bluuebunny/crossref_metadata_2025 huggingface dataset:
Rapid Antimicrobial Susceptibility Determination of Uropathogens in Clinical Urine Specimens by Use of ATP Bioluminescence
Authors: Ivančić Vesna , Mastali Mitra , Percy Neil , Gornbein Jeffrey , Babbitt Jane T. , Li Yang , Landaw Elliot M. , Bruckner David A. , Churchill Bernard M. , Haake David A.
Published: February 2008

We describe the first direct testing of the antimicrobial susceptibilities of bacterial pathogens in human clinical fluid samples by the use of ATP bioluminescence. We developed an ATP bioluminescence assay that eliminates somatic sources of ATP to selectively quantify the bacterial load in clinical urine specimens with a sensitivity of <1,000 CFU per milliliter. There was a log-log relationship between light emission and the numbers of CFU in clinical urine specimens. A clinical study was performed to evaluate the accuracy of the ATP bioluminescence assay for determination of the antimicrobial susceptibilities of uropathogens in clinical urine specimens tested in a blinded manner. ATP bioluminescent bacterial density quantitation was used to determine the inoculation volume in growth medium with and without antibiotics. After incubation at 37°C for 120 min, the ATP bioluminescence assay was repeated to evaluate the uropathogen response to antibiotics. The ability of the ATP bioluminescence assay to discriminate between antimicrobial susceptibility and resistance was determined by comparison of the results obtained by the ATP bioluminescence assay with the results obtained by standard clinical microbiology methods. Receiver operator characteristic curves were used to determine the optimal threshold for discriminating between susceptibility and resistance. Susceptibility and resistance were correctly predicted in 87% and 95% of cases, respectively, for an overall unweighted accuracy of 91%, when the results were stratified by antibiotic. For samples in which the pathogen was susceptible, the accuracy improved to 95% when the results for samples with less than a 25-fold increase in the amount of bacterial ATP in the medium without antibiotics were excluded. These data indicate that a rapid bioluminescent antimicrobial susceptibility assay may be useful for the management of urinary tract infections.
Evaluation of the Abbott RealTime HBV DNA Assay and Comparison to the Cobas AmpliPrep/Cobas TaqMan 48 Assay in Monitoring Patients with Chronic Cases of Hepatitis B
Authors: Ciotti Marco , Marcuccilli Fabbio , Guenci Tania , Prignano Maria Grazia , Perno Carlo Federico
Published: February 2008

The new Abbott RealTime hepatitis B virus (HBV) assay was compared to the Cobas AmpliPrep/Cobas TaqMan assay with 128 serum samples from patients with chronic hepatitis B. There was an excellent correlation (r= 0.961) between the two assays, with the Abbott RealTime test showing at least equivalent sensitivity and a slightly wider dynamic range than the Cobas TaqMan assay. By coupling high sensitivity with a large dynamic range, the Abbott RealTime HBV assay is useful in monitoring the response to antiviral therapy.
Molecular Epidemiology of Norovirus Infections in Children with Acute Gastroenteritis in South Korea in November 2005 through November 2006
Authors: Yoon Jong-Sub , Lee Sung-Geun , Hong Seong-Karp , Lee Su-A , Jheong Weon-Hwa , Oh Sang-Suk , Oh Mi-Hwa , Ko Gwang-Pyo , Lee Chan-Hee , Paik Soon-Young
Published: February 2008

Norovirus infections were detected in 114 of 762 children with acute gastroenteritis in South Korea from November 2005 to November 2006. Seasonality peaks in December, March, and October were also assessed in this study. We identified seven noroviral genotypes (GI-6, GII-2, GII-3, GII-4, GII-5, GII-6, and GII-8) and a C1-120 strain showing low identity (79.3%) with GII-13 and GII-17.
Negative and Positive mRNA Splicing Elements Act Competitively To Regulate Human Immunodeficiency Virus Type 1 Vif Gene Expression
Authors: Exline C. M. , Feng Z. , Stoltzfus C. M.
Published: February 2008

Over 40 different human immunodeficiency virus type 1 (HIV-1) mRNAs are produced by alternative splicing of the primary HIV-1 RNA transcripts. In addition, approximately half of the viral RNA remains unspliced and is used as genomic RNA and as mRNA for the Gag and Pol gene products. Regulation of splicing at the HIV-1 3′ splice sites (3′ss) requires suboptimal polypyrimidine tracts, and positive or negative regulation occurs through the binding of cellular factors to
cis
-acting splicing regulatory elements. We have previously shown that splicing at HIV-1 3′ss A1, which produces single-spliced
vif
mRNA and promotes the inclusion of HIV exon 2 into both completely and incompletely spliced viral mRNAs, is increased by optimizing the 5′ splice site (5′ss) downstream of exon 2 (5′ss D2). Here we show that the mutations within 5′ss D2 that are predicted to lower or increase the affinity of the 5′ss for U1 snRNP result in reduced or increased Vif expression, respectively. Splicing at 5′ss D2 was not necessary for the effect of 5′ss D2 on Vif expression. In addition, we have found that mutations of the GGGG motif proximal to the 5′ss D2 increase exon 2 inclusion and Vif expression. Finally, we report the presence of a novel exonic splicing enhancer (ESE) element within the 5′-proximal region of exon 2 that facilitates both exon inclusion and Vif expression. This ESE binds specifically to the cellular SR protein SRp75. Our results suggest that the 5′ss D2, the proximal GGGG silencer, and the ESE act competitively to determine the level of
vif
mRNA splicing and Vif expression. We propose that these positive and negative splicing elements act together to allow the accumulation of
vif
mRNA and unspliced HIV-1 mRNA, compatible with optimal virus replication.
Genital Ulcers Facilitate Rapid Viral Entry and Dissemination following Intravaginal Inoculation with Cell-Associated Simian Immunodeficiency Virus SIVmac239
Authors: Weiler Andrea M. , Li Qingsheng , Duan Lijie , Kaizu Masahiko , Weisgrau Kim L. , Friedrich Thomas C. , Reynolds Matthew R. , Haase Ashley T. , Rakasz Eva G.
Published: February 2008

