Two possible approaches to form sub-millisecond pulsars

Translation and GenderHistorical BackgroundThe women's Movement and the Idea of GenderSimon de Beauvoir wrote in 1949"on ne nait pas femme, on le devient". E.M.Parshley translated this in 1953 as "one is not born, but rather becomes a woman". Beauvoir suggests that a girlbaby is turned into a woman by the society she grows up in and in response to the expectations that society has of women. The final product 'woman' is a result of education and conditioning, and differs according to the dominant influences she is subject to in the culture.Gender refers to the sociocultural construction of both sexes. Feminist thinkers of the late 1960s and early 1970s developed the term in the interests of examining and understanding women's socialized difference from men, and their comitant cultural and political powerlessness.Women and LanguageMany feminists think that language is not only a tool for communication but also a manipulative tool.Two different approaches to questions about women and language: The reformormist approach: view conventional language as a symptom of the society that spawned it. The radical approach: view conventional language as an important cause of women's oppression, the medium through which women were taught and came to know their subordinate place in the world. (Cameron 1985)The women's movement of the late 1960s and early 1970s focused on two aspects of women's difference:First, it tried to show how women's difference from men was in many ways due to the artificial behavioural stereotypes that come with gender conditioning. Second, the movement de-emphasized differences between women, stressing instead shared experiences, their commonality, their solidarity.Gender and the Practice of TranslationGender awareness in translation practice poses questions about the links between social stereotypes and linguistic forms, about the politics of language and cultural difference, about the ethics of translation, and about reviving inaccessible works for contemporary readers.It highlights the importance of the cultural context in which translation is done.Experimental Feminist Writing and Its TranslationThe radical feminist writing of the 1970s was experimental. It was radical as it sought to undermine, subvert, even destroy the conventional everyday language maintained by institutions such as schools and universities, publishing houses and the media, dictionaries, writing manuals, and the 'great works' of literature. Thus, they took on the radical position of attacking language itself, rather than just the messages carried by the language.Radical feminist writing in the late twentieth century has been experimental in that it explores new ground, seeking to develop new ideas and a new language for women. The theory is that the language women have at their disposal will influence their creativity, affecting their ability to think in revolutionary terms and their capacity to produce new work.Experiments have blossomed in every Western European and North American country, and in all languages due to the fact that writers are deconstructing different languages as well as different cultures, which require feminist attention in different places.Translating Experiments with LanguageWhen the grammar of a language such as French dictates that nouns, adj. and participles need to be gender-identified, feminist writers can subvert this gender requirement and the symbolic system that underlies it by applying the grammar system differently. This could mean feminizing words to give them new meanings. Similarly, when the syntax of a language or its conventions of style are too restrictive for women's new vision. the writer can change it.Assertive Feminist TranslationNo act of writing or translation is neutral and rewriting in the feminine is a conscious act that puts its cards on the table from the very beginning . Its project is to imbue translation praxis with feminist consciousness. Translation thus becomes a political activity that has the objective of making women visible and resident in language and society.Issues of sexism or women's silencing need not only be pointed out, they need to be solved with deliberate feminist intervention that redresses the imbalance and places women directly into the language.Descriptive Translation Studies and and Poly-system Theory Describing TranslationWhat confronted the translation researchers first is the relationship between a text and one or more translations of it. They try to analyze it from the perspective of description and empirical assessment.The main differences between systematic attempts at description concern approach and procedure. Some are source-text based, while others treat the source and target text on an equal basis.Toury’s AT TheoryIn 1980, Toury argued that the tertium comparatist should take into account the unequal status of a translation in relation to its source. The tertium comparatist, which Toury calls the A T or Adequate Translation, results from an analysis of the source text. A T is a hypothetical construct consisting of an “explicitation of [source text] textual relations and functions”(Descriptive Translation Studies and Beyond 1980:116)A T embodies the principle of a wholly retentive, source-text-oriented translation. This principle, which also constitutes a practical translation strategy, is termed ‘adequacy’. It refers to a mode of translation “which realizes in the target language the textual relationships of a source text with no breach oThe comparison between textual relations and functions presented in the source text and the target text:The identification of textual relations and functions in the source text and the formulation of the A TMapping target-text units on the A T and on the corresponding source-text unitsMeasuring shifts and deviations between target text, source text and A T so as to be able to characterize the overall relation between the translation and its sourceToury’s NormsNorms：external and socio-cultural constraintsThey are seen as “performance instructions”, both in a general sociological sense and, with reference to communication and translation, in the sense of controlling linguistic usage.Norms operate at the intermediate level between competence and performance. Competence stands for the set of options translators have at their disposal. Performance refers to the options actually selected Decisions and Norms:Jiri Levy’s ‘generative model’emphasized that at every level the translator had to choose one option from among a set of alternatives, in the knowledge that every decision will affect all subsequent decisions.The process covers everything from the selection of a text to be translated, via the overall orchestration at macro-level, down to individual sentence constructions, word choice, punctuation marks and even spelling.Preliminary norms（初步准则）, which concerns such things as the choices of the text to translate, or the decision to work directly from the original language or from an existing translation in another language, the decision to translate into the native or into a second or third languagethe initial norm（首要准则）, which governs the translator’s choice between two polar