bluuebunny/crossref_metadata_2025_split huggingface dataset:
Milk of Cow (
Bos taurus
), Buffalo (
Bubalus bubalis
), and Goat (
Capra hircus
): a Better Alternative than Fetal Bovine Serum in Media for Primary Isolation, In Vitro Cultivation, and Maintenance of
Leishmania donovani
Promastigotes
Authors: Muniaraj M. , Lal C. S. , Kumar S. , Sinha P. K. , Das P. 
Published: February 2007

ABSTRACT

Tyndalized milk of goat, cow, and buffalo was found to be a potential substitute for fetal bovine serum (FBS) in the medium for the cultivation of
Leishmania donovani
promastigotes. The numbers (means) of promastigotes reached 2.6 × 10
7
, 2.3 × 10
7
, and 2.1 × 10
7
/ml, respectively, in the medium supplemented with 10% milk of goat, cow, and buffalo, in comparison to 1.9 × 10
7
/ml in the control with 10% FBS. In primary isolation, the milk-supplemented medium showed that 22 out of 26 samples were positive for promastigotes (84.6%) and the cells were maintained successfully during the observed period of 6 months.
The Nucleocytoplasmic Rabies Virus P Protein Counteracts Interferon Signaling by Inhibiting both Nuclear Accumulation and DNA Binding of STAT1
Authors: Vidy Aurore , El Bougrini Jamila , Chelbi-Alix Mounira K. , Blondel Danielle 
Published: February 2007

ABSTRACT
Rabies virus P protein inhibits alpha interferon (IFN-α)- and IFN-γ-stimulated Jak-STAT signaling by retaining phosphorylated STAT1 in the cytoplasm. Here, we show that P also blocks an intranuclear step that is the STAT1 binding to the DNA promoter of IFN-responsive genes. As P is a nucleocytoplasmic shuttling protein, we first investigated the effect of the cellular distribution of P on the localization of STAT1 and consequently on IFN signaling. We show that the localization of STAT1 is correlated with the localization of P: in cells expressing a nuclear form of P (the short P3 isoform or the complete P in the presence of the export inhibitor leptomycin B), STAT1 is nuclear, whereas in cells expressing a cytoplasmic form of P, STAT1 is cytoplasmic. However, the expression of nuclear forms of P inhibits the signaling of both IFN-γ and IFN-α, demonstrating that the retention of STAT1 in the cytoplasm is not the only mechanism involved in the inhibition of IFN signaling. Electrophoretic mobility shift analysis indicates that P expression in the cell extracts of infected cells or in stable cell lines prevents IFN-induced DNA binding of STAT1. The loss of the DNA binding of STAT1 and ISGF3 was also observed when purified recombinant P or P3 was added to the extracts of IFN-γ- or IFN-α-treated cells, indicating that P directly affects the DNA binding activity of STAT1. Then products of the rabies virus P gene are able to counteract IFN signaling by creating both cytoplasmic and nuclear blocks for STAT1.
Antigenic and Genetic Evolution of Swine Influenza A (H3N2) Viruses in Europe
Authors: de Jong J. C. , Smith D. J. , Lapedes A. S. , Donatelli I. , Campitelli L. , Barigazzi G. , Van Reeth K. , Jones T. C. , Rimmelzwaan G. F. , Osterhaus A. D. M. E. , Fouchier R. A. M. 
Published: February 2007

ABSTRACTIn the early 1970s, a human influenza A/Port Chalmers/1/73 (H3N2)-like virus colonized the European swine population. Analyses of swine influenza A (H3N2) viruses isolated in The Netherlands and Belgium revealed that in the early 1990s, antigenic drift had occurred, away from A/Port Chalmers/1/73, the strain commonly used in influenza vaccines for pigs. Here we show that Italian swine influenza A (H3N2) viruses displayed antigenic and genetic changes similar to those observed in Northern European viruses in the same period. We used antigenic cartography methods for quantitative analyses of the antigenic evolution of European swine H3N2 viruses and observed a clustered virus evolution as seen for human viruses. Although the antigenic drift of swine and human H3N2 viruses has followed distinct evolutionary paths, potential cluster-differentiating amino acid substitutions in the influenza virus surface protein hemagglutinin (HA) were in part the same. The antigenic evolution of swine viruses occurred at a rate approximately six times slower than the rate in human viruses, even though the rates of genetic evolution of the HA at the nucleotide and amino acid level were similar for human and swine H3N2 viruses. Continuous monitoring of antigenic changes is recommended to give a first indication as to whether vaccine strains may need updating. Our data suggest that humoral immunity in the population plays a smaller role in the evolutionary selection processes of swine H3N2 viruses than in human H3N2 viruses.
Sulfated Homologues of Heparin Inhibit Hepatitis C Virus Entry into Mammalian Cells
Authors: Basu Arnab , Kanda Tatsuo , Beyene Aster , Saito Kousuke , Meyer Keith , Ray Ranjit 
Published: February 2007

