Mfold web server for nucleic acid folding and hybridization prediction
The abbreviated name, 'mfold web server', describes a number of closely related software applications available on the World Wide Web (WWW) for the prediction of the secondary structure of single stranded nucleic acids. The objective of this web server is to provide easy access to RNA and DNA folding and hybridization software to the scientific community at large. By making use of universally available web GUIs (Graphical User Interfaces), the server circumvents the problem of portability of this software. Detailed output, in the form of structure plots with or without reliability information, single strand frequency plots and 'energy dot plots', are available for the folding of single sequences. A variety of 'bulk' servers give less information, but in a shorter time and for up to hundreds of sequences at once. The portal for the mfold web server is http://www.bioinfo.rpi.edu/applications/mfold. This URL will be referred to as 'MFOLDROOT'.
Technology Acceptance Model 3 and a Research Agenda on Interventions
Prior research has provided valuable insights into how and why employees make a decision about the adoption and use of information technologies (ITs) in the workplace. From an organizational point of view, however, the more important issue is how managers make informed decisions about interventions that can lead to greater acceptance and effective utilization of IT. There is limited research in the IT implementation literature that deals with the role of interventions to aid such managerial decision making. Particularly, there is a need to understand how various interventions can influence the known determinants of IT adoption and use. To address this gap in the literature, we draw from the vast body of research on the technology acceptance model (TAM), particularly the work on the determinants of perceived usefulness and perceived ease of use, and: (i) develop a comprehensive nomological network (integrated model) of the determinants of individual level (IT) adoption and use; (ii) empirically test the proposed integrated model; and (iii) present a research agenda focused on potential pre- and postimplementation interventions that can enhance employees' adoption and use of IT. Our findings and research agenda have important implications for managerial decision making on IT implementation in organizations.
Enrichr: a comprehensive gene set enrichment analysis web server 2016 update
Enrichment analysis is a popular method for analyzing gene sets generated by genome-wide experiments. Here we present a significant update to one of the tools in this domain called Enrichr. Enrichr currently contains a large collection of diverse gene set libraries available for analysis and download. In total, Enrichr currently contains 180 184 annotated gene sets from 102 gene set libraries. New features have been added to Enrichr including the ability to submit fuzzy sets, upload BED files, improved application programming interface and visualization of the results as clustergrams. Overall, Enrichr is a comprehensive resource for curated gene sets and a search engine that accumulates biological knowledge for further biological discoveries. Enrichr is freely available at: http://amp.pharm.mssm.edu/Enrichr.
ExPASy: the proteomics server for in-depth protein knowledge and analysis
The ExPASy (the Expert Protein Analysis System) World Wide Web server (http://www.expasy.org), is provided as a service to the life science community by a multidisciplinary team at the Swiss Institute of Bioinformatics (SIB). It provides access to a variety of databases and analytical tools dedicated to proteins and proteomics. ExPASy databases include SWISS-PROT and TrEMBL, SWISS-2DPAGE, PROSITE, ENZYME and the SWISS-MODEL repository. Analysis tools are available for specific tasks relevant to proteomics, similarity searches, pattern and profile searches, post-translational modification prediction, topology prediction, primary, secondary and tertiary structure analysis and sequence alignment. These databases and tools are tightly interlinked: a special emphasis is placed on integration of database entries with related resources developed at the SIB and elsewhere, and the proteomics tools have been designed to read the annotations in SWISS-PROT in order to enhance their predictions. ExPASy started to operate in 1993, as the first WWW server in the field of life sciences. In addition to the main site in Switzerland, seven mirror sites in different continents currently serve the user community.
Deciphering key features in protein structures with the new ENDscript server
ENDscript 2 is a friendly Web server for extracting and rendering a comprehensive analysis of primary to quaternary protein structure information in an automated way. This major upgrade has been fully re-engineered to enhance speed, accuracy and usability with interactive 3D visualization. It takes advantage of the new version 3 of ESPript, our well-known sequence alignment renderer, improved to handle a large number of data with reduced computation time. From a single PDB entry or file, ENDscript produces high quality figures displaying multiple sequence alignment of proteins homologous to the query, colored according to residue conservation. Furthermore, the experimental secondary structure elements and a detailed set of relevant biophysical and structural data are depicted. All this information and more are now mapped on interactive 3D PyMOL representations. Thanks to its adaptive and rigorous algorithm, beginner to expert users can modify settings to fine-tune ENDscript to their needs. ENDscript has also been upgraded as an open platform for the visualization of multiple biochemical and structural data coming from external biotool Web servers, with both 2D and 3D representations. ENDscript 2 and ESPript 3 are freely available at http://endscript.ibcp.fr and http://espript.ibcp.fr, respectively.
