bluuebunny/crossref_metadata_2025_split huggingface dataset:
Generating, growing and transforming skeletal shape: insights from amphibian pharyngeal arch cartilages
Authors: Rose Christopher 
Published: March 2009

AbstractAmphibians that undergo a metamorphosis provide an unparalleled opportunity to investigate how skeletal shape is generated, preserved, and transformed in development. Their pharyngeal arch (PA) cartilages, which support breathing and feeding behaviors, form embryonically from cranial neural crest cells, grow isometrically at larval stages, and abruptly change shape during metamorphosis. Further, the shape changes occur in three different ways: some adult cartilages form de novo, others emerge from within resorbing larval cartilages and some larval cartilages reshape themselves at the cellular level. Isometric growth followed by abrupt shape change is unique to amphibian PA cartilages, which suggests that the origin and evolution of amphibian metamorphosis has been influenced by the tissue properties of cartilage. This essay reviews the functional role of the PA skeleton in frogs and salamanders and presents a mechanistic framework for understanding how its shape is generated, preserved, and transformed at the levels of cell behavior and specification mechanisms.
Close encounters of the third kind: disordered domains and the interactions of proteins
Authors: Tompa Peter , Fuxreiter Monika , Oldfield Christopher J. , Simon Istvan , Dunker A. Keith , Uversky Vladimir N. 
Published: March 2009

AbstractProtein–protein interactions are thought to be mediated by domains, which are autonomous folding units of proteins. Recently, a second type of interaction has been suggested, mediated by short segments termed linear motifs, which are related to recognition elements of intrinsically disordered regions. Here, we propose a third kind of protein–protein recognition mechanism, mediated by disordered regions longer than 20–30 residues. Bioinformatics predictions and well‐characterized examples, such as the kinase‐inhibitory domain of Cdk inhibitors and the Wiskott–Aldrich syndrome protein (WASP)‐homology domain 2 of actin‐binding proteins, show that these disordered regions conform to the definition of domains rather than motifs, i.e., they represent functional, evolutionary, and structural units. Their functions are distinct from those of short motifs and ordered domains, and establish a third kind of interaction principle. With these points, we argue that these long disordered regions should be recognized as a distinct class of biologically functional protein domains.
Chromatin loops, illegitimate recombination, and genome evolution
Authors: Kantidze Omar L. , Razin Sergey V. 
Published: March 2009

AbstractChromosomal rearrangements frequently occur at specific places (“hot spots”) in the genome. These recombination hot spots are usually separated by 50–100 kb regions of DNA that are rarely involved in rearrangements. It is quite likely that there is a correlation between the above‐mentioned distances and the average size of DNA loops fixed at the nuclear matrix. Recent studies have demonstrated that DNA loop anchorage regions can be fairly long and can harbor DNA recombination hot spots. We previously proposed that chromosomal DNA loops may constitute the basic units of genome organization in higher eukaryotes. In this review, we consider recombination between DNA loop anchorage regions as a possible source of genome evolution.
A tale of tails: insights into the coordination of 3′ end processing during homologous recombination
Authors: Lyndaker Amy M. , Alani Eric 
Published: March 2009

AbstractEukaryotic genomes harbor a large number of homologous repeat sequences that are capable of recombining. Their potential to disrupt genome stability highlights the need to understand how homologous recombination processes are coordinated. The Saccharomyces cerevisiae Rad1–Rad10 endonuclease performs an essential role in recombination between repeated sequences, by processing 3′ single‐stranded intermediates formed during single‐strand annealing and gene conversion events. Several recent studies have focused on factors involved in Rad1–Rad10‐dependent removal of 3′ nonhomologous tails during homologous recombination, including Msh2–Msh3, Slx4, and the newly identified Saw1 protein. Together, this new work provides a model for how Rad1–Rad10‐dependent end processing is coordinated: Msh2–Msh3 stabilizes and prepares double‐strand/single‐strand junctions for Rad1–Rad10 cleavage, Saw1 recruits Rad1–Rad10 to 3′ tails, and Slx4 mediates crosstalk between the DNA damage checkpoint machinery and Rad1–Rad10.
The “safe zone” in medial percutaneous calcaneal pin placement
Authors: Gamie Zakareya , Donnelly Leo , Tsiridis Eleftherios 
Published: March 2009

