bluuebunny/crossref_metadata_2025_split huggingface dataset:
Phagocytosis Inhibits F-Actin-Enriched Membrane Protrusions Stimulated by Fractalkine (CX3CL1) and Colony-Stimulating Factor 1
Authors: Luo Yong , Isaac Beth M. , Casadevall Arturo , Cox Dianne 
Published: July 2009

ABSTRACTCryptococcus neoformansis the only encapsulated human-pathogenic fungus and a facultative intracellular pathogen that can reside in macrophages without host cell lysis. In the present study, we investigated how phagocytosis ofC. neoformansaffected the macrophage response to chemoattractants such as fractalkine (FKN) (CX3CL1) and colony-stimulating factor 1 (CSF-1). Phagocytosis of immunoglobulin G (IgG)-opsonizedC. neoformansand IgG- or C3bi-opsonized sheep erythrocytes was performed using a RAW 264.7 subline (LR5 cells) and bone marrow-derived macrophages (BMM). The chemotactic response to FKN or CSF-1 was quantitated by measurement of the formation of F-actin-enriched membrane protrusions (ruffles), which showed that FKN or CSF-1 stimulated strong transient ruffling in both LR5 cells and BMM. This stimulated cell ruffling was inhibited by phagocytosis in an intracellular-pathogen-number-dependent manner. The inhibition of ruffling was not simply a result of reduced membrane availability since membrane sequestration by sucrose treatment did not inhibit the ruffling response. The phagocytosis process was required to inhibit ruffling as BMM from FcγR−/−mice that boundC. neoformansbut did not ingest it retained the ability to ruffle in response to chemoattractants. These results imply that the inhibition of FKN- or CSF-1-stimulated cell ruffling was a direct consequence of the phagocytosis process. Since cell ruffling is a prelude to chemotaxis, this observation links two functions of macrophages that are critical to host defense, chemotaxis and phagocytosis. Phagocytosis-induced chemotactic suppression may enhance host defense by keeping these antimicrobial effector cells at infected sites and reduce the likelihood of microbial spread by wandering macrophages containing infectious cargo.
Distinguishing citation quality for journal impact assessment
Authors: Lim Andrew , Ma Hong , Wen Qi , Xu Zhou , Cheang Brenda 
Published: July 2009

Introduction

The research community has long and often been fervently keen on debating the topic of journal impact. Well, just what is the impact of a journal? Today, the Science Citation Index (SCI) recognizes over 7,000 journals. The sheer number of available journals renders it pivotal for researchers to accurately gauge a journal's impact when submitting their papers, as it has become commonplace that researchers regard publishing their work in established journals to have significant influence on peer recognition. For journals in Management Information System (MIS), such research studies have continuously been published since the 1990s. Nine of them have been summarized by Carol Saunders, whereby seven were based on respondent perceptions by surveying experts, and two were based on the citation quantity to indicate the journal impact.
It is generally accepted that citation analysis is purported to be a more objective method than the expert survey. The main reason is citation analysis uses objective measurements, which are based on the viewpoint that the influence of a journal and its articles is determined by their usefulness to other journals and articles, and where their usage can be reflected by citations that they have received. However, using citation quantity only is also considered to have bias to a certain degree, due to a widely held notion that citation quantity does not represent citation quality. Regarding the impact in the MIS discipline for example, a citation by a paper published in a prestigious MIS journal should far outweigh a citation by a paper published in an unremarkable MIS journal or in an external journal outside the MIS field. Such intuition suggests that the citation quality can be divided into the following two aspects:
• Citation Relevance (CR): indicating how relevant the journal giving the citation is to the discipline we are interested in;
• Citation Importance (CI): indicating how important the journal giving the citation is in the discipline we are interested in.
However, these concerns about citation quality have not been properly addressed in citation analysis literature.
To address our concerns about citation quality for assessing journal impact, we propose a method, which first clusters "pure" MIS journals to identify relevant citations, and then score the impact for each journal, according to its citations that are received from pure MIS journals and weighted by citation importance. Although our method is only applied to MIS journals, it is general enough to evaluate the impact of journals in other disciplines.
Modelling Bedriaga's rock lizard distribution in Sardinia: An ensemble approach
Authors: Vignoli Leonardo , Bologna Marco , Bombi Pierluigi , Salvi Daniele 
Published: July 2009

