bluuebunny/crossref_metadata_2025 huggingface dataset:
Changes in the Abundance and Diversity of Proteaceae in South‐western Australia: a Review of an Integrated Palaeoenvironmental Study
Authors: ITZSTEIN‐DAVEY FREEA
Published: February 2007

South‐western Australia is a globally significant hotspot of Proteaceae diversity. This review reports on changes in the abundance and diversity of Proteaceae in south‐western Australia. Using palynology, the data were obtained from three sediment sequences from the Eocene, Pliocene and Holocene, as well as a modern pollen rain study, in the context of a vegetation history framework. The total percentages of Proteaceae pollen in pollen counts indicate that the number of Proteaceae in the vegetation are highest at present, slightly lower, yet still high in the Eocene, reduced by the Pliocene and lowest in the Holocene. It was found that Proteaceous genera can contribute up to 50% of the total modern pollen rain. Sediment from Lake Lefroy showed Nothofagus‐dominated rainforest occurred in the Middle to Late Eocene. Proteaceae species were at least as diverse as today, contributing up to a maximum of 42% of the total pollen rain, and varying across small lateral distances. A laminated Pliocene age sequence from Yallalie confirmed other studies that south‐western Australia was covered by a rich vegetation mosaic consisting of heath and wet rainforest elements. Proteaceae species were a consistent component of the counts, although diversity and abundance (maximum 5%) were low. A Holocene record from Two Mile Lake, near the Stirling Range, recorded little environmental change. Proteaceae species were noted in low abundance, at a maximum of 3.5% of the total pollen count. It is likely that both changing pollination mechanisms and changes in associated vegetation are important in determining the dispersal of Proteaceous pollen.
Judicial Review
Authors: Waluchow W. J.
Published: February 2007

Courts are sometimes called upon to review a law or some other official act of government to determine its constitutionality, its reasonableness, rationality, or its compatibility with fundamental principles of justice. In some jurisdictions, this power of judicial review includes the ability to ‘strike down’ or nullify a law duly passed by a legislature body. This article examines this practice and various criticisms of it, including the charge that it is fundamentally undemocratic. The focus is on the powerful critique mounted by Jeremy Waldron, the foremost philosophical opponent of judicial review.
Are UK genetic databases governed adequately? A comparative legal analysis
Authors: Gibbons Susan MC
Published: February 2007

Given the burgeoning of genetic research and proliferation of human genetic databases, especially in the biomedical sphere, this paper explores whether the existing laws and regulatory structures for governing genetic databases in England and Wales are adequate. Through a critical survey of relevant rules, bodies and practices, it argues that the current UK framework is far from ideal in at least five major areas: (1) forms and styles of law used, especially the separate legislative regimes for physical biomaterial and data; (2) core definitions; (3) formal regulatory bodies, licensing and notification requirements; (4) ethics committees and other advisory panels; and (5) enforcement powers and sanctions. Such shortcomings could have major implications for stakeholders, hamper efforts to achieve European or international harmonisation of genetic database principles and practices, and undermine the UK’s standing as a world leader in genetics and biotechnology. Drawing on comparative analysis of governance strategies adopted in Estonia, Iceland and Sweden, the paper identifies alternative options and lessons from experiences abroad, suggesting possible avenues for reform that may warrant serious consideration in the UK.
Improving Grape Quality Using Microwave Vacuum Drying Associated with Temperature Control
Authors: Clary C. D. , Mejia‐Meza E. , Wang S. , Petrucci V. E.
Published: January 2007

ABSTRACT:  Microwave (MW) vacuum dehydration using temperature to control the level of MW power demonstrated potential in improving the performance of the process. Product surface temperature measured by an infrared temperature sensor was used to control MW power at any level between 0 and 3 kW. Multiple linear regression analysis indicated an r2= 0.942 for prediction of final moisture content and r2= 0.985 for prediction of puffed character of grapes based on product temperature, time, specific energy, fresh fruit sugar, and fresh fruit moisture content. Temperature was found to be the most significant predictor. The elemental and compound contents of grapes dried using MW vacuum was compared to sun‐dried raisins. The grapes dried using MW vacuum exhibited better preservation. Vitamin A was found in the MW‐vacuum‐dried grapes but none was detected in the raisins, and Vitamin C, thiamine, and riboflavin were also higher in the MW‐vacuum‐dried grapes than in the raisins.
Quantitative assessment of human muscle glycogen granules size and number in subcellular locations during recovery from prolonged exercise
Authors: Marchand I. , Tarnopolsky M. , Adamo K. B. , Bourgeois J. M. , Chorneyko K. , Graham T. E.
Published: February 2007

Although data relating to muscle glycogen are interpreted as showing it is homogenous when quantified biochemically, it is actually in granules in specific subcellular locations. We hypothesized that postexercise restoration of muscle glycogen would occur initially by an increase in granule number followed by an increase in size, and also that restoration would differ in various subcellular locations. Five men performed prolonged exercise and had muscle biopsies taken at 0, 4, 24 and 48 h of recovery. We quantified granule number and size as well as the total volume of glycogen in the subsarcolemmal and the intra‐ and intermyofibrillar regions, using transmission electron microscopy. Muscle glycogen was reduced to 36 ± 8.3 mmol glucosyl units (kg dry weight)−1 at exhaustion, and was preferentially depleted and subsequently repleted in the intramyofibrillar space. The repletion rate was greatest in the first 4 h; this was associated with a 186% increase in number (P≤ 0.05) and no change in particle size (P≥ 0.05). From 4 h to 48 h, there was an increase in particle size (P≤ 0.05) but not number (P≥ 0.05). Net rate of G volume synthesis per unit area was 50% greater (P≤ 0.05) in the subsarcolemmal than the myofibrillar compartment. Conversely, the net rate of single‐particle volume synthesis was greater (P≤ 0.05) in the myofibrillar than the subsarcolemmal compartment. Glycogen granules varied in size and number depending on location, and in all compartments resynthesis of glycogen was characterized initially by an increase in granule number and later by an increase in size.
Single‐channel properties of glycine receptors of juvenile rat spinal motoneurones in vitro
Authors: Beato Marco , Sivilotti Lucia G.
Published: February 2007

