2,081 results on '"Unfolding"'
Search Results
2. Constructing cospectral graphs by unfolding non-bipartite graphs.
- Author
-
Kannan, M. Rajesh, Pragada, Shivaramakrishna, and Wankhede, Hitesh
- Subjects
- *
BIPARTITE graphs , *TENSOR products , *LAPLACIAN matrices - Abstract
In 2010, Butler introduced the unfolding operation on a bipartite graph to produce two bipartite graphs, which are cospectral for the adjacency and the normalized Laplacian matrices. In this article, we describe how the idea of unfolding a bipartite graph with respect to another bipartite graph can be extended to nonbipartite graphs. In particular, we describe how unfoldings involving reflexive bipartite, semi-reflexive bipartite, and multipartite graphs are used to obtain cospectral nonisomorphic graphs for the adjacency matrix. [ABSTRACT FROM AUTHOR]
- Published
- 2024
- Full Text
- View/download PDF
3. Copula-Based Non-Metric Unfolding on Augmented Data Matrix.
- Author
-
Nai Ruscone, Marta, Fernández, Daniel, and D'Ambrosio, Antonio
- Subjects
- *
MEASUREMENT - Abstract
A multidimensional unfolding technique that is not prone to degenerate solutions and is based on multidimensional scaling of a complete data matrix is proposed. We adopt the strategy of augmenting the data matrix, trying to build a complete dissimilarity matrix, by using copula-based association measures among rankings (the individuals), and between rankings and objects (namely, a rank-order representation of the objects through tied rankings). The proposed technique leads to acceptable recovery of given preference structures. [ABSTRACT FROM AUTHOR]
- Published
- 2024
- Full Text
- View/download PDF
4. Potenziale entfalten: Einwände gegen eine verbreitete Forderung.
- Author
-
Meyer, Kirsten
- Subjects
EDUCATIONAL planning ,RESPECT - Abstract
Copyright of Zeitschrift für Pädagogik is the property of Julius Beltz GmbH & Co. KG Beltz Juventa and its content may not be copied or emailed to multiple sites or posted to a listserv without the copyright holder's express written permission. However, users may print, download, or email articles for individual use. This abstract may be abridged. No warranty is given about the accuracy of the copy. Users should refer to the original published version of the material for the full abstract. (Copyright applies to all Abstracts.)
- Published
- 2024
- Full Text
- View/download PDF
5. Monomer unfolding of a bacterial ESCRT‐III superfamily member is coupled to oligomer disassembly.
- Author
-
Quarta, Ndjali, Bhandari, Tika Ram, Girard, Martin, Hellmann, Nadja, and Schneider, Dirk
- Abstract
The inner membrane associated protein of 30 kDa (IM30), a member of the endosomal sorting complex required for transport (ESCRT‐III) superfamily, is crucially involved in the biogenesis and maintenance of thylakoid membranes in cyanobacteria and chloroplasts. In solution, IM30 assembles into various large oligomeric barrel‐ or tube‐like structures, whereas upon membrane binding it forms large, flat carpet structures. Dynamic localization of the protein in solution, to membranes and changes of the oligomeric states are crucial for its in vivo function. ESCRT‐III proteins are known to form oligomeric structures that are dynamically assembled from monomeric/smaller oligomeric proteins, and thus these smaller building blocks must be assembled sequentially in a highly orchestrated manner, a still poorly understood process. The impact of IM30 oligomerization on function remains difficult to study due to its high intrinsic tendency to homo‐oligomerize. Here, we used molecular dynamics simulations to investigate the stability of individual helices in IM30 and identified unstable regions that may provide structural flexibility. Urea‐mediated disassembly of the IM30 barrel structures was spectroscopically monitored, as well as changes in the protein's tertiary and secondary structure. The experimental data were finally compared to a three‐state model that describes oligomer disassembly and monomer unfolding. In this study, we identified a highly stable conserved structural core of ESCRT‐III proteins and discuss the advantages of having flexible intermediate structures and their putative relevance for ESCRT‐III proteins. [ABSTRACT FROM AUTHOR]
- Published
- 2024
- Full Text
- View/download PDF
6. Regularization-based methods for ordinal quantification.
- Author
-
Bunse, Mirko, Moreo, Alejandro, Sebastiani, Fabrizio, and Senz, Martin
- Subjects
LINEAR orderings ,DATA mining ,PRIOR learning ,ALGORITHMS ,ASTROPHYSICS - Abstract
Quantification, i.e., the task of predicting the class prevalence values in bags of unlabeled data items, has received increased attention in recent years. However, most quantification research has concentrated on developing algorithms for binary and multi-class problems in which the classes are not ordered. Here, we study the ordinal case, i.e., the case in which a total order is defined on the set of n > 2 classes. We give three main contributions to this field. First, we create and make available two datasets for ordinal quantification (OQ) research that overcome the inadequacies of the previously available ones. Second, we experimentally compare the most important OQ algorithms proposed in the literature so far. To this end, we bring together algorithms proposed by authors from very different research fields, such as data mining and astrophysics, who were unaware of each others' developments. Third, we propose a novel class of regularized OQ algorithms, which outperforms existing algorithms in our experiments. The key to this gain in performance is that our regularization prevents ordinally implausible estimates, assuming that ordinal distributions tend to be smooth in practice. We informally verify this assumption for several real-world applications. [ABSTRACT FROM AUTHOR]
- Published
- 2024
- Full Text
- View/download PDF
7. Dynamics and Thermodynamics Study of the Adsorption of Lysozyme to 2D SnSe Nanoflake Surfaces with Associated Unfolding.
- Author
-
Samui, Rajesh, Saha, Satyajit, Guha, Prasanta Kumar, and Bhunia, Amit Kumar
- Subjects
- *
BINDING constant , *ENERGY transfer , *LYSOZYMES , *BINDING sites , *SURFACE interactions - Abstract
In this work, we explore the interaction as well as corona formation and interfacial phenomena of lysozyme (LYZ) and 2D SnSe nanoflake. The optical results indicate formation of ground state complex with an apparent association constant of 1.5 × 103 (mol)−1. The dynamics of the in situ interaction exhibited surface reorganization (t2 = 73.5 min) and unfolding, which were more prominent than binding (t1 = 3 min) for tryptophan residues of LYZ. The formations of soft and hard corona of the LYZ structure were clearly observed from HRTEM. The emission quenching exhibited tertiary deformation of the LYZ structure with positive cooperative binding (n > 1) and dynamics of quenching followed the sigmoidal Boltzmann nature of the energy transfer process. The ultrafast lifetime of the bioconjugate varied from 1.9–1.35 ns with a maximum 63% energy transfer efficiency within 300 min of the corona evolution. The decrement of α helix (58.87%–21.78%) and increment of β sheet (5.27%–23.98%) were observed after interaction, with the conversion of large amount of α helix into β sheet. The ITC results showed that the injection heat results followed two‐site binding model, and the exothermic binding was dominate over the interaction. The second phase binding is driven by larger positive entropy, where the first binding site has a stronger association. [ABSTRACT FROM AUTHOR]
- Published
- 2024
- Full Text
- View/download PDF
8. La educación individualizada en el pensamiento pedagógico de Edith Stein.
- Author
-
MUÑOZ-ARRANZ, MILAGROS
- Subjects
- *
PHILOSOPHERS , *VOCABULARY , *AUTHORS - Abstract
For Edith Stein, individualized education cannot be separated from personalized education, without these notions being synonymous. For our study we take the concepts of potency (Potenz) and act (Akt), developed in her work Finite and Eternal Being, and we link them to the words commonly used by the philosopher: unfolding (Entfaltung) and development (Entwicklung). The objective is to argue, from the point of view of Edith Stein's pedagogical thought, the individualized nature of all educational interventions, anthropologically justify it is need, and present the relationship that the author establishes with the concept of personalized education. [ABSTRACT FROM AUTHOR]
- Published
- 2024
- Full Text
- View/download PDF
9. 还原型谷胱甘肽诱导溶菌酶界面组装 成膜机制及膜性能分析.
