"Validation" simulation model

CONTEXT: Parkinson's disease is a neurodegenerative condition characterized by the degeneration of dopaminergic neurons, resulting in motor disabilities such as rigidity, bradykinesia, postural instability, and resting tremors. While the exact cause of Parkinson's remains uncertain, both familial and sporadic forms are often associated with the G2019S mutation found in the kinase domain of LRRK2. Roco4 is an analogue of LRRK2 protein in Dictyostelium discoideum which is an established model organism to investigate LRRK2 inhibitors...

Thermodynamic and dynamic anomalies of water play a crucial role in supporting life on our planet. The two-state theory attributes these anomalies to a dynamic equilibrium between locally favored tetrahedral structures (LFTSs) and disordered normal liquid structures. This theory provides a straightforward, phenomenological explanation for water's unique thermodynamic and dynamic characteristics. To validate this two-state feature, it is critical to unequivocally identify these structural motifs in a dynamically fluctuating disordered liquid...

A prosthetic knee is designed to replace the functionality of an anatomical knee in transfemoral amputees. The purpose of a prosthetic knee is to restore mobility and compensate amputees for their impairment. In the present research numerical modelling and simulation of a carbon fabric reinforced polymer made polycentric prosthetic knee with four-bar mechanism was performed. Virtual prototyping with computer-aided design and computer-aided engineering software ensured geometric and structural stability of the knee design...

Mycobacteria are causative agents of tuberculosis (TB), which is a global health concern. Drug-resistant TB strains are rapidly emerging, thereby necessitating the urgent development of new drugs. Two-component signal transduction systems (TCSs) are signaling pathways involved in the regulation of various bacterial behaviors and responses to environmental stimuli. Applying specific inhibitors of TCSs can disrupt bacterial signaling, growth, and virulence, and can help combat drug-resistant TB. We conducted a comprehensive pharmacophore-based inhibitor screening and biochemical and biophysical examinations to identify, characterize, and validate potential inhibitors targeting the response regulators PhoP and MtrA of mycobacteria...

This data article describes the extensive experimental dataset of friction hysteresis measured during the round robin test of the original research article [1]. The round robin test was performed on the two different fretting rigs of Imperial College London and Politecnico di Torino, and consisted of recording comparable friction hysteresis loops on specimen pairs manufactured from the same batch of raw stainless steel. The reciprocating motion of the specimens was performed at room temperature under a wide range of test conditions, including different normal loads, displacement amplitudes, nominal areas of contact and excitation frequencies of 100 Hz and 175 Hz...

Biphasic models have been widely used to simulate the time-dependent biomechanical response of soft tissues. Modelling techniques of joints with biphasic weight-bearing soft tissues have been markedly improved over the last decade, enhancing our understanding of the function, degenerative mechanism and outcomes of interventions of joints. This paper reviews the recent advances, challenges and opportunities in computational models of joints with biphasic weight-bearing soft tissues. The review begins with an introduction of the function and degeneration of joints from a biomechanical aspect...

With the outbreak of the novel coronavirus SARS-CoV2, many countries have faced problems because of their available hospital capacity. Health systems must be prepared to restructure their facilities and meet the requirements of the pandemic while keeping their services and specialties active. This process, known as hospital reconversion, contributes to minimizing the risk of contagion between hospital staff and patients and optimizing the efficient treatment and disposal of healthcare wastes that represent a risk of nosocomial infection contagion...

OBJECTIVE: Real-time measurement of biological joint moment could enhance clinical assessments and generalize exoskeleton control. Accessing joint moments outside clinical and laboratory settings requires harnessing non-invasive wearable sensor data for indirect estimation. Previous approaches have been primarily validated during cyclic tasks, such as walking, but these methods are likely limited when translating to non-cyclic tasks where the mapping from kinematics to moments is not unique...

Table tennis is a sport that demands high levels of technical proficiency and body coordination from players. Biomechanical fingerprints can provide valuable insights into players' habitual movement patterns and characteristics, allowing them to identify and improve technical weaknesses. Despite the potential, few studies have developed effective methods for generating such fingerprints. To address this gap, we propose TacPrint, a framework for generating a biomechanical fingerprint for each player. TacPrint leverages machine learning techniques to extract comprehensive features from biomechanics data collected by inertial measurement units (IMU) and employs the attention mechanism to enhance model interpretability...

In the field of digital humanities, color research aims to discover explanations for painting history and color usage habits. However, researchers analyzing color relationships is challenging and time-consuming, as it requires color extraction and a detailed review of many painting images for reference and comparison of color relationships. In our work, we propose ColorNetVis, an interactive color network analysis tool that enables researchers to explore color relationships through color networks. The core of ColorNetVis is a bipartite network model that establishes a bipartite relationship between colors and Chinese painting within a scope based on color difference measurement...

