jablonkagroup/rise_ai_scientists huggingface dataset:
Authors: Christian Chukwujindu | Max Kolton | Oladepo Fasakin | Ashish Pathak | John C. Seaman | Ashvini Ashok Chauhan
Source: Frontiers in Microbiology (article, 2026-01-28)
Field: Chemistry — Inorganic Chemistry

Microbial community structure and functional potential in a long-term uranium–nickel contaminated ecosystem This study examined the microbial community structure, functional potential, and resistance determinants in uranium (U)- and nickel (Ni)-contaminated soils from the Savannah River Site (SRS), a former nuclear materials production and waste collection facility operated by the U. S. Department of Energy (DOE). Soil cores were collected from the Steed Pond area, where long-term discharge of acidic wastewater resulted in spatially variable contamination levels. Concentrations of U and Ni in the collected samples ranged from 0.22-10.44 g kg<sup>-1</sup> and 0.79-2.28 g kg<sup>-1</sup>, respectively. Shotgun metagenomic and high-throughput quantitative PCR (HT-qPCR) analyses revealed bacterial communities dominated by Pseudomonadota, Actinomycetota, and Acidobacteriota, with enrichment of taxa affiliated with genera known to include diazotrophic members (e.g., <i>Bradyrhizobium</i> and <i>Burkholderia</i>), alongside increased abundance of nitrogen fixation-related functional genes. Carbon and nitrogen cycle genes were generally well represented across samples, with selective shifts observed in acetate assimilation genes (acsA/acsE) and comparatively low abundance of hydrazine oxidoreductase (hzo), indicating pathway-specific variation rather than broad metabolic suppression. A total of 117 resistance-associated genes were identified, comprising 93 antibiotic-resistance genes (ARGs), 3 metal-resistance genes (MRGs), and 21 mobile genetic elements (MGEs). Strong positive correlations among ARGs, MRGs, and MGEs indicate co-selection and horizontal gene transfer, forming a genetically mobile resistome. Collectively, these findings demonstrate that long-term U-Ni contamination selects for metabolically versatile, diazotroph-enriched, and genetically mobile microbiomes. Such communities exhibit both resistance proliferation and bioremediation potential, providing key insights into microbial adaptation and ecosystem recovery in legacy nuclear-contaminated soils. Microbial population biology ; Bioremediation ; Metagenomics ; Mobile genetic elements ; Ecosystem ; Abundance (ecology) ; Contamination ; Nitrogen cycle ; Wastewater Radioactive element chemistry and processing ; Radioactive contamination and transfer ; Chromium effects and bioremediation
Authors: Jaydn Su
Source: American journal of student research. (article, 2026-01-01)
Field: Materials Science — Materials Chemistry

Inputting Missing Values in Mechanical Materials Data: Accuracy and Statistical Effect of Mean, Median, and KNN Methods This study explores how different methods for handling missing data change the accuracy of mechanical property datasets. A dataset containing ultimate tensile strength (Su) and related mechanical properties was used, with 100 Su values randomly removed to simulate realistic data loss. Three commonly used methods were tested: mean substitution, median substitution, and k-nearest neighbor (KNN) imputation. Each completed dataset was then compared to the original to see how well statistical relationships were maintained. The results indicated that the median imputation method produced the most accurate reconstruction in this dataset and under MCAR simulation among the tested methods, maintaining an almost exact correlation with the original Su values with a Pearson correlation coefficient (r) value of 0.9987 and a coefficient of determination (R²) value of 0.9487 in the linear regression model. Both mean and KNN imputation performed sufficiently, but introduced larger deviations from the original relationships. Overall, the findings show that under the MCAR missingness simulation used here and within this specific mechanical-property dataset, the median imputation method provides the most effective balance between accuracy and preservation of statistical structure among the three methods tested, suggesting that median imputation may serve as a practical solution for researchers and engineers who regularly work with incomplete mechanical property data. Missing data ; Imputation (statistics) ; Correlation coefficient ; Linear regression ; Pearson product-moment correlation coefficient ; Regression ; Correlation ; Statistical analysis Machine Learning in Materials Science ; Optimal Experimental Design Methods ; Material Selection and Properties
Authors: Аnatoliy Pavlenko
Source: Preprints.org (preprint, 2026-01-27)
Field: Materials Science — Materials Chemistry

