bluuebunny/crossref_metadata_2025 huggingface dataset:
Mathematical Modeling of Pneumatic Pipes in a Simulation of Heterogeneous Engineering Systems
Authors: Kamiński Zbigniew
Published: December 2011

Pipes are widely used in hydraulic and pneumatic subsystems for transferring energy or signals. Accurate prediction of pressure transients is very important in the drive and control circuits of complex fluid-line systems. Based on the approximation of Navier-Stokes equations for one-dimensional flow, a mathematical model of the pneumatic pipe with lumped parameters was developed using ordinary differential equations, which can be easily implemented in most computer programs for the simulation of complex heterogeneous engineering systems. Implemented in Matlab-Simulink software, the computer model of the pipe makes it possible to determine the influence of capacitance, inertance, resistance and heat exchange on the dynamic characteristics of the control and power circuits of pneumatic systems. An advantage of the model is that various functions can be selected to describe linear resistances and local resistances are taken into account, particularly at the inlet and outlet. Such resistances largely affect flow resistances in short tubes (up to 10 m) that can be found, e.g., in pneumatic brake systems of road vehicles. Confirmed by Kolmogorov-Smirnov test results, the consistency of the pressure curves obtained in experimental and simulation tests proves the implemented tube model to be useful for the calculations of pneumatic system dynamics.
Well Completion for Effective Deliquification of Natural Gas Wells
Authors: Yilin Wang John
Published: December 2011

Liquid loading has been a problem in natural gas wells for several decades. With gas fields becoming mature and gas production rates dropping below the critical rate, deliquification becomes more and more critical for continuous productivity and profitability of gas wells. Current methods for solving liquid loading in the wellbore include plunger lift, velocity string, surfactant, foam, well cycling, pumps, compression, swabbing, and gas lift. All these methods are to optimize the lifting of liquid up to surface, which increases the operating cost, onshore, and offshore. However, the near-wellbore liquid loading is critical but not well understood. Through numerical reservoir simulation studies, effect of liquid loading on gas productivity and recovery has been quantified in two aspects: backup pressure and near-wellbore liquid blocking by considering variable reservoir permeability, reservoir pressure, formation thickness, liquid production rate, and geology. Based on the new knowledge, we have developed well completion methods for effective deliquifications. These lead to better field operations and increased ultimate gas recovery.
An Analysis of Noise Characteristics of Drill Bits
Authors: Gradl Christian , Eustes Alfred W. , Thonhauser Gerhard
Published: December 2011

There have been papers that analyze the relationship between bit design and a bit’s vibrational characteristics. These papers typically are based on the analysis of three-axis near-bit down-hole vibration sensors. In this paper, the authors take a simpler approach. Using a standard microphone literally pointed at the bit, they record the noise of the bit/rock interaction while drilling and analyze the resulting noise for these bit vibrational characteristics. The data were gathered at the Colorado School of Mines in Golden, CO. The noise of a PDC core, roller cone, and diamond core bits were recorded under various weight and rotary speeds using a microphone and a vertically mounted uniaxial geophone (used for confirming the data recorded on the microphones). Using a Fast Fourier Transform, the frequency spectra were extracted from the recorded data and analyzed. The data were normalized for rotational speed. The results of the frequency analysis of the roller cone, the PDC, and the natural diamond bits are presented in this paper. The major differences in the three bit frequency characteristics could be detected and furthermore, for drag bits, the frequency characteristics could be related to the bit’s design. The frequency spectra of the roller cone bit can best be described with a general high amplitude level that is relatively evenly distributed over the whole frequency spectrum. The drag bit data showed a strong relationship between the number and arrangement of cutting elements and frequency peaks on a plot of amplitude versus cycles per revolution. Frequency peaks were observed at multiples of the number of cutting elements. In general this relationship was strongly visible on the PDC bit data but not as strongly visible on the diamond bit data. The conclusion is that bit characteristics can be determined using only the noise of a bit. Potential applications of this research include detecting and diagnosing bit problems (e.g., broken teeth and bit balling) in real time using simple microphone based acoustic data.
Electrokinetic Flow Dynamics of Weakly Aggregated λDNA Confined in Nanochannels
Authors: Uehara Satoshi , Shintaku Hirofumi , Kawano Satoyuki
Published: December 2011

Flow dynamics in nano-scaled structures such as nanochannels and nanopores have recently become important in developing next-generation high-speed DNA sequencers. In the present paper, we report the electrokinetic flow dynamics of λDNA confined in nanochannels having heights that are smaller than the molecular radius of gyration. Nanochannels of varying heights of from 330 to 650 nm were used in the experiments in order to systematically investigate the effect of confinement. Weakly aggregated λDNA flowed in a direction opposite to an applied electric field as a result of the competition of electrophoresis and electroosmotic flows. The terminal velocity of λDNA was proportional to the strength of the electric field, and the mobility was found to decrease with the channel height. A simple theoretical model explaining the decrease in the mobility was developed taking into account the shear stress due to small clearances between λDNA and the walls of nanochannels. The validity of the model was confirmed by reasonable agreement between the theoretical and experimental results. The theoretical model and the transport properties under confinement provide basic design data for the development of next-generation DNA sequencers.
Experimental and Numerical Investigation of Single Bubble Dynamics in a Two-Phase Bubbly Medium
Authors: Jayaprakash Arvind , Singh Sowmitra , Chahine Georges
Published: December 2011