An essential step in understanding fast synaptic transmission is to establish the activation mechanism of synaptic receptors. The purpose of this work was to extend our detailed single‐channel kinetic characterization of α1β glycine channels from rat recombinant receptors to native channels from juvenile (postnatal day 12–16) rat spinal cord slices. In cell‐attached patches from ventral horn neurones, 1 mm glycine elicited clusters of channel openings to a single conductance level (41 ± 1 pS, n= 12). This is similar to that of recombinant heteromers. However, fewer than 1 in 100 cell‐attached patches from spinal neurones contained glycine channels. Outside‐out patches gave a much higher success rate, but glycine channels recorded in this configuration appeared different, in that clusters opened to three conductance levels (28 ± 2, 38 ± 1 and 46 ± 1 pS, n= 7, one level per cluster, all levels being detected in each patch). Furthermore, open period properties were different for the different conductances. As a consequence of this, the only recordings suitable for kinetic analysis were the cell‐attached ones. Low channel density precluded recording at glycine concentrations other than 1 mm, but the 1 mm data allowed us to estimate the fully bound gating constants by global model fitting of the ‘flip’ mechanism of Burzomato and co‐workers. Our results suggest that glycine receptors on ventral horn neurones in the juvenile rat are heteromers and have fast gating, similar to that of recombinant α1β receptors.
Assistive technology and robotic control using motor cortex ensemble‐based neural interface systems in humans with tetraplegia
Authors: Donoghue John P. , Nurmikko Arto , Black Michael , Hochberg Leigh R.
Published: February 2007

This review describes the rationale, early stage development, and initial human application of neural interface systems (NISs) for humans with paralysis. NISs are emerging medical devices designed to allow persons with paralysis to operate assistive technologies or to reanimate muscles based upon a command signal that is obtained directly from the brain. Such systems require the development of sensors to detect brain signals, decoders to transform neural activity signals into a useful command, and an interface for the user. We review initial pilot trial results of an NIS that is based on an intracortical microelectrode sensor that derives control signals from the motor cortex. We review recent findings showing, first, that neurons engaged by movement intentions persist in motor cortex years after injury or disease to the motor system, and second, that signals derived from motor cortex can be used by persons with paralysis to operate a range of devices. We suggest that, with further development, this form of NIS holds promise as a useful new neurotechnology for those with limited motor function or communication. We also discuss the additional potential for neural sensors to be used in the diagnosis and management of various neurological conditions and as a new way to learn about human brain function.
Binding and direct activation of the epithelial Na+ channel (ENaC) by phosphatidylinositides
Authors: Pochynyuk Oleh , Tong Qiusheng , Staruschenko Alexander , Stockand James D.
Published: February 2007

Several distinct types of ion channels bind and directly respond to phosphatidylinositides, including phosphatidylinositol (3,4,5)‐trisphosphate (PI(3,4,5)P3) and phosphatidylinositol (4,5)‐bisphosphate (PI(4,5)P2). This regulation is physiologically relevant for its dysfunction, in some instances, causes disease. Recent studies identify the epithelial Na+ channel (ENaC) as a channel sensitive to phosphatidylinositides. ENaC appears capable of binding both PI(4,5)P2 and PI(3,4,5)P3 with binding stabilizing channel gating. The binding sites for these molecules within ENaC are likely to be distinct with the former phosphoinositide interacting with elements in the cytosolic NH2‐terminus of the β‐ and γ‐ENaC subunits and the latter with cytosolic regions immediately following the second transmembrane domains in these two subunits. PI(4,5)P2 binding to ENaC appears saturated at rest and necessary for channel gating. Thus, decreases in cellular PI(4,5)P2 levels may serve as a convergence point for inhibitory regulation of ENaC by G‐protein coupled receptors and receptor tyrosine kinases. In contrast, apparent PI(3,4,5)P3 binding to ENaC is not saturated. This enables the channel to respond with gating changes in a rapid and dynamic manner to signalling input that influences cellular PI(3,4,5)P3 levels.
Destruction of Cryogenic Pressure Vessel and Piping by Shock Wave
Authors: Watanabe Toshiaki , Hokamoto Kazuyuki , Itoh Shigeru
Published: February 2007

In recent years, the usage of cryogenic fluids as coolant are gaining more attention due to their capability to fulfill the requirements of today’s advancing low temperature industrial applications. As a result, the use of a cryogenic pressure vessel and piping in LNG-tank, LN2, O2 tank for food processing applications and medical applications are becoming more important. In a cryogenic pressure vessel and piping, the reduction of thermal insulation by a small initial damage leads to an internal pressure rise and occurrence of flashing, which leads to a secondary crush of the vessel. In this study, a shock wave was applied to a pressure vessel and piping filled with cryogenic fluid and various observations were made. The internal pressure time history was measured and the safety of the cryogenic pressure vessel and piping was considered.
Plastic Zone Coalescence and Edge Break Conditions of Internal Cracks in a Semi-infinite Sheet
Authors: Nishimura Toshihiko
Published: February 2007