AbstractPercutaneous pin insertion into the medial calcaneus places a number of structures at risk. Evidence suggests that the greatest risk is to the medial calcaneal nerve (MCN). The medial calcaneal region of 24 cadavers was dissected to determine the major structures at risk. By using four palpable anatomical landmarks, the inferior tip of the medial malleolus (point A), the posterior superior portion of the calcaneal tuberosity (point B), the navicular tuberosity (point C), and the medial process of the calcaneal tuberosity (point D), we attempted to define the safe zone taking into account all possible variables in our dissections including ankle position, side, gender, and possible anatomical variations of the MCN. The commonest arrangement of the MCN was two MCNs that arose independently, one arising before the bifurcation of the tibial nerve and the other arising from the medial plantar nerve. A zone could be defined posterior to 75% of the distance along the lines AB, CD, AD, and CB which would avoid most structures. The posterior branches of the MCN, however, would still be at risk and placing the pin too far posteriorly risks an avulsion fracture. This is the first study to employ four palpable anatomical landmarks to identify a zone to minimize damage to neurovascular structures. It may not be possible, however, to avoid injury of the MCN and consequent sensory loss to the sole of the foot. foot. Clin. Anat. 22:523–529, 2009. © 2009 Wiley‐Liss, Inc.
Origin of the radial nerve branch innervating the brachialis muscle
Authors: Oh Chang‐Seok , Won Hyung‐Sun , Lee Kyu‐Seok , Chung In‐Hyuk 
Published: March 2009

AbstractThe brachialis muscle is dually innervated by the musculocutaneous nerve running via the anterior division of the brachial plexus and the radial nerve running via the posterior division of the plexus. There have been inconsistent descriptions of the pathway of the radial nerve branch at the brachial plexus. This study investigated the route of the radial nerve branch innervating the brachialis muscle at the brachial plexus. In 20 samples, the radial nerve branch innervating the brachialis muscle was separated and traced up to the cervical nerve under a surgical microscope. All the radial nerve branches innervating the muscle ran via the posterior cord, the posterior division, and the superior or middle trunk at the brachial plexus. The radial nerve branches arose from C5 in 5 cases, C6 in 11 cases, C5 and C6 in 3 cases, and C6 and C7 in 1 case. Clin. Anat. 22:495–499, 2009. © 2009 Wiley‐Liss, Inc.
A web‐based training framework in automotive electric education
Authors: Liang Janus S. 
Published: March 2009

AbstractIn this study, the mechanism of network information is applied together with CAD, open software and virtual reality technology to generate a web‐based learning framework for measuring components and circuit design of automobile electric system. Different from traditional teaching methods, this web‐based system is very helpful for students to learn skills of measurements and circuit design. There are three topics discussed in this study: (1) developing the learning module for measuring electric parts; (2) building the platform for practice of electric circuit; (3) creating the online study tools and effectiveness analysis. The effectiveness of this training system was tested after experiment instruction. Close to 100% attendance was observed during the practice sessions, which demonstrates the success in generating interest among the students. The training platform developed through this study was tested capable of improving learning efficiency on technology content and promoting students' ability of troubleshooting on automotive electrical system. © 2009 Wiley Periodicals, Inc. Comput Appl Eng Educ 18: 619–633, 2010; View this article online atwileyonlinelibrary.com; DOI 10.1002/cae.20257
Teaching and learning enhancement in undergraduate machine dynamics
Authors: Aziz El‐Sayed 
Published: March 2009

AbstractCurrently, information technology (IT) is playing a significant role in the development of learning environments. The integration of IT into the classroom provides innovative learning environments that allow for more interactive, relevant, and effective applications to give students valuable experiences. This article presents the design and implementation of more active and collaborative methods of teaching and learning in a course on mechanisms and machine dynamics. Through the use of virtual collaborative environments such as cooperative learning, problem‐based learning (PBL), critical thinking, and more in the context of IT‐enabled environments, students are given the opportunity to experiment with ideas and see the results of their efforts on the computer screen. These interactive learning modules impose more responsibility on students for their own learning than the traditional lecture‐based passive learning methodology. © 2009 Wiley Periodicals, Inc. Comput Appl Eng Educ 19: 244–255, 2011
Bridging the gap between textbook and real applications: A teaching methodology in digital electronics education
Authors: Wang Guoping 
Published: March 2009

