Development and validation of a consistency based multiple structure alignment algorithm
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Issues in Informing Science and Information TechnologyDevelopment and Validation of an Instrument for Assessing Users’ Views about the Usability ofDigital LibrariesAlex KoohangUniversity of Wisconsin – Milwaukee, USAkoohang@AbstractThis paper attempted to develop and validate an instrument that measures users’ views about the usability of digital libraries. Users’ views toward the usability of digital libraries may serve as the major conduit to user acceptance and satisfaction, thus promoting positive learning experiences. The instrument, digital library usability , consisted of 12 items that described usability properties of digital libraries. The content validity of the instrument was determined by a panel of experts. The instrument was administered to 293 subjects. The construct validity was determined by con-ducting a set of statistical procedures, including a principal component analysis. The results re-vealed a single component solution that assessed one particular trait. All items of the instrument achieved high loading values indicating that each item contributed to the assessment of the single component that accounted for a high variation among the items. The internal consistency (Cron-bach alpha) was .96. These results suggest that the digital library usability instrument is a valid and reliable instrument that can measure users’ views about the usability of digital libraries. This instrument can be the basis for future research regarding users’ views toward the usability of digi-tal libraries.Keywords : Usability, Usability Attributes, Usability Properties, Digital Library, Electronic Li-brary, Virtual Library, Users’ views, Instrument Validation, Content Validity, Construct Validity, ReliabilityIntroductionA digital library is a blend of “(1) a service; (2) an architecture; (3) a set of information resources, databases of text, numbers, graphics, sound and video etc.; and (4) a set of tools and capabilities to locate, retrieve and utilize the information resources available” Borgman (2000, p. 41). Wat-stein, Calarco, & Ghaphery, (1999) reported that terms such as virtual libraries, on-line libraries, and electronic libraries are used simultaneously and/or interchangeability with the term digital libraries.The Association of Research Libraries (ARL) has suggested a definition for digital libraries that was advanced by Drabenstott (1994). This definition consists of elements that are common toterms used to explain digital libraries.These elements are: • The digital library is not asingle entity;Material published as part of this journal, either on-line or in print,is copyrighted by Informing Science. Permission to make digital orpaper copy of part or all of these works for personal or classroomuse is granted without fee provided that the copies are not made or distributed for profit or commercial advantage AND that copies 1) bear this notice in full and 2) give the full citation on the first page. It is permissible to abstract these works so long as credit is given. To copy in all other cases or to republish or to post on a server or to redistribute to lists requires specific permission from the pub-lisher at Publisher@Usability of Digital Library56 •The digital library requires technology to link the resources of many;•The linkages between the many digital libraries and information services are transparent to the end users;•Universal access to digital libraries and information services is a goal; and•Digital library collections are not limited to document surrogates: they extend to digital artifacts that cannot be represented or distributed in printed formats.Digital libraries are increasingly becoming a part of the digital learning communities, in particu-lar, distance education. Roes (2001) stated that digital libraries are natural complements to elec-tronic learning settings. Digital libraries have many benefits such as bringing information to us-ers; providing enhanced searching, sharing; collaboration, and use of information; and lessening the digital divide (Arms 2000).McCray & Gallagher (2001) stated that designing a usable system is one of the major principles in developing digital libraries. The authors believe that characteristics such as accessibility, sim-plicity, user control, and clear navigation should be incorporated into the design for usability of digital libraries.Usability is generally characterized as the determining aspect of a product or system’s capability to satisfy the needs and specifications of users. Usability is the extent of how users easily and ef-fectively use a product or system. It plays a vital role in user acceptance of a product or system (Dumas & Redish, 1993; Guillemette, 1989; Holms, 2002; Nielsen 1993; Nielsen, 2000; Rosenbaum, 1989; Rubin, 1994; Shackel 1991).A digital library is a system that must be usable. Much of the literature in the area of usability of digital libraries has been on testing and evaluation (Dickstein & Mills, 2000; McGillis & Toms, 2001; McMullen, 2001; Walbridge, 2000). A critical, yet largely unexamined facet of usability of digital libraries is the users’ views of the usability of digital libraries. Research has acknowledged that users’ views play a vital role in determining the usability of digital libraries (Blanford, Stel-maszewska, & Byyan-Kinns, 2001; Covi and Kling 1997). One’s behavior based on his or her views about the usability of digital libraries may play an important role in the success of learning in general. Therefore, this study attempted to develop and validate an instrument that measures users’ views about the usability of digital libraries. Users’ views may serve as the major interme-diary to user acceptance and satisfaction, thus promoting positive learning experience.Development of the Instrument: Content ValidityThe literature has documented many usability attributes that are the end result of a usable product or system. In general the following usability attributes are reported in the literature: effectiveness, learnability, flexibility, and attitude (Shackle, 1991); learnability, efficiency, memorability, er-rors, and satisfaction (Nielsen, 1993); effectiveness, efficiency, and satisfaction (ISO 9241-11, 1998); and understandability, learnability, operability, and attractiveness (ISO 9126-1, 1991). Each usability attribute may be linked to one or more properties that describe a usable system. The properties are elements such as simplicity, recognition, navigability, etc. that are designed into a product or system to make it usable. Many usability properties are reported in the literature (Dumas & Redish, 1993; Guillemette, 1989; Holms, 2002; Nielsen 1993; Nielsen, 2000; Rosenbaum, 1989; Rubin, 1994; Shackel 1991). For example, simplicity is a usability property. If this property is designed into a product or system then that product or system can be considered usable. The presence of this property may influence one or more usability attributes such as user satisfaction, learnability, efficiency, and positive attitude.Similar to any product or system, a digital library must possess usability properties. In otherKoohang57words, in designing digital libraries for usability, appropriate usability properties must be used. For the purpose of this study, a set of usability properties were chosen from the literature that would describe usability of digital libraries. These usability properties for digital libraries were taken to the next step of instrument development and validation – content validity.The content validity of the instrument was determined by a panel of experts consisting of five university professors whose expertise included the fields of information technology, information systems, and information science. The items of the instrument were usability properties that were chosen from an original pool of 15 items. These items described usability of digital libraries. Sev-eral items were modified from their original form to maximize the accuracy and clarity of the items. Three items were eliminated because the panel of experts had determined that they were duplicates of other items. It was the consensus of the panel of experts that the individual items chosen assessed the intended concepts, and that the instrument as a whole was a valid measure of usability of digital libraries. The final instrument consisted of 12 items that described the usability of digital libraries. These items are described below:• Simplicity: A digital library must be simple to use. Simplicity may be linked to usabilityattributes such as learnability, efficiency, satisfaction, and attitude. • Comfort: Users must feel comfortable using a digital library. The usability attributeslinked to comfort may include learnability, efficiency, satisfaction, and attitude. • User friendliness: A digital library must be user-friendly. The attributes connected to thisproperty may include attractiveness, learnability, efficiency, satisfaction, and attitude. • Control: Users must be in control of using a digital library. The usability attributes thataffect this property may include operability, learnability, effectiveness, efficiency, satis-faction, and attitude. • Readability: Accessed information by users from a digital library must be uncluttered andreadable. The usability attributes linked to readability may include understandability, at-tractiveness, learnability, effectiveness, efficiency, satisfaction, and attitude. • Information Adequacy/Task Match: The accessed information from a digital librarymust be adequate. In other words, a digital library is much more usable if there is ade-quate information – no more, no less. The usability attributes connected to this property may include effectiveness, efficiency, satisfaction, and attitude. • Navigability: Users must be able to navigate with ease, freely, and without problemthroughout a digital library. The usability attributes linked to this property may include operability, learnability, effectiveness, efficiency, satisfaction, and attitude. • Recognition: Users must be able to quickly understand the features and functions avail-able in a digital library. The attributes linked to this property may include memorability, error, learnability, efficiency, satisfaction, and attitude. • Access time: The information queried from a digital library must be loaded in a reason-able time. The attributes linked to this property may include flexibility, effectiveness, ef-ficiency, satisfaction, and attitude. • Relevancy: The information accessed from a digital library must be relevant. The attrib-utes linked to this property may include effectiveness, efficiency, satisfaction, and atti-tude.Usability of Digital Library58 •Consistency: The consistency of terms, words, and actions must be present throughout a digital library. The attributes linked to this property may include memorability, learnabil-ity, efficiency, satisfaction, and attitude.•Visual Presentation: Appropriate visual presentation such as text boldfacing, underlin-ing, and italicizing must be present in a digital library. The attributes linked to this prop-erty may include effectiveness, efficiency, attractiveness, satisfaction, and attitude.The instrument used the Likert technique. A five-point scale was developed with five response choices. They were: strongly agree = 5, agree = 4, neither agree nor disagree = 3, disagree = 2, and strongly disagree = 1. Listed below are the instrument items:1.Simplicity: The digital library was simple to use.fort: I felt at ease using the digital library.er friendliness: The digital library was user-friendly.4.Control: I felt in control of using the digital library.5.Readability: The information I accessed from the digital library was uncluttered andreadable.6.Adequacy/Task Match: The accessed information from the digital library was adequate.7.Navigability: I was able to move around throughout the digital library with ease.8.Recognition: I quickly understood the features and functions available in the digital li-brary.9.Access time: The information I asked for from the digital library loaded in a reasonabletime.10.Relevancy: The information I got from the digital library was relevant.11.Consistency: The consistency of terms, words, and actions used throughout the digital li-brary was evident.12.Visual Presentation: Text boldfacing, italicizing, and underlining were present in thedigital library to grab my attention.This instrument uses the Human Computer Interaction (HCI) participative evaluation method using a questionnaire. This method entails collecting data about usability of digital libraries di-rectly from users’ subjective point of views. This method has the ability to acquire all characteris-tics related to “users’ needs, desires, thought processes, and experiences that are difficult to ob-tain otherwise” (Hilbert & Redmiles, 2000, p. 389).MethodSubjectsA total of 293 students who were enrolled in an undergraduate hybrid program in management completed the instrument. The subjects were males and females from a multi-campus university in the Midwest, USA. They were enrolled in courses such as supervision, communication, re-search design, organizational behavior, and human resources. All subjects had completed at least several