The problem of two cracks in a semi-infinite sheet is analyzed. The critical conditions when adjacent plastic zones just coalesced are obtained. Also, the conditions when a plastic zone just reached the sheet edge are obtained. Assuming the crack and plastic zones as a fictitious crack, the integral equations are formulated in terms of surface traction, nonsingular stress, and zero crack face displacement at the coalescent point or at the sheet edge. By solving the equations, critical remote stress, plastic zone sizes, and crack tip opening displacements are obtained. Numerical results are presented.
Eddy Current Examination of Fatigue Cracks in Inconel Welds
Authors: Cheng Weiying , Komura Ichiro , Shiwa Mitsuharu , Kanemoto Shigeru
Published: February 2007

Basic studies on the eddy current examination of defects in Inconel, a typical nickel-base alloy used in the reactor vessel, pressurizer, and core internal of nuclear power plants, are carried out. The detecting and sizing capability of the eddy current method is investigated through analytical and experimental approaches. Probe’s detectability is numerically evaluated, and appropriate probe and examination conditions are correspondingly selected. The numerical signal calculation and crack reconstruction approach is confirmed in terms of the study of the eddy current examination of electrodischarge machining notches in Inconel base metal, and further applied to eddy current examination of fatigue cracks in Inconel welds. The profiles of fatigue cracks are reconstructed using eddy current testing signals. Crack depths estimated by eddy current reconstruction agree well with that of ultrasonic testing and are consistent with the crack depths revealed from destructive testing. The research presented in this paper shows that by choosing a proper testing situation, eddy current examination is feasible for detecting and sizing of surface-breaking cracks in Inconel welds.
Quantitative Phylogenetic Assessment of Microbial Communities in Diverse Environments
Authors: von Mering C. , Hugenholtz P. , Raes J. , Tringe S. G. , Doerks T. , Jensen L. J. , Ward N. , Bork P.
Published: February 2007

The taxonomic composition of environmental communities is an important indicator of their ecology and function. We used a set of protein-coding marker genes, extracted from large-scale environmental shotgun sequencing data, to provide a more direct, quantitative, and accurate picture of community composition than that provided by traditional ribosomal RNA–based approaches depending on the polymerase chain reaction. Mapping marker genes from four diverse environmental data sets onto a reference species phylogeny shows that certain communities evolve faster than others. The method also enables determination of preferred habitats for entire microbial clades and provides evidence that such habitat preferences are often remarkably stable over time.
Developing a Different Perspective on Disease
Authors: Adair Linda
Published: February 2007

Developmental Origins of Health and Disease
.
Peter Gluckman and Mark Hanson, Eds.
. Cambridge University Press, Cambridge, 2006. 541 pp. $150, £90. ISBN 9780521847438.

Emphasizing public health issues and an evo-devo perspective, the contributors explore the biological bases for the link between early development and chronic diseases.
Martian Atmospheric Erosion Rates
Authors: Barabash Stas , Fedorov Andrei , Lundin Rickard , Sauvaud Jean-Andre
Published: January 2007

Mars was once wet but is now dry, and the fate of its ancient carbon dioxide atmosphere is one of the biggest puzzles in martian planetology. We have measured the current loss rate due to the solar wind interaction for different species: Q(O
+
) = 1.6·10
23
per second = 4 grams per second (g s
–1
), Q(O
+
2
) = 1.5·10
23
s
–1
= 8 g s
–1
, and Q(CO
+
2
) = 8·10
22
s
–1
= 6 g s
–1
in the energy range of 30 to 30,000 electron volts per charge. These rates can be propagated backward over a period of 3.5 billion years, resulting in the total removal of 0.2 to 4 millibar of carbon dioxide and a few centimeters of water. The escape rate is low, and thus one has to continue searching for water reservoirs and carbon dioxide stores on or beneath the planetary surface and investigate other escape channels.
Coupling Coherence Distinguishes Structure Sensitivity in Protein Electron Transfer
Authors: Prytkova Tatiana R. , Kurnikov Igor V. , Beratan David N.
Published: February 2007

Quantum mechanical analysis of electron tunneling in nine thermally fluctuating cytochrome b
562
derivatives reveals two distinct protein-mediated coupling limits. A structure-insensitive regime arises for redox partners coupled through dynamically averaged multiple-coupling pathways (in seven of the nine derivatives) where heme-edge coupling leads to the multiple-pathway regime. A structure-dependent limit governs redox partners coupled through a dominant pathway (in two of the nine derivatives) where axial-ligand coupling generates the single-pathway limit and slower rates. This two-regime paradigm provides a unified description of electron transfer rates in 26 ruthenium-modified heme and blue-copper proteins, as well as in numerous photosynthetic proteins.
Species Interactions Reverse Grassland Responses to Changing Climate
Authors: Suttle K. B. , Thomsen Meredith A. , Power Mary E.
Published: February 2007