A Study of the Influence of Thermodynamic Parameters on the Dynamics of Cavitation Bubbles Numerical studies on the dynamics of bubble clusters in a compressible fluid, including interfacial heat and mass transfer, were performed to investigate the behaviour of bubble clusters in cavita-tion devices. The influence of operational and system parameters on the intensity of cavitation processes was considered. Physicochemical transformations during the cavitation treatment of liquids are caused not only by the action of shock waves and emitted pressure pulses but also by extreme thermal effects. At the stage of ultimate bubble compression, the vapour inside the bubble and the liquid in its vicinity transition to a supercritical fluid state. The presented model analyses the nature of microflows in the inter-bubble space and performs a quantitative calculation of the local values of velocity and pressure field parameters. Cavitation ; Bubble ; Supercritical fluid ; Shock wave ; Compressibility ; Shock (circulatory) ; Dynamics (music) ; Thermal Ultrasound and Cavitation Phenomena ; Cavitation Phenomena in Pumps ; Fluid Dynamics and Heat Transfer
Authors: Jéssica Ataide Batista Nigro | Sophia da Silva Vidal | Carlos Eduardo Malavasi Bruno | Eliana de Fátima Marques de Mesquita
Source: Boletim do Instituto de Pesca (article, 2026-01-26)
Field: Materials Science — Biomaterials

Histological and histochemical analysis to identify type I and III collagen in the skins of different shark species During fishing activities, solid waste such as shark skin is often discarded by the processing industry, contributing to environmental pollution and representing the loss of a material with high biotechnological potential, especially as a source of collagen. The objective of this research was to characterize the structure of the skin and identify the types of collagen present in four shark species: Rhizoprionodon lalandii, Squalus albicaudus, Sphyrna lewini, and Squatina guggenheim. The samples were obtained from artisanal fishing in the municipality of Saquarema, Rio de Janeiro, and specimens provided by the Santos Fisheries Institute, São Paulo, all from bycatch and already dead. For histological analysis, tissue fragments were collected from the left side of the animals and stained with haematoxylin-eosin, Masson’s trichrome and Picrosirius red. The results revealed structures already described in the literature, such as mucus, epidermis, dermis, muscle fiber, haemolymphatic vessels and type I collagen, in addition to the presence of type III collagen, not yet evidenced. The result reinforces the high healing capacity of sharks, highlighting the thicker and more resistant skin, with more condensed collagen in S. guggenheim, a demersal species, and the preservation of mucus in S. lewini, associated with the accumulation of collagen fiber, broadening prospects for future biomedical applications. Demersal zone ; Trichrome ; Fishing ; Bycatch ; Mucus ; Chondrichthyes Collagen: Extraction and Characterization ; Corneal Surgery and Treatments ; Skin and Cellular Biology Research
Authors: Antonia Fecke | Luiza Martins Nascentes Melo | Ann-Cathrin Groba | Gabriele Allies | Feyza Cansiz | Siva Swapna Kasarla | Sven Heiles | Albert Sickmann | Alpaslan Tasdogan | Karl W. Smith
Source: ChemRxiv (article, 2026-02-05)
Field: Chemistry — Spectroscopy

