bluuebunny/crossref_metadata_2025 huggingface dataset:
Evaluation of Chlamydia trachomatis and Neisseria gonorrhoeae Detection in Urine, Endocervical, and Vaginal Specimens by a Multiplexed Isothermal Thermophilic Helicase-Dependent Amplification (tHDA) Assay
Authors: O'Neil Dominic , Doseeva Victoria , Rothmann Thomas , Wolff John , Nazarenko Irina
Published: September 2011

We have developed a new research assay that combines sequence-specific sample preparation and isothermal amplification for the detection of
Chlamydia trachomatis
and
Neisseria gonorrhoeae
infections. The assay targets both the
omp
gene and the cryptic plasmid of
C. trachomatis
and the multicopy
opa
gene of
N. gonorrhoeae
, which are amplified and detected in a single reaction. We evaluated the ability of the assay to detect
C. trachomatis
and
N. gonorrhoeae
infections in first-catch urine, swab, and liquid-based cytology samples. Total agreement between the new assay and APTIMA Combo 2 varied between 95.3% and 100%, depending on the sample type and target detected. Total agreement between the new assay and BD ProbeTec varied between 96.7% and 100%, depending on the sample type and target detected. The assay has a simple work flow, and endpoint results can be achieved in 3 h, including sample preparation. The assay described here was evaluated for research use and was compared to commercially available assays.
Systematic Survey of Clonal Complexity in Tuberculosis at a Populational Level and Detailed Characterization of the Isolates Involved
Authors: Navarro Yurena , Herranz Marta , Pérez-Lago Laura , Martínez Lirola Miguel , Ruiz-Serrano Maria Jesús , Bouza Emilio , García de Viedma Darío
Published: September 2011

Clonally complex infections by
Mycobacterium tuberculosis
are progressively more accepted. Studies of their dimension in epidemiological scenarios where the infective pressure is not high are scarce. Our study systematically searched for clonally complex infections (mixed infections by more than one strain and simultaneous presence of clonal variants) by applying mycobacterial interspersed repetitive-unit (MIRU)–variable-number tandem-repeat (VNTR) analysis to
M. tuberculosis
isolates from two population-based samples of respiratory (703 cases) and respiratory-extrapulmonary (R+E) tuberculosis (TB) cases (71 cases) in a context of moderate TB incidence. Clonally complex infections were found in 11 (1.6%) of the respiratory TB cases and in 10 (14.1%) of those with R+E TB. Among the 21 cases with clonally complex TB, 9 were infected by 2 independent strains and the remaining 12 showed the simultaneous presence of 2 to 3 clonal variants. For the 10 R+E TB cases with clonally complex infections, compartmentalization (different compositions of strains/clonal variants in independent infected sites) was found in 9 of them. All the strains/clonal variants were also genotyped by IS
6110
-based restriction fragment length polymorphism analysis, which split two MIRU-defined clonal variants, although in general, it showed a lower discriminatory power to identify the clonal heterogeneity revealed by MIRU-VNTR analysis. The comparative analysis of IS
6110
insertion sites between coinfecting clonal variants showed differences in the genes coding for a cutinase, a PPE family protein, and two conserved hypothetical proteins. Diagnostic delay, existence of previous TB, risk for overexposure, and clustered/orphan status of the involved strains were analyzed to propose possible explanations for the cases with clonally complex infections. Our study characterizes in detail all the clonally complex infections by
M. tuberculosis
found in a systematic survey and contributes to the characterization that these phenomena can be found to an extent higher than expected, even in an unselected population-based sample lacking high infective pressure.
Differing Neisseria gonorrhoeae Bacterial Loads in the Pharynx and Rectum in Men Who Have Sex with Men: Implications for Gonococcal Detection, Transmission, and Control
Authors: Bissessor M. , Tabrizi S. N. , Fairley C. K. , Danielewski J. , Whitton B. , Bird S. , Garland S. , Chen M. Y.
Published: September 2011

The bacterial loads for gonococcal infections of the pharynx and rectum were determined among men with male sexual partners. The median bacterial load for rectal infections (18,960 copies/swab) was significantly higher than the load for pharyngeal infections (2,100 copies/swab;
P
= 0.001). Bacterial loads among men with symptomatic proctitis were strikingly high (median, 278,000 copies/swab).
Target Cell-Mediated Editing of HIV-1 cDNA by APOBEC3 Proteins in Human Macrophages
Authors: Koning Fransje A. , Goujon Caroline , Bauby Hélène , Malim Michael H.
Published: September 2011

Apolipoprotein B mRNA-editing enzyme catalytic polypeptide-like 3 (APOBEC3) proteins are encapsidated by assembling HIV-1 virions and edit viral cDNA in the next round of infection. Using alpha interferon (IFN-α)-treated monocyte-derived macrophages, we show that infrequent editing of HIV-1 reverse transcripts can also be mediated by APOBEC3 proteins supplied by the targets of infection. Based on the local sequence contexts of these mutations and the established characteristics of APOBEC3 protein expression in myeloid cells, we speculate that APOBEC3A may be responsible for a substantial proportion of this activity.
Hypoxia Induces the Gene Expression and Extracellular Transmission of Persistent Lymphocytic Choriomeningitis Virus
Authors: Tomaskova Jana , Oveckova Ingrid , Labudova Martina , Lukacikova Lubomira , Laposova Katarina , Kopacek Juraj , Pastorekova Silvia , Pastorek Jaromir
Published: September 2011