The dynamics of a bubble in a dilute bubbly water-air mixture is investigated experimentally and the results compared with a simple homogeneous compressible fluid model in order to elucidate the requirements from a better advanced numerical solution. The experiments are conducted in view of providing input and validation for an advanced bubbly flow numerical model we are developing. Corrections for classical approaches where in the two-phase flow modeling the dynamics of individual bubble is based on spherical isolated bubble dynamics in the liquid or an equivalent homogeneous medium are sought. The main/primary bubble is produced by an underwater spark discharge from charged capacitors, while the bubbly medium is generated using electrolysis. The size of the main bubble is controlled by the discharge voltage, the capacitors size, and the ambient pressure in the container. The size and concentration of the fine bubbles is controlled by the electrolysis voltage, the length, diameter, arrangement, and type of the wires, and also by the pressure imposed in the container. This enables parametric study of the factors controlling the dynamics of the primary bubble and development of relationships between the primary bubble characteristic quantities such as achieved maximum bubble radius and bubble period and the characteristics of the surrounding two-phase medium: micro bubble sizes and void fraction. The dynamics of the main bubble and of the mixture is observed using high speed video photography. The void fraction of the bubbly mixture in the fluid domain is deduced from image analysis of the high speed movies and obtained as a function of time and space. The interaction between the primary bubble and the bubbly medium is analyzed using both field pressure measurements and high-speed videography. Parameters such as the primary bubble energy and the bubble mixture density (void fraction) are varied, and their effects studied. The experimental data is then compared to a simple compressible fluid medium model which accounts for the change in the medium properties in space and time. This helps illustrate where such simple models are valid and where they need improvements. This information is valuable for the parallel development of an Eulerian-Lagrangian code, which accounts for the dynamics of bubbles in the field and their interaction.
Concepts in nuclear science illustrated by experiments with radon
Authors: Angell C. T. , Kaplan A. C. , Seelig J. D. , Norman E. B. , Pedretti M.
Published: December 2011

Basic concepts in nuclear science can be difficult for students to grasp. To address this problem, we have developed a set of experiments using radon gas to enable students to explore the concepts of decay modes, half-lives, decay chains, and secular equilibrium. The measurements can be performed at several levels of sophistication. Measurements using Geiger-Mueller counters, high-purity germanium detectors, and surface barrier silicon detectors are described.
Modeling the exit velocity of a compressed air cannon
Authors: Rohrbach Z. J. , Buresh T. R. , Madsen M. J.
Published: December 2011

The use of compressed air cannons in an undergraduate laboratory provides a way to illustrate the connection between diverse physics concepts, such as conservation of momentum, the work-kinetic energy theorem, gas expansion, air drag, and elementary Newtonian mechanics. However, it is not clear whether the expansion of the gas in the cannon is an adiabatic or an isothermal process. We built an air cannon that utilizes a diaphragm valve to release the pressurized gas and found that neither process accurately predicts the exit velocity of our projectile. We discuss a model based on the flow of air through the valve, which is in much better agreement with our data.
Fossilized Nuclei and Germination Structures Identify Ediacaran “Animal Embryos” as Encysting Protists
Authors: Huldtgren Therese , Cunningham John A. , Yin Chongyu , Stampanoni Marco , Marone Federica , Donoghue Philip C. J. , Bengtson Stefan
Published: December 2011

High-resolution imaging of 570-million-year-old fossils suggests that they were not remnants of early animals.
Polymerase Exchange During Okazaki Fragment Synthesis Observed in Living Cells
Authors: Lia Giuseppe , Michel Bénédicte , Allemand Jean-François
Published: December 2011

Dynamic Replication

In all organisms, DNA replication involves a multiprotein complex called the replisome. Active
Escherichia coli
replisomes contain three copies of DNA polymerase III (Pol III).

Lia
et al.

(p.
328
, published online 22 December) used single-molecule spectroscopy to probe the dynamics of single proteins during
E. coli
replication in vivo. The results confirmed the presence of three Pol III molecules in the active replisome, with regular exchange of one of these Pol III's with one from the pool. Coordination with single-stranded DNA content suggests the Pol III that performs lagging-strand synthesis is exchanged so that a new Pol III is used for the synthesis of each Okazaki fragment.
Angular Momentum Conservation in Dipolar Energy Transfer
Authors: Guo Dong , Knight Troy E. , McCusker James K.
Published: December 2011

Spin states restrict energy transfer between donor and acceptor chromophores that appear otherwise compatible.
Genomic and Physiological Characterization of the Verrucomicrobia Isolate Diplosphaera colitermitum gen. nov., sp. nov., Reveals Microaerophily and Nitrogen Fixation Genes
Authors: Wertz John T. , Kim Eunji , Breznak John A. , Schmidt Thomas M. , Rodrigues Jorge L. M.
Published: December 2011

Previously we reported the cultivation of novel verrucomicrobia, including strain TAV2 (93% 16S rRNA gene identity to its nearest cultivated representative,
Opitutus terreae
PB90-1) from the gut of the termite
Reticulitermes flavipes
. To gain better insight into the
Verrucomicrobia
as a whole and understand the role of verrucomicrobia within the termite gut ecosystem, we analyzed a draft genome and undertook a physiological characterization of TAV2. Strain TAV2 is an autochthonous member of the
R. flavipes
gut microbiota and groups phylogenetically among diverse
Verrucomicrobia
from
R. flavipes
and other termites that are represented by 16S rRNA gene sequences alone. TAV2 is a microaerophile, possessing a high-affinity
cbb
3
-type terminal oxidase-encoding gene and exhibiting an optimum growth rate between 2 and 8% (vol/vol) oxygen. It has the genetic potential to degrade cellulose, an important function within termite guts, but its
in vitro
substrate utilization spectrum was limited to starch and a few mono- and disaccharides. Growth occurred on nitrogen-free medium, and genomic screening revealed genes for dinitrogenases, heretofore detected in only a few members of the
Verrucomicrobia
. This represents the first (i) characterization of a verrucomicrobial species from the termite gut, (ii) report of
nif
and
anf
genes in a nonacidophilic verrucomicrobial species, and (iii) description of a microaerophilic genotype and phenotype in this phylum of bacteria. The genetic and physiological distinctiveness of TAV2 supports its recognition as the type strain of a new genus and species, for which the name
Diplosphaera colitermitum
gen. nov., sp. nov., is proposed.
Calcium Increases Xylella fastidiosa Surface Attachment, Biofilm Formation, and Twitching Motility
Authors: Cruz Luisa F. , Cobine Paul A. , De La Fuente Leonardo
Published: December 2011