mini-research paper/essay assignments that required the extensive use of the university’s digital library.The terms electronic library and digital library were used interchangeably by subjects. The digital library used by subjects of this study is a virtual library that is a subset of the actual physical li-brary. It is accessed via the Internet using computer networks. In particular, this digital library included a large number of databases that contain digital full-text of scholarly journals, substan-tive news periodicals, general interest periodicals, and popular periodicals. Other features of the digital library included on-line catalogs for finding books and periodical list, a comprehensive on-Koohang59line tutorial, and asynchronous support by e-mail. All students were required to attend a two-hour library orientation session in the beginning of their program.The subjects were told that their participation in completing the instrument were entirely volun-tarily. All participants were 18 years or older. They were told not to put their names on the in-strument. The subjects were guaranteed anonymity with regard to the publication of the results.Data analysesThe following statistical analyses were conducted using SPSS:1. Kaiser-Meyer-Olkin Measure of Sampling Adequacy was conducted to ensure that therewas adequate and high variability in the collected data.2. Bartlett Test of Sphericity was conducted to ensure that the items of the instrument weresufficiently correlated.3. Principal component analysis with Varimax rotation was conducted on the collected data.This method was used to determine the number of components to retain.4. Reliability test (Cronbach alpha) was conducted to find internal consistencyamong the items.ResultsConstruct ValidityThe data were inspected with regard to their appropriateness for component analysis through the Kaiser-Meyer-Olkin Measure of Sampling Adequacy and the Bartlett Test of Sphericity. The Kaiser-Meyer-Olkin Measure for the date was .885, which suggested that there was sufficient and high variability in the data to conduct component analysis. The results of Bartlett Test of Spheric-ity (Approximate Chi-Square = 4828.65, df = 66, Sig. = .000) suggested that the items were suffi-ciently correlated to conduct component analysis. (See Table 1)Table 1: KMO and Bartlett's TestKaiser-Meyer-Olkin Measure of Sampling Adequacy.888 Bartlett's Test of SphericityApprox. Chi-Square4701.567df 66Sig..000All items were retained and achieved loading values of greater than .64, which suggested that each item contributed to the assessment of the single component solution (See Tables 2 & 3). The single component model accounted for 73.04% of the variation among the items. No rotation was attempted by SPSS after finding a single component solution.Usability of Digital Library60Table 2: CommunalitiesInitial ExtractionSimplicity 1.000 .715Comfort 1.000 .723User friendliness 1.000 .707Control 1.000 .760Readability 1.000 .783 Information Adequacy/Task Match 1.000 .649Navigability 1.000 .765Recognition 1.000 .744Access time 1.000 .764Relevancy 1.000 .692Consistency 1.000 .732Visual Presentation 1.000 .729Table 3: Principal Component Analysis (Component Matrix)Component 1Simplicity .846Comfort .851User friendliness .841Control .872Readability .885 Information Adequacy/Task Match .806Navigability .874Recognition .863Access time .874Relevancy .832Consistency .856Visual Presentation.854Table 4: Descriptive StatisticsN Min Max Mean SDSimplicity 293 1.00 5.00 3.8976 .95968Comfort 293 1.00 5.00 3.9010 .97596 User friendliness 293 1.00 5.00 3.9556 .94075Control 293 1.00 5.00 3.9352 .92856Readability 293 1.00 5.00 3.6826 1.00594 Information Adequacy/Task Match 293 1.00 5.00 3.7543 1.03419Navigability 293 1.00 5.00 3.8020 1.03784Recognition 293 1.00 5.00 3.7884 1.04173Access time 293 1.00 5.00 3.7747 1.01552Relevancy 293 1.00 5.00 3.7440 1.05630Consistency 293 1.00 5.00 3.9386 .91579 Visual Presentation293 1.00 5.00 3.8191 1.00242Koohang61ReliabilityA reliability coefficient (Cronbach alpha) was calculated using the internal consistency method. The calculated coefficient alpha reliability from the results was .96, which suggests that this in-strument is highly suitable to measure users’ views about the usability of digital libraries. The results of correlation matrix, means, and standard deviations are shown in Tables 4 & 5.Table 5: Correlation MatrixV1 V2 V3 V4 V5 V6 V7 V8 V9 V10 V11 V12 V1 1.00 V2 0.87 1.00 V3 0.81 0.83 1.00 V4 0.70 0.69 0.71 1.00 V5 0.69 0.70 0.72 0.78 1.00 V6 0.59 0.59 0.64 0.66 0.74 1.00 V7 0.64 0.65 0.62 0.70 0.75 0.73 1.00 V8 0.68 0.67 0.65 0.68 0.73 0.73 0.80 1.00 V9 0.72 0.74 0.69 0.70 0.75 0.63 0.74 0.74 1.00 V10 0.68 0.69 0.68 0.66 0.70 0.64 0.69 0.69 0.84 1.00 V11 0.68 0.68 0.69 0.97 0.77 0.63 0.68 0.68 0.68 0.63 1.00 V12 0.62 0.630.590.680.730.710.970.780.710.650.691.00V6 = Information Adequacy/Task Match, V7 = Navigability, V8 = Recognition, V9 = Access time,V10 = Relevancy, V11 = Consistency, V12 = Visual PresentationConclusionThe literature has documented that usability of a system or product contributes to attributes such as users’ effectiveness, learnability, flexibility, attitude, efficiency, memorability, satisfaction, and understandability, thus creating a positive learning environment for users to accomplish tasks that meet their goals. A usable system contains usability properties that lead to usability attrib-utes.Digital libraries are increasingly becoming a part of the digital learning settings. For this reason, the usability of digital libraries becomes an important issue for both users and designers. Unques-tionably, a digital library must possess usability properties which results in attributes that affect users’ positive and successful learning experience.One’s positive views toward the usability of digital libraries may play an important role in his or her successful accomplishment of tasks, thus ensuring rewarding learning experience. This study attempted to develop and validate an instrument that measures users’ views toward the usability of digital libraries. A set of usability properties that described usability of digital libraries was selected for the instrument. Each property was formed into an item/statement. A panel of experts concluded that the items of the instrument were suitable to measure users’ views toward the us-ability of digital libraries. In other words, the instrument as a whole was a valid measure of us-ability of digital libraries.Initial analyses of the collected data for the instrument suggested that the items of the instrument were sufficiently correlated and that there was adequate and high variability in the collected data to conduct principal component analysis. The results of principal component analysis indicated that the digital library usability instrument measured one particular trait. The analysis revealed a single component solution. All items of the instrument achieved high loading values indicating that each item contributed to the assessment of the single component that accounted for a high variation among the items. The internal consistency (reliability estimate) for the instrument wasUsability of Digital Library62.96 indicating a very high reliability. The Cronbach alpha showed a homogeneous set of items that measure users’ views toward the usability of digital libraries.Currently, the multitudes of commercial digital libraries contain many databases that do not fol-low universal techniques for system usability. Such techniques are perhaps being developed, however; the digital libraries lack the same standardization for system usability. Measuring users’ views about the usability of digital libraries may assist designers of digital libraries to be sensitive to the needs and specifications of users regarding the usability of digital libraries. It may also as-sist the designers of digital libraries in initiating usability standardization within and across all digital libraries.The results of this study were indicative of a valid and reliable instrument that can measure users’ views toward the usability of digital libraries. This instrument represents an initial step toward the establishment of a measurement technique for users’ views toward the usability of digital librar-ies. However, efforts must be made to further improve this instrument by possibly expanding emerging usability properties that might further describe the usability of digital libraries. Fur-thermore, this instrument may be used as the foundation for future research regarding users’ views toward the usability of digital libraries.ReferencesArms, E. (2000). Digital libraries . Cambridge, MA: MIT Press.Borgman, C. (2000). From Gutenberg to the global information infrastructure: Access to information in thenetworked world . Cambridge, MA: MIT Press Blandford, A. E., Harrison, M. D. & Barnard, P. J. (1995). Using interaction framework to guide the designof interactive systems. International Journal of Human-Computer Studies , 43, 101-130. Covi, L. & Kling, R. (1997). Organisational dimensions of effective digital library use: Closed rational andopen natural systems model. In S. Kiesler, Culture of the Internet (pp. 343-360). New Jersey: Law-rence Erlbaum. Dickstein, R. & Mills, R. (2000). Usability testing at the University of Arizona Library: How to let the us-ers in on the design . Information Technology & Libraries , 19 (3), 144-151. Drabenstott, Karen M. (1994). Analytical review of the library of the future. Washington, DC: Council Li-brary Resources. Dumas, J. & Redish, J. (1993). A practical guide to usability testing . Norwood, New Jersey: Ablex. Guillemette, R. A. (1989). Usability in computer documentation design: Conceptual and methodologicalconsiderations. IEEE Transactions on Professional Communication , 32, 217-28. Hilbert, D. & Redmiles, D. (2000). Extracting usability information from user interface events. ACM Com-puting Surveys , 32 (4). Holms, M. (2002). Web usability & navigation . New York: McGraw-HillISO 9241-11 (1998). Ergonomic requirements for office work with visual display terminals (VDT)s - Part11 Guidance on usability . ISO 9126 -1 (1991). Software product evaluation - Quality characteristics and guidelines for their use . McCray A. & Gallagher, M. (2001). Principles for Digital Library Development . Communications of theACM , 44(5), 49-54. McGill, L. & Toms, L. (2001). Usability of the academic library web site: Implications for design. College& Research Libraries , 62 (4), 355-367. McMullen, S. (2001). Usability testing in a library web site redesign project. Reference Service Review , 29(1), 7-22.Koohang63Nielsen, J., (1993). Usability engineering . San Diego, CA: Academic Press.Nielsen, J. (2000). Designing Web usability: The practice of simplicity . Indianapolis: New Riders. Robins, S. (2001). Organizational behavior (9th ed.). New Jersey: Prentice-Hall.Roes, H. (2001). Digital libraries and education: Trends and opportunities. D-Lib Magazine , 7 (7/8). Rosenbaum, S. (1989). Usability evaluations vs. usability testing: When and Why? IEEE Transactions onProfessional Communication , 32, 210-16. Rubin, J. (1994). Handbook of usability testing . New York: John Wiley.Shackel, B., (1991). Usability - context, framework, design and evaluation. In B. Shackel, & S. Richardson(Eds.). Human Factors for Informatics Usability (pp. 21-28). Cambridge: Cambridge University Press. Walbridge, S. (2000). Usability testing and libraries: The WSU experience. ALKI , 16 (3), 23-4.Watstein, S., Calarco, P. & Ghaphery, J. (1999). Digital library: Keywords. Reference Services Review , 27(4), 344-352.BiographyDr. Alex Koohang is an associate professor and director of undergraduate program in the School of Information Studies at University of Wisconsin - Milwaukee, USA. Dr. Koohang has designed, developed, and implemented various traditional, non-traditional, hybrid, and on-linecourses/programs. He has been involved in the development of on-line education, having initiated and administered some of the earliest asynchronous learning networks. His current research inter-ests are in the areas of distance/e-learning, system usability, learning objects and reusability.。