AbstractMany techniques for predicting species potential distribution were recently developed. Despite the international interest for these procedures, applications of predictive approaches to the study of Italian fauna distribution are exceptionally rare. This paper aimed at: (a) detecting climatic exigencies of A. bedriagae in Sardinia; (b) predicting the Archaeolacerta bedriagae Sardinian potential distribution; (c) identifying the most vulnerable Italian populations of the species. Literature and field data were utilized as presence records. Six modelling procedures (BIOCLIM, DOMAIN, ENFA, GAM, GLM, and MAXENT) were adopted. The species climatic requirements were defined using the WorldClim databank for deriving the environmental predictors. AUC and Kappa values were calculated for models validation. AUC values were compared by using Anova Monte Carlo. The best four models were combined through the weighted average consensus method for producing a univocal output. GAM and MAXENT had the best performances (respectively: AUC = 0.93 ± 0.03, Kappa = 0.77 ± 0.08; AUC = 0.93 ± 0.03, Kappa = 0.78 ± 0.07). Good results were also obtained by GLM and DOMAIN (respectively: AUC = 0.89 ± 0.04, Kappa = 0.72 ± 0.05; AUC = 0.88 ± 0.04, Kappa = 0.69 ± 0.07). BIOCLIM and ENFA gained relatively low performances (respectively: AUC = 0.78 ± 0.07, Kappa = 0.57 ± 0.14; AUC = 0.75 ± 0.06; Kappa = 0.49 ± 0.10). In Sardinia A. bedriagae is mainly influenced by seasonality, which causes the evidenced range fragmentation. Moreover, the general importance of multi-methods approaches and consensus techniques in predicting species distribution was highlighted.
Are sex ratios of larval alpine newts (Mesotriton alpestris) biased in high-altitude spawning sites with different temperature regimes?
Authors: Schabetsberger Robert , Grabherr Helmut , Sztatecsny Marc 
Published: July 2009

AbstractAmphibians generally have genetic sex determination which should lead to equal sex ratios. However, populations of the alpine newt (Mesotriton alpestris) from cold, high-altitude breeding sites in the Austrian Alps showed strongly female-biased sex ratios of up to 3.7 females to 1 male over 6 years. Temperature dependent sex determination has therefore been considered as possible reason to explain the observed skews. To investigate if a female excess already exists during gonadal differentiation of M. alpestris larvae before metamorphosis, we assessed larval sex ratios in high-altitude spawning sites with different temperature regimes. The sex was determined by histological analyses of cross sections of the gonads. In no case a significant divergence from a 1:1 sex ratio was found. Based on these results and previous karyological, skeletochronological, and ecological work we conclude that higher mortality rates of adult males are the most plausible explanation for the female excess in high-altitude populations of alpine newts. However, future studies should focus on the development of sex-specific genetic markers to allow early determination of gender in embryos and larvae.
Assessing whether disinfectants against the fungus Batrachochytrium dendrobatidis have negative effects on tadpoles and zooplankton
Authors: von Rütte Mirjam , Peyer Niklaus , Schmidt Benedikt , Keller Nina , Geiser Céline 
Published: July 2009

AbstractChytridiomycosis is an emerging disease of amphibians that has led to global population declines and possible extinctions. Vectoring of the pathogen, Batrachochytrium dendrobatidis (Bd) by anthropogenic means is thought to be important in its spread. To limit further increase in the distribution of Bd, field biologists and amateur naturalists ought to disinfect their boots and materials. However, imprudent use of potentially harmful disinfectants may have unwanted negative side effects on amphibians. We used a factorial experiment to test whether commonly used disinfectants (bleach and Virkon S) affect tadpole performance and zooplankton abundance. At the high dose of bleach, all tadpoles and zooplankton died. Tadpole performance and zooplankton abundance in the low dose of bleach and Virkon S treatments were undistinguishable from the control. Therefore, when bleach is used as a disinfectant, it must not get in contact with amphibians. Virkon S appears to be a disinfectant that can be used against Bd with no detectable negative effects on tadpoles and zooplankton.
Activation of endothelial intrinsic NF-κB pathway impairs protein C anticoagulation mechanism and promotes coagulation in endotoxemic mice
Authors: Song Dongmei , Ye Xiaobing , Xu Honglei , Liu Shu Fang 
Published: July 2009

