bluuebunny/crossref_metadata_2025_split huggingface dataset:
Analyzing Protein‐Protein Interactions from Affinity Purification‐Mass Spectrometry Data with SAINT
Authors: Choi Hyungwon , Liu Guomin , Mellacheruvu Dattatreya , Tyers Mike , Gingras Anne‐Claude , Nesvizhskii Alexey I. 
Published: September 2012

AbstractSignificance Analysis of INTeractome (SAINT) is a software package for scoring protein‐protein interactions based on label‐free quantitative proteomics data (e.g., spectral count or intensity) in affinity purification–mass spectrometry (AP‐MS) experiments. SAINT allows bench scientists to select bona fide interactions and remove nonspecific interactions in an unbiased manner. However, there is no ‘one‐size‐fits‐all’ statistical model for every dataset, since the experimental design varies across studies. Key variables include the number of baits, the number of biological replicates per bait, and control purifications. Here we give a detailed account of input data format, control data, selection of high‐confidence interactions, and visualization of filtered data. We explain additional options for customizing the statistical model for optimal filtering in specific datasets. We also discuss a graphical user interface of SAINT in connection to the LIMS system ProHits, which can be installed as a virtual machine on Mac OS X or Windows computers. Curr. Protoc. Bioinform. 39:8.15.1‐8.15.23. © 2012 by John Wiley & Sons, Inc.
Using ProHits to Store, Annotate, and Analyze Affinity Purification–Mass Spectrometry (AP‐MS) Data
Authors: Liu Guomin , Zhang Jianping , Choi Hyungwon , Lambert Jean‐Philippe , Srikumar Tharan , Larsen Brett , Nesvizhskii Alexey I. , Raught Brian , Tyers Mike , Gingras Anne‐Claude 
Published: September 2012

AbstractAffinity purification coupled with mass spectrometry (AP‐MS) is a robust technique used to identify protein‐protein interactions. With recent improvements in sample preparation, and dramatic advances in MS instrumentation speed and sensitivity, this technique is becoming more widely used throughout the scientific community. To meet the needs of research groups both large and small, we have developed software solutions for tracking, scoring and analyzing AP‐MS data. Here, we provide details for the installation and utilization of ProHits, a Laboratory Information Management System designed specifically for AP‐MS interaction proteomics. This protocol explains: (i) how to install the complete ProHits system, including modules for the management of mass spectrometry files and the analysis of interaction data, and (ii) alternative options for the use of pre‐existing search results in simpler versions of ProHits, including a virtual machine implementation of our ProHits Lite software. We also describe how to use the main features of the software to analyze AP‐MS data. Curr. Protoc. Bioinform. 39:8.16.1‐8.16.32. © 2012 by John Wiley & Sons, Inc.
Selecting, Acquiring, and Using Small Molecule Libraries for High‐Throughput Screening
Authors: Dandapani Sivaraman , Rosse Gerard , Southall Noel , Salvino Joseph M. , Thomas Craig J. 
Published: September 2012

AbstractThe selection, acquisition, and use of high‐quality small molecule libraries for screening is an essential aspect of drug discovery and chemical biology programs. Screening libraries continue to evolve as researchers gain a greater appreciation of the suitability of small molecules for specific biological targets, processes, and environments. The decision surrounding the makeup of any given small molecule library is informed by a multitude of variables, and opinions vary on best practices. The fitness of any collection relies upon upfront filtering to avoid problematic compounds, assess appropriate physicochemical properties, install the ideal level of structural uniqueness, and determine the desired extent of molecular complexity. These criteria are under constant evaluation and revision as academic and industrial organizations seek out collections that yield ever‐improving results from their screening portfolios. Practical questions including cost, compound management, screening sophistication, and assay objective also play a significant role in the choice of library composition. This overview attempts to offer advice to all organizations engaged in small molecule screening based upon current best practices and theoretical considerations in library selection and acquisition. Curr. Protoc. Chem. Biol. 4:177‐191 © 2012 by John Wiley & Sons, Inc.
Dealing with the Data Deluge: Handling the Multitude of Chemical Biology Data Sources
Authors: Guha Rajarshi , Nguyen Dac‐Trung , Southall Noel , Jadhav Ajit 
Published: September 2012

