Article
Polymer Science
Raffaele Pastore, Ciro Siviello, Domenico Larobina
Summary: Research suggests that anomalous aging in soft glassy materials is closely related to ultra-long-range dynamical correlations, which may be a common feature.
Article
Developmental Biology
Kelsey H. Elliott, Sai K. Balchand, Christian Louis Bonatto Paese, Ching-Fang Chang, Yanfen Yang, Kari M. Brown, Daniel T. Rasicci, Hao He, Konrad Thorner, Praneet Chaturvedi, Stephen A. Murray, Jing Chen, Aleksey Porollo, Kevin A. Peterson, Samantha A. Brugmann
Summary: This study provides a searchable transcriptomic resource for the primary ciliome, revealing differentially expressed genes with tissue and temporal specificity. The genes within the differentially expressed ciliome show a lower level of functional constraint across species, indicating organism and cell-specific functional adaptation. The functional validation of ciliary heterogeneity was performed by disrupting ciliary genes using Cas9 gene editing, which exhibited dynamic gene expression profiles during osteogenic differentiation of multipotent neural crest cells. Overall, this novel primary cilia-focused resource allows researchers to explore the correlation between tissue and cell-type specific functions, ciliary heterogeneity, and the range of phenotypes associated with ciliopathies.
Article
Automation & Control Systems
Zuogong Yue, Johan Thunberg, Wei Pan, Lennart Ljung, Jorge Goncalves
Summary: This paper addresses the reconstruction of dynamic networks from heterogeneous datasets under the assumption that the underlying networks share the same Boolean structure across all experiments. Parametric models and group sparsity methods are proposed to assure network sparsity and structure consistency. The performance of the proposed methods is benchmarked in numerical simulation.
Article
Thermodynamics
S. Gupta, A. Chauhan, C. Sasmal
Summary: This study investigates the influence of adding solid polymers on mixed convective heat transfer phenomena. The results show that the addition of polymers can induce elastic instability and elastic turbulence, leading to an increase in heat transfer rate.
INTERNATIONAL JOURNAL OF HEAT AND MASS TRANSFER
(2022)
Article
Engineering, Industrial
Andrea Gelei, Zsofia Kenesei
Summary: This study focuses on the impact of suppliers' technological heterogeneity on the performance of buyer companies, finding that it has a significant positive effect on the buyer's actual business performance and research and development capability, mediated by the buyer's supply chain management efforts.
JOURNAL OF MANUFACTURING TECHNOLOGY MANAGEMENT
(2022)
Article
Engineering, Environmental
Vy Le, Sophia Thompson, Eric Roden, Christopher Zahasky
Summary: Prevention, mitigation, and regulation of bacterial contaminants in groundwater require a fundamental understanding of the mechanisms of transport and attachment in complex geological materials. The highest bacterial attachment occurs at the interfaces between sand layers oriented orthogonal to the direction of flow. By studying the distribution of attachment coefficients, a better understanding of bacterial transport mechanisms and accurate predictions of bacterial fate and transport in groundwater can be achieved.
ENVIRONMENTAL SCIENCE & TECHNOLOGY
(2023)
Article
Thermodynamics
Qian Zhou, Lihong Wei, Yinbo Yang, Tong Hao, Hui Liu
Summary: This study investigated the effects of different loadings of iron on coal-derived char for the heterogeneous reduction of NO. The catalytic mechanism of Fe was revealed through theoretical calculations. The experimental results showed that the char containing 0.4% FeCl3 exhibited the highest catalytic performance, with an NO reduction rate 18.8% higher than that of demineralized char. The catalytic mechanism of Fe was attributed to the creation of new active sites, reduction of energy barriers, and facilitation of N-N bond formation and N-2 desorption from the char surface.
COMBUSTION AND FLAME
(2023)
Article
Mechanics
B. Veltkamp, K. P. Velikov, D. Bonn
Summary: In this study, the squeeze flow of thin fluid layers during high velocity impact on a solid surface was experimentally investigated. It was found that the amount of viscous dissipation determines the remaining fluid in the contact after the object's kinetic energy is absorbed. Newtonian and shear thinning fluids can be completely drained from the contact on a short time scale, while viscoelastic liquids cannot be drained due to their elastic tendency to retract back into the contact after rapid squeezing. Furthermore, the experimental results were consistent with the predictions of hydrodynamic theory applied to the fluid flow in the gap.