AbstractThis paper describes a teaching methodology in digital electronics education. Its purpose is to bridge the gap between traditional textbooks using out‐of‐date discrete 74‐series TTL chips and the current industry in which FPGA components and EDA design tools are becoming the standard. The principles and practices of digital components are presented to the students from five aspects, that is, classroom lecture, Multisim homework assignments, breadboard lab practices, Xilinx ISE computer design and simulation, and FPGA board verification. This approach is expected to help students better prepare for the current trends of digital systems design while not sacrificing the basic theories and principles. © 2009 Wiley Periodicals, Inc. Comput Appl Eng Educ 19: 268–279, 2011
Effect of S Replacement on the Mechanism of Unimolecular Reactions for Ground‐state Thioacetic Acid: A Theoretical Study
Authors: LU Aimei , KE Ming , DING Wanjian , LIU Ruozhuang 
Published: March 2009

AbstractThe potential energy surfaces of nine molecular reactions for the ground‐state CH3C(O)SH and CH3C(S)OH have been investigated with a B3LYP method in conjugation with 6‐31G∗︁∗︁, cc‐pVDZ, aug‐cc‐pVDZ, and cc‐pVTZ basis sets. The present calculations predict that thioacetic acid mainly exists as a CH3C(O)SH tautomer, and both tautomers predominately adopt syn conformations, which reproduces the experimental observations. By comparison of the reactivity difference among CH3C(O)SH, CH3C(S)OH, and CH3C(O)OH, it can be concluded that the replacement of atom O by S in –OH group of CH3C(O)OH has a big effect on the molecular decompositions only when –SH takes part in the reaction as one group, while the CO or CS group has minor contribution to the reactivity difference.
Investigation of Vapor‐Liquid Nucleation for Associating Fluids by Density Gradient Theory
Authors: FU Dong , LIU Jianmin 
Published: March 2009

AbstractAn equation of state (EOS) applicable to both the uniform and non‐uniform associating fluids was established by using the density‐gradient expansion, in which the influence parameter κ is formulated as a function of temperature. The molecular parameters were regressed by fitting to the experimental data of vapor pressures and liquid densities. Within the framework of density gradient theory (DGT), the nucleation rates for water, heavy water, methanol, ethanol, 1‐propanol, 1‐butanol, 1‐pentanol and 1‐hexanol were calculated. The results were satisfactory compared with the experimental data. Our study shows that DGT preserves all the advantages of density functional theory (DFT) in capturing the structure and properties of nucleus but gives much more accurate nucleation rates by adjusting the influence parameter.
Electrochemical Studies of 1,4‐Bis[2‐(2‐pyridyl)‐vinyl] Benzene and 1,4‐Bis[2‐(4‐pyridyl) vinyl] Benzene Laser Dyes via Cyclic Voltammetry, Convolutive Voltammetry and Digital Simulation Methods
Authors: EL‐DALY Samy A. , EL‐HALLAG Ibrahim S , EBEED Ezeiny M , GHONEIM Mohamed M 
Published: March 2009

AbstractElectrochemical properties of two diolefinic laser dyes namely 1,4‐bis[2‐(2‐pyridyl)‐vinyl] benzene (2PVB) and 1,4‐bis[2‐(4‐pyridyl) vinyl] benzene (4PVB) have been investigated using cyclic voltammetry and convolutive voltammetry combined with digital simulation at a platinum electrode in 0.1 mol/L tetrabutyl ammonium perchlorate (TBAP) in the two different solvents acetonitrile (CH3CN) and dimethylformamide (DMF). The species were reduced via consumption of two sequential electrons to form radical anion and dianion. In switching the potential to positive direction, the two compounds were oxidized by loss of one electron, which was followed by a fast isomerisation process. The electrode reaction pathway and the electrochemical parameters of the investigated compounds were determined using cyclic voltammetry. The extracted electrochemical parameters were verified and confirmed via digital simulation and convolutive voltammetry methods.
Photoelectrochemical Study of Corrosion Resisting Property of Cupronickel B10 in Simulated Cooling Water
Authors: XU Qunjie , WAN Zongyue , ZHOU Guoding , YIN Renhe , CAO Weimin , LIN Changjian 
Published: March 2009