Here we report the results of studies in the simian immunodeficiency virus (SIV)-rhesus macaque model of intravaginal transmission of human immunodeficiency virus type 1 in the setting of genital ulcerative diseases. We document preferential association of vRNA with induced ulcers during the first days of infection and show that allogeneic cells of the inoculum traffic from the vaginal lumen to lymphatic tissues. This surprisingly rapid systemic dissemination in this cell-associated SIV challenge model thus reveals the challenges of preventing transmission in the setting of genital ulcerative diseases and illustrates the utility of this animal model in tests of strategies aimed at reducing transmission under these conditions.
Role of Cellular Phosphatase cdc25C in Herpes Simplex Virus 1 Replication
Authors: Smith-Donald Benjamin A. , Durand Lizette O. , Roizman Bernard
Published: February 2008

Earlier studies have shown that in herpes simplex virus 1-infected cells, ICP22 upregulates the accumulation of a subset of γ
2
proteins exemplified by the products of the U
L
38, U
L
41, and U
S
11 genes. The ICP22-dependent process involves degradation of cyclins A and B1, the stabilization and activation of cdc2, physical interaction of activated cdc2 with the U
L
42 DNA synthesis processivity factor, and recruitment and phosphorylation of topoisomerase IIα by the cdc2/U
L
42 complex. Activation of cdc2, the first step in the process, is a key function of the mitotic phosphatase cdc25C. To define the role of cdc25C, we probed some features of the ICP22-dependent pathway of upregulation of γ
2
genes in cdc25C
−/−
cells and in cdc25C
+/+
cells derived from sibling mice. We report that cyclin B1 turned over in cdc25C
+/+
or cdc25C
−/−
cells at the same rate, that cdc2 increased in amount, and that U
S
11 and U
L
38 proteins and infectious virus accumulated in smaller amounts than in wild-type infected cells. The reduction in U
L
38 protein accumulation and virus was greater in cdc25C
−/−
cells infected with virus lacking ICP22 than in cells infected with wild-type virus. We conclude that cdc25C phosphatase plays a role in viral replication and that this role extends beyond its function of activating cdc2 for initiation of the ICP22-dependent cascade for upregulation of γ
2
gene expression.
The Interaction of Herpes Simplex Virus 1 Regulatory Protein ICP22 with the cdc25C Phosphatase Is Enabled In Vitro by Viral Protein Kinases U
S
3 and U
L
13
Authors: Smith-Donald Benjamin A. , Roizman Bernard
Published: February 2008

Earlier studies have shown that ICP22 and the U
L
13 protein kinase but not the U
S
3 kinase are required for optimal expression of a subset of late (γ
2
) genes exemplified by U
L
38, U
L
41, and U
S
11. In primate cells, ICP22 mediates the disappearance of inactive isoforms of cdc2 and degradation of cyclins A and B1. Active cdc2 acquires a new partner, the viral DNA synthesis processivity factor U
L
42. The cdc2-U
L
42 complex recruits and phosphorylates topoisomerase IIα for efficient expression of the γ
2
genes listed above. In uninfected cells, the cdc25C phosphatase activates cdc2 by removing two inhibitory phosphates. The accompanying report shows that in the absence of cdc25C, the rate of degradation of cyclin B1 is similar to that occurring in infected wild-type mouse embryo fibroblast cells but the levels of cdc2 increase, and the accumulation of a subset of late proteins and virus yields are reduced. This report links ICP22 with cdc25C. We show that in infected cells, ICP22 and U
S
3 protein kinase mediate the phosphorylation of cdc25C at its C-terminal domain. In in vitro assays with purified components, both U
L
13 and U
S
3 viral kinases phosphorylate cdc25C and ICP22. cdc25C also interacts with cdc2. However, in infected cells, the ability of cdc25C to activate cdc2 by dephosphorylation of the inactive cdc2 protein is reduced. Coupled with the phosphorylation of cdc25C by the U
S
3 kinase, the results raise the possibility that herpes simplex virus 1 diverts cdc25C to perform functions other than those performed in uninfected cells.
Antiviral Therapy during Primary Simian Immunodeficiency Virus Infection Fails To Prevent Acute Loss of CD4
+
T Cells in Gut Mucosa but Enhances Their Rapid Restoration through Central Memory T Cells
Authors: Verhoeven David , Sankaran Sumathi , Silvey Melanie , Dandekar Satya
Published: February 2008