Refined on-tissue chemical derivatization expands MALDI-MSI capabilities for spatial metabolomics of mammalian organs using EDC and 4-APEBA Matrix-assisted laser desorption/ionization mass spectrometry imaging (MALDI-MSI) is widely used in metabolomics because it enables high-resolution spatial characterization of molecular distributions directly from tissue. Nevertheless, comprehensive analysis of small, polar metabolites remains difficult due to limited ionization efficiencies and diverse chemical structures. On-tissue chemical derivatization (OTCD) has emerged as an effective strategy to improve ionization efficiency, sensitivity, and selectivity for these analytes. In this study, we established and systematically optimized an OTCD approach for spatial analysis of carbonyl-and carboxyl-containing metabolites in murine tissues using 4-APEBA in combination with carbodiimide crosslinker EDC. Optimization of reagent concentrations, solvent composition, and spray parameters resulted in robust and reproducible derivatization across multiple tissue types. Application to metastatic liver and lung tissue demonstrated the method’s performance in biologically complex environments. Pronounced metabolic heterogeneity correlated with histopathological features in tumor-rich liver sections, and clear tumor-specific localizations were obtained in lung tissue with only small metastatic foci. Metabolic differences between tumor and adjacent healthy regions were consistent with established cancer metabolism pathways, including glycolytic reprogramming. These findings establish a reliable OTCD workflow for MALDI-MSI-based spatial metabolomics capable of interrogating metabolic heterogeneity in clinically relevant tumor models and demonstrate its value for future investigations of tumor metabolism. Metabolomics ; Derivatization ; Metabolic pathway ; Metabolome ; Reagent ; Mass spectrometry ; Glycolysis Mass Spectrometry Techniques and Applications ; Metabolomics and Mass Spectrometry Studies ; Advanced Proteomics Techniques and Applications
Authors: Mazen M. Al Fayez | Khaled I. Alyousef | Bader I. Al Tamran | Fahad N. Abu-Khalil | Faisal H. Alruways | Somaiah K. Almubayedh
Source: Frontiers in Nutrition (article, 2026-03-17)
Field: Chemistry — Analytical Chemistry

Identification and determination of synthetic colors in fine bakery wares (cakes) sold in Riyadh City, Saudi Arabia: a comparative study of the specifications set by the Gulf standardization organization and the European Union The findings indicate the presence of synthetic colorants in a large proportion of bakery products, with a notable number of samples failing to comply with regulatory standards, particularly when evaluated against European limits. These results highlight the need for strengthened regulatory oversight and stricter enforcement of food color regulations to ensure compliance with Gulf standards, safeguard consumer health, and improve the quality and safety of bakery products available in the local market. Tartrazine ; European union ; Indigo ; Magenta ; Standardization ; Directive Dye analysis and toxicity ; Microbial Metabolism and Applications ; Melamine detection and toxicity
Authors: Chao Yang | Zhen Ma | Xiao Wang | Ullah Yaseen | Kexin Xu | Mingrui Fan | Xiangmin Yan | Zongsheng Zhao | Lei Chen
Source: Frontiers in Veterinary Science (article, 2026-03-09)
Field: Chemistry — Spectroscopy

TMT-based proteomic profiling of serum reveals the impact of developmental stage and generation in beef cattle This study reveals that the breeding strategy for Xinjiang Brown cattle prioritizes shaping a proteomic landscape that promotes growth and metabolism, potentially at the cost of atten- uated immune-vascular reactivity. The identified panel of candidate proteins pro- vides a molecular framework for evaluating breeding outcomes and designing balanced selection strategies. Follow-up research should further investigate the functions of these candidate proteins and validate their predictive value for health and production performance in independent herds. Beef cattle ; Breed ; Proteomics ; Downregulation and upregulation ; Regulator ; Lipid metabolism ; Phenotype Advanced Proteomics Techniques and Applications ; Reproductive Physiology in Livestock ; Growth Hormone and Insulin-like Growth Factors
Authors: Keke Yu | Zhenwang Zhang | Tao Liu | Huijie Fu | Penghui Lv | Zhe Zhang | Ping Cong | Huaixu Zhan | Lina Tang | Zhiyuan Li | Jianxin Dong
Source: Frontiers in Plant Science (article, 2026-01-12)
Field: Materials Science — Biomaterials