Predictions of ecological response to climate change are based largely on direct climatic effects on species. We show that, in a California grassland, species interactions strongly influence responses to changing climate, overturning direct climatic effects within 5 years. We manipulated the seasonality and intensity of rainfall over large, replicate plots in accordance with projections of leading climate models and examined responses across several trophic levels. Changes in seasonal water availability had pronounced effects on individual species, but as precipitation regimes were sustained across years, feedbacks and species interactions overrode autecological responses to water and reversed community trajectories. Conditions that sharply increased production and diversity through 2 years caused simplification of the food web and deep reductions in consumer abundance after 5 years. Changes in these natural grassland communities suggest a prominent role for species interactions in ecosystem response to climate change.
Abortive Phage Resistance Mechanism AbiZ Speeds the Lysis Clock To Cause Premature Lysis of Phage-Infected
Lactococcus lactis
Authors: Durmaz Evelyn , Klaenhammer Todd R.
Published: February 2007

The conjugative plasmid pTR2030 has been used extensively to confer phage resistance in commercial
Lactococcus
starter cultures. The plasmid harbors a 16-kb region, flanked by insertion sequence (IS) elements, that encodes the restriction/modification system LlaI and carries an abortive infection gene,
abiA
. The AbiA system inhibits both prolate and small isometric phages by interfering with the early stages of phage DNA replication. However,
abiA
alone does not account for the full abortive activity reported for pTR2030. In this study, a 7.5-kb region positioned within the IS elements and downstream of
abiA
was sequenced to reveal seven additional open reading frames (ORFs). A single ORF, designated
abiZ
, was found to be responsible for a significant reduction in plaque size and an efficiency of plaquing (EOP) of 10
−6
, without affecting phage adsorption. AbiZ causes phage φ31-infected
Lactococcus lactis
NCK203 to lyse 15 min early, reducing the burst size of φ31 100-fold. Thirteen of 14 phages of the P335 group were sensitive to AbiZ, through reduction in either plaque size, EOP, or both. The predicted AbiZ protein contains two predicted transmembrane helices but shows no significant DNA homologies. When the phage φ31 lysin and holin genes were cloned into the nisin-inducible shuttle vector pMSP3545, nisin induction of holin and lysin caused partial lysis of NCK203. In the presence of AbiZ, lysis occurred 30 min earlier. In holin-induced cells, membrane permeability as measured using propidium iodide was greater in the presence of AbiZ. These results suggest that AbiZ may interact cooperatively with holin to cause premature lysis.
Unraveling the Regulatory Network in
Streptococcus pyogenes
: the Global Response Regulator CovR Represses
rivR
Directly
Authors: Roberts Samantha A. , Churchward Gordon G. , Scott June R.
Published: February 2007

The response regulator CovR acts as a master regulator of virulence in
Streptococcus pyogenes
by repressing transcription of approximately 15% of the group A streptococcus genome directly or indirectly. We demonstrate that phosphorylated CovR represses transcription of
rivR
directly by binding to conserved sequences located downstream from the promoter to block procession of RNA polymerase. This establishes the first link in a regulatory network where CovR interacts directly with other proteins that modulate gene expression.
Population Structure of Plasmid-Containing Strains of
Streptococcus mutans
, a Member of the Human Indigenous Biota
Authors: Caufield Page W. , Saxena Deepak , Fitch David , Li Yihong
Published: February 2007

There are suggestions that the phylogeny of
Streptococcus mutans
, a member of the human indigenous biota that is transmitted mostly mother to child, might parallel the evolutionary history of its human host. The relatedness and phylogeny of plasmid-containing strains of
S. mutans
were examined based on chromosomal DNA fingerprints (CDF), a hypervariable region (HVR) of a 5.6-kb plasmid, the rRNA gene intergenic spacer region (IGSR), serotypes, and the genotypes of mutacin I and II. Plasmid-containing strains were studied because their genetic diversity was twice as great as that of plasmid-free strains. The CDF of
S. mutans
from unrelated human hosts were unique, except those from Caucasians, which were essentially identical. The evolutionary history of the IGSR, with or without the serotype and mutacin characters, clearly delineated an Asian clade. Also, a continuous association with mutacin II could be reconstructed through an evolutionary lineage with the IGSR, but not for serotype e. DNA sequences from the HVR of the plasmid produced a well-resolved phylogeny that differed from the chromosomal phylogeny, indicating that the horizontal transfer of the plasmid may have occurred multiple times. The plasmid phylogeny was more congruent with serotype e than with mutacin II evolution, suggesting a possible functional correlation. Thus, the history of this three-tiered relationship between human, bacterium, and plasmid supported both coevolution and independent evolution.
Evaluation of the Performance of the Automated NucliSENS easyMAG and EasyQ Systems versus the Roche AmpliPrep-AMPLICOR Combination for High-Throughput Monitoring of Human Immunodeficiency Virus Load
Authors: Stevens W. , Horsfield P. , Scott L. E.
Published: February 2007

