bluuebunny/crossref_metadata_2025_split huggingface dataset:
MR Myelography of Sacral Meningeal Cysts
Authors: Tsuchiya K. , Katase S. , Hachiya J. 
Published: January 2010

Purpose: To describe the findings of sacral meningeal cysts (SMCs) on MR myelography and assess its value for the diagnosis of SMCs. Material and Methods: We evaluated the MR images and MR myelograms obtained from 10 patients with SMC. MR myelograms were obtained using a 2D or 3D single-shot fast spin-echo sequence. In 5 patients, X-ray myelograms and postmyelographic CT images were compared with the MR myelograms. Results: A total of 33 SMCs were diagnosed within the spinal canal and/or sacral foramen. MR myelograms clearly revealed each cyst as a well-defined mass showing hyperintensity (10 cysts) or isointensity (23 cysts) compared to cerebrospinal fluid. MR myelograms demonstrated SMCs better than X-ray myelograms and postmyelographic CT images in 3 of the 5 patients. Conclusion: MR myelography can be an adjunct to conventional imaging techniques when surgical treatment is indicated, because it can precisely delineate the extent of SMCs.
Clinical Practice Guidelines for the Management of Cryptococcal Disease: 2010 Update by the Infectious Diseases Society of America
Authors: Perfect John R. , Dismukes William E. , Dromer Francoise , Goldman David L. , Graybill John R. , Hamill Richard J. , Harrison Thomas S. , Larsen Robert A. , Lortholary Olivier , Nguyen Minh-Hong , Pappas Peter G. , Powderly William G. , Singh Nina , Sobel Jack D. , Sorrell Tania C. 
Published: January 2010

AbstractCryptococcosis is a global invasive mycosis associated with significant morbidity and mortality. These guidelines for its management have been built on the previous Infectious Diseases Society of America guidelines from 2000 and include new sections. There is a discussion of the management of cryptococcal meningoencephalitis in 3 risk groups: (1) human immunodeficiency virus (HIV)–infected individuals, (2) organ transplant recipients, and (3) non–HIV-infected and nontransplant hosts. There are specific recommendations for other unique risk populations, such as children, pregnant women, persons in resource-limited environments, and those with Cryptococcus gattii infection. Recommendations for management also include other sites of infection, including strategies for pulmonary cryptococcosis. Emphasis has been placed on potential complications in management of cryptococcal infection, including increased intracranial pressure, immune reconstitution inflammatory syndrome (IRIS), drug resistance, and cryptococcomas. Three key management principles have been articulated: (1) induction therapy for meningoencephalitis using fungicidal regimens, such as a polyene and flucytosine, followed by suppressive regimens using fluconazole; (2) importance of early recognition and treatment of increased intracranial pressure and/or IRIS; and (3) the use of lipid formulations of amphotericin B regimens in patients with renal impairment. Cryptococcosis remains a challenging management issue, with little new drug development or recent definitive studies. However, if the diagnosis is made early, if clinicians adhere to the basic principles of these guidelines, and if the underlying disease is controlled, then cryptococcosis can be managed successfully in the vast majority of patients.
Paramecium tetraurelia: The Renaissance of an Early Unicellular Model
Authors: Beisson Janine , Bétermier Mireille , Bré Marie-Hélène , Cohen Jean , Duharcourt Sandra , Duret Laurent , Kung Ching , Malinsky Sophie , Meyer Eric , Preer John R. , Sperling Linda 
Published: January 2010