AbstractOver the last 20 years, there has been an explosion in the amount and type of biological and chemical data that has been made publicly available in a variety of online databases. While this means that vast amounts of information can be found online, there is no guarantee that it can be found easily (or at all). A scientist searching for a specific piece of information is faced with a daunting task—many databases have overlapping content, use their own identifiers and, in some cases, have arcane and unintuitive user interfaces. In this overview, a variety of well‐known data sources for chemical and biological information are highlighted, focusing on those most useful for chemical biology research. The issue of using data from multiple sources and the associated problems such as identifier disambiguation are highlighted. A brief discussion is then provided on Tripod, a recently developed platform that supports the integration of arbitrary data sources, providing users a simple interface to search across a federated collection of resources. Curr. Protoc. Chem. Biol. 4:193‐209 © 2012 by John Wiley & Sons, Inc.
One‐Pot Multienzyme Synthesis of Lewis x and Sialyl Lewis x Antigens
Authors: Yu Hai , Lau Kam , Li Yanhong , Sugiarto Go , Chen Xi 
Published: September 2012

AbstractL‐Fucose has been found abundantly in human milk oligosaccharides, bacterial lipopolysaccharides, glycolipids, and many N‐ and O‐linked glycans produced by mammalian cells. Fucose‐containing carbohydrates have important biological functions. Alterations in the expression of fucosylated oligosaccharides have been observed in several pathological processes such as cancer and atherosclerosis. Chemical formation of fucosidic bonds is challenging due to its acid lability. Enzymatic construction of fucosidic bonds by fucosyltransferases is highly efficient and selective but requires the expensive sugar nucleotide donor guanosine 5′‐diphosphate‐L‐fucose (GDP‐Fuc). Here, we describe a protocol for applying a one‐pot three‐enzyme system in synthesizing structurally defined fucose‐containing oligosaccharides from free L‐fucose. In this system, GDP‐Fuc is generated from L‐fucose, adenosine 5′‐triphosphate (ATP), and guanosine 5′‐triphosphate (GTP) by a bifunctional L‐fucokinase/GDP‐fucose pyrophosphorylase (FKP). An inorganic pyrophosphatase (PpA) is used to degrade the by‐product pyrophosphate (PPi) to drive the reaction towards the formation of GDP‐Fuc. In situ generated GDP‐Fuc is then used by a suitable fucosyltransferase for the formation of fucosides. The three‐enzyme reactions are carried out in one pot without the need for high‐cost sugar nucleotide or isolation of intermediates. The time for the synthesis is 4 to 24 hr. Purification and characterization of products can be completed in 2 to 3 days. Curr. Protoc. Chem. Biol. 4:233‐247 © 2012 by John Wiley & Sons, Inc.
Recent Progress in Redox Flow Battery Research and Development
Authors: Wang Wei , Luo Qingtao , Li Bin , Wei Xiaoliang , Li Liyu , Yang Zhenguo 
Published: September 2012

AbstractWith the increasing need to seamlessly integrate renewable energy with the current electricity grid, which itself is evolving into a more intelligent, efficient, and capable electrical power system, it is envisioned that energy‐storage systems will play a more prominent role in bridging the gap between current technology and a clean sustainable future in grid reliability and utilization. Redox flow battery technology is a leading approach in providing a well‐balanced solution for current challenges. Here, recent progress in the research and development of redox flow battery technology, including cell‐level components of electrolytes, electrodes, and membranes, is reviewed. The focus is on new redox chemistries for both aqueous and non‐aqueous systems.
Microribbon‐Like Elastomers for Fabricating Macroporous and Highly Flexible Scaffolds that Support Cell Proliferation in 3D
Authors: Han Li‐Hsin , Yu Stephanie , Wang Tianyi , Behn Anthony W. , Yang Fan 
Published: September 2012

