Active Database Research Articles

New Zealand Active Faults Database: the high-resolution dataset v2.0

ABSTRACT The New Zealand Active Faults Database (NZAFD) contains underpinning data to help mitigate the impacts of future surface-rupturing earthquakes in Aotearoa New Zealand. However, defining the associated hazards and risks must be undertaken at relevant scales and as such, the NZAFD contains two scale-based datasets each serving complementary, but different, purposes. The high-resolution (‘NZAFD-HighRes’) dataset contains enough detail on surface traces for cadastral scale land-use planning purposes, while the other dataset is generalised to 1:250,000 scale (‘NZAFD-AF250’). Here we document for the first time the NZAFD-HighRes dataset (v2.0) and describe the recent efforts that have focused on updating the dataset structure to increase useability, compiling data and improving GIS infrastructure. The NZAFD-HighRes and NZAFD-AF250 datasets, along with Fault Avoidance Zones and Fault Awareness Areas – land-use planning tools used to mitigate surface rupture hazard – are publicly accessible via the active faults web service and a webmap application at https://data.gns.cri.nz/af/. This upgraded webmap enables active fault data to be discovered and used for informing future surface rupture hazard assessments. The relationship of the NZAFD to other active fault datasets and models is also discussed, along with future directions and challenges.

Analysis of Straw Degradation and Whole Genome of Acrophialophora multiforma.

Lignin is one of the main components in plants, which can transform value-added bioenergy and chemicals. At the same time, due to the close combination of lignin and hemicellulose in the structure, it becomes a barrier for cellulose utilization. Therefore, the effective degradation of lignin is of great significance for the utilization of these resources. In this study, the lignin degrading ability of Acrophialophora multiforma strain GZUIFR 22.397 was preliminarily investigated through straw degradation experiments and enzyme activity determination. Then, the whole genome of strain A. multiforma GZUIFR 22.397 was sequentially analyzed and annotated through multiple gene function annotation databases to comprehensively evaluate its lignin degrading potential. The results showed that the weight loss of straw reached 5.98 ± 3.95%. Laccase activity was 77.49 ± 2.65 U/L, lignin peroxidase activity was 160.57 ± 29.07 U/L, and manganese peroxidase activity was 294.83 ± 3.77 U/L. The genome of A. multiforma strain GZUIFR 22.397 spans 33.81 megabases and encompasses 9,370 genes. Among these, 6,122 genes have been annotated in the Gene Ontology (GO), 2,286 in the Cluster of Orthologous Groups of proteins (KOG), 2,283 in the Kyoto Encyclopedia of Genes and Genomes (KEGG), and 603 in the Carbohydrate Active enZYmes Database (CAZy). Concurrently, the genome analysis predicted the presence of 9 genes for laccase, 2 genes for lignin peroxidase, and 2 genes for manganese peroxidase. In summary, these results indicated that A. multiforma GZUIFR 22.397 has lignin degrading ability, and laid the foundation for deciphering the molecular mechanism of A. multiforma GZUIFR 22.397 to degrade lignin.

Probabilistic seismic hazard analysis for the Dominican Republic

The Dominican Republic experiences moderate to high seismic hazard mostly caused by oblique convergence at the Caribbean/North American plate boundary that manifests as subduction zones, less-pronounced subduction-like trenches with thrust faulting, long strike-slip faults parallel to the plate boundary, and onshore deformation. Historical earthquakes have damaged the Dominican Republic’s large cities and those in neighboring Haiti, once requiring relocation. Given this, the Dominican Republic joined the “Training and Communication for Earthquake Risk Assessment” (TREQ) project funded by the United States Agency for International Development, which aimed to increase earthquake risk assessment capacity in Latin American cities. The TREQ project was the basis for developing an openly available probabilistic seismic hazard model for the Dominican Republic. The input model was developed from two main datasets: a homogenized earthquake catalog and an active faults database that combines results of recent local projects with a global database. The seismic source characterization used these to constrain source geometries and occurrence rates for active shallow crustal earthquakes, subduction interfaces and subduction-like thrusts, and intraslab earthquakes. Shallow crustal earthquakes, including those on subduction-like thrusts, are modeled by smoothed seismicity and fault sources, the latter using pre-defined geometries that permit multi-fault ruptures. Seismicity on the Puerto Rico Trench subduction interface is modeled as a fault source, while intraslab sources use pre-defined gridded ruptures inside the intraslab volume. The source characterization applies epistemic uncertainties to modeling assumptions affecting occurrence rates and maximum magnitudes. The ground motion characterization used residual analyses from past regional projects as a basis, updating some components with more recent ground motion models. Computed hazard results reinforce those from recent studies in terms of geographical hazard patterns and levels. For 475-year return periods, peak ground acceleration (PGA) in Santiago de los Caballeros reaches 0.50 g, controlled by the Septentrional Fault, while all tectonic region types contribute to the PGA 0.31 g computed for Santo Domingo.

