bluuebunny/crossref_metadata_2025_split huggingface dataset:
Conservation of the rare British lichen Vulpicida pinastri: changing climate, habitat loss and strategies for mitigation
Authors: BINDER Mark D. , ELLIS Christopher J. 
Published: February 2008

Abstract:Autecological information targeted towards rare and threatened lichen species is severely lacking. This study adopts the rare British lichen Vulpicida pinastri as a case study species and examines its ecological response to emerging threats: climate change and the recurrent loss of its primary habitat (juniper scrub). We used predictive niche modelling to examine the response of V. pinastri to a range of present-day climatic variables. A successful model was projected for a period during the 2050s based on IPCC climate change scenarios (UKCIP02 data), and threat was estimated as the proportional change in bioclimatic space. To estimate the potential range now and during the 2050s, projected bioclimatic space was masked by a habitat map equivalent to (i) the present-day distribution of juniper and (ii) theoretical juniper distribution based on existing rates of decline. Our results point to potential range loss of V. pinastri with climate warming, exacerbated by the recurrent decline in juniper habitat. This predictive modelling approach was complemented by an assessment of local stand-scale effects. At four sites in north-east Scotland we examined the occurrence and abundance of V. pinastri thalli, in response to juniper spatial distribution, and the life-stage and structure of individual shrubs. Vulpicida pinastri appeared to be dispersal limited at small-scales, and was significantly more abundant on old and degenerate juniper shrubs. Our results evidence a close relationship between management for habitat quality and effective lichen conservation. Effective conservation of V. pinastri must ensure cohorts of older and degenerate juniper shrubs are maintained at sites where the species is expected to be most resistant to long-term climate warming, i.e. in the uplands of north-east Scotland.
Allicin from garlic suppresses TNF-α and augments IFN-γ expressions in monocyte cultures from patients with Vaginitis
Authors: Islam Najmul , Iqbal Jawed , Hasan Nazarul , Fatima Zeeshan , Thakur Hamida , Hasan Nazia , Mahdi Abbas Ali , Khan Tamkin , Bano Farzana , Ansari Irfan Ahmad 
Published: February 2008

Abstract
Objective:
We tried to explore beneficial effects of allicin- a natural antioxidant from garlic in the possible management of vaginitis. Methods: Peripheral blood mononuclear cells (PBMC’s) were isolated from blood of patients having vaginal infections as well as normal healthy subjects as per our published protocol. Monocytes (MN’s) from above PBMC’s were adhered, rested overnight and cultured without or with varying doses of allicin (0-500 ng/ml). Some cultures received SN50 and SN50M (100 ug/ml). After 24 hrs cultures, the cells were harvested and the supernatants subjected to secreted TNF-α and sIFN-γ assays by ELISA. Treated/untreated harvested cells were subjected to glutathione peroxidase (GPx) activity assay.

Results:
We show involvement of inflammatory cytokines and reactive oxygen species (ROS) in vaginitis. Augmented secreted TNF-α and decreased sIFN-γ levels were observed in monocyte cultures of vaginal patients. Relative to healthy controls, a decrease by 2.5-fold in glutathione peroxidase (GPx) activity in cultures of vaginal patients was observed. Treatment with allicin from garlic appreciably decreased secreted TNF-α with simultaneous amelioration in sIFN-γ and GPx activity. Allicin (500 ng/ml) ameliorated GPx activity by ~ 2.16-folds in patient monocyte cultures. The anti-oxidant and anti-inflammatory actions of allicin induced in monocyte cultures of vaginal infection patients were mediated via NF-κB.