QbR Frequently Asked QuestionsDisclaimer: These are general answers and may not be applicable to every product. Each ANDA is reviewed individually. This document represents the Office of Generic Drugs’s (OGD’s) current thinking on these topics.Format and SubmissionHow should QbR ANDAs be submitted?OGD’s QbR was designed with the expectation that ANDA applications would beorganized according to the Common Technical Document (CTD) format, a submissionformat adopted by multiple regulatory bodies including FDA. Generic firms are strongly recommended to submit their ANDAs in the CTD format (either eCTD or paper) tofacilitate implementation of the QbR. The ANDA Checklist for completeness andacceptability of an application for filing can be found on the OGD web page:/cder/ogd/anda_checklist.pdf .What is a QOS?The Quality Overall Summary (QOS) is the part of the CTD format that provides asummary of the CMC aspects of the application. It is an important tool to make the QbR review process more efficient.How long should a QOS be?OGD believes the CTD guidance1 recommendation of 40 pages to be an appropriatecompromise between level of detail and concision. The CTD guidance recommendation does not include tables and figures.The same information should not be included in multiple locations in the QOS. Instead of repeating information, refer to the first location of the original information in the QOS by CTD section number.Should the QOS be submitted electronically?All applications should include an electronic QOS. For paper submissions, it isrecommended that both an electronic QOS and a paper QOS be included.What file format should be used for the QOS?All applications, both eCTD and paper submissions, should have an electronic QOS. The electronic QOS should be contained in one document. Do not provide separate files foreach section or question.The electronic QOS should be provided as both a pdf and a Microsoft Word file. Microsoft Word files should be readable by Word 2003.1 Guidance for Industry M4Q: The CTD – Quality (August 2001) /cder/guidance/4539Q.htmWhat fonts should be used in the QOS?Because of FDA’s internal data management systems, please use only use these TrueType fonts: Times New Roman, Arial, Courier New. Times New Roman is recommended as the main text font.Should the applicable QbR question be presented within the body of Module 2 of the relevant section, followed by sponsor's answer?Yes, include all the QbR questions without deletion in the QOS.Can the granularity of module 3 be used in module 2?Yes, the granularity can be used for section and subsection headings. However, the QOS should always be submitted as a single file.Can color be used in the QOS?Yes, but sponsors should ensure that the QOS is legible when printed in black and white.Colored text should not be used.Is the QOS format available on OGD webpage and questions therein mandatory to be followed?For an efficient review process, OGD desires all applications to be in a consistent format.See the OGD QbR questions and example QOS:/cder/ogd/QbR-Quality_Overall_Summary_Outline.doc/cder/ogd/OGD_Model_Quality_Overall_ Summary.pdf/cder/ogd/OGD_Model_QOS_IR_Product.pdfFor amendments to applications, should the documentation consist of a revision of the QOS? Would new PD reports be required?The QOS should not be updated after submission of the original ANDA. Any additional data (including any new PD reports) should be provided as a stand alone amendment.Responses to deficiencies should be provided in electronic format as both a pdf andMicrosoft Word file.After January 2007, what will happen to an application that does not have a QOS or contains an incomplete QOS?OGD will contact the sponsor and ask them to provide a QOS. If the sponsor provides the QOS before the application comes up for review, OGD will use the sponsor’s QOS.OGD’s QbR questions represent the current thinking about what information is essential to evaluate an ANDA. Reviewers will use deficiency letters to ask ANDA sponsors thequestions that are not answered in the sponsor’s QOS.In February 2007, 75% of ANDAs submitted contained a QOS.If a question is not applicable to a specific formulation or dosage form, should the question be deleted or unanswered?Sponsors should never delete a QbR question, but instead answer as not applicable, with a brief justification. Please answer all parts of multi-part questions.For sterile injectables, to what extent should sterility assurance be covered in QOS?The current QbR was not intended to cover data recommendations for Sterility Assurance information. In the future, other summaries will cover other disciplines.MAPP 5040.1, effective date 5/24/04, specifies location of the microbiology information in the CTD format.Where in the CTD should an applicant provide comparative dissolution data between the generic and RLD?The comparison between the final ANDA formulation and the RLD should be provided in5.3.1, this comparison should be summarized in the QOS. Comparisons with otherformulations conducted during development should be included in 3.P.2.Is it possible to submit an amendment in CTD format for a product that was already submitted in the old ANDA format?No, all amendments to an application under review should use the same format as theoriginal submission.How is a paper CTD to be paginated?“Page numbering in the CTD format should be at the document level and not at the volume or module level. (The entire submission should never be numbered consecutively by page.) In general, all documents should have page numbers. Since the page numbering is at the document level, there should only be one set of page numbers for each document.”2. For paper submission, tabs locating sections and subsections are useful.For the ANDA submitted as in paper CTD format, can we submit the bioequivalence study report electronically? Or does the Agency require paper copy only?The bioequivalence summary tables should always be provided in electronic format.Will QbR lead to longer review times?Many of the current long review times result from applications that do not completelyaddress all of the review issues and OGD must request additional information through the deficiency process. This iterative process will be reduced with the use of the QbR template.Sponsors that provide a QOS that clearly and completely addresses all the questions in the QbR should find a reduction in the overall review time.Will DMFs for the drug substance be required to be in CTD if the ANDA is in CTD format?No. CTD format DMFs are recommended.What should be included in 3.2.R.1.P.2, Information on Components?COA’s for drug substance, excipients and packaging components used to produce theexhibit batch.2 Submitting Marketing Applications According to the ICH/CTD Format: General Considerations/cder/guidance/4707dft.pdfHow should an ANDA sponsor respond to deficiencies?OGD requests that sponsors provide a copy of the response to deficiencies in electronic format as both a pdf file and a Microsoft Word file.QUALITY OVERALL SUMMARY CONTENT QUESTIONS2.3 Introduction to the Quality Overall SummaryWhat information should be provided in the introduction?Proprietary Name of Drug Product:Non-Proprietary Name of Drug Product:Non-Proprietary Name of Drug Substance:Company Name:Dosage Form:Strength(s):Route of Administration:Proposed Indication(s):Maximum Daily Dose:2.3.S DRUG SUBSTANCEWhat if an ANDA contains two or more active ingredients?Prepare separate 2.3.S sections of the QOS for each API. Label them 2.3.S [API 1] and2.3.S [API 2].What if an ANDA contains two or more suppliers of the same active ingredient?Provide one 2.3.S section. Information that is common between suppliers should not be repeated. Information that is not common between suppliers (e.g. different manufacturing processes) should have separate sections and be labeled accordingly (drug substance,manufacturer 1) and (drug substance, manufacturer 2).Can information in this section be provided by reference to a DMF?See individual questions for details. As a general overview:•Information to be referenced to the DMFo Drug substance structure elucidation;o Drug substance manufacturing process and controls;o Container/closure system used for packaging and storage of the drugsubstance;o Drug substance stability.•Information requested from ANDA Sponsoro Physicochemical properties;o Adequate drug substance specification and test methods including structure confirmation;o Impurity profile in drug substance (process impurity or degradant);o Limits for impurity/residual solvent limits;o Method validation/verification;o Reference standard.2.3.S.1 General InformationWhat are the nomenclature, molecular structure, molecular formula, and molecular weight?What format should be used for this information?Chemical Name:CAS #:USAN:Molecular Structure:Molecular Formula:Molecular Weight:What are the physicochemical properties including physical description, pKa, polymorphism, aqueous solubility (as function of pH), hygroscopicity, melting point, and partition coefficient?What format should be used for this information?Physical Description:pKa:Polymorphism:Solubility Characteristics:Hygroscopicity:Melting Point:Partition Coefficient:Should all of these properties be reported? Even if they are not critical?Report ALL physicochemical properties listed in the question even if they are not critical.If a property is not quantified, explain why, for example: “No pKa because there are no ionizable groups in the chemical structure” or “No melting point because compounddegrades on heating”.What solubility data should be provided?The BCS solubility classification3 of the drug substance should be determined for oral dosage forms.Report aqueous solubility as a function of pH at 37º C in tabular form. Provide actualvalues for the solubility and not descriptive phrases such as “slightly soluble”.3 See BCS guidance /cder/guidance/3618fnl.pdf for definitionSolvent Media and pH Solubility Form I(mg/ml) Solubility Form II(mg/ml)Should pH-solubility profiles be provided for all known polymorphic forms?No, it is essential that the pH-solubility profile be provided for the form present in the drug product. The relative solubility (at one pH) should be provided for any other more stable forms.Physicochemical information such as polymorphic form, pKa, solubility, is usually in the confidential section of DMF. Is reference to a DMF acceptable for this type of information?No, knowledge of API physicochemical properties is crucial to the successful development of a robust formulation and manufacturing process. In view of the critical nature of thisinformation, OGD does not consider simple reference to the DMF to be acceptable.The Guidance for Industry: M4Q: The CTD-Quality Questions and Answers/ Location Issues says only the polymorphic form used in the drug product should be described in S.1 and other known polymorphic forms should be described in S.3. OGD’s examples placed information about all known polymorphic forms in S.1. Where does OGD want this information?This information may be included in either S.1 or in S.3. Wherever presented, list allpolymorphic forms reported in literature and provide brief discussion (i.e., which one is the most stable form) and indicate which form is used for this product.Other polymorph information should be presented by the ANDA applicant as follows: • 2.3.S.3 Characterization: Studies performed (if any) and methods used to identify the potential polymorphic forms of the drug substance. (x-ray, DSC, and literature) • 2.3.S.4 Specification: Justification of whether a polymorph specification is needed and the proposed analytical method• 2.3.P.2.1.1 Pharmaceutical Development –Drug Substance: Studies conducted to evaluate if polymorphic form affects drug product propertiesWhy does OGD need to know the partition coefficient and other physicochemical properties?Physical and chemical properties may affect drug product development, manufacture, or performance.2.3.S.2 ManufactureWho manufactures the drug substance?How should this be answered?Provide the name, address, and responsibility of each manufacturer, including contractor, and each proposed production site or facility involved in manufacturing and testing.Include the DMF number, refer to the Letter of Authorization in the body of data, andidentify the US Agent (if applicable)How do the manufacturing processes and controls ensure consistent production of the drug substance?Can this question be answered by reference to a DMF?Yes. It is preferable to mention the source of the material (synthetic or natural) when both sources are available.The DMF holder’s COA for the batch used to manufacture the exhibit batches should be provided in the body of data at 3.2.S.4.4.If there is no DMF, what information should be provided?A complete description of the manufacturing process and controls used to produce the drugsubstance.2.3.S.3 CharacterizationHow was the drug substance structure elucidated and characterized?Can structure elucidation be answered by reference to a DMF?Yes.What information should be provided for chiral drug substances?When the drug substance contains one or more chiral centers, the applicant should indicate whether it is a racemate or a specific enantiomer.When the drug substance is a specific enantiomer, then tests to identify and/or quantify that enantiomer should be included. Discussion of chirality should include the potential forinterconversion between enantiomers (e.g. racemization/epimerization).How were potential impurities identified and characterized?List related compounds potentially present in the drug substance. Identify impurities bynames, structures, or RRT/HPLC. Under origin, classify impurities as process impurities and/or degradants.Structure Origin ID ChemicalName[SpecifiedImpurity]Is identification of potential impurities needed if there is a USP related substances method?Yes.Can this question be answered by reference to a DMF?The ANDA should include a list of potential impurities and their origins. The methodsused to identify and characterize these impurities can be incorporated by reference to the DMF.According to the CTD guidance, section S.3 should contain a list of potential impurities and the basis for the acceptance criteria for impurities, however in the OGD examples this information was in section S.4. Where should it go?This information may be included in either S.3 or in S.4.2.3.S.4 Control of Drug SubstanceWhat is the drug substance specification? Does it include all the critical drug substance attributes