bluuebunny/crossref_metadata_2025_split huggingface dataset:
New insights into structure‐function relationships between archeal ATP synthase (A1A0) and vacuolar type ATPase (V1V0)
Authors: Grüber Gerhard , Marshansky Vladimir 
Published: February 2009

AbstractAdenosine triphosphate, ATP, is the energy currency of living cells. While ATP synthases of archae and ATP synthases of pro‐ and eukaryotic organisms operate as energy producers by synthesizing ATP, the eukaryotic V‐ATPase hydrolyzes ATP and thus functions as energy transducer. These enzymes share features like the hydrophilic catalytic‐ and the membrane‐embedded ion‐translocating sector, allowing them to operate as nano‐motors and to transform the transmembrane electrochemical ion gradient into ATP or vice versa. Since archaea are rooted close to the origin of life, the A‐ATP synthase is probably more similar in its composition and function to the “original” enzyme, invented by Nature billion years ago. On the contrary, the V‐ATPases have acquired specific structural, functional and regulatory features during evolution. This review will summarize the current knowledge on the structure, mechanism and regulation of A‐ATP synthases and V‐ATPases. The importance of V‐ATPase in pathophysiology of diseases will be discussed. BioEssays 30:1096–1109, 2008. © 2008 Wiley Periodicals, Inc.
Bacterial microcompartments: their properties and paradoxes
Authors: Cheng Shouqiang , Liu Yu , Crowley Christopher S. , Yeates Todd O. , Bobik Thomas A. 
Published: February 2009

AbstractMany bacteria conditionally express proteinaceous organelles referred to here as microcompartments (Fig. 1). These microcompartments are thought to be involved in a least seven different metabolic processes and the number is growing. Microcompartments are very large and structurally sophisticated. They are usually about 100–150 nm in cross section and consist of 10,000–20,000 polypeptides of 10–20 types. Their unifying feature is a solid shell constructed from proteins having bacterial microcompartment (BMC) domains. In the examples that have been studied, the microcompartment shell encases sequentially acting metabolic enzymes that catalyze a reaction sequence having a toxic or volatile intermediate product. It is thought that the shell of the microcompartment confines such intermediates, thereby enhancing metabolic efficiency and/or protecting cytoplasmic components. Mechanistically, however, this creates a paradox. How do microcompartments allow enzyme substrates, products and cofactors to pass while confining metabolic intermediates in the absence of a selectively permeable membrane? We suggest that the answer to this paradox may have broad implications with respect to our understanding of the fundamental properties of biological protein sheets including microcompartment shells, S‐layers and viral capsids. BioEssays 30:1084–1095, 2008. © 2008 Wiley Periodicals, Inc.
The role of the ubiquitin proteasome system in synapse remodeling and neurodegenerative diseases
Authors: Ding Mei , Shen Kang 
Published: February 2009

AbstractThe ubiquitin proteasome system is a potent regulatory mechanism used to control protein stability in numerous cellular processes, including neural development. Many neurodegenerative diseases are featured by the accumulation of UPS‐associated proteins, suggesting the UPS dysfunction may be crucial for pathogenesis. Recent experiments have highlighted the UPS as a key player during synaptic development. Here we summarize recent discoveries centered on the role of the UPS in synapse remodeling and draw attention to the potential link between the synaptic UPS dysfunction and the pathology of neurodegenerative diseases. BioEssays 30:1075–1083, 2008. © 2008 Wiley Periodicals, Inc.
Proposed three‐letter abbreviations for homologues of the coded amino acids
Authors: Burton James A. 
Published: February 2009

AbstractDEAR EDITOR:A three‐letter code to identify homologues of the coded amino acids is proposed. The first letter is taken from the one‐letter code used for amino acids and identifies the side chain functional group that distinguishes the coded amino acid. To this is added two lower case letters identifying the number of carbon atoms in the homologue. © 2009 Wiley Periodicals, Inc. Biopolymers (Pept Sci) 92: 132–136, 2009.This article was originally published online as an accepted preprint. The “Published Online” date corresponds to the preprint version. You can request a copy of the preprint by emailing the Biopolymers editorial office at biopolymers@wiley.com
T7 phage display as a method of peptide ligand discovery for PDZ domain proteins
Authors: Sharma Sudhir C. , Memic Adnan , Rupasinghe Chamila N. , Duc Anne‐Cécile E. , Spaller Mark R. 
Published: February 2009

