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Article ; Online: Sequential quadrature methods for RDO

Peri Daniele

Communications in Applied and Industrial Mathematics, Vol 7, Iss 1, Pp 23-

2016 Volume 47

Abstract: This paper presents a comparative study between a large number of different existing sequential quadrature schemes suitable for Robust Design Optimization (RDO), with the inclusion of two partly original approaches. Efficiency of the different ... ...

Abstract	This paper presents a comparative study between a large number of different existing sequential quadrature schemes suitable for Robust Design Optimization (RDO), with the inclusion of two partly original approaches. Efficiency of the different integration strategies is evaluated in terms of accuracy and computational effort: main goal of this paper is the identification of an integration strategy able to provide the integral value with a prescribed accuracy using a limited number of function samples. Identification of the different qualities of the various integration schemes is obtained utilizing both algebraic and practical test cases. Differences in the computational effort needed by the different schemes is evidenced, and the implications on their application to practical RDO problems is highlighted.
Keywords	Quadrature schemes ; Robust Design Optimization ; Industrial Design ; Science ; Q ; Mathematics ; QA1-939
Publishing date	2016-03-01T00:00:00Z
Publisher	Società Italiana di Matematica Applicata e Industriale (SIMAI)
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: Time-Constrained Node Visit Planning for Collaborative UAV-WSN Distributed Applications.

Augello, Andrea / Gaglio, Salvatore / Lo Re, Giuseppe / Peri, Daniele

Sensors (Basel, Switzerland)

2022 Volume 22, Issue 14

Abstract: Unmanned Aerial Vehicles (UAVs) are often studied as tools to perform data collection from Wireless Sensor Networks (WSNs). Path planning is a fundamental aspect of this endeavor. Works in the current literature assume that data are always ready to be ... ...

Abstract	Unmanned Aerial Vehicles (UAVs) are often studied as tools to perform data collection from Wireless Sensor Networks (WSNs). Path planning is a fundamental aspect of this endeavor. Works in the current literature assume that data are always ready to be retrieved when the UAV passes. This operational model is quite rigid and does not allow for the integration of the UAV as a computational object playing an active role in the network. In fact, the UAV could begin the computation on a first visit and retrieve the data later. Potentially, the UAV could orchestrate the distributed computation to improve its performance, change its parameters, and even upload new applications to the sensor network. In this paper, we analyze a scenario where a UAV plays an active role in the operation of multiple sensor networks by visiting different node clusters to initiate distributed computation and collect the final outcomes. The experimental results validate the effectiveness of the proposed method in optimizing total flight time, Average Age of Information, Average cluster computation end time, and Average data collection time compared to prevalent approaches to UAV path-planning that are adapted to the purpose.
Language	English
Publishing date	2022-07-15
Publishing country	Switzerland
Document type	Journal Article
ZDB-ID	2052857-7
ISSN	1424-8220 ; 1424-8220
ISSN (online)	1424-8220
ISSN	1424-8220
DOI	10.3390/s22145298
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Article ; Online: Wearable Multisensor Ring-Shaped Probe for Assessing Stress and Blood Oxygenation: Design and Preliminary Measurements.

Valenti, Simone / Volpes, Gabriele / Parisi, Antonino / Peri, Daniele / Lee, Jinseok / Faes, Luca / Busacca, Alessandro / Pernice, Riccardo

Biosensors

2023 Volume 13, Issue 4

Abstract: The increasing interest in innovative solutions for health and physiological monitoring has recently fostered the development of smaller biomedical devices. These devices are capable of recording an increasingly large number of biosignals simultaneously, ...

Abstract	The increasing interest in innovative solutions for health and physiological monitoring has recently fostered the development of smaller biomedical devices. These devices are capable of recording an increasingly large number of biosignals simultaneously, while maximizing the user's comfort. In this study, we have designed and realized a novel wearable multisensor ring-shaped probe that enables synchronous, real-time acquisition of photoplethysmographic (PPG) and galvanic skin response (GSR) signals. The device integrates both the PPG and GSR sensors onto a single probe that can be easily placed on the finger, thereby minimizing the device footprint and overall size. The system enables the extraction of various physiological indices, including heart rate (HR) and its variability, oxygen saturation (SpO
MeSH term(s)	Humans ; Photoplethysmography/methods ; Monitoring, Physiologic ; Heart Rate/physiology ; Galvanic Skin Response ; Wearable Electronic Devices
Language	English
Publishing date	2023-04-05
Publishing country	Switzerland
Document type	Journal Article
ZDB-ID	2662125-3
ISSN	2079-6374 ; 2079-6374
ISSN (online)	2079-6374
ISSN	2079-6374
DOI	10.3390/bios13040460
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Article ; Online: In Silico Mixed Ligand/Structure-Based Design of New CDK-1/PARP-1 Dual Inhibitors as Anti-Breast Cancer Agents.

