Structural Database Research Articles

Perancangan Sistem Informasi Peminjaman dan Pengembalian Berkas Rekam Medis Rawat Jalan dengan Metode Waterfall

Wiyung Sejahtera Hospital in recording the borrowing and returning of outpatient medical records still uses expedition books which are recorded manually. The research aims to design and develop an information system to facilitate the process of borrowing and returning outpatient medical record files using the Waterfall method approach. The Waterfall method was chosen because of its ability to divide system development into structured stages, starting from requirements analysis to maintenance. The needs analysis stage involves an in-depth study of existing processes and user needs. Next, system design is carried out by building a design plan that includes database structure, user interface design, and system workflow. System implementation is carried out by developing applications based on previous designs, while system testing is carried out thoroughly to ensure quality and performance before full implementation. The maintenance stage is carried out to ensure system operation and carry out continuous repairs and improvements. As a result, it is hoped that this system can improve the efficiency and quality of outpatient medical record file management and health services as a whole. The conclusion of this research is the successful design and development of a computer-based information system for borrowing and returning outpatient medical records at Wiyung Sejahtera Hospital using the waterfall method.

Enhancing Security in Industrial Application Development: Case Study on Self-Generating Artificial Intelligence Tools

The emergence of security vulnerabilities and risks in software development assisted by self-generated tools, particularly with regard to the generation of code that lacks due consideration of security measures, could have significant consequences for industry and its organizations. This manuscript aims to demonstrate how such self-generative vulnerabilities manifest in software programming, through a case study. To this end, this work undertakes a methodology that illustrates a practical example of vulnerability existing in the code generated using an AI model such as ChatGPT, showcasing the creation of a web application database, SQL queries, and PHP server-side. At the same time, the experimentation details a step-by-step SQL injection attack process, highlighting the hacker’s actions to exploit the vulnerability in the website’s database structure, through iterative testing and executing SQL commands to gain access to sensitive data. Recommendations on effective prevention strategies include training programs, error analysis, responsible attitude, integration of tools and audits in software development, and collaboration with third parties. As a result, this manuscript discusses compliance with regulatory frameworks such as GDPR and HIPAA, along with the adoption of standards such as ISO/IEC 27002 or ISA/IEC 62443, for industrial applications. Such measures lead to the conclusion that incorporating secure coding standards and guideline—from organizations such as OWASP and CERT training programs—further strengthens defenses against vulnerabilities introduced by AI-generated code and novice programming errors, ultimately improving overall security and regulatory compliance.

In silico structures, mass spectra and retention indices database development for purposes of chemical weapons convention

The Chemical Weapons Convention (CWC) is a science-based international treaty for the disarmament and non-proliferation of chemical weapons. However, reference Orgaization for prohibition of chemical weapons (OPCW) central analytical database (OCAD) of structures with mass spectra (MS) and retention indices (RI) includes only minor part of all possible chemical species defined in the Schedules of CWC. In this work we employed OCAD in silico augmentation based on chemoinformatics approach for chemical structures enumeration, MS data generation based on message passing neural network and based on P-alkyl molecular pairs RI prediction to support the verification activities as provided for in the CWC. Enumerated 879 noncyclic and 5270 monocyclic alcohols became the basis for generating hundreds of thousands molecules of Schedule 1 toxic chemicals like Sarin, Tabun, VX and Novichok. Trained on ordinary and neutral loss electron ionization mass spectrometry (EI-MS) a message-passing neural network (MPNN) outperformed other quantum chemistry and machine learning methods. Generated by this MPNN in silico EI-MS are very similar to the library's spectra and allowed to reach desired match factor above 800 within a scale of 0–1000. Statistical data for molecular pairs based on P-alkyl fragments was collected and used to predict RIs within desired 20 RI window for some toxic chemicals of Schedule 1.A.01, for which in the current OCAD version RIs are absent.

In – Silico Biological Evaluation of Antifungal Drugs - Molinspiration

The aim of this research work is to evaluate In – Silico Antifungal Drugs, in this work Molinspiration is used to provide predictive tools for essential molecular properties, such as lipophilicity, aqueous solubility and pKa, which are critical in drug discovery and cheminformatics. It operates based on a comprehensive database of chemical structures and employs algorithms to calculate these properties. Molinspiration is a renowned software and informatics company that plays a pivotal role in the pharmaceutical and biotechnology industries. With a primary focus on providing cutting-edge cheminformatics tools and software solutions, Molinspiration has significantly contributed to the field of drug discovery and medicinal chemistry. Molinspiration's software is an indispensable resource for the pharmaceutical and biotechnology sectors.