Xylella fastidiosais a plant-pathogenic bacterium that forms biofilms inside xylem vessels, a process thought to be influenced by the chemical composition of xylem sap. In this work, the effect of calcium on the production ofX. fastidiosabiofilm and movement was analyzed underin vitroconditions. After a dose-response study with 96-well plates using eight metals, the strongest increase of biofilm formation was observed when medium was supplemented with at least 1.0 mM CaCl2. The removal of Ca by extracellular (EGTA, 1.5 mM) and intracellular [1,2-bis(o-aminophenoxy)ethane-N,N,N′,N′-tetraacetic acid acetoxymethyl ester (BAPTA/AM), 75 μM] chelators reduced biofilm formation without compromising planktonic growth. The concentration of Ca influenced the force of adhesion to the substrate, biofilm thickness, cell-to-cell aggregation, and twitching motility, as shown by assays with microfluidic chambers and other assays. The effect of Ca on attachment was lost when cells were treated with tetracycline, suggesting that Ca has a metabolic or regulatory role in cell adhesion. A double mutant (fimA pilO) lacking type I and type IV pili did not improve biofilm formation or attachment when Ca was added to the medium, while single mutants of type I (fimA) or type IV (pilB) pili formed more biofilm under conditions of higher Ca concentrations. The concentration of Ca in the medium did not significantly influence the levels of exopolysaccharide produced. Our findings indicate that the role of Ca in biofilm formation may be related to the initial surface and cell-to-cell attachment and colonization stages of biofilm establishment, which rely on critical functions by fimbrial structures.
Isolation of a Novel Cutinase Homolog with Polyethylene Terephthalate-Degrading Activity from Leaf-Branch Compost by Using a Metagenomic Approach
Authors: Sulaiman Sintawee , Yamato Saya , Kanaya Eiko , Kim Joong-Jae , Koga Yuichi , Takano Kazufumi , Kanaya Shigenori
Published: December 2011

The gene encoding a cutinase homolog, LC-cutinase, was cloned from a fosmid library of a leaf-branch compost metagenome by functional screening using tributyrin agar plates. LC-cutinase shows the highest amino acid sequence identity of 59.7% to
Thermomonospora curvata
lipase. It also shows the 57.4% identity to
Thermobifida fusca
cutinase. When LC-cutinase without a putative signal peptide was secreted to the periplasm of
Escherichia coli
cells with the assistance of the pelB leader sequence, more than 50% of the recombinant protein, termed LC-cutinase*, was excreted into the extracellular medium. It was purified and characterized. LC-cutinase* hydrolyzed various fatty acid monoesters with acyl chain lengths of 2 to 18, with a preference for short-chain substrates (C
4
substrate at most) most optimally at pH 8.5 and 50°C, but could not hydrolyze olive oil. It lost activity with half-lives of 40 min at 70°C and 7 min at 80°C. LC-cutinase* had an ability to degrade poly(ε-caprolactone) and polyethylene terephthalate (PET). The specific PET-degrading activity of LC-cutinase* was determined to be 12 mg/h/mg of enzyme (2.7 mg/h/μkat of
p
NP-butyrate-degrading activity) at pH 8.0 and 50°C. This activity is higher than those of the bacterial and fungal cutinases reported thus far, suggesting that LC-cutinase* not only serves as a good model for understanding the molecular mechanism of PET-degrading enzyme but also is potentially applicable for surface modification and degradation of PET.
Accurate, Rapid Taxonomic Classification of Fungal Large-Subunit rRNA Genes
Authors: Liu Kuan-Liang , Porras-Alfaro Andrea , Kuske Cheryl R. , Eichorst Stephanie A. , Xie Gary
Published: December 2011

Taxonomic and phylogenetic fingerprinting based on sequence analysis of gene fragments from the large-subunit rRNA (LSU) gene or the internal transcribed spacer (ITS) region is becoming an integral part of fungal classification. The lack of an accurate and robust classification tool trained by a validated sequence database for taxonomic placement of fungal LSU genes is a severe limitation in taxonomic analysis of fungal isolates or large data sets obtained from environmental surveys. Using a hand-curated set of 8,506 fungal LSU gene fragments, we determined the performance characteristics of a naïve Bayesian classifier across multiple taxonomic levels and compared the classifier performance to that of a sequence similarity-based (BLASTN) approach. The naïve Bayesian classifier was computationally more rapid (>460-fold with our system) than the BLASTN approach, and it provided equal or superior classification accuracy. Classifier accuracies were compared using sequence fragments of 100 bp and 400 bp and two different PCR primer anchor points to mimic sequence read lengths commonly obtained using current high-throughput sequencing technologies. Accuracy was higher with 400-bp sequence reads than with 100-bp reads. It was also significantly affected by sequence location across the 1,400-bp test region. The highest accuracy was obtained across either the D1 or D2 variable region. The naïve Bayesian classifier provides an effective and rapid means to classify fungal LSU sequences from large environmental surveys. The training set and tool are publicly available through the Ribosomal Database Project (
http://rdp.cme.msu.edu/classifier/classifier.jsp
).
Desiccation as a Long-Term Survival Mechanism for the Archaeon Methanosarcina barkeri
Authors: Anderson Kimberly L. , Apolinario Ethel E. , Sowers Kevin R.
Published: December 2011

