scholarly journals Bringing radiomics into a multi-omics framework for a comprehensive genotype–phenotype characterization of oncological diseases

2019 ◽  
Vol 17 (1) ◽  
Author(s):  
Mario Zanfardino ◽  
Monica Franzese ◽  
Katia Pane ◽  
Carlo Cavaliere ◽  
Serena Monti ◽  
...  
Keyword(s):  
Data Integration ◽  
Data Structures ◽  
R Package ◽  
Biological Information ◽  
Phenotype Definition ◽  
Current State ◽  
Oncological Diseases ◽  
Cancer Phenotype

Abstract Genomic and radiomic data integration, namely radiogenomics, can provide meaningful knowledge in cancer diagnosis, prognosis and treatment. Despite several data structures based on multi-layer architecture proposed to combine multi-omic biological information, none of these has been designed and assessed to include radiomic data as well. To meet this need, we propose to use the MultiAssayExperiment (MAE), an R package that provides data structures and methods for manipulating and integrating multi-assay experiments, as a suitable tool to manage radiogenomic experiment data. To this aim, we first examine the role of radiogenomics in cancer phenotype definition, then the current state of radiogenomics data integration in public repository and, finally, challenges and limitations of including radiomics in MAE, designing an extended framework and showing its application on a case study from the TCGA-TCIA archives. Radiomic and genomic data from 91 patients have been successfully integrated in a single MAE object, demonstrating the suitability of the MAE data structure as container of radiogenomic data.

scholarly journals GWENA: gene co-expression networks analysis and extended modules characterization in a single Bioconductor package

2021 ◽  
Vol 22 (1) ◽  
Author(s):  
Gwenaëlle G. Lemoine ◽  
Marie-Pier Scott-Boyer ◽  
Bathilde Ambroise ◽  
Olivier Périn ◽  
Arnaud Droit
Keyword(s):  
Muscle Development ◽  
R Package ◽  
Topological Information ◽  
Old Patients ◽  
Network Modules ◽  
Extended Analysis ◽  
Networks Analysis ◽  
Underlying Processes

Abstract Background Network-based analysis of gene expression through co-expression networks can be used to investigate modular relationships occurring between genes performing different biological functions. An extended description of each of the network modules is therefore a critical step to understand the underlying processes contributing to a disease or a phenotype. Biological integration, topology study and conditions comparison (e.g. wild vs mutant) are the main methods to do so, but to date no tool combines them all into a single pipeline. Results Here we present GWENA, a new R package that integrates gene co-expression network construction and whole characterization of the detected modules through gene set enrichment, phenotypic association, hub genes detection, topological metric computation, and differential co-expression. To demonstrate its performance, we applied GWENA on two skeletal muscle datasets from young and old patients of GTEx study. Remarkably, we prioritized a gene whose involvement was unknown in the muscle development and growth. Moreover, new insights on the variations in patterns of co-expression were identified. The known phenomena of connectivity loss associated with aging was found coupled to a global reorganization of the relationships leading to expression of known aging related functions. Conclusion GWENA is an R package available through Bioconductor (https://bioconductor.org/packages/release/bioc/html/GWENA.html) that has been developed to perform extended analysis of gene co-expression networks. Thanks to biological and topological information as well as differential co-expression, the package helps to dissect the role of genes relationships in diseases conditions or targeted phenotypes. GWENA goes beyond existing packages that perform co-expression analysis by including new tools to fully characterize modules, such as differential co-expression, additional enrichment databases, and network visualization.

