scholarly journals Estimating the quality of eukaryotic genomes recovered from metagenomic analysis

2019 ◽  
Author(s):  
Paul Saary ◽  
Alex L. Mitchell ◽  
Robert D. Finn
Keyword(s):  
Large Fraction ◽  
Marker Gene ◽  
Single Copy ◽  
Dynamic Selection ◽  
Microbial Eukaryotes ◽  
Gene Sets ◽  
Eukaryotic Genomes ◽  
Eukaryote Genome ◽  
Selection Of

AbstractEukaryotes make up a large fraction of microbial biodiversity. However, the field of metagenomics has been heavily biased towards the study of just the prokaryotic fraction. This focus has driven the necessary methodological developments to enable the recovery of prokaryotic genomes from metagenomes, which has reliably yielded genomes from thousands of novel species. More recently, microbial eukaryotes have gained more attention, but there is yet to be a parallel explosion in the number of eukaryotic genomes recovered from metagenomic samples. One of the current deficiencies is the lack of a universally applicable and reliable tool for the estimation of eukaryote genome quality. To address this need, we have developed EukCC, a tool for estimating the quality of eukaryotic genomes based on the dynamic selection of single copy marker gene sets, with the aim of applying it to metagenomics datasets. We demonstrate that our method outperforms current genome quality estimators and have applied EukCC to datasets from two different biomes to enable the identification of novel genomes, including a eukaryote found on the human skin and a Bathycoccus species obtained from a marine sample.

scholarly journals Estimating the quality of eukaryotic genomes recovered from metagenomic analysis with EukCC

2020 ◽  
Vol 21 (1) ◽  
Author(s):  
Paul Saary ◽  
Alex L. Mitchell ◽  
Robert D. Finn
Keyword(s):  
Marker Gene ◽  
Single Copy ◽  
High Quality ◽  
Dynamic Selection ◽  
Microbial Eukaryotes ◽  
Gene Sets ◽  
Current Availability ◽  
Eukaryotic Genomes ◽  
Selection Of

Abstract Microbial eukaryotes constitute a significant fraction of biodiversity and have recently gained more attention, but the recovery of high-quality metagenomic assembled eukaryotic genomes is limited by the current availability of tools. To help address this, we have developed EukCC, a tool for estimating the quality of eukaryotic genomes based on the automated dynamic selection of single copy marker gene sets. We demonstrate that our method outperforms current genome quality estimators, particularly for estimating contamination, and have applied EukCC to datasets derived from two different environments to enable the identification of novel eukaryote genomes, including one from the human skin.

scholarly journals Loss of MAR1 Function is a Marker for Co-Selection of CRISPR-Induced Mutations in Plants

2021 ◽  
Vol 3 ◽  
Author(s):  
Jannis Rinne ◽  
Claus-Peter Witte ◽  
Marco Herde
Keyword(s):  
Tissue Culture ◽  
Plant Species ◽  
Target Gene ◽  
Iron Homeostasis ◽  
Marker Gene ◽  
Single Copy ◽  
Kanamycin Resistance ◽  
Control Population ◽  
Induced Mutations ◽  
Selection Of

In this study, we describe the establishment of the knockout marker gene MAR1 for selection of CRISPR/Cas9-edited Arabidopsis seedlings and tomato explants in tissue culture. MAR1 encodes a transporter that is located in mitochondria and chloroplasts and is involved in iron homeostasis. It also opportunistically transports aminoglycoside antibiotics into these organelles and defects of the gene render plants insensitive to those compounds. Here, we show that mutations of MAR1 induced by the CRISPR system confer kanamycin-resistance to Arabidopsis plants and tomato tissues. MAR1 is single-copy in a variety of plant species and the corresponding proteins form a distinct phylogenetic clade allowing easy identification of MAR1 orthologs in different plants. We demonstrate that in multiplexing approaches, where Arabidopsis seedlings were selected via a CRISPR/Cas9-induced kanamycin resistance mediated by MAR1 mutation, a mutation in a second target gene was observed with higher frequency than in a control population only selected for the presence of the transgene. This so called co-selection has not been shown before to occur in plants. The technique can be employed to select for edited plants, which might be particularly useful if editing events are rare.

