bluuebunny/crossref_metadata_2025_split huggingface dataset:
Evaluation of Versant Hepatitis C Virus Genotype Assay (LiPA) 2.0
Authors: Verbeeck Jannick , Stanley Mark J. , Shieh Jen , Celis Linda , Huyck Els , Wollants Elke , Morimoto Judy , Farrior Alice , Sablon Erwin , Jankowski-Hennig Margaret , Schaper Carl , Johnson Pamela , Van Ranst Marc , Van Brussel Marianne 
Published: April 2008

ABSTRACT

Hepatitis C virus (HCV) genotyping is a tool used to optimize antiviral treatment regimens. The newly developed Versant HCV genotype assay (LiPA) 2.0 uses sequence information from both the 5′ untranslated region and the core region, allowing distinction between HCV genotype 1 and subtypes c to l of genotype 6 and between subtypes a and b of genotype 1. HCV-positive samples were genotyped manually using the Versant HCV genotype assay (LiPA) 2.0 system according to the manufacturer's instructions. For the comparison study, Versant HCV genotype assay (LiPA) 1.0 was used. In this study, 99.7% of the samples could be amplified, the genotype of 96.0% of samples could be determined, and the agreement with the reference method was 99.4% when a genotype was determined. The reproducibility study showed no significant differences in performance across sites (
P
= 0.43) or across lots (
P
= 0.88). In the comparison study, 13 samples that were uninterpretable or incorrectly genotyped with Versant HCV genotype assay (LiPA) 1.0 were correctly genotyped by Versant HCV genotype assay (LiPA) 2.0. Versant HCV genotype assay (LiPA) 2.0 is a sensitive, accurate, and reliable assay for HCV genotyping. The inclusion of the core region probes in Versant HCV genotype assay (LiPA) 2.0 results in a genotyping success rate higher than that of the current Versant HCV genotype assay (LiPA) 1.0.
Characterization of Neutralizing Antibody Responses Elicited by Clade A Envelope Immunogens Derived from Early Transmitted Viruses
Authors: Kraft Zane , Strouss Katharine , Sutton William F. , Cleveland Brad , Tso For Yue , Polacino Patricia , Overbaugh Julie , Hu Shiu-Lok , Stamatatos Leonidas 
Published: April 2008

ABSTRACT
The vast majority of studies with candidate immunogens based on the human immunodeficiency virus envelope (Env) have been conducted with Env proteins derived from clade B viruses isolated during chronic infection. Whether non-clade B Env protein immunogens will elicit antibodies with epitope specificities that are similar to those of antibodies elicited by clade B Envs and whether the antibodies elicited by Envs derived from early transmitted viruses will be similar to those elicited by Envs derived from viruses isolated during chronic infection are currently unknown. Here we performed immunizations with four clade A Envs, cloned directly from the peripheral blood of infected individuals during acute infection, which differed in lengths and extents of glycosylation. The antibody responses elicited by these four Envs were compared to each other and to those elicited by a well-characterized clade B Env immunogen derived from the SF162 virus, which was isolated during chronic infection. Only one clade A Env, the one with the fewer glycosylation sites, elicited homologous neutralizing antibodies (NAbs); these did not target the V1, V2, or V3 regions. In contrast, all four clade A Envs elicited anti-V3 NAbs against “easy-to-neutralize” clade B and clade A isolates, irrespective of the variable region length and extent of glycosylation of the Env used as an immunogen. These anti-V3 NAbs did not access their epitopes on homologous and heterologous clade A, or B, neutralization-resistant viruses. The length and extent of glycosylation of the variable regions on the clade A Env immunogens tested did not affect the breadth of the elicited NAbs. Our data also indicate that the development of cross-reactive NAbs against clade A viruses faces similar hurdles to the development of cross-reactive anti-clade B NAbs.
E Protein Domain III Determinants of Yellow Fever Virus 17D Vaccine Strain Enhance Binding to Glycosaminoglycans, Impede Virus Spread, and Attenuate Virulence
Authors: Lee Eva , Lobigs Mario 
Published: April 2008

