [GM], sulfamethazine [SN], and sulfamethoxazole [SL]). To monitor functional gene expression, we constructed a 9,600-feature anonymous DNA microarray platform onto which cDNA from the biofilms was hybridized. Pharmaceutical treatments induced both positive and negative transcriptional responses from biofilm microorganisms. For instance, ER induced the transcription of several stress, transcription, and replication genes, while GM, a lipid regulator, induced transcriptional responses from several genes involved in lipid metabolism. SN caused shifts in genes involved in energy production and conversion, and SL induced responses from a range of cell membrane and outer envelope genes, which in turn could affect biofilm formation. The results presented here demonstrate for the first time that low concentrations of small molecules can induce transcriptional changes in a complex microbial community. The relevance of these results also demonstrates the usefulness of anonymous DNA microarrays for large-scale metatranscriptomic studies of communities from differing aquatic ecosystems.
Epigenetics in Plasmodium: What Do We Really Know?
Authors: Merrick Catherine J. , Duraisingh Manoj T.
Published: June 2010

In the burgeoning field ofPlasmodiumgene expression, there are—to borrow some famous words from a former U.S. Secretary of Defense—“known knowns, known unknowns, and unknown unknowns.” This is in itself an important achievement, since it is only in the past decade that facts have begun to move from the third category into the first. Nevertheless, much remains in the middle ground of known or suspected “unknowns.” It is clear that the malaria parasite controls vital virulence processes such as host cell invasion and cytoadherence at least partly via epigenetic mechanisms, so a proper understanding of epigenetic transcriptional control in this organism should have great clinical relevance.Plasmodium, however, is an obligate intracellular parasite: it operates not in a vacuum but rather in the complicated context of its metazoan hosts. Therefore, as valuable data about the parasite's basic epigenetic machinery begin to emerge, it becomes increasingly important to relatein vitrostudies to the situationin vivo. This review will focus upon the challenge of understandingPlasmodiumepigenetics in an integrated manner, in the human and insect hosts as well as the petri dish.
Molybdenum Incorporation in Tungsten Aldehyde Oxidoreductase Enzymes from
Pyrococcus furiosus
Authors: Sevcenco Ana-Maria , Bevers Loes E. , Pinkse Martijn W. H. , Krijger Gerard C. , Wolterbeek Hubert T. , Verhaert Peter D. E. M. , Hagen Wilfred R. , Hagedoorn Peter-Leon
Published: June 2010

The hyperthermophilic archaeon
Pyrococcus furiosus
expresses five aldehyde oxidoreductase (AOR) enzymes, all containing a tungsto-bispterin cofactor. The growth of this organism is fully dependent on the presence of tungsten in the growth medium. Previous studies have suggested that molybdenum is not incorporated in the active site of these enzymes. Application of the radioisotope
99
Mo in metal isotope native radioautography in gel electrophoresis (MIRAGE) technology to
P. furiosus
shows that molybdenum can in fact be incorporated in all five AOR enzymes. Mo(V) signals characteristic for molybdopterin were observed in formaldehyde oxidoreductase (FOR) in electron paramagnetic resonance (EPR)-monitored redox titrations. Our finding that the aldehyde oxidation activity of FOR and WOR5 (W-containing oxidoreductase 5) correlates only with the residual tungsten content suggests that the Mo-containing AORs are most likely inactive. An observed W/Mo antagonism is indicative of tungstate-dependent negative feedback of the expression of the tungstate/molybdate ABC transporter. An intracellular selection mechanism for tungstate and molybdate processing has to be present, since tungsten was found to be preferentially incorporated into the AORs even under conditions with comparable intracellular concentrations of tungstate and molybdate. Under the employed growth conditions of starch as the main carbon source in a rich medium, no tungsten- and/or molybdenum-associated proteins are detected in
P. furiosus
other than the high-affinity transporter, the proteins of the metallopterin insertion machinery, and the five W-AORs.
The Native 67-Kilodalton Minor Fimbria ofPorphyromonas gingivalisIs a Novel Glycoprotein with DC-SIGN-Targeting Motifs
Authors: Zeituni Amir E. , McCaig William , Scisci Elizabeth , Thanassi David G. , Cutler Christopher W.
Published: June 2010

