bluuebunny/crossref_metadata_2025_split huggingface dataset:
Effects of impurities and their redistribution during recrystallization of ice crystals
Authors: Iliescu D. , Baker I. 
Published: July 2008

AbstractIn order to examine the effects of solutes on recrystallization and subsequent grain growth in ice, both doped and undoped ice single crystals were extruded through a 120° equal-channel angular extrusion jig, in order to impart a large shear strain (∼1.15). Upon subsequent annealing at −3°C, the original single crystals recrystallized, in most cases to a new single crystal with a different orientation. Increasing the solute concentration (for H2SO4 to ∼200–300 ppb, and for NaCl, KCl and MgSO4 to >5 ppm) was found to significantly retard the growth and possibly, for H2SO4-doped ice, the nucleation of new grains in the strained ice single crystals. This is indicative of how soluble impurities can retard grain growth in ice cores. It was also found that the migrating grain boundaries surrounding the newly formed grains contained large concentrations of impurities, often observed as filaments. These could have formed by the grain boundaries sweeping up impurities from the lattice into the boundary or by their diffusion to the boundary – mechanisms whereby impurities could be concentrated into the grain boundaries in ice cores – although the latter mechanism seems unlikely since it would require very high diffusion rates.
Effects of Pin-up Oxygen on [60]Fullerene for Enhanced Antioxidant Activity
Authors: Matsubayashi Kenji , Goto Tadashi , Togaya Kyoko , Kokubo Ken , Oshima Takumi 
Published: July 2008

Abstract
The introduction of pin-up oxygen on C60, such as in the oxidized fullerenes C60O and C60On, induced noticeable increase in the antioxidant activity as compared to pristine C60. The water-soluble inclusion complexes of fullerenes C60O and C60Onreacted with linoleic acid peroxyl radical 1.7 and 2.4 times faster, respectively.
Interleukin‐10 improves left ventricular function in rats with heart failure subsequent to myocardial infarction
Authors: Stumpf Christian , Seybold Katrin , Petzi Sebastian , Wasmeier Gerald , Raaz Dorette , Yilmaz Atilla , Anger Thomas , Daniel Werner G. , Garlichs Christoph D. 
Published: July 2008

AbstractEvidence has shown that pro‐inflammatory cytokines, especially TNF‐α, are involved in the inflammatory response in the remodelling process after myocardial infarction (MI). Although IL‐10, an anti‐inflammatory cytokine, has been shown to antagonize some of the deleterious effects of TNF‐α, little is known about its role in post‐MI left ventricular (LV) dysfunction. The aim of the present study was to investigate whether a therapy with rhIL‐10 could be beneficial in an animal model of post‐MI heart failure (HF).Rats with experimental MI were treated with rhIL‐10 (75 mn;g/kg/d sc) starting directly after MI induction, and continuing for 4 weeks. Controls were untreated MI and sham‐operated rats. Cardiac function was assessed by echocardiography and cardiac catheterization 4 weeks after MI induction. Membrane‐bound and soluble fractions of TNF‐α, IL‐6 and IL‐10, the ratio of TNF‐α to IL‐10, serum levels of MCP‐1 as well as myocardial macrophage infiltration, were analyzed. Treatment with rhIL‐10 significantly improved post‐MI LV function (FS +127%;, dP/dtmax +131%; LVEDP–36%). This effect was associated with a significant decrease in pro‐inflammatory cytokine and chemokine levels (TNF‐α, IL‐6, MCP‐1) and furthermore resulted in a reduced myocardial infiltration of macrophages.
ChemmineR: a compound mining framework for R
Authors: Cao Yiqun , Charisi Anna , Cheng Li-Chang , Jiang Tao , Girke Thomas 
Published: July 2008

Abstract
Motivation: Software applications for structural similarity searching and clustering of small molecules play an important role in drug discovery and chemical genomics. Here, we present the first open-source compound mining framework for the popularstatistical programming environment R. The integration with a powerful statistical environment maximizes the flexibility, expandability and programmability of the provided analysis functions.
Results: We discuss the algorithms and compound mining utilities provided by the R package ChemmineR. It contains functions for structural similarity searching, clustering of compound libraries with a wide spectrum of classification algorithms and various utilities for managing complex compound data. It also offers a wide range of visualization functions for compound clusters and chemical structures. The package is well integrated with the online ChemMine environment and allows bidirectional communications between the two services.
Availability: ChemmineR is freely available as an R package from the ChemMine project site: http://bioweb.ucr.edu/ChemMineV2/chemminer
Contact: thomas.girke@ucr.edu
Coherent coupling of feedback loops: a design principle of cell signaling networks
Authors: Kwon Yung-Keun , Cho Kwang-Hyun 
Published: July 2008