Viable methanogens have been detected in dry, aerobic environments such as dry reservoir sediment, dry rice paddies and aerobic desert soils, which suggests that methanogens have mechanisms for long-term survival in a desiccated state. In this study, we quantified the survival rates of the methanogenic archaeon
Methanosarcina barkeri
after desiccation under conditions equivalent to the driest environments on Earth and subsequent exposure to different stress factors. There was no significant loss of viability after desiccation for 28 days for cells grown with either hydrogen or the methylotrophic substrates, but recovery was affected by growth phase, with cells desiccated during the stationary phase of growth having a higher rate of recovery after desiccation. Synthesis of methanosarcinal extracellular polysaccharide (EPS) significantly increased the viability of desiccated cells under both anaerobic and aerobic conditions compared with that of non-EPS-synthesizing cells. Desiccated
M. barkeri
exposed to air at room temperature did not lose significant viability after 28 days, and exposure of
M. barkeri
to air after desiccation appeared to improve the recovery of viable cells compared with that of desiccated cells that were never exposed to air. Desiccated
M. barkeri
was more resistant to higher temperatures, and although resistance to oxidative conditions such as ozone and ionizing radiation was not as robust as in other desiccation-resistant microorganisms, the protection mechanisms are likely adequate to maintain cell viability during periodic exposure events. The results of this study demonstrate that after desiccation
M. barkeri
has the innate capability to survive extended periods of exposure to air and lethal temperatures.
Small-Molecule Modulators of Listeria monocytogenes Biofilm Development
Authors: Nguyen Uyen T. , Wenderska Iwona B. , Chong Matthew A. , Koteva Kalinka , Wright Gerard D. , Burrows Lori L.
Published: December 2011

Listeria monocytogenes
is an important food-borne pathogen whose ability to form disinfectant-tolerant biofilms on a variety of surfaces presents a food safety challenge for manufacturers of ready-to-eat products. We developed here a high-throughput biofilm assay for
L. monocytogenes
and, as a proof of principle, used it to screen an 80-compound protein kinase inhibitor library to identify molecules that perturb biofilm development. The screen yielded molecules toxic to multiple strains of
Listeria
at micromolar concentrations, as well as molecules that decreased (≤50% of vehicle control) or increased (≥200%) biofilm formation in a dose-dependent manner without affecting planktonic cell density. Toxic molecules—including the protein kinase C antagonist sphingosine—had antibiofilm activity at sub-MIC concentrations. Structure-activity studies of the biofilm inhibitory compound palmitoyl-
d,l
-carnitine showed that while
Listeria
biofilm formation was inhibited with a 50% inhibitory concentration of 5.85 ± 0.24 μM,
d,l
-carnitine had no effect, whereas palmitic acid had stimulatory effects. Saturated fatty acids between C
9:0
and C
14:0
were
Listeria
biofilm inhibitors, whereas fatty acids of C
16:0
or longer were stimulators, showing chain length specificity.
De novo
-synthesized short-chain acyl carnitines were less effective biofilm inhibitors than the palmitoyl forms. These molecules, whose activities against bacteria have not been previously established, are both useful probes of
L. monocytogenes
biology and promising leads for the further development of antibiofilm strategies.
HAVCR1 Gene Haplotypes and Infection by Different Viral Hepatitis C Virus Genotypes
Authors: Abad-Molina Cristina , Garcia-Lozano José-Raúl , Montes-Cano Marco-Antonio , Torres-Cornejo Almudena , Torrecillas Fuensanta , Aguilar-Reina José , Romero-Gómez Manuel , López-Cortés Luis-Fernando , Núñez-Roldan Antonio , González-Escribano María-Francisca
Published: December 2011

The hepatitis A virus cellular receptor 1 (HAVCR1) gene is highly polymorphic, and several variants have been associated with susceptibility to allergic and autoimmune diseases. The HAVCR1 gene region was identified as a candidate for hepatitis C virus (HCV) natural clearance in a genotyping study of selected immune response genes in both European-American and African-American populations. The aim of the present study was to explore the influence of HAVCR1 in the outcome of HCV infection in the Spanish population. Three cohorts, consisting of 354 subjects with persistent HCV infection (285 with persistent HCV monoinfection and 69 with natural clearance), 182 coinfected HIV/HCV patients, and 320 controls, were included. Samples were genotyped in several polymorphic positions, insertion/deletion variants in exon 4 and tag single nucleotide polymorphisms (SNPs), in order to define previously described HAVCR1 haplotypes (haplotypes A to D). No statistically significant differences were observed with spontaneous resolution of infection or with viral clearance after treatment. Nevertheless, different rates of infection by viral genotypes (G's) were observed among the HAVCR1 haplotypes. Individuals bearing haplotype C had the highest viral G1 infection rate when compared to individuals bearing other haplotypes (75.82% versus 57.72%, respectively; correctedPvalue [Pc], 3.2 × 10−4; odds ratio [OR], 2.30; 95% confidence interval [CI], 1.51 to 3.47). Thus, HAVCR1 could be involved in susceptibility or resistance to infection by a particular HCV genotype.
Helicobacter pylori Relies Primarily on the Purine Salvage Pathway for Purine Nucleotide Biosynthesis
Authors: Liechti George , Goldberg Joanna B.
Published: December 2011

