Miracle-dz/UniFAR-FTUs huggingface dataset:
Alternative role of motif B in template dependent polymerase inhibition

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) relies on the central molecular machine RNA-dependent RNA polymerase (RdRp) for the viral replication and transcription. Remdesivir at the template strand has been shown to effectively inhibit the RNA synthesis in SARS-CoV-2 RdRp by deactivating not only the complementary UTP incorporation but also the next nucleotide addition. How-ever, the underlying molecular mechanism of the second inhibitory point remains unclear. In this work, we have performed molecular dynamics simulations and demonstrated that such inhibition has not directly acted on the nucleotide addition at the active site. Instead, the translocation of Remdesivir from + 1 to − 1 site is hindered thermodynamically as the post-translocation state is less stable than the pre-translocation state due to the motif B residue G683. Moreover, another conserved residue S682 on motif B further hinders the dynamic translocation of Remdesivir due to the steric clash with the 1′-cyano substitution. Overall, our study has unveiled an alternative role of motif B in mediating the translocation when Remdesivir is present in the template strand and complemented our understanding about the inhibitory mechanisms exerted by Remdesivir on the RNA synthesis in SARS-CoV-2 RdRp.
Social Distancing elaboration for indoor environment using machine learning techniques

The last two years witnessed a rapid outbreak of the COVID-19 virus with an exponential increase of critical cases leading to death of many infected people, the social distancing remains the common technique adopted by all countries to reduce the contamination risk and is also recommended by WHO (World Health Organization). According to previous research studies in virology, it is reasonable to maintain a distance between people in public areas. In this paper, we propose a method based on wireless localization and distance between wireless users using both machine learning techniques and correlation-distance model elaboration. We collected indoor RSSI data of WIFI stations using smartphones, perform data pre-processing RSSI and feature selection, we apply classification techniques to determine the location, and finally use the correlation between measurements to estimate distance using a proposed model. Results are assessed in terms of classification and fitting accuracy. Our model is able to determine user's location with an accuracy of 91.1 % using classification and distance discrimination method is proposed to detect any breach of social distancing standard.
A stochastic approximation method for convex programming with many semidefinite constraints

In this paper, we consider a type of semidefinite programming problem (MSDP), which involves many (not necessarily finite) of semidefinite constraints. MSDP can be established in a wide range of applications, including covering ellipsoids problem and truss topology design. We propose a random method based on a stochastic approximation technique for solving MSDP, without calculating and storing the multiplier. Under mild conditions, we establish the almost sure convergence and expected convergence rates of the proposed method. A variety of simulation experiments are carried out to support our theoretical results.
Graph Neural Network Modelling as a potentially effective Method for predicting and analyzing Procedures based on Patient Diagnoses

Currently, the healthcare sector strives to increase the quality of patient management and improve the economic performance of healthcare providers. The data contained in electronic health records (EHRs) offer the potential to discover relevant patterns that aim to relate diseases and therapies, and thus discover patterns that could help identify empirical medical guidelines that reflect best practices in the healthcare system. Based on this pattern identification, it is then possible to implement recommendation systems based on the idea that a higher volume of procedures is associated with high-quality models. Although there are several applications that use machine learning methods to identify these patterns, this identification is still a challenge, in part because these methods often ignore the basic structure of the population, considering the similarity of diagnoses and patient typology. To this end, we have developed graph methods that aim to cluster similar patients. In such models, patients are linked when the same or similar patterns can be observed for these patients, a concept that enables the construction of a network-like structure. This structure can then be analyzed with Graph Neural Networks (GNN) to identify relevant labels, in this case the appropriate medical procedures. We report the construction of a patient Graph structure based on basic patient information like age and gender as well as the diagnoses and trained GNNs models to identify the corresponding patient therapies using a synthetic patient database. We compared our GNN models against different baseline models (using the SCIKIT-learn library of python) and compared the performance of the different model methods. We have found that GNNs are superior, with an average improvement of the f1 score of 6.48% respect to the baseline models. In addition, the GNNs are useful for performing additional clustering analyses that allow specific identification of specific therapeutic clusters related to a particular combination of diagnoses. We found that GNNs are a promising way to model the distribution of diagnoses in a patient population and thus better model how similar patients can be identified based on the combination of morbidities and comorbidities. Nevertheless, network building is still challenging and prone to prejudice, as it depends on how ICD distribution affects the patient network embedding space. This network setup requires not only a high quality of the underlying diagnostic ecosystem, but also a good understanding of how to identify related patients by disease. For this reason, additional work is needed to improve and better standardize patient embedding in graph structures for future investigations and applications of services based on this technology, and therefore is not yet an interventional study.
Genetic Characteristics and Enzymatic Activities of Bacillus velezensis KS04AU as a Stable Biocontrol Agent against Phytopathogens