ABSTRACT
The yellow fever virus (YFV) 17D strain is one of the most effective live vaccines for human use, but the in vivo mechanisms for virulence attenuation of the vaccine and the corresponding molecular determinants remain elusive. The vaccine differs phenotypically from wild-type YFV by the loss of viscerotropism, despite replicative fitness in cell culture, and genetically by 20 amino acid changes predominantly located in the envelope (E) protein. We show that three residues in E protein domain III inhibit spread of 17D in extraneural tissues and attenuate virulence in type I/II interferon-deficient mice. One of these residues (Arg380) is a dominant glycosaminoglycan-binding determinant, which mainly accounts for more rapid in vivo clearance of 17D from the bloodstream in comparison to 17D-derived variants with wild-type-like E protein. While other mutations will account for loss of neurotropism and phenotypic stability, the described impact of E protein domain III changes on virus dissemination and virulence is the first rational explanation for the safety of the 17D vaccine in humans.
Silencing of Rotavirus NSP4 or VP7 Expression Reduces Alterations in Ca
2+
Homeostasis Induced by Infection of Cultured Cells
Authors: Zambrano José Luis , Díaz Yuleima , Peña Franshelle , Vizzi Esmeralda , Ruiz Marie-Christine , Michelangeli Fabián , Liprandi Ferdinando , Ludert Juan Ernesto 
Published: April 2008

ABSTRACT

Rotavirus infection of cells in culture induces major changes in Ca
2+
homeostasis. These changes include increases in plasma membrane Ca
2+
permeability, cytosolic Ca
2+
concentration, and total cell Ca
2+
content and a reduction in the amount of Ca
2+
released from intracellular pools sensitive to agonists. Various lines of evidence suggest that the nonstructural glycoprotein NSP4 and possibly the major outer capsid glycoprotein VP7 are responsible for these effects. In order to evaluate the functional roles of NSP4 and other rotavirus proteins in the changes in Ca
2+
homeostasis observed in infected cells, the expressions of NSP4, VP7, and VP4 were silenced using the short interfering RNA (siRNA) technique. The transfection of specific siRNAs resulted in a strong and specific reduction of the expression of NSP4, VP7, and VP4 and decreased the yield of new viral progeny by more than 90%. Using fura-2 loaded cells, we observed that knocking down the expression of NSP4 totally prevented the increase in Ca
2+
permeability of the plasma membrane and cytosolic Ca
2+
concentration measured in infected cells. A reduction in the levels of VP7 expression partially reduced the effect of infection on plasma membrane Ca
2+
permeability and Ca
2+
pools released by agonist (ATP). In addition, the increase of total Ca
2+
content (as measured by
45
Ca
2+
uptake) observed in infected cells was reduced to the levels in mock-infected cells when NSP4 and VP7 were silenced. Finally, when the expression of VP4 was silenced, none of the disturbances of Ca
2+
homeostasis caused by rotaviruses in infected cells were affected. These data altogether indicate that NSP4 is the main protein responsible for the changes in Ca
2+
homeostasis observed in rotavirus-infected cultured cells. Nevertheless, VP7 may contribute to these effects.
The use of prolotherapy in the sacroiliac joint
Authors: Cusi M , Saunders J , Hungerford B , Wisbey-Roth T , Lucas P , Wilson S 
Published: April 2008

ObjectiveIn this study the effectiveness of prolotherapy in the treatment of deficient load transfer of the sacroiliac joint (SIJ) was determined.DesignA prospective descriptive study.SettingAuthors’ private practice.Participants25 patients who consented to treatment and attended for at least one follow-up visit and assessment.Study periodFrom April 2004 to July 2007.InterventionThree injections of hypertonic dextrose solution into the dorsal interosseous ligament of the affected SIJ, under CT control, 6 weeks apart.Main outcome measuresQuebec Back Pain Disability Scale, Roland–Morris 24, Roland–Morris 24 Multiform questionnaires and clinical examination by two authors independently.ResultsAll patients included in this study attended at least one follow-up visit at 3, 12 or 24 months.. The number of patients at follow-up decreased at 12 and 24 months. Functional questionnaires demonstrated significant improvements for those followed-up at 3, 12 and 24 months (p<0.05). Clinical scores showed significant improvement from commencement to 3, 12 and 24 months (p<0.001).ConclusionsThis descriptive study of prolotherapy in private practice has shown positive clinical outcomes for the 76% of patients who attended the 3-month follow-up visit (76% at 12 months and 32% at 24 months). Similar results were found in the questionnaires (Quebec Back Pain Disability Scale, Roland–Morris 24 and Roland–Morris 24 Multiform questionnaires) at 3, 12 and 24 months.
FAST FACTORIZATION BY SIMILARITY OF FUZZY CONCEPT LATTICES WITH HEDGES
Authors: BĚLOHLÁVEK RADIM , OUTRATA JAN , VYCHODIL VILEM 
Published: April 2008