ОСОБЛИВОСТІ СТРУКТУРИ БАЗИ ДАНИХ ДЛЯ ЗБЕРЕЖЕННЯ РІЗНОТИПНОЇ ІНФОРМАЦІЇ В СИСТЕМАХ КОМПЛЕКСНОГО МОНІТОРИНГУ

Modern integrated monitoring systems of territories and objects, such as countries, regions, cities, districts, enterprises, or even natural resources, deal with a vast amount of diverse information. Indicators characterizing the state of these objects may differ fundamentally and have distinct components, specifics of data processing, and storage. This diversity poses a challenge for standardizing data under a single template, as it requires accommodating the peculiarities of each indicator. The creation of a unified database structure for such systems is a complex and extremely important aspect that can significantly enhance monitoring efficiency and productivity. This paper discusses the peculiarities of developing a database structure for complex monitoring systems of ecological, economic, energy, and social parameters of territories, where comprehensive analysis requires consideration of data from different fields, emphasizing the importance of creating a flexible database structure that can be easily modified. A vertical data storage principle is proposed for preserving heterogeneous information, which eliminates the problem of information redundancy and facilitates the development of a universal database structure. The proposed structure remains unchanged when adding new parameters, allowing various experts to work with the system and analyze the environmental state using different indicators, without requiring database restructuring or changes to the software modules utilizing it. A database structure for storing calculations and formulas employing the vertical data storage principle is developed and presented, aiming to increase data processing speed and reduce time spent on programming new mathematical tools and analysis. The described database structure is successfully utilized in a comprehensive eco-energetic-economic monitoring system.

DMXP: A De Novo Small-Molecule 3D Structure Predictor with Graph Attention Networks.

Generating the three-dimensional (3D) structure of small molecules is crucial in both structure- and ligand-based drug design. Structure-based drug design needs bioactive conformations of compounds for lead identification and optimization. Ligand-based drug design techniques, such as 3D shape similarity search, 3D pharmacophore model, 3D-QSAR, etc., all require high-quality small-molecule ligand conformations to obtain reliable results. Although predicting a small molecular bioactive conformer requires information from the receptor, a crystal structure of the molecule is a proper approximation to its bioactive conformer in a specific receptor because the binding pose of a small molecule in its receptor's binding pockets should be energetically close to the crystal structures. This study presents a de novo small molecular structure predictor (dMXP) with graph attention networks based on crystal data derived from the Cambridge Structural Database (CSD) combined with molecular electrostatic information calculated by density-functional theory (DFT). Two featuring strategies (topological and atomic partial change features) were employed to explore the relation between these features and the 3D crystal structure of a small molecule. These features were then assembled to construct the holistic 3D crystal structure of a molecule. Molecular graphs were encoded using a graph attention mechanism to deal with the issues of the inconsistencies of local substructures contributing to the entire molecular structure. The root-mean-square deviation (RMSDs) of approximately 80% dMXP predicted structures and the native binding poses within receptors are less than 2.0 Å.

Educational Web Portal Software for Teachers, Tutors and Students

This article substantiates the feasibility of using the Data-Driven approach in education and creating a "one-stop shop" platform. The paper describes the advantages and disadvantages of modern domestic and foreign ED Tech products, on the basis of which a conclusion is made about the necessary functionality of the designed platform. The article describes the software requirements for the UML design methodology, describes the choice of creation tools, and considers the program for implementing the tool system, including the database structure. It is shown that such a scheme is scalable and can be easily supplemented with other functionality. Based on the requirements, a project prototype was created, located at kuzovkin.info; the project consists of several parts, including a database with tasks, an online simulator, an online board, a voice messenger and articles with task theory. In addition, in the future, it is planned to use an adaptive learning algorithm using artificial intelligence. It is shown that this prototype is successfully used for teaching students. In the future, a web portal with similar tools is planned to be introduced into the work of online schools.

Can AlphaFold's breakthrough in protein structure help decode the fundamental principles of adaptive cellular immunity?