The physiological context of virus-infected cells can markedly affect multiplication and spread of the virus progeny. During persistent infection, the virus exploits the host cell without disturbing its vital functions. However, microenvironmental hypoxia can uncouple this intimate relationship and escalate virus pathogenesis. Accumulating evidence suggests that hypoxia-inducible factor (HIF) modulates gene expression of the viruses that pass through a DNA stage, contain hypoxia-responsive promoter elements, and replicate in the nucleus. Here we show that hypoxia can influence the gene expression and transmission of the cytoplasmic RNA virus lymphocytic choriomeningitis virus (LCMV), which is a neglected human pathogen and teratogen. The MX strain of LCMV, which we used as a model, replicates in a persistent mode in human HeLa cells, fails to produce mature envelope glycoproteins, and spreads through cell-cell contacts in the absence of extracellular infectious virions. Both exposure of MX-infected HeLa cells to chronic hypoxia and gene transfer approaches led to increased virus RNA transcription and higher levels of the viral proteins via a HIF-dependent mechanism. Moreover, hypoxia enhanced the formation of infectious virions capable of transmitting LCMV by cell-free medium. This LCMV “reactivation” might have health-compromising consequences in hypoxia-associated situations, such as fetal development and ischemia-related pathologies.
Retrofitting the Genome: L1 Extinction Follows Endogenous Retroviral Expansion in a Group of Muroid Rodents
Authors: Erickson Issac K. , Cantrell Michael A. , Scott LuAnn , Wichman Holly A.
Published: September 2011

Long interspersed nuclear element 1 (LINE-1; L1) retrotransposons are the most common retroelements in mammalian genomes. Unlike individual families of endogenous retroviruses (ERVs), they have remained active throughout the mammalian radiation and are responsible for most of the retroelement movement and much genome rearrangement within mammals. They can be viewed as occupying a substantial niche within mammalian genomes. Our previous demonstration that L1s and B1 short interspersed nuclear elements (SINEs) are inactive in a group of South American rodents led us to ask if other elements have amplified to fill the empty niche. We identified a novel and highly active family of ERVs (mysTR). To determine whether loss of L1 activity was correlated with expansion of mysTR, we examined mysTR activity in four South American rodent species that have lost L1 and B1 activity and four sister species with active L1s. The copy number of recent mysTR insertions was extremely high, with an average of 4,200 copies per genome. High copy numbers exist in both L1-active and L1-extinct species, so the mysTR expansion appears to have preceded the loss of both SINE and L1 activity rather than to have filled an empty niche created by their loss. It may be coincidental that two unusual genomic events—loss of L1 activity and massive expansion of an ERV family—occur in the same group of mammals. Alternatively, it is possible that this large ERV expansion set the stage for L1 extinction.
A Genetic Interaction between the Core and NS3 Proteins of Hepatitis C Virus Is Essential for Production of Infectious Virus
Authors: Jones Daniel M. , Atoom Ali M. , Zhang Xiaozhen , Kottilil Shyamasundaran , Russell Rodney S.
Published: September 2011

By analogy to other members of the
Flaviviridae
family, the hepatitis C virus (HCV) core protein is presumed to oligomerize to form the viral nucleocapsid, which encloses the single-stranded RNA genome. Core protein is directed to lipid droplets (LDs) by domain 2 (D2) of the protein, and this process is critical for virus production. Domain 1 (D1) of core is also important for infectious particle morphogenesis, although its precise contribution to this process is poorly understood. In this study, we mutated amino acids 64 to 75 within D1 of core and examined the ability of these mutants to produce infectious virus. We found that residues 64 to 66 are critical for generation of infectious progeny, whereas 67 to 75 were dispensable for this process. Further investigation of the defective 64 to 66 mutant (termed JFH1
T
-64–66) revealed it to be incapable of producing infectious intracellular virions, suggesting a fault during HCV assembly. Furthermore, isopycnic gradient analyses revealed that JFH1
T
-64–66 assembled dense intracellular species of core, presumably representing nucleocapsids. Thus, amino acids 64 to 66 are seemingly not involved in core oligomerization/nucleocapsid assembly. Passaging of JFH1
T
-64–66 led to the emergence of a single compensatory mutation (K1302R) within the helicase domain of NS3 that completely rescued its ability to produce infectious virus. Importantly, the same NS3 mutation abrogated virus production in the context of wild-type core protein. Together, our results suggest that residues 64 to 66 of core D1 form a highly specific interaction with the NS3 helicase that is essential for the generation of infectious HCV particles at a stage downstream of nucleocapsid assembly.
Fusion of Epstein-Barr Virus with Epithelial Cells Can Be Triggered by αvβ5 in Addition to αvβ6 and αvβ8, and Integrin Binding Triggers a Conformational Change in Glycoproteins gHgL
Authors: Chesnokova Liudmila S. , Hutt-Fletcher Lindsey M.
Published: September 2011

