scholarly journals What is Normalization? The Strategies Employed in Top-Down and Bottom-Up Proteome Analysis Workflows

Proteomes ◽  
2019 ◽  
Vol 7 (3) ◽  
pp. 29 ◽  
Author(s):  
Matthew B. O’Rourke ◽  
Stephanie E. L. Town ◽  
Penelope V. Dalla ◽  
Fiona Bicknell ◽  
Naomi Koh Belic ◽  
...  
Keyword(s):  
Normal State ◽  
Proteome Analysis ◽  
Biological Condition ◽  
Sample Handling ◽  
Analysis Process ◽  
Starting Point ◽  
Wide Range ◽  
Experimental Process ◽  
Definition Of ◽  
Accurate Quantification

The accurate quantification of changes in the abundance of proteins is one of the main applications of proteomics. The maintenance of accuracy can be affected by bias and error that can occur at many points in the experimental process, and normalization strategies are crucial to attempt to overcome this bias and return the sample to its regular biological condition, or normal state. Much work has been published on performing normalization on data post-acquisition with many algorithms and statistical processes available. However, there are many other sources of bias that can occur during experimental design and sample handling that are currently unaddressed. This article aims to cast light on the potential sources of bias and where normalization could be applied to return the sample to its normal state. Throughout we suggest solutions where possible but, in some cases, solutions are not available. Thus, we see this article as a starting point for discussion of the definition of and the issues surrounding the concept of normalization as it applies to the proteomic analysis of biological samples. Specifically, we discuss a wide range of different normalization techniques that can occur at each stage of the sample preparation and analysis process.

scholarly journals АНАЛІЗ СУЧАСНОГО СТАНУ РОЗВИТКУ БЕЗПІЛОТНИХ ЛІТАЛЬНИХ МІКРОАПАРАТІВ МУЛЬТИКОПТЕРНОГО ТИПУ

2021 ◽  
pp. 125-134
Author(s):  
О. Г. Гребеніков
Keyword(s):  
Unmanned Aerial Vehicles ◽  
Statistical Data ◽  
Weather Conditions ◽  
Future Research ◽  
Prototype Model ◽  
Aerial Vehicles ◽  
Starting Point ◽  
Wide Range ◽  
Range Of Functions ◽  
Definition Of

The development of unmanned aerial vehicles is of great interest to both the largest aircraft companies and design enthusiasts, and among the total volume of developments, the volume of multicopter unmanned aerial vehicles occupies one of the leading positions. In this regard, the analysis of existing developments and the definition of future research in this direction is relevant. Multi-helicopter drones have a wide range of functions in both military and civilian use.The paper collects and analyzes statistical data of micro-unmanned aerial vehicles of the multicopter type to determine the achievements in the field of design of micro-unmanned aerial vehicles (UAVs). The current classification of UAVs is considered; as a result of the analysis of statistical data its expansion is offered. The take-off and mass characteristics of the micro UAV are described. The tables showing the existing UAVs are given. In addition, the flight characteristics, aerodynamic schemes and type of engine that are most rationally suited for micro-unmanned aerial vehicles according to their purpose and class are determined.Based on the obtained data, a prototype model of a micro-UAV with improved characteristics was built. The model successfully completed all tasks. This indicates that the new UAV "Fear-1" is a successful project and it has the ability to remotely control by phone or any other equipment designed for this purpose. In addition, the designed device can additionally hang in the specified coordinates."Fear-1" confidently performs tasks in automatic mode, as well as independently decides to return to the starting point of takeoff, if: there is a loss of communication, the battery level has reached a certain level, the UAV has completed its task or used more miles -amperes than specified by the output parameters. The drone has the ability to fly in "Follow me" mode on the selected GPS transmitter. The quadcopter was tested in difficult weather conditions, when the wind force reached 8 points (about 22 m / s). Noise immunity tests were also performed in the industrial frequency range (from 2.4 GHz to 5.8 GHz).