that affect the manufacturing and quality of the drug product?What format should be used for presenting the specification?Include a table of specifications. Include the results for the batch(es) of drug substance used to produce the exhibit batch(es). Identify impurities in a footnote. Test results and acceptance criteria should be provided as numerical values with proper units whenapplicable.Tests Acceptancecriteria AnalyticalprocedureTest results for Lot#AppearanceIdentificationA:B:AssayResidualSolventsSpecified ImpuritiesRC1RC2RC3Any UnspecifiedImpurityTotal Impurities[AdditionalSpecification]*RC 1: [impurity identity]RC 2: [impurity identity]RC 3: [impurity identity]What tests should be included in the drug substance specification?USP drugs must meet the USP monograph requirements, but other tests should be included when appropriate. For USP and non USP drugs, other references (EP, BP, JP, the DMF holder’s specifications, and ICH guidances) can be used to help identify appropriate tests.Only relevant tests should be included in the specification. Justify whether specific tests such as optical rotation, water content, impurities, residual solvents; solid state properties(e.g. polymorphic form, particle size distribution, etc) should be included in thespecification of drug substance or not.Does OGD accept foreign pharmacopeia tests and criteria for drug substances?There are several examples where a drug substance is covered by a monograph in EP or JP, but not in the USP. ANDA and DMF holders can obtain information regardingphysicochemical properties, structure of related impurities, storage conditions, analytical test methods, and reference standards from EP or JP to support their submission to OGD.Although the USP remains our official compendium, we usually accept EP when the drug substance is not in USP (However, a complete validation report for EP methods should be provided in the ANDA).For each test in the specification, is the analytical method(s) suitable for its intended use and, if necessary, validated? What is the justification for the acceptance criterion?What level of detail does OGD expect for the analytical method justifications and validations?Provide a summary of each non-USP method. This can be in a tabular or descriptive form.It should include the critical parameters for the method and system suitability criteria ifapplicable. See an example in section 2.3.P.5 of this document.For each analytical procedure, provide a page number/link to the location of validationinformation in Module 3. For quantitative non-compendial analytical methods, provide a summary table for the method validation. See an example in section 2.3.P.5 of thisdocument.Is validation needed for a USP method?No, but USP methods should be verified and an ANDA sponsor should ensure that theUSP assay method is specific (e.g. main peak can be separated from all process impurities arising from their manufacturing process and from degradation products) and the USPrelated substance method is specific (e.g. all the process impurities and degradants can be separated from each other and also separated from main peak).Is validation needed if the USP method is modified or replaced by an in-house method?Yes. Data supporting the equivalence or superiority of the in-house method should beprovided. In case of a dispute, the USP method will be considered the official method.Is reference to the DMF for drug substance analytical method validations acceptable?No. ANDA sponsors need to either provide full validation reports from the ANDA holder or reference full validation reports from the DMF holder (provided there is a copy of the method validation report in the ANDA and method verification from the ANDA holder). AppearanceIdentityAssayImpurities (Organic impurities)What format should be used for related substances?List related compounds potentially present in the drug substance. (Either here or S.3)Name Structure Origin[SpecifiedImpurity]Provide batch results and justifications for the proposed acceptance criteria. See guidance on ANDA DS impurities4 for acceptable justifications. If the DS is compendial, include the USP limits in the table. If the RLD product is used for justification/qualification, then its results should also be included. If an ICH justification is used, then the calculation of the ICH limits should be explained.To use the ICH limits, determine the Maximum Daily Dose (MDD) indicated in the label and use it to calculate the ICH Thresholds: Reporting Threshold (RT), Identification1. The amount of drug substance administered per day2. Higher reporting thresholds should be scientifically justified3. Lower thresholds can be appropriate if the impurity is unusually toxicSponsors can use the ICH limits to ensure the LOQ for the analytical method is equal or below the RT, establish the limit for “Any Unspecified Impurity” to equal or below the IT, and establish limits for each “Specified Identified Impurity” and each “SpecifiedUnidentified Impurity”5 to equal or below the QT.An impurity must be qualified if a limit is established above the QT. Options forqualification include reference to the specific impurity listed in a USP monograph,comparison to the RLD product, identifying the impurity as a significant metabolite of the drug substance, literature references including other compendial monographs (EP, BP, JP), or conducting a toxicity study.4/cder/guidance/6422dft.pdf5 The ANDA DS guidance states “For unidentified impurities to be listed in the drug substance specification, we recommend that you clearly state the procedure used and assumptions made in establishing the level of the impurity. It is important that unidentified specified impurities be referred to by an appropriate qualitative analytical descriptive label (e.g., unidentified A, unidentified with relative retention of 0.9)”. Q3A(R) states “When identification of an impurity is not feasible, a summary of the laboratory studies demonstrating the unsuccessful effort should be included in the application.”Name DrugSubstance(Lot #)USPLimit forDrugSubstanceRLDDrugProduct(Lot #)ProposedAcceptancecriteriaJustification[Specified Impurity,Identified][BatchResults][BatchResults][SpecifiedImpurity,Unidentified]Any UnspecifiedImpurityTotalImpuritiesInclude the column for RLD drug product only if that data is used to justify the drugsubstance limit (example a process impurity that is also found in the RLD).What is OGD’s policy on genotoxic impurities?FDA is developing a guidance for genotoxic impurities. According to the ICH Q3A lower thresholds are appropriate for impurities that are unusally toxic.If impurities levels for an approved generic drug are higher than the RLD, can the approved generic drug data be used as justification for a higher impurity specification?According to ANDA DP and DS Impurity guidances, any approved drug product can be used to qualify an impurity level. However, the guidances qualify this by later stating “This approved human drug product is generally the reference listed drug (RLD). However, you may also compare the profile to a different drug product with the same route ofadministration and similar characteristics (e.g. tablet versus capsule) if samples of thereference listed drug are unavailable or in the case of an ANDA submitted pursuant to a suitability petition.”What if there are no impurities’ tests found in the USP monograph for a USP drug substance? What should the ANDA sponsor do?Please work with your supplier (DMF Holder) to ensure that potential synthetic process impurities (e.g. isomers (if any), side reaction products), degradation impurities, metalcatalysts, and residual solvents are adequately captured by your impurities test method.There may be information available in published literature as well, regarding potentialimpurities.Can levels of an impurity found in the RLD and identified by RRT be used for qualification?Qualification of a specified unidentified impurity by means of comparative RRT, UVspectra, and mass spectrometry with the RLD may be acceptable. However, the ANDAsponsor should make every attempt to identify the impurity.If levels are higher than in an approved drug product then the sponsor should provide data for qualification of the safety of this impurity at this level.Can a limit from a USP monograph for “any unspecified impurity” be used to justify a limit for “any unspecified impurity” greater than the ICH Q3 identification threshold?No. Any unspecified impurity (any unknown) limit should not exceed ICH Q3A “IT”based on MDD. Non-specific compendial acceptance criteria (e.g. Any Individual Impurity is NMT 0.5%) should not be used for justification of proposed impurity acceptance criteria.However, if the USP limit is less than the ICH threshold, then the USP limit should be used. Can a limit for an identified impurity in the drug substance be qualified with data obtained from RLD drug product samples treated under the stressed conditions?No. Test various samples of marketed drug product over the span of its shelf life (ideally, near the end of shelf-life). Data generated from accelerated or stressed studies of the RLD is considered inappropriate.Impurities (Residual Solvents)Will OGD base residual solvent acceptance limits on ICH limits or process capability?The ICH guidance on residual solvents6 provides safety limits for residual solvents but also indicates that “residual solvents should be removed to the extent possible”. ANDA residual solvent limits should be within the ICH safety limits, but the review of the ANDA includes both of these considerations.OGD generally accepts the ICH limits when they are applied to the drug product.What about solvents that are not listed in Q3C?Levels should be qualified for safety.Impurities (Inorganic impurities)Polymorphic FormWhen is a specification on polymorphic form necessary?See ANDA polymorphism guidance7 for a detailed discussion.Particle SizeWhen is a drug substance particle size specification necessary?A specification should be included when the particle size is critical to either drug productperformance or manufacturing.For example, in a dry blending process, the particle size distribution of the drug substance and excipients may affect the mixing process. For a low solubility drug, the drug substance particle size may have a critical impact on the dissolution of the drug product. For a high solubility drug, particle size is often not critical to product performance.6 /cder/guidance/Q3Cfnl.pdf7/cder/guidance/6154dft.pdfWhat justification is necessary for drug substance particle size specifications?As for other API properties, the specificity and range of acceptance criteria for particle size, and the justification thereof, could vary from none to very tight limits, depending upon the criticality of this property for that drug product.Particle size specifications should be justified based on whether a change in particle sizewill affect the ability to manufacture the product or the final product performance.In general, a sponsor either should demonstrate through mechanistic understanding orempirical experiments how changes in material characteristics such as particle size affecttheir product.In the absence of pharmaceutical development studies, the particle size specificationshould represent the material used to produce the exhibit batch.When should the particle size be specified as distribution [d90,d50,d10] and when is a single point limit appropriate?When critical, a particle size should be specified by the distribution. There may be othersituations when a single point limit can be justified by pharmaceutical development studies.2.3.S.5 Reference StandardsHow were the primary reference standards certified?For non-compendial, in-house reference standards, what type of qualification data is recommended? Will a COA be sufficient?COA should be included in Module 3, along with details of its preparation, qualification,and characterization. This should be summarized in the QOS.In terms of the qualification data that may be requested, it is expected that these reference standards be of the highest possible purity (e.g. may necessitate an additionalrecrystallization beyond those used in the normal manufacturing process of the activeingredient) and be fully characterized (e.g. may necessitate in the qualification reportadditional characterization information such as proof of structure via NMR) beyond theidentification tests that are typically reported in a drug substance COA. StandardLaboratory Practice for preparation of reference standards entails recrystallization toconstant physical measurements or to literature values for the pure material.2.3.S.6 Container Closure SystemWhat container closure is used for packaging and storage of the drug substance?Can this question be answered by reference to a DMF?Yes.。
《国际中文教育中文水平等级标准》(GF0025-2021)(以下简称《标准》)经国家语委语言文字规范标准审定委员会审定,2021年3月由教育部、国家语言文字工作委员会发布,作为国家语委语言文字规范自2021年7月1日起正式实施。
以下是《标准》研发组专家对《标准》内容及研发情况做出的部分解读。