Graphitic Carbon Nitride (g-C3N4)-Based Photocatalysts for Artificial Photosynthesis and Environmental Remediation: Are We a Step Closer To Achieving Sustainability?
As a fascinating conjugated polymer, graphitic carbon nitride (g-C3N4) has become a new research hotspot and drawn broad interdisciplinary attention as a metal-free and visible-light-responsive photocatalyst in the arena of solar energy conversion and environmental remediation. This is due to its appealing electronic band structure, high physicochemical stability, and "earth-abundant" nature. This critical review summarizes a panorama of the latest progress related to the design and construction of pristine g-C3N4 and g-C3N4-based nanocomposites, including (1) nanoarchitecture design of bare g-C3N4, such as hard and soft templating approaches, supramolecular preorganization assembly, exfoliation, and template-free synthesis routes, (2) functionalization of g-C3N4 at an atomic level (elemental doping) and molecular level (copolymerization), and (3) modification of g-C3N4 with well-matched energy levels of another semiconductor or a metal as a cocatalyst to form heterojunction nanostructures. The construction and characteristics of each classification of the heterojunction system will be critically reviewed, namely metal-g-C3N4, semiconductor-g-C3N4, isotype g-C3N4/g-C3N4, graphitic carbon-g-C3N4, conducting polymer-g-C3N4, sensitizer-g-C3N4, and multicomponent heterojunctions. The band structures, electronic properties, optical absorption, and interfacial charge transfer of g-C3N4-based heterostructured nanohybrids will also be theoretically discussed based on the first-principles density functional theory (DFT) calculations to provide insightful outlooks on the charge carrier dynamics. Apart from that, the advancement of the versatile photoredox applications toward artificial photosynthesis (water splitting and photofixation of CO2), environmental decontamination, and bacteria disinfection will be presented in detail. Last but not least, this comprehensive review will conclude with a summary and some invigorating perspectives on the challenges and future directions at the forefront of this research platform. It is anticipated that this review can stimulate a new research doorway to facilitate the next generation of g-C3N4-based photocatalysts with ameliorated performances by harnessing the outstanding structural, electronic, and optical properties for the development of a sustainable future without environmental detriment.
Information Technology Adoption Across Time: A Cross-Sectional Comparison of Pre-Adoption and Post-Adoption Beliefs
The process of information technology adoption and use is critical to deriving the benefits of information technology. Yet from a conceptual standpoint, few empirical studies have made a distinction between individuals' pre-adoption and post-adoption (continued use) beliefs and attitudes. This distinction is crucial in understanding and managing this process over time. The current study combines innovation diffusion and attitude theories in a theoretical framework to examine differences in pre-adoption and post-adoption beliefs and attitudes. The examination of Windows technology in a single organization indicates that users and potential adopters of information technology differ on their determinants of behavioral intention, attitude, and subjective norm. Potential adopter intention to adopt is solely determined by normative pressures, whereas user intention is solely determined by attitude. In addition, potential adopters base their attitude on a richer set of innovation characteristics than users. Whereas pre-adoption attitude is based on perceptions of usefulness, ease-of-use, result demonstrability, visibility, and trialability, post-adoption attitude is only based on instrumentality beliefs of usefulness and perceptions of image enhancements.
Adoption of Agricultural Innovations in Developing Countries: A Survey
This is a working document published informally by The World Bank: To present the results of research with the least possible delay, the typescript has not been prepared in accordance with the procedures appropriate to formal printed texts, and The World Bank accepts no responsibility for errors. The publication is supplied at a token charge to defray part of the cost of manufacture and distribution...
HMMER web server: interactive sequence similarity searching
HMMER is a software suite for protein sequence similarity searches using probabilistic methods. Previously, HMMER has mainly been available only as a computationally intensive UNIX command-line tool, restricting its use. Recent advances in the software, HMMER3, have resulted in a 100-fold speed gain relative to previous versions. It is now feasible to make efficient profile hidden Markov model (profile HMM) searches via the web. A HMMER web server (http://hmmer.janelia.org) has been designed and implemented such that most protein database searches return within a few seconds. Methods are available for searching either a single protein sequence, multiple protein sequence alignment or profile HMM against a target sequence database, and for searching a protein sequence against Pfam. The web server is designed to cater to a range of different user expertise and accepts batch uploading of multiple queries at once. All search methods are also available as RESTful web services, thereby allowing them to be readily integrated as remotely executed tasks in locally scripted workflows. We have focused on minimizing search times and the ability to rapidly display tabular results, regardless of the number of matches found, developing graphical summaries of the search results to provide quick, intuitive appraisement of them.