The paper presents results on factorization by similarity of fuzzy concept lattices with hedges. A fuzzy concept lattice is a hierarchically ordered collection of clusters extracted from tabular data. The basic idea of factorization by similarity is to have, instead of a possibly large original fuzzy concept lattice, its factor lattice. The factor lattice contains less clusters than the original concept lattice but, at the same time, represents a reasonable approximation of the original concept lattice and provides us with a granular view on the original concept lattice. The factor lattice results by factorization of the original fuzzy concept lattice by a similarity relation. The similarity relation is specified by a user by means of a single parameter, called a similarity threshold. Smaller similarity thresholds lead to smaller factor lattices, i.e. to more comprehensible but less accurate approximations of the original concept lattice. Therefore, factorization by similarity provides a trade-off between comprehensibility and precision. We first describe the notion of factorization. Second, we present a way to compute the factor lattice directly from input data, i.e. without the need to compute the possibly large original concept lattice. Third, we provide an illustrative example to demonstrate our method.
Monochromosome Transfer and Microarray Analysis Identify a Critical Tumor-Suppressive Region Mapping to Chromosome 13q14 and THSD1 in Esophageal Carcinoma
Authors: Ko Josephine M.Y. , Chan Pui Ling , Yau Wing Lung , Chan Ho Kin , Chan King Chi , Yu Zhuo You , Kwong Fung Mei , Miller Lance D. , Liu Edison T. , Yang Li Chun , Lo Paulisally H.Y. , Stanbridge Eric J. , Tang Johnny C.O. , Srivastava Gopesh , Tsao Sai Wah , Law Simon , Lung Maria L. 
Published: April 2008

Abstract
Loss of chromosome 13q regions in esophageal squamous cell carcinoma (ESCC) is a frequent event. Monochromosome transfer approaches provide direct functional evidence for tumor suppression by chromosome 13 in SLMT-1, an ESCC cell line, and identify critical regions at 13q12.3, 13q14.11, and 13q14.3. Differential gene expression profiles of three tumor-suppressing microcell hybrids (MCH) and their tumorigenic parental SLMT-1 cell line were revealed by competitive hybridization using 19k cDNA oligonucleotide microarrays. Nine candidate 13q14 tumor-suppressor genes (TSG), including RB1, showed down-regulation in SLMT-1, compared with NE1, an immortalized normal esophageal epithelial cell line; their average gene expression was restored in MCHs compared with SLMT-1. Reverse transcription-PCR validated gene expression levels in MCHs and a panel of ESCC cell lines. Results suggest that the tumor-suppressing effect is not attributed to RB1, but instead likely involves thrombospondin type I domain-containing 1 (THSD1), a novel candidate TSG mapping to 13q14. Quantitative reverse transcription-PCR detected down-regulation of THSD1 expression in 100% of ESCC and other cancer cell lines. Mechanisms for THSD1 silencing in ESCC involved loss of heterozygosity and promoter hypermethylation, as analyzed by methylation-specific PCR and clonal bisulfite sequencing. Transfection of wild-type THSD1 into SLMT-1 resulted in significant reduction of colony-forming ability, hence providing functional evidence for its growth-suppressive activity. These findings suggest that THSD1 is a good candidate TSG. (Mol Cancer Res 2008;6(4):592–603)
Arachidonic Acid–Induced Ca2+ Entry Is Involved in Early Steps of Tumor Angiogenesis
Authors: Pla Alessandra Fiorio , Grange Cristina , Antoniotti Susanna , Tomatis Cristiana , Merlino Annalisa , Bussolati Benedetta , Munaron Luca 
Published: April 2008

AbstractGrowth factor–induced intracellular calcium signals in endothelial cells regulate cytosolic and nuclear events involved in the angiogenic process. Among the intracellular messengers released after proangiogenic stimulation, arachidonic acid (AA) plays a key role and its effects are strictly related to calcium homeostasis and cell proliferation. Here, we studied AA-induced intracellular calcium signals in endothelial cells derived from human breast carcinomas (B-TEC). AA promotes B-TEC proliferation and organization of vessel-like structures in vitro. The effect is directly mediated by the fatty acid without a significant contribution of its metabolites. AA induces Ca2+i signals in the entire capillary-like structure during the early phases of tubulogenesis in vitro. No such responses are detectable in B-TECs organized in more structured tubules. In B-TECs growing in monolayer, AA induces two different signals: a Ca2+i increase due to Ca2+ entry and an inhibition of store-dependent Ca2+ entry induced by thapsigargin or ATP. An inhibitor of Ca2+ entry and angiogenesis, carboxyamidotriazole, significantly and specifically decreases AA-induced B-TEC tubulogenesis, as well as AA-induced Ca2+ signals in B-TECs. We conclude that (a) AA-activated Ca2+ entry is associated with the progression through the early phases of angiogenesis, mainly involving proliferation and tubulogenesis, and it is down-regulated during the reorganization of tumor-derived endothelial cells in capillary-like structures; and (b) inhibition of AA-induced Ca2+ entry may contribute to the antiangiogenic action of carboxyamidotriazole. (Mol Cancer Res 2008;6(4):535–45)
A Different View on DNA Amplifications Indicates Frequent, Highly Complex, and Stable Amplicons on 12q13-21 in Glioma
Authors: Fischer Ulrike , Keller Andreas , Leidinger Petra , Deutscher Stephanie , Heisel Sabrina , Urbschat Steffi , Lenhof Hans-Peter , Meese Eckart 
Published: April 2008