AbstractMotivation:It is widely accepted that cell signaling networks have been evolved to be robust against perturbations. To investigate the topological characteristics resulting in such robustness, we have examined large-scale signaling networks and found that a number of feedback loops are present mostly in coupled structures. In particular, the coupling was made in a coherent way implying that same types of feedback loops are interlinked together.Results: We have investigated the role of such coherently coupled feedback loops through extensive Boolean network simulations and found that a high proportion of coherent couplings can enhance the robustness of a network against its state perturbations. Moreover, we found that the robustness achieved by coherently coupled feedback loops can be kept evolutionarily stable. All these results imply that the coherent coupling of feedback loops might be a design principle of cell signaling networks devised to achieve the robustness.Contact: ckh@kaist.ac.krSupplementary information: Supplementary data are available at Bioinformatics online.
Impaired Gamma Interferon Response to
Mycobacterium vaccae
Antigens in Patients with Cavitary Pulmonary Tuberculosis
Authors: Rodríguez-Güell Elisabeth , Agustí Gemma , Corominas Mercè , Luquin Marina , Julián Esther 
Published: July 2008

ABSTRACT

The ability of tuberculosis patients to recognize
Mycobacterium vaccae
-specific antigens before starting chemotherapy and according to disease severity was analyzed. We report that the
M. vaccae
cell wall skeleton fraction triggers more enhanced cytokine production than the whole bacterium. Moreover, a tendency was observed for a lower gamma interferon/interleukin-10 ratio in patients with cavitary disease induced by
M. vaccae
antigens.
Vancomycin Heteroresistance in Bloodstream Isolates of
Staphylococcus capitis
Authors: D'mello Danaë , Daley Andrew J. , Rahman Muhammad Shihab , Qu Yue , Garland Suzanne , Pearce Christopher , Deighton Margaret A. 
Published: July 2008

ABSTRACT

Nine
Staphylococcus capitis
isolates from blood cultures of newborns were examined for resistance to vancomycin. MICs were within the susceptible range, but population profiling revealed a resistant subpopulation. Only isolates with the largest subpopulation were identified as heteroresistant to vancomycin by Etest. This finding may have therapeutic implications.
In Vitro Activity of Tigecycline against Gram-Positive and Gram-Negative Pathogens as Evaluated by Broth Microdilution and Etest
Authors: Pillar Chris M. , Draghi Deborah C. , Dowzicky Michael J. , Sahm Daniel F. 
Published: July 2008

ABSTRACT

The current surveillance establishes the activity profile of tigecycline against recent clinical U.S. isolates of target pathogens. Findings from a distributed surveillance that utilized Etest yielded a tigecycline activity profile that varied from that observed in a separate centralized broth microdilution (BMD) surveillance (D. C. Draghi et al., Poster D-0701, 46th Intersci. Conf. Antimicrob. Agents Chemother., San Francisco, CA). Differences were noted among
Acinetobacter
spp. and
Serratia marcescens
and, to a lesser extent, with
Streptococcus pyogenes
. To address whether these differences were due to discordance in testing methodology or to variations among the analyzed populations, isolates from the current surveillance were concurrently tested by BMD and Etest. In all, 1,800
Staphylococcus aureus
, 259
S. pyogenes
, 226
Streptococcus pneumoniae
, 93
Enterococcus faecalis
, 1,356
Enterobacteriaceae
, and 227
Acinetobacter baumannii
strains were evaluated. Tigecycline had potent activity by BMD, with >99.6% susceptibility (%S) observed for all pathogens with interpretive criteria, excluding
Enterobacter cloacae
(98.3% S) and
E. faecalis
(86.0% S), and MIC
90
s ranged from 0.03 μg/ml (
S. pyogenes
/
S. pneumoniae
) to 1 μg/ml (
Enterobacteriaceae
/
A. baumannii
). Similar profiles were observed by Etest, with the exception of
A. baumannii
, although for most evaluated pathogens Etest MICs trended one doubling-dilution higher than BMD MICs. Major or very major errors were infrequent, and a high degree of essential agreement was observed, excluding
A. baumannii, S. marcescens
, and
S. pneumoniae
, for which ≥4-fold differences in MICs were observed for 29, 27.1, and 34% of the isolates, respectively. Further analysis regarding the suitability of the tigecycline Etest for testing
S. marcescens, Acinetobacter
spp., and
S. pneumoniae
is warranted.
Salmonella
Infections in the Common Raccoon (
Procyon lotor
) in Western Pennsylvania
Authors: Compton Justin A. , Baney Jason A. , Donaldson Sarah C. , Houser Beth A. , San Julian Gary J. , Yahner Richard H. , Chmielecki Wayne , Reynolds Stanley , Jayarao Bhushan M. 
Published: July 2008