Conclusion:
Thus, the above results may help in understanding the use of allicin as an adjunct in vaginal infection therapy, and in turn, may address the globally female health.
Azadirachta indica induced suppression of Mycobacterium tuberculosis secreted proteins in human monocyte
Authors: Iqbal Jawed , Kumar Ajay , Islam Najmul 
Published: February 2008

AbstractThe H37Rv strain of MTB was grown in modified Sauton’s medium till mid-log phase. Peripheral blood mononuclear cells (PBMC) were isolated by density gradient sedimentation on Ficoll-Paque separation medium. Adherent monocytes obtained from PBMC’s were infected with H37Rv for 90 min. in the ratio of 1:1 (1 bug: 1 cell). Thereafter, after washing, infected cells were co-cultured with varying doses of neem extract for 24 hrs, and harvested subsequently. Modulation of secreted TNF-[alpha], iNOS and MTB Ag85 complex expressions in culture supernatants was estimated by ELISA.We report the high basal expression of secreted tumor necrosis factor-[alpha] (TNF-[alpha]), inducible nitric oxide synthase (iNOS) and MTB Ag85 complex in MTB-infected monocytes was suppressed by neem extract in a dose-dependent manner (P<0.001 for all). A concentration of 1ug/ml of neem extract showed a suppression by ~ 2.5-fold (P<0.001), 1.7-fold (P<0.001) and 1.8-fold (P<0.001) in the expressions ofsecreted TNF-[alpha], iNOS and MTB Ag85 respectively in 24 hr culture supernatants of MTB-infected monocytes.Thus, neem extract seems to be a potential future adjunct for in-depth studies in the management of tuberculosis.
Downward Trends in Surgical Site and Urinary Tract Infections After Cesarean Delivery in a French Surveillance Network, 1997–2003
Authors: Vincent Agnès , Ayzac Louis , Girard Raphaële , Caillat-Vallet Emmanuelle , Chapuis Catherine , Depaix Florence , Dumas Anne-Marie , Gignoux Chantal , Haond Catherine , Lafarge-Leboucher Joëlle , Launay Carine , Tissot-Guerraz Françoise , Fabry Jacques ,   Mater Sud-Est Study Group
Published: February 2008

Objective.To evaluate whether the adjusted rates of surgical site infection (SSI) and urinary tract infection (UTI) after cesarean delivery decrease in maternity units that perform active healthcare-associated infection surveillance.Design.Trend analysis by means of multiple logistic regression.Setting.A total of 80 maternity units participating in the Mater Sud-Est surveillance network.Patients.A total of 37,074 cesarean deliveries were included in the surveillance from January 1, 1997, through December 31, 2003.Methods.We used a logistic regression model to estimate risk-adjusted post–cesarean delivery infection odds ratios. The variables included were the maternity units' annual rate of operative procedures, the level of dispensed neonatal care, the year of delivery, maternal risk factors, and the characteristics of cesarean delivery. The trend of risk-adjusted odds ratios for SSI and UTI during the study period was studied by linear regression.Results.The crude rates of SSI and UTI after cesarean delivery were 1.5% (571 of 37,074 patients) and 1.8% (685 of 37,074 patients), respectively. During the study period, the decrease in SSI and UTI adjusted odds ratios was statistically significant (R = −0.823 [P = .023] and R = −0.906 [P = .005], respectively).Conclusion.Reductions of 48% in the SSI rate and 52% in the UTI rate were observed in the maternity units. These unbiased trends could be related to progress in preventive practices as a result of the increased dissemination of national standards and a collaborative surveillance with benchmarking of rates.
Biological pathway kinetic rate constants are scale-invariant
Authors: Grandison Scott , Morris Richard J. 
Published: February 2008

Abstract
Motivation: Scale-free networks have had a profound impact in Biology. Network theory is now used routinely to visualize, navigate through, and help understand gene networks, protein–protein interactions, regulatory networks and metabolic pathways. Here we analyse the numerical rather than topological properties of biological networks and focus on the study of kinetic rate constants within pathways.
Results: We have analysed all current entries in the BioModels database and show that the kinetic rate parameters follow Benford's; law closely. The cumulative histogram plot reveals an underlying power-law. This implies that these data are scale-invariant, thus placing biological network topology and their chemistry on an equivalent ‘scale-free’ power-law foundation.
Contact: Richard.Morris@bbsrc.ac.uk
(In)visibility: Dislocation in French and the Voice of the Translator
Authors: McLaughlin Mairi 
Published: February 2008