JOURNAL OF FLUID MECHANICS
(2022)
Article
Environmental Sciences
Yanqing Lian, Lisha Zhen, Xi Chen, Yang Li, Xiaona Li
Summary: The present study collected water samples and conducted water quality analysis in river segments surrounding the urban areas in Xi'an, China. The results showed that hydrologic conditions and inflow sources significantly influenced the microbial community distributions. Sewage effluents impacted the microbial communities in Chan and Zao Rivers, while the Ba and Feng Rivers were enriched with soil and freshwater microbial communities. The findings of this study highlight the importance of understanding microbial pollution in urban rivers and its potential threats to public health and eco-environments.
ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH
(2023)
Article
Computer Science, Artificial Intelligence
Lin Zhang, Jiawen Guo, Qijie Bai, Chunyao Song
Summary: Graph representation learning aims to learn low-dimensional representations of graph structured data, which has various applications in graph analysis tasks. However, learning high-quality graph representations for dynamic heterogeneous networks is challenging due to their complex properties and rapidly evolving structures. Existing methods for representation learning of temporal heterogeneous networks are insufficient, relying on meta-paths or network snapshots. In this paper, we propose a novel graph neural network model called THGAT to address these limitations, improving the aggregation of neighborhood information and considering the importance of neighbor nodes through heterogeneous and temporal information. We also introduce three node signature methods for encoding heterogeneous information and directly representing temporal information. Experimental results on real-world datasets demonstrate the effectiveness of THGAT compared to state-of-the-art methods in link prediction, node classification, and node clustering. Additionally, we analyze the applicable scenarios of the three node signature methods through experiments.
Article
Management
Zhuzhu Song, Wansheng Tang, Ruiqing Zhao
Summary: This study examines service competition between two liner companies and finds that forming an alliance on the primary route can result in a win-win outcome, especially for the company with a lower price level. The alliance can also benefit some shippers, leading to a triple-win situation.
OMEGA-INTERNATIONAL JOURNAL OF MANAGEMENT SCIENCE
(2021)
Review
Biotechnology & Applied Microbiology
Yating Mao, Paige Nielsen, Jamel Ali
Summary: Microrheology is a method for measuring the mechanical properties of soft materials by characterizing the motion of microscopic particles. It extends the range of conventional bulk rheology and has advantages such as eliminating the need for large sample sizes and obtaining spatiotemporal information. It has significant applications in understanding structurally complex fluids in biomedical systems.
FRONTIERS IN BIOENGINEERING AND BIOTECHNOLOGY
(2022)
Article
Materials Science, Multidisciplinary
Leonid K. Leshchinskiy, Vitaliy P. Ivanov, Elena V. Lavrova, Dmitry P. Il'yaschenko
Summary: This paper presents the experimental analysis of data that shows the increased resistance of heterogeneous multilayer clad composites to dynamic loading destruction compared to homogeneous materials. The crack retardation caused by lamination at the boundary of the layers is believed to be the reason for this. The study also demonstrates the crack retardation in the destruction of heterogeneous compact composite samples by cyclic off-center stretching, with the fractogram clearly showing the transverse tightening of the sample section. It argues that crack nucleation plays a decisive role in the process of dynamic destruction of heterogeneous composites obtained by both multilayer cladding and explosion welding.
Article
Engineering, Multidisciplinary
Marcio A. Murad, Maicon R. Correa, Marcio R. Borges, Jesus A. Luizar-Obregon, Tuane Lopes
Summary: The study proposes a new computational model for two-phase immiscible flow in a poroelastic medium overlain by a saline formation, solving hydrodynamics and geomechanics subsystems using mixed finite element methods and a higher-order non-oscillatory finite volume central scheme. Numerical simulations illustrate the impact of viscoelastic effects in the cap rock on subsidence, reservoir compaction, and finger growth. Comparisons with traditional formulations are also presented.
COMPUTER METHODS IN APPLIED MECHANICS AND ENGINEERING
(2021)
Article
Mathematics, Applied
Santanu Manna, Akash Kumar
Summary: This paper focuses on the surface wave field in functionally graded multi-layer transversely isotropic heterogeneous magneto-elastic reinforced media and explores the mechanical properties and wave scattering relation in such media. By applying Haskell's technique and finite difference technique, the wave scattering relation and group velocity, phase velocity in the media are obtained, indicating that these characteristics are influenced by factors such as heterogeneity, reinforcement, magneto-elastic coupling parameters, and stability ratio.
