ARTICLE | doi:10.20944/preprints202009.0006.v2
Subject: Life Sciences, Biochemistry 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: Life Sciences, 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/preprints202007.0132.v1
Subject: Life Sciences, 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: Mathematics & Computer Science, Other 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, General 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: 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.
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.
REVIEW | doi:10.20944/preprints202203.0032.v1
Subject: Chemistry, 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: Life Sciences, 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 & 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/preprints202112.0225.v1
Subject: Chemistry, 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.
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, 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/preprints201912.0374.v1
Subject: 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/preprints201810.0771.v2
Subject: Social Sciences, Education Studies 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 & 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/preprints202005.0407.v1
Subject: 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/preprints202205.0304.v1
Subject: Mathematics & Computer Science, Other 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/preprints202202.0335.v1
Subject: Biology, Agricultural Sciences & 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/preprints201902.0160.v1
Subject: Mathematics & Computer Science, Artificial Intelligence & Robotics 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/preprints202209.0283.v1
Subject: Medicine & 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: 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/preprints201911.0189.v1
Subject: Medicine & Pharmacology, Nutrition 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/preprints201901.0198.v1
Subject: Mathematics & Computer Science, Information Technology & Data Management 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 & Pharmacology, Pathology & 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.
ARTICLE | doi:10.20944/preprints201810.0513.v1
Subject: Engineering, General 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.
REVIEW | doi:10.20944/preprints202204.0156.v1
Subject: 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/preprints201912.0069.v1
Subject: Mathematics & Computer Science, 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/preprints202010.0351.v1
Subject: Life Sciences, Biochemistry 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/preprints201809.0466.v1
Subject: Mathematics & Computer Science, Information Technology & Data Management 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/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/preprints201805.0234.v1
Subject: Biology, Other 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/preprints202007.0606.v1
Subject: Social Sciences, Business And Administrative Sciences 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/preprints201611.0041.v1
Subject: Chemistry, 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.
ARTICLE | doi:10.20944/preprints202111.0125.v1
Subject: Chemistry, 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/preprints202011.0446.v1
Subject: Chemistry, 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: Mathematics & Computer Science, Geometry & 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.
CONCEPT PAPER | doi:10.20944/preprints202005.0182.v1
Subject: 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/preprints201903.0166.v1
Subject: Chemistry, 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/preprints202002.0097.v1
Subject: Engineering, Biomedical & Chemical Engineering 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.
CONCEPT PAPER | doi:10.20944/preprints202106.0578.v1
Subject: Biology, Animal Sciences & 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: Life Sciences, Biochemistry 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: 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
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.
REVIEW | doi:10.20944/preprints201607.0012.v1
Subject: Mathematics & Computer Science, Information Technology & Data Management 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/preprints202107.0191.v1
Subject: Mathematics & Computer Science, Algebra & 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: 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/preprints202010.0010.v1
Subject: Engineering, Electrical & 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/preprints202112.0296.v1
Subject: Medicine & Pharmacology, Pharmacology & 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 & 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/preprints201610.0080.v1
Subject: Chemistry, 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/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.
ARTICLE | doi:10.20944/preprints201608.0069.v1
Subject: Earth Sciences, Environmental Sciences 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.
ARTICLE | doi:10.20944/preprints201910.0124.v1
Subject: Biology, Other 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.
Subject: Life Sciences, Other 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: Mathematics & Computer Science, 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, Other 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.
REVIEW | doi:10.20944/preprints202112.0027.v2
Subject: Biology, Animal Sciences & 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.
Subject: Chemistry, Other 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/preprints201807.0307.v1
Subject: Social Sciences, 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
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/preprints202111.0108.v1
Subject: Chemistry, 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, Other 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.
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/preprints201709.0139.v1
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.
ARTICLE | doi:10.20944/preprints202002.0249.v1
Subject: Biology, Agricultural Sciences & Agronomy Keywords: Fungal diversity; Saccharomyces; genetic diversity; glyphosate-based herbicides; copper-based fungicides; RoundUp Ready™ corn; phylogenetics
Online: 17 February 2020 (15:37:11 CET)
Saccharomyces cerevisiae are a phenotypically diverse species that adapt to a wide variety of environments by exploiting standing genetic diversity and selecting for advantageous mutations. Glyphosate and copper-based herbicides/ fungicides affect non-target organisms, these incidental exposures can impact microbial populations. In this study, glyphosate resistance was found in the historical collection of yeast which was collected over the last century, but only in yeast isolated after the introduction of glyphosate. The highest glyphosate-resistant yeasts were isolated from agricultural sites. However, herbicide application at these sites was not recorded. In an effort to assess glyphosate resistance and impact on non-target microorganisms, yeast were harvested from 15 areas with known herbicidal histories, including an organic farm, conventional farm, remediated coal mine, suburban locations, state park, and a national forest. Yeast representing 23 genera were isolated from 237 samples of plant, soil, spontaneous fermentation, nut, flower, fruit, feces, and tree material samples. Saccharomyces, Candida, Metschnikowia, Klyveromyces, Hanseniaspora, and Pichia were other genera commonly found across our sampled environments. Managed areas had less species diversity and at the brewery, only Saccharomyces and Pichia were isolated. A conventional farm growing RoundUp Ready™ corn had the lowest phylogenetic diversity and the highest glyphosate resistance. The mine was sprayed with multiple herbicides including a commercial formulation of glyphosate; however, the yeast did not have elevated glyphosate resistance. In contrast to the conventional farm, the mine was exposed to glyphosate only one year prior to sample isolation. Glyphosate resistance is an example of the anthropogenic selection of nontarget organisms.
