bluuebunny/crossref_metadata_2025 huggingface dataset:
Methods of control and monitoring of organophosphorus compounds in natural environments
Authors:   Saratov State Technical University named after Gagarina Yu.A., Rastegaev O. Y. , Ashikhmina T. Ya. ,   Vyatka State University,   Institute of Biology of the Komi Scientific Center of the Ural Branch of the Russian Academy of Sciences, Chernikov S. N. ,   Saratov State Technical University named after Gagarina Yu.A.
Published: January 2025

Methods of control and monitoring of organophosphorus compounds in natural environments while organophosphorus compounds (OPCs – Vx) utilization are proposed. It was found that environmental control standards and quality standards of natural environments were not exceeded. Environmental control was carried out as a planned control of pollutant sources (emissions, discharges, process waters, waste and reaction masses), while environmental monitoring analyzed the main objects of the natural environment (atmospheric air, soil cover, natural and groundwater, snow cover) was carried out. The volume of eco-analytical studies conducted within the framework of environmental control and monitoring amounted to 200 plots and objects of control and monitoring, more than 250 indicators. Natural water, groundwater, snow cover were monitored according to 57 indicators, atmospheric air – for 10 indicators, soil cover, bottom sediments – for 11 indicators. Summary data of the state environmental control and monitoring in 2006–2009 during the period of utilization of organophosphorus compounds (FOS – Vx) are presented. The methodological base of eco-analytical support for the utilization of FOS has been supplemented and implemented, 14 methods for the determination of phosphorus-containing substances – O-isobutylmethylphosphonate, methylphosphonic acid, their total content (the indicator “total phosphorus”) were developed and adapted. The development of methods is based on the justification of the ranges of determined concentrations, taking into account the technological parameters of the disposal processes, experimental justification of sampling, sample preparation and analytical termination on target substances. These methods were tested on real control and monitoring objects and certified in accordance with the established procedure. The OPCs disposal process was carried out normally. No OPCs and their degradation products were detected in environmental objects during the entire observation period, and no negative environmental effect was established.
Monitoring of ground and surface water in the area of hazardous industrial waste disposal enterprises
Authors:   Vyatka State University, Ashikhmina T. Ya. ,   Institute of Biology of the Komi Science Centre of the Ural Branch of the Russian Academy of Sciences, Dabakh E. V. ,   Institute of Biology of the Komi Science Centre of the Ural Branch of the Russian Academy of Sciences, Kantor G. Ya. ,   Vyatka State University,   Institute of Biology of the Komi Science Centre of the Ural Branch of the Russian Academy of Sciences, Timonov A. S. ,   Vyatka State University,   Institute of Biology of the Komi Science Centre of the Ural Branch of the Russian Academy of Sciences, Domnina Е. А. ,   Vyatka State University,   Institute of Biology of the Komi Science Centre of the Ural Branch of the Russian Academy of Sciences, Kutyavina T. I. ,   Vyatka State University
Published: January 2025

On the territory of the Mirny Ecotechnopark, a production and technical complex for processing, recycling and rendering harmless waste of I and II hazard classes, it is planned to conduct environmental monitoring of all natural environments and objects within the framework of the integrated environmental monitoring program. This paper presents some principles and approaches to organizing the monitoring of groundwater and surface water, bottom sediments. It is shown that when organizing the monitoring of the created object, it is necessary to take into account the features of the monitoring system of previously existing objects in this territory and the results of long-term observations of the state of natural waters in this area. In particular, when organizing the monitoring network, it is recommended to use observation wells drilled to monitor chemical weapons storage and destruction facilities. When selecting monitoring indicators, it is necessary to take into account elevated concentrations of pollutants and indicators indicating deterioration in water quality identified during monitoring of existing objects. It is recommended to include 38 indicators in the list of environmental monitoring of the facility being created for groundwater, and 40 for surface water. To form a priority list of observed parameters of natural waters and water bodies, a logarithmic index of pollutant toxicity based on toxicity classes and maximum permissible concentration values is proposed. It is recommended to use bioindication and biotesting methods to assess the state of natural waters and bottom sediments, in particular, to conduct an analysis of the taxonomic composition of bottom invertebrates and quantitative indicators of benthic communities, as well as a qualitative assessment of the state of water bodies using bioindication indices.
Taxonomic structure of the flora of water bodies located in the zone of influence of the JSC “SLPC” (Komi Republic)
Authors:   Institute of Biology of the Komi Science Centre of the Ural Branch of the Russian Academy of Sciences, Teteryuk B. Yu. , Panyukov A. A. ,   Institute of Biology of the Komi Science Centre of the Ural Branch of the Russian Academy of Sciences, Lapteva E. M. ,   Institute of Biology of the Komi Science Centre of the Ural Branch of the Russian Academy of Sciences, Rafikov R. R. ,   Institute of Biology of the Komi Science Centre of the Ural Branch of the Russian Academy of Sciences
Published: January 2025