ABSTRACTThe mechanism of entry of hepatitis C virus (HCV) through interactions between the envelope glycoproteins and specific cell surface receptors remains unclear at this time. We have previously shown with the vesicular stomatitis virus (VSV)/HCV pseudotype model that the hypervariable region 1 of the HCV E2 envelope glycoprotein helps in binding with glycosaminoglycans present on the cell surface. In this study, we have examined the binding of HCV envelope glycoproteins with chemically modified derivatives of heparin. Furthermore, we have determined the functional relevance of the interaction of heparin derivatives with HCV envelope glycoproteins for infectivity by using a human immunodeficiency virus (HIV)/HCV pseudotype, a VSV/HCV pseudotype, and cell culture-grown HCV genotype 1a. Taken together, our results suggest that the HCV envelope glycoproteins rely upon O-sulfated esters of a heparin homologue to facilitate entry into mammalian cells.
Distinct Sites on the Sindbis Virus RNA-Dependent RNA Polymerase for Binding to the Promoters for the Synthesis of Genomic and Subgenomic RNA
Authors: Li Mei-Ling , Stollar Victor 
Published: February 2007

ABSTRACT
Sindbis virus-infected cells make two positive-strand RNAs, a genomic (G) RNA and a subgenomic (SG) RNA. Here we report the amino acid sequence in nonstructural protein 4 (nsP4), the viral RNA-dependent RNA polymerase, that binds to the promoter for the synthesis of G RNA. In addition, using a cell-free system that makes both G and SG RNA, we show that specific amino acid changes in nsP4 that abolish the synthesis of SG RNA have no effect on the synthesis of G RNA. Our findings indicate that nsP4 has distinct sites for the recognition of the G and SG promoters.
A Phase 1 Escalating Single-Dose and Weekly Fixed-Dose Study of Cetuximab: Pharmacokinetic and Pharmacodynamic Rationale for Dosing
Authors: Fracasso Paula M. , Burris Howard , Arquette Matthew A. , Govindan Ramaswamy , Gao Feng , Wright Lisa P. , Goodner Sherry A. , Greco F. Anthony , Jones Suzanne F. , Willcut Noel , Chodkiewicz Catherine , Pathak Amit , Springett Gregory M. , Simon George R. , Sullivan Daniel M. , Marcelpoil Raphaël , Mayfield Shelley D. , Mauro David , Garrett Christopher R. 
Published: February 2007

Abstract
Purpose: This phase 1 study evaluated the pharmacokinetic and pharmacodynamic effects of cetuximab on patients with epithelial malignancies.
Experimental Design: Following a skin and tumor biopsy, patients with advanced epithelial malignancies were randomized to receive a single dose of cetuximab at 50, 100, 250, 400, or 500 mg/m2 i.v. Repeat skin (days 2, 8, 15, and 22) and tumor (day 8) biopsies were obtained. Immunohistochemical expression of epidermal growth factor receptor (EGFR) and its pathway members was done on biopsies. Blood samples were obtained over 22 days for pharmacokinetic analyses. After day 22, all patients received weekly 250 mg/m2 cetuximab until disease progression or unacceptable toxicity.
Results: Thirty-nine patients enrolled. Rash was noted in 26 (67%) patients. Three patients (two with colon cancer and one with laryngeal cancer) achieved a partial response and 13 patients had stable disease. Pharmacokinetic data revealed mean maximum observed cetuximab concentrations and mean area under the concentration-time curve from time zero to infinity increased in a dose-dependent manner up to 400 mg/m2 cetuximab. Mean clearance was similar at cetuximab doses ≥100 mg/m2, supporting saturation of EGFR binding at 250 mg/m2. Pharmacodynamic evaluation revealed that patients with partial response/stable disease had a higher-grade rash and higher cetuximab trough levels than those with progressive disease (P = 0.032 and 0.002, respectively). Administration of single doses (250-500 mg/m2) of cetuximab resulted in a dose-dependent decrease in EGFR protein expression levels in skin over time, supporting a minimal dose of cetuximab at 250 mg/m2 for a pharmacodynamic effect.
Conclusion: This study provides a pharmacokinetic and pharmacodynamic rationale for the dosing of cetuximab.
Nitric Oxide and Its Gatekeeper Thrombospondin-1 in Tumor Angiogenesis
Authors: Roberts David D. , Isenberg Jeffery S. , Ridnour Lisa A. , Wink David A. 
Published: February 2007