- Author
-
周 彬, 李俊娇, 郭大山, 武 璨, 胡煜莹, and 崔 冰
- Subjects
X-ray photoelectron spectroscopy ,TRANSMISSION electron microscopy ,LYSOZYMES ,SULFHYDRYL group ,FLUORESCENCE spectroscopy - Abstract
Copyright of Shipin Kexue/ Food Science is the property of Food Science Editorial Department and its content may not be copied or emailed to multiple sites or posted to a listserv without the copyright holder's express written permission. However, users may print, download, or email articles for individual use. This abstract may be abridged. No warranty is given about the accuracy of the copy. Users should refer to the original published version of the material for the full abstract. (Copyright applies to all Abstracts.)
- Published
- 2024
- Full Text
- View/download PDF
10. Resveratrol Effect on α-Lactalbumin Thermal Stability.
- Author
-
Precupas, Aurica, Gheorghe, Daniela, Leonties, Anca Ruxandra, and Popa, Vlad Tudor
- Subjects
PEPTIDE mass fingerprinting ,DIFFERENTIAL scanning calorimetry ,THERMAL stability ,CIRCULAR dichroism ,PROTEIN structure - Abstract
The effect of resveratrol (RESV) on α-lactalbumin (α-LA) thermal stability was evaluated using differential scanning calorimetry (DSC), circular dichroism (CD) and dynamic light scattering (DLS) measurements. Complementary information offered by molecular docking served to identify the binding site of the ligand on the native structure of protein and the type of interacting forces. DSC thermograms revealed a double-endotherm pattern with partial overlapping of the two components. The most relevant effect of RESV is manifested in the narrowing of the protein thermal fingerprint: the first process (peak temperature T
1 ) is shifted to higher temperatures while the second one (peak temperature T2 ) to lower values. The CD data indicated partial conformational changes in the protein non-α-helix domain at T1 , resulting in a β-sheet richer intermediate (BSRI) with an unaffected, native-like α-helix backbone. The RESV influence on this process may be defined as slightly demoting, at least within DSC conditions (linear heating rate of 1 K min−1 ). On further heating, unfolding of the α-helix domain takes place at T2 , with RESV acting as a promoter of the process. Long time incubation at 333 K produced the same type of BSRI: no significant effect of RESV on the secondary structure content was detected by CD spectroscopy. Nevertheless, the size distribution of the protein population obtained from DLS measurements revealed the free (non-bound) RESV action manifested in the developing of larger size aggregates. [ABSTRACT FROM AUTHOR]- Published
- 2024
- Full Text
- View/download PDF
11. Formation Mechanism and Performance of Films through Reduced Glutathione-Induced Lysozyme Interface Assembly
- Author
-
ZHOU Bin, LI Junjiao, GUO Dashan, WU Can, HU Yuying, CUI Bing
- Subjects
reduced glutathione ,lysozyme ,unfolding ,self-assembly ,film ,Food processing and manufacture ,TP368-456 - Abstract
In this study, the mechanism of film formation through glutathione-induced lysozyme interface assembly was verified by spectroscopic methods, and the formed film was characterized by ellipsometry. N-(1-pyrenyl)maleimide (NPM) staining demonstrated that reduced glutathione broken the disulfide bonds of lysozyme leading to release of free sulfhydryl groups. Together, tryptophan fluorescence spectroscopy and lysozyme activity assay verified that the disulfide bond Cys6-Cys127 in lysozyme was broken. In addition, the unfolded lysozyme was found to still have antibacterial activity. The lysozyme film was transparent and colorless. Atom force microscopy (AFM) and transmission electron microscopy (TEM) revealed that it was composed of lysozyme aggregates with a uniform, smooth and dense surface. The results of X-ray photoelectron spectroscopy (XPS) and laser confocal Raman spectroscopy (LCRS) indicated that the lysozyme nanofilm might possess interfacial adhesion. The results of ellipsometry showed that the maximum thickness of the film was approximately 900 nm, and did not increase without limit with the increase in incubation time or the concentration of the reactants. Its stiffness value, elastic modulus and hardness were 29.32–34.21 μN/nm, 24.00–27.93 GPa, and 0.44–0.49 GPa, respectively, which were in the strength range of the protein film. The three-phase contact angle of the film was around 70°, indicating good hydrophilicity. Its thermal stability was high, and no degradation occurred at 200 ℃. The preparation of the lysozyme nanofilm provides a good idea and reference for the construction of novel edible coatings.
- Published
- 2024
- Full Text
- View/download PDF
12. Profile-based latent class distance association analyses for sparse tables:application to the attitude of European citizens towards sustainable tourism.
- Author
-
Bassi, Francesca, Vera, José Fernando, and Marmolejo Martín, Juan Antonio
- Abstract
Social and behavioural sciences often deal with the analysis of associations for cross-classified data. This paper focuses on the study of the patterns observed on European citizens regarding their attitude towards sustainable tourism, specifically their willingness to change travel and tourism habits to be more sustainable. The data collected the intention to comply with nine sustainable actions; answers to these questions generated individual profiles; moreover, European country belonging is reported. Therefore, unlike a variable-oriented approach, here we are interested in a person-oriented approach through profiles. Some traditional methods are limited in their performance when using profiles, for example, by sparseness of the contingency table. We removed many of these limitations by using a latent class distance association model, clustering the row profiles into classes and representing these together with the categories of the response variable in a low-dimensional space. We showed, furthermore, that an easy interpretation of associations between clusters' centres and categories of a response variable can be incorporated in this framework in an intuitive way using unfolding. Results of the analyses outlined that citizens mostly committed to an environmentally friendly behavior live in Sweden and Romania; citizens less willing to change their habits towards a more sustainable behavior live in Belgium, Cyprus, France, Lithuania and the Netherlands. Citizens preparedness to change habits however depends also on their socio-demographic characteristics such as gender, age, occupation, type of community where living, household size, and the frequency of travelling before the Covid-19 pandemic. [ABSTRACT FROM AUTHOR]
- Published
- 2024
- Full Text
- View/download PDF
13. Understanding Osaka mutation polymorphic Aβ fibril response to static and oscillating electric fields: insights from computational modeling
- Author
-
Mukhriddin Makhkamov, Artyom Baev, Erkin Kurganov, and Jamoliddin Razzokov
- Subjects
Alzheimer’s disease ,Polymorphic Aβ fibril ,Osaka mutation ,Molecular dynamics ,Electric field ,Unfolding ,Medicine ,Science - Abstract
Abstract Alzheimer’s disease (AD) is a prevalent neurodegenerative disorder, impacting millions of individuals worldwide. Among its defining characteristics is the accumulation of senile plaques within the brain’s gray matter, formed through the self-assembly of misfolded proteins contributing to the progressive symptoms of AD. This study investigates a polymorphic Aβ fibril under static and oscillating electric fields using molecular dynamics simulation. Specifically, we utilized a polymorphic fibrillar complex composed of two intertwined pentamer-strands of the Aβ1–40 peptide with the Osaka mutation (E22Δ), known for its toxicity and stable structure. Our findings demonstrate that a 0.3 and 0.4 V/nm electric field combined with a 0.20 GHz frequency effectively disrupts the polymorphic conformation of Aβ fibrils. Furthermore, we elucidate the molecular mechanisms underlying this disruption, providing insights into the potential therapeutic use of oscillating electric fields for AD. This research offers valuable insights into novel therapeutic approaches for combating AD pathology.
- Published
- 2024
- Full Text
- View/download PDF
14. Understanding Osaka mutation polymorphic Aβ fibril response to static and oscillating electric fields: insights from computational modeling.