ON THE EXPERT’S RIGHT TO BE PRESENT AT LEGAL PROCEEDINGS

2016 ◽  
Vol 15 ◽  
pp. 163-171
Author(s):  
M. G. Shcherbakovskiy
Keyword(s):  
Initial Data ◽  
Legal Proceedings ◽  
Reliable Assessment ◽  
Data Acquiring ◽  
Selection Of

The article discusses the reasonsfor an expert to participate in legal proceedings. The gnoseological reason for that consists of the bad quality of materials subject to examination that renders the examination either completely impossible or compromises objective, reasoned and reliable assessment of the findings. The procedural reason consists ofa proscription for an expert to collect evidence himself or herself. The author investigates into the ways of how an expert can participate in legal proceedings. If the defense invites an expert to participate in the proceedings, then it is recommended that his or her involvement should be in the presence of attesting witnesses and recorded in the protocol. In the course of the legal proceedings an expert has the following tasks: adding initial data, acquiring new initial data, understanding the situation of the incident, acquiring new objects to be studied, including samples for examination. An expert’s participation in legal proceedings differs from the participation of a specialist or an examination on the scene of the incident. The author describes the tasks that an expert solves in the course of legal proceedings, the peculiarities ofan investigation experiment practices, the selection of samples for an examination, inspection, interrogation.

Implementasi Voip Server Berbasis IPV6 Dengan Raspberry PI

2019 ◽  
Vol 9 (01) ◽  
pp. 47-54
Author(s):  
Rabbai San Arif ◽  
Yuli Fitrisia ◽  
Agus Urip Ari Wibowo
Keyword(s):  
Internet Protocol ◽  
Wireless Transmission ◽  
Raspberry Pi ◽  
Test Results ◽  
Average Delay ◽  
Ipv6 Network ◽  
Ip Network ◽  
Selection Of ◽  
Better Than

Voice over Internet Protocol (VoIP) is a telecommunications technology that is able to pass the communication service in Internet Protocol networks so as to allow communicating between users in an IP network. However VoIP technology still has weakness in the Quality of Service (QoS). VOPI weaknesses is affected by the selection of the physical servers used. In this research, VoIP is configured on Linux operating system with Asterisk as VoIP application server and integrated on a Raspberry Pi by using wired and wireless network as the transmission medium. Because of depletion of IPv4 capacity that can be used on the network, it needs to be applied to VoIP system using the IPv6 network protocol with supports devices. The test results by using a wired transmission medium that has obtained are the average delay is 117.851 ms, jitter is 5.796 ms, packet loss is 0.38%, throughput is 962.861 kbps, 8.33% of CPU usage and 59.33% of memory usage. The analysis shows that the wired transmission media is better than the wireless transmission media and wireless-wired.

DESIGN, SIMULATION AND IMPLEMENTATION MONITORING SYSTEM FOR SYSTEM CONTROL C4 FEEDING PUMP FOR FEED VAPORIZATION IN THE BUTADIENE PLANT

2020 ◽  
Vol 1 (1) ◽  
pp. 31-35
Author(s):  
Fahmi Yunistyawan ◽  
Yunistyawan J Berchmans ◽  
Gembong Baskoro
Keyword(s):  
Motor Control ◽  
Control System ◽  
Field Operator ◽  
System Control ◽  
Variable Speed ◽  
Variable Speed Drive ◽  
Software And Hardware ◽  
Discharge Pressure ◽  
Selection Of

This study implements the auto start control system on an electric motor 3 phase C4Feeding pump when the discharge pressure is low-low (4.3 kg /cm²). The C4 feeding pumpmotor was initially manually operated from the local control station, this was very ineffectiveand inefficient because it still relied on the field operator to operate the pump motor and whenthe plant was in normal operating it is very risk if the field operator late to operate motor then itwill impact to quality of the product, and if the delay time to operate motor is too long then planthave to shut down, therefore improvement is needed in the C4 feeding pump motor controlsystem. In this paper, various types of 3-phase motor control are explained which allow it to beapplied to the C4 feeding pump motor that are on-off, inverter, and variable speed drive andefficient selection of the three systems control of the motor. Software and hardware used in thisthesis work are DCS CENTUM VP Yokogawa.

Thomas More’s Correspondence in a Spanish Ambiance

Moreana ◽  
2002 ◽  
Vol 39 (Number 149) (1) ◽  
pp. 41-60 ◽  
Author(s):  
Eugenio M. Olivares Merino
Keyword(s):  
The Subject ◽  
Selection Of

The recent reprinting of Álvaro de Silva’s 1998 edition of a selection of More’s letters prompts the author to examine the subject of Spanish translations of More, and of de Silva’s general commentary on More’s correspondence and on his relationship to other humanists. The author reflects on aspects of More’s personality as exposed in his letters and uses what he finds as a corrective to several biographical misconceptions. He points out the strengths and weaknesses of de Silva’s work and compares it with that of other translators, particularly Elizabeth Rogers, and notes the particularly Spanish quality of de Silva’s edition.