ABSTRACT

Ten
Salmonella enterica
serotypes were isolated from fecal samples collected from anesthetized raccoons (
n
= 738) trapped in six Pennsylvania counties from 2003 to 2005. Comparison of raccoon pulsed-field gel electrophoresis (PFGE) pulse type data with the Pennsylvania Department of Health PFGE database revealed that the patterns of seven
Salmonella
serotypes matched those isolated from humans with salmonellosis.
Dermatitis Caused by
Neosartorya hiratsukae
Infection in a Hedgehog
Authors: Han Jae-Ik , Na Ki-Jeong 
Published: July 2008

ABSTRACT

This case report describes the fungal dermatitis caused by
Neosartorya hiratsukae
infection in a household hedgehog confirmed by microscopic examination of conidiophores and DNA analyses including the internal transcribed spacer region, partial β-tubulin, and the calmodulin gene. It is the first report of a natural
N. hiratsukae
infection in animals.
Genetic Classification of Severe Early Childhood Caries by Use of Subtracted DNA Fragments from
Streptococcus mutans
Authors: Saxena Deepak , Caufield Page W. , Li Yihong , Brown Stuart , Song Jinmei , Norman Robert 
Published: July 2008

ABSTRACT

Streptococcus mutans
is one of several members of the oral indigenous biota linked with severe early childhood caries (S-ECC). Because most humans harbor
S. mutans
, but not all manifest disease, it has been proposed that the strains of
S. mutans
associated with S-ECC are genetically distinct from those found in caries-free (CF) children. The objective of this study was to identify common DNA fragments from
S. mutans
present in S-ECC but not in CF children. Using suppressive subtractive hybridization, we found a number of DNA fragments (biomarkers) present in 88 to 95% of the S-ECC
S. mutans
strains but not in CF
S. mutans
strains. We then applied machine learning techniques including support vector machines and neural networks to identify the biomarkers with the most predictive power for disease status, achieving a 92% accurate classification of the strains as either S-ECC or CF associated. The presence of these gene fragments in 90 to 100% of the 26 S-ECC isolates tested suggested their possible functional role in the pathogenesis of
S. mutans
associated with dental caries.
Cost-Effectiveness of Detection of Intestinal Amebiasis by Using Serology and Specific-Amebic-Antigen Assays among Persons with or without Human Immunodeficiency Virus Infection
Authors: Chang Sui-Yuan , Sun Hsin-Yun , Ji Dar-Der , Lo Yi-Chun , Wu Cheng-Hsin , Wu Pei-Ying , Liu Wen-Chun , Hung Chien-Ching , Chang Shan-Chwen 
Published: July 2008

ABSTRACT

Among 345 persons who underwent indirect hemagglutination (IHA) serological assays and assays of specific amebic antigens in their stool samples, 24 of 36 (66.7%) who were seropositive for
Entamoeba histolytica
had intestinal amebiasis as determined by antigen assays compared with 2 of 309 (0.2%) who were seronegative (odds ratio, 307; 95% confidence interval, 64.9 to 1,451). The estimated cost to detect a case of intestinal amebiasis by serology followed by antigen assays ($52) could be reduced by 74.3% and 69.9%, respectively, compared with the costs of the concurrent use of both assays ($202) and the antigen assays alone ($173). Our finding suggests that IHA assays followed by specific-amebic-antigen assays can be cost-effective in the diagnosis of intestinal amebiasis among persons with or without human immunodeficiency virus infection who are at risk for
E. histolytica
infection.
Performance of Three Commercial Viral Load Assays, Versant Human Immunodeficiency Virus Type 1 (HIV-1) RNA bDNA v3.0, Cobas AmpliPrep/Cobas TaqMan HIV-1, and NucliSens HIV-1 EasyQ v1.2, Testing HIV-1 Non-B Subtypes and Recombinant Variants
Authors: Holguín Africa , López Marisa , Molinero Mar , Soriano Vincent 
Published: July 2008

