scholarly journals Ethnically relevant consensus Korean reference genome towards personal reference genomes

2016 ◽  
Author(s):  
Yun Sung Cho ◽  
Hyunho Kim ◽  
Hak-Min Kim ◽  
Sungwoong Jho ◽  
JeHoon Jun ◽  
...  
Keyword(s):  
Large Scale ◽  
New Technologies ◽  
Reference Genome ◽  
Genomic Structure ◽  
Personal Genomic ◽  
Personal Reference ◽  
Human Genomes ◽  
Scale Population ◽  
Genome Assemblies ◽  
Universal Reference

AbstractHuman genomes are routinely compared against a universal reference. However, this strategy could miss population-specific or personal genomic variations, which may be detected more efficiently using an ethnically-relevant and/or a personal reference. Here we report a hybrid assembly of Korean reference (KOREF) as a pilot case for constructing personal and ethnic references by combining sequencing and mapping methods. KOREF is also the first consensus variome reference, providing information on millions of variants from additional ethnically homogeneous personal genomes. We found that this ethnically-relevant consensus reference was beneficial for efficiently detecting variants. Systematic comparison of KOREF with previously established human assemblies showed the importance of assembly quality, suggesting the necessity of using new technologies to comprehensively map ethnic and personal genomic structure variations. In the era of large-scale population genome projects, the leveraging of ethnicity-specific genome assemblies as well as the human reference genome will accelerate mapping all human genome diversity.

scholarly journals An ethnically relevant consensus Korean reference genome is a step towards personal reference genomes

2016 ◽  
Vol 7 (1) ◽  
Author(s):  
Yun Sung Cho ◽  
Hyunho Kim ◽  
Hak-Min Kim ◽  
Sungwoong Jho ◽  
JeHoon Jun ◽  
...  
Keyword(s):  
Large Scale ◽  
New Technologies ◽  
Reference Genome ◽  
Genomic Structure ◽  
Genome Project ◽  
Personal Genome ◽  
Personal Genomic ◽  
Personal Reference ◽  
Scale Population ◽  
Genome Assemblies

Abstract Human genomes are routinely compared against a universal reference. However, this strategy could miss population-specific and personal genomic variations, which may be detected more efficiently using an ethnically relevant or personal reference. Here we report a hybrid assembly of a Korean reference genome (KOREF) for constructing personal and ethnic references by combining sequencing and mapping methods. We also build its consensus variome reference, providing information on millions of variants from 40 additional ethnically homogeneous genomes from the Korean Personal Genome Project. We find that the ethnically relevant consensus reference can be beneficial for efficient variant detection. Systematic comparison of human assemblies shows the importance of assembly quality, suggesting the necessity of new technologies to comprehensively map ethnic and personal genomic structure variations. In the era of large-scale population genome projects, the leveraging of ethnicity-specific genome assemblies as well as the human reference genome will accelerate mapping all human genome diversity.

scholarly journals Population analysis of retrotransposons in giraffe genomes supports RTE decline and widespread LINE1 activity in Giraffidae

Mobile DNA ◽  
2021 ◽  
Vol 12 (1) ◽  
Author(s):  
Malte Petersen ◽  
Sven Winter ◽  
Raphael Coimbra ◽  
Menno J. de Jong ◽  
Vladimir V. Kapitonov ◽  
...  
Keyword(s):  
Large Scale ◽  
Population Analysis ◽  
Model Organism ◽  
Population Level ◽  
Data Sets ◽  
Ltr Retrotransposons ◽  
Scale Population ◽  
Mammalian Genomes ◽  
Genome Assemblies ◽  
First Time