APPLIED MATHEMATICS AND COMPUTATION
(2021)
Article
Biochemical Research Methods
Mattia Miotto, Alexandros Armaos, Lorenzo Di Rienzo, Giancarlo Ruocco, Edoardo Milanetti, Gian Gaetano Tartaglia
Summary: In this study, a webserver called Thermometer was developed to assess the thermal stability of proteins using structural information. The server is publicly available and has a user-friendly interface.
Article
Chemistry, Physical
Marco Benedetti, Enrico Ventura, Enzo Marinari, Giancarlo Ruocco, Francesco Zamponi
Summary: This study compares the Hebbian unlearning algorithm with a symmetric perceptron algorithm and finds that they have similar properties in terms of basin size and convergence region. The study also proposes a geometric interpretation of Hebbian unlearning and explores its potential applications in memory storage in materials.
JOURNAL OF CHEMICAL PHYSICS
(2022)
Article
Biochemistry & Molecular Biology
Lorenzo Di Rienzo, Luca De Flaviis, Giancarlo Ruocco, Viola Folli, Edoardo Milanetti
Summary: This study proposes a new computational approach based on Zernike polynomials for identifying binding sites of specific ligands on GPCRs. By analyzing the shape complementarity of local molecular surfaces, the method can distinguish binding pockets from randomly sampled regions on the receptor surface. The method achieves an Area Under ROC curve of 0.77 in experiments, demonstrating its ability for rapid and efficient screening of potential drugs.
JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN
(2022)
Article
Biology
Mattia Miotto, Lorenzo Di Rienzo, Giorgio Gosti, Leonardo Bo', Giacomo Parisi, Roberta Piacentini, Alberto Boffi, Giancarlo Ruocco, Edoardo Milanetti
Summary: The researchers conducted molecular dynamics simulations to assess the stabilizing effect of several possible SARS-CoV-2 spike variants on the molecular complex. They found that several variants exhibited greater stability compared to the wild type and negative control systems. The study highlights the importance of characterizing the effects of these variants' mutations on contagiousness and antigenicity.
COMMUNICATIONS BIOLOGY
(2022)
Article
Biochemistry & Molecular Biology
Roberta Piacentini, Laura Centi, Mattia Miotto, Edoardo Milanetti, Lorenzo Di Rienzo, Martina Pitea, Paolo Piazza, Giancarlo Ruocco, Alberto Boffi, Giacomo Parisi
Summary: This study investigates the interactions among human lactoferrin, SARS-CoV-2 receptor-binding domain, and human angiotensin-converting enzyme 2 receptor. The results suggest that lactoferrin can bind to ACE2 receptor but not to RBD. This reveals a potential mechanism for lactoferrin's preventive effect against CoV-2 infection by interfering with RBD-ACE2 binding.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2022)
Article
Multidisciplinary Sciences
Greta Grassmann, Mattia Miotto, Lorenzo Di Rienzo, Giorgio Gosti, Giancarlo Ruocco, Edoardo Milanetti
Summary: This research introduces a new theoretical and computational algorithm for reducing the number of sampling points while preserving key information of the molecular surface. By testing local shape properties, the method proves to be effective in identifying hot spots.
Article
Multidisciplinary Sciences
Walter Schirmacher, Taras Bryk, Giancarlo Ruocco
Summary: This study investigates the instantaneous normal mode spectrum of a simulated soft-sphere liquid at different equilibrium temperatures. The findings reveal a sharp maximum near (but not at) lambda = 0 in the spectrum of eigenvalues rho(lambda), which decreases monotonically with |lambda| on both stable and unstable sides. The temperature strongly affects the spectral shape, with asymmetry at low temperatures and symmetry at high temperatures. A mean-field theory for rho(lambda) based on a heterogeneous elasticity model is proposed and shows good agreement with simulation data.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2022)
Article
Multidisciplinary Sciences
Alessandro Soloperto, Deborah Quaglio, Paola Baiocco, Isabella Romeo, Mattia Mori, Matteo Ardini, Caterina Presutti, Ida Sannino, Silvia Ghirga, Antonia Iazzetti, Rodolfo Ippoliti, Giancarlo Ruocco, Bruno Botta, Francesca Ghirga, Silvia Di Angelantonio, Alberto Boffi
Summary: Numerous studies have shown a strong correlation between the number of neurofibrillary tangles of the tau protein and Alzheimer's disease progression, making the quantitative detection of tau very promising from a clinical point of view. However, the lack of highly reliable fluorescent probes for selective imaging of tau neurofibrillary tangles is a major challenge. In this study, a small-size library of fluorescent probes was designed and evaluated in silico. The synthesized probe BT1 showed excellent photophysical properties and high selectivity for imaging hyperphosphorylated tau protein filaments in vitro.
