scholarly journals BioJS-HGV Viewer: Genetic Variation Visualizer

2015 ◽  
Author(s):  
Saket Choudhary ◽  
Leyla Garcia ◽  
Andrew Nightingale ◽  
Maria-Jesus Martin
Keyword(s):  
Genetic Variation ◽  
Genetic Variants ◽  
Biological Diversity ◽  
Source Code ◽  
Disease States ◽  
Levels Of Detail ◽  
Key Driver ◽  
User Friendly ◽  
Different Sources ◽  
Different Levels

Studying the pattern of genetic variants is a primary step in deciphering the basis of biological diversity, identifying key `driver variants' that affect disease states and evolution of a species. Catalogs of genetic variants contain vast numbers of variants and are growing at an exponential rate, but lack an interactive exploratory interface. We present BioJS-HGV Viewer, a BioJS component to represent and visualize genetic variants pooled from different sources. The tool displays sequences and variants at different levels of detail, facilitating representation of variant sites and annotations in a user friendly and interactive manner. Source code for BioJS-HGV Viewer is available at: https://github.com/saketkc/biojs-genetic-variation-viewer A demo is available at: http://saketkc.github.io/biojs-genetic-variation-viewer

Development of a Simulation-Based Process Chain – Strategy for Different Levels of Detail for the Preprocessing Definitions

2011 ◽  
Vol 21 (3-4) ◽  
pp. 135-140 ◽  
Author(s):  
Toni A. Krol ◽  
Sebastian Westhäuser ◽  
M. F. Zäh ◽  
Johannes Schilp ◽  
G. Groth
Keyword(s):  
Process Chain ◽  
Levels Of Detail ◽  
Simulation Based ◽  
Different Levels

scholarly journals Velody 2—Resilient High-Capacity MIDI Steganography for Organ and Harpsichord Music

2020 ◽  
Vol 11 (1) ◽  
pp. 39
Author(s):  
Eric Järpe ◽  
Mattias Weckstén
Keyword(s):  
Mean Absolute Error ◽  
Signal To Noise Ratio ◽  
High Capacity ◽  
Absolute Error ◽  
Music Technology ◽  
Alternative Methods ◽  
File Size ◽  
User Friendly ◽  
Different Levels ◽  
Better Than

A new method for musical steganography for the MIDI format is presented. The MIDI standard is a user-friendly music technology protocol that is frequently deployed by composers of different levels of ambition. There is to the author’s knowledge no fully implemented and rigorously specified, publicly available method for MIDI steganography. The goal of this study, however, is to investigate how a novel MIDI steganography algorithm can be implemented by manipulation of the velocity attribute subject to restrictions of capacity and security. Many of today’s MIDI steganography methods—less rigorously described in the literature—fail to be resilient to steganalysis. Traces (such as artefacts in the MIDI code which would not occur by the mere generation of MIDI music: MIDI file size inflation, radical changes in mean absolute error or peak signal-to-noise ratio of certain kinds of MIDI events or even audible effects in the stego MIDI file) that could catch the eye of a scrutinizing steganalyst are side-effects of many current methods described in the literature. This steganalysis resilience is an imperative property of the steganography method. However, by restricting the carrier MIDI files to classical organ and harpsichord pieces, the problem of velocities following the mood of the music can be avoided. The proposed method, called Velody 2, is found to be on par with or better than the cutting edge alternative methods regarding capacity and inflation while still possessing a better resilience against steganalysis. An audibility test was conducted to check that there are no signs of audible traces in the stego MIDI files.

scholarly journals A Framework for Visualizing Heterogeneous Construction Data Using Semantic Web Standards

2018 ◽  
Vol 2018 ◽  
pp. 1-11
Author(s):  
Mostafa Ali ◽  
Yasser Mohamed
Keyword(s):  
Ad Hoc ◽  
3D Visualization ◽  
Heterogeneous Data ◽  
Data Merging ◽  
Levels Of Detail ◽  
Heterogeneous Data Sources ◽  
Web Standards ◽  
Visualization Process ◽  
Merging Process ◽  
Different Sources