Fusion of herpesviruses with their target cells requires a minimum of three glycoproteins, namely, gB and a complex of gH and gL. Epstein-Barr virus (EBV) fusion with an epithelial cell requires no additional virus glycoproteins, and we have shown previously that it can be initiated by an interaction between integrin αvβ6 or αvβ8 and gHgL. We now report that integrin αvβ5 can also bind to gHgL and trigger fusion. Binding of gHgL to integrins is a two-step reaction. The first step, analyzed by surface plasmon resonance, was fast, with high association and low dissociation rate constants. The second step, detected by fluorescence spectroscopy of gHgL labeled at cysteine 153 at the domain I-domain II interface with the environmentally sensitive probes acrylodan and IANBD, involved a slower conformational change. Interaction of gHgL with neutralizing monoclonal antibodies or Fab′ fragments was also consistent with a two-step reaction involving fast high-affinity binding and a subsequent slower conformational change. None of the antibodies bound to the same epitope, and none completely inhibited integrin binding. However, binding of each decreased the rate of conformational change induced by integrin binding, suggesting that neutralization might involve a conformational change that precludes fusion. Overall, the data are consistent with the interaction of gHgL with an integrin inducing a functionally important rearrangement at the domain I-domain II interface.
Regulation of Vaccinia Virus E3 Protein by Small Ubiquitin-Like Modifier Proteins
Authors: González-Santamaría José , Campagna Michela , García María Angel , Marcos-Villar Laura , González Dolores , Gallego Pedro , Lopitz-Otsoa Fernando , Guerra Susana , Rodríguez Manuel S. , Esteban Mariano , Rivas Carmen
Published: September 2011

The vaccinia virus (VACV) E3 protein is essential for virulence and has antiapoptotic activity and the ability to impair the host innate immune response. Here we demonstrate that E3 interacts with SUMO1 through a small ubiquitin-like modifier (SUMO)-interacting motif (SIM). SIM integrity is required for maintaining the stability of the viral protein and for the covalent conjugation of E3 to SUMO1 or SUMO2, a modification that has a negative effect on the E3 transcriptional transactivation of the p53-upregulated modulator of apoptosis (PUMA) and APAF-1 genes. We also demonstrate that E3 is ubiquitinated, a modification that does not destabilize the wild-type protein but triggers the degradation of an E3-ΔSIM mutant. This report constitutes the first demonstration of the important roles that both SUMO and ubiquitin play in the regulation of the VACV protein E3.
Immunovirological Analyses of Chronically Simian Immunodeficiency Virus SIVmnd-1- and SIVmnd-2-Infected Mandrills (Mandrillus sphinx)
Authors: Apetrei Cristian , Sumpter Beth , Souquiere Sandrine , Chahroudi Ann , Makuwa Maria , Reed Patricia , Ribeiro Ruy M. , Pandrea Ivona , Roques Pierre , Silvestri Guido
Published: September 2011

Simian immunodeficiency virus (SIV) infection in African nonhuman primate (NHP) natural hosts is usually nonpathogenic, despite high levels of virus replication. We have previously shown that chronic SIV infection in sooty mangabeys (SMs) and African green monkeys (AGMs) is associated with low levels of immune activation and bystander T cell apoptosis. To compare these features with those observed in another natural host, the mandrill (MND), we conducted a cross-sectional survey of the 23 SIV-infected and 25 uninfected MNDs from the only semifree colony of mandrills available worldwide. Viral loads (VLs) were determined and phenotypic and functional analysis of peripheral blood- and lymph node-derived lymphocytes was performed. We found that mandrills chronically infected with SIVmnd-1 or SIVmnd-2 have similar levels of viral replication, and we observed a trend toward lower CD4
+
T cell counts in chronically SIVmnd-2-infected MNDs than SIVmnd-1-infected MNDs. No correlation between CD4
+
T cell counts and VLs in SIV-infected MNDs could be established. Of note, the levels of T cell activation, proliferation, and apoptosis were comparable between SIVmnd-1- and SIVmnd-2-infected MNDs and to those observed in uninfected animals, with the only exception being an increase in tumor necrosis factor alpha-producing CD8
+
T cells in SIVmnd-2-infected MNDs. Overall, these findings recapitulate previous observations in SIV-infected SMs and AGMs and lend further evidence to the hypothesis that low levels of immune activation protect natural SIV hosts from disease progression.
CD8+T Cell Escape Mutations in Simian Immunodeficiency Virus SIVmac239 Cause Fitness DefectsIn Vivo, and Many Revert after Transmission
Authors: Mudd Philip A. , Ericsen Adam J. , Walsh Andrew D. , León Enrique J. , Wilson Nancy A. , Maness Nicholas J. , Friedrich Thomas C. , Watkins David I.
Published: September 2011

Virus-specific CD8+T lymphocytes select for escape mutations in human immunodeficiency virus (HIV) and simian immunodeficiency virus (SIV). To assess the effects of these mutations on viral fitness, we introduced escape mutations into 30 epitopes (bound by five major histocompatibility complex class I [MHC-I] molecules) in three different viruses. Two of these MHC-I alleles are associated with elite control. Two of the three viruses demonstrated reduced fitnessin vivo, and 27% of the introduced mutations reverted. These findings suggest that T cell epitope diversity may not be such a daunting problem for the development of an HIV vaccine.
Poliovirus Unlinks TIA1 Aggregation and mRNA Stress Granule Formation
Authors: White James P. , Lloyd Richard E.
Published: September 2011