AbstractAlthough the role of systemic activation of the nuclear factor κB (NF-κB) pathway in septic coagulation has been well documented, little is known about the contribution of endothelial-specific NF-κB signaling in this pathologic process. Here, we used transgenic mice that conditionally overexpress a mutant I-κBα, an inhibitor of NF-κB, selectively on endothelium, and their wild-type littermates to define the role of endothelial-specific NF-κB in septic coagulation. In wild-type mice, lipopolysaccharide (LPS) challenge (5 mg/kg intraperitoneally) caused markedly increased plasma markers of coagulation, decreased plasma fibrinogen level, and widespread tissue fibrin deposition, which were abrogated by endothelial NF-κB blockade in transgenic mice. Endothelial NF-κB blockade inhibited tissue factor expression in endothelial cells, but not in leukocytes. Endothelial NF-κB blockade did not inhibit LPS-induced tissue factor expression in heart, kidney, and liver. Endothelial NF-κB blockade prevented LPS down-regulation of endothelial protein C receptor (EPCR) and thrombomodulin protein expressions, inhibited tissue tumor necrosis factor-α converting enzyme activity, reduced EPCR shedding, and restored plasma protein C level. Our data demonstrate that endothelial intrinsic NF-κB signaling plays a pivotal role in septic coagulation and suggests a link between endothelial-specific NF-κB activation and the impairment of the thrombomodulin-protein C-EPCR anticoagulation pathway.
Apolipoprotein-mediated lipid antigen presentation in B cells provides a pathway for innate help by NKT cells
Authors: Allan Lenka L. , Hoefl Katrin , Zheng Dong-Jun , Chung Brian K. , Kozak Frederick K. , Tan Rusung , van den Elzen Peter 
Published: July 2009

AbstractNatural killer T (NKT) cells are innate-like lymphocytes that recognize lipid antigens and have been shown to enhance B-cell activation and antibody production. B cells typically recruit T-cell help by presenting internalized antigens recognized by their surface antigen receptor. Here, we demonstrate a highly efficient means whereby human B cells present lipid antigens to NKT cells, capturing the antigen using apolipoprotein E (apoE) and the low-density lipoprotein receptor (LDL-R). ApoE dramatically enhances B-cell presentation of alpha-galactosylceramide (αGalCer), an exogenous CD1d presented antigen, inducing activation of NKT cells and the subsequent activation of B cells. B cells express the LDL-R on activation, and the activation of NKT cells by B cells is completely LDL-R dependent, as shown by blocking experiments and the complete lack of presentation when using apoE2, an isoform of apoE incapable of LDL-R binding. The dependence on apoE and the LDL-R is much more pronounced in B cells than we had previously seen in dendritic cells, which can apparently use alternate pathways of lipid antigen uptake. Thus, B cells use an apolipoprotein-mediated pathway of lipid antigen presentation, which constitutes a form of innate help for B cells by NKT cells.
A species delimitation approach in the Trochulus sericeus/hispiduscomplex reveals two cryptic species within a sharp contact zone
Authors: Dépraz Aline , Hausser Jacques , Pfenninger Markus 
Published: July 2009

Abstract

Background
Mitochondrial DNA sequencing increasingly results in the recognition of genetically divergent, but morphologically cryptic lineages. Species delimitation approaches that rely on multiple lines of evidence in areas of co-occurrence are particularly powerful to infer their specific status. We investigated the species boundaries of two cryptic lineages of the land snail genus Trochulus in a contact zone, using mitochondrial and nuclear DNA marker as well as shell morphometrics.

Results
Both mitochondrial lineages have a distinct geographical distribution with a small zone of co-occurrence. In the same area, we detected two nuclear genotype clusters, each being highly significantly associated to one mitochondrial lineage. This association however had exceptions: a small number of individuals in the contact zone showed intermediate genotypes (4%) or cytonuclear disequilibrium (12%). Both mitochondrial lineage and nuclear cluster were statistically significant predictors for the shell shape indicating morphological divergence. Nevertheless, the lineage morphospaces largely overlapped (low posterior classification success rate of 69% and 78%, respectively): the two lineages are truly cryptic.

Conclusion
The integrative approach using multiple lines of evidence supported the hypothesis that the investigated Trochulus lineages are reproductively isolated species. In the small contact area, however, the lineages hybridise to a limited extent. This detection of a hybrid zone adds an instance to the rare reported cases of hybridisation in land snails.
Polymorphic segmental duplication in the nematode Caenorhabditis elegans
Authors: Vergara Ismael A , Mah Allan K , Huang Jim C , Tarailo-Graovac Maja , Johnsen Robert C , Baillie David L , Chen Nansheng 
Published: July 2009

Abstract

Background
The nematode Caenorhabditis elegans was the first multicellular organism to have its genome fully sequenced. Over the last 10 years since the original publication in 1998, the C. elegans genome has been scrutinized and the last gaps were filled in November 2002, which present a unique opportunity for examining genome-wide segmental duplications.