3D Visualization provides a mean for communicating different construction activities to diverse audiences. The scope, level of detail, and time resolution of the 3D visualization process are determined based on the targeted audiences. Developing the 3D visualization requires obtaining and merging heterogeneous data from different sources (such as BIM model and CPM schedule). The data merging process is usually carried out on ad hoc basis for a specific visualization case which limits the reusability of the process. This paper discusses a framework for automatic merging of heterogeneous data to create a visualization. The paper describes developing an ontology which captures concepts related to the visualization process. Then, heterogeneous data sources that are commonly used in construction are fed into the ontology which can be queried to produce different visualization scenarios. The potential of this approach has been demonstrated by providing multiple visualization scenarios that cover different audiences, levels of detail, and time resolutions.

Studying how genetic variants affect mechanism in biological systems

2018 ◽  
Vol 62 (4) ◽  
pp. 575-582
Author(s):  
Francesco Raimondi ◽  
Robert B. Russell
Keyword(s):  
Genetic Variation ◽  
Molecular Mechanism ◽  
Genetic Variants ◽  
Biological Function ◽  
Biological Systems ◽  
Protein Structures ◽  
Clinical Applications ◽  
Biological Pathways ◽  
The Relationship

Genetic variants are currently a major component of system-wide investigations into biological function or disease. Approaches to select variants (often out of thousands of candidates) that are responsible for a particular phenomenon have many clinical applications and can help illuminate differences between individuals. Selecting meaningful variants is greatly aided by integration with information about molecular mechanism, whether known from protein structures or interactions or biological pathways. In this review we discuss the nature of genetic variants, and recent studies highlighting what is currently known about the relationship between genetic variation, biomolecular function, and disease.

scholarly journals IPEV: a web server for inferring pathogenic enhancers with variants

2019 ◽  
Author(s):  
Guanxiong Zhang ◽  
Aimin Xie ◽  
Jing Bai ◽  
Tao Luo ◽  
Huating Yuan ◽  
...  
Keyword(s):  
Transcription Factor ◽  
Genetic Variants ◽  
Target Genes ◽  
Genetic Alterations ◽  
Enhancer Activity ◽  
Web Environment ◽  
One Stop ◽  
User Friendly ◽  
Coding Variants ◽  
Interactive User

Abstract Background Enhancer has been recognized as an important driver whose genetic alterations contribute to disease progression. However, there is still no easy-to-use tools to identify pathogenic enhancers, allowing for deciphering functional influence of genetic variants on enhancer. Results We developed a user-friendly one-stop shop platform, named inferring pathogenic enhancer with variant (IPEV), only requiring variants as input, to quickly infer the pathogenic enhancers that harbor variants affecting their activities. Results of IPEV are explored in an interactive, user-friendly web environment, which is designed to highlight the most probable pathogenic enhancers and their target genes. Furthermore, IPEV provides intuitive visualizations of how a variant affects the corresponding enhancer activity by mediating TF binding changes. Conclusions IPEV is specially designed to prioritize the potentially pathogenic enhancers with genetic variants, and provides intuitive visualizations how a variant affects the corresponding enhancer activity by mediating which transcription factor binding changes. The use of IPEV does not require any specialized computer skills. We believe that IPEV will be useful in interpreting non-coding variants by the inferring pathogenic enhancers. It is freely available at http://biocc.hrbmu.edu.cn/IPEV/ or http://210.46.80.168/IPEV and supports recent versions of all major browsers.

Prevalence and Adaptive Impact of Introgression

2021 ◽  
Vol 55 (1) ◽  
Author(s):  
Nathaniel B. Edelman ◽  
James Mallet
Keyword(s):  
Genetic Variation ◽  
Adaptive Evolution ◽  
Genetic Variants ◽  
Genomic Data ◽  
Annual Review ◽  
Publication Date ◽  
Adaptive Introgression ◽  
Changing Environments ◽  
Potential Benefits

Alleles that introgressed between species can influence the evolutionary and ecological fate of species exposed to novel environments. Hybrid offspring of different species are often unfit, and yet it has long been argued that introgression can be a potent force in evolution, especially in plants. Over the last two decades, genomic data have increasingly provided evidence that introgression is a critically important source of genetic variation and that this additional variation can be useful in adaptive evolution of both animals and plants. Here, we review factors that influence the probability that foreign genetic variants provide long-term benefits (so-called adaptive introgression) and discuss their potential benefits. We find that introgression plays an important role in adaptive evolution, particularly when a species is far from its fitness optimum, such as when they expand their range or are subject to changing environments. Expected final online publication date for the Annual Review of Genetics, Volume 55 is November 2021. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.