T cells are essential immune cells responsible for identifying and eliminating pathogens. Through interactions between their T-cell antigen receptors (TCRs) and antigens presented by major histocompatibility complex molecules (MHCs) or MHC-like molecules, T cells discriminate foreign and self peptides. Determining the fundamental principles that govern these interactions has important implications in numerous medical contexts. However, reconstructing a map between T cells and their antagonist antigens remains an open challenge for the field of immunology, and success of in silico reconstructions of this relationship has remained incremental. In this Perspective, we discuss the role that new state-of-the-art deep-learning models for predicting protein structure may play in resolving some of the unanswered questions the field faces linking TCR and peptide-MHC properties to T-cell specificity. We provide a comprehensive overview of structural databases and the evolution of predictive models, and highlight the breakthrough AlphaFold provided the field.

Halogen Bond via an Electrophilic π-Hole on Halogen in Molecules: Does It Exist?

This study reveals a new non-covalent interaction called a π-hole halogen bond, which is directional and potentially non-linear compared to its sister analog (σ-hole halogen bond). A π-hole is shown here to be observed on the surface of halogen in halogenated molecules, which can be tempered to display the aptness to form a π-hole halogen bond with a series of electron density-rich sites (Lewis bases) hosted individually by 32 other partner molecules. The [MP2/aug-cc-pVTZ] level characteristics of the π-hole halogen bonds in 33 binary complexes obtained from the charge density approaches (quantum theory of intramolecular atoms, molecular electrostatic surface potential, independent gradient model (IGM-δginter)), intermolecular geometries and energies, and second-order hyperconjugative charge transfer analyses are discussed, which are similar to other non-covalent interactions. That a π-hole can be observed on halogen in halogenated molecules is substantiated by experimentally reported crystals documented in the Cambridge Crystal Structure Database. The importance of the π-hole halogen bond in the design and growth of chemical systems in synthetic chemistry, crystallography, and crystal engineering is yet to be fully explicated.

Rancang Bangun Sistem Informasi Manajemen Asset Berbasis Web Dengan Metode Waterfall

This research is an effort to design and build a web-based Asset Management Information System (SIMA) by applying the Waterfall Method. SIMA is an important component in managing an organization's assets, including the efficient procurement, maintenance and monitoring of assets. The Waterfall method was chosen because it has a systematic and structured approach, starting from the needs analysis stage to the implementation and system maintenance stages. The aim of this research is to optimize the asset management process by integrating web technology so that it can provide real-time and efficient access to information. This is expected to have a positive impact on more effective and measurable asset management in various industrial sectors. This research will focus on the key steps in developing a web-based SIMA using the Waterfall Method. The first stage is requirements analysis, where the functional and non-functional requirements of SIMA will be identified in detail. Next, system design will be carried out based on the results of the analysis, including designing the user interface and database structure. The implementation phase will change the system design into program codes that can run, followed by the testing phase to ensure the quality and performance of the system. Finally, the system will be fully implemented and maintained according to needs and changes that occur. Thus, it is hoped that this research can make a significant contribution in increasing the efficiency and effectiveness of asset management through the use of appropriate and structured information technology..

Investigation of approaches to designing complex database structures in systems of integrated monitoring of environmental, economic, energy and social parameters of the territory

The object of research is the traditional and universal approach of designing the database structure in systems of integrated monitoring of ecological, economic, energy and social parameters of the territory, which include diverse data from various subject areas. In the course of the study, an analysis was performed based on a set of criteria such as scalability, ease of updating data, absence of empty fields, volume of the database, number of tables and fields, ease and speed of execution of requests for a sample set of indicators of the research object. The comparison of these approaches took place on the example of water resources monitoring, since it has several subsystems and a large number of indicators that are used for assessment. It is established that the proposed universal approach to designing complex database structures made it possible to reduce the volume of the database by 2.25 times due to the absence of empty fields. In particular, in the considered example, the filling factor of the database with the traditional approach is 1.75 times less than with the proposed universal approach. It should be noted that the rate of table filling for the traditional design approach can vary depending on the number of indicator values, while the table filling rate for the universal approach is always close to 100 %. Also, the proposed database design approach makes it possible to speed up data loading and processing. For example, with the same volume of significant information, the minimum speed of sampling the characteristics of one research object is 3.87 times greater in a database developed according to the principles of the universal approach than according to the rules of the traditional approach. The proposed structure of the database is successfully used in the system of complex eco-energy-economic monitoring. The developed structure of the database can serve as an effective basis for the formation of an electronic data bank at the level of the enterprise, region and country.

