scholarly journals SPADIS: An Algorithm for Selecting Predictive and Diverse SNPs in GWAS

2018 ◽  
Author(s):  
Serhan Yilmaz ◽  
Oznur Tastan ◽  
A. Ercument Cicek
Keyword(s):  
Complex Traits ◽  
Biological Network ◽  
Predictive Performance ◽  
Constant Factor ◽  
Biological Processes ◽  
Novel Method ◽  
Submodular Set Function ◽  
Set Function ◽  
First Time ◽  
Selection Of

AbstractPhenotypic heritability of complex traits and diseases is seldom explained by individual genetic variants. Algorithms that select SNPs which are close and connected on a biological network have been successful in finding biologically-interpretable and predictive loci. However, we argue that the connectedness constraint favors selecting redundant features that affect similar biological processes and therefore does not necessarily yield better predictive performance. In this paper, we propose a novel method called SPADIS that selects SNPs that cover diverse regions in the underlying SNP-SNP network. SPADIS favors the selection of remotely located SNPs in order to account for the complementary additive effects of SNPs that are associated with the phenotype. This is achieved by maximizing a submodular set function with a greedy algorithm that ensures a constant factor (1−1/e) approximation. We compare SPADIS to the state-of-the-art method SConES, on a dataset of Arabidopsis Thaliana genotype and continuous flowering time phenotypes. SPADIS has better regression performance in 12 out of 17 phenotypes on average, it identifies more candidate genes and runs faster. We also investigate the use of Hi-C data to construct SNP-SNP network in the context of SNP selection problem for the first time, which yields slight but consistent improvements in regression performance. SPADIS is available at http://ciceklab.cs.bilkent.edu.tr/spadis

Competition of Verb Aspects and Its Resolution as a Creative Act (Based on the Material of Aspects Variants in the Texts by F. M. Dostoevsky)

2020 ◽  
Vol 81 (2) ◽  
pp. 56-63
Author(s):  
S. A. Karpukhin
Keyword(s):  
Traditional Method ◽  
Contextual Analysis ◽  
Verb Aspect ◽  
Component Theory ◽  
Two Component ◽  
Artistic Interpretation ◽  
New Perspective ◽  
First Time ◽  
Selection Of ◽  
Aspectual Meaning

The article considers the competition of verbal aspects from a new perspective. Instead of employing the traditional method of demonstrating this phenomenon — an empirical replacement of the aspect of a verb in a phrase with the opposite — the author examines Dostoevsky’s choice between the variants found in different manuscripts of the same text. For the first time, based on a two-component theory of the semantic invariant of a verb type, the aspectual meaning of the selection of a verb aspect is revealed and, as a result of contextual analysis, an artistic interpretation of the selected type is proposed.

Peculiarities of the juvenile period of the native Chechen genotypes of willow leaf pear (Pyrus salicifolia Pall.)

2020 ◽  
Vol 62 ◽  
pp. 32-38
Author(s):  
E. A. Dolmatov ◽  
R. B. Borzayev ◽  
A. N. Shaipov
Keyword(s):  
Chestnut Soil ◽  
Crop Breeding ◽  
Juvenile Period ◽  
Period 2 ◽  
Russian Research Institute ◽  
The Common ◽  
One Year ◽  
First Time ◽  
Selection Of ◽  
Creative Cooperation

The results of the study of the duration of the juvenile period of indigenous Chechen willow leaf pear genotypes (Pyrus salicifolia Pall.) are given in connection with the acceleration of the breeding process and the use of selected forms in pear breeding for high precocity. The studies were carried out in 2016-2019 at OOO “Orchards of Chechnya” in accordance with the Agreement on creative cooperation with the Russian Research Institute of Fruit Crop Breeding. The work was carried out in accordance with generally accepted programs and methods. The objects of the study were one-year and two-year-old pear seedlings obtained from sowing seeds of selected dwarf and low-growing local Chechen forms of willow pear (P. salicifolia Pall.), laying fruit buds on annual growths and seedlings of Caucasian pear (P. caucasica Fed.), 20 500 pcs. of each specie. The aim of the research was to study the potential of precocity of willow pear seedlings and to reveal of selected forms with the greatest degree of this trait. Stratified seeds were sown in the sowing department of the OOO “Orchards of Chechnya” production nursery in April, 2017. The seedlings were grown according to the common technology in dryland conditions on the plot with chestnut soil. The first fl owering of plants was noted in the spring, 2019. As a result of the research, for the first time on a large number of the experimental material it was found that in the off spring of the indigenous Chechen willow leaf pear genotypes, the selection of a little more than 2% of seedlings with a very short juvenile period (2 years) was possible. They are of great interest in accelerating the breeding process and in the selection of new pear varieties with high precocity. 20 willow leaf pear genotypes were selected for the further use in breeding for high precocity and as sources of the trait of short juvenile period.