AbstractThe use of bacteriophage T7 is presented as a peptide display platform to identify short binding sequences for PDZ domain proteins. Two different domains are examined, the 10th PDZ domain (PDZ10) of the multi‐PDZ domain protein 1 (MUPP1) and the third PDZ domain (PDZ3) of postsynaptic density‐95 (PSD‐95) protein. Using the T7Select 415‐1b construct, which displays 415 peptides per phage particle, a random heptapeptide and focused octapeptide libraries were constructed and subjected to iterative selection‐enrichment cycles against surface‐immobilized PDZ3 and PDZ10 proteins. The derived consensus sequences, together with those of high‐frequency clones, were used as the basis for individual chemically synthesized peptides. Each peptide was subjected to isothermal titration calorimetry binding determinations against the corresponding PDZ domain under standard solution conditions. For MUPP1 PDZ10, binding analysis demonstrated that one of the heptapeptides, Ac‐IGRISRV, displayed a two‐fold improved affinity over the octapeptide derived from the carboxy terminus of the hc‐Kit protein, which we had recently demonstrated as among the highest affinity ligands reported to date for that domain. In the case of PSD‐95 PDZ3, peptides were found that possessed low‐micromolar dissociation constants, as well as those that rediscovered the C‐terminal sequence (KQTSV) of the protein CRIPT, a known natural binding protein of PDZ3. These successful examples of ligand discovery against two distinctly different PDZ domains demonstrate that the T7 phage platform could prove broadly applicable to the numerous other PDZ domains for which binding peptides are absent or of insufficient affinity. © 2009 Wiley Periodicals, Inc. Biopolymers (Pept Sci) 92: 183–193, 2009.This article was originally published online as an accepted preprint. The “Published Online” date corresponds to the preprint version. You can request a copy of the preprint by emailing the Biopolymers editorial office at biopolymers@wiley.com
Multivalent interactions with gp120 are required for the anti‐HIV activity of Cyanovirin
Authors: Liu Yinan , Carroll Jacob R. , Holt Lindsey A. , McMahon James , Giomarelli Barbara , Ghirlanda Giovanna 
Published: February 2009

AbstractCyanovirin‐N (CV‐N) is a cyanobacterial lectin that binds to specific oligomannoses on the surface of gp120, resulting in nanomolar antiviral activity against HIV. In its monomeric form, CV‐N contains two functional carbohydrate‐binding domains, A and B. When refolded at high concentration, the protein can form a domain‐swapped dimer. To clarify the role of multiple‐binding sites in CV‐N, we previously designed a monomeric mutant, P51G‐m4‐CVN, in which the binding site on domain A was rendered ineffective by four mutations (m4); in addition, a hinge region mutation (P51G) hinders the formation of a domain swapped dimer. The protein bound gp120 with diminished affinity and was completely inactive against HIV. Here, we present two mutants, ΔQ50‐m4‐CVN and S52P‐m4‐CVN, which fold exclusively as domain‐swapped dimers while containing the four mutations that abolish domain A. The dimers contain two intact B domains, thus restoring multivalency. ΔQ50‐m4‐CVN and S52P‐m4‐CVN bind gp120 at low‐nanomolar concentrations and recover in part the antiviral activity of wt CV‐N. These results indicate that the number of carbohydrate binding domains, rather than their identity, is crucial to CV‐N functionality. © 2009 Wiley Periodicals, Inc. Biopolymers (Pept Sci) 92: 194–200, 2009.This article was originally published online as an accepted preprint. The “Published Online” date corresponds to the preprint version. You can request a copy of the preprint by emailing the Biopolymers editorial office at biopolymers@wiley.com
Local‐loop based robot action control module using independent microprocessors
Authors: Chen Chao Hung , Lin Hsiung Cheng , Liu Ying Chu , Hsu Wei Chung 
Published: February 2009