Chinese Proficiency Standards for International Chinese Language Education (GF0025-2021) (hereinafter referred to as The Standards) was validated by the Standard Validation Committee of the State Language Commission for Language Specifications and released by the Ministry of Education and the State Language Commission in March 2021. It has been officially implemented as the national language standards since July 1, 2021. The following is an interpretation of The Standards by the experts who participated in its making.H ow long did the preparation of The Standards take? Howmany experts were involved? What was the starting pointand basis for it?At present, 75 countries around the world have included Chinesein their national education systems, more than 4,000 foreignuniversities have offered Chinese language courses, 25 million people have been studying Chinese, and 40 million Chinese language tests have been taken. The international Chinese language education has undergone significant changes in terms of many aspects including its scale and form. In order to further improve international Chinese language education and meet diversified needs of learning, there is an urgent need to introduce a new set of standards that is scientific, inclusive and easy to implement to guide the learning, teaching, testing and assessment of Chinese language, and to provide reference and services for countries around the world to carry out Chinese language education. Since May 2017, commissioned by Center for Language Education and Cooperation, Chinese Testing International has formed a task force of more than 20 experts in related fields from Peking University, Beijing Language and Culture University, Beijing Normal University, Renmin University of China, Capital Normal University, Chinese Academy of Social Sciences, East China Normal University, Shanghai University and other institutions to develop The Standards . The group has consulted more than 80 Chinese and foreign experts and scholars from more than 30 institutions in countries including the United States, the United Kingdom, France, Germany, Japan, Korea, and conducted more than 50 interviews and focused discussions. After three and a half years of discussion and revision, The Standards eventually came into being in early 2021.《标准》从筹备到正式出台,经历了多长时间?有多少专家参与?修改的动机和依据是什么?目前全球已有75个国家将中文纳入国民教育体系,4,000多所国外大学开设了中文课程,2,500多万人学习中文,4,000多万人次参加各类中文考试,国际中文教育的规模、形式等都发生了重大变化。
Annex 4附件4Supplementary guidelines on good manufacturing practices: validation 药品生产质量管理规范补充指南:验证1Introduction简介2Scope范围3Glossary术语4Relationship between validation and qualification验证和确认之间的联系5. Validation5.1. Approaches to validation验证方法5.2. Scope of validation验证范围5Qualification确认6Calibration and verification校准和核实7Validation master plan验证主计划8Qualification and validation protocols确认和验证方案9Qualification and validation reports确认和验证报告10Qualification stages确认程序11Change control变更控制12Personnel人员References参考文献Appendix 1附录1Validation of heating, ventilation and air-conditioning systems采暖、通风和空气净化系统的验证Appendix 2附录2Validation of water systems for pharmaceutical use制药用水系统的验证Appendix 3附录3Cleaning validation清洁验证Appendix 4附录4Analytical method validation分析方法验证Appendix 5附录5Validation of computerized systems计算机系统的验证Appendix 6附录6Qualification of systems and equipment系统和设备的确认Appendix 7附录7Non-sterile process validation非灭菌工艺的验证1. Introduction简介Validation is an essential part of good manufacturing practices (GMP). It is, therefore, an element of the quality assurance programme associated with a particular product or process. The basic principles of quality assurance have as their goal the production of products that are fit for their intended use. These principles are as follows:验证是药品生产管理规范(GMP)的一个重要组成部分;也正因如此,所以它同时也是产品或工艺的质量保证计划的一个不可或缺的要素。
高一英语大学专业选择因素单选题50题(带答案)1.Which of the following is the most important factor when choosinga college major according to your interests?A.Good job prospectsB.High salaryC.Personal interestD.Famous university答案:C。
解析:根据兴趣选择大学专业时,个人兴趣是最重要的因素。
选项A“良好的就业前景”、选项B“高薪水”和选项D“著名大学”虽然也很重要,但如果没有个人兴趣作为支撑,可能会在学习过程中感到枯燥和困难。
2.If you are interested in art, which college major is the most suitable for you?puter ScienceB.English LiteratureC.Fine ArtsD.Mathematics答案:C。
解析:如果对艺术感兴趣,美术专业是最适合的。
选项A“计算机科学”、选项B“英语文学”和选项D“数学”与艺术的相关性较小。
3.Your hobby is playing musical instruments. Which major might you be interested in?A.MusicB.PhysicsC.BiologyD.History答案:A。
解析:爱好是演奏乐器,那么音乐专业可能会感兴趣。
选项B“物理”、选项C“生物”和选项D“历史”与乐器演奏的关联性不大。
4.You love reading novels. Which college major could be a good choice?A.LiteratureB.ChemistryC.EngineeringD.Accounting答案:A。
2025年研究生考试考研英语(一201)模拟试题及答案指导一、完型填空(10分)研究生考试考研英语(一201)一、完形填空(共20题,每小题1分,满分20分)Passage:In recent years, there has been a surge in interest in mindfulness. Mindfulness, simply put, is the practice of paying attention to the present moment without judgment. It involves observing your thoughts, feelings, and sensations (1)they arise, acknowledging them without getting caught up in them.This approach to awareness has its roots in ancient Eastern traditions, such as Buddhism, where it was (2) as a path to enlightenment. However, mindfulness has gained widespread (3) in the West (4) research has shown its numerous benefits for mental and physical health.Practicing mindfulness can help reduce stress, improve focus, (5)emotional regulation, and boost overall well-being. Studies have (6) a link between mindfulness and a decreased risk of chronic diseases, such as heart disease and depression. (7), mindfulness can enhance (8)skills, such as communication and empathy.Some people (9) mindfulness through formal meditation practices, while others (10) it into their daily lives by paying attention (11) while walking, eating, or (12) to music. Regardless of the approach, the key is (13) present and (14) judgment.Mindfulness is not a quick fix. It requires (15) and (16). However, with (17) practice, it can become a powerful tool for (18) stress, enhancing well-being, and living a more (19) life.(20) all, mindfulness teaches us to be present and appreciate the beauty of the now.Answer Key:1.as2.viewed3.acceptance4.because5.enhance6.established7.Furthermore8.interpersonal9.cultivate10.incorporate11.fully12.listening13.staying14.non-judgmentally15.patiencemitment17.consistent18.managing19.fulfilling20.Above二、传统阅读理解(本部分有4大题,每大题10分,共40分)第一题文章正文:Title: The Last of the TitansIn the heart of the Indian Ocean, lies a small, obscure island known as Kikonyogo. Unlike the grandeur of Maldives or the allure of Bali, Kikonyogo is a place many would scarcely bother to find on a map. Yet, it holds within its shrunken frame a peculiar secret: it is home to the largest living tree in the world.This colossal tree, estimated to be over 70 meters in circumference and with a girth thick enough to wrap around four average-sized cars, towers above the surrounding vegetation. Its branches stretch out like ancient fingers reaching for the sky, embracing the sunlight that filters through the dense canopy. Thetree, though largely surrounded by ruins of what once was a thriving civilization, stands tall, its roots deeply entrenched in the earth and its leaves whispering tales of centuries passed.The locals, a remnant of the once vibrant community that thrived around these ancient woods, have long held traditions of respecting and protecting this solitary tree. They believe it to be sacred, a guardi an of the island’s life force, a reminder of the these lands’ untouched beauty before human intervention. Despite the passage of time and the changes that have swept over Kikonyogo, the last of the titans, as it is affectionately called, remains steadfast, a testament to resilience and endurance.1.How old is the largest living tree in Kikonyogo?The largest living tree in Kikonyogo is estimated to be over 70 meters in circumference, indicating it is significantly older than any living tree on Earth.2.What does the tree look like?The tree looks like a colossal structure, with an estimated circumference of over 70 meters and a girth thick enough to wrap around four average-sized cars. Its branches stretch out like ancient fingers, and its leaves whisper tales of centuries passed.3.What role does the tree play in the local community’s traditions?The tree plays a role of being a guardian of the island’s life force and a reminder of the untouched beauty of the land before human intervention. It is considered sacred and is respected and protected by the local community.4.What is the significance of Kikonyogo’s colossal tree?The significance of Kikonyogo’s colossal tree is that it stands as a testament to resilience and endurance, surviving years and changes that have swept over Kikonyogo.5.According to the text, how does the tree fit into the natural landscape of Kikonyogo?The tree fits into the natural landscape of Kikonyogo as a solitary tree surrounded by ruins of what once was a thriving civilization. It stands tall, embracing the sunlight, and its presence is deeply intertwined with the island’s history and the local community’s traditions.第二题阅读下列短文,从每题所给的四个选项中,选出最佳答案。
BETTER COMMUNICATION | GREATER VALUEThe most stringent food standards to be developed by 2035Upgrading food safety standards to the international advanced level is stressed in the Opinions onDeepening Reform and Guaranteeing Food Safety issued by the Central Committee of the CPC and the State Council in May.It puts forward developing the most stringent standards to ensure that every one can trust the food they eat, mainly through the following work:· Speed up the development and revision of common food safety standards related to pesticide and veterinary drug residues, food contaminant and pathogenic microorganisms. The number of limit indicators for pesticide and veterinary drug residues is expected to reach up to 10,000 by 2020, which will be in line with international food code. Accelerate the development of standards catering to the urgent needs of industrial development and regulation.· I n n o v a t e s t a n d a r d i z a t i o n w o r k mechanism. International food safet y standards can be referenced and converted. Streamline standard development and revision processes and encourage enterprises to implement enterprise standards more stringent than national standards or local s t andards. Ac tively par ticipate in the development of international food code as well as the evaluation analysis and management decision making of emerging risk factors.· Strengthen standards implementation. Intensify the explanation, propaganda and training on food safety standards, and prompt food producers and traders to accurately understand and use those standards and guarantee their mandatory nature. Track and evaluate the use of those standards.The leading role of green technology standards is highlighted in the guiding opinions on building market-driven green technology innovation system recently issued by the National Development and Reform Commission and the Ministry of Science and Technology of China.Green technology innovation is becoming an important momentum for green development. It reduces pollution control, and boosts ecological civilization and high-quality development, as China has established a robust system for supporting green, low carbon circular economy.To that end, the leading role of green technology standards is underlined in the Opinions. It defines the key areas for the development and revision ofsuch standards, such as eco environmental pollution protection and control, resources conservation and recycling, green urban development, and new energy. The document also defines its key performance and technical indicators, and encourages the research on common standards of green technology with the evaluation and verification of such results.On the other hand, mandatory standards on product energy efficiency, water efficiency, energy consumption limits, carbon emission, and pollutant emission are to be improved in accordance with the law. The evaluation of such standards is to be conducted on a regular basis, and standards are updated and revised if needed.Standards shall also be developed for the assessment and certification of green technological innovation. A special action will be launched to cultivate ten leading enterprises with the annual output value higher than RMB 50 billion in the area, support 100 enterprises to create national green enterprise technological centers and certificate 1,000 enterprises conducting green technological innovation.Standards and innovation lead to green lifeBETTER COMMUNICATION | GREATER VALUEThe 18th Forum on Industrial Automation and Standardization, which focused on the digitalization and networking of manufacturing equipment and produc tion process, took place in Beijing on May 22. It was hosted by the secretariat of national standardization committee on industrial-process measurement and control (SAC/TC 124).Themed on standardization promoting high-quality development of manufacturing industry, the event probed into the development trend ofcutting-edge technologies in advanced manufacturing field and displayed key solutions for quality and efficiency improvement of enterprises. It attracted some 600 representatives from 17 areas including energy, aerospace, machine tools, shipping, robotics and rail transport.