ABSTRACT

Monitoring antiretroviral therapy requires that human immunodeficiency virus type 1 (HIV-1) viremia assays are applicable to all distinct variants. This study evaluates the performance of three commercial viral load assays—Versant HIV-1 RNA bDNA v3.0, Cobas AmpliPrep/Cobas TaqMan HIV-1, and NucliSens HIV-1 EasyQ v1.2—in testing 83 plasma specimens from patients carrying HIV-1 non-B subtypes and recombinants previously defined by phylogenetic analysis of the
pol
gene. All 28 specimens from patients under treatment presented viremia values below the detection limit with the three methods. In the remaining 55 specimens from naive individuals viremia could not be detected in 32.7, 20, and 14.6% using the NucliSens, Versant, or TaqMan tests, respectively, suggesting potential viral load underestimation of some samples by all techniques. Only 32 (58.2%) samples from naive subjects were quantified by the three methods; the NucliSens test provided the highest HIV RNA values (mean, 4.87 log copies/ml), and the Versant test provided the lowest (mean, 4.16 log copies/ml). Viremia differences of greater than 1 log were seen in 8 (14.5%) of 55 specimens, occurring in 10.9, 7.3, and 5.4%, respectively, of the specimens in comparisons of Versant versus NucliSens, Versant versus TaqMan, and TaqMan versus NucliSens. Differences greater than 0.5 log, considered significant for clinicians, occurred in 45.5, 27.3, and 29% when the same assays were compared. Some HIV-1 strains, such as subtype G and CRF02_AG, showed more discrepancies in distinct quantification methods than others. In summary, an adequate design of primers and probes is needed for optimal quantitation of plasma HIV-RNA in non-B subtypes. Our data emphasize the need to use the same method for monitoring patients on therapy and also the convenience of HIV-1 subtyping.
Human Immunodeficiency Virus Type 1 Nef Expression Prevents AP-2-Mediated Internalization of the Major Histocompatibility Complex Class II-Associated Invariant Chain
Authors: Toussaint Hélène , Gobert François-Xavier , Schindler Michael , Banning Carina , Kozik Patrycja , Jouve Mabel , Kirchhoff Frank , Benaroch Philippe 
Published: July 2008

ABSTRACT

The lentiviral Nef protein has been studied extensively for its ability to induce the downregulation of several immunoreceptors on the surfaces of infected cells. However, Nef expression is unique in inducing highly effective upregulation of the major histocompatibility complex class II-associated chaperone invariant (Ii) chain complexes in different cell types. Under normal conditions, endocytosis of the Ii chain and other molecules, like the transferrin receptor and CD4, is rapid and AP-2 dependent. Human immunodeficiency virus type 1 (HIV-1) Nef expression strongly reduces the internalization of the Ii chain, enhances that of CD4, and does not modify transferrin uptake. The mutation of AP-2 binding motifs LL164 and DD174 in Nef leads to the inhibition of Ii chain upregulation. In AP-2-depleted cells, surface levels of the Ii chain are high and remain unmodified by Nef expression, further indicating that Nef regulates Ii chain internalization via the AP-2 pathway. Immunoprecipitation experiments revealed that the Ii chain can interact with Nef in a dileucine-dependent manner. Importantly, we have shown that Nef-induced CD4 downregulation and Ii chain upregulation are genetically distinguishable. We have identified natural
nef
alleles that have lost one of the two functions but not the other one. Moreover, we have characterized Nef mutant forms possessing a similar phenotype in the context of HIV-1 infection. Therefore, the Nef-induced accumulation of Ii chain complexes at the cell surface probably results from a complex mechanism leading to the impairment of AP-2-mediated endocytosis rather than from direct competition between Nef and the Ii chain for binding AP-2.
Viral Genome Methylation as an Epigenetic Defense against Geminiviruses
Authors: Raja Priya , Sanville Bradley C. , Buchmann R. Cody , Bisaro David M. 
Published: July 2008

ABSTRACT

Geminiviruses encapsidate single-stranded DNA genomes that replicate in plant cell nuclei through double-stranded DNA intermediates that associate with cellular histone proteins to form minichromosomes. Like most plant viruses, geminiviruses are targeted by RNA silencing and encode suppressor proteins such as AL2 and L2 to counter this defense. These related proteins can suppress silencing by multiple mechanisms, one of which involves interacting with and inhibiting adenosine kinase (ADK), a cellular enzyme associated with the methyl cycle that generates
S
-adenosyl-methionine, an essential methyltransferase cofactor. Thus, we hypothesized that the viral genome is targeted by small-RNA-directed methylation. Here, we show that
Arabidopsis
plants with mutations in genes encoding cytosine or histone H3 lysine 9 (H3K9) methyltransferases, RNA-directed methylation pathway components, or ADK are hypersensitive to geminivirus infection. We also demonstrate that viral DNA and associated histone H3 are methylated in infected plants and that cytosine methylation levels are significantly reduced in viral DNA isolated from methylation-deficient mutants. Finally, we demonstrate that
Beet curly top virus L2
−
mutant DNA present in tissues that have recovered from infection is hypermethylated and that host recovery requires AGO4, a component of the RNA-directed methylation pathway. We propose that plants use chromatin methylation as a defense against DNA viruses, which geminiviruses counter by inhibiting global methylation. In addition, our results establish that geminiviruses can be useful models for genome methylation in plants and suggest that there are redundant pathways leading to cytosine methylation.
Differential Antigen Presentation Kinetics of CD8+T-Cell Epitopes Derived from the Same Viral Protein
Authors: Sacha Jonah B. , Reynolds Matthew R. , Buechler Matthew B. , Chung Chungwon , Jonas Anna K. , Wallace Lyle T. , Weiler Andrea M. , Lee Wonhee , Piaskowski Shari M. , Soma Taeko , Friedrich Thomas C. , Wilson Nancy A. , Watkins David I. 
Published: July 2008

