bluuebunny/crossref_metadata_2025_split huggingface dataset:
Delivery of Small Interfering RNA (siRNA) Using the Sleeping Beauty Transposon: Figure 1.
Authors: Fletcher Bradley S. 
Published: November 2010

INTRODUCTIONRNA interference (RNAi) is an evolutionarily conserved process that silences gene expression through double-stranded RNA species in a sequence-specific manner. Small interfering RNAs (siRNAs) can promote sequence-specific degradation and/or translational repression of target RNA by activation of the RNA-induced silencing complex (RISC). Traditionally, silencing in mammalian cells had been achieved by transfection of synthetically derived siRNA duplexes, resulting in transient gene suppression of the target sequence. As the technology was advanced, inhibitory short-hairpin-shaped RNAs (shRNAs) could be produced by transcription from RNA polymerase-III (pol-III)-driven promoters, such as H1, U6, or cytomegalovirus (CMV)-enhanced pol III promoters. Following transcription, the shRNAs are processed by the enzyme Dicer into active siRNA. This approach allows for the continuous production of siRNA within cells using a DNA template and offers increased options for delivery of the pol-III-driven transcriptional units. A number of different viral vectors, as well as plasmid DNAs, have been utilized to deliver shRNA to mammalian cells. Here, the Tc1/mariner DNA transposon Sleeping Beauty (SB) is used as a tool to deliver shRNA-encoding transcriptional units. The SB transposon system uses a “cut-and-paste” mechanism to insert the transposon into random TA dinucleotides within the target genome. The shRNAs are then processed and used for gene knockdown.
Culturing the Antarctic Nematode Plectus murrayi
Authors: Adhikari Bishwo N. , Tomasel Cecilia M. , Li Grace , Wall Diana H. , Adams Byron J. 
Published: November 2010

INTRODUCTIONThe Antarctic terrestrial nematode Plectus murrayi is an excellent model organism for the study of stress response mechanisms in various types of environmental conditions. In this procedure, we describe a method for culturing P. murrayi extracted from soil and sediment samples from the McMurdo (MCM) Dry Valleys of Antarctica. Nematodes are cultured on sand agar plates and incubated at various temperatures, and feed on bacteria growing on the agar media. They can be subcultured and stored at 15°C for >2 mo. This method is easy to carry out and can produce nematodes in quantities sufficient for ecological and molecular studies.
Array Tomography: Rodent Brain Fixation and Embedding
Authors: Micheva Kristina D. , O’Rourke Nancy , Busse Brad , Smith Stephen J. 
Published: November 2010

INTRODUCTIONArray tomography is a volumetric microscopy method based on physical serial sectioning. Ultrathin sections of a plastic-embedded tissue are cut using an ultramicrotome, bonded in an ordered array to a glass coverslip, stained as desired, and imaged. The resulting two-dimensional image tiles can then be reconstructed computationally into three-dimensional volume images for visualization and quantitative analysis. The minimal thickness of individual sections permits high-quality rapid staining and imaging, whereas the array format allows reliable and convenient section handling, staining, and automated imaging. Also, the physical stability of the arrays permits images to be acquired and registered from repeated cycles of staining, imaging, and stain elution, as well as from imaging using multiple modalities (e.g., fluorescence and electron microscopy). Array tomography makes it possible to visualize and quantify previously inaccessible features of tissue structure and molecular architecture. However, careful preparation of the tissue is essential for successful array tomography; these steps can be time-consuming and require some practice to perfect. This protocol describes the fixation and processing required to prepare tissues for immunofluorescence array tomography.
Array Tomography: Production of Arrays
Authors: Micheva Kristina D. , O’Rourke Nancy , Busse Brad , Smith Stephen J. 
Published: November 2010