The growing role of structural mass spectrometry in the discovery and development of therapeutic antibodies

The Analyst ◽  
2018 ◽  
Vol 143 (11) ◽  
pp. 2459-2468 ◽  
Author(s):  
Yuwei Tian ◽  
Brandon T. Ruotolo
Keyword(s):  
Mass Spectrometry ◽  
State Of The Art ◽  
Therapeutic Antibodies ◽  
Critical Importance ◽  
Current State ◽  
Measurement Science ◽  
Structural Mass Spectrometry ◽  
Structural Mass

The comprehensive structural characterization of therapeutic antibodies is of critical importance for the successful discovery and development of such biopharmaceuticals, yet poses many challenges to modern measurement science. Here, we review the current state-of-the-art mass spectrometry technologies focusing on the characterization of antibody-based therapeutics.

scholarly journals ProMetIS, deep phenotyping of mouse models by combined proteomics and metabolomics analysis

2021 ◽  
Vol 8 (1) ◽  
Author(s):  
Alyssa Imbert ◽  
Magali Rompais ◽  
Mohammed Selloum ◽  
Florence Castelli ◽  
Emmanuelle Mouton-Barbosa ◽  
...  
Keyword(s):  
Mouse Models ◽  
Physiological Role ◽  
R Package ◽  
Level Data ◽  
Molecular Information ◽  
Number Of Individuals ◽  
Deep Phenotyping ◽  
Omics Data Integration

AbstractGenes are pleiotropic and getting a better knowledge of their function requires a comprehensive characterization of their mutants. Here, we generated multi-level data combining phenomic, proteomic and metabolomic acquisitions from plasma and liver tissues of two C57BL/6 N mouse models lacking the Lat (linker for activation of T cells) and the Mx2 (MX dynamin-like GTPase 2) genes, respectively. Our dataset consists of 9 assays (1 preclinical, 2 proteomics and 6 metabolomics) generated with a fully non-targeted and standardized approach. The data and processing code are publicly available in the ProMetIS R package to ensure accessibility, interoperability, and reusability. The dataset thus provides unique molecular information about the physiological role of the Lat and Mx2 genes. Furthermore, the protocols described herein can be easily extended to a larger number of individuals and tissues. Finally, this resource will be of great interest to develop new bioinformatic and biostatistic methods for multi-omics data integration.

The Search for a Survival Value of Music

1984 ◽  
Vol 1 (3) ◽  
pp. 350-356 ◽  
Author(s):  
Juan G. Roederer
Keyword(s):  
Music Perception ◽  
Biological Information ◽  
Speech Communication ◽  
Emotional States ◽  
Short Term ◽  
Current State ◽  
Basic Issue ◽  
Complete Detachment ◽  
The Brain

A most basic issue in the study of music perception is the question of why humans are motivated to pay attention to, or create, musical messages, and why they respond emotionally to them, when such messages seem to convey no real-time relevant biological information as do speech, animal utterances, and environmental sounds. Expanding on previous work (Roederer, 1979,1982) three possibly concurrent factors will be examined: (1) The inborn motivation to train language-handling networks of the brain in the processing of simple, organized sound patterns as a prelude to the acquisition of language; (2) The need to extract the information contained in the "musical" components of speech; (3) The value of music as a means of transmitting information on emotional states and its effect in congregating and behaviorally equalizing masses of people. In the discussion, special attention will be paid to the role of motivation and emotion in auditory perception, to the fact that in humans limbic system functions can be activated by internally evoked images in complete detachment from the current state of environment and organism, and to the existence of two distinct strategies of cerebral information processing, namely short-term time sequencing, as required in speech communication and thinking, and holistic pattern recognition, as required in music perception.

Directions of improving legal education

2020 ◽  
Vol 22 (1) ◽  
pp. 85-91
Author(s):  
OLEG V. ZAITSEV ◽  
◽  
DENIS V. NOVAK ◽  
Keyword(s):  
Legal Education ◽  
Current State ◽  
Foreign Law ◽  
Wide Range ◽  
History Of ◽  
Market Transformation ◽  
State Accreditation