Helicobacter pylori
is a chronic colonizer of the gastric epithelium and plays a major role in the development of gastritis, peptic ulcer disease, and gastric cancer. In its coevolution with humans, the streamlining of the
H. pylori
genome has resulted in a significant reduction in metabolic pathways, one being purine nucleotide biosynthesis. Bioinformatic analysis has revealed that
H. pylori
lacks the enzymatic machinery for
de novo
production of IMP, the first purine nucleotide formed during GTP and ATP biosynthesis. This suggests that
H. pylori
must rely heavily on salvage of purines from the environment. In this study, we deleted several genes putatively involved in purine salvage and processing. The growth and survival of these mutants were analyzed in both nutrient-rich and minimal media, and the results confirmed the presence of a robust purine salvage pathway in
H. pylori
. Of the two phosphoribosyltransferase genes found in the
H. pylori
genome, only
gpt
appears to be essential, and an Δ
apt
mutant strain was still capable of growth on adenine, suggesting that adenine processing via Apt is not essential. Deletion of the putative nucleoside phosphorylase gene
deoD
resulted in an inability of
H. pylori
to grow on purine nucleosides or the purine base adenine. Our results suggest a purine requirement for growth of
H. pylori
in standard media, indicating that
H. pylori
possesses the ability to utilize purines and nucleosides from the environment in the absence of a
de novo
purine nucleotide biosynthesis pathway.
Generation of Transmitted/Founder HIV-1 Infectious Molecular Clones and Characterization of Their Replication Capacity in CD4 T Lymphocytes and Monocyte-Derived Macrophages
Authors: Ochsenbauer Christina , Edmonds Tara G. , Ding Haitao , Keele Brandon F. , Decker Julie , Salazar Maria G. , Salazar-Gonzalez Jesus F. , Shattock Robin , Haynes Barton F. , Shaw George M. , Hahn Beatrice H. , Kappes John C.
Published: December 2011

Genome sequences of transmitted/founder (T/F) HIV-1 have been inferred by analyzing single genome amplicons of acute infection plasma viral RNA in the context of a mathematical model of random virus evolution; however, few of these T/F sequences have been molecularly cloned and biologically characterized. Here, we describe the derivation and biological analysis of ten infectious molecular clones, each representing a T/F genome responsible for productive HIV-1 clade B clinical infection. Each of the T/F viruses primarily utilized the CCR5 coreceptor for entry and replicated efficiently in primary human CD4
+
T lymphocytes. This result supports the conclusion that single genome amplification-derived sequences from acute infection allow for the inference of T/F viral genomes that are consistently replication competent. Studies with monocyte-derived macrophages (MDM) demonstrated various levels of replication among the T/F viruses. Although all T/F viruses replicated in MDM, the overall replication efficiency was significantly lower compared to prototypic “highly macrophage-tropic” virus strains. This phenotype was transferable by expressing the
env
genes in an isogenic proviral DNA backbone, indicating that T/F virus macrophage tropism mapped to Env. Furthermore, significantly higher concentrations of soluble CD4 were required to inhibit T/F virus infection compared to prototypic macrophage-tropic virus strains. Our findings suggest that the acquisition of clinical HIV-1 subtype B infection occurs by mucosal exposure to virus that is not highly macrophage tropic and that the generation and initial biological characterization of 10 clade B T/F infectious molecular clones provides new opportunities to probe virus-host interactions involved in HIV-1 transmission.
THE DARK MAGNETISM OF THE UNIVERSE
Authors: JIMÉNEZ JOSE BELTRÁN , MAROTO ANTONIO L.
Published: December 2011

Despite the success of Maxwell's electromagnetism in the description of the electromagnetic interactions on small scales, we know very little about the behavior of electromagnetic fields on cosmological distances. Thus, it has been suggested recently that the problems of dark energy and the origin of cosmic magnetic fields could be pointing to a modification of Maxwell's theory on large scales. Here, we review such a proposal in which the scalar state which is usually eliminated by means of the Lorenz condition is allowed to propagate. On super-Hubble scales, the new mode is essentially given by the temporal component of the electromagnetic potential and contributes as an effective cosmological constant to the energy–momentum tensor. The new state can be generated from quantum fluctuations during inflation and it is shown that the predicted value for the cosmological constant agrees with observations, provided inflation took place at the electroweak scale. We also consider more general theories including non-minimal couplings to the spacetime curvature in the presence of the temporal electromagnetic background. We show that both in the minimal and non-minimal cases, the modified Maxwell's equations include new effective current terms which can generate magnetic fields from sub-galactic scales up to the present Hubble horizon. The corresponding amplitudes could be enough to seed a galactic dynamo or even to account for observations just by collapse and differential rotation in the protogalactic cloud.
ON THE WEAKLY NONLINEAR KELVIN–HELMHOLTZ INSTABILITY OF TANGENTIAL DISCONTINUITIES IN MHD
Authors: HUNTER JOHN K. , THOO J. B.
Published: December 2011

We derive a quadratically nonlinear equation that describes the motion of a tangential discontinuity in incompressible magnetohydrodynamics near the onset of a Kelvin–Helmholtz instability. We show that nonlinear effects enhance the instability and give a criterion for it to occur in terms of a longitudinal strain of the fluid motion along the discontinuity.
Autocrine regulation of biliary pathology by activated cholangiocytes
Authors: Jensen Kendal , Marzioni Marco , Munshi Kamruzzaman , Afroze Syeda , Alpini Gianfranco , Glaser Shannon
Published: December 2011

