Light Functional Interpretation

2005 ◽  
pp. 477-492 ◽  
Author(s):  
Mircea-Dan Hernest
Keyword(s):  
Functional Interpretation

scholarly journals Expression and regulatory roles of lncRNAs in G-CIMP-low vs G-CIMP-high Glioma: an in-silico analysis

2021 ◽  
Vol 19 (1) ◽  
Author(s):  
Indrani Datta ◽  
Houtan Noushmehr ◽  
Chaya Brodie ◽  
Laila M. Poisson
Keyword(s):  
Cpg Island ◽  
Rank Order ◽  
In Silico Analysis ◽  
Good Prognosis ◽  
Cpg Island Methylator Phenotype ◽  
Functional Interpretation ◽  
Protein Coding ◽  
Upstream Regulator ◽  
Methylator Phenotype ◽  
Molecular Relationships

Abstract Background Clinically relevant glioma subtypes, such as the glioma-CpG island methylator phenotype (G-CIMP), have been defined by epigenetics. In this study, the role of long non-coding RNAs in association with the poor-prognosis G-CMIP-low phenotype and the good-prognosis G-CMIP-high phenotype was investigated. Functional associations of lncRNAs with mRNAs and miRNAs were examined to hypothesize influencing factors of the aggressive phenotype. Methods RNA-seq data on 250 samples from TCGA’s Pan-Glioma study, quantified for lncRNA and mRNAs (GENCODE v28), were analyzed for differential expression between G-CIMP-low and G-CIMP-high phenotypes. Functional interpretation of the differential lncRNAs was performed by Ingenuity Pathway Analysis. Spearman rank order correlation estimates between lncRNA, miRNA, and mRNA nominated differential lncRNA with a likely miRNA sponge function. Results We identified 4371 differentially expressed features (mRNA = 3705; lncRNA = 666; FDR ≤ 5%). From these, the protein-coding gene TP53 was identified as an upstream regulator of differential lncRNAs PANDAR and PVT1 (p = 0.0237) and enrichment was detected in the “development of carcinoma” (p = 0.0176). Two lncRNAs (HCG11, PART1) were positively correlated with 342 mRNAs, and their correlation estimates diminish after adjusting for either of the target miRNAs: hsa-miR-490-3p, hsa-miR-129-5p. This suggests a likely sponge function for HCG11 and PART1. Conclusions These findings identify differential lncRNAs with oncogenic features that are associated with G-CIMP phenotypes. Further investigation with controlled experiments is needed to confirm the molecular relationships.

scholarly journals The Limits of Computation

Axiomathes ◽  
2021 ◽  
Author(s):  
Andrew Powell
Keyword(s):  
Natural Number ◽  
Set Theory ◽  
Lambda Calculus ◽  
Second Order ◽  
Functional Interpretation ◽  
Arbitrary Type ◽  
Computable Functions

AbstractThis article provides a survey of key papers that characterise computable functions, but also provides some novel insights as follows. It is argued that the power of algorithms is at least as strong as functions that can be proved to be totally computable in type-theoretic translations of subsystems of second-order Zermelo Fraenkel set theory. Moreover, it is claimed that typed systems of the lambda calculus give rise naturally to a functional interpretation of rich systems of types and to a hierarchy of ordinal recursive functionals of arbitrary type that can be reduced by substitution to natural number functions.

scholarly journals CpGmotifs: a tool to discover DNA motifs associated to CpG methylation events

2021 ◽  
Vol 22 (1) ◽  
Author(s):  
Giovanni Scala ◽  
Antonio Federico ◽  
Dario Greco
Keyword(s):  
Dna Methylation ◽  
Motif Discovery ◽  
Cpg Methylation ◽  
Functional Interpretation ◽  
Dna Motifs ◽  
Molecular Alterations ◽  
Link Type ◽  
Dna Motif ◽  
Quantitative Manner ◽  
Dna Motif Discovery

