scholarly journals Large-scale quality assessment of prokaryotic genomes with metashot/prok-quality

F1000Research ◽  
2021 ◽  
Vol 10 ◽  
pp. 822
Author(s):  
Davide Albanese ◽  
Claudio Donati
Keyword(s):  
Quality Assessment ◽  
Large Scale ◽  
Metagenomic Sequencing ◽  
Link Type ◽  
Archaeal Species ◽  
Prokaryotic Genomes ◽  
Genomic Characterization ◽  
Computational Workflow ◽  
Quality Tool

Metagenomic sequencing allows large-scale identification and genomic characterization. Binning is the process of recovering genomes from complex mixtures of sequence fragments (metagenome contigs) of unknown bacteria and archaeal species. Assessing the quality of genomes recovered from metagenomes requires the use of complex pipelines involving many independent steps, often difficult to reproduce and maintain. A comprehensive, automated and easy-to-use computational workflow for the quality assessment of draft prokaryotic genomes, based on container technology, would greatly improve reproducibility and reusability of published results. We present metashot/prok-quality, a container-enabled Nextflow pipeline for quality assessment and genome dereplication. The metashot/prok-quality tool produces genome quality reports that are compliant with the Minimum Information about a Metagenome-Assembled Genome (MIMAG) standard, and can run out-of-the-box on any platform that supports Nextflow, Docker or Singularity, including computing clusters or batch infrastructures in the cloud. metashot/prok-quality is part of the metashot collection of analysis pipelines. Workflow and documentation are available under GPL3 licence on GitHub.

scholarly journals A REVIEW ON SPATIAL QUALITY ASSESSMENT METHODS FOR EVALUATION OF PAN-SHARPENED SATELLITE IMAGERY

2019 ◽  
Vol XLII-4/W18 ◽  
pp. 255-261
Author(s):  
F. Dadras Javan ◽  
F. Samadzadegan ◽  
S. Mehravar ◽  
A. Toosi
Keyword(s):  
Remote Sensing ◽  
Quality Assessment ◽  
Satellite Imagery ◽  
Urban Areas ◽  
Large Scale ◽  
Spatial Distortion ◽  
Sensing Applications ◽  
Fused Image ◽  
Spatial Quality

Abstract. Nowadays, high-resolution fused satellite imagery is widely used in multiple remote sensing applications. Although the spectral quality of pan-sharpened images plays an important role in many applications, spatial quality becomes more important in numerous cases. The high spatial quality of the fused image is essential for extraction, identification and reconstruction of significant image objects, and will result in producing high-quality large scale maps especially in the urban areas. This paper introduces the most sensitive and effective methods in detecting the spatial distortion of fused images by implementing a number of spatial quality assessment indices that are utilized in the field of remote sensing and image processing. In this regard, in order to recognize the ability of quality assessment indices for detecting the spatial distortion quantity of fused images, input images of the fusion process are affected by some intentional spatial distortions based on non-registration error. The capabilities of the investigated metrics are evaluated on four different fused images derived from Ikonos and WorldView-2 initial images. Achieved results obviously explicate that two methods namely Edge Variance Distortion and the spatial component of QNR metric called Ds are more sensitive and responsive to the imported errors.

scholarly journals METHODOLOGICAL TOOLS FOR THE IMPLEMENTATION OF INFORMATION TECHNOLOGY FOR EXPERT ASSESSMENT OF THE QUALITY OF HEAVY AUTOMOBILE EQUIPMENT IN THE PROCESS OF ITS EXPLOITATION

2021 ◽  
pp. 69-77
Author(s):  
Volodymyr Rudnytskyi ◽  
Amineh Hadi
Keyword(s):  
Information Technology ◽  
Quality Assessment ◽  
Large Scale ◽  
System Analysis ◽  
Fuzzy Mathematics ◽  
Expert Assessment ◽  
Comprehensive Model ◽  
Infrastructure Projects ◽  
Heavy Vehicles