COMBINATORIAL POLYNOMIALLY COMPUTABLE CHARACTERISTICS OF SUBSTITUTIONS AND THEIR PROPERTIES

2020 ◽  
Vol 7 (2) ◽  
pp. 34-41
Author(s):  
VLADIMIR NIKONOV ◽  
◽  
ANTON ZOBOV ◽  
Keyword(s):  
Mathematical Expectation ◽  
Point Of View ◽  
Small Range ◽  
Computational Point ◽  
Wide Range ◽  
Bijective Function ◽  
The Difference ◽  
Element Base ◽  
Selection Of

The construction and selection of a suitable bijective function, that is, substitution, is now becoming an important applied task, particularly for building block encryption systems. Many articles have suggested using different approaches to determining the quality of substitution, but most of them are highly computationally complex. The solution of this problem will significantly expand the range of methods for constructing and analyzing scheme in information protection systems. The purpose of research is to find easily measurable characteristics of substitutions, allowing to evaluate their quality, and also measures of the proximity of a particular substitutions to a random one, or its distance from it. For this purpose, several characteristics were proposed in this work: difference and polynomial, and their mathematical expectation was found, as well as variance for the difference characteristic. This allows us to make a conclusion about its quality by comparing the result of calculating the characteristic for a particular substitution with the calculated mathematical expectation. From a computational point of view, the thesises of the article are of exceptional interest due to the simplicity of the algorithm for quantifying the quality of bijective function substitutions. By its nature, the operation of calculating the difference characteristic carries out a simple summation of integer terms in a fixed and small range. Such an operation, both in the modern and in the prospective element base, is embedded in the logic of a wide range of functional elements, especially when implementing computational actions in the optical range, or on other carriers related to the field of nanotechnology.

Spatial Autocorrelation in the Study of Neighbourhoods towards Smart Cities: Empirical Evidence from Kerman, Iran

2012 ◽  
Vol 9 (2) ◽  
pp. 1
Author(s):  
Asra Hosseini
Keyword(s):  
Spatial Autocorrelation ◽  
Urban Areas ◽  
Smart Cities ◽  
Moran’S I ◽  
Moran's I ◽  
Urban Planner ◽  
Universal Feature ◽  
Autocorrelation Method ◽  
Selection Of

From earliest cities to the present, spatial division into residential zones and neighbourhoods is the universal feature of urban areas. This study explored issue of measuring neighbourhoods through spatial autocorrelation method based on Moran's I index in respect of achieving to best neighbourhoods' model for forming cities smarter. The research carried out by selection of 35 neighbourhoods only within central part of traditional city of Kerman in Iran. The results illustrate, 75% of neighbourhoods' area in the inner city of Kerman had clustered pattern, and it shows reduction in Moran's index is associated with disproportional distribution of density and increasing in Moran's I and Z-score have monotonic relation with more dense areas and clustered pattern. It may be more efficient for urban planner to focus on spatial autocorrelation to foster neighbourhood cohesion rather than emphasis on suburban area. It is recommended characteristics of historic neighbourhoods can be successfully linked to redevelopment plans toward making city smarter, and also people's quality of life can be related to the way that neighbourhoods' patterns are defined. 

Spatial Autocorrelation in the Study of Neighbourhoods towards Smart Cities: Empirical Evidence from Kerman, Iran

2012 ◽  
Vol 9 (2) ◽  
pp. 1
Author(s):  
Asra Hosseini
Keyword(s):  
Spatial Autocorrelation ◽  
Smart Cities ◽  
Moran’S I ◽  
Moran's I ◽  
Urban Planner ◽  
Universal Feature ◽  
Autocorrelation Method ◽  
Selection Of ◽  
Monotonic Relation

From earliest cities to the present, spatial division into residential zones and neighbourhoods is the universal feature ofurban areas. This study explored issue ofmeasuring neighbourhoods through spatial autocorrelation method based on Moran's I index in respect of achieving to best neighbourhoods' model for forming cities smarter. The research carried out by selection of 35 neighbourhoods only within central part of traditional city of Kerman in Iran. The results illustrate, 75% ofneighbourhoods, area in the inner city of Kerman had clustered pattern, and it shows reduction in Moran's index is associated with disproportional distribution of density and increasing in Moran's I and Z-score have monotonic relation with more dense areas and clustered pattern. It may be more efficient for urban planner to focus on spatial autocorrelation to foster neighbourhood cohesion rather than emphasis on suburban area. It is recommended characteristics of historic neighbourhoods can be successfully linked to redevelopment plans toward making city smarter, and also people's quality of life can be related to the way that neighbourhoods' patterns are defined.

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