AbstractNitric oxide (NO) plays a central role in angiogenesis as a mediator of signaling by vascular endothelial growth factor and other angiogenic factors. Low concentrations of NO produced in response to angiogenic factors stimulate angiogenesis, whereas higher concentrations typical of inflammatory responses inhibit angiogenesis. The proangiogenic activity of NO is mediated by activation of soluble guanylyl cyclase, leading to cyclic guanosine 3′,5′-monophosphate accumulation and activation of its target kinases and ion channels. The four angiogenesis inhibitors currently approved for clinical use target components of the signaling cascade upstream of NO. New research has identified components downstream of NO as the primary target of the endogenous angiogenesis inhibitor thrombospondin-1 and has shown that circulating levels of thrombospondin-1 are sufficient to limit angiogenic responses by antagonizing NO signaling. This provides new insights into the significance of the widespread loss of thrombospondin-1 expression during malignant progression. Although clinical trials suggest that blocking NO signaling can inhibit tumor angiogenesis, this approach also inactivates inhibitory signaling from thrombospondin-1. We discuss the implications of the balance between these pathways for applying thrombospondin-1 mimetics and redox modifiers as cancer therapeutics.
CpG Island Methylator Phenotype Association with Elevated Serum α-Fetoprotein Level in Hepatocellular Carcinoma
Authors: Zhang Changsong , Li Zhengyou , Cheng Yue , Jia Fengqi , Li Rong , Wu Mengchao , Li Ke , Wei Lixin 
Published: February 2007

Abstract
Purpose: CpG island methylator phenotype (CIMP) involves hypermethylation targeted toward the promoters of multiple genes. To gain insight into the role of epigenetic aberration of tumor-related genes in hepatocarcinogenesis, we determined a hypermethylation profile in hepatocellular carcinoma (HCC).
Experimental Design: We examined the promoter methylation status of nine genes in 50 HCCs, 50 paired nontumor tissues, and 6 normal liver tissues by methylation-specific PCR. CIMP+ was defined as having five genes that are concordantly methylated.
Results: The frequency of promoter methylation of nine genes in 50 HCCs varied from 10% in P53 to 94% in c-Myc. The methylation status of P14, P15, P16, ER, RASSF1A, WT1, and c-Myc was significantly correlated with HCC and nontumor tissues (P &lt; 0.05). Hypermethylation of one or more genes was found in 96% of HCC. CIMP was more frequent in HCC than in nontumor tissues (70% and 12%, P &lt; 0.001). There is a significant association between CIMP and methylation of P14, P15, P16, ER, RSAAF1A, and WT1 (P &lt; 0.05) and serum α-fetoprotein (AFP) level (P = 0.017). CIMP+ was more frequent in HCC with AFP ≥ 30 μg/L than those with AFP &lt; 30 μg/L (P = 0.005). In addition, the promoter hypermethylation of P15 and P16 was associated with elevated serum AFP levels in 35 HCC samples with CIMP+ (P &lt; 0.05).
Conclusions: Positive correlation of CIMP and AFP levels in HCC suggests that CIMP can serve as a molecular marker of late-stage HCC development.
Radiation-Induced Hepatitis B Virus Reactivation in Liver Mediated by the Bystander Effect from Irradiated Endothelial Cells
Authors: Chou Chia Hung , Chen Pei-Jer , Lee Po-Huang , Cheng Ann-Lii , Hsu Hui-Chen , Cheng Jason Chia-Hsien 
Published: February 2007

Abstract
Purpose: Hepatitis B virus (HBV) reactivation is one unique pathogenesis in Asian carriers with liver toxicity after radiotherapy for hepatobiliary malignancies. This study attempts to delineate the biological mechanism of radiation-induced HBV reactivation.
Experimental Design: Primary cultures of hepatocytes (PCC) were prepared from the noncancerous liver tissue removed perioperatively from 12 HBV carriers with hepatocellular carcinoma (HCC). The conditioned medium of irradiated PCCs, HCC, and endothelial cells from patients was transferred to PCCs or HepG2.2.15 cells (a human hepatoblastoma cell line transfected with HBV DNA) before subsequent irradiation. Forty-eight hours after irradiation, HBV DNA was measured by real-time quantitative PCR. Specific cytokines were determined by cytokine array and ELISA analysis. Preradiotherapy and postradiotherapy sera from 10 HBV carriers and 16 non-HBV carriers were analyzed for viral loads and cytokine activities.
Results: Radiation induced HBV DNA replication in (a) irradiated PCCs cultured with the conditioned medium from irradiated PCCs (2.74-fold; P = 0.004) and endothelial cells (9.50-fold; P = 3.1 × 10−10), but not from HCCs (1.07-fold), and in (b) irradiated HepG2.2.15 cells (17.7-fold) cocultured with human umbilical vascular endothelial cells. Cytokine assay revealed increased expression of interleukin-6 (IL-6) in conditioned medium from irradiated human umbilical vascular endothelial cells. All 16 patients with liver irradiated had the increased serum IL-6 compared with 3 of 10 patients with irradiation excluding liver (P &lt; 0.001). All nine HBV carriers with liver irradiated had postradiotherapy increases in both HBV DNA and IL-6.
Conclusions: Radiation-induced liver toxicity with HBV reactivation is from a bystander effect on irradiated endothelial cells releasing cytokines, including IL-6.
Women and the Dura-Europos Synagogue Paintings
Authors: Steinberg Faith 
Published: February 2007