The algal-bacterial shortcut nitrogen removal (ABSNR) process can be used to treat high ammonia strength wastewaters without external aeration. However, prior algal-bacterial SNR studies have been conducted under fixed light/dark periods that were not representative of natural light conditions. In this study, laboratory-scale photo-sequencing batch reactors (PSBRs) were used to treat anaerobic digester sidestream under varying light intensities that mimicked summer and winter conditions in Tampa, FL, USA. A dynamic mathematical model was developed for the ABSNR process, which was calibrated and validated using data sets from the laboratory PSBRs...

Isothiazolinones represent a class of heterocyclic compounds widely used in various applications, including as biocides in cosmetics, detergents, and paints, as well as in industrial wastewater treatment. Indeed, the presence of isothiazolinones in the environment and their associated potential health hazards have raised significant concerns. In this study, a non-adiabatic dynamics investigation was conducted using state-of-the-art methodologies to explore the photochemistry of isothiazolinones. A simplified model, isothiazol-3( 2H )-one (ISO), was employed to represent this compound class...

The rodent-borne Arenavirus in humans has led to the emergence of regional endemic situations and has deeply emerged into pandemic-causing viruses. Arenavirus have a bisegmented ambisense RNA that produces four proteins: glycoprotein, nucleocapsid, RdRp and Z protein. The peptide-based vaccine targets the glycoprotein of the virus encountered by the immune system. Screening of B-Cell and T-Cell epitopes was done based on their immunological properties like antigenicity, allergenicity, toxicity and anti-inflammatory properties were performed...

Identifying optimal collective variables to model transformations using atomic-scale simulations is a long-standing challenge. We propose a new method for the generation, optimization, and comparison of collective variables that can be thought of as a data-driven generalization of the path collective variable concept. It consists of a kernel ridge regression of the committor probability, which encodes a transformation's progress. The resulting collective variable is one-dimensional, interpretable, and differentiable, making it appropriate for enhanced sampling simulations requiring biasing...

BACKGROUND: Despite the successes of the Global Polio Eradication Initiative, substantial challenges remain in eradicating the poliovirus. The Sabin-strain (live-attenuated) virus in oral poliovirus vaccine (OPV) can revert to circulating vaccine-derived poliovirus (cVDPV) in under-vaccinated communities, regain neurovirulence and transmissibility, and cause paralysis outbreaks. Since the cessation of type 2-containing OPV (OPV2) in 2016, there have been cVDPV type 2 (cVDPV2) outbreaks in four out of six geographical World Health Organization regions, making these outbreaks a significant public health threat...

This work challenges the conventional approach of using NdIII 4 F3/2 lifetime changes for evaluating the experimental NdIII → YbIII energy transfer rate and efficiency. Using near-infrared (NIR) emitting Nd:Yb mixed-metal coordination polymers (CPs), synthesized via solvent-free thermal grinding, we demonstrate that the NdIII [2 H11/2 → 4 I15/2 ] → YbIII [2 F7/2 → 2 F5/2 ] pathway, previously overlooked, dominates energy transfer due to superior energy resonance and J -level selection rule compatibility...

Recent usage of Virtual Reality (VR) technology in surgical training has emerged because of its cost-effectiveness, time savings, and cognition-based feedback generation. However, the quantitative evaluation of its effectiveness in training is still not studied thoroughly. This paper demonstrates the effectiveness of a VR-based surgical training simulator in laparoscopic surgery and investigates how stochastic modeling represented as Continuous-time Markov-chain (CTMC) can be used to explicit the training status of the surgeon...

In this study, we combined AlphaFold-based approaches for atomistic modeling of multiple protein states and microsecond molecular simulations to accurately characterize conformational ensembles and binding mechanisms of convergent evolution for the SARS-CoV-2 Spike Omicron variants BA.1, BA.2, BA.2.75, BA.3, BA.4/BA.5 and BQ.1.1. We employed and validated several different adaptations of the AlphaFold methodology for modeling of conformational ensembles including the introduced randomized full sequence scanning for manipulation of sequence variations to systematically explore conformational dynamics of Omicron Spike protein complexes with the ACE2 receptor...

Nowadays dog bite is becoming a world public health problem. Therefore, the study aimed to develop a dog bite animal model that is helpful to solve these problems. In this study, the skull of an adult dog was scanned. The three-dimensional model of the dog maxillofacial bones and dentition was built by MIMICS. Next, the model was printed with Co-Cr alloy by using selective laser sintering technology to develop the dog bite simulation pliers. Then, to simulate dog bite to most, the maximum bite force of the pliers was measured and actions contained in dog bite process was analyzed...

The amygdala (AMY) is widely implicated in fear learning and fear behaviour, but it remains unclear how the many biological components present within AMY interact to achieve these abilities. Building on previous work, we hypothesize that individual AMY nuclei represent different quantities and that fear conditioning arises from error-driven learning on the synapses between AMY nuclei. We present a computational model of AMY that (a) recreates the divisions and connections between AMY nuclei and their constituent pyramidal and inhibitory neurons; (b) accommodates scalable high-dimensional representations of external stimuli; (c) learns to associate complex stimuli with the presence (or absence) of an aversive stimulus; (d) preserves feature information when mapping inputs to salience estimates, such that these estimates generalize to similar stimuli; and (e) induces a diverse profile of neural responses within each nucleus...