AbstractHydrogel‐based scaffolds are widely used for culturing cells in three dimensions due to their tissue‐like water content and tunable biochemical and physical properties. Most conventional hydrogels lack the macroporosity desirable for efficient cell proliferation and migration and have limited flexibility when subject to mechanical load. Here microribbon‐like elastomers that, when photocrosslinked, can form macroporous and highly flexible scaffolds that support cell proliferation in 3D are developed. These microribbons are produced by wet‐spinning gelatin solution into microfibers, followed by drying in acetone, which causes asymmetrical collapse of microfibers to form microribbon‐like structures. Gelatin microribbons are then modified using methacrylate anhydride to allow further photocrosslinking into 3D scaffolds. The macroporosity and mechanical properties of the microribbon‐based scaffold may be tuned by varying wet‐spinning rate, drying temperature, choice of drying agent, level of glutaraldehyde crosslinking, and microribbon density. When encapsulated in the microribbon‐based scaffold, human adipose‐derived stromal cells proliferated up to 30‐fold within 3 weeks. Furthermore, microribbons‐based scaffold demonstrate great flexibility and can sustain up to 90% strain and 3 MPa stress without failing. The unique mechanical properties of microribbon‐based scaffolds make them promising tools for engineering shock‐absorbing tissues such as cartilage and intervertebral discs.
Heterogeneous Nucleation Promotes Carrier Transport in Solution‐Processed Organic Field‐Effect Transistors
Authors: Li Ruipeng , Khan Hadayat Ullah , Payne Marcia M. , Smilgies Detlef‐M. , Anthony John E. , Amassian Aram 
Published: September 2012

AbstractA new way to investigate and control the growth of solution‐cast thin films is presented. The combination of in situ quartz crystal microbalance measurements with dissipation capabilities (QCM‐D) and in situ grazing‐incidence wide‐angle X‐ray scattering (GIWAXS) in an environmental chamber provides unique quantitative insights into the time‐evolution of the concentration of the solution, the onset of nucleation, and the mode of growth of the organic semiconductor under varied drying conditions. It is demonstrated that careful control over the kinetics of solution drying enhances carrier transport significantly by promoting phase transformation predominantly via heterogeneous nucleation and sustained surface growth of a highly lamellar structure at the solid‐liquid interface at the expense of homogeneous nucleation.
Influence of the Injection‐Molding Parameters on the Cellular Structure and Thermo‐Mechanical Properties of Ethylene‐Propylene Block Copolymer Foams
Authors: Gómez‐gómez J. F. , Arencón D. , Sánchez‐soto M. A. , Martínez A. B. 
Published: September 2012

AbstractMicrocellular injection‐molding technology is capable of producing lightweight polymeric products. The foam morphology is determined by the injection‐molding parameters, and it has been observed that depending on the parameter variations, the cell structure may exhibit substantial morphological differences through the entire section along the melt flow direction of the injected part. The effects of varying injection‐molding parameters on foam morphology and thermal mechanical properties of a multiphase ethylene‐propylene block copolymer (EPBC) were tested on 5‐mm plaque specimens using a constant temperature profile. It has been found that injection speed does not have a significant effect on the thermal‐mechanical properties of the foam, whereas shot volume and mold temperature do have a significant influence. Low shot volume produces uniform density cellular structures and larger cores, whereas lower mold temperatures help maintain small cell sizes. Furthermore, the effect of the copolymer's crystalline phase on foam morphology has been observed. This study identifies the achievable foam morphologies and the thermal‐mechanical performance of cellular molded EPBC parts. © 2012 Wiley Periodicals, Inc. Adv Polym Techn 32: E692–E704, 2013; View this article online at wileyonlinelibrary.com. DOI 10.1002/adv.21311
Synthesis and Antitubercular Activity Evaluation of Novel Unsymmetrical Cyclohexane‐1,2‐diamine Derivatives
Authors: Beena  , Joshi Seema , Kumar Nitin , Kidwai Saqib , Singh Ramandeep , Rawat Diwan S. 
Published: September 2012

