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Article ; Online: RNA-Based Strategies for Cancer Therapy: In Silico Design and Evaluation of ASOs for Targeted Exon Skipping.

Pacelli, Chiara / Rossi, Alice / Milella, Michele / Colombo, Teresa / Le Pera, Loredana

International journal of molecular sciences

2023 Volume 24, Issue 19

Abstract: Precision medicine in oncology has made significant progress in recent years by approving drugs that target specific genetic mutations. However, many cancer driver genes remain challenging to pharmacologically target ("undruggable"). To tackle this issue, ...

Abstract	Precision medicine in oncology has made significant progress in recent years by approving drugs that target specific genetic mutations. However, many cancer driver genes remain challenging to pharmacologically target ("undruggable"). To tackle this issue, RNA-based methods like antisense oligonucleotides (ASOs) that induce targeted exon skipping (ES) could provide a promising alternative. In this work, a comprehensive computational procedure is presented, focused on the development of ES-based cancer treatments. The procedure aims to produce specific protein variants, including inactive oncogenes and partially restored tumor suppressors. This novel computational procedure encompasses target-exon selection, in silico prediction of ES products, and identification of the best candidate ASOs for further experimental validation. The method was effectively employed on extensively mutated cancer genes, prioritized according to their suitability for ES-based interventions. Notable genes, such as NRAS and VHL, exhibited potential for this therapeutic approach, as specific target exons were identified and optimal ASO sequences were devised to induce their skipping. To the best of our knowledge, this is the first computational procedure that encompasses all necessary steps for designing ASO sequences tailored for targeted ES, contributing with a versatile and innovative approach to addressing the challenges posed by undruggable cancer driver genes and beyond.
MeSH term(s)	Humans ; Oligonucleotides, Antisense/genetics ; Oligonucleotides, Antisense/therapeutic use ; RNA ; Neoplasms/therapy ; Neoplasms/drug therapy ; RNA Splicing ; Exons/genetics
Chemical Substances	Oligonucleotides, Antisense ; RNA (63231-63-0)
Language	English
Publishing date	2023-10-03
Publishing country	Switzerland
Document type	Journal Article
ZDB-ID	2019364-6
ISSN	1422-0067 ; 1422-0067 ; 1661-6596
ISSN (online)	1422-0067
ISSN	1422-0067 ; 1661-6596
DOI	10.3390/ijms241914862
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Book ; Online: Convolutional neural networks and multi-threshold analysis for contamination detection in the apparel industry

Boresta, Marco / Colombo, Tommaso / De Santis, Alberto

2022

Abstract: Quality control of apparel items is mandatory in modern textile industry, as consumer's awareness and expectations about the highest possible standard is constantly increasing in favor of sustainable and ethical textile products. Such a level of quality ... ...

Abstract	Quality control of apparel items is mandatory in modern textile industry, as consumer's awareness and expectations about the highest possible standard is constantly increasing in favor of sustainable and ethical textile products. Such a level of quality is achieved by checking the product throughout its life cycle, from raw materials to boxed stock. Checks may include color shading tests, fasteners fatigue tests, fabric weigh tests, contamination tests, etc. This work deals specifically with the automatic detection of contaminations given by small parts in the finished product such as raw material like little stones and plastic bits or materials from the construction process, like a whole needle or a clip. Identification is performed by a two-level processing of X-ray images of the items: in the first, a multi-threshold analysis recognizes the contaminations by gray level and shape attributes; the second level consists of a deep learning classifier that has been trained to distinguish between true positives and false positives. The automatic detector was successfully deployed in an actual production plant, since the results satisfy the technical specification of the process, namely a number of false negatives smaller than 3% and a number of false positives smaller than 15%. Comment: 23 pages, 8 figures
Keywords	Computer Science - Computer Vision and Pattern Recognition
Subject code	670
Publishing date	2022-07-26
Publishing country	us
Document type	Book ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: A Census and Categorization Method of Epitranscriptomic Marks.