scholarly journals Jointly Defining Cell Types from Multiple Single-Cell Datasets Using LIGER

2020 ◽  
Author(s):  
Jialin Liu ◽  
Chao Gao ◽  
Joshua Sodicoff ◽  
Velina Kozareva ◽  
Evan Z. Macosko ◽  
...  
Keyword(s):  
Single Cell ◽  
Nonnegative Matrix ◽  
Cell Types ◽  
Data Types ◽  
Sequencing Technologies ◽  
Analysis Process ◽  
Wide Range ◽  
Dataset Size ◽  
Single Nucleus ◽  
Definition Of

AbstractHigh-throughput single-cell sequencing technologies hold tremendous potential for defining cell types in an unbiased fashion using gene expression and epigenomic state. A key challenge in realizing this potential is integrating single-cell datasets from multiple protocols, biological contexts, and data modalities into a joint definition of cellular identity. We previously developed an approach called Linked Inference of Genomic Experimental Relationships (LIGER) that uses integrative nonnegative matrix factorization to address this challenge. Here, we provide a step-by-step protocol for using LIGER to jointly define cell types from multiple single-cell datasets. The main steps of the protocol include data preprocessing and normalization, joint factorization, quantile normalization and joint clustering, and visualization. We describe how to jointly define cell types from single-cell RNA-seq and single-nucleus ATAC-seq data, but similar steps apply across a wide range of other settings and data types, including cross-species analysis, single-nucleus DNA methylation, and spatial transcriptomics. Our protocol contains examples of expected results, describes common pitfalls, and relies only on our freely available, open-source R implementation of LIGER. We also provide Rmarkdown tutorials showing the outputs from each individual code segment. The analysis process can be performed in 1 - 4 h depending on dataset size and assumes no specialized bioinformatics training.

Typologization of security regulation

2020 ◽  
pp. 20-27
Author(s):  
Denis Tikhomirov
Keyword(s):  
Social Relations ◽  
Scientific Literature ◽  
Legal Regulation ◽  
Procedural Understanding ◽  
Limited Ability ◽  
Methodological Basis ◽  
Wide Range ◽  
The Subject ◽  
Definition Of ◽  
Legal Understanding

The purpose of the article is to typologize terminological definitions of security, to find out the general, to identify the originality of their interpretations depending on the subject of legal regulation. The methodological basis of the study is the methods that made it possible to obtain valid conclusions, in particular, the method of comparison, through which it became possible to correlate different interpretations of the term "security"; method of hermeneutics, which allowed to elaborate texts of normative legal acts of Ukraine, method of typologization, which made it possible to create typologization groups of variants of understanding of the term "security". Scientific novelty. The article analyzes the understanding of the term "security" in various regulatory acts in force in Ukraine. Typological groups were understood to understand the term "security". Conclusions. The analysis of the legal material makes it possible to confirm that the issues of security are within the scope of both legislative regulation and various specialized by-laws. However, today there is no single conception on how to interpret security terminology. This is due both to the wide range of social relations that are the subject of legal regulation and to the relativity of the notion of security itself and the lack of coherence of views on its definition in legal acts and in the scientific literature. The multiplicity of definitions is explained by combinations of material and procedural understanding, static - dynamic, and conditioned by the peculiarities of a particular branch of legal regulation, limited ability to use methods of one or another branch, the inter-branch nature of some variations of security, etc. Separation, common and different in the definition of "security" can be used to further standardize, in fact, the regulatory legal understanding of security to more effectively implement the legal regulation of the security direction.

