ARTICLE | doi:10.20944/preprints202009.0006.v2
Subject: Biology And Life Sciences, Biochemistry And Molecular Biology Keywords: COVID-19; SARS-CoV-2; protein design; complementarity; competitive inhibitor; homology-based threading in rational protein design
Online: 4 March 2021 (10:14:39 CET)
COVID-19 is characterized by an unprecedented abrupt increase in the viral transmission rate (SARS-CoV-2) relative to its pandemic evolutionary ancestor, SARS-CoV (2003). The complex molecular cascade of events related to the viral pathogenicity is triggered by the Spike protein upon interacting with the ACE2 receptor on human lung cells through its receptor binding domain (RBDSpike). One potential therapeutic strategy to combat COVID-19 could thus be limiting the infection by blocking this key interaction. In this current study, we adopt a protein design approach to predict and propose non-virulent structural mimics of the RBDSpike which can potentially serve as its competitive inhibitors in binding to ACE2. The RBDSpike is an independently foldable protein domain, resilient to conformational changes upon mutations and therefore an attractive target for strategic re-design. Interestingly, in spite of displaying an optimal shape fit between their interacting surfaces (attributed to a consequently high mutual affinity), the RBDSpike–ACE2 interaction appears to have a quasi-stable character due to a poor electrostatic match at their interface. Structural analyses of homologous protein complexes reveal that the ACE2 binding site of RBDSpike has an unusually high degree of solvent-exposed hydrophobic residues, attributed to key evolutionary changes, making it inherently ‘reaction-prone’. The designed mimics aimed to block the viral entry by occupying the available binding sites on ACE2, are tested to have signatures of stable high-affinity binding with ACE2 (cross-validated by appropriate free energy estimates), overriding the native quasi-stable feature. The results show the apt of directly adapting natural examples in rational protein design, wherein, homology-based threading coupled with strategic ‘hydrophobic ↔ polar’ mutations serve as a potential breakthrough.
ARTICLE | doi:10.20944/preprints201701.0040.v1
Subject: Biology And Life Sciences, Biochemistry And Molecular Biology Keywords: Sarcocystis neurona; EPM; docking; apicomplexans; phylogeny; homology modeling
Online: 9 January 2017 (05:19:32 CET)
The apicomplexan parasite, Sarcocystis neurona causes the degenerative neurological equine protozoal myeloencephalitis (EPM) disease of horses. Due to its host range expansion, S. neurona is an emerging threat that requires close monitoring. In apicomplexans, protein kinases (PKs) have been implicated in a myriad of critical functions such as host cell invasion, cell cycle progression and host immune responses evasion. Here, we used various bioinformatics methods to define the kinome of S. neurona and phylogenetic relatedness of its PKs to other apicomplexans. Further, three-dimensional (3D) homology models for selected S. neurona putative PKs were constructed and evaluated for inhibitor docking. We identified 92 putative PKs clustering within the AGC, CAMK, CK1, CMGC, STE, TKL, aPK and OPK groups. Although containing the universally conserved PKA (AGC group), S. neurona kinome was devoid of PKB and PKC, but contained the six apicomplexan conserved CDPKs (CAMK group). The OPK group was represented by ROPKs 19A, 27, 30, 33, 35 and 37, but was devoid of the virulence-associated ROPKs 5, 6, 18 and 38. Two out of the three S. neurona CK1 enzymes had high sequence similarities to T. gondii TgCK1-α and TgCK1-β and the Plasmodium PfCK1. Docking of four inhibitors onto homology models of putative ROP27 and PKA indicated that inhibition of S. neurona PKs is feasible, but needs to be experimentally tested. The essentiality of apicomplexan PKs makes the elucidation of S. neurona kinome a key milestone for development of novel therapeutics for EPM.
ARTICLE | doi:10.20944/preprints202306.0194.v1
Subject: Biology And Life Sciences, Virology Keywords: insect viruses; arthropod virus; distant homology detection; remote homology detection; virulence factor; tospovirus; structure prediction; cypovirus; small protrusion domain
Online: 2 June 2023 (11:45:35 CEST)
Today, the most powerful approach to detect distant homologs of a protein is based on structure prediction and comparison. Yet this approach is still inapplicable to many viral proteins. Therefore, we developed a powerful sequence-based procedure to identify distant homologs of viral proteins. It relies on 3 main principles: 1) Traces of sequence similarity with a protein can persist beyond the significance cutoff of homology detection programs; 2) Candidate homologs can be identified among proteins with weak sequence similarity to the query, by using "contextual" information, e.g. taxonomy or type of host infected; 3) These candidate homologs can be validated using highly sensitive profile-profile comparison.As a test case, we applied our approach to a protein without known homologs, ORF4 of Lake Sinai virus (which infects bees). We discovered that ORF4 is composed of a domain that has homologs in proteins from >20 taxa of viruses infecting arthropods. We called it “Widespread, Intriguing, Versatile” (WIV) domain because it is found in proteins with a wide variety of domain organizations and functions. For example, WIV is encoded by the NSs protein of tospoviruses, a global threat to food security, which infect plants through arthropod vectors; by the protein encoded by RNA2 ORF1 of chronic bee paralysis virus, a widespread virus of bees; and by various proteins of cypoviruses, which infect the silkworm bombyx mori. WIV has a previously unknown structural fold, according to Alphafold predictions. In some viral species, WIV facilitates infection of arthropods, according to bibliographical evidence
ARTICLE | doi:10.20944/preprints202007.0132.v1
Subject: Biology And Life Sciences, Biology And Biotechnology Keywords: coronavirus; spike protein; database; sequence alignment; mutation; homology model; hydrophobic amino acids
Online: 7 July 2020 (16:49:04 CEST)
Analysis of SARS-CoV-2 spike protein sequences of over 19 countries from biological databases submitted around the globe was carried out with help of bioinformatics tools and structure prediction databases. Initial data analysis showed entry of virus into different geographic regions started in the month of January 2020. Meanwhile, alignment of spike protein sequences of SARS-CoV-2 isolates from China and other countries revealed a critical mutation of D614G. Surprisingly, mutation D614G was not seen in early samples submitted in the month of January but gradually it started appearing globally from the month of March 2020. However, the mutations of amino acids in the spike protein other than D614G exhibiting similar pI and altered polarity were found to be specific to geographical regions. Besides, prediction of homology model for interaction of spike protein showed predominant role of chain C of trimeric spike protein in adhering receptor binding domain (RBD) of human ACE2 receptor. Furthermore, the prediction of glycosylation points has revealed that there are about 20 N-glycosylation potential sites on spike protein. We believe that the information present here would not only help in thorough understanding of infectivity but also enhance the knowledge of the scientific community in developing prophylactics and/or therapeutics for SARS-CoV19-2 virus.
ARTICLE | doi:10.20944/preprints201807.0523.v1
Subject: Social Sciences, Education Keywords: game-based learning; game design; project-based teaching; informatics and society, cybersecurity
Online: 26 July 2018 (16:38:48 CEST)
This article discusses the use of game design as a method for interdisciplinary project-based teaching in secondary school education to convey informatics and society topics. There is a lot of knowledge about learning games but little background on project-based teaching using game design as a method. We present the results of an analysis of student-created games and an evaluation of a student-authored database on learning contents found in commercial off-the-shelf games. We further contextualise these findings using a group discussion with teachers. Results underline the effectiveness of project-based teaching to raise awareness for informatics and society topics. We further outline informatics and society topics that are particularly interesting to students, genre preferences and potentially engaging game mechanics stemming from our analyses.
ARTICLE | doi:10.20944/preprints202003.0150.v1
Subject: Engineering, Control And Systems Engineering Keywords: CFD; numerical optimization; CAD parametrization; cloud-based; design space exploration; SSIM
Online: 9 March 2020 (09:50:23 CET)
In this manuscript, an automated framework dedicated to design space exploration and design optimization studies is presented. The framework integrates a set of numerical simulation, computer-aided design, numerical optimization, and data analytics tools using scripting capabilities. The tools used are open-source and freeware, and can be deployed on any platform. The main feature of the proposed methodology is the use of a cloud-based parametrical computer-aided design application, which allows the user to change any parametric variable defined in the solid model. We demonstrate the capabilities and flexibility of the framework using computational fluid dynamics applications; however, the same workflow can be used with any numerical simulation tool (e.g., a structural solver or a spread-sheet) that is able to interact via a command line interface or using scripting languages. We conduct design space exploration and design optimization studies using quantitative and qualitative metrics, and to reduce the high computing times and computational resources intrinsic to these kinds of studies, concurrent simulations and surrogate-based optimization are used.
DATASET | doi:10.20944/preprints202003.0011.v1
Subject: Biology And Life Sciences, Biochemistry And Molecular Biology Keywords: antigen-antibody complex structure; interfacial electrostatic feature; Machine Learning-Based Antibody Design; Protein Data Bank
Online: 1 March 2020 (12:39:55 CET)
The importance of antibodies in health care and the biotechnology research and development demands not only knowledge of their experimental structures at high resolution, but also practical implementation of this knowledge for both effective and efficient design and production of antibody for its use in both medical and research applications. While the experimental wet-lab approach is usually costly, laborious and time-consuming, computational (dry-lab) approaches, in spite of their intrinsic limitations in comparison with its experimental (wet-lab) counterpart, provide a cheaper and faster alternative option. For the first time, this article reports a comprehensive set of structural electrostatic features extracted from experimentally determined antigen-antibody-related structures, including especially those structural electrostatic features at the interfaces of all experimentally determined antigen-antibody complex structures as of February 29, 2020, to facilitate effective and efficient machine learning-based computational antibody design using currently available experimental structures inside Protein Data Bank.
Subject: Engineering, Automotive Engineering Keywords: Automotive development; Secure SDLC; Evidence-based standard; ISO/SAE 21434; UNECE cybersecurity regulation
Online: 9 December 2020 (10:59:57 CET)
Although traditional automotive development has mainly focused on functional safety, as the number of automotive hacking cases has increased due to the growing Internet connectivity of automotive control systems, security is also becoming more important. Accordingly, various international organizations are preparing cybersecurity regulations or standards to ensure security in automotive development by emphasizing the concept of security-by-design(i.e. security engineering) which emphasizes trustworthiness from the beginning of development. The problem, however, is that no specific methodology has been suggested. In this paper, we propose a specific security-by-design methodology for automotive development based on Secure System Development Life Cycle (secure SDLC) standards and evidence-based standards. Our methodology could be easily used in the actual field as it is more general and detailed than existing secure SDLC standards and research. Also, since it satisfies all requirements of United Nations Economic Commission for Europe (UNECE) regulation, automobile manufacturers could respond to the upcoming cybersecurity regulation with our methodology.
TECHNICAL NOTE | doi:10.20944/preprints202310.1109.v1
Subject: Biology And Life Sciences, Biophysics Keywords: EnCPdock; Complementarity Plot; Artificial Intelligence; Structure based Thermodynamics; web-server
Online: 18 October 2023 (08:26:54 CEST)
The combined efect of shape and electrostatic complementarities (Sc, EC) at the interface of the interacting protein partners (PPI) serves as the physical basis for such associations and is a strong detterminant of their binding energetics. EnCPdock (https://www.scinetmol.in/EnCPdock/) presents a comprehensive web-platform for the direct conjoint comparative analyses of complementarity and binding energetics in PPIs. It elegantly interlinks the dual nature of local (Sc) and non-local complementarity (EC) in PPIs using the Complementarity Plot. It further derives an AI-based ∆Gbinding with a prediction accuracy comparable to the state-of-the-art. This book-chapter presents a practical manual to conceptualize and implement EnCPdock with its various features and functionalities, collectively having the potential to serve as a valuable protein engineering tool in the design of novel protein interfaces.
ARTICLE | doi:10.20944/preprints201912.0374.v1
Subject: Biology And Life Sciences, Biophysics Keywords: alpha-fetoprotein; estrogens; selective estrogen receptor modulators; homology-based modeling; molecular docking; protein-ligand interaction; amino acid substitutions
Online: 29 December 2019 (08:08:23 CET)
Alpha-fetoprotein (AFP) is a major embryo- and tumor-associated protein capable of binding and transporting variety of hydrophobic ligands including estrogens. AFP has been shown to inhibit estrogen receptor (ER)-positive tumor growth and this can be attributed to its estrogen-binding ability. Despite AFP has long been investigated, its three-dimensional (3D) structure has not been experimentally resolved and molecular mechanisms underlying AFP-ligand interaction remain obscure. In our study we constructed homology-based 3D model of human AFP (HAFP) with the purpose to perform docking of ERα ligands, three agonists (17β-estradiol, estrone and diethylstilbestrol) and three antagonists (tamoxifen, afimoxifene and endoxifen) into the obtained structure. Based on ligand docked scoring function, we identified three putative estrogen- and antiestrogen-binding sites with different ligand binding affinities. Two high-affinity sites were located in (i) a tunnel formed within HAFP subdomains IB and IIA and (ii) opposite side of the molecule in a groove originating from cavity formed between domains I and III, while (iii) the third low-affinity site was found at the bottom of the cavity. 100 ns MD simulation allowed studying their geometries and showed that HAFP-estrogen interactions occur due to van der Waals forces, while both hydrophobic and electrostatic interactions were almost equally involved in HAFP-antiestrogen binding. MM/GBSA rescoring method estimated binding free energies (ΔGbind) and showed that antiestrogens have higher affinities to HAFP as compared to estrogens. We performed in silico point substitutions of amino acid residues to confirm their roles in HAFP-ligand interactions and showed that Thr132, Leu138, His170, Phe172, Ser217, Gln221, His266, His316, Lys453, and Asp478 residues along two disulfide bonds, Cys224-Cys270 and Cys269-Cys277 have key roles in both HAFP-estrogen and HAFP-antiestrogen binding. Data obtained in our study contribute to understanding mechanisms underlying protein-ligand interactions and anti-cancer therapy strategies based on ER-binding ligands.
ARTICLE | doi:10.20944/preprints202012.0395.v1
Subject: Engineering, Automotive Engineering Keywords: Innovation; Up-scaling; NBS Nature-based solutions (NBS); Hydrometeorological hazards; PHUSICOS project; Flooding; Landslides; Avalanches; Rockfall; Europe
Online: 16 December 2020 (08:33:57 CET)
Impact in the form of innovation and commercialisation is an essential component of publicly funded research projects. PHUSICOS, an H2020 Innovation Action project, aims at demonstrating the use of nature-based solutions for mitigating hydrometeorological hazards in rural and mountainous areas. The work program is built around key innovation actions, and each WP leader specifically responsible for nurturing innovation processes, maintaining market focus and ensuring relevance for the intended recipients of the project results. Key success criteria for PHUSICOS include up-scaling and mainstreaming of NBS to reach broader market access. An innovation strategy and supporting tools for implementing this within PHUSICS has been developed and key concepts forming the basis for this strategy are presented in this research note.
ARTICLE | doi:10.20944/preprints202112.0225.v1
Subject: Chemistry And Materials Science, Medicinal Chemistry Keywords: RNA targeting; RNA-based interactions; bis-3-chloropiperidines
Online: 14 December 2021 (11:13:29 CET)
After a long limbo, RNA has gained its credibility as a druggable target, fully earning its de-served role in the next-generation area of pharmaceutical R&D. We have recently probed the Trans-Activation Response element (TAR), a RNA stem–bulge–loop domain of the HIV-1 genome with bis-3-chloropiperidines (B-CePs), and revealed the compounds unique behavior in stabiliz-ing TAR structure, thus impairing in vitro the chaperone activity of the HIV-1 nucleocapsid (NC) protein. Seeking to elucidate the determinants of B-CePs inhibition, we have further characterized here their effects on the target TAR and its NC recognition, while developing quantitative analyti-cal approaches for the study of multicomponent RNA-based interactions.
REVIEW | doi:10.20944/preprints202203.0032.v1
Subject: Chemistry And Materials Science, Medicinal Chemistry Keywords: artificial intelligence; machine learning; drug design; covid-19; structure-based drug design; ligand-based drug design
Online: 2 March 2022 (03:00:37 CET)
The recent covid crisis has proven important lessons for academia and industry regarding digital reorganization. Among fascinating lessons from these times is the huge potential of data analytics and artificial intelligence. The crisis exponentially accelerated the adoption of analytics and artificial intelligence, and this momentum is predicted to continue into the 2020s and over. Moreover, drug development is a costly and time-consuming business, and only a minority of approved drugs return the revenue that exceeds the research and development costs. As a result, there is a huge drive to make drug discovery cheaper and faster. With modern algorithms and hardware, it is not too surprising that the new technologies of artificial intelligence and other computational simulation tools can help drug developers. In only two years of covid research, many novel molecules have been designed/identified using artificial intelligence methods with astonishing results in terms of time and effectiveness. This paper will review the most significant research on artificial intelligence in the de novo drug design for COVID-19 pharmaceutical research.