Mathlin, Julia / Le Pera, Loredana / Colombo, Teresa

International journal of molecular sciences

2020 Volume 21, Issue 13

Abstract: In the past few years, thorough investigation of chemical modifications operated in the cells on ribonucleic acid (RNA) molecules is gaining momentum. This new field of research has been dubbed "epitranscriptomics", in analogy to best-known epigenomics, ... ...

Abstract	In the past few years, thorough investigation of chemical modifications operated in the cells on ribonucleic acid (RNA) molecules is gaining momentum. This new field of research has been dubbed "epitranscriptomics", in analogy to best-known epigenomics, to stress the potential of ensembles of RNA modifications to constitute a post-transcriptional regulatory layer of gene expression orchestrated by writer, reader, and eraser RNA-binding proteins (RBPs). In fact, epitranscriptomics aims at identifying and characterizing all functionally relevant changes involving both non-substitutional chemical modifications and editing events made to the transcriptome. Indeed, several types of RNA modifications that impact gene expression have been reported so far in different species of cellular RNAs, including ribosomal RNAs, transfer RNAs, small nuclear RNAs, messenger RNAs, and long non-coding RNAs. Supporting functional relevance of this largely unknown regulatory mechanism, several human diseases have been associated directly to RNA modifications or to RBPs that may play as effectors of epitranscriptomic marks. However, an exhaustive epitranscriptome's characterization, aimed to systematically classify all RNA modifications and clarify rules, actors, and outcomes of this promising regulatory code, is currently not available, mainly hampered by lack of suitable detecting technologies. This is an unfortunate limitation that, thanks to an unprecedented pace of technological advancements especially in the sequencing technology field, is likely to be overcome soon. Here, we review the current knowledge on epitranscriptomic marks and propose a categorization method based on the reference ribonucleotide and its rounds of modifications ("stages") until reaching the given modified form. We believe that this classification scheme can be useful to coherently organize the expanding number of discovered RNA modifications.
MeSH term(s)	Epigenesis, Genetic ; Epigenomics/methods ; RNA/metabolism ; RNA Processing, Post-Transcriptional ; Ribonucleosides/metabolism ; Transcriptome
Chemical Substances	Ribonucleosides ; RNA (63231-63-0)
Language	English
Publishing date	2020-06-30
Publishing country	Switzerland
Document type	Journal Article ; Review
ZDB-ID	2019364-6
ISSN	1422-0067 ; 1422-0067 ; 1661-6596
ISSN (online)	1422-0067
ISSN	1422-0067 ; 1661-6596
DOI	10.3390/ijms21134684
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Article ; Online: Mining sponge phenomena in RNA expression data.

Angiulli, Fabrizio / Colombo, Teresa / Fassetti, Fabio / Furfaro, Angelo / Paci, Paola

Journal of bioinformatics and computational biology

2021 Volume 20, Issue 1, Page(s) 2150022

Abstract: In the last few years, the interactions among competing endogenous RNAs (ceRNAs) have been recognized as a key post-transcriptional regulatory mechanism in cell differentiation, tissue development, and disease. Notably, such sponge phenomena substracting ...