The bile duct system of the liver is lined by epithelial cells (i.e., cholangiocytes) that respond to a large number of neuroendocrine factors through alterations in their proliferative activities and the subsequent modification of the microenvironment. As such, activation of biliary proliferation compensates for the loss of cholangiocytes due to apoptosis and slows the progression of toxic injury and cholestasis. Over the course of the last three decades, much progress has been made in identifying the factors that trigger the biliary epithelium to remodel and grow. Because a large number of autocrine factors have recently been identified as relevant clinical targets, a compiled review of their contributions and function in cholestatic liver diseases would be beneficial. In this context, it is important to define the specific processes triggered by autocrine factors that promote cholangiocytes to proliferate, activate neighboring cells, and ultimately lead to extracellular matrix deposition. In this review, we discuss the role of each of the known autocrine factors with particular emphasis on proliferation and fibrogenesis. Because many of these molecules interact with one another throughout the progression of liver fibrosis, a model speculating their involvement in the progression of cholestatic liver disease is also presented.
The effect of aging on adrenergic and nonadrenergic receptor expression and responsiveness in canine skeletal muscle
Authors: DeLorey D. S. , Clifford P. S. , Mittelstadt S. , Anton M. M. , Kluess H. A. , Tune J. D. , Dincer U. D. , Buckwalter J. B.
Published: December 2011

We tested the hypothesis that adrenergic and nonadrenergic receptor responsiveness and protein expression would be altered with advancing age. Young ( n = 6; 22 ± 1 mo; mean ± SE) and old ( n = 6; 118 ± 9 mo) beagles were instrumented with flow probes and an indwelling catheter for continuous measurement of external iliac blood flow and arterial blood pressure. Vascular conductance (VC) was calculated as hindlimb blood flow/mean arterial pressure. Selective agonists for α-1, α-2, neuropeptide-Y (NPY), and purinergic (P2X) receptors were infused at rest and during treadmill running at moderate (2.5 mph) and heavy (4 mph with 2.5% grade) exercise intensities. Feed arteries were dissected from gracilis muscles, and α-1D, α-1B, α-2A, P2X-4, P2X-1, and NPY-Y1 receptor protein expression was determined. Phenylephrine produced similar decreases ( P > 0.05) in VC in young and old beagles at rest (young: −62 ± 5%; old: −59 ± 5%) and during moderate (young: −67 ± 5%; old: −62 ± 4%) and heavy (young: −54 ± 4%; old: −49 ± 3%) exercise. Clonidine caused similar ( P > 0.05) decreases in VC in old compared with young dogs at rest (young: −59 ± 8%; old: −70 ± 6%) and during moderate (young: −52 ± 6%; old: −47 ± 5%)- and heavy (young: −42 ± 5%; old: −43 ± 5%)-intensity exercise. NPY infusion resulted in a similar decline in VC in young and old beagles at rest (young: −40 ± 7%; old: −39 ± 9%) and during moderate (young: −47 ± 6%; old: −40 ± 6%)- and heavy (young: −40 ± 3%; old: −38 ± 4%)-intensity exercise. α-β-Methylene-ATP also produced similar decreases in VC in young and old beagles at rest (young: −36 ± 6%; old: −40 ± 8%) and during exercise at moderate (young: −42 ± 5%; old: −40 ± 9%) and heavy (young: −47 ± 5%; old: −42 ± 8%) intensities. α-1B receptor protein expression was elevated ( P < 0.05) in old compared with young dogs, whereas there were no age-related differences in α-1D or α-2A receptor expression and nonadrenergic P2X-4, P2X-1, and NPY-Y1 receptor expression. The present findings indicate that postsynaptic adrenergic and nonadrenergic receptor responsiveness was not altered by advancing age. Moreover, the expression of adrenergic and nonadrenergic receptors in skeletal-muscle feed arteries was largely unaffected by aging.
Regulation of V̇o2 kinetics by O2 delivery: insights from acute hypoxia and heavy-intensity priming exercise in young men
Authors: Spencer Matthew D. , Murias Juan M. , Grey Tyler M. , Paterson Donald H.
Published: December 2011

This study examined the separate and combined effects of acute hypoxia (Hypo) and heavy-intensity “priming” exercise (Hvy) on pulmonary O2 uptake (V̇o2p) kinetics during moderate-intensity exercise (Mod). Breath-by-breath V̇o2p and near-infrared spectroscopy-derived muscle deoxygenation {deoxyhemoglobin concentration [HHb]} were monitored continuously in 10 men (23 ± 4 yr) during repetitions of a Mod 1-Hvy-Mod 2 protocol, where each of the 6-min (Mod or Hvy) leg-cycling bouts was separated by 6 min at 20 W. Subjects were exposed to Hypo [fraction of inspired O2 (FiO2) = 15%, Mod 2 + Hypo] or “sham” (FiO2 = 20.9%, Mod 2-N) 2 min following Hvy in half of these repetitions; Mod was also performed in Hypo without Hvy (Mod 1 + Hypo). On-transient V̇o2p and [HHb] responses were modeled as a monoexponential. Data were scaled to a relative percentage of the response (0–100%), the signals were time-aligned, and the individual [HHb]-to-V̇o2 ratio was calculated. Compared with control (Mod 1), τV̇o2p and the O2 deficit (26 ± 7 s and 638 ± 144 ml, respectively) were reduced ( P < 0.05) in Mod 2-N (20 ± 5 s and 529 ± 196 ml) and increased ( P < 0.05) in Mod 1 + Hypo (34 ± 14 s and 783 ± 184 ml); in Mod 2 + Hypo, τV̇o2p was increased (30 ± 8 s, P < 0.05), yet O2 deficit was unaffected (643 ± 193 ml, P > 0.05). The modest “overshoot” in the [HHb]-to-V̇o2 ratio (reflecting an O2 delivery-to-utilization mismatch) in Mod 1 (1.06 ± 0.04) was abolished in Mod 2-N (1.00 ± 0.05), persisted in Mod 2 + Hypo (1.09 ± 0.07), and tended to increase in Mod 1 + Hypo (1.10 ± 0.09, P = 0.13). The present data do not support an “O2 delivery-independent” speeding of τV̇o2p following Hvy (or Hvy + Hypo); rather, this study suggests that local muscle O2 delivery likely governs the rate of adjustment of V̇o2 at τV̇o2p greater than ∼20 s.
Piperacillin-Induced Immune Hemolysis Presenting with Tachycardia and Cardiac Arrest
Authors: Lohiya Ghan-Shyam , Tan-Figueroa Lilia , Krishna Vamsi
Published: December 2011

