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1. Isometry invariants of crystal structures based on Voronoi domains and interatomic distances

Author

Mosca, Marco Michele

Abstract

The need for comparison methods between crystal structures led the research to look for proper descriptors that could encode the chemical properties of different materials. Many crystal structures exist in theory, but only some of them may be synthesized in a laboratory and used in the real world for practical applications. To discover new materials, Crystal Structure Prediction is vital in predicting various crystal structure forms or generating new ones by building blocks or molecules. Usually, a structure prediction computes chemical features that are not correct properties because they do not consider the entire 3-dimensional structure of a crystal. However, they rely on rules considering only the type of particles involved. For example, some chemical properties are used frequently to select a good candidate for synthesis because, in theory, they could tell if a crystal may exist in its solid form under some environmental conditions. This thesis project aims to design and develop new geometric tools or properties that can properly distinguish 3-dimensional structures starting from the raw atom coordinates. The Geometric features developed in this document are fast properties or numerical characteristics that map crystal structure to a different space for a more reliable and efficient comparison. Firstly, we solved the comparison problem between crystal lattices by designing a property that maps a crystal lattice to the space of polyhedra and a metric that can distinguish them. Secondly, we designed a new and faster geometric property that relies on vectors of interatomic distances that are proved to change continuously under atom perturbations. Finally, the chemical property prediction was addressed in our last work, where we attempted to predict the chemical properties of crystals by using our geometric features.

Published
2022
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2. Fast predictions of lattice energies by continuous isometry invariants of crystal structures

Author

Ropers, Jakob, Mosca, Marco M, Anosova, Olga, Kurlin, Vitaliy, and Cooper, Andrew I

Subjects
Condensed Matter - Materials Science, Computer Science - Computational Engineering, Finance, and Science, Computer Science - Machine Learning
Abstract

Crystal Structure Prediction (CSP) aims to discover solid crystalline materials by optimizing periodic arrangements of atoms, ions or molecules. CSP takes weeks of supercomputer time because of slow energy minimizations for millions of simulated crystals. The lattice energy is a key physical property, which determines thermodynamic stability of a crystal but has no simple analytic expression. Past machine learning approaches to predict the lattice energy used slow crystal descriptors depending on manually chosen parameters. The new area of Periodic Geometry offers much faster isometry invariants that are also continuous under perturbations of atoms. Our experiments on simulated crystals confirm that a small distance between the new invariants guarantees a small difference of energies. We compare several kernel methods for invariant-based predictions of energy and achieve the mean absolute error of less than 5kJ/mole or 0.05eV/atom on a dataset of 5679 crystals., Comment: To appear in the proceedings of DACOMSIN (Data and Computation for Materials Science and Innovation) 2021, https://en.misis.ru/university/colleges/sound/thermochemistry/dacomsin/

Published
2021

3. The asymptotic behaviour and a near linear time algorithm for isometry invariants of periodic sets

Author

Widdowson, Daniel, Mosca, Marco, Pulido, Angeles, Kurlin, Vitaliy, and Cooper, Andrew I

Subjects
Condensed Matter - Materials Science, 51-08 (Primary) 51K05 14L24, 74E15 (Secondary), G.0, J.2, I.3.5
Abstract

The fundamental model of a periodic structure is a periodic point set up to rigid motion or isometry. Our recent paper in SoCG 2021 defined isometry invariants (density functions), which are complete in general position and continuous under perturbations. This work introduces much faster isometry invariants (average minimum distances), which are also continuous and distinguish some sets that have identical density functions. We explicitly describe the asymptotic behaviour of the new invariants for a wide class of sets including non-periodic. The proposed near linear time algorithm processed a dataset of hundreds of thousands of real structures in a few hours on a modest desktop., Comment: The main paper and appendices A,B are written for mathematicians and computer scientists, while appendices C,D focus on applications to crystals

Published
2020

4. Voronoi-based similarity distances between arbitrary crystal lattices

Author

Mosca, Marco Michele and Kurlin, Vitaliy

Subjects
Computer Science - Computational Geometry, Physics - Computational Physics
Abstract