Optimizing the application of potassium sulfate fertilizer based on the variation in soil mineral accumulation and tobacco growth: a 10-year field experiment Potassium (K) is an essential element in tobacco production, especially in Shandong, the main tobacco-growing province in China, where the improvement of tobacco yield and quality is limited by soil K deficiency, thus potassium sulfate (K<sub>2</sub>SO<sub>4</sub>) fertilizer is popularly applied by farmers. However, it is unknown how soil physicochemical characteristics and tobacco growth respond to the utilization of K<sub>2</sub>SO<sub>4</sub> fertilizer in the long term. This study aimed to determine the optimal application amount of K<sub>2</sub>SO<sub>4</sub> fertilizer to improve soil health and enhance tobacco leaf K content without yield loss. Four treatments were tested, namely mixes of 82.5 kg a.i. ha <sup>-1</sup> K<sub>2</sub>O + 66.0 kg a.i. ha <sup>-1</sup> sulfur (K<sub>82.5</sub> + S<sub>66</sub>), 165.0 + 95.7 (K<sub>165</sub> + S<sub>95.7</sub>), 247.5 + 125.4 (K<sub>247.5</sub> + S<sub>125.4</sub>) and no fertilizer (CK). Excessive use of K<sub>2</sub>SO<sub>4</sub> fertilizer led to soil acidification and a significant decrease in arylsulfatase activity. Soil available potassium (AK) and pH, that exhibited diverse responses over course of 10 years, increased and decreased with the amount of K<sub>2</sub>SO<sub>4</sub> fertilizer applied, respectively. Moreover, the K content in tobacco plants significantly increased after K<sub>2</sub>SO<sub>4</sub> fertilizer application, with that in tobacco leaves being 162.3% and 45.2% higher than that in tobacco roots and stems, respectively. Soil AK exhibited a significant positive correlation with the K content in tobacco roots, stems, and leaves, while soil pH showed the opposite performance. Soil pH is a pivotal factor influencing soil physicochemical characteristics, total dry matter and the K content in tobacco tissue. The application of K<sub>165</sub> + S<sub>95.7</sub> was more reasonable and economical in terms of matter accumulation. We concluded that the optimal application rate in Shandong was K<sub>165</sub> + S<sub>95.7</sub>, which not only improved soil health and tobacco leaf K content but also reduced input without causing yield loss. Fertilizer ; Potassium ; Potassium sulfate ; Curing of tobacco ; Potash ; Soil water ; Field experiment ; Soil pH ; Soil fertility Clay minerals and soil interactions ; Nitrogen and Sulfur Effects on Brassica ; Plant nutrient uptake and metabolism
Authors: G. V. Nesvetaev | Ju. I. Koryanova | V. V. Shut
Source: Modern Trends in Construction Urban and Territorial Planning (article, 2026-03-30)
Field: Materials Science — Materials Chemistry

Analysis of Timing Results during Continuous Concreting of a Massive Foundation Slab Introduction. Risk assessment of early cracking during hardening of massive monolithic reinforced concrete foundation slabs due to temperature gradients enhances the relevance of studies of a host of factors related to a concreting technology given the technical capabilities of workers and suppliers of concrete mixtures, as well as weather conditions. While developing technological regulations for concreting with a calculation of the thermal stress state in the early period in order to reduce and control heat dissipation, studies in the field of assignment and regulation of time parameters of the process of forming the body of the foundation slab taking into account the prescription features of concrete mixtures and weather conditions are relevant. The aim of the study is to obtain new data for calculating the time parameters of concreting massive structures using concrete pumps with technical characteristics that are not available in the regulatory framework. Materials and Methods. The paper presents the results of timing the process parameters of continuous concreting of a massive foundation slab with a volume of 1642 m 3 in 13.6 h. The numerical values of the concrete mixture pumping speed, maneuvering time of concrete mixer trucks as well as the coefficients of transition from technical to operational performance of concrete pump trucks with a technical capacity of 170 and 180 m 3 /h are obtained. The use of concrete pumps with such a capacity at an actual unloading speed of concrete mixer trucks of up to 2.3 m 3 /min ensures an actual pumping performance coefficient of up to 0.81, which basically corresponds to normal operation. Research Results. The values of the concrete pump utilization coefficient over a time period ranging from 0.478 to 0.841 with an average value of ≈ 0.66 were obtained. The actual average productivity of one concrete pump during the concreting period was ≈ 61 m 3 /h. Discussion and Conclusion. With a distance from the concrete pump truck to the concrete mixer truck waiting area within 25–50 m, the maneuvering time does not depend greatly on the distance, according to 69 measurements, it is no more than 5.76 min with a reliability of 0.95 and is identified by the convenience of an area for maneuvering concrete mixer and access roads. The results can be used in developing process regulations for continuous concreting of similar massive structures. Slab ; Truck ; Mass concrete ; Foundation (evidence) ; Cracking ; Hardening (computing) Structural mechanics and materials ; Innovations in Concrete and Construction Materials ; Construction Management and Sustainability
Authors: Ehsan Zangene | Elham Gholizadeh | Uladzislau Vadadokhau | Danilo Ritz | Amirata Saei | Mohieddin JAFARI
Source: bioRxiv (Cold Spring Harbor Laboratory) (article, 2026-03-23)
Field: Chemistry — Spectroscopy