Active Dwarf Galaxy Database. I. Overlap between Active Galactic Nuclei Selected by Different Techniques

We assemble a sample of 733 dwarf galaxies (M * ≤ 109.5 M ⊙) with signatures of active galactic nuclei (AGN) and explore the intersection between different AGN-selection techniques. Objects in our database are compiled from previous studies that identify AGN in dwarf galaxies through spectroscopy, X-ray emission, infrared colors, and optical photometric variability. We apply a uniform set of AGN diagnostic tools to the database using archival data. We find that any single selection method captures no more than half of the overall AGN population, and there is a general disagreement among the AGN-selection methods in this stellar-mass regime. The largest overlap between methods is found when both methods use optical spectroscopic data. In contrast, the populations of AGN intersect the least when comparing those methods that use photometric data at different wavelengths. These results can be used to better constrain the active fraction in dwarf galaxies, which is in turn an important constraint for black hole seed formation models. In a follow-up paper, we will explore links between the effectiveness of each selection technique and host galaxy properties.

The China Active Faults Database (CAFD) and its web system

Abstract. Active faults serve as potential sources of destructive earthquakes. Studies and investigations of active faults are necessary for earthquake disaster prevention. This study presents a nation-scale database of active faults in China and its adjacent regions, in tandem with an associated web-based query system. This database is an updated version of the active faults data included in the Seismotectonic Map of China and its Adjacent Regions (1:4 000 000), which is one of the four essential maps of the mandatory Chinese standard GB 18306-2015 Seismic Ground Motion Parameter Zonation Maps of China. The data update and integration stem from regional-scale studies and surveys conducted over the past 2 decades (at reference scales from 1:250 000 to 1:50 000). The information amassed from these regional-scale studies and surveys encompasses geophysical probing, drill logging, measurement of offset landforms, sample dating, as well as geometric and kinematic parameters of exposed and blind faults, paleo-earthquake sequences, and recurrence intervals. These data have been acquired and analyzed utilizing a uniform technical standard framework and reviewed by expert panels in both field and laboratory settings. Our system hosts this nation-scale database accessible through a Web Geographic Information System (GIS) application, enabling browsing, querying, and downloading functionalities via a web browser. The system we built also publishes the Open Geospatial Consortium (OGC) Web Feature Service and the OGC Web Map Service of active faults data. Users can incorporate map layers and obtain fault data in OGC-compliant GIS software for further analysis through these services. The Chinese government, research institutions, and companies have widely used the active faults data from the previous versions of the database. The database is available at https://doi.org/10.12031/activefault.china.400.2023.db (Xu, 2023) and via the web system (https://data.activetectonics.cn/arcportal/apps/webappviewer/index.html?id=684737e8849c4170bbca14447608c451, CEFIS, 2023; http://data.activetectonics.cn/arcserver/services/Hosted/CAFD400_2022_WFS/MapServer/WFSServer, CAFD WFS, 2024).

Identification of potential PIM-2 inhibitors via ligand-based generative models, molecular docking and molecular dynamics simulations.