- Author
-
Makhkamov, Mukhriddin, Baev, Artyom, Kurganov, Erkin, and Razzokov, Jamoliddin
- Abstract
Alzheimer’s disease (AD) is a prevalent neurodegenerative disorder, impacting millions of individuals worldwide. Among its defining characteristics is the accumulation of senile plaques within the brain’s gray matter, formed through the self-assembly of misfolded proteins contributing to the progressive symptoms of AD. This study investigates a polymorphic Aβ fibril under static and oscillating electric fields using molecular dynamics simulation. Specifically, we utilized a polymorphic fibrillar complex composed of two intertwined pentamer-strands of the Aβ1–40 peptide with the Osaka mutation (E22Δ), known for its toxicity and stable structure. Our findings demonstrate that a 0.3 and 0.4 V/nm electric field combined with a 0.20 GHz frequency effectively disrupts the polymorphic conformation of Aβ fibrils. Furthermore, we elucidate the molecular mechanisms underlying this disruption, providing insights into the potential therapeutic use of oscillating electric fields for AD. This research offers valuable insights into novel therapeutic approaches for combating AD pathology. [ABSTRACT FROM AUTHOR]
- Published
- 2024
- Full Text
- View/download PDF
15. The experimental internal bremsstrahlung spectrum of 14C isotope.
- Author
-
Almaz, Ekrem, Çelıktaş, Cüneyt, Aygör, Hasan Ali, and Saritaş, Turgut
- Abstract
The continuous internal bremsstrahlung spectrum accompanying a beta and neutrino from the 14 C isotope was measured by magnetic deflection method in the region of 10–150 keV using a 7.62 cm × 7.62 cm NaI(Tl) scintillation spectrometer. The NaI(Tl) detector was calibrated by the standard radioactive sources. The detector response functions are generated for single-energy gamma photons with the help of experimental detector parameters and the Monte Carlo method. The experimental set-up and the geometry were adjusted carefully to minimise the external bremsstrahlung effect and the undesirable gamma counts from the surroundings in the detector. The raw experimental data were unfolded from the detector response effects by applying the singular value decomposition method. The experimental spectrum was compared with both theoretical and Monte Carlo calculation spectra. [ABSTRACT FROM AUTHOR]
- Published
- 2024
- Full Text
- View/download PDF
16. Probing the structural stability of R‐phycocyanin under pressure.
- Author
-
Minic, Simeon, Velickovic, Luka, Annighöfer, Burkhard, Thureau, Aurélien, Gligorijevic, Nikola, Jovanovic, Zorana, Brûlet, Annie, and Combet, Sophie
- Abstract
The red macroalgae Porphyra, commonly known as Nori, is widely used as food around the world due to its high nutrient content, including the significant abundance of colored phycobiliproteins (PBPs). Among these, R‐phycocyanin (R‐PC) stands out for its vibrant purple color and numerous bioactive properties, making it a valuable protein for the food industry. However, R‐PC's limited thermal stability necessitates alternative processing methods to preserve its color and bioactive properties. Our study aimed to investigate the in‐situ stability of oligomeric R‐PC under high pressure (HP) conditions (up to 4000 bar) using a combination of absorption, fluorescence, and small‐angle X‐ray scattering (SAXS) techniques. The unfolding of R‐PC is a multiphase process. Initially, low pressure induces conformational changes in the R‐PC oligomeric form (trimers). As pressure increases above 1600 bar, these trimers dissociate into monomers, and at pressures above 3000 bar, the subunits begin to unfold. When returned to atmospheric pressure, R‐PC partially refolds, retaining 50% of its original color absorbance. In contrast, heat treatment causes irreversible and detrimental effects on R‐PC color, highlighting the advantages of HP treatment in preserving both the color and bioactive properties of R‐PC compared to heat treatment. [ABSTRACT FROM AUTHOR]
- Published
- 2024
- Full Text
- View/download PDF
17. Unfolding experimental distortions in beta spectrometry.
- Author
-
Craveiro, Gael, Leblond, Sylvain, Mougeot, Xavier, Vivier, Matthieu, Estienne, Magali, and Commara, Marco La
- Subjects
TIKHONOV regularization ,COVARIANCE matrices ,SPECTROMETRY ,RADIOISOTOPES - Abstract
The distortions of measured beta spectra are addressed by means of unfolding algorithms. Two different approaches, the Maximum-Likelihood ExpectationMaximization and the Tikhonov regularization, are tested on various simulated spectra, for which the initial spectrum to retrieve is known, and on a
99 Tc spectrum measured with our dedicated setup. Statistical uncertainties of distorted measured spectra are propagated by determining the covariance matrices. Both algorithms provide satisfactory results but Tikhonov performs overall better for most of the studied radionuclides. Highlight is made on the necessity to employ at least two independent methods to ensure the accuracy of the unfolded spectra and to estimate the internal bias of each algorithm. [ABSTRACT FROM AUTHOR]- Published
- 2024
- Full Text
- View/download PDF
18. Homogenization of quasilinear problems with semilinear terms and Signorini boundary conditions in perforated domains.
- Author
-
Avila, Jake
- Abstract
This paper studies the upscaling of an elliptic problem with a highly oscillating quasilinear matrix coefficient, a quasilinear term, and a semilinear term in domains periodically perforated with holes of critical size. A Signorini boundary condition is imposed on the boundary of the holes, while a Dirichlet boundary condition is prescribed on the exterior boundary. Using the periodic unfolding method, we obtain an obstacle problem with a nonnegativity spreading effect. [ABSTRACT FROM AUTHOR]
- Published
- 2024
- Full Text
- View/download PDF
19. Unfolding and de-confounding: biologically meaningful causal inference from longitudinal multi-omic networks using METALICA
- Author
-
Daniel Ruiz-Perez, Isabella Gimon, Musfiqur Sazal, Kalai Mathee, and Giri Narasimhan
- Subjects
longitudinal microbiome analysis ,multi-omic integration ,causal inference ,unfolding ,de-confounding ,Microbiology ,QR1-502 - Abstract
ABSTRACT A key challenge in the analysis of microbiome data is the integration of multi-omic datasets and the discovery of interactions between microbial taxa, their expressed genes, and the metabolites they consume and/or produce. In an effort to improve the state of the art in inferring biologically meaningful multi-omic interactions, we sought to address some of the most fundamental issues in causal inference from longitudinal multi-omics microbiome data sets. We developed METALICA, a suite of tools and techniques that can infer interactions between microbiome entities. METALICA introduces novel unrolling and de-confounding techniques used to uncover multi-omic entities that are believed to act as confounders for some of the relationships that may be inferred using standard causal inferencing tools. The results lend support to predictions about biological models and processes by which microbial taxa interact with each other in a microbiome. The unrolling process helps identify putative intermediaries (genes and/or metabolites) to explain the interactions between microbes; the de-confounding process identifies putative common causes that may lead to spurious relationships to be inferred. METALICA was applied to the networks inferred by existing causal discovery, and network inference algorithms were applied to a multi-omics data set resulting from a longitudinal study of IBD microbiomes. The most significant unrollings and de-confoundings were manually validated using the existing literature and databases.IMPORTANCEWe have developed a suite of tools and techniques capable of inferring interactions between microbiome entities. METALICA introduces novel techniques called unrolling and de-confounding that are employed to uncover multi-omic entities considered to be confounders for some of the relationships that may be inferred using standard causal inferencing tools. To evaluate our method, we conducted tests on the inflammatory bowel disease (IBD) dataset from the iHMP longitudinal study, which we pre-processed in accordance with our previous work. From this dataset, we generated various subsets, encompassing different combinations of metagenomics, metabolomics, and metatranscriptomics datasets. Using these multi-omics datasets, we demonstrate how the unrolling process aids in the identification of putative intermediaries (genes and/or metabolites) to explain the interactions between microbes. Additionally, the de-confounding process identifies potential common causes that may give rise to spurious relationships to be inferred. The most significant unrollings and de-confoundings were manually validated using the existing literature and databases.
