bluuebunny/crossref_metadata_2025_split huggingface dataset:
Tissue Collection for Systematic Phenotyping in the Mouse
Authors: Antal Cristina , Teletin Marius , Wendling Olivia , Dgheem Mounzer , Auwerx Johan , Mark Manuel 
Published: October 2007

AbstractIn this unit, a procedure for post‐mortem examination of mice and tissue collection is provided. This procedure is performed for post‐mortem analysis of anatomical defects (necropsy) and histological analysis and/or tissue collection destined for molecular biology applications. In both cases, tissue preservation is the major issue, but the way to achieve it depends on the objective. When histological analysis is the aim, tissue preservation is achieved by rapid transfer into fixative solutions. In contrast, molecular biology applications require rapid freezing of tissue samples to preserve mRNA integrity. Consequently, performing both procedures simultaneously may be at the expense of the final product quality. Curr. Protoc. Mol. Biol. 80:29A.4.1‐29A.4.23. © 2007 by John Wiley & Sons, Inc.
Overview of Genetic Diagnosis in Cancer
Authors: Korf Bruce , M. Mikhail Fady 
Published: October 2007

AbstractBoth cytogenetic and molecular genetic studies can contribute to the management of patients with cancer. In some cases genetic markers are specific to particular tumor types and are useful in diagnosis. This can be helpful in distinguishing histologically similar tumors that may respond differently to treatment and can sometimes be of prognostic value. Genetic markers can also be tools for following the response of a tumor to therapy, providing a sensitive means of detection of relapse. This introductory unit considers some of the types of genetic changes that occur in association with malignancies and major approaches used in their detection. Curr. Protoc. Hum. Genet. 55:10.1.1‐10.1.8. © 2007 by John Wiley & Sons, Inc.
Flow Cytometric Sorting of Bacterial Surface‐Displayed Libraries
Authors: Kenrick Sophia , Rice Jeffrey , Daugherty Patrick 
Published: October 2007

AbstractThe protocols herein detail methods for isolating binding peptides from a combinatorial library displayed on the surface of bacterial cells. These methods are appropriate for a variety of display scaffolds and a large range of library sizes, up to ∼5 × 109 or more. Instructions have been provided for isolating peptides that bind to both proteins and non‐protein targets, such as whole cells or inorganic particles. Qualitative analysis by flow cytometry can be exploited for bacterial libraries to characterize a displayed peptide's binding properties with a target of interest, and sorting conditions can be tuned to maximize binding affinity. Curr. Protocol. Cytom. 42:4.6.1‐4.6.27. © 2007 by John Wiley & Sons, Inc.
SYTO Probes: Markers of Apoptotic Cell Demise
Authors: Wlodkowic Donald , Skommer Joanna 
Published: October 2007

AbstractAs mechanistic studies on tumor cell death advance towards their ultimate translational goal, there is a need for specific, rapid, and high‐throughput analytical tools to detect diverse cell demise modes. Patented DNA‐binding SYTO probes, for example, are gaining increasing interest as easy‐to‐use markers of caspase‐dependent apoptotic cell death. They are proving convenient for tracking apoptosis in diverse hematopoietic cell lines and primary tumor samples, and, due to their spectral characteristics, appear to be useful for the development of multiparameter flow cytometry assays. Herein, several protocols for multiparametric assessment of apoptotic events using SYTO probes are provided. There are protocols describing the use of green fluorescent SYTO 16 and red fluorescent SYTO 17 dyes in combination with plasma membrane permeability markers. Another protocol highlights the multiparametric use of SYTO 16 dye in conjunction with the mitochondrial membrane potential sensitive probe, tetramethylrhodamine methyl ester (TMRM), and the plasma membrane permeability marker, 7‐aminoactinomycin D (7‐AAD). Curr. Protocol. Cytom. 42:7.33.1‐7.33.12. © 2007 by John Wiley & Sons, Inc.
Alternatives to Log‐Scale Data Display
Authors: Trotter Joseph 
Published: October 2007

AbstractTraditional log‐scale data display of multiparameter immunofluorescence cytometry data has several perplexing intrinsic problems that are largely mitigated by recent transformation alternatives that are log‐like at the high end of the scale, near linear at the low end of the scale, and symmetrical about zero. These alternative log‐like display transformations provide a means for better interpretation and analysis of compensated data. Curr. Protocol. Cytom. 42:10.16.1‐10.16.11. © 2007 by John Wiley & Sons, Inc.
Detecting Protein‐Protein Interactions In Vivo with FRET using Multiphoton Fluorescence Lifetime Imaging Microscopy (FLIM)
Authors: Llères David , Swift Samuel , Lamond Angus I. 
Published: October 2007

