Areas Of Science Research Articles

Revealing Missing Protein–Ligand Interactions Using AlphaFold Predictions

Protein–ligand interactions represent an essential step to understand the bases of molecular recognition, an intense field of research in many scientific areas. Structural biology has played a central role in unveiling protein–ligand interactions, but current techniques are still not able to reliably describe the interactions of ligands with highly flexible regions. In this work, we explored the capacity of AlphaFold2 (AF2) to estimate the presence of interactions between ligands and residues belonging to disordered regions. As these interactions are missing in the crystallographic-derived structures, we called them “ghost interactions”. Using a set of protein structures experimentally obtained after AF2 was trained, we found that the obtained models are good predictors of regions associated with order–disorder transitions. Additionally, we found that AF2 predicts residues making ghost interactions with ligands, which are mostly buried and show differential evolutionary conservation with the rest of the residues located in the flexible region. Our findings could fuel current areas of research that consider, given their biological relevance and their involvement in diseases, intrinsically disordered proteins as potentially valuable targets for drug development.

New Integral Transforms of the Extended k- Generalized Mittag-Leffler Function with Graphical Representations

Different integral transforms have extensive applications in the various areas of science and engineering. Some of the new integral transforms of extended k-generalized Mittag-Leffler function are discussed in this paper. We examine integral transforms such as the Euler-Beta, Laplace, Mohand, Aboodh, SEE, and Sadik transform. Moreover, we also tried to establish the graphical representations of these transforms.

Educational Data Mining: A Foundational Overview

Educational data mining (EDM) is a novel scientific area that focuses on developing and applying methods to analyze datasets generated within educational settings. This paper outlines the evolution, significance, and applications of EDM. With the increasing popularity of e-learning in web-based educational systems, EDM has expanded to include a variety of analytical methods and data sources. Some key methodologies addressed include classification, regression analysis, clustering techniques, association rule mining, and Natural Language Processing, among others. Additionally, this paper looks at how EDM can facilitate data-driven decision-making among other areas such as curriculum development and customization of learners’ experiences. It also touches on issues related to the challenges of the scientific field. Finally, some projections about EDM’s future trends are made, especially concerning its integration into AI technologies and development trends like augmented reality or virtual reality, which imply greater possibilities for changes than any other series witnessed before within this sphere.

Neurology and Neurosurgery as Reflected by A Number of Collectible Means

This research article examines the results of the study conducted by its author on the representation of phaleristics and numismatic materials, in all their diversity, dedicated to both neurology and neurosurgery and their heroes, practitioners and scientists-specialists in these areas of medical science. All illustrative materials presented in this article are presented in the form of their screenshot copies, supplied with short explanatory comments to them.

AI- and LLM-driven search tools: A paradigm shift in information access for education and research

The article reports on an exploratory study that assesses the results produced by emerging artificial intelligence (AI)- and large language model-driven search tools in response to a series of queries and prompts based on four scenarios of information-intensive tasks of university students and researchers. Sixteen questions and prompts were created based on four scenarios of information-intensive tasks of university students. Each of these questions and prompts was presented to six AI-driven search tools, and the results were manually checked to assess their suitability for specific user needs and contexts. Based on the findings, it was argued that while the AI-driven tools bring a paradigm shift in information access for education and research, outputs generated by these tools vary quite significantly. Choice of the right tool, framing the question and further prompting play a key role. Also, users need to scrutinise each output to check their quality and reliability in the context of the specific search tasks. It was concluded that further research is needed involving different user groups, scenarios and search tasks and different AI-driven search tools. Implications of the use of AI-driven search tools for libraries and scholarly databases, as well as for research and scholarship in different areas of information science, are discussed.

