bluuebunny/crossref_metadata_2025_split huggingface dataset:
Intracellular Concentrations of Posaconazole in Different Compartments of Peripheral Blood
Authors: Farowski Fedja , Cornely Oliver A. , Vehreschild Jörg J. , Hartmann Pia , Bauer Tim , Steinbach Angela , Rüping Maria J. G. T. , Müller Carsten 
Published: May 2010

ABSTRACT

Therapeutic drug monitoring (TDM) of antifungal plasma concentrations is increasingly recommended. However, data on antifungal concentrations in the other compartments of the peripheral blood are limited. Hence, we collected 23 blood samples from 14 patients receiving posaconazole for prophylaxis of fungal infections. These samples were separated by double-discontinuous Ficoll-Hypaque density gradient centrifugation. The intracellular posaconazole concentrations of the obtained cells, i.e., the peripheral blood mononuclear cells (PBMCs), polymorphonuclear leukocytes (PMNs), and red blood cells (RBCs), were determined by liquid chromatography-tandem mass spectrometry. The intracellular concentrations of the PBMCs and PMNs were significantly higher than those of surrounding media (
P
< 0.001). The ratios between the intracellular and extracellular concentrations (C/E) were 22.5 ± 21.2, 7.66 ± 6.50, and 0.09 ± 0.05 for the PBMCs, PMNs, and RBCs, respectively. Posaconazole reaches high concentrations within human PBMCs and PMNs and is, to a lesser extent, present in RBCs. The high intracellular concentrations might contribute to posaconazole efficacy and distribution.
The VirSR Two-Component Signal Transduction System Regulates NetB Toxin Production in
Clostridium perfringens
Authors: Cheung Jackie K. , Keyburn Anthony L. , Carter Glen P. , Lanckriet Anouk L. , Van Immerseel Filip , Moore Robert J. , Rood Julian I. 
Published: May 2010

ABSTRACT

Clostridium perfringens
causes several diseases in domestic livestock, including necrotic enteritis in chickens, which is of concern to the poultry industry due to its health implications and associated economic cost. The novel pore-forming toxin NetB is a critical virulence factor in the pathogenesis of this disease. In this study, we have examined the regulation of NetB toxin production. In
C. perfringens
, the quorum sensing-dependent VirSR two-component signal transduction system regulates genes encoding several toxins and extracellular enzymes. Analysis of the sequence upstream of the
netB
gene revealed the presence of potential DNA binding sites, or VirR boxes, that are recognized by the VirR response regulator.
In vitro
binding experiments showed that purified VirR was able to recognize and bind to these
netB
-associated VirR boxes. Furthermore, using a reporter gene assay, the
netB
VirR boxes were shown to be functional. Mutation of the
virR
gene in two avian
C. perfringens
strains was shown to significantly reduce the production of the NetB toxin; culture supernatants derived from these strains were no longer cytotoxic to Leghorn male hepatoma cells. Complementation with the
virRS
operon restored the toxin phenotypes to wild type. The results also showed that the VirSR two-component system regulates the expression of
netB
at the level of transcription. We postulate that in the gastrointestinal tract of infected birds, NetB production is upregulated when the population of
C. perfringens
cells reaches a threshold level that leads to activation of the VirSR system.
Pseudomonas aeruginosa
Evasion of Phagocytosis Is Mediated by Loss of Swimming Motility and Is Independent of Flagellum Expression
Authors: Amiel Eyal , Lovewell Rustin R. , O'Toole George A. , Hogan Deborah A. , Berwin Brent 
Published: May 2010