This study presents the data of an evaluation of the automated Nuclisens easyMAG and EasyQ systems versus the Roche AmpliPrep-AMPLICOR combination for testing of high-volume human immunodeficiency virus (HIV) load. This represents a follow-up of a previous study investigating the performance of the real-time Nuclisens assay using the semiautomated NucliSENS miniMAG extraction procedure. Three hundred eighteen patient samples were analyzed using both methods. The easyMAG-EasyQ HIV type 1 system has a higher sensitivity and broader dynamic range than the Cobas AmpliPrep-AMPLICOR system when the standard Roche assay is used alone, 25 to 3,000,000 IU/ml versus 400 to 750,000 HIV RNA copies/ml, respectively. There was significant correlation between the assays (0.93;
P
< 0.0001), with good accuracy (percent similarity mean μ = 96%), good precision (percent similarity standard deviation = 4.97%), and overall good agreement with a low percent similarity coefficient of variation of 5.17 to 6.11%. Bland-Altman analysis revealed that the AMPLICOR assay generated higher values than the EasyQ combination, with 95% of results within clinically acceptable limits. The throughput of samples was greatly improved using the easyMAG-EasyQ system, allowing 144 samples to be processed within 6 h. The potential for contamination has been dramatically reduced using the automated extraction system. Additional negative controls have been added to the kit to monitor for contamination based on the South African experience. This assay thus presents a real option for monitoring HIV load assays in high-volume testing environments.
Evaluation of Microscopic Observation Drug Susceptibility Assay for Detection of Multidrug-Resistant
Mycobacterium tuberculosis
Authors: Shiferaw Girum , Woldeamanuel Yimtubezinash , Gebeyehu Mekdes , Girmachew Feven , Demessie Daniel , Lemma Eshetu
Published: January 2007

Early detection of multidrug-resistant
Mycobacterium tuberculosis
(MDR-TB) is of primary importance for both patient management and infection control. Optimal methods for identifying drug-resistant
Mycobacterium tuberculosis
in a timely and affordable way in resource-limited settings are not yet available. This study prospectively evaluated a low-technology but rapid drug susceptibility testing method, the microscopic observation drug susceptibility assay (MODS), in the concurrent detection of
M. tuberculosis
and its susceptibilities to isoniazid and rifampin (two drugs defining multidrug-resistant
M. tuberculosis
) directly from sputum specimens. Sputum samples were collected from 262 smear-positive TB patients in Addis Ababa, Ethiopia. To undertake MODS, 100 μl of decontaminated samples was inoculated into a 24-well plate containing 1 ml of 7H9 broth with and without appropriate drugs. The assay uses an inverted-light microscope to detect characteristic mycobacterial growth in liquid culture. Of 262 smear-positive patients, MODS detected 254 (96.9%) and culture in Löwenstein-Jensen medium detected 247 (94.3%) (
P
= 0.016). For the 247 cultures, the sensitivity, specificity, and accuracy of MODS for detecting MDR-TB were 92.0, 99.5, and 98.8%, respectively, using the method of proportion as a reference (concordance, 98.8%; kappa value, 0.932). Results for MODS were obtained in a median time of 9 days. MODS is an optimal alternative method for identifying MDR-TB in a timely and affordable way in resource-limited settings.
Molecular Identification of Unusual Pathogenic Yeast Isolates by Large Ribosomal Subunit Gene Sequencing: 2 Years of Experience at the United Kingdom Mycology Reference Laboratory
Authors: Linton Christopher J. , Borman Andrew M. , Cheung Grace , Holmes Ann D. , Szekely Adrien , Palmer Michael D. , Bridge Paul D. , Campbell Colin K. , Johnson Elizabeth M.
Published: January 2007

Rapid identification of yeast isolates from clinical samples is particularly important given their innately variable antifungal susceptibility profiles. We present here an analysis of the utility of PCR amplification and sequence analysis of the hypervariable D1/D2 region of the 26S rRNA gene for the identification of yeast species submitted to the United Kingdom Mycology Reference Laboratory over a 2-year period. A total of 3,033 clinical isolates were received from 2004 to 2006 encompassing 50 different yeast species. While more than 90% of the isolates, corresponding to the most common
Candida
species, could be identified by using the AUXACOLOR2 yeast identification kit, 153 isolates (5%), comprised of 47 species, could not be identified by using this system and were subjected to molecular identification via 26S rRNA gene sequencing. These isolates included some common species that exhibited atypical biochemical and phenotypic profiles and also many rarer yeast species that are infrequently encountered in the clinical setting. All 47 species requiring molecular identification were unambiguously identified on the basis of D1/D2 sequences, and the molecular identities correlated well with the observed biochemical profiles of the various organisms. Together, our data underscore the utility of molecular techniques as a reference adjunct to conventional methods of yeast identification. Further, we show that PCR amplification and sequencing of the D1/D2 region reliably identifies more than 45 species of clinically significant yeasts and can also potentially identify new pathogenic yeast species.
Testing the Interaction between NOD-2 Status and Serological Response toMycobacterium paratuberculosisin Cases of Inflammatory Bowel Disease
Authors: Bernstein Charles N. , Wang Ming-Hsi , Sargent Michael , Brant Steven R. , Collins Michael T.
Published: January 2007