Abstract Background The investigation of molecular alterations associated with the conservation and variation of DNA methylation in eukaryotes is gaining interest in the biomedical research community. Among the different determinants of methylation stability, the DNA composition of the CpG surrounding regions has been shown to have a crucial role in the maintenance and establishment of methylation statuses. This aspect has been previously characterized in a quantitative manner by inspecting the nucleotidic composition in the region. Research in this field still lacks a qualitative perspective, linked to the identification of certain sequences (or DNA motifs) related to particular DNA methylation phenomena. Results Here we present a novel computational strategy based on short DNA motif discovery in order to characterize sequence patterns related to aberrant CpG methylation events. We provide our framework as a user-friendly, shiny-based application, CpGmotifs, to easily retrieve and characterize DNA patterns related to CpG methylation in the human genome. Our tool supports the functional interpretation of deregulated methylation events by predicting transcription factors binding sites (TFBS) encompassing the identified motifs. Conclusions CpGmotifs is an open source software. Its source code is available on GitHub https://github.com/Greco-Lab/CpGmotifs and a ready-to-use docker image is provided on DockerHub at https://hub.docker.com/r/grecolab/cpgmotifs.

scholarly journals Genetic association studies of alterations in protein function expose recessive effects on cancer predisposition

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Nadav Brandes ◽  
Nathan Linial ◽  
Michal Linial
Keyword(s):  
Cancer Risk ◽  
Protein Function ◽  
Association Studies ◽  
Genetic Effects ◽  
Cancer Predisposition ◽  
Genome Wide Association Studies ◽  
Genetic Associations ◽  
Functional Interpretation ◽  
Gene Damage ◽  
Genomic Regions

AbstractThe characterization of germline genetic variation affecting cancer risk, known as cancer predisposition, is fundamental to preventive and personalized medicine. Studies of genetic cancer predisposition typically identify significant genomic regions based on family-based cohorts or genome-wide association studies (GWAS). However, the results of such studies rarely provide biological insight or functional interpretation. In this study, we conducted a comprehensive analysis of cancer predisposition in the UK Biobank cohort using a new gene-based method for detecting protein-coding genes that are functionally interpretable. Specifically, we conducted proteome-wide association studies (PWAS) to identify genetic associations mediated by alterations to protein function. With PWAS, we identified 110 significant gene-cancer associations in 70 unique genomic regions across nine cancer types and pan-cancer. In 48 of the 110 PWAS associations (44%), estimated gene damage is associated with reduced rather than elevated cancer risk, suggesting a protective effect. Together with standard GWAS, we implicated 145 unique genomic loci with cancer risk. While most of these genomic regions are supported by external evidence, our results also highlight many novel loci. Based on the capacity of PWAS to detect non-additive genetic effects, we found that 46% of the PWAS-significant cancer regions exhibited exclusive recessive inheritance. These results highlight the importance of recessive genetic effects, without relying on familial studies. Finally, we show that many of the detected genes exert substantial cancer risk in the studied cohort determined by a quantitative functional description, suggesting their relevance for diagnosis and genetic consulting.

Taxonomic efforts in the description of leader behavior: A synthesis and functional interpretation

1991 ◽  
Vol 2 (4) ◽  
pp. 245-287 ◽  
Author(s):  
Edwin A. Fleishman ◽  
Michael D. Mumford ◽  
Stephen J. Zaccaro ◽  
Kerry Y. Levin ◽  
Arthur L. Korotkin ◽  
...  
Keyword(s):  
Leader Behavior ◽  
Functional Interpretation

The Court of the Psalms: A Functional Interpretation of the Mari Palace

1980 ◽  
Vol 100 (2) ◽  
pp. 190
Author(s):  
A. Finet ◽  
Yasin M. Al-Khalesi
Keyword(s):  
Functional Interpretation

