bluuebunny/crossref_metadata_2025 huggingface dataset:
The use of information sources by internet users in answering questions
Authors: Oh Sanghee , Oh Jung Sun , Shah Chirag
Published: June 2009

The purpose of this study was to investigate what kinds of sources people prefer to use when they answer questions online, especially, in the context of social Q&A. Social Q&A is a Web‐based service, that allows people to ask questions and receive answers from their fellow users. In social Q&A, people often cite sources of information when they answer questions. It could be a name, a short description, or hyperlinks to the original sources. Yahoo! Answers was chosen for this study due to its popularity as a top ranked social Q&A service as well as its capability for separately indicating sources for the answers in its format. We collected data with a crawler that used Yahoo! Answers APIs. A total number of 5,391 sources were identified and analyzed with the following three approaches: (1) source distribution by online accessibility, (2) source distribution by genre, and (3) source distribution by subjects. At the early stage of this study, it was expected that the results of source preferences heavily relied on sources online, since people ask and answer questions on the Web‐based service. Nevertheless, it was found that human (56.4%) was the most frequently cited type of source, and it was followed by online (40%) and offline sources (4%). According to the source distribution by genre, human (56.4%) was followed by the Internet (38.1%), books (3.6%), and mass media (1.6%), and the sub‐categories of these sources were analyzed. Additionally, the patterns of source distribution were shown differently across subjects. The categories of Health, Home & Electronics, and Society & Culture relied heavily on human sources, while Computers & the Internet included most of the Internet‐based sources of information.
A new design structure for a classification system in Korean Traditional Performing Arts
Authors: nam Park Ok , Oh Sam Gyun
Published: June 2009

Discussions of classification system design are limited to providing technical ‘recipes,’ lacking detailed “how‐to's.” In addition, previous literature has addressed collaboration in classification system design; however, there has been a lack of discussion on how collaborative system design could be formed, or on the benefits and challenges that exist in system design. This study aims to introduce a generic design model of a collaborative classification system with technical ‘recipes’. A collaborative model for classification system design involves diverse stakeholders and describes how collaboration works throughout the design process. The limitations of the current discussion of classification system design and the value of collaborative design are investigated. The results of a case study in the field of Korean Traditional Performing Arts and a design structure adopted within that field are presented. It is also noted that a collaborative model adopts process analysis techniques from social process models. The paper discusses the benefits of collaborative design in relation to specifying roles and tasks of stakeholders as well as the challenges of collaborative design in classification system.
A repository for learning objects: Supporting the reuse and repurposing of redesigned courses and their content
Authors: Barnes Svetlana , Li Fei , Polyakov Serhiy , Xu Hong , Moen William
Published: June 2009

This paper describes the design and development of a learning object repository for a new statewide higher education initiative. The Texas Higher Education Coordinating Board is funding the redesign of large undergraduate courses; the redesigned courses are intended to improve student learning, retention and outcomes. The learning object repository stores and provides access to content from these courses. Content has been decomposed into discrete learning object varying in levels of granularity. The paper provides details on the proof‐of‐concept implementation developed in Phase I of a two‐phase project. Special attention is given to key aspects such as the levels of granularity, metadata, technology, and user testing. Issues that emerged in Phase I are informing all facets of the next iteration of the repository.
Toward successful institutional repositories: Listening to IR staff's experiences
Authors: St. Jean Beth , Rieh Soo Young , Markey Karen , Yakel Elizabeth , Kim Jihyun
Published: June 2009

This poster presents a study of what is required to plan, implement, maintain, and sustain successful institutional repositories (IRs). This study is part of the MIRACLE (Making Institutional Repositories a Collaborative Learning Environment) Project, which aims to identify the factors contributing to the success of IRs and effective ways of accessing and using repositories. The data for this study were collected through telephone interviews with IR managers and staff members. Interviews focused on participants' motivations, experiences, and viewpoints in regard to IRs, among other IR deployment issues. The transcriptions of interviews were analyzed using content analysis. The findings indicate that IRs are more than the sum of their component parts (i.e., collections, systems, policies, staff, contributors, and end‐users); rather, they are a knowledge sharing and content management tool that works together with other types of open access infrastructure in colleges and universities.
Web searching model: Integrating multitasking, cognitive coordination and cognitive shifts
Authors: Du Jia T. , Spink Amanda
Published: June 2009

Web search models are a significant and important area of Web research. This paper outlines dissertation research to develop a Web search model that integrates processes involving multitasking, cognitive coordination and cognitive shifts. Based on previous studies, we present a preliminary conceptual model of Web search interaction incorporating multitasking, cognitive coordination and cognitive shifts. Research questions and research design are also discussed.
Web ecology: Information needs of different user groups in the context of a community college website
Authors: Yadamsuren Borchuluun , Paul Anindita , Wang Jiazhen , Wang Xin , Erdelez Sanda
Published: June 2009

College websites play an increasingly important role in the lives of students, faculty, and parents providing them with necessary information and communication opportunities. A number of researchers have studied the effectiveness of college websites, however, most of these studies focused on the needs of students. There is a research gap in understanding the information needs of multiple audiences of college websites.