INTRODUCTIONParamecium tetraurelia is a widely distributed, free-living unicellular organism that feeds on bacteria and can easily be cultured in the laboratory. Its position within the phylum Ciliophora, remote from the most commonly used models, offers an interesting perspective on the basic cellular and molecular processes of eukaryotic life. Its large size and complex cellular organization facilitate morphogenetic studies of conserved structures, such as cilia and basal bodies, as well as electrophysiological studies of swimming behavior. Like all ciliates, P. tetraurelia contains two distinct types of nuclei, the germline micronucleus (MIC) and the somatic macronucleus (MAC), which differentiate from copies of the zygotic nucleus after fertilization. The sexual cycle can be managed by controlling food uptake, allowing the study of a developmentally regulated differentiation program in synchronous cultures. Spectacular genome rearrangements occur during the development of the somatic macronucleus. Their epigenetic control by RNA-mediated homology-dependent mechanisms, which might underlie long-known cases of non-Mendelian inheritance, provides evolutionary insight into the diversity of small RNA pathways involved in genome regulation. Being endowed with two alternative modes of sexual reproduction (conjugation and autogamy), P. tetraurelia is ideally suited for genetic analyses, and the recent sequencing of its macronuclear genome revealed one of the largest numbers of genes in any eukaryote. Together with the development of new molecular techniques, including complementation cloning and an easily implemented technique for reverse genetics based on RNA interference (RNAi), these features make P. tetraurelia a very attractive unicellular model.
Measurement of Free Ca2+ Concentration in the Lumen of Neuronal Endoplasmic Reticulum
Authors: Solovyova Natasha , Verkhratsky Alexei 
Published: January 2010

INTRODUCTIONThis protocol describes a technique for the simultaneous monitoring of free calcium concentrations in the cytosol ([Ca2+]i) and within the lumen of the endoplasmic reticulum (ER) ([Ca2+]L) of cultured/freshly isolated dorsal root ganglia (DRG) neurons. The method uses two synthetic fluorescent Ca2+ probes (fluo-3 and mag-fura-2) in combination with fluorescence microscopy and a whole-cell patch-clamp technique. This approach has been used successfully in acutely isolated/cultured DRG neurons, in Purkinje neurons, acutely isolated from cerebellar slices, and in cultured astrocytes. In this protocol, isolated neurons are first loaded with the membrane-permeant, low-affinity Ca2+ indicator, mag-fura-2, which preferentially, though not exclusively, accumulates in the ER. Cells are then loaded with the membrane-impermeant, high-affinity calcium indicator fluo-3 using the whole-cell patch-clamp configuration. This second loading removes the majority of cytosolic mag-fura-2, replacing it with fluo-3. Mag-fura-2 and fluo-3 signals can be separated by virtue of their distinct excitation properties (340 nm and 380 nm for mag-fura-2, and 488 nm for fluo-3). An equation is provided to determine [Ca2+]L values using the 340/380 nm ratio.
Rabbit Mating and Embryo Isolation
Authors: Püschel Bernd , Viebahn Christoph 
Published: January 2010

INTRODUCTIONThis protocol describes how to generate and collect rabbit embryos of defined developmental stages for experiments such as live embryo micromanipulation and culture or whole-mount in situ hybridization and immunofluorescence. Most values and measurements given in the procedure are optimally suited for the New Zealand White strain (the most commonly used strain because of its relatively large size and therefore large blood volumes for polyclonal antiserum collection). Successful embryo generation and isolation depend on a well-equipped animal care facility and dedicated veterinary care.
Live Rabbit Embryo Culture: Figure 1.
Authors: Püschel Bernd , Bitzer Eva , Viebahn Christoph 
Published: January 2010

INTRODUCTIONThis protocol outlines methods for culturing rabbit embryos. Such cultures can be used to study the impact of micromanipulation, transplantation, and the influence of signaling molecules on embryonic development. They can be performed on whole blastocysts submerged in culture medium (suspension culture) or on explanted parts of the embryo spread out on a semisolid agarose support (flat or ring culture). Cultures can be adapted to many desired growth conditions by varying the parameters, but culture length is limited to ~24 h because longer incubation times lead either to bursting of the blastocyst and subsequent rolling up of the embryonic disc or to inadequate growth, resulting in deformed embryos.
Staining and Imaging of Live Rabbit Embryos: Figure 1.
Authors: Püschel Bernd , Viebahn Christoph 
Published: January 2010

INTRODUCTIONThis protocol describes methods for supravital labeling of cellular proliferation and movement in rabbit embryos as well as for imaging of live cell movements. The techniques use localized labeling of epiblast cells with DiI by injection or by using comprehensive nuclear staining of all cell layers before and during early gastrulation. Because rabbit embryos implant relatively late during embryonic development, gastrulation-stage embryos can be isolated by flushing them from the uterus. Moreover, the embryonic disc is flat and translucent, providing a direct uncompromised overview of gastrulation while the whole blastocyst is protected by the zona pellucida. These properties allow examination of whole blastocysts either under the impact of changing environmental conditions (e.g., medium additives, oxygen concentrations) or following mechanical manipulation of the embryonic disc using a needle penetrating the zona pellucida. Further manipulation (e.g., transplantation) can be performed after removing the embryo from the zona and explantation of the embryonic disc. These techniques allow embryonic growth centers to be identified and single-cell movements to be recorded.
Whole-Mount In Situ Immunofluorescence of Early Rabbit Embryos
Authors: Püschel Bernd , Viebahn Christoph 
Published: January 2010