Holism, Chinese Medicine and Systems Ideologies: Rewriting the Past to Imagine the Future

2018 ◽  
Author(s):  
Volker Scheid
Keyword(s):  
Eighteenth Century ◽  
Chinese Medicine ◽  
Medical Humanities ◽  
Science And Technology Studies ◽  
Human Beings ◽  
The Past ◽  
Starting Point ◽  
The Us ◽  
Shared Objective ◽  
Definition Of

This chapter explores the articulations that have emerged over the last half century between various types of holism, Chinese medicine and systems biology. Given the discipline’s historical attachments to a definition of ‘medicine’ that rather narrowly refers to biomedicine as developed in Europe and the US from the eighteenth century onwards, the medical humanities are not the most obvious starting point for such an inquiry. At the same time, they do offer one advantage over neighbouring disciplines like medical history, anthropology or science and technology studies for someone like myself, a clinician as well as a historian and anthropologist: their strong commitment to the objective of facilitating better medical practice. This promise furthermore links to the wider project of critique, which, in Max Horkheimer’s definition of the term, aims at change and emancipation in order ‘to liberate human beings from the circumstances that enslave them’. If we take the critical medical humanities as explicitly affirming this shared objective and responsibility, extending the discipline’s traditional gaze is not a burden but becomes, in fact, an obligation.

Music after the Fall

2017 ◽  
Author(s):  
Tim Rutherford-Johnson
Keyword(s):  
New Media ◽  
Contemporary Music ◽  
The United States ◽  
Art Music ◽  
Sound Art ◽  
Musical Composition ◽  
Western Art ◽  
Wide Range ◽  
Definition Of ◽  
The Cold War

By the start of the 21st century many of the foundations of postwar culture had disappeared: Europe had been rebuilt and, as the EU, had become one of the world’s largest economies; the United States’ claim to global dominance was threatened; and the postwar social democratic consensus was being replaced by market-led neoliberalism. Most importantly of all, the Cold War was over, and the World Wide Web had been born. Music After The Fall considers contemporary musical composition against this changed backdrop, placing it in the context of globalization, digitization, and new media. Drawing on theories from the other arts, in particular art and architecture, it expands the definition of Western art music to include forms of composition, experimental music, sound art, and crossover work from across the spectrum, inside and beyond the concert hall. Each chapter considers a wide range of composers, performers, works, and institutions are considered critically to build up a broad and rich picture of the new music ecosystem, from North American string quartets to Lebanese improvisers, from South American electroacoustic studios to pianos in the Australian outback. A new approach to the study of contemporary music is developed that relies less on taxonomies of style and technique, and more on the comparison of different responses to common themes, among them permission, fluidity, excess, and loss.

Discovery of Antibacterial Agents Inhibiting the Energy-Coupling Factor (ECF) Transporters by Structure-Based Virtual Screening

2020 ◽  
Author(s):  
Eleonora Diamanti ◽  
Inda Setyawati ◽  
Spyridon Bousis ◽  
leticia mojas ◽  
lotteke Swier ◽  
...  
Keyword(s):  
Virtual Screening ◽  
Antibacterial Agents ◽  
Antimicrobial Agents ◽  
Energy Coupling ◽  
Coupling Factor ◽  
Design Synthesis ◽  
Screening Design ◽  
Starting Point ◽  
Wide Range ◽  
Vitamin Uptake

Here, we report on the virtual screening, design, synthesis and structure–activity relationships (SARs) of the first class of selective, antibacterial agents against the energy-coupling factor (ECF) transporters. The ECF transporters are a family of transmembrane proteins involved in the uptake of vitamins in a wide range of bacteria. Inhibition of the activity of these proteins could reduce the viability of pathogens that depend on vitamin uptake. Because of their central role in the metabolism of bacteria and their absence in humans, ECF transporters are novel potential antimicrobial targets to tackle infection. The hit compound’s metabolic and plasma stability, the potency (20, MIC Streptococcus pneumoniae = 2 µg/mL), the absence of cytotoxicity and a lack of resistance development under the conditions tested here suggest that this scaffold may represent a promising starting point for the development of novel antimicrobial agents with an unprecedented mechanism of action.<br>

scholarly journals Size-adjusted aortic valve area: refining the definition of severe aortic stenosis