- Published
- 2024
- Full Text
- View/download PDF
20. A temperature-dependent investigation of the impact of metal nanoparticles on the structural integrity of serum albumin
- Author
-
Ajamaluddin Malik, Abdulaziz Alamri, Javed Masood Khan, Nojood Altwaijry, Abir Alamro, Abdullah S. Alhomida, Hamza Odeibat, and Mohammad Shamsul Ola
- Subjects
Metal nanoparticles ,Nanotoxicity ,Nanomaterial ,Corona ,Unfolding ,Far UV CD ,Science (General) ,Q1-390 - Abstract
Nanoparticles (NPs) have distinct properties due to their small size and high surface area-to-volume ratio. These characteristics result in unique features not seen in bulk materials. Metals, semiconductors, and polymers are among the many varieties. Nanomaterials are used in various industries, including medical, electronics, and environmental cleanup. However, their potential environmental and health consequences must be carefully considered. Metal nanoparticles (MNPs) have received significant attention due to their outstanding physicochemical features and diverse applications in various sectors. MNPs are utilized in different fields, from electronics to health. Previously, the effect of various metal nanoparticles on the structure, stability, and functionality of metabolic enzymes was investigated. Copper (Cu) NPs were found to have significant negative impacts on these enzymes. The focus of the current investigation turned to serum albumin, a vital plasma protein containing oxidized cysteine residues. The findings demonstrated that NPs had a minor impact on the structure and stability of serum albumin, in contrast to the effects observed on reduced cysteine-containing enzymes.
- Published
- 2024
- Full Text
- View/download PDF
21. Whole-grain Petri Nets and Processes.
- Author
-
KOCK, JOACHIM
- Subjects
PETRI nets ,SEMANTICS ,GROUPOIDS - Abstract
We present a formalism for Petri nets based on polynomial-style finite-set configurations and etale maps. The formalism supports both a geometric semantics in the style of Goltz and Reisig (processes are etale maps from graphs) and an algebraic semantics in the style of Meseguer and Montanari, in terms of free coloured props, and allows the following unification: for P a Petri net, the Segal space of P-processes is shown to be the free coloured prop-in-groupoids on P. There is also an unfolding semantics à la Winskel, which bypasses the classical symmetry problems: with the new formalism, every Petri net admits a universal unfolding, which in turn has associated an event structure and a Scott domain. Since everything is encoded with explicit sets, Petri nets and their processes have elements. In particular, individual-token semantics is native. (Collectivetoken semantics emerges from rather drastic quotient constructions à la Best–Devillers, involving taking π0 of the groupoids of states [ABSTRACT FROM AUTHOR]
- Published
- 2023
- Full Text
- View/download PDF
22. Token Trail Semantics II - Petri Nets And Their Net Language
- Author
-
Kovář, Jakub, Bergenthum, Robin, Goos, Gerhard, Series Editor, Hartmanis, Juris, Founding Editor, van Leeuwen, Jan, Series Editor, Hutchison, David, Editorial Board Member, Kanade, Takeo, Editorial Board Member, Kittler, Josef, Editorial Board Member, Kleinberg, Jon M., Editorial Board Member, Kobsa, Alfred, Series Editor, Mattern, Friedemann, Editorial Board Member, Mitchell, John C., Editorial Board Member, Naor, Moni, Editorial Board Member, Nierstrasz, Oscar, Series Editor, Pandu Rangan, C., Editorial Board Member, Sudan, Madhu, Series Editor, Terzopoulos, Demetri, Editorial Board Member, Tygar, Doug, Editorial Board Member, Weikum, Gerhard, Series Editor, Vardi, Moshe Y, Series Editor, Bertino, Elisa, Editorial Board Member, Gao, Wen, Editorial Board Member, Steffen, Bernhard, Editorial Board Member, Yung, Moti, Editorial Board Member, Woeginger, Gerhard, Editorial Board Member, Kristensen, Lars Michael, editor, and van der Werf, Jan Martijn, editor
- Published
- 2024
- Full Text
- View/download PDF
23. Molecular dynamics simulations suggest the potential toxicity of fluorinated graphene to HP35 protein via unfolding the α-helix structure
- Author
-
Fangrong Zou, Zonglin Gu, Jose Manuel Perez-Aguilar, and Yuqi Luo
- Subjects
Fluorinated graphene ,HP35 protein ,Unfolding ,Toxicity ,Molecular dynamics simulation ,Medicine ,Science - Abstract
Abstract Fluorinated graphene, a two-dimensional nanomaterial composed of three atomic layers, a central carbon layer sandwiched between two layers of fluorine atoms, has attracted considerable attention across various fields, particularly for its potential use in biomedical applications. Nonetheless, scant effort has been devoted to assessing the potential toxicological implications of this nanomaterial. In this study, we scrutinize the potential impact of fluorinated graphene on a protein model, HP35 by utilizing extensive molecular dynamics (MD) simulation methods. Our MD results elucidate that upon adsorption to the nanomaterial, HP35 undergoes a denaturation process initiated by the unraveling of the second helix of the protein and the loss of the proteins hydrophobic core. In detail, substantial alterations in various structural features of HP35 ensue, including alterations in hydrogen bonding, Q value, and RMSD. Subsequent analyses underscore that hydrophobic and van der Waals interactions (predominant), alongside electrostatic energy (subordinate), exert influence over the adsorption of HP35 on the fluorinated graphene surface. Mechanistic scrutiny attests that the unrestrained lateral mobility of HP35 on the fluorinated graphene nanomaterial primarily causes the exposure of HP35's hydrophobic core, resulting in the eventual structural denaturation of HP35. A trend in the features of 2D nanostructures is proposed that may facilitate the denaturation process. Our findings not only substantiate the potential toxicity of fluorinated graphene but also unveil the underlying molecular mechanism, which thereby holds significance for the prospective utilization of such nanomaterials in the field of biomedicine.
- Published
- 2024
- Full Text
- View/download PDF
24. Averaged Deep Denoisers for Image Regularization.
- Author
-
Nair, Pravin and Chaudhury, Kunal N.
- Abstract
Plug-and-Play (PnP) and Regularization-by-Denoising (RED) are recent paradigms for image reconstruction that leverage the power of modern denoisers for image regularization. In particular, they have been shown to deliver state-of-the-art reconstructions with CNN denoisers. Since the regularization is performed in an ad-hoc manner, understanding the convergence of PnP and RED has been an active research area. It was shown in recent works that iterate convergence can be guaranteed if the denoiser is averaged or nonexpansive. However, integrating nonexpansivity with gradient-based learning is challenging, the core issue being that testing nonexpansivity is intractable. Using numerical examples, we show that existing CNN denoisers tend to violate the nonexpansive property, which can cause PnP or RED to diverge. In fact, algorithms for training nonexpansive denoisers either cannot guarantee nonexpansivity or are computationally intensive. In this work, we construct contractive and averaged image denoisers by unfolding splitting-based optimization algorithms applied to wavelet denoising and demonstrate that their regularization capacity for PnP and RED can be matched with CNN denoisers. To our knowledge, this is the first work to propose a simple framework for training contractive denoisers using network unfolding. [ABSTRACT FROM AUTHOR]
- Published
- 2024
- Full Text
- View/download PDF
25. Molecular dynamics simulations suggest the potential toxicity of fluorinated graphene to HP35 protein via unfolding the α-helix structure.