AbstractWith increasing demand of robot applications in industry or other areas, the development of both reliable and low‐cost robot action control system is getting much attention in recent years. This paper has proposed a local‐loop based robot action control module using independent microprocessors. The robot action commands transmitted from PC via RS232 can be received by the individual authorized microprocessor. There are up to tens of modules to be operated for a variety of robot actions simultaneously and independently. Real world performance results are presented to demonstrate the effectiveness of the proposed approach in term of simple, flexible and efficient performance. © 2009 Wiley Periodicals, Inc. Comput Appl Eng Educ 18: 593–606, 2010; View this article online atwileyonlinelibrary.com; DOI 10.1002/cae.20250
Real‐time motor current signature analysis tool for undergraduate laboratory
Authors: Idowu Peter , Root Christopher 
Published: February 2009

AbstractThe typical electrical engineering (EE) undergraduate curriculum is packed with foundational materials and offers limited room for other desirable materials that could be readily applied in the power industry. A Motor Current Signature Analysis (MCSA) tool is developed for effectively teaching the concepts of induction motor fault detection within one lecture or laboratory period. © 2009 Wiley Periodicals, Inc. Comput Appl Eng Educ 18: 634–639, 2010; View this article online at wileyonlinelibrary.com; DOI 10.1002/cae.20263
Simulations as a new physics teaching tool
Authors: Martinez Elvira , Carbonell Victoria , Florez Mercedes , Amaya Jose 
Published: February 2009

AbstractIn the past 15 years, physics education research has shed light on the difficulties students encounter in learning physics. In response, a wide variety of new models of physics instruction have become available. In the last 4 years, we developed a physics remedial course to decrease the dropout rate of university students while promoting more efficient learning of the principles and laws of physics. To motivate students to do research on physical phenomena we focused our attention on simulations to help students learn different subjects concerning physics word. This article presents examples of simulations generated by the authors using Modellus software for interactive learning of simple harmonic motion. In addition, videotapes, tests and other didactic material are available for students in a virtual environment. © 2009 Wiley Periodicals, Inc. Comput Appl Eng Educ 18: 757–761, 2010; View this article online at wileyonlinelibrary.com; DOI 10.1002/cae.20266
A remotely accessible and configurable electronics laboratory implementation by using LabVIEW
Authors: Azaklar Sezen , Korkmaz Hayriye 
Published: February 2009

AbstractIn this article, selected applications from the experiments included in undergraduate Electronics and Computer Education curriculum are transformed into remotely accessible and configurable manner. The experiment user interfaces and publishing over the internet is developed in LabVIEW. These experiments are suitable for online conduction where students are either in‐class or laboratory on‐campus and/or at home. In this work, four different remotely configurable experiment modules are designed and implemented. Remotely configurable facility in a predefined range is performed by using switches activated by DO terminals of a data acquisition card through a web‐based application. In this way, students can select the desired experiment from the ones stored on the PCB, adjust the voltage applied to the input terminal of the circuit and change the circuit elements values by using telepresence methodology. © 2009 Wiley Periodicals, Inc. Comput Appl Eng Educ 18: 709–720, 2010; View this article online atwileyonlinelibrary.com; DOI 10.1002/cae.20276
Scaffolding for automotive air conditioning learning environment
Authors: Liang Janus S. 
Published: February 2009

AbstractThis research is to construct a scaffold‐based learning environment of automotive air conditioning system repair and maintenance by using technologies of Internet, virtual reality, CAD graphic processing and 2D animation. It is a useful system of air conditioning system troubleshooting training for such learners as colleague or vocational school students or novices in automotive repair industry, etc. This environment is composed of different units, helping learns to understand different types of automotive air conditioning system troubles, their causes and corresponding troubleshooting steps. In this research, an experiment composed of a pre‐test and a post‐test on the sampled learners was conducted to measure if the learning environment was helpful for them in improving their automotive air conditioning system troubleshooting knowledge and skills. In addition, a user satisfaction questionnaire survey was also conducted and the user satisfaction rate reached as high as nearly 0.98, indicating the learners did find the learning system satisfactory and helpful. In conclusion, the learning system developed in this research can help promote the training of automotive air conditioning system maintenance and repair. © 2009 Wiley Periodicals, Inc. Comput Appl Eng Educ 18: 736–749, 2010; View this article online atwileyonlinelibrary.com; DOI 10.1002/cae.20280
Description and evaluation of an introductory course to Matlab for a heterogeneous group of university students
Authors: Soria‐Olivas Emilio , Martín‐Guerrero José David , Martínez‐Sober Marcelino , Ayuso‐Moya Amparo 
Published: February 2009