Gut-associated lymphoid tissue (GALT) is an early target of human immunodeficiency virus (HIV) and simian immunodeficiency virus (SIV) and a site for severe CD4
+
T-cell depletion. Although antiretroviral therapy (ART) is effective in suppressing HIV replication and restoring CD4
+
T cells in peripheral blood, restoration in GALT is delayed. The role of restored CD4
+
T-cell help in GALT during ART and its impact on antiviral CD8
+
T-cell responses have not been investigated. Using the SIV model, we investigated gut CD4
+
T-cell restoration in infected macaques, initiating ART during either the primary stage (1 week postinfection), prior to acute CD4
+
cell loss (PSI), or during the chronic stage at 10 weeks postinfection (CSI). ART led to viral suppression in GALT and peripheral blood mononuclear cells of PSI and CSI animals at comparable levels. CSI animals had incomplete CD4
+
T-cell restoration in GALT. In PSI animals, ART did not prevent acute CD4
+
T-cell loss by 2 weeks postinfection in GALT but supported rapid and complete CD4
+
T-cell restoration thereafter. This correlated with an accumulation of central memory CD4
+
T cells and better suppression of inflammation. Restoration of CD4
+
T cells in GALT correlated with qualitative changes in SIV gag-specific CD8
+
T-cell responses, with a dominance of interleukin-2-producing responses in PSI animals, while both CSI macaques and untreated SIV-infected controls were dominated by gamma interferon responses. Thus, central memory CD4
+
T-cell levels and qualitative antiviral CD8
+
T-cell responses, independent of viral suppression, were the immune correlates of gut mucosal immune restoration during ART.
The Specificities of Kaposi's Sarcoma-Associated Herpesvirus-Encoded E3 Ubiquitin Ligases Are Determined by the Positions of Lysine or Cysteine Residues within the Intracytoplasmic Domains of Their Targets
Authors: Cadwell Ken , Coscoy Laurent
Published: February 2008

Kaposi's sarcoma-associated herpesvirus encodes two homologous E3 ligases, MIR1 and MIR2, that mediate the ubiquitination and subsequent downregulation of several cell surface proteins, and in particular major histocompatibility complex class I (MHC-I) molecules. We have previously shown that, in addition to lysine ubiquitination, MIR1 has the unique ability of transferring ubiquitin onto MHC-I molecules lacking available lysine residues, in a cysteine-dependent manner. Here we report that MIR1 activity is maximal when either a lysine or cysteine residue is placed approximately 15 amino acids away from the transmembrane domain, whereas MIR2 preferentially targets residues, including cysteines, that are closer to the transmembrane domain. Thus MIR1 and -2 can distinguish their substrates based on the position of the lysine or cysteine residues, suggesting that these proteins have evolved to target different sets of surface molecules. These results indicate that the position of target residues within a substrate is an essential determinant of E3 ubiquitin ligase specificity.
The Role of T Cells in the Enhancement of Respiratory Syncytial Virus Infection Severity during Adult Reinfection of Neonatally Sensitized Mice
Authors: Tregoning John S. , Yamaguchi Yuko , Harker James , Wang Belinda , Openshaw Peter J. M.
Published: February 2008

Respiratory syncytial virus (RSV) is the major cause of infantile bronchiolitis and hospitalization. Severe RSV disease is associated with the development of wheezing in later life. In a mouse model of the delayed effects of RSV, the age at primary infection determines responses to reinfection in adulthood. During primary RSV infection, neonatal BALB/c mice developed only mild disease and recruited CD8 cells that were defective in gamma interferon production. Secondary reinfection of neonatally primed mice caused enhanced inflammation and profuse lung T-cell recruitment. CD4 cell depletion during secondary RSV challenge attenuated disease (measured by weight loss); depletion of CD8 cells also markedly attenuated disease severity but enhanced lung eosinophilia, and depletion of both CD4 and CD8 cells together completely abrogated weight loss. Depletion of CD8 (but not CD4) cells during primary neonatal infection was protective against weight loss during adult challenge. Therefore, T cells, in particular CD8 T cells, play a central role in the outcome of neonatal infection by enhancing disease during secondary challenge. These findings demonstrate a crucial role for T cells in the regulation of immune responses after neonatal infection.
Tobacco Rattle Virus 16-Kilodalton Protein Encodes a Suppressor of RNA Silencing That Allows Transient Viral Entry in Meristems
Authors: Martín-Hernández Ana M. , Baulcombe David C.
Published: February 2008

RNA silencing is a host defense mechanism that limits the accumulation and spread of viruses in infected plants. Correspondingly, plant viruses encode suppressors of silencing. In the positive-strand RNA virus Tobacco rattle virus (TRV), the suppressor of silencing is a 16-kDa (16K) protein encoded by RNA1. The suppressor action of the 16K protein is transient and weaker than that of the P19 suppressor, encoded by tomato bushy stunt virus. Mutant TRV that does not produce its suppressor, unlike other suppressor-defective viruses, is competent to accumulate and spread systemically in the infected plant. However, this mutant virus does not exhibit the transient invasion of the meristem that is characteristic of the wild-type virus. Based on this analysis, we propose that the 16K suppressor of silencing allows TRV to transiently invade the meristem. Our data are consistent with a mechanism of long-term meristem virus exclusion that is dependent on a transient invasion of the meristem early in the infection cycle. This novel mechanism of meristem exclusion may be associated with the phenomenon of recovery in virus-infected plants in which upper leaves have little or no virus and are immune to secondary infection by the same virus.
CD4
+
Target Cell Availability Determines the Dynamics of Immune Escape and Reversion In Vivo
Authors: Petravic Janka , Loh Liyen , Kent Stephen J. , Davenport Miles P.
Published: February 2008