deepTools2: a next generation web server for deep-sequencing data analysis
We present an update to our Galaxy-based web server for processing and visualizing deeply sequenced data. Its core tool set, deepTools, allows users to perform complete bioinformatic workflows ranging from quality controls and normalizations of aligned reads to integrative analyses, including clustering and visualization approaches. Since we first described our deepTools Galaxy server in 2014, we have implemented new solutions for many requests from the community and our users. Here, we introduce significant enhancements and new tools to further improve data visualization and interpretation. deepTools continue to be open to all users and freely available as a web service at deeptools.ie-freiburg.mpg.de. The new deepTools2 suite can be easily deployed within any Galaxy framework via the toolshed repository, and we also provide source code for command line usage under Linux and Mac OS X. A public and documented API for access to deepTools functionality is also available.
Electronic Data Interchange and Small Organizations: Adoption and Impact of Technology
Many EDI researchers and practitioners have recognized the importance of high penetration levels for the success of EDI. Unfortunately, such penetration is partly impeded by the resistance of small companies to become EDI capable. To investigate this issue, we identify three major factors that influence the EDI adoption practices of small firms. These factors are: organizational readiness (because of the low levels of IT sophistication and resource availability of small firms), external pressures to adopt (because of the weak market positions of small firms and the network nature of the technology), and perceived benefits (because of the limited impact that IT has on small firms due to under-utilization and lack of integration). By combining the anticipated effects of these factors, we developed a framework of EDI adoption by small businesses. The applicability of this framework is empirically demonstrated using the results of seven case studies. Lastly, recommendations are made for the development of successful EDI partner expansion plans. These include the development of a long term EDI partner expansion plan from the very beginning, the individual assessment of each partner's EDI preparedness level, and the selection of appropriate influence tactics to expedite adoption by small partners. Specifically, it is suggested that EDI initiators pursue promotional efforts to improve partners' perceptions of EDI benefits, provide financial and technological assistance to partners with low organizational readiness, and carefully select and enact influence strategies to reduce resistance.
A survey on visual surveillance of object motion and behaviors
Visual surveillance in dynamic scenes, especially for humans and vehicles, is currently one of the most active research topics in computer vision. It has a wide spectrum of promising applications, including access control in special areas, human identification at a distance, crowd flux statistics and congestion analysis, detection of anomalous behaviors, and interactive surveillance using multiple cameras, etc. In general, the processing framework of visual surveillance in dynamic scenes includes the following stages: modeling of environments, detection of motion, classification of moving objects, tracking, understanding and description of behaviors, human identification, and fusion of data from multiple cameras. We review recent developments and general strategies of all these stages. Finally, we analyze possible research directions, e.g., occlusion handling, a combination of twoand three-dimensional tracking, a combination of motion analysis and biometrics, anomaly detection and behavior prediction, content-based retrieval of surveillance videos, behavior understanding and natural language description, fusion of information from multiple sensors, and remote surveillance.
Understanding and Predicting Electronic Commerce Adoption: An Extension of the Theory of Planned Behavior
This paper extends Ajzen's (1991) theory of planned behavior (TPB) to explain and predict the process of e-commerce adoption by consumers. The process is captured through two online consumer behaviors: (1) getting information and (2) purchasing a product from a Web vendor. First, we simultaneously model the association between these two contingent online behaviors and their respective intentions by appealing to consumer behavior theories and the theory of implementation intentions, respectively. Second, following TPB, we derive for each behavior its intention, attitude, subjective norm, and perceived behavioral control (PBC). Third, we elicit and test a comprehensive set of salient beliefs for each behavior. A longitudinal study with online consumers supports the proposed e-commerce adoption model, validating the predictive power of TPB and the proposed conceptualization of PBC as a higher-order factor formed by self-efficacy and controllability. Our findings stress the importance of trust and technology adoption variables (perceived usefulness and ease of use) as salient beliefs for predicting e-commerce adoption, justifying the integration of trust and technology adoption variables within the TPB framework. In addition, technological characteristics (download delay, Website navigability, and information protection), consumer skills, time and monetary resources, and product characteristics (product diagnosticity and product value) add to the explanatory and predictive power of our model. Implications for Information Systems, e-commerce, TPB, and the study of trust are discussed.
Sustainability and Cities: Overcoming Automobile Dependence
The book examines the urban aspect of sustainability issues, arguing that cities are a necessary focus for that global agenda. The authors make the case that the essential caracter of a city's land use results from how it manages its transportation, and that only by reducing our automobile dependence will we be able to successfully accommodate all elements of the sustainability agenda. The table of contents lists the following chapter headings: Chapter 1 - The Concept of Sustainability and Its Relationship to Cities; Chapter 2 - The Problem of Automobile Dependence at the End of the Twentieth Century; Chapter 3 - The Pattern of Automobile Dependence and Global Cities; Chapter 4 - A Vision of Reduced Automobile Dependence; Chapter 5 - Greening the Automobile Dependent City; Chapter 6 - Promoting Sustainable Urban Change; and Chapter 7 - Ethics, Spirituality, and Community in the Sustainable City.
