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Article ; Online: Tubulin-Based Polymorphism (TBP) in Plant Genotyping.

Braglia, Luca / Gavazzi, Floriana / Gianì, Silvia / Morello, Laura / Breviario, Diego

Methods in molecular biology (Clifton, N.J.)

2023 Volume 2638, Page(s) 387–401

Abstract: Tubulin-based polymorphism (TBP) is an intron length polymorphism (ILP) method widely applicable to any plant species and particularly suitable for a first and rapid classification of any plant genome. It is based on the selective, polymerase chain ... ...

Abstract	Tubulin-based polymorphism (TBP) is an intron length polymorphism (ILP) method widely applicable to any plant species and particularly suitable for a first and rapid classification of any plant genome. It is based on the selective, polymerase chain reaction (PCR)-based amplification of the two introns present at conserved positions within the coding sequences of plant β-tubulin genes. Amplification releases a simple yet distinctive genomic profile.
MeSH term(s)	Tubulin/genetics ; Polymorphism, Genetic ; Genotype ; Plants/genetics ; Genes, Plant ; Introns/genetics
Chemical Substances	Tubulin
Language	English
Publishing date	2023-02-13
Publishing country	United States
Document type	Journal Article
ISSN	1940-6029
ISSN (online)	1940-6029
DOI	10.1007/978-1-0716-3024-2_28
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Book ; Online: An Artificial Intelligence System for Combined Fruit Detection and Georeferencing, Using RTK-Based Perspective Projection in Drone Imagery

Baird, Angus / Giani, Stefano

2021

Abstract: This work presents an Artificial Intelligence (AI) system, based on the Faster Region-Based Convolution Neural Network (Faster R-CNN) framework, which detects and counts apples from oblique, aerial drone imagery of giant commercial orchards. To reduce ... ...

Abstract	This work presents an Artificial Intelligence (AI) system, based on the Faster Region-Based Convolution Neural Network (Faster R-CNN) framework, which detects and counts apples from oblique, aerial drone imagery of giant commercial orchards. To reduce computational cost, a novel precursory stage to the network is designed to preprocess raw imagery into cropped images of individual trees. Unique geospatial identifiers are allocated to these using the perspective projection model. This employs Real-Time Kinematic (RTK) data, Digital Terrain and Surface Models (DTM and DSM), as well as internal and external camera parameters. The bulk of experiments however focus on tuning hyperparameters in the detection network itself. Apples which are on trees and apples which are on the ground are treated as separate classes. A mean Average Precision (mAP) metric, calibrated by the size of the two classes, is devised to mitigate spurious results. Anchor box design is of key interest due to the scale of the apples. As such, a k-means clustering approach, never before seen in literature for Faster R-CNN, resulted in the most significant improvements to calibrated mAP. Other experiments showed that the maximum number of box proposals should be 225; the initial learning rate of 0.001 is best applied to the adaptive RMS Prop optimiser; and ResNet 101 is the ideal base feature extractor when considering mAP and, to a lesser extent, inference time. The amalgamation of the optimal hyperparameters leads to a model with a calibrated mAP of 0.7627. Comment: 12 pages, 12 figures
Keywords	Computer Science - Computer Vision and Pattern Recognition ; Computer Science - Machine Learning ; Electrical Engineering and Systems Science - Image and Video Processing
Subject code	006
Publishing date	2021-01-01
Publishing country	us
Document type	Book ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: Effectiveness and acceptability of conversational agents for sexual health promotion: a systematic review and meta-analysis.

Balaji, Divyaa / He, Linwei / Giani, Stefano / Bosse, Tibor / Wiers, Reinout / de Bruijn, Gert-Jan

Sexual health

2022 Volume 19, Issue 5, Page(s) 391–405

Abstract: Digital health interventions for sexual health promotion have evolved considerably alongside innovations in technology. Despite these efforts, studies have shown that they do not consistently result in the desired sexual health outcomes. This could be ... ...