alternatives regarding the translation’s overall orientation, one which leans as far as possible to the source text, the other subscribing to usage in the receptor culture; the first pole Toury calls that of ‘adequacy’, the other that of ‘acceptability’③operational norms（操作准则），which guide decision-making during the actual business of translating;here Toury distinguishes between.Matricial norms（母体规范）, which help determine the macro-structure of the text and govern decisions concerning translating all or part of the source text, division into chapters, acts, stanzas, paragraphs and the like. Texutual-linguistic norms（文本规范）, which affect the text’s micro-level, the detail of sentence construction, word choice, the use of italics or capitals for emphasis, and so on.Andrew Chesterman’s NormsHis approach is descriptive.Chesterman’s discussion covers social, ethical and technical norms of translationThe social norm regulate interpersonal coordinationThe ethical norms : translators’wish to uphold the values of clarity, truth, trust and understandingThe technical norms: relating the four values(clarity, truth, trust, understanding)Process(or production) norm, which operate at a lower level than expectancy norms, regulate the translation process itself.T he accountability norm,which is ethical in nature, assumes that translators owe loyalty to the original writer, to the commissioner of the translation job, to themselves, and to their clients and prospective readers.The communicative norm is social in character and stipulates that translators should act in such a way as to optimize communication, as required by the situation, between all the parties involved.The relation norm urges the translator to ensure that “an appropriate relation of relevant similarity is established and maintained between the source text and the target text”Norm TheoryNorm refers to both a regularity in behavior and to the underlying mechanism which accounts for this regularity.The mechanism is a psychological and social entity. It mediates between the individual and the collective, between the individual’s intentions, choices and actions, and collectively held beliefs, values and preferences.Poly-system TheoryIt was developed in the 1970s by the Isreali scholar Itamar Even-Zohar brorrowing ideas from the Russian Formalists of the 1920s.Even-Zohar emphasizes that translated literature operates as a system: in the way the TL selects works for translation. in the way translation norms, behaviour and policies are influenced by other co-system According to Shuttleworth and Cowie:The poly-system is conceived as a heterogeneous, hierarchized conglomerate (or system) of systems which interact to bring about an ongoing, dynamic process of evolution within the poly-system as a whole.The hierarchy referred to the positioning and interaction at a given historical moment of the different strata of the poly-system.This 'dynamic process of evolution' is vital to the poly-system, indicating that the relations between innovatory and conservative systems are in a constant state of flux and competition.The position of translated literature is not fixed due to the flux.It may occupy a primary or a secondary position in the poly-system. If it is primary, 'it participates actively in shaping the centre of the poly-system'(Even-Zohar 1978/2000:193)Even-Zohar gives three major cases when translated literature occupies the primary position:when a 'young' literature is being established and looks initially to 'older' literatures for ready-made models when a literature is 'peripheral' or 'weak' and imports those literary types which it is lackingwhen there is a critical turning point in literary history at which established models are no longer considered sufficient, or when there is a vacuum in the literature of the country. (Jeremy Munday 2010:112) If translated literature assumes a secondary position, then it represents a peripheral system within thepolysyetem. It has no majoy influence over the central system and even becomes a conservative element, preserving conventional forms and conforming to the literary norms of the target system.Even-Zohar suggests that the position occupied by translated literature in the polysystem conditions the translation strategy.If it primary, translators do not feel constrained to follow target literature models and are more prepared to break conventions. They often produce a TT that is a close match in terms of adequacy, reproducing the textual relations of the ST.If it is secondary, tranlators tend to use existing target-culture models for the TT and produce more 'non-adequate' translations.The advantages of poly-system:Literature itself if studied alongside the social, historical and cultural forcesEven-Zohar moves away from the isolated study of individual texts toward the study of translation within the cultural and literary systems in which it functionsThe non-prescriptive definition of equivalence and adequacy allows for variation according to the historical and cultural situation of the text.The criticisms of poly-system theory:overgeneralization to 'universal laws' of translation based on relatively little evidencean over-reliance on a historically based 1920s' Formalist model which might be inappropriate for translated texts in the 1970s.the tendency to focus on the abstract model rather than the 'real-life' constraints placed on texts and translators the question as to how far the supposed scientific model is really objectivity.Even-Zohar suggests that the position occupied by translated literature in the polysystem conditions the translation strategy.If it primary, translators do not feel constrained to follow target literature models and are more prepared to break conventions. They often produce a TT that is a close match in terms of adequacy, reproducing the textual relations of the ST.If it is secondary, translators tend to use existing target-culture models for the TT and produce more 'non-adequate' translations.。

6th International Conference on Social Science, Education and Humanities Research (SSEHR 2017)Exploring Newmark’s Communicative Translation and Text TypologyWang ZhengXiamen University Tan Kah Kee CollegeKeywords: communicative; translation; text typologyAbstract. Translation, as an important means of communication, in all aspects of cross-culture communication, is playing a crucial role. Translation theory’s main concerns are to determine appropriate translation methods for the widest possible range of texts or text-categories. When a lot of pragmatic texts, science and technology texts appeared in the translation areas, the interrelation between the text type and transfer method began to arouse the interest of translation scholars. Many translation scholars presented the concept of standards for classifying the correlation between the text type and translation method. There are two famous theorists of Functionalism who made a major contribution to the theory of text typology: Katherina Reiss and Peter Newmark. Peter Newmark, a famous British translation theorist, who linked language function to translation in his theory and further bring the theory of text typology to translation practices. Communicative translation is an