We recently reported that the oral mucosal pathogenPorphyromonas gingivalis, through its 67-kDa Mfa1 (minor) fimbria, targets the C-type lectin receptor DC-SIGN for invasion and persistence within human monocyte-derived dendritic cells (DCs). The DCs respond by inducing an immunosuppressive and Th2-biased CD4+T-cell response. We have now purified the native minor fimbria by ion-exchange chromatography and sequenced the fimbria by tandem mass spectrometry (MS/MS), confirming its identity and revealing two putative N-glycosylation motifs as well as numerous putative O-glycosylation sites. We further show that the minor fimbria is glycosylated by ProQ staining and that glycosylation is partially removed by treatment with β(1-4)-galactosidase, but not by classic N- and O-linked deglycosidases. Further monosaccharide analysis by gas chromatography-mass spectrometry (GC-MS) confirmed that the minor fimbria contains the DC-SIGN-targeting carbohydrates fucose (1.35 nmol/mg), mannose (2.68 nmol/mg),N-acetylglucosamine (2.27 nmol/mg), andN-acetylgalactosamine (0.652 nmol/mg). Analysis by transmission electron microscopy revealed that the minor fimbria forms fibers approximately 200 nm in length that could be involved in targeting or cross-linking DC-SIGN. These findings shed further light on molecular mechanisms of invasion and immunosuppression by this unique mucosal pathogen.
1885 Cholera Controversy: Klein versus Koch: Figure 1
Authors: Atalic Bruno
Published: June 2010

This paper will try to give new insight into the Cholera Controversy, which occurred 125 years ago. The majority of papers already written on the topic have emphasised the role of Robert Koch who described the comma bacillus as the cause of cholera epidemics. At the same time they have marginalised the role of Emanuel Edward Klein by stating that he was wrong when he objected to Robert Koch's statement, because as an employee of the British government he was politically motivated. Moreover, they have paid barely any attention to Klein's writings on the subject. In this paper I will try to approach his attitudes from the scientific, not political, perspective and try to explain the reasons why he challenged Koch.
THERMOSIZE EFFECTS IN CONFINED QUANTUM GAS SYSTEMS
Authors: LIN TONGLING , SU GUOZHEN , OU CONGJIE , LIN BIHONG , LE MÉHAUTÉ A. , WANG QIUPING A. , CHEN JINCAN
Published: June 2010

Based on the grand potentials of ideal quantum gases, the number of particles, internal energy, three diagonal components of the pressure tensor, and other thermodynamic quantities of the ideal quantum gas systems confined in a rectangular box are analytically derived. It is found that the internal energy of the systems is non-extensive and that the other thermodynamic quantities, which are extensive under the thermodynamic limit condition, are also non-extensive. It is also found that the pressure tensor of the quantum gas systems in a confined space is, in general, no longer isotropic because of the geometric effect of the boundary. Moreover, the influence of the size effect of the containers on the properties of the systems and the thermosize effects in the confined quantum gas systems such as the Seebeck-like, Peltier-like and Thomson-like thermosize effects are discussed with the help of the assumption of local equilibrium. It is very significant to note that the new concept of the "mix" heat capacity, which is neither the heat capacity at constant pressure nor the heat capacity at constant volume, must be introduced in the investigation of Thomson-like thermosize effect. The results obtained may be directly used to analyze the thermodynamic properties and thermosize effects of the confined classical gas.
TWO-MODE ENTANGLEMENT AND SQUEEZING IN A THREE-LEVEL CASCADE ATOMIC SYSTEM
Authors: PING YUN-XIA
Published: June 2010

The generation and evolution of entanglement and squeezing for the two-mode fields are discussed in a cascade three-level atomic system. Two photons of a strong external pump field induce atomic coherence between the top and bottom levels. The dynamics of this system in the presence of cavity losses is studied. It is shown that entanglement and squeezing between the two modes increase initially, then decrease and eventually disappear. The periods of them are extended with the increasing of the pump field intensity. The effects of the cavity losses on squeezing and entanglement are also discussed.
ATOMISTIC SIMULATION OF THE MECHANICAL BEHAVIOR OF Ni3Al NANOWIRES
Authors: CHENG DENGMU , WANG SHENGJIE , WANG CHUNDONG , WANG ZHIGUO
Published: June 2010