ARTICLE | doi:10.20944/preprints202001.0032.v1
Subject: Mathematics & Computer Science, Artificial Intelligence & Robotics Keywords: model based diagnosis; applications; diagnosis; physiotherapy; education
Online: 4 January 2020 (06:34:25 CET)
Many physiotherapy treatments begin with a diagnosis process. The patient describes symptoms, upon which the physiotherapist decides which tests to perform until a final diagnosis is reached. The relationships between the anatomical components are too complex to keep in mind and the possible actions are abundant. A trainee physiotherapist with little experience naively applies multiple tests to reach the root cause of the symptoms, which is a highly inefficient process. This work proposes to assist students in this challenge by presenting three main contributions: (1) A compilation of the neuromuscular system as components of a system in a Model-Based Diagnosis problem; (2) The PhysIt is an AI-based tool that enables an interactive visualization and diagnosis to assist trainee physiotherapists; and (3) An empirical evaluation that comprehends performance analysis and a user study. The performance analysis is based on evaluation of simulated cases and common scenarios taken from anatomy exams. The user study evaluates the efficacy of the system to assist students in the beginning of the clinical studies. The results show that our system significantly decreases the number of candidate diagnoses, without discarding the correct diagnosis, and that students in their clinical studies find PhysIt helpful in the diagnosis process.
DATA DESCRIPTOR | doi:10.20944/preprints202104.0351.v1
Subject: Keywords: lecture based instruction; actual community-based instruction; maternal and child care; social competency skills; community awareness
Online: 13 April 2021 (12:47:52 CEST)
Maternal-child care is one of the foundations of primary health care. Nurses’ competency skills they have been taught. Community awareness is an important part of preventive healthcare, and nurses must be aware of the factors that impact the health of the community. This study examines the effectiveness of lecture-based instructions in maternal and child care and its implications to students' social competency skills and community awareness in Nursing Colleges in Nueva Ecija, Philippines. The researcher uses survey questionnaire and employed the descriptive design where fifteen (15) nursing students and five (5) teachers were purposively selected. The findings revealed that the weighted mean for the effectiveness of lecture based instruction in maternal and child care is 3.91 with verbal description of “Effective”, the effects of lecture based instruction in maternal and childcare to students’ social competency skills and community awareness got the weighted mean of 3.87 and interpreted as “very satisfactory” and the effectiveness of actual community-based instruction is very effective with weighted mean of 4.25 and is higher compare to lecture based instruction. The results also revealed that students and teachers were challenged in lecture-based instruction in maternal and chi8ldcare during distance learning. Recommendations for the enhancement of lecture-based instruction in maternal and childcare in social competency skills and community awareness were also made.
ARTICLE | doi:10.20944/preprints202107.0698.v1
Online: 30 July 2021 (11:43:12 CEST)
Background: In an age where information is generally accessible, most of the interest these days has focused on how accessible and convenient technology can be. So small and personal, mobile devices can transform our perception of learning by combining both mobility and convenience. Mobile learning is part of the digital learning landscape alongside e-learning and serious games. However, knowledge about effective design of mobile learning experiences remains of interest with a focus on appropriate design models and the embodiments that can be implemented to achieve the intended educational outcomes. Exploring the instructor's perspective on mobile learning is essential. Therefore, the aim of this study was to investigate the Moroccan instructors' perception and practice of mobile learning to inform the development of an ecologically valid mobile learning integration model. Methods: Higher education Instructors (n=41) were recruited to the study. The Moroccan instructors' perception and their experiences regarding their adoption of mobile learning were collected using an online survey. The analysis focused on their mobile use, perceived IT competency, and opinions on mobile learning. Results: We described most of the instructors' considerations regarding integrating mobile technologies into their teaching activities. We found that most of the mobile learning activities defined by the respondents corresponded to relatively advanced use of mobile devices. More promising, instructors have found innovative ways to use the educational potential of mobile devices. However, the prospect of mobile devices was still to challenge. No or poor Wi-Fi connection, number of devices or limited access, sometimes fees or applications incompatibility were identified as reasons and obstacles to mobile learning usage. Conclusion: Mobile learning is mostly perceived positively among Moroccan instructors allowing many applications and usage to enhance teaching and learning. In this study, a better understanding of aspects and factors influencing the integration of mobile learning in the Moroccan educational context is exposed, helping further the development of an ecologically valid mobile learning integration model. Future work on mobile learning should consider the highly paced evolution of mobile technologies, emphasizing the flexibility of integration frameworks to support instructors and learners.
ARTICLE | doi:10.20944/preprints201908.0011.v1
Subject: Earth Sciences, Atmospheric Science Keywords: rain cell; tracking; PIV; feature-based verification
Online: 1 August 2019 (10:16:12 CEST)
This study proposes a new algorithm termed rain cell identification and tracking (RCIT) to identify and track rain cells from high resolution weather radar data. Previous algorithms have limitations when tracking non-consequent rain cells owing to their use of maximum correlation coefficient methods and their lack of an alternative way to handle the variation stages of rain cells during their life cycles. To address these deficiencies, various methods are implemented in the new algorithm. These include the particle image velocimetry (PIV) method for motion estimation and the rain cell matching rule to obtain the stage changes of rain cells. High resolution (5-min and 1-km) radar reflectivity data from three rainy days over the German federal state North Rhine Westphalia (NRW) are used to evaluate the proposed algorithm. The performance of the new algorithm is compared with a radar reflectivity map and verified by two object-oriented methods: structure–amplitude–location (SAL) and geometric index. The verification results suggest that the performance of the new algorithm is good. Application of the RCIT algorithm to the selected cases shows that the inner structure of rainfall events in the experimental region present extreme value distributions, with most rainfall events having a short duration with less intensity. The new algorithm can effectively capture the stage changes of rain cells during their life cycles. The proposed algorithm can serve as the basis for further hydro-meteorological applications such as spatial and temporal analysis of rainfall events and short-term flood forecasting.