This paper presents the preliminary findings of the study on information needs of multiple user groups of a community college website: traditional students, non‐traditional students, employees, parents, and prospective students. The preliminary analysis of data shows that in general, community college website users need course‐related information, information about the college, financial information, contact information, admission and career‐related information pertaining to the college. On the other hand, each group of users has distinct information needs that should be taken into account in the architecture, design, and content of community college websites to make them more effective.
User satisfaction versus retrieval effectiveness in interactive retrieval
Authors: Ma Hongyan
Published: June 2009

The current study investigates how retrieval effectiveness measured by recall and precision is related to user satisfaction in interactive retrieval. User satisfaction, the multi‐dimensional measure, is decomposed into 11 semantic differentials that are related to tasks, results, and search processes respectively. A user‐centered experiment was conducted with 24 participants and six simulated search tasks. Results demonstrated that instance precision is significantly correlated to relevant and useful search results and restful search processes. Instance recall is significantly correlated to clear, simple, and familiar tasks, relevant and useful search results, and relaxing, easy, and restful search processes. Through principal component factor analysis, two major factors underling the 11 semantic differentials are identified to correlate closely to retrieval effectiveness.
I give up! Five factors that contribute to the abandonment of information management strategies
Authors: Jones Elisabeth , Bruce Harry , Klasnja Predrag , Jones William
Published: June 2009

In this paper, we present initial findings from a six‐month study involving qualitative interviews on the topic of project‐related personal information management. Specifically, we report on the emergent theme of information management strategy abandonment ‐ that is, what factors in particular might cause people to give up on their systems for managing documents, calendars, email, and other sorts of project information. In exploring the recurrence of this theme throughout the interview data, five factors emerged as particularly compelling and frequently‐cited reasons for system abandonment: (1) visibility, (2) integration, (3) co‐adoption, (4) scalability, and (5) return on investment. We describe each of these factors in turn, using examples from the interviews for illustration. These findings, though preliminary in nature, provide a starting point for understanding why systems fail and how future systems might be designed to improve their success rate.
Legal discovery: Does domain expertise matter?
Authors: Efthimiadis Efthimis N. , Hotchkiss Mary A.
Published: June 2009

The study investigates whether legal expertise matters to find more relevant documents during the discovery phase of a request for information.
Making Faceted Classification more acceptable on the Web: A comparison of Faceted Classification and ontologies
Authors: Choi Yunseon
Published: June 2009

Both Faceted Classification and ontologies offer a consistent structure to organize web resources effectively. This paper compares Faceted Classification and ontologies to introduce the concept of making Faceted Classification work more efficiently on the Web. It concludes that if complemented by ontologies, Faceted Classification could be more usefully accepted on the Web with increased conceptual expressiveness among facets.
Undergraduates' source selection behavior: A correspondence analysis
Authors: Yoo Eun‐Young , Kim Kyung‐Sun
Published: June 2009

With advances in information technologies, a wide variety of sources and channels have been made available to provide access to information. As different sources offer information with varying qualities, evaluating and selecting quality information sources is crucial and has become a key element in bibliographic instruction and information literacy training. Despite efforts in helping them to select optimal sources, individuals choose to use sources that are not necessarily accurate or reliable. Users often turn to information sources that are not suitable to their tasks. This study aims at understanding the relationship between the perception and selection of information sources.

Surveying undergraduate students, this study examines three aspects related to their source selection behavior: (1) perceived characteristics of different sources; (2) source characteristics considered to be important for the source selection; and (3) frequently selected/used sources. The study will help understand how users view sources differently and how such perception is related to the source selection behavior. Based on the study findings, suggestions will be made to improve information literacy programs that can support the selection of the best sources.
The intersection of information behavior and coping among women undergoing breast lump diagnosis
Authors: Rubenstein Ellen
Published: June 2009

Few studies have examined the intersection of information behavior and coping of women during the time period between the discovery of a breast lump and receiving a diagnosis. Those that do look at particular segments of this time without taking the full period into consideration, leaving a gap as to the range of behaviors that may occur throughout the waiting period. This study sought to understand how information behavior interacts with the coping strategies of women who undergo the potentially stressful experience of waiting for a breast lump diagnosis.
Children's questions about science fair: Preliminary results of an analysis of digital library reference questions
Authors: Mardis Marcia A.
Published: June 2009

In this study, the researcher used a data set that contained science‐related questions from the Internet Public Library's Kidspace Ask A Question email reference form. The data showed that the majority of the questions were asked by middle school students in the United States who were preparing for science fair. A closer inspection of the question text showed that students are concerned about the process of assembling a project as well as the project's content. This finding suggests that digital libraries can support young science learners by developing a metadata vocabulary for process.
Visiting human errors in interacting with IR systems from decision making perspective
Authors: Zhang Yan
Published: June 2009