Infections with human immunodeficiency virus (HIV) and the closely related monkey viruses simian-human immunodeficiency virus (SHIV) and simian immunodeficiency virus (SIV) are characterized by progressive waves of immune responses, followed by viral mutation and “immune escape.” However, escape mutation usually leads to lower replicative fitness, and in the absence of immune pressure, an escape mutant (EM) virus “reverts” to the wild-type phenotype. Analysis of the dynamics of immune escape and reversion has suggested it is a mechanism for identifying the immunogens best capable of controlling viremia. We have analyzed and modeled data of the dynamics of wild-type (WT) and EM viruses during SHIV infection of macaques. Modeling suggests that the dynamics of reversion and immune escape should be determined by the availability of target cells for infection. Consistent with this suggestion, we find that the rate of reversion of cytotoxic T-lymphocyte (CTL) EM virus strongly correlates with the number of CD4
+
T cells available for infection. This phenomenon also affects the rate of immune escape, since this rate is determined by the balance of CTL killing and the WT fitness advantage. This analysis predicts that the optimal timing for the selection of immune escape variants will be immediately after the peak of viremia and that the development of escape variants at later times will lead to slower selection. This has important implications for comparative studies of immune escape and reversion in different infections and for identifying epitopes with high fitness cost for use as vaccine targets.
Genome Analysis of a
Glossina pallidipes
Salivary Gland Hypertrophy Virus Reveals a Novel, Large, Double-Stranded Circular DNA Virus
Authors: Abd-Alla Adly M. M. , Cousserans François , Parker Andrew G. , Jehle Johannes A. , Parker Nicolas J. , Vlak Just M. , Robinson Alan S. , Bergoin Max
Published: February 2008

Several species of tsetse flies can be infected by the
Glossina pallidipes
salivary gland hypertrophy virus (GpSGHV). Infection causes salivary gland hypertrophy and also significantly reduces the fecundity of the infected flies. To better understand the molecular basis underlying the pathogenesis of this unusual virus, we sequenced and analyzed its genome. The GpSGHV genome is a double-stranded circular DNA molecule of 190,032 bp containing 160 nonoverlapping open reading frames (ORFs), which are distributed equally on both strands with a gene density of one per 1.2 kb. It has a high A+T content of 72%. About 3% of the GpSGHV genome is composed of 15 sequence repeats, distributed throughout the genome. Although sharing the same morphological features (enveloped rod-shaped nucleocapsid) as baculoviruses, nudiviruses, and nimaviruses, analysis of its genome revealed that GpSGHV differs significantly from these viruses at the level of its genes. Sequence comparisons indicated that only 23% of GpSGHV genes displayed moderate homologies to genes from other invertebrate viruses, principally baculoviruses and entomopoxviruses. Most strikingly, the GpSGHV genome encodes homologues to the four baculoviral per os infectivity factors (p74 [pif-0], pif-1, pif-2, and pif-3). The DNA polymerase encoded by GpSGHV is of type B and appears to be phylogenetically distant from all DNA polymerases encoded by large double-stranded DNA viruses. The majority of the remaining ORFs could not be assigned by sequence comparison. Furthermore, no homologues to DNA-dependent RNA polymerase subunits were detected. Taken together, these data indicate that GpSGHV is the prototype member of a novel group of insect viruses.
Identification of a Coronavirus Transcription Enhancer
Authors: Moreno José L. , Zúñiga Sonia , Enjuanes Luis , Sola Isabel
Published: February 2008

Coronavirus
(CoV) transcription includes a discontinuous mechanism during the synthesis of sub-genome-length minus-strand RNAs leading to a collection of mRNAs in which the 5′ terminal leader sequence is fused to contiguous genome sequences. It has been previously shown that transcription-regulating sequences (TRSs) preceding each gene regulate transcription. Base pairing between the leader TRS (TRS-L) and the complement of the body TRS (cTRS-B) in the nascent RNA is a determinant factor during CoV transcription. In fact, in transmissible gastroenteritis CoV, a good correlation has been observed between subgenomic mRNA (sg mRNA) levels and the free energy (ΔG) of TRS-L and cTRS-B duplex formation. The only exception was sg mRNA N, the most abundant sg mRNA during viral infection in spite of its minimum ΔG associated with duplex formation. We postulated that additional factors should regulate transcription of sg mRNA N. In this report, we have described a novel transcription regulation mechanism operating in CoV by which a 9-nucleotide (nt) sequence located 449 nt upstream of the N gene TRS core sequence (CS-N) interacts with a complementary sequence just upstream of CS-N, specifically increasing the accumulation of sg mRNA N. Alteration of this complementarity in mutant replicon genomes showed a correlation between the predicted stability of the base pairing between 9-nt sequences and the accumulation of sg mRNA N. This interaction is exclusively conserved in group 1a CoVs, the only CoV subgroup in which the N gene is not the most 3′ gene in the viral genome. This is the first time that a long-distance RNA-RNA interaction regulating transcriptional activity specifically enhancing the transcription of one gene has been described to occur in CoVs.
Effect of sample size on shear strength of basaltic residual soils
Authors: Garga Vinod K.
Published: February 2008

This paper first provides a brief review of the very limited data available on the size effect on strength of soils. Then it presents the results of an investigation of this effect on the drained strength of two residual soils derived from basalt. The dense basaltic soil, derived from weathering of columnar basalt, is fissured, whereas the vesicular basaltic soil, product of weathering of amygdaloidal basalt, is remarkably free of discontinuities. The results of tests on 500 mm square, 100 mm square, and 63.5 mm diameter direct shear tests, as well as on 36 mm diameter triaxial samples were obtained. The data clearly indicate the significant effect of fissures on the strength of dense basaltic soil, whereas the effect is absent in the vesicular soil. The reduction in strength with size in the former can be attributed almost totally to a loss of the cohesive component of shear strength. In the absence of tests on large-sized samples, a method is suggested to estimate the mass strength of such soils from results of tests on small-sized samples. Key words: fissures, residual soil, size effect, shear, strength, testing.
Density of granular materials derived from X-ray photographs: calibration, reliability, and recommended procedures
Authors: Morin Pierre
Published: February 2008