Abstract
To further understand the biological significance of amplifications for glioma development and recurrencies, we characterized amplicon frequency and size in low-grade glioma and amplicon stability in vivo in recurring glioblastoma. We developed a 12q13-21 amplicon–specific genomic microarray and a bioinformatics amplification prediction tool to analyze amplicon frequency, size, and maintenance in 40 glioma samples including 16 glioblastoma, 10 anaplastic astrocytoma, 7 astrocytoma WHO grade 2, and 7 pilocytic astrocytoma. Whereas previous studies reported two amplified subregions, we found a more complex situation with many amplified subregions. Analyzing 40 glioma, we found that all analyzed glioblastoma and the majority of pilocytic astrocytoma, grade 2 astrocytoma, and anaplastic astrocytoma showed at least one amplified subregion, indicating a much higher amplification frequency than previously suggested. Amplifications in low-grade glioma were smaller in size and displayed clearly different distribution patterns than amplifications in glioblastoma. One glioblastoma and its recurrencies revealed an amplified subregion of 5 Mb that was stable for 6 years. Expression analysis of the amplified region revealed 10 overexpressed genes (i.e., KUB3, CTDSP2, CDK4, OS-9, DCTN2, RAB3IP, FRS2, GAS41, MDM2, and RAP1B) that were consistently overexpressed in all cases that carried this amplification. Our data indicate that amplifications on 12q13-21 (a) are more frequent than previously thought and present in low-grade tumors and (b) are maintained as extended regions over long periods of time. (Mol Cancer Res 2008;6(4):576–84)
MUC1 Initiates Src-CrkL-Rac1/Cdc42–Mediated Actin Cytoskeletal Protrusive Motility after Ligating Intercellular Adhesion Molecule-1
Authors: Shen Qiang , Rahn Jennifer J. , Zhang Jing , Gunasekera Nirosha , Sun Xuejun , Shaw Andrew R.E. , Hendzel Michael J. , Hoffman Pat , Bernier Ashlyn , Hugh Judith C. 
Published: April 2008

AbstractMUC1, a transmembrane glycoprotein of the mucin family, when aberrantly expressed on breast cancer cells is correlated with increased lymph node metastases. We have previously shown that MUC1 binds intercellular adhesion molecule-1 (ICAM-1) on surrounding accessory cells and facilitates transendothelial migration of MUC1-bearing cells. Nevertheless, the underlying molecular mechanism is still obscure. In the present study, we used a novel assay of actin cytoskeletal reorganization to show that by ligating ICAM-1, MUC1 triggers Rac1- and Cdc42-dependent actin cytoskeletal protrusive activity preferentially at the heterotypic cell-cell contact sites. Further, we show that these MUC1/ICAM-1 interaction–initiated lamellipodial and filopodial protrusions require Src family kinase and CT10 regulator of kinase like (CrkL) accompanied by the rapid formation of a Src-CrkL signaling complex at the MUC1 cytoplasmic domain. Through inhibition of Src kinase activity, we further revealed that Src is required for recruiting CrkL to the MUC1 cytoplasmic domain as well as mediating the observed actin cytoskeleton dynamics. These findings suggest a novel MUC1-Src-CrkL-Rac1/Cdc42 signaling cascade following ICAM-1 ligation, through which MUC1 regulates cytoskeletal reorganization and directed cell motility during cell migration. (Mol Cancer Res 2008;6(4):555–67)
Overgrowing forest as a possible cause for the local extinction of Vipera aspis in the northern Swiss Jura mountains
Authors: Jaggi Christoph , Baur Bruno 
Published: April 2008