REVIEW | doi:10.20944/preprints202007.0478.v2
Subject: Biology And Life Sciences, Biochemistry And Molecular Biology Keywords: Bioinformatics; Drug Design; Small Organic Molecule; Target identification; Web-based Server
Online: 25 July 2020 (17:50:30 CEST)
Drug design is used for different applications of bioinformatics tools analyze DNA, genome, and sequence target region of a small organic molecule in order to understand the molecules of disease. Bioinformatics tools are identified a newly wide research field and minimize future risks through web servers and data mining. Clinical sample test performed with the bioinformatics tools as the biomedical detective. A particular structure and configuration of protein obliging in Drug design concluded Bioinformatics. This review bioinformatics tools and webserver will discuss functions of small organic molecules according to clinical pharmacology.
ARTICLE | doi:10.20944/preprints201709.0074.v1
Subject: Engineering, Electrical And Electronic Engineering Keywords: recommendation system; context awareness; location based services; mobile computing, cloud-based computing
Online: 18 September 2017 (08:54:04 CEST)
The ubiquity of mobile sensors (such as GPS, accelerometer and gyroscope) together with increasing computational power have enabled an easier access to contextual information, which proved its value in next generation of the recommender applications. The importance of contextual information has been recognized by researchers in many disciplines, such as ubiquitous and mobile computing, to filter the query results and provide recommendations based on different user status. A context-aware recommendation system (CoARS) provides a personalized service to each individual user, driven by his or her particular needs and interests at any location and anytime. Therefore, a contextual recommendation system changes in real time as a user’s circumstances changes. CoARS is one of the major applications that has been refined over the years due to the evolving geospatial techniques and big data management practices. In this paper, a CoARS is designed and implemented to combine the context information from smartphones’ sensors and user preferences to improve efficiency and usability of the recommendation. The proposed approach combines user’s context information (such as location, time, and transportation mode), personalized preferences (using individuals past behavior), and item-based recommendations (such as item’s ranking and type) to personally filter the item list. The context-aware methodology is based on preprocessing and filtering of raw data, context extraction and context reasoning. This study examined the application of such a system in recommending a suitable restaurant using both web-based and android platforms. The implemented system uses CoARS techniques to provide beneficial and accurate recommendations to the users. The capabilities of the system is evaluated successfully with recommendation experiment and usability test.
ARTICLE | doi:10.20944/preprints202005.0407.v1
Subject: Biology And Life Sciences, Virology Keywords: SARS-CoV-2; spike protein; D614G mutation; genotype distribution; furin cleavage site; secondary structure; sequence analysis; homology modeling
Online: 24 May 2020 (20:31:16 CEST)
We analyzed the SARS-CoV-2 spike (S) protein amino acid sequence extracted from 11,542 viral genomic sequences submitted to the Global Initiative on Sharing All Influenza Data (GISAID) database through April 27, 2020. Consistent with prior reports, we found a major S protein mutation, D614 to G614, that was represented in 56% of all the analyzed sequences. All other mutations combined were less than 10%. After parsing the data geographically, we found most of the Chinese patient samples showed D614 (97%). By contrast, most patient samples in many European countries showed G614 (51 to 88%). In the United States, the genotypic distribution in California and Washington was similar to Asian countries, while the distribution in other US states was comparable to Europe. We observed a dramatic increase in the frequency of G614 over time in multiple regions, surpassing D614 when both were present, suggesting G614 S protein virus outcompetes D614 S protein virus. To gain insight into the consequences of the D614G mutation, homology modeling using a multi-template threading mechanism with ab initio structural refinement was performed for a region of the S protein (S591 to N710) spanning the D614G mutation and the S1 furin cleavage site. Molecular models of this region containing D614 or G614 revealed a major difference in secondary structure at the furin domain (RRARS, R682 to S686). The D614 model predicted a random coil structure in the furin domain whereas the G614 model predicted an alpha helix. Critical residues in the cleavage domain of G614 model were found to better align with the PDB structure of a furin inhibitor. Thus, homology modeling studies suggest a potential mechanism whereby the D614G mutation may confer a competitive advantage at the furin binding domain that may contribute to the rise of the D614G SARS-CoV-2 mutant.
ARTICLE | doi:10.20944/preprints202007.0121.v1
Subject: Engineering, Civil Engineering Keywords: performance-based building design; PBBD; high-rise residential.
Online: 7 July 2020 (09:46:46 CEST)
The complexity of the design in high-rise residential projects is a challenge for the construction industry in completing projects that fit the needs of users. Performance-Based Building Design (PBBD) appears as a design concept that can describe these needs into performance requirements. In this case designing a building can be considered as an iterative process of exploration, where desired functional properties can be created, the shapes are suggested, and evaluation processes is used, so as to bring together the shapes and functions of the building. This concept is a container for designers to produce high-performance buildings. This study aimed to identify the performance-based building design factors applied by architect designers and engineers in high-rise residential building in Surabaya. As part of this study, primary data was collected based on surveys conducted through observation and questionnaire distributed to designers who had or were involved in the high-rise residential design process in Surabaya. A total of sixty-eight respondents were included in this study. Descriptive analysis through a mean and standard deviation scatter plot was used to rank the application of PBBD. Meanwhile, factor analysis was used in the analysis of PBBD application factors. From the results of the analysis, four factors were obtained for the application of PBBD in high-rise residential buildings in Surabaya, namely; the interests of occupants, the sustainability of building operations, the design collaboration process, and the risk of loss. Future research is the influence relationships and measure the success model of PBBD at a higher level into BIM (Building Information Modeling) interoperability.
ARTICLE | doi:10.20944/preprints201907.0220.v1
Subject: Chemistry And Materials Science, Medicinal Chemistry Keywords: diversity; fragment-based drug discovery; library design; library size
Online: 19 July 2019 (07:54:41 CEST)
Fragment-based drug discovery (FBDD) has become a major strategy to derive novel lead candidates for various therapeutic targets, as it promises efficient exploration of chemical space by employing fragment-sized (MW < 300) compounds. One of the first challenges in implementing a FBDD approach is the design of a fragment library, and more specifically, the choice of its size and individual members. A diverse set of fragments is required to maximise the chances of discovering novel hit compounds. However, the exact diversity of a certain collection of fragments remains underdefined, which hinders direct comparisons among different selections of fragments. Based on structural fingerprints, we herein introduced quantitative metrics for the structural diversity of fragment libraries. Structures of commercially available fragments were retrieved from the ZINC database, from which libraries with sizes ranging from 100 to 100,000 compounds were selected. The selected libraries were evaluated and compared quantitatively, resulting in interesting size-diversity relationships. Our results demonstrated that while library size does matter for its diversity, there exists an optimal size for structural diversity. It is also suggested that such quantitative measures can guide the design of diverse fragment libraries under different circumstances.
ARTICLE | doi:10.20944/preprints201902.0160.v1
Subject: Computer Science And Mathematics, Computer Science Keywords: holes; grid; shapes; homology; uncertainty
Online: 18 February 2019 (10:49:02 CET)
Starting from unidentified objects moving inside a two-dimensional Euclidean manifold, we propose a simple method to detect the topological changes that occur during their reciprocal interactions and shape morphing. This method, which allows the detection of topological holes development and disappearance, makes it possible to solve the uncertainty due to disconnectedness, lack of information and absence of objects’ sharp boundaries, i.e., the three troubling issues which prevent scientists to select the required proper sets/subsets during their experimental assessment of natural and artificial dynamical phenomena, such as fire propagation, wireless sensor networks, migration flows, neural networks’ and cosmic bodies’ analysis.
ARTICLE | doi:10.20944/preprints201810.0771.v2
Subject: Social Sciences, Education Keywords: scientific competence; competence-based education; educational planning; Education for Sustainable Development; evaluation of digital resources
Online: 29 November 2019 (03:17:18 CET)
Educating for Sustainability involves promoting sustainable competences in students. Not in vain, wider societal changes that ensure a balance between economic growth, respect for the environment and social justice must start with individual actions, implying knowledge, capacity and willingness to act. However, and although there is wide consensus that education should promote the development of competences for life, putting this theoretical tenet into may entail more problems. Competence is most often expressed in general terms without a specific definition of the intervening elements (knowledge, skills, values, attitudes), which may collide with the necessity of teachers – as learning planners - concrete entities on which to base their process of design. So that, in this work we propose a series of indicators that serve to characterize the four dimensions of scientific competence – contents of science, contents about science, value of science and utility of science-. Although they are primarily intended to be used to filter multimedia resources in an educational platform, this proposal of indicators can be extrapolated to the management and selection of a variety of resources and activities, and for sharing the objectives and evidences for the acquisition of competencies.
ARTICLE | doi:10.20944/preprints201806.0493.v1
Subject: Engineering, Electrical And Electronic Engineering Keywords: electromagnetically actuated cantilevers; nanometrology; multiobjective optimisation; active cantilevers; SOI-based prototyping
Online: 29 June 2018 (15:52:53 CEST)
In this paper we present the numerical and experimental results of a design optimization of electromagnetic cantilevers. In particular, a cost-effective technique of evolutionary computing enabling the simultaneous minimization of multiple criteria is applied. A set of optimal solutions are subsequently fabricated and measured. The designed structures are fabricated in arrays, which makes the comparison and measurements of the sensor properties reliable. The microfabrication process, based on the silicon on insulator (SOI) technology, is proposed in order to minimize parasitic phenomena and enable efficient electromagnetic actuation. Measurements on the fabricated prototypes assessed the proposed methodological approach.
ARTICLE | doi:10.20944/preprints202205.0304.v1
Subject: Computer Science And Mathematics, Robotics Keywords: Safe-drone; Emergency Detection; Time-window; Event-based Control; UAV(Unmanned Aerial Vehicle)/Quadrotor Drone
Online: 23 May 2022 (10:57:36 CEST)
Quadrotor drones have rapidly gained interest recently. Numerous studies are underway for the commercial use of autonomous drones, and especially the distribution businesses are taking serious reviews on drone delivery services. However, there are still many concerns about urban drone operations. The risk of failures and accidents makes it difficult to provide drone-based services in the real world with ease. There have been many studies that introduced supplementary methods to handle drone failures and emergencies. However, we discovered the limitation of the existing methods. The majority of approaches were improving PID-based control algorithms which is the dominant drone control method. This type of low-level approach lacks situation awareness and the ability to handle unexpected situations. This study introduces an event-based control methodology that takes a high-level diagnosing approach that can implement situation awareness via time-window. While leaving the low-level controller to involve in operating the drone for most of the time in normal situations, our controller operates at a higher level and detects unexpected behaviors and abnormal situations of the drone. We tested our method with real-time 3D computer simulation environments with Unreal Engine and AirSim. We were able to verify that our approach can provide enhanced double safety and better ensure safe drone operations. We hope our discovery to possibly contribute to the advance of real-world drone services in the near future.
ARTICLE | doi:10.20944/preprints202212.0157.v1
Subject: Engineering, Control And Systems Engineering Keywords: self-adaption; wireless sensors; model-based design; control engineering
Online: 8 December 2022 (10:24:09 CET)
The main objective of this work is the design and implementation of self-adaptive capabilities in wireless sensors by applying control engineering and model-based design methodologies. It has been addressed the problem related to the changes in the flow of data packets through the network connection and the excess energy consumption that this causes in these devices. To design the solution, a systemic characterization of the scheduling and execution process of embedded tasks on the device has been carried out. This means defining cause-effect relationships in the system and its modelling theoretically and/or experimentally. In turn, these models facilitate the design of control strategies to improve the dynamic behavior of the system. As a solution, a self-adaptation strategy based on feedforward control algorithm has been designed and developed, which has been applied to improve the dynamic behavior and resource consumption. The developed solution has been satisfactorily evaluated experimentally.
ARTICLE | doi:10.20944/preprints202209.0283.v1
Subject: Medicine And Pharmacology, Veterinary Medicine Keywords: Wolinella; Virulence genes; Helicobacter pylori; genomic homology
Online: 20 September 2022 (02:06:43 CEST)
Wolinella spp. and Helicobacter spp. have been repeatedly reported in the oral cavity of dogs and are associated with periodontal disease. Wolinella strains predominate in the oral cavity of dogs. The only known species of this genus, Wolinella succinogenes, was considered non-pathogenic until sequence analysis of its genome revealed homologous genes resembling virulence factors in Helicobacter pylori. This has led researchers to question the nonpathogenic status of W. succinogenes. The cagA and babA genes are examples of crucial virulence factors in H. pylori pathogenesis; thus, the present study evaluated the prevalence of these genera and assessed the Wolinella strain genome in terms of the presence of these virulence factors. Multiple specific PCR tests were performed on oral secretion samples collected from 62 dogs by sterile cytobrush to evaluate the genera, species, and presence of virulence genes. The species-specific 16s rRNA genes from the Helicobacter and Wolinella genera were detected in 58.06% and 83.87% of the oral samples, respectively. H. pylori were not detected in the specimens. No cagA and babA genes were detected in the Wolinella spp. or non-pylori Helicobacter genomes. Our results confirmed that Wolinella spp. is the predominant population compared to Helicobacter in the oral cavity of dogs. Apparently, the incidence of Helicobacter infections is generally associated with non-pylori Helicobacter organisms. Despite the hypothesis of genomic homology between W. succinogenes and H. pylori, cagA and babA virulence genes were not identified in any of the oral samples from the dogs.
ARTICLE | doi:10.20944/preprints202206.0201.v1
Subject: Biology And Life Sciences, Virology Keywords: human coronaviruses; envelope protein; PDZ-binding motif (PBM), homology-based modelling; docking; HADDOCK; protein-protein interaction; PALS1; pathogenesis; SARS-CoV-2
Online: 14 June 2022 (09:52:47 CEST)
The less virulent human (h) coronaviruses (CoVs) 229E, NL63, OC43, and HKU1 cause mild, self-limiting respiratory tract infections, while the more virulent SARS-CoV-1, MERS-CoV, and SARS-CoV-2 have caused severe outbreaks. The CoV envelope (E) protein, an important contributor to the pathogenesis of severe hCoVs infections, may provide insight into this disparate severity of the disease. We, therefore, generated full-length E protein models for SARS-CoV-1, -2, MERS-CoV, HCoV-229E, and HCoV-NL63 and docked C-terminal peptides of each model to the PDZ domain of the human PALS1 protein. The PDZ-binding motif (PBM) of the SARS-CoV-1, -2, and MERS-CoV models adopted a more flexible, extended coil while the HCoV-229E and HCoV-NL63 models adopted a less flexible alpha helix. All the E peptides docked to PALS1 occupied the same binding site and the more virulent hCoV E peptides generally interacted more stably with PALS1 than the less virulent ones. We propose that the increased flexibility of the PBM in more virulent hCoVs may permit more stable binding to various host proteins, thereby possibly contributing to more severe disease. This is the first paper to model full-length 3D structures for both more virulent and less virulent hCoVs E proteins, providing novel insights for possible drug and/or vaccine development.
ARTICLE | doi:10.20944/preprints202308.1858.v1
Subject: Biology And Life Sciences, Biochemistry And Molecular Biology Keywords: Deep Learning, ELECTRA; Ion binding site prediction; Transformer; Natural Language Processing; Sequence-based prediction
Online: 29 August 2023 (02:50:38 CEST)
Interactions between proteins and ions are essential for various biological functions like structural stability, metabolism, and signal transport. Given that more than half of all proteins bind to ions, it becomes crucial to identify ion-binding sites. Accurate identification of protein-ion binding sites helps us to understand proteins’ biological functions and plays a significant role in drug discovery. While several computational approaches have been proposed, this remains a challenging problem due to the small size and high versatility of metals and acid radicals. In this study, we propose IonPred, a sequence-based approach that employs ELECTRA (Efficiently Learning an Encoder that Classifies Token Replacements Accurately) to predict ion binding sites using only raw protein sequences. We successfully fine-tuned our pretrained model to predict the binding sites for nine metal ions (Zn2+, Cu2+, Fe2+, Fe3+, Ca2+, Mg2+, Mn2+, Na+, and K+) and four acid radical ion ligands (CO32−, SO42−, PO43−, NO2−). IonPred surpassed six current state-of-the-art tools by over 44.65% and 28.46% respectively in F1 score and MCC when compared on an independent test dataset. Our method is more computationally efficient than existing tools producing prediction results for a hundred sequences for a specific ion in under ten minutes.