ARTICLE | doi:10.20944/preprints201810.0316.v1
Subject: Social Sciences, Finance Keywords: estimation error; shrinkage; target matrix; risk-based portfolios
Online: 15 October 2018 (13:10:56 CEST)
Portfolio weights solely based on risk avoid estimation error from the sample mean, but they are still affected from the misspecification in the sample covariance matrix. To solve this problem, we shrink the covariance matrix towards the Identity, the Variance Identity, the Single-index model, the Common Covariance, the Constant Correlation and the Exponential Weighted Moving Average target matrices. By an extensive Monte Carlo simulation, we offer a comparative study of these target estimators, testing their ability in reproducing the true portfolio weights. We control for the dataset dimensionality and the shrinkage intensity in the Minimum Variance, Inverse Volatility, Equal-risk-contribution and Maximum Diversification portfolios. We find out that the Identity and Variance Identity have very good statistical properties, being well-conditioned also in high-dimensional dataset. In addition, the these two models are the best target towards to shrink: they minimise the misspecification in risk-based portfolio weights, generating estimates very close to the population values. Overall, shrinking the sample covariance matrix helps reducing weights misspecification, especially in the Minimum Variance and the Maximum Diversification portfolios. The Inverse Volatility and the Equal-Risk-Contribution portfolios are less sensitive to covariance misspecification, hence they benefit less from shrinkage.
ARTICLE | doi:10.20944/preprints202110.0336.v1
Subject: Biology, Ecology Keywords: nature-based solutions; climate change adaptation; biodiversity; ecosystem-based adaptation
Online: 23 October 2021 (14:19:30 CEST)
Nature-based solutions (NbS) are increasingly recognised for their potential to address both the climate and biodiversity crises. These outcomes are interdependent, and both rely on the capacity of NbS to support and enhance the health of an ecosystem: its biodiversity, the condition of its abiotic and biotic elements, and its capacity to function normally despite environmental change. However, while understanding of ecosystem health outcomes of nature-based interventions for climate change mitigation is growing, the outcomes of those implemented for adaptation remain poorly understood with evidence scattered across multiple disciplines. To address this, we conducted a systematic review of the outcomes of 109 nature-based interventions for climate change adaptation using 33 indicators of ecosystem health across eight broad categories (e.g. diversity, biomass, ecosystem functioning and population dynamics). We showed that 88% of interventions with positive outcomes for climate change adaptation also reported measurable benefits for ecosystem health. We also showed that interventions were associated with a 67% average increase in local species richness. All eight studies that reported benefits in terms of both climate change mitigation and adaptation also supported ecosystem health, leading to a triple win. However, there were also trade-offs, mainly for forest management and creation of novel ecosystems such as monoculture plantations of non-native species. Our review highlights two major limitations of research to date. First, only a limited selection of metrics are used to assess ecosystem health and these rarely include key aspects such as functional diversity and habitat connectivity. Second, taxonomic coverage is poor: 67% of outcomes assessed only plants and 57% did not distinguish between native and non-native species. Future research addressing these issues will allow the design and adaptive management of NbS to support healthy and resilient ecosystems, and thereby enhance their effectiveness for meeting both climate and biodiversity targets.
ARTICLE | doi:10.20944/preprints202012.0437.v1
Subject: Medicine & Pharmacology, Allergology Keywords: malnutrition; translation; physiologically based pharmacokinetics; PBPK; pediatrics
Online: 17 December 2020 (16:03:40 CET)
Malnutrition in children is a global health problem, particularly in developing countries. The effects of an insufficient supply of nutrients on body composition and physiological functions may have implications for drug disposition and ultimately affect the clinical outcome in this vulnerable population. Physiologically based pharmacokinetic (PBPK) modeling can be used to predict the effect of malnutrition as it links physiological changes to pharmacokinetic (PK) consequences. However, the absence of detailed information on body composition and the limited availability of controlled clinical trials in malnourished children complicates the establishment and evaluation of a generic PBPK model in this population. In this manuscript we describe the creation of physiologically-based bridge to a malnourished pediatric population, by combining information on a) the differences in body composition between healthy and malnourished adults and b) the differences in physiology between healthy adults and children. Model performance was confirmed using clinical reference data. This study presents a physiologically-based translational framework for prediction of drug disposition in malnourished children. The model is readily applicable for dose recommendation strategies to address the urgent medicinal needs of this vulnerable population.
ARTICLE | doi:10.20944/preprints201810.0156.v1
Subject: Earth Sciences, Environmental Sciences Keywords: Health care risk waste, home-based caregivers
Online: 8 October 2018 (16:02:59 CEST)
The quadruple burden of diseases, early discharge from hospital and hospital at home have resulted in home-based care services becoming a requirement in South Africa. The home-based care services generate a significant amount of health care risk waste that is mismanaged. However, more attention is given to the health care risk waste generated in hospitals and clinics than to health care risk waste generated by home-based caregivers. Therefore, this study investigates the health care risk waste management practices by home-based caregivers. The study adopted a mixed research approach, qualitative and quantitative methods, using a literature review, interviews, and questionnaires as means of data collection. Results show that there are different types of health care risk waste generated as a result of different activities performed by home-based caregivers, but that the waste was found to be managed in an unsafe manner. The majority of households receiving home-based care did not have basic sanitation facilities such as toilets, running water and waste removal services, aggravating the issue of health care risk waste mismanagement. The study recommends a new policy framework that will lead to safe management practices of generated health care risk waste to be adopted by home-based caregivers.
ARTICLE | doi:10.20944/preprints202007.0439.v1
Subject: Social Sciences, Other Keywords: Participation; Wildlife; Community–Based Conservation; India; Interaction; Northeast India
Online: 19 July 2020 (20:42:21 CEST)
Participation by local communities in wildlife conservation projects have long been advocated since it is socially just and is effective to reach conservation and development goals. Socio–economic variables that drive participation and impact of participation have been studied, but the contextual process that stir up local community participation remains understudied. In this paper, we studied factors facilitating community participation in three wildlife conservation projects in Northeast India. Through ethnographic fieldwork at these sites we identified conservation actors and examined interactions between them.We found common modes of participation at these sites and these were related to gaining material incentives, providing labour, attending consultative workshops. Levels of interaction and coercion were found to be different in three sites. Three critical factors that drive participation were: (1) trigger, (2) negotiation and (3) sustenance. Trigger factors kickstart participation through establishment of a crisis narrative and facilitation by external actors. Negotiation factors emerge from day–to–day interaction between local community and external actors and involve effective entry stage activities, income opportunity, mediating voices within the community and intra–community dynamics. Sustenance factors affect the long term participation by community in the conservation project and involve tangible/intangible results, capability development of locals, funding and availability to critical information. In our paper we argue that investment of time and fund to understand the stakeholders and their concept of participation, periodic feedback sessions, capacity development of locals for self–mobilization, innovative information dissemination and securing long term funding are necessary for effective local community participation.