In a population-based case-control study we have previously shown that 14% of healthy Manitobans carry one or two mutations in the NOD-2 locus, a gene highly associated with Crohn's disease (CD). The NOD-2 protein is the receptor responsible for recognition of bacterial peptidoglycans, and it is plausible that NOD-2 is involved in the recognition of mycobacteria. Thirty-seven percent of Manitobans with CD had ≥1 NOD-2 mutation, leading to a threefold increased risk of CD for single-mutant carriers and a 30-fold increased risk for double-mutant carriers. In the same population groups, we assessed the seroprevalence forMycobacterium paratuberculosisand found it to be 35%, with no differences between CD, ulcerative colitis (UC), and controls. Because of high rates of CD and UC in Manitoba, we assessed whether there was an interaction between carrying a NOD-2 mutation andM. paratuberculosisseropositivity. An enzyme-linked immunosorbent assay for serum antibodies toM. paratuberculosisin cattle was adapted for human use. DNA was purified from whole blood. Subjects were genotyped for three NOD-2 variants, G908R, Cins1007fs, and R702W. Multivariate logistic regression analysis showed that NOD-2 gene mutations significantly associated with CD, butM. paratuberculosisserology did not. Furthermore, there was no interaction between NOD-2 mutation status andM. paratuberculosisserology status. For those with the NOD-2 mutation, the likelihood of CD subjects having positiveM. paratuberculosisserology was similar to that of controls (odds ratio, 1.31; 95% confidence interval, 0.55-3.11). No interaction could be proven for UC or by combining CD and UC compared to controls. In conclusion, we could not find an interaction between the NOD-2 genotype andM. paratuberculosisserology in relationship to CD or UC.
International Quality Assurance Study for Characterization ofStreptococcus pyogenes
Authors: Neal Shona , Beall Bernard , Ekelund Kim , Henriques-Normark Birgitta , Jasir Aftab , Johnson Dwight , Kaplan Edward , Lovgren Marguerite , Reinert Ralf Rene ,   Members of the Strep-EURO Study Group and International Streptococcus Reference Laboratories, Efstratiou Androulla
Published: February 2007

Surveillance of group A streptococcal (GAS) infections was undertaken as a major component of the European Commission-funded project on severe GAS disease in Europe (strep-EURO). One aim of strep-EURO was to improve the quality of GAS characterization by standardization of methods. An external quality assurance study (EQA) was therefore carried out to evaluate current global performance. Eleven strep-EURO and seven other streptococcal reference centers received a panel of 20 coded GAS isolates for typing. Conventional phenotypic typing (based on cell surface T and M protein antigens and opacity factor [OF] production) and molecular methods (emmgene typing) were used either as single or combined approaches to GAS typing. T typing was performed by 16 centers; 12 centers found one or more of the 20 strains nontypeable (typeability, 89%), and 11 centers reported at least one incorrect result (concordance, 93%). The 10 centers that tested for OF production achieved 96% concordance. Limited availability of antisera resulted in poor typeability values from the four centers that performed phenotypic M typing (41%), three of which also performed anti-OF typing (typeability, 63%); however, concordance was high for both M (100%) and anti-OF (94%) typing. In contrast, the 15 centers that performedemmgene sequencing achieved excellent typeability (97%) and concordance (98%), although comparison of the performance between centers yielded typeability rates from 65 to 100% and concordance values from 83 to 100%. With the rapid expansion and use of molecular genotypic methods to characterize GAS, continuation of EQA is essential in order to achieve international standardization and comparison of type distributions.
Impact of V2 Mutations on Escape from a Potent Neutralizing Anti-V3 Monoclonal Antibody during In Vitro Selection of a Primary Human Immunodeficiency Virus Type 1 Isolate
Authors: Shibata Junji , Yoshimura Kazuhisa , Honda Akiko , Koito Atsushi , Murakami Toshio , Matsushita Shuzo
Published: January 2007

KD-247, a humanized monoclonal antibody to an epitope of gp120-V3 tip, has potent cross-neutralizing activity against subtype B primary human immunodeficiency virus type 1 (HIV-1) isolates. To assess how KD-247 escape mutants can be generated, we induced escape variants by exposing bulked primary R5 virus, MOKW, to increasing concentrations of KD-247 in vitro. In the presence of relatively low concentrations of KD-247, viruses with two amino acid mutations (R166K/D167N) in V2 expanded, and under high KD-247 pressure, a V3 tip substitution (P313L) emerged in addition to the V2 mutations. However, a virus with a V2 175P mutation dominated during passaging in the absence of KD-247. Using domain swapping analysis, we demonstrated that the V2 mutations and the P313L mutation in V3 contribute to partial and complete resistance phenotypes against KD-247, respectively. To identify the V2 mutation responsible for the resistance to KD-247, we constructed pseudoviruses with single or double amino acid mutations in V2 and measured their sensitivity to neutralization. Interestingly, the neutralization phenotypes were switched, so that amino acid residue 175 (Pro or Leu) located in the center of V2 was exchanged, indicating that the amino acid at position 175 has a crucial role, dramatically changing the Env oligomeric state on the membrane surface and affecting the neutralization phenotype against not only anti-V3 antibody but also recombinant soluble CD4. These data suggested that HIV-1 can escape from anti-V3 antibody attack by changing the conformation of the functional envelope oligomer by acquiring mutations in the V2 region in environments with relatively low antibody concentrations.
Downregulation of CD4 by Human Immunodeficiency Virus Type 1 Nef Is Dependent on Clathrin and Involves Direct Interaction of Nef with the AP2 Clathrin Adaptor
Authors: Chaudhuri Rittik , Lindwasser O. Wolf , Smith William J. , Hurley James H. , Bonifacino Juan S.
Published: February 2007

Nef, an accessory protein of human and simian immunodeficiency viruses, is a critical determinant of pathogenesis that promotes the progression from infection to AIDS. The pathogenic effects of Nef are in large part dependent on its ability to downregulate the macrophage and T-cell coreceptor, CD4. It has been proposed that Nef induces downregulation by linking the cytosolic tail of CD4 to components of the host-cell protein trafficking machinery. To identify these components, we developed a novel Nef-CD4 downregulation system in
Drosophila melanogaster
S2 cells. We found that human immunodeficiency virus type 1 (HIV-1) Nef downregulates human CD4 in S2 cells and that this process is subject to the same sequence requirements as in human cells. An RNA interference screen targeting protein trafficking genes in S2 cells revealed a requirement for clathrin and the clathrin-associated, plasma membrane-localized AP2 complex in the downregulation of CD4. The requirement for AP2 was confirmed in the human cell line HeLa. We also used a yeast three-hybrid system and glutathione
S
-transferase pull-down analyses to demonstrate a robust, direct interaction between HIV-1 Nef and AP2. This interaction requires a dileucine motif in Nef that is also essential for downregulation of CD4. Together, these results support a model in which HIV-1 Nef downregulates CD4 by promoting its accelerated endocytosis by a clathrin/AP2 pathway.
Understanding frailty
Authors: Lally Frank , Crome Peter
Published: February 2007