A 20-year-old nonverbal patient with profound developmental disabilities was treated with intravenous piperacillin-tazobactam for respiratory infection. After 8 days, he became afebrile with normal pulmonary status,but his pulse remained inexplicably rapid (114/minute). Investigations revealed severe normochromic normocytic hemolytic anemia (hemoglobin: 40 g/L, reticulocytes: 9.4%, nucleated erythrocytes: 5%). While being hospitalized, patient experienced sudden cardiac arrest from which he was successfully resuscitated. He had no blood loss or intrinsic heart disease to explain the acute anemia or cardiac arrest. He had uneventfully received piperacillin-tazobactam on 7 occasions during the preceding 5 years for >50 days. Patient was treated with intravenous crystalloids, methylprednisolone and transfusion of 3 units of packed erythrocytes. Piperacillin-tazobactam was discontinued. A direct antiglobulin test was positive for immunoglobulin G and complement. Antibody to piperacillin was detected in patient's serum by the “immune-complex” method confirming “piperacillin-induced immune hemolytic anemia (PIHA)”. On discharge (day 15), patient's hemoglobin improved to 115 g/L (baseline: 131 g/L). Vigilantclinicaland hematological monitoring for anemia is indicated in piperacillin-treated patients, particularly in those unable to verbalize their discomfort. Repeated piperacillin exposure may sensitize and predispose patients to PIHA.
Towards Defining a Rigidity-Associated Pathogenic Pathway in Idiopathic Parkinsonism
Authors: Dobbs R. John , Charlett André , Dobbs Sylvia M. , Weller Clive , Iguodala Owens , Smee Cori , Bowthorpe James , Taylor David , Bjarnason Ingvar T.
Published: December 2011

Helicobacter pylori eradication has a differential effect on the facets of idiopathic parkinsonism (IP): brady/hypokinesia improves, but rigidity worsens. Small intestinal bacterial overgrowth is common in IP and has been described as a sequel to Helicobacter eradication. The hyperhomocysteinaemia of IP is, in part, explained by serum vitamin B12, but the concentration is not explained by Helicobacter status. Moreover, Helicobacter-associated gastric atrophy is uncommon in IP. However, overgrowth both increases B12 utilization and provides a source of inflammation to drive homocysteine production. It is not a bystander event in IP: clouds of lysosomes are seen in duodenal enterocytes. Its candidature for causality of a rigidity-associated pathway is circumstantial: there are biological gradients of rigidity on natural killer and T-helper blood counts, both being higher with hydrogen breath test positivity for overgrowth.
Bioabsorbable Staple-Line Reinforcement for Pancreatectomy in a Porcine Model: A Preliminary Study
Authors: Hornez E. , Garnier E. , Sastre B. , Garcia S. , Mayet A. , Berdah S.V.
Published: December 2011

Background: We conducted an exploratory study to assess the use of FOREseal® bioabsorbable reinforcement sleeves in stapling of the pancreatic parenchyma. Methods: A left pancreatectomy was carried out with linear stapler on 12 pigs: in the FOREseal group (n = 6), the stapling was reinforced with FOREseal, while in the control group (n = 6), simple stapling was applied. Results: The mean operating time was not different between the two groups. No additional haemostasis of the stapling transection was necessary with FOREseal, while in the control group, four pigs required additional haemostasis (p = 0.03). The mean postoperative drainage volume and the mean duration of drainage were, respectively, in the FOREseal group versus the control group: 82 versus 204 ml (p = 0.2) and 3.2 versus 4.7 days (p = 0.3). No adverse event occurred in the FOREseal group. There was no anatomopathological difference between the two groups. Conclusion: A good tolerance of FOREseal was observed when used on the pancreatic stump. In this study, it was demonstrated a better haemostatic control of the pancreatic stump with FOREseal which also tends to reduce the volume of postoperative drainage liquid.
Accelerated Atherosclerosis in

Apoe
−/−

Mice Heterozygous for the Insulin Receptor and the Insulin Receptor Substrate-1
Authors: Galkina Elena V. , Butcher Matthew , Keller Susanna R. , Goff Matthew , Bruce Anthony , Pei Hong , Sarembock Ian J. , Sanders John M. , Nagelin Melissa H. , Srinivasan Suseela , Kulkarni Rohit N. , Hedrick Catherine C. , Lattanzio Frank A. , Dobrian Anca D. , Nadler Jerry L. , Ley Klaus
Published: December 2011

Objective—

Prediabetic states are associated with accelerated atherosclerosis, but the availability of mouse models to study connections between these diseases has been limited. The aim of this study was to test the selective role of impaired insulin receptor/insulin receptor substrate-1 signaling on atherogenesis.

Methods and Results—

To address the effects of impaired insulin signaling associated with hyperinsulinemia on atherosclerosis in the absence of obesity and hyperglycemia, we generated insulin receptor (
Insr
)/insulin receptor substrate-1 (
Insr1
) double heterozygous apolipoprotein (
Apoe
)-knockout mice (

Insr
+/−
Irs1
+/−
Apoe
−/−

) mice.