Bacillus velezensis has a broad application in the agricultural and industrial sectors for its biocontrol properties and its potential active secondary metabolites. The defined phenotypic characteristics of a strain vary according to its ecosystem. We report the complete genomic analysis of B. velezensis KS04AU compared to four strains of B. velezensis (SRCM102752, ONU-553, FZB42, and JS25R) and two closely related Bacillus amyloliquefaciens (LL3 and IT-45). A total of 4771 protein coding genes comprises the KS04AU genome, in comparison with 3334 genes core genes found in the six other strains and the remaining 1437 shell genes. Average nucleotide identity of the target strain to the six other strains showed 99.65% to B. velezensis ONU-553, sharing 60 orthologous genes. Secondary metabolite gene cluster analysis of all strains showed that KS04AU has a mersacidin cluster gene, which is absent in the genome of the other strains. PHASTER analysis also showed KS04AU harboring two phages (Aeribacllus AP45 NC_048651 and Paenibacillus_Tripp NC_028930), which were also unique in comparison with the other strains. Analysis on anti-microbial resistance genes showed no difference in the genome of KS04AU to any of the other genomes, with the exception of B. amyloliquefaciens IT-45 which had one unique small multidrug-resistance antibiotic efflux-pump gene (qacJ). The CRISPR-Cas systems in the strains were also compared showing one CRISPR gene found only in KS04AU. Hydrolytic activity, antagonistic activity against phytopathogens (Fusarium oxysporum, Fusarium graminearum, Alternaria alternata and Pseudomonas syringae) and biocontrol against tomato foot and root rot experiments were carried out. B. velezensis KS04AU inhibits the growth of all phytopathogens tested, produces hydrolytic activity, and reduces Fusarium oxysporum f.sp. radicis-lycopersici (Forl) ZUM2407 lesions up to 46.02 ± 0.12%. The obtained results confirm B. velezensis KS04AU as a potential biocontrol strain for plant protection.
Time-Dependent Seismic Fragility of Typical Concrete Girder Bridges under Chloride-Induced Corrosion

Recent studies highlighted the importance of the combined effects of prestress loss and corrosion deterioration for concrete girder bridge structures when the effect of damage on the performance level is estimated. The multi-deterioration mechanisms connected with chloride erosion include the cross-sectional area loss of longitudinal bars and stirrups, the reduction in the ductility, the decrease in the strength of steels and the strength loss of concrete in RC columns. For the corroded RC columns and corroded elastomeric bridge bearings, analytical models of the material degradation phenomena were employed for performing the probabilistic seismic performance analysis, which could obtain the system seismic fragility of aging bridges by considering the failure functionality of multiple correlated components (e.g., columns, bearings). The combined effects of prestress loss and cracking were also considered when developing time-dependent system seismic fragility functions. Here, a typical multi-span reinforced concrete girder bridge was used as a case study for studying the time-variant seismic performance. The results revealed the importance of the joint effects of the multi-deterioration mechanisms when modeling the time-dependent seismic fragility of aging bridge systems, as well as the significance of considering the combined effects of prestress loss and cracking.
Thermodynamics and sustainable development

It is the objective of this thesis to demonstrate exergy analysis as a powerful instrument to obtain sustainable development. An important aspect of sustainable development is the minimisation of irreversibilities caused by the use of non-renewables. In order to limit the scope of this thesis sustainable development associated with production is considered only. The demonstration cases from practice are selected on four levels: components from process units, process units, complete production processes and, finally, products from production processes. This approach requires life cycle analysis aspects to be included in the exergy analysis.
The role of innovation type and country context in diffusion of innovative technologies in organisations – a meta-analytic review

ABSTRACT As innovative information technologies (IT) become increasingly available, there is a need to understand how these technologies diffuse in organisations. Several studies on IT innovation have investigated the relationship of key innovation attributes, namely relative advantage, compatibility, complexity, trialability, and observability with either ‘intention to use’ or ‘adoption’ in the organisations. However, those studies have observed contradictory results regarding these relationships. Additionally, there is a lack of investigation on how contingencies of innovation type (IT service vs IT product) and country context (developing vs developed) influence these relationships. Considering these gaps, the present research undertakes a meta-analysis of 86 studies published during 2001–2020 to examine how organisational ‘intention to use’ and ‘adoption’ of IT innovations are influenced by key innovation attributes. We also examine how contingencies of innovation type and country context influence these relationships. Results contribute to the diffusion of innovations as well as information systems literature.
Adoption of Audit Data Analytics - The Moderation Effect of Audit, Firm Size, and Voluntariness to Use