ARTICLE | doi:10.20944/preprints202202.0335.v1
Subject: Biology And Life Sciences, Agricultural Science And Agronomy Keywords: Cereals; Grain protein; Near Infrared Spectroscopy (NIRS)-based sensors; Prediction algorithms; FOSS; Hone Lab
Online: 25 February 2022 (11:21:57 CET)
Achieving global goals on sustainable nutrition, health, and wellbeing will depend on delivering enhanced diets to humankind. This will require, among others, instantaneous access to information on food quality at key points within agri-food systems. Although stationary methods are usually used to quantify grain quality (wet-lab chemistry, benchtop NIR spectrometer); these do not suit many required user-cases, such as stakeholders in decentralized agri-food-chains that are typical for emerging economies. Therefore, we explored new technologies and models that might aid these particular user-cases. For this purpose, we generated the NIR spectra of 328 grain samples from multiple cereals (finger millet, foxtail millet, maize, pearl millet, sorghum) with a standard benchtop NIR Spectrometer (DS2500, FOSS) and a novel mobile NIR-based sensor (HL-EVT5, Hone). We explored a range of classical deterministic and novel machine learning (ML)-driven models to build calibrations out of the NIR spectra. We were able to build relevant calibrations out of both types of spectra. At the same time, ML-based methods enhanced the prediction capacity of calibration models compared to classical deterministic methods. We also documented that the prediction of grain protein content based on NIR spectra generated by a mobile sensor (HL-EVT5, Hone) was highly relevant for quantitative protein predictions (R2 = 0.91, RMSE = 0.97, RPD = 3.48). Thus, the findings of this study lay the foundations on which to expand the utilization of NIR spectroscopy applications for agricultural research and development.
ARTICLE | doi:10.20944/preprints201901.0198.v1
Subject: Computer Science And Mathematics, Information Systems Keywords: Dark Proteome, Molecular Structure, Homology Modelling
Online: 21 January 2019 (08:50:48 CET)
The dark proteome as we define it, is the part of the proteome where 3D structure has not been observed either by homology modeling or by experimental characterization in the protein universe. From the 550.116 proteins available in Swiss-Prot (as of July 2016) 43.2% of the Eukarya universe and 49.2% of the Virus universe are part of the dark proteome. In Bacteria and Archaea, the percentage of the dark proteome presence is significantly less, with 12.6% and 13.3% respectively. In this work, we present the map of the dark proteome in Human and in other model organisms. The most significant result is that around 40%- 50% of the proteome of these organisms are still in the dark, where the higher percentages belong to higher eukaryotes (mouse and human organisms). Due to the amount of darkness present in the human organism being more than 50%, deeper studies were made, including the identification of ‘dark’ genes that are responsible for the production of the so-called dark proteins, as well as, the identification of the ‘dark’ organs where dark proteins are over represented, namely heart, cervical mucosa and natural killer cells. This is a step forward in the direction of the human dark proteome.
ARTICLE | doi:10.20944/preprints201811.0310.v1
Subject: Medicine And Pharmacology, Pathology And Pathobiology Keywords: tessellation; forensic picture; bullets; homology; proximity
Online: 13 November 2018 (10:41:14 CET)
Here we show how a recently-introduced method from algebraic topology, namely proximal planar vortex 1-cycles, might be helpful in detecting hidden features of the shapes and holes in images, therefore contributing to the solution of both cold and fresh forensic cases. In particular, we test the efficacy of this technique by assessing one of the most puzzling cases of recent history, i.e., Aldo Moro’s death. Terrorists of the Red Brigades claimed that they killed Moro when he was placed inside the trunk of a car,shooting him with a barrage of bullets. We demonstrate, based on the analysis of the photographs taken during the autoptic procedure, that the terrorist’s account does not hold true. Our results, showing different series of shots, point towards a three-step execution, with the first phasestaking place outside the car. In conclusion, the novel forensic analysis method introduced in this paper permits the evaluation of a collection of vortex cycles/nerves equipped with a connectedness proximity, which makes it possible to assess unexpected spatial clusters in photographs.
REVIEW | doi:10.20944/preprints202204.0156.v1
Subject: Biology And Life Sciences, Biophysics Keywords: nanovesicles; flow; homology; vortex; Betti number; Borsuk–Ulam theorem
Online: 18 April 2022 (06:14:33 CEST)
Mechanical properties such as shape, volume and size affect the dynamics of biological systems. Most of the current methodological approaches are inclined to remove the existence of holes and impurities from systems’ description, regarding them as routes toward mechanical failure. On the contrary, we suggest that the occurrence of holes might be of utmost functional importance, allowing reversible transformations of cellular structures. The focus here is on the widespread occurrence of intracytoplasmic holes, that deeply modifies the topology of living cells and provides researchers with novel operational tools to investigate intracellular dynamics. We take as example the prokaryotic gas vesicles, i.e., intracellular cavities filled with gases spreading from the nearby medium. The mechanical and topological cellular properties dictated by intracytoplasmic holes are investigated, focusing on the physical constraints imposed by their very existence. For instance, the presence of gas vesicles breaks the cytoplasmic homogeneity, leading to inhomogeneity in functional activities and modifications in intracellular flows. Also, a topological approach to cytoplasmic holes suggests novel physiological roles for gas vesicles. For example, the gas vesicles’ ability to increase/decrease cellular volumes provides a mechanism that counteracts the detrimental effects of the surface/volume ratio. In conclusion, a structural/methodological approach based on the occurrence of holes testifies once again how the simple biophysical structure alone can dictate the function.
ARTICLE | doi:10.20944/preprints201911.0189.v1
Subject: Biology And Life Sciences, Food Science And Technology Keywords: protein; plant-based protein; whey protein; essential amino acids; leucine, healthy men
Online: 16 November 2019 (00:58:01 CET)
This study assessed bio-equivalence of high-quality, plant-based protein blends versus Whey Protein Isolate (WPI) in healthy, resistance-trained men. The primary endpoint was incremental area under the curve (iAUC) of blood essential Amino Acids (eAAs) 4 hours after consumption of each product. Cmax and Tmax of blood leucine were secondary outcomes. Subjects (n=18) consumed three plant-based protein blends and WPI (control). Analysis of Variance model was used to assess for bio-equivalence of total sum of blood eAA concentrations. The total blood eAA iAUC ratios of the three blends were: [90% CI]: #1: 0.66 [0.58-0.76]; #2: 0.71 [0.62-0.82]; #3: 0.60 [0.52-0.69], not completely within the pre-defined equivalence range [0.80-1.25], indicative of 30-40% lower iAUC versus WPI. Leucine Cmax of the three blends was not equivalent to WPI, #1: 0.70 [0.67-0.73]; #2: 0.72 [0.68-0.75]; #3: 0.65 [0.62 – 0.68], indicative of a 28-35% lower response. Leucine Tmax for two blends were similar to WPI (#1: 0.94 [0.73-1.18]; #2: 1.56 [1.28-1.92]; #3: 1.19 [0.95-1.48]). The plant-based protein blends were not bio-equivalent. However, blood leucine kinetic data across the blends approximately doubled from fasting concentrations whereas blood Tmax data across two blends was similar to WPI. This suggests evidence of rapid hyperleucinemia, which correlates with a protein’s anabolic potential.
ARTICLE | doi:10.20944/preprints201912.0069.v1
Subject: Computer Science And Mathematics, Computational Mathematics Keywords: statistical mirroring; genomic mirrors; comparative optinalysis; multiple comparison; inferences; homology
Online: 5 December 2019 (11:36:25 CET)
Sequence alignment and comparison through pairwise, multiple, global and local techniques are the main principles that underpin comparative genomics. However, most of the algorithms used are alignment-based which imposed some limitations on their use and application. In an attempt to provide an alignment-free alternative approaches, a methodology of comparative optinalysis and statistical mirroring was used and adopted to provide a suitable alternative for multiple genomic sequence comparison. In this article, methods comparison with MUSCLE, MUFFT, Clustal Omega, and T-Coffee was designed to assess the suitability and statistical power of statistical mirroring as an alternative method for multiple genomic sequences comparison using different sets of logically generated biological sequence datasets with different problems and computational complications. The results of the comparisons validate that statistical mirroring is a suitable alignment-free alternative approach for multiple genomic sequence comparison. The applied method (statistical mirroring) distinguishes itself over MUSCLE, MUFFT, Clustal Omega, and T-Coffee in specificity to a position-specific changes, specificity to a base-specific changes, cladogram and phylogenetic linearity, alignment independency, computational simplicity, and limit of input capacity.
ARTICLE | doi:10.20944/preprints202305.1806.v1
Subject: Chemistry And Materials Science, Paper, Wood And Textiles Keywords: phenol-formaldehyde resin; soybean meal; soy-based adhesives; curing; plywood
Online: 25 May 2023 (10:55:13 CEST)
To develop a lower-cost, excellent performance, and environmentally friendly phe-nol-formaldehyde (PF) resin, soybean meal was used to modify PF resin, and soybean meal-phenol-formaldehyde (SMPF) resins were prepared. Their physicochemical properties and curing performance were investigated, showing that SMPF resins have higher curing tempera-tures than PF resin. The Fourier transform infrared spectroscopy (FTIR) results indicated that the cross-linking reaction occurred between the amino groups of soybean protein and the hy-droxymethyl phenol. Moreover, with the addition of soybean meal, the viscosity of SMPF in-creased while the gel time decreased. It is worth mentioning that SMPF-2 resin has favorable viscosity, short gel time, low curing temperature (135.78 °C), and high water resistance and bonding strength (1.01 MPa). Finally, all the plywoods bonded with SMPF resins have good water resistance and bonding strength, which could meet the Standard (GB/T 17657-2013, type I) for plywood. The optimized SMPF resins showed the potential application to replace part of PF resin in the wood industry.
REVIEW | doi:10.20944/preprints202303.0072.v1
Subject: Engineering, Bioengineering Keywords: glycosylation, glycoengineering, biologic, therapeutic protein, gene therapy, cell-based therapy, monoclonal antibody
Online: 3 March 2023 (10:43:51 CET)
Over recent decades, therapeutic proteins have had widespread success in treating a myriad of diseases. Glycosylation, a near universal feature of this class of drugs, is a critical quality attribute that significantly influences the physical properties, safety profile and biological activity of therapeutic proteins. Optimizing protein glycosylation, therefore, offers an important avenue to developing more efficacious therapies. In this review, we discuss specific examples of how variations in glycan structure and glycoengineering impacts the stability, safety, and clinical efficacy of protein-based drugs that are already in the market as well as those that are still in preclinical development. We also highlight the impact of glycosylation on next generation biologics such as T cell-based cancer therapy and gene therapy.
ARTICLE | doi:10.20944/preprints202310.1331.v1
Subject: Arts And Humanities, Architecture Keywords: inclusive park; disabilities; research-based design; research through designing
Online: 23 October 2023 (05:13:53 CEST)
Public parks are a community resource with an important role in improving liveability, physical, and mental wellbeing. However, exercise facilities that are suitable for people with disabilities typically have been neglected in public park design. As such, people with disabilities often are unable to independently or safely use the park. To address this shortcoming, the objective of this paper was to employ a pragmatic research through designing process in developing the design for an inclusive park. We used a mixed-methods approach in the research that included review of previous studies, semi-structured interviews, and questionnaire surveys with stakeholders were applied as design integration. Persons with disabilities specifically were consulted to express their views on all matters of inclusive park design.
ARTICLE | doi:10.20944/preprints202302.0386.v1
Subject: Chemistry And Materials Science, Physical Chemistry Keywords: gelatinized starch; maltose-binding protein; microplate based assay; protein-protein interaction; dissociation constant determination
Online: 22 February 2023 (14:53:42 CET)
The detection and quantification of protein–protein interactions (PPIs) is a crucial technique that often involves the use of recombinant proteins with fusion-protein tags, such as maltose-binding protein (MBP) and glutathione-S-transferase (GST). In this study, we improved the cohesive and sticky properties of gelatinized starch by supplementing it with agarose, resulting in a harder gel that could coat the bottom of a microtiter plate. The resulting gelatinized starch/agarose mixture allowed for the efficient immobilization of MBP-tagged proteins on the coated plates, enabling the use of indirect ELISA-like PPI assays. By using the enzymatic activity of GST as an indicator, we succeeded in determining the dissociation constants between MBP-tagged and GST-tagged proteins on 96-well microtiter plates and a microplate reader without any expensive specialized equipment.
REVIEW | doi:10.20944/preprints202211.0444.v1
Subject: Chemistry And Materials Science, Electrochemistry Keywords: Density functional theory; Descriptor; Carbon-based materials; Electrocatalysis; Low dimension
Online: 23 November 2022 (11:04:03 CET)
Low-dimensional carbon-based (LDC) materials have attracted extensive research attentions in electrocatalysis because of their unique advantages such as structural diversity, low cost, and chemical tolerance. They have been widely used in a broad range of electrochemical reactions to relief environmental pollution and energy crisis. Typical examples include hydrogen evolution reaction (HER), oxygen evolution reaction (OER), oxygen reduction reaction (ORR), carbon dioxide reduction reaction (CO2RR), and nitrogen reduction reaction (NRR). Traditional “trial and error” strategies seriously slowed down the rational design of electrocatalysts for these important applications. Recent studies show that the combination of density functional theory (DFT) calculations and experimental research is capable of accurately predicting the structures of electrocatalysts, thus could reveal the catalytic mechanisms. Herein, current well-recognized collaboration methods of theory and practice are reviewed. The history of modern DFT, commonly used calculation methods, and basic functionals are briefly summarized. Special attention is paid to descriptors that are widely accepted as a bridge links the structure and activity, and the breakthroughs for high-volume accurate prediction of electrocatalysts. Importantly, correlating multiple descriptors are used to systematically describe the complicated interfacial electrocatalytic processes of LDC catalysts. In addition, machine learning and high-throughput simulations are crucial in assisting the discovery of new multiple descriptors and reaction mechanisms. This review will guide the further development of LDC electrocatalysts for extended applications from the aspect of DFT computations.
ARTICLE | doi:10.20944/preprints201809.0466.v1
Subject: Computer Science And Mathematics, Information Systems Keywords: topological data analysis; text mining; computational topology; style; persistent homology
Online: 24 September 2018 (15:33:02 CEST)
Topological Data Analysis (TDA) refers to a collection of methods that find the structure of shapes in data. Although recently, TDA methods have been used in many areas of data mining, it has not been widely applied to text mining tasks. In most text processing algorithms, the order in which different entities appear or co-appear is being lost. Assuming these lost orders are informative features of the data, TDA may play a significant role in the resulted gap on text processing state of the art. Once provided, the topology of different entities through a textural document may reveal some additive information regarding the document that is not reflected in any other features from traditional text processing methods. In this paper, we introduce a novel approach that hires TDA in text processing in order to capture and use the topology of different same-type entities in textural documents. First, we will show how to extract some topological signatures in the text using persistent homology-i.e., a TDA tool that captures topological signature of data cloud. Then we will show how to utilize these signatures for text classification.
ARTICLE | doi:10.20944/preprints202305.1202.v1
Subject: Engineering, Aerospace Engineering Keywords: Generative model; Knowledge-Based Engineering; Design automation; Conceptual design; Aerospace Engineering; Computer Aided Design
Online: 17 May 2023 (07:14:32 CEST)
This thesis presents the effects of work done on a software project for generative models and spreadsheets, allowing for a quick creation of the conceptual model of the aircraft. The subject of the work is a response to the current trends and needs prevailing in the field of computer design engineering CAD and aviation. In the initial chapters, theoretical issues related to the work being carried out were introduced and the methodology of creating software for construction and verification of the structure of aircraft along with the needs of interchange between databases of generative models was presented. In the next stages, the concepts and selected solutions for the user interface supporting the knowledge base were presented along with a set of procedures for its operation. Furthermore, the method of database integration with the methods of determining design features for the developed generative models and with the Siemens NX system. Furthermore, problems encountered in software development, as well as solution examples for model application are specified. The results obtained and the models generated on their basis were subjected to a strength analysis using Autodesk Inventor software and analysed in terms of meeting the initial assumptions. In the end, conclusions and observations resulting from the effects of the work presented in the project were formulated.