An Insight into Oligopeptide Transporter 3 (OPT3) family proteins

2020 ◽  
Vol 27 ◽  
Author(s):  
Fırat Kurt
Keyword(s):  
Stress Responses ◽  
Chelating Agent ◽  
Biological Processes ◽  
Biotic And Abiotic Stress ◽  
Oligopeptide Transporter ◽  
Binding Residues ◽  
Fe Homeostasis ◽  
Proteins Interactions ◽  
Insight Into ◽  
Selection Of

: Oligopeptide transporter 3 (OPT3) proteins are one of the subsets of OPT clade, yet little is known about these transporters. Therefore, homolog OPT3 proteins in several plant species were investigated and characterized using bioinformatical tools. Motif and co-expression analyses showed that OPT3 proteins may be involved in both biotic and abiotic stress responses as well as growth and developmental processes. AtOPT3 usually seemed to take part in Fe homeostasis whereas ZmOPT3 putatively interacted with proteins involved in various biological processes from plant defense system to stress responses. Glutathione (GSH), as a putative alternative chelating agent, was used in the AtOPT3 and ZmOPT3 docking analyses to identify their putative binding residues. The information given in this study will contribute to the understanding of OPT3 proteins’ interactions in various pathways and to the selection of potential ligands for OPT3s.

Organic Reactivity Control by Means of Neighboring Groups and Organometallics. A Personal Account

1994 ◽  
Vol 59 (1) ◽  
pp. 1-74 ◽  
Author(s):  
Pavel Kočovský
Keyword(s):  
Transition Metals ◽  
Cyclopropane Ring ◽  
Allylic Substitutions ◽  
Recent Developments ◽  
Cardioactive Drug ◽  
Novel Method ◽  
Metal Catalyzed ◽  
Electrophilic Additions ◽  
Near Future ◽  
First Time

This review summarizes the main topics of our research and covers the period of the last 15 years. The prime interest is focused on various ways of controlling the regio- and stereoselectivity of selected organic reactions, in particular electrophilic additions, cleavage of cyclopropane rings, and allylic substitutions by means of neighboring groups and/or transition and non-transition metals. In the first part, the factors governing the course of electrophilic additions are assessed, culminating in the formulation of selection rules for the reactivity of cyclohexene systems, and in a concise synthesis of the natural cardioactive drug, strophanthidin. These studies also contribute to a better understanding of the mechanisms of electrophilic additions. The second part describes recent developments in the stereo- and regiocontrolled cleavage of cyclopropane rings by non-transition metals (Tl and Hg), and the reactivity and transmetalation (with Pd) of the primary products. This methodology has resulted in novel routes to unique polycyclic structures, and will have synthetic applications in the near future. Evidence for the stereospecific "corner" cleavage of the cyclopropane ring has been provided for the first time for Tl and later for Hg. The third part deals with transition metal-catalyzed allylic substitution. Evidence for a new "syn" mechanism for the formation of the intermediate (π-allyl)palladium complex has been provided, which runs counter to the generally accepted "anti" mechanism. A novel method for a Pd-catalyzed allylic oxidation has been developed and employed in the synthesis of natural sesquiterpenes. The increasing importance of transition and non-transition metals for synthetic organic chemistry is demonstrated by their unique reactivity in a number of the papers included in this review.