This paper develops a new continuous approach to a similarity between periodic lattices of ideal crystals. Quantifying a similarity between crystal structures is needed to substantially speed up the Crystal Structure Prediction, because the prediction of many target properties of crystal structures is computationally slow and is essentially repeated for many nearly identical simulated structures. The proposed distances between arbitrary periodic lattices of crystal structures are invariant under all rigid motions, satisfy the metric axioms and continuity under atomic perturbations. The above properties make these distances ideal tools for clustering and visualizing large datasets of crystal structures. All the conclusions are rigorously proved and justified by experiments on real and simulated crystal structures reported in the Nature 2017 paper "Functional materials discovery using energy-structure-function maps"., Comment: Paper accepted in Crystal Research and Technology Journal

Published
2020

9. Soy phytochemicals decrease nonsmall cell lung cancer growth in female athymic mice

Author

Gallo, Daniela, Zannoni, Gian Franco, De Stefano, Ilaria, Mosca, Marco, Ferlini, Cristiano, Mantuano, Elisabetta, and Scambia, Giovanni

Subjects
Phytochemicals -- Health aspects, Phytochemicals -- Chemical properties, Lung cancer, Non-small cell -- Development and progression, Soybean products -- Composition, Soybean products -- Health aspects, Mice -- Health aspects, Food/cooking/nutrition
Abstract

This study investigated the effects of a phytoestrogen-containing standardized soy extract (SSE) on the growth of nonsmall cell lung cancer (NSCLC; A549) xenografts in female athymic mice. Tumor-bearing mice received either sterile water or SSE [50 or 100 mg/(kg-d), per os], 5 d/wk, until the mean tumor weight in each group was at least 900 mg. Treatment with SSE reduced tumor growth in the high-dose group compared with control (P < 0.01 ); tumors in both treated groups had reduced proliferation and greater apoptosis compared with controls (P < 0.05). SSE treatment also induced diffuse central necrosis, reducing the viable tissue mass within the tumor. Whereas tumor levels of epidermal growth factor receptor were comparable in control and treated mice, the expression of phosphorylated protein kinase B (p-Akt) was lower in tumors of mice treated with 100 mg SSE/(kg.d) than in controls (P < 0.01). The protein level of phosphorylated mitogen-activated protein kinase also tended to be lower (P = 0.07) in this group than in controls. Estrogen receptor (ER)[alpha] and ER[beta] were present in tumors, but their expression levels did not differ among groups. Serum insulin-like growth factor-1 concentrations also were not affected by the treatments. In conclusion, we found that soy phytochemicals slow the in vivo growth of NSCLC xenografts; the modulation of the Akt-signaling pathway observed in tumors of SSE-treated mice may have a role in the activity observed. Our research provides further support for the concept that consumption of phytoestrogens may be effective in delaying lung cancer progression.

Published
2008

12. Dot2dot: accurate whole-genome tandem repeats discovery.

Author

Genovese, Loredana M, Mosca, Marco M, Pellegrini, Marco, and Geraci, Filippo

Subjects
*EUKARYOTIC cells, *NUCLEOTIDE sequencing, *ALGORITHMS, *GENE expression, *NUCLEOTIDE sequence
Abstract

Motivation Large-scale sequencing projects have confirmed the hypothesis that eukaryotic DNA is rich in repetitions whose functional role needs to be elucidated. In particular, tandem repeats (TRs) (i.e. short, almost identical sequences that lie adjacent to each other) have been associated to many cellular processes and, indeed, are also involved in several genetic disorders. The need of comprehensive lists of TRs for association studies and the absence of a computational model able to capture their variability have revived research on discovery algorithms. Results Building upon the idea that sequence similarities can be easily displayed using graphical methods, we formalized the structure that TRs induce in dot-plot matrices where a sequence is compared with itself. Leveraging on the observation that a compact representation of these matrices can be built and searched in linear time, we developed Dot2dot : an accurate algorithm fast enough to be suitable for whole-genome discovery of TRs. Experiments on five manually curated collections of TRs have shown that Dot2dot is more accurate than other established methods, and completes the analysis of the biggest known reference genome in about one day on a standard PC. Availability and implementation Source code and datasets are freely available upon paper acceptance at the URL: https://github.com/Gege7177/Dot2dot. Supplementary information Supplementary data are available at Bioinformatics online. [ABSTRACT FROM AUTHOR]

Published
2019
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13. D2.1 Evaluation Criteria and Methods

Author

Drachsler, Hendrik, Greller, Wolfgang, Stoyanov, Slavi, Fetahu, Besnik, Daga, Enrico, Parodi, Elisabetta, Mosca, Marco, Adamou, Allesandro, and Herder, Eelco