“We shall intensify efforts in building a manufacturing standards system and promote the integration of international and national standards,” stressed Xu Changxing, Deputy Director General of Standards Technology Management Department, SAMR, in the opening address.Attendees were also inspired by keynote speeches on hot issues like digital twins, reconfigurable manufacturing, collaborative optimization of energy efficiency of production process, and new-generation industrial wide band. The speakers shared the technologies enabling the transformation of manufacturing industry to automation, digitalization, networking and intelligence, implementation experience as well as specific products and solutions, and demonstrated relevant systems.For instance, CRRC Corporation Limited introduced its smart manufacturing model covering the whole industry chain and all business areas. After technological transformation, operation cost was reduced by over 20 percent, product R&D cycle down by 33 percent, production efficiency up by 30 percent, and energy utilization rate up by over 5 percent. Those exchanges and sharing at the forum provide valuable insights for identifying the R&D direction of cutting-edge fundamental technologies and fostering technological innovation in enterprises.Advancing the high-quality development of manufacturing industryWorkshop looks at the forefront of standards data applicationNational Library of Standards of CNIS organized a workshop on the forefront of standards data application in Suzhou, Jiangsu Province on June 13-14, bringing together some 70 researchers and technical experts from related institutions and enterprises including Jilin Provincial Institute of Standards, Shenzhen Institute of Standards and Technology, Mystuff Standard Firm and IHS Markit, to exchange latest development and innovation of data research and application in the area.With a distinct advantage in standards document and resources, CNIS will increase efforts in the research on standards data, providing technical support for improving standardizers’ ability in standards data processing, application, research and services.First national standard on data asset announcedThe standard on data asset GB/T 37550-2019, E-commerce data asset evaluation index system , the first of its kind in China, developed by CNIS was officially published on June 4.It specifies the principles for establishing a data asset evaluation system, index classification, index system and evaluation process, which is applicable to the quantitative calculation and assessment of the value of data asset in e-commerce.Filling the gap in the area, the standard is conducive to the conversion of data resources into asset, and provides technical support for data trading, exchange, sharing and value increase.BETTER COMMUNICATION | GREATER VALUESmart grid standardization empowers energy networkingThe State Grid Corporation of China developed and released the Action Plan onConstructing the National Technical Standard Innovation Base of Smart Grid (2019-2021) to fulfill innovation-driven development strategy and promote the transformation of innovations to technical standards.It put forwards two major tasks: constructing a technical standards system in the smart grid field and promoting the application of advanced standards in the field. Such work is safeguarded by the special fund for “technological innovation + standards development” and a coordination mechanism with standardization organizations. The innovation base as an effective measure for boosting the high-quality development of smart grid by standardization is beneficial to the simultaneous development of science and technology, standards, and industry, finally safeguarding the healthy, advanced development of energy networking.Nursing homes to be graded and evaluated by standardChina’s elderly population continues to rise, with 249.49 million citizens aged 60 or above by the end of 2018, representing 17.9 percent of the country’s total population. The need for elderly care services arise rapidly.The first standard on nursing homes grading and evaluation came into effect on July 1, which is expected to provide reference for the elderly in making selections and encourage service quality improvement in those institutions.Nursing homes are divided into five levels based on the evaluation of their environment, equipment, operation & management, and services. For instance, services can be assessed in terms of hospital admission and discharge, diet, sanitary service, medical care, and hospice nursing. Those institutions can voluntarily apply for grading and evaluation. Higher level represents stronger ability to provide comprehensive services.Despite voluntary, the standard is animportant monitoring measure. Subsequently,the Minis tr y of Civil Af fairs will issuecorresponding regulations and managementmeasures to ensure its implementation.Nursing homes failing to meet the standardshould be closed down or suspended forrectification. It will additionally develop andpublish a mandatory national standard onservice quality and safety in nursing homewithin the coming two years.The implementation of the new standardwill promote the development of nursingservice industry in the long run, since nursinghomes need to earn profits by increasinginvestment and upgrading both hard and softservices to attract more elderly, especiallyprivate-owned ones.。
In the modern era,the importance of technological information security cannot be overstated.With the rapid development of the internet and digital technology,our lives have become increasingly intertwined with cyberspace.However,this has also brought about numerous security challenges.Here are some key points to consider when discussing the topic of technological information security in an English composition.1.The Importance of Information Security:Information security is crucial for protecting personal data,intellectual property,and national security.It ensures the confidentiality,integrity,and availability of information.2.Threats to Information Security:Cyber threats such as hacking,phishing,malware,and viruses pose significant risks to information security.These threats can lead to data breaches,financial losses,and compromised privacy.3.Measures for Enhancing Information Security:To safeguard information,various measures can be implemented,including strong passwords,encryption,firewalls,and regular software updates.Additionally,educating users about safe online practices is essential.4.Role of Encryption:Encryption is a method of converting information into a code to prevent unauthorized access.It plays a vital role in securing data during transmission and storage.5.Importance of Regular Updates:Keeping software and systems uptodate is critical for patching security vulnerabilities. Regular updates help protect against the latest threats.6.The Role of Legislation:Governments around the world are enacting laws and regulations to combat cybercrime and enforce information security standards.These legal frameworks help to hold individuals and organizations accountable for protecting data.7.Ethical Considerations:Ethics in information security involve respecting privacy,ensuring transparency,and promoting responsible use of technology.Ethical considerations guide the development and application of security measures.8.The Impact of Information Security on Business:For businesses,information security is not just a technical issue but also a strategic one.Itaffects the companys reputation,customer trust,and operational efficiency.9.The Future of Information Security:As technology advances,so do the methods of securing information.Emerging technologies like artificial intelligence and blockchain offer new ways to enhance security measures.10.Personal Responsibility:Individuals must take personal responsibility for their information security by being vigilant and proactive in protecting their digital footprint.In conclusion,technological information security is a multifaceted issue that requires a combination of technical solutions,legal frameworks,and individual responsibility.As we continue to rely on technology for various aspects of our lives,it is imperative that we prioritize and invest in robust security measures to safeguard our digital world.。
合规的临床使用验收的质量检测要求的英文全文共四篇示例,供读者参考第一篇示例:Quality Inspection Requirements for Compliance with Clinical Use AcceptanceWith the increasing focus on compliance and regulations in the healthcare industry, it has become crucial for organizations to ensure that their clinical use acceptance processes meet the necessary standards. This includes conducting quality inspections to verify that products or services comply with established protocols and guidelines.Quality inspection requirements for compliance with clinical use acceptance involve several key aspects that must be considered. These include:1. Documentation: Ensuring that all relevant documentation, such as test reports, certificates of analysis, and validation reports, are complete and accurate. This documentation should be reviewed and verified to confirm that the product or service meets the required specifications.2. Training: Ensuring that all personnel involved in the clinical use acceptance process are properly trained and qualified to perform their respective tasks. This may involve providing training on relevant protocols, procedures, and regulations.3. Equipment: Verifying that all equipment used in the clinical use acceptance process is calibrated, maintained, and in proper working condition. This includes ensuring that equipment is appropriate for the intended use and meets all necessary specifications.4. Sampling and testing: Conducting sampling and testing of products or services to verify compliance with specified requirements. This may involve conducting physical, chemical, or biological tests to assess the quality and safety of the product or service.5. Record keeping: Maintaining accurate records of all inspections, tests, and evaluations conducted during the clinical use acceptance process. These records should be kept in a secure and accessible manner for future reference and audit purposes.6. Compliance with regulations: Ensuring that all clinical use acceptance processes comply with relevant regulations, standards, and guidelines. This may involve conducting regularaudits and reviews to verify compliance and identify areas for improvement.By adhering to these quality inspection requirements, organizations can ensure that their clinical use acceptance processes are conducted in a compliant and efficient manner. This can help to enhance patient safety, improve overall quality of care, and minimize the risk of regulatory issues or legal liabilities.In conclusion, quality inspection requirements for compliance with clinical use acceptance are essential for ensuring that products or services meet the necessary standards and regulations. By following these requirements, organizations can demonstrate their commitment to quality and compliance in the healthcare industry.第二篇示例:Quality testing requirements for compliance in clinical use acceptanceIn the field of healthcare, ensuring that medical devices and pharmaceutical products meet regulatory requirements is essential to guarantee their safety and effectiveness when used by healthcare professionals. Clinical use acceptance refers to theprocess of evaluating and approving medical devices or drugs for use in clinical settings, after they have undergone necessary testing and regulatory approval. To ensure compliance in clinical use acceptance, it is important to establish quality testing requirements that help verify the safety, efficacy, and quality of these products.第三篇示例:Quality Testing Requirements for Regulatory Clinical Use Approval1. Safety Testing:Safety testing is one of the most critical aspects of quality testing for regulatory clinical use approval. This testing is designed to assess the potential risks and side effects associated with the medical product. Safety testing may include tests such as toxicology studies, genotoxicity studies, and carcinogenicity studies. The results of these tests help regulatory authorities determine if the product is safe for use in clinical settings.第四篇示例:Quality Inspection Requirements for Compliance Clinical Trial AcceptanceClinical trial acceptance is an essential step in the process of drug development and marketing. It ensures that a new drug meets regulatory requirements and is safe and effective for patient use. To ensure the quality of clinical trial acceptance, it is important to have rigorous quality inspection requirements in place.1. Quality Management System3. Data Collection and Analysis4. Regulatory Compliance5. Oversight and Monitoring。