important part of Newmark's translation theories. In this thesis, the author will focus on the comparison of semantic translation and communicative translation, then further explore the framework of Newmark’s text typology.Peter Newmark and Communicative TranslationThe Definition of Communicative Translation. “Communicative translation attempts to produce on its readers an effect as close as possible to that obtained on the readers of the original. Semantic translation attempts to render, as closely as the semantic and syntactic structures of the second language allow, the exact contextual meaning of the original” (Newmark, 2006: 39). It is obvious that communicative translation focuses on producing an equivalent effect on the target readers. On the contrary, semantic translation remains within the original culture at the author’s linguistic level. Newmark’s one major contribution to translation is the communicative translation versus semantic translation.Difference Between Communicative Translation and Semantic Translation. In theory, there are only two methods of translation: communicative translation and semantic translation. There are wide differences between the two methods. Communicative translation addressed itself solely to the second reader, who does not anticipate difficulties or obscurities, and would expect a generous transfer of foreign elements into his own culture as well as his language where necessary. But even here the translator still has to respect and work on the form of the source language text as the only material basis for his work. Semantic translation remains within the original culture and assists the reader only in its connotations if they constitute the essential human (non-ethnic) message of the text.Communicative translation attempts to produce on its readers an effect as close as possible to that obtained on the readers of the original. Semantic translation attempts to render, as closely as the semantic and syntactic structures of the second language allow, the exact contextual meaning of the original.The functionalism theory demonstrates the possible translation procedures and the various arguments for and against the use of one translation rather than another in a particular context. Translators should accordingly adopt respective appropriate translation strategies and relative approaches, either semantic translation or communicative translation according to different text types.Peter Newmark’s Text TypologyAccording to functionalist approaches, it is the intended purpose or function of the target text that determines the translation method. This means that the translator needs to determine the translation purpose first, and next whether the translation intended to show the different aspects of the source text or to achieve the same functions as the original text. Lastly, the translator must then decide the suitable translation strategies and methods. Text typology is a very useful tool to explore translation approaches for different types of text.Text type and genre are used to refer to a distinctive category of discourse of any type, spoken or written, with and without literary aspiration. Text type as an essential pattern of text embodies linguistic functions, thinking modes and cultural conventions. The study of text types in the text-oriented translation will help the translator to have a thorough understanding of the text and to obtain adequate equivalence in target language text from the source language text. Every text is characterized by one or several basic communication functions. Different text type should require different transfer methods (Reiss 1982:112) .The Classification of Text Type. Based on Karl Buhler’s theory of language function and Reiss’s text typology, Newmark (1981:21) classifies different texts into three categories: expressive text, informative text, vocative text.According to Newmark (1998:40), expressive texts include serious imaginative literature, authoritative statements, autobiographies, and personal correspondences; informative texts include textbooks, reports, papers, articles, memos, minutes, and legal documents, etc. with scientific, technological, commercial, industrial, and economic content; vocative texts include notices, propaganda, publicity, and popular fiction.Text Type and Its Corresponding Translation Criteria and Method. Newmark holds that different texts require different translation criteria and methods. He proposes that semantic translation is used for expressive texts and communicative for informative and vocative texts. In translating expressive texts, the expressive components should be rendered closely. However, for informative and vocative texts, the translator should focus on the accuracy of message and the main force of the texts, trying to produce a pragmatically equivalent effect on readers. Badly and/or inaccurately written passages should be corrected in communicative translation (Newmark,1998: 47).Translation Methods for Different Text TypesTranslation Methods for Expressive Text. Newmark also points out that the core of expressive text is the author’s status in the process of translation. The core of expressive texts is the author’s ideology, which is sacred in the texts. The author’s personal components constitute the “expressive” elements of an expressive text and become the idiolect which displays the author’s personal language style. So, Newmark suggests adopting the approach of semantic translation when translating this type of text. That is, attempt to render, as closely as the semantic and syntactic structures of the second language allow, the exact contextual meaning of the original, in order to display the personal components of the text and make the translated text follow as close to the original as possible. The aim is to highlight the expressive function of the text. (Newmark, 1981).Translation Methods for Vocative Text. The core of vocative texts is the readership since the status of their authors is not important. Instead, what is important is the effect of information transmission and the readers’ affective response, which is to call upon the readers to act, to think, to feel, and to react in the way intended by the text (Newmark, 1998:41). Therefore, to attract readers and perform the vocative function of the text, and achieve the expected effect intended by the original, the translator must observe readers’ reading habits and feelings and try to use their familiar expressions. In the process of translating, the translator frequently prefers to adopt the approach of explanation rather than reproduction. The translator has the right to correct or improve the logic of the text, to replace clumsy syntactical structures with elegant ones, to discard any expressions of wayward, obscurities, ambiguity, and tautology, and to correct barriers of idiolect in the text. Hedoesn’t have to follow the form of the original. Instead, he can rearrange the sentence structures of the text, and make the translated text natural, fluent, and easily understood (Newmark, 1982:42).Translation Methods For Informative Text. The function of informative texts focuses on the external situation, the facts of a topic, and the reality outside of the