People's interaction and negotiation with an information retrieval (IR) system is a constant decision making process, where people make errors as they do in their daily lives. Knowledge of biases and heuristics inherent in human reasoning as suggested by decision‐making theories provides us a useful tool to explore the underlying cognitive processes of human errors in using IR systems. In this pilot study, we explore the potential of decision‐making theories for explaining human IR errors and propose a tentative knowledge structure of human errors in IR systems.
Remote users in our midst: Insights from the archival metrics project
Authors: Krause Magia G.
Published: June 2009

Are there any differences between in‐person and remote users of archives? This paper addresses this question through the development and testing of two survey instruments intended to help archivists conduct user evaluations of their online resources. The surveys are part of a larger toolkit developed by the Archival Metrics project consisting of five assessment instruments to help archivists evaluate the services and resources they provide to researchers. This paper focuses on the two sampling methods developed by the Archival Metrics team to elicit responses to the online surveys and the resulting differences between on‐site researchers and online users.
Mediated information retrieval in Web searching
Authors: Lee Hyuk‐Jin
Published: June 2009

This study investigated whether the existence of either the mediated condition through a collection in a specific domain or the combined display of a clustered structure and a linear ranked list of search results would affect the three main measures of the user's Web searching behaviors: effectiveness, efficiency, and usability. That is, mediated access through a structured collection helps the user explore a small well‐structured document collection covering a specific subject domain in order to clarify her/his information needs before search on the World Wide Web. The results of the study demonstrated that all the measures had interesting results via the adaptive process on the system and the search task. The findings of this research contribute to a better understanding of how the mediation system or the combined display supports a Web information user.
Factors that influence users to leave, acquire, and retain information items: A case study of college students' Personal Information Management
Authors: Finneran Christina M.
Published: June 2009

Personal Information Management (PIM) research has primarily focused on how users manage information items that are in their local collection, under their control. This investigation will broadly study PIM, additionally looking at items that users decide not to acquire, and seeks to identify factors that influence the leaving, acquiring, and retaining behavior. A theoretical framework developed for the study introduces the hoarding literature into the Personal Information Management (PIM) domain. The study uses a multiple‐embedded case study design to naturalistically study students' PIM within the context of a college course.
The Archival Metrics Toolkit: Development and implementation
Authors: Yakel Elizabeth , McKay Aprille , Duff Wendy , Cherry Joan , Tibbo Helen
Published: June 2009

User based evaluation in archives and manuscript repositories lags behind that of libraries and museums. This paper discusses the development and testing of the Archival Metrics Toolkit which is designed to support archivists in conducting user‐based evaluations. The current Toolkit includes 5 different questionnaires focused on assessing various archival services in Colleges and Universities as well as instructions for administration and data analysis. The questionnaires aim to gather feedback from (1) onsite users of the reading room, (2) students who have attended an orientation session and (3) instructors who use the archives for teaching, as well as (4) online users of the website and (5) online users of finding aids.
Searcher adaptation: A response to topic difficulty
Authors: Smith Catherine L.
Published: June 2009

Some search topics pose little challenge to a search system (“easy”), and some are more difficult (“hard”). We investigated the relationship between one measure of searcher behavior (queries entered per minute), and one measure of system response (the average length of the lists returned) for topics at two levels of difficulty. Specifically, each of 36 participants searched for information about 12 topics: 2 that were “easy” and 10 that were “hard”. We find that when working on easy topics, searchers entered queries less frequently over the course of the search. We also find that lists of retrieved items, as returned by the system, were longer on average for easy topics. We propose that these findings may be useful in designing interactive search systems capable of “awareness” of search difficulty.
Identifying reusable resources in digital reference answers
Authors: Pomerantz Jeffrey , Haas Stephanie W. , Hecht Eliah
Published: June 2009

What can we learn from resources provided in answers to digital reference questions? Using the Internet Public Library's archive of over 60,000 records of answered reference questions, this project aims to determine (1) characteristics of resources provided in answers to digital reference questions, (2) the extent to which these resources are reusable in future answers, and (3) the useful lifespan of a resource that has been provided. As part of our research, we have developed an XML schema for digital reference questions and answers.
A categorical comparison between user‐supplied tags and web search queries for images
Authors: Chung EunKyung , Yoon JungWon
Published: June 2009

Although social tagging has received attention in the LIS field as a promising information organization mechanism, there is little research comparing user‐supplied tags and search queries. For using user‐supplied tags as an alternative or supplementary tool for existing image representation schemes, there should be evidence which demonstrate to what extent there are similarities and/or differences between user‐supplied tags and search terms. Based on these considerations, this study investigates categorical differences between user supplied tags and Web search queries. Using Shatford's categories, the study identifies categorical characteristics of tags and queries. Using the 1st level of categories, a rough comparison was made. User‐supplied tags contain Generic terms for the majority, but Web search queries include Specific terms, rather than Generic terms. For a more detailed comparison between tags and queries, the 2nd level of categories from Shatford's was adopted. In most of subcategories, the categorical comparisons between tags and queries demonstrate considerable differences. Although this result is based on a small size of data sets, the result of this study can impact the way of social tagging systems and indexing/ranking systems of Web search engines for images.
Application of Hadamard spectroscopy to automated structure verification in high‐throughput NMR
Authors: Ruan Ke , Yang Shengtian , Van Sant Karey A. , Likos John J.
Published: June 2009