AbstractA library of unsymmetrical cyclohexane‐1,2‐diamine derivatives were synthesized and evaluated for their activity against Mycobacterium tuberculosis H37Rv in vitro. Out of the 46 compounds synthesized, eight compounds (11h, 13a, 13e, 13f, 14a, 14c, 14d, and 15d) were found to be active at or below 6.25 µM concentration, with negligible toxicity to human red blood cells at a concentration much higher than the MIC99. Compound 13a was the best active compound showing inhibition at 3.125–6.25 µM, and was found to be non‐hemolytic up to 500 µg/mL concentration.
Observability Analysis and Improved Zero‐Speed Position Observer Design of Synchronous Motor with Experimental Results
Authors: Zaltni D. , Ghanes M. 
Published: September 2012

AbstractThis paper deals with the permanent magnet synchronous motor (PMSM) observability analysis for sensorless control design. The problem of loss of observability at low frequency range is always recognized in experimental settings. Nevertheless, there are no sufficient theoretical observability analyses for the PMSM. In the literature, only the sufficient observability condition has been presented. Therefore, the current work is aimed especially towords the necessary observability condition analysis. Furthermore, improved zero‐speed observation is presented here for a surface PMSM (SPMSM) to overcome position observability problems at zero‐speed which is an unobservable state point. The proposed observer based on higher order sliding mode (HOSM) is designed in order to ensure robustness against disturbances and to avoid the chattering phenomenon which is inherent in standard first order sliding modes. The stability and finite time convergence of the developed observer are studied and discussed. Experimental results are carried out to illustrate the effectiveness and robustness of the proposed observer.
Theoretische Untersuchungen zum Stofftransport in turbulenter Rohrströmung zu Ringelektroden
Authors: Dreesen E. W. , Vielstich W. 
Published: September 2012

AbstractDie Differentialgleichung der konvektiven Diffusion für den Stofftransport zu Ringelektroden in turbulenter Rohrströmung wird durch Transformationen in eine Form gebracht, die es erlaubt, den Stofftransport durch Einführung von sogenannten normierten Nusseltzahlen Nu+ explizit unabhängig von der Reynoldszahl (Re), der Prandtlzahl (Pr), der Ausdehnung der Elektrode in Strömungsrichtung und dem Rohrdurchmesser darzustellen.Es werden Kriterien dafür angegeben, wann die übliche Darstellung des Stofftransports durch eine Beziehung der Art Nu ∼ Rea · Prb, zutrifft.
Nahordnung in Flüssigkeiten, IV LCAO‐MO‐Modellrechnungen zur Lösungsmittelabhängigkeit der 13C‐NMR‐Verschiebung
Authors: Schröer Wolffram 
Published: September 2012

AbstractBin LCAO‐MO‐Verfahren zur Berechnung von 13C‐NMR‐chemischen Verschiebungen wird angegeben. Die 13C‐Verschiebungen der Äthylenkohlenstoffatome verschiedener Äthylenderivate werden damit berechnet. Außerdem werden die NMR‐Verschiebungen von Acrylnitril bei Wechselwirkung mit einem H+ ‐ oder CN−‐Ion, die als Modell für ein polares Lösungsmittel dienen, abgeschätzt. Die experimentellen Lösungsmittelverschiebungen von Acrylnitril in Mischungen von CCl4 und Hexamethylphosphorsäure‐Triamid entsprechen diesen Berechnungen und zeigen somit Veränderungen der Elektronenstruktur an, wie sie entsprechend der chemischen Reaktivität α,β‐ungesättigter Karbonyl‐Verbindungen erwartet werden.
The Influence of Chemical Exchange on NMR Spin Lattice Relaxation
Authors: Strehlow H. , Frahm J. 
Published: September 2012