language (Newmark, 1998:40), so the truth conveyed by the information is the core of this type of text. Meanwhile, the author’s status in the text is anonymous. The translation of this type calls for receptors’ understanding and response, that is, the effect of information transmission. Therefore, Newmark (1982:39) suggests adopting the approach of communicative translation, with the attempt to produce the effect to the target readers as close as possible to that obtained by the original readers, emphasizing the accuracy and truth of the process in information transmission. On this aspect, Newmark’s assertion is quite similar to the “functional equivalence” that Nida claims. The readers of a translated text should be able to comprehend it to the point that they can conceive how the original reader of the text must have understood and appreciated it (Nida, 1993:118).Significance of Newmark’sThe text typology by Newmark is quite brief, definite, and easily utilized, which is not only a guide to literary translation, but more important, a feasible approach to pragmatic translation. According to the three types of texts he mentions above, Newmark (1998:47) further points out that, semantic translation is used for “expressive” texts, communicative for “informative” and “vocative” texts. The difference in the two translation approaches is that the former demands that the translated text should be as close to the original as possible in the form, structure, and word order; and the latter focuses on readers’ understanding and response, i.e., the effect of information transmission.Newmark (1998:42) also claims that, in translation practice, few texts are purely expressive, informative or vocative: most include all three functions, with an emphasis on one of the three. Therefore, the translator must first determine the primary function of a single text, or determine the language function of each part of the same text, and accordingly adopt respective appropriate translation strategies and relative approaches, either semantic translation or communicative translation.References[1] Reiss, K. Text types, translation types and translation assessment. In: Chesterman, A. (ed.) (1989). Readings in Translation Theory. Oy Finn Lectura Ab,1989.[2] Holz-Manttari, J. Theory and Method [M]. Helsinki: Rodopi, 1991.[3] Newmark, P. Approaches to Translation [M]. Oxford: Pergamon. 1981.[4] Newmark, P. A Textbook of Translation [M]. New York: Prentice Hall International, 1988.[5] Newmark P. 1998. More Paragraphs on Translation [M]. Multilingual Matters Limited.1998.[6] Newmark, P. (2006). About Translation [M]. Beijing: Foreign Language Teaching and Research Press.[7] Nida, E. A. and Taber, C. R. The Theory and Practice of Translation [M]. Leiden: The Netherlands, 1964.。

QualitySNP Pipeline ManualIndex1.Introduction of QualitySNP2.How to compile the programs3.How to use the programs4．How to use the results1.Introduction to QualitySNPQualitySNP is an efficient tool for SNP detection, storage and retrieval. It implements a new algorithm developed by us to reliably detect single nucleotide polymorphisms (SNPs) and insertions/deletions (indels) in expressed sequence tag (EST) data, both with and without quality files. The new algorithm uses a haplotype based strategy on potential SNPs, which predicts reliable SNPs, as well as reliable haplotypes.The pipeline consists of six steps:1)The first step performs EST assembling using cross_match forremoving vectors and CAP3 for sequence clustering.2)The second step is the analysis of the alignment information to selectclusters with at least 4 EST members; this is done by the Perl script“Getalignmentinfo”. If sequences with quality information are available,another Perl script “Getalignmentinfoqual” is used instead of “Getalignmentinfo”.3)The third part performs SNP and haplotype detection, anddistinguishes variations between or within genotypes. This is the corepart of the pipeline, using the C program named “QualitySNP” thatimplements the algorithms for prediction haplotypes and SNPs. Thehelper programs “Getavailcontigseq” and “Getavailcontigqual” extractthe sequences from the contigs and get the quality information ofcontigs.In the case of sequences with quality information, the program“QualitySNPqual” should be used instead of “QualitySNP”. Beforeusing “QualitySNPqual”, another program “GetavailESTqual” shouldbe run to get quality score for each sequence in each cluster thatcontains at least 4 sequences.4)Step four is the non-synonymous SNP discovery using FASTY, fromPearson’s FASTA package. A C program named “GetnonsySNPfasty” isused to analyze FASTY results, detect the ORFs and find non-synonymous SNPs.5)The fifth step transfers the final results into a SNP database. Itincludes two C programs: “Getsnpindexcontig” (for sequences withoutquality information) or “Getsnpindexcontigqual” (for sequences withquality information) formats all information of contigs and the locationand types of SNPs for insertion into the MySQL database; the secondprogram “Transfersnpfasta” is used to convert SNP-containing probesfor micro-array analysis into the format for the MySQL database.There are two SQL scripts to create the database and to load the datainto the database. “dbcreater.sql” (for sequences without qualityinformation) or “dbcreaterQ.sql” (for sequences with quality information) can create the database and tables that are used by theretrieval system, and “dataload.sql” puts the formatted data intodatabase.6)The final part is the retrieval system that is written in PHP. All PHPscripts and HTML pages are stored in the website’s directory tree.The QualitySNP pipeline itself is implemented in standard C-Shell script on a UNIX/Linux workstation. The Perl program is written in Perl5.8.0, the database uses MySQL3.23 (or better) and the retrieval system uses PHP4.3.1 (or better).2.How to compile the programs1)Download the packed file named QualitySNP11102007.tar.gz2)Unpack the tar file by the following command% tar xzvf QualitySNP11102007.tar.gzor, if your tar command lacks the build-in unzip function, use% zcat QualitySNP11102007.tar.gz | tar xvf -3)Compile the programs using the command% make all3.How to use the programsThere are two possible approaches to run these programs, the first way by running the programs manually one after the other, and the second way by running a C shell script name “QualitySNPpipeline” (see below).I. The first (manual) way is as follows:1)Make sure that the programs that you installed are in your search path.This can be done by adding the program-directory to your PATH variable.In the C-shell you can add the following to your “.login” file:set path = ( my_program_dir $path )and in the bash by adding the following to the “.profile” file:export PATH=my_program_dir:$PATHOf course, “my_program_dir” should be the path leading to your program directory (e.g. /usr/local/bin/).2)Run CAP3 in a sequence file directory, containing the sequence file whichincludes all sequences in FASTA format. The CAP3 program can be obtained from /cap/cap3.html.The commands are:% formcon filename 500 4000% cap3 filename –p similarity –o 100The parameters in these commands are:filename is the file with sequences in FASTA