scholarly journals SBML Level 3 package: Qualitative Models, Version 1, Release 1

2015 ◽  
Vol 12 (2) ◽  
pp. 691-730 ◽  
Author(s):  
Claudine Chaouiya ◽  
Sarah M. Keating ◽  
Duncan Berenguier ◽  
Aurélien Naldi ◽  
Denis Thieffry ◽  
...  
Keyword(s):  
Biological Networks ◽  
Quantitative Methods ◽  
Expression Data ◽  
Qualitative Modelling ◽  
The Core ◽  
Qualitative Models ◽  
Level 3 ◽  
Influence Graphs ◽  
Definition Of ◽  
Modelling Methods

Summary Quantitative methods for modelling biological networks require an in-depth knowledge of the biochemical reactions and their stoichiometric and kinetic parameters. In many practical cases, this knowledge is missing. This has led to the development of several qualitative modelling methods using information such as, for example, gene expression data coming from functional genomic experiments. The SBML Level 3 Version 1 Core specification does not provide a mechanism for explicitly encoding qualitative models, but it does provide a mechanism for SBML packages to extend the Core specification and add additional syntactical constructs.The SBML Qualitative Models package for SBML Level 3 adds features so that qualitative models can be directly and explicitly encoded. The approach taken in this package is essentially based on the definition of regulatory or influence graphs. The SBML Qualitative Models package defines the structure and syntax necessary to describe qualitative models that associate discrete levels of activities with entity pools and the transitions between states that describe the processes involved. This is particularly suited to logical models (Boolean or multi-valued) and some classes of Petri net models can be encoded with the approach.

Translationese and interlanguage in inverse translation: A case study

2021 ◽  
Vol 22 (1) ◽  
pp. 45-63
Author(s):  
Ming Yue ◽  
Boyang Sun
Keyword(s):  
Quantitative Methods ◽  
Comparative Method ◽  
Translation Studies ◽  
Language Complexity ◽  
Complexity Metrics ◽  
Working Definition ◽  
Level 3 ◽  
Definition Of ◽  
Inverse Translation

AbstractCurrent translation studies do not present a clear distinction between ‘translationese’ and ‘interlanguage’, giving rise to conceptual and terminology confusion. To disentangle these two concepts, we start with a relatively conservative working definition of translationese, then find it necessary to first differentiate between direct and inverse translations, according to whether the translator's L1 equals to TL or not. Taking Zhuangzi (a Daoist classic) as a case, we made both inter- and intra-speaker comparisons among Lin Yu-tang's inverse translation, James Legge's direct translation, and the two translators' creative works in English, with well-established language complexity metrics and quantitative methods. Results show that: (1) Inverse and direct translations are remarkably different in terms of complexity; (2) Inverse translation demonstrates both features of interlanguage and translationese, with the former mostly at lexical level and the latter at syntactic level; (3) Similar patterns are also discovered in Lin's other inverse translated works, suggesting our quantitative comparative method proposed may be reliable to some extent. Such results support our proposal that translationese and interlanguage should and can be differentiated for both theoretical and practical purposes.

Methodological challenges in historical linguistics

2017 ◽  
Author(s):  
Gard B. Jenset ◽  
Barbara McGillivray
Keyword(s):  
Qualitative Methods ◽  
Quantitative Research ◽  
Quantitative Methods ◽  
Historical Linguistics ◽  
Quantitative Research Methods ◽  
The Core ◽  
Qualitative Models ◽  
General Linguistics

Chapter 1 sets out the aims of the book, and introduces the core topics of models in historical linguistics, and the role of quantitative vs. qualitative methods in historical linguistics. The importance of use of both quantitative and qualitative models simultaneously is discussed. The chapter also introduces the ‘chasm’ metaphor for the current situation in historical linguistics, where quantitative methods are still confined to a minority of researchers in the field, but a methodological ‘chasm’ seems to separate them from the majority. A meta study of current research in historical linguistics is presented to substantiate this claim. The meta study shows that, compared to the leading general linguistics journal, historical linguistics is lagging behind in adopting quantitative research methods.