In response to environmental stress and viral infection, mammalian cells form foci containing translationally silenced mRNPs termed stress granules (SGs). As aggregates of stalled initiation complexes, SGs are defined by the presence of translation initiation machinery in addition to mRNA binding proteins. Here, we report that cells infected with poliovirus (PV) can form SGs early that contain T-cell-restricted intracellular antigen 1 (TIA1), translation initiation factors, RNA binding proteins, and mRNA. However, this response is blocked as infection progresses, and a type of pseudo-stress granule remains at late times postinfection and contains TIA but lacks translation initiation factors, mRNA binding proteins, and most polyadenylated mRNA. This result was observed using multiple stressors, including viral infection, oxidative stress, heat shock, and endoplasmic reticulum stress. Multiple proteins required for efficient viral internal ribosome entry site-dependent translation are localized to SGs under stress conditions, providing a potential rationale for the evolution and maintenance of the SG inhibition phenotype. Further, the expression of a noncleavable form of the RasGAP-SH3 domain binding protein in PV-infected cells enables SGs whose constituents are consistent with the presence of stalled 48S translation preinitiation complexes to persist throughout infection. These results indicate that in poliovirus-infected cells, the functions of TIA self-aggregation and aggregation of stalled translation initiation complexes into stress granules are severed, leading to novel foci that contain TIA1 but lack other stress granule-defining components.
CD8
+
T Cell Immunodominance in Lymphocytic Choriomeningitis Virus Infection Is Modified in the Presence of Toll-Like Receptor Agonists
Authors: Siddiqui Sarah , Basta Sameh
Published: September 2011

Currently, we have limited understanding of how Toll-like receptor (TLR) engagement by microbial products influences the immune response during a concurrent virus infection. In this study, we established that dual TLR2 plus TLR3 (designated TLR2+3) stimulation alters the immunodominance hierarchies of lymphocytic choriomeningitis virus (LCMV) epitopes by reducing NP396-specific CD8
+
T cell responses and shifting it to a subdominant position. The shift in immunodominance occurred due to a reduction in antigen uptake and the reduced cross-presentation of NP396, a major LCMV immunodominant epitope that is efficiently cross-presented. Moreover, the altered immunodominance was dependent on TLR stimulation occurring at the site of infection. Finally, as lipopolysaccharide failed to induce the same phenomenon, the data suggest that these findings are dependent not only on the dual engagement of the TRIF/MyD88 pathways but also on how TLR agonists activate antigen-presenting cells. Taken together, our data demonstrate a novel role for TLR ligands in regulating antiviral CD8
+
T cell responses due to the regulation of the cross-presentation of cell-associated antigens.
In Vitro
Generation of High-Titer Prions
Authors: Shikiya Ronald A. , Bartz Jason C.
Published: September 2011

Prions are composed mainly, if not entirely, of PrP
Sc
, an infectious misfolded isoform of PrP
C
, the normal isoform of the prion protein. Here we show that protein misfolding cyclic amplification (PMCA)-generated hypertransmissible mink encephalopathy (HY TME) PrP
Sc
is highly infectious and has a titer that is similar, if not identical, to that associated with brain tissue from animals infected with the HY TME agent that are in the terminal stage of disease. These data demonstrate that PMCA efficiently replicates the prion agent and provide further support for the hypothesis that
in vitro
-generated prions are bona fide and are not due to contamination.
Curative effect of topical treatment of digital dermatitis with a gel containing activated copper and zinc chelate
Authors: Holzhauer M. , Bartels C. J. , van Barneveld M. , Vulders C. , Lam T.
Published: September 2011

The efficacy of two topical treatments for painful ulcerative stage (M2) of bovine digital dermatitis (BDD) lesions was compared in a clinical trial conducted on five dairy farms in 2009 to 2010. The first treatment was a water‐based gel with active components copper and zinc (Intra Hoof‐fit gel [IHF]) and the second treatment was a topical chlortetracycline spray (CTC spray). The experimental unit for this study was the hindleg with the presence of a BDD lesion. Cure was defined as the transition of an M2 lesion into a healed (M0) or a non‐painful chronic stage (M4) of BDD at D28. On day 0, cows with M2 BDD lesions were photographed and were treated with either IHF or CTC. Subsequently, feet were photographed and scored on D28. The cure rate of M2 BDD lesions treated with IHF at D28 was 0.92 (CI 0.84 to 0.96) and was significantly better than for M2 BDD lesions treated with CTC, which was 0.58 (CI 0.47 to 0.68).
Survey to determine the seroprevalence of Toxoplasma gondii infection in British sheep flocks
Authors: Hutchinson J. P. , Wear A. R. , Lambton S. L. , Smith R. P. , Pritchard G. C.
Published: September 2011

A serological survey of Toxoplasma gondii infection in adult breeding sheep in Great Britain was conducted using surplus sera taken during a seroprevalence study of Brucella melitensis in 2009. Of the 3539 sera collected from 227 flocks, 2619 (74 per cent) were found to be positive for T gondii specific antibody when tested using latex agglutination. Multilevel logistic modelling suggested that the likelihood of infection increased with age and this effect appeared to be amplified in animals vaccinated against T gondii. The model also indicated that the odds of sheep being seropositive were increased on premises where cattle were also kept. These results suggest a high level of Toxoplasma infection in breeding sheep in Great Britain and provide further evidence to suggest that postnatal infection is more common than congenital infection in sheep.
A MODIFIED MODEL OF NONLOCALLY CORRECTED GRAVITY: COSMOLOGY AND THE NEWTONIAN LIMIT
Authors: LIU DAO-JUN , YANG BIN , JIN XING-HUA
Published: September 2011

A modified form of nonlocally corrected theory of gravity is investigated in the context of cosmology and the Newtonian limit. This form of nonlocal correction to classic Einstein–Hilbert action can be locally represented by a triple-scalar–tensor theory in which one of the scalar degrees of freedom is phantom-like and the other two are quintessence-like. We show that there exists a stable de Sitter solution for the cosmological dynamics if a suitable form of potential function V(ϕ) (or equivalently, f(R)) is selected. However, no matter what a potential function is selected, there is always an early time repeller solution corresponding to a radiation dominated universe. Besides, the equations for linear scalar perturbations are presented and it is shown that the form of potential function V(ϕ) is stringently constrained by the solar system test, although the post-Newtonian parameter γ is not directly affected by this function.
MODEL DEPENDENCE OF OUTFLOW RATES FROM AN ACCRETION DISK IN PRESENCE OF A DISSIPATIVE STANDING SHOCK
Authors: SINGH CHANDRA B. , CHAKRABARTI SANDIP K.
Published: September 2011