The article is a continuation of the expert discussion ‘Legal education and the labor market. Transformation or stagnation in the digital economy’, uniting the leaders of leading Russian and foreign law schools, the scientific, pedagogical community at the Gaidar Forum 2020. The authors consider a wide range of issues related to the characterization of the current state of legal education, its integration into the Bologna system, noting the importance of the application of traditional methods and means of teaching law, taking into account modern realities. Particular attention is paid to the traditions of teaching law laid down by Roman lawyers, the history of the formation and development of domestic jurisprudence, as well as modern discussions on a given topic, in which representatives of the scientific community and practical lawyers take part. The authors draw attention to issues related to the new content of curricula and new ways of regulating legal education. The topic of state accreditation of educational programs in the field of jurisprudence and the role of the Association of Russian Lawyers in this process also seems important. The analysis of the main features of modern law is carried out, necessitating the comprehensive improvement of modern legal education. As a possible measure of the quality of legal education, the introduction of a single exam for entering the profession is proposed.

Digital x-ray mapping of nanometer-size supported bimetallic catalysts

1988 ◽  
Vol 46 ◽  
pp. 530-531
Author(s):  
L. T. Germinario
Keyword(s):  
Background Radiation ◽  
Metal Cluster ◽  
Single Element ◽  
Beam Diameter ◽  
X Rays ◽  
X Ray ◽  
Major Interest ◽  
Induced Changes

Understanding the role of metal cluster composition in determining catalytic selectivity and activity is of major interest in heterogeneous catalysis. The electron microscope is well established as a powerful tool for ultrastructural and compositional characterization of support and catalyst. Because the spatial resolution of x-ray microanalysis is defined by the smallest beam diameter into which the required number of electrons can be focused, the dedicated STEM with FEG is the instrument of choice. The main sources of errors in energy dispersive x-ray analysis (EDS) are: (1) beam-induced changes in specimen composition, (2) specimen drift, (3) instrumental factors which produce background radiation, and (4) basic statistical limitations which result in the detection of a finite number of x-ray photons. Digital beam techniques have been described for supported single-element metal clusters with spatial resolutions of about 10 nm. However, the detection of spurious characteristic x-rays away from catalyst particles produced images requiring several image processing steps.

Consideraciones en torno a la reducción solipsista

1970 ◽  
Vol 11 ◽  
Author(s):  
Natalia Carolina Petrillo

ResumenEn el presente trabajo se intentará mostrar que la fenomenología no conduce a una postura solipsista. Para ello, se caracterizará en qué consiste el solipsismo. Luego, se intentará refutar a lo que se ha de llamar “solipsismo metafísico” y “solipsismo gnoseológico”, con el objetivo principal de poner de manifiesto el fundamento de motivación para la salida de la ficción solipsista.Palabras claves:Phenomenology – solipsim – empatía - HusserlAbstractWith the aim of showing that phenomenology does not lead in solipsism, I will first attempt a characterization of it. Then, I will attempt a refutation of the so-called “metaphysical” and “epistemological” solipsisms. Finally, the nature and role of Husserl´s solipsistic fiction is examined, and the grounds that motivate the overcoming of this standpoint are disclosed.key wordsFenomenología – solipsismo - empathy – Husserl

ANALYSIS OF APPLICATION OF BLOCKCHAIN TECHNOLOGIES FOR THE BANKING SECTOR

2017 ◽  
Author(s):  
Svitlana Ilkovych ◽  
◽  
Maryna Korol ◽  
Keyword(s):  
Banking Sector ◽  
Blockchain Technology ◽  
Current State ◽  
Global Banking ◽  
Banking Institutions ◽  
Pros And Cons ◽  
Further Development

The article considers the essence of blockchain technology and the possibility of its application in the banking sector. The current state of development and application of blockchain technologies in various industries is analyzed. The pros and cons of using blockchain technologies for the banking sector are identified. Emphasis is placed on the role of blockchain technologies in the further development of the banking sector. The most promising directions of development of this technology are considered. Particular attention is paid to examples of the use of blockchain technology by global banking institutions.

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