Abstract Background The majority of structural variation in genomes is caused by insertions of transposable elements (TEs). In mammalian genomes, the main TE fraction is made up of autonomous and non-autonomous non-LTR retrotransposons commonly known as LINEs and SINEs (Long and Short Interspersed Nuclear Elements). Here we present one of the first population-level analysis of TE insertions in a non-model organism, the giraffe. Giraffes are ruminant artiodactyls, one of the few mammalian groups with genomes that are colonized by putatively active LINEs of two different clades of non-LTR retrotransposons, namely the LINE1 and RTE/BovB LINEs as well as their associated SINEs. We analyzed TE insertions of both types, and their associated SINEs in three giraffe genome assemblies, as well as across a population level sampling of 48 individuals covering all extant giraffe species. Results The comparative genome screen identified 139,525 recent LINE1 and RTE insertions in the sampled giraffe population. The analysis revealed a drastically reduced RTE activity in giraffes, whereas LINE1 is still actively propagating in the genomes of extant (sub)-species. In concert with the extremely low activity of the giraffe RTE, we also found that RTE-dependent SINEs, namely Bov-tA and Bov-A2, have been virtually immobile in the last 2 million years. Despite the high current activity of the giraffe LINE1, we did not find evidence for the presence of currently active LINE1-dependent SINEs. TE insertion heterozygosity rates differ among the different (sub)-species, likely due to divergent population histories. Conclusions The horizontally transferred RTE/BovB and its derived SINEs appear to be close to inactivation and subsequent extinction in the genomes of extant giraffe species. This is the first time that the decline of a TE family has been meticulously analyzed from a population genetics perspective. Our study shows how detailed information about past and present TE activity can be obtained by analyzing large-scale population-level genomic data sets.

scholarly journals General Attitudes Towards Robots Scale (GAToRS): A New Versatile Instrument for Social Surveys

2021 ◽  
Author(s):  
Mika Koverola ◽  
Anton Kunnari ◽  
Jukka Reima Ilmari Sundvall ◽  
Michael Laakasuo
Keyword(s):  
Large Scale ◽  
New Technologies ◽  
Population Based ◽  
Context Dependency ◽  
Equal Weight ◽  
Human Society ◽  
Social Scientists ◽  
New Instrument ◽  
Scale Population ◽  
People’S Attitudes

Psychometric scales are useful tools in understanding people’s attitudes towards different aspects of life. As societies develop and new technologies arise, new validated scales are needed. Robots and artificial intelligences of various kinds are about to occupy just about every niche in human society. Several tools to measure fears and anxieties about robots do exist, but there is a definite lack of tools to measure hopes and expectations for these new technologies. Here, we cre-ate and validate a novel multi-dimensional scale which measures people’s attitudes towards ro-bots, giving equal weight to positive and negative attitudes. Our scale reliably differentiated a) comfort and enjoyment around robots, b) discomfort and anxiety around robots, c) rational hopes about robots in general and d) rational worries about robots in general. In addition to its psycho-metric qualities our scale is compact (only 20 items), aesthetically pleasing (5 items in each of the four sub-scales) and produces reliably the same factor structure in different samples. In contrast to previous tools our new instrument also allows large-scale population based and intercultural re-search without context dependency. Due to its easy-to-use nature, we hope our scale will be a use-ful instrument for social scientists who wish to study human-technology relations with a validated scale in efficient and generalizable ways.

Financial and Economic Support of Innovation Processes in the Russian Fuel and Energy Complex

2019 ◽  
Vol 12 (3) ◽  
pp. 77-85
Author(s):  
L. D. Kapranova ◽  
T. V. Pogodina
Keyword(s):  
Oil Recovery ◽  
Large Scale ◽  
Oil And Gas ◽  
New Technologies ◽  
Innovative Development ◽  
Oil Reserves ◽  
Energy Complex ◽  
Innovation Activities ◽  
Substantial Investment ◽  
The Government