Symmetry classification of 2D materials: layer groups versus space groups

The symmetry of a crystal structure with a three-dimensional (3D) lattice can be classified by one of the 230 space group types. For some types of crystals, e.g. crystalline films, surfaces, or planar interfaces, it is more appropriate to assume a two-dimensional (2D) lattice. With this assumption the structure can be classified by one of the 80 layer group types. We have implemented an algorithm to determine the layer group type of a 3D structure with a 2D lattice, and applied it to more than 15 000 monolayer structures in the Computational 2D Materials Database (C2DB). We compare the classification of monolayers by layer groups and space groups, respectively. The latter is defined as the space group of the 3D bulk structure obtained by repeating the monolayer periodically in the direction perpendicular to the 2D lattice (AA-stacking). By this correspondence, nine pairs of layer group types are mapped to the same space group type due to the inability of the space group to distinguish the in-plane and out-of-plane axes. In total 18% of the monolayers in the C2DB belong to one of these layer group pairs and are thus not properly classified by the space group type. Our results show that symmetry classification of 2D materials should be based on layer groups rather than the commonly used space groups.

Time-series analysis of rhenium(I) organometallic covalent binding to a model protein for drug development.

Metal-based complexes with their unique chemical properties, including multiple oxidation states, radio-nuclear capabilities and various coordination geometries yield value as potential pharmaceuticals. Understanding the interactions between metals and biological systems will prove key for site-specific coordination of new metal-based lead compounds. This study merges the concepts of target coordination with fragment-based drug methodologies, supported by varying the anomalous scattering of rhenium along with infrared spectroscopy, and has identified rhenium metal sites bound covalently with two amino acid types within the model protein. A time-based series of lysozyme-rhenium-imidazole (HEWL-Re-Imi) crystals was analysed systematically over a span of 38 weeks. The main rhenium covalent coordination is observed at His15, Asp101 and Asp119. Weak (i.e. noncovalent) interactions are observed at other aspartic, asparagine, proline, tyrosine and tryptophan side chains. Detailed bond distance comparisons, including precision estimates, are reported, utilizing the diffraction precision index supplemented with small-molecule data from the Cambridge Structural Database. Key findings include changes in the protein structure induced at the rhenium metal binding site, not observed in similar metal-free structures. The binding sites are typically found along the solvent-channel-accessible protein surface. The three primary covalent metal binding sites are consistent throughout the time series, whereas binding to neighbouring amino acid residues changes through the time series. Co-crystallization was used, consistently yielding crystals four days after setup. After crystal formation, soaking of the compound into the crystal over 38 weeks is continued and explains these structural adjustments. It is the covalent bond stability at the three sites, their proximity to the solvent channel and the movement of residues to accommodate the metal that are important, and may prove useful for future radiopharmaceutical development including target modification.