Proviral Integrations of Moloney-2 (PIM-2) kinase is a promising target for various cancers and other diseases, and its inhibitors hold potential for treating related diseases. However, there is currently no clinically available PIM-2 inhibitor. In this study, we constructed a generative model for de novo PIM-2 inhibitor design based on artificial intelligence, performed molecular docking and molecular dynamics (MD) simulations to develop an efficient PIM-2 inhibitor generative model and discover potential PIM-2 inhibitors. First, we designed a generative model based on a Bi-directional Long Short-Term Memory (BiLSTM) framework combined with a transfer learning strategy and generated a new PIM-2 small molecule library using existing active drug databases. The generated compound library was then virtually screened by molecular docking and scaffold similarity comparison, identifying 10 initial hit compounds with better performance. Next, using the inhibitor in the crystal structure as a positive control, we performed two rounds of MD simulations, with lengths of 100ns and 500ns, respectively, to study the dynamic stability of the protein-ligand systems of the 10 compounds with PIM-2. Analyzed the interactions with key hinge region residues, binding free energies, and changes in the ATP pocket size. The generative model demonstrates good molecular generation capability and can generate efficient novel molecules with similar physicochemical properties as active PIM-2 drugs. Among the 10 initially selected hit compounds, 5 compounds C3 (-29.69kcal/mol), C4 (-33.31kcal/mol), C5 (-28.59kcal/mol), C8 (-34.68kcal/mol), and C9 (-25.88kcal/mol) have higher binding energies with PIM-2 than the positive drug 3YR (-26.18kcal/mol). The MD simulation results are consistent with the docking analysis, these compounds have lower and more stable RMSD values for the complex systems with the reported positive drug 3YR and PIM-2 complex system. They can form long-term stable interactions with active site and the hinge region of PIM-2, which suggests these compounds are likely to have potent inhibitory effects on PIM-2. This study provides an efficient generative model for PIM-2 inhibitor research and discovers 5 potential novel PIM-2 inhibitors.

A novel glycoside hydrolase 43-like enzyme from Clostridium boliviensis is an endo-xylanase and a candidate for xylooligosaccharide production from different xylan substrates.

The genome of Clostridium boliviensis strain E-1 encodes a number of hypothetical enzymes, annotated as glycoside hydrolase-like but not classified in the Carbohydrate Active Enzyme Database (CAZy). A novel thermostable GH43-like enzyme is here characterized as an endo-β-xylanase of interest in the production of prebiotic xylooligosaccharides (XOs) from different xylan sources. CbE1Xyn43-l is a two-domain enzyme composed of a catalytic GH43-l domain and a CBM6 domain, producing xylotriose as main XO product. The enzyme has homologs in many related Clostridium strains which may indicate a similar function and be a previously unknown type of endo-xylanase in this evolutionary lineage of microorganisms.

Scenario-based tsunami hazard assessment for Northeastern Adriatic coasts

Significant tsunamis in the Northern Adriatic are rare, and only a few historical events have been reported in the literature, with sources mostly located along central and southern parts of the Adriatic coasts. Recently, a tsunami alert system has been established for the whole Mediterranean area; however, a detailed description of the potential impact of tsunami waves on coastal areas is still missing for several sites. This study aims to model the hazard associated with possible tsunamis generated by offshore earthquakes, with the purpose of contributing to tsunami risk assessment for selected urban areas along the Northeastern Adriatic coasts. Tsunami modelling is performed by the NAMI DANCE software, which allows accounting for seismic source properties, variable bathymetry, and nonlinear effects in wave propagation. Hazard scenarios at the shoreline are developed for the coastal areas of Northeastern Italy and at selected cities (namely, Trieste, Monfalcone, Lignano and Grado). An extensive set of potential tsunamigenic sources of tectonic origin located in three distance ranges (namely at Adriatic-wide, regional and local scales) are considered for the modelling. Sources are defined according to available literature, which includes catalogues of historical tsunamis and existing active faults databases. Accordingly, a set of tsunami-related parameters and maps are obtained (e.g. maximum run-up, arrival times, synthetic mareograms) that are relevant to planning mitigation actions at the selected sites.

HTNpedia: A Knowledge Base for Hypertension Research.

Hypertension is notably a serious public health concern due to its high prevalence and strong association with cardiovascular disease and renal failure. It is reported to be the fourth leading disease that leads to death worldwide. Currently, there is no active operational knowledge base or database for hypertension or cardiovascular illness. The primary data source was retrieved from the research outputs obtained from our laboratory team working on hypertension research. We have presented a preliminary dataset and external links to the public repository for detailed analysis to readers. As a result, HTNpedia was created to provide information regarding hypertension-related proteins and genes. The complete webpage is accessible via www.mkarthikeyan.bioinfoau.org/HTNpedia.