ARTICLE | doi:10.20944/preprints201811.0230.v1
Subject: Engineering, Civil Engineering Keywords: accident; construction project; causes; Bangladesh; RII based rank
Online: 9 November 2018 (03:29:17 CET)
Bangladeshi construction industry suffers a lot of safety and accidental issues than other developing countries in the world. Among many of these, accident of construction project goes far beyond and shape a horrific figure of death for every year. The aims of this study is that analysis and discussion of causes of accident at construction project in Bangladesh. A widespread statistical data collection and data analysis take place to identify the causes and design the questionnaire. The questionnaire-based survey was used to elicit the attitude of four stakeholders as workers, owners, consultants, and contractors towards passive causes of fatal accident at construction site. These study also identify 77 passive causes under 14 major groups and ranked them based on Relative Importance Index (RII). The top 5 major group of causes are (1) Management related, (2) Consultant related, (3) Technology related, (4) Labour related and (5) Contractor related. The top 5 passive causes are: (1) Unaware of safety-related issue, (2) Lack of personal protective equipment, (3) Lack of safety eliminating/ avoiding design, (4) Unfit equipment, (5) Lack of knowledge and training on equipment.
REVIEW | doi:10.20944/preprints202202.0212.v1
Subject: Mathematics & Computer Science, Analysis Keywords: Knowledge Graphs; Link Prediction; Semantic-Based Models; Translation Based Embedded Models
Online: 17 February 2022 (11:49:24 CET)
For disciplines like biological science, security, and the medical field, link prediction is a popular research area. To demonstrate the link prediction many methods have been proposed. Some of them that have been demonstrated through this review paper are TransE, Complex, DistMult, and DensE models. Each model defines link prediction with different perceptions. We argue that the practical performance potential of these methods, having similar parameter values, using the fine-tuning technique to evaluate their reliability and reproducibility of results. We describe those methods and experiments; provide theoretical proofs and experimental examples, demonstrating how current link prediction methods work in such settings. We use the standard evaluation metrics for testing the model's ability.
ARTICLE | doi:10.20944/preprints202011.0677.v1
Online: 26 November 2020 (23:08:59 CET)
High levels ofmeat consumption are increasingly being criticised for ethical, environmental, 2 and social reasons. Plant-based meat substitutes have been identified as healthy sources of protein in 3 comparison to meat. This alternative offers several social, environmental and health benefits and may 4 play a role in reducing meat consumption. However, there has been a lack of research on how specific 5 meat substitute attributes can influence consumers to replace or partially replace meat in their diets. 6 Research demonstrates that in many countries consumers are highly attached to meat.They consider 7 it as an essential and integral element of their daily diet. For these consumers which are not interested 8 in vegan or vegetarian alternatives to meat, so-called meathybrids could be a low-threshold option 9 for a more sustainable food consumption behaviour. In meathybrids only a fraction of the meat 10 product (e.g. 20% to 50%) is replaced with plant-based proteins. In this paper, the results of an online 11 survey with 500 German consumers are presented with focus on preferences and attitudes relating 12 to meathyrids. The results show that more than fifty percent of consumers substitute meat at least 13 occasionally. Thus, about half of the respondents reveal an eligible consumption behaviour in respect 14 to sustainability and healthiness to a certain degree. Concerning the determinants of choosing either 15 meathybrid or meat it becomes evident that the highest effect is exerted by the health perception. The 16 healthier meathybrids are perceived, the higher is the choice probability. Thus, this egoistic motive 17 seems to outperform altruistic motives like animal welfare or environmental concerns when it comes 18 to choice for this new product category.
ARTICLE | doi:10.20944/preprints202003.0267.v1
Subject: Chemistry, Physical Chemistry Keywords: COVID-19; SARS-CoV-2; RNA-dependent RNA polymerase (RdRp); remdesivir; homology model; molecular dynamics; free energy perturbation
Online: 17 March 2020 (04:07:15 CET)
Starting from December 2019, coronavirus disease 2019 (COVID-19) has emerged as a once-in-a-century pandemic with deadly consequences, which urgently calls for new treatments, cures and supporting apparatuses. Remdesivir was reported by World Health Organization (WHO) as the most promising drug currently available for the treatment of COVID-19. Here, we use molecular dynamics simulations and free energy perturbation methods to study the inhibition mechanism of remdesivir to its target SARS-CoV-2 virus RNA-dependent RNA polymerase (RdRp). In the absence of a crystal structure of the SARS-CoV-2 RdRp, we first construct the homology model of this polymerase based on a previously available structure of SARS-CoV NSP12 RdRp (with a sequence identify of 95.8%). We then build the putative binding mode by aligning the remdesivir + RdRp complex to the ATP bound poliovirus RdRp. The putative binding structure is further optimized with molecular dynamics simulations and demonstrated to be stable, indicating a reasonable binding mode for remdesivir. The relative binding free energy of remdesivir is calculated to be -8.28 ± 0.65 kcal/mol, much stronger than the natural substrate ATP (-4.14 ± 0.89 kcal/mol) which is needed for the polymerization. The ~800-fold improvement in the Kd from remdesivir over ATP indicates an effective replacement of APT in blocking of the RdRp binding pocket. Key residues D618, S549 and R555 are found to be the contributors to the binding affinity of remdesivir. These findings demonstrate that remdesivir can potentially act as a SARS-CoV-2 RNA-chain terminator, effectively stopping its RNA reproduction, with key residues also identified for future lead optimization and/or drug resistance studies.