Colloquial features in Word Englishes

2013 ◽  
Vol 18 (4) ◽  
pp. 479-505 ◽  
Author(s):  
Peter Collins ◽  
Xinyue Yao
Keyword(s):  
Twentieth Century ◽  
American English ◽  
World Englishes ◽  
Evolutionary Status ◽  
First Person ◽  
Functional Interpretation ◽  
Person Plural ◽  
World English ◽  
First Person Plural ◽  
Grammatical Change

A powerful discourse-pragmatic agent of grammatical change in English since the mid-twentieth century has been the increasing acceptance of colloquialism. Little is known, however, about its influence on grammatical developments in regional varieties of World English other than the two inner circle ‘supervarieties’, British and American English. This paper reports findings from a corpus-based study of three grammatical categories known to be undergoing a colloquialism-related rise in contemporary English, across a range of registers in ten World Englishes: quasi-modals (have to, have got to, be going to, want to), get-passives, and first person plural inclusive let’s. In each case comparisons are drawn with non-colloquial variants: modals (must, should, will, shall), be-passives, and let us. Subsequent functional interpretation of the data is used to explore the effect upon the quantitative patterns identified of the phenomenon of colloquialism and of further factors with which it interacts (including Americanism, prescriptivism, and evolutionary status).

scholarly journals Dental functional traits of mammals resolve productivity in terrestrial ecosystems past and present

2012 ◽  
Vol 279 (1739) ◽  
pp. 2793-2799 ◽  
Author(s):  
Liping Liu ◽  
Kai Puolamäki ◽  
Jussi T. Eronen ◽  
Majid M. Ataabadi ◽  
Elina Hernesniemi ◽  
...  
Keyword(s):  
Net Primary Productivity ◽  
Terrestrial Ecosystems ◽  
Functional Trait ◽  
Geological Time ◽  
Crown Height ◽  
Short Term ◽  
Functional Interpretation ◽  
Terrestrial Mammals ◽  
Terrestrial Biomes ◽  
The Relationship

We have recently shown that rainfall, one of the main climatic determinants of terrestrial net primary productivity (NPP), can be robustly estimated from mean molar tooth crown height (hypsodonty) of mammalian herbivores. Here, we show that another functional trait of herbivore molar surfaces, longitudinal loph count, can be similarly used to extract reasonable estimates of rainfall but also of temperature, the other main climatic determinant of terrestrial NPP. Together, molar height and the number of longitudinal lophs explain 73 per cent of the global variation in terrestrial NPP today and resolve the main terrestrial biomes in bivariate space. We explain the functional interpretation of the relationships between dental function and climate variables in terms of long- and short-term demands. We also show how the spatially and temporally dense fossil record of terrestrial mammals can be used to investigate the relationship between biodiversity and productivity under changing climates in geological time. The placement of the fossil chronofaunas in biome space suggests that they most probably represent multiple palaeobiomes, at least some of which do not correspond directly to any biomes of today's world.

Constructing a Second Language

2009 ◽  
Vol 7 ◽  
pp. 111-139 ◽  
Author(s):  
Nick C. Ellis ◽  
Teresa Cadierno
Keyword(s):  
Second Language ◽  
Second Language Acquisition ◽  
Language Learning ◽  
Corpus Linguistics ◽  
Special Section ◽  
Functional Interpretation ◽  
Linguistic Evidence ◽  
Cognitive Principles ◽  
Conceptual Transfer ◽  
Language Meaning

This Special Section brings together researchers who adopt a constructional approach to Second Language Acquisition (SLA) as informed by Cognitive and Corpus Linguistics, approaches which fall under the general umbrella of Usage-based Linguistics. The articles present psycholinguistic and corpus linguistic evidence for L2 constructions and for the inseparability of lexis and grammar. They consider the psycholinguistics of language learning following general cognitive principles of category learning, with schematic constructions emerging from usage. They analyze how learning is driven by the frequency and frequency distribution of exemplars within construction, the salience of their form, the significance of their functional interpretation, the match of their meaning to the construction prototype, and the reliability of their mappings. They explore conceptual transfer and the acquisition of second language meaning. They consider the implications of these phenomena for L2 instruction.

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