Solutions of black hole accretion flows with axisymmetric shocks are obtained self-consistently when the dissipation at the post-shock flow is taken into account. The Rankine–Hugoniot relationships had to be modified suitably to incorporate the energy loss as well as possible matter loss due to outflows in the post-shock region. The outflow rate from the post-shock region is also computed self-consistently. This was done by considering the quantities in the subsonic post-shock flow as the initial condition for the conical outflow. We have several major results: we find the analytical expression of the ratio of the outflow rate and the inflow rate Rṁ. We find that Rṁ strongly depends on the model assumptions which govern the flow geometry. It appears that, (a) the outflow rate is at most a few percent of the inflow rate, (b) the outflow is absent when the shock is relatively weak, (c) the outflow rate decreases with the increase in the energy loss at the post-shock region. These conclusions are very important as they have direct bearings on the observational effects. Since spectrally soft states are generally believed to be caused by the dominance of the soft photons and almost total loss of thermal energy of the Compton cloud by inverse Comptonization, a spectrally softer state should have less outflows. The opposite is generally true: A spectrally harder state will have a stronger outflow, but the result depends on the compression ratio and the adopted model. The other major result is that the model independence of the transonic properties of the flow does not hold in presence of the loss of the energy (radiation) and mass (outflow).
Altered sleep and behavioral activity phenotypes in PER3-deficient mice
Authors: Hasan Sibah , van der Veen Daan R. , Winsky-Sommerer Raphaelle , Dijk Derk-Jan , Archer Simon N.
Published: September 2011

Sleep homeostasis and circadian rhythmicity interact to determine the timing of behavioral activity. Circadian clock genes contribute to circadian rhythmicity centrally and in the periphery, but some also have roles within sleep regulation. The clock gene Period3 ( Per3) has a redundant function within the circadian system and is associated with sleep homeostasis in humans. This study investigated the role of PER3 in sleep/wake activity and sleep homeostasis in mice by recording wheel-running activity under baseline conditions in wild-type (WT; n = 54) and in PER3-deficient ( Per3−/−; n = 53) mice, as well as EEG-assessed sleep before and after 6 h of sleep deprivation in WT ( n = 7) and Per3−/− ( n = 8) mice. Whereas total activity and vigilance states did not differ between the genotypes, the temporal distribution of wheel-running activity, vigilance states, and EEG delta activity was affected by genotype. In Per3−/− mice, running wheel activity was increased, and REM sleep and NREM sleep were reduced in the middle of the dark phase, and delta activity was enhanced at the end of the dark phase. At the beginning of the baseline light period, there was less wakefulness and more REM and NREM sleep in Per3−/− mice. Per3−/− mice spent less time in wakefulness and more time in NREM sleep in the light period immediately after sleep deprivation, and REM sleep accumulated more slowly during the recovery dark phase. These data confirm a role for PER3 in sleep-wake timing and sleep homeostasis.
Impact of a single session of intermittent pneumatic leg compressions on skeletal muscle and isolated artery gene expression in rats
Authors: Roseguini Bruno T. , Arce-Esquivel Arturo A. , Newcomer Sean C. , Laughlin M. H.
Published: September 2011

Intermittent pneumatic leg compressions (IPC) have proven to be an effective noninvasive approach for treatment of patients with claudication, but the mechanisms underlying the clinical benefits remain elusive. In the present study, a rodent model of claudication produced by bilateral ligation of the femoral artery was used to investigate the acute impact of a single session of IPC (150 min) on hemodynamics, skeletal muscle (tibialis anterior), and isolated collateral artery (perforating artery) expression of a subset of genes associated with inflammation and vascular remodeling. In addition, the effect of compression frequency (15 vs. 3 compressions/min) on the expression of these factors was studied. In ligated animals, IPC evoked an increase of monocyte chemoattractant protein-1 (MCP-1) and cytokine-induced neutrophil chemoattractant 1 (CXCL1) mRNA ( P < 0.01) and immunostaining ( P < 0.05), as well as a minor increase in VEGF immunostaining in the muscle endomysium 150 min postintervention. Further, collateral arteries from these animals showed an increased expression of MCP-1 (approximately twofold, P = 0.02). These effects were most evident in the group exposed to the high-frequency protocol (15 compressions/min). In contrast, IPC in sham-operated control animals evoked a modest initial upregulation of VEGF ( P = 0.01), MCP-1 ( P = 0.02), and CXCL1 ( P = 0.03) mRNA in the muscle without concomitant changes in protein levels. No changes in gene expression were observed in arteries isolated from sham animals. In conclusion, IPC acutely up-regulates the expression of important factors involved in vascular remodeling in the compressed muscle and collateral arteries in a model of hindlimb ischemia. These effects appear to be dependent on the compression frequency, such that a high compression frequency (15 compressions/min) evokes more consistent and robust effects compared with the frequency commonly employed clinically to treat patients with claudication (3 compressions/min).
AMPK protects proximal tubular cells from stress-induced apoptosis by an ATP-independent mechanism: potential role of Akt activation
Authors: Lieberthal Wilfred , Zhang Leiqing , Patel Vimal A. , Levine Jerrold S.
Published: September 2011