A Hierarchical Prediction Method for Pedestrian Head Injury in Intelligent Vehicle with Combined Active and Passive Safety System.

With the development of intelligent vehicle technology, the probability of road traffic accidents occurring has been effectively reduced to a certain extent. However, there is still insufficient research on head injuries in human vehicle collisions, making it impossible to effectively predict pedestrian head injuries in accidents. To study the efficacy of a combined active and passive safety system on pedestrian head protection through the combined effect of the exterior airbag and the braking control systems of an intelligent vehicle, a "vehicle-pedestrian" interaction system is constructed in this study and is verified by real collision cases. On this basis, a combined active and passive system database is developed to analyze the cross-influence of the engine hood airbag and the vehicle braking curve parameters on pedestrian HIC (head injury criterion). Meanwhile, a hierarchy design strategy for a combined active and passive system is proposed, and a rapid prediction of HIC is achieved via the establishment of a fitting equation for each grading. The results show that the exterior airbag can effectively protect the pedestrian's head, prevent the collision between the pedestrian's head and the vehicle front structure, and reduce the HIC. The braking parameter H2 is significantly correlated with head injury, and when H2 is less than 1.8, the HIC value is less than 1000 in nearly 90% of cases. The hierarchy design strategy and HIC prediction method of the combined active and passive system proposed in this paper can provide a theoretical basis for rapid selection and parameter design.

Managing Active Fault Surface Rupture Risk through Land Use Planning:

This article reflects on the management of active fault surface rupture hazard after the Canterbury and Kaikōura earthquakes. To understand mitigation barriers, interviews were conducted with planners and natural hazard risk specialists in selected districts with active faults, but without land use provisions. The interviews revealed issues with the interpretation and implementation of the Ministry for the Environment’s Active Fault Guidelines, Planning for Development of Land on or Close to Active Faults: a guideline to assist resource management planners in New Zealand. The purpose and intended use of the New Zealand Active Faults Database (NZAFD) is also explored.

INTEGRATED GIS TECHNIQUES FOR LAND SUITABILITY ASSESSMENT IN SOUTHERN IDAHO FOR SPRING WHEAT

The accurate evaluation of land suitability for special agriculture production plays an important role to decrease the negative environmental impacts. The current study aimed to apply GIS techniques for analyzing land suitability to wheat production in 5474.27 ha of semi-arid regions of Bingham and Bonneville counties of southern Idaho. This research used the Idaho West State Plane projection for the least distorted projection for its investigation. "Convert feature class to feature class" and "copy raster" procedures were used to ensure that all required data layers are stored in the active database. DEM data was gathered in the form of multiple rasters and then turned into a single mosaic dataset so that all of the data are converted to a single mosaic dataset. The results indicated that Bingham County is more suitable for wheat than Bonneville County. A change in irrigation, cropping pattern, rotation, and land use type of Bonneville County might be helpful to increase its wheat production. It was concluded that integrating GIS techniques could be an accurate and effective method for better land use planning and management for agriculture productions.

Characterization of Focal Mechanisms for Upper Crustal Distributed Seismicity in Aotearoa New Zealand

AbstractApplying distributed seismicity models for seismic hazard analysis requires postulating the styles of faulting and nodal planes for anticipated earthquakes. Here, we present a model describing focal mechanisms, or more specifically, strike, dip, and rake angles, for the ruptures of shallow (hypocentral depth ≤40 km) crustal earthquakes in Aotearoa New Zealand. This model is based on delineations of neotectonic domains and analysis of pre-existing datasets, including an active fault database, geological map-based fault datasets, the New Zealand Community Fault Model, and a regional moment tensor catalog. We demonstrate that the focal mechanism model is broadly consistent with the regional moment tensor catalog, with respect to spatial distributions of P and T axes and in terms of the Kagan angle. This characterization of focal mechanisms complements the distributed seismicity component of the New Zealand National Seismic Hazard Model 2022.