The subject of the research is the current state of the fuel and energy complex (FEC) that ensures generation of a significant part of the budget and the innovative development of the economy.The purpose of the research was to establish priority directions for the development of the FEC sectors based on a comprehensive analysis of their innovative and investment activities. The dynamics of investment in the fuel and energy sector are considered. It is noted that large-scale modernization of the fuel and energy complex requires substantial investment and support from the government. The results of the government programs of corporate innovative development are analyzed. The results of the research identified innovative development priorities in the power, oil, gas and coal sectors of the fuel and energy complex. The most promising areas of innovative development in the oil and gas sector are the technologies of enhanced oil recovery; the development of hard-to-recover oil reserves; the production of liquefied natural gas and its transportation. In the power sector, the prospective areas are activities aimed at improving the performance reliability of the national energy systems and the introduction of digital technologies. Based on the research findings, it is concluded that the innovation activities in the fuel and energy complex primarily include the development of new technologies, modernization of the FEC technical base; adoption of state-of-the-art methods of coal mining and oil recovery; creating favorable economic conditions for industrial extraction of hard-to-recover reserves; transition to carbon-free fuel sources and energy carriers that can reduce energy consumption and cost as well as reducing the negative FEC impact on the environment.

The sugar and alcohol industry in the biofuels and cogeneration era: a paradigm change (part II)

2014 ◽  
pp. 97-104 ◽  
Author(s):  
Electo Eduardo Silv Lora ◽  
Mateus Henrique Rocha ◽  
José Carlos Escobar Palacio ◽  
Osvaldo José Venturini ◽  
Maria Luiza Grillo Renó ◽  
...  
Keyword(s):  
Large Scale ◽  
New Technologies ◽  
Process Integration ◽  
Animal Feed ◽  
Raw Materials ◽  
Biofuel Production ◽  
New Paradigm ◽  
Alcohol Industry ◽  
Feed Production ◽  
Steam Parameters

The aim of this paper is to discuss the major technological changes related to the implementation of large-scale cogeneration and biofuel production in the sugar and alcohol industry. The reduction of the process steam consumption, implementation of new alternatives in driving mills, the widespread practice of high steam parameters use in cogeneration facilities, the insertion of new technologies for biofuels production (hydrolysis and gasification), the energy conversion of sugarcane trash and vinasse, animal feed production, process integration and implementation of the biorefinery concept are considered. Another new paradigm consists in the wide spreading of sustainability studies of products and processes using the Life Cycle Assessment (LCA) and the implementation of sustainability indexes. Every approach to this issue has as an objective to increase the economic efficiency and the possibilities of the sugarcane as a main source of two basic raw materials: fibres and sugar. The paper briefly presents the concepts, indicators, state-of-the-art and perspectives of each of the referred issues.

scholarly journals Genome Assembly of the Canadian Two-row Malting Barley Cultivar AAC Synergy

2021 ◽  
Author(s):  
Wayne Xu ◽  
James R Tucker ◽  
Wubishet A Bekele ◽  
Frank M You ◽  
Yong-Bi Fu ◽  
...  
Keyword(s):  
Reference Genome ◽  
Single Copy ◽  
Barley Cultivar ◽  
Malting Barley ◽  
Orthologous Genes ◽  
Hordeum Vulgare L ◽  
Chromosome Conformation ◽  
Mate Pair ◽  
Genome Assemblies ◽  
First Time

Abstract Barley (Hordeum vulgare L.) is one of the most important global crops. The six-row barley cultivar Morex reference genome has been used by the barley research community worldwide. However, this reference genome can have limitations when used for genomic and genetic diversity analysis studies, gene discovery, and marker development when working in two-row germplasm that is more common to Canadian barley. Here we assembled, for the first time, the genome sequence of a Canadian two-row malting barley, cultivar AAC Synergy. We applied deep Illumina paired-end reads, long mate-pair reads, PacBio sequences, 10X chromium linked read libraries, and chromosome conformation capture sequencing (Hi-C) to generate a contiguous assembly. The genome assembled from super-scaffolds had a size of 4.85 Gb, N50 of 2.32 Mb and an estimated 93.9% of complete genes from a plant database (BUSCO, benchmarking universal single-copy orthologous genes). After removal of small scaffolds (< 300 Kb), the assembly was arranged into pseudomolecules of 4.14 Gb in size with seven chromosomes plus unanchored scaffolds. The completeness and annotation of the assembly were assessed by comparing it with the updated version of six-row Morex and recently released two-row Golden Promise genome assemblies.