- Author
-
Zou, Fangrong, Gu, Zonglin, Perez-Aguilar, Jose Manuel, and Luo, Yuqi
- Abstract
Fluorinated graphene, a two-dimensional nanomaterial composed of three atomic layers, a central carbon layer sandwiched between two layers of fluorine atoms, has attracted considerable attention across various fields, particularly for its potential use in biomedical applications. Nonetheless, scant effort has been devoted to assessing the potential toxicological implications of this nanomaterial. In this study, we scrutinize the potential impact of fluorinated graphene on a protein model, HP35 by utilizing extensive molecular dynamics (MD) simulation methods. Our MD results elucidate that upon adsorption to the nanomaterial, HP35 undergoes a denaturation process initiated by the unraveling of the second helix of the protein and the loss of the proteins hydrophobic core. In detail, substantial alterations in various structural features of HP35 ensue, including alterations in hydrogen bonding, Q value, and RMSD. Subsequent analyses underscore that hydrophobic and van der Waals interactions (predominant), alongside electrostatic energy (subordinate), exert influence over the adsorption of HP35 on the fluorinated graphene surface. Mechanistic scrutiny attests that the unrestrained lateral mobility of HP35 on the fluorinated graphene nanomaterial primarily causes the exposure of HP35's hydrophobic core, resulting in the eventual structural denaturation of HP35. A trend in the features of 2D nanostructures is proposed that may facilitate the denaturation process. Our findings not only substantiate the potential toxicity of fluorinated graphene but also unveil the underlying molecular mechanism, which thereby holds significance for the prospective utilization of such nanomaterials in the field of biomedicine. [ABSTRACT FROM AUTHOR]
- Published
- 2024
- Full Text
- View/download PDF
26. Unfolding experimental distortions in beta spectrometry
- Author
-
Gaël Craveiro, Sylvain Leblond, Xavier Mougeot, and Matthieu Vivier
- Subjects
beta spectra ,experimental distortions ,unfolding ,MLEM ,Tikhonov ,uncertainties ,Physics ,QC1-999 - Abstract
The distortions of measured beta spectra are addressed by means of unfolding algorithms. Two different approaches, the Maximum-Likelihood Expectation-Maximization and the Tikhonov regularization, are tested on various simulated spectra, for which the initial spectrum to retrieve is known, and on a 99Tc spectrum measured with our dedicated setup. Statistical uncertainties of distorted measured spectra are propagated by determining the covariance matrices. Both algorithms provide satisfactory results but Tikhonov performs overall better for most of the studied radionuclides. Highlight is made on the necessity to employ at least two independent methods to ensure the accuracy of the unfolded spectra and to estimate the internal bias of each algorithm.
- Published
- 2024
- Full Text
- View/download PDF
27. High Hydrostatic Pressure: Influences on Allergenicity, Bioactivities, and Structural and Functional Properties of Proteins from Diverse Food Sources.
- Author
-
Braspaiboon, Sukan and Laokuldilok, Thunnop
- Abstract
High hydrostatic pressure (HHP) has gained prominence in the food processing industry over the last decade. In addition to the effectiveness of microbial and enzymatic inactivation, HHP directly impacts protein structures and properties. Accordingly, this review article aims to consolidate relevant research findings elucidating the effects of HHP on protein structure, allergenicity, bioactivities, and functional properties across diverse protein sources. They encompass cereals, legumes, nuts, meat, poultry products, milk, eggs, seafood, algae, insects, seeds, and vegetables. This review provides insights into the consistent trends of HHP effects on each protein source. In conclusion, HHP induces alterations in non-covalent bonds within protein structures, leading to the unfolding of their interior regions and consequential changes in their properties. Remarkably, the allergenicity of cereals, legumes, and nuts decreases while their bioactivities and digestibility escalate. The disruption of non-covalent bonds during HHP results in the exposure of the interior hydrophobic regions to the surface microenvironment, thereby enhancing the surface hydrophobicity of proteins, particularly those derived from seeds and vegetables. HHP weakens the allergenicity and elevates the foaming properties of proteins from dairy products, including improving the gelling properties and antioxidant activities of egg proteins. Texture profiles of meat and poultry, particularly hardness, are enhanced. Furthermore, HHP demonstrates the potential to diminish the allergenicity of seafood proteins and augment insect protein bioactivities. Lastly, HHP enhances the extraction of algal bioactive components, improving their nutritional quality. [ABSTRACT FROM AUTHOR]
- Published
- 2024
- Full Text
- View/download PDF
28. Organic Personality: Divine and Human Personality in Herman Bavinck.
- Author
-
Flowers, Skyler R.
- Subjects
- *
MODERN philosophy , *DOCTRINAL theology - Abstract
Bavinck's critical appropriation of modern grammar in discussing Christian doctrine has led to his being described as a thinker who is "modern yet orthodox." His appropriation of modern philosophy and psychology is clearly seen in his use of 'personality' in his doctrine of God and anthropology. This article argues that his use in these two areas demonstrates the organic ontology of creatures created in the image of their Creator. Thus, in understanding divine personality, human personality comes into focus, both theologically and psychologically. The article concludes with reflections on how the study of personality in Bavinck's writings helps one to understand his entire project. [ABSTRACT FROM AUTHOR]
- Published
- 2024
- Full Text
- View/download PDF
29. Resveratrol Effect on α-Lactalbumin Thermal Stability
- Author
-
Aurica Precupas, Daniela Gheorghe, Anca Ruxandra Leonties, and Vlad Tudor Popa
- Subjects
lactalbumin ,resveratrol ,aggregates ,unfolding ,DSC ,CD ,Biology (General) ,QH301-705.5 - Abstract
The effect of resveratrol (RESV) on α-lactalbumin (α-LA) thermal stability was evaluated using differential scanning calorimetry (DSC), circular dichroism (CD) and dynamic light scattering (DLS) measurements. Complementary information offered by molecular docking served to identify the binding site of the ligand on the native structure of protein and the type of interacting forces. DSC thermograms revealed a double-endotherm pattern with partial overlapping of the two components. The most relevant effect of RESV is manifested in the narrowing of the protein thermal fingerprint: the first process (peak temperature T1) is shifted to higher temperatures while the second one (peak temperature T2) to lower values. The CD data indicated partial conformational changes in the protein non-α-helix domain at T1, resulting in a β-sheet richer intermediate (BSRI) with an unaffected, native-like α-helix backbone. The RESV influence on this process may be defined as slightly demoting, at least within DSC conditions (linear heating rate of 1 K min−1). On further heating, unfolding of the α-helix domain takes place at T2, with RESV acting as a promoter of the process. Long time incubation at 333 K produced the same type of BSRI: no significant effect of RESV on the secondary structure content was detected by CD spectroscopy. Nevertheless, the size distribution of the protein population obtained from DLS measurements revealed the free (non-bound) RESV action manifested in the developing of larger size aggregates.
- Published
- 2024
- Full Text
- View/download PDF
30. pH-Based Molecular Dynamics Simulation for Analysing Protein Structure and Folding
- Author
-
Sasidharan, Santanu, Shukla, Rohit, Tripathi, Timir, Saudagar, Prakash, Saudagar, Prakash, editor, and Tripathi, Timir, editor
- Published
- 2023
- Full Text
- View/download PDF
31. Principles, Methods, and Applications of Protein Folding Inside Cells
- Author
-
Sahoo, Subhashree, Shivani, Kummari, Padhy, Amrita Arpita, Kumari, Varsha, Mishra, Parul, Saudagar, Prakash, editor, and Tripathi, Timir, editor
- Published
- 2023
- Full Text
- View/download PDF
32. Investigating Protein Unfolding and Stability Using Chaotropic Agents and Molecular Dynamics Simulation
- Author
-
Shukla, Rohit, Tripathi, Timir, Saudagar, Prakash, editor, and Tripathi, Timir, editor