scholarly journals bioLQM: a java library for the manipulation and conversion of Logical Qualitative Models of biological networks

2018 ◽  
Author(s):  
Aurélien Naldi
Keyword(s):  
Biological Networks ◽  
Regulatory Networks ◽  
Model Simulation ◽  
Biological Regulatory Networks ◽  
Interactive Tools ◽  
Graphical Interfaces ◽  
Qualitative Models ◽  
Import And Export ◽  
Definition Of ◽  
Java Library

AbstractHere we introduce bioLQM, a new Java software toolkit for the conversion, modification, and analysis of Logical Qualitative Models of biological regulatory networks, aiming to foster the development of novel complementary tools by providing core modelling operations. Based on the definition of multi-valued logical models, it implements import and export facilities, notably for the recent SBML-qual exchange format, as well as for formats used by several popular tools, facilitating the design of workflows combining these tools. Model modifications enable the definition of various perturbations, as well as model reduction, easing the analysis of large models. Another modification enables the study of multi-valued models with tools limited to the Boolean case. Finally, bioLQM provides a framework for the development of novel analysis tools. The current version implements the usual updating modes for model simulation (notably synchronous, asynchronous, and random asynchronous), as well as some static analysis features for the identification of attractors. The bioLQM software can be integrated into analysis workflows through command line and scripting interfaces. As a Java library, it further provides core data structures to the GINsim and EpiLog interactive tools, which supply graphical interfaces and additional analysis methods for cellular and multi-cellular qualitative models.

Ways and Voices in the Psychoanalysis of Links According to Enrique Pichon-Rivière

2016 ◽  
Vol 6 (2) ◽  
Author(s):  
Rosa Jaitin
Keyword(s):  
Couple Therapy ◽  
Clinical Observation ◽  
Clinical Work ◽  
The Core ◽  
The Social ◽  
The 1960S ◽  
Definition Of ◽  
Relationship Of ◽  
The Voice ◽  
Different Levels

This article covers several stages of the work of Pichon-Rivière. In the 1950s he introduced the hypothesis of "the link as a four way relationship" (of reciprocal love and hate) between the baby and the mother. Clinical work with psychosis and psychosomatic disorders prompted him to examine how mental illness arises; its areas of expression, the degree of symbolisation, and the different fields of clinical observation. From the 1960s onwards, his experience with groups and families led him to explore a second path leading to "the voices of the link"—the voice of the internal family sub-group, and the place of the social and cultural voice where the link develops. This brought him to the definition of the link as a "bi-corporal and tri-personal structure". The author brings together the different levels of the analysis of the link, using as a clinical example the process of a psychoanalytic couple therapy with second generation descendants of a genocide within the limits of the transferential and countertransferential field. Body language (the core of the transgenerational link) and the couple's absences and presence during sessions create a rhythm that gives rise to an illusion, ultimately transforming the intersubjective link between the partners in the couple and with the analyst.

Historical text archives and prosopography: the COEL database system

1998 ◽  
Vol 10 (1-3) ◽  
pp. 57-72 ◽  
Author(s):  
K. S. B. Keats-Rohan
Keyword(s):  
Research Tool ◽  
Direct Access ◽  
Specific Situation ◽  
Core Data ◽  
Secondary Sources ◽  
The Core ◽  
Level 3 ◽  
Full Discussion ◽  
Available Information ◽  
Level 2