format, andsimilarity is the similarity of overlap for CAP3.For example, using a sequence file named testseq, and a similarity score of 95 like we used in our study, the commands would be:% formcon testseq 500 4000% cap3 testseq –p 95 –o 100Please note: If sequences with quality information are used, the quality file with quality scores of all sequences should be formatted in FASTA format and should be named “filename.qual”. For instance, for a sequence file named “testseq”, the quality file should be named “testseq.qual”.3)Run Getalignmentinfo in the directory, by issuing the command:% Getalignmentinfo filename.cap min-clustersize where filename is the sequence file, and min-clustersize is the minimum cluster size. The default minimal cluster size is 4, you can set this according to your requirements. For example:% Getalignmentinfo testseq.cap 4Please note: if sequences with quality information are used, please run “Getalignmentinfoqual” instead of “Getalignmentinfo”. The parameters of “Getalignmentinfoqual” are identical to those for “Getalignmentinfo”.4)Run QualitySNP in the same directory. The commands are:% Getavailcontigseq filename.capfilename.capGetavailcontigqual%% QualitySNP filename.cap min-allelesize lowqual5sidelowqual3sideweightlowqualsimilarity2similarity1min-confidencescoreThe parameters used in these commands are:Min-allelesize is the minimum size of alleles of each SNP (2 in our study)lowqual5side is the length of the low quality region at the 5’ end of sequence (30 nucleotides in our study)similarity1 is the similarity on one polymorphic site (0.75)similarity2 is the similarity on all polymorphic sites (0.8)lowqual3side is the low quality region of 3’ side (0.2, 20% of the wholesequence in our study).weightlowqual is the weight value of the low quality region (0.5)min-confidencscore is the minimal confidence score（2）For example:% Getavailcontigseq testseq.cap% Getavailcontigqual testseq.cap% QualitySNP testseq.cap 2 30 0.75 0.8 0.2 0.5 2Please note: if sequences with quality information are used, first run “GetavailESTqual’” to get quality scores for each sequence, and then run “QualitySNPqual” instead of “QualitySNP”. Besides parameters used by QualitySNP, one more parameter of min-SNPqualityscore is required by QualitySNPqual (the default value is 20 PHRED score). The usage of “QualitySNPqual” is the same as for “QualitySNP”. For example: % GetavailESTqual testseq% QualitySNPqual testseq.cap 2 30 0.75 0.8 0.2 0.5 2 205)Run FASTY and the analysis of non-synonymous SNP (this step is notnecessary). FASTY can be obtained from / as part of the FASTA package.The command to run (the threaded version of) FASTY is:% fasty34_t allavailcontigseqwithSNP Uniprot –b 6 –d 6 –Q >allavailcontigseqwithSNP.fastyThe command for the detection of non-synonymous SNPs is:% GetnonsySNPfasty availcontigseq allavailcontigseqwithSNPallavailcontigseqwithSNP.fastyParameters used:Uniprot is the Uniprot (or any other) protein database. This can beeither the full path leading to a FASTA-formatted protein database, ora single letter to indicate the database, in case the FASTLIBSenvironment variable is used to specify databases in the FASTA suite.The files “availcontigseq” and “allavailcontigseqwithSNP” arefrom the results of QualitySNP, File “availcontigseq” contains theconsensus sequences of contigs with SNPs, as produced by CAP3. Asthese sequences are not curated, they may contain padding symbols(“*”), which may indicate either insertions and/or deletions in the ESTs, but in many cases these may be caused by sequencing errors. File“allavailcontigseqwithSNP” contains the consensus sequences ofSNP-containing contigs which did not contain any insertions ordeletions.For example:% fasty34_t allavailcontigseqwithSNP Uniprot –b 6 –d 6 –Q> allavailcontigseqwithSNP.fasty% GetnonsySNPfasty availcontigseq allavailcontigseqwithSNPallavailcontigseqwithSNP.fastyNote: a program called “transeq” that is used in GetnonsySNPfasty is from the package of EMBOSS. Please make sure that you have installed it. If not, please download it from /6) Format all information of SNPs and haplotypes, and transfer them to the database.Commands for formatting data:% Getsnpindexcontig filename% TransfersnpfastaIf sequence quality is available, sequence quality score is used as additional criterion, a different command is used to format the output: % Getsnpindexcontigqual filename% TransfersnpfastaCommands for moving results to one directory named “snpdb”: % mkdir snpdb% mv estdata snpdb% mv snpindexdata snpdb% mv contigindexdata snpdb% mv snpcontigdata snpdb% mv allsnpmicro snpdbIf you run step 5, please also move the 9 output files in step 5 to “snpdb”% mv ssnpcodingdata snpdb% mv nssnpcodingdata snpdb% mv ssnpfastydata snpdb% mv nssnpfastydata snpdb% mv indelsnpdata snpdb% mv contigorfdata snpdb% mv utrsnpdata snpdb% mv snptagdata snpdbCommands for creating databases and loading data:If sequences without quality files, run the command:% mysql –u root –p < dbcreater.sqlIf sequence with quality files, run the command:% mysql –u root –p < dbcreaterQ.sqlData loading command for both cases:% mysql –u root –p < dataload.sqlNote: edit dataload.sql and change to the correct data directory; Also ifyou run step 5, please remove ‘#’ before the 9 lines.Parameters:snpdb is the name of the directory for storing dataFor example:% Getsnpindexcontig testseq% TansfersnpfastaIf sequence quality is available, the example is:% Getsnpindexcontigqual testseq% TansfersnpfastaPut all data to one directory “snpdb”:% mkdir snpdb% mv estdata snpindexdata contigindexdata snpdb% mv snpcontigdata allsnpmicro snpdbCreate the database and load the data into database for sequences without quality files:% mysql –u root –p < dbcreater.sql% mysql –u root –p < dataload.sqlCreate the database and load the data into database for sequences with quality files:% mysql -u root –p < dbcreaterQ.sql% mysql –u root –p < dataload.sql7) Set up your retrieval system1.Start your apache server or other web server.2.Put the website directory with PHP scripts and HTML pages in yourserver’s “DocumentRoot” directory.3.Edit reference species of the “search.php” page and put yourspecies there. Edit “searchdb.php”, put correct name of yourdatabase thereII. The second way of running the pipeline is MUCH easier: just run the C-shell script QualitySNPpipeline:1. Edit QualitySNPpipeline program:Change program_path1 to your alignment program CAP3 directoryChange program_path2 to your QualitySNP directory2. Run QualitySNPpipeline:% path_to_QualitySNPdir/QualitySNPpipeline [-q] filename similarityCAP3 min-clustersize min-allelesize lowqual5side similarity1 similarity2 lowqual3side weightlowqualmin-confidencescoreThe parameters used are:1.filename is the name of sequence file2.similarityCAP3 is the similarity of overlap for CAP33.min-clustersize of the minimum size of a cluster (4)4.min-allelesize is the minimal size of alleles for each SNP (2)5.lowqual5side is the size of the low quality region at the 5’ side of theEST sequence (30 nucleotides in our study)6.similarity1 is the similarity on one polymorphic site (we used 0.75 inour study)7.similarity2 is the similarity on all polymorphism sites (0.8)8.lowqual3side is the length of the low quality region at the 3’ end (0.2;20% of the whole sequence in our study)9.weightlowqual is the weight value of the low quality region (0.5 in ourstudy)10.m in-confidencscore is the minimum confidence score (2)For example% QualitySNPpipeline testseq 95 4 2 30 0.75 0.8 0.2 0.5 211.