2020 ◽  
Author(s):  
Branka Vulesevic ◽  
Naozumi Kubota ◽  
Ian G Burwash ◽  
Claire Cimadevilla ◽  
Sarah Tubiana ◽  
...  
Keyword(s):  
Aortic Valve ◽  
Predictive Accuracy ◽  
Severe Aortic Stenosis ◽  
Aortic Valve Area ◽  
Obese Patients ◽  
Derivation Cohort ◽  
Wide Range ◽  
Definition Of ◽  
Diagnostic And Prognostic Value ◽  
Valve Area

Abstract Aims Severe aortic valve stenosis (AS) is defined by an aortic valve area (AVA) &lt;1 cm2 or an AVA indexed to body surface area (BSA) &lt;0.6 cm/m2, despite little evidence supporting the latter approach and important intrinsic limitations of BSA indexation. We hypothesized that AVA indexed to height (H) might be more applicable to a wide range of populations and body morphologies and might provide a better predictive accuracy. Methods and results In 1298 patients with degenerative AS and preserved ejection fraction from three different countries and continents (derivation cohort), we aimed to establish an AVA/H threshold that would be equivalent to 1.0 cm2 for defining severe AS. In a distinct prospective validation cohort of 395 patients, we compared the predictive accuracy of AVA/BSA and AVA/H. Correlations between AVA and AVA/BSA or AVA/H were excellent (all R2 &gt; 0.79) but greater with AVA/H. Regressions lines were markedly different in obese and non-obese patients with AVA/BSA (P &lt; 0.0001) but almost identical with AVA/H (P = 0.16). AVA/BSA values that corresponded to an AVA of 1.0 cm2 were markedly different in obese and non-obese patients (0.48 and 0.59 cm2/m2) but not with AVA/H (0.61 cm2/m for both). Agreement for the diagnosis of severe AS (AVA &lt; 1 cm2) was significantly higher with AVA/H than with AVA/BSA (P &lt; 0.05). Similar results were observed across the three countries. An AVA/H cut-off value of 0.6 cm2/m [HR = 8.2(5.6–12.1)] provided the best predictive value for the occurrence of AS-related events [absolute AVA of 1 cm2: HR = 7.3(5.0–10.7); AVA/BSA of 0.6 cm2/m2 HR = 6.7(4.4–10.0)]. Conclusion In a large multinational/multiracial cohort, AVA/H was better correlated with AVA than AVA/BSA and a cut-off value of 0.6 cm2/m provided a better diagnostic and prognostic value than 0.6 cm2/m2. Our results suggest that severe AS should be defined as an AVA &lt; 1 cm2 or an AVA/H &lt; 0.6 cm2/m rather than a BSA-indexed value of 0.6 cm2/m2.

scholarly journals Consumer Neuroscience Techniques in Advertising Research: A Bibliometric Citation Analysis

2021 ◽  
Vol 13 (3) ◽  
pp. 1589
Author(s):  
Juan Sánchez-Fernández ◽  
Luis-Alberto Casado-Aranda ◽  
Ana-Belén Bastidas-Manzano
Keyword(s):  
Self Report ◽  
Future Research ◽  
Complex Nature ◽  
Clear Understanding ◽  
Continuous Growth ◽  
Main Research ◽  
Consumer Neuroscience ◽  
Starting Point ◽  
Wide Range ◽  
Performance Analysis Tools

The limitations of self-report techniques (i.e., questionnaires or surveys) in measuring consumer response to advertising stimuli have necessitated more objective and accurate tools from the fields of neuroscience and psychology for the study of consumer behavior, resulting in the creation of consumer neuroscience. This recent marketing sub-field stems from a wide range of disciplines and applies multiple types of techniques to diverse advertising subdomains (e.g., advertising constructs, media elements, or prediction strategies). Due to its complex nature and continuous growth, this area of research calls for a clear understanding of its evolution, current scope, and potential domains in the field of advertising. Thus, this current research is among the first to apply a bibliometric approach to clarify the main research streams analyzing advertising persuasion using neuroimaging. Particularly, this paper combines a comprehensive review with performance analysis tools of 203 papers published between 1986 and 2019 in outlets indexed by the ISI Web of Science database. Our findings describe the research tools, journals, and themes that are worth considering in future research. The current study also provides an agenda for future research and therefore constitutes a starting point for advertising academics and professionals intending to use neuroimaging techniques.