Bono, Alessia / La Monica, Gabriele / Alamia, Federica / Mingoia, Francesco / Gentile, Carla / Peri, Daniele / Lauria, Antonino / Martorana, Annamaria

International journal of molecular sciences

2023 Volume 24, Issue 18

Abstract: CDK-1 and PARP-1 play crucial roles in breast cancer progression. Compounds acting as CDK-1 and/or PARP-1 inhibitors can induct cell death in breast cancer with a selective synthetic lethality mechanism. A mixed treatment by means of CDK-1 and PARP-1 ... ...

Abstract	CDK-1 and PARP-1 play crucial roles in breast cancer progression. Compounds acting as CDK-1 and/or PARP-1 inhibitors can induct cell death in breast cancer with a selective synthetic lethality mechanism. A mixed treatment by means of CDK-1 and PARP-1 inhibitors resulted in radical breast cancer cell growth reduction. Inhibitors with a dual target mechanism of action could arrest cancer progression by simultaneously blocking the DNA repair mechanism and cell cycle, resulting in advantageous monotherapy. To this aim, in the present work, we identified compound
MeSH term(s)	Poly(ADP-ribose) Polymerase Inhibitors/pharmacology ; Ligands ; Antineoplastic Agents/pharmacology ; Mammaplasty ; Cell Cycle ; Neoplasms
Chemical Substances	Poly(ADP-ribose) Polymerase Inhibitors ; Ligands ; Antineoplastic Agents
Language	English
Publishing date	2023-09-06
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/ijms241813769
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Article ; Online: Knowledge-Based Verification of Concatenative Programming Patterns Inspired by Natural Language for Resource-Constrained Embedded Devices.

Gaglio, Salvatore / Lo Re, Giuseppe / Martorella, Gloria / Peri, Daniele

Sensors (Basel, Switzerland)

2020 Volume 21, Issue 1

Abstract: We propose a methodology to verify applications developed following programming patterns inspired by natural language that interact with physical environments and run on resource-constrained interconnected devices. Natural language patterns allow for the ...

Abstract	We propose a methodology to verify applications developed following programming patterns inspired by natural language that interact with physical environments and run on resource-constrained interconnected devices. Natural language patterns allow for the reduction of intermediate abstraction layers to map physical domain concepts into executable code avoiding the recourse to ontologies, which would need to be shared, kept up to date, and synchronized across a set of devices. Moreover, the computational paradigm we use for effective distributed execution of symbolic code on resource-constrained devices encourages the adoption of such patterns. The methodology is supported by a rule-based system that permits runtime verification of Software Under Test (SUT) on board the target devices through automated oracle and test case generation. Moreover, verification extends from syntactic and semantic checks to the evaluation of the effects of SUT execution on target hardware. Additionally, by exploiting rules tying sensors and actuators to physical quantities, the effects of code execution on the physical environment can be verified. The system is also able to build test code to highlight software issues that may arise during repeated SUT execution on the target hardware.
Language	English
Publishing date	2020-12-26
Publishing country	Switzerland
Document type	Journal Article
ZDB-ID	2052857-7
ISSN	1424-8220 ; 1424-8220
ISSN (online)	1424-8220
ISSN	1424-8220
DOI	10.3390/s21010107
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Article ; Online: Identification of biological targets through the correlation between cell line chemosensitivity and protein expression pattern.

Lauria, Antonino / La Monica, Gabriele / Gentile, Carla / Mannino, Giuseppe / Martorana, Annamaria / Peri, Daniele

Drug discovery today

2021 Volume 26, Issue 10, Page(s) 2431–2438

Abstract: Matching biological data sequences is one of the most interesting ways to discover new bioactive compounds. In particular, matching cell chemosensitivity with a protein expression profile can be a useful approach to predict the activity of compounds ... ...