The study is one of the first empirical studies that focuses on the evolution of BDAs in the auditing field. This study aims to examine the moderation effect of audit firm characteristics such as audit firm size and voluntariness to use have on the relationships between the factors affecting auditors’ ATT towards using ADAs. The study is supported by the TAM model and the UTAUT model. A survey is the main research instrument used in the current study; the survey is administrated on Google forms and in direct collect form as well. The data examined for both Big4 and Non-Big4 auditors and the results shows mixed significance level for the different variables.
Mathematical Modeling of Real-Time Scheduling for Microgrid Considering Uncertainties of Renewable Energy Sources

This paper deals with the real-time scheduling of a microgrid considering uncertainties of renewable energy sources (RESs). A two-step mathematical model based on real-time scheduling and demand responses (DRs) is proposed. DR programs, time of use (TOU) and emergency demand response programs (EDRP), are used to minimize the operation cost of microgrid. The proposed real-time scheduling is based on spinning and load reserves to deal with uncertainties of RESs. In the first step, the day-ahead scheduling is run for 24 hours with forecasted RESs. The second step deals with the actual RESs and the microgrid operation is rescheduled in the real time. The effectiveness of DR programs on the electrical demand for each interval is also shown in this study. The mixed-integer linear programming (MILP) method using CPLEX optimization program is used to solve the proposed two-step mathematical model.
Antecedents on Customer Satisfaction Tuku Coffee Shop: A Perspective Expectation-Confirmation Theory and Kano's Model

The purpose of this study was to test the antecedents of overall customer satisfaction using the expectation confirmation theory and Kano's model. Data analysis methods used PLS-SEM. The sampling technique used purposive sampling. The sample analyzed in this study amounted to 200 respondents. The results show that packaging has a significant effect on customer satisfaction, service quality has an impact on customer satisfaction, meaning that the hypothesis is supported so that coffee shop management should pay more attention to packaging and service to consumers which can offer a more memorable experience for customers to create customer satisfaction. But sales promotion does not Significant effect on customer satisfaction means that the hypothesis is rejected. This study is limited in the sample size, research domain and participant coverage. This study suggests a practical canoe model approach and expectation confirmation theory for related organizations and practitioners to correctly identify customer needs and channel resources in the right direction. Fulfilling customer requirements by providing customer satisfaction and pleasure is essential as a golden rule to maintain business continuity in this competitive world. Keywords: packaging, sales promotion, service quality, customer satisfaction
Simulation and visualization framework for selecting appropriate urban-scale climate mitigation and adaptation strategies

At present mitigation and adaptations strategies compete for constrained resources within a future of uncertain climate impacts. Meeting decarbonisation goals while implementing robust and resilient adaptation strategies requires an analysis structure that can account for uncertainty as well as depict how the intermingling of strategies may hinder or beneﬁt the ultimate trajectory of actions. The marginal abatement cost curve (MACC) is an indispensable tool for planning mitigation pathways, but has historically not relied upon robust experimental analysis making it notional at best nor has it included a view of adaptation pathways. This study utilizes a newly developed, medium-density residential community in Van-couver, British Columbia, Canada as a case study for developing a pathway-based MACC. Multiple mitigation and adaptation measures are modeled individually and through exhaustive combination to test their sensitivity on marginal abatement cost and residual cost of climate change. Several visualizations are created to demonstrate several ways of analyzing the resulting large set of data.
Mortality of NBA Players: Risk Factors and Comparison with the General US Population

Concerns have been raised recently by players’ associations regarding the risk of death among retired players. Using a retrospective cohort study, we analyzed factors associated with the mortality of National Basketball Association (NBA) players and compared their life expectancy with that of the general population. We analyzed a cohort of 3985 players who participated in the NBA from its inception in 1946 to April 2015 (481 active and 3504 former players). We used the data for the 3504 former NBA players, of whom 687 (19.1%) died before 15 April 2015, to study the elapsed time between the end of their NBA careers until death. Cox proportional hazards models were employed in the multivariate survival analysis. After adjusting for age at the end of the NBA career and calendar year, we found that mortality is associated with height and ethnicity. Taller players and African-American players had a higher instantaneous risk of death than shorter players or white players. In addition, the life expectancy of players (regardless of height and ethnicity) has increased since the inception of the NBA. This is one of the first studies using such an extensive cohort of professional basketball players and Cox proportional hazards models. Results confirmed that height is associated with mortality. In addition, ethnicity is also linked to mortality; white players and small players live longer. Our study is useful for devising strategies for health interventions and the proper allocation of resources with respect to the general population.
Viral and Cellular Factors Contributing to the Hematogenous Dissemination of Human Cytomegalovirus via Polymorphonuclear Leukocytes