Insr
+/−
Irs1
+/−
Apoe
−/−

mice fed a Western diet for 15 weeks showed elevated levels of fasting insulin compared to

Insr
+/+
Irs1
+/+
Apoe
−/−

mice. There were no significant differences in glucose, triglyceride, HDL, VLDL, cholesterol levels or free fatty acid in the plasma of

Insr
+/−
Irs1
+/−
Apoe
−/−

and

Insr
+/+
Irs1
+/+
Apoe
−/−

mice. Atherosclerotic lesions were increased in male (brachiocephalic artery) and female (aortic tree)

Insr
+/−
Irs1
+/−
Apoe
−/−

compared to

Insr
+/+
Irs1
+/+
Apoe
−/−

mice. Bone marrow transfer experiments demonstrated that nonhematopoietic cells have to be

Insr
+/−
Irs1
+/−

to accelerate atherosclerosis. Impaired insulin signaling resulted in decreased levels of vascular phospho-eNOS, attenuated endothelium-dependent vasorelaxation and elevated VCAM-1 expression in aortas of

Insr
+/−
Irs1
+/−
Apoe
−/−

mice. In addition, phospho-ERK and vascular smooth muscle cell proliferation were significantly elevated in aortas of

Insr
+/−
Irs1
+/−
Apoe
−/−

mice.

Conclusion—

These results demonstrate that defective insulin signaling is involved in accelerated atherosclerosis in

Insr
+/−
Irs1
+/−
Apoe
−/−

mice by promoting vascular dysfunction and inflammation.
Bone Marrow–Specific Deficiency of Nuclear Receptor Nur77 Enhances Atherosclerosis
Authors: Hamers Anouk A.J. , Vos Mariska , Rassam Fadi , Marinković Goran , Kurakula Kondababu , van Gorp Patrick J. , de Winther Menno P.J. , Gijbels Marion J.J. , de Waard Vivian , de Vries Carlie J.M.
Published: December 2011

Rationale:

Nuclear receptor Nur77, also known as NR4A1, TR3, or NGFI-B, is expressed in human atherosclerotic lesions in macrophages, endothelial cells, T cells and smooth muscle cells. Macrophages play a critical role in atherosclerosis and the function of Nur77 in lesion macrophages has not yet been investigated.

Objective:

This study aims to delineate the function of Nur77 in macrophages and to assess the effect of bone marrow–specific deficiency of Nur77 on atherosclerosis.

Methods and Results:

We investigated Nur77 in macrophage polarization using bone marrow-derived macrophages (BMM) from wild-type and Nur77-knockout (Nur77
−/−
) mice. Nur77
−/−
BMM exhibit changed expression of M2-specific markers and an inflammatory M1-phenotype with enhanced expression of interleukin-12, IFNγ, and SDF-1α and increased NO synthesis in (non)-stimulated Nur77
−/−
BMM cells. SDF-1α expression in nonstimulated Nur77
−/−
BMM is repressed by Nur77 and the chemoattractive activity of Nur77
−/−
BMM is abolished by SDF-1α inhibiting antibodies. Furthermore, Nur77
−/−
mice show enhanced thioglycollate-elicited migration of macrophages and B cells. The effect of bone marrow–specific deficiency of Nur77 on atherosclerosis was studied in low density lipoprotein receptor-deficient (Ldlr
−/−
) mice. Ldlr
−/−
mice with a Nur77
−/−
-deficient bone marrow transplant developed 2.1-fold larger atherosclerotic lesions than wild-type bone marrow–transplanted mice. These lesions contain more macrophages, T cells, smooth muscle cells and larger necrotic cores. SDF-1α expression is higher in lesions of Nur77
−/−
-transplanted mice, which may explain the observed aggravation of lesion formation.

Conclusions:

In conclusion, in bone marrow–derived cells the nuclear receptor Nur77 has an anti-inflammatory function, represses SDF-1α expression and inhibits atherosclerosis.
Why do New Zealand high school students carry weapons?
Authors: Marsh Louise , McGee Rob , Williams Sheila
Published: December 2011

This study examined weapon carrying, including both the type of weapons being carried and reasons for carrying, in a sample of New Zealand high school students. A self-report online survey was administered to 1169 secondary students in the Otago region of New Zealand. Overall, 17 per cent had carried a weapon in the past year at school, and 24 per cent hadcarried outside school. The most common type of weapon was a pocket knife or knife, and the most common reason for carrying it at school was because it was in their bag or on their key ring, and for hunting or self-defence outside school. When psychological intention was taken into account, 9 per cent reported carrying for potential use as a weapon in the past year and 6 per cent in the past month. These students were also more likely to have been in a fight, to have missed school due to feeling unsafe, to have felt lonely, been bullied, bullied others and have few self-perceived competencies. In estimating the prevalence of weapon carrying, it is important to understand the psychological context of these behaviours.
The resource boom's underbelly: Criminological impacts of mining development
Authors: Carrington Kerry , Hogg Russell , McIntosh Alison
Published: December 2011

Australia is currently in the midst of a major resources boom. Resultant growing demands for labour in regional and remote areas have accelerated the recruitment of non-resident workers, mostly contractors, who work extended block rosters of 12-hour shifts and are accommodated in work camps, often adjacent to established mining towns. Serious social impacts of these practices, including violence and crime, have generally escaped industry, government and academic scrutiny. This paper highlights some of these impacts on affected regional communities and workers and argues that post-industrial mining regimes serve to mask and privatize these harms and risks, shifting them on to workers, families and communities.