The analysis of the taxonomic structure of the flora of water bodies located in the zone of influence of the largest forestry enterprise in the European North-East of Russia – joint stock company (JSC) “SLPC”. The flora of impact reservoirs in the zone of influence of JSC “SLPC” unites 119 species of macrophytes belonging to 77 genera and 43 families. Flowering plants in its composition are represented by 114 species, and cryptogamic ones by five: vascular spore plants by two, bryophytes by three. It was found that the role of the Potamogetonaceae family and the genus Potamogeton was significantly reduced in the floras of impact reservoirs, while the role of the Asteraceae and Poaceae families was simultaneously increased. The flora of reservoirs located in the zone of influence of JSC “SLPC” have a high degree of transformation: the flora of anthropogenic reservoirs is 100.0% composed of synanthropic species. The most active among them are Bidens cernua L., Bidens tripartita L., Lycopus europaeus L. and Typha latifolia L. The flora of anthropogenically transformed reservoirs are also significantly synanthropized (Is=98.4–100.0%), the basis of their flora is apophytes. In anthropogenic reservoirs, vascular spore and moss-like plants are completely absent. The taxonomic structure of the flora of anthropogenically transformed reservoirs retains similarities with the flora of the reservoirs of the region. The analyzed flora includes species protected on the territory of the Komi Republic: Riccia cavernosa Hoffm. and Carex pseudocyperus L.
Epidemiological situation and organization of specialized medical care for infectious diseases in the Republic of Sakha (Yakutia)
Authors:   MD, Associate Professor, Head of the Department of Infectious Diseases, M.K. Ammosov North-Eastern Federal University, Yakutsk, Sleptsova S.S. , Sleptsov S.S. ,   Yakut Science Centre of Complex Medical Problems (YSC CMP), Yakutsk, Ru, Danilova M.A. ,   chief specialist of the Ministry of Health of the Republic of Sakha (Yakutia), Yakutsk, Burtseva T.E. ,   MD, Associate Professor, Professor of the Department of Pediatrics and Pediatric Surgery, Medical Institute M.K. Ammosov North-Eastern Federal University, Yakutsk
Published: January 2025

The article presents a content analysis of the epidemiology of infectious diseases in the Republic of Sakha (Yakutia) in the period from 2020-2023. An increase in the incidence of infectious pathology in the Republic of Sakha (Yakutia) by 20 nosological forms was revealed. Taking into account the epidemiological situation, as well as the available capacities of medical facilities and staffing, recommendations are proposed to improve the organization of specialized medical care for infectious diseases in the Republic of Sakha (Yakutia).
Keywords: infectious diseases service, morbidity, infectious diseases, pandemic, mortality, bed stock, staffing, Yakutia.
Emergency surgical aid to patients with colorectal cancer in the Republic of Sakha (Yakutia)
Authors:   Doctor of Medical Sciences, Professor, Head of General Surgery Department, Medical institute, M.K. Ammosov North-Eastern federal university, Ignatyev V.G. , Krivoshapkina L.A. ,   coloproctologist surgeon, Republic hospital №2- Emergency Medical Center, Dyagileva T.S. ,   PhD, Associate Professor, Department of General Surgery, Medical institute, M.K. Ammosov North-Eastern federal university, Kholtosunov I.A. ,   coloproctology surgeon, Republic hospital №2- Emergency Medical Center, Savvina I.L. ,   PhD, Associate Professor of Foreign Languages and Regional Studies Institute, M.K. Ammosov North-Eastern Federal University
Published: January 2025

The article presents materials of the coloproctology department of the Republic hospital №2 - Emergency Medical Center for the last five years (2018-2022). Diagnosis and treatment of 399 patients with complicated colorectal cancer admitted by emergency indications were analyzed. 115 patients (28.8%) were delivered from the districts of the Republic by air ambulance. The remaining 284 patients (71.2%) were hospitalized from Yakutsk and its suburbs. 90% of patients were operated by emergency. The mortality rate after emergency surgical interventions amounted to 20.2%.
Keywords: neoplasms, colon, colorectal cancer, surgical treatment.
Dynamics of the main medical and demographic indicators of maternal and child health care in the Arctic regions of the Republic of Sakha (Yakutia)
Authors:   MD, Associate Professor, Professor of the Department of Pediatrics and Pediatric Surgery of the Medical Institute FSAE HE M.K. Ammosov North-Eastern Federal University, Burtseva T.E. , Sleptsova S.S. ,   MD, Associate Professor, Head of the Department of Infectious Diseases, Phthisiology and Dermatovenerology of the Medical Institute FSAE HE M.K. Ammosov North-Eastern Federal University, Gogolev N.M. ,   PhD, Associate Professor, Director of the Medical Institute FSAE HE M.K. Ammosov North-Eastern Federal University, Vikhreva O.A. ,   Candidate of Physical and Mathematical Sciences, Associate Professor, Department of Higher Mathematics, Institute of Mathematics and Informatics, FSAE HE M.K. Ammosov North-Eastern Federal University, Afanasyeva L.N. ,   Minister of Health of the RS (Ya), Candidate of Medical Sciences, Associate Professor of the Basic Department of Oncology of the Medical Institute FSAE HE M.K. Ammosov North-Eastern Federal University, Nikitina A.M. ,   chief physician of the State Budgetary Institution of the RS (Ya) Republican Center of Public Health and Medical Prevention
Published: January 2025