Combined verification using 1‐D proton and HSQC has been proved to be quite successful; the acquisition time of HSQC spectra, however, can be limiting in its high‐throughput applications. The replacement with Hadamard HSQC can significantly enhance the throughput. We hereby propose a protocol to optimize the grouping of the predicted carbon chemical shifts from the proposed structure and the associated Hadamard frequencies and bandwidths. The resulting Hadamard HSQC spectra compare favorably with their Fourier‐transformed counterparts, and have demonstrated to perform equivalently in terms of combined verification, but with several fold enhancement in throughput, as illustrated for 21 commercial available molecules and 16 prototypical drug compounds. Further improvement of the verification accuracy can be achieved by the cross validation from Hadamard TOCSY, which can be acquired without much sacrifice in throughput. Copyright © 2009 John Wiley & Sons, Ltd.
Relationships among bleeding severity, health‐related quality of life, and platelet count in children with immune thrombocytopenic purpura
Authors: Neunert Cindy E. , Buchanan George R. , Blanchette Victor , Barnard Dorothy , Young Nancy L. , Curtis Christine , Klaassen Robert J.
Published: June 2009

Important outcomes for children with immune thrombocytopenic purpura (ITP) include health‐related quality of life (HRQOL) and bleeding severity. A HRQOL instrument for children with ITP, the Kids' ITP Tools (KIT), was recently validated. Secondary analysis of the KIT database was performed to determine relationships among platelet count, bleeding severity and HRQOL. Bleeding severity grade correlated with platelet count in chronic ITP but not in acute ITP. Platelet count and bleeding severity failed to have any statistically significant correlations with the KIT scores. These findings suggest that relationships among outcome measures in children with ITP, using currently available instruments, remain poorly defined. Pediatr Blood Cancer 2009;53:652–654. © 2009 Wiley‐Liss, Inc.
Hypercalcemia and osteoblastic lesions induced by 13‐Cis‐retinoic acid mimicking relapsed neuroblastoma
Authors: Cross Siobhan F. , Pozza Luciano Dalla , Munns Craig F.
Published: June 2009

A 6‐year‐old male diagnosed with extensive neuroblastoma was treated with chemotherapy, surgery, autotransplantation, and radiotherapy. He was then enrolled on a study to assess the monoclonal antibody Ch14.18 (anti‐GD2) with 13 cis‐retinoic acid. 13‐cis‐retinoic acid therapy caused severe bone pain and hypercalcemia. Bone scans showed multiple osteoblastic lesions suggesting recurrent disease however MIBG scans were negative. Serum markers of bone turnover were increased and the patient required pamidronate therapy to treat persistent hypercalcemia. Retinoic acid toxicity needs to be considered in the differential of painful osteoblastic lesions and/or hypercalcemia. MIBG scans can assist in differentiating from recurrent disease. Pediatr Blood Cancer 2009;53:666–668. © 2009 Wiley‐Liss, Inc.
Health care utilization and expenditures for privately and publicly insured children with sickle cell disease in the United States
Authors: Mvundura Mercy , Amendah Djesika , Kavanagh Patricia L. , Sprinz Philippa G. , Grosse Scott D.
Published: June 2009

Background

There are no current national estimates on health care utilization and expenditures for US children with sickle cell disease (SCD).

Procedure

We used the MarketScan® Medicaid Database and the MarketScan® Commercial Claims and Encounters Database for 2005 to estimate health services use and expenditures. The final samples consisted of 2,428 Medicaid‐enrolled and 621 privately insured children with SCD.

Results

The percentage of children with SCD enrolled in Medicaid with an inpatient admission was higher compared to those privately insured (43% vs. 38%), yet mean expenditures per admission were 35% lower ($6,469 vs. $10,013). The mean number of emergency department (ED) visits was 49% higher for Medicaid‐enrolled children compared to those with private insurance (1.36 vs. 0.91), but mean expenditures per ED visit were 28% lower. The mean number of non‐ED outpatient visits was similar (12.6 vs. 11.5) but mean expenditures were 40% lower for the Medicaid‐enrolled children ($3,557 vs. $5,908). The mean expenditures on drug claims were higher among those with Medicaid than private insurance ($1,049 vs. $531). Mean total expenditures for children with SCD enrolled in Medicaid were 25% lower than for privately insured children ($11,075 vs. $14,722). The samples were comparable with respect to SCD‐related inpatient discharge diagnoses and use of outpatient blood transfusions.