Abstract	Digital health interventions for sexual health promotion have evolved considerably alongside innovations in technology. Despite these efforts, studies have shown that they do not consistently result in the desired sexual health outcomes. This could be attributed to low levels of user engagement, which can hinder digital health intervention effectiveness, as users do not engage with the system enough to be exposed to the intervention components. It has been suggested that conversational agents (automated two-way communication systems e.g. Alexa) have the potential to overcome the limitations of prior systems and promote user engagement through the increased interactivity offered by bidirectional, natural language-based interactions. The present review, therefore, provides an overview of the effectiveness and user acceptability of conversational agents for sexual health promotion. A systematic search of seven databases provided 4534 records, and after screening, 31 articles were included in this review. A narrative synthesis of results was conducted for effectiveness and acceptability outcomes, with the former supplemented by a meta-analysis conducted on a subset of studies. Findings provide preliminary support for the effectiveness of conversational agents for promoting sexual health, particularly treatment adherence. These conversational agents were found to be easy to use and useful, and importantly, resulted in high levels of satisfaction, use and intentions to reuse, whereas user evaluations regarding the quality of information left room for improvement. The results can inform subsequent efforts to design and evaluate these interventions, and offer insight into additional user experience constructs identified outside of current technology acceptance models, which can be incorporated into future theoretical developments.
MeSH term(s)	Communication ; Health Promotion/methods ; Humans ; Mass Screening ; Sexual Behavior ; Sexual Health
Language	English
Publishing date	2022-07-19
Publishing country	Australia
Document type	Journal Article ; Meta-Analysis ; Systematic Review ; Research Support, Non-U.S. Gov't
ZDB-ID	2256731-8
ISSN	1449-8987 ; 1448-5028
ISSN (online)	1449-8987
ISSN	1448-5028
DOI	10.1071/SH22016
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Article ; Online: Characterization of the cryptic interspecific hybrid Lemna × mediterranea by an integrated approach provides new insights into duckweed diversity.

Braglia, Luca / Ceschin, Simona / Iannelli, M Adelaide / Bog, Manuela / Fabriani, Marco / Frugis, Giovanna / Gavazzi, Floriana / Gianì, Silvia / Mariani, Flaminia / Muzzi, Maurizio / Pelella, Emanuele / Morello, Laura

Journal of experimental botany

2024

Abstract: Lemnaceae taxonomy is challenged by the particular morphology of these tiny free-floating angiosperms. Although molecular taxonomy has helped clarify the phylogenetic history of this family, some inconsistency with morphological data leads to frequent ... ...

Abstract	Lemnaceae taxonomy is challenged by the particular morphology of these tiny free-floating angiosperms. Although molecular taxonomy has helped clarify the phylogenetic history of this family, some inconsistency with morphological data leads to frequent misclassifications in the genus Lemna. Recently, the finding that Lemna japonica is an interspecific hybrid between Lemna minor and Lemna turionifera, provided a clear explanation to one of such taxonomic questions. Here we demonstrated that L. minor is also capable to hybridize with Lemna gibba, generating a cryptic but widespread taxon in the Mediterranean area. The nothotaxon Lemna × mediterranea is described and compared with clones of the putative parental species L. minor and L. gibba. Genetic analysis by nuclear and plastid markers, as well as genome size measurement, revealed that two different cytotypes, diploid and triploid, originated by at least two independent hybridization events. Despite high overall similarity, morphometrical, physiological and biochemical analyses showed an intermediate position of L. × mediterranea between its parental species in most qualitative and quantitative characters, and also separation of the two hybrid cytotypes by some criteria. These data provide evidence that hybridization and polyploidization, driving forces of terrestrial plant evolution, contribute to the duckweed genetic diversity and may have shaped the phylogenetic history of these mainly asexual, aquatic plants.
Language	English
Publishing date	2024-02-22
Publishing country	England
Document type	Journal Article
ZDB-ID	2976-2
ISSN	1460-2431 ; 0022-0957
ISSN (online)	1460-2431
ISSN	0022-0957
DOI	10.1093/jxb/erae059
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Article: New Insights into Interspecific Hybridization in

Braglia, Luca / Breviario, Diego / Gianì, Silvia / Gavazzi, Floriana / De Gregori, Jacopo / Morello, Laura

Plants (Basel, Switzerland)

2021 Volume 10, Issue 12

Abstract: Duckweeds have been increasingly studied in recent years, both as model plants and in view of their potential applications as a new crop in a circular bioeconomy perspective. In order to select species and clones with the desired attributes, the correct ... ...

Abstract	Duckweeds have been increasingly studied in recent years, both as model plants and in view of their potential applications as a new crop in a circular bioeconomy perspective. In order to select species and clones with the desired attributes, the correct identification of the species is fundamental. Molecular methods have recently provided a more solid base for taxonomy and yielded a consensus phylogenetic tree, although some points remain to be elucidated. The duckweed genus
Language	English
Publishing date	2021-12-15
Publishing country	Switzerland
Document type	Journal Article
ZDB-ID	2704341-1
ISSN	2223-7747
ISSN	2223-7747
DOI	10.3390/plants10122767
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Article: Tubulin-Based DNA Barcode: Principle and Applications to Complex Food Matrices.

Morello, Laura / Braglia, Luca / Gavazzi, Floriana / Gianì, Silvia / Breviario, Diego

Genes

2019 Volume 10, Issue 3

Abstract: The DNA polymorphism diffusely present in the introns of the members of the Eukaryotic beta-tubulin gene families, can be conveniently used to establish a DNA barcoding method, named tubulin-based polymorphism (TBP), that can reliably assign specific ... ...