ARTICLE | doi:10.20944/preprints201805.0234.v1
Subject: Biology And Life Sciences, Cell And Developmental Biology Keywords: non-coding RNA; telomerase RNA; secondary structure; synteny; homology search; yeast
Online: 16 May 2018 (11:58:28 CEST)
The telomerase RNA in yeasts is large, usually >1000 nt, and contains functional elements that have been extensively studied experimentally in several disparate species. Nevertheless, they are very difficult to detect by homology-based methods and so far have escaped annotation in the majority of the genomes of Saccharomycotina. This is a consequence of sequences that evolve rapidly at nucleotide level, are subject to large variations in size, and are highly plastic with respect to their secondary structures. Here we report on a survey that was aimed at closing this gap in RNA annotation. Despite considerable efforts and the combination of a variety of different methods, it was only partially successful. While 27 new telomerase RNAs were identified, we had to restrict our efforts to the subgroup Saccharomycetacea because even this narrow subgroup was diverse enough to require different search models for different phylogenetic subgroups. More distant branches of the Saccharomycotina still remain without annotated telomerase RNA.
ARTICLE | doi:10.20944/preprints202302.0164.v1
Subject: Environmental And Earth Sciences, Environmental Science Keywords: coastal transformation; ecosystem services; transdisciplinarity; nature-based solutions; southern North Sea; Gute Küste Niedersachsen
Online: 9 February 2023 (11:17:26 CET)
Novel strategies in coastal protection are needed to cope with climate change-induced sea level rise. They aim at the sustainable development of coastal areas in light of an intensification and land use changes. A promising approach is the design of nature-based solutions (NbS), complementing the safety levels of technical infrastructures. However, NbS lack a widespread and large-scale implementation. To address this deficit, co-design concepts are needed that combine experiences from science and practice. This work presents and discusses the approach of a coast-specific real-world laboratory (RwL) addressing the inclusive design of ecosystem-based coastal protection. Strategies of RwLs are applied for the first time in a coastal context along the North Sea coastline in Germany. We found the concept of RwLs suitable for coastal transdisciplinary research, although adaptions in the spatial reference level or flexibility in location and time of experimentation are necessary. A profound actor analysis is indispensable to specify participatory processes and interaction levels. A criteria-based cooperative selection of RwL sites helps to reveal and solve conflicting interests to achieve trust between science and practice. Addressing site-specific characteristics and practitioners’ needs, our coastal RwL provides a mutual learning space to develop and test NbS to complement technical coastal protection.
ARTICLE | doi:10.20944/preprints201810.0513.v1
Subject: Engineering, Control And Systems Engineering Keywords: project based learning; human powered vehicles; sustainable transportation design
Online: 23 October 2018 (03:42:42 CEST)
In this work, the decennial experience of Policumbent student team at Politecnico di Torino is summarized by focusing on the acquired knowledge in design of Human Powered Vehicles (HPVs) and on soft skills developed by both students and staff. Policumbent was funded by the authors at the end of 2008 in order to gather engineering students interested in design and construction of HPVs. In the last decade, the team has grown from 10 up to 50 students enrolled per year, exploring a range of HPV design for sports and mobility. Even when focusing on sport vehicles and extreme HPVs for speed record, such kind of projects allows students to familiarize with important concepts related to sustainable mobility: the amount of resistive forces and dissipated power, the role of vehicle weight and the impact of acceleration on the overall energetic balance as far as fundamental concepts about energy consumption, efficiency and emissions of the ``human engine'' in comparison with other kind of engines. By touching with hands such topics in the framework of a ``human-centred'' design project, the students have opportunity to develop awareness about the impact of design choices on sustainability of any kind of vehicle for transportation. Also, the paper retraces the team evolution path by focusing on a thorough analysis of what factors contributed to the success of this project.
ARTICLE | doi:10.20944/preprints202010.0351.v1
Subject: Biology And Life Sciences, Biochemistry And Molecular Biology Keywords: Streptococcus mutans; adhesion proteins; Antigen I/II; Structure-based virtual screening; molecular dynamics
Online: 16 October 2020 (13:48:43 CEST)
Streptococcus mutans is well known for having virulence factors associated with its cariogenic role, such as glucosyltransferases, which have been used as targets for the virtual screening of molecules with inhibitory capacity. The Antigen I/II of S. mutans is involved in the adhesion to the surface of the tooth and the bacterial co-aggregation in the biofilm formation, despite that, this protein has not been used as a target in a virtual strategy search for inhibitors. In this study we identified in silico and evaluated in vitro molecules with adhesion inhibitory potential on S. mutans Ag I/II. A virtual screening of 883,551 molecules was conducted, cytotoxicity analysis on fibroblast cells, S. mutans adhesion studies, scanning electron microscopy analysis for bacterial integrity, and molecular dynamics simulation were also performed. We have found three molecules (ZI-187, ZI-939, ZI-906) that were not cytotoxic and inhibited the adhesion of S. mutans to polystyrene microplates. Molecular dynamic simulation by 300 nanoseconds showed stability of the interaction between ZI-187 and Ag I/II (PDB: 3IPK). This work provides three new molecules that targets Ag I/II and have the capacity to inhibit in vitro the S. mutans adhesion on polystyrene microplates and provides a new computational line for the search and selection of safe inhibitory molecules against different pathogens.
ARTICLE | doi:10.20944/preprints202311.0355.v1
Subject: Chemistry And Materials Science, Food Chemistry Keywords: rice protein; spirulina protein; pea protein; soy protein; plant-based diet; thermal properties; rheological properties; protein processing
Online: 6 November 2023 (13:48:26 CET)
Reducing meat consumption is better for the environment. Unfortunately, commercial plant-based meat substitutes are often more expensive than meat and thus have not seen widespread adoption. This paper analyzes commercially-available spirulina, soy, pea, and brown rice protein isolates characteristics to provide data for non-meat protein cost reductions. Thermal and rheological properties, viscosity, density, and particle size distribution are analyzed for further study on alternative protein-based food processing. Differential scanning calorimetry analysis produced dry amorphous-shaped curves and paste curves with a more distinct endothermic peak. Extracted linear temperature ranges for processing in food production for spirulina was 70-90ºC; soy protein was 87-116ºC; pea protein was 67-77ºC; and brown rice protein was 87-97ºC. Viscosity analysis determined each protein material was shear-thinning and that viscosity increased with decreased water concentration, with rice being an exception to the latter trend. The obtained viscosity range for spirulina was 15,100-78,000cP; soy protein was 3,200-80,000cP; pea protein was 1,400-32,700cP; and brown rice protein was 600-3,500cP. The results indicate that extrusion is a viable method for further processing of the protein isolates as this technique has a large temperature operating range and variable screw speed. Data provided here can be used to make single or multi-component protein substitutes.
ARTICLE | doi:10.20944/preprints202310.0425.v1
Subject: Biology And Life Sciences, Virology Keywords: hepatitis B; antiviral; drug discovery; HBc protein; pharmacophore-based screening; drug repurposing
Online: 8 October 2023 (05:11:37 CEST)
Background: Chronic Hepatitis B Virus (HBV) infection is a global health concern, associated with severe liver diseases, necessitating ongoing research on novel drug candidates. This study aims to identify potential drug candidates targeting HBV core protein (HBcAg) and disrupting capsid assembly, a critical step in the virus's life cycle. Methods: HBcAg in complex with HBV inhibitors were obtained from the Protein Data Bank (PDB). CavityPlus server was used for analysis of druggable cavity. Structure-based pharmacophores were extracted from identified cavities, and potential allosteric ligand binding sites were assessed using CavPharmer, CorrSite, and CovCys. LigandScout was employed for ligand-based pharmacophore screening against an FDA-approved library. The ZINC database was screened with features extracted from CavPharmer. Molecular docking studies were conducted using Autodock Vina. Lead compounds were selected based on docking scores, binding modes, and interactions within the druggable cavity. Results: Strong druggable pockets were found for Ciclopirox, while Compound 24, NVR10-001E2, and others showed medium to weak pockets. Ligand-based pharmacophores varied in size and complexity. Screening revealed potential hits matching these pharmacophores, including Ciclopirox olamine, Voriconazole, Enasidenib, and Statins. A large compound database search yielded additional hits like ZINC86859997 and ZINC63280172. Docking analyses confirmed these hits' potential, highlighting their interactions with critical HBc protein residues, offering promising leads for hepatitis B drug development. Conclusions: Voriconazole, Enasidenib, and Lovastatin have shown promises. These hits displayed favorable interactions with crucial HBc protein residues, indicating their potential as lead compounds The mechanism of action of statins with anti-HBV activities also highlighted. This comprehensive approach offers valuable insights into targeting HBc protein for antiviral drug discovery.
ARTICLE | doi:10.20944/preprints202011.0446.v1
Subject: Chemistry And Materials Science, Medicinal Chemistry Keywords: Alkaloids; Anti-Onchocercal; Bisindoles; Docking; Homology Modeling; Monoindoles.
Online: 17 November 2020 (11:13:54 CET)
A new iboga-vobasine-type isomeric bisindole alkaloid named voacamine A (1), along with eight known compounds, voacangine (2), voacristine (3), coronaridine (4), tabernanthine (5), iboxygaine (6), voacamine (7), voacorine (8), and conoduramine (9), were isolated from the stem bark of Voacanga africana. The structures of the compounds were determined by comprehensive spectroscopic analyses (1D- and 2D-NMR). Compounds 1, 2, 3, 4, 6, 7 and 8 were found to inhibit the motility of both the microfilariae (Mf) and adult male worms of Onchocerca ochengi, in a dose-dependent manner, but were only moderately active on the adult female worms upon biochemical assessment at 30 μM drug concentrations. The IC50 values of the isolates are 2.49-5.49 µM for microfilariae and 3.45-17.87 µM for adult males. Homology modeling was used to generate a 3D model of the the O. ochengi thioredoxin reductase target and docking simulation attempted to offer an explanation of the anti-onchocercal structure-activity relationship (SAR) of the isolated compounds. These alkaloids are new potential leads for the development of antifilirial drugs. The results of this study validate the traditional use of V. africana in the treatment of human onchocerciasis.
ARTICLE | doi:10.20944/preprints202003.0068.v1
Subject: Computer Science And Mathematics, Geometry And Topology Keywords: Tournaments; Semi-Simplicial Sets; Neural networks; Persistent homology
Online: 4 March 2020 (11:40:12 CET)
Complete digraphs are referred to in the combinatorics literature as tournaments. We consider a family of semi-simplicial complexes, that we refer to as ``tournaplexes'', whose simplices are tournaments. In particular, given a digraph G, we associate with it a ``flag tournaplex'' which is a tournaplex containing the directed flag complex of G, but also the geometric realisation of cliques that are not directed. We define several types of filtrations on tournaplexes, and exploiting persistent homology, we observe that flag tournaplexes provide finer means of distinguishing graph dynamics than the directed flag complex. We then demonstrate the power of these ideas by applying them to graph data arising from the Blue Brain Project's digital reconstruction of a rat's neocortex.
ARTICLE | doi:10.20944/preprints201902.0024.v1
Subject: Engineering, Civil Engineering Keywords: infiltration based BMP’s; flood; infiltration; clogging; soil permeability; underdrain; soil saturation rate; drainage basin; urban drainage
Online: 3 February 2019 (03:05:39 CET)
Infiltration based stormwater best management practices bring considerable economic, social and ecological benefits. Controlling stormwater quantity and quality are primarily important to prevent urban flooding and minimizing loads of pollutants to the receiving waters. However, there have been growing concerns about how the traditional design approach contributes to the failure of infiltration based BMP’s that have caused flooding, ponding, prolonged movement of surface water, and frequent clogging, etc. Many of these problems were due to the fact that the current design approaches of stormwater BMP’s only focus on surface hydrology and give little or no attention to the underline subsoil permeability rate and other constraints during the design and sizing process. As a result, we are exhibiting many newly constructed infiltration based BMP’s are failing to function well. This paper presents and demonstrates a new paradigm shift in designing infiltration-based stormwater BMP’s by combining subsurface hydrology and undelaying native soil constraints to establish acceptable criteria for sizing infiltration based BMPs.
ARTICLE | doi:10.20944/preprints201611.0041.v1
Subject: Chemistry And Materials Science, Analytical Chemistry Keywords: M-polynomial; degree-based index; boron nanotubes
Online: 7 November 2016 (07:41:36 CET)
Recent discovery of triangular boron Nanotubes makes it a competitor of carbon in many respects. Closed forms of M-polynomial of nanotubes produce closed forms of many degree-based topological indices which are numerical parameters of the structure and, in combination, determine properties of the concerned nanotubes. In this report, we give M-polynomials of triangular boron nanotubes and recover many important topological degree-based indices of these nanotubes. We also plot surfaces associated to these nanotubes.
CONCEPT PAPER | doi:10.20944/preprints202005.0182.v1
Subject: Biology And Life Sciences, Virology Keywords: Coronavirus Nsp proteins; ribosomal proteins homology; inhibition of ribosome turn over; rRNA methyltransferase; protein synthesis inhibition; low ATP formation; blood clotting; low blood pressure and coma
Online: 10 May 2020 (18:14:55 CEST)
Multi-Alignment method coupled with phylogenetic analysis we disclosed the Nsp9 and Nsp10 non-structural proteins of Corona Virus as rRNA RlmH/K methyltransferases with similarities with bin recombinase and int-core integrase fold. Further, Nsp9 has similarities to S8 ribosomal protein and Nap10 has similarity to S10 ribosomal protein. Previously, we showed Nsp13, Nsp14, Nsp15 and Nsp16 are also different types of rRNA RlmE/N and Cfr-like methyltransferases-ribonuclease with RNA helicase domains. Two domains of Nsp13 astonishingly have similarities to ribosomal proteins L6 and L9. Taken together, Nsp9/10 and Nsp13-16 proteins could mimic host ribosome assembly and also could methylate rRNA of mitobibosome preventing mitochondrial protein synthesis and oxidative phosphorylation. Low ATP synthesis causes lowering blood pressure following coma but very ATP concentration (1-10nM) surely induces platelets aggregation through vWA, collagen and GpIIb/IIIa proteins followed by fibrin formation and blood clotting as recently have seen in the lung of many Corona virus infected patients. We have also postulated that two polyproteins itself resemble like 28S and 38S mitoribosome subunits and compete with rRNAs inhibiting the ribosome turnover and new protein synthesis due to their similarities with many ribosomal proteins. Such finding may be valuable in computer-based novel drug design against Corona virus.
ARTICLE | doi:10.20944/preprints202310.1181.v1
Subject: Biology And Life Sciences, Immunology And Microbiology Keywords: recombinant probiotic -based vaccines; probiotic strain E. faecium L3; mucosal vaccines; SARS-CoV-2 spike protein; vaccine efficacy.
Online: 18 October 2023 (11:29:09 CEST)
The COVID-19 pandemic was declared in March 2020 and is still ongoing. The course of the epidemic remains uncertain, and mutations in the coronavirus, as well as the emergence of new variants of concern, make it possible that there will be periodic surges in the number of cases. Moreover, it is not clear how quickly and to what extent the effectiveness of vaccination will decline as the virus continues to mutate. One possible solution to combat the rapidly mutating coronavirus is the development of pan-coronavirus vaccines that stimulate the production of antibodies against conserved elements of the virus. Another approach could be the creation of safe vaccine platforms that can be rapidly adapted to deliver new, specific antigens in response to viral mutations. Recombinant probiotic microorganisms that can produce viral antigens by inserting specific viral DNA fragments into their genome show promise as a platform and vector for mucosal vaccine antigen delivery. With a well-established safety profile and the ability to transform into vaccine candidates, probiotic bacteria have significant research potential. The authors of this study have developed a convenient and universal technique for inserting the DNA sequences of pathogenic bacteria and viruses into the gene that encodes the pili protein of the probiotic strain E. faecium L3. The paper presents data on the immunogenic properties of two E. faecium L3 vaccine strains, which produce two different fragments of the coronavirus S1 protein, and provides an assessment of the protective efficacy of these oral vaccines against coronavirus infection in Syrian hamsters.