The analysis of the main medical and demographic indicators of maternal and child health care in 13 Arctic regions of the Republic of Sakha (Yakutia) is presented in the article. It is demonstrated that the studied period is marked by a decrease in population size, and despite this, there are high birth rates, as well as high rates of total mortality, a significant decrease in the infant mortality rate, and high rates of child morbidity.
Keywords: demography, birth rate, mortality, morbidity, Arctic, Yakutia.
Risk factors for chronic kidney disease in the Arctic zone of the Republic of Sakha (Yakutia)
Authors:   nephrologist, Director of Diamed Sakha LLC, manager of the branch of Dialog Medical Center LLC, Anisimova A.I. , Krylova M.I. ,   PhD, Associate Professor of the Department of Hospital Therapy, Occupational Diseases and Clinical Pharmacology of the Medical Institute of M.K. Ammosov Northeastern Federal University, nephrologist of the State Medical University of RS(Ya) RH No. 1 - M.E. Nikolaev NCM, Emelyanova E.A. ,   PhD, Associate Professor of the Department Hospital Therapy, Occupational Diseases and Clinical Pharmacology of the Medical Institute of M.K. Ammosov Northeastern Federal University, Argunova A.N. ,   PhD, Head of the Department Hospital Therapy, Occupational Diseases and Clinical Pharmacology of the Medical Institute of M.K. Ammosov Northeastern Federal University, Palshina A.M. ,   PhD, Associate Professor of the Department Hospital Therapy, Occupational Diseases and Clinical Pharmacology of the Medical Institute of M.K. Ammosov Northeastern Federal University, Northeastern Federal University, Gryaznukhina N.N. ,   PhD, Head of the Quality Control and Safety Department of Medical activity of State budgetary institution of the Republic of Sakha (Yakutia) Mirninskaya Central District Hospital, Berezhnev Ya.R. ,   Chief physician of State budgetary institution of the Republic of Sakha (Yakutia) Momskaya Central District Hospital, Essaian A.M. ,   MD, Professor, Head of the Department of Nephrology and Dialysis of the Faculty of Postgraduate Education of Academician I.P. Pavlov PSPbSMU
Published: January 2025

To date, there is a worldwide trend of increasing morbidity and mortality in patients with chronic kidney disease. Given the secondary nature of kidney damage, prevention and early detection of risk factors are the main priority of modern medicine.
The purpose of our work was to conduct a screening study of the population of the Momsky district (5 settlements) of the Republic of Sakha (Yakutia) for early detection of damage and decreased kidney function.
Results. The study involved 222 people, of whom 14 (6,3%) had chronic kidney disease (GFR less than 60 ml/min/1.73 m2). An early predictor of the development of chronic kidney disease, albuminuria was found in 70 (31.5%) of the examined patients. The main risk factors affecting the development of chronic kidney disease were hypertension (54.3%), burden of cardiovascular diseases (50%) and obesity (37.1%), burden of kidney diseases were in 11 (15.7%) of the examined patients.
Keywords: chronic kidney disease, Arctic zones, albuminuria, glomerular filtration rate, risk factors.
The role of proinflammatory cytokines in the development of chronic discogenic pain syndrome
Authors:   V.M. Bekhterev Institute of Personalized Psychiatry and Neurology SMRC PN (St. Petersburg), Ashkhotov A.V. , Schnaider N.A. ,   V.M. Bekhterev Institute of Personalized Psychiatry and Neurology SMRC PN (St. Petersburg), Trefilova V.V. ,   V.M. Bekhterev Institute of Personalized Psychiatry and Neurology SMRC PN (St. Petersburg), Novitsky M.A. ,   Department of Neurology of the Hospital for War Veterans (St. Petersburg), Petrova M.M. ,   Center for Collective Use Molecular and Cellular Technologies, V.F. Voino-Yasenetsky Krasnoyarsk State Medical University (Krasnoyarsk), Nasyrova R.F. ,   V.M. Bekhterev Institute of Personalized Psychiatry and Neurology SMRC PN (St. Petersburg)
Published: January 2025

The purpose of this review is to update the knowledge of neurologist doctors about the role of pro-inflammatory cytokines in the evelopment and chronicity of discogenic pain syndrome in patients with intervertebral disc degeneration.
Keywords: cytokines; cytokine status; disk degeneration; biomarker; chronic inflammation, discogenic pain syndrome.
АНАЛИЗ ПРОБЛЕМ УСТОЙЧИВОГО РАЗВИТИЯ СИСТЕМЫ " КЛИМАТ-ОБЩЕСТВО"
Authors: КРАПИВИН В Ф. , ПОТАПОВ И И. , СОЛДАТОВ В Ю.
Published: January 2025

Затрагиваемые в статье проблемы охватывают широкий спектр теоретических и прикладных задач, решение которых неизбежно приводит к проблеме изменения глобального климата. Поиск причин этих изменений сводится к построению геоэкологической информационно-моделирующей системы (ГИМС), охватывающей наиболее значимые прямые и обратные связи в окружающей среде. Поэтому предметом работы является критический взвешенный анализ имеющихся подходов к определению понятия «устойчивое развитие современной цивилизации и выбор наиболее адекватного критерия выживания человечества». Проблемаустойчивого развития рассматривается совместно с проблемой глобализации при учете различных факторов неравномерного экономического, политического и социального развития стран. Проанализированы фактические данные об использовании природных ресурсов и изменениях окружающей среды, отображающие глобальную динамику современного общества потребления и его возможные перспективы. Особое внимание уделено при этом проблеме энергопотребления и водным ресурсам. Отмечено, что важным элементом системы обеспечения устойчивого развития является моделирование динамики численности населения планеты.

