scholarly journals YHP: Y-chromosome Haplogroup Predictor for predicting male lineages based on Y-STRs

2021 ◽  
Author(s):  
Mengyuan Song ◽  
Feng Song ◽  
Chenxi Zhao ◽  
Yiping Hou
Keyword(s):  
High Resolution ◽  
Y Chromosome ◽  
Software Package ◽  
Tandem Repeats ◽  
Evolutionary Process ◽  
Lineage Tracing ◽  
Software Packages ◽  
Specific Distribution ◽  
The Cost ◽  
Male Lineage

AbstractHuman Y chromosome reflects the evolutionary process of males. Male lineage tracing by Y chromosome is of great use in evolutionary, forensic, and anthropological studies when male samples exist or especially when the biological sample is a mixture of male and female individuals. Identifying the male lineage based on the specific distribution of Y haplogroups narrows down the investigation scope. Integrating previously published datasets with genotypes of Y chromosome short tandem repeats (Y-STRs) and high-resolution haplogroups (122 haplogroups in total), we developed YHP (Y Haplogroup Predictor), an open-access and userfriendly software package to predict haplogroups, compare the similarity, and conduct mismatch analysis of samples with Y-STR profiles. The software is available at Github (https://github.com/cissy123/YHP-Y-Haplogroup-Predictor-).Author SummaryFamilial searching has been used in forensic, anthropologic, and personalized scenarios. Software packages have been developed to assist in male familial searching, such as predicting Y-SNP haplogroups by Y-STRs. However, these software packages, in general, achieve this goal with a rough resolution. In this study, we developed a software package to conduct high-resolution haplogroup inference to help familial searching and at the same time reduce the cost, since it does not require tiresome Y-SNP sequencing.

Population Genetics of Y-Chromosome Short Tandem Repeats in Humans

1997 ◽  
Vol 45 (3) ◽  
pp. 265-270 ◽  
Author(s):  
Anna Pérez-Lezaun ◽  
Francesc Calafell ◽  
Mark Seielstad ◽  
Eva Mateu ◽  
David Comas ◽  
...  
Keyword(s):  
Population Genetics ◽  
Y Chromosome ◽  
Short Tandem Repeats ◽  
Tandem Repeats ◽  
Short Tandem

scholarly journals A Back Migration from Asia to Sub-Saharan Africa Is Supported by High-Resolution Analysis of Human Y-Chromosome Haplotypes

2002 ◽  
Vol 70 (5) ◽  
pp. 1197-1214 ◽  
Author(s):  
Fulvio Cruciani ◽  
Piero Santolamazza ◽  
Peidong Shen ◽  
Vincent Macaulay ◽  
Pedro Moral ◽  
...  
Keyword(s):  
High Resolution ◽  
Y Chromosome ◽  
Sub Saharan Africa ◽  
High Resolution Analysis ◽  
Resolution Analysis ◽  
Sub Saharan ◽  
Human Y Chromosome

scholarly journals Sex-Specific Migration Patterns in Central Asian Populations, Revealed by Analysis of Y-Chromosome Short Tandem Repeats and mtDNA

1999 ◽  
Vol 65 (1) ◽  
pp. 208-219 ◽  
Author(s):  
Anna Pérez-Lezaun ◽  
Francesc Calafell ◽  
David Comas ◽  
Eva Mateu ◽  
Elena Bosch ◽  
...  
Keyword(s):  
Y Chromosome ◽  
Short Tandem Repeats ◽  
Tandem Repeats ◽  
Migration Patterns ◽  
Asian Populations ◽  
Central Asian ◽  
Short Tandem

scholarly journals mixIndependR: a R package for statistical independence testing of loci in database of multi-locus genotypes

2021 ◽  
Vol 22 (1) ◽  
Author(s):  
Bing Song ◽  
August E. Woerner ◽  
John Planz
Keyword(s):  
Population Genetics ◽  
Linkage Disequilibrium ◽  
Genetic Markers ◽  
Software Package ◽  
Tandem Repeats ◽  
Population Data ◽  
Real Data ◽  
R Package ◽  
Nucleotide Polymorphisms ◽  
Mutual Independence