ABSTRACT

Pseudomonas aeruginosa
is a pathogenic Gram-negative bacterium that causes severe opportunistic infections in immunocompromised individuals; in particular, severity of infection with
P. aeruginosa
positively correlates with poor prognosis in cystic fibrosis (CF) patients. Establishment of chronic infection by this pathogen is associated with downregulation of flagellar expression and of other genes that regulate
P. aeruginosa
motility. The current paradigm is that loss of flagellar expression enables immune evasion by the bacteria due to loss of engagement by phagocytic receptors that recognize flagellar components and loss of immune activation through flagellin-mediated Toll-like receptor (TLR) signaling. In this work, we employ bacterial and mammalian genetic approaches to demonstrate that loss of motility, not the loss of the flagellum
per se
, is the critical factor in the development of resistance to phagocytosis by
P. aeruginosa
. We demonstrate that isogenic
P. aeruginosa
mutants deficient in flagellar function, but retaining an intact flagellum, are highly resistant to phagocytosis by both murine and human phagocytic cells at levels comparable to those of flagellum-deficient mutants. Furthermore, we show that loss of MyD88 signaling in murine phagocytes does not recapitulate the phagocytic deficit observed for either flagellum-deficient or motility-deficient
P. aeruginosa
mutants. Our data demonstrate that loss of bacterial motility confers a dramatic resistance to phagocytosis that is independent of both flagellar expression and TLR signaling. These findings provide an explanation for the well-documented observation of nonmotility in clinical
P. aeruginosa
isolates and for how this phenotype confers upon the bacteria an advantage in the context of immune evasion.
Generation ofTrypanosoma cruzi-Specific CD8+T-Cell Immunity Is Unaffected by the Absence of Type I Interferon Signaling
Authors: Martin Diana L. , Murali-Krishna Kaja , Tarleton Rick L. 
Published: May 2010

ABSTRACTTrypanosoma cruziis a protozoan parasite that causes human Chagas’ disease, a leading source of congestive heart failure in Central and South America. CD8+T cells are critical for control ofT. cruziinfection, and CD8+T cells recognizing the immunodominanttrans-sialidase gene-encoded peptide TSKB20 (ANYKFTLV) account for approximately 30% of the total CD8+T-cell population at the peak of infection in C57BL/6 mice. Type I interferons (IFN-I) are pleiotropic cytokines that play a critical role in both innate and adaptive immunity against a variety of infections, but their induction and their role in infection are dictated by the infectious agent. Because type I IFNs and IFN-responsive genes are evident early afterT. cruziinfection of host cells, we examined the influence of IFN-I on the development of CD8+T-cell responses during this infection. Mice lacking the receptor for IFN-I (IFNARKO) and their wild-type counterparts both developed chronic infections and generated similar frequencies of immunodominant TSKB20- and subdominant TSKB18-specific CD8+T cells followingT. cruziinfection. In contrast, peak TSKB20-specific CD8+T-cell responses generated during infection with vaccinia virus engineered to express TSKB20 were approximately 2.5-fold lower in IFNARKO mice than B6 mice, although after viral clearance, the frequencies of TSKB20-specific CD8+T cells stabilized at similar levels. Together, these data suggest that IFN-I induction and biology are dependent upon the microbial context and emphasize the need to investigate various infection models for a full understanding of CD8+T-cell development.
Convergence Theorems on Asymptotically Pseudocontractive Mappings in the Intermediate Sense
Authors: Qin Xiaolong , Cho SunYoung , Kim JongKyu 
Published: May 2010

AbstractA new nonlinear mapping is introduced. The convergence of Ishikawa iterative processes for the class of asymptotically pseudocontractive mappings in the intermediate sense is studied. Weak convergence theorems are established. A strong convergence theorem is also established without any compact assumption by considering the so-called hybrid projection methods.
Some Variational Results Using Generalizations of Sequential Lower Semicontinuity
Authors: Bottaro Aruffo Ada , Bottaro Gianfranco 
Published: May 2010

AbstractKirk and Saliga and then Chen et al. introduced lower semicontinuity from above, a generalization of sequential lower semicontinuity, and they showed that well-known results, such as Ekeland's variational principle and Caristi's fixed point theorem, remain still true under lower semicontinuity from above. In a previous paper we introduced a new concept that generalizes lower semicontinuity from above. In the present one we continue such study, also introducing other two new generalizations of lower semicontinuity from above; we study such extensions, compare each other five concepts (sequential lower semicontinuity, lower semicontinuity from above, the one by us previously introduced, and the two here defined) and, in particular, we show that the above quoted well-known results remain still true under one of our such generalizations.
From Prestimulus Alpha Oscillation to Visual-evoked Response: An Inverted-U Function and Its Attentional Modulation
Authors: Rajagovindan Rajasimhan , Ding Mingzhou 
Published: May 2010