ARTICLE | doi:10.20944/preprints202011.0695.v1
Subject: Earth Sciences, Atmospheric Science Keywords: COVID-19; NO2; Monitoring; traffic volume; urban; ground-based
Online: 27 November 2020 (14:30:08 CET)
The air pollutant NO2 is derived largely from transportation sources and is known to cause respiratory disease. A substantial reduction in transport and industrial processes around the globe from the novel SARS-CoV-2 coronavirus and subsequent pandemic resulted in sharp declines in emissions, including for NO2. Additionally, the COVID-19 disease that results from the coronavirus may present in its most severe form in those who have been exposed to high levels of air pollution. To explore these links, we compared ground-based NO2 sensor data from 11 US cities from a two-month window (March-April) over the previous five years versus the same window during 2020 shutdowns. NO2 declined roughly 12-41% in the 11 cities. This decreased coincided with a sharp drop in vehicular traffic from shutdown-related travel restrictions. To explore this link more closely, we gathered more detailed traffic count data in one city, Indianapolis, Indiana, and found a strong correlation between traffic counts/classification and vehicle miles travelled, and a moderate correlation between NO2 and traffic related data. This finding indicates that we can use such analysis in targeting reduction in pollutants like NO2 by examining and manipulating traffic patterns, thus potentially leading to more population-level health resilience in the future.
REVIEW | doi:10.20944/preprints202208.0105.v1
Subject: Medicine & Pharmacology, Oncology & Oncogenics Keywords: asian breast cancers; mammography screening; risk-based screening
Online: 4 August 2022 (06:20:25 CEST)
Close to half (45.4%) of 2.3 million breast cancers (BC) diagnosed in 2020 were from Asia. While the burden of breast cancer has been examined on the level of broad geographic regions, literature on more in-depth coverage of the individual countries and subregions of the Asian continent is lacking. This review examines the breast cancer burden in 47 Asian countries. Breast cancer screening guidelines and risk-based screening initiatives are discussed.
ARTICLE | doi:10.20944/preprints202105.0632.v1
Subject: Medicine & Pharmacology, Allergology Keywords: suicide; men; help-seeking; engagement; community-based intervention
Online: 26 May 2021 (11:12:38 CEST)
Due to the continuing high suicide rates among young men, there is a need to understand help-seeking behaviour and engagement with tailored suicide prevention interventions. The aim of this study was to compare help-seeking among younger and older men who attended a therapeutic centre for men in a suicidal crisis. In this case series study, data were collected from 546 men who were referred into a community-based therapeutic service in North West England. Of the 546 men, 337 (52%) received therapy; 161 (48%) were aged between 18 and 30 years (mean age 24 years, SD=3.4). Analyses included baseline differences, symptom trajectories for the CORE-34 Clinical Outcome Measure (CORE-OM) and engagement with the therapy. For the CORE-OM there was a clinically significant reduction in mean scores between assessment and discharge (p<0.001) for both younger and older men. At initial assessment, younger men were less affected by entrapment (46% v 62%; p=.02), defeat (33% v 52%; p=.01), not engaging in new goals (38% v 47%; p=.02), and positive attitudes towards suicide (14% v 18%; p=.001) than older men. At discharge assessment, older men were significantly more likely to have an absence of positive future thinking (15% v 8%; p=0.03), have less social support (45% v 33%; p=.02) and feelings of entrapment (17% v 14%; p=.02) than younger men. Future research needs to assess the long-term effects of help-seeking using a brief psychological intervention for young men in order to understand whether the effects of the therapy are sustainable over a period of time following discharge from the service.
ARTICLE | doi:10.20944/preprints201706.0112.v1
Subject: Social Sciences, Education Studies Keywords: HE course management； evidence-based practice； professionalism； practice
Online: 26 June 2017 (04:33:02 CEST)
This paper outlines evidence-based practice in the context of professionalism, and highlights the contribution evidence-based practice can make to the professional practice of higher education course managers. Implications of the changing HE landscape for the status of academics as professionals are reviewed, and evidence-based practice is proposed as a solution for both enhanced course management and to remedy perceived deprofessionalisation. Finally, questions regarding researching professional practice within one’s own institution are addressed.
ARTICLE | doi:10.20944/preprints202012.0539.v1
Online: 21 December 2020 (16:01:59 CET)
Starting from the importance of risk perception for taking certain preventive measures to protect people and their property from disasters, the subject of the research is to examine the factors influencing public perception of mythically-based human behavior in disaster conditions. Using the random sampling method, 250 adult respondents were surveyed in the city of Belgrade, using a specially created and adapted survey questionnaire. The results of the research show that there is no statistically significant influence of gender, age, educational and economic factors on the public perception of human behavior in disaster conditions. The results of the research can be used to improve strategies and campaigns based on risk assessment, aimed at improving the safety of people in disasters.
ARTICLE | doi:10.20944/preprints202010.0148.v2
Subject: Social Sciences, Accounting Keywords: Sustainable Teaching; multidisciplinary; multicultural; teams; Case-based Learning; Problem-based Learning; teamwork
Online: 26 April 2021 (15:38:20 CEST)
This article investigates the prospect of implementing multidisciplinary and multicultural student teamwork (MMT) involving Case-based Learning (CBL) and Problem-based Learning (PBL) as a sustainable teaching practice. Based on a mixed methods approach, which includes direct observation (both physical and virtual), questionnaire distribution and focus-group interviews the study reveals that MMT through CBL and PBL can both facilitate and hinder sustainable learning. Our findings show that while MMT enhances knowledge sharing, it also poses a wide range of challenges, raising questions about its social significance as a sustainable teaching practice. The study suggests the implementation of certain mechanisms, such as ‘Teamwork Training’ and ‘Pedagogical Mentors’, aiming to strengthen the sustainable orientation of MMT through CBL and PBL.