- Published
- 2023
- Full Text
- View/download PDF
33. Algorithm unfolding for block-sparse and MMV problems with reduced training overhead.
- Author
-
Hauffen, Jan Christian, Jung, Peter, Mücke, Nicole, Junhong Lin, and Kunis, Stefan
- Subjects
ALGORITHMS ,CONVOLUTIONAL neural networks ,SUPERVISED learning ,THRESHOLDING algorithms - Abstract
In this study, we consider algorithm unfolding for the multiple measurement vector (MMV) problem in the case where only few training samples are available. Algorithm unfolding has been shown to empirically speed-up in a data-driven way the convergence of various classical iterative algorithms, but for supervised learning, it is important to achieve this with minimal training data. For this, we consider learned block iterative shrinkage thresholding algorithm (LBISTA) under different training strategies. To approach almost data-free optimization at minimal training overhead, the number of trainable parameters for algorithm unfolding has to be substantially reduced. We therefore explicitly propose a reduced-size network architecture based on the Kronecker structure imposed by the MMV observation model and present the corresponding theory in this context. To ensure proper generalization, we then extend the analytic weight approach by Liu and Chen to LBISTA and the MMV setting. Rigorous theoretical guarantees and convergence results are stated for this case. We show that the network weights can be computed by solving an explicit equation at the reduced MMV dimensions which also admits a closed-form solution. Toward more practical problems, we then considered convolutional observation models and show that the proposed architecture and the analytical weight computation can be further simplified and thus open new directions for convolutional neural networks. Finally, we evaluate the unfolded algorithms in numerical experiments and discuss connections to other sparse recovering algorithms. [ABSTRACT FROM AUTHOR]
- Published
- 2023
- Full Text
- View/download PDF
34. A two‐step log‐linear procedure for graphical representation and inference of associations in cross‐classified data for disease diagnosis.
- Author
-
Vera, J. Fernando and Roldán‐Nofuentes, José A.
- Subjects
- *
DIAGNOSIS , *LOG-linear models , *ODDS ratio , *CORONARY disease , *DIAGNOSIS methods - Abstract
Biometrical sciences and disease diagnosis in particular, are often concerned with the analysis of associations for cross‐classified data, for which distance association models give us a graphical interpretation for non‐sparse matrices with a low number of categories. In this framework, usually binary exploratory and response variables are present, with analysis based on individual profiles being of great interest. For saturated models, we show the usual linear relationship for log‐linear models is preserved in full dimension for the distance association parameterization. This enables a two‐step procedure to facilitate the analysis and the interpretation of associations in terms of unfolding after the overall and main effects are removed. The proposed procedure can deal with cross‐classified data for profiles by binary variables, and it is easy to implement using traditional statistical software. For disease diagnosis, the problems of a degenerate solution in the unfolding representation, and that of determining significant differences between the profile locations are addressed. A hypothesis test of independence based on odds ratio is considered. Furthermore, a procedure is proposed to determine the causes of the significance of the test, avoiding the problem of error propagation. The equivalence between a test for equality of odds ratio pairs and the test for equality of location for two profiles in the unfolding representation in the disease diagnosis is shown. The results have been applied to a real example on the diagnosis of coronary disease, relating the odds ratios with performance parameters of the diagnostic test. [ABSTRACT FROM AUTHOR]
- Published
- 2023
- Full Text
- View/download PDF
35. AUTOLISP FUNCTION FOR UNFOLDING THE OBLIQUE CONE OR FRUSTUM OF OBLIQUE CONE, IN AUTOCAD.
- Author
-
STROE, Iulius
- Subjects
CONES ,DIAMETER ,TIME measurements ,TUBES - Abstract
In production areas dedicated to the manufacturing of small series or unique products, i.e. in sectors which require frequent calculations for geometric determinations (such as the case of obtaining the unfolded shape of oblique cones frustums from the joints of different tubes (pipes) of varying diameters and/or orientations it is useful to achieve their development within a short timeframe, accurately and with minimal effort. Regarding this, an AutoLisp function was created for the rapid development of an oblique cone frustum, capable of being used in the current working session of the drawing executed in AutoCAD, without requiring additional calculations or drawings [ABSTRACT FROM AUTHOR]
- Published
- 2023
36. Unfolding polyhedra via tabu search
- Author
-
Zawallich, Lars
- Published
- 2024
- Full Text
- View/download PDF
37. Measurements of hadronic tt differential cross sections with ATLAS and unfolding with Gaussian processes
- Author
-
Bozson, Adam
- Subjects
top quark ,Top Physics ,Particle physics ,Unfolding ,Gaussian Processes ,Large Hadron Collider ,machine learning ,proton collisions - Abstract
Measurements of tt production cross sections at the Large Hadron Collider are presented. Proton-proton collision data with a centre-of-momentum energy of 13 TeV were collected using the ATLAS detector, totalling an integrated luminosity of 36.1 fb⁻¹. The measurements are performed for the fully hadronic decay channel where the jets can be resolved. This allows all tt decay components to be measured along with additional QCD radiation. The results are presented as absolute and normalised unfolded differential cross sections at particle level, as functions of several kinematic variables. Some cross sections are also unfolded to parton level, and some two-dimensional differential cross sections are presented. These distributions are compared to several Monte Carlo simulations. Potential uses for Gaussian processes in particle physics are discussed, and a novel method for unfolding with Gaussian processes is introduced. The method is derived and assessed in terms of the unfolded estimators, statistical covariance matrices, and flexibility of the model.
- Published
- 2020
38. Algorithm unfolding for block-sparse and MMV problems with reduced training overhead
- Author
-
Jan Christian Hauffen, Peter Jung, and Nicole Mücke
- Subjects
unfolding ,compressed sensing ,multiple measurement vector problem ,deep learning ,block-sparsity ,Applied mathematics. Quantitative methods ,T57-57.97 ,Probabilities. Mathematical statistics ,QA273-280 - Abstract
In this study, we consider algorithm unfolding for the multiple measurement vector (MMV) problem in the case where only few training samples are available. Algorithm unfolding has been shown to empirically speed-up in a data-driven way the convergence of various classical iterative algorithms, but for supervised learning, it is important to achieve this with minimal training data. For this, we consider learned block iterative shrinkage thresholding algorithm (LBISTA) under different training strategies. To approach almost data-free optimization at minimal training overhead, the number of trainable parameters for algorithm unfolding has to be substantially reduced. We therefore explicitly propose a reduced-size network architecture based on the Kronecker structure imposed by the MMV observation model and present the corresponding theory in this context. To ensure proper generalization, we then extend the analytic weight approach by Liu and Chen to LBISTA and the MMV setting. Rigorous theoretical guarantees and convergence results are stated for this case. We show that the network weights can be computed by solving an explicit equation at the reduced MMV dimensions which also admits a closed-form solution. Toward more practical problems, we then considered convolutional observation models and show that the proposed architecture and the analytical weight computation can be further simplified and thus open new directions for convolutional neural networks. Finally, we evaluate the unfolded algorithms in numerical experiments and discuss connections to other sparse recovering algorithms.
- Published
- 2023
- Full Text
- View/download PDF
39. AUTOLISP FUNCTION FOR UNFOLDING THE OBLIQUE CONE OR FRUSTUM OF OBLIQUE CONE, IN AUTOCAD
- Author
-
Iulius STROE
- Subjects
AutoCAD ,AutoLISP ,oblique cone ,frustum ,unfolding ,Architectural engineering. Structural engineering of buildings ,TH845-895 ,Engineering design ,TA174 - Abstract
In production areas dedicated to the manufacturing of small series or unique products, i.e. in sectors which require frequent calculations for geometric determinations (such as the case of obtaining the unfolded shape of oblique cones frustums from the joints of different tubes (pipes) of varying diameters and/or orientations it is useful to achieve their development within a short timeframe, accurately and with minimal effort. Regarding this, an AutoLisp function was created for the rapid development of an oblique cone frustum, capable of being used in the current working session of the drawing executed in AutoCAD, without requiring additional calculations or drawings.