ARTICLE | doi:10.20944/preprints202309.2178.v1
Subject: Biology And Life Sciences, Biochemistry And Molecular Biology Keywords: leucyl-aminopeptidase; Bacillus cereus; expression; homology modeling; molecular docking
Online: 2 October 2023 (11:18:37 CEST)
Leucyl-aminopeptidase (LAP), an important metallopeptidase, hydrolyses amino acid residues from the N-terminal of polypeptides and proteins, acting preferentially on the peptide bond formed by N- terminus leucine. A new leucyl-aminopeptidase was found in Bacillus cereus CZ. Its gene (bclap) contained a 1485 bp ORF encoding 494 amino acids with a molecular weight of 54 kDa. The bcLAP protein was successfully expressed in E. coli BL21(DE3). Optimal activity is obtained at pH 9.0 and 58°C. The bcLAP displays a moderate thermostability and an alkaline pH adaptation range. Enzymatic activity is dramatically enhanced by Ni2+. EDTA significantly inhibits the enzymatic activity, and bestatin and SDS also show strong inhibition. The three-dimensional model of bcLAP monomer and homohexamer is simulated by Phyre2 server and SWISS-MODEL server. The docking of bestatin, Leu-Trp, Asp-Trp and Ala-Ala-Gly to bcLAP is performed using AutoDock4.2.5 , respectively. Molecular docking results show that the residues Lys260, Asp265, Lys272, Asp283, Asp342, Glu344, Arg346, Gly372, His437 are involved in the hydrogen bonding with the ligands and zinc ions. There may be two nucleophilic catalytic mechanisms in bcLAP, one involving His 437 or Arg346 and the other involving His437 and Arg346. The bcLAP can hydrolyse the peptide bonds in Leu-Trp, Leu-Trp and Ala-Ala-Gly.
CONCEPT PAPER | doi:10.20944/preprints202106.0578.v1
Subject: Biology And Life Sciences, Animal Science, Veterinary Science And Zoology Keywords: homology; developmental mechanism; evidential integration; eumetazoan body plan; phylogenetics
Online: 23 June 2021 (11:45:06 CEST)
Reconstructing ancestral species is a challenging endeavour: fossils are often scarce or enigmatic, and inferring ancestral characters based on novel molecular approaches (e.g. comparative genomics or developmental genetics) has long been controversial. A key philosophical challenge pertinent at present is the lack of a theoretical framework capable of evaluating inferences of homology made through integration of multiple kinds of evidence (e.g. molecular, developmental, or morphological). Here, I present just such a framework. I start with a brief history and critical assessment of attempts at inferring morphological homology through developmental genetics. I then bring attention to a recent model of homology, namely Character Identity Mechanisms (DiFrisco, Love, & Wagner, 2020), intended partly to elucidate the relationships between morphological characters, developmental genetics, and homology. I utilise and build on this model to construct the evaluative framework mentioned above, which judges the epistemic value of evidence of each kind in each particular case based on three proposed criteria: effectiveness, admissibility, and informativity, as well as providing a generalised guideline on how it can be scientifically operationalised. I then point out the evolution of the eumetazoan body plan as a case in point where the application of this framework can yield satisfactory results, both empirically and conceptually. I will conclude with a discussion on some potential implications for more general philosophy of biology and philosophy of science, especially surrounding evidential integration, models and explanation, and reductionism.
ARTICLE | doi:10.20944/preprints202012.0281.v1
Subject: Biology And Life Sciences, Biochemistry And Molecular Biology Keywords: covid-19; drug repurposing; topological data analysis; persistent homology
Online: 11 December 2020 (12:57:28 CET)
Since its emergence in March 2020, the SARS-CoV-2 global pandemic has produced more than 65 million cases and one point five million deaths worldwide. Despite the enormous efforts carried out by the scientific community, no effective treatments have been developed to date. We created a novel computational pipeline aimed to speed up the process of repurposable candidate drug identification. Compared with current drug repurposing methodologies, our strategy is centered on filtering the best candidate among all selected targets focused on the introduction of a mathematical formalism motivated by recent advances in the fields of algebraic topology and topological data analysis (TDA). This formalism allows us to compare three-dimensional protein structures. Its use in conjunction with two in silico validation strategies (molecular docking and transcriptomic analyses) allowed us to identify a set of potential drug repurposing candidates targeting three viral proteins (3CL viral protease, NSP15 endoribonuclease, and NSP12 RNA-dependent RNA polymerase), which included rutin, dexamethasone, and vemurafenib among others. To our knowledge, it is the first time that a TDA based strategy has been used to compare a massive amount of protein structures with the final objective of performing drug repurposing
REVIEW | doi:10.20944/preprints202008.0516.v1
Subject: Medicine And Pharmacology, Epidemiology And Infectious Diseases Keywords: Coronavirus, sequence homology, transmission, virology, diagnosis, virus control, vaccination.
Online: 24 August 2020 (09:31:38 CEST)
Emerging and reemerging pathogens is a global challenge for public health. Recently, a novel coronavirus disease emerged in Wuhan, Hubei province of China, in December 2019. It is named COVID-19 by World Health Organization (WHO). It is known to be caused by Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) that affects the lower respiratory tract and manifests as pneumonia in humans. Coronaviruses (CoVs) are structurally more complicated as compared to other RNA viruses. This viral epidemic has led to the deaths of many, including the elderly or those with chronic disease or compromised immunity. Viruses cause infection and diseases in humans of varying degrees, upper respiratory tract infections (URTIs) cause common cold while lower respiratory tract infections induce pneumonia, bronchitis, and even severe acute respiratory syndrome (SARS). The costs of COVID-19 are not limited. It equally affects all the medical, sociological, psychological, and economic aspects globally. This is regarded as the third deadly outbreak in the last two decades after Severe Acute Respiratory Syndrome SARS (2002–2003) and Middle East Respiratory Syndrome MERS (2012). Based on the sequence homology of SARS-CoV-2, different animal sources including bats, snakes, and pangolins have been reported as potential carriers of this viral strain. Real-time RT-PCR represents the primary method for the diagnosis of new emerging viral strain SARS-CoV-2. The transmission dynamics suggest that SARS-CoV-2 is transmitted from person-to-person through direct contact or coughing, sneezing, and by respiratory droplets. Several anti-viral treatments including lopinavir/ritonavir, remdesivir, chloroquine phosphate, and abidor are also suggested with different recommendations and prescriptions. Protective and preventive strategies as suggested by various health organization i.e. WHO and US Center for Disease Control and Prevention (CDC) must be adopted by everyone. This review covers the important aspects of novel COVID-19 including characteristics, virology, symptoms, diagnostics, clinical aspects, transmission dynamics, and protective measures of COVID-19.
ARTICLE | doi:10.20944/preprints202002.0061.v1
Subject: Medicine And Pharmacology, Medicine And Pharmacology Keywords: Coronavirus; Deep learning; Drug screening; homology modeling; main protease
Online: 5 February 2020 (10:59:09 CET)
A novel coronavirus called 2019-nCoV was recently found in Wuhan, Hubei Province of China, and now is spreading across China and other parts of the world. 2019-nCoV spreads more rapidly than SARS-CoV. Unfortunately, there is no drug to combat the virus. It is of high significance to develop a drug that can combat the virus effectively before the situation gets worse. It usually takes a much longer time to develop a drug using traditional methods. For 2019-nCoV, it is now better to rely on some alternative methods to develop drugs that can combat such a disease effectively since 2019-nCoV is highly homologous to SARS-CoV. In this paper, we first collected virus RNA sequences from the GISAID database, translated the RNA sequences into protein sequences, and built a protein 3D model using homology modeling. Coronavirus main protease is considered to be a major therapeutic target, thus this paper focused on drug screening based on the modeled 2019-nCov_main_protease structure. The deep learning based method DFCNN, developed by our group, can identify/rank the protein-ligand interactions with relatively high accuracy. DFCNN is capable of performing virtual screening quickly since no docking or molecular dynamic simulation is needed. DFCNN identifies potential drugs for 2019-nCoV protease by performing drug screening against 4 chemical compound databases. Also, we performed drug screening for all tripeptides against the binding site of 2019-nCov_main_protease since peptides often show better stability, more bio-availability and negligible immune responses. In the end, we provided the list of possible chemical ligands and peptide drugs for experimental validation.
ARTICLE | doi:10.20944/preprints202212.0020.v2
Subject: Biology And Life Sciences, Biochemistry And Molecular Biology Keywords: spinal cord injury; apoptotic cell death; XIAP; neuroprotection; miRNA-based therapies
Online: 11 January 2023 (11:39:24 CET)
Altered expression of microRNAs (miRNAs) after spinal cord injury (SCI) has been described as being responsible for the main secondary responses, such as apoptosis. X-linked inhibitor apoptosis protein (XIAP) is a key apoptotic component involved in the progression of apoptotic programmed cell death. Several regulators have been described to modulate the XIAP's function, including the post-transcriptional regulator's miRNAs. The main aim of the present work is to identify miRNAs with altered expression after SCI which can regulate XIAP expression. Our bioinformatic analyses identified several candidate miRNAs that may regulate XIAP, among which miR-199a-5p may be involved in the downregulation of XIAP after SCI. Gene reporter assays and in vitro analyses in the neural C6 cell line confirmed the targeting of miR-199a-5p on the 3-UTR of the rat XIAP and its post-transcriptional regulation of XIAP protein level, but not at mRNA level. Analyses in a rat model of SCI revealed a trend towards increased expression of miR-199a-5p and a decrease in XIAP protein level at 3 days after injury. Finally, using a specific fluorescent in situ hybridization (FISH) probe for miR-199a-5p, we characterized the expression pattern of miR-199a-5p in cells of uninjured and rat-contused spinal cords. These findings provide new insights into apoptotic miRNA-mediated mechanisms after SCI, which will help us develop therapeutic strategies based on miRNAs for treating SCI.
ARTICLE | doi:10.20944/preprints202007.0606.v1
Subject: Business, Economics And Management, Business And Management Keywords: Design Thinking; hydrosocial contract; web-based prototype; household engagement; Product Service Systems; clustering; ICT; sustainable use of water; customization
Online: 25 July 2020 (11:27:24 CEST)
This article shows the numerical results and the analysis of households' degree of knowledge in an intermediary city such as Huelva (Andalusia, Spain) about the sustainable use of urban water. It analyzes the needs and values regarding water and the attitudes that households maintain regarding the acceptance of reclaimed water and the use of new technologies to achieve more efficient and sustainable consumption. These results are part of the stages of needfinding and synthesis of Design Thinking methodology, adopted as a framework to improve the efficiency and sustainability of urban water among households in this city. Different statistical analysis techniques of surveys sent to households and the use of clustering are the mathematical tools used to draw conclusions and recommendations that allow the design of a web-based prototype grounded on Product Service Systems methodology, as a tool to improve the engagement of households concerning water and align citizens with the sustainability of their city. Strategies of customization and technological facilitators will be the means to improve the hydrosocial contract among households in Huelva in future later stages of the project.
ARTICLE | doi:10.20944/preprints202211.0001.v1
Subject: Computer Science And Mathematics, Hardware And Architecture Keywords: smart attendance system; attendance monitoring system; students’ absenteeism; Bluetooth Low Energy technology; beacon-based application
Online: 1 November 2022 (01:07:13 CET)
Student attendance serves many other important purposes aside from monitoring. In certain universities, the attendance of students in a course is also used as one of the requirements for students to be allowed to sit for the final examination. Traditionally, among most Malaysian Institutions of Higher Learning (IHL), attendance recording is usually done using pen and paper, or uses simple web-based system that is time consuming and difficult for faculty periodic monitoring. To address the identified drawbacks, this research aims to develop a Smart Attendance for Faculty Monitoring System using the Bluetooth Low Energy (BLE) technology to assist faculty in recording, managing and monitoring students’ attendance and class schedules effectively. The system is developed for Android-based devices using an agile methodology consists of iteration and incremental approaches. Thus, to evaluate the effectiveness of the system, a survey was conducted on 140 respondents involving lecturers and students of Kolej Universiti Poly-Tech MARA (KUPTM). Respondents were selected using purposive sampling. The descriptive analysis showed that 87.9% of the respondents strongly agreed that the system is effective in assisting lecturers to record attendance, manage class schedules and student attendance as well as to assist faculty in monitoring students’ absenteeism.
ARTICLE | doi:10.20944/preprints202111.0125.v1
Subject: Chemistry And Materials Science, Medicinal Chemistry Keywords: artificial intelligence; de novo design; fragment-based drug discovery; HIV-1 inhibitors; pseudo natural products
Online: 8 November 2021 (09:23:49 CET)
The acquired immunodeficiency syndrome (AIDS) caused by the human immunodeficiency virus (HIV) continues to be a public health problem. In 2020, 680,000 people died from HIV-related causes, and 1.5 million people were infected. Antiretrovirals are only a way to control HIV infection but not to cure AIDS. As such, effective treatment must be developed to control AIDS. Developing a drug is not an easy task, and there is an enormous amount of work and economic resources invested. For this reason, it is highly convenient to employ computer-aided drug design methods, which can help generate and identify novel molecules. Using the de novo design, new novel molecules can be developed using fragments as building blocks. In this work, we develop a virtual-focused compound library of HIV-1 viral protease inhibitors from natural product fragments. Natural products are characterized by a large diversity of functional groups, many sp3 atoms, and chiral centers. Pseudo-natural products are a combination of natural products fragments that keep the desired structural characteristics from different natural products. An interactive version of chemical space visualization of virtual compounds focused on HIV-1 viral protease inhibitors from natural product fragments is freely available at https://figshare.com/s/ceb58d58e8f5585ce67e.
ARTICLE | doi:10.20944/preprints202305.1275.v1
Subject: Biology And Life Sciences, Food Science And Technology Keywords: Natural dye; pH sensor; Smart packaging; Surimi-based, Tilapia protein
Online: 18 May 2023 (05:24:02 CEST)
The use of intelligent sensor-based packaging in food products provide quick evaluation of the quaility of the food. This study was done to develop bio-based color sensor from surimi-based color sensor incorporated with sappan wood extract (SWE) for smart food packaging. The SWE with different concentration (0.15%, 0.25%, and 0.35%) was incorporated to the myofibrillar protein-based edible film. The sappan wood-surimi edible film (SSEF) was subjected to physical properties analysis and the color changes at different pH values and soaking time at different condition were evaluated. Based on the results, different concentration of the SWE significantly (p<0.05) affected the physical properties of the film. With the increasing of pH values, the darkness, redness, and blueness of the film was increased. Based on the evaluation of the SSEF with different soaking condition, the color changes of the film in acidic condition were more stable than in neutral and alkaline condition. The results from this study showed that SSEF have the possibilities to be used as a smart food packaging possessing the capabilities to act as color sensor due to its sensitivity to the changes in pH condition of the product.
ARTICLE | doi:10.20944/preprints202308.1376.v1
Subject: Engineering, Architecture, Building And Construction Keywords: air supply optimization; double-objective optimization; surrogate-based optimization; Kriging model; genetic algorithm
Online: 21 August 2023 (03:23:07 CEST)
When using meta-heuristic optimization approaches for optimization, a large number of samples are required. In particular, when generating subgeneration, the utilization of existing samples is low and the number of individuals is high. Therefore, surrogate-based optimization has been developed, which greatly reduces the number of individuals in the subgeneration and the cost of optimization. In complex air supply scenarios, single-objective optimization results may not be comprehensive; therefore, this paper developed a double-objective air supply optimization method based on the Kriging surrogate model and Non-dominated Sorting Genetic Algorithms-II. And proposed the infill criteria based on clustering to advance the Pareto Frontier. The method was validated by an inverse prediction case, and in particular, the problems when based on 3D steady-state simulations were analyzed. The results showed that the method can quickly achieve an approximate prediction of the boundary conditions (when prediction were made based on experimental data, the number of simulations was 82 and the average error was 6.8%). Finally, the method was used to optimize the air supply parameters of a dual-aisle, single-row cabin. The Pareto set suggested that an airflow organization with dual circulation may be optimal.
ARTICLE | doi:10.20944/preprints202107.0191.v1
Subject: Computer Science And Mathematics, Algebra And Number Theory Keywords: topology; simplicial complex; homology; Mayer-Vietoris sequence; RNA; secondary structure
Online: 8 July 2021 (10:43:11 CEST)
In this paper we establish a topological framework of τ-structures to quantify the evolutionary transitions between two RNA sequence-structure pairs. τ-structures developed here consist of a pair of RNA secondary structures together with a non-crossing partial matching between the two backbones. The loop complex of a τ-structure captures the intersections of loops in both secondary structures. We compute the loop homology of τ-structures. We show that only the zeroth, first and second homology groups are free. In particular, we prove that the rank of the second homology group equals the number γ of certain arc-components in a τ-structure, and the rank of the first homology is given by γ−χ+1, where χ is the Euler characteristic of the loop complex.