An AluYa5 Insertion in the 3′UTR of COL4A1 and Cerebral Small Vessel Disease

Cerebral small vessel diseases (CSVDs) account for one-fifth of stroke cases. Numerous familial cases remain unresolved after routine screening of known CSVD genes. To identify novel genes and mechanisms associated with familial CSVD. This 2-stage study involved linkage analysis and a case-control study; linkage analysis and whole exome and genome sequencing were used to identify candidate gene variants in 2 large families with CSVD (9 patients with CSVD). Then, a case-control analysis was conducted on 246 unrelated probands, including probands from these 2 families and 244 additional probands. All probands (clinical onset <age 55 years and ≥1 first-degree relative with CSVD) were referred to the French cerebrovascular referral center between 2013 and 2023. The large-scale gnomAD structural variant database and 467 healthy individuals of French ancestry were used as a control group. A pathogenic AluYa5 insertion was identified within the COL4A1 3'UTR in the 2 large families with CSVD. Reverse transcriptase-quantitative polymerase chain reaction (RT-qPCR), Western blot, and long-read RNA sequencing were used to investigate outcomes associated with the insertion using patient fibroblasts. Clinical and magnetic resonance imaging features of probands with variants and available relatives were assessed. Among 246 probands (141 females [57.3%]; median [IQR] age at referral, 56 [49-64] years), 7 patients of French ancestry carried the insertion. This insertion was absent in 467 healthy French individuals in a control group (odds ratio, ∞; 95% CI, 2.78 to ∞; P = 5 × 10-4) and 10 847 individuals from the gnomAD structural variant database (odds ratio, ∞; 95% CI, 64.77 to ∞; P = 2.42 × 10-12). In these 7 patients' families, 19 family members with CSVD carried the insertion. RT-qPCR and Western blot showed an upregulation of COL4A1 mRNA (10.6-fold increase; 95% CI, 1.4-fold to 17.1-fold increase) and protein levels (2.8-fold increase; 95% CI, 2.1-fold to 3.5-fold increase) in patient vs control group fibroblasts. Long-read RNA sequencing data showed that the insertion was associated with perturbation in the use of canonical COL4A1 polyadenylation signals (approximately 87% of isoforms transcribed from the wild type allele vs 5% of isoforms transcribed from the allele with the insertion used the 2 distal canonical polyadenylation signals). The main clinical feature of individuals with CSVD was the recurrence of pontine ischemic lesions starting at an early age (17 of 19 patients [89.5%]). This study found a novel mechanism associated with COL4A1 upregulation and a highly penetrant adult-onset CSVD. These findings suggest that quantitative alterations of the cerebrovascular matrisome are associated with CSVD pathogenesis, with diagnostic and therapeutic implications.

Material Property Prediction Using Graphs Based on Generically Complete Isometry Invariants

The structure–property hypothesis says that the properties of all materials are determined by an underlying crystal structure. The main obstacle was the ambiguity of conventional crystal representations based on incomplete or discontinuous descriptors that allow false negatives or false positives. This ambiguity was resolved by the ultra-fast pointwise distance distribution, which distinguished all periodic structures in the world’s largest collection of real materials (Cambridge structural database). State-of-the-art results in property prediction were previously achieved by graph neural networks based on various graph representations of periodic crystals, including the Crystal Graph with vertices at all atoms in a crystal unit cell. This work adapts the pointwise distance distribution for a simpler graph whose vertex set is not larger than the asymmetric unit of a crystal structure. The new Distribution Graph reduces mean absolute error by 0.6–12% while having 44–88% of the number of vertices when compared to the Crystal Graph when applied on the Materials Project and Jarvis-DFT datasets using CGCNN and ALIGNN. Methods for hyper-parameters selection for the graph are backed by the theoretical results of the pointwise distance distribution and are then experimentally justified.

DEVELOPMENT OF A DATABASE CONCEPT FOR DIGITALISING THE EXPERIENCE OF BUILDINGS AND STRUCTURES OPERATING

Problem statement. These days, the main method of monitoring the buildings and structures state is through periodic technical state assessment and monitoring. This is an important practice that guarantees the reliability and safety of the operation of buildings and structures, helping to identify and establish the obvious and possible causes of defects and damages. However, the current practice of storing the results of surveys and monitoring is often limited to records in paper reports, which makes it difficult to analyse over time. Thus, there is a need to create a digital information system designed to record and store the results of monitoring of buildings and structures. This will make the data accessible and organised for specialists, simplifying analysis and ensuring their effective use for decision-making. Such a system will significantly improve the safety and efficiency of buildings and structures management. The purpose of the article is the development of a database architecture for the digitalisation of information related to the inspection and monitoring of the technical state of buildings and structures. Conclusions. The developed database structure will allow storing information about buildings, their owners, location, structures, defects and damage identified during visual and instrumental inspections, as well as organisational and technical measures aimed at bringing structures back to normal technical state or reducing the impact of negative factors. This will contribute to more efficient management and help maintain the property in good working order, reducing the probability of emergency situations.