Subject: Engineering, Control & Systems Engineering Keywords: Model-based systems engineering (MBSE); Model informatics and analytics; Model-based collaboration
Online: 12 March 2021 (16:52:34 CET)
In MBSE there is yet no converged terminology. The term ’system model’ is used in different contexts in literature. In this study we elaborated the definitions and usages of the term ’system model’, to find a common definition. 104 publications have been analyzed in depth for their usage and definition as well as their meta-data e.g., the publication year and publication background to find some common patterns. While the term is gaining more interest in recent years it is used in a broad range of contexts for both analytical and synthetic use cases. Based on this three categories of system models have been defined and integrated into a more precise definition.
REVIEW | doi:10.20944/preprints201811.0127.v1
Subject: Mathematics & Computer Science, Artificial Intelligence & Robotics Keywords: IoT search; access control; attribute-based access control; survey
Online: 6 November 2018 (04:18:40 CET)
With the development of IoT technology, various information resources, such as social resources and physical resources, are deeply integrated for different comprehensive applications. Social networking, car networking, medical services, video surveillance and other forms of IoT information Service model gradually change people's daily life. Facing the vast amounts of IoT information data, IoT search technology is used to quickly find accurate information to meet real-time search needs of users. However, IoT search requires to use a large number of user privacy Information, such as personal health information, location information, social relations information, to provide personalized services. User privacy information will meet security problems if an effective access control mechanism is missing during the IoT search process. Access control mechanism can effectively monitor the access activities of resources, and ensure authorized users to access information resources under legitimate conditions. This survey examines the growing literature on access control for IoT search. Problems and challenges of access control mechanism are analyzed to facilitate the adoption of access control solutions in real-life settings. This paper aims to provides theoretical, methodological and technical guidance for IoT search access control mechanism in large-scale dynamic heterogeneous environment. Based on the literature study, we also analyzed future development direction of access control in the age of IoT.
ARTICLE | doi:10.20944/preprints202109.0001.v1
Subject: Keywords: Sacred groves; biodiversity conservation; Community-based conservation; Indigenous People; Nigeria.
Online: 1 September 2021 (08:42:18 CEST)
Globally, sacred groves represent a traditional form of community-based conservation system, recognized for their capacity to preserve areas that are of cultural and religious importance to local people. In most cases, the entire community takes on a watchdog role to guard against encroachment and unauthorized access either by its members or outsiders who might desecrate such sites. Our paper investigates the effects of different governance arrangements on three sacred groves in southwest Nigeria⎯Osun Osogbo Sacred Grove (UNESCO World Heritage Site); Idanre Hills (Nigerian National Monument) and Igbo-Olodumare (local cultural site)⎯on their socio-economic and religio-cultural benefits and contribution to biodiversity conservation. Using a mixed-methods design of a semi-structured questionnaire (n=167), key informant interviews (n=2), and focus groups (n=7), we collected data from local community members, traditional priests, sacred grove devotees and tourism officials. We found that customary institutions have guided reverence for sacralized spaces and wise utilization of their unique resources. The growing recognition of sacred groves has paved the way for socioeconomic rewards for individuals and government as cultural tourism increases. We found that the involvement of formal institutions alongside customary institutions in sacred grove management reinforces compliance with conservation laws within the sacred groves, especially where traditional norms are weak or may be disregarded. We discuss the implications of these observations and offer suggestions to improve community engagement, uphold traditional ecological knowledge, and develop ecotourism within the groves. We conclude that the co-existence of community-based conservation through a system of established traditional norms and prohibitions as well as formal government legislation and management, offers assurance for the long-term preservation of sacred groves and their biodiversity.
ARTICLE | doi:10.20944/preprints201611.0073.v1
Subject: Earth Sciences, Atmospheric Science Keywords: rainfall; TMPA; CMORPH; Pra basin; satellite-based precipitation; Ghana
Online: 14 November 2016 (07:39:44 CET)
Satellite-based rainfall estimation products provide a vital alternative source of rainfall data in areas where conventional precipitation measurement is not readily available. In order to facilitate the use of these products there is the need to evaluate their accuracies. This study evaluated the accuracy of three satellite rainfall products; TMPA 3B42RT, TMPA 3B42 and CMORPH in the Pra basin (23,330 km2) of Ghana. The evaluation was through the point-to-pixel method by comparing 0.25°x 0.25° satellite grids to gauged rainfall based on gauge locations and analyzed statistically using correlation coefficient (r), bias and percent bias (pBias) as the performance verification methods. Seven (7) gauge stations with no missing data for the period of 2003-2008 was used in the evaluation. The analysis was based on daily, monthly, annual and seasonal timescales. Our results showed a good correlation between the TMPA products and the gauged data on all timescales considered. The CMORPH on the other hand showed huge overestimation at all gauge locations. The TMPA 3B42 was seen to be the best amongst the three products. The overall rainfall in the basin was well depicted by the TMPA 3B42 and 3B42RT. Although there wasn’t a perfect match between the 3B42RT and 3B42 products and the gauged rainfall, these products can be used to supplement gauged rainfall measurements in the basin and in estimation of rainfall in ungauged basins with similar characteristics.
ARTICLE | doi:10.20944/preprints202103.0526.v1
Subject: Medicine & Pharmacology, Allergology Keywords: suicide, men, help-seeking, engagement, community-based intervention
Online: 22 March 2021 (12:04:18 CET)
Due to the continuing high suicide rates among young men, there is a need to understand help-seeking behaviour and engagement with tailored suicide prevention interventions. The aim of this study was to explore help-seeking behaviour and engagement for young men aged 18 to 30 years who attended a therapeutic centre for men in a suicidal crisis. In this prospective cohort study, data were collected from 546 men who were referred into a community-based therapeutic service in North West England. Of the 546 men, 337 (52%) received therapy; 161 (48%) were aged between 18 and 30 years (mean age 24 years, SD=3.4). One third (n=54; 34%) of the men were seen within 48 hours of their referral. Analyses included baseline differences, symptom trajectories for the CORE-34 Clinical Outcome Measure (CORE-OM) and engagement with the therapy. For the CORE 34 there was a clinically significant reduction in mean scores between assessment and discharge (p<0.001), with all outcomes demonstrating a large effect size. Future research needs to assess the long-term effects of help-seeking using a brief psychological intervention for young men in order to understand whether the effects of the therapy are sustainable over a period of time following discharge from the service.