AbstractThe corrosion behavior for cupronickel B10 electrode in simulated cooling water has been studied by using cyclic voltammetry, a photocurrent response method and electrochemical impedance spectroscopy (EIS). The cupronickel electrode shows a p‐type photoresponse to positive and negative potential scan, which comes from Cu2O layer on its surface, but its iph,max is less than that in borax buffer solution. The corrosion resisting property of the cupronickel B10 electrode appeared worse with the increase in the concentrations of Cl−, SO42− and S2− ions, as well as with increasing pH. The rise in the temperature may result in a photoresponse changes from p‐type to n‐type, and the corrosion resisting property fell simultaneously. The results of the EIS measurement agree well with those obtained by a photoelectrochemical method.
Highly Selective Perchlorate Membrane Electrode Based on Cobalt(III) Schiff Base as a Neutral Carrier
Authors: SHOKROLLAHI Ardeshir , GHAEDI Mehrorang , RAJABI Hamid Reza , KIANFAR Ali Hossein 
Published: March 2009

AbstractA highly selective poly(vinyl chloride) (PVC) membrane electrode based on Co(III)‐Schiff base [Co(5‐NO2‐ Salen)(PBu3)]ClO4·H2O (where 5‐NO2‐SalenHbis(5‐nitrosalycilaldehyde)ethylenediamine) as a new carrier for construction of perchlorate‐selective electrode by incorporating the membrane ingredients on the surface of a graphite electrodes has been reported. The proposed electrode possesses a very wide Nernestian potential linear range to perchlorate from 1.0×10−6 to 5.0×10−1 mol·L−1 with a slope of (59.4±0.9) mV per decade of perchlorate concentration with a low detection limit of 5.0×10−7 mol·L−1 and good perchlorate selectivity over the wide variety of other anions. The developed electrode has an especially fast response (<5 s) and a wide pH independent range (3.0–12.0) in comparison with recent reported electrodes and can be used for at least 2 months without any considerable divergence in their potential response. This electrode was used for the determination of perchlorate in river water, drinking water, sludgy water and human urine with satisfactory results without complicated and time consuming pretreatment.
One Step Preparation of Controlled Drug Release Systems in Supercritical Carbon Dioxide
Authors: CAO Liqin , WANG Chengwei , CHEN Liuping 
Published: March 2009

AbstractDrug delivery systems based on copolymers of N‐isopropylacrylamide were first prepared by a one step method, in which supercritical carbon dioxide was simultaneously used as a polymerization medium and an impregnation agent. The obtained microspheres were characterized by scanning electronic microscopy (SEM), differential scanning calorimetry (DSC), transmission electron microscopy (TEM) and X‐ray diffraction (XRD). The release effect of the in situ prepared microgels impregnated with ibuprofen was presented through in vitro release simulation.
Mechanism for OH‐Initiated Oxidation of n‐Octane in the Presence of O2 and NO: A DFT Study
Authors: ZHAO Yan , WANG Hui , SUN Xiaomin , ZHANG Qingzhu , WANG Wenxing 
Published: March 2009

AbstractDensity functional theory was used to study the mechanism for the OH‐initiated atmospheric oxidation of n‐octane in the presence of O2 and NO. The geometries and frequencies of the reactants, transition states, intermediates, and products were calculated at the B3LYP/6‐31G(d) level and single‐point energy calculations were carried out with a large basis set, 6‐311+G(3df, 2p). All of the possible product channels have been studied, but only the main ones are reported. The main products obtained are hydroxynitrates and hydroxycarbonyls, which have relative low vapor pressure and are inclined to form secondary organic aerosol. The theoretical results were compared with the available experimental observations.
Peroxo Complexes of Molybdenum(VI) Containing Mannich Base Ligands
Authors: SHARMA Mohita , SALEEM Mohd. , PATHANIA M. S. , SHEIKH H. N. , KALSOTRA B. L. 
Published: March 2009

AbstractThe molybdenum(VI)‐peroxo complexes containing Mannich base ligands having a formula as [MoO(O2)2(L‐L)] [where L‐L=morpholinobenzyl benzamide (MBB), piperidinobenzyl benzamide (PBB), morpholinobenzyl urea (MBU), piperidinobenzyl urea (PBU), morpholinobenzyl thiourea (MBTU), piperdinobenzyl thiourea (PBTU)] have been synthesized and characterized by physico‐chemical, electrochemical techniques and TGA/DTA studies. The complexes have been prepared by stirring ammonium molybdate and excess of 30% aqueous‐H2O2 and then treatment with ethanolic solution of the ligand. Studies revealed that these complexes were non‐electrolytes and diamagnetic in nature. The ligands are bound to metal in a bidentate mode through carbonyl oxygen/thiocarbonyl sulphur and the ring nitrogen. The cyclic voltammograms of the complexes show two quasi‐reversible steps involving complexes. The complexes have also been tested for antibacterial activity against Salmonella and Kleibsella. The antibacterial study of the ligands and complexes indicate that the complexes exhibit higher activity than the free ligands.
Synthesis and Characterization of Three Diverse Coordination Frameworks under Co‐ligand Intervention
Authors: LIU Ping , LIU Jianqiang , WANG Yaoyu , LIANG Yanping , WU Zhensen , SHI Qizhen 
Published: March 2009