The COEL database and database software, a combined reference and research tool created by historians for historians, is presented here through Screenshots illustrating the underlying theoretical model and the specific situation to which that has been applied. The key emphases are upon data integrity, and the historian's role in interpreting and manipulating what is often contentious data. From a corpus of sources (Level 1) certain core data are extracted for separate treatment at an interpretive level (Level 3), based upon a master list of the core data (Level 2). The core data are interdependent: each record in Level 2 is of interest in itself; and it either could or should be associated with an(other) record(s) as a specific entity. Sometimes the sources are ambiguous and the association is contentious, necessitating a probabilty-coding approach. The entities created by the association process can then be treated at a commentary level, introducing material external to the database, whether primary or secondary sources. A full discussion of the difficulties is provided within a synthesis of available information on the core data. Direct access to the source texts is only ever a mouse click away. Fully query able, COEL is formidable look-up and research tool for users of all levels, who remain free to exercise an alternative judgement on the associations of the core data. In principle, there is no limit on the type of text or core data that could be handled in such a system.

ДОМИНАНТНО-ФУНКЦИОНАЛЬНАЯ СТРУКТУРА ИДИОСТИЛЯ М.Ф. ДОРОНОВИЧА// Humanitarian and Socio-Economic Sciences Journal/ OEAPS Inc., Berlin, Germany, pp.46-55

2018 ◽  
Author(s):  
Olga Dorofeeva ◽  
Любовь Викторовна Чернова
Keyword(s):  
Functional Structure ◽  
The Core ◽  
Definition Of

Обращаясь к рассмотрению вопроса о доминантно-функциональной структуреидиостиля, авторы раскрывают дефиницию «идиостиль» в его связи с экстра- и интралингвистическими факторами. Рассматривая творчество публициста М.Ф. Дороновича через призму одножанровых текстов, авторы выделяют доминанты, составляющие ядро идиостиля публициста. К числу таковых относятся оценочная метафоричность, гиперболичность, фразеологичность, реализующиеся как на уровне тропов, так и на уровне синтаксических фигур.Addressing the issue of dominant-functional structure of idiostyle, the authors reveal the definition of "idiostyle" in its connection with extra- and intralinguistic factors. Considering the creativity of the writer M.F. Doronovich through the lens of various genres of texts, the authors identify the dominant components of the core of the idiostyle of the writer. These include evaluative metaphoricity, hyperbolicity, phraseology, which are implemented both at the level of tropes and at the level of syntactic figures.СВЕДЕНИЯ О ГРАНТАХ И ФИНАНСИРОВАНИИИсследование подготовлено при поддержке Российского фонда фундаментальных исследований (отделение гуманитарных и общественных наук) и Министерства образования, науки и молодёжной политики Краснодарского края в рамках научного проекта № 18-412-230008 а(р) «Язык и стиль публикаций М.Ф. Дороновича в кубанских дореволюционных газетах». Руководитель проекта – О.А. Дорофеева.

Reference Conundrum: The Broad Definition of Peer-Review

2018 ◽  
Author(s):  
Cody Fullerton
Keyword(s):  
Peer Review ◽  
Gold Standard ◽  
Review Process ◽  
Peer Review Process ◽  
Academic Publishing ◽  
Inaccurate Information ◽  
The Core ◽  
Literature Reviews ◽  
Reference Interactions ◽  
Definition Of

For years, the gold-standard in academic publishing has been the peer-review process, and for the most part, peer-review remains a safeguard to authors publishing intentionally biased, misleading, and inaccurate information. Its purpose is to hold researchers accountable to the publishing standards of that field, including proper methodology, accurate literature reviews, etc. This presentation will establish the core tenants of peer-review, discuss if certain types of publications should be able to qualify as such, offer possible solutions, and discuss how this affects a librarian's reference interactions.