INTRODUCTIONIn this procedure for whole-mount immunostaining of early rabbit embryos, embryonic tissues are immersed in a small volume of buffer containing detergents to permeabilize tissues and the cells, allowing antibodies access to intracellular structures. This method allows the detection of specific cell types and the identification of subcellular characteristics. Correlating the position of the cells of interest with the stage of development allows conclusions to be drawn as to cell differentiation and embryonic development. This method can be applied to rabbit embryos from the early cleavage stages up to neurulating embryos at day 8 of embryonic development.
Artificial Insemination in Rabbits
Authors: Daniel Nathalie , Renard Jean-Paul 
Published: January 2010

INTRODUCTIONArtificial insemination (AI) is used in rabbit husbandry to improve breeding management. Conception rates after AI with fresh semen are equivalent to or even better than those obtained by natural mating. Also, AI has the advantage of avoiding contact between animals. Furthermore, AI with frozen sperm is particularly useful for assisted reproduction and conservation of rabbit genetic resources, and in some cases, frozen semen produce results similar to those obtained in AI using fresh sperm. This protocol describes the most commonly used protocol for AI using fresh sperm.
Immunocytochemistry of Paramecium Cytoskeletal Structures
Authors: Beisson Janine , Bétermier Mireille , Bré Marie-Hélène , Cohen Jean , Duharcourt Sandra , Duret Laurent , Kung Ching , Malinsky Sophie , Meyer Eric , Preer John R. , Sperling Linda 
Published: January 2010

INTRODUCTIONParamecium has a highly complex cellular structure. The cytoskeleton of these organisms interacts with cilia at the cell surface to control cell movement, feeding, and environmental responses. Basal bodies anchored in the cortex organize the cytoskeleton and determine cell shape, and a conspicuous cytoskeletal network, the infraciliary lattice, underlies the cell surface and plays an important role in cellular Ca2+ homeostasis. This protocol describes methods to visualize the cytoskeleton, especially cortical structures. It is not directly applicable for visualization of membrane proteins.
Preparation and Culture of Limb Blastema Stem Cells from Regenerating Larval and Adult Salamanders
Authors: Kumar Anoop , Godwin James W. 
Published: January 2010

INTRODUCTIONAdult salamanders show extensive ability to regenerate their body parts, and this can be attributed at least in part to their cellular plasticity. Cell reprogramming, dedifferentiation, proliferation and redifferentiation occur naturally in adult salamanders in response to tissue damage or removal. Limb regeneration proceeds by mesenchymal dedifferentiation and cell migration at the end of the stump. This generates a cohort of mesenchymal stem cells called blastema cells, which accumulate under the wound epithelium. The “limb blastema” is an autonomous structure that retains the positional identity of its location of origin as well as morphogenetic cues for reconstructing a new limb. At the cellular level, blastema stem cells maintain characteristics such as positional memory derived from their location, while expressing new markers relevant to the process of limb regeneration. In this protocol, a nonenzymatic method is described for the dissociation of blastema stem cells from newts (Notophthalmus viridescens) and axolotls (Ambystoma mexicanum).
Using the Metagenomics RAST Server (MG-RAST) for Analyzing Shotgun Metagenomes
Authors: Glass Elizabeth M. , Wilkening Jared , Wilke Andreas , Antonopoulos Dionysios , Meyer Folker 
Published: January 2010