ARTICLE | doi:10.20944/preprints201812.0184.v1
Subject: Computer Science And Mathematics, Mathematical And Computational Biology Keywords: Metagenomics; Metatranscriptomics; Environmental sample; Homology searches; Taxonomic profile; Functional profile
Online: 17 December 2018 (09:51:22 CET)
Data generated by metagenomic and metatranscriptomic experiments is both enormous and inherently noisy . When using taxonomy-dependent alignment-based methods to classify and label reads, such as MEGAN , the first step consists in performing homology searches against sequence databases. To obtain the most information from the samples, nucleotide sequences are usually compared to various databases (i.e., nucleotide and protein) using local sequence aligners such as BLASTN and BLASTX . Nevertheless, the analysis and integration of these results can be problematic because the outputs from these searches usually show differences, which can be notorious when working with RNA-seq (Personal observation; Graphical abstract). These inconsistencies led us to develop the HoSeIn workflow to determine the unequivocal taxonomic and functional profile of environmental samples, based on the assumption that the sequences that correspond to a certain taxon are composed of (Graphical abstract): 1) sequences that were assigned to the same taxon by both homology searches, plus 2) sequences that were assigned to that taxon by one of the homology searches but returned no hits in the other one, and vice versa.
ARTICLE | doi:10.20944/preprints201903.0166.v1
Subject: Chemistry And Materials Science, Medicinal Chemistry Keywords: Structure-based design; glycogen phosphorylase inhibitor; glycogen metabolism; type 2 diabetes; X-ray crystallography; N-acyl-β-D-glucopyranosylamine
Online: 15 March 2019 (14:06:06 CET)
Structure-based design and synthesis of two biphenyl-N-acyl-β-D-glucopyranosylamine derivatives as well as their assessment as inhibitors of human liver glycogen phosphorylase (hlGPa, a pharmaceutical target for type 2 diabetes) is presented. X-ray crystallography revealed the importance of structural water molecules and that the inhibitory efficacy correlates with the degree of disturbance caused by the inhibitor binding to a loop crucial for the catalytic mechanism. The in silico derived models of the binding mode generated during the design process corresponded very well with the crystallographic data.
ARTICLE | doi:10.20944/preprints202310.1838.v1
Subject: Engineering, Mechanical Engineering Keywords: Particle swarm optimization algorithm; Reliability-based design and optimization; Simulated annealing algorithm; Most probable point
Online: 30 October 2023 (07:14:52 CET)
With the engineering system becoming more and more complex, the uncertainty factors have a more and more profound influence on the reliability and security of the engineering system. In recent years, Reliability-Based Design Optimization (RBDO) has been studied extensively in complex engineering system design. The research on reliability optimization design considering stochastic uncertainty has been comprehensive and widely used. However, the reliability optimization design considering mixed uncertainty has the disadvantages of large computation and imprecise convergence. This study proposes an RBDO method based on Particle Swarm Optimization (PSO) and Simulated Annealing (SA) to overcome this challenge. In the method, PSO is used to solve the most probable point, while SA has excellent global optimization capability to acquire the global optimal solution. Finally, three examples are given to illustrate the advantages of the proposed method.
ARTICLE | doi:10.20944/preprints202002.0097.v1
Subject: Biology And Life Sciences, Biochemistry And Molecular Biology Keywords: Protein structure and dynamics; Molecular structure and modeling; Protein and macromolecules; Computational methods and bioinformatics; Computer-based teaching tools; Learning materials and teaching tools; Multimedia teaching tools
Online: 7 February 2020 (11:42:09 CET)
Biomolecular structure drives function, and computational capabilities have progressed such that the prediction and computational design of biomolecular structures is increasingly feasible. Because computational biophysics attracts students from many different backgrounds and with different levels of resources, teaching the subject can be challenging. One strategy to teach diverse learners is with interactive multimedia material that promotes self-paced, active learning. We have created a hands-on education strategy with a set of fifteen modules that teach topics in biomolecular structure and design, from fundamentals of conformational sampling and energy evaluation to applications like protein docking, antibody design, and RNA structure prediction. Our modules are based on PyRosetta, a Python library that encapsulates all computational modules and methods in the Rosetta software package. The workshop-style modules are implemented as Jupyter Notebooks that can be executed in the Google Colaboratory, allowing learners access with just a web browser. The digital format of Jupyter Notebooks allows us to embed images, molecular visualization movies, and interactive coding exercises. This multimodal approach may better reach students from different disciplines and experience levels as well as attract more researchers from smaller labs and cognate backgrounds to leverage PyRosetta in their science and engineering research. All materials are freely available at https://github.com/RosettaCommons/PyRosetta.notebooks.
ARTICLE | doi:10.20944/preprints202306.0771.v1
Subject: Engineering, Metallurgy And Metallurgical Engineering Keywords: Solder Alloys; Mechanical Properties; Alloy Design; Sn-based Alloys; Data Science; Predictive models; Machine Learning
Online: 12 June 2023 (05:23:12 CEST)
In this study, an extensive data set was based on existing literature records in order to enable the suitability of several predictive models, from Multiple Linear Regression (MLR) to Neural Networks (NN). The main objective was to, through regression analyses, generate model computations to correlate tensile properties (UTS- Ultimate Tensile Strength, YTS – Yield Tensile Strength and EF – Elongation-to-Fracture) to a given alloy composition and microstructural spacing. This investigation led to positive results, as the highest accuracies of the trained modules (in 80% of the database) were found to be above ~82% (UTS and EF) and a maximum of ~98% (YTS), when analyzing the results to a test data set. Later, these models were used to define trends for possible next solder alloy commercial compositions. Overall, using the standard model’s setup, the Random Forest and Decision Tree models showed the highest accuracy results, with 0.958 for YTS as opposed to 0.907 for MLR. Moreover, Multilayer Perceptron (MLP)-optimized models yielded the best results for each variable, with the highest increases in accuracy associated with the YTS and EF. The present contribution might imply an important milestone towards alloy design research based on data science guidelines to unlock the full potential of former experiments and their extensive set of results.
REVIEW | doi:10.20944/preprints201607.0012.v1
Subject: Computer Science And Mathematics, Information Systems Keywords: role-based access control; attribute-based access control; attribute-based encryption
Online: 8 July 2016 (10:12:21 CEST)
Cloud Computing is a promising and emerging technology that is rapidly being adopted by many IT companies due to a number of benefits that it provides, such as large storage space, low investment cost, virtualization, resource sharing, etc. Users are able to store a vast amount of data and information in the cloud and access it from anywhere, anytime on a pay-per-use basis. Since many users are able to share the data and the resources stored in the cloud, there arises a need to provide access to the data to only those users who are authorized to access it. This can be done through access control schemes which allow the authenticated and authorized users to access the data and deny access to unauthorized users. In this paper, a comprehensive review of all the existing access control schemes has been discussed along with analysis. Keywords: role-based access control, attribute-based access control, attribute-based encryption
ARTICLE | doi:10.20944/preprints202302.0428.v1
Subject: Biology And Life Sciences, Biology And Biotechnology Keywords: hybrid cheese; faba bean protein; insect protein; desirability-based mixture design; spreadability texture analysis; sensory analysis
Online: 27 February 2023 (01:44:30 CET)
As a result of the growing demand for foods with reduced animal protein content, many new alternative diets are now emerging. Nevertheless, recent studies have shown that the Western population is unprepared for drastic changes and is disinclined to accept foods based on alternative proteins. However, hybrid products might become a good transitional offer. This study used a desirability-based mixture design to model hybrid spreadable cheese analogues (SCAs). The design combined the dairy protein (MPC), Tenebrio molitor (IF) and faba bean (FBP) flours. Nine SCAs with different MPC/FBP/IF ratios were formulated, representing 0, 50 and 100% MPC replacement (7.1% of the formula). Incorporating the IF negatively impacted the desirable texture properties. The FBP flour improved the texture (achieving increased firmness and stickiness and decreased spreadability), but only when combined with MPC. Changing the MPC/FBP/IF ratio affected the colour of SCAs. Sensory analysis showed that hybrid SCAs (≤ 50% MPC) had a more characteristic cheesy flavour than the commercial plant-based reference, and sample C2 had a texture profile similar to the dairy reference. Samples containing IF showed a better flavour profile than the products without IF. The SCAs had higher protein and lower saturated fat, starch and sugar con-tent than commercial analogues.This study demonstrates that the inclusion of alternative proteins can be effective as a strategy to reduce dairy protein content in hybrid product formulations.
ARTICLE | doi:10.20944/preprints202010.0010.v1
Subject: Engineering, Electrical And Electronic Engineering Keywords: Totem-pole power factor correction; energy storage systems (ESS); digital control; Gallium Nitride (GaN) based; current harmonic distortion mitigation; efficiency and power quality improvement
Online: 1 October 2020 (09:12:36 CEST)
With the unceasing advancement in wide-bandgap (WBG) semiconductor technology, the minimal reverse-recovery charge Qrr and other more powerful natures of WBG transistors enable totem-pole bridgeless PFC to become a dominant solution for energy storage systems (ESS). This paper focuses on design and implementation of a control structure for a totem-pole boost PFC with newfangled enhancement-mode Gallium Nitride (eGaN) FETs, not only to simplify the control implementation, but also to achieve high power quality and efficiency. The converter is designed to convert a 90-264-VAC input to a 385-VDC output for a 2.6-kW output power. Lastly, to validate the methodology, an experimental prototype is characterized and fabricated. The uttermost efficiency at 230 VAC attains 99.14%. The lowest total harmonic distortion in the current (ITHD) at high line condition (230 V) reaches 1.52% while the power factor gains 0.9985.
ARTICLE | doi:10.20944/preprints202212.0556.v1
Subject: Environmental And Earth Sciences, Environmental Science Keywords: Three Lines One Permit; web-based interactive analysis; online environmental planning analysis platform; EIA approval; Web-GIS; geospatial data; Guangzhou
Online: 29 December 2022 (08:56:25 CET)
Currently, an interactive environmental planning analysis system platform based on " Three Lines One Permit " (TLOP) is being developed to support environmental planning, construction project approval, and the application of TLOP outcome data in Guangzhou. The main objective is to provide governments, businesses and the public with environmental planning analysis tools to determine the site of construction projects. The platform is using the system architecture of the browser and server. Its core functions are interactive environmental planning analysis tool for construction project and the results display tool supporting map viewing. It provides users with a large number of detailed geospatial data and TLOP results data access and environmental planning analysis functions. This article describes the system architecture and implementation of the system platform and has a case study illustrating the system functionality. At present, the platform has been deployed and trial-operated. The content of the analysis framework is constantly expanding. This promotes the matching of environmental planning and analysis with local conditions. This will implement the application of TLOP and improve the efficiency of project construction and the level of ecological environment planning and management.
ARTICLE | doi:10.20944/preprints202310.0396.v1
Subject: Biology And Life Sciences, Life Sciences Keywords: Pyrimidine; Homology Modelling; Pharmacophore Mapping; 3D-QSAR; Molecular Docking; ADMET; Drug Design
Online: 9 October 2023 (09:36:05 CEST)
(1) Background: Type-2 Diabetes (T2DM) is a long-term medical disorder characterized by Insulin deficiency and high blood glucose levels. Among other medication to cure T2DM, the review of the literature found that various Pyrimidine derivative act as an agonist for G-protein-coupled receptor 119 (GPR119) was proposed to control blood glucose levels by enhancing the function of pancreatic beta-cells and its mechanism of action with fewer adverse effects.; (2) Methods: In the present research work, in-silico investigations were carried out to investigate the potential of Pyrimidine analogue as an agonists to the protein target GPR119 receptor. We performed exhaustive molecular modelling and protein modelling methodologies such as homology mod-elling, molecular docking along with various drug designing tools such as 3D-QSAR and pharmacophore mapping to ascertain the design of better GPR119 agonists.; (3) Results: On the basis of in-depth computa-tional studies, we designed new pyrimidine moiety and analyzed them for GPR-119 receptor agonist and fur-ther explored the ADME properties. Designed compounds found to exhibit better predicted activities as com-pared to reference compound; (4) Conclusions: The current research on pyrimidine derivatives, using molec-ular docking, 3D-QSAR and Pharmacophore mapping demonstrated that the obtained computational model has significant properties and the designed molecules and Dataset from this model, produced antidiabetic compound against the target GPR119 i.e., compound 1S, 1Z and 1D with the docking score of −11.696, -9.314 and -8.721 respectively. The pharmacokinetics and drug-likeness studies revealed that these compounds may be the future candidate for the treatment of diabetes acting via GPR119 agonist mechanism.
Subject: Biology And Life Sciences, Virology Keywords: Sars-CoV-2; homology modelling; envelope membrane glycoprotein; Bat; Pangolin; Sars-CoV
Online: 9 May 2020 (08:43:08 CEST)
The Coronavirus Disease 2019 (COVID-19) is a new viral infection caused by the severe acute respiratory coronavirus 2 (SARS-CoV-2). Genomic analyses have revealed that SARS-CoV-2 is related to Pangolin and Bat coronaviruses. In this report, a structural comparison between the Sars-CoV-2 Envelope and Membrane proteins from different human isolates with homologous proteins from closely related viruses is described. The analyses here reported show the high structural similarity of Envelope and Membrane proteins to the counterparts from Pangolin and Bat coronavirus isolates. However, the comparisons have also highlighted structural differences specific of Sars-CoV-2 proteins which may be correlated to the cross-species transmission and/or to the properties of the virus. Structural modelling has been applied to map the variant sites onto the predicted three-dimensional structure of the Envelope and Membrane proteins.
ARTICLE | doi:10.20944/preprints201911.0366.v1
Subject: Computer Science And Mathematics, Computational Mathematics Keywords: neural networks; topology; directed graphs; directed flag complexes; persistent homology; computaional software
Online: 29 November 2019 (03:03:36 CET)
We present a new computing package Flagser, designed to construct the directed flag complex of a finite directed graph, and compute persistent homology for flexibly defined filtrations on the graph and the resulting complex. The persistent homology computation part of Flagser is based on the program Ripser , but is optimised specifically for large computations. The construction of the directed flag complex is done in a way that allows easy parallelisation by arbitrarily many cores. Flagser also has the option of working with undirected graphs. For homology computations Flagser has an Approximate option, which shortens compute time with remarkable accuracy. We demonstrate the power of Flagser by applying it to the construction of the directed flag complex of digital reconstructions of brain microcircuitry by the Blue Brain Project and several other examples. In some instances we perform computation of homology. For a more complete performance analysis, we also apply Flagser to some other data collections. In all cases the hardware used in the computation, the use of memory and the compute time are recorded.
ARTICLE | doi:10.20944/preprints201807.0085.v1
Subject: Biology And Life Sciences, Biochemistry And Molecular Biology Keywords: CagA; phosphatidylserine; phosphatidylserine mutations; conservation N-terminal CagA; homology modeling; molecular docking
Online: 5 July 2018 (08:34:40 CEST)
Helicobacter pylori cytotoxin-associated gene A protein (CagA) has been associated with the increase in virulence and risk of cancer. It has been demonstrated that CagA's translocation is dependent on its interaction with phosphatidylserine. We evaluated the variability of the N-terminal CagA in 127 sequences reported in NCBI, by referring to molecular interaction forces with the Phosphatidylserine and the docking of 3 mutations chosen from variations in specific positions. The major sites of conservation of the residues involved in CagA-Phosphatidylserine interaction were 617, 621 and 626 which had no amino acid variation. Position 636 had the lowest conservation score, so mutations in this position were evaluated to observe the differences in intermolecular forces of the CagA-Phosphatidylserine complex. We evaluated the docking of 3 mutations: K636A, K636R and K636N. The models of the crystal and mutations presented a ΔG of −8.919907, −8.665261, −8.701923, −8.515097 Kcal/mol, respectively, while mutations K636A, K636R, K636N and the crystal structure presented 0, 3, 4 and 1 H-bonds, respectively. Likewise, the bulk effect of the ΔG and amount of H-bonds was estimated in all of the docking models. The type of mutation affected both the ΔG (χ2(1) = 93.82, p-value < 2.2 × 10−16) and the H-bonds (χ2(1) = 91.93, p-value < 2.2 × 10−16). In all the data, 76.9% of the strains that exhibit the K636N mutation produced a severe pathology. The average H-bond count diminished when comparing the mutations with the crystal structure of all the docking models, which means that other molecular forces are involved in the CagA-Phosphatidylserine complex interaction.
ARTICLE | doi:10.20944/preprints201610.0080.v1
Subject: Chemistry And Materials Science, Analytical Chemistry Keywords: degree-based topological index; Zagreb index; general Randic index; symmetric division index; M-polynomial, titania nanotubes
Online: 19 October 2016 (12:44:36 CEST)
Titania is one of the most comprehensively studied nanostructures due to its widespread applications in production of catalytic, gas- sensing and corrosion- resistance materials . M-polynomial of nanotubes has been vastly investigated as it produces many degree-based topological indices which are numerical parameters capturing structural and chemical properties. These indices are used in the development of quantitative structure-activity relationships (QSARs) in which the biological activity and other properties of molecules are correlated with their structure like boiling point, stability, strain energy etc of chemical compounds. In this paper, we determine M-polynomials of single-walled titanium (SW TiO2) nanotubes and recover important topological degree based indices of them to theoretically judge these nanotubes. We also use Maple to plot surfaces associated to different types of single-walled titanium (SW TiO2) nanotubes.