Abstract
Understanding the relation between prestimulus neural activity and subsequent stimulus processing has become an area of active investigation. Computational modeling, as well as in vitro and in vivo single-unit recordings in animal preparations, have explored mechanisms by which background synaptic activity can influence the responsiveness of cortical neurons to afferent input. How these mechanisms manifest in humans is not well understood. Although numerous EEG/MEG studies have considered the role of prestimulus alpha oscillations in the genesis of visual-evoked potentials, no consensus has emerged, and divergent reports continue to appear. The present work addresses this problem in three stages. First, a theoretical model was developed in which the background synaptic activity and the firing rate of a neural ensemble are related through a sigmoidal function. The derivative of this function, referred to as local gain, has an inverted-U shape and is postulated to be proportional to the trial-by-trial response evoked by a transient stimulus. Second, the theoretical model was extended to noninvasive studies of human visual processing, where the model variables are reinterpreted in terms of ongoing EEG oscillations and event-related potentials. Predictions were derived from the model and tested by recording high-density scalp EEG from healthy volunteers performing a trial-by-trial cued spatial visual attention task. Finally, enhanced stimulus processing by attention was linked to an increase in the overall slope of the sigmoidal function. The commonly observed reduction of alpha magnitude with attention was interpreted as signaling a shift of the underlying neural ensemble toward an optimal excitability state that enables the increase in global gain.
Osteochondral Tissue Cell Viability Is Affected by Total Impulse during Impaction Grafting
Authors: Balash Paul , Kang Richard W. , Schwenke Thorsten , Cole Brian J. , Wimmer Markus A. 
Published: May 2010

Objective: Osteochondral graft transplantation has garnered significant attention because of its ability to replace the lesion with true hyaline cartilage. However, surgical impaction of the graft to anchor it into the defect site can be traumatic and lead to cell death and cartilage degeneration. This study aimed to test the hypothesis that increasing impulse magnitude during impaction of osteochondral plugs has a direct effect on loss of cell viability. Design: In this controlled laboratory study, the impaction force was kept constant while the impulse was varied. Ninety-six osteochondral plugs were extracted from the trochlea of bovine stifle joints and were randomly assigned into 3 experimental and 1 (nonimpacted) control group. The transferred impulse of the experimental groups reflected the median and the lower and upper quartiles of preceding clinical measurements. Data were obtained at day 0, day 4, and day 8; at each point, cell viability was assessed using the Live/Dead staining kit and histological assessments were performed to visualize matrix structural changes. Results: After impaction, cartilage samples stayed intact and did not show any histological signs of matrix disruption. As expected, higher impulse magnitudes introduced more cell death; however, this relationship was lost at day 8 after impaction. Conclusion: Impulse magnitude has a direct effect on cell viability of the graft. Because impulse magnitude is mostly governed by the press-fit characteristics of the recipient site, this study aids in the definition of optimal insertion conditions for osteochondral grafts.
Systemic autoimmunity and defective Fas ligand secretion in the absence of the Wiskott-Aldrich syndrome protein
Authors: Nikolov Nikolay P. , Shimizu Masaki , Cleland Sophia , Bailey Daniel , Aoki Joseph , Strom Ted , Schwartzberg Pamela L. , Candotti Fabio , Siegel Richard M. 
Published: May 2010

AbstractAutoimmunity is a surprisingly common complication of primary immunodeficiencies, yet the molecular mechanisms underlying this clinical observation are not well understood. One widely known example is provided by Wiskott-Aldrich syndrome (WAS), an X-linked primary immunodeficiency disorder caused by mutations in the gene encoding the WAS protein (WASp) with a high incidence of autoimmunity in affected patients. WASp deficiency affects T-cell antigen receptor (TCR) signaling and T-cell cytokine production, but its role in TCR-induced apoptosis, one of the mechanisms of peripheral immunologic tolerance, has not been investigated. We find that WASp-deficient mice produce autoantibodies and develop proliferative glomerulonephritis with immune complex deposition as they age. We also find that CD4+ T lymphocytes from WASp-deficient mice undergo reduced apoptosis after restimulation through the TCR. While Fas-induced cell death is normal, WASp deficiency affects TCR-induced secretion of Fas ligand (FasL) and other components of secretory granules by CD4+ T cells. These results describe a novel role of WASp in regulating TCR-induced apoptosis and FasL secretion and suggest that WASp-deficient mice provide a good model for the study of autoimmune manifestations of WAS and the development of more specific therapies for these complications.
Protein sequences classification by means of feature extraction with substitution matrices
Authors: Saidi Rabie , Maddouri Mondher , Mephu Nguifo Engelbert 
Published: May 2010