Abstract Background Multi-locus genotype data are widely used in population genetics and disease studies. In evaluating the utility of multi-locus data, the independence of markers is commonly considered in many genomic assessments. Generally, pairwise non-random associations are tested by linkage disequilibrium; however, the dependence of one panel might be triplet, quartet, or other. Therefore, a compatible and user-friendly software is necessary for testing and assessing the global linkage disequilibrium among mixed genetic data. Results This study describes a software package for testing the mutual independence of mixed genetic datasets. Mutual independence is defined as no non-random associations among all subsets of the tested panel. The new R package “mixIndependR” calculates basic genetic parameters like allele frequency, genotype frequency, heterozygosity, Hardy–Weinberg equilibrium, and linkage disequilibrium (LD) by mutual independence from population data, regardless of the type of markers, such as simple nucleotide polymorphisms, short tandem repeats, insertions and deletions, and any other genetic markers. A novel method of assessing the dependence of mixed genetic panels is developed in this study and functionally analyzed in the software package. By comparing the observed distribution of two common summary statistics (the number of heterozygous loci [K] and the number of share alleles [X]) with their expected distributions under the assumption of mutual independence, the overall independence is tested. Conclusion The package “mixIndependR” is compatible to all categories of genetic markers and detects the overall non-random associations. Compared to pairwise disequilibrium, the approach described herein tends to have higher power, especially when number of markers is large. With this package, more multi-functional or stronger genetic panels can be developed, like mixed panels with different kinds of markers. In population genetics, the package “mixIndependR” makes it possible to discover more about admixture of populations, natural selection, genetic drift, and population demographics, as a more powerful method of detecting LD. Moreover, this new approach can optimize variants selection in disease studies and contribute to panel combination for treatments in multimorbidity. Application of this approach in real data is expected in the future, and this might bring a leap in the field of genetic technology. Availability The R package mixIndependR, is available on the Comprehensive R Archive Network (CRAN) at: https://cran.r-project.org/web/packages/mixIndependR/index.html.

Impact of High Resolution 3D Geomechanics on Well Optimization in the Southern Gulf of Suez, Egypt

2021 ◽  
Author(s):  
Mohamed Elkhawaga ◽  
Wael A. Elghaney ◽  
Rajarajan Naidu ◽  
Assef Hussen ◽  
Ramy Rafaat ◽  
...  
Keyword(s):  
High Resolution ◽  
Pore Pressure ◽  
Cost Optimization ◽  
Oil Field ◽  
Wellbore Stability ◽  
Gulf Of Suez ◽  
Geomechanical Model ◽  
3D Geomechanical Model ◽  
The Cost ◽  
The Impact

Abstract Optimizing the number of casing strings has a direct impact on cost of drilling a well. The objective of the case study presented in this paper is the demonstration of reducing cost through integration of data. This paper shows the impact of high-resolution 3D geomechanical modeling on well cost optimization for the GS327 Oil field. The field is located in the Sothern Gulf of Suez basin and has been developed by 20 wells The conventional casing design in the field included three sections. In this mature field, especially with the challenge of reducing production cost, it is imperative to look for opportunites to optimize cost in drilling new wells to sustain ptoduction. 3D geomechanics is crucial for such cases in order to optimize the cost per barrel at the same time help to drill new wells safely. An old wellbore stability study did not support the decision-maker to merge any hole sections. However, there was not geomechanics-related problems recorded during the drilling the drilling of different mud weights. In this study, a 3D geomechanical model was developed and the new mud weight calculations positively affected the casing design for two new wells. The cost optimization will be useful for any future wells to be drilled in this area. This study documents how a 3D geomechanical model helped in the successful delivery of objectives (guided by an understanding of pore pressure and rock properties) through revision of mud weight window calculations that helped in optimizing the casing design and eliminate the need for an intermediate casing. This study reveals that the new calculated pore pressure in the GS327 field is predominantly hydrostatic with a minor decline in the reservoir pressure. In addition, rock strength of the shale is moderately high and nearly homogeneous, which helped in achieving a new casing design for the last two drilled wells in the field.

scholarly journals Development and Validation of a High-Resolution Melting Assay To Detect Azole Resistance in Aspergillus fumigatus

2017 ◽  
Vol 61 (12) ◽  
Author(s):  
L. Bernal-Martínez ◽  
H. Gil ◽  
O. Rivero-Menéndez ◽  
S. Gago ◽  
M. Cuenca-Estrella ◽  
...  
Keyword(s):  
High Resolution ◽  
Aspergillus Fumigatus ◽  
Tandem Repeats ◽  
High Resolution Melting ◽  
Screening Method ◽  
Melting Curve ◽  
Health Concern ◽  
Azole Resistance ◽  
Content Type ◽  
Selection Of

ABSTRACT The global emergence of azole-resistant Aspergillus fumigatus strains is a growing public health concern. Different patterns of azole resistance are linked to mutations in cyp51A. Therefore, accurate characterization of the mechanisms underlying azole resistance is critical to guide selection of the most appropriate antifungal agent for patients with aspergillosis. This study describes a new sequencing-free molecular screening tool for early detection of the most frequent mutations known to be associated with azole resistance in A. fumigatus. PCRs targeting cyp51A mutations at positions G54, Y121, G448, and M220 and targeting different tandem repeats (TRs) in the promoter region were designed. All PCRs were performed simultaneously, using the same cycling conditions. Amplicons were then distinguished using a high-resolution melting assay. For standardization, 30 well-characterized azole-resistant A. fumigatus strains were used, yielding melting curve clusters for different resistance mechanisms for each target and allowing detection of the most frequent azole resistance mutations, i.e., G54E, G54V, G54R, G54W, Y121F, M220V, M220I, M220T, M220K, and G448S, and the tandem repeats TR34, TR46, and TR53. Validation of the method was performed using a blind panel of 80 A. fumigatus azole-susceptible or azole-resistant strains. All strains included in the blind panel were properly classified as susceptible or resistant with the developed method. The implementation of this screening method can reduce the time needed for the detection of azole-resistant A. fumigatus isolates and therefore facilitate selection of the best antifungal therapy in patients with aspergillosis.