Abstract The chelating organic ligands of 2,2′‐bipyridine (2,2′‐bipy), di(pyrid‐2‐yl)amine (dpa) and 2,6‐di(pyrid‐2‐ylamino)pyridine (dpap) were respectively applied to react with H2fum (fumaric acid) and copper salts, affording three different complexes [Cu2(fum)(2,2′‐bipy)4]·2ClO4 (1), [Cu2(µ‐OH)2(fum)(dpa)2]·2H2O (2) and [Cu(SO4)(H2O)(dpap)]·H2O (3). These complexes were determined by single‐crystal X‐ray diffraction. Each penta‐coordinated Cu(II) ion exhibits a distorted trigonal bipyramidal geometry in 1. The fum ligand links copper ions to form a dinuclear copper unit. While in 2, the fum ligands connect [Cu2(µ‐OH)2(dpa)2] unit to construct a 1D zigzag chain. Unexpectedly, when dpap instead of dpa was used under the same conditions, only one mononuclear complex 3 was formed. Crystal packings show that 1–3 form 3D supramolecular architectures through non‐covalent interactions (multiple hydrogen bonds and C–H··· π/π‐π interactions). In addition, the study of the magnetic property reveals dominating ferromagnetic interactions between Cu(II) atoms in 1.
Interaction Study of 2,6‐Bis[4‐(4‐amino‐2‐trifluoromethyl phenoxy)benzoyl] Pyridine with Human Immunoglobulin by Optical Spectroscopy and Molecular Modeling
Authors: HE Wenying , ZHANG Qiongmei , GAO Wenhua , DONG Yuming , YAO Xiaojun 
Published: March 2009

Abstract The interaction between human immunoglobulin (HIgG) and BAFP (2,6‐bis[4‐(4‐amino‐2‐trifluoromethyl phenoxy)benzoyl] pyridine was studied by fluorescence quenching, Fourier transform infrared (FT‐IR) spectra and molecule modeling. The synchronous fluorescence spectra indicated the information on qualitative changes of the protein secondary structure in the presence of BAFP in aqueous solution. The quantitative alterations of the protein secondary structure were estimated by the evidences from FT‐IR spectra with increases of α helices by about 2.6%–10.2%, increases of β‐sheet structure by about 13.6%–27.7%, and reductions of β‐turn structure by about 23.8%–30.3%. Molecular docking suggests that BAFP can strongly bind to HIgG. There are four hydrogen bond interactions between the drug and the residues Trp 170, Val 105, Met 139 and Asn 52. It was also considered that BAFP bound to HIgG mainly by a hydrophobic interaction, which is in good agreement with the results from the experimental thermodynamic parameters (the enthalpy change ΔH⊖ and the entropy change ΔS⊖ were calculated to be −6.70 kJ·mol−1 and 71.93 J·mol−1·K−1, respectively, according to the Van't Hoff equation).
Iterative Non‐m/z‐sharing Rule for Confident and Sensitive Protein Identification of Non‐shotgun Proteomics
Authors: YUN Dong , LU Haojie , WANG Haijian , ZHANG Yang , CHENG Gang , JIN Hong , YU Yanbao , XU Yawei , YANG Pengyuan , HE Fuchu 
Published: March 2009

AbstractSelecting reasonable matches from the database search results is crucial to mass spectrometry‐based proteomics identification. However, the current score‐based filter solution and decoy database methods are not effective enough to prevent all false positive and false negative selections. In this study, a systematic search strategy named iterative non‐m/z‐sharing (INMZS) analysis was proposed to address the problem. In the strategy, all search results were screened based on the share status of corresponding matched m/z, only the proteins that matched with exclusive m/z information were reserved for the confident matches. The researchers did further iterative search to improve the identification of minor components in a spot. Finally, identifications were confirmed by decoy database evaluation for the final phase of protein identification. Simulation and application tests of INMZS were implemented on a large human liver data set and standard protein cocktails. The result shows that INMZS plus decoy database evaluation is efficient in ensuring the confidence and sensitivity of 2‐DE or similar non‐shotgun based proteome identification.