Predicting E-Services Adoption: A Perceived Risk Facets Perspective
Internet-delivered e-services are increasingly being made available to consumers; however, little is known about how consumers evaluate them for potential adoption. Past Technology Adoption Research has focused primarily on the positive utility gains attributable to system adoption. This research extends that approach to include measures of negative utility (potential losses) attributable to e-service adoption. Drawing from Perceived Risk Theory, specific risk facets were operationalized, integrated, and empirically tested within the Technology Acceptance Model resulting in a proposed e-services adoption model. Results indicated that e-services adoption is adversely affected primarily by performance-based risk perceptions, and perceived ease of use of the e-service reduced these risk concerns. Implications of integrating perceived risk into the proposed e-services adoption model are discussed.
Factors Influencing the Adoption of Internet Banking
A research framework based on the theory of planned behavior (Ajzen 1985) and the diffusion of innovations theory (Rogers 1983) was used to identify the attitudinal, social and perceived behavioral control factors that would influence the adoption of Internet banking. An online questionnaire was designed on the World Wide Web (WWW). Respondents participated through extensive personalized e-mail invitations as well as postings to newsgroups and hyperlinks from selected Web sites. The results revealed that attitudinal and perceived behavioral control factors, rather than social influence, play a significant role in influencing the intention to adopt Internet banking. In particular, perceptions of relative advantage, com-Journal of the Association for Information Systems 2 patibility, trialability, and risk toward using the Internet were found to influence intentions to adopt Internet banking services. In addition, confidence in using such services as well as perception of government support for electronic commerce were also found to influence intentions. The implications of the study are discussed and suggestions for future research presented.
IUPred: web server for the prediction of intrinsically unstructured regions of proteins based on estimated energy content
Intrinsically unstructured/disordered proteins and domains (IUPs) lack a well-defined three-dimensional structure under native conditions. The IUPred server presents a novel algorithm for predicting such regions from amino acid sequences by estimating their total pairwise interresidue interaction energy, based on the assumption that IUP sequences do not fold due to their inability to form sufficient stabilizing interresidue interactions. Optional to the prediction are built-in parameter sets optimized for predicting short or long disordered regions and structured domains.
Factors Influencing the Adoption of Internet Banking
A research framework based on the theory of planned behavior (Ajzen 1985) and the diffusion of innovations theory (Rogers 1983) was used to identify the attitudinal, social and perceived behavioral control factors that would influence the adoption of Internet banking. An online questionnaire was designed on the World Wide Web (WWW). Respondents participated through extensive personalized email invitations as well as postings to newsgroups and hyperlinks from selected Web sites.
Generating representative Web workloads for network and server performance evaluation
One role for workload generation is as a means for understanding how servers and networks respond to variation in load. This enables management and capacity planning based on current and projected usage. This paper applies a number of observations of Web server usage to create a realistic Web workload generation tool which mimics a set of real users accessing a server. The tool, called Surge (Scalable URL Reference Generator) generates references matching empirical measurements of 1) server file size distribution; 2) request size distribution; 3) relative file popularity; 4) embedded file references; 5) temporal locality of reference; and 6) idle periods of individual users. This paper reviews the essential elements required in the generation of a representative Web workload. It also addresses the technical challenges to satisfying this large set of simultaneous constraints on the properties of the reference stream, the solutions we adopted, and their associated accuracy. Finally, we present evidence that Surge exercises servers in a manner significantly different from other Web server benchmarks.
The FoldX web server: an online force field
FoldX is an empirical force field that was developed for the rapid evaluation of the effect of mutations on the stability, folding and dynamics of proteins and nucleic acids. The core functionality of FoldX, namely the calculation of the free energy of a macromolecule based on its high-resolution 3D structure, is now publicly available through a web server at . The current release allows the calculation of the stability of a protein, calculation of the positions of the protons and the prediction of water bridges, prediction of metal binding sites and the analysis of the free energy of complex formation. Alanine scanning, the systematic truncation of side chains to alanine, is also included. In addition, some reporting functions have been added, and it is now possible to print both the atomic interaction networks that constitute the protein, print the structural and energetic details of the interactions per atom or per residue, as well as generate a general quality report of the pdb structure. This core functionality will be further extended as more FoldX applications are developed.
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