AbstractProtein interactions are critical for many processes in mammalian cells. Such interactions include the stable association of proteins within multi‐subunit complexes and the transient association of regulatory proteins. Information about protein interactions in cells has previously come from either in vitro analyses using recombinant expressed proteins, or from yeast 2–hybrid studies. A limitation of this approach is that the protein interaction is studied in isolation, without regard to the many competing protein interactions that can occur within cells. This unit presents a light microscopy approach for detecting protein‐protein interactions in vivo based on the measurement of FRET using the multiphoton fluorescence lifetime imaging microscopy (FLIM) technique. By using the FLIM‐FRET technique, the spatial organization and quantification of such interactions in a living cell can be characterized. A detailed protocol describing the complete microscope procedure and the choice of the appropriate experimental controls as well as the FRET calculations is also included. Curr. Protocol. Cytom. 42:12.10.1‐12.10.19. © 2007 by John Wiley & Sons, Inc.
Standing Wave Meters and Network Analyzers
Authors: Rolfes Ilona , Gronefeld Andreas , Schiek Burkhard 
Published: October 2007

AbstractThe sections in this article areMeasurement of Networks at Microwave FrequenciesReflection Measurement TechniquesError Models, Calibration, and Error CorrectionModern Self‐Calibration Techniques for Four‐ReceiverVNAsOutlook and Related Topics
Fullerene Polymers: Synthetic Strategies, Properties and Applications
Authors: Giacalone Francesco , Martín Nazario 
Published: October 2007

AbstractA general overview of the different C60‐containing polymers according to their chemical structure and the general synthetic routes followed for their preparation as well as their potential applications is presented. The many fullerene‐containing polymers reported in the recent literature have been classified depending upon the position of the fullerenes within the polymer chain and considering the type of chemical connectivity between them.The combination of fullerenes and polymer chemistry is a new interdisciplinary field in which all the knowledge on the synthesis and study of natural, as well as artificial macromolecules, can be applied to fullerenes to achieve novel fullerene‐based architectures. The combination of the unique properties of C60with the characteristics of well‐known polymers, often allow chemists to create new materials with combined features. In some cases, novel unprecedented properties open the doors to new realistic applications.In this article, a general overview of the different types of C60‐containing polymers according to their chemical structure and the consideration of their general synthetic routes as well as their plausible applications is given.The aim of this work is to establish a classification of the many fullerene‐containing polymers reported in the literature in order to clarify the field for all those chemists interested in the topic. Nevertheless to say that not all the examples known are covered, but those more representative or appealing for the authors. For a more comprehensive presentation the readers are referred to a recent review on the same topic.
Fundamentals of Atom Transfer Radical Polymerization
Authors: Golas Patricia L. , Mueller Laura A. , Matyjaszewski Krzysztof 
Published: October 2007

AbstractThe development of living polymerization enabled the production of polymers with precisely controlled molecular weight, narrow molecular weight distribution, and well‐defined architecture and composition. There are a number of advantages of controlled/living radical polymerization (CRP) as compared to ionic polymerization. Such advantages include applicability to a wide range of monomers and solvents, tolerance to impurities and functional groups, and ease of experimental set‐up. The most widely used CRP techniques include atom transfer radical polymerization (ATRP), nitroxide‐mediated polymerization, organometallic‐mediated radical polymerization, and degenerative transfer polymerization. In each case, control is maintained via fast dynamic equilibrium between dormant species and propagating chains. This article gives details on ATRP fundamentals, mechanistic considerations, conducting ATRP, materials, and functionality. Recent advances in catalyst design, initiation systems, and material synthesis have expanded the potential of ATRP as an environmentally benign process.
Isolation of Human Embryonic Stem Cell–Derived Teratomas for the Assessment of Pluripotency
Authors: Gertow Karin , Przyborski Stefan , Loring Jeanne F. , Auerbach Jonathan M. , Epifano Olga , Otonkoski Timo , Damjanov Ivan , Ährlund‐Richter Lars 
Published: October 2007