Evolution and Selection of Quantitative Traits

2018 ◽  
Author(s):  
Bruce Walsh ◽  
Michael Lynch
Keyword(s):  
Mathematical Models ◽  
Quantitative Genetics ◽  
Complex Traits ◽  
Evolutionary Biology ◽  
Quantitative Traits ◽  
Specific Gene ◽  
Real World Data ◽  
Holistic Treatment ◽  
Genetics And Genomics ◽  
Selection Of

Quantitative traits—be they morphological or physiological characters, aspects of behavior, or genome-level features such as the amount of RNA or protein expression for a specific gene—usually show considerable variation within and among populations. Quantitative genetics, also referred to as the genetics of complex traits, is the study of such characters and is based on mathematical models of evolution in which many genes influence the trait and in which non-genetic factors may also be important. Evolution and Selection of Quantitative Traits presents a holistic treatment of the subject, showing the interplay between theory and data with extensive discussions on statistical issues relating to the estimation of the biologically relevant parameters for these models. Quantitative genetics is viewed as the bridge between complex mathematical models of trait evolution and real-world data, and the authors have clearly framed their treatment as such. This is the second volume in a planned trilogy that summarizes the modern field of quantitative genetics, informed by empirical observations from wide-ranging fields (agriculture, evolution, ecology, and human biology) as well as population genetics, statistical theory, mathematical modeling, genetics, and genomics. Whilst volume 1 (1998) dealt with the genetics of such traits, the main focus of volume 2 is on their evolution, with a special emphasis on detecting selection (ranging from the use of genomic and historical data through to ecological field data) and examining its consequences. This extensive work of reference is suitable for graduate level students as well as professional researchers (both empiricists and theoreticians) in the fields of evolutionary biology, genetics, and genomics. It will also be of particular relevance and use to plant and animal breeders, human geneticists, and statisticians.

scholarly journals A Virtual Telescope for the Open University Science Foundation Course

1998 ◽  
Vol 162 ◽  
pp. 100-105
Author(s):  
Andrew J. Norton ◽  
Mark H. Jones
Keyword(s):  
Social Science ◽  
Open University ◽  
Distance Teaching ◽  
The Arts ◽  
Wide Range ◽  
University Science ◽  
First Time ◽  
Degree Level ◽  
Selection Of

The Open University is the UK's foremost distance teaching university. For over twenty five years we have been presenting courses to students spanning a wide range of degree level and vocational subjects. Since we have no pre-requisites for entry, a major component of our course profile is a selection of foundation courses comprising one each in the Arts, Social Science, Mathematics, Technology and Science faculties. The Science Faculty's foundation course is currently undergoing a substantial revision. The new course, entitled “S103: Discovering Science”, will be presented to students for the first time in 1998.

scholarly journals Incorporating radiomics into clinical trials: expert consensus on considerations for data-driven compared to biologically driven quantitative biomarkers

2021 ◽  
Author(s):  
Laure Fournier ◽  
Lena Costaridou ◽  
Luc Bidaut ◽  
Nicolas Michoux ◽  
Frederic E. Lecouvet ◽  
...  
Keyword(s):  
Clinical Trials ◽  
Quantitative Imaging ◽  
A Priori ◽  
External Validation ◽  
Data Driven ◽  
Imaging Biomarkers ◽  
Clinical Validation ◽  
Biological Processes ◽  
Imaging Data ◽  
Selection Of

Abstract Existing quantitative imaging biomarkers (QIBs) are associated with known biological tissue characteristics and follow a well-understood path of technical, biological and clinical validation before incorporation into clinical trials. In radiomics, novel data-driven processes extract numerous visually imperceptible statistical features from the imaging data with no a priori assumptions on their correlation with biological processes. The selection of relevant features (radiomic signature) and incorporation into clinical trials therefore requires additional considerations to ensure meaningful imaging endpoints. Also, the number of radiomic features tested means that power calculations would result in sample sizes impossible to achieve within clinical trials. This article examines how the process of standardising and validating data-driven imaging biomarkers differs from those based on biological associations. Radiomic signatures are best developed initially on datasets that represent diversity of acquisition protocols as well as diversity of disease and of normal findings, rather than within clinical trials with standardised and optimised protocols as this would risk the selection of radiomic features being linked to the imaging process rather than the pathology. Normalisation through discretisation and feature harmonisation are essential pre-processing steps. Biological correlation may be performed after the technical and clinical validity of a radiomic signature is established, but is not mandatory. Feature selection may be part of discovery within a radiomics-specific trial or represent exploratory endpoints within an established trial; a previously validated radiomic signature may even be used as a primary/secondary endpoint, particularly if associations are demonstrated with specific biological processes and pathways being targeted within clinical trials. Key Points • Data-driven processes like radiomics risk false discoveries due to high-dimensionality of the dataset compared to sample size, making adequate diversity of the data, cross-validation and external validation essential to mitigate the risks of spurious associations and overfitting. • Use of radiomic signatures within clinical trials requires multistep standardisation of image acquisition, image analysis and data mining processes. • Biological correlation may be established after clinical validation but is not mandatory.