- Published
- 2023
40. The 0:1 resonance bifurcation associated with the supercritical Hamiltonian pitchfork bifurcation.
- Author
-
Zhou, Xing
- Subjects
- *
RESONANCE , *DUFFING equations , *BIFURCATION diagrams , *DEGREES of freedom , *ORBITS (Astronomy) , *MATHEMATICS - Abstract
We consider the non-semisimple 0:1 resonance (i.e. the unperturbed equilibrium has two purely imaginary eigenvalues ± i α ( α ∈ R and α > 0) and a non-semisimple double-zero one) Hamiltonian bifurcation with one distinguished parameter, which corresponds to the supercritical Hamiltonian pitchfork bifurcation. Based on BCKV singularity theory established by [H.W. Broer, S. -N. Chow, Y. Kim, and G. Vegter, A normally elliptic Hamiltonian bifurcation, Z. Angew. Math. Phys. 44 (3) (1993), pp. 389–432], this bifurcation essentially triggered by the reversible universal unfolding M = 1 2 p 2 + 1 4 q 4 + (λ + I 1) q 2 with respect to BCKV-restricted morphisms of the planar non-semisimple singularity 1 2 p 2 + 1 4 q 4 (the I 1 is regarded as distinguished parameter with respect to the external parameter λ). We first give the plane bifurcation diagram of the integrable Hamiltonian on each level of integral in detail, which is related to the usual supercritical Hamiltonian pitchfork bifurcation. Then, we use the S 1 -symmetry generated by the additional pair of imaginary eigenvalues ± i α to reconstruct the above plane bifurcation phenomenon caused by the zero eigenvalue pair into the case with two degrees of freedom. Finally, we prove the persistence of typical bifurcation scenarios (e.g. 2-dimensional invariant tori and the symmetric homoclinic orbit) under the small Hamiltonian perturbations, as proposed by [H.W. Broer, S. -N. Chow, Y. Kim, and G. Vegter, A normally elliptic Hamiltonian bifurcation, Z. Angew. Math. Phys. 44 (3) (1993), pp. 389–432]. An example system (the coupled Duffing oscillator) with strong linear coupling and weak local nonlinearity is given for this bifurcation. [ABSTRACT FROM AUTHOR]
- Published
- 2023
- Full Text
- View/download PDF
41. Depth-First Net Unfoldings and Equivalent Reduction.
- Author
-
Yang, Xu, Ye, Chen, and Chen, Yijun
- Subjects
- *
BRANCHING processes , *TREE branches , *PETRI nets - Abstract
In Petri net unfolding, according to the strategies of breadth first and depth first, the biggest problem lies in the potential explosion of the state space. Unfolding generates either accessible trees or branch processes. Making marking reduction or branch cutting accessible proves to be an effective approach to mitigating the state space expansion. In this paper, we propose three reduction rules based on similarity equivalence, conduct state space reduction, present three theorems supported by a case study, and propose a new unfolding algorithm for the unfolding process. In both the new case and the experiments, the completeness, optimality, completeness, and memory and time consumption are reduced by about 60%. [ABSTRACT FROM AUTHOR]
- Published
- 2023
- Full Text
- View/download PDF
42. Molecular basis of conformational changes and mechanics of integrins.
- Author
-
Gaikwad, Hanmant K., Jaswandkar, Sharad V., Katti, Kalpana S., Haage, Amanda, and Katti, Dinesh R.
- Subjects
- *
INTEGRINS , *EPIDERMAL growth factor , *FIBRONECTINS , *TORSIONAL load , *EXTRACELLULAR matrix , *LIGAND binding (Biochemistry) , *MOLECULAR dynamics - Abstract
Integrin, as a mechanotransducer, establishes the mechanical reciprocity between the extracellular matrix (ECM) and cells at integrin-mediated adhesion sites. This study used steered molecular dynamics (SMD) simulations to investigate the mechanical responses of integrin αvβ3 with and without 10th type III fibronectin (FnIII10) binding for tensile, bending and torsional loading conditions. The ligand-binding integrin confirmed the integrin activation during equilibration and altered the integrin dynamics by changing the interface interaction between β-tail, hybrid and epidermal growth factor domains during initial tensile loading. The tensile deformation in integrin molecules indicated that fibronectin ligand binding modulates its mechanical responses in the folded and unfolded conformation states. The bending deformation responses of extended integrin models reveal the change in behaviour of integrin molecules in the presence of Mn2+ ion and ligand based on the application of force in the folding and unfolding directions of integrin. Furthermore, these SMD simulation results were used to predict the mechanical properties of integrin underlying the mechanism of integrin-based adhesion. The evaluation of integrin mechanics provides new insights into understanding the mechanotransmission (force transmission) between cells and ECM and contributes to developing an accurate model for integrin-mediated adhesion. This article is part of a discussion meeting issue 'Supercomputing simulations of advanced materials'. [ABSTRACT FROM AUTHOR]
- Published
- 2023
- Full Text
- View/download PDF
43. Comparison of End-Point Energies of Bremsstrahlung Photons from 28- GHz ECR Ion Source in Three Measurement Locations.
- Author
-
Kumwenda, Mwingereza J.
- Subjects
- *
BREMSSTRAHLUNG , *PHOTONS , *DETECTORS , *ENGINEERING instruments , *ELECTRONS - Abstract
Bremsstrahlung photons measurement show elevated energy emission beyond critical energy in 28-GHz ECR and its nature is not revealed. Thus, the aim of this study is to unveil the nature of high end-point energies at the three measurement locations. Bremsstrahlung photons from a 28-GHz ECR ion source were measured at Busan center of Korean Basic Science Institute (KBSI). The gamma-ray detection system consists of three round type NaI(Tl) scintillation detectors placed 62 cm radially from the beam axis at the three measurement locations namely injection, centre and extraction sides of an ECR ion source, and a NaI(Tl) scintillation detector placed at the view port for monitoring photon intensity along the beam axis. Such design of the experiment was based on the inner structure of the ECR ion source and the shape of the ECR plasma. Bremsstrahlung photons energy spectra were measured at RF power of 1 kW to extract O16 beam with a dominant fraction of O3+ and O4+. Also, bremsstrahlung photons were measured by exchanging the detector positions for studying systematic uncertainties. Monte Carlo simulation based on the Geant4 package was performed to take geometrical acceptance and the energydependent detection efficiency into account due to large non-uniformity in the material budget. True bremsstrahlung energy spectra from the 28-GHz ECR ion source were extracted using an inverse matrix unfolding method. The measured high end-point energies at the three measurement locations were 1.68 MeV, 1.72 MeV and 2.04 MeV for the injection, centre and extraction sides, respectively. The high end-point energy values of the measured bremsstrahlung photons beyond the theoretical energy value of 1.33 MeV were found to be correlated with the structure of the ECR ion source and the shape of the ECR plasma. Furthermore, the high end-point energy values resulting from the bremsstrahlung photons measurements in the 28-GHz ECR plasma are due to the higher number of unconfined electrons arriving at the chamber wall easily, and producing higher bremsstrahlung photons. The unconfined electrons are the results of imperfect magnetic confinement that cause electrons to escape from the plasma volume. This study suggests a new design of magnetic confinement that will not allow an electron to escape. [ABSTRACT FROM AUTHOR]
- Published
- 2023
- Full Text
- View/download PDF
44. The Nature of the Enthalpy–Entropy Compensation and "Exotic" Arrhenius Parameters in the Denaturation Kinetics of Proteins.
- Author
-
Baklanov, Alexey V. and Kiselev, Vitaly G.