Abstract	The DNA polymorphism diffusely present in the introns of the members of the Eukaryotic beta-tubulin gene families, can be conveniently used to establish a DNA barcoding method, named tubulin-based polymorphism (TBP), that can reliably assign specific genomic fingerprintings to any plant or/and animal species. Similarly, many plant varieties can also be barcoded by TBP. The method is based on a simple cell biology concept that finds a conveniently exploitable molecular basis. It does not depend on DNA sequencing as the most classically established DNA barcode strategies. Successful applications, diversified for the different target sequences or experimental purposes, have been reported in many different plant species and, of late, a new a version applicable to animal species, including fishes, has been developed. Also, the TBP method is currently used for the genetic authentication of plant material and derived food products. Due to the use of a couple of universal primer pairs, specific for plant and animal organisms, respectively, it is effective in metabarcoding a complex matrix allowing an easy and rapid recognition of the different species present in a mixture. A simple, dedicated database made up by the genomic profile of reference materials is also part of the analytical procedure. Here we will provide some example of the TBP application and will discuss its features and uses in comparison with the DNA sequencing-based methods.
MeSH term(s)	Animals ; DNA Barcoding, Taxonomic/methods ; Food/classification ; Food/standards ; Food Industry ; Plant Proteins/genetics ; Plants/classification ; Plants/genetics ; Polymorphism, Genetic ; Sequence Analysis, DNA ; Tubulin/genetics
Chemical Substances	Plant Proteins ; Tubulin
Language	English
Publishing date	2019-03-18
Publishing country	Switzerland
Document type	Journal Article ; Research Support, Non-U.S. Gov't ; Review
ZDB-ID	2527218-4
ISSN	2073-4425
ISSN	2073-4425
DOI	10.3390/genes10030229
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Article: Tubulin-based polymorphism genome profiling: a novel method for animal species authentication in meat and poultry

Gianì, Silvia / Di Cesare, Verdiana / Gavazzi, Floriana / Morello, Laura / Breviario, Diego

Food control. 2020 Apr., v. 110

2020

Abstract: We present a new method for the authentication of the biological identity of raw meat and processed meat products that is based on length polymorphism found in the introns of the members of the animal beta-tubulin gene family. The method, denominated ... ...

Abstract	We present a new method for the authentication of the biological identity of raw meat and processed meat products that is based on length polymorphism found in the introns of the members of the animal beta-tubulin gene family. The method, denominated aTBP for animal Tubulin-Based-Polymorphism, is shown to be capable of assigning an exclusive genomic fingerprinting to ten different animal species, eight of which are largely consumed as food products. Besides an exclusive DNA profiling, each species is characterized by the presence of specific diagnostic fragments, that assist their selective recognition in admixtures and products sold in the market. The aTBP method is also shown to be effective in both DNA/DNA and weight/weight mixtures where the presence of the low abundance species can be detected at the level of 0.5% and 1% respectively. Detection by aTBP genome profiling is also obtained from either frozen/thawed or cooked samples. The composition of 25 market products made by meat was also assessed with respect to what declared in the label. The results are discussed with reference to biosurveillance and disclosure of frauds and contaminations in comparison with other DNA-based diagnostic methods currently used.
Keywords	DNA ; DNA fingerprinting ; diagnostic techniques ; freeze-thaw cycles ; genomics ; introns ; markets ; poultry ; processed meat ; raw meat ; tubulin
Language	English
Dates of publication	2020-04
Publishing place	Elsevier Ltd
Document type	Article
ZDB-ID	1027805-9
ISSN	0956-7135
ISSN	0956-7135
DOI	10.1016/j.foodcont.2019.107010
Database	NAL-Catalogue (AGRICOLA)

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Article: On the applicability of the Tubulin-Based Polymorphism (TBP) genotyping method: a comprehensive guide illustrated through the application on different genetic resources in the legume family.

Braglia, Luca / Gavazzi, Floriana / Morello, Laura / Gianì, Silvia / Nick, Peter / Breviario, Diego

Plant methods

2020 Volume 16, Page(s) 86

Abstract: Background: Plant discrimination is of relevance for taxonomic, evolutionary, breeding and nutritional studies. To this purpose, evidence is reported to demonstrate TBP (Tubulin-Based-Polymorphism) as a DNA-based method suitable for assessing plant ... ...