Abstract	In the last few years, the interactions among competing endogenous RNAs (ceRNAs) have been recognized as a key post-transcriptional regulatory mechanism in cell differentiation, tissue development, and disease. Notably, such sponge phenomena substracting active microRNAs from their silencing targets have been recognized as having a potential oncosuppressive, or oncogenic, role in several cancer types. Hence, the ability to predict sponges from the analysis of large expression data sets (e.g. from international cancer projects) has become an important data mining task in bioinformatics. We present a technique designed to mine sponge phenomena whose presence or absence may discriminate between healthy and unhealthy populations of samples in tumoral or normal expression data sets, thus providing lists of candidates potentially relevant in the pathology. With this aim, we search for pairs of elements acting as ceRNA for a given miRNA, namely, we aim at discovering miRNA-RNA pairs involved in phenomena which are clearly present in one population and almost absent in the other one. The results on tumoral expression data, concerning five different cancer types, confirmed the effectiveness of the approach in mining interesting knowledge. Indeed, 32 out of 33 miRNAs and 22 out of 25 protein-coding genes identified as top scoring in our analysis are corroborated by having been similarly associated with cancer processes in independent studies. In fact, the subset of miRNAs selected by the sponge analysis results in a significant enrichment of annotation for the KEGG32 pathway "microRNAs in cancer" when tested with the commonly used bioinformatic resource DAVID. Moreover, often the cancer datasets where our sponge analysis identified a miRNA as top scoring match the one reported already in the pertaining literature.
MeSH term(s)	Computational Biology ; Data Mining ; Gene Expression Regulation ; Gene Expression Regulation, Neoplastic ; Gene Regulatory Networks ; Humans ; MicroRNAs/genetics ; MicroRNAs/metabolism ; Neoplasms/genetics ; RNA, Long Noncoding/genetics
Chemical Substances	MicroRNAs ; RNA, Long Noncoding
Language	English
Publishing date	2021-11-18
Publishing country	Singapore
Document type	Journal Article
ZDB-ID	2115015-1
ISSN	1757-6334 ; 0219-7200
ISSN (online)	1757-6334
ISSN	0219-7200
DOI	10.1142/S0219720021500220
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Article ; Online: Supervised and unsupervised learning to classify scoliosis and healthy subjects based on non-invasive rasterstereography analysis.

Colombo, Tommaso / Mangone, Massimiliano / Agostini, Francesco / Bernetti, Andrea / Paoloni, Marco / Santilli, Valter / Palagi, Laura

PloS one

2021 Volume 16, Issue 12, Page(s) e0261511

Abstract: The aim of our study was to classify scoliosis compared to to healthy patients using non-invasive surface acquisition via Video-raster-stereography, without prior knowledge of radiographic data. Data acquisitions were made using Rasterstereography; ... ...

Abstract	The aim of our study was to classify scoliosis compared to to healthy patients using non-invasive surface acquisition via Video-raster-stereography, without prior knowledge of radiographic data. Data acquisitions were made using Rasterstereography; unsupervised learning was adopted for clustering and supervised learning was used for prediction model Support Vector Machine and Deep Network architectures were compared. A M-fold cross validation procedure was performed to evaluate the results. The accuracy and balanced accuracy of the best supervised model were close to 85%. Classification rates by class were measured using the confusion matrix, giving a low percentage of unclassified patients. Rasterstereography has turned out to be a good tool to distinguish subject with scoliosis from healthy patients limiting the exposure to unnecessary radiations.
MeSH term(s)	Adolescent ; Adult ; Female ; Humans ; Imaging, Three-Dimensional/methods ; Male ; Retrospective Studies ; Scoliosis/classification ; Scoliosis/diagnosis ; Supervised Machine Learning ; Unsupervised Machine Learning ; Young Adult
Language	English
Publishing date	2021-12-23
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2267670-3
ISSN	1932-6203 ; 1932-6203
ISSN (online)	1932-6203
ISSN	1932-6203
DOI	10.1371/journal.pone.0261511
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Article ; Online: Low-Risk Antenatal Care Enhanced by Telemedicine: A Practical Guideline Model.

Colombo, Talita / Todeschini, Lorenza Bridi / Orlandini, Mariana / Nascimento, Hallana do / Gabriel, Franciele Cordeiro / Alves, Rafael José Vargas / Stein, Airton Tetelbom

Revista brasileira de ginecologia e obstetricia : revista da Federacao Brasileira das Sociedades de Ginecologia e Obstetricia

2022 Volume 44, Issue 9, Page(s) 845–853

Abstract: Objective: To develop a protocol for hybrid low-risk prenatal care adapted to Brazilian guidelines, merging reduced face-to-face consultations and remote monitoring.: Methods: The PubMed, Embase, and Cochrane Library databases were systematically ... ...