The problems considered in this paper include wide spectrum of theoretical and applied tasks solution of which inevitably lead to the problem of global climate change. A search of the causes of these changes is came to the synthesis of geoecological information-modeling system (GIMS) involving the most signifi cant direct and indirect correlations in the environment. Therefore, critical weighed analysis of existing approaches to the defi nition of sustainable development of present civilization and choice of the most adequate criterion for the humanity survivability is the subject of this paper. A sustainable development problem is considered together with the globalization problem taking into consideration of different factors connected with irregular economic, politic and social development of countries. Actual data are discussed concerning the natural resources use and environmental changes that refl ect global ecodynamics of present consumption society and its perspectives. Under this, specifi c attention is given to the problem connected with energy consumption and to the water resources. It is marked that modeling the dynamics of the world population size is important component of sustainable development.
ИОСИФ СЕМЕНОВИЧ ГОНОРОВСКИЙ И ЕГО ВКЛАД В ТЕОРЕТИЧЕСКУЮ РАДИОТЕХНИКУ
Authors: ЕРОФЕЕВ Ю Н.
Published: January 2025

В статье рассказывается о жизни и творческой деятельности Иосифа Семеновича Гоноровского (1907-1995) - выдающегося советского ученого в области теоретической радиотехники и педагога высшей школы. У него слушал лекции на вузовском факультете ускоренной подготовки радиоспециалистов А.А. Расплетин; он был научным руководителем на этапе подготовки кандидатской диссертации у Б.В. Бункина - будущих академиков, наших прославленных Генеральных конструкторов зенитно-ракетных комплексов.

In the article the life and creative activity of Iosif Semenovich Gonorovcky (1907-1995), an outstanding Soviet scientist in the field of theoretical radio engineering and tutor of the Higher School, are narrated. A.A. Raspletin attended lectures of Gonorovcky in the radio engineering specialists fast training faculty of the Higher School; he was scientific adviser of B.V. Bunkin at the stage of his Ph. D thesis preparation and adviser of future academicians , our renowned chief designers of air defense missile complexes.
Metaproteomics beyond databases: addressing the challenges and potentials of de novo sequencing
Authors: Van Den Bossche Tim , Beslic Denis , van Puyenbroeck Sam , Suomi Tomi , Holstein Tanja , Martens Lennart , Elo Laura L. , Muth Thilo
Published: January 2025

Metaproteomics enables the large-scale characterization of microbial community proteins, offering crucial insights into their taxonomic composition, functional activities, and interactions within their environments. By directly analyzing proteins, metaproteomics offers insights on community phenotypes and the roles individual members play in diverse ecosystems. While database-dependent search engines are commonly used for peptide identification, they rely on pre-existing protein databases, which can be limiting for complex, poorly characterized microbiomes. De novo sequencing presents a promising alternative, which derives peptide sequences directly from mass spectra without requiring a database. Over time, this approach has evolved from manual annotation to advanced graph-based, tag-based, and deep learning-based methods, significantly improving the accuracy of peptide identification. This Viewpoint explores the evolution, advantages, limitations, and future opportunities of de novo sequencing in metaproteomics. We highlight recent technological advancements that have improved its potential for detecting unsequenced species and for providing deeper functional insights into microbial communities.
Modeling Boltzmann weighted structural ensembles of proteins using AI based methods
Authors: Aranganathan Akashnathan , Gu Xinyu , Wang Dedi , Vani Bodhi , Tiwary Pratyush
Published: January 2025

This review highlights recent advances in AI-driven methods for generating Boltzmann-weighted structural ensembles, which are crucial for understanding biomolecular dynamics and drug discovery. With the rise of deep learning models like AlphaFold2, there has been a shift toward more accurate and efficient sampling of structural ensembles. The review discusses the integration of AI with traditional molecular dynamics techniques as well as experiments, the challenges of conformational sampling, and future directions for AI-driven research in structural biology, particularly in drug discovery and protein dynamics.
Solvation Thermodynamic Costs of Cognate Binding Site Formation
Authors: Ji Yeonji , Molino Vjay , Ramsey Steven , Kurtzman Tom
Published: January 2025

Conformational flexibility complicates the identification of lead molecules that are shape and charge complementary to target proteins. Solvation thermodynamics has typically not been integrated into the exploration of alternate protein conformations. Here, we study the variation of solvation thermodynamic potentials as proteins adopt different conformations. Specifically, we analyze solvation thermodynamics of protein binding cavities with conformations obtained from molecular dynamics simulations with mobile side chains and side chains restrained about their cognate bound structure. We find that the reorganization of protein side chains has a significant effect on the structure and thermodynamics of binding site solvation and, in the vast majority of cases, that there is a significant solvation free energetic cost to forming cognate ligand bound structures when the ligand is absent. We discuss how understanding the interplay between solvation thermodynamics and protein structural fluctuations is crucial for discovering alternative binding pockets, estimating the contribution to binding affinity of displacing water upon ligand binding, and assessing revealed cryptic pocket bindability.
Poly(lactic acid) nanoplastics through laser ablation: Establishing a reference model for mimicking biobased nanoplastics in aquatic environments
Authors: Manju Sudheer Malavika , Fazli Arezou , Sganga Stefania , Tirelli Nicolla , Carzino Riccardo , Veronesi Marina , Khabarov Kirill , Athanassiou Athanassia , Fragouli Despina
Published: January 2025