We examined the role of AMP-activated protein kinase (AMPK) in modulating the viability of cultured kidney proximal tubular cells subjected to metabolic stress induced by either dextrose deprivation, inhibition of glycolysis, or inhibition of mitochondrial respiration. We used BU.MPT cells, a conditionally immortalized kidney epithelial cell line derived from the proximal tubules of transgenic mice bearing a temperature-sensitive mutation of the simian virus 40 large-tumor antigen. All three forms of metabolic stress increased the phosphorylation and activity of AMPK. Activation of AMPK led to changes in the phosphorylation of two downstream targets of AMPK, acetyl coenzyme A carboxylase and p70 S6 kinase. Inhibition of AMPK, either pharmacologically with compound C (CC) or by gene silencing, significantly increased the amount of apoptosis in response to all three forms of metabolic stress. Although the amount of apoptosis was directly related to the severity of ATP depletion, inhibition of AMPK had no effect on cellular ATP levels. Notably, metabolic stress increased the phosphorylation and activity of Akt. Furthermore, inhibition of AMPK, with CC or gene silencing, abrogated the ability of metabolic stress to activate Akt. The augmentation of apoptosis induced by inhibition of AMPK was comparable to that induced by inhibition of Akt. We conclude that activation of AMPK following acute metabolic stress plays a major role in promoting the viability of cultured proximal tubular cells. Protection by AMPK appears to be due not to AMPK-mediated conservation of cell energy stores, but rather, at least in part, to AMPK-mediated activation of Akt.
INK4a deletion results in improved kidney regeneration and decreased capillary rarefaction after ischemia-reperfusion injury
Authors: Lee David H. , Wolstein Jesse M. , Pudasaini Basu , Plotkin Matthew
Published: September 2011

The molecular mechanisms that lead to tubular atrophy, capillary loss, and fibrosis following acute kidney injury are not very clear but may involve cell cycle inhibition by increased expression of cyclin kinase inhibitors. The INK4a/ARF locus encodes overlapping genes for two proteins, a cyclin kinase inhibitor, p16INK4a, and a p53 stabilizer, p19ARF, from independent promoters. To determine if decreased INK4a gene expression results in improved kidney regeneration, INK4a knockout (KO) and wild-type (WT) mice were subjected to ischemia-reperfusion injury (IRI). p16INK4a and p19ARF levels were increased markedly in WT mice at 1–28 days after injury. Kidneys were examined to determine the localization and levels of p16INK4a, apoptosis, cell proliferation, and capillary rarefaction. KO mice displayed decreased tubular cell apoptosis, increased cell proliferation, and lower creatinine levels after injury. KO mice had significantly higher capillary density compared with WT mice at 14–42 days after IRI. Plasma granulocyte colony-stimulating factor (G-CSF) increased after ischemia in both WT and KO mice and was elevated markedly in KO compared with WT mice. KO kidney digests contained higher counts of Gr-1+/Cd11b+ myeloid cells by flow cytometry. KO mice treated with a Gr-1-depleting antibody displayed reduced vascular endothelial growth factor mRNA, plasma G-CSF, and capillary density, and an increase in serum creatinine and medullary myofibroblasts, compared with untreated KO mice 14 days after ischemia. The anti-angiogenic effect of Gr-1 depletion in KO mice was confirmed by Matrigel angiogenesis assays. These results suggest that the absence of p16INK4a and p19ARF following IRI has a protective effect on the kidney through improved epithelial and microvascular repair, in part by enhancing the mobilization of myeloid cells into the kidney.
Task-level feedback can explain temporal recruitment of spatially fixed muscle synergies throughout postural perturbations
Authors: Safavynia Seyed A. , Ting Lena H.
Published: September 2011

Recent evidence suggests that complex spatiotemporal patterns of muscle activity can be explained with a low-dimensional set of muscle synergies or M-modes. While it is clear that both spatial and temporal aspects of muscle coordination may be low dimensional, constraints on spatial versus temporal features of muscle coordination likely involve different neural control mechanisms. We hypothesized that the low-dimensional spatial and temporal features of muscle coordination are independent of each other. We further hypothesized that in reactive feedback tasks, spatially fixed muscle coordination patterns—or muscle synergies—are hierarchically recruited via time-varying neural commands based on delayed task-level feedback. We explicitly compared the ability of spatially fixed (SF) versus temporally fixed (TF) muscle synergies to reconstruct the entire time course of muscle activity during postural responses to anterior-posterior support-surface translations. While both SF and TF muscle synergies could account for EMG variability in a postural task, SF muscle synergies produced more consistent and physiologically interpretable results than TF muscle synergies during postural responses to perturbations. Moreover, a majority of SF muscle synergies were consistent in structure when extracted from epochs throughout postural responses. Temporal patterns of SF muscle synergy recruitment were well-reconstructed by delayed feedback of center of mass (CoM) kinematics and reproduced EMG activity of multiple muscles. Consistent with the idea that independent and hierarchical low-dimensional neural control structures define spatial and temporal patterns of muscle activity, our results suggest that CoM kinematics are a task variable used to recruit SF muscle synergies for feedback control of balance.
Persistent activity in a cortical-to-subcortical circuit: bridging the temporal gap in trace eyelid conditioning
Authors: Siegel Jennifer J. , Kalmbach Brian , Chitwood Raymond A. , Mauk Michael D.
Published: September 2011