AbstractBetween 1928 and 1937, during excavations at a site in Mesopotamia, archaeologists uncovered an ancient city, Dura-Europos, on the Euphrates River. Among their many findings, which included numerous pagan temples, were a Christian house and a synagogue. A room in the house had been converted into a baptistery with frescoes. In a large assembly room of the synagogue, murals depicting biblical narratives were painted in three registers on all four walls. The Second Commandment forbids the use of imagery, and the finding, the earliest and only one of such magnitude to date, caused a stir and has generated an extensive literature. Many scholars attribute this phenomenon to the rise of Christianity. But there is an aspect of the paintings that has not been investigated. In the most visually accessible and most holy area of the room, the Torah shrine, heroic Jewish women of the Bible were depicted. In light of the patriarchal nature of historical Judaism, this paper examines the murals and the architectural and archeological findings in an effort to understand this anomaly.
Tomb Stone of the Sons of Attes from Myrmekion
Authors: Tokhtasiev Sergei 
Published: February 2007

AbstractThe author publishes a tomb stone of the 1st half of the 4th century BC discovered at the necropolis of the Bosporan city of Myrmekion (on the territory of Kerch). The name of the second buried person Kυαιανιζ should be probably read as Kυλιανιζ. The latter is known from a 4th century epitaph CIRB 162 and is often to be found on the ceramic stamps of Sinope as the name factory-owners. The name seems to be Paphlagonian, derived from the Hittito-Luvian anthroponymic stem Kul(a)-. Anatolian name of the father "Aττηζ known on the Bosporus from some other inscriptions of the 4th century BC, is attested in Myrmekion in CIRB 178. The author gives other examples from Bosporan epigraphy of how immigrant families from Asia Minor preserved their traditional names. The epigraphic data make it possible to speak about a mass migration of super ficially Hellenized barbarians (often with their families) from the northern parts of Asia Minor to the Bosporus in the 5th and 4th centuries BC.
On the Dating of one Group of Chian Amphoras (Based on Finds from the Pichvnari Greek Necropolis of the 5th Century BC)
Authors: Khalvashi Merab , Kakhidze Amiran 
Published: February 2007

AbstractOn the basis of the evidence of the Pichvnari Greek Necropolis of the 5th century BC, the present publication offers a new dating of the late period Chian amphoras with swollen necks. It is obvious that the manufacture of this kind of amphoras ceased in the mid-5th century BC. From the second quarter of the 5th century BC a new variety of pottery emerged, which can be regarded as a transitional form between Chian amphoras with swollen necks and amphoras with straight necks.
Epitaph of Onesimos the Son of Kallisthenes
Authors: Azarnert Leonid 
Published: February 2007

AbstractThis note analyses one of the Bosporan sepulchral inscriptions. The analysis suggests that the epitaph of Onesimos the son of Kallisthenes is a metric epigram cast in two iambic trimesters and not a prose inscription as has been previously believed.
SCaFoS: a tool for Selection, Concatenation and Fusion of Sequences for phylogenomics
Authors: Roure Béatrice , Rodriguez-Ezpeleta Naiara , Philippe Hervé 
Published: February 2007

Abstract

Background
Phylogenetic analyses based on datasets rich in both genes and species (phylogenomics) are becoming a standard approach to resolve evolutionary questions. However, several difficulties are associated with the assembly of large datasets, such as multiple copies of a gene per species (paralogous or xenologous genes), lack of some genes for a given species, or partial sequences. The use of undetected paralogous or xenologous genes in phylogenetic inference can lead to inaccurate results, and the use of partial sequences to a lack of resolution. A tool that selects sequences, species, and genes, while dealing with these issues, is needed in a phylogenomics context.