Subject matter. Justification of the choice of a model range of heavy vehicles when organizing purchases in the framework of large-scale infrastructure projects. Goal. Increasing the efficiency of the process of determining the model range of heavy automobile equipment, in terms of its operation, at the stage of initiating large-scale infrastructure projects, by creating a special methodological approach, and on its basis - an appropriate information technology for decision support. Tasks. To develop a complex fuzzy model for assessing the quality of heavy automobile equipment during its operation. To propose a method for collective expert assessment of the quality of heavy automobile equipment during its operation. To develop an applied information technology to support decision-making on the formation of a model range of purchased heavy vehicles. Methods. System analysis – in the development of a comprehensive model of the quality of heavy automotive equipment; fuzzy mathematics – to ensure the process of fuzzy assessment by experts of the quality of heavy automobile equipment during its operation; expertology – when creating a method for forming a generalized quality assessment by means of collective expert assessment; software engineering – when creating applied information technology for collective expert assessment of the quality of heavy automobile equipment. Results. An approach to the creation of a number of applied information technologies for complex expert assessment of the quality of operation of a wide class of vehicles using the example of heavy automobile equipment. Conclusions. A comprehensive model has been developed for assessing the quality of heavy automobile equipment, at the stage of its operation, using the principles and approaches that are generally accepted in system analysis. The method of presentation and further implementation of a complex quality assessment model by means of fuzzy mathematics, which makes it possible to increase the efficiency of expert assessment, is described. A method for forming a team of experts is proposed, which implements the selection of an expert from several applicants, while taking into account the communication capabilities of individual members of the team of experts. The applied information technology for complex assessment of the quality of heavy automobile equipment in the aspect of its operation is described, in order to justify the choice of a model range for the acquisition of this equipment in the implementation of large-scale infrastructure projects.

scholarly journals Blue poo: impact of gut transit time on the gut microbiome using a novel marker

Gut ◽  
2021 ◽  
pp. gutjnl-2020-323877
Author(s):  
Francesco Asnicar ◽  
Emily R Leeming ◽  
Eirini Dimidi ◽  
Mohsen Mazidi ◽  
Paul Franks ◽  
...  
Keyword(s):  
Transit Time ◽  
Gut Microbiome ◽  
Large Scale ◽  
Characteristic Curve ◽  
Stool Consistency ◽  
Cardiometabolic Health ◽  
Blue Dye ◽  
Metagenomic Sequencing ◽  
Clinical Trial Registry ◽  
Link Type

Background and aimsGut transit time is a key modulator of host–microbiome interactions, yet this is often overlooked, partly because reliable methods are typically expensive or burdensome. The aim of this single-arm, single-blinded intervention study is to assess (1) the relationship between gut transit time and the human gut microbiome, and (2) the utility of the ‘blue dye’ method as an inexpensive and scalable technique to measure transit time.MethodsWe assessed interactions between the taxonomic and functional potential profiles of the gut microbiome (profiled via shotgun metagenomic sequencing), gut transit time (measured via the blue dye method), cardiometabolic health and diet in 863 healthy individuals from the PREDICT 1 study.ResultsWe found that gut microbiome taxonomic composition can accurately discriminate between gut transit time classes (0.82 area under the receiver operating characteristic curve) and longer gut transit time is linked with specific microbial species such as Akkermansia muciniphila, Bacteroides spp and Alistipes spp (false discovery rate-adjusted p values <0.01). The blue dye measure of gut transit time had the strongest association with the gut microbiome over typical transit time proxies such as stool consistency and frequency.ConclusionsGut transit time, measured via the blue dye method, is a more informative marker of gut microbiome function than traditional measures of stool consistency and frequency. The blue dye method can be applied in large-scale epidemiological studies to advance diet-microbiome-health research. Clinical trial registry website https://clinicaltrials.gov/ct2/show/NCT03479866 and trial number NCT03479866.

scholarly journals Quality of top webpages providing abortion pill information for Google searches in the USA: An evidence-based webpage quality assessment

PLoS ONE ◽  
2021 ◽  
Vol 16 (1) ◽  
pp. e0240664
Author(s):  
Elizabeth Pleasants ◽  
Sylvia Guendelman ◽  
Karen Weidert ◽  
Ndola Prata
Keyword(s):  
Quality Assessment ◽  
Assessment Tool ◽  
Pregnancy Termination ◽  
The United States ◽  
Evidence Based ◽  
Online Information ◽  
Search Results ◽  
Link Type ◽  
Google Search