Due to the well-documented negative environmental impacts of conventional plastics, the use of bioplastics has been increasing. Poly(lactic acid) (PLA) is currently among the most common and industrially available bioplastics. Although PLA is compostable under industrial conditions and generally degrades more quickly than conventional plastics, its breakdown in typical environmental settings remains problematic. PLA’s potential to contribute to plastic pollution through the release of microplastics and nanoplastics makes it crucial to understand how these particles behave, especially in marine environments. However, as for all nanoplastics, identifying, isolating, and quantifying PLA nanoplastics in water presents significant challenges. This study proposes a versatile approach to fabricate PLA nanoplastics through laser ablation in a water environment to mimic realworld samples. Commencing with bulk PLA films, this top-down method yields the formation of nanoplastics with an average diameter of 54.7 ± 26.7 nm. Surface and chemical analyses confirm the presence of carboxylic groups on their surface, potentially resembling the environmental degradation pathway of PLA under exposure to sunlight and humid environments. This indicates that the proposed process results in a PLA nanoplastics system that serves as an invaluable reference model, enabling realistic environmental scenario explorations and simulations for risk assessment evaluations on bio-based nanoplastics.
Self-Assembled PROTACs Enable Glycoproteins Degradation in the Living Cells.
Authors: Chen Haoyu , Kielkowski Pavel
Published: January 2025

We report here a two-component proteolysis targeting chimeras (PROTACs) strategy selectively targeting O-GalNAcylated and O-GlcNAcylated proteins for proteasomal degradation, which leads to severe toxicity in human cancer cell lines through perturbation of critical metabolic and signaling pathways governed by glycoproteins. Our approach termed as GlyTAC leverages from metabolic incorporation of easily accessible and cell-permeable peracetylated N-acetylglucosamine (GlcNAc) or N-acetylgalactosamine (GalNAc) analogues bearing an azido group into glycoproteins. In the living cells, the azido-modified glycoproteins serve as covalent anchors for the introduction of thalidomide moiety by strain-promoted azide-alkyne cycloaddition (SPAAC) to recruit E3 ligase cereblon (CRBN), resulting in stepwise ubiquitination of ‘sensitized’ proteins and their degradation by proteasome. We show the efficiency of the system in a series of human cancer cell lines and verify the mechanistic pathway by performing control experiments at each stage of the process. Given the characteristic features of cancer cells including fast nutrient turnover, and overall increase of protein glycosylation, as well as the low cytotoxicity of the individual components, our approach may open a feasible strategy in cancer therapy.
Separating critical elements from a NdFeB magnet with aminophosphonic acid functionalised 3D printed filters and their detailed structural characterisation with X-ray tomography
Authors: Virtanen Emilia J. , Yliharju Janne , Kukkonen Esa , Christiansen Tia , Tuomisto Minnea , Miettinen Arttu , Väisänen Ari , Moilanen Jani O.
Published: January 2025

3D printed filters containing 70 wt% of polyamide (PA) nylon-12 as a polymer matrix and either 30 wt% of a commercial aminophosphonic acid functionalised resin (Lewatit TP260) or a synthetized aminobisphosphonic acid (1) as an additive were investigated for the separation of elements from a NdFeB magnet waste. Before separation studies, the magnet was leached with 10 v/v% methanesulfonic acid using S/L ratio of 5 g/l for 20 h at 60 °C. The PA-TP260 filters adsorbed rare earth elements (REE) more efficiently than transition and main group elements and showed greater uptake than the PA-1 filters at the studied pH range of 0.15–4.00. Thus, the PA-TP260 filters were selected for the separation process, wherein Fe was selectively precipitated from the leachate, while solid-phase extraction was used to separate the remaining elements from the leachate to four distinct fractions: REEs; B, Co; Cu; and Al. Neither significant decrease in the adsorption and desorption percentages of the PA-TP260 filters over 50 adsorption-desorption cycles, nor structural changes, as confirmed by the detailed X-ray tomography studies, were observed. The results indicate that the PA-TP260 filters are robust and fully reusable. Overall, the results demonstrated that the highly porous 3D printed filters efficiently separate critical elements from the NdFeB magnet leachate only by using ecofriendly MSA, ammonium chloride, and potassium oxalate solutions paving the way towards greener separation processess for the critical elements.
HSADab2025: AI-powered Modelling of Human Serum Albumin
Authors: Zheng Lei , Wang Xiaohui , Liu Xiao , Wang Mao , Zhang John Zeng Hui , Zhang Zuo-yuan , Sun Zhaoxi
Published: January 2025

Human serum albumin (HSA) as the most prevalent protein constitutes ~60% of the protein mass. In this work, we augment our previously released HSA database (HSADab) via the incorporation of AI-powered modelling. The constructed webserver www.hsadab.cn enables instant prediction of HSA binding affinities for drug-like molecules through various machine-learning predictors, hosts the most comprehensive affinity and structure banks containing all HSA-relevant data published so far, and contains a complete set of deep-learning assisted docking structures for molecules presented in the database. We additionally present comprehensive analyses on the protein conformational space, docking performance and AlphaFold modelling, and further open source the most robust fingerprints-based model in the GitHub repository https://github.com/proszxppp/HSADab.
Thermodynamics of the Condensation of the Si8O20(SnMe3)8 Building Block with M–X (M = B, Al, Si, P, Ti, V, Zn, Sn, Sb, X = Cl, Me, Et) Precursors by DFT-D3 Calculations
Authors: Kejik Martin , Semrad Hugo , Styskalik Ales , Pinkas Jiri
Published: January 2025