INTRODUCTIONArray tomography is a volumetric microscopy method based on physical serial sectioning. Ultrathin sections of a plastic-embedded tissue are cut using an ultramicrotome, bonded in an ordered array to a glass coverslip, stained as desired, and imaged. The resulting two-dimensional image tiles can then be reconstructed computationally into three-dimensional volume images for visualization and quantitative analysis. The minimal thickness of individual sections permits high-quality rapid staining and imaging, whereas the array format allows reliable and convenient section handling, staining, and automated imaging. Also, the physical stability of the arrays permits images to be acquired and registered from repeated cycles of staining, imaging, and stain elution, as well as from imaging using multiple modalities (e.g., fluorescence and electron microscopy). Array tomography makes it possible to visualize and quantify previously inaccessible features of tissue structure and molecular architecture. However, careful preparation of the tissue is essential for successful array tomography; these steps can be time consuming and require some practice to perfect. This protocol describes the sectioning of embedded tissues and the mounting of the serial arrays. The procedures require some familiarity with the techniques used for ultramicrotome sectioning for electron microscopy.
Array Tomography: Immunostaining and Antibody Elution
Authors: Micheva Kristina D. , O’Rourke Nancy , Busse Brad , Smith Stephen J. 
Published: November 2010

INTRODUCTIONArray tomography is a volumetric microscopy method based on physical serial sectioning. Ultrathin sections of a plastic-embedded tissue are cut using an ultramicrotome, bonded in an ordered array to a glass coverslip, stained as desired, and imaged. The resulting two-dimensional image tiles can then be reconstructed computationally into three-dimensional volume images for visualization and quantitative analysis. The minimal thickness of individual sections permits high-quality rapid staining and imaging, whereas the array format allows reliable and convenient section handling, staining, and automated imaging. Also, the physical stability of the arrays permits images to be acquired and registered from repeated cycles of staining, imaging, and stain elution, as well as from imaging using multiple modalities (e.g., fluorescence and electron microscopy). Array tomography makes it possible to visualize and quantify previously inaccessible features of tissue structure and molecular architecture. However, careful preparation of the tissue is essential for successful array tomography; these steps can be time-consuming and require some practice to perfect. In this protocol, tissue arrays are prepared for imaging by tagging with primary antibodies against specific cellular targets, followed by labeling with fluorescent secondary antibodies. Alternatively, fluorescent proteins that have been introduced into the tissue before dissection can be used.
Array Tomography: Semiautomated Image Alignment
Authors: Micheva Kristina D. , O’Rourke Nancy , Busse Brad , Smith Stephen J. 
Published: November 2010

INTRODUCTIONArray tomography is a volumetric microscopy method based on physical serial sectioning. Ultrathin sections of a plastic-embedded tissue are cut using an ultramicrotome, bonded in an ordered array to a glass coverslip, stained as desired, and imaged. The resulting two-dimensional image tiles can then be reconstructed computationally into three-dimensional volume images for visualization and quantitative analysis. The minimal thickness of individual sections permits high-quality rapid staining and imaging, whereas the array format allows reliable and convenient section handling, staining, and automated imaging. Also, the physical stability of the arrays permits images to be acquired and registered from repeated cycles of staining, imaging, and stain elution, as well as from imaging using multiple modalities (e.g., fluorescence and electron microscopy). Array tomography makes it possible to visualize and quantify previously inaccessible features of tissue structure and molecular architecture. However, careful preparation of the tissue is essential for successful array tomography; these steps can be time-consuming and require some practice to perfect. Successful array tomography requires that the captured images be properly stacked and aligned, and the software to achieve these ends is freely available. This protocol describes the construction of volumetric image stacks from images of fluorescently labeled arrays for three-dimensional image visualization, analysis, and archiving.
Constructing and Expressing Fluorescent Protein Fusions
Authors: Spector David L. , Goldman Robert D. 
Published: November 2010

INTRODUCTIONFluorescent protein fusions (FPFs) have been used to address a wide range of questions in individual cells as well as in specific tissues of a particular organism. However, investigators must take extreme care when using FPFs to ensure that the resultant fusion protein is expressed at or close to the endogenous level of the parent protein, and also that it is full length, localizes correctly, and behaves normally once incorporated in the cell. Because the molecular mass of the fluorescent protein (FP) itself is 27 kDa, one must consider the potential effects of placing such a large tag in association with a protein under investigation. This article discusses how these goals can be achieved and provides examples to assist the investigator in designing and implementing experiments using FPFs.
Spinning-Disk Microscopy Systems
Authors: Wilson Tony 
Published: November 2010