Results
Here, we present SCaFoS, a tool that quickly assembles phylogenomic datasets containing maximal phylogenetic information while adjusting the amount of missing data in the selection of species, sequences and genes. Starting from individual sequence alignments, and using monophyletic groups defined by the user, SCaFoS creates chimeras with partial sequences, or selects, among multiple sequences, the orthologous and/or slowest evolving sequences. Once sequences representing each predefined monophyletic group have been selected, SCaFos retains genes according to the user's allowed level of missing data and generates files for super-matrix and super-tree analyses in several formats compatible with standard phylogenetic inference software. Because no clear-cut criteria exist for the sequence selection, a semi-automatic mode is available to accommodate user's expertise.

Conclusion
SCaFos is able to deal with datasets of hundreds of species and genes, both at the amino acid or nucleotide level. It has a graphical interface and can be integrated in an automatic workflow. Moreover, SCaFoS is the first tool that integrates user's knowledge to select orthologous sequences, creates chimerical sequences to reduce missing data and selects genes according to their level of missing data. Finally, applying SCaFoS to different datasets, we show that the judicious selection of genes, species and sequences reduces tree reconstruction artefacts, especially if the dataset includes fast evolving species.
Molecular characterization, biofilm analysis and experimental biofouling study of Fusariumisolates from recent cases of fungal keratitis in New York State
Authors: Dyavaiah Madhu , Ramani Rama , Chu David S , Ritterband David C , Shah Mahendra K , Samsonoff William A , Chaturvedi Sudha , Chaturvedi Vishnu 
Published: February 2007

Abstract

Background
To characterize Fusarium isolates from recent cases of fungal keratitis in contact lens wearers, and to investigate fungal association with MoistureLoc solution.

Methods
We studied six fungal isolates from recent cases of keratitis in New York State. The isolates were characterized by nucleotide sequencing and phylogenetic analyses of multiple genes, and then typed using minisatellite and microsatellite probes. Experimental fungal biofilm formation was tested by standard methods. MoistureLoc solutions were tested in biofouling studies for their efficacy in elimination of Fusarium contamination.

Results

Fusarium solani – corneal ulcers (2 isolates), lens case (1 isolate), and F. oxysporum – corneal ulcer (1 isolate), eye (1 isolate), were recovered from five patients. An opened bottle of MoistureLoc solution provided by a patient also yielded F. solani. Two distinct genotypes of F. solani as well as of F. oxysporum were present in the isolated strains. Remarkably, F. solani strains from the lens case and lens solution in one instance were similar, based on phylogenetic analyses and molecular typing. The solution isolate of F. solani formed biofilm on contact lenses in control conditions, but not when co-incubated with MoistureLoc solution. Both freshly opened and 3-month old MoistureLoc solutions effectively killed F. solani and F. oxysporum, when fungal contamination was simulated under recommended lens treatment regimen (4-hr). However, simulation of inappropriate use (15 – 60 min) led to the recovery of less than 1% of original inoculum of F. solani or F. oxysporum.

Conclusion
Temporary survival of F. solani and F. oxysporum in MoistureLoc suggested that improper lens cleaning regimen could be a possible contributing factor in recent infections.
Integrative analysis of a cancer somatic mutome
Authors: Hernández Pilar , Solé Xavier , Valls Joan , Moreno Víctor , Capellá Gabriel , Urruticoechea Ander , Pujana Miguel Angel 
Published: February 2007

Abstract

Background
The consecutive acquisition of genetic alterations characterizes neoplastic processes. As a consequence of these alterations, molecular interactions are reprogrammed in the context of highly connected and regulated cellular networks. The recent identification of the collection of somatically mutated genes in breast tumors (breast cancer somatic "mutome") allows the comprehensive study of its function and organization in complex networks.

Results
We analyzed functional genomic data (loss of heterozygosity, copy number variation and gene expression in breast tumors) and protein binary interactions from public repositories to identify potential novel components of neoplastic processes, the functional relationships between them, and to examine their coordinated function in breast cancer pathogenesis. This analysis identified candidate tumor suppressors and oncogenes, and new genes whose expression level predicts survival rate in breast cancer patients. Mutome network modeling using different types of pathological and healthy functional relationships unveils functional modules significantly enriched in genes or proteins (genes/proteins) with related biological process Gene Ontology terms and containing known breast cancer-related genes/proteins.

Conclusion
This study presents a comprehensive analysis of the breast somatic mutome, highlighting those genes with a higher probability of playing a determinant role in tumorigenesis and better defining molecular interactions related to the neoplastic process.