AbstractThis paper presents the experience of the authors in teaching the Matlab™ software to students with different levels of academic training, even though all of them belong to the field of Science. Matlab™ is a worldwide standard in technical programming and computing, and its use is still growing; therefore, it is taught in many different university degree programs (Physics, Mathematics, Engineering, etc.). The course analyzed in this paper contains examples of different fields of knowledge to show the students the versatility and power of this tool. At the end of each course, which consists of 30 h, the students expressed their opinions about the content in a private opinion poll (questionnaire). The results of these opinion polls show that the methodology followed is considered appropriate and useful by the students who attended the course. © 2009 Wiley Periodicals, Inc. Comput Appl Eng Educ 18: 750–756, 2010; View this article online at wileyonlinelibrary.com; DOI 10.1002/cae.20282
A computer application for teaching and learning approximation and interpolation algorithms of curves
Authors: Gutiérrez de Ravé E. , Jiménez‐Hornero F. J. , Giráldez J. V. 
Published: February 2009

AbstractA computer teaching and learning application to help to understand the approximation and interpolation algorithms most used in engineering design has been developed. It is aimed at providing students with a visual, practical and easy‐to‐manage tool for learning and applying the principles of modelling and depicting the results of different curve generation algorithms. This application permits the user to carry out any operation related to the handling of curves depending on the characteristics and parameters of each of the algorithms included within an interactive interface. © 2009 Wiley Periodicals, Inc. Comput Appl Eng Educ 19: 40–47, 2011
Computer‐aided power system fault analysis
Authors: Ekici Sami 
Published: February 2009

AbstractMost of power systems courses contain mathematical analysis, animations, simulations, and technical tours to power stations. However, experimental studies particularly in fault analysis are very difficult due to high voltages and currents passed through short circuits. Although there are experimental equipments and prototype systems for the students, they are very expensive. This paper presents a new computer‐aided approach for power system analysis course at The University of Firat. The new course covers the previous course which contains only a short experiment by using a prototype power system. The sequence of new updated course for high‐voltage fault analysis is following: experimental implementations, simulation, signal processing and fault classification. A questionnaire containing 11 questions has been applied to students to determine the effectiveness of the new course. According to questionnaire; the updated course has been found more useful to analyze and understand the transmission line faults than the previous course. © 2009 Wiley Periodicals, Inc. Comput Appl Eng Educ 19: 66–70, 2011
Comparison of the most popular object‐oriented software languages and criterions for introductory programming courses with analytic network process: A pilot study
Authors: Anik Zelal , Baykoç Ömer Faruk 
Published: February 2009

AbstractThis study has primarily aimed at finding a tool which will facilitate the choice of programming language and making this program well‐arranged. But, choosing the proper programming language is a kind of decision making problem with multiple criterions which require the consideration of many factors which are closely interrelated. The Analytic Network Process (ANP) methodology is particularly useful for decision making in a multi‐criteria context where interaction exists between the criterions. A set of criteria for the selection of a programming language for introductory courses proposed in Parker et al. [J Inform Technol Edu USA 5: 135–142, 2006] is used in this study. These selection criterions and the criterion groups were analyzed by using the ANP, and the obtained ranking for software languages and criteria were given. © 2009 Wiley Periodicals, Inc. Comput Appl Eng Educ 19: 89–96, 2011
Remote monitoring and control of horticultural cool storage over the Internet
Authors: Omid M. , Sajjadiye S. M. , Alimardani R. 
Published: February 2009