Synthesis of porous metallosilicate materials from siloxane oligomers is a promising approach to constructing well-defined structures at a molecular level. Here, we use quantum chemistry DFT methods and demonstrate a computationally cheap method for screening potential precursors for synthesizing porous metallosilicates. We estimate the thermodynamic parameters of condensation reactions of the octakis(trimethyltin)spherosilicate Si8O20(SnMe3)8 (CUBE) building block with metal chlorides and alkyl metals. These reactions represent the initial steps in the non-hydrolytic synthesis of metallosilicate gels containing potentially uniform single-site metal centers. Our main emphasis was on the spontaneity and irreversibility of the condensation and the computational screening of potential metal center sources. The precursors previously reported in successful condensations with CUBE, such as AlCl3, [AlCl4]–, Si–Cl compounds, PCl3, TiCl4, and VOCl3, are shown to undergo sufficiently irreversible reactions, as are the untested precursors BCl3, VCl4, and POCl3. Interestingly, AlMe3 proves to be twice as exoergic as AlCl3. The first chloride in Cp2TiCl2 reacts readily, but the second may be partially reversible. SbCl3 and Ph3SbCl2 are borderline cases and reversibility of their condensations might pose a problem. SnCl4 was found unsuitable as a precursor to stannosilicates. It should be possible to prepare zincosilicates from ZnEt2, but not from ZnCl2 as the affinity of Zn for Cl– is so high that in the presence of a source of Cl–, zincosilicate structures will dissolve back to CUBE and ZnCl2. The oxophilicity of the metal in the precursor is the main factor in the driving force for the condensation with CUBE. Alkyl metals and lighter elements are more prone to the reaction than the corresponding metal chlorides and heavier analogs. The propensity of [SnMe3]+ to bind to Cl– in preference to CUBE has a supporting effect. At low temperatures, the condensation is slightly disfavored, while at the experimentally used temperature of 100 °C, this process contributes over 20 kJ mol–1 of the additional driving force and helps to complete the condensation. The reliability of B3LYP-D3 and PBE0-D3, together with the CBS extrapolation scheme, is also evaluated in calculations.
Data Efficient Learning of Molecular Slow Modes from Nonequilibrium Metadynamics
Authors: Hanni Jack , Ray Dhiman
Published: January 2025

Enhanced sampling simulations help overcome free energy barriers and explore molecular conformational space by applying external bias potential along suitable collective variables (CVs). However, identifying optimal CVs that align with the slow modes of complex molecular systems with many coupled degrees of freedom can be a significant challenge. Deep time-lagged independent component analysis (Deep-TICA) addresses this issue by employing an artificial neural network that generates non-linear combinations of molecular descriptors to learn the slowest degrees of freedom. Training Deep-TICA CVs, however, typically requires long equilibrium simulations that can sample multiple recrossing events across various metastable conformations of the molecule. This requirement can often be prohibitively expensive, thereby limiting its widespread application. In this study, we present an algorithm that enables the training of Deep-TICA CVs using a limited amount of trajectory data obtained from short non-equilibrium metadynamics simulations that only sample one forward transition from the initial to the final state. We achieve this by utilizing the variational Koopman algorithm, which reweights short off-equilibrium trajectories to reflect the equilibrium probability densities. We demonstrate that enhanced sampling simulations conducted along the Koopman reweighted Deep-TICA CV can accurately and efficiently converge the free energy surface for systems such as the Muller-Brown Potential, Alanine Dipeptide, and the chignolin mini-protein. Our approach, therefore, addresses the key challenge of inferring slow modes from limited trajectory data, making it more feasible to use deep learning CVs to study molecular processes of practical relevance.
Enhanced compound selection using holistic virtual screening for gatifloxacin analogues to overcome dysglycemic effects
Authors: Majalekar P.P. , Shirote P.J.
Published: January 2025

Gatifloxacin, a fluoroquinolone-class antibacterial agent, is effective but has been associated with dysglycemic side effects, leading to the withdrawal of its oral formulation. Patients treated with gatifloxacin have shown notable decrease blood glucose level and after four days of treatment there will be increases in blood glucose levels. To mitigate this issue, novel gatifloxacin derivatives were designed and assessed for their efficacy and safety through in silico molecular docking studies. The derivatives aim to prevent dysglycemia by blocking human pancreatic alpha-amylase (PDB ID: 5TD4). These modifications are hypothesized to retain antibacterial effectiveness while minimizing blood glucose fluctuations. Using AutoDock, molecular docking of gatifloxacin and its derivatives with α -amylase (PDB ID: 5TD4) revealed binding energies, with gatifloxacin exhibiting a binding interaction of -7.1 Kcal/mol; meanwhile derivatives i) Gati I = -9.0 Kcal/mol, ii) Gati-II showed -8.2 Kcal/mol; iii) Gati III -8.5 Kcal/mol; iv) Gati IV = -9.3 Kcal/mol; v) Gati V = -8.9 Kcal/mol; vi) Gati VI = -7.6 Kcal/mol; Acarbose = -13.8 Kcal/mol. Unlike gatifloxacin, these derivatives demonstrated stronger binding interactions with 5TD4, potentially reducing dysglycemic risks. This study contributes to design the targeted antibacterial agents that minimize dysglycemia-related complications, thus enhancing clinical outcomes.
Molecular docking study of 2,4 disubstituted thiazole derivatives as antiulcer activity
Authors: Wadave D.B. , S.C. Daswadkar
Published: January 2025