Evaluation and risk assessment of heavy metals in wetland soil in the University of Lagos

A study was conducted to evaluate the concentration of heavy metals, and the physicochemical and microbiological properties of wetland soils at the University of Lagos. Soil samples were randomly collected from the Faculty of Science (FSC), Lagoon Front, and Distance Learning Institute areas at depths of 5 cm, 10 cm, 15 cm, and 20 cm using a soil auger. The samples were stored in sterile nylon bags, appropriately labelled, and transported to the University of Lagos Central Research Laboratory for chemical analysis. The physicochemical characteristics measured included soil pH, determined using a pH meter, and moisture content, assessed through the oven-drying method. Heavy metal concentrations were analyzed using an Atomic Absorption Spectrophotometer. Microbial population diversity was examined using the disc diffusion method. Statistical analysis was performed using SPSS version 20, and mean values were evaluated using Tukey’s multiple comparison test at a probability level of P < 0.05. The results revealed that soil pH ranged from 7.20 to 8.81, with the highest value (8.81) recorded near the Faculty of Science (FSC-3). Eight heavy metals, including Pb, Ni, Cr, Cd, Fe, Cu, Mn, and Zn, were analyzed. Lead concentrations ranged from 0.02 to 0.29 ppm, followed by nickel, which ranged from 0.01 to 0.13 ppm. Chromium ranged from 0.0 to 0.25 ppm, cadmium from 0.03 to 0.08 ppm, iron from 1.02 to 2.96 ppm, copper from 3.31 to 4.60 ppm, manganese from 3.31 to 5.16 ppm, and zinc from 1.67 to 9.17 ppm. Lead and zinc concentrations were found to be below the permissible limit at all locations, while chromium and cadmium were within permissible limits. However, Zn, Mn, Cu, Fe, and Ni exceeded the permissible limits. Correlation analysis revealed a significant correlation (P < 0.05) between Pb and Zn, likely due to effluents from human waste and seepage from nearby dumpsites into the lagoon, streams, or beaches. The isolated microbial flora included three bacterial genera, Bacillus megaterium, Bacillus spp, and Enterobacter spp, as well as four fungal genera, Aspergillus, Penicillium, Aspergillus flavus, and Fusarium. Bacterial counts were lower than fungal counts in polluted soils, likely due to the nutrient status of the soil. The isolates were found to be tolerant to slightly alkaline pH and heavy metal pollutants, with microbial variation attributed to the impact of pH and heavy metals on the microbial population.

Quantum Fundamentalism and Theological Liberty

Quantum mechanics (QM) is astonishingly successful as a theoretical framework, underpinning countless scientific areas and providing the impetus behind entire technologies. Many scientists suspect that physical reality is fundamentally quantum in nature, even if we perceive little of this in our everyday human experience. This is the viewpoint of “quantum fundamentalism.” Yet, the conceptual implications of QM defy common sense, to such an extent that popular culture largely perceives of QM as a source of counterintuitive weirdness. At the same time, bestselling self-help manuals portray QM as a source of hidden healing power within, while spiritual readings invoke QM as a bridge to the divine, or as a source of theological analogies. Scientists often denounce these mystical approaches as “quantum quackery,” but I examine their serious side. I argue that, for quantum fundamentalism to function as a worldview, it should inform a sense of human purpose, something for which theological analysis is well equipped.

RadicalPy: A Tool for Spin Dynamics Simulations.

Radical pairs (electron-hole pairs, polaron pairs) are transient reaction intermediates that are found and exploited in all areas of science, from the hard realm of physics in the form of organic semiconductors, spintronics, quantum computing, and solar cells to the soft domain of chemistry and biology under the guise of chemical reactions in solution, biomimetic systems, and quantum biology. Quantitative analysis of radical pair phenomena has historically been successful by a few select groups. With this in mind, we present an intuitive open-source framework in the Python programming language that provides classical, semiclassical, and quantum simulation methodologies. A radical pair kinetic rate equation solver, Monte Carlo-based spin dephasing rate estimations, and molecule database functionalities are implemented. We introduce the kine-quantum method, a new approach that amalgamates classical rate equations, semiclassical, and quantum techniques. This method resolves the prohibitively large memory requirement issues of quantum approaches while achieving higher accuracy, and it also offers wavelength-resolved simulations, producing time- and wavelength-resolved magnetic field effect simulations. Model examples illustrate the versatility and ease of use of the software, including the new approach applied to the magnetosensitive absorption and fluorescence of flavin adenine dinucleotide photochemistry, spin-spin interaction estimation from molecular dynamics simulations on radical pairs inside reverse micelles, radical pair anisotropy inside proteins, and triplet exciton pairs in anthracene crystals. The intuitive interface also allows this software to be used as a teaching or learning aid for those interested in the field of spin chemistry. Furthermore, the software aims to be modular and extensible, with the aim to standardize how spin dynamics simulations are performed.