AbstractIn this article, a distributed architecture that allows remote control and monitoring of horticultural cool storage (HCS) is presented. The various stages in the design and implementation of system for monitoring temperature and relative humidity and controlling HCS environment conditions are presented and discussed. The required hardware include a microcontroller and accompanying electronic circuitry, a server computer, serial port, temperature and relative humidity sensors and two actuators. Microcontroller transfers the sensors data to the server via serial port. Both the client and the server side programs are coded in VB programming language. They use VB MSComm control in order to communicate with the microcontroller. Internet communications is relied on socket programming. Winsock is used for network communications via the TCP/IP protocol. Sockets are configured to listen to a data port or to connect and then transmit to a remote one. Consequently information can be easily and reliably transmitted, monitored and/or controlled by the two machines. The performance of system was evaluated for 2 weeks and the results were quite satisfactory. This system can be easily adapted in other agricultural facilities such as greenhouses and silos. © 2009 Wiley Periodicals, Inc. Comput Appl Eng Educ 19: 136–145, 2011
Learning by developing a satellite navigation simulator
Authors: Aydin Serkan , Kaptan Hakan 
Published: February 2009

AbstractThis article describes a methodology to explain and understand Satellite Navigation concepts by developing simulators in the Marmara University, Technical Education Faculty, Electronics and Computer Education Department (MUTEFEC) Istanbul. At present, senior students of MUTEFEC take graduation projects interested in their professional skills. In addition some students have got developing projects related with Global Positioning System (GPS)/Galileo (EU Satellite Navigation System). In this study; to help students and accelerate their perceptions while building their project, a teaching concept for simulator‐based project developing issues in computerized environment supports the possibility of distance learning as well as a computer‐aided teaching is presented. © 2009 Wiley Periodicals, Inc. Comput Appl Eng Educ 19: 501–507, 2011
Rapid Matrix‐Assisted Refolding of Histidine‐Tagged Proteins
Authors: Dashivets Tetyana , Wood Nichole , Hergersberg Christoph , Buchner Johannes , Haslbeck Martin 
Published: February 2009

AbstractMatrix refolded: The formation of inclusion bodies, which are amorphous aggregates of misfolded insoluble protein, during recombinant protein expression, is one of the biggest bottlenecks in protein science. We report a stepwise, rational optimization procedure for refolding of insoluble proteins (see scheme). In comparison to refolding in‐solution, this parallelized, matrix‐assisted approach allows the refolding of various proteins in a fast and efficient manner.magnified imageThe formation of inclusion bodies (IBs)—amorphous aggregates of misfolded insoluble protein—during recombinant protein expression, is still one of the biggest bottlenecks in protein science. We have developed and analyzed a rapid parallel approach for matrix‐assisted refolding of recombinant His6‐tagged proteins. Efficiencies of matrix‐assisted refolding were screened in a 96‐well format. The developed methodology allowed the efficient refolding of five different test proteins, including monomeric and oligomeric proteins. Compared to refolding in‐solution, the matrix‐assisted refolding strategy proved equal or better for all five proteins tested. Interestingly, specifically oligomeric proteins displayed significantly higher levels of refolding compared to refolding in‐solution. Mechanistically, matrix‐assisted folding seems to differ from folding in‐solution, as the reaction proceeds more rapidly and shows a remarkably different concentration dependence—it allows refolding at up to 1000‐fold higher protein concentration than folding in‐solution.
Cover Picture: Two‐Dimensional Oligo(phenylene‐ethynylene‐butadiynylene)s: All‐Covalent Nanoscale Spoked Wheels (Chem. Eur. J. 11/2009)
Authors: Lei Shengbin , Ver Heyen An , De Feyter Steven , Surin Mathieu , Lazzaroni Roberto , Rosenfeldt Sabine , Ballauff Matthias , Lindner Peter , Mössinger Dennis , Höger Sigurd 
Published: February 2009

AbstractDefined two‐dimensional…︁organic structures in the 5 nm regime have been rarely produced without meeting the limits of solubility, synthetic feasibility, or uniformity. In their full paper on page 2518 ff., S. Höger, S. De Feyter, R. Lazzaroni, S. Rosenfeldt et al. present a spoked wheel that is molecularly defined, shape‐persistent, and yet fully characterizable. The 2D oligomer is formed by sixfold coupling of rim modules to a central hub and subsequent template‐directed cyclization. The structure and rigidity are confirmed by detailed STM/AFM and SANS experiments.magnified image