SCIENTIFIC REPORTS
(2022)
Article
Multidisciplinary Sciences
Emmanouil Xypakis, Giorgio Gosti, Taira Giordani, Raffaele Santagati, Giancarlo Ruocco, Marco Leonetti
Summary: Blind-structured illumination microscopy (blind-SIM) is enhanced by a custom convolutional neural network architecture (BS-CNN) which outperforms other blind-SIM deconvolution algorithms. It provides a resolution improvement of 2.17 and reduces artifacts. Additionally, BS-CNN is robust in cross-database variability.
SCIENTIFIC REPORTS
(2022)
Article
Materials Science, Multidisciplinary
Martina Marcotulli, Maria Celeste Tirelli, Marina Volpi, Jakub Jaroszewicz, Chiara Scognamiglio, Piotr Kasprzycki, Karol Karnowski, Wojciech Swieszkowski, Giancarlo Ruocco, Marco Costantini, Gianluca Cidonio, Andrea Barbetta
Summary: 3D printing systems have evolved greatly in the last decade, becoming a top technology for academic and industrial applications. However, manufacturing polymeric materials with trabecular porosity and functionally graded architecture through additive platforms remains a technical challenge. This study presents a 3D extrusion printing strategy that enables the construction of high-accuracy polymeric foams with varying density and composition.
ADVANCED MATERIALS TECHNOLOGIES
(2023)
Review
Cell Biology
Ilaria Genovese, Ersilia Fornetti, Giancarlo Ruocco
Summary: The relationships between mitochondria, ER, and lysosomes play a crucial role in cell homeostasis regulation and stress response. Protein aggregation can lead to cellular damage and stress. This review summarizes the complex liaison between mitochondria, ER, and lysosomes, with a particular focus on their role in cancer.
FRONTIERS IN CELL AND DEVELOPMENTAL BIOLOGY
(2022)
Article
Biochemical Research Methods
Riccardo Reale, Giovanna Peruzzi, Maryamsadat Ghoreishi, Helena Stabile, Giancarlo Ruocco, Marco Leonetti
Summary: This article introduces a microfluidic scanning flow cytometer (mu SFC) that can achieve accurate angle-resolved scattering measurements within a standard polydimethylsiloxane microfluidic chip. In contrast to conventional flow cytometers and fluorescence activated cell sorters, the mu SFC yields linearly correlated size estimates and quantitative refractive index estimates for particles, making it suitable for characterizing biological samples and potentially applicable in diagnostic settings.
Article
Multidisciplinary Sciences
N. Shashaank, Mahalakshmi Somayaji, Mattia Miotto, Eugene V. Mosharov, Emily A. Makowicz, David A. Knowles, Giancarlo Ruocco, David L. Sulzer
Summary: Dopamine neurotransmission in the striatum plays a crucial role in normal and disease functions. This study utilizes computational models to analyze fast-scan cyclic voltammetry recordings in mice and provides insight into the modulation of dopamine release and reuptake. The findings support previous research and reveal the involvement of synuclein proteins in dopamine neurotransmission.
Meeting Abstract
Cell & Tissue Engineering
Gianluca Cidonio, Federico Salaris, Janos Kanczler, Alessandro Soloperto, Chiara Scognamiglio, Andrea Barbetta, Jonathan Dawson, Richard Oreffo, Alessandro Rosa, Giancarlo Ruocco
TISSUE ENGINEERING PART A
(2022)
Article
Chemistry, Physical
Marco Benedetti, Enrico Ventura, Enzo Marinari, Giancarlo Ruocco, Francesco Zamponi
Summary: This study compared the Hebbian unlearning algorithm with a supervised algorithm in neural networks, finding similarities in stability of stored memories and learning paths. The proposed geometric interpretation explained the optimal performance of the Hebbian unlearning algorithm.
JOURNAL OF CHEMICAL PHYSICS
(2022)