In this study, 2,4 disubstituted thiazole derivatives were used to create an antiulcer agent. These compounds were chosen based on molecular properties and a drug-likeness score, ensuring their suitability for oral absorption. The molecular docking of 2,4 disubstituted thiazole derivatives was performed using AutoDock Vina Ver.1.1.2. The thiazole derivatives were constructed using Cambridge's Chem Draw Ultra 8.0 software. The program Chem 3D Ultra 8.0 was used to convert 2D structures to 3D structures. Thiazole derivatives were docked into the H2 blocker, with nizatidine binding at the active site (PDB ID: 2XZB) as the target protein obtained from the protein data bank. The current study reported anti-ulcer activity of newly synthesized derivatives with electron releasing and electron withdrawing groups on thiazole derivative. The study provided potential derivatives exhibiting significant anti-ulcer activity with fast onset and extended duration of action, which is the most promising expectation of any anti-ulcer agent, especially when administered in conjunction with complaint-specific therapy.
Phytochemical Screening, HPTLC and FT-IR analysis of methanolic bark extract of Syzygium stocksii (Duthie) Gamble – a critically endangered taxon in Myrtaceae
Authors: A.E. Johns  , P.M. Radhamany
Published: January 2025

Syzygium is a large genus with numerous species in the Family Myrtaceae. The genus Syzygium is a treasure trove of phytochemicals with immene therapeutic potential. Syzygium stocksii (Duthie) Gamble syn. Syzygium travancoricum, a critically endangered plant collected from Thrissur District in Kerala, India. The present study aims at the preliminary phytochemical screening, HPTLC and FT-IR analysis of the plant. Qualitative phytochemical studies revealed the presence of alkaloids, phenolics, flavonoids, tannins, and terpenoids. The preliminary phytochemical screening results revealed the presence of more constituents on the methanolic bark extract, and hence, this was further subjected to an HPTLC analysis to determine the number of compounds in the crude extract.  FTIR analysis was also conducted to identify the major functional groups in the compounds in the extract. From this study, it can be concluded that Syzygium stocksii contains various bioactive compounds. This study calls for the importance of excavating the phytochemical and pharmacological potential of this relatively unexplored species.
Use of local raw materials to obtain glass used in glazing of ceramic products
Authors: Satayeva S. , Akhmetova F. , Yermukhanova S. , G. Gubaidullina  , A. Abdrakhmanova  , Ibrayeva M. , Ozturk M. , Utepova T.
Published: January 2025

Glass is one of the widely used materials in the construction industry and in everyday life. The year-on-year growing demand for various types of glass products pushes the glass-making industries to increase their production volumes and not to lower their quality levels. The scientific and technical progress in glass extraction has gradually expanded the area of ​​its effective use. In recent years, significant changes have taken place in the glassmaking technique. New production methods and ways of improving existing technological processes appeared, and new areas of glass application began to open. The chemical composition of the product was changed and different types of glass were made. In this regard, the study of the method of obtaining glass with different properties is one of the most important issues. In order to prepare the composition of colored glass used in the production of various products, colored glass was obtained in laboratory conditions. Physico-chemical properties of the obtained colored glass were studied in order to determine the area of application. Based on the research results, the obtained colored glass can be used for decorative purposes.
Genetic markers of sports performance, interpretation of individual genotypes in the athlete’s genetic passport
Authors: Altynova N.K. , Tokmurzina S.S. , Kassymbekova A.M. , Kereyev T.N. , Musralina L.Z. , Lebedeva L.P. , Djansugurova L.B.
Published: January 2025

Identifying and studying genetic polymorphisms that determine the phenotype of elite athletes is a highly relevant task, as it forms the basis for developing so-called sports genetic passports. The aim of this manuscript was to analyze genetic markers for the development of athletic qualities (strength, power, speed, and endurance) through a selective systematic review of the literature. This review allowed to select SNPs that are responsible for individual athletic qualities based on the functions of their gene products, proposing an interpretation of sports markers for genetic passports. These markers can provide scientists in physical culture and sports medicine with the latest and most compelling evidence in the field of exercise genomics. A panel of 40 of the most popular genetic markers associated with athletic performance, responsible for strength, speed, and endurance, has been presented.
Theoretical determination of the biological activities of some benzimidazolederivative compounds with potential as active pharmaceutical agents
Authors: İslamoğlu F.
Published: January 2025

The biological activities of twelve different benzimidazole derivative compounds synthesized and registered in the literature were theoretically calculated with Way2Drug PASS software. Seven different biological activities, including acute rat toxicity, adverse drug effects, antibacterial activity, antifungal activity, anti-HIV activity, antiviral activity, and cell line cytotoxicity, were calculated for each benzimidazole derivative compound examined here. Rat acute toxicity was calculated in four different ways. These are Rat IP (intraperitoneal administration route) LD50, Rat IV (intravenous administration route) LD50, Rat Oral (oral administration route) LD50, and Rat SC (subcutaneous administration route) LD50. According to the results, a classification was also made for each method. Adverse effects that the molecules may show were determined with the help of the calculated Pa (probability of activity) and Pi (probability of inactivity) values. The antibacterial effect of each molecule against which bacteria was determined and the confidence value of this effect was calculated. Likewise, it was determined whether the molecules showed antifungal properties. It was determined against which fungus the molecules showing antifungal properties showed this effect, and the confidence value was calculated. The anti-HIV properties of the molecules were studied for five different targets (protease (HIV-1), reverse transcriptase (HIV-1), integrase (HIV-1), REV (regulator of virion) (HIV-1), and TAT (trans-activator of transcription) (HIV-1)) and the p function of the IC50 (half maximal inhibitory concentration) values obtained were analyzed. Anti-viral effects of molecules examined. Here, the viruses against which they show this effect were determined, and the confidence value was calculated together with the target protein. Finally, cancer cell line and non-tumor cell line properties of the molecules were determined by Pa and Pi values as well as tissue and tumor type.
Novel 3-benzylbenzo[d]thiazol-2(3H)-iminium salts as potent DNA benzylating agents: design, synthesis, MTT assay, and DFT calculation
Authors: Bahmani A. , Rajaee M.H. , Ebadi A. , Najafi Z. , Dastan D. , Chehardoli G.
Published: January 2025