X-ray photographs of sample cores are commonly used to describe undisturbed sedimentary structures such as bedding planes, cracks, shells, etc. An improved X-ray film density method is presented; it allows for a quantitative measurement of physical parameters, for example, water content or density, provided adequate calibration and interpretation are used. The influence of the grain size, chemical composition of the materials, and the pore fluid has been investigated. A simple procedure is recommended and illustrated with an example. Key words: radiography, X ray, density, granular materials, film density method.
Determination of the shear strength parameters of an unsaturated soil using the direct shear test
Authors: Gan J. K. M. , Fredlund D. G. , Rahardjo H.
Published: February 2008

Multistage direct shear tests have been performed on saturated and unsaturated specimens of a compacted glacial till. A conventional direct shear apparatus was modified in order to use the axis-translation technique for direct shear tests on unsaturated soils. The soil can be subjected to a wide range of matric suctions. The testing procedure and some typical results are presented. Nonlinearity in the failure envelope with respect to matric suction was observed. Suggestions are made as to how best to handle the nonlinearity from a practical engineering standpoint. Key words: shear strength, unsaturated soils, negative pore-water pressures, soil suction, direct shear.
The induced trench method—a critical review and case history
Authors: Sladen J. A. , Oswell J. M.
Published: February 2008

The "induced trench" method for buried pipe protection is reviewed. By installing a zone of relatively compressible material within the backfill above a pipe, soil arching is induced. This has the effect of reducing the vertical earth load on the pipe, permitting the pipe to be buried at a greater depth than would otherwise be tolerable. In many circumstances, the method can offer significant economic benefits over alternatives. Although the literature includes several case histories describing the use of this technique, geotechnical aspects have received little attention. The theory on which currently available design methods are based is somewhat outdated and fails to address many factors that affect performance. For a recent project in Calgary, Alberta, a nonlinear finite element simulation was carried out to optimize the design. Performance during and after installation was monitored. Vertical pressures on the pipe were significantly less than those predicted by conventional theory. There is a need for the development of a more rational approach that is suitable for routine design. Key words: induced trench, soil–structure interaction, buried pipes, soil arching.
The shear strength of soils containing undulating shear zones—a numerical study
Authors: Dounias George T. , Potts David M. , Vaughan Peter R.
Published: February 2008

This paper investigates the behaviour of a clay layer containing an undulating shear surface, when sheared across the undulations. A relatively long soil block containing an undulating weak zone of finite thickness is assumed. A finite element study is undertaken, examining the effect of the thickness and the amplitude of the weak zone on the overall strength and deformation of the block. Also examined is the behaviour of the block when either only the weak zone or both the weak zone and the intact soil are strain softening. Key words: undulating shear surface, finite elements, strain softening.
Determination of horizontal geostatic stress in clay with self-bored pressuremeter
Authors: Jefferies M. G.
Published: February 2008

The Gibson–Anderson theory for interpretation of pressuremeter data in clay is extended to include the unloading part of the test for the particular circumstances that prevail with a self-bored pressuremeter (SBP). Incorporation of the extended theory in a computer-aided modelling procedure allows horizontal geostatic stress to be unambiguously determined from SBP data by image matching irrespective of imperfections in the self-boring process. The procedure is illustrated by example on a previously reported test carried out in Beaufort Shelf clay. Key words: clay, in situ tests, self-bored pressuremeter, K0.
Postsurcharge secondary compression equation for clays
Authors: Juárez-Badillo Eulalio
Published: February 2008

A general time – volume change equation for soils is used to describe the initial swelling and further secondary compression of clay samples when surcharges are used. The procedure is illustrated by a practical application to México City clay. Key words: clay, secondary compression, secondary consolidation, postsurcharge, time-dependent compression, constitutive equations.
Extraction and characterization of organics from two Champlain Sea subsurface soils
Authors: Yong Raymond N. , Mourato Diana
Published: February 2008

The focus of this investigation is to establish whether organic materials are present in subsurface soils in measurable and significant quantities. Two subsurface soils from the Champlain Sea region were chosen for study. Organic carbon concentrations of 0.5% as total organic carbon (TOC) were detected in the soils studied at depths up to 14.2 m. The extraction and subsequent analyses of organic compounds permitted one to classify these as humic acids, fulvic acids, humins, and nonhumic materials. Extraction of these subsurface soil organics was achieved using a modified HCl–NaOH extraction method. The extracted organics were analyzed for TOC to confirm their organic nature as well as for study of their surface chemistry. The compositional and structural characteristics of the extracts were investigated using infrared spectroscopy and scanning electron microscopy. Key words: subsurface soil organics, humic materials, nonhumic organics, organics extraction, Champlain Sea clays.
2 × 2-SCROLL ATTRACTORS GENERATED IN A THREE-DIMENSIONAL SMOOTH AUTONOMOUS SYSTEM
Authors: LIU WENBO , TANG WALLACE K. S. , CHEN GUANRONG
Published: February 2008

In this letter, a three-dimensional continuous-time smooth autonomous system with quadratic nonlinear terms is proposed for generating multiscroll chaotic attractors. Observation of 2 × 2-scroll attractors generated from this kind of system is reported for the first time. The result is confirmed by both numerical simulations and electronic circuit experiments.
ESTIMATION OF THE DOMAIN CONTAINING ALL COMPACT INVARIANT SETS OF THE OPTICALLY INJECTED LASER SYSTEM
Authors: STARKOV KONSTANTIN E.
Published: February 2008