AbstractBackgroundThis paper deals with the preprocessing of protein sequences for supervised classification. Motif extraction is one way to address that task. It has been largely used to encode biological sequences into feature vectors to enable using well-known machine-learning classifiers which require this format. However, designing a suitable feature space, for a set of proteins, is not a trivial task. For this purpose, we propose a novel encoding method that uses amino-acid substitution matrices to define similarity between motifs during the extraction step.ResultsIn order to demonstrate the efficiency of such approach, we compare several encoding methods using some machine learning classifiers. The experimental results showed that our encoding method outperforms other ones in terms of classification accuracy and number of generated attributes. We also compared the classifiers in term of accuracy. Results indicated that SVM generally outperforms the other classifiers with any encoding method. We showed that SVM, coupled with our encoding method, can be an efficient protein classification system. In addition, we studied the effect of the substitution matrices variation on the quality of our method and hence on the classification quality. We noticed that our method enables good classification accuracies with all the substitution matrices and that the variances of the obtained accuracies using various substitution matrices are slight. However, the number of generated features varies from a substitution matrix to another. Furthermore, the use of already published datasets allowed us to carry out a comparison with several related works.ConclusionsThe outcomes of our comparative experiments confirm the efficiency of our encoding method to represent protein sequences in classification tasks.
Core promoter structure and genomic context reflect histone 3 lysine 9 acetylation patterns
Authors: Kratz Anton , Arner Erik , Saito Rintaro , Kubosaki Atsutaka , Kawai Jun , Suzuki Harukazu , Carninci Piero , Arakawa Takahiro , Tomita Masaru , Hayashizaki Yoshihide , Daub Carsten O 
Published: May 2010

Abstract

Background
Histone modifications play an important role in gene regulation. Acetylation of histone 3 lysine 9 (H3K9ac) is generally associated with transcription initiation and unfolded chromatin, thereby positively influencing gene expression. Deep sequencing of the 5' ends of gene transcripts using DeepCAGE delivers detailed information about the architecture and expression level of gene promoters. The combination of H3K9ac ChIP-chip and DeepCAGE in a myeloid leukemia cell line (THP-1) allowed us to study the spatial distribution of H3K9ac around promoters using a novel clustering approach. The promoter classes were analyzed for association with relevant genomic sequence features.

Results
We performed a clustering of 4,481 promoters according to their surrounding H3K9ac signal and analyzed the clustered promoters for association with different sequence features. The clustering revealed three groups with major H3K9ac signal upstream, centered and downstream of the promoter. Narrow single peak promoters tend to have a concentrated activity of H3K9ac in the upstream region, while broad promoters tend to have a concentrated activity of H3K9ac and RNA polymerase II binding in the centered and downstream regions. A subset of promoters with high gene expression level, compared to subsets with low and medium gene expression, shows dramatic increase in H3K9ac activity in the upstream cluster only; this may indicate that promoters in the centered and downstream clusters are predominantly regulated at post-initiation steps. Furthermore, the upstream cluster is depleted in CpG islands and more likely to regulate un-annotated genes.

Conclusions
Clustering core promoters according to their surrounding acetylation signal is a promising approach for the study of histone modifications. When examining promoters clustered into groups according to their surrounding H3K9 acetylation signal, we find that the relative localization and intensity of H3K9ac is very specific depending on characteristic sequence features of the promoter. Experimental data from DeepCAGE and ChIP-chip experiments using undifferentiated (monocyte) and differentiated (macrophage) THP-1 cells leads us to the same conclusions.
NGX6 gene mediated by promoter methylation as a potential molecular marker in colorectal cancer
Authors: Liu Minji , Peng Ya , Wang Xiaoyan , Guo Qin , Shen Shourong , Li Guiyuan 
Published: May 2010

Abstract

Background
Nasopharyngeal carcinoma associated gene 6 (NGX6) is down-regulated in most colon cancer cell lines and tumor tissues when compared with their normal tissue samples. As a novel suppress tumor gene, it could inhibit colon cancer cell growth and cell cycle progression. However, little is known about the transcriptional mechanisms controlling NGX6 gene expression. Recent findings suggest that epigenetic inactivation of multiple tumor suppressor genes plays an important role in the tumorigenesis of colorectal carcinoma (CRC). In this study, we explored the role of DNA methylation in regulation of NGX6 transcription.