The term “frailty” is used loosely to describe a range of conditions in older people, including general debility and cognitive impairment. There is no clear consensus on the definition of frailty; however, it is proposed that frailty comprises a collection of biomedical factors which influences an individual's physiological state in a way that reduces his or her capacity to withstand environmental stresses. Only a subset of older people are at risk of becoming frail; these are vulnerable, prone to dependency and have reduced life expectancy. These health outcomes contribute to an increased demand for medical and social care, and are associated with increased economic costs. As demographic trends indicate a rise in the older population, this healthcare burden will increase. This review aims to encapsulate the current debate surrounding the concept of frailty, with emphasis on proposed definitions of frailty which may be relevant to its identification in the clinical setting.
RELAXED STABILITY CONDITIONS FOR DELAYED RECURRENT NEURAL NETWORKS WITH POLYTOPIC UNCERTAINTIES
Authors: ZHANG BAOYONG , XU SHENGYUAN , ZOU YUN
Published: February 2007

This paper investigates the problem of stability analysis for recurrent neural networks with time-varying delays and polytopic uncertainties. Parameter-dependent Lypaunov functionals are employed to obtain sufficient conditions that guarantee the robust global exponential stability of the equilibrium point of the considered neural network. The derived stability criteria are expressed in terms of a set of relaxed linear matrix inequalities, which can be easily tested by using commercially available software. Two numerical examples are provided to demonstrate the effectiveness of the proposed results.
ANALYTICAL AND NUMERICAL INVESTIGATION OF ANT BEHAVIOR UNDER CROWDED CONDITIONS
Authors: PETERS KARSTEN , JOHANSSON ANDERS , DUSSUTOUR AUDREY , HELBING DIRK
Published: February 2007

Swarm intelligence is widely recognized as a powerful paradigm of self-organized optimization, with numerous examples of successful applications in distributed artificial intelligence. However, the role of physical interactions in the organization of traffic flows in ants under crowded conditions has only been studied very recently. The related results suggest new ways of congestion control and simple algorithms for optimal resource usage based on local interactions and, therefore, decentralized control concepts. Here, we present a mathematical analysis of such concepts for an experiment with two alternative ways with limited capacities between a food source and the nest of an ant colony. Moreover, we carry out microscopic computer simulations for generalized setups, in which ants have more alternatives or the alternative ways are of different lengths. In this way and by variation of interaction parameters, we can get a better idea of how powerful congestion control based on local repulsive interactions may be. Finally, we discuss potential applications of this design principle to routing in traffic or data networks and machine usage in supply systems.
Nitric oxide inhibits enterocyte migration through activation of RhoA-GTPase in a SHP-2-dependent manner
Authors: Cetin Selma , Leaphart Cynthia L. , Li Jun , Ischenko Irene , Hayman Michael , Upperman Jeffrey , Zamora Ruben , Watkins Simon , Ford Henri R. , Wang James , Hackam David J.
Published: February 2007

Diseases of intestinal inflammation like necrotizing enterocolitis (NEC) are associated with impaired epithelial barrier integrity and the sustained release of intestinal nitric oxide (NO). NO modifies the cytoskeletal regulator RhoA-GTPase, suggesting that NO could affect barrier healing by inhibiting intestinal restitution. We now hypothesize that NO inhibits enterocyte migration through RhoA-GTPase and sought to determine the pathways involved. The induction of NEC was associated with increased enterocyte NO release and impaired migration of bromodeoxyuridine-labeled enterocytes from terminal ileal crypts to villus tips. In IEC-6 enterocytes, NO significantly inhibited enterocyte migration and activated RhoA-GTPase while increasing the formation of stress fibers. In parallel, exposure of IEC-6 cells to NO increased the phosphorylation of focal adhesion kinase (pFAK) and caused a striking increase in cell-matrix adhesiveness, suggesting a mechanism by which NO could impair enterocyte migration. NEC was associated with increased expression of pFAK in the terminal ileal mucosa of wild-type mice and a corresponding increase in disease severity compared with inducible NO synthase knockout mice, confirming the dependence of NO for FAK phosphorylation in vivo and its role in the pathogenesis of NEC. Strikingly, inhibition of the protein tyrosine phosphatase SHP-2 in IEC-6 cells prevented the activation of RhoA by NO, restored focal adhesions, and reversed the inhibitory effects of NO on enterocyte migration. These data indicate that NO impairs mucosal healing by inhibiting enterocyte migration through activation of RhoA in a SHP-2-dependent manner and support a possible role for SHP-2 as a therapeutic target in diseases of intestinal inflammation like NEC.
Gata4andHnf1αare partially required for the expression of specific intestinal genes during development
Authors: Bosse Tjalling , Fialkovich John J. , Piaseckyj Christina M. , Beuling Eva , Broekman Henrike , Grand Richard J. , Montgomery Robert K. , Krasinski Stephen D.
Published: February 2007