Simulations have been carried out on [001]-oriented Ni 3 Al nanowires with square cross-section with the purpose to investigate the mechanism of failure under tensile and compressive strain. Simulation results show that the elastic limit of the nanowire is up to about 15% strain with the yield stress of 5.99–6.48 GPa under tensile strain. Under the elastic stage, the deformation is carried mainly through the uniform elongation of the bonds between atoms. With more tensile strain, the slips in the {111} planes occur to accommodate the applied strain at room temperature under tensile strain. And the nanowires accommodate the compressive strain by forming the twins within the nanowires.
AN INVESTIGATION ON THE DIELECTRIC PROPERTIES OF POLYANILINE-BASED NANOCOMPOSITE
Authors: JIANG J. , AI L. H.
Published: June 2010

Polyaniline/ LiNi 0.5 Gd 0.08 Fe 1.92 O 4 nanocomposite was synthesized by an in-situ polymerization of aniline in the presence of LiNi 0.5 Gd 0.08 Fe 1.92 O 4 particles. The dielectric properties of the as-prepared polyaniline-based nanocomposite were investigated using an Agilent E4991A RF Impedance/Material Analyzer at room temperature in the frequency range from 1 MHz to 1 GHz. The real (ε') and imaginary part (ε″) of complex permittivity, and dissipation factor ( tan δ) were found to be frequency-dependent, which decreased with increasing of frequency. It was shown that ε', ε″ and tan δ of the nanocomposite were lower than those of pristine polyaniline. In order to investigate the dielectric process in detail, the complex electric modulii derived from the complex permittivity were analyzed as a function of the frequency.
INTEGRABILITY AND SUPERINTEGRABILITY OF TODA SYMPLECTIC MAP WITH MULTIPLE EIGENPARAMETERS
Authors: CHENG JUNWEI , ZHOU RUGUANG
Published: June 2010

The integrability and superintegrability of Toda symplectic map with multiple eigenparameters is studied. We show that if the multiplicity of an eigenparameter is r for the Toda symplectic map on a 2N-dimensional phase space then N + r - 2 functionally independent invariants can be constructed. Therefore, if the multiplicity r is greater than 2, the Toda symplectic map is not only integrable but also superintegrable.
A SLICE THEOREM FOR QUIVERS WITH AN INVOLUTION
Authors: BOCKLANDT RAF
Published: June 2010

We study the Luna slice theorem in the case of quivers with an involution or supermixed quivers as introduced by Zubkov in [6]. We construct an analogue to the notion of a local quiver setting described in [3]. We use this technique to determine dimension vectors of simple supermixed representations.
ANALYSIS OF qPCR DATA BY CONVERTING EXPONENTIALLY RELATED Ct VALUES INTO LINEARLY RELATED X0 VALUES
Authors: THOMSEN RUNE , SØLVSTEN CHRISTINA ANE ELISABETH , LINNET TOKE ELBEK , BLECHINGBERG JENNY , NIELSEN ANDERS LADE
Published: June 2010

A common method for calculating results from qPCR experiments is the comparative Ct method, also called the 2-ΔΔCt method. However, several assumptions are included in the 2-ΔΔCt method and standard statistical analyses are not directly applicable. Here, we describe a different method, the X0 method, for result calculations and statistical analysis from qPCR experiments. The X0 method differs from the 2-ΔΔCt method by introducing a conversion of the exponentially related Ct values into linearly related X0 values, which represent the amount of starting material in a qPCR experiment. Results calculated by the X0 method are illustrated for qPCR experiments with technical and biological replicates, including procedures to calculate standard deviations. Incorporation of primer efficiencies in calculations by the X0 method is also described. Altogether, the X0 method constitutes a very simple and accurate alternative to the 2-ΔΔCt method for result calculations from qPCR data.