scholarly journals OpenStats: A Robust and Scalable Software Package for Reproducible Analysis of High-Throughput Phenotypic Data

2020 ◽  
Author(s):  
Hamed Haselimashhadi ◽  
Jeremy C Mason ◽  
Ann-Marie Mallon ◽  
Damian Smedley ◽  
Terrence F Meehan ◽  
...  
Keyword(s):  
High Throughput ◽  
Software Package ◽  
Computational Time ◽  
Phenotypic Data ◽  
Creative Commons ◽  
International Mouse Phenotyping Consortium ◽  
Software Packages ◽  
Current Production ◽  
High Throughput Phenotyping ◽  
Reproducible Analysis

AbstractReproducibility in the statistical analyses of data from high-throughput phenotyping screens requires a robust and reliable analysis foundation that allows modelling of different possible statistical scenarios. Regular challenges are scalability and extensibility of the analysis software. In this manuscript, we describe OpenStats, a freely available software package that addresses these challenges. We show the performance of the software in a high-throughput phenomic pipeline in the International Mouse Phenotyping Consortium (IMPC) and compare the agreement of the results with the most similar implementation in the literature. OpenStats has significant improvements in speed and scalability compared to existing software packages including a 13-fold improvement in computational time to the current production analysis pipeline in the IMPC. Reduced complexity also promotes FAIR data analysis by providing transparency and benefiting other groups in reproducing and re-usability of the statistical methods and results. OpenStats is freely available under a Creative Commons license at www.bioconductor.org/packages/OpenStats.

scholarly journals AUTOMATIC MRF-BASED REGISTRATION OF HIGH RESOLUTION SATELLITE VIDEO DATA

2016 ◽  
Vol III-1 ◽  
pp. 121-128 ◽  
Author(s):  
C. Platias ◽  
M. Vakalopoulou ◽  
K. Karantzalos
Keyword(s):  
High Resolution ◽  
Markov Random Fields ◽  
Video Data ◽  
Registration Accuracy ◽  
Registration Method ◽  
Computational Performance ◽  
Markov Random ◽  
Video Frames ◽  
Reference Map ◽  
The Cost

In this paper we propose a deformable registration framework for high resolution satellite video data able to automatically and accurately co-register satellite video frames and/or register them to a reference map/image. The proposed approach performs non-rigid registration, formulates a Markov Random Fields (MRF) model, while efficient linear programming is employed for reaching the lowest potential of the cost function. The developed approach has been applied and validated on satellite video sequences from Skybox Imaging and compared with a rigid, descriptor-based registration method. Regarding the computational performance, both the MRF-based and the descriptor-based methods were quite efficient, with the first one converging in some minutes and the second in some seconds. Regarding the registration accuracy the proposed MRF-based method significantly outperformed the descriptor-based one in all the performing experiments.

scholarly journals Quantum GIS (QGIS): An introduction to a free alternative to more costly GIS platforms

EDIS ◽  
2020 ◽  
Vol 2020 (2) ◽  
pp. 7
Author(s):  
Jeffry M. Flenniken ◽  
Steven Stuglik ◽  
Basil V. Iannone
Keyword(s):  
Information System ◽  
Geographic Information System ◽  
Spatial Analysis ◽  
Natural Resources ◽  
Software Package ◽  
Forest Resources ◽  
Software Packages ◽  
Land Cover Map ◽  
Gis Software ◽  
Florida Springs

Geographic information system (GIS) software packages can be prohibitively expensive, causing many to shy away from mapping and spatial analysis. This 7-page fact sheet written by Jeffry M. Flenniken, Steven Stuglik, and Basil V. Iannone III and published by the UF/IFAS School of Forest Resources and Conservation introduces the reader to a free GIS software package called Quantum GIS (QGIS), walking the reader through simple GIS processes that can be used to visualize spatial patterns of importance to a variety of fields, including natural resources, agriculture, and urban planning. Learn how to create a land-cover map for a county of interest and create heatmaps that illustrate the density of a given attribute (Florida Springs for this example). This publication will benefit those interested in incorporating GIS into their work but who are unable to afford expensive proprietary GIS software packages, as well as anyone interested in learning a new GIS software package. https://edis.ifas.ufl.edu/fr428

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