BRIEF REPORT | doi:10.20944/preprints202311.1305.v1
Subject: Computer Science And Mathematics, Other Keywords: artificial intelligence; patient management
Online: 21 November 2023 (10:00:01 CET)
Dementia is a major issue for healthcare systems worldwide, necessitating the development of creative and effective strategies for its management. This paper examines the use of Artificial Intelligence (AI) technologies in caring for and managing people with dementia. AI-driven solutions can improve diagnosis, personalize care, optimize medication management, and reduce the burden on caregivers. This paper discusses the implementation of an AI-based framework for creating videos related to people’s memories to support train-therapy or travel- therapy, a non-pharmacological intervention for Alzheimer’s disease patients
BRIEF REPORT | doi:10.20944/preprints202310.0289.v1
Subject: Computer Science And Mathematics, Mathematical And Computational Biology Keywords: Aging; Network Science
Online: 5 October 2023 (13:02:46 CEST)
Dyslipidemia (Dys) is a disease characterised by abnormally high levels of lipids in the 1 blood. It causes the deposits of lipids on the arterial wall, leading to the insurgence of atherosclerosis, 2 i.e. the increased thickness of arterial walls, which finally increases the risk of cardiovascular diseases. 3 Dyslipidemia is as comorbidity of Type 2 Diabetes Mellitus (T2DM). A set of genes has been associated 4 with dyslipidemia, but examining the regulation of such genes in age and sex is still an open research 5 field. In this study, starting from publicly available databases, we select genes associated with 6 dyslipidemia and we analyse their basal level changes by means of age and sex. Also studying the 7 networks associated to the genes, we identify the rewiring changes showing that there exists a set of 8 genes whose expression changes with age in: artery tibial, artery aorta and blood. Finally, we report 9 about changes associated to gender atributes in the extracted data
BRIEF REPORT | doi:10.20944/preprints202209.0172.v1
Subject: Computer Science And Mathematics, Mathematical And Computational Biology Keywords: ageing GTEx analysis
Online: 13 September 2022 (10:36:35 CEST)
Recently, many independent research project focus on the study of the molecular basis of aging processes. I parallel, the different progression of many diseaes between sex is a hot topic research area. These studies require many data, models and tools for inferring aging and sex specific molecular machinaries. Among the others, the Genotype-Tissue Expression (GTEx) database is one of the preminent resources for the analysis of expression data related to tissues, sex and age. The current version of the database has a lot of querying interface that enable many analysis centered on the expression of genes on tissues. Despite this the database lacks on the analysis at sex/age level, thus the researcher has to download data and then write queries by hand. Nevertheless it lacks on the integration with existing protein interaction data. Therefore, the need for the introduction of tools enabling easy access and powerful analysis capabilities (i.e. state of the art network based analysis and integration), arises. We here present NOMA-DB a framework for the analysis of age related genes based on the GTEx database that enable easy querying at sex/age level, network based analysis. The framework is based on wrapping the GTEx database and on building an application logic level on top of existing data. The current version enables the analysis of genes by tissue, gene and age, thus it may be used in potentially future directions of analysis towards better comprehension of aging/sex-related molecular machineries based on the analysis of expression dat
ARTICLE | doi:10.20944/preprints201804.0008.v1
Subject: Computer Science And Mathematics, Information Systems Keywords: SNP; multiple analysis pipeline; pharmacogenomics; overall survival curves; data mining: statistical analysis
Online: 2 April 2018 (07:53:23 CEST)
Personalized medicine is an aspect of the P4 medicine (predictive, preventive, personalized and participatory) based precisely on the customization of all medical characters of each subject. In personalized medicine, the development of medical treatments and drugs is tailored to the individual characteristics and needs of each subject, according to the study of diseases at different scales from genotype to phenotype scale. To make concrete the goal of personalized medicine, it is necessary to employ high-throughput methodologies such as Next Generation Sequencing (NGS), Genome-Wide Association Studies (GWAS), Mass Spectrometry or Microarrays, that are able to investigate a single disease from a broader perspective. For example, by using genotyping microarrays (e.g. collections of Single Nucleotide Polymorphism - SNP) it is possible to uncover the reasons (i.e. mutation in genes) because a treatment works properly in some patients (for example absence of mutated genes), but it does not work (presence of mutated genes) in others. A side effect of high-throughput methodologies is the massive amount of data produced for each single experiment, that poses several challenges (e.g. high execution time and required memory) to bioinformatic software. Thus a main requirement of modern bioinformatic software is the use of good software engineering methods and efficient programming techniques, able to face those challenges, that include the use of parallel programming and efficient and compact data structures. Thus, to exploit all the potential of this massive amount of data in the short possible time (before that data becomes obsolete), the necessity to develop parallel software tools for efficient data collection and analysis arise. Moreover, due to the heterogeneity of the data produced by the different kinds of experimental platforms, it is necessary to automatize in a comprehensive software pipeline, the various steps that compose a bioinformatic analysis, such as: the preprocessing of raw data to remove noise or corrupted data; the annotation of data with external knowledge (e.g. Gene Ontology), and the integration of molecular data with clinical data. It should be noted that such steps are necessary to make statistical or data mining analysis more effective. This paper presents the design and the experimentation of a comprehensive software pipeline, named microPipe, for the preprocessing, annotation and analysis of microarray-based SNP genotyping data. A case study in pharmacogenomics is presented. The main advantages of using microPipe are: the reduction of errors that may happen when trying to make data compatible among different tools; the possibility to analyze in parallel huge datasets; the easy annotation and integration of data.