Results
Here, we performed analysis of the C. elegans genome in search for segmental duplications using a new tool–OrthoCluster–we have recently developed. We detected 3,484 duplicated segments–duplicons–ranging in size from 234 bp to 108 Kb. The largest pair of duplicons, 108 kb in length located on the left arm of Chromosome V, was further characterized. They are nearly identical at the DNA level (99.7% identity) and each duplicon contains 26 putative protein coding genes. Genotyping of 76 wild-type strains obtained from different labs in the C. elegans community revealed that not all strains contain this duplication. In fact, only 29 strains carry this large segmental duplication, suggesting a very recent duplication event in the C. elegans genome.

Conclusion
This report represents the first demonstration that the C. elegans laboratory wild-type N2 strains has acquired large-scale differences.
OPA1-related dominant optic atrophy is not strongly influenced by mitochondrial DNA background
Authors: Pierron Denis , Ferré Marc , Rocher Christophe , Chevrollier Arnaud , Murail Pascal , Thoraval Didier , Amati-Bonneau Patrizia , Reynier Pascal , Letellier Thierry 
Published: July 2009

Abstract

Background
Leber's hereditary optic neuropathy (LHON) and autosomal dominant optic atrophy (ADOA) are the most frequent forms of hereditary optic neuropathies. LHON is associated with mitochondrial DNA (mtDNA) mutations whereas ADOA is mainly due to mutations in the OPA1 gene that encodes a mitochondrial protein involved in the mitochondrial inner membrane remodeling. A striking influence of mtDNA haplogroup J on LHON expression has been demonstrated and it has been recently suggested that this haplogroup could also influence ADOA expression. In this study, we have tested the influence of mtDNA backgrounds on OPA1 mutations.

Methods
To define the relationships between OPA1 mutations and mtDNA backgrounds, we determined the haplogroup affiliation of 41 French patients affected by OPA1-related ADOA by control-region sequencing and RFLP survey of their mtDNAs.

Results
The comparison between patient and reference populations did not revealed any significant difference.

Conclusion
Our results argue against a strong influence of mtDNA background on ADOA expression. These data allow to conclude that OPA1 could be considered as a "severe mutation", directly responsible of the optic atrophy, whereas OPA1-negative ADOA and LHON mutations need an external factor(s) to express the pathology (i.e. synergistic interaction with mitochondrial background).
Diagnostic accuracy of the vegetative and minimally conscious state: Clinical consensus versus standardized neurobehavioral assessment
Authors: Schnakers Caroline , Vanhaudenhuyse Audrey , Giacino Joseph , Ventura Manfredi , Boly Melanie , Majerus Steve , Moonen Gustave , Laureys Steven 
Published: July 2009

Abstract

Background
Previously published studies have reported that up to 43% of patients with disorders of consciousness are erroneously assigned a diagnosis of vegetative state (VS). However, no recent studies have investigated the accuracy of this grave clinical diagnosis. In this study, we compared consensus-based diagnoses of VS and MCS to those based on a well-established standardized neurobehavioral rating scale, the JFK Coma Recovery Scale-Revised (CRS-R).

Methods
We prospectively followed 103 patients (55 ± 19 years) with mixed etiologies and compared the clinical consensus diagnosis provided by the physician on the basis of the medical staff's daily observations to diagnoses derived from CRS-R assessments performed by research staff. All patients were assigned a diagnosis of 'VS', 'MCS' or 'uncertain diagnosis.'

Results
Of the 44 patients diagnosed with VS based on the clinical consensus of the medical team, 18 (41%) were found to be in MCS following standardized assessment with the CRS-R. In the 41 patients with a consensus diagnosis of MCS, 4 (10%) had emerged from MCS, according to the CRS-R. We also found that the majority of patients assigned an uncertain diagnosis by clinical consensus (89%) were in MCS based on CRS-R findings.