Applications of Graphene Materials in Optoelectronic Devices

Graphene is a groundbreaking material at the forefront of material science and nanotechnology area. Graphene exhibit special qualities, including great mechanical strength, strong electrical conductivity and thermal conductivity. Consequently, the optical property of graphene is focused in this work. The excellent optical properties of graphene make it a good candidate material for optoelectronic devices. In recent years, a great deal of research has been conducted on the use of graphene for optoelectronic devices. Therefore, conducting research in this field is of great significance. In this work, researches are analyzed and studied to gain new insights into this area. In addition, a summary of the prevalent synthesis methods utilized for the production of graphene is provided, accompanied by a detailed examination of the merits and demerits associated with each technique. Finally, the applications of graphene materials in optoelectronic devices are discussed in depth to further understand the development status of graphene materials. This work seeks to generate new ideas and directions for the future development of optoelectronic technology.

Commentary Innovations in Tissue Regeneration and Wound Healing: A Comparative Study of Nigeria and South Africa

Tissue regeneration and wound healing represent critical areas in medical science, with significant advance-ments in recent years. These fields involve restoring damaged tissues and promoting recovery, which are essential for improv-ing patient outcomes and quality of life. Innovations such as biomaterials, stem cell therapy, advanced wound dressings, and regenerative medicine have significantly impacted these areas. This study provides a comparative analysis of innovations in tissue regeneration and wound healing in Nigeria and South Africa. The focus includes technological advancements, research contributions, and statistical data to highlight progress and challenges in both countries. Data from various healthcare institu-tions, research publications, and government reports form the basis of this analysis.Additionally, surgical innovations that minimize wound occurrence and improve wound healing, such as mini-mally invasive surgery, negative pressure wound therapy (NPWT), and the use of advanced suture materials, are transforming clinical outcomes in both Nigeria and South Africa. Minimally invasive techniques reduce tissue damage, leading to smaller wounds and faster recovery. NPWT has proven effective in managing chronic wounds and reducing infection rates, while an-timicrobial and absorbable sutures have lowered complications related to wound closure. Cold plasma therapy and stem cell applications are also emerging as promising approaches for chronic wound care and tissue regeneration. These innovations, coupled with the efforts in regenerative medicine and biomaterials, are providing both nations with effective tools to manage wound healing more efficiently. This comparative study aims to shed light on the current state of tissue regeneration and wound healing in these nations, offering insights into the advancements made, the effectiveness of various approaches, and the potential future devel-opments in this vital medical field.

Unveiling pharmacogenomics: insights from Portuguese pharmacists on quaternary prevention

Abstract Background Public health genomics recognises the potential of genomic knowledge for enhancing population health. Adverse drug reactions (ADR) and lack of efficacy have significant clinical and economic burdens, which can be mitigated by pharmacogenomics (PGx) testing. Pharmacists can play a vital role in facilitating the implementation of PGx into routine clinical care. This will promote quaternary prevention, to protect individuals from medical intervention that can cause more harm than good. Objectives To assess attitudes, opinions, expectations, practices, and concerns of Portuguese pharmacists regarding PGx implementation. Methods An observational cross-sectional web-based survey was developed based on literature review, adapted to the national context, and validated in a focus group. The target population were adults residing in Portugal with a degree in Pharmaceutical Sciences or equivalent, with convenience sampling. Descriptive statistics were performed. Results From 303 participants, 98% believe that PGx is an important area of pharmaceutical sciences and 97% indicate that PGx should be included in continuing education. Almost all (99%) anticipate that PGx implementation will prevent the administration of ineffective drugs and inappropriate doses, 98% expect PGx will reduce ADR. Major concerns are related with direct-to-consumer sale of PGx tests via internet (78%) and unauthorized access to test results (91%). Currently, 25% are familiar with reliable sources of information on PGx, but only 11% feel qualified to recommend PGx testing, and 10% have analysed PGx reports. Conclusions There are positive opinions and expectations regarding the potential benefits of PGx tests. However, there are regulatory concerns and lack of readiness for immediate application. Pharmacists express interest in learning more about PGx, highlighting the need for continuous education and training to integrate it effectively into routine pharmaceutical practice. Key messages • Pharmacists recognize the benefits of PGx implementation for quaternary prevention. • Regulatory concerns and readiness gaps in PGx emphasise a need for training and life-long education of pharmacists.