ARTICLE | doi:10.20944/preprints201710.0073.v1
Subject: Computer Science And Mathematics, Data Structures, Algorithms And Complexity Keywords: graph alignment; brain network; human connectome
Online: 12 October 2017 (04:07:33 CEST)
A growing area in neurosciences is focused on the modeling and analysis the complex system of connections in neural systems, i.e. the connectome. Here we focus on the representation of connectomes by using graph theory formalisms. The human brain connectomes are usually derived from neuroimages; the analyzed brains are co-registered in the image domain and brought to a common anatomical space. An atlas is then applied in order to define anatomically meaningful regions that will serve as the nodes of the network - this process is referred to as parcellation. Recently, it has been proposed to perform atlas-free random brain parcellation into nodes and align brains in the network space instead of the anatomical image space to define network nodes of individual brain networks. In the network domain, the question of comparison of the structure of networks arises. Such question is tackled by modeling the comparison of brain network as a network alignment (NA) problem. In this paper, we first defined the NA problem formally, then we applied three existing state of the art of multiple alignment algorithms (MNA) on diffusion MRI-derived brain networks and we compared the performances. The results confirm that MNA algorithms may be applied in cases of atlas-free parcellation for a fully network-driven comparison of connectomes.
ARTICLE | doi:10.20944/preprints201710.0018.v1
Subject: Computer Science And Mathematics, Computer Vision And Graphics Keywords: Biological Network; Graphs; Statistical Analysis
Online: 3 October 2017 (16:52:13 CEST)
Graphs are largely used in computer science to model relations, or associations, among entities the compose complex systems. More recently, they found a broad field of application in bioinformatics and medical informatics supporting modelling, analysis of many systems. The applications span from representing interactions among molecules within cells, to model the functions of the brains. In order to support research, algorithms from graph theory that are able to extract knowledge from network should be coupled to efficient visualisation techniques. Although the importance of such topic, we retain that many challenges should be faced in the futures, such as automated pathway and network layout to better match biologists’ needs, the developing of a standard able to give more and better choices to represent nodes, edges finally, the developing of automated mechanism able to improve the network navigation methods that help users manage large and complex networks with the goal to improve the usability.
ARTICLE | doi:10.20944/preprints202308.0546.v1
Online: 8 August 2023 (10:16:00 CEST)
Dyslipidemia (Dys) is a disease characterised by abnormally high levels of lipids in the blood. It causes the deposits of lipids on the arterial wall leading to the insurgence of atherosclerosis, i.e. the increased thickness of arterial walls, which finally increases the risk of cardiovascular diseases. Dyslipidemia is a comorbidity of Type 2 Diabetes Mellitus (T2DM). A set of genes has been associated with dyslipidemia, but examining the regulation of such genes in age and sex is still an open research field. In this study, we select from publicly available databases the genes associated with dyslipidemia and analyse changes in the basal level of such genes by age and sex. Moreover, we also distinct differential rewiring of the related gene association network in males and females. Our results show that there exist a set of genes whose expression changes with age in artery tibial, artery aorta and blood. Moreover, there exist significant differences between sex.
ARTICLE | doi:10.20944/preprints202204.0027.v1
Online: 5 April 2022 (12:02:35 CEST)
Protein Contact Network (PCN) is an emerging paradigm for modelling protein structure. A common approach to interpreting such data is through network-based analyses. It has been shown that clustering analysis may discover allostery in PCN. Nevertheless Network Embedding has shown good performances in discovering hidden communities and structures in network. In this work, we compare some approaches for graph embedding with respect to some classical clustering approaches for annotating protein structures.