ARTICLE | doi:10.20944/preprints201904.0270.v1
Subject: Mathematics & Computer Science, Numerical Analysis & Optimization Keywords: structural bias, algorithmic design, differential evolution, population-based algorithms, optimisation
Online: 24 April 2019 (12:16:42 CEST)
This paper investigates a range of popular differential evolution (DE) configurations to identify components responsible for emergence of structural bias – a recently identified tendency of algorithms to prefer some regions of search space over others, for reasons unrelated to objective function values. Previous work has explored this tendency for genetic algorithms (GA) and particle swarm optimisation (PSO), finding a relationship between population size and extent of structural bias, hence highlighting potential weaknesses of those algorithms. In current article, we focus on DE, extend the investigation to include consideration of an algorithmic component that is often overlooked – constraint handling mechanism. Towards this end, a wide range of DE configurations was tested here. Results suggest that DE is generally robust to structural bias. Unlike the case with GA and PSO, population size seems to have no influence on DE structural bias. Only one of variants studied – DE/current-to-best/1/bin – shows clear signs of bias, however, we show that this effect is mitigated by a judicious choice of constraint handling technique. These findings contribute towards explaining widespread success of DE variants in algorithm comparison studies; its robustness to structural bias represents the absence of a factor that may confound other algorithms.
ARTICLE | doi:10.20944/preprints202107.0259.v1
Subject: Engineering, Automotive Engineering Keywords: Driveability; low-frequency; energy path analysis; powertrain; model-based engineering
Online: 12 July 2021 (12:21:24 CEST)
Vehicle driveability is one of the important vehicle attributes in range-extender electric vehicles due to the electric motor torque characteristics at low-speed events. The process of validating and rectifying vehicle driveability attributes is typically utilised by a physical vehicle prototype that can be expensive and required several design iterations. In this paper, a model-based energy method to assess vehicle driveability is presented based on a high-fidelity 49 degree-of-freedom powertrain and vehicle systems. Multibody dynamics components were built according to their true centre of gravity relative to the vehicle datum for providing an accurate system interaction. The work covered a frequency at less than 20 Hz. The results that consisted of the component frequency domination are structured and examined to identify the low-frequency sensitivity based on different operating parameters such as a road surface coefficient. An energy path technique was also implemented on the dominant component by decoupling its compliances to study the effect on the vehicle driveability and low-frequency response. The outcomes of the research provided a good understanding of the interaction across the sub-systems levels. The powertrain rubber mounts were the dominant components that controlled the low-frequency contents (< 15.33 Hz) and can change the vehicle driveability quality.
REVIEW | doi:10.20944/preprints202111.0089.v1
Subject: Engineering, Industrial & Manufacturing Engineering Keywords: Latent Dirichlet Allocation; Natural Language Processing; Condition based maintenance
Online: 3 November 2021 (14:59:02 CET)
In the field of industrial process monitoring, more and more interest is being shown in specific process categories. These include time-varying processes, that is, those processes whereby the response one receives as output from the system depends on when the input signal is sent into it. There are many reasons for this process variability and such contexts are not always analyzed with this operational characteristic at their core. At the same time, interest in certain categories of techniques is also becoming more prominent, to meet certain application needs. Among these, clustering and unsupervised techniques in general are gaining ground. This is largely due to the difficulty of finding fault data with which to train, for example, supervised models. On the other hand, the clustering technique, on which this contribution focuses, also makes it possible to compensate for the lack of complete knowledge of the structure of the process itself. With these two considerations in mind, this contribution proposes a literature review on the topic of clustering applied in time-varying contexts, in the maintenance field. The aim is to present an overview of the main fields of study, the role of clustering in this context and the main clustering techniques used.
REVIEW | doi:10.20944/preprints202201.0073.v1
Subject: Medicine & Pharmacology, Other Keywords: Messenger RNA • Hospital-based mRNA therapeutics • circular mRNA • self-amplifying mRNA • RNA-based CAR T-cell • RNA-based gene-editing tools
Online: 6 January 2022 (11:20:59 CET)
Hospital-based programs democratize mRNA therapeutics by facilitating the processes to translate a novel RNA idea from the bench to the clinic. Because mRNA is essentially biological software, therapeutic RNA constructs can be rapidly developed. The generation of small batches of clinical grade mRNA to support IND applications and first-in-man clinical trials, as well as personalized mRNA therapeutics delivered at the point-of-care, is feasible at a modest scale of cGMP manufacturing. Advances in mRNA manufacturing science and innovations in mRNA biology, are increasing the scope of mRNA clinical applications.
REVIEW | doi:10.20944/preprints202109.0150.v1
Subject: Social Sciences, Education Studies Keywords: medical moulage; low-cost; healthcare simulation; simulation-based learning
Online: 8 September 2021 (12:39:35 CEST)
Background: Simulation plays a crucial role in health studies, as it helps medical students apply their theoretical knowledge in real-life situations. Moulage is one of the techniques that helps in making simulation more realistic or high-fidelity. It uses special effects to emulate wounds for a better understanding of what the wound is like visually. Still, moulage is expensive, time-consuming, resource-intensive, and requires the training of staff, which is why we need to find low-cost substitutes for moulage materials. Method: When searching the database “PubMed” for the terms “Low-cost and Medical moulage”, we retrieved 222 studies, out of which when excluding results not related to low-cost, we obtained 62 studies, from which when removing studies that do not contain information regarding moulage, we found two papers, after referring to citations and cited articles of those papers, we ended up with six studies. Based on the selected articles and additional articles sourced from their reference list, a total of 11 studies were included in the review. Results: We understand that moulage is a technique that helps make simulations come alive, but the resources required to use it are at times, expensive, which is why we need to find methods to do low-cost moulage, and many studies address that it can be as simple as using homemade ingredients. Students from a previous study have talked about their opinions regarding the realistic component of moulage and whether if it is any different from other moulages. Most of the students agreed that the moulage ranked well in face and content validity. However, further innovations must be introduced in the field to be widely spread and lead to newer opportunities. Conclusion: Although the research done under moulage is limited, it is accepted that moulage is helpful for simulation-based studies and that low-cost moulage can help make medical studies a better experience for students studying it. Students have a favorable opinion on the realistic aspect of the low-cost moulage applied to them. Newer methods can be introduced to moulage, and it can be implemented in low-income countries.