Analysis of Historical Federal R&D Priorities: The OMB-OSTP Memorandum and the R&D Section of the Analytical Perspectives in the President's Budget

Each year, the directors of the White House Office of Science and Technology Policy (OSTP) and the Office of Management and Budget (OMB) jointly produce a memorandum of research and development priorities and how those priorities align with the fiscal year budget. This memo guides the actions of executive branch departments and agencies towards the administration’s science and technology priorities. By presenting these priorities yearly, these memoranda serve as a record of the science and technology priorities of respective Presidential administrations and, in turn, can reflect a changing science and technology policy landscape over the duration of several Presidential terms. This paper assesses how science and technology policy priorities, as established in these memoranda, are reflected in the Presidential budget within and across administrations. Additionally, this paper compares and analyzes priority topic areas from the OMB/OSTP memos with another representation of science and technology areas of emphasis: the research and development (R&D) section of the Analytical Perspectives in the President’s budget. The Analytical Perspectives document highlights items from the Presidential budget requests. This paper discerns the extent to which these two sources of priority-setting become aligned in order to identify trends in which science and technology topics are prioritized by the White House across time and administration. This study addresses two core research questions: 1) How do science and technology priorities change over time, both across and/or within Presidential administrations?; and 2) To what extent, if any, are the ideas in the OMB/OSTP science and technology priorities memoranda and the Analytical Perspectives documents aligned?

Stem Cells Treatment for Subarachnoid Hemorrhage.

Subarachnoid hemorrhage (SAH) refers to bleeding in the subarachnoid space, which is a serious neurologic emergency. However, the treatment effects of SAH are limited. In recent years, stem cell (SC) therapy has gradually become a very promising therapeutic method and advanced scientific research area for SAH. The SCs used for SAH treatment are mainly bone marrow mesenchymal stem cells (BMSCs), umbilical cord mesenchymal stem cells (hUC-MSCs), dental pulp stem cells (DPSCs), neural stem cells (NSCs)/neural progenitor cell (NPC), and endothelial progenitor cell (EPC). The mechanisms mainly included differentiation and migration of SCs for tissue repair; alleviating neuronal apoptosis; anti-inflammatory effects; and blood-brain barrier (BBB) protection. The dosage of SCs was generally 106 orders of magnitude. The administration methods included intravenous injection, nasal, occipital foramen magnum, and intraventricular administration. The administration time is generally 1 hour after SAH modeling, but it may be as late as 24 hours or 6 days. Existing studies have confirmed the neuroprotective effect of SCs in the treatment of SAH. SC has great potential application value in SAH treatment, a few case reports have provided support for this. However, the relevant research is still insufficient and there is still a lack of clinical research on the SC treatment for SAH to further evaluate the effectiveness and safety before it can go from experiment to clinical application.

Two-Staged Technology for CoCr Stent Production by SLM.