AbstractA method is presented for the determination of chemical rate constants from spin‐lattice relaxation times T1. The exchange rate of water molecules between the inner‐hydration sphere of nickel ions and the bulk has thus been obtained in Ni(NO3)2 solutions. The results indicate a nitrate inner‐sphere complex with a stability constant of about 0.2 M−1. The ratio of the Ni2+ ion‐water proton distances in the first and second hydration layers is estimated. A combined T1 — T2 technique is proposed which improves the accuracy of the measurement of fast chemical reactions.
Messung der Stoßfrequenz in Gasentladungen verschiedener mehratomiger Gase
Authors: Janzen G. , Staib W. , Kruppa G. , Schücker U. , Suhr H. 
Published: September 2012

AbstractDie Stoßfrequenzen in den Plasmen von Ar, He, H2, CO, O2, H2O, CO2, NH3, CH4, CH3OH, CH3COCH3 wurden bei verschiedenen Werten von Entladungsstrom und Druck über die Resonanzverbreitung eines Mikrowellen‐Hohlraumresonators gemessen. Aus Längsfeldstärke und Elektronendichte berechnete Stoßfrequenzwerte stimmen gut mit diesen Werten überein.
Die Reaktionen von atomarem Wasserstoff mit Cyclohexen, Cyclohexadien‐1,3 und Benzol
Authors: Hoyermann K. , Preuss A. W. , Gg. Wagner H. 
Published: September 2012

AbstractDie Reaktionen von atomarem Wasserstoff mit cyclischen C6‐Kohlenwasserstoffen (Cyclohexen, Cyclohexadien‐1,3, Benzol) wurden in einem isothermen Strömungssystem (gekoppelt an ESR, Massenspektrometer, Gaschromatograph) bei Temperaturen von 296 ≤ T ≤ 493 K und Drücken von 1,9 ≤ p ≤ 14,7 Torr bei Unterschuß von atomarem Wasserstoff untersucht.Die Messungen der Geschwindigkeitskonstanten der Reaktionen ergaben:

Für Drücke p > 5 Torr und hohe Überschußverhältnisse ([Reaktand]0/[H]0) bleibt das Ringsystem auch bei Ablauf der Folgereaktionen hauptsächlich erhalten. (Hauptreaktionsprodukte für Cyclohexen: Cyclohexan; für Cyclohexadien‐1,3: Cyclohexen, Cyclohexan; für Benzol: Cyclohexen; Cyclohexadiene, Cyclohexan). Die Reaktionsmechanismen werden diskutiert.
Complex Formation in Reactive and Inelastic Scattering: Statistical Adiabatic Channel Model of Unimolecular Processes III
Authors: Quack M. , Troe J. 
Published: September 2012

AbstractThe statistical adiabatic channel model developed previously [25] for unimolecular dissociation reactions is extended to describe bimolecular collisions proceeding via a strongly bound intermediate complex. As examples three cases are considered, in which the intermediate complex corresponds to a known stable molecule: O + O2 → O3*, O + NO → NO2* and Cl + NO → ClNO*. Using known molecular properties and the experimental high pressure recombination rate constants, the specific dissociation rate constants k(E,J), state to state inelastic scattering cross sections σ(v,j → v',j') and center of mass translational energy distributions are calculated with the same simple potential model. Rate constants kvv, for vibrational relaxation are computed and found to be in good agreement with experimental results available for the O + O2 vibrational relaxation. The dependence of cross sections and final state distributions as a function of initial state is illustrated in some detail. Even within the statistical model, there is found to be a marked memory of initial conditions. The range of validity of statistical models is discussed.
Thermal Transpiration in a Dissociating Gas
Authors: Wright P. G. 
Published: September 2012