CoPISA: Combinatorial Proteome Integral Solubility/Stability Alteration analysis Abstract Combination therapies are widely used in acute myeloid leukemia (AML), but systematic datasets capturing proteome-wide responses to multi-drug perturbations remain limited. Here we present CoPISA (Combinatorial Proteome Integral Solubility/Stability Alteration), a quantitative proteomics assay designed to profile protein solubility and stability responses to single and combined drug treatments. The dataset includes two AML drug pairs (LY3009120–sapanisertib and ruxolitinib–ulixertinib) applied to four AML cell lines (MOLM-13, MOLM-16, SKM-1, and NOMO-1) under control, single-agent, and combination conditions in both lysate and intact-cell formats. Thermal solubility profiling coupled with TMT-based multiplexed LC–MS/MS generated 16 TMT16-plex experiments comprising 192 LC–MS/MS raw files, providing deep proteome coverage across treatments and biological contexts. The resource includes raw and processed proteomics data, detailed experimental metadata in Sample and Data Relationship Format (SDRF), and reproducible analysis scripts for reporter normalization, protein-level aggregation, statistical modeling, and classification of combinatorial response patterns. The experimental design enables identification of proteins responding uniquely to combination treatments as well as overlapping single-agent effects. Technical validation demonstrates reproducible quantification across multiplex experiments and assay formats. All data are publicly available through the PRIDE repository (PXD066812) together with analysis code, enabling independent reanalysis and method development. This dataset provides a benchmark resource for studying proteome responses to drug combinations, comparing lysate and intact-cell perturbation profiles, developing computational approaches for combinatorial target inference, and supporting training in computational proteomics. Proteome ; Proteomics ; Multiplex ; Quantitative proteomics ; Profiling (computer programming) ; Cheminformatics ; Identification (biology) Advanced Proteomics Techniques and Applications ; Single-cell and spatial transcriptomics ; vaccines and immunoinformatics approaches
Authors: S. K. Mbepa | M. L. Smith | J. E. Williams
Source: The Chemical Educator (article, 2026-01-01)
Field: Chemistry — Physical and Theoretical Chemistry

Drug Docking in the Organic Chemistry Curriculum This article presents a feasible 3-week lab project that introduces drug docking with proteins to undergraduate Organic Chemistry students. In week 1, students are briefly introduced to docking by demonstrating the use of Autodock, OpenBabel, Protox, PyMol, and Protein Ligand Interaction Profiler. In week 2, students use a known drug of their choice and study its docking to a protein known to bind to the drug from literature searches. In week 3, students modify the structure of the drug and study the modified drug’s docking to the same protein. The toxicity and hydrophobicity of both drugs are predicted using ProTox. Based on binding energies, students predict the drug that is likely to bind better to the binding site. Docking (animal) ; Drug ; Protein–ligand docking ; Drug discovery ; Binding site Various Chemistry Research Topics ; Cancer and biochemical research ; Science Education and Pedagogy
Authors: Safa Y. Mohammed | Abdulqadir J. Nashwan
Source: Kidney International Reports (article, 2026-03-25)
Field: Materials Science — Materials Chemistry