–q is the command line switch to instruct the pipeline to processsequences with quality information. The parameter MINQUAL in thepipeline is for the parameter min-SNPqualityscore of QualitySNPqual.The default value is 20 PHRED score, which can be changed by usersas well (see line 58 of QualitySNPpipeline). The usage is as following: % QualitySNPpipeline –q testseq 95 4 2 30 0.75 0.8 0.2 0.5 2 3. Create a database and upload the data to the database, and set up the website:Create a database and upload the data under ‘snpdb’ to the database according to the instructions mentioned before.Set up the website:a. make sure that PHP and apache are installed and worked well on yourcomputer.b. put these PHP scripts under the directory for websites, Please read“readme” file under websites in the QualitySNP package.Note: please check the IP address for the computer with the MySQL database, and change it in the “searchdb.php” script4. How to use the resultsThere programs will output a number of results files: some files contain information about SNPs and haplotypes, and others contain contig sequences and statistical information.Important files for SNPs and haplotypes:1.File “realsnpinfo” includes all SNPs in the clusters, excluding thosefrom single haplotypes.2.File “SNPquality” includes all relevant information for identifyingreliable SNPs, such as confidence scores and allele haplotype scores,as well as quality score of SNPs if sequence quality available.3.File “availcontigwithSNP” includes haplotype and SNP information forevery contig, as well as statistical information of SNPs for all contigswith SNPs.Other information for SNPs haplotypes:4.File “SNPinfo2” includes all potential SNPs for all clustered sequences.5.File “haplotypes” includes all information for the haplotype definition.6.File “SNPdiff” includes the D-values of the contigs, which are used fordetecting paralogs.7.File “allavailsnp” contains 25 nucleotides sense and reverse stringsurrounding the SNP, the SNP at the middle position (residue 13).These can be used for designing probes for inclusion on microarraychips.8.File “SNPblocks” includes block information for every SNP in onecluster.9.File “SNPpattern” includes pattern information for every SNP in onecluster.Important files for contigs1.File “contigstatisticinfo” includes the statistical information of clustersize and number of clusters. In this file, the first column is the number of ESTs in any cluster, the second column is the number of clusters of this particular size.2.File “availcontigseq” contains the consensus sequences of contigs withSNPs, as produced by CAP3. As these sequences are not curated, they may contain padding symbols (“*”), which may indicate eitherinsertions and/or deletions in the ESTs, but in many cases these may be caused by sequencing errors.3.File “allavailcontigseqwithSNP” contains the consensus sequences ofSNP-containing contigs which did not contain any insertions ordeletions.4.File “availcontiglist” shows a list of the contigs with sizes larger thanthe minimum cluster size, the number of ESTs in them, and length of the longest EST therein.5.File “availcontigseq” contains the sequence of the contigs whose size islarger than minimum cluster size.6.File “availcontigqual” contains the quality scores of the contigs in file“availcontigseq”, as obtained from CAP3.。

N.B. This OMCL Quality Management System document is applicable to members of the European OMCL Network only. Other laboratories might use the document on a voluntary basis. However, please note thatGeneral European OMCL Network (GEON) QUALITY MANAGEMENT DOCUMENTPA/PH/OMCL (18) 24 R1QUALIFICATION OF EQUIPMENTQUALIFICATION OF IR SPECTROPHOTOMETERSFull document titleand reference Qualification of EquipmentAnnex 4: Qualification of IR Spectrophotometers PA/PH/OMCL (18) 24 R1 Document typeGuidelineLegislative basisThe present document was also accepted by EA as recommendation document to be used in the context of Quality Management System audits of OMCLs Date of first adoptionMay 2007 Date of original entry into forceJuly 2007 Date of entry into force of revised documentSeptember 2019Previous titles/other references / last valid version This document replaces document PA/PH/OMCL (07) 12 DEF CORR in force since December 2007 Custodian Organisation The present document was elaborated by the OMCL Network / EDQM of the Council of Europe Concerned NetworkGEONANNEX 4 OF THE OMCL NETWORK GUIDELINE“QUALIFICATION OF EQUIPMENT”QUALIFICATION OF IR SPECTROPHOTOMETERSNote: Mandatory requirements in this annex are defined using the terms “shall” or “must”. The use of “should” indicates a recommendation. For these parts of the text other appropriately justified approaches are acceptable. The term “can” indicates a possibility or an example w ith non-binding character.1.INTRODUCTIONThe present document is the 4th Annex of the core document “Qualification of Equipment”, and it shall be used in combination with it when planning, performing and documenting the qualification process of Infrared (IR) spectrophotometers.The core document contains the Introduction and general forms for Levels I (Selection of instruments and suppliers) and II (Installation and release for use) of qualification, which are common to all types of instruments.The present Annex 4 contains a general introduction and requirements for IR spectrophotometers. Level III (Periodic and motivated instrument calibration/checks) and IV (In-use instrument checks) qualifications must be carried out as an ISO 17025 requirement.Requirements and (if applicable) corresponding typical acceptance limits given in bold should be applied; however other appropriately justified approaches are acceptable.Exemplary procedures provided in this document have non-binding character. They can be helpful when carrying out the required qualification. Nevertheless, it is left to the professional judgement and background experience of each OMCL to decide on the most relevant procedures to be undertaken in order to provide evidence that their IR spectrophotometers are working properly and are suitable for their intended use.If the qualification of equipment is done by the manufacturer or an external service provider, it is the responsibility of the OMCL to make sure that this is in line with the requirements set out in this guideline.TABLE ILevel III. Periodic and motivated instrument checksRequirements and related typical acceptance limits are indicated in boldParameter to be checked Typical acceptance limits* Accuracy of wavenumber scale*Refer to Ph. Eur. Chapter 2.2.24.“Control of equipment performance”Spectral Resolution*Refer to Ph. Eur. Chapter 2.2.24.