AbstractThis unit describes protocols on how to assess the developmental potency of human embryonic stem cells (hESCs) by performing xenografting into immunodeficient mice to induce teratoma formation. hESCs can be injected under the testis capsule, or alternatively into the kidney or subcutaneously. Teratomas that develop from grafted hESCs are surgically removed, fixed in formaldehyde, and paraffin embedded. The tissues in the teratoma are analyzed histologically to determine whether the hESCs are pluripotent and form tissues derived from of all three embryonic germ layers (ectoderm, mesoderm, and endoderm). Teratomas can also be fixed in Bouin's or cryosectioned for analysis, and they can be analyzed by immunohistochemistry for tissue markers. Methods for these procedures are included in this unit. Curr. Protoc. Stem Cell Biol. 3:1B.4.1‐1B.4.29. © 2007 by John Wiley & Sons, Inc.
Formation and Hematopoietic Differentiation of Human Embryoid Bodies by Suspension and Hanging Drop Cultures
Authors: Cerdan Chantal , Hong Seok Ho , Bhatia Mickie 
Published: October 2007

AbstractThe in vitro aggregation of human embryonic stem cells (hESCs) into clusters termed embryoid bodies (EBs) allows for the spontaneous differentiation of cells representing endoderm, mesoderm, and ectoderm lineages. This stochastic process results however, in the generation of low numbers of differentiated cells, and can be enhanced to some extent by the addition of exogenous growth factors or overexpression of regulatory genes. In the authors' laboratory, the use of hematopoietic cytokines in combination with the mesoderm inducer bone morphogenetic protein‐4 (BMP‐4) was able to generate up to 90% of CD45+ hematopoietic cells with colony‐forming unit (CFU) activity. This unit describes two protocols that have been successfully applied in the authors' laboratory for the generation of EBs in (1) suspension and (2) hanging drop (HD) cultures from enzymatically digested clumps of undifferentiated hESC colonies. Curr. Protoc. Stem Cell Biol. 3:1D.2.1‐1D.2.16. © 2007 by John Wiley & Sons, Inc.
Simple Route to Hydrophilic Microfluidic Chip Fabrication Using an Ultraviolet (UV)‐Cured Polymer
Authors: Kim S. H. , Yang Y. , Kim M. , Nam S.‐W. , Lee K.‐M. , Lee N. Y. , Kim Y. S. , Park S. 
Published: October 2007

AbstractHerein, we introduce a simple route to fabricating hydrophilic microfluidic chips with an alternative material, a UV‐cured polyurethane‐related polymer, known as Norland Optical Adhesive (NOA 63). Conventionally, polydimethylsiloxane (PDMS) is widely used to fabricate microfluidic chips as an alternative to glass or SiO2 because PDMS is easily molded and relatively cheap. However, despite these advantages, the hydrophobicity of PDMS entails critical problems when it is used in microfluidic chips because microchannels inside the microfluidic chips, which have extremely low surface tension, are difficult to fill with aqueous solution without an extra pumping system. To overcome these problems, significant efforts have been focused on developing procedures to change the PDMS surface to be hydrophilic. However, the resulting hydrophilicity is generally short‐lived and the modification procedures require cumbersome multi‐steps. In the present study, we demonstrate that microchannel‐molding and microfluidic chip construction are easier using NOA 63 than when using PDMS and that the hydrophilicity of the NOA surface, which is induced by treatment with O2 plasma, lasts longer, for at least one month. Due to the longer lasting hydrophilicity, microchannels in NOA 63 microfluidic chips are spontaneously filled with solution by capillary reaction without any extra pumping over the period. The feasibility of NOA 63‐based microfabrication is verified by demonstrating NOA 63 microfluidic platforms with antibody‐immobilized beads for immunoassays.
Poly(vinyl alcohol) Scaffolds with Tailored Morphologies for Drug Delivery and Controlled Release
Authors: Gutiérrez M. C. , García‐Carvajal Z. Y. , Jobbágy M. , Rubio F. , Yuste L. , Rojo F. , Ferrer M. L. , del Monte F. 
Published: October 2007