Conclusions

Children with SCD enrolled in Medicaid had lower expenditures than privately insured children, despite higher utilization of medical care, which indicates lower average reimbursements. Research is needed to assess the quality of care delivered to Medicaid‐enrolled children with SCD and its relation to health outcomes. Pediatr Blood Cancer 2009;53:642–646. Published 2009 Wiley‐Liss, Inc.
Protein–protein interactions at an enzyme–substrate interface: Characterization of transient reaction intermediates throughout a full catalytic cycle of Escherichia coli thioredoxin reductase
Authors: Negri Ana , Rodríguez‐Larrea David , Marco Esther , Jiménez‐Ruiz Antonio , Sánchez‐Ruiz José M. , Gago Federico
Published: June 2009

A large collection of structural snapshots along a full catalytic cycle of Escherichia coli thioredoxin reductase (TrxR) has been generated and characterized using a combination of theoretical methods. Molecular models were built starting from the available X‐ray crystallographic structures of dimeric wild‐type TrxR in the flavin‐oxidizing conformation and a C135S TrxR mutant enzyme in a flavin‐reducing conformation “trapped” by a cross‐link between Cys138 of TrxR and Cys32 of C35S mutant thioredoxin (Trx). The transition between these two extreme states, which is shown to be reproduced in a normal mode analysis, as well as natural cofactor binding and dissociation, were simulated for the wild‐type species using unrestrained and targeted molecular dynamics following docking of oxidized Trx to reduced TrxR. The whole set of simulations provides a comprehensive structural framework for understanding the mechanism of disulfide reduction in atomic detail and identifying the most likely intermediates that facilitate entry of NADPH and exit of NADP+. The crucial role assigned to Arg73 and Lys36 of Trx in substrate binding and complex stabilization was ascertained when R73G, R73D, and K36A site‐directed mutants of Trx were shown to be impaired to different extents in their ability to be reduced by TrxR. On the basis of previous findings and the results reported herein, E. coli TrxR appears as a beautifully engineered molecular machine that is capable of synchronizing cofactor capture and ejection with substrate binding and redox activity through an interdomain twisting motion. Proteins 2010. © 2009 Wiley‐Liss, Inc.
Prediction of global and local model quality in CASP8 using the ModFOLD server
Authors: McGuffin Liam J.
Published: June 2009

The development of effective methods for predicting the quality of three‐dimensional (3D) models is fundamentally important for the success of tertiary structure (TS) prediction strategies. Since CASP7, the Quality Assessment (QA) category has existed to gauge the ability of various model quality assessment programs (MQAPs) at predicting the relative quality of individual 3D models. For the CASP8 experiment, automated predictions were submitted in the QA category using two methods from the ModFOLD server–ModFOLD version 1.1 and ModFOLDclust. ModFOLD version 1.1 is a single‐model machine learning based method, which was used for automated predictions of global model quality (QMODE1). ModFOLDclust is a simple clustering based method, which was used for automated predictions of both global and local quality (QMODE2). In addition, manual predictions of model quality were made using ModFOLD version 2.0—an experimental method that combines the scores from ModFOLDclust and ModFOLD v1.1. Predictions from the ModFOLDclust method were the most successful of the three in terms of the global model quality, whilst the ModFOLD v1.1 method was comparable in performance to other single‐model based methods. In addition, the ModFOLDclust method performed well at predicting the per‐residue, or local, model quality scores. Predictions of the per‐residue errors in our own 3D models, selected using the ModFOLD v2.0 method, were also the most accurate compared with those from other methods. All of the MQAPs described are publicly accessible via the ModFOLD server at: http://www.reading.ac.uk/bioinf/ModFOLD/. The methods are also freely available to download from: http://www.reading.ac.uk/bioinf/downloads/. Proteins 2009. © 2009 Wiley‐Liss, Inc.
Identification of specificity and promiscuity of PDZ domain interactions through their dynamic behavior
Authors: Gerek Z. Nevin , Keskin Ozlem , Ozkan S. Banu
Published: June 2009

PDZ domains (PDZs), the most common interaction domain proteins, play critical roles in many cellular processes. PDZs perform their job by binding specific protein partners. However, they are very promiscuous, binding to more than one protein, yet selective at the same time. We examined the binding related dynamics of various PDZs to have insight about their specificity and promiscuity. We used full atomic normal mode analysis and a modified coarse‐grained elastic network model to compute the binding related dynamics. In the latter model, we introduced specificity for each single parameter constant and included the solvation effect implicitly. The modified model, referred to as specific‐Gaussian Network Model (s‐GNM), highlights some interesting differences in the conformational changes of PDZs upon binding to Class I or Class II type peptides. By clustering the residue fluctuation profiles of PDZs, we have shown: (i) binding selectivities can be discriminated from their dynamics, and (ii) the dynamics of different structural regions play critical roles for Class I and Class II specificity. s‐GNM is further tested on a dual‐specific PDZ which showed only Class I specificity when a point mutation exists on the βA‐βB loop. We observe that the binding dynamics change consistently in the mutated and wild type structures. In addition, we found that the binding induced fluctuation profiles can be used to discriminate the binding selectivity of homolog structures. These results indicate that s‐GNM can be a powerful method to study the changes in binding selectivities for mutant or homolog PDZs. Proteins 2009. © 2009 Wiley‐Liss, Inc.
Two modes of electroluminescence from single‐walled carbon nanotubes
Authors: Lefebvre Jacques , Austing D. Guy , Finnie Paul
Published: June 2009