ABSTRACTThe kinetics of peptide presentation by major histocompatibility complex class I (MHC-I) molecules may contribute to the efficacy of CD8+T cells. Whether all CD8+T-cell epitopes from a protein are presented by the same MHC-I molecule with similar kinetics is unknown. Here we show that CD8+T-cell epitopes derived from SIVmac239 Gag are presented with markedly different kinetics. We demonstrate that this discrepancy in presentation is not related to immunodominance but instead is due to differential requirements for epitope generation. These results illustrate that significant differences in presentation kinetics can exist among CD8+T-cell epitopes derived from the same viral protein.
Preferential Cytolysis of Peripheral Memory CD4
+
T Cells by In Vitro X4-Tropic Human Immunodeficiency Virus Type 1 Infection before the Completion of Reverse Transcription
Authors: Zhou Yan , Shen Lin , Yang Hung-Chih , Siliciano Robert F. 
Published: July 2008

ABSTRACT

CD4
+
T-cell depletion is the hallmark of AIDS pathogenesis. Multiple mechanisms may contribute to the death of productively infected CD4
+
T cells and innocent-bystander cells. In this study, we characterize a novel mechanism in which human immunodeficiency virus type 1 (HIV-1) infection preferentially depletes peripheral memory CD4
+
T cells before the completion of reverse transcription. Using a recombinant HIV-1 carrying the green fluorescent protein reporter gene, we demonstrate that memory CD4
+
T cells were susceptible to infection-induced cell death at a low multiplicity of infection. Infected memory CD4
+
T cells underwent rapid necrotic cell death. Killing of host cells was dependent on X4 envelope-mediated viral fusion, but not on virion-associated Vpr or Nef. In contrast to peripheral resting CD4
+
T cells, CD4
+
T cells stimulated by mitogen or certain cytokines were resistant to HIV-1-induced early cell death. These results demonstrate that early steps in HIV-1 infection have a detrimental effect on certain subsets of CD4
+
T cells. The early cell death may serve as a selective disadvantage for X4-tropic HIV-1 in acute infection but may play a role in accelerated disease progression, which is associated with the emergence of X4-tropic HIV-1 in the late stage of AIDS.
Vaccinia Virus L1 Protein Is Required for Cell Entry and Membrane Fusion
Authors: Bisht Himani , Weisberg Andrea S. , Moss Bernard 
Published: July 2008

ABSTRACT
Genetic and biochemical studies have provided evidence for an entry/fusion complex (EFC) comprised of at least eight viral proteins (A16, A21, A28, G3, G9, H2, J5, and L5) that together with an associated protein (F9) participates in entry of vaccinia virus (VACV) into cells. The genes encoding these proteins are conserved in all poxviruses, are expressed late in infection, and are components of the mature virion membrane but are not required for viral morphogenesis. In addition, all but one component has intramolecular disulfides that are formed by the poxvirus cytoplasmic redox system. The L1 protein has each of the characteristics enumerated above except that it has been reported to be essential for virus assembly. To further investigate the role of L1, we constructed a recombinant VACV (vL1Ri) that inducibly expresses L1. In the absence of inducer, L1 synthesis was repressed and vL1Ri was unable to form plaques or produce infectious progeny. Unexpectedly, assembly and morphogenesis appeared normal and the noninfectious virus particles were indistinguishable from wild-type VACV as determined by transmission electron microscopy and analysis of the component polypeptides. Notably, the L1-deficient virions were able to attach to cells but the cores failed to penetrate into the cytoplasm. In addition, cells infected with vL1Ri in the absence of inducer did not form syncytia following brief low-pH treatment even though extracellular virus was produced. Coimmunoprecipitation experiments demonstrated that L1 interacted with the EFC and indirectly with F9, suggesting that L1 is an additional component of the viral entry apparatus.