ARTICLE | doi:10.20944/preprints202308.1787.v1
Subject: Engineering, Bioengineering Keywords: Vaccination strategy; Covid-19; epidemiology; vaccines distributions
Online: 25 August 2023 (07:30:25 CEST)
Vaccination has been the most effective way to control the outbreak of the Covid pandemic. The numbers and types of vaccines have reached considerable proportions, even if the question of vaccine procedures and frequency still needs to be resolved. We learn the necessity of defining a vaccination distribution strategies with regard to Covid that could be used for any future pandemics of similar gravity. In fact, vaccine monitoring implies the existence of a strategy that should be measurable in terms of input and output, based on a mathematical model, including death rates, spread of infections, symptoms, hospitalization and so on. This paper addresses the issue of vaccine diffusion and strategies for monitoring the pandemic. It provides a description of the importance and take up of vaccines and the links between procedures and the containment of Covid variants, as well as the long-term effects. Finally, the paper focuses on the global scenario in a world undergoing profound social and political change, with particular attention on current and future health provision. This contribution would represent an example of vaccination experiences which can be useful in other pandemic or epidemiological contexts.
BRIEF REPORT | doi:10.20944/preprints202303.0207.v2
Subject: Computer Science And Mathematics, Mathematical And Computational Biology Keywords: Annotation; Biological Databases; Aging Analysis
Online: 15 March 2023 (02:00:02 CET)
There is increasing evidence that many molecular processes exhibit differences with age 1 and sex. Such differences produces also differences in the insurgence and progression of many 2 complex diseases. For instances, demographic data on insurgence of comorbidities of mellitus 3 diabetes, on lethality of COVID-19, and on some cancers, shows differences between sex and age 4 groups. Therefore, the growing interest on such area requires the management of related data as 5 well as the development of algorithms and tool for the analysis. The availability of omics data 6 annotated with metadata related to age and sex is mandatory for building pipeline of the analysis. 7 The number of databases containing data related to age and sex is hencefort growing. We here show 8 some databases and tools storing such data. Finally, future research direction are highlighte
BRIEF REPORT | doi:10.20944/preprints202301.0101.v1
Subject: Computer Science And Mathematics, Artificial Intelligence And Machine Learning Keywords: SI4CARE; TELEMEDICINE; ARTIFICIAL INTELLIGENCE; RURAL AREAS
Online: 5 January 2023 (09:11:00 CET)
The SI4CARE project is a transnational project which aims to develop both strategy and 1 action plans to improve health and social care in the Adriatic-Ionian region. Starting from the 2 survey of the status quo, each partner has developed some pilots to to support the development 3 and monitoring of the policy actions. In particular Partner number three, Municipality of Miglierina, 4 designed and developed a pilot related to the use of wearable device for monitoring elderly patients 5 in rural areas. With the collaboration of the complex unity of primary cares (UCCP) of the Reventino 6 area, the pilot is based on the use of smart wearable device to monitor some parameters of elderly 7 people after the vaccination for flu and covid. This paper focuses on the design and implementation 8 of the system and describe its application in the Municipality of Miglierina, the presentation of the 9 results and the discussion of the strengths and weaknesses will be presented in detail in a future work. 10 Finally, the possibility of extending the experiment to the other Adriatic-Ionian region is presented.
CASE REPORT | doi:10.20944/preprints202301.0427.v2
Subject: Computer Science And Mathematics, Hardware And Architecture Keywords: Wearable Device; Dementia
Online: 29 January 2023 (09:29:03 CET)
The improvement of health and social care needs the introduction of shared solution at transnational level. The SI4CARE (Social Innovation for Integrated Health Care) project is a transnational initiative within the Adriatic-Ionian regions aiming to develop strategies to improve the current status of health and social care. The Municipality of Miglierina, a small rural town in Calabria, which is a member the project, is developing a pilot action related to the use of wearable device for monitoring people affected by dementia with the project partner Ra.Gi.. Ra.Gi. is a non-profit organization dedicated to assisting people with dementia in day care centers and so-called dementia-friendly communities. The pilot is based on the use of smart wearable devices to monitor these patients during their daily lifetime. This paper focuses on the design and implementation of the system discussing the proposed application, the strengths and weaknesses. Finally, the possibility of extending the experiment to the other Adriatic-Ionian region is presented.