scholarly journals mRNA-Based Vaccines

Vaccines ◽  
2021 ◽  
Vol 9 (4) ◽  
pp. 390
Author(s):  
Frank Kowalzik ◽  
Daniel Schreiner ◽  
Christian Jensen ◽  
Daniel Teschner ◽  
Stephan Gehring ◽  
...  
Keyword(s):  
Large Scale ◽  
New Technologies ◽  
Vaccine Development ◽  
Effective Means ◽  
Cost Effective ◽  
Clinical Applications ◽  
Cell Mediated Immunity ◽  
Healthy Individuals ◽  
Emerging Pathogens ◽  
Cell Genome

Increases in the world’s population and population density promote the spread of emerging pathogens. Vaccines are the most cost-effective means of preventing this spread. Traditional methods used to identify and produce new vaccines are not adequate, in most instances, to ensure global protection. New technologies are urgently needed to expedite large scale vaccine development. mRNA-based vaccines promise to meet this need. mRNA-based vaccines exhibit a number of potential advantages relative to conventional vaccines, namely they (1) involve neither infectious elements nor a risk of stable integration into the host cell genome; (2) generate humoral and cell-mediated immunity; (3) are well-tolerated by healthy individuals; and (4) are less expensive and produced more rapidly by processes that are readily standardized and scaled-up, improving responsiveness to large emerging outbreaks. Multiple mRNA vaccine platforms have demonstrated efficacy in preventing infectious diseases and treating several types of cancers in humans as well as animal models. This review describes the factors that contribute to maximizing the production of effective mRNA vaccine transcripts and delivery systems, and the clinical applications are discussed in detail.

scholarly journals Publisher Correction: A link between appendectomy and gastrointestinal cancers: a large-scale population-based cohort study in Korea

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Youn Young Park ◽  
Kil‑yong Lee ◽  
Seong Taek Oh ◽  
Sang Hyun Park ◽  
Kyung Do Han ◽  
...  
Keyword(s):  
Cohort Study ◽  
Large Scale ◽  
Population Based ◽  
Gastrointestinal Cancers ◽  
Scale Population

An amendment to this paper has been published and can be accessed via a link at the top of the paper.

scholarly journals Using Bus Ticketing Big Data to Investigate the Behaviors of the Population Flow of Chinese Suburban Residents in the Post-COVID-19 Phase

2021 ◽  
Vol 18 (11) ◽  
pp. 6066
Author(s):  
Yanbing Bai ◽  
Lu Sun ◽  
Haoyu Liu ◽  
Chao Xie
Keyword(s):  
Travel Behavior ◽  
Large Scale ◽  
Behavior Patterns ◽  
Population Movements ◽  
Economic Level ◽  
Passenger Travel ◽  
Scale Population ◽  
Travel Behaviors ◽  
Railway Passenger ◽  
And Control

Large-scale population movements can turn local diseases into widespread epidemics. Grasping the characteristic of the population flow in the context of the COVID-19 is of great significance for providing information to epidemiology and formulating scientific and reasonable prevention and control policies. Especially in the post-COVID-19 phase, it is essential to maintain the achievement of the fight against the epidemic. Previous research focuses on flight and railway passenger travel behavior and patterns, but China also has numerous suburban residents with a not-high economic level; investigating their travel behaviors is significant for national stability. However, estimating the impacts of the COVID-19 for suburban residents’ travel behaviors remains challenging because of lacking apposite data. Here we submit bus ticketing data including approximately 26,000,000 records from April 2020–August 2020 for 2705 stations. Our results indicate that Suburban residents in Chinese Southern regions are more likely to travel by bus, and travel frequency is higher. Associated with the economic level, we find that residents in the economically developed region more likely to travel or carry out various social activities. Considering from the perspective of the traveling crowd, we find that men and young people are easier to travel by bus; however, they are exactly the main workforce. The indication of our findings is that suburban residents’ travel behavior is affected profoundly by economy and consistent with the inherent behavior patterns before the COVID-19 outbreak. We use typical regions as verification and it is indeed the case.

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