Methods
In the present study, we cloned the NGX6 promoter with characteristics of a CpG island by luciferase reporter assay. Then, the CpG methylation status around the NGX6 promoter region in colon cancer cell lines and colorectal tumor tissues was examined by methylation-specific PCR and bisulfite DNA sequencing. Finally, 5-Aza-2'-deoxycytidine (5-Aza-dC) treatment was used to confirm the correlation between NGX6 promoter methylation and its gene inactivation.

Results
The sequence spanning positions -157 to +276 was identified as the NGX6 promoter, in which no canonical TATA boxes were found, while two CAAT boxes and GC boxes were discovered. Methylation status was observed more frequently in 40 colorectal cancer samples than in 40 adjacent normal mucosa samples (18/40 versus 7/40; P < 0.05). An analysis correlating gene methylation status with clinicopathological cancer features revealed that dense methylation of the NGX6 promoter was associated with colorectal cancer patients age (P < 0.05). Moreover, a trend was shown toward metastasis status and primary site in colorectal carcinomas with NGX6 promoter methylation (p = 0.056 and P = 0.067, respectively). In addition, 5-Aza-dC could induce NGX6 mRNA expression and NGX6 promoter demethylation in HT-29 cells.

Conclusions
Down-regulation of NGX6 gene is related to the promoter methylation. DNA methylation of NGX6 promoter might be a potential molecular marker for diagnosis or prognosis, or serve as a therapeutic target.
Antitumor and antiangiogenic effect of the dual EGFR and HER-2 tyrosine kinase inhibitor lapatinib in a lung cancer model
Authors: Diaz Roque , Nguewa Paul A , Parrondo Ricardo , Perez-Stable Carlos , Manrique Irene , Redrado Miriam , Catena Raul , Collantes Maria , Peñuelas Ivan , Díaz-González Juan Antonio , Calvo Alfonso 
Published: May 2010

Abstract

Background
There is strong evidence demonstrating that activation of epidermal growth factor receptors (EGFRs) leads to tumor growth, progression, invasion and metastasis. Erlotinib and gefitinib, two EGFR-targeted agents, have been shown to be relevant drugs for lung cancer treatment. Recent studies demonstrate that lapatinib, a dual tyrosine kinase inhibitor of EGFR and HER-2 receptors, is clinically effective against HER-2-overexpressing metastatic breast cancer. In this report, we investigated the activity of lapatinib against non-small cell lung cancer (NSCLC).

Methods
We selected the lung cancer cell line A549, which harbors genomic amplification of EGFR and HER-2. Proliferation, cell cycle analysis, clonogenic assays, and signaling cascade analyses (by western blot) were performed in vitro. In vivo experiments with A549 cells xenotransplanted into nude mice treated with lapatinib (with or without radiotherapy) were also carried out.

Results
Lapatinib dramatically reduced cell proliferation (P < 0.0001), DNA synthesis (P < 0.006), and colony formation capacity (P < 0.0001) in A549 cells in vitro. Furthermore, lapatinib induced G1 cell cycle arrest (P < 0.0001) and apoptotic cell death (P < 0.0006) and reduced cyclin A and B1 levels, which are regulators of S and G2/M cell cycle stages, respectively. Stimulation of apoptosis in lapatinib-treated A549 cells was correlated with increased cleaved PARP, active caspase-3, and proapoptotic Bak-1 levels, and reduction in the antiapoptic IAP-2 and Bcl-xL protein levels. We also demonstrate that lapatinib altered EGFR/HER-2 signaling pathways reducing p-EGFR, p-HER-2, p-ERK1/2, p-AKT, c-Myc and PCNA levels. In vivo experiments revealed that A549 tumor-bearing mice treated with lapatinib had significantly less active tumors (as assessed by PET analysis) (P < 0.04) and smaller in size than controls. In addition, tumors from lapatinib-treated mice showed a dramatic reduction in angiogenesis (P < 0.0001).

Conclusion
Overall, these data suggest that lapatinib may be a clinically useful agent for the treatment of lung cancer.