AbstractPoly(vinyl alcohol) (PVA) scaffolds are prepared by a cryogenic process that consists of the unidirectional freezing of a PVA solution. The scaffolds exhibit a microchanneled structure, the morphology of which (in terms of pore diameter, surface area, and thickness of matter accumulated between adjacent microchannels) can be finely tailored by the averaged molecular weight of PVA, the PVA concentration in the solution, and the freezing rate of the PVA solution. The resulting PVA scaffolds are suitable substrates for drug‐delivery purposes, the drug release being controlled (from tens of minutes up to several days) by the morphology of the microchanneled structure. In vitro experiments reveal the efficiency of PVA scaffolds for controlling the release of ciprofloxacin into a bacteria culture medium.
Thickness‐Dependent Structural Evolutions and Growth Models in Relation to Carrier Transport Properties in Polycrystalline Pentacene Thin Films
Authors: Cheng H.‐L. , Mai Y.‐S. , Chou W.‐Y. , Chang L.‐R. , Liang X.‐W. 
Published: October 2007

AbstractThickness‐dependent crystal structure, surface morphology, surface energy, and molecular structure and microstructure of a series of polycrystalline pentacene films with different film thickness ranging from several monolayers to the several hundred nanometers have been investigated using X‐ray diffraction (XRD), atomic force microscopy (AFM), contact angle meter, and Raman spectroscopy. XRD studies indicate that thin film polymorphs transformation behaviours are from the orthorhombic phase to the thin‐film phase and then to the triclinic bulk phase as measured by the increased tilt angle (θtilt) of the pentacene molecule from the c‐axis toward the a‐axis. We propose a growth model that rationalizes the θtilt increased along with increasing film thickness in terms of grain size and surface energy varying with film growth using AFM combined with contact angle measurements. The vibrational characterizations of pentacene molecules in different thickness films were investigated by Raman spectroscopy compared to density functional theory calculations of an isolated molecule. In combination with XRD and AFM the method enables us to distinguish the molecular microstructures in different thin film polymorphs. We proposed a methodology to probe the microscopic parameters determining the carrier transport properties based on Davydov splitting and the characteristics of aromatic C–C stretching modes in Raman spectra. When compared to the triclinic bulk phase at a high thickness, we suggest that the first few monolayer structures located at the dielectric surface could have inferior carrier transport properties due to weak intermolecular interactions, large molecular relaxation energy, and more grain boundaries.
Tuning the Emitting Color of Organic Light‐Emitting Diodes Through Photochemically Induced Transformations: Towards Single‐Layer, Patterned, Full‐Color Displays and White‐Lighting Applications
Authors: Vasilopoulou M. , Georgiadou D. , Pistolis G. , Argitis P. 
Published: October 2007

AbstractPhotochemically induced emission tuning for the definition of pixels emitting the three primary colors, red, green, blue (RGB), in a single conducting polymeric layer is investigated. The approach proposed is based on an acid‐induced emission shift of the (1‐[4‐(dimethylamino)phenyl]‐6‐phenylhexatriene) (DMA‐DPH) green emitter and acid‐induced quenching of the red fluorescent emitter (4‐dimethylamino‐4′‐nitrostilbene) (DANS). The two emitters are dispersed in the wide bandgap conducting polymer poly(9‐vinylcarbazole) (PVK), along with a photoacid generator (PAG). In the unexposed film areas, red emission is observed because of efficient energy transfer from PVK and DMA‐DPH to DANS. Exposure of selected areas of the film at different doses results in quenching of the red emitter's fluorescence and the formation of green, blue, or even other color‐emitting pixels, depending on the exposure dose and the relative concentrations of the different compounds in the film. Organic light‐emitting diodes having the PVK polymer containing the appropriate amounts of DMA‐DPH, DANS, and PAG as the emitting layer are fabricated and electroluminescence spectra are recorded. The time stability of induced emission spectrum changes and the color stability during device operation are also examined, and the first encouraging results are obtained.
A Europium Complex With Excellent Two‐Photon‐Sensitized Luminescence Properties
Authors: Hao R. , Li M. , Wang Y. , Zhang J. , Ma Y. , Fu L. , Wen X. , Wu Y. , Ai X. , Zhang S. , Wei Y. 
Published: October 2007