Abstract
This article presents the results of the investigation of a corpus consisting of translated and original French taken from contemporary prize-winning fiction. The focus of the inquiry is the difference between original and translated French and the consequences for the voice of the translator. The differences between the two language types are examined through a case study of the syntactic structure known as dislocation. Through careful analysis of the form, function and usage of this construction in the two language types, I arrive at several conclusions. First, the very existence of formal, functional and usage variation highlights the differences between translated and original language, and this may in future play a greater role in governing the composition of corpora in linguistic research. Second, the way in which this variation manifests itself has consequences for the status that translation holds in a specific culture and the effects that translation can have on the target language. Finally, variation between the two language types is shown to be relevant to the debate regarding the voice of the translator: Lawrence Venuti's invisibility theory is reworked to include three types of invisibility.
Cavemen Among Us: Genealogies of Atavism from Zola's
La Bête humaine
to Chabrol's
Le Boucher
Authors: Bell Dorian 
Published: February 2008

Abstract

Although critics have rightly linked Claude Chabrol's film
Le Boucher
(1969) to Zola's novel
La Bête humaine
(1890), the two have yet to be considered in the context of the century-long tradition of thought about atavism that informs them both. This article reconstructs that tradition, examining how
Le Boucher
's modern-day caveman suggests twentieth-century cultural continuities with nineteenth-century notions of man's relation to his evolutionary forebears. Noting
Le Boucher
's debt to a Freudian conception of atavism — a conception heavily influenced by the very same scientific paradigm that shaped Zola's fascination with man's prehistoric self — I argue that Chabrol's film revives a nineteenth-century European anxiety of proximity whereby technological and scientific advances prompted unease about ever closer contact with the distant reaches of humanity. Chabrol achieves this by building on Zola's proto-cinematic vision, refracting it through a Freudian lens in which atavism and the cinema occupy common psychological space, and updating the thematics of atavism for a twentieth century chastised by the colonial experiment.
Influence of the Columbia River plume (USA) on the vertical and horizontal distribution of mesozooplankton over the Washington and Oregon shelf
Authors: Peterson Jay O. , Peterson William T. 
Published: February 2008

Abstract
Peterson, J. O., and Peterson, W. T. 2008. Influence of the Columbia River plume (USA) on the vertical and horizontal distribution of mesozooplankton over the Washington and Oregon shelf. – ICES Journal of Marine Science, 65: 477–483. River plumes extending out over continental shelf waters have distinct frontal boundaries along their leading edges that concentrate highly buoyant particles, including zooplankton. The margin between the base of the plume and the underlying oceanic waters is often many times larger in spatial extent than the visible surface front, but the influence of this region of a river plume on the vertical and horizontal distribution of zooplankton is less well understood. Using a laser optical plankton counter (LOPC) and a conductivity–temperature–depth sensor (CTD) mounted to a rapidly undulating tow body, we examined the horizontal and vertical distribution of zooplankton proximate to the Columbia River plume, to study how plume waters affect zooplankton over the continental shelf. Overall, vertically integrated zooplankton abundance and biovolume was elevated close to “aged” plume waters. Zooplankton tended to aggregate near the surface close to river plume waters. When plume waters are present at the surface, zooplankton aggregations tended to be in the upper 10 m of the water column, compared with 25 m when the plume was not present. The presence of river plumes may be ecologically and energetically important to surface feeding planktivores such as larval and juvenile fish.
Preparation of Double-Stranded RNA for Drosophila RNA Interference (RNAi)
Authors: Misquitta Leonie , Wei Qin , Paterson Bruce M. 
Published: February 2008

INTRODUCTIONRNA interference (RNAi) is a powerful method for determining the role of specific genes during Drosophila embryogenesis. It has been used in our laboratory to phenocopy a series of known mutations in Drosophila, including twist, engrailed, daughterless, Dmef2, and, to a lesser extent, white in the adult eye. This protocol describes the preparation of dsRNA by in vitro transcription of complementary strands of a cloned DNA fragment that codes for all or a portion of the gene of interest, followed by annealing of the transcribed RNA.
Injection of dsRNA into Drosophila Embryos for RNA Interference (RNAi): Figure 1.
Authors: Misquitta Leonie , Wei Qin , Paterson Bruce M. 
Published: February 2008