Background In the United States, the internet is widely used to seek health information. Despite an estimated 18 million Google searches on abortion per year and the demonstrated importance of the abortion pill as an option for pregnancy termination, the top webpage search results for abortion pill searches, as well as the content and quality of those webpages, are not well understood. Methods We used Google’s Custom Search Application Programming Interface (API) to identify the top 10 webpages presented for “abortion pill” searches on August 06, 2018. We developed a comprehensive, evidence-based Family Planning Webpage Quality Assessment Tool (FPWQAT), which was used to assess webpage quality for the five top webpages presenting text-based educational content. Results Of the top webpages for “abortion pill” searches, a plannedparenthood.com page was the top result and scored highest on our assessment (81%), providing high-quality and useable information. The other four webpages, a Wikipedia.com page and three anti-abortion information webpages, scored much lower on our assessment (14%-43%). These four webpages had lower quality of information in less useable formats. The anti-abortion pages also presented a variety of disinformation about the abortion pill. Conclusions Both the lack of accurate clinical content on the majority of top webpages and the concerning disinformation they contained raise concerns about the quality of online abortion pill information, while underlining challenges posed by Google search results to informed choice for consumers. Healthcare providers and consumers must be informed of online abortion pill content that is not based in current clinical evidence, while advocates and policymakers should push for online information that is credible and useable. These changes are imperative given the importance of sound abortion pill information for reproductive decision-making at a time when in-person abortion services are further challenged in the US.

Assessment of quality of life in patients with the effects of transient ischemic stroke

2016 ◽  
pp. 37-39
Author(s):  
A. Babirad
Keyword(s):  
Quality Of Life ◽  
Ischemic Stroke ◽  
Large Scale ◽  
Cerebrovascular Diseases ◽  
Control Measures ◽  
Sociological Research ◽  
Cerebrovascular Events ◽  
Sf 36 ◽  
Angioplasty And Stenting

Cerebrovascular diseases are a problem of the world today, and according to the forecast, the problem of the near future arises. The main risk factors for the development of ischemic disorders of the cerebral circulation include oblique and aging, arterial hypertension, smoking, diabetes mellitus and heart disease. An effective strategy for the prevention of cerebrovascular events is based on the implementation of large-scale risk control measures, including the use of antiagregant and anticoagulant therapy, invasive interventions such as atheromectomy, angioplasty and stenting. In this connection, the efforts of neurologists, cardiologists, angiosurgery, endocrinologists and other specialists are the basis for achieving an acceptable clinical outcome. A review of the SF-36 method for assessing the quality of life in patients with the effects of transient ischemic stroke is presented. The assessment of quality of life is recognized in world medical practice and research, an indicator that is also used to assess the quality of the health system and in general sociological research.

Expert System for Quality Assessment of Electronic Book Exhibitions

2013 ◽  
pp. 32-39
Author(s):  
Svetlana V. Savkina
Keyword(s):  
Expert System ◽  
Quality Assessment ◽  
Electronic Book ◽  
Electronic Books ◽  
Comparison Of The Results

The article presents the results of testing the complex methodology of assessment of quality of electronic books exhibitions (EBE). The author describes the project of the expert system, allowing to implement the EBE assessment without the experts’ participation. There is given the comparison of the results of assessments, carried out by experts and by the expert system.

Quality of cytogenetic investigations: problems and ways for improvement

2020 ◽  
pp. 22-24
Author(s):  
В.Г. Антоненко ◽  
Н.В. Шилова ◽  
Е.Н. Лукаш ◽  
Э.Р. Бабкеева ◽  
В.Н. Малахов
Keyword(s):  
Quality Assessment ◽  
Russian Federation ◽  
Chromosomal Analysis ◽  
Common Causes

Представлены результаты экспертной оценки качества цитогенетических исследований в лабораториях РФ в системе межлабораторных сличительных испытаний «ФСВОК» в 2018-2019 гг. Обсуждаются наиболее частые причины неудовлетворительных результатов экспертизы и возможные пути улучшения качества цитогенетических исследований. We report the results of quality assessment for preparation of cytogenetic slides and chromosomal analysis in the laboratories of Russian Federation in the system of the interlaboratory comparative examinations “FSVOK” in 2018-2019. Common causes of poor results of assessment and the ways for improvement of quality for cytogenetic investigations are discussed.