“Control of equipment performance” Detector energy ratio Limit to be set based on OMCLexperience/service provider’s instructionsSignal-to-Noise ratio Limit to be set based on OMCLexperience/service provider’s instructionsZero test Limit to be set based on OMCLexperience/service provider’s instructionsContamination check (only for ATR instruments)Wavenumber (cm-1) Upper limit (A) 3100.0 – 2800.0 0.1 1800.0 – 1600.0 0.1 1400.0 – 1100.0 0.2Throughput check (only for ATR instruments)T min = 80 % (n=3 wavenumbers)(The lower limit of the transmittance for the 3 wavenumbers must be 80 %)TABLE IILevel IV. In-use instrument checksExamples of requirements for IR spectrophotometersParameter to be checked/Typical acceptance limitsSystem suitability check: according to Ph. Eur. Chapter 2.2.24. “Control of equipment performance” or specific Monographs or MAH dossier or validated in-house method2. LEVEL III: examples of periodic and motivated instrument checksThis section contains practical examples of tests and their associated tolerance limits for several parameters related to the performance of an IR spectrophotometer.These examples can be considered by OMCLs as possible approaches to perform Level III of the equipment qualification process: “Periodic and motivated instrument checks”.Note: if available and judged appropriate, the use of the automatic internal calibration function of the instrument is encouraged. Please refer to the manufacturer’s instructions.2.1 DETECTOR ENERGY RATIOMethod:Record the minimum energy ratio value for at least one of the following measurement points and compare it to the vendor’s specifications:-Energy at 3990 cm-1 / energy at 2000 cm-1-Energy at 4000 cm-1 / energy at 2000 cm-1-Energy at 3400 cm-1 / energy at 1300 cm-1-Energy at 2000 cm-1 / energy at 1000 cm-1Energy ratio test specifications vary for each spectrometer configuration.2.2 SIGNAL-TO-NOISE RATIOMethod:Record the maximum noise level for each of the following regions:Peak-to-peak noise between:4050 cm-1 and 3950 cm-12050 cm-1 and 1950 cm-11050 cm-1 and 950 cm-1550 cm-1 and 450 cm-1(systems with DTGS detector only)RMS (root mean square) noise between:4050 cm-1 and 3950 cm-12050 cm-1 and 1950 cm-11050 cm-1 and 950 cm-1550 cm-1 and 450 cm-1(systems with DTGS detector only)Noise level test specifications vary for each spectrometer configuration.2.3 ZERO TESTMethod:When using a polystyrene film of approximately 35 µm in thickness as standard at wavelengths of 2925 cm-1and 700 cm-1, almost complete absorption of the irradiated energy can be observed. With this test, the remaining transmission is measured. As the maximum absorption can be observed at 700 cm-1, a negative value may be observed. The objective of the test is to evaluate whether, despite the fact that there is almost complete absorption, energy is still detectable.Non-valid results are an indication of non-linear behaviour of the detector and the electronic system.2.4 CONTAMINATION TEST (only for Attenuated Total Reflection (ATR) instruments)Note: if an automated system is available, this test can be run more frequently or it can be transferred to Level IV, to be run before each analysis.Method:This test checks the presence of peaks that signal a contamination problem.Use the automated function of the instrument (if available) to perform this test. If not available, a background spectrum should be recorded and compared with the one generated during the instrument qualification or provided by the supplier.2.5 THROUGHPUT CHECK (only for Attenuated Total Reflection (ATR) instruments)Note: if an automated system is available, this test can be run more frequently or it can be transferred to Level IV, to be run before each analysis.Method:This test checks for an unexpected reduction of the transmittance. An instrument-specific automated test can be used.A background spectrum is recorded and the transmittance is measured at 3 wavenumbers e.g. 4000, 2600 and 1000 cm-1. The background spectrum should be compared with the one generated during the instrument qualification or provided by the supplier.3.LEVEL IV: examples of in-use instrument checksThis section contains practical examples of tests and their associated tolerance limits for several parameters related to the performance of an IR spectrophotometer.These examples can be considered by OMCLs as possible approaches to perform Level IV of the equipment qualification process: “In-use instrument checks”.Note: if available and judged appropriate, the use of the automatic internal calibration function of the instrument is encouraged. Please refer to the manufacturer’s instructions.3.1 SYSTEM SUITABILITY TEST OF THE METHODMethod:This test should be performed according to the Ph. Eur. 2.2.24. “Control of equipment performance”, the MAH dossier or a suitably validated in-house method.Note: regeneration or replacement of the desiccant should be done if the system suitability test fails (e.g. by drying it for 8-12h at 250°C, then flushing with N2).REFERENCES(For all references, the latest version applies)1)Ph. Eur. 2.2.24, Absorption spectrophotometry, Infrared.。

直译和意译的异同英语作文英文回答：Literal translation and interpretative translation are two different approaches to translating texts. Literal translation aims to render the source text as closely as possible to the target language, word-for-word and structure-for-structure. The focus is on preserving the original meaning and form of the text, with minimal adaptation to the target language's conventions and cultural context.Interpretative translation, on the other hand, prioritizes conveying the meaning and intent of the source text while allowing for more freedom in adapting the language and structure to suit the target audience. The translator assumes a more active role in interpreting the original text, taking into account cultural differences, idioms, and the overall context.The choice between literal and interpretative translation depends on the specific purpose and context of the translation. Literal translation may be more appropriate for technical or legal documents where accuracy and precision are paramount. Interpretative translation is often used for literary works, marketing materials, and other texts where cultural sensitivity and readability are important.中文回答：直译和意译是两种不同的翻译方法。

1. A decision whether to pump or to transport concrete in buckets will directly affect the cost and duration of tasks involved in building construction.用泵送混凝土还是用吊斗浇筑混凝土的决定将直接影响建筑物施工中各项任务的成本和时间2.In selecting among alternative methods and technologies, it may be necessary to formulate a number of construction plans based on alternative methods or assumptions. 在选择施工方法和技术时，有必要根据各种备选的施工方法和假设制订若干套施工计划。

3.This examination of several alternatives is often made explicit in bidding competitions in which several alternative designs may be proposed or value engineering for alternative construction methods may be permitted这种对几个备选方案之间的评比在公开招标中表现的十分明显：在设计招标中会要求提交数个设计方案；在施工招标中会用到价值工程的方法4. In this case, potential constructors may wish to prepare plans for each alternative design using the suggested construction method as well as to prepare plans for alternative construction methods which would be proposed as part of the value engineering process.在这个案例中，潜在的承包商需要针对每个备选设计方案根据被建议的施工方法来制定具体的计划；也需要针对每个备选施工方法制定具体计划，而这些施工方法选择会被推荐应用价值工程方法5.In forming a construction plan, a useful approach is to simulate the construction process either in the imagination of the planner or with a formal computer based simulation technique.根据施工计划人员的想象或者利用以计算机为工具的仿真技术队施工过程进行模拟。