- Subjects
- *
DENATURATION of proteins , *UNIMOLECULAR reactions , *CELL death , *ENTHALPY , *DIMERS - Abstract
Protein unfolding is a ubiquitous process responsible for the loss of protein functionality (denaturation), which, in turn, can be accompanied by the death of cells and organisms. The nature of enthalpy–entropy compensation (EEC) in the kinetics of protein unfolding is a subject of debate. In order to investigate the nature of EEC, the "completely loose" transition state (TS) model has been applied to calculate the Arrhenius parameters for the unfolding of polyglycine dimers as a model process. The calculated Arrhenius parameters increase with increasing dimer length and demonstrate enthalpy–entropy compensation. It is shown that EEC results from the linear correlations of enthalpy and entropy of activation with dimer length, which are derived directly from the properties of the transition state. It is shown that EEC in solvated (hydrated, etc.) proteins is a direct consequence of EEC in proteins themselves. The suggested model allows us also to reproduce and explain "exotic" very high values of the pre-exponential factor measured for the proteins unfolding, which are drastically higher than those known for unimolecular reactions of organic molecules. A similar approach can be applied to analyzing the nature of EEC phenomena observed in other areas of chemistry. [ABSTRACT FROM AUTHOR]
- Published
- 2023
- Full Text
- View/download PDF
45. Model selection and signal extraction using Gaussian Process regression
- Author
-
Abhijith Gandrakota, Amit Lath, Alexandre V. Morozov, and Sindhu Murthy
- Subjects
Hadron-Hadron Scattering ,Beyond Standard Model ,Higgs Physics ,Unfolding ,Nuclear and particle physics. Atomic energy. Radioactivity ,QC770-798 - Abstract
Abstract We present a novel computational approach for extracting localized signals from smooth background distributions. We focus on datasets that can be naturally presented as binned integer counts, demonstrating our procedure on the CERN open dataset with the Higgs boson signature, from the ATLAS collaboration at the Large Hadron Collider. Our approach is based on Gaussian Process (GP) regression — a powerful and flexible machine learning technique which has allowed us to model the background without specifying its functional form explicitly and separately measure the background and signal contributions in a robust and reproducible manner. Unlike functional fits, our GP-regression-based approach does not need to be constantly updated as more data becomes available. We discuss how to select the GP kernel type, considering trade-offs between kernel complexity and its ability to capture the features of the background distribution. We show that our GP framework can be used to detect the Higgs boson resonance in the data with more statistical significance than a polynomial fit specifically tailored to the dataset. Finally, we use Markov Chain Monte Carlo (MCMC) sampling to confirm the statistical significance of the extracted Higgs signature.
- Published
- 2023
- Full Text
- View/download PDF
46. Reflecting and Unfolding
- Author
-
Cantini, Andrea, Rahman, Shahid, Series Editor, Clerbout, Nicolas, Managing Editor, Symons, John, Founding Editor, van Bendegem, Jean Paul, Editorial Board Member, Benis Sinaceur, Hourya, Editorial Board Member, van Benthem, Johan, Editorial Board Member, Chemla, Karine, Editorial Board Member, Dubucs, Jacques, Editorial Board Member, Fagot-Largeault, Anne, Editorial Board Member, Van Fraassen, Bas C, Editorial Board Member, Gabbay, Dov M., Editorial Board Member, McNamara, Paul, Editorial Board Member, Priest, Graham, Editorial Board Member, Sandu, Gabriel, Editorial Board Member, Smets, Sonja, Editorial Board Member, Street, Tony, Editorial Board Member, Sundholm, Göran, Editorial Board Member, Wansing, Heinrich, Editorial Board Member, Williamson, Timothy, Editorial Board Member, Ademollo, Francesco, editor, Amerini, Fabrizio, editor, and De Risi, Vincenzo, editor
- Published
- 2022
- Full Text
- View/download PDF
47. The Synthesis Problem for Repeatedly Communicating Petri Games
- Author
-
Hannibal, Paul, Olderog, Ernst-Rüdiger, Goos, Gerhard, Founding Editor, Hartmanis, Juris, Founding Editor, Bertino, Elisa, Editorial Board Member, Gao, Wen, Editorial Board Member, Steffen, Bernhard, Editorial Board Member, Yung, Moti, Editorial Board Member, Bernardinello, Luca, editor, and Petrucci, Laure, editor
- Published
- 2022
- Full Text
- View/download PDF
48. Garment Type Agnostic Robotic Unfolding of Garments from Random Configuration
- Author
-
Triantafyllou, Dimitra, Aspragathos, Nikolaos, Ceccarelli, Marco, Series Editor, Agrawal, Sunil K., Advisory Editor, Corves, Burkhard, Advisory Editor, Glazunov, Victor, Advisory Editor, Hernández, Alfonso, Advisory Editor, Huang, Tian, Advisory Editor, Jauregui Correa, Juan Carlos, Advisory Editor, Takeda, Yukio, Advisory Editor, Müller, Andreas, editor, and Brandstötter, Mathias, editor
- Published
- 2022
- Full Text
- View/download PDF
49. The Promise and Challenge of High Pressure Macromolecular Crystallography.
- Author
-
Kurpiewska, Katarzyna, Sławek, Joanna, Klonecka, Agnieszka, and Kozak, Maciej
- Subjects
CRYSTALLOGRAPHY ,PROTEIN stability ,PROTEIN conformation ,DIAMOND anvil cell ,CRYSTAL structure - Abstract
Since its introduction in the early 1970s, high pressure crystallography (HPX) has shown great potential for the investigation of different types of matter. Using diamond anvil cells, HPX is an emerging technique that has been rapidly implemented, making it available to biologists, and there is immense potential for utilizing this technique in biological systems in the future. At the molecular level, high-pressure crystallographic investigation provides information on structural characteristics that not only determine the native conformation of a protein but also the conformations with higher free-energy, thus revealing function-related structural changes and properties that can be modified as a result of pressurization. The increase in the number of crystal structures of different macromolecules determined under high pressure over the last five decades can be ascribed mainly to two factors: the emergence of high-pressure cells with very large, open angles, and the advent of third generation synchrotron sources. The use of high pressure crystallography as a research tool has been shown to contribute to the advancements in the basic fields of biochemistry (protein misfolding and aggregation), biophysics (protein stability), and biotechnology (food processing). Presently, with a growing interest in biomedicine and nanotechnology, this nonstandard method appears to be a valid instrument for probing more challenging and complex systems. In this review, we present the method, highlight a selection of recent applications, and describe challenges for high pressure macromolecular crystallography (HPMX). [ABSTRACT FROM AUTHOR]
- Published
- 2023
- Full Text
- View/download PDF
50. High Hydrostatic Pressure: Influences on Allergenicity, Bioactivities, and Structural and Functional Properties of Proteins from Diverse Food Sources
- Author
-
Sukan Braspaiboon and Thunnop Laokuldilok
- Subjects
high pressure processing ,unfolding ,surface hydrophobicity ,texture ,allergenicity ,Chemical technology ,TP1-1185 - Abstract
High hydrostatic pressure (HHP) has gained prominence in the food processing industry over the last decade. In addition to the effectiveness of microbial and enzymatic inactivation, HHP directly impacts protein structures and properties. Accordingly, this review article aims to consolidate relevant research findings elucidating the effects of HHP on protein structure, allergenicity, bioactivities, and functional properties across diverse protein sources. They encompass cereals, legumes, nuts, meat, poultry products, milk, eggs, seafood, algae, insects, seeds, and vegetables. This review provides insights into the consistent trends of HHP effects on each protein source. In conclusion, HHP induces alterations in non-covalent bonds within protein structures, leading to the unfolding of their interior regions and consequential changes in their properties. Remarkably, the allergenicity of cereals, legumes, and nuts decreases while their bioactivities and digestibility escalate. The disruption of non-covalent bonds during HHP results in the exposure of the interior hydrophobic regions to the surface microenvironment, thereby enhancing the surface hydrophobicity of proteins, particularly those derived from seeds and vegetables. HHP weakens the allergenicity and elevates the foaming properties of proteins from dairy products, including improving the gelling properties and antioxidant activities of egg proteins. Texture profiles of meat and poultry, particularly hardness, are enhanced. Furthermore, HHP demonstrates the potential to diminish the allergenicity of seafood proteins and augment insect protein bioactivities. Lastly, HHP enhances the extraction of algal bioactive components, improving their nutritional quality.
- Published
- 2024
- Full Text
- View/download PDF
Catalog
Discovery Service for Jio Institute Digital Library
For full access to our library's resources, please sign in.