The terminal differentiation phases of intestinal development in mice occur during cytodifferentiation and the weaning transition. Lactase-phlorizin hydrolase (LPH), liver fatty acid binding protein (Fabp1), and sucrase-isomaltase (SI) are well-characterized markers of these transitions. With the use of gene inactivation models in mature mouse jejunum, we have previously shown that a member of the zinc finger transcription factor family ( Gata4) and hepatocyte nuclear factor-1α ( Hnf1α) are each indispensable for LPH and Fabp1 gene expression but are both dispensable for SI gene expression. In the present study, we used these models to test the hypothesis that Gata4 and Hnf1α regulate LPH, Fabp1, and SI gene expression during development, specifically focusing on cytodifferentiation and the weaning transition. Inactivation of Gata4 had no effect on LPH gene expression during either cytodifferentiation or suckling, whereas inactivation of Hnf1α resulted in a 50% reduction in LPH gene expression during these same time intervals. Inactivation of Gata4 or Hnf1α had a partial effect (∼50% reduction) on Fabp1 gene expression during cytodifferentiation and suckling but no effect on SI gene expression at any time during development. Throughout the suckling period, we found a surprising and dramatic reduction in Gata4 and Hnf1α protein in the nuclei of absorptive enterocytes of the jejunum despite high levels of their mRNAs. Finally, we show that neither Gata4 nor Hnf1α mediates the glucocorticoid-induced precocious maturation of the intestine but rather are downstream targets of this process. Together, these data demonstrate that specific intestinal genes have differential requirements for Gata4 and Hnf1α that are dependent on the developmental time frame in which they are expressed.
Frequency-dependent contractile strength in mice over- and underexpressing the sarco(endo)plasmic reticulum calcium-ATPase
Authors: Hiranandani Nitisha , Raman Sripriya , Kalyanasundaram Anuradha , Periasamy Muthu , Janssen Paul M. L.
Published: January 2007

One of the prominent markers of end-stage heart failure at the molecular level is a decrease in function and/or expression of the sarcoplasmic reticulum ATPase protein [sarco(endo)plasmic reticulum calcium-ATPase, SERCA]. It has been often postulated that a decrease in SERCA pump activity can contribute in a major way to decreased cardiac function. To establish a functional relationship, we assessed how alterations in SERCA activity level affect basic contractile function in healthy myocardium devoid of other significant molecular changes. We investigated baseline contractile function, frequency-dependent activation, and β-adrenergic response in ultrathin trabeculae isolated from hearts of mice overexpressing SERCA (transgenic, TG), underexpressing SERCA2a (heterozygous knockout, Het), and their respective wild-type (WT) littermates. At physiological temperature and frequency, compared with their respective WT littermates, SERCA1a mice displayed increased developed force at frequencies of 4–8 Hz (∼90% increase at 4 Hz) and force equal to WT mice at 10–14 Hz. Force development at 4 Hz in presence of 1 μM isoproterenol was similar in TG and WT mice. In Het mice, developed force was nearly identical at the lower end of the frequency range (4–8 Hz) but slightly depressed at higher frequency ( P < 0.05 at 14 Hz). In presence of 1 μM isoproterenol, developed force at 4 Hz was equal to that in WT mice. Compared with normal levels, increased SERCA activity enhanced force development only at subphysiological frequencies. A reduction in SERCA activity only showed a depression of force at the higher frequency range. Thus generalizations regarding the correlation between SERCA activity and contractility can be highly ambiguous, because this relationship is critically dependent on other factors including stimulation frequency.
Rapid regulation of Na+fluxes and ammonia excretion in response to acute environmental hypoxia in the Amazonian oscar,Astronotus ocellatus
Authors: Wood Chris M. , Kajimura Makiko , Sloman Katherine A. , Scott Graham R. , Walsh Patrick J. , Almeida-Val Vera M. F. , Val Adalberto L.
Published: February 2007

The Amazonian oscar is extremely resistant to hypoxia, and tolerance scales with size. Overall, ionoregulatory responses of small (∼15 g) and large oscars (∼200 g) to hypoxia were qualitatively similar, but the latter were more effective. Large oscars exhibited a rapid reduction in unidirectional Na+uptake rate at the gills during acute hypoxia (Po2∼10 mmHg), which intensified with time (7 or 8 h); Na+efflux rates were also reduced, so net balance was little affected. The inhibitions were virtually immediate (1st h) and preceded a later 60% reduction (at 3 h) in gill Na+-K+-ATPase activity, reflected in a 60% reduction in maximum Na+uptake capacity without change in affinity (Km) for Na+. Upon acute restoration of normoxia, recovery of Na+uptake was delayed for 1 h. These data suggest that dual mechanisms may be involved (e.g., immediate effects of O2availability on transporters, channels, or permeability, slower effects of Na+-K+-ATPase regulation). Ammonia excretion appeared to be linked indirectly to Na+uptake, exhibiting a Michaelis-Menten relationship with external [Na+], but the Km was less than for Na+uptake. During hypoxia, ammonia excretion fell in a similar manner to Na+fluxes, with a delayed recovery upon normoxia restoration, but the relationship with [Na+] was blocked. Reductions in ammonia excretion were greater than in urea excretion. Plasma ammonia rose moderately over 3 h hypoxia, suggesting that inhibition of excretion was greater than inhibition of ammonia production. Overall, the oscar maintains excellent homeostasis of ionoregulation and N-balance during severe hypoxia.