ABOUT NECESSITY OF MATHEMATICAL MODELING OF THE BUSINESS PROCESS OF COST ESTIMATE CALCULATIONS IN THE CONSTRUCTION OF OIL AND GAS FACILITIES

2017 ◽  
pp. 139-145
Author(s):  
R. I. Hamidullin ◽  
L. B. Senkevich
Keyword(s):  
Mathematical Modeling ◽  
Quality Assessment ◽  
Business Process ◽  
Oil And Gas ◽  
Oil And Gas Industry ◽  
Gas Industry ◽  
Construction Organizations ◽  
The Cost ◽  
Cost Of Construction

A study of the quality of the development of estimate documentation on the cost of construction at all stages of the implementation of large projects in the oil and gas industry is conducted. The main problems that arise in construction organizations are indicated. The analysis of the choice of the perfect methodology of mathematical modeling of the investigated business process for improving the activity of budget calculations, conducting quality assessment of estimates and criteria for automation of design estimates is performed.

Model and Method for Contributor’s Quality Assessment in Community Image Tagging Systems

2018 ◽  
pp. 45-51
Author(s):  
A. V. Ponomarev
Keyword(s):  
Large Scale ◽  
Wide Spectrum ◽  
Preference Relation ◽  
Pairwise Comparison ◽  
Ground Truth ◽  
Comparison Method ◽  
Characteristic Matrix ◽  
Image Tagging ◽  
Proposed Model

Introduction: Large-scale human-computer systems involving people of various skills and motivation into the information processing process are currently used in a wide spectrum of applications. An acute problem in such systems is assessing the expected quality of each contributor; for example, in order to penalize incompetent or inaccurate ones and to promote diligent ones.Purpose: To develop a method of assessing the expected contributor’s quality in community tagging systems. This method should only use generally unreliable and incomplete information provided by contributors (with ground truth tags unknown).Results:A mathematical model is proposed for community image tagging (including the model of a contributor), along with a method of assessing the expected contributor’s quality. The method is based on comparing tag sets provided by different contributors for the same images, being a modification of pairwise comparison method with preference relation replaced by a special domination characteristic. Expected contributors’ quality is evaluated as a positive eigenvector of a pairwise domination characteristic matrix. Community tagging simulation has confirmed that the proposed method allows you to adequately estimate the expected quality of community tagging system contributors (provided that the contributors' behavior fits the proposed model).Practical relevance: The obtained results can be used in the development of systems based on coordinated efforts of community (primarily, community tagging systems). 

Translation and Validation of the Thai Version of the Wisconsin Quality of Life Questionnaire (TH WISQoL) for Kidney Stone Patients

2020 ◽  
Vol 103 (11) ◽  
pp. 1194-1199
Keyword(s):  
Quality Of Life ◽  
Internal Consistency ◽  
Kidney Stone ◽  
Convergent Validity ◽  
Large Scale ◽  
Short Form ◽  
Outcome Measurement ◽  
Life Questionnaire ◽  
Sf 36

Objective: To develop and validate a Thai version of the Wisconsin Quality of Life (TH WISQoL) Questionnaire. Materials and Methods: The authors developed the TH WISQoL Questionnaire based on a standard multi-step process. Subsequently, the authors recruited patients with kidney stone and requested them to complete the TH WISQoL and a validated Thai version of the 36-Item Short Form Survey (TH SF-36). The authors calculated the internal consistency and interdomain correlation of TH WISQoL and compared the convergent validity between the two instruments. Results: Thirty kidney stone patients completed the TH WISQoL and the TH SF-36. The TH WISQoL showed acceptable internal consistency for all domains (Cronbach’s alpha 0.768 to 0.909). Interdomain correlation was high for most domains (r=0.698 to 0.779), except for the correlation between Vitality and Disease domains, which showed a moderate correlation (r=0.575). For convergent validity, TH WISQoL demonstrated a good overall correlation to TH SF-36, (r=0.796, p<0.05). Conclusion: The TH WISQoL is valid and reliable for evaluating the quality of life of Thai patients with kidney stone. A further large-scale multi-center study is warranted to confirm its applicability in Thailand. Keywords: Quality of life, Kidney stone, Validation, Outcome measurement

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