INTRODUCTIONThe popularity of the confocal microscope in life science laboratories around the world is undoubtedly due to its ability to permit volume objects to be imaged and to be rendered in three dimensions. It is important to realize that the confocal microscope itself does not produce three-dimensional images. Indeed, it does the opposite. The critical property that the confocal microscope possesses, which the conventional microscope does not, is its ability to image efficiently (and in-focus) only those regions of a volume specimen that lie within a thin section in the focal region of the microscope. In other words, it is able to reject (i.e., vastly attenuate) light originating from out-of-focus regions of the specimen. To image a three-dimensional volume of a thick specimen, it is necessary to take a whole series of such thin optical sections as the specimen is moved axially through the focal region. Once this through-focus series of optically sectioned images has been recorded, it is a matter of computer processing to decide how the three-dimensional information is to be presented. There are many methods for producing optical sections, of which the confocal optical system is just one. This article reviews these methods and describes a number of convenient methods of implementation that can lead to, among other things, real-time image formation.
Array Tomography: High-Resolution Three-Dimensional Immunofluorescence
Authors: Micheva Kristina D. , O’Rourke Nancy , Busse Brad , Smith Stephen J. 
Published: November 2010

INTRODUCTIONArray tomography, which is described in this article, is a volumetric microscopy method based on physical serial sectioning. Ultrathin sections of a plastic-embedded tissue are cut using an ultramicrotome, bonded in an ordered array to a glass coverslip, stained as desired, and imaged. The resulting two-dimensional image tiles can then be reconstructed computationally into three-dimensional volume images for visualization and quantitative analysis. The minimal thickness of individual sections permits high-quality rapid staining and imaging, whereas the array format allows reliable and convenient section handling, staining, and automated imaging. Also, the physical stability of the arrays permits images to be acquired and registered from repeated cycles of staining, imaging, and stain elution, as well as from imaging using multiple modalities (e.g., fluorescence and electron microscopy). Although the fabrication procedures can be relatively difficult, the high resolution, depth invariance, and molecular discrimination offered by array tomography justify the effort involved. Array tomography makes it possible to visualize and quantify previously inaccessible features of tissue structure and molecular architecture.
A COVERING PROJECTION FOR ROBOT NAVIGATION UNDER STRONG ANISOTROPY
Authors: ANGHINOLFI ANDREA , COSTA LUCA , FERRI MASSIMO , VIARANI ENRICO 
Published: November 2010

Path planning can be subject to different types of optimization. Some years ago a German researcher, U. Leuthäusser, proposed a new variational method for reducing most types of optimization criteria to one and the same: minimization of path length. This can be done by altering the Riemannian metric of the domain, so that optimal paths (with respect to whatever criterion) are simply seen as shortest. This method offers an extra feature, which has not been exploited so far: it admits direction–dependent criteria. In this paper we make this feature explicit, and apply it to two different anisotropic settings. One is that of different costs for different directions: E.g. the situation of a countryside scene with ploughed fields. The second is dependence on oriented directions, which is called here "strong" anisotropy: the typical scene is that of a hill side. A covering projection solves the additional difficulty. We also provide some experimental results on synthetic data.
CONSTRAINED POINT-SET EMBEDDABILITY OF PLANAR GRAPHS
Authors: DI GIACOMO EMILIO , DIDIMO WALTER , LIOTTA GIUSEPPE , MEIJER HENK , WISMATH STEPHEN K. 
Published: November 2010

This paper starts the investigation of a constrained version of the point-set embed-dability problem. Let G = (V,E) be a planar graph with n vertices, G′ = (V′,E′) a subgraph of G, and S a set of n distinct points in the plane. We study the problem of computing a point-set embedding of G on S subject to the constraint that G′ is drawn with straight-line edges. Different drawing algorithms are presented that guarantee small curve complexity of the resulting drawing, i.e. a small number of bends per edge. It is proved that: • If G′ is an outerplanar graph and S is any set of points in convex position, a point-set embedding of G on S can be computed such that the edges of E\E′ have at most 4 bends each. • If S is any set of points in general position and G′ is a face of G or if it is a simple path, the curve complexity of the edges of E\E′ is at most 8. • If S is in general position and G′ is a set of k disjoint paths, the curve complexity of the edges of E \ E′ is O(2k).
On Equivalence of Some Iterations Convergence for Quasi-Contraction Maps in Convex Metric Spaces
Authors: Xue Zhiqun , Lv Guiwen , Rhoades BE 
Published: November 2010