Additive manufacturing of porous materials with a specific macrostructure and tunable mechanical properties is a state-of-the-art area of material science. Additive technologies are widely used in industry due to numerous advantages, including automation, reproducibility, and freedom of design. Selective laser melting (SLM) is one of the advanced techniques among 3D fabrication methods. It is widely used to produce various medical implants and devices including stents. It should be noticed that there is a lack of information on its application in stent production. The paper presents the technological aspects of CoCr stent SLM fabrication, including design of stents and development of regimes for their manufacturing. Physical, chemical, and technological properties of CoCr powder were initially determined. Parametric design of mesh stent models was adopted. A two-stage approach was developed to ensure dimensional accuracy and quality of stents. The first stage involves a development of the single-track fusion process. The second stage includes the stent manufacturing according to determined technological regimes. The single-track fusion process was simulated to assign laser synthesis parameters for stent fabrication. Melting bath temperature and laser regimes providing such conditions were determined. Twenty-seven SLM manufacturing regimes were realized. Dependence of single-tracks width and height on the laser power, exposition time, and point distance was revealed. The qualitative characteristics of tracks imitating the geometry of the stent struts as well as favorable and unfavorable fusion regimes were determined. The results of surface roughness regulating of the stents' structural elements by various methods were analyzed. Thus, this two-staged approach can be considered as a fundamental approach for CoCr stent SLM fabrication.

A Trans-Theoretical Systematization of Clinical Interventions Based on Dynamical Systems Research (DSR)

The scientific literature focused on the categorization of therapists’ interventions in clinical sessions, and their effects on patients, is not very extensive and often autoreferential. The most relevant findings clearly show the eclecticism of clinicians, grounding only 10–14% of their interventions on the specific theoretical approach to which they belong. Despite that, a trans-theoretical systematization of clinical interventions is lacking. The present work aims to verify the feasibility of a trans-theoretical categorization of clinical interventions based on Dynamical Systems Research in psychotherapy (DSR). For this purpose, the authors present the results of three literature reviews. The first sections of this paper present the literature on the historical development of clinical interventions within the psychodynamic and cognitive-behavioral approaches. In the fourth section, the review of the DSR literature in psychotherapy and the systematization of clinical interventions according to such a unifying framework are introduced. Clinical interventions can be aimed at increasing the patient’s stability and flexibility, with the final objective of promoting H-L Synchronization and S-F Oscillations. The connections between the DSR-based categorization and the literature pertaining to the psychodynamic and cognitive-behavioral approaches are highlighted. Finally, in the conclusions, the limitations and potential developments of this scientific area are discussed.

The development and applications of multidimensional biomolecular spectroscopy illustrated by photosynthetic light harvesting.

The parallel and synergistic developments of atomic resolution structural information, new spectroscopic methods, their underpinning formalism, and the application of sophisticated theoretical methods have led to a step function change in our understanding of photosynthetic light harvesting, the process by which photosynthetic organisms collect solar energy and supply it to their reaction centers to initiate the chemistry of photosynthesis. The new spectroscopic methods, in particular multidimensional spectroscopies, have enabled a transition from recording rates of processes to focusing on mechanism. We discuss two ultrafast spectroscopies - two-dimensional electronic spectroscopy and two-dimensional electronic-vibrational spectroscopy - and illustrate their development through the lens of photosynthetic light harvesting. Both spectroscopies provide enhanced spectral resolution and, in different ways, reveal pathways of energy flow and coherent oscillations which relate to the quantum mechanical mixing of, for example, electronic excitations (excitons) and nuclear motions. The new types of information present in these spectra provoked the application of sophisticated quantum dynamical theories to describe the temporal evolution of the spectra and provide new questions for experimental investigation. While multidimensional spectroscopies have applications in many other areas of science, we feel that the investigation of photosynthetic light harvesting has had the largest influence on the development of spectroscopic and theoretical methods for the study of quantum dynamics in biology, hence the focus of this review. We conclude with key questions for the next decade of this review.