INTRODUCTIONShotgun metagenomics creates millions of fragments of short DNA reads, which are meaningless unless analyzed appropriately. The Metagenomics RAST server (MG-RAST) is a web-based, open source system that offers a unique suite of tools for analyzing these data sets. After de-replication and quality control, fragments are mapped against a comprehensive nonredundant database (NR). Phylogenetic and metabolic reconstructions are computed from the set of hits against the NR. The resulting data are made available for browsing, download, and most importantly, comparison against a comprehensive collection of public metagenomes. A submitted metagenome is visible only to the user, unless the user makes it public or shares with other registered users. Public metagenomes are available to all.
Dual-Color ELISPOT Assay for the Simultaneous Detection of IL-2 and/or IFN-γ Secreting T Cells
Authors: Boulet Salix , Ndongala Michel L. , Bernard Nicole F. 
Published: January 2010

INTRODUCTIONThe enzyme-linked immunospot (ELISPOT) assay measures the secretion intensity of effector molecules released by immune cells in response to ex vivo antigenic stimulation, as well as the frequency of these responding cells. This assay is highly sensitive, quantitative, easy to use, and amenable to high-throughput screening. For these reasons, the ELISPOT assay is considered by many as a gold standard for monitoring cellular immune responses. Until recently, ELISPOT assays using chromophores to detect the T cell secretion of cytokines were limited to the characterization of a single effector molecule. Notably, studies evaluating the immune response to chronic viral infections often measured IFN-γ secretion by ELISPOT because of the known antiviral effects of this cytokine as well as its correlation to the cytotoxic capacity of T cells. However, maintenance of both IFN-γ and IL-2 secretion by pathogen-specific T cells has been linked to a more favorable clinical outcome in human immunodeficiency virus (HIV) and Leishmania infections. Therefore, an ELISPOT assay able to simultaneously characterize T cell responses in terms of IL-2 and IFN-γ secretion is potentially relevant for the monitoring of immune responses to certain infectious agents. In this protocol, we describe an ELISPOT assay for the simultaneous detection of IL-2 and IFN-γ upon stimulation with viral peptides.
The conflation of ignorance and knowledge in the inference of clade posteriors
Authors: Randle Christopher P. , Pickett Kurt M. 
Published: January 2010

AbstractThe objective Bayesian approach relies on the construction of prior distributions that reflect ignorance. When topologies are considered equally probablea priori, clades cannot be. Shifting justifications have been offered for the use of uniform topological priors in Bayesian inference. These include: (i) topological priors do not inappropriately influence Bayesian inference when they are uniform; (ii) although clade priors are not uniform, their undesirable influence is negated by the likelihood function, even when data sets are small; and (iii) the influence of nonuniform clade priors is an appropriate reflection of knowledge. The first two justifications have been addressed previously: the first is false, and the second was found to be questionable. The third and most recent justification is inconsistent with the first two, and with the objective Bayesian philosophy itself. Thus, there has been no coherent justification for the use of nonflat clade priors in Bayesian phylogenetics. We discuss several solutions: (i) Bayesian inference can be abandoned in favour of other methods of phylogenetic inference; (ii) the objective Bayesian philosophy can be abandoned in favour of a subjective interpretation; (iii) the topology with the greatest posterior probability, which is also the tree of greatest marginal likelihood, can be accepted as optimal, with clade support estimated using other means; or (iv) a Bayes factor, which accounts for differences in priors among competing hypotheses, can be used to assess the weight of evidence in support of clades. ©The Willi Hennig Society 2009
Population size of lions in Yankari Game Reserve as revealed by faecal DNA sampling
Authors: Tende Talatu , Ottosson Ulf , Hansson Bengt , Åkesson Mikael , Bensch Staffan 
Published: January 2010

AbstractStudies have shown that lion (Panthera leo) populations in West Africa are small, isolated and fragmented. In Nigeria, lions have disappeared from unprotected areas and are nowadays found only in parks and reserves where these populations may still decline. It is therefore urgent to obtain reliable estimates of population sizes at different localities. Direct observational surveys may either fail to count all individuals or count some individuals repeatedly and are therefore associated with unknown levels of estimation errors. More accurate estimates can be obtained if direct counting is combined with DNA‐based individual identification. As lions are difficult to identify individually, presented here is a method that can be a valuable addition to the existing census methods.
Systematic review: the effects of carbonated beverages on gastro‐oesophageal reflux disease
Authors: JOHNSON T. , GERSON L. , HERSHCOVICI T. , STAVE C. , FASS R. 
Published: January 2010