ARTICLE | doi:10.20944/preprints202112.0296.v1
Subject: Medicine And Pharmacology, Pharmacology And Toxicology Keywords: Plasmodium falciparum dihydroorotate dehydrogenase; fragment-based drug design; 2D-QSAR; DFT calculation; Lead optimization; Induced Fit docking
Online: 20 December 2021 (09:39:42 CET)
Plasmodium falciparum dihydroorotate dehydrogenase (PfDODH) is one of the enzymes currently explored in the treatment of malaria. Although there is currently no clinically approved drug targeting PfDODH, many of the compounds in clinical trials have [1, 2, 4,] triazolo [1, 5-a] pyrimidin-7-amine backbone structure. This study sought to design new compounds from the fragments of known experimental inhibitors of PfDODH. Nine experimental compounds retrieved from Drug Bank online were downloaded and broken into fragments using Schrodinger power shell; the fragments were recombined to generate new ligand structures using BREED algorithm. The new compounds were docked with PfDODH crystal structure, after which the compounds were filtered with extensive drug-likeness and toxicity parameters. A 2D-QSAR model was built using the multiple linear regression method and externally validated. The compounds electronic behaviours were studied using DFT calculations. Structural investigation of the six designed compounds, which had lower binding energies than the standard inhibitors, showed that five of them had [1, 2, 4,] triazolo [1, 5-a] pyrimidin-7-amine moieties and interacted with essential residues at the PfDODH binding site. In addition to their drug-like and pharmacokinetic properties, they also showed minimal toxicities. The externally validated 2D-QSAR model with R2 and Q2 values of 0.6852 and 0.6691, confirmed the inhibitory prowess of these compounds against PfDODH. The DFT calculations showed regions of the molecules prone to electrophilic and nucleophilic attack. The current study thus provides insight into the development of a new set of potent PfDODH inhibitors.
ARTICLE | doi:10.20944/preprints202111.0083.v2
Subject: Engineering, Control And Systems Engineering Keywords: RAMI4.0; Asset Administration Shell (AAS); Multi-Agent Systems (MAS); Evolutionary Assembly Systems (EAS); Engineering Capabilities Based, Production Flow Scheme (PFS); Petri Net (PN).
Online: 18 November 2021 (14:26:42 CET)
Manufacturing systems need to meet I4.0 guidelines to deal with uncertainty in scenarios of turbulent demand for products. The engineering concepts to define the service’s resources to manufacture the products will be more flexible, ensuring the possibility of re-planning in operation. These can follow the engineering paradigm based on capabilities. The virtualization of industry components and assets achieves the RAMI 4.0 guidelines and (I4.0C), which describes the Asset Administration Shell (AAS). However, AAS are passive components that provide information about I4.0 assets. The proposal of specific paradigms is exposed for managing these components, as is the case of multi-agent systems (MAS) that attribute intelligence to objects. The implementation of resource coalitions with evolutionary architectures (EAS) applies cooperation and capabilities’ association. Therefore, this work focuses on designing a method for modeling the asset administration shell (AAS) as virtual elements orchestrating intelligent agents (MAS) that attribute cooperation and negotiation through contracts to coalitions based on the engineering capabilities concept. The systematic method suggested in this work is partitioned for the composition of objects, AAS elements, and activities that guarantee the relationship between entities. Finally, Production Flow Schema (PFS) refinements are applied to generate the final Petri net models (PN) and validate them with Snoopy simulations. The results achieved demonstrate the validation of the procedure, eliminating interlocking and enabling liveliness to integrate elements behavior.
ARTICLE | doi:10.20944/preprints201910.0124.v1
Subject: Biology And Life Sciences, Biochemistry And Molecular Biology Keywords: intrinsically disordered protein; IDP; protein-protein interaction; mutual synergistic folding; coupled folding and binding; structural analysis; structure-based classification; fold recognition
Online: 11 October 2019 (04:00:32 CEST)
Intrinsically disordered proteins mediate crucial biological functions through their interactions with other proteins. Mutual synergistic folding (MSF) occurs when all interacting proteins are disordered, folding into a stable structure in the course of the complex formation. In these cases, the folding and binding processes occur in parallel, lending the resulting structures uniquely heterogeneous features. Currently there are no dedicated classification approaches that would take into account the particular biological and biophysical properties of MSF complexes. Here we present a scalable clustering-based classification scheme, built on redundancy-filtered features that describe the sequence and structure properties of the complexes, and the role of the interaction, which is directly responsible for structure formation. Using this approach, we define six major types of MSF complexes, corresponding to biologically meaningful groups. Hence, the presented method also shows that differences in binding strength, subcellular localization, and regulation are encoded in the sequence and structural properties of proteins. While current structure classification methods can also handle complex structures, we show that the developed scheme is fundamentally different, and since it takes into account defining features of MSF complexes, it serves as a better representation of structures arising through this specific interaction mode.
ARTICLE | doi:10.20944/preprints201608.0069.v1
Subject: Environmental And Earth Sciences, Environmental Science Keywords: Rubber (Hevea brasiliensis) plantation; phenology; Xishuangbanna; Landsat; object-based approach; pixel-based approach
Online: 6 August 2016 (11:54:28 CEST)
Effectively mapping and monitoring rubber plantation is still changing. Previous studies have explored the potential of phenology features for rubber plantation mapping through a pixel-based approach (pixel-based phenology approach). However, in fragmented mountainous Xishuangbanna, it could lead to noises and low accuracy of resultant maps. In this study, we investigated the capability of an integrated approach by combining phenology information with an object-based approach (object-based phenology approach) to map rubber plantations in Xishuangbanna. Moderate Resolution Imaging Spectroradiometer (MODIS) data were firstly used to acquire the temporal profile and phenological features of rubber plantations and natural forests, which delineates the time windows of defoliation and foliation phases. Landsat images were then used to extract a phenology algorithm comparing three different approaches: pixel-based phenology, object-based phenology, and extended object-based phenology to separate rubber plantations and natural forests. The results showed that the two object-based approaches achieved higher accuracy than the pixel-based approach, having overall accuracies of 96.4%, 97.4%, and 95.5%, respectively. This study proved the reliability of a phenology-based rubber mapping in fragmented landscapes with a distinct dry/cool season using Landsat images. This study indicated that the object-based phenology approaches can effectively improve the accuracy of the resultant maps in fragmented landscapes.
REVIEW | doi:10.20944/preprints202306.0141.v1
Subject: Chemistry And Materials Science, Medicinal Chemistry Keywords: Mycobacterium tuberculosis; target identification; activity-based probes; affinity-based probes
Online: 2 June 2023 (07:39:37 CEST)
Mycobacterium tuberculosis (Mtb) is the etiological agent of tuberculosis (TB), a disease that alt-hough preventable and curable, remains a global epidemic due to the emergence of resistance and a latent form responsible for a long period of treatment. Drug discovery in TB is a challenging task due to the heterogeneity of the disease, the emergence of resistance and an uncomplete knowledge of the pathophysiology of the disease. The limited permeability of the cell wall and the presence of multiple efflux pumps remain a major barrier to achieve effective intracellular drug accumulation. While the complete genome sequence of Mtb has been determined and several potential protein targets have been validated, the lack of adequate models for in vitro and in vivo studies is a limit-ing factor in TB drug discovery programs. In current therapeutic regimens, less than 0.5% of bac-terial proteins are targeted being the biosynthesis of the cell wall and the energetic metabolism two of the most important processes exploited for TB chemotherapeutics. This review provides an overview on the current challenges in TB drug discovery and emerging Mtb druggable proteins, and how chemical probes for protein profiling enabled the identification of new targets and bi-omarkers, paving the way to disruptive therapeutic regimens and diagnostic tools.
ARTICLE | doi:10.20944/preprints202111.0241.v1
Subject: Engineering, Marine Engineering Keywords: Collaborative robotics; Human-Robot Collaboration (HRC); Knowledge-Based Approach (KBA); collaborative workplace design; systematic layout planning; digital layout optimization; what-if analysis.
Online: 12 November 2021 (17:17:02 CET)
The innovation driven Industry 5.0, in agreement with Industry 4.0, leads to consider human in a prominence position as the center of manufacturing field. This pushes towards the hybridization of manufacturing plants promoting a fully collaboration between human and robot. Furthermore, the new paradigm of "human centred design" and "anthropocentric design" allows enabling a synergistic combination of human and robot skills. However, properly collaborative workplaces are currently very few. Industry is still not confident, and systems integrators hesitate to venture into Human-Robot Collaboration (HRC). Despite the effort in collaborative robotics, a general solution to overcome the current limitations in designing of collaborative workplaces still misses. In the current work, a Knowledge-Based Approach (KBA) is adopted to face collaborative workplace designing problem. The framework resulting from the KBA allows developing a modelling paradigm that enable to define a streamlined approach for the layout designing of a collaborative workplace. Finally, a what-if analysis and a ANOVA analysis are performed to generate and evaluate a set of scenarios related to a collaborative workplace for quality inspection of welded parts. Facing the high complexity and multidisciplinary of HRC can be conveyed to develop a general design approach aimed at overcoming the difficulties that limit the spread of HRC in the manufacturing field.
Subject: Chemistry And Materials Science, Polymers And Plastics Keywords: poly(vinyl chloride); tri-functional additive; mannitol stearate ester-based aluminum alkoxides; synergistic effect
Online: 26 April 2019 (11:57:11 CEST)
The thermal stabilizers, lubricant, and plasticizers are three crucial additives for processing poly (vinyl chloride) (PVC). In this study, a new mannitol stearate ester-based aluminum alkoxides (MSE-Al) was designed and synthesized as a novel additive for PVC. The thermal stability and processing performance of PVC stabilized by MSE-Al were evaluated by Congo red test, conductivity measurement, thermal aging test, ultravioletevisible (UV-vis) spectroscopy test, and torque rheometer test. Results showed that the addition of MSE-Al can not only markedly improve the long-term thermal stability of PVC, but also greatly accelerate the plasticizing and decrease the balance torque which demonstrated that MSE-Al possesses the lubricating property. Thus, MSE-Al was demonstrated to be able to provide tri-functional additive roles, e.g., thermal stabilizer, plasticizer, and lubricant. The test results for the thermal stability of PVC indicated that the initial whiteness of PVC stabilized with MSE-Al was not good enough, thus the synergistic effect of MSE-Al with zinc stearates (ZnSt2) on the thermal stability of PVC was also investigated. The results showed that there exhibited an appreciable synergistic effect between MSE-Al and ZnSt2. The thermal stabilization mechanism and synergism effect of MSE-Al with ZnSt2 were then discussed.
ARTICLE | doi:10.20944/preprints202111.0108.v1
Subject: Chemistry And Materials Science, Medicinal Chemistry Keywords: Plasmodium; malaria; type III beta phosphatidylinositol 4-kinase; virtual screening; homology modeling; molecular dynamics
Online: 5 November 2021 (08:44:31 CET)
Plasmodium species that cause malaria, a disease responsible for about half a million deaths per annum despite concerted efforts to combat it. The causative agent depends on type III beta phosphatidylinositol 4-kinase (PPI4K) during the development of merozoite. PPI4K is the only clinically validated Plasmodium kinase so far and its inhibitors are effective both in vitro and in vivo. In this work, a small library of ~22 000 fragments was virtually screened using PPI4K homology model to discover potential ligands of the enzyme. 16 virtual hits were selected based on ≤ -9.0 kcal/mol binding energy cut off and were subjected to similarity and substructure searching after they had passed PAINS screening. The derivatives obtained showed improved binding energies, which ranged from -10.00 to -13.80 kcal/mol. Moreover, the topmost ranking compound 31, with interesting drug-like quality was stable within the protein’s binding cavity during the 10 ns molecular dynamics simulation period. In addition, analysis of its binding pose revealed some unique binding interactions with PPI4K active site residues as the basis for the observed improved binding affinity. Overall, compound 31 appears to be a viable starting point for the development of PPI4K inhibitors with antimalarial activity.
ARTICLE | doi:10.20944/preprints201912.0083.v1
Subject: Biology And Life Sciences, Biochemistry And Molecular Biology Keywords: hydrogenases; hydrogen fuel cells; homology modeling; fes clusters; transmembrane helices; molecular docking; molecular tunnels
Online: 6 December 2019 (11:47:06 CET)
Three-dimensional structure of six closely related hydrogenases from purple bacteria has been modeled by combining template-based and ab initio modeling approach. The results lead to conclusion that there should be 4Fe3S-cluster in the structure of these enzymes. Thus, these hydrogenases could drive attention for exploring their oxygen tolerance and practical applicability in hydrogen fuel cells. Analysis of 4Fe3S-cluster's microenvironment showed intragroup heterogeneity. Possible function of the C-terminal part of the small subunit in membrane binding has been discussed. Comparison of the built models with existing hydrogenases of the same subgroup (membrane-bound oxygen-tolerant hydrogenases) has been carried out. Analysis of intramolecular interactions in the large subunits showed statistically reliable differences in number of hydrophobic interactions and number of ionic interactions. Molecular tunnels were mapped in the models and compared with structures from PDB. Protein-protein docking showed that these enzymes could exchange electrons in oligomeric state, which is important for oxygen-tolerant hydrogenases. Molecular docking with model electrode compounds showed mostly the same results as with hydrogenases from E.coli, H. marinus, R. eutropha, S. enterica; some interesting results were shown in case of HupSL from Rba. sphaeroides and Rvx. gelatinosus.
REVIEW | doi:10.20944/preprints202112.0027.v2
Subject: Biology And Life Sciences, Animal Science, Veterinary Science And Zoology Keywords: Zoo animal welfare; Five Domains; Validity; Animal-based; Resource-based; Scoring
Online: 22 December 2021 (11:59:32 CET)
Zoos are increasingly putting in place formalized animal welfare assessment programs to allow monitoring of welfare over time, as well as to aid in resource prioritization. These programs tend to rely on assessment tools that incorporate resource-based and observational animal- focused measures since it is rarely feasible to obtain measures of physiology in zoo-housed animals. A range of assessment tools are available which commonly have a basis in the Five Domains framework. A comprehensive review of the literature was conducted to bring together recent studies examining welfare assessment methods in zoo animals. A summary of these methods is provided with advantages and limitations of the approach es presented. We then highlight practical considerations with respect to implementation of these tools into practice, for example scoring schemes, weighting of criteria, and innate animal factors for consideration. It is concluded that would be value in standardizing guidelines for development of welfare assessment tools since zoo accreditation bodies rarely prescribe these. There is also a need to develop taxon or species- specific assessment tools to inform welfare management.
ARTICLE | doi:10.20944/preprints202306.0429.v1
Online: 6 June 2023 (09:43:32 CEST)
Many theoretical models of iron-based superconductors have been proposed but Tc calculations based on the models are usually missing. We have chosen two models of iron-based superconductors in the literature and then compute the Tc values accordingly: Recently two models have been announced which suggest that superconducting electron concentration involved in the pairing mechanism of iron-based superconductors may have been underestimated, and that the antiferromagnetism and the induced xy potential may even have a dramatic amplification effect on electron-phonon coupling. We use bulk FeSe, LiFeAs and NaFeAs data to calculate the Tc based on these models and test if the combined model can predict the superconducting transition temperature (Tc) of the nanostructured FeSe monolayer well. To substantiate the recently announced xy potential in the literature, we create a two-channel model to separately superimpose the dynamics of the electron in the upper and lower tetrahedral plane. The results of our two-channel model support the literature data. While scientists are still searching for a universal DFT functional that can describe the pairing mechanism of all iron-based superconductors, we base on the ARPES data to propose an empirical combination of DFT functional for revising the electron-phonon scattering matrix in the superconducting state, which ensures that all electrons involved in iron-based superconductivity are included in the computation. Our computational model takes into account this amplifying effect of antiferromagnetism and the correction of the electron-phonon scattering matrix together with the abnormal soft out-of-plane lattice vibration of the layered structure, which allows us to calculate theoretical Tc values of LiFeAs, NaFeAs and FeSe as a function of pressure that correspond reasonably well to the experimental values. More importantly, by taking into account the interfacial effect between an FeSe monolayer and its SrTiO3 substrate as an additional gain factor, our calculated Tc value is up to 91 K high, and provides evidence that the strong Tc enhancement recently observed in such monolayers with Tc reaching 100 K may be contributed from the electrons within the ARPES range.