国际会计第七版课后答案（第五章）作者：弗雷德里克Chapter 5Reporting and DisclosureDiscussion Questions1. Accounting measurement is the process of assigning numerical symbols to eventsor objects. Disclosure, on the other hand, is the communication of accounting measurements to intended users. Advances in financial disclosure are likely to outpace those related to accounting measurement for a number of reasons.First, many would argue that financial disclosure is a less controversial area than accounting measurement. Second, changes in disclosure requirements are more rapidly implemented than changes in accounting measurement rules.Finally, whereas a single set of accounting measurement rules may not serve users equally well under different social, economic and legal systems, a company can disclose without necessarily sacrificing its accounting measurement system.2.Four reasons why multinational corporations are increasingly being heldaccountable to constituencies other than traditional investor groups:a.The development and growth of the influence of trade unions.b.The growing recognition of the view that those who are significantlyaffected by decisions made by institutions in general must be given theopportunity to influence those decisions.c.The rejection by many governments of classical economic premises such asthe belief that the regulated pursuit of private gain maximizessociety’s welfare.d.The increasing concern over the social and economic impact ofmultinational corporations in host countries.3.Arguments in favor of equal disclosure include:a.The absence of equal disclosure would create an unfair playing field forU.S. companies. Non-U.S. companies would have a competitive advantagein that they would not have to disclose the same information and sowould not incur the costs involved in generating and publishing it.b.Investors in non-U.S. companies have the same information needs as thosewho invest in U.S. companies. A market concerned with investorprotection would make sure that investors have timely and materialinformation on all listed companies, not just those domiciled in theUnited States.c.Unequal disclosure might impede cross-company comparisons involving U.S.and non-U.S. companies.Possible reasons against equal disclosure include:a.The high cost of meeting equal disclosure requirements may deter foreignissuers from listing in the United States.b.The extra costs involved work against the benefits of listing to theforeign companies.Evaluation of arguments:All of these arguments have merit. There is no unambiguously correct answer as to what disclosure requirements should be imposed on foreign issuers, and there has been a contentious debate on this subject in the U.S. in recent years. In practice, fairness arguments often carry great weight in public debate, even when objective economic analysis does not support them.4.Managers in Continental Europe and in Japan have for many years stronglyobjected to disclosing information about business segment financial results.These managers have argued that the information can be used by their competitors. In addition, Continental Europe and Japan have had traditions of low disclosure.Requirements for disclosure about segment results have become more stringent in Japan, France, and Germany in response to strong investor and analyst demand for the information. More generally, the three countries are striving to improve the quality of their financial reporting standards in order to improve the reputation and credibility of their capital markets.5.The simple answer is that mandatory disclosures are corporate disclosures madein response to regulatory requirements (for example, rules issued by national regulators or stock exchanges), and thatvoluntary disclosures are purely discretionary in nature. The distinction between mandatory and voluntary disclosures can be ambiguous in some settings, however. For example, the requirement that U.S. companies must file Form 10-Ks with the U.S. Securities and Exchange Commission is straightforward. However, measurement and disclosure approaches for some of the items in the Form 10-K are not.Similarly, there are widely divergent views concerning what types of press announcements are mandatory versus voluntary.Two possible explanations for differences in managers’ voluntary disclosure practices are: (1) Managers in highly competitive industries may be less forthcoming than managers in less competitive industries due to the expected cost of releasing information of potential use to their competitors. (2) Managers are expected to be more forthcoming when there is good news to disclose, than when there is bad news, particularly when the news can be expected to affect share prices.Two explanations for differences in managers’ mandatory disclosure practices are: (1) Cross-jurisdictional differences in disclosure requirements. (2) Differences in the extent of compliance with disclosure rules due to cross-jurisdictional differences in enforcement.6. Triple bottom line reporting refers to reporting on a company’s ec onomic,social, and environmental performance. It is a form of social responsibility reporting designed to demonstrate good corporate citizenship. So-called “sustainability” reports are an increasingly popular means of triple bottom line reporting. There is substantial variation in social reporting today.More regulation would improve comparability, but it might also stifle reporting innovations. The usefulness of social reporting to outside parties, particularly investors, needs to be demonstrated before implementing more regulation for it.6.Often we expect to observe less voluntary disclosure by companies in emergingmarket countries than by those in developed countries:a.Equity markets are relatively less developed in many emerging marketcountries, resulting in lower total demand for company information byinvestors and analysts.b.In many emerging market countries, most financing is supplied by banksand insiders such as family groups. This also leads to less demand fortimely, credible public disclosure, and in these markets enhanceddisclosure may have limited benefits.8. In general, for the same reasons as in Discussion Question 7, we expect toobserve fewer regulatory disclosure requirements in emerging market countries than in developed countries. The equity markets and disclosure requirements in many emerging market countries are not yet well developed, and accounting and auditing systems in emerging market countries are less well developed than in more developed market countries.9. The two broad objectives of investor-oriented equity markets are investorprotection and market quality. In the absence of investorprotection, investors will not be willing to participate in a market. However, in the absence of market quality, markets will not function satisfactorily. Many would consider the objectives equally important.10. It certainly is possible that more required disclosure will further encourageinvestor participation in capital markets by providing more and better information on which to base investment decisions. Benefits of increasedinvestor participation include increased liquidity, reduced transaction costs, and more accurate and efficient market pricing.。