Enhancing distribution generator impact mitigation using an adaptive protection scheme based on modified pelican optimization algorithm and active database management system

AbstractThis paper addresses the challenge of protecting electrical networks in the presence of distribution generators (DGs). The use of DGs affects fault currents, leading to miscoordination between protection relays and causing constraints on network reliability. To tackle this issue, the authors propose an adaptive protection scheme (APS) based on a modified pelican optimization algorithm (MPOA) and active database management system (ADBMS). The APS coordinates directional overcurrent relays and distance relays, while the MPOA simulates a pelican mating strategy and includes a modified internal equation. The proposed APS is further upgraded with ADBMS to save system resources by storing relay settings in the database and calling them when the state of DGs changes without running optimization algorithms. The effectiveness of the proposed APS is validated on the Institute of Electrical and Electronics Engineers (IEEE) eight‐bus test system and the IEEE 14‐bus distribution network. Results indicate that the APS can effectively protect electrical networks in the presence of DGs, while the ADBMS upgrade saves system resources.

A Private and Efficient Triple-Entry Accounting Protocol on Bitcoin

The ‘Big Four’ accountancy firms dominate the auditing market, auditing almost all the Financial Times Stock Exchange (FTSE) 100 companies. This leads to people having to accept auditing results even if they may be poor quality and/or for inadequate purposes. In addition, accountants may provide different auditing results with the same financial data. These issues are hard for regulators such as the Financial Reporting Council to identify because of insufficient resources or inconsistent compliance. In this paper, we proposed a triple-entry accounting protocol to allow users to report Bitcoin transactions to a third-party auditor to comply with regulations such as the travel rule. It allows the auditor to easily detect anomalies and identify the non-compliant parties, whilst the blockchain itself provides a transparent and immutable record of these anomalies. Despite building on a public ledger, our solution preserves privacy and offers an interoperability layer for information exchange. Merkle proofs were used to record non-compliant transactions whilst allowing compliant transactions to be pruned from an auditor’s active database.

Navigating the Landscape: A Comprehensive Review of Current Virus Databases.

Viruses are abundant and diverse entities that have important roles in public health, ecology, and agriculture. The identification and surveillance of viruses rely on an understanding of their genome organization, sequences, and replication strategy. Despite technological advancements in sequencing methods, our current understanding of virus diversity remains incomplete, highlighting the need to explore undiscovered viruses. Virus databases play a crucial role in providing access to sequences, annotations and other metadata, and analysis tools for studying viruses. However, there has not been a comprehensive review of virus databases in the last five years. This study aimed to fill this gap by identifying 24 active virus databases and included an extensive evaluation of their content, functionality and compliance with the FAIR principles. In this study, we thoroughly assessed the search capabilities of five database catalogs, which serve as comprehensive repositories housing a diverse array of databases and offering essential metadata. Moreover, we conducted a comprehensive review of different types of errors, encompassing taxonomy, names, missing information, sequences, sequence orientation, and chimeric sequences, with the intention of empowering users to effectively tackle these challenges. We expect this review to aid users in selecting suitable virus databases and other resources, and to help databases in error management and improve their adherence to the FAIR principles. The databases listed here represent the current knowledge of viruses and will help aid users find databases of interest based on content, functionality, and scope. The use of virus databases is integral to gaining new insights into the biology, evolution, and transmission of viruses, and developing new strategies to manage virus outbreaks and preserve global health.

An objective criterion to evaluate sequence-similarity networks helps in dividing the protein family sequence space.

The deluge of genomic data raises various challenges for computational protein annotation. The definition of superfamilies, based on conserved folds, or of families, showing more recent homology signatures, allow a first categorization of the sequence space. However, for precise functional annotation or the identification of the unexplored parts within a family, a division into subfamilies is essential. As curators of an expert database, the Carbohydrate Active Enzymes database (CAZy), we began, more than 15 years ago, to manually define subfamilies based on phylogeny reconstruction. However, facing the increasing amount of sequence and functional data, we required more scalable and reproducible methods. The recently popularized sequence similarity networks (SSNs), allows to cope with very large families and computation of many subfamily schemes. Still, the choice of the optimal SSN subfamily scheme only relies on expert knowledge so far, without any data-driven guidance from within the network. In this study, we therefore decided to investigate several network properties to determine a criterion which can be used by curators to evaluate the quality of subfamily assignments. The performance of the closeness centrality criterion, a network property to indicate the connectedness within the network, shows high similarity to the decisions of expert curators from eight distinct protein families. Closeness centrality also suggests that in some cases multiple levels of subfamilies could be possible, depending on the granularity of the research question, while it indicates when no subfamily emerged in some family evolution. We finally used closeness centrality to create subfamilies in four families of the CAZy database, providing a finer functional annotation and highlighting subfamilies without biochemically characterized members for potential future discoveries.