AbstractWe report the synthesis and excellent two‐photon‐sensitized luminescence properties of a new complex [Eu(tta)3dmbpt] (tta = henoyltrifluoroacetonate; dmbpt = 2‐(N,N‐diethyl‐2,6‐dimethylanilin‐4‐yl)‐4,6‐bis(3,5‐dimethylpyrazol‐1‐yl)‐1,3,5‐triazine) that exhibits the highest efficiency of lanthanide luminescence when excited by near‐infrared (NIR) laser pulses (action cross section of two‐photon‐excited fluorescence δ × ΦF: 85 GM at 812 nm and 56 GM at 842 nm; 1 GM = 10–50 cm4 s photon–1 molecule–1). Compared to a previously reported [Eu(tta)3dpbt] complex, (dpbt = 2‐(N,N‐diethylanilin‐4‐yl)‐4,6‐bis(3,5‐dimethylpyrazol‐1‐yl)‐1,3,5‐triazine), [Eu(tta)3dmbpt] has two excess methyl groups at the 2,6‐positions of the phenyl ring. Crystallographic data of dmbpt show that the 2,6‐dimethyl substitutes bring about a significant twist in the conformation of the diethylamino group compared to that in dpbt, which severely influences the conjugation in the ground state between the electron lone pair of N in the –N(CH2–)2 moiety and the aromatic electron system in dmbpt. The large two‐photon absorption (TPA) cross section of dmbpt is mainly derived from its large static dipole moment difference between the S0 and the S1 states, which is partly responsible for the high capability of two‐photon‐sensitized luminescence of [Eu(tta)3dmbpt]. The broader two‐ and single‐photon excitation windows and the superior two‐photon‐sensitized luminescent properties in the long‐wavelength NIR region of [Eu(tta)3dmbpt] compared to [Eu(tta)3dpbt] are also explained according to the calculated results and twisted structure.
All‐Optical Operation Cycle on Molecular Bits with 250‐GHz Clock‐Rate Based on Photochromic Fulgides
Authors: Malkmus S. , Koller F. O. , Draxler S. , Schrader T. E. , Schreier W. J. , Brust T. , DiGirolamo J. A. , Lees W. J. , Zinth W. , Braun M. 
Published: October 2007

AbstractThe prototype operation of an ultrafast write–readout–erase–readout cycle of an all‐optical system based on photochromic indolylfulgides is demonstrated. In the employed dye the molecular structure is switched using light of different wavelengths between two thermally stable states to allow binary encoding of information. Non‐destructive readout of the bit states using infrared light completes the scheme of an all‐optical memory. For ultrafast operation femtosecond light pulses are applied and it is demonstrated that two consecutive write/erase processes separated by less than 4 ps still allow the defined readout of the bit state. The short time between the write/erase and readout actions demonstrates that an all‐optical data storage system based on indolylfulgides may be operated at memory clock rates that exceed 250 GHz.
Increasing the Complexity of Magnetic Core/Shell Structured Nanocomposites for Biological Applications
Authors: Salgueiriño‐Maceira V. , Correa‐Duarte M. A. 
Published: October 2007

AbstractThis Review article ponders core/shell structured nanoparticles that can be prepared with features that combine properties of different materials, including ligands that enhance their biocompatibility. These nanocomposites are not classified in terms of synthesis, but rather by how these features are distributed in the final morphology, attending to connected or isolated materials that end up in interacting or not‐interacting functionalities. In particular, we have focused on magnetic core/shell‐structured particles with a directly connected, coupled, or isolated second functionality. The current progress on methods in colloidal solution that have allowed the great development of these multifunctional magnetic and active spheres on biological and biomedical fields is reported.
Peeling Back the Layers: Controlled Erosion and Triggered Disassembly of Multilayered Polyelectrolyte Thin Films
Authors: Lynn D. M. 
Published: October 2007

AbstractMethods for the layer‐by‐layer deposition of oppositely charged polymers on surfaces can be used to assemble thin multilayered films using a broad range of natural, synthetic, and biologically relevant materials. These methods also permit precise, nanometer‐scale control over the compositions and internal structures of multicomponent assemblies. Provided that the individual components of these materials are selected or designed appropriately, these methods provide tantalizing new opportunities to design thin films and coatings that provide spatial, temporal, or active control over the release of one or several different agents from surfaces. The last two years have seen a significant increase in reports describing the development of new chemical, physical, and biomolecular approaches to the controlled erosion, triggered disassembly, or general deconstruction of multilayered polymer films. In this Progress Report, we highlight recent work from our laboratory and several other groups toward the design of ultrathin multilayered assemblies that i) permit broad, tunable, and sophisticated control over film erosion, and ii) provide new opportunities for the localized release of macromolecular therapeutics, such as DNA and proteins, from surfaces.