Ionized AGN outflows are less powerful than assumed: A multi-wavelength census of outflows in type II AGN

2019 ◽  
Vol 15 (S356) ◽  
pp. 225-225
Author(s):  
Dalya Baron
Keyword(s):  
Optical Emission ◽  
Infrared Emission ◽  
Type Ii ◽  
Ionized Gas ◽  
Kinetic Coupling ◽  
Mass Outflow ◽  
Multi Wavelength ◽  
Novel Method ◽  
First Time ◽  
Ionization Parameter

AbstractIn this talk I will show that multi-wavelength observations can provide novel constraints on the properties of ionized gas outflows in AGN. I will present evidence that the infrared emission in active galaxies includes a contribution from dust which is mixed with the outflow and is heated by the AGN. We detect this infrared component in thousands of AGN for the first time, and use it to constrain the outflow location. By combining this with optical emission lines, we constrain the mass outflow rates and energetics in a sample of 234 type II AGN, the largest such sample to date. The key ingredient of our new outflow measurements is a novel method to estimate the electron density using the ionization parameter and location of the flow. The inferred electron densities, ∼104.5 cm−3, are two orders of magnitude larger than found in most other cases of ionized outflows. We argue that the discrepancy is due to the fact that the commonly-used [SII]-based method underestimates the true density by a large factor. As a result, the inferred mass outflow rates and kinetic coupling efficiencies are 1–2 orders of magnitude lower than previous estimates, and 3–4 orders of magnitude lower than the typical requirement in hydrodynamic cosmological simulations. These results have significant implications for the relative importance of ionized outflows feedback in this population.

A novel method for the design and selection of neutron-attenuating media

2021 ◽  
Vol 160 ◽  
pp. 108368
Author(s):  
Abdullah G. Weiss ◽  
Moiz I. Butt ◽  
Pavel V. Tsvetkov ◽  
Mark L. Kimber ◽  
Sean M. McDeavitt
Keyword(s):  
Novel Method ◽  
Selection Of

scholarly journals Combining QTL Mapping and Gene Expression Analysis to Elucidate the Genetic Control of ‘Crumbly’ Fruit in Red Raspberry (Rubus idaeus L.)

Agronomy ◽  
2021 ◽  
Vol 11 (4) ◽  
pp. 794
Author(s):  
Luca M. Scolari ◽  
Robert D. Hancock ◽  
Pete E. Hedley ◽  
Jenny Morris ◽  
Kay Smith ◽  
...  
Keyword(s):  
Genetic Control ◽  
Developmental Disorder ◽  
Molecular Mechanisms ◽  
Developmental Stages ◽  
Microarray Experiment ◽  
Rubus Idaeus ◽  
Red Raspberry ◽  
Genotype By Sequencing ◽  
First Time ◽  
Selection Of

‘Crumbly’ fruit is a developmental disorder in raspberry that results in malformed and unsaleable fruits. For the first time, we define two distinct crumbly phenotypes as part of this work. A consistent crumbly fruit phenotype affecting the majority of fruits every season, which we refer to as crumbly fruit disorder (CFD) and a second phenotype where symptoms vary across seasons as malformed fruit disorder (MFD). Here, segregation of crumbly fruit of the MFD phenotype was examined in a full-sib family and three QTL (Quantitative Trait Loci) were identified on a high density GbS (Genotype by Sequencing) linkage map. This included a new QTL and more accurate location of two previously identified QTLs. A microarray experiment using normal and crumbly fruit at three different developmental stages identified several genes that were differentially expressed between the crumbly and non-crumbly phenotypes within the three QTL. Analysis of gene function highlighted the importance of processes that compromise ovule fertilization as triggers of crumbly fruit. These candidate genes provided insights regarding the molecular mechanisms involved in the genetic control of crumbly fruit in red raspberry. This study will contribute to new breeding strategies and diagnostics through the selection of molecular markers associated with the crumbly trait.

Sign in / Sign up

Export Citation Format

Share Document