Abstract	Background: Plant discrimination is of relevance for taxonomic, evolutionary, breeding and nutritional studies. To this purpose, evidence is reported to demonstrate TBP (Tubulin-Based-Polymorphism) as a DNA-based method suitable for assessing plant diversity. Results: Exploiting one of the most valuable features of TBP, that is the convenient and immediate application of the assay to groups of individuals that may belong to different taxa, we show that the TBP method can successfully discriminate different agricultural species and their crop wild relatives within the Papilionoideae subfamily. Detection of intraspecific variability is demonstrated by the genotyping of 27 different accessions of Conclusions: These data illustrate TBP as a useful and versatile tool for plant genotyping. Since its potential has not yet been fully appreciated by the scientific community, we carefully report all the experimental details of a successful TBP protocol, while describing different applications, so that the method can be replicated in other laboratories.
Language	English
Publishing date	2020-06-12
Publishing country	England
Document type	Journal Article
ZDB-ID	2203723-8
ISSN	1746-4811
ISSN	1746-4811
DOI	10.1186/s13007-020-00627-z
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Article ; Online: aTBP: A versatile tool for fish genotyping.

Gianì, Silvia / Silletti, Silvia / Gavazzi, Floriana / Morello, Laura / Spinsanti, Giacomo / Parati, Katia / Breviario, Diego

PloS one

2020 Volume 15, Issue 8, Page(s) e0237111

Abstract: Animal Tubulin-Based-Polymorphism (aTBP), an intron length polymorphism method recently developed for vertebrate genotyping, has been successfully applied to the identification of several fish species. Here, we report data that demonstrate the ability of ...

Abstract	Animal Tubulin-Based-Polymorphism (aTBP), an intron length polymorphism method recently developed for vertebrate genotyping, has been successfully applied to the identification of several fish species. Here, we report data that demonstrate the ability of the aTBP method to assign a specific profile to fish species, each characterized by the presence of commonly shared amplicons together with additional intraspecific polymorphisms. Within each aTBP profile, some fragments are also recognized that can be attributed to taxonomic ranks higher than species, e.g. genus and family. Versatility of application across different taxonomic ranks combined with the presence of a significant number of DNA polymorphisms, makes the aTBP method an additional and useful tool for fish genotyping, suitable for different purposes such as species authentication, parental recognition and detection of allele variations in response to environmental changes.
MeSH term(s)	Animals ; Fish Proteins/genetics ; Fishes/genetics ; Genotyping Techniques/methods ; Polymorphism, Genetic ; Tubulin/genetics
Chemical Substances	Fish Proteins ; Tubulin
Language	English
Publishing date	2020-08-04
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ISSN	1932-6203
ISSN (online)	1932-6203
DOI	10.1371/journal.pone.0237111
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Article ; Online: Communication in refugee and migrant mental healthcare: A systematic rapid review on the needs, barriers and strategies of seekers and providers of mental health services.

Krystallidou, Demi / Temizöz, Özlem / Wang, Fang / de Looper, Melanie / Di Maria, Emilio / Gattiglia, Nora / Giani, Stefano / Hieke, Graham / Morganti, Wanda / Pace, Cecilia Serena / Schouten, Barbara / Braun, Sabine

Health policy (Amsterdam, Netherlands)

2023 Volume 139, Page(s) 104949

Abstract: Background: Migrants and refugees may not access mental health services due to linguistic and cultural discordance between them and health and social care professionals (HSCPs). The aim of this review is to identify the communication needs and barriers ... ...

Abstract	Background: Migrants and refugees may not access mental health services due to linguistic and cultural discordance between them and health and social care professionals (HSCPs). The aim of this review is to identify the communication needs and barriers experienced by third-country nationals (TCNs), their carers, and HSCPs, as well as the strategies they use and their preferences when accessing/providing mental health services and language barriers are present. Methods: We undertook a rapid systematic review of the literature (01/01/2011 - 09/03/2022) on seeking and/or providing mental health services in linguistically discordant settings. Quality appraisal was performed, data was extracted, and evidence was reviewed and synthesised qualitatively. Results: 58/5,650 papers met the inclusion criteria. Both TCNs (and their carers) and HSCPs experience difficulties when seeking or providing mental health services and language barriers are present. TCNs and HSCPs prefer linguistically and culturally concordant provision of mental health services but professional interpreters are often required. However, their use is not always preferred, nor is it without problems. Conclusions: Language barriers impede TCNs' access to mental health services. Improving language support options and cultural competency in mental health services is crucial to ensure that individuals from diverse linguistic and cultural backgrounds can access and/or provide high-quality mental health services.
MeSH term(s)	Humans ; Communication ; Communication Barriers ; Health Services Accessibility ; Mental Health Services ; Refugees/psychology ; Transients and Migrants
Language	English
Publishing date	2023-11-28
Publishing country	Ireland
Document type	Journal Article ; Review ; Systematic Review
ZDB-ID	605805-x
ISSN	1872-6054 ; 0168-8510
ISSN (online)	1872-6054
ISSN	0168-8510
DOI	10.1016/j.healthpol.2023.104949
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