Abstract
In the northern Swiss Jura mountains, the Asp viper Vipera aspis was common until the 1940ies. During the past 50 years many local populations went extinct and nowadays the species is considered as threatened. We compared habitat characteristics of localities with extant viper populations with those of localities where the species became extinct. These two groups of localities did not differ in exposure, altitude, inclination, soil structure and cover of ground vegetation. However, localities where the species is still found were situated more frequently at forest edges, in dry meadows and at roadsides, whereas localities in which V. aspis became extinct were situated more frequently in forests. Tree density was lower at localities where the viper is still present. The results suggest that former habitats of V. aspis became overgrown by bushes and trees, which in turn may have led to a colder, more humid and thus unfavourable microclimate for V. aspis. We conclude that logging is an essential tool to maintain suitable habitat for this thermophilous ovoviviparous reptile.
Cranial morphology of Rafetus euphraticus (Daudin, 1801) from Southeastern Anatolia
Authors: Taşkavak Ertan 
Published: April 2008

AbstractObservations on cranial morphology were made on Euphrates soft-shelled turtles, Rafetus euphraticus, sampled in the Euphrates and Tigris rivers and tributaries, Southeastern Anatolia. The vomer separates the maxillaries in half of the specimens, whereas the maxillae meet on the vomer in others. The parietal has no contribution in the formation of the foramen nervi trigemini due to the contact between the prootic and the epipterygoid. There are variations in the contacts of the basisphenoid and in the formation of the trigeminal region, a prootic-epipterygoid contact participates in the trigeminal region. The contacts of the vomer-pterygoid, the vomer-basisphenoid and the vomer-pterygoid-basisphenoid are observed in some specimens. In one specimen, the parietal contacts the opisthotic. All specimens have the symphyseal ridge, althought it is weak and barely discernible.
Interactions between branchiate mole salamanders (Ambystoma talpoideum) and lesser sirens (Siren intermedia): asymmetrical competition and intraguild predation
Authors: Fauth John E. 
Published: April 2008

AbstractUsing field sampling and experiments in natural and artificial ponds, I studied interactions between branchiate adult mole salamanders (Ambystoma talpoideum) and lesser sirens (Siren intermedia), two top predators in temporary ponds of the southeastern United States. The abundance and distribution of these two salamanders were independent among ponds, with A. talpoideum more numerous and widespread than S. intermedia. Both species were more likely to be found in ponds near other intermittent wetlands. Within a pond, captures of these two species were negatively correlated, and a field experiment showed that paedomorphic A. talpoideum avoided traps containing S. intermedia. An experiment in artificial ponds confirmed that interactions between these two species were highly asymmetrical; S. intermedia reduced the growth and recruitment of A. talpoideum without experiencing reciprocal. positive or negative effects. These results suggest that S. intermedia competes with and is an intraguild predator of A. talpoideum, limiting its growth and controlling its recruitment.
Ecology and conservation of the Milos viper, Macrovipera schweizeri (Werner, 1935)
Authors: Nilson Göran , Andrén Claes , Ioannidis Yiannis , Dimaki Maria 
Published: April 2008

Abstract
The Milos viper (Macrovipera schweizeri) is nocturnal from early summer until mid-September. The typical habitat was maquis terrain with small and large bushes on gravel or rocky ground. Telemetric studies showed that cryptic basking behaviour was used during 23.5% of the localisations, and a preference for large bushes (77.7%). The mean distance moved between two succeeding days was 28.5 m (with s_x, of 47.9), and in general, the male home range covered an area of 10 to 20 ha, while the female home range was smaller. Hibernacula were south facing and situated in the middle of the home ranges. Population density was 50 adult vipers per km2 in the optimal habitats. The total population for western Milos was estimated to be around 2,500 adult vipers during the study period (1993-98). The present total population on Milos seems to be below 3,000 adult animals. The species has been isolated since the Pliocene, and adapted to a diet of passerine birds. A pattern of twice-a-year foraging during spring and autumn bird migrations was highlighted. During spring, the vipers tend to be concentrated around water pools; in the dry autumn nights they climb up trees for resting birds. In years with a cold spring or autumn, critical situations may occur with starvation, resulting in cyclic population patterns. Mid-May is the mating period. The female reproductive cycle is biennial. The sex ratio is nearly equal. Around 600 specimens reach adulthood and participate in the reproductive activities each year. Mining and fires destroy habitat. The yearly estimated removal by man and road killing of vipers is up to 500-600 adult specimens. Thus, the input and out-take of adult specimens is of the same magnitude, and equal to a yearly 25% turnover. This indicates a very delicate balance, and even a small change that increases the removed number can lead towards a rapid extinction. A conservation program is urgently needed and should include the establishment of protected areas, the closing of roads for night-time driving, and prohibition of increased mining activities.