Abstract 18134: Phenome-wide Study of Electronic Medical Record Data Reveals Novel Association of Natriuretic Peptide A Genetic Variant With Rheumatoid Arthritis

Circulation ◽  
2015 ◽  
Vol 132 (suppl_3) ◽  
Author(s):  
Naveen Pereira ◽  
Gregory Jenkins ◽  
Ifthikar Kullo ◽  
Suzette Bielinski ◽  
John Burnett ◽  
...  
Keyword(s):  
Rheumatoid Arthritis ◽  
Genetic Variation ◽  
Medical Record ◽  
Electronic Medical Record ◽  
Natriuretic Peptide ◽  
Genetic Variants ◽  
Association Studies ◽  
Disease Phenotypes ◽  
Novel Association ◽  
The Relationship

Introduction: Phenome-wide association studies (PheWAS) using electronic medical record (EMR)-linked biobanks have been used not only to identify and replicate known associations of genetic variants with disease phenotypes but have also resulted in the discovery of potentially novel genotype-phenotype relationships. The natriuretic peptide (NP) system plays an important role in a broad range of disease processes including cardiovascular and inflammatory diseases. We hypothesized that performing a PheWAS using previously known functional genetic variants of the NP system may result in novel disease associations that could provide mechanistic insights in an unbiased manner. Methods: We scanned for associations between 9 single-nucleotide polymorphisms (SNPs) in the NP system and 27 EMR-derived chronic disease phenotypes in 3,025 individuals participating in a case-control study of peripheral arterial disease. The EMR phenotypes were identified using two or more ICD-9-CM diagnosis codes based on the AHRQ Clinical Classifications Software (CCS). The relationship of SNPs and phenotypes were modeled using logistic regression adjusting for gender. Results: We identified rs5065, a SNP located in the stop codon of exon 3 of the NPPA gene, to be the strongest associated SNP with rheumatoid arthritis (RA) (OR=0.78, p=0.0008, q-value=0.11). The SNP leads to the extension of atrial natriuretic peptide (ANP) by 2 additional arginines at the C terminus. Cardiovascular disease is known to be the leading cause of death in patients with RA and ANP plays an important immunomodulatory role by inhibiting inducible nitric oxide synthase, reducing TNF-α production and attenuating prostaglandin E2 production in macrophages. Circulating NPs have been used to screen for occult cardiac disease and are associated with mortality in RA. This study demonstrates for the first time the importance of the relationship between genetic variation in the NP system and RA. Conclusions: PheWAS was successfully used as a tool to identify a novel association of functional genetic variation in the NPPA gene with RA. The observation is hypothesis generating and further replication studies are required to determine the role of rs5065 in cardiovascular outcomes of RA.

scholarly journals 132 Effects of high-energy diet on viscera and progeny carcass yield in sheep

2019 ◽  
Vol 97 (Supplement_1) ◽  
pp. 71-71
Author(s):  
Sarita Bonagurio Gallo ◽  
Sophia Honigmann ◽  
Luciano Brochine ◽  
Giuliana Micai de Oliveira ◽  
Luis Orlindo Tedeschi
Keyword(s):  
Maternal Diet ◽  
High Energy ◽  
Control Group ◽  
Animal Science ◽  
Carcass Yield ◽  
Orthogonal Contrasts ◽  
Food Engineering ◽  
Omental Fat ◽  
Different Sources ◽  
Different Levels