The electroluminescence from single‐walled carbon nanotube field effect transistors is spectrally resolved, and shows two distinct modes of light emission. The vast majority of nanotubes have spectrally broad emission consistent with the spectrum of blackbody radiation. Much more rarely, superposed on the broad emission is a single narrow (<50 meV) peak which is consistent with expectation for electron–hole recombination. The narrow emission is strong even at lower biases and in general has greater peak intensity than the broadband emission. (© 2009 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Simplification of the CBS‐QB3 method for predicting gas‐phase deprotonation free energies
Authors: Casasnovas Rodrigo , Frau Juan , Ortega‐Castro Joaquín , Salvà Antoni , Donoso Josefa , Muñoz Francisco
Published: June 2009

Simplified versions of CBS‐QB3 model chemistry were used to calculate the free energies of 36 deprotonation reactions in the gas phase. The best such version, S9, excluded coupled cluster calculation [CCSD(T)], and empirical (ΔEemp) and spin‐orbit (ΔEint) correction terms. The mean absolute deviation and root mean square thus obtained (viz. 1.24 and 1.56 kcal/mol, respectively) were very‐close to those provided by the original CBS‐QB3 method (1.19 and 1.52 kcal/mol, respectively). The high‐accuracy of the proposed simplification and its computational expeditiousness make it an excellent choice for energy calculations on gas‐phase deprotonation reactions in complex systems. © 2009 Wiley Periodicals, Inc. Int J Quantum Chem, 2010
First‐principles calculation of magnetic circular dichroism of transition‐metal L2,3‐edge X‐ray absorption near‐edge structures
Authors: Ogasawara K. , Chaya A. , Watanabe S. , Yoshida H.
Published: June 2009

We performed first‐principles calculations for the magnetic circular dichroism of transition‐metal (TM) L2,3‐edge X‐ray absorption near‐edge structures of some rock‐salt type TM oxides using the relativistic discrete‐variational multielectron method. We also investigated the validity of the sum rules quantitatively by comparing the magnetic moments calculated from the theoretical spectra using the sum rules and those calculated directly from the explicit many‐electron wave functions. It was found that discrepancy is significant in the case of the spin moment. The configuration analysis of the many‐electron wave function indicated that the magnitude of the mixing between L2 and L3 edges could be the major cause of this discrepancy. © 2009 Wiley Periodicals, Inc. Int J Quantum Chem, 2009
Interpretation of the emission fluorescence spectra of two fluoroionophores: DMABN‐Crown4 and DMABN‐Crown5
Authors: Carlotto Silvia , Ferrante Camilla , Polimeno Antonino , Benzi Caterina , Barone Vincenzo
Published: June 2009

We discuss an interpretation of the emission signal of a class of dimethylaminobenzonitrile (DMABN) derivatives, based on a stochastic model approach. This study is prompted by the interest in building relatively simple theoretical tools for understanding the static and dynamic properties of metal chelation‐controlled fluorescent molecular systems with internal flexibility and solvation effects, which can be used as fluorescent sensors of metal ions. We proceed by extending a stochastic modeling approach, previously used for DMABN, in which internal degrees of freedom are coupled to an effective solvent relaxation variable. The model is based on an integrated approach that combines stochastic methods and QM calculations. The static and dynamic properties of the molecule are obtained by a combination of a continuum treatment and a detailed solute dynamics. Simple computational approximations lead to a semianalytical treatment of the resulting equations, which reproduce correctly the static spectra at room temperature of 4‐(1‐aza‐4,7,10‐trioxacyclododecyl) benzonitrile (DMABN‐Crown4) and 4‐(1‐aza‐4,7,10,13‐tetraoxacyclododecyl) benzonitrile (DMABN‐Crown5) in solvents with different polarity. A qualitative analysis of the dynamic spectra of the DMABN‐Crown4 is also presented. A discussion is finally provided on how combined quantum and classical methods can be used to define a general robust and reliable computational approach for predicting fluorescence properties of organic molecules in solution. © 2009 Wiley Periodicals, Inc. Int J Quantum Chem, 2010
Magnetic vortex dynamics induced by an electrical current
Authors: Gaididei Yuri , Kravchuk Volodymyr P. , Sheka Denis D.
Published: June 2009

A magnetic nanoparticle in a vortex state is a promising candidate for the information storage. One bit of information corresponds to the upward or downward magnetization of the vortex core (vortex polarity). The dynamics of the magnetic vortex driven by a spin current is studied theoretically. Using a simple analytical model and numerical simulations, we show that a nondecaying vortex motion can be excited by a dc spin–polarized current, whose intensity exceeds a first threshold value as a result of the balance between a spin‐torque pumping and damping forces. The irreversible switching of the vortex polarity takes place for a current above a second threshold. The mechanism of the switching, which involves the process of creation and annihilation of a vortex–antivortex pair is described analytically, using a rigid model, and confirmed by detailed spin–lattice simulations. © 2009 Wiley Periodicals, Inc. Int J Quantum Chem, 2010
Models for the adsorption and self‐assembly of ethanol and 1‐decanethiol on Au(111) surfaces. A comparative study by computer simulation
Authors: Fartaria Rui P. S. , Freitas Filomena F. M. , Silva Fernandes Fernando M. S.
Published: June 2009