In this paper we study the localization problem of compact invariant sets of the optically injected laser system by applying the first order extremum conditions and cylindrical coordinates. Our main results consist in finding localization sets of simple forms which can be easily computed. Special attention is focussed on the case where we obtain a compact localization set.
GENERATION OF n × m-SCROLL ATTRACTORS UNDER A CHUA-CIRCUIT FRAMEWORK
Authors: YU SIMIN , TANG WALLACE K. S. , CHEN G.
Published: February 2008

In this paper, the generation of n × m-scroll attractors under a Chua-circuit framework is presented. By using a sawtooth function, f1(x), and a staircase function, f2(y), n × m-scroll attractors can be generated and observed from a third-order circuit. Its dynamical behaviors are investigated by means of theoretical analysis as well as numerical simulation. Moreover, two electronic circuits are designed for its realization, and experimental observations of n × m-scroll attractors based on Chua's circuit are reported, for the first time in the literature.
PHENOMENOLOGY OF RETAINED EXCITATION
Authors: ADAMATZKY ANDREW
Published: February 2008

In a two-dimensional cellular automaton model of retained excitation every excited cell stays excited if the number of excited neighbors belong to some interval, the cell takes refractory state otherwise. Every resting cell is excited if the number of excited cells in its neighborhood belong to some other interval; cell-state transition from refractory to resting state is unconditional. We classify 1296 rules of retained excitation based on how dynamics of excitable lattices develop after initial stimulation. Several modes of space-time activity dynamics are discovered: not growing but persistent domains of activity, domains with rectangular, octagonal and almost circular growth, amoeba-like growing patterns, mobile and still localizations.
THE CORRESPONDENCE BETWEEN STOCHASTIC RESONANCE AND BIFURCATION OF MOMENT EQUATIONS OF NOISY NONLINEAR DYNAMICAL SYSTEM
Authors: ZHANG GUANG-JUN , XU JIAN-XUE
Published: February 2008

There is a kind of correspondence between stochastic resonance and bifurcation of the moment equations of a noisy nonlinear system with the same noise intensity as the resonance independent variable and the bifurcation parameter, respectively. In this paper, this correspondence is examined and revealed in the noisy one-dimensional bistable system and the noisy two-dimensional Duffing oscillator. The bifurcation of the moment equations of each noisy system is the bifurcation with double-branch of fixed-point shift. Besides classical stochastic resonance, a kind of complex stochastic resonance corresponds to the bifurcation of moment equations. This complex stochastic resonance is induced by the stochastic transitions of system motion among the three fixed point attractors on both sides of the bifurcation point of the original system, which is predicted semi-analytically. Finally, due to this correspondence being examined, the mechanism of stochastic resonance can be provided through analyzing the change of the energy transfer induced by the bifurcation of the moment equations.
BIFURCATION OF LIMIT CYCLES IN A FOURTH-ORDER NEAR-HAMILTONIAN SYSTEM
Authors: HAN MAOAN , SHANG DESHENG , ZHENG WANG , YU PEI
Published: February 2008

This paper is concerned with bifurcation of limit cycles in a fourth-order near-Hamiltonian system with quartic perturbations. By bifurcation theory, proper perturbations are given to show that the system may have 20, 21 or 23 limit cycles with different distributions. This shows that H(4) ≥ 20, where H(n) is the Hilbert number for the second part of Hilbert's 16th problem. It is well known that H(2) ≥ 4, and it has been recently proved that H(3) ≥ 12. The number of limit cycles obtained in this paper greatly improves the best existing result, H(4) ≥ 15, for fourth-degree polynomial planar systems.
Mechanism of Eukaryotic Homologous Recombination
Authors: San Filippo Joseph , Sung Patrick , Klein Hannah
Published: February 2008

Homologous recombination (HR) serves to eliminate deleterious lesions, such as double-stranded breaks and interstrand crosslinks, from chromosomes. HR is also critical for the preservation of replication forks, for telomere maintenance, and chromosome segregation in meiosis I. As such, HR is indispensable for the maintenance of genome integrity and the avoidance of cancers in humans. The HR reaction is mediated by a conserved class of enzymes termed recombinases. Two recombinases, Rad51 and Dmc1, catalyze the pairing and shuffling of homologous DNA sequences in eukaryotic cells via a filamentous intermediate on ssDNA called the presynaptic filament. The assembly of the presynaptic filament is a rate-limiting process that is enhanced by recombination mediators, such as the breast tumor suppressor BRCA2. HR accessory factors that facilitate other stages of the Rad51- and Dmc1-catalyzed homologous DNA pairing and strand exchange reaction have also been identified. Recent progress on elucidating the mechanisms of action of Rad51 and Dmc1 and their cohorts of ancillary factors is reviewed here.
How Does Synaptotagmin Trigger Neurotransmitter Release?
Authors: Chapman Edwin R.
Published: February 2008

Neurotransmitter release at synapses involves a highly specialized form of membrane fusion that is triggered by Ca2+ions and is optimized for speed. These observations were established decades ago, but only recently have the molecular mechanisms that underlie this process begun to come into view. Here, we summarize findings obtained from genetically modified neurons and neuroendocrine cells, as well as from reconstituted systems, which are beginning to reveal the molecular mechanism by which Ca2+—acting on the synaptic vesicle (SV) protein synaptotagmin I (syt)—triggers rapid exocytosis. This work sheds light not only on presynaptic aspects of synaptic transmission, but also on the fundamental problem of membrane fusion, which has remained a puzzle that has yet to be solved in any biological system.
Structural Principles From Large RNAs
Authors: Holbrook Stephen R.
Published: February 2008