Abstract	Matching biological data sequences is one of the most interesting ways to discover new bioactive compounds. In particular, matching cell chemosensitivity with a protein expression profile can be a useful approach to predict the activity of compounds against definite biological targets. In this review, we discuss this correlation. First, we analyze case studies in which some known drugs, acting on known targets, show a good correlation between their antiproliferative activities and protein expression when a large panel of tumor cells is considered. Then, we highlight how the application of in silico methods based on the correlation between cell line chemosensitivity and gene/protein expression patterns might be a quick, cheap, and interesting approach to predict the biological activity of investigated molecules.
MeSH term(s)	Antineoplastic Agents/pharmacology ; Cell Line, Tumor ; Computer Simulation ; Drug Discovery/methods ; Gene Expression Regulation, Neoplastic ; Humans ; Molecular Targeted Therapy ; Neoplasms/drug therapy ; Neoplasms/genetics ; Neoplasms/pathology
Chemical Substances	Antineoplastic Agents
Language	English
Publishing date	2021-05-26
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't ; Review
ZDB-ID	1324988-5
ISSN	1878-5832 ; 1359-6446
ISSN (online)	1878-5832
ISSN	1359-6446
DOI	10.1016/j.drudis.2021.05.013
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Article ; Online: Antiproliferative Activity Predictor: A New Reliable In Silico Tool for Drug Response Prediction against NCI60 Panel.

Martorana, Annamaria / La Monica, Gabriele / Bono, Alessia / Mannino, Salvatore / Buscemi, Silvestre / Palumbo Piccionello, Antonio / Gentile, Carla / Lauria, Antonino / Peri, Daniele

International journal of molecular sciences

2022 Volume 23, Issue 22

Abstract: In vitro antiproliferative assays still represent one of the most important tools in the anticancer drug discovery field, especially to gain insights into the mechanisms of action of anticancer small molecules. The NCI-DTP (National Cancer Institute ... ...

Abstract	In vitro antiproliferative assays still represent one of the most important tools in the anticancer drug discovery field, especially to gain insights into the mechanisms of action of anticancer small molecules. The NCI-DTP (National Cancer Institute Developmental Therapeutics Program) undoubtedly represents the most famous project aimed at rapidly testing thousands of compounds against multiple tumor cell lines (NCI60). The large amount of biological data stored in the National Cancer Institute (NCI) database and many other databases has led researchers in the fields of computational biology and medicinal chemistry to develop tools to predict the anticancer properties of new agents in advance. In this work, based on the available antiproliferative data collected by the NCI and the manipulation of molecular descriptors, we propose the new in silico Antiproliferative Activity Predictor (AAP) tool to calculate the GI
MeSH term(s)	Antineoplastic Agents/pharmacology ; Antineoplastic Agents/chemistry ; Cell Line, Tumor ; Curcumin ; Databases, Factual
Chemical Substances	Antineoplastic Agents ; Curcumin (IT942ZTH98)
Language	English
Publishing date	2022-11-19
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/ijms232214374
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Article ; Online: Numerical optimization of plasmid DNA delivery combined with hyaluronidase injection for electroporation protocol.

Peri, Daniele / Deville, Manon / Poignard, Clair / Signori, Emanuela / Natalini, Roberto

Computer methods and programs in biomedicine

2019 Volume 186, Page(s) 105204

Abstract: Background and objective: The paper focuses on the numerical strategies to optimize a plasmid DNA delivery protocol, which combines hyaluronidase and electroporation.: Methods: A well-defined continuum mechanics model of muscle porosity and advanced ... ...

Abstract	Background and objective: The paper focuses on the numerical strategies to optimize a plasmid DNA delivery protocol, which combines hyaluronidase and electroporation. Methods: A well-defined continuum mechanics model of muscle porosity and advanced numerical optimization strategies have been used, to propose a substantial improvement of a pre-existing experimental protocol of DNA transfer in mice. Our work suggests that a computational model might help in the definition of innovative therapeutic procedures, thanks to the fine tuning of all the involved experimental steps. This approach is particularly interesting in optimizing complex and costly protocols, to make in vivo DNA therapeutic protocols more effective. Results: Our preliminary work suggests that computational model might help in the definition of innovative therapeutic protocol, thanks to the fine tuning of all the involved operations. Conclusions: This approach is particularly interesting in optimizing complex and costly protocols for which the number of degrees of freedom prevents a experimental test of the possible configuration.
MeSH term(s)	Algorithms ; Animals ; DNA/administration & dosage ; Electroporation/methods ; Hyaluronoglucosaminidase/administration & dosage ; Mice ; Models, Biological ; Plasmids ; Transfection
Chemical Substances	DNA (9007-49-2) ; Hyaluronoglucosaminidase (EC 3.2.1.35)
Language	English
Publishing date	2019-11-15
Publishing country	Ireland
Document type	Journal Article
ZDB-ID	632564-6
ISSN	1872-7565 ; 0169-2607
ISSN (online)	1872-7565
ISSN	0169-2607
DOI	10.1016/j.cmpb.2019.105204
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Article ; Online: In Silico Identification of Small Molecules as New Cdc25 Inhibitors through the Correlation between Chemosensitivity and Protein Expression Pattern.