Bioinformatics Advance Access published February 10, 2006© The Author (2006). Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oxford Development and Validation of a Consistency Based Multiple Structure AlignmentAlgorithmRunning title: Consistency Based Multiple AlignmentJessica EbertProgram in Biophysics and Department of BiochemistryStanford UniversityStanford, CA 94305 USADouglas Brutlag*Program in Biophysics and Department of BiochemistryStanford UniversityStanford, CA 94305 USAAssociate Editor: Thomas Lengauer*To whom correspondence should be addressedAbstractSummary: We introduce an algorithm that uses the information gained from simultaneous consideration of an entire group of related proteins to create multiple structure alignments. CBA (consistency-based alignment) first harnesses the information contained within regions that are consistently aligned among a set of pairwise superpositions in order to realign pairs of proteins through both global and local refinement methods. It then constructs a multiple alignment that is maximally consistent with the improved pairwise alignments. We validate CBA’s alignments by assessing their accuracy in regions where at least two of the aligned structures contain the same conserved sequence motif.Results: CBA correctly aligns well over 90% of motif residues in superpositions of proteins belonging to the same family or superfamily, and outperforms a number of previously reported multiple structure alignment algorithms.Availability: CBA is available at /, and source code is freely available at /software/.IntroductionMethods for the alignment of multiple proteins, whether guided by sequence, structure, or both sources of information, are the cornerstone of many techniques in the biological sciences. A number of current areas of research depend on the ability to identify structurally equivalent residues across a group of proteins, including a variety of fold recognition and prediction techniques (Bystroff and Shao, 2002), homology modeling (Madej et al.,1995,Panchenko et al.,1999), evolutionary studies of both protein families and entire organisms, and investigations into the relationships among structure, function, and sequence (Thornton et al.,2000,Todd et al.,2001). As factors that contribute to errors and ambiguity often differ between sequence alignment and structure superposition algorithms (Marchler-Bauer et al.,2002), multiple structure alignment (MSTA) has a place nearly everywhere multiple sequence alignment (MSA) is used. In particular, since structure is often more conserved than sequence, structural alignment has the potential to be more accurate than sequence alignment below the so-called twilight zone of sequence similarity (Doolittle, 1986). However, relatively few MSTA algorithms exist, and even fewer have been subjected to meaningful and clear validation.Early MSTA efforts often focused on placing all structures in a common frame of reference by aligning each of them to a stationary reference, such as the structure that is in some sense the centroid of the group (Akutsu and Sim, 1999). This approach, however, does little to take advantage of the fact that more information can be obtained from simultaneous consideration of all of the structures than from independent analyses of pairs of proteins. Similar methods instead iterate this process, in each phase aligning the structures to the previous iteration’s MSTA, typically by defining the consensus or average structure implied by the multiple alignment (Gerstein and Levitt, 1996, Taylor et al.,1994). Progressive algorithms align the most closely related structures first and eventually incorporate the more distantly related ones, and some perform a final optimization step once all structures have been aligned (Russell and Barton, 1992, Saliand Blundell, 1990, Yang and Honig, 2000). Since early iterations examine only a subset of the proteins, they may discard the optimal alignment as suboptimal. Alternatively, it is possible to use pairwise alignments as a starting point for building an MSTA and then determine which residues should be aligned by using either structure-based scoring functions (Guda et al.,2004) or graph theoretic methods designed to find the best set of residue equivalencies across all structures that do not conflict with one another (Sandelin, 2005). Some recent algorithms make greater use of simultaneous consideration of all structures in the input set, typically by building up a multiple alignment out of aligned structural fragments (Dror et al.,2003,Shatsky et al.,2004)or by using methods such as geometric hashing to identify structural equivalences across a group of proteins (Leibowitz et al.,2001).MSTA algorithms that explicitly or implicitly rely on pairwise superpositions in some way depend on the principle of transitivity, often referred to as consistency, among the pairwise alignments (Gotoh, 1990). Mathematically, the three possible pairwise alignments among three structures are said to be consistent if the residue registrations of two of the alignments predict that of the third. Though a set of pairwise alignments will be fully consistent with one another only in the simplest cases, consistency has successfully been used as a driving force in the multiple alignment of both sequences (Do et al.,2005)and structures (Ochagavia and Wodak, 2004). In fact, one recent algorithm for obtaining the residue correspondences necessary for a multiple sequence or structure alignment is based entirely on the premise of “relaxed transitivity” (Van Walle et al., 2003). This method constructs a graph whose nodes are residues and whose edges connect residues that are either aligned in a set of pairwise alignments or that, if aligned, would create transitive cycles in the graph.Here, we present CBA (consistency-based alignment), an MSTA algorithm that uses information from consistent and nearly consistent regions of pairwise alignments to create a multiple structure alignment. CBA focuses almost entirely on the problem of determining which residues should be aligned given the relative orientations of the proteins once they have been superimposed. We use consistency first to find residue equivalencies across some or all structures in the input set and then to correct residue registration errors and gaps in the pairwise alignments in order to add additional aligned residues to the MSTA. We also introduce changes to the LOCK 2 pairwise protein superposition algorithm (Shapiro and Brutlag, 2004) that significantly enhance consistency among the alignments that are the starting point for CBA. CBA is a general framework for multiple structure alignment consisting of several modules that can be independently modified or even replaced. Simple modifications would also adapt it to perform multiple sequence alignment. Because CBA never uses sequence information, its alignments are well suited to the study of the relationships among sequence, structure, and functionTo date, very few validation techniques have been proposed for multiple structure or sequence alignment methods. Alignment algorithms are often validated by comparison to databases containing multiple alignments whose construction has been fully or partially guided by structure, such as HOMSTRAD (Mizuguchi et al.,1998), BaliBASE (Thompson et al.,1999), and OXBench (Raghava et al.,2003), but even alignments that are manually corrected or built entirely by hand are subject to error. Fully or semi-automated databases such as HOMSTRAD require explicit trust in the algorithms used toproduce their alignments, thus establishing these methods as de facto gold standards. While the HOMSTRAD authors state that alignments are validated by hand, an incorrect automated alignment could easily prove to be a misleading starting point for manual analysis, particularly given the difficulty of visualizing multiple structure superpositions. Comparison of an algorithm to a database such as HOMSTRAD is therefore an implicit comparison to the alignment methods used to produce it, and thus lacks the generality we desire for validation of a new algorithm. Other attempts to quantify alignment quality through the use of simple measurements such as the alignment length and the distances between aligned alpha carbons lack substantive connections to alignment accuracy for anything other than closely related proteins. Though many complex scoring functions have been proposed, even a seemingly reasonable one is nonetheless arbitrary.We instead validate CBA by examining alignments of protein structures containing the same conserved sequence motifs. Although global sequence alignments of proteins that share only limited sequence similarity are too prone to error to be used as gold standards for multiple structure alignment, distantly related proteins may nonetheless contain conserved local sequence motifs that are expected to align to one another. This method avoids the problem of ambiguous or incorrect global sequence alignments in regions of low sequence similarity (< 20%) while still retaining the ability to assess alignments of proteins with low overall sequence identity in a fully automated fashion. We apply this benchmark to several previously reported multiple structure alignment algorithms and demonstrate that CBA outperforms them for multiple alignments of structures from the same family or superfamily.MethodsValidation data setsWe have aligned structures from each family and superfamily in release 1.65 of the Structural Classification of Proteins (SCOP) (Murzin et al.,1995)that contains at least three sequences with the same PROSITE pattern (Sigrist et al.,2002)or eMOTIF hit (Nevill-Manning et al.,1998). These structures come from an ASTRAL subset of the SCOP database created such that no two sequences share greater than 40% sequence identity (Brenner et al.,2000). Since not all PROSITE patterns have high specificity, we excluded as too general for our purposes any pattern that recognizes structures from multiple SCOP folds. Only structures from SCOP’s all alpha, all beta, alpha+beta, and alpha/beta classes were considered.The 478 family validation sets have an average of 6.3 members, among which the average sequence identity as determined by BLAST (Altschul et al.,1990) is approximately 16.7%, while the 197 superfamily validation sets have an average of 13.4 members whose pairwise sequence identities average 14%. Hence, relatively few pairs of sequences in any given validation set reach the upper limit of 40% sequence identity, and many pairs are within or below the twilight zone of sequence similarity. Among the family and superfamily data sets that contain at least two examples of the same eMOTIF, an average of 4.0 structures share the motif. Since more than one eMOTIF may be built to recognize the same functional region, slightly different versions of the same motif may cover different members of the validation data set. On average, the number of structurescontaining any eMOTIF is 4.6 and 5.7 for family and superfamily validation sets, respectively. The average number of structures containing the same PROSITE motif is 2.6 in the family validation data sets and 4.7 in the superfamily data sets. All data sets are available for download in text format at/distributions/CBA/validationsets.html.LOCK 2Though the pairwise structural alignments CBA uses to build a multiple alignment may be created by any structural superposition algorithm, we use an improved version of LOCK 2 by default. LOCK 2 produces an initial superposition by aligning secondary structure elements as previously reported (Shapiro and Brutlag, 2004), and replaces the residue alignment phase developed by Singh and Brutlag (Singh and Brutlag, 1997) with a dynamic programming algorithm that scores the alignment of a query and target residue pair according to both the distances between their beta carbons and also the angles between the vectors defined by the alpha and beta carbons (Figure 1). The use of the beta carbon allows LOCK 2 to encode a preference to align residues whose side chains point in the same general direction. Glycine residues’ alpha hydrogens are replaced with beta carbons, whose positions are determined using ideal bond lengths and angles.Assessment of motif alignment accuracyWhen two or more structures in a multiple alignment contain the same local sequence motif, we assess the accuracy of the alignment in the motif region using the sequence motif as a gold standard. We sum the number of motif residues correctly aligned over all pairs of structures containing the motif and normalize to the number of residue pairs examined to give the percent of motif residues correctly aligned. If two or more motifs overlap, we count each position only once.AlgorithmSteps 1-3: Obtaining an initial multiple superposition.Because pairwise structural alignment algorithms consider only two proteins at a time, they cannot use information regarding the full extent of the variability observed in a given fold to resolve ambiguous regions of the alignment. Both imperfect scoring functions and this rather limited view of fold space lead to registration errors, and hence the pairwise alignments among a group of proteins tend to contain residue registrations that are not consistent with one another. This problem is exacerbated by the use of rigid body transformation methods, which may be unable to optimize the superposition in all structurally similar regions simultaneously. CBA seeks to resolve inconsistencies in alignments by considering an entire group of structures at once and extracting from them more information than is available from independent analysis of pairs of proteins.The CBA algorithm consists of seven steps, each of which incorporates additional information into the alignment (Figure 2). After computing the pairwise alignments among the proteins in the input set (Figure 2, step 1), CBA places all of the structures in the input set into a common frame of reference (Figure 2, step 2). This is particularly helpful in cases involving structures with repeated subdomains. Given three structures, two with multiple copies of the same subdomain and one with only one copy, LOCK 2 might align the smaller structure to different repeats in the two larger structures, thus yielding completely inconsistent pairwise alignments. While this is not necessarily incorrect, it is inconvenient for analyzing similarities across all three proteins. Following a number of progressive