Aliment Pharmacol Ther 31, 607–614SummaryBackground  Carbonated beverages have unique properties that may potentially exacerbate gastro‐oesophageal reflux disease (GERD), such as high acidity and carbonation. Cessation of carbonated beverage consumption is commonly recommended as part of lifestyle modifications for patients with GERD.Aims  To evaluate the relationship of carbonated beverages with oesophageal pH, oesophageal motility, oesophageal damage, GERD symptoms and GERD complications.Methods  A systematic review.Results  Carbonated beverage consumption results in a very short decline in intra‐oesophageal pH. In addition, carbonated beverages may lead to a transient reduction in lower oesophageal sphincter basal pressure. There is no evidence that carbonated beverages directly cause oesophageal damage. Carbonated beverages have not been consistently shown to cause GERD‐related symptoms. Furthermore, there is no evidence that these popular drinks lead to GERD complications or oesophageal cancer.Conclusions  Based on the currently available literature, it appears that there is no direct evidence that carbonated beverages promote or exacerbate GERD.
Does strong selection promote host specialisation and ecological speciation in insect herbivores? Evidence from Neochlamisus leaf beetles
Authors: FUNK DANIEL J. 
Published: January 2010

1. Outstanding issues in evolutionary ecology include: (1) the prevalence of host‐associated ecological specialisation among herbivorous insects, and (2) the speciation processes contributing to the tremendous species‐level diversity of herbivores.2. Neochlamisus leaf beetle species are generally monophagous, but cumulatively employ a disparate array of host plants. These patterns occur in microcosm within the putatively oligophagous Neochlamisus bebbianae, which uses specific host species within each of six plant genera representing five families. I refer to all beetle populations associated with any one of these hosts as a particular ‘host form’.3. This paper describes aspects of Neochlamisus biology and some experimental findings relevant to both host‐use evolution and host specialisation in Neochlamisus, and to ecological divergence, reproductive isolation, and genetic differentiation among N. bebbianae host forms. It thereby reviews a research programme focused on ecological speciation.4. With respect to these host forms, our findings include: (1) ubiquitous host specialisation, (2) constraints on ‘multitasking’ that select for host specialisation, (3) ubiquitous ecological divergence, (4) pre‐ and post‐mating reproductive barriers, (5) genetic and environmental contributions to ecological divergence and reproductive isolation, (6) positive statistical associations between ecological divergence and reproductive isolation, (7) strongly differentiated loci despite gene flow, reflecting divergent host‐related selection, and (8) possible host race formation. We additionally describe a unique example of intimate host adaptation in another species, Neochlamisus platani.5. The intimate and discrete nature of herbivore–host associations may generate unusually strong (host‐related) selection that could simultaneous explain pronounced rates of herbivore specialisation and speciation.
DNA profiling of host–herbivore interactions in tropical forests
Authors: NAVARRO SARA PINZÓN , JURADO‐RIVERA JOSÉ A. , GÓMEZ‐ZURITA JESÚS , LYAL CHRISTOPHER H. C. , VOGLER ALFRIED P. 
Published: January 2010

1. The diversity of insects in tropical forests remains poorly known, in particular regarding the critical feeding associations of herbivores, which are thought to drive species richness in these ecosystems.2. Host records remain elusive and traditionally require labour‐intensive feeding trials. A recent approach analyses plant DNA ingested by herbivorous insects; direct PCR amplification from DNA extracts from weevils (Curculionoidea) using chloroplast (trnL intron) primers was successful in 41 of 115 cases, resulting in 40 different sequences.3. The resulting trnL intron sequences were identified against public databases to various hierarchical levels based on their position in phylogenetic trees and shown to be members of 26 plant families from different major groups of angiosperms.4. Among the trnL intron sequences, seven pairs or triplets of close relatives (0–2 bp difference) were found which may represent intraspecific variation in the respective host plants.5. Molecular clock calibrations of mitochondrial cox1 sequences of weevils established great distances of lineages obtained (all splits estimated >20 Mya). Distant taxa were found to feed on the same or similar hosts in some cases, showing low evolutionary conservation of host associations among deeper levels.6. The technique provides a new means of studying species diversity and plant–herbivore interactions in tropical forests, and removes the constraints of the need for actual observations of feeding in ecological and evolutionary studies.