New derivatives of 3-benzylbenzo[d]thiazol-2(3H)-iminium salt were developed, synthesized, and assessed for their cytotoxic effects on the MCF-7 cell line. Among them, two molecules, identified as 3g and 3i, demonstrated notable cytotoxic activity with IC50 values of 41.76 and 58.34 µmol/L respectively, compared to the reference drug Cis-platin, which has an IC50 of 22.36 ± 2.98 µmol/L. Subsequent DNA interaction docking studies were conducted with these compounds. The docking data revealed that both 3g and 3i effectively bind within the minor groove of DNA, showing a preference for interaction with AT-rich sequences over CG-rich sequences. These findings suggest that 3g and 3i are effective DNA-binding agents. Further analysis using Density Functional Theory (DFT) was performed to explore the potential of DNA benzylation by compound 3g. The DFT studies suggested that the benzylation of guanine bases by 3g could occur at room temperature. Nonetheless, further experimental investigations are necessary to validate this hypothesis. The DFT studies suggested that the benzylation of guanine bases by 3g could occur at room temperature. Nonetheless, further experimental investigations are necessary to validate this hypothesis.
Antioxidant potencies in enzymatic hydrolysates from cup and corner sections
of edible bird's nest
Authors: Turiman N.S.R. , Muttalib S.A.A. , Sunarharum W.B. , S. Raseetha , Tan E.T.T.
Published: January 2025

Edible Bird's Nest (EBN) has many health-promoting properties, including antioxidants.
Although the antioxidant properties of the EBN hydrolysates have been reported in the
previous literature, little study has been done on the antioxidant potencies of the
enzymatic hydrolysates within different sections of EBN. Thus, this study investigated the
antioxidant potencies of the enzymatic hydrolysates from both the cup and corner sections
of EBN. Therefore, using different enzymatic hydrolysis durations (1, 2, and 3 hr), this
study examined the antioxidant potencies of enzymatic hydrolysates from cup and corner
sections of EBN. The antioxidant potencies of alcalase-treated EBN hydrolysates were
evaluated using in-vitro chemical assays (DPPH, FRAP, and ABTS). The hydrolysates
from the corner section of EBN consistently exhibited significantly higher (p<0.05)
DPPH, FRAP, and ABTS values compared to the hydrolysates from the cup section of
EBN at all hydrolysis times, except FRAP assay at the 2-hr hydrolysis time. Meanwhile,
the antioxidant values obtained from this study suggest that, despite the variations in
hydrolysis time, certain data points exhibited comparable antioxidant potencies between
cup and corner samples in FRAP and ABTS assays. It is also noteworthy that the ABTS
assay demonstrated higher sensitivity in detecting antioxidant activity in the hydrolysates
of EBN compared to DPPH and FRAP. In conclusion, the hydrolysates from the corner
section of EBN showed stronger antioxidant potencies when treated with alcalase
compared to the cup hydrolysates. These results open way for further investigation into
the factors influencing the antioxidant activity of the hydrolysates from the cup and corner
sections of EBN.
Consumer perceptions of rabbit meat as an alternative animal protein source: a
university-based study
Authors: Goli Z. , Akinmoladun O.F. , Mpetile Z. , Mazhangara I.R. , Jaja I.F.
Published: January 2025

The need to meet the daily animal protein requirements of the teeming human population
requires that other protein sources, including rabbit meat, be explored. Rabbit meat can be
used as an alternate protein source to combat protein deficiency in South Africa as it is
healthier and has a higher proportion of digestible proteins compared to currently
popularly consumed meats such as pork, beef, and chicken. However, consumers should
be the primary focus when promoting any product since they are the end users and make
purchasing decisions based on their perceptions. The study's objective was to investigate
the perceptions of the University of Fort Hare students towards using rabbit meat as an
alternative animal protein source. Structured questionnaires from 400 respondents were
used to gather information on consumer perceptions of rabbit meat as an alternate animal
protein source. Information regarding socio-demographic and meat characteristics that
affect consumer purchasing behaviour was also gathered. The data obtained were analyzed
using the Statistical Package for Social Science (SPSS) software. Most respondents (75%)
had never consumed rabbit meat. The main reason was the unfamiliarity (46%) with rabbit
meat. A total of 45% of the respondents were likely to buy and consume rabbit meat at
restaurants, whereas 44% and 62% were likely to buy rabbit meat from grocery stores or
consume it when offered by friends and relatives, respectively. Approximately 19% of the
respondents perceived rabbit meat as similar to chicken. The quality of meat is positively
correlated with the health aspect of the meat (P = 0.02). Presentation and meat quality are
also positively correlated (P = 0.01). This study discovered that most respondents were
unfamiliar with rabbit meat and, therefore, had limited knowledge of the meat quality
attributes of the product.