multiple structure alignment algorithms, CBA clusters all of the structures in the input set by average linkage using LOCK 2’s global alignment scores as measures of similarity. This creates a binary guide tree that we use to progressively transform all structures into the same frame of reference beginning at the bottom of the tree, where clusters contain the most similar structures, and proceeding towards the root node. In the trivial case of a node at the bottom of the tree with only two descendants, we transform one child structure onto the other using the transformation matrix from the pairwise alignment and label the parent node with the resulting superposition. When a node has more than two descendants, we choose one descendant of the left child and one from the right such that the two selected structures have the highest alignment score among all such pairs, and then use their pairwise transformation to add all descendants from the left child to the right child’s MSTA.Since this process may change some pairwise superpositions, we run LOCK 2’s residue alignment phase a second time to obtain improved pairwise residue correspondences (Figure 2, step 3). Though LOCK 2’s residue alignment phase does employ an iterative algorithm in which each cycle uses the previous cycle’s residue registration to update the transformation of one protein onto the other, these changes in the overlap between the query and target proteins are minor and serve only to make the correct residue registration more clear. CBA discards the changes to the transformations and retains only the new residue registration, thus maintaining the common frame of reference obtained in step 2. From this point forward, the positions of the proteins in space remain fixed.Step 4: Obtaining an initial residue registration across all structures.Although the third step of CBA places all proteins in the same frame of reference, this superposition does not directly imply an unambiguous residue registration across all of the structures in any but the simplest of alignment problems. For the sake of clarity, we make a distinction between the superposition of a group of proteins, which defines their relative positions in space, and their residue registration, which specifies the groups of structurally equivalent residues that are aligned to one another. The superposition is fixed from this point forward, and the remaining phases of the algorithm focus on the more difficult problem of determining the residue registration without using sequence information.The fourth step of CBA applies a fast implementation of the Markov cluster algorithm (MCL) (Van Dongen, 2000) to find the residue registration across all of the proteins that is maximally consistent with the pairwise alignments obtained at the end of step 3 (Figure 2, step 4). One may view this task as the problem of finding clusters in agraph whose nodes are residues and whose edges connect nodes aligned in the pairwise superpositions (Figure 3). Edge weights, which reflect CBA’s confidence that the residue correspondences from the pairwise alignments are correct, are proportional to the LOCK 2residue alignment scores described in the Methods section. If the pairwise alignments were perfectly consistent, this graph would consist of a series of fully connected clusters, such as the leftmost cluster of figure 3, and it would have no edges connecting nodes in different clusters.The MCL algorithm operates under the paradigm that a random walk beginning in a region of the graph that corresponds to a cluster – in this case, a column in the multiple alignment – will visit many of the nodes in that cluster before leaving it for another region. That is, regions of the proteins that are structurally equivalent will give rise to groups of nodes in the graph that are connected to one another by many edges and that have relatively few edges connecting them to other regions of the graph. If the structural similarity in the region is strong, the edges connecting these nodes will furthermore be associated with large weights.Formally, MCL maximizes the flow through the graph where it is already relatively strong and weakens it where it is already weak, thus strengthening correct residue correspondences, eliminating edges that describe incorrect correspondences, and adding edges between residues not aligned by LOCK 2 when the principle of transitivity suggests that they are structurally equivalent. Each resulting cluster contains equivalent residues across a subset of the proteins in the input set and is the basis for a column in the multiple alignment. Since the MCL method does not enforce sequence order constraints and does not require that each cluster contain only one residue from each protein, CBA must deal with these matters in subsequent steps of the algorithm. In the meantime, one can consider the latter issue in particular as a reflection of uncertainty in the residue registration.Steps 5-6: Realignment of secondary structure elements.Even when large portions of two protein structures align well, individual helices and strands may superimpose poorly, thus making identification of residue correspondences difficult. Realigning each pair of superimposed secondary structure elements in isolation circumvents this limitation of rigid body superposition algorithms, which cannot always optimally superimpose all structurally similar regions of two proteins simultaneously (Figure 2, step 5). Since more than one registration of two secondary structure elements of the same type is possible, CBA initially superimposes them onto one other using the residue correspondences identified by the MCL algorithm in step 4. This produces a new superposition that is fully consistent with the current multiple structure alignment but that is better suited to LOCK 2’s scoring functions than was the overlap of the two secondary structure elements in the global pairwise alignment.We run the LOCK 2 residue alignment phase on the newly superimposed pair of secondary structure elements to fill in gaps and to correct mistakes in the current multiple alignment’s residue registration. We then transfer the resulting residue correspondences to the global pairwise alignment, but discard the changes in the superposition of the two secondary structure elements so that the positions of the proteins in space remain unchanged. After repeating this process for all pairs of aligned secondary structureelements in all pairs of proteins, we run the MCL algorithm on the new pairwise alignments in order to update the MSTA’s residue correspondences (Figure 2, step 6). Step 7: Realignment of local regions.The final stage of the CBA algorithm seeks to identify and realign small regions of the multiple alignment that could not be resolved in any previous step (Figure 2, step 7). Regions to be realigned are derived both from secondary structure elements with gaps and from areas containing MSTA columns established by the MCL algorithm that violate sequence order constraints or that contain more than one residue from the same protein. Each region contains one target domain whose alignment is suspect, and each secondary structure element or loop may be marked for realignment more than once with different target domains.CBA realigns the target domain’s residues within a particular region by scoring the placement of a residue into a column according to the number of pairwise alignments that agree with the assignment. The assessment of structural similarity is therefore not based on an isolated and possibly misleading local perspective, but is instead derived solely from the global pairwise alignments obtained at the end of the sixth step of CBA. As was the case up to this point in the algorithm, sequence similarity is not considered. Dynamic programming then determines the new registration of the target domain in this region. This process thus uses the consistency among the pairwise alignments to correct local regions of the multiple alignment. After realigning all regions marked as potentially incorrect, we iterate until no further changes are made or for a maximum of ten iterations. ResultsWithin the 391 superfamilies in SCOP version 1.67 containing at least three members in an ASTRAL subset of domains constructed such that no two share greater than 25% sequence identity, LOCK 2’s pairwise residue registrations are on average 68.2% consistent. This number is calculated from every triple of aligned residues from each triple of structures within the same superfamily. This high level of consistency among pairwise alignments often allows CBA to align distantly related protein structures. The average consistency within a superfamily increases to 80.4% after obtaining a common frame of reference and recalculating the residue registration in the implied pairwise alignments in steps 2 and 3. After the realignment of secondary structure elements in step 5, the average consistency reaches 84.2%. In the 351 families in SCOP containing at least three members in the 25% sequence identity ASTRAL subset, the consistency among the initial LOCK 2 pairwise alignments averages 76.7%. This value increases to 85.1% and 87.7% after steps 3 and 5, respectively. These increases in consistency occur without a decrease in the number of aligned residues.Because CBA observes sequence order constraints, we can read off a sequence alignment from the structural superposition. Figure 4a shows a portion of an alignment of the seventeen structures in SCOP’s globin-like superfamily that are included in the ASTRAL-25 subset; members of three families, including two phycocyanin domains, are included in the superposition. The full alignment (see supplementary information) required 2.2 minutes of CPU time (1.5 minutes user time, 42 seconds system time) on a3.06Ghz Intel Xeon processor.Though gaps do occasionally appear in secondary structure elements, many are justified structurally or occur in regions where the correct residue alignment might be considered ambiguous. For example, the superposition of two of the structures, SCOP domains d1itha_ and d1b0b__, shows the insertion of a residue in SCOP domain d1itha_ (asparagine 17) that induces a gap in globin helix A (Figure 4b). The alignment of d1itha_ and d1b0b__ shown in figure 4b suggests that it is reasonable to leave either 16L or 17N of d1itha_ unaligned. In cases such as this, CBA tends to align the residue that is most consistently aligned in the pairwise alignments. Many other gaps in helices and strands are induced by insertions of loop residues that do not align to the secondary structure element.Validation by comparison to sequence motifsSince manual analysis and validation of multiple structural alignments can be both prone to error and too time consuming to approach on a large scale, we sought to validate CBA by examining its alignments in regions containing conserved sequence motifs. Even when a set of proteins is so diverse that sequence alignment methods are not reliable enough to be used as a gold standard, a subset of the sequences may still contain the same local sequence motif. If the motifs themselves are reliable, then the alignment accuracy can be assessed in these regions by assuming that residues at the same position of the motif should align to one another. We use both PROSITE patterns (Sigrist et al., 2002), which are constructed manually to represent known functional regions, and eMOTIFs (Nevill-Manning et al.,1998), which are built automatically from high quality multiple alignments of proteins sharing strong sequence similarity. Since CBA never uses sequence information, this is an independent test of its accuracy.In an ASTRAL subset of SCOP (version 1.65) created such that no two structures have greater than 40% sequence identity, there are 478 families and 153 superfamilies in which at least two structures contain the same PROSITE pattern. Similarly, there are 123 families and 121 superfamilies in which at least two structures contain the same eMOTIF. All members of the SCOP family or superfamily represented in the ASTRAL-40 database are included regardless of whether they contain the sequence motif; this allows for a more difficult test by increasing both the number of structures to be superimposed and the overall structural variability. The average pairwise sequence identity as determined by BLAST within these validation sets is approximately 17% for families and 14% for superfamilies.For each pair of proteins in a validation set that contain a given sequence motif, we count the number of motif positions that CBA correctly aligned to produce a sum of pairs measurement of alignment accuracy. When a motif occurs in more than one location in one or both proteins, we consider only the pair of hits that is best aligned according to this criterion. Summing over all pairs of proteins with the motif yields a measure of the accuracy of the CBA alignments in these regions. CBA correctly aligns 96.4% of eMOTIF residues and 97.4% of PROSITE residues in the family validation sets (Table 1). Interestingly, only 92% of eMOTIF residues were correctly aligned in the LOCK 2 pairwise superpositions used by CBA. Hence, CBA was able to take advantage of the information contained in a set of related structures in order to increase alignment accuracy. In the significantly more challenging superfamily validation sets, CBA。