Subjects
data competition, education, evaluation framework, open web data, linked data, data in education, LinkedUp, data mashups, dataTEL
Abstract

The main purposes of the current deliverable D2.1 is to provide the foundations of an Evaluation Framework that can be applied to compare Open Web Data applications and rank them according to their achievements. D2.1 contains the information gained from Task 2.1 - Evaluation criteria and method review and Task 2.2 - Validation of the evaluation criteria and methods of WP2 (DoW. p. 8). According to those tasks, we conducted an expert survey with the Group Concept Mapping method to identify relevant indicators and criteria for the Evaluation Framework. In a second step, we conducted a focused literature review to extend the outcomes of the expert survey with latest indicators reported in the literature. We finally, present the initial concept of the Evaluation Framework and its criteria and indicators. This deliverable provides the theoretical foundations for the Evaluation Framework that is further developed into a scoring sheet for the judges of LinkedUp challenge in deliverable D2.2.1. The Evaluation Framework will be further developed and amended according to the experiences collected in the three LinkedUp data competitions during the LinkedUp challenge

Published
2013

14. Crucial pathophysiological role of CXCR2 in experimental ulcerative colitis in mice

Author

Buanne, Pasquale, primary, Di Carlo, Emma, additional, Caputi, Lorenzo, additional, Brandolini, Laura, additional, Mosca, Marco, additional, Cattani, Franca, additional, Pellegrini, Luigi, additional, Biordi, Leda, additional, Coletti, Gino, additional, Sorrentino, Carlo, additional, Fedele, Guido, additional, Colotta, Francesco, additional, Melillo, Gabriella, additional, and Bertini, Riccardo, additional

Published
2007
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15. Muscle activations during functional tasks in individuals with chronic ankle instability: a systematic review of electromyographical studies

Author

Luciana Labanca, Massimiliano Mosca, Maria Grazia Benedetti, Marco Ghislieri, Marco Knaflitz, Valentina Agostini, and Luciana Labanca, Massimiliano Mosca , Marco Ghislieri , Valentina Agostini , Marco Knaflitz , Maria Grazia Benedetti

Subjects
Joint Instability, medicine.medical_specialty, Movement, Biophysics, Electromyography, surface electromyography, Physical medicine and rehabilitation, Peroneus longus, Hip strategy, Medicine, Humans, Orthopedics and Sports Medicine, muscle activation, hip strategy, joint instability, movement, Treadmill, Muscle, Skeletal, Functional movement, Balance (ability), medicine.diagnostic_test, business.industry, Rehabilitation, Motor control, Surface electromyography, medicine.anatomical_structure, Chronic Disease, Proximal Muscle, Muscle activation, Ankle, business, Ankle Joint
Abstract

Background: It has been reported that individuals with chronic ankle instability (CAI) show motor control abnormalities. The study of muscle activations by means of surface electromyography (sEMG) plays a key role in understanding some of the features of movement abnormalities. Research question: Do common sEMG activation abnormalities and strategies exists across different functional movements? Methods: Literature review was conducted on PubMed, Web-of-Science and Cochrane databases. Studies published between 2000 and 2020 that assessed muscle activations by means of sEMG during any type of functional task in individuals with CAI, and used healthy individuals as controls, were included. Methodological quality was assessed using the modified Downs&Black checklist. Since the methodologies of different studies were heterogeneous, no meta-analysis was conducted. Results: A total of 63 articles investigating muscle activations during gait, running, responses to perturbations, landing and hopping, cutting and turning; single-limb stance, star excursion balance task, forward lunges, ball-kicking, y-balance test and single-limb squatting were considered. Individuals with CAI showed a delayed activation of the peroneus longus in response to sudden inversion perturbations, in transitions between double- and single-limb stance, and in landing on unstable surfaces. Apparently, while walking on ground there are no differences between CAI and controls, walking on a treadmill increases the variability of muscles activations, probably as a "safety strategy" to avoid ankle inversion. An abnormal activation of the tibialis anterior was observed during a number of tasks. Finally, hip/spine muscles were activated before ankle muscles in CAI compared to controls. Conclusion: Though the methodology of the studies herein considered is heterogeneous, this review shows that the peroneal and tibialis anterior muscles have an abnormal activation in CAI individuals. These individuals also show a proximal muscle activation strategy during the performance of balance challenging tasks. Future studies should investigate whole-body muscle activation abnormalities in CAI individuals.

Published
2021

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