AbstractWe show the equivalence of the convergence of Picard and Krasnoselskij, Mann, and Ishikawa iterations for the quasi-contraction mappings in convex metric spaces.
Extracranial venous stenosis is an unlikely cause of multiple sclerosis
Authors: Yamout Bassem , Herlopian Aline , Issa Zeinab , Habib Robert H , Fawaz Ahmad , Salame Joseph , Wadih Antoine , Awdeh Haytham , Muallem Nadime , Raad Roy , Al-Kutoubi Aghiab 
Published: November 2010

Background: Extracranial venous stenosis (EVS) has recently been implicated as the primary cause of multiple sclerosis (MS). Objective: The aim of this study was to determine the presence of EVS in MS patients. Methods: We performed selective extracranial venography on 42 patients with early MS (EMS): clinically isolated syndrome (CIS) or relapsing—remitting MS (RRMS) of less than 5 years duration, and late MS (LMS): RRMS of more than 10 years duration. Magnetic resonance imaging (MRI) and clinical relapse data were reviewed for all patients with EVS. Results: EVS was present in 7/29 patients with EMS and 12/13 patients with LMS, a highly significant statistical difference ( p< 0.001). Only 3/42 patients (all in the LMS group) had two vessel stenoses, while the rest had only one vessel involved. EVS was seen in 1/11 patients with CIS compared with 6/18 RRMS patients of less than 5 years duration. Disease duration was greater in patients with EVS overall ( p < 0.005). LMS remained an independent predictor of EVS following multivariate adjustment for gender, age at disease onset and Expanded Disability Status Scale (EDSS) (Adjusted Odds Ratio = 29 (3—298); p = 0.005]. Within the EMS group, patients with ( n = 7) and without ( n = 22) EVS had similar EDSS and disease duration, suggesting similar disease severity. No clear correlation could be found between site of EVS and anatomic localization of either clinical relapses or MRI gadolinium-enhancing lesions. Conclusions: We conclude that EVS is an unlikely cause of MS since it is not present in most patients early in the disease and rarely involves more than one extracranial vein. It is likely to be a late secondary phenomenon.
Application of Water-Soluble Titanium Complexes as Precursors for Synthesis of Titanium-Containing Oxides via Aqueous Solution Processes
Authors: Kakihana Masato , Kobayashi Makoto , Tomita Koji , Petrykin Valery 
Published: November 2010

Abstract
The growing significance of nanocrystalline inorganic functional materials in the fields of catalysis, electronics, and energy conversion together with the increasing demand of the society for safer, softer, and “greener” technologies has drawn considerable attention of the researchers toward water-based solution processes for synthesis of such materials. In this respect complex oxides, containing d0-transition metals, such as Ti, Nb, Ta, or Si represent an outstanding challenge for materials chemists due to the extremely narrow range or almost complete absence of suitable precursor compounds compatible with aqueous systems. In the recent 10 years, a remarkable progress has been achieved in the development of new water-soluble complexes of titanium and considerable experience was accumulated in the application of these compounds for synthesis of nanocrystalline titanium-containing materials. The essential knowledge of coordination chemistry of such water-soluble titanium complexes is reviewed in this work, which succeeded to identify the key structural features responsible for stability of the compounds against hydrolysis and to provide guidelines for synthesis of these complexes. Finally, an extensive overview of highly selective aqueous solution based synthesis of TiO2 polymorphs as well as complex oxide materials with the help of the novel water-soluble titanium complexes is provided.
Synthesis of New Thiophene-Based π-Conjugated Organic Compounds and Polymer
Authors: Usui Motoaki , Fukumoto Hiroki , Yamamoto Takakazu 
Published: November 2010

Abstract
p-Dibromobenzenes and p-phenylenediboronate with π-conjugated bithiophene and terthiophene arms were synthesized. They showed UV–vis absorption peaks in the range of 376–417 nm. p-Phenylenediboronate with bithiophene arms were used for synthesis of a new π-conjugated polymer consisting of isothianaphthene and the p-phenylene units with π-conjugated bithiophene side chains.
Multivariate Optimization Strategies in the Development of an Electroanalytical Method for the Assay of Metoclopramide Using Mercury-Film-Modified Carbon Nanotube Paste Electrode
Authors: Mendes Camila Bitencourt , Andrade Felipe Nascimento , Segatelli Mariana Gava , Pereira Arnaldo César , Dragunski Douglas Cardoso , Tarley César Ricardo Teixeira 
Published: November 2010