POSSIBILITIES OF SYNTHESIS OF UNCHARGED STABLE LATEX PARTICLES FOR IMMUNOANALYSIS

Objective: The objective of this study is to find a method for synthesizing uncharged polystyrene latex particles whose surface can be easily modified. Theoretical basis: The main method of latex synthesis is emulsion polymerization. Latexes for a specific purpose can be obtained by polymerization in heterogeneous monomer-water systems, without the use of emulsifiers, both with intensive mixing of the system and under static conditions. In this work, polymerization was carried out without the use of emulsifiers in a static monomer-water system. Method: To achieve the set goal, the possibility of obtaining latex particles using a hydrophobic initiator - ditrile of azoisobutyric acid - was investigated by carrying out polymerization in a diffusion mode in a three-phase system monomer - water - initiator. Results and discussion: The results of the study showed that the latex obtained in the three-phase system is stable. It is assumed that the stability is due to the presence of hydroxyl end groups groups of polymer molecules on the surface of the latex particles, which are formed as a result of the reaction of the initiator with water and initiate polymerization. The synthesized latexes retained stability for a year. Practical value: Latexes can be used in all those areas of science and technology where the absence of a charge on the surface of latex particles is required. Originality/value: The originality of the work lies in the fundamental simplicity of the synthesis and the unambiguity of the results obtained.

The extended Adomian decomposition method and its application to the rotating shallow water system for the numerical pulsrodon solutions

The rotating shallow water system is an important physical model, which has been widely used in many scientific areas, such as fluids, hydrodynamics, geophysics, oceanic and atmospheric dynamics. In this paper, we extend the application of the Adomian decomposition method from the single equation to the coupled system to investigate the numerical solutions of the rotating shallow water system with an underlying circular paraboloidal basin. By introducing some special initial values, we obtain interesting approximate pulsrodon solutions corresponding to pulsating elliptic warm-core rings, which take the form of realistic series solutions. Numerical results reveal that the numerical pulsrodon solutions can quickly converge to the exact solutions derived by Rogers and An, which fully shows the efficiency and accuracy of the proposed method. Note that the method proposed can be effectively used to construct numerical solutions of many nonlinear mathematical physics equations. The results obtained provide some potential theoretical guidance for experts to study the related phenomena in geography, oceanic and atmospheric science.

Statistical monitoring applied to data science in classification: continuous validation in predictive models

PurposeThis study aims to analyze the performance of quality indices to continuously validate a predictive model focused on the control chart classification.Design/methodology/approachThe research method used analytical statistical methods to propose a classification model. The project science research concepts were integrated with the statistical process monitoring (SPM) concepts using the modeling methods applied in the data science (DS) area. For the integration development, SPM Phases I and II were associated, generating models with a structured data analysis process, creating a continuous validation approach.FindingsValidation was performed by simulation and analytical techniques applied to the Cohen’s Kappa index, supported by voluntary comparisons in the Matthews correlation coefficient (MCC) and the Youden index, generating prescriptive criteria for the classification. Kappa-based control charts performed well for m = 5 sample amounts and n = 500 sizes when Pe is less than 0.8. The simulations also showed that Kappa control requires fewer samples than the other indices studied.Originality/valueThe main contributions of this study to both theory and practitioners is summarized as follows: (1) it proposes DS and SPM integration; (2) it develops a tool for continuous predictive classification models validation; (3) it compares different indices for model quality, indicating their advantages and disadvantages; (4) it defines sampling criteria and procedure for SPM application considering the technique’s Phases I and II and (5) the validated approach serves as a basis for various analyses, enabling an objective comparison among all alternative designs.

Long-Range Three-Dimensional Tracking of Nanoparticles Using Interferometric Scattering Microscopy.

Tracking nanoparticle movement is highly desirable in many scientific areas, and various imaging methods have been employed to achieve this goal. Interferometric scattering (iSCAT) microscopy has been particularly successful in combining very high spatial and temporal resolution for tracking small nanoparticles in all three dimensions. However, previous works have been limited to an axial range of only a few hundred nanometers. Here, we present a robust and efficient measurement and analysis strategy for three-dimensional tracking of nanoparticles at high speed and with nanometer precision. After discussing the principle of our approach using synthetic data, we showcase the performance of the method by tracking gold nanoparticles with diameters ranging from 10 to 80 nm in water, demonstrating an axial tracking range from 4 μm for the smallest particles up to over 30 μm for the larger ones. We point out the limitations and robustness of our system across various noise levels and discuss its promise for applications in cell biology and material science, where the three-dimensional motion of nanoparticles in complex media is of interest.