INTRODUCTIONRNA interference (RNAi) is a powerful method for determining the role of specific genes during Drosophila embryogenesis. This protocol describes a technique by which Drosophila embryos can be injected with dsRNA in order to disrupt targeted gene function. The approach is straightforward, utilizing improved methods for injecting the dsRNA directly through the chorion of the embryo. This strategy minimizes problems normally associated with desiccation of the dechorionated embryo and facilitates post-injection analysis of gene expression.
Labeling the Components of the Plasma Membrane with Fluorescent Dyes for Imaging
Authors: Chazotte Brad 
Published: February 2008

INTRODUCTIONThe eukaryotic cell has evolved to compartmentalize its functions and transport various metabolites among cellular compartments. Therefore, in cell biology, the study of organization and structure/function relationships are of great importance. The plasma membrane provides the essential dynamic boundary and a vital selective interface between the cell compartment and its environment. This article describes four methods for labeling the plasma membrane with fluorescent probes. Each method labels a distinct class of membrane molecules.
Labeling the Golgi Apparatus with BODIPY-FL-Ceramide (C5-DMB-ceramide) for Imaging
Authors: Chazotte Brad 
Published: February 2008

INTRODUCTIONThe eukaryotic cell has evolved to compartmentalize its functions and transport various metabolites among cellular compartments. Therefore, in cell biology, the study of organization and structure/function relationships are of great importance. The Golgi apparatus is composed of a series of flattened, disk-shaped cisternae typically located near the cell nucleus. It is thought that the Golgi may be a principal organizer of macromolecular traffic in the cell because many molecules, such as secreted proteins, glycoproteins, glycolipids, and plasma membrane glycoproteins, pass through the Golgi during their maturation. In this protocol, fluorescent probes of the Golgi make use of this function to allow labeling of the Golgi.
Calculation of Spot Reliability Evaluation Scores (SRED) for DNA Microarray Data
Authors: Shimokawa Kazuro , Kodzius Rimantas , Matsumura Yonehiro , Hayashizaki Yoshihide 
Published: February 2008

INTRODUCTIONIn terms of cost per measurement, the use of DNA microarrays for comprehensive and quantitative expression measurements is vastly superior to other methods such as Northern blotting or quantitative reverse transcriptase polymerase chain reaction (QRT-PCR). However, the output values of DNA microarrays are not always highly reliable or accurate compared with other techniques, and the output data sometimes consist of measurements of relative expression (treated sample vs. untreated) rather than absolute expression values as desired. In effect, some measurements from some laboratories do not represent absolute expression values (such as the number of transcripts) and as such are experimentally deficient. This protocol addresses one problem in some microarray data: the absence of accurate measurements. Spot reliability evaluation score for DNA microarrays (SRED) offers a reliability value for each spot in the microarray. SRED does not require an entire microarray to assess the reliability, but rather analyzes the reliability of individual spots of the microarray. The calculation of a reliability index can be used for different microarray systems, which facilitates the analysis of multiple microarray data sets from different experimental platforms.
Calculation of Absolute Expression Values for DNA Microarray Data
Authors: Shimokawa Kazuro , Kodzius Rimantas , Matsumura Yonehiro , Hayashizaki Yoshihide 
Published: February 2008

INTRODUCTIONIn terms of cost per measurement, the use of DNA microarrays for comprehensive and quantitative expression measurements is vastly superior to other methods such as Northern blotting or quantitative reverse transcriptase polymerase chain reaction (QRT-PCR). However, the output values of DNA microarrays are not always highly reliable or accurate compared with other techniques, and the output data sometimes consist of measurements of relative expression (treated sample vs. untreated) rather than absolute expression values as desired. In effect, some measurements from some laboratories do not represent absolute expression values (such as the number of transcripts) and as such are experimentally deficient. To address the problem that some microarray data sets fail to reflect the number of mRNA molecules sufficiently in a given sample (i.e., fail to provide absolute expression levels), additional methods are required. The procedure described here provides a new method for converting microarray data to absolute expression values with the use of external data such as expressed sequence tags (ESTs) and cap analysis of gene expression (CAGE) tags.
In Vitro Histone Methyltransferase Assay
Authors: Fingerman Ian M. , Du Hai-Ning , Briggs Scott D. 
Published: February 2008