Title translation	Atenção ao pré-natal de baixo risco potencializada por telemedicina: Diretriz clínica prática.
Abstract	Objective: To develop a protocol for hybrid low-risk prenatal care adapted to Brazilian guidelines, merging reduced face-to-face consultations and remote monitoring. Methods: The PubMed, Embase, and Cochrane Library databases were systematically searched on telemedicine and antenatal care perspectives and adaptation of the low-risk prenatal care protocols recommended by the Ministry of Health and by the Brazilian Federation of Gynecology and Obstetrics Associations. Results: Five relevant articles and three manuals were included in the review, for presented criteria to develop this clinical guideline. We identified, in these studies, that the schedule of consultations is unevenly distributed among the gestational trimesters, and ranges from 7 to 14 appointments. In general, the authors propose one to two appointments in the first trimester, two to three appointments in the second trimester, and two to six appointments in the third trimester. Only three studies included puerperal evaluations. The routine exams recommended show minimal variations among authors. To date, there are no validated Brazilian protocols for prenatal care by telemedicine. The included studies showed that pregnant women were satisfied with this form of care, and the outcomes of interest, except for hypertensive diseases, were similar between the groups exposed to traditional and hybrid prenatal care. Conclusion: The presented guideline comprises the Ministry of Health recommendations for low-risk prenatal care and reduces exposure to the hospital environment and care costs. A randomized clinical trial, to be developed by this group, will provide real-world data on safety, effectiveness, satisfaction, and costs.
MeSH term(s)	Female ; Humans ; Obstetrics ; Postpartum Period ; Practice Guidelines as Topic ; Pregnancy ; Pregnant Women ; Prenatal Care/methods ; Randomized Controlled Trials as Topic ; Telemedicine
Language	English
Publishing date	2022-07-19
Publishing country	Brazil
Document type	Journal Article
ZDB-ID	2105176-8
ISSN	1806-9339 ; 0100-7203
ISSN (online)	1806-9339
ISSN	0100-7203
DOI	10.1055/s-0042-1753505
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Article ; Online: Risk of bias and certainty of evidence on the association between obesity and mortality in patients with SARS-COV-2: An umbrella review of meta-analyses.

Silva, Flávia M / Lima, Julia / Teixeira, Paula P / Grezzana, Guilherme B / Figueiro, Mabel / Colombo, Talita / Souto, Katia / Stein, Airton T

Clinical nutrition ESPEN

2022 Volume 53, Page(s) 13–25

Abstract: Background & aims: This umbrella review of systematic reviews with meta-analysis (SR-MAs) aimed to evaluate the risk of bias and the certainty of the evidence of SR-MAs on the association between obesity and mortality in patients with SARS-CoV-2.: ... ...