AbstractBy use of the dusty‐gas model, an analysis is given of the gradient of pressure set up in the steady state in a dissociating gas in local chemical equilibrium in a gradient of temperature in a porous medium (or in a capillary tube). For a dissociating gas, though not for an isomerising gas, the gradient of pressure thereby induced can be appreciably greater than for a non‐reacting gas (though the enhancement is less marked than the corresponding enhancement of the thermal conductivity). The enhancement remains appreciable even for a gas in which there is only a small proportion of the associated species; and for a porous medium with very small pores the steady state could in consequence be one with (p−1 δp/δz)/(T−1 δT/δz) detectably greater than the conventional 0.5000.It is shown in passing that a result previously established for a dusty gas at uniform temperature, that the Stefan‐Maxwell equations for diffusion can be compounded with relevant equations for viscous contributions to the resultant fluxes, to give a set of equations of the unaugmented Stefan‐Maxwell form but with modified values for coefficients appearing in them, also holds for a dusty gas in a gradient of temperature.
Der Dampfdruck‐Isotopie‐Effekt von deuterierten Neopentanen
Authors: Höpfner A. , Parekh N. , Hörner Ch. , Abdel‐Hamid A. 
Published: September 2012

AbstractDer Dampfdruck von Neopentan und die Dampfdruck‐Isotopie‐Effekte von 6 deuterierten Neopentanen (C(CD3)4, C(CH3)(CD3)3, C(CH3)2(CD3)2, C(CH2D)4, C(CH3)3(CD3) und C(CH3)3(CH2D)) im Temperaturbereich zwischen ‐60 und +20°C werden mitgeteilt. Der Effekt ist in allen Fällen wie erwartet invers. Die beobachteten Tripelpunkte liegen zwischen ‐16,64 (Neopentan) und ‐18,66°C (Neopentan‐D12). Die beobachteten Dampfdrücke und die aus ihnen abgeschätzten Verdampfungsenthalpien werden mit Literatur‐Daten verglichen.
Homogeneous Particle Growth from the Reaction of SO2 with n‐Butane
Authors: Jordan H. , Penzhorn R.‐D. 
Published: September 2012

AbstractPhotolysis of SO2 with n‐butane results in several products wich can condense to particles. The particle mass concentration (pmc) and the rate of product formation were measured in this system during and after photolysis. After a certain irradiation time a maximum pmc is reached. The hight of the pmc maximum is a function of the photochemical reaction rate. Based on simple model considerations, we show that the photochemically produced aerosols are lost mainly by sedimentation, are monodisperse and that the particle size is relatively insensitive to the photochemical reaction rate.
Kinetics of Redox Couples at Solid Electrodes: II ‐ Ferro‐Ferricyanide System in Nearly Neutral Media on Rotating Disk Electrodes of Polycristalline Spinel Manganites CuxMn3‐xO4, with x = 1.2
Authors: Beley M. , Brenet J. , Chartier P. 
Published: September 2012

AbstractDie Kinetik der Durchtrittsreaktion des Redox‐Systems Fe(CN)64‐/Fe(CN)63‐ ist mit einer aus CuxMn3‐xO4 (x = 1,2) bestehenden rotierenden Scheibenelektrode untersucht worden. Der kathodische Strom wird teilweise inhibiert. Es ergeben sich Durchtrittsfaktoren α = β = 0,50. Die scheinbare Standardreaktionsgeschwindigkeitskonstante ist in der Größenordnung von (3 ± 2) · 10−3 cm s−1. Nur mit äquimolaren Lösungen wird eine Reaktionsordnung 1 beobachtet, und der Einfluß der Fe(CN)63‐‐Ionen auf die Oxydation der Fe(CN)64‐‐Ionen wird nahegelegt.
High‐Temperature Viscometer for Fluid Liquids Part I: On‐line Computer‐facilitated Torsion Pendulum
Authors: Ohta T. , Borgen O. , Brockner W. , Fremstad D. , Grjotheim K. , Tørklep K. , Øye H. A. 
Published: September 2012

AbstractAn oscillation viscometer, interfaced to an on‐line minicomputer for measurement of the viscosity of low‐viscous hygroscopic melts up to 1200°C, is described. The paper gives a discussion of changes in experimental technique facilitated by use of the computer, and the resulting improvements in the viscometer performance.