Lauria, Antonino / Martorana, Annamaria / La Monica, Gabriele / Mannino, Salvatore / Mannino, Giuseppe / Peri, Daniele / Gentile, Carla

International journal of molecular sciences

2021 Volume 22, Issue 7

Abstract: The cell division cycle 25 (Cdc25) protein family plays a crucial role in controlling cell proliferation, making it an excellent target for cancer therapy. In this work, a set of small molecules were identified as Cdc25 modulators by applying a mixed ... ...

Abstract	The cell division cycle 25 (Cdc25) protein family plays a crucial role in controlling cell proliferation, making it an excellent target for cancer therapy. In this work, a set of small molecules were identified as Cdc25 modulators by applying a mixed ligand-structure-based approach and taking advantage of the correlation between the chemosensitivity of selected structures and the protein expression pattern of the proposed target. In the first step of the in silico protocol, a set of molecules acting as Cdc25 inhibitors were identified through a new ligand-based protocol and the evaluation of a large database of molecular structures. Subsequently, induced-fit docking (IFD) studies allowed us to further reduce the number of compounds biologically screened. In vitro antiproliferative and enzymatic inhibition assays on the selected compounds led to the identification of new structurally heterogeneous inhibitors of Cdc25 proteins. Among them, J3955, the most active inhibitor, showed concentration-dependent antiproliferative activity against HepG2 cells, with GI
MeSH term(s)	Binding Sites ; CDC2 Protein Kinase/metabolism ; Computer Simulation ; Drug Discovery ; Drug Screening Assays, Antitumor ; Hep G2 Cells ; Humans ; Ligands ; Molecular Targeted Therapy ; Phosphorylation/drug effects ; cdc25 Phosphatases/antagonists & inhibitors ; cdc25 Phosphatases/metabolism
Chemical Substances	Ligands ; CDC2 Protein Kinase (EC 2.7.11.22) ; CDK1 protein, human (EC 2.7.11.22) ; cdc25 Phosphatases (EC 3.1.3.48)
Language	English
Publishing date	2021-04-02
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/ijms22073714
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Article ; Online: DRUDIT: web-based DRUgs DIscovery Tools to design small molecules as modulators of biological targets.

Lauria, Antonino / Mannino, Salvatore / Gentile, Carla / Mannino, Giuseppe / Martorana, Annamaria / Peri, Daniele

Bioinformatics (Oxford, England)

2019 Volume 36, Issue 5, Page(s) 1562–1569

Abstract: Motivation: New in silico tools to predict biological affinities for input structures are presented. The tools are implemented in the DRUDIT (DRUgs DIscovery Tools) web service. The DRUDIT biological finder module is based on molecular descriptors that ... ...

Abstract	Motivation: New in silico tools to predict biological affinities for input structures are presented. The tools are implemented in the DRUDIT (DRUgs DIscovery Tools) web service. The DRUDIT biological finder module is based on molecular descriptors that are calculated by the MOLDESTO (MOLecular DEScriptors TOol) software module developed by the same authors, which is able to calculate more than one thousand molecular descriptors. At this stage, DRUDIT includes 250 biological targets, but new external targets can be added. This feature extends the application scope of DRUDIT to several fields. Moreover, two more functions are implemented: the multi- and on/off-target tasks. These tools applied to input structures allow for predicting the polypharmacology and evaluating the collateral effects. Results: The applications described in the article show that DRUDIT is able to predict a single biological target, to identify similarities among biological targets, and to discriminate different target isoforms. The main advantages of DRUDIT for the scientific community lie in its ease of use by worldwide scientists and the possibility to be used also without specific, and often expensive, hardware and software. In fact, it is fully accessible through the WWW from any device to perform calculations. Just a click or a tap can start tasks to predict biological properties for new compounds or repurpose drugs, lead compounds, or unsuccessful compounds. To date, DRUDIT is supported by four servers each able to execute 8 jobs simultaneously. Availability and implementation: The web service is accessible at the www.drudit.com URL and its use is free of charge. Supplementary information: Supplementary data are available at Bioinformatics online.
MeSH term(s)	Computer Simulation ; Drug Discovery ; Internet ; Polypharmacology ; Software
Language	English
Publishing date	2019-10-11
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	1422668-6
ISSN	1367-4811 ; 1367-4803
ISSN (online)	1367-4811
ISSN	1367-4803
DOI	10.1093/bioinformatics/btz783
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