Conclusion
Despite the importance of diagnostic accuracy, the rate of misdiagnosis of VS has not substantially changed in the past 15 years. Standardized neurobehavioral assessment is a more sensitive means of establishing differential diagnosis in patients with disorders of consciousness when compared to diagnoses determined by clinical consensus.
A novel chalcone derivative which acts as a microtubule depolymerising agent and an inhibitor of P-gp and BCRP in in-vitro and in-vivoglioblastoma models
Authors: Boumendjel Ahcene , McLeer-Florin Anne , Champelovier Pierre , Allegro Diane , Muhammad Dima , Souard Florence , Derouazi Madiha , Peyrot Vincent , Toussaint Bertrand , Boutonnat Jean 
Published: July 2009

AbstractBackgroundOver the past decades, in spite of intensive search, no significant increase in the survival of patients with glioblastoma has been obtained. The role of the blood-brain barrier (BBB) and especially the activity of efflux pumps belonging to the ATP Binding Cassette (ABC) family may, in part, explain this defect.MethodsThein-vitroactivities of JAI-51 on cell proliferation were assessed by various experimental approaches in four human and a murine glioblastoma cell lines. Using drug exclusion assays and flow-cytometry, potential inhibitory effects of JAI-51 on P-gp and BCRP were evaluated in sensitive or resistant cell lines. JAI-51 activity onin-vitromicrotubule polymerization was assessed by tubulin polymerization assay and direct binding measurements by analytical ultracentrifugation. Finally, a model of C57BL/6 mice bearing subcutaneous GL26 glioblastoma xenografts was used to assess the activity of the title compoundin vivo. An HPLC method was designed to detect JAI-51 in the brain and other target organs of the treated animals, as well as in the tumours.ResultsIn the four human and the murine glioblastoma cell lines tested, 10 μM JAI-51 inhibited proliferation and blocked cells in the M phase of the cell cycle, via its activity as a microtubule depolymerising agent. This ligand binds to tubulin with an association constant of 2 × 105M-1, overlapping the colchicine binding site. JAI-51 also inhibited the activity of P-gp and BCRP, without being a substrate of these efflux pumps. Thesein vitrostudies were reinforced by ourin vivoinvestigations of C57BL/6 mice bearing GL26 glioblastoma xenografts, in which JAI-51 induced a delay in tumour onset and a tumour growth inhibition, following intraperitoneal administration of 96 mg/kg once a week. In accordance with these results, JAI-51 was detected by HPLC in the tumours of the treated animals. Moreover, JAI-51 was detected in the brain, showing that the molecule is also able to cross the BBB.ConclusionThesein vitroandin vivodata suggest that JAI-51 could be a good candidate for a new treatment of tumours of the CNS. Further investigations are in progress to associate the title compound chemotherapy to radiotherapy in a rat model.
Claudin-containing exosomes in the peripheral circulation of women with ovarian cancer
Authors: Li Jianghong , Sherman-Baust Cheryl A , Tsai-Turton Miyun , Bristow Robert E , Roden Richard B , Morin Patrice J 
Published: July 2009

Abstract

Background
The absence of highly sensitive and specific serum biomarkers makes mass screening for ovarian cancer impossible. The claudin proteins are frequently overexpressed in ovarian cancers, but their potential as prognostic, diagnostic, or detection markers remains unclear. Here, we have explored the possible use of these proteins as screening biomarkers for ovarian cancer detection.

Methods
Claudin protein shedding from cells was examined by immunoblotting of conditioned culture media. The presence of claudins in exosomes released from ovarian cancer cells was demonstrated by sucrose gradient separation and immunogold electron microscopy experiments. Claudin-4-containing exosomes in the plasma of ovarian cancer patients were evaluated in a pilot panel of 63 ovarian cancer patients and 50 healthy volunteers. The CA125 marker was also assessed in these samples and compared with claudin-4 positivity.

Results
We show that full-length claudins can be shed from ovarian cancer cells in culture and found in the media as part of small lipid vesicles known as exosomes. Moreover, 32 of 63 plasma samples from ovarian cancer patients exhibited the presence of claudin-4-containing exosomes. In contrast, only one of 50 samples from individuals without cancer exhibited claudin-4-positive exosomes. In our small panel, at a specificity of 98%, the claudin-4 and CA125 tests had sensitivities of 51% and 71%, respectively. The two tests did not appear to be independent and were strongly correlated.

Conclusion
Our work shows for the first time that claudin-4 can be released from ovarian cancer cells and can be detected in the peripheral circulation of ovarian cancer patients. The development of sensitive assays for the detection of claudin-4 in blood will be crucial in determining whether this approach can be useful, alone or in combination with other screening methods, for the detection of ovarian cancer.