Deep Learning of Quasar Lightcurves in the LSST Era

Deep learning techniques are required for the analysis of synoptic (multi-band and multi-epoch) light curves in massive data of quasars, as expected from the Vera C. Rubin Observatory Legacy Survey of Space and Time (LSST). In this follow-up study, we introduce an upgraded version of a conditional neural process (CNP) embedded in a multi-step approach for the analysis of large data of quasars in the LSST Active Galactic Nuclei Scientific Collaboration data challenge database. We present a case study of a stratified set of u-band light curves for 283 quasars with very low variability ∼0.03. In this sample, the CNP average mean square error is found to be ∼5% (∼0.5 mag). Interestingly, besides similar levels of variability, there are indications that individual light curves show flare-like features. According to the preliminary structure–function analysis, these occurrences may be associated with microlensing events with larger time scales of 5–10 years.

Spatial access to buprenorphine-waivered prescribers in the HEALing communities study: Enhanced 2-step floating catchment area analyses in Massachusetts, Ohio, and Kentucky

IntroductionThe opioid overdose epidemic continues to impact a large swath of the population in the US. Medications for opioid use disorders (MOUD) are an effective resource to combat the epidemic; however, there is limited research on MOUD treatment access that accounts for both supply of and demand for services. We aimed to examine access to buprenorphine prescribers in the HEALing Communities Study (HCS) Wave 2 communities in Massachusetts, Ohio, and Kentucky during 2021, and the association between buprenorphine access and opioid-related incidents, specifically fatal overdoses and opioid-related responses by emergency medical services (EMS). MethodsWe calculated Enhanced 2-Step Floating Catchment Area (E2SFCA) accessibility indices for each state, as well as Wave 2 communities in each state, based on the location of providers (buprenorphine-waivered clinicians from the US Drug Enforcement Agency Active Registrants database), population-weighted centroids at the census block group level, and catchment areas defined by the state or community's average commute time. In advance of intervention initiation, we quantified the opioid-related risk environment of communities. We assessed gaps in services by using bivariate Local Moran's I analysis, incorporating accessibility indices and opioid-related incident data. ResultsMassachusetts Wave 2 HCS communities had the highest rates of buprenorphine prescribers per 1000 patients (median: 165.8) compared to Kentucky (38.8) and Ohio (40.1). While urban centers in all three states had higher E2SFCA index scores compared to rural communities, we observed that suburban communities often had limited access. Through bivariate Local Moran's I analysis, we identified numerous locations with low buprenorphine access surrounded by high opioid-related incidents, particularly in communities that surrounded Boston, Massachusetts; Columbus, Ohio; and Louisville, Kentucky. ConclusionRural communities demonstrated a great need for additional access to buprenorphine prescribers. However, policymakers should also direct attention toward suburban communities that have experienced significant increases in opioid-related incidents.

New assessment of the probabilistic seismic hazard analysis for the greater Jakarta area, Indonesia

The greater Jakarta area is located in west Java and has a high earthquake risk due to the subduction of the Australian Plate beneath the Eurasian Plate. Previous hazard studies have been carried out using various seismic probability approaches. This study presents a new probabilistic seismic hazard analysis (PSHA) by developing an updated seismic model for the crustal active fault database, using a new set of ground motion prediction equations (GMPE), and taking into consideration the effect of site amplification. The logic tree method was used to quantify the epistemic uncertainty of the source parameter components and the attenuation equation was used. We calculate the peak ground acceleration (PGA) and spectral acceleration (SA) for West Java, including metropolitan Jakarta, Bogor and Serang, which have the greatest concentrations of population and business. We found that the mean PGA reaches 1.0 g or a 2% probability of exceedance in 50 years, including site amplification factors. The seismic hazard is dominated by the shallow crustal fault near metropolitan Jakarta. The result of this study may be useful for updating the existing Indonesian hazard map.