Polymorphonuclear leukocytes (PMNs) presumably transmit human cytomegalovirus (HCMV) between endothelial cells in blood vessels and thereby facilitate spread to peripheral organs. We aimed to identify viral components that contribute to PMN-mediated transmission and test the hypothesis that cellular adhesion molecules shield transmission sites from entry inhibitors. Stop codons were introduced into the genome of HCMV strain Merlin to delete pUL74 of the trimeric and pUL128 of the pentameric glycoprotein complex and the tegument proteins pp65 and pp71. Mutants were analyzed regarding virus uptake by PMNs and transfer of infection to endothelial cells. Cellular adhesion molecules were evaluated for their contribution to virus transmission using function-blocking antibodies, and hits were further analyzed regarding shielding against inhibitors of virus entry. The viral proteins pUL128, pp65, and pp71 were required for efficient PMN-mediated transmission, whereas pUL74 was dispensable. On the cellular side, the blocking of the αLβ2-integrin LFA-1 reduced virus transfer by 50% and allowed entry inhibitors to reduce it further by 30%. In conclusion, these data show that PMN-mediated transmission depends on the pentameric complex and an intact tegument and supports the idea of a virological synapse that promotes this dissemination mode both directly and via immune evasion.
TOP-CT: Trajectory With Overlapping Projections X-Ray Computed Tomography

TOP-CT (Trajectory with Overlapping Projections X-ray Computed Tomography) is a new class of CT scanning geometries for high throughput industrial CT scanning. In TOP-CT multiple objects move with a constant spacing over the same trajectory between a stationary X-ray source and detector. The projections of multiple objects can overlap, which provides additional flexibility when designing CT scanning geometries. Reconstruction algorithms were developed to reconstruct objects one by one from the overlapping projection data as soon as the objects move out of the field of view of the scanning setup. This makes it possible to make reconstructions while new objects with overlapping projections keep being added. The forward problem of TOP-CT is linear with a band block Toeplitz structure, and the matrix of the forward problem can be constructed from multiple copies of a non-overlapping CT projection matrix, so existing software toolkits can be used for TOP-CT with only a small modification. Simulation experiments and a real life experiment were performed on a U-turn TOP-CT geometry. One experiment showed that reconstructions from an overlapping projection setup have a slightly higher SSIM (0.828 vs 0.811) and similar PSNR (33.50 vs 33.34) compared to a non-overlapping setup, using the same scan time per object and the same reconstruction algorithm (SIRT). Another experiment showed that a reconstruction algorithm making reconstructions one by one using only local projection data performed without loss of quality compared to a baseline reconstruction method using all projection data.
Heritage Tourism and Nation-Building: Politics of the Production of Chinese National Identity at the Mausoleum of Yellow Emperor

As an important embodiment and carrier of Chinese traditional culture, the rituals and ceremonies in heritage tourism not only carry profound spiritual and cultural connotations, such as respecting nature and worshiping ancestors, they also enable people to gain a sense of identity. Therefore, this paper aims to explore the relationship between heritage tourism and the politics of identity-building from the perspective of critical toponymy based on the case study of the Mausoleum of the Yellow Emperor. Drawing on five years’ of fieldwork at the Mausoleum of the Yellow Emperor in Shaanxi Province, China, this paper unfolds how heritage tourism has evolved into a certain kind of political agenda and a social engineering of nation-building. Relying on in-depth interviews and R language text analysis, this paper examines how Chinese national identity is produced, performed, and established through landscape naming and ritual performance in heritage tourism. This paper finds that (1) the naming and interpretation of ancestral roots cultural landscapes, as well as ritual performance in heritage tourism, are closely associated with cultural representations and reproductions of national identity. (2) The naming and interpretation of landscapes, as well as the performance of ritual practices in heritage tourism, are closely associated with national history and mythology. The tourists’ behaviors and emotions, as well as their performance and experiences during the ritual practice at the heritage tourism site, help to construct national identity. The cultural production and invention are combined with actions enacted by governments and local residents, as well as visitors from different backgrounds. (3) The mausoleum creates cultural links for Taiwanese tourists to understand their ancestral roots culture and thus to enhance their connection with the mainland. This paper tries to explore the relationship between heritage tourism and identity-building from the perspective of critical toponymy, which has implications for place branding and marketing projects when promoting ancestral roots culture and place-named tourism. This research not only helps the individuals to realize and reappreciate the value of traditional culture and heritage, it also motivates the individuals to rethink their responsibilities in cultural inheritance and the innovative development of culture. It also helps to enhance the consciousness of the people on both sides of the strait as a community of the Chinese nation, as well as to promote the peaceful development of cross-strait relations.