Abstract	Background & aims: This umbrella review of systematic reviews with meta-analysis (SR-MAs) aimed to evaluate the risk of bias and the certainty of the evidence of SR-MAs on the association between obesity and mortality in patients with SARS-CoV-2. Methods: We conducted a comprehensive literature search until April 22, 2022, in several databases and assessed the risk of bias of SR-MAs according to AMSTAR-2 and the certainty of evidence using the GRADE approach. The degree of overlap between meta-analyses was based on the corrected covered area (CCA) index. The results of each MA [relative risk (RR), hazard ratio (HR), or odds ratio (OR)] were extracted to evaluate the magnitude of the association between obesity and mortality. Results: A total of 24 SR-MAs were eligible, and the association between obesity and mortality was not statistically significant in eight (33.3%) of them, while the OR/HR/RR ranged from 1.14 to 3.52 in the other SR-MAs. The overlap was slight (CCA = 4.82%). The majority of SR-MAs presented critically low quality according to AMSTAR-2 (66.7%), and the certainty of the evidence for most of them (83.4%) was "very low". Conclusions: Obesity was associated with an increased risk of death in patients with SARS-CoV-2 infection in most SR-MAs; however, a critical appraisal pointed to a high risk of bias, and the certainty of their evidence was not well graded. The dissemination of poor SR-MAs may limit the interpretation of findings, and we should always aspire to trustworthy scientific evidence. Prospero: PROSPERO 2021 CRD42021253142.
MeSH term(s)	Humans ; SARS-CoV-2 ; COVID-19 ; Systematic Reviews as Topic ; Obesity/complications
Language	English
Publishing date	2022-08-17
Publishing country	England
Document type	Meta-Analysis ; Journal Article
ISSN	2405-4577
ISSN (online)	2405-4577
DOI	10.1016/j.clnesp.2022.08.014
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Article: La ricerca del sostituto valvolare "ideale" in sede aortica.

Colombo, T

Giornale italiano di cardiologia

1997 Volume 27, Issue 2, Page(s) 146–151

Title translation	Research for the "ideal" aortic valve substitute.
MeSH term(s)	Aortic Valve/surgery ; Heart Valve Prosthesis ; Humans
Language	Italian
Publishing date	1997-02
Publishing country	Italy
Document type	Journal Article ; Review
ZDB-ID	184670-x
ISSN	0046-5968
ISSN	0046-5968
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Article: Plant and fungus transcriptomic data from grapevine berries undergoing artificially-induced noble rot caused by Botrytis cinerea

Lovato, A. / Zenoni, S. / Tornielli, G. B. / Colombo, T. / Vandelle, E. / Polverari, A.

Data in Brief

2019 Volume 25, Issue Art. 104150, Page(s) 6 pp.

Abstract: Noble rot is a latent infection of grape berries caused by the necrotrophic fungus Botrytis cinerea, which develops under specific climatic conditions. The infected berries undergo biochemical and metabolic changes, associated with a rapid withering, ... ...

Institution	University of Verona, Biotechnology Department, Strada le Grazie, Cà Vignal 1, 37134 Verona, Italy
Abstract	Noble rot is a latent infection of grape berries caused by the necrotrophic fungus Botrytis cinerea, which develops under specific climatic conditions. The infected berries undergo biochemical and metabolic changes, associated with a rapid withering, which altogether offer interesting organoleptic features to sweet white wines. In this paper, we provide RNAseq datasets (raw and normalized counts as well as differentially expressed genes lists) of the transcriptome profiles of both grapevine berries (Vitis vinifera cv. Garganega) and B. cinerea during the establishment of noble rot, artificially induced in controlled conditions. The sequencing data are available in the NCBI GEO database under accession number GSE116741. These data were exploited in a comprehensive meta-analysis of gene expression during noble rot infection, gray mold and post-harvest withering. This highlighted an important common transcriptional reprogramming in different botrytized grape berry varieties and led to the identification of key genes specifically modulated during noble rot infection, which are described in the article entitled “Specific molecular interactions between Vitis vinifera and Botrytis cinerea are required for noble rot development in grape berries” Lovato et al., 2019.
Language	English
Document type	Article
ZDB-ID	2786545-9
ISSN	2352-3409
ISSN	2352-3409
Database	Viticulture and Oenology Abstracts

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Article: Specific molecular interactions between Vitis vinifera and Botrytis cinerea are required for noble rot development in grape berries

Lovato, A. / Zenoni, S. / Tornielli, G. B. / Colombo, T. / Vandelle, E. / Polverari, A.

Postharvest biology and technology

2019 Volume 156, Issue -, Page(s) 110924

Document type	Article
ZDB-ID	1082798-5
ISSN	0925-5214
Database	Current Contents Nutrition, Environment, Agriculture

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