Abstract
The present work describes an electroanalytical method based on adsorptive preconcentration of metoclopramide (MCP) onto mercury-film-modified carbon nanotube paste electrode followed by anodic stripping measures. The method presented a good linear range from 2.0 up 100 µmol L−1 (r = 0.998) and a limit of detection of 0.51 µmol L−1. The determination of MCP was successfully carried out in solid and liquid pharmaceutical formulations, as well as in urine samples without intense sample treatment.
Aggregation and Adsorption Behaviors of Sodium Deoxycholate in Water–Ethylene Glycol Medium
Authors: Das Sujit , Thapa Uttam , Ismail Kochi 
Published: November 2010

Abstract
Critical micelle concentrations (cmcs) of sodium deoxycholate (SDC) were determined at 25 °C in water + ethylene glycol (EG) medium (mass fraction of EG, wEG × 102 = 0, 10, 20, 30, 40, 50, and 60) by measuring surface tension, fluorescence emission intensities of pyrene probe, and conductance. Cmc was also determined in the presence of NaCl from the surface tension isotherms, and counter ion binding constants (β) of SDC were evaluated by applying the Corrin–Harkins equation and slope-ratio method. The value of β in water is about 0.18 and becomes almost half of this value in water + EG. Surface excess at the cmc decreases as the EG amount increases, but increases on adding NaCl. Gordon parameter and ratio of surface tension of the medium to that of the surfactant solution at the cmc are used to represent solvophobicity.
Total Syntheses of Sterically Locked Phycocyanobilin Derivatives Bearing a 15Z-anti or a 15E-anti CD-Ring Component
Authors: Nishiyama Kaori , Kamiya Ayumi , Hammam Mostafa A S , Kinoshita Hideki , Fujinami Shuhei , Ukaji Yutaka , Inomata Katsuhiko 
Published: November 2010

Abstract
Total syntheses of sterically locked phycocyanobilin derivatives with a 15Z-anti or a 15E-anti CD-ring component were performed toward elucidation of the stereochemistry and function of the chromophore in phytochromes. In the course of the construction of a sterically locked 15E-anti CD-ring component employing 5-tosylpyrrolin-2-one derivatives as the D-ring, the Ts group was found to be rearranged under acidic conditions to give a mixture of regioisomers, both of which could be transformed into the same CD-ring precursor via detosylation with a base followed by Wittig-like coupling reaction. In addition, a sterically locked 15E-anti biliverdin derivative was also synthesized.
Two-Dimensional Melting and Phase Change of Binary Mixtures of CCl4 and CHCl3 Confined in ACF Nanospace Studied Using Solid-State 1H NMR
Authors: Ueda Takahiro , Omichi Hiroaki , Chen Yu , Kobayashi Hirokazu , Kubota Osamu , Miyakubo Keisuke , Eguchi Taro 
Published: November 2010

Abstract
Two-dimensional melting and phase changes of binary mixtures of CCl4 and CHCl3 confined in activated carbon fiber were examined using differential thermal analysis and 1H wide-line NMR. Molecular assembly of CCl4 confined in ACF nanospace with a slit width of 1.1 nm showed succeeding thermal anomalies corresponding to crystal–hexatic and hexatic–liquid transitions. Results showed that these thermal anomalies did not occur in a mixture of CHCl3 and CCl4. This behavior differed greatly from the phase diagram for the bulk mixture between CHCl3 and CCl4. Furthermore, the dynamic features of CHCl3 molecule were examined using the 1H wide-line NMR spectrum. The activation energy of the hopping motion changed from 7 kJ mol−1 for pure CHCl3 to 13 kJ mol−1 for CHCl3 with a 0.016 molar ratio in CCl4. In particular, a drastic increase in the activation energy was observed for doping with a trace amount of CHCl3, suggesting that molecular self-assembly of CCl4 takes place in the ACF nanoslit because of the effective intermolecular interaction between CCl4 molecules. The existence of CHCl3 in CCl4 brings about the remarkable impurity effect on two-dimensional melting and phase transition of CCl4 confined in ACF nanospace.