Since the year 2000 a number of large RNA three-dimensional structures have been determined by X-ray crystallography. Structures composed of more than 100 nucleotide residues include the signal recognition particle RNA, group I intron, the GlmS ribozyme, RNAseP RNA, and ribosomal RNAs from Haloarcula morismortui, Escherichia coli, Thermus thermophilus, and Deinococcus radiodurans. These large RNAs are constructed from the same secondary and tertiary structural motifs identified in smaller RNAs but appear to have a larger organizational architecture. They are dominated by long continuous interhelical base stacking, tend to segregate into domains, and are planar in overall shape as opposed to their globular protein counterparts. These findings have consequences in RNA folding, intermolecular interaction, and packing, in addition to studies of design and engineering and structure prediction.
Biophysics of Catch Bonds
Authors: Thomas Wendy E. , Vogel Viola , Sokurenko Evgeni
Published: February 2008

Receptor-ligand bonds strengthened by tensile mechanical force are referred to as catch bonds. This review examines experimental data and biophysical theory to analyze why mechanical force prolongs the lifetime of these bonds rather than shortens the lifetime by pulling the ligand out of the binding pocket. Although many mathematical models can explain catch bonds, experiments using structural variants have been more helpful in determining how catch bonds work. The underlying mechanism has been worked out so far only for the bacterial adhesive protein FimH. This protein forms catch bonds because it is allosterically activated when mechanical force pulls an inhibitory domain away from the ligand-binding domain. Other catch bond–forming proteins, including blood cell adhesion proteins called selectins and the motor protein myosin, show evidence of allosteric regulation between two domains, but it remains unclear if this is related to their catch bond behavior.
Single-Molecule Approach to Molecular Biology in Living Bacterial Cells
Authors: Xie X. Sunney , Choi Paul J. , Li Gene-Wei , Lee Nam Ki , Lia Giuseppe
Published: February 2008

Recent developments on fluorescent proteins and microscopy techniques have allowed the probing of single molecules in a living bacterial cell with high specificity, millisecond time resolution, and nanometer spatial precision. Recording movies and analyzing dynamics of individual macromolecules have brought new insights into the mechanisms of many processes in molecular biology, such as DNA-protein interactions, gene regulation, transcription, translation, and replication, among others. Here we review the key methods of single-molecule detection and highlight numerous examples to illustrate how these experiments are contributing to the quantitative understanding of the fundamental processes in a living cell.
Spike Timing–Dependent Plasticity: A Hebbian Learning Rule
Authors: Caporale Natalia , Dan Yang
Published: February 2008

Spike timing–dependent plasticity (STDP) as a Hebbian synaptic learning rule has been demonstrated in various neural circuits over a wide spectrum of species, from insects to humans. The dependence of synaptic modification on the order of pre- and postsynaptic spiking within a critical window of tens of milliseconds has profound functional implications. Over the past decade, significant progress has been made in understanding the cellular mechanisms of STDP at both excitatory and inhibitory synapses and of the associated changes in neuronal excitability and synaptic integration. Beyond the basic asymmetric window, recent studies have also revealed several layers of complexity in STDP, including its dependence on dendritic location, the nonlinear integration of synaptic modification induced by complex spike trains, and the modulation of STDP by inhibitory and neuromodulatory inputs. Finally, the functional consequences of STDP have been examined directly in an increasing number of neural circuits in vivo.
Reproductive Biology, Technology, and Gender Inequality: An Autobiographical Essay
Authors: Huber Joan N.
Published: February 2008

Ignorance of biodata is costly in sociology. Gender theorists remain unaware that until the demographic transition, infants were suckled every 15 minutes for two years, less often another two. A nearly continuous cycle of pregnancy and lactation barred women from the activities that brought the most prestige and power until the advent of modern sanitation after 1880. Women entered the public arena in large number only after technology altered the social consequences of human physiology. Yet wives still spend twice as much time in housework and child care as husbands. Data about the effects of both biology and culture on social interaction would enhance studies of ethnocentrism within the household.
Fluid pressure modulates L-type Ca2+ channel via enhancement of Ca2+-induced Ca2+ release in rat ventricular myocytes
Authors: Lee Sunwoo , Kim Joon-Chul , Li Yuhua , Son Min-Jeong , Woo Sun-Hee
Published: February 2008

This study examines whether fluid pressure (FP) modulates the L-type Ca2+ channel in cardiomyocytes and investigates the underlying cellular mechanism(s) involved. A flow of pressurized (∼16 dyn/cm2) fluid, identical to that bathing the myocytes, was applied onto single rat ventricular myocytes using a microperfusion method. The Ca2+ current ( ICa) and cytosolic Ca2+ signals were measured using a whole cell patch-clamp and confocal imaging, respectively. It was found that the FP reversibly suppressed ICa (by 25%) without altering the current-voltage relationships, and it accelerated the inactivation of ICa. The level of ICa suppression by FP depended on the level and duration of pressure. The Ba2+ current through the Ca2+ channel was only slightly decreased by the FP (5%), suggesting an indirect inhibition of the Ca2+ channel during FP stimulation. The cytosolic Ca2+ transients and the basal Ca2+ in field-stimulated ventricular myocytes were significantly increased by the FP. The effects of the FP on the ICa and on the Ca2+ transient were resistant to the stretch-activated channel inhibitors, GsMTx-4 and streptomycin. Dialysis of myocytes with high concentrations of BAPTA, the Ca2+ buffer, eliminated the FP-induced acceleration of ICa inactivation and reduced the inhibitory effect of the FP on ICa by ≈80%. Ryanodine and thapsigargin, abolishing sarcoplasmic reticulum Ca2+ release, eliminated the accelerating effect of FP on the ICa inactivation, and they reduced the inhibitory effect of FP on the ICa. These results suggest that the fluid pressure indirectly suppresses the Ca2+ channel by enhancing the Ca2+-induced intracellular Ca2+ release in rat ventricular myocytes.
Physiological and hypoxic O2 tensions rapidly regulate NO production by stimulated macrophages
Authors: Robinson Mary A. , Baumgardner James E. , Good Virginia P. , Otto Cynthia M.
Published: February 2008