We have addressed the source and nature of the persistent neural activity that bridges the stimulus-free gap between the conditioned stimulus (CS) and unconditioned stimulus (US) during trace eyelid conditioning. Previous work has demonstrated that this persistent activity is necessary for trace eyelid conditioning: CS-elicited activity in mossy fiber inputs to the cerebellum does not extend into the stimulus-free trace interval, which precludes the cerebellar learning that mediates conditioned response expression. In behaving rabbits we used in vivo recordings from a region of medial prefrontal cortex (mPFC) that is necessary for trace eyelid conditioning to test the hypothesis that neurons there generate activity that persists beyond CS offset. These recordings revealed two patterns of activity during the trace interval that would enable cerebellar learning. Activity in some cells began during the tone CS and persisted to overlap with the US, whereas in other cells, activity began during the stimulus-free trace interval. Injection of anterograde tracers into this same region of mPFC revealed dense labeling in the pontine nuclei, where recordings also revealed tone-evoked persistent activity during trace conditioning. These data suggest a corticopontine pathway that provides an input to the cerebellum during trace conditioning trials that bridges the temporal gap between the CS and US to engage cerebellar learning. As such, trace eyelid conditioning represents a well-characterized and experimentally tractable system that can facilitate mechanistic analyses of cortical persistent activity and how it is used by downstream brain structures to influence behavior.
Characterization of an Effective CTL Response against HIV and SIV Infections
Authors: Genescà Meritxell
Published: September 2011

A vaccine inducing protective immunity in mucosal tissues and secretions may stop or limit HIV infection. Although cytotoxic T lymphocytes (CTLs) are clearly associated with control of viral replication in HIV and simian immunodeficiency virus (SIV) infections, there are examples of uncontrolled viral replication in the face of strong CD8+ T‐cell responses. The number of functions, breadth, avidity, and magnitude of CTL response are likely to be important factors in the effectiveness of anti‐HIV T‐cell response, but the location and persistence of effector CD8+ T cells are also critical factors. Although the only HIV vaccine clinical trial targeting cellular immunity to prevent HIV infection failed, vaccine strategies using persistent agents against pathogenic mucosal challenge in macaque models are showing unique success. Thus, the key to control the initial focus of viral replication at the portal of entry may rely on the continuous generation of effector CTL responses at mucosal level.
The Role of Prophylactic Central Neck Dissection in Differentiated Thyroid Carcinoma: Issues and Controversies
Authors: Wong Kai-Pun , Lang Brian Hung-Hin
Published: September 2011

Prophylactic central neck dissection (pCND) in differentiated thyroid carcinoma (DTC) is one of the most controversial surgical subjects in recent times. To date, there is little evidence to support the practice of pCND in patients with DTC undergoing total thyroidectomy. Although the recently revised American Thyroid Association (ATA) guideline has clarified many inconsistencies regarding pCND and has recommended pCND in “high-risk” patients, many issues and controversies surrounding the subject of pCND in DTC remain. The recent literature has revealed an insignificant trend toward lower recurrence rate in patients with DTC who undergo total thyroidectomy and pCND than those who undergo total thyroidectomy alone. However, this was subjected to biases, and there are concerns whether pCND should be performed by all surgeons who manage DTC because of increased surgical morbodity. Performing a unilateral pCND may be better than a bilateral pCND given its lower surgical morbidity. Further studies in this controversial subject are much needed.
Applications of an HIDS Theorem to the Existence of Fixed Point, Abstract Equilibria and Optimization Problems
Authors: Du Wei-Shih
Published: September 2011

By applying hybrid inclusion and disclusion systems (HIDS), we establish several vectorial variants
of system of Ekeland′s variational principle on topological vector spaces, some existence theorems of system of parametric vectorial quasi‐equilibrium
problem, and an existence theorem of system of the Stampacchia‐type vectorial equilibrium problem. As an application, a vectorial minimization theorem is
also given. Moreover, we discuss some equivalence relations between our vectorial variant of Ekeland′s variational principle, common fixed point
theorem, and maximal element theorem.
Antisynchronization of Nonidentical Fractional‐Order Chaotic Systems Using Active Control
Authors: Bhalekar Sachin , Daftardar-Gejji Varsha
Published: September 2011

Antisynchronization phenomena are studied in nonidentical fractional‐order differential systems. The characteristic feature of antisynchronization is that the sum of relevant state‐variables vanishes for sufficiently large value of time variable. Active control method is used first time in the literature to achieve antisynchronization between fractional‐order Lorenz and Financial systems, Financial and Chen systems, and Lü and Financial systems. The stability analysis is carried out using classical results. We also provide numerical results to verify the effectiveness of the proposed theory.
Skin Autofluorescence, as Marker of Accumulation of Advanced Glycation Endproducts and of Cumulative Metabolic Stress, Is Not Increased in Patients with Systemic Sclerosis
Authors: Hettema M. E. , Bootsma H. , Graaff R. , de Vries R. , Kallenberg C. G. M. , Smit A. J.
Published: September 2011