Abstract The energy required during gestation in sheep is high, and when restricted, fetal development may be affected; thus, knowledge of its deficit needs to be better understood. The objective was to evaluate different levels and sources of energy in the diet of sheep and their influence on the viscera and carcass yield of the offspring. The experiment was carried out at the Faculty of Animal Science and Food Engineering of USP, Brazil, using 56 pregnant ewes, Dorper and Santa Ines breeds, randomly distributed in four treatments: control group (fed according to the 2007 NRC recommendation); and groups with 10% more energy with different sources (starch, ST; protected fat, PF; and chromium, Cr). Ewes were fed the experimental diets at the beginning (50 days) and end of the gestation (50 days). The middle of gestation the ewes received the diet as recommended by the NRC (2007). After weaning at 60 days, 32 uncastrated male lambs were confined for a period of 60 days. In the confinement the lambs received a growth diet, being the same for all the animals. After this period, lambs were slaughtered, and the non-carcass components were weighed, the warm and cold carcass yields were calculated. The experimental design was completely randomized, with eight replicates and four treatments, the means were analyzed by orthogonal contrasts, assuming a significant threshold of 5%. Lambs in the PF treatment had lower cold carcass yield (50.8%, PPP > 0.05). The sheep fed according to the energy recommendation had lambs with greater weight of omental fat, testicular, kidney and rumen. These lambs also had a smaller spleen, heart, liver, and intestine. We concluded that the maternal diet affected the growth and development of progeny by altering the viscera and the carcass yields. Acknowledgment to FAPESP (process 2017/20555–8).

Metal distribution and biological diversity of crusts in paddy fields polluted with different levels of cadmium

2019 ◽  
Vol 184 ◽  
pp. 109620 ◽  
Author(s):  
Huijuan Song ◽  
Liang Peng ◽  
Zhiyi Li ◽  
Xiaozhou Deng ◽  
Jihai Shao ◽  
...  
Keyword(s):  
Biological Diversity ◽  
Paddy Fields ◽  
Metal Distribution ◽  
Different Levels

scholarly journals Evidence for polygenic and oligogenic basis of Australian sporadic amyotrophic lateral sclerosis

2020 ◽  
pp. jmedgenet-2020-106866 ◽  
Author(s):  
Emily P McCann ◽  
Lyndal Henden ◽  
Jennifer A Fifita ◽  
Katharine Y Zhang ◽  
Natalie Grima ◽  
...  
Keyword(s):  
Amyotrophic Lateral Sclerosis ◽  
Genetic Variation ◽  
Genetic Analysis ◽  
Genetic Variants ◽  
Age Of Onset ◽  
Sporadic Amyotrophic Lateral Sclerosis ◽  
Whole Genome ◽  
Identity By Descent ◽  
Sporadic Als ◽  
Lateral Sclerosis

BackgroundAmyotrophic lateral sclerosis (ALS) is a fatal neurodegenerative disease with phenotypic and genetic heterogeneity. Approximately 10% of cases are familial, while remaining cases are classified as sporadic. To date, >30 genes and several hundred genetic variants have been implicated in ALS.MethodsSeven hundred and fifty-seven sporadic ALS cases were recruited from Australian neurology clinics. Detailed clinical data and whole genome sequencing (WGS) data were available from 567 and 616 cases, respectively, of which 426 cases had both datasets available. As part of a comprehensive genetic analysis, 853 genetic variants previously reported as ALS-linked mutations or disease-associated alleles were interrogated in sporadic ALS WGS data. Statistical analyses were performed to identify correlation between clinical variables, and between phenotype and the number of ALS-implicated variants carried by an individual. Relatedness between individuals carrying identical variants was assessed using identity-by-descent analysis.ResultsForty-three ALS-implicated variants from 18 genes, including C9orf72, ATXN2, TARDBP, SOD1, SQSTM1 and SETX, were identified in Australian sporadic ALS cases. One-third of cases carried at least one variant and 6.82% carried two or more variants, implicating a potential oligogenic or polygenic basis of ALS. Relatedness was detected between two sporadic ALS cases carrying a SOD1 p.I114T mutation, and among three cases carrying a SQSTM1 p.K238E mutation. Oligogenic/polygenic sporadic ALS cases showed earlier age of onset than those with no reported variant.ConclusionWe confirm phenotypic associations among ALS cases, and highlight the contribution of genetic variation to all forms of ALS.

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