Assessment of multimorbidity of diseases in geriatric practice

2020 ◽  
pp. 17-21
Author(s):  
Mark Oprenko
Keyword(s):  
Quality Of Life ◽  
The Core ◽  
Definition Of

The definition of the multimorbidity concept reveals insufficient specificity of the comorbidity and multimorbidity definitions and, as a result, confusion in the use of these terms. Most authors are unanimous that the “core” of multimorbidity is presence of more than one disease in a patient. These coexisting diseases can be pathogenetically interconnected and non-interconnected. Regardless, the degree of multimorbidity always affects prognosis and quality of life.

scholarly journals Definition of the Mycobacterial SOS Box and Use To Identify LexA-Regulated Genes in Mycobacterium tuberculosis

2002 ◽  
Vol 184 (12) ◽  
pp. 3287-3295 ◽  
Author(s):  
Elaine O. Davis ◽  
Edith M. Dullaghan ◽  
Lucinda Rand
Keyword(s):  
Dna Damage ◽  
Mycobacterium Tuberculosis ◽  
Dna Polymerase ◽  
Expression Data ◽  
Repeat Family ◽  
New Genes ◽  
Lexa Binding ◽  
Definition Of ◽  
Inducible Genes ◽  
Single Mismatch

ABSTRACT The bases of the mycobacterial SOS box important for LexA binding were determined by replacing each base with every other and examining the effect on the induction of a reporter gene following DNA damage. This analysis revealed that the SOS box was longer than originally thought by 2 bp in each half of the palindromic site. A search of the Mycobacterium tuberculosis genome sequence with the new consensus, TCGAAC(N)4GTTCGA, identified 4 sites which were perfect matches and 12 sites with a single mismatch which were predicted to bind LexA. Genes which could potentially be regulated by these SOS boxes were ascertained from their positions relative to the sites. Examination of expression data for these genes following DNA damage identified 12 new genes which are most likely regulated by LexA as well as the known M. tuberculosis DNA damage-inducible genes recA, lexA, and ruvC. Of these 12 genes, only 2 have a predicted function: dnaE2, a component of DNA polymerase III, and linB, which is similar to 1,3,4,6-tetrachloro-1,4-cylcohexadiene hydrolase. Curiously, of the remaining 10 genes predicted to be LexA regulated, 7 are members of the M. tuberculosis 13E12 repeat family, which has some of the characteristics of mobile elements.

scholarly journals A Genomic Distance Based on MUM Indicates Discontinuity between Most Bacterial Species and Genera

2008 ◽  
Vol 191 (1) ◽  
pp. 91-99 ◽  
Author(s):  
Marc Deloger ◽  
Meriem El Karoui ◽  
Marie-Agnès Petit
Keyword(s):  
Dna Sequences ◽  
Dna Content ◽  
Core Genome ◽  
Biological Diversity ◽  
Bacterial Species ◽  
Genomic Distance ◽  
The Core ◽  
Intraspecies Diversity ◽  
Genome Level ◽  
Definition Of

ABSTRACT The fundamental unit of biological diversity is the species. However, a remarkable extent of intraspecies diversity in bacteria was discovered by genome sequencing, and it reveals the need to develop clear criteria to group strains within a species. Two main types of analyses used to quantify intraspecies variation at the genome level are the average nucleotide identity (ANI), which detects the DNA conservation of the core genome, and the DNA content, which calculates the proportion of DNA shared by two genomes. Both estimates are based on BLAST alignments for the definition of DNA sequences common to the genome pair. Interestingly, however, results using these methods on intraspecies pairs are not well correlated. This prompted us to develop a genomic-distance index taking into account both criteria of diversity, which are based on DNA maximal unique matches (MUM) shared by two genomes. The values, called MUMi, for MUM index, correlate better with the ANI than with the DNA content. Moreover, the MUMi groups strains in a way that is congruent with routinely used multilocus sequence-typing trees, as well as with ANI-based trees. We used the MUMi to determine the relatedness of all available genome pairs at the species and genus levels. Our analysis reveals a certain consistency in the current notion of bacterial species, in that the bulk of intraspecies and intragenus values are clearly separable. It also confirms that some species are much more diverse than most. As the MUMi is fast to calculate, it offers the possibility of measuring genome distances on the whole database of available genomes.

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