Objective. To investigate whether advanced glycation endproducts (AGEs) in the skin are increased in patients with systemic sclerosis (SSc) and are related to the presence of disease-related and traditional cardiovascular risk factors.Methods. Skin autofluorescence, as a measure for the accumulation of AGEs, was assessed by measuring UV-A light excitation-emission matrices (AF-EEMS) in 41 SSc patients and 41 age- and sex-matched controls. Traditional cardiovascular risk factors and disease-related risk factors were recorded.Results. Skin AF-EEMS did not differ between SSc patients and controls (1.68±0.58 a.u. versus1.63±0.41 a.u.,P=0.684). Skin AF-EEMS in SSc patients was associated with levels of CRP (r=0.44,P=0.004), Medsger's severity scale (r=0.45,P=0.006), and use of agents intervening in the renin-angiotensin system (r=0.33,P=0.027). When analysing SSc patients and controls together, in multivariate analysis, only age and use of agents intervening in the renin-angiotensin system were independently associated with AF-EEMS.Conclusion. These data demonstrate that skin AGEs are not increased in SSc patients.
Homology‐Driven Proteomics of Dinoflagellates with Unsequenced Genomes Using MALDI‐TOF/TOF and Automated De Novo Sequencing
Authors: Wang Da-Zhi , Li Cheng , Xie Zhang-Xian , Dong Hong-Po , Lin Lin , Hong Hua-Sheng
Published: September 2011

This study developed a multilayered, gel‐based, and underivatized strategy for de novo protein sequence analysis of unsequenced dinoflagellates using a MALDI‐TOF/TOF mass spectrometer with the assistance of DeNovo Explorer software. MASCOT was applied as the first layer screen to identify either known or unknown proteins sharing identical peptides presented in a database. Once the confident identifications were removed after searching against the NCBInr database, the remainder was searched against the dinoflagellate expressed sequence tag database. In the last layer, those borderline and nonconfident hits were further subjected to de novo interpretation using DeNovo Explorer software. The de novo sequences passing a reliability filter were subsequently submitted to nonredundant MS‐BLAST search. Using this layer identification method, 216 protein spots representing 158 unique proteins out of 220 selected protein spots from Alexandrium tamarense, a dinoflagellate with unsequenced genome, were confidently or tentatively identified by database searching. These proteins were involved in various intracellular physiological activities. This study is the first effort to develop a completely automated approach to identify proteins from unsequenced dinoflagellate databases and establishes a preliminary protein database for various physiological studies of dinoflagellates in the future.
Validation of Fuel‐Coolant Interaction Model for Severe Accident Simulations
Authors: Melikhov Vladimir , Melikhov Oleg , Yakush Sergey , Rtishchev Nikita
Published: September 2011

A specialized module VAPEX‐M has been developed and implemented as a part of an integral code, SOCRAT, to enable the modeling of fuel‐coolant interactions (FCIs) during severe accidents. The mathematical model and correlations for the main physical processes are described. Results of computational analysis of three experimental series reported in the literature are presented. The calculations were carried out by the combined SOCRAT/VAPEX code and were aimed at validation of the predictive capabilities of the code. The experiments chosen cover a wide range of physical parameters, which enables different aspects of the code to be verified, that is, drag correlations (MAGICO‐2000), evaporation rate (QUEOS), fuel fragmentation, and interaction with the coolant in all complexity (FARO). Generally, reasonable agreement between the measured data and calculated results was obtained, which allows one to use the combined SOCRAT/VAPEX code for severe accidents analysis.
Multiply Recurrent Episodes of Gastric Emphysema
Authors: Pauli Eric M. , Tomasko Jonathan M. , Jain Vishal , Dye Charles E. , Haluck Randy S.
Published: September 2011

Introduction. Gastric emphysema can present both a diagnostic challenge and a life-threatening condition for patients and has only once been reported as being recurrent.Background. A 64-year-old male presented with chronic abdominal pain and was found to have gastric pneumatosis on CT scan. The patient was successfully managed conservatively. The cause was attributed to aberrant arterial anatomy and atherosclerosis along with hypotension. The patient has since had 3 episodes of recurrent gastric emphysema, all managed nonoperatively.Discussion. To our knowledge, this is the first case of both serial episodes of gastric pneumatosis and gastric mucosal ischemia as a precipitating factor for the development of gastric emphysema.
Positive Solutions to a Second‐Order Discrete Boundary Value Problem
Authors: Lin Xiaojie , Liu Wenbin
Published: September 2011

We are concerned with second‐order discrete boundary value problems and obtain some sufficient conditions for the existence of at least one positive solution by using the fixed point theorem due to Krasnosel′skii on a cone.
Intraperitoneal Oxygen/Ozone Treatment Decreases the Formation of Experimental Postsurgical Peritoneal Adhesions and the Levels/Activity of the Local Ubiquitin-Proteasome System
Authors: Di Filippo Clara , Capuano Annalisa , Rinaldi Barbara , Luongo Margherita , Lettieri Biagio , Rossi Francesco , D'Amico Michele
Published: September 2011

We have investigated whether an oxygen/ozone (95%O2/5%O3) mixture would have potential against the formation of experimental postsurgical peritoneal adhesions. In two groups of rats, one control intraperitoneally injected with 3 mL/rat of O2and one intraperitoneally injected with oxygen/ozone mixture (3 mL/rat equivalent to 300 μg/kg ozone), we induced a midline laparotomy and an enterotomy at the level of the ileum to encourage the formation of peritoneal adhesions. Samples were taken from the parietal peritoneal tissue to assess the formation of adhesions 0 and 10 days after the surgical procedure and to assess the levels of ubiquitin and 20S proteasome. We found decreased formation of postsurgical peritoneal adhesions after treatment of the rats with 300 μg/kg ozone associated with a decreased levels of ubiquitin and 20S proteasome subunit within the adhered tissue. Oxygen/ozone mixture is potentially useful for approaching the post-surgical peritoneal adhesions, and the UPS system is involved in this.