Nitric oxide (NO) production by inducible NO synthase (iNOS) is dependent on O2 availability. The duration and degree of hypoxia that limit NO production are poorly defined in cultured cells. To investigate short-term O2-mediated regulation of NO production, we used a novel forced convection cell culture system to rapidly (response time of 1.6 s) and accurately (±1 Torr) deliver specific O2 tensions (from <1 to 157 Torr) directly to a monolayer of LPS- and IFNγ-stimulated RAW 264.7 cells while simultaneously measuring NO production via an electrochemical probe. Decreased O2 availability rapidly (≤30 s) and reversibly decreased NO production with an apparent KmO2 of 22 (SD 6) Torr (31 μM) and a Vmax of 4.9 (SD 0.4) nmol·min−1·10−6 cells. To explore potential mechanisms of decreased NO production during hypoxia, we investigated O2-dependent changes in iNOS protein concentration, iNOS dimerization, and cellular NO consumption. iNOS protein concentration was not affected ( P = 0.895). iNOS dimerization appeared to be biphasic [6 Torr ( P = 0.008) and 157 Torr ( P = 0.258) >36 Torr], but it did not predict NO production. NO consumption was minimal at high O2 and NO tensions and negligible at low O2 and NO tensions. These results are consistent with O2 substrate limitation as a regulatory mechanism during brief hypoxic exposure. The rapid and reversible effects of physiological and pathophysiological O2 tensions suggest that O2 tension has the potential to regulate NO production in vivo.
Dysregulation of hepatic iron with aging: implications for heat stress-induced oxidative liver injury
Authors: Bloomer Steven A. , Brown Kyle E. , Buettner Garry R. , Kregel Kevin C.
Published: February 2008

Environmental heat stress is associated with an age-related increase in hepatic oxidative damage and an exaggerated state of oxidative stress. The purpose of this investigation was to evaluate the regulation of hepatic iron after heat stress. A secondary aim was to determine a potential role for iron in heat stress-induced liver injury. Hyperthermia-induced alterations in hepatic iron were evaluated in young (6 mo) and old (24 mo) Fischer 344 rats by exposing them to a two-heat stress protocol. Livers were harvested at several time points after the second heating and assayed for labile and nonheme iron. In the control condition, there was no difference in labile iron between age groups. Both labile iron and storage iron were not altered by hyperthermia in young rats, but both were increased immediately after heating in old rats. To evaluate a role for iron in liver injury, hepatic iron content was manipulated in young and old rats, and then both groups were exposed to heat stress. Iron administration to young rats significantly increased hepatic iron content and ferritin but did not affect markers of lipid peroxidation under control conditions or after heat stress. In old rats, iron chelation with deferoxamine prevented the increase in nonheme iron, labile iron, ferritin, and lipid peroxidation after heat stress. These results suggest that iron may play a role in hepatic injury after hyperthermia. Thus, dysregulation of iron may contribute to the gradual decline in cellular and physiological function that occurs with aging.
PACAP is expressed in sympathoexcitatory bulbospinal C1 neurons of the brain stem and increases sympathetic nerve activity in vivo
Authors: Farnham Melissa M. J. , Li Qun , Goodchild Ann K. , Pilowsky Paul M.
Published: February 2008

Pituitary adenylate cyclase-activating polypeptide (PACAP) is an excitatory neuropeptide present in the rat brain stem. The extent of its localization within catecholaminergic groups and bulbospinal sympathoexcitatory neurons is not established. Using immunohistochemistry and in situ hybridization, we determined the extent of any colocalization with catecholaminergic and/or bulbospinal projections from the brain stem was determined. PACAP mRNA was found in tyrosine hydroxylase-immunoreactive (TH-ir) neurons in the C1-C3 cell groups. In the rostral ventrolateral medulla (RVLM), PACAP mRNA was found in 84% of the TH-ir neurons and 82% of bulbospinal TH-ir neurons. The functional significance of these PACAP mRNA positive bulbospinal neurons was tested by intrathecal administration of PACAP-38 in anaesthetized rats. Splanchnic sympathetic nerve activity doubled (110%) and heart rate rose significantly (19%), although blood pressure was unaffected. In addition, as previously reported, PACAP was found in the A1 cell group but not in the A5 cell group or in the locus coeruleus. The RVLM is the primary site responsible for the tonic and reflex control of blood pressure through the activity of bulbospinal presympathetic neurons, the majority of which contain TH. The results indicate 1) that pontomedullary neurons containing both TH and PACAP that project to the intermediolateral cell column originate from C1-C3 and not A5, and 2) intrathecal PACAP-38 causes a prolonged, sympathoexcitatory effect.