REVIEW | doi:10.20944/preprints202304.1108.v1
Subject: Medicine And Pharmacology, Pharmacy Keywords: biopolymers; nanogels; drug delivery; polysaccharide-based nanogels; protein-based nanogels; nanotechnology
Online: 28 April 2023 (04:32:57 CEST)
Due to their increased surface area, extent of swelling and active substance loading capacity and flexibility, nanogels made from natural and synthetic polymers have gained significant interest in the scientific and industrial areas. Especially, customized design and implementation of non-toxic, biocompatible, and biodegradable micro/nano carriers makes their usage very feasible for a range of biomedical applications, including drug delivery, tissue engineering, and bioimaging. The design and application methodologies of nanogels have been outlined in this review. Additionally, the most recent advancements in nanogel biomedical applications have been discussed, with a particular emphasis on applications for the delivery of drugs and biomolecules.
ARTICLE | doi:10.20944/preprints201807.0307.v1
Subject: Business, Economics And Management, Marketing Keywords: sustainable outcomes; dedication-based mechanism; constraint-based mechanism; perceived switching costs; loyalty program
Online: 17 July 2018 (10:55:47 CEST)
Given the increase in consumers’ preferences for coffee, it is becoming important to understand their decision-making processes in the coffee chain context. To deepen the understanding of sustainable outcomes in this context, this study investigates the role of dedication- and constraint-based mechanisms in forming consumers’ repurchase and positive word-of-mouth (WOM) intentions, two critical sustainable outcomes. We examined the effects of coffee quality, the quality of the physical environment, and service quality in accelerating the formation of dedication-based factors. Moreover, this study offers an in-depth understanding of the enablers of perceived switching costs. Data collected from 238 university students that frequently visit coffee chains are empirically tested against the proposed theoretical framework by using structural equation modeling. The results confirm that both dedication- and constraint-based factors substantially predict consumers’ sustainable outcomes in the coffee chain context. Brand image and perceived switching costs play an important role in enhancing consumers’ repurchase and positive WOM intentions compared with customer satisfaction. Coffee quality is significantly associated with both customer satisfaction and brand image, whereas the quality of the physical environment and service quality are only significantly associated with brand image. Habit is found to be the key enabler of perceived switching costs, while loyalty programs have no significant impact on perceived switching costs.
ARTICLE | doi:10.20944/preprints201907.0131.v1
Subject: Business, Economics And Management, Economics Keywords: Knowledge Based Economy Saudi Arabia
Online: 9 July 2019 (14:15:17 CEST)
Saudi Arabia is an oil-reliant nation as a large percentage of its GDP comes from oil resources. Oil dependency leaves a county at the mercy of the international crude market, and a decrease in the price of crude can seriously destabilize the economy of such nations. An example is the case of Venezuela whose dependence on oil caused a national disaster (McCarthy, 2017). As such, the nation’s exports, GDP, and government revenue are primarily dependent on oil revenue, and the recent decrease in the oil prices has decreased Venezuela’s national revenue resulting in economic collapse as well as inflation. A shift from a resource based economy to a knowledge based economy will help Saudi Arabia become less reliant on its oil revenues for its economic stability and growth (Nurunnabi, 2017).
ARTICLE | doi:10.20944/preprints202305.0276.v1
Subject: Chemistry And Materials Science, Medicinal Chemistry Keywords: fibroblast activation protein α (FAP-α); cancer-associated fibroblasts (CAFs); FAP inhibitors (FAPIs); PET imaging; gallium-68; (R)-pyrrolidin-2-yl-boronic acid-based radiopharmaceuticals
Online: 5 May 2023 (02:40:01 CEST)
Fibroblast activation protein (FAP) is a membrane-tethered serine protease overexpressed in the reactive stromal fibroblasts of > 90% human carcinomas, which makes it a promising target for developing radiopharmaceuticals for imaging and therapy of carcinomas. Here, we synthesized two novel (R)-pyrrolidin-2-yl-boronic acid-based FAP-targeted ligands; SB02055 (DOTA-conjugated (R)-(1-((6-(3-(piperazin-1-yl)propoxy)quinoline-4-carbonyl)glycyl)pyrrolidin-2-yl)boronic acid) and SB04028 (DOTA-conjugated ((R)-1-((6-(3-(piperazin-1-yl)propoxy)quinoline-4-carbonyl)-D-alanyl)pyrrolidin-2-yl)boronic acid). natGa- and 68Ga-complexes of both ligands were evaluated in preclinical studies and compared to previously reported natGa/68Ga-complexed PNT6555. Enzymatic assays showed that FAP binding affinities (IC50) of natGa-SB02055, natGa-SB04028 and natGa-PNT6555 were 0.41±0.06, 13.9±1.29 and 78.1±4.59 nM, respectively. PET imaging and biodistribution studies in HEK293T:hFAP tumor-bearing mice showed that while [68Ga]Ga-SB02055 presented with a nominal tumor uptake (1.08±0.37 %ID/g), [68Ga]Ga-SB04028 demonstrated clear tumor visualization with ~1.5-fold higher tumor uptake (10.1±0.42 %ID/g) compared to [68Ga]Ga-PNT6555 (6.38±0.45 %ID/g). High accumulation in the bladder indicated renal excretion of all three tracers. [68Ga]Ga-SB04028 displayed low background level uptake in most normal organs, and comparable to [68Ga]Ga-PNT6555. However, since its tumor uptake was considerably higher than [68Ga]Ga-PNT6555, the corresponding tumor-to-organ uptake ratios for [68Ga]Ga-SB04028 were also significantly greater than [68Ga]Ga-PNT6555. Our data demonstrate that (R)-(((quinoline-4-carbonyl)-D-alanyl)pyrrolidin-2-yl)boronic acid is a promising pharmacophore for the design of FAP-targeted radiopharmaceuticals for cancer imaging and radioligand therapy.
REVIEW | doi:10.20944/preprints202310.1708.v1
Subject: Biology And Life Sciences, Life Sciences Keywords: target based screening; phenotypic based screening; targets; transcriptional reprogramming, highthroughput screening, cancer therapeutics
Online: 26 October 2023 (10:31:24 CEST)
Drug discovery utilizes high-throughput screening (HTS) methods applying target and cell-based assays. This review discusses the challenges and benefits associated with these assays in HTS. Discussed the strategies that can be applied for the development of screening assays through primary and secondary screens for target identification. Further discussion on identify-ing the most efficacious drugs following these approaches in cancer. Even though various drugs have been identified to treat cancer, there is high demand of more relevant phenotypic assays to produce desired diseased phenotype to only highlighting the specific targets instead of off-targets. Hopefully, the new developing strategies could provide innovative drugs to treat cancer patients to reduce mortality rate.
ARTICLE | doi:10.20944/preprints202304.0886.v1
Subject: Social Sciences, Education Keywords: POGIL-based instruction; lecture-based instruction; unit of circular motion; science performance
Online: 25 April 2023 (04:23:47 CEST)
The aim of this study was to investigate the impact of Process Oriented Guided Inquiry Learning (POGIL)-based instruction versus lecture-based instruction on Grade 12 students’ performance in circular motion unit. A quasi-experimental, pretest-posttest design, the impact of POGIL-based instruction versus lecture-based instruction on students’ performance as measured by three types of cognitive outcomes: Knowing, Applying and Reasoning (KAR). The total number of participants was approximately 110 students (N=110); 54 were assigned to treatment groups (25 girls and 29 boys) and 56 were assigned to control groups (27 girls and 29 boys). The treatment group was taught a unit of circular motion in physics using POGIL-based instruction while the control group was taught the unit using lecture-based instruction. The findings of the study showed statistically significant differences between students of the control group and the treatment group in favor of the later regarding their circular motion performance, suggesting the superiority of the POGIL in enhancing student understanding of the circular motion.
ARTICLE | doi:10.20944/preprints202108.0425.v1
Subject: Engineering, Civil Engineering Keywords: road pavement design; design based on materials science; material mineralogy; New-age (Nano) Modified Emulsions (NME); naturally available materials; material stabilisation; basic engineering requirements; Unconfined Compressive Strengths (UCS); Indirect Tensile Strengths (ITS); Retained Compressive Strengths (RCT) and; Retained Tensile Strengths (RTS)
Online: 23 August 2021 (10:38:52 CEST)
The use of naturally available materials not conforming to traditional specifications or standards, in the base and sub-base layers of road pavement structures, stabilised with New-age (Nano) Modified Emulsions (NME), have been tested, implemented and successfully verified through Accelerated Pavement Testing (APT) in South Africa. This was made possible through the development and use of a design procedure addressing fundamental principles and based on scientific concepts, which are universally applicable. The understanding of and incorporation of the chemical interaction between the mineralogy of the materials and a NME stabilising agent (compatibility between the chemistry of the reactive agents and material mineralogy) into the design approach is key to achieving the required engineering properties. Stabilised materials evaluation is done using tests indicative of the basic engineering properties (physics) of compressive strengths, tensile strengths and durability. This article describes the basic materials design approach developed to ensure that organofunctional nano-silane modified emulsions can successfully be used for pavement layer construction utilising naturally available materials, at a low risk. The enablement of the use of naturally available materials in all pavement layers can have a considerable impact on the unit cost and life-cycle costs of road transportation infrastructure. TRANSLATE with x English ArabicHebrewPolish BulgarianHindiPortuguese CatalanHmong DawRomanian Chinese SimplifiedHungarianRussian Chinese TraditionalIndonesianSlovak CzechItalianSlovenian DanishJapaneseSpanish DutchKlingonSwedish EnglishKoreanThai EstonianLatvianTurkish FinnishLithuanianUkrainian FrenchMalayUrdu GermanMalteseVietnamese GreekNorwegianWelsh Haitian CreolePersian TRANSLATE with COPY THE URL BELOW Back EMBED THE SNIPPET BELOW IN YOUR SITE Enable collaborative features and customize widget: Bing Webmaster Portal Back
ARTICLE | doi:10.20944/preprints202311.0107.v1
Subject: Engineering, Electrical And Electronic Engineering Keywords: Inverter-based resources; Measure-based method; Model identification; Non-linear dynamics; Power system; SINDy; Synchronous generators; System-level nonlinearity; Volterra-based nonlinearity index
Online: 1 November 2023 (17:22:36 CET)
The complexity of modern power grids, exacerbated by integrating diverse energy sources, espe-cially inverter-based resources (IBRs), presents a significant challenge to grid operation and plan-ning since linear models fail to capture the intricate IBR dynamics. This study employs the Sparse Identification of Nonlinear Dynamics (SINDy) method to bridge the gap between theoretical un-derstanding and practical implementation in power system analysis. It introduces the novel Volterra-based Nonlinearity Index (VNI) to examine system-level nonlinearity comprehensively. The distinction of dynamics into first-order linearizable terms, second-order nonlinear dynamics, and third-order noise elucidates the intricacy of power systems. The findings demonstrate a fundamental shift in system dynamics as power sources transit to IBRs, revealing system-level nonlinearity compared to module-level nonlinearity in conventional syn-chronous generators. The VNI quantifies nonlinear-to-linear relationships, enriching our comprehension of power system behavior and offering a versatile tool for distinguishing between different nonlinearities and visualizing their distinct patterns through the proposed VIN profile.
REVIEW | doi:10.20944/preprints202305.1646.v1
Subject: Medicine And Pharmacology, Oncology And Oncogenics Keywords: graphene-based nanomaterials; graphene-based drug delivery systems; lysosomes; cancer; endosomal/lysosomal escape; lysosomal cell death
Online: 23 May 2023 (10:52:24 CEST)
Graphene-based nanomaterials (GNMs), including graphene, graphene oxide, reduced graphene oxide, and graphene quantum dots, may have direct anticancer activity or be used as nanocarri-ers for antitumor drugs. GNMs usually enter tumor cells by endocytosis and can accumulate in lysosomes. This accumulation prevents drugs bound to GNMs from reaching their targets, sup-pressing their anticancer effects. A number of chemical modifications are made to GNMs to facili-tate the separation of anticancer drugs from GNMs at low lysosomal pH and to enable lysosomal escape of drugs. Lysosomal escape may be associated with oxidative stress, permeabilization of the unstable membrane of cancer cell lysosomes, release of lysosomal enzymes into the cytoplasm, and cell death. GNMs can prevent or stimulate tumor cell death by inducing protective autopha-gy or suppressing autolysosomal degradation, respectively. Furthermore, because GNMs prevent bound fluorescent agents from emitting light, their separation in lysosomes may enable tumor cell identification and therapy monitoring. In this review, we explain how the characteristics of the lysosomal microenvironment and the unique features of tumor cell lysosomes can be exploited for GNM-based cancer therapy.
REVIEW | doi:10.20944/preprints202309.1571.v1
Subject: Environmental And Earth Sciences, Geography Keywords: social-environmental systems; agent-based complex systems; sustainability science; agent-based models; artificial intelligence; data science
Online: 22 September 2023 (13:39:57 CEST)
A significant number and range of challenges besetting sustainability can be traced to the actions and interactions of multiple autonomous agents (people mostly) and the entities they create (e.g., institutions, policies, social network) in the corresponding social-environmental systems (SES). To address these challenges, we need to understand decisions made and actions taken by agents, the outcomes of their actions, including the feedbacks on the corresponding agents and environment. The science of Agent-based Complex Systems—ACS science—has a significant potential to handle such challenges. The advantages of ACS science for sustainability are addressed by way of identifying the key elements and challenges in sustainability science, the generic features of ACS, and the key advances and challenges in modeling ACS. Artificial intelligence and data science promise to improve understanding of agents’ behaviors, detect SES structures, and formulate SES mechanisms.
ARTICLE | doi:10.20944/preprints202304.1213.v1
Subject: Social Sciences, Education Keywords: POGIL-based instruction; lecture-based instruction; the unit of circular motion; science performance self-efficacy
Online: 29 April 2023 (05:21:26 CEST)
This study compares the effects of lecture-based instruction and process-oriented guided inquiry learning (POGIL)-based instruction on the self-efficacy performance of Grade 12 students. A quasi-experimental, pretest-posttest design was adopted to investigate and assess the impact of POGIL-based instruction versus lecture-based instruction on students’ performance as measured by three types of cognitive outcomes; Knowing, Applying and Reasoning (KAR). Two government high schools in Alain were selected as research sites, one for the boys and one for the girls. The total number of participants was approximately 110 students (N=110); 54 were assigned to treatment groups (25 girls and 29 boys), and 56 were assigned to control groups (27 girls and 29 boys). The treatment group was taught a circular motion unit in physics using POGIL-based instruction, while the control group was taught the unit using lecture-based instruction. The study's findings showed statistically significant differences between students of the control group and the treatment group in favour of the latter regarding their science performance, self-efficacy and science-related attitudes. Moreover, positive correlations were found between participants’ performance at the KAR test, self-efficacy and scientific attitudes towards scientific inquiry after the intervention. In conclusion, it is recommended to shift teaching towards POGIL-based instruction due to its positive impact on students’ performance and self-efficacy. It is also suggested to replicate the study to include government and private schools, elementary and high schools, teachers and advisors.
ARTICLE | doi:10.20944/preprints201709.0139.v1
Subject: Social Sciences, Geography, Planning And Development Keywords: Accuracy; Uncertainties; Object-Based; Slums; Jakarta
Online: 27 September 2017 (16:45:25 CEST)
Object-Based Image Analysis (OBIA) has been successfully used to map slums. In general, the occurrence of uncertainties in producing geographic data is inevitable. However, most studies concentrated solely on assessing the classification accuracy and neglecting the inherent uncertainties. Our research analyses the impact of uncertainties in measuring the accuracy of OBIA-based slum detection. We selected Jakarta as our case study area, because of a national policy of slum eradication, which is causing rapid changes in slum areas. Our research comprises of four parts: slum conceptualization, ruleset development, implementation, and accuracy and uncertainty measurements. Existential and extensional uncertainty arise when producing reference data. The comparison of a manual expert delineations of slums with OBIA slum classification results into four combinations: True Positive, False Positive, True Negative and False Negative. However, the higher the True Positive (which lead to a better accuracy), the lower the certainty of the results. This demonstrates the impact of extensional uncertainties. Our study also demonstrates the role of non-observable indicators (i.e., land tenure), to assist slum detection, particularly in areas where uncertainties exist. In conclusion, uncertainties are increasing when aiming to achieve a higher classification accuracy by matching manual delineation and OBIA classification.