Results from computer simulations, based on different models to study theadsorption and self‐assembly of the ethanol and 1‐decanethiol on gold surfaces, Au(111), are presented. Canonical ensemble Monte Carlo simulations were performed at 298 K using two different force fields. One from DFT calculations, where the gold electrode has an explicit structure (corrugated electrode), and the other representing an electrode, in which the structure is taken into account on an average way (flat electrode). The behavior of the ethanol adsorption on gold surfaces, with and without the 1‐decanethiol presence, is analyzed. The introduction of molecular flexibility is also discussed. The relative surface density for the ethanol oxygen, adsorbed on gold, and the density profiles, in different conditions, show that the structure of the surface has a fundamental role on the way the adsorption takes place, not only on the preferential adsorption sites of the surface but also on the ethanol distribution over the electrodes. Potentials of mean force have also been calculated for the two surface models, giving the free energy barriers to the 1‐decanethiol crossing of the solvent adsorption layers. The average tilt angle, obtained with a single thiol molecule in the simulation box, presents the values: ∼26° for the rigid molecule model and 74° ± 18° for the flexible one. These differences are analyzed. © 2009 Wiley Periodicals, Inc. Int J Quantum Chem, 2010
Three computational mise‐en‐scènes of red‐ and blue‐shifted hydrogen bonding motifs: Concept of negative intramolecular coupling—What else?
Authors: Kryachko Eugene S.
Published: June 2009

This work is a kind of attempt to rethink some problems which are related to the blue‐shifted “hydrogen bonds” and which have been left in the past decade as not yet fully resolved. The impetus for such rethink is originated from the three computational mise‐en‐scènes on red‐ and blue‐shifted hydrogen bonding motifs, which are aimed to be thoroughly studied in this work, thus resolving the above problems. © 2009 Wiley Periodicals, Inc. Int J Quantum Chem, 2010
Conditions on the Kohn–Sham kinetic energy and associated density
Authors: Trickey S. B. , Karasiev V. V. , Jones R. S.
Published: June 2009

Effective, explicitly density‐dependent (i.e., orbital‐free) approximations to the Kohn–Sham kinetic energy functional Ts remain elusive. In the course of developing such functionals in collaboration with Frank Harris, various issues have arisen that have gone unaddressed. We consider four of them here: positivity of the KS kinetic energy density, supposed requirements on its functional dependence, the use of cutoffs to insure positivity, and the role of the Coulomb virial theorem in the asymptotic analysis of Ts. © 2009 Wiley Periodicals, Inc. Int J Quantum Chem, 2009
Gas‐phase fragmentation study of biotin reagents using electrospray ionization tandem mass spectrometry on a quadrupole orthogonal time‐of‐flight hybrid instrument
Authors: Sioud Salim , Genestie Benoit , Jahouh Farid , Martin Patrick , Banoub Joseph
Published: June 2009

In this study, we evaluated, by electrospray ionization mass spectrometry (ESI‐MS) and collision‐induced dissociation tandem mass spectrometry (CID‐MS/MS) using a quadrupole orthogonal time‐of‐flight (QqToF)‐MS/MS hybrid instrument, the gas‐phase fragmentations of some commercially available biotinyl reagents. The biotin reagents used were: psoralen‐BPE 1, p‐diazobenzoyl biocytin (DBB) 2, photoreactive biotin 3, biotinyl‐hexaethyleneglycol dimer 4, and the sulfo‐SBED 5. The results showed that, during ESI‐MS and CID‐MS/MS analyses, the biotin reagents followed a similar gas‐phase fragmentation pattern and the cleavages usually occurred at either end of the spacer arm of the biotin reagents. In general we have observed that the CID‐MS/MS fragmentation routes of the five precursor protonated molecules obtained from the biotin linkers 1–5 afforded a series of product ions formed essentially by similar routes. The genesis and the structural identities of all the product ions obtained from the biotin linkers 1–5 have been assigned. All the exact mass assignments of the protonated molecules and the product ions were verified by conducting separate CID‐MS/MS analysis of the deuterium‐labelled precursor ions. Copyright © 2009 John Wiley & Sons, Ltd.
Fuzzy pole placement based on piecewise Lyapunov functions
Authors: Tognetti Eduardo S. , Oliveira Vilma A.
Published: June 2009

This paper presents a controller design method for fuzzy dynamic systems based on piecewise Lyapunov functions with constraints on the closed‐loop pole location. The main idea is to use switched controllers to locate the poles of the system to obtain a satisfactory transient response. It is shown that the global fuzzy system satisfies the requirements for the design and that the control law can be obtained by solving a set of linear matrix inequalities, which can be efficiently solved with commercially available softwares. An example is given to illustrate the application of the proposed method. Copyright © 2009 John Wiley & Sons, Ltd.
Site‐specific dual ink dip pen nanolithography™
Authors: Nafday Omkar A. , Haaheim Jason R. , Villagran Fredy
Published: June 2009