ARTICLE | doi:10.20944/preprints201903.0084.v1
Subject: Chemistry, Applied Chemistry Keywords: titanium-based alloys; microstructure; passivity breakdown; pitting corrosion
Online: 7 March 2019 (06:49:58 CET)
The effect of microstructure and chemistry of passive films on the kinetics of passive layer growth and passivity breakdown of some Ti-based alloys, namely Ti-6Al-4V, Ti-6Al-7Nb and TC21 alloys was studied. The rate of pitting corrosion was evaluated using cyclic polarization measurements. Chronoamperometry was applied to assess the passive layer growth kinetics and breakdown. Microstructure influence on the uniform corrosion rate of these alloys was also investigated employing Tafel extrapolation and dynamic electrochemical impedance spectroscopy. Corrosion studies were performed in 0.9% NaCl solution at 37 oC, and the obtained results were compared with ultrapure Ti (99.99%). The different phases of the microstructure were characterized by X-ray diffraction and scanning electron microscopy. Chemical composition and chemistry of the corroded surfaces were studied using X-ray photoelectron analysis. For all studied alloys, the microstructure consisted of α matrix, which was strengthened by β phase. The highest and the lowest values of the β phase’s volume fraction were recorded for TC21 and Ti-Al-Nb alloys, respectively. The uniform corrosion rate and pitting corrosion resistance (Rpit) of the studied alloys were enhanced following the sequence: Ti-6Al-7Nb < Ti-6Al-4V << TC21. The corrosion resistance of Ti-Al-Nb alloy approached that of pure Ti. The obvious changes in the microstructure of these alloys, together with XPS findings, were adopted to interpret the pronounced variation in their corrosion rates.
ARTICLE | doi:10.20944/preprints201812.0077.v1
Subject: Keywords: biodiversity; climate change; forests; nature-based solutions; policy; resilience
Online: 6 December 2018 (07:39:13 CET)
The current focus on afforestation in climate policy runs the risk of compromising both longterm carbon storage and human adaptation. It also works against efforts to stem the tide of biodiversity loss. We outline why an emphasis on diverse, intact natural ecosystems—as opposed to tree plantations with fast-growing exotic species—will help nations deliver the goals of the Paris Agreement and much more.
ARTICLE | doi:10.20944/preprints202208.0523.v1
Subject: Mathematics & Computer Science, Other Keywords: angle-based outlier detection: percentile-based outlier detection; multiphilda, noise; irrelevant software requirements
Online: 30 August 2022 (11:25:24 CEST)
Noise in requirements has been known to be a defect in software requirements specifications (SRS). Detecting defects at an early stage is crucial in the process of software development. Noise can be in the form of irrelevant requirements that are included within a SRS. A previous study had attempted to detect noise in SRS, in which noise was considered as an outlier. However, the resulting method only demonstrated a moderate reliability due to the overshadowing of unique actor words by unique action words in the topic-word distribution. In this study, we propose a framework to identify irrelevant requirements based on the MultiPhiLDA method. The proposed framework distinguishes the topic-word distribution of actor words and action words as two separate topic-word distributions with two multinomial probability functions. Weights are used to maintain a proportional contribution of actor and action words. We also explore the use of two outlier detection methods, namely Percentile-based Outlier Detection (PBOD) and Angle-based Outlier Detection (ABOD), to distinguish irrelevant requirements from relevant requirements. The experimental results show that the proposed framework was able to exhibit better performance than previous methods. Furthermore, the use of the combination of ABOD as the outlier detection method and topic coherence as the estimation approach to determine the optimal number of topics and iterations in the proposed framework outperformed the other combinations and obtained sensitivity, specificity, F1-score, and G-mean values of 0.59, 0.65, 0.62, and 0.62, respectively.
ARTICLE | doi:10.20944/preprints202111.0196.v1
Subject: Life Sciences, Other Keywords: crocodilian; animal welfare; animal-based measure; animal-based indicator; welfare assessment; welfare measure
Online: 10 November 2021 (08:46:54 CET)
Animal-based measures are the measure of choice in animal welfare assessment protocols as they can often be applied completely independently to the housing or production system employed. Although there has been a small body of work on potential animal-based measures for farmed crocodilians [1-3], they have not been studied in the context of an animal welfare assessment protocol. Potential animal-based measures, that could be used to reflect the welfare state of farmed crocodilians, were identified and aligned with the Welfare Quality® principles of good housing, good health, good feeding and appropriate behaviour. A consultation process with a panel of experts was used to evaluate and score the potential measures in terms of validity and feasibility. This resulted in a toolbox of measures being identified for further development and integration into animal welfare assessment on the farm. Animal-based measures related to ‘good feeding’ and ‘good health’ received the highest scores for validity and feasibility by the experts. There was less agreement on the animal-based measures that could be used to reflect ‘appropriate behaviour’. Where no animal-based measures were deemed to reliably reflect a welfare criterion nor be useful as a measure on the farm, additional measures of resources or management were suggested as alternatives. Future work in this area should focus on the reliability of the proposed measures and involve further evaluation of their validity and feasibility as they relate to different species of crocodilian and farming system.