INTRODUCTIONHistone methyltransferases catalyze the addition of one or more methyl groups to a specific lysine or arginine residue within histones. Currently, there is a great deal of interest in histone methyltransferases, because mutations and misregulation of the genes encoding these proteins have been linked to various cancers and other diseases. Many genes encoding putative histone methyltransferases have been identified in eukaryotes, but the proteins they encode have not been functionally characterized. This protocol describes an in vitro assay for histone methyltransferase activity that uses bacterial cell extracts in which expression of a methyltransferase of interest is induced. In many cases, purification of the enzyme is unnecessary, making this experiment ideal for pilot studies. Bacterial cell extract containing the methyltransferase of interest is incubated with S-adenosyl-L-[methyl-3H]-methionine and various histone substrates, many of which are commercially available. Incorporation of the methyl-3H can be measured easily by scintillation counting. The labeled substrate is visualized by SDS-polyacrylamide gel electrophoresis (PAGE) followed by fluorography. This allows the substrate specificity and activity of a histone methyltransferase of interest to be readily characterized.
Stable Isotope Labeling of Mammals (SILAM)
Authors: McClatchy Daniel B. , Yates John R. 
Published: February 2008

INTRODUCTIONA general approach in quantitative mass spectrometry is to mix a protein sample containing only natural-abundance isotopes with an identical protein sample containing proteins labeled with heavy stable isotopes (e.g., 2H, 13C, 15N, or 18O). Introduction of stable isotope labels into proteins alters their molecular weight and such changes can be observed on the mass spectrometer. The relative protein expression is calculated from the ion chromatograms of the labeled and unlabeled peptides. Introduction of stable isotopes via metabolic labeling is an efficient and quantitative method compared to in vitro covalent labeling strategies, because it ensures that every protein is enriched with a heavy stable isotope. Metabolic labeling is routinely performed with cultured cells, ranging from bacteria and yeast to mammalian cells. However, analysis of mammalian tissue allows greater insight into physiology compared to cultured cells. In this protocol, we describe a procedure to metabolically label Rattus norvegicus with 15N for quantitative mass spectrometry analysis. Stable isotope labeling of mammals (SILAM) allows the global quantitative analysis of any mammalian model of human disease.
Nonradioactive In Situ Hybridization of RNA Probes to Sections of Plant Tissues
Authors: Ferrandiz Cristina , Sessions Allen 
Published: February 2008

INTRODUCTIONBoth radioactive and nonradioactive probes can be used to detect RNA in situ. Radioactive in situ hybridizations are believed by many to be more sensitive, but the localization of signal is considerably less precise than for nonradioactive in situs, and each experiment takes much longer. Thus, nonradioactive in situ hybridization is generally preferred. Antisense RNA is typically labeled using digoxygenin (DIG), which is subsequently detected with an anti-DIG antibody coupled to alkaline phosphatase. This protocol describes in situ hybridization of a DIG-labeled probe to paraffin-embedded sections of plant tissue. Double labeling using both DIG- and fluorescein isothiocyanate (FITC)-conjugated ribonucleotides is also described.
Immunohistochemistry on Sections of Plant Tissues Using Enzyme-Coupled Avidin-Biotin Complex
Authors: Weigel Detlef , Glazebrook Jane 
Published: February 2008

INTRODUCTIONLike RNA, proteins can be localized in situ on tissue sections. In situ localization or immunohistochemistry provides information on the cellular and subcellular distribution of proteins in different tissues. The technique described in this protocol employs a biotinylated secondary antibody in conjunction with a preformed Avidin:Biotinylated enzyme Complex (ABC) for immunohistochemistry. It allows for sensitive detection of antigens while avoiding fluorescent secondary antibodies, which produce a much less stable signal. Formation of the complex is achieved by mixing avidin and biotinylated enzyme in dilute solution and in defined amounts prior to use. The complex is then allowed to bind to biotinylated secondary antibodies, thus linking the antigen via primary and secondary antibodies to the enzyme used to generate the signal. Kits for this procedure are available from Vector Laboratories. The VECTASTAIN ABC kits are of three types, using the enzymes horseradish peroxidase, alkaline phosphatase, or glucose oxidase. This protocol assumes use of the peroxidase kit, but can be easily modified for the other kits.