Does the Central Nitrogen Atom Make a Difference? A Comparison of Non‐Coordinating Pyridine and Benzene Spacers in Multitopic Ligands

AbstractIn metal coordination compounds of the divergent ligands 4,2′:6′,4“‐terpyridine and 3,2′:6′,3”‐terpyridine and their 4′‐functionalized derivatives, the central pyridine ring of the 4,2′:6′,4“‐terpyridine and 3,2′:6′,3”‐terpyridine domains is non‐coordinated. We present an overview of data from the Cambridge Structural Database to assess whether there are structural similarities between the coordination compounds of 4,2′:6′,4“‐tpy and 1,3‐di(pyridin‐4‐yl)benzene, and between 3,2′:6′,3”‐tpy and 1,3‐di(pyridin‐3‐yl)benzene. Based upon structurally characterized compounds, it emerges that the coordination chemistry of ligands including one or more 4,2′:6′,4“‐terpyridine or 3,2′:6′,3”‐terpyridine metal‐binding domains is more abundantly exemplified than that of corresponding ligands based upon 1,3‐di(pyridin‐4‐yl)benzene and 1,3‐di(pyridin‐3‐yl)benzene. We provide an overview of metallamacrocycles and cages, 1D‐coordination polymers and 2D‐ and 3D‐networks.

Koncepcja ujednolicenia wzajemnie niekompatybilnych modeli informacyjnych oraz danych przechowywanych w relacyjnych bazach danych zarządców dróg

Road Administrations (RAs) implement Building Information Modelling (BIM) through pilot projects developed for new or reconstructed structures. Each model is processed with respect to BIM standards and practices valid at the time of its creation. Consequently, models are incompatible and cannot be interconnected to create a combined model of the managed network or even its selected parts. Existing structures are often not included in the BIM effort until some major repair is planned. In addition, RAs usually store data on fixed and variable parameters of structures in relational databases. This results in a situation in which a relatively small number of structures are included in mutually incompatible models and data regarding the majority of structures is contained in relational databases. It creates a heterogeneous data environment for RAs. The goals of the paper are as follows: to analyse the described problem, to propose a method of model unification models, a method of creation of simplified compatible information models using data on existing structures stored in relational databases and a method of storing data at the level of the managed network, to support RA asset management systems which can be treated as a dynamic part of BIM.

Synthesis of new analogs of N-substituted(benzoylamino)-1,2,3,6-tetrahydropyridines

Abstract The tetrahydropyridine (THP) moiety is notably present in synthetic and natural products, playing a cardinal role in the food, cosmetic, and pharmaceutical industries. The THP structure is an instrumental constituent and is widely found in alkaloids that have therapeutic properties against inflammation, cancer, the nervous system, and bacterial infections. The use of THPs has gained traction, so it is imperative to increase the structural database through the synthesis of THP derivatives. The focus of this study is to make structural modifications to the benzene ring portion of the lead compound while keeping the pyridine ring constant. Eleven novel THP analogs were synthesized using a four-step synthetic approach involving partial reduction of N-substituted ylides into 1,2,3,6-THPs. The results illustrate that 11 THPs were successfully synthesized in low to moderate yields. Flash chromatography was utilized for purification. Proton nuclear magnetic resonance, deuterium oxide exchange, carbon nuclear magnetic resonance, infrared spectroscopy, and CHN elemental analysis were utilized to characterize the THP analogs. This study aids in contributing knowledge to the THP database.

MEDI ASSIST PORTAL

Service institutions are considered one of the most important institutions in our time, and they have become a great place in our lives The health institutions are considered the most important, because they provide many types of required health services and related to the safety of the health of individuals, and through cooperation between the academic study and the health sector. This research paper presented a proposal Medical assist portal system project is primarily focused on managing medical-related records within a hospital. More precisely, this system helps track medical reports. The system also shows all available employees and patients. more ever, the system can total inventory and pharmacy records, this system containing of two major sections: database structure, and GUI frames (created in PHP, HTML, and CSS). The database constructed with MYSQL and the GUI frame make it easier for novitiate users to utilize the suggested system. at the latest this paper describes a hospital system that can be used to manage and analyses hospital information related to patients, treatments, and appointments. The practical implications of this system are: It can help hospitals to manage their operations more easily by providing a centralized system for managing patient info, treat records, The system can be of assistance hospital administrators to make data-driven decisions by providing them with real-time information about hospital operations, and improve patient care by providing doctors with easy and user friendly access to patient information and treatment records, The system can be beneficial to reduce errors and improve accuracy by automating many of the manual processes involved in managing hospital information. Overall, the MH described in this paper has the ability to increase efficiency, accuracy, and quality of hospital operations, which can ultimately lead to better patient outcomes. Keywords: hospital system, pharmacy, health, patient