Cubical Agda: A dependently typed programming language with univalence and higher inductive types

2021 ◽  
Vol 31 ◽  
Author(s):  
ANDREA VEZZOSI ◽  
ANDERS MÖRTBERG ◽  
ANDREAS ABEL
Keyword(s):  
Programming Language ◽  
Type Theory ◽  
Type Checking ◽  
Dependent Type Theory ◽  
Wide Range ◽  
General Schema ◽  
Direct Definition ◽  
Inductive Types ◽  
Definition Of ◽  
Cubical Type Theory

Abstract Proof assistants based on dependent type theory provide expressive languages for both programming and proving within the same system. However, all of the major implementations lack powerful extensionality principles for reasoning about equality, such as function and propositional extensionality. These principles are typically added axiomatically which disrupts the constructive properties of these systems. Cubical type theory provides a solution by giving computational meaning to Homotopy Type Theory and Univalent Foundations, in particular to the univalence axiom and higher inductive types (HITs). This paper describes an extension of the dependently typed functional programming language Agda with cubical primitives, making it into a full-blown proof assistant with native support for univalence and a general schema of HITs. These new primitives allow the direct definition of function and propositional extensionality as well as quotient types, all with computational content. Additionally, thanks also to copatterns, bisimilarity is equivalent to equality for coinductive types. The adoption of cubical type theory extends Agda with support for a wide range of extensionality principles, without sacrificing type checking and constructivity.

scholarly journals Definitions and Prevalence of Multimorbidity in Large Database Studies: A Scoping Review

2021 ◽  
Vol 18 (4) ◽  
pp. 1673
Author(s):  
Ying Pin Chua ◽  
Ying Xie ◽  
Poay Sian Sabrina Lee ◽  
Eng Sing Lee
Keyword(s):  
Scoping Review ◽  
Chronic Conditions ◽  
Meta Analysis ◽  
Epidemiological Studies ◽  
Cross Sectional ◽  
Coding Systems ◽  
Wide Range ◽  
Scoping Reviews ◽  
Retrospective Cohort Studies ◽  
Definition Of

Background: Multimorbidity presents a key challenge to healthcare systems globally. However, heterogeneity in the definition of multimorbidity and design of epidemiological studies results in difficulty in comparing multimorbidity studies. This scoping review aimed to describe multimorbidity prevalence in studies using large datasets and report the differences in multimorbidity definition and study design. Methods: We conducted a systematic search of MEDLINE, EMBASE, and CINAHL databases to identify large epidemiological studies on multimorbidity. We used the Preferred Reporting Items for Systematic Reviews and Meta-analysis Extension for Scoping Reviews (PRISMA-ScR) protocol for reporting the results. Results: Twenty articles were identified. We found two key definitions of multimorbidity: at least two (MM2+) or at least three (MM3+) chronic conditions. The prevalence of multimorbidity MM2+ ranged from 15.3% to 93.1%, and 11.8% to 89.7% in MM3+. The number of chronic conditions used by the articles ranged from 15 to 147, which were organized into 21 body system categories. There were seventeen cross-sectional studies and three retrospective cohort studies, and four diagnosis coding systems were used. Conclusions: We found a wide range in reported prevalence, definition, and conduct of multimorbidity studies. Obtaining consensus in these areas will facilitate better understanding of the magnitude and epidemiology of multimorbidity.

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