The ability to deposit different materials with nanoscale precision at user‐specified locations is a very important attribute of dip pen nanolithography (DPN®). However, the potential of DPN goes beyond simple deposition since DPN used in conjunction with lateral force microscopy (LFM) allows site‐specific investigations of nanoscale properties. In this work, we use two different inks, 16‐mercaptohexadecanoic acid (MHA) and 1‐octadecanethiol (ODT) to show site‐specific dual ink DPN enabled exclusively by our proprietary software. A diamond‐dot pattern was created by using a layer‐to‐layer alignment (LLA) algorithm, which enables a MHA pattern (diamond) to be written concentric with another ODT (central dot) pattern. This simple demonstration of multi‐ink DPN is not specific to alkanethiol ink systems, but is also applicable to other multi‐material patterning, interaction, and exchange studies. SCANNING 31: 122–126, 2009. © 2009 Wiley Periodicals, Inc.
M X‐ray production cross sections for heavy elements by proton impact
Authors: Deghfel B. , Nekkab M. , Kahoul A.
Published: June 2009

We present in this paper, M‐shell ionization cross sections and M X‐ray production cross sections calculated within the Energy loss, Coulomb deflection, Perturbed Stationary State and Relativistic effects (ECPSSR) theory for elements with 72 ≤ Z ≤ 90 for protons with 0.1–4.0 MeV energy. Our results are compared to the plane wave Born approximation (PWBA) predictions, the relativistic plane‐wave Born approximation including corrections for binding and Coulomb deflection effect (RPWBA‐BC) results and the ECPSSR calculations from earlier works. On the other hand, semiempirical and empirical M X‐ray production cross sections are deduced from the polynomial fitting of the available experimental data collected from different sources. A comparison is made between the different sets of results. The differences between the above calculations and the experimental results are pointed out and discussed. Copyright © 2009 John Wiley & Sons, Ltd.
Acute activation of acid ceramidase affects cytokine‐induced cytotoxicity in rat islet β‐cells
Authors: Zhu Qun , Shan Xiaohong , Miao Heng , Lu Yibing , Xu Jiarong , You Na , Liu Chao , Liao Duan-fang , Jin Junfei
Published: June 2009

Ceramidase hydrolyzes ceramide and produces sphingosine as a substrate of sphingosine kinase (SPHK), which transforms sphingosine to sphingosine‐1‐phosphate. It has been reported that cytokines elicit SPHK activation in rat β‐cells. As a sphingosine provider, ceramidase should also be activated. In our previous work, we showed that the increase in mRNA and protein levels in cytokine‐treated INS‐1 rat β‐cells resulted in chronic activation of neutral ceramidase. Here we found that acid ceramidase (AC) is activated by cytokines at an early stage via tyrosine phosphorylation. In addition, basal AC activity was first detected in INS‐1 cells and isolated rat islets, and cytokine‐induced cell growth was significantly repressed when AC was pharmacologically inhibited.
Dietary polyunsaturated fatty acids and adaptation to chronic hypoxia alter acyl composition of serum and heart lipids
Authors: Balková Patricie , Ježková Jana , Hlaváčková Markéta , Neckář Jan , Staňková Barbora , Kolář František , Novák František , Nováková Olga
Published: June 2009

The effects of dietary supplementation with fat of different fatty acid profile and chronic intermittent hypoxia (CIH) on the fatty acid composition of serum and heart lipids were analysed. Adult male Wistar rats were fed a standard non-fat diet enriched with 10 % of lard, fish oil (n-3 PUFA) or maize oil (n-6 PUFA) for 10 weeks. After 4 weeks on the diets, each group was divided in two subgroups, either exposed to CIH in a barochamber (7000 m, twenty-five exposures) or kept at normoxia. In normoxic rats, the fish oil diet increased the level of conjugated dienes. Then-6:n-3 PUFA ratio in serum TAG, phospholipids (PL), cholesteryl esters (CE) and heart TAG, PL and diacylglycerols (DAG) followed the ratio in the fed diet (in the sequence maize oil>lard>fish oil). In heart TAG, PL and DAG, 20 : 4n-6 and 18 : 2n-6 were replaced by 22 : 6n-3 in the fish oil group. The main fatty acid in CE was 20 : 4n-6 in the lard and maize oil groups whereas in the fish oil group, half of 20 : 4n-6 was replaced by 20 : 5n-3. CIH further increased 20 : 5n-3 in CE in the fish oil group. CIH decreased then-6:n-3 PUFA ratio in serum CE, heart TAG, PL and DAG in all dietary groups and stimulated the activity of catalase in the maize and fish oil groups. In conclusion, PUFA diets and CIH, both interventions considered to be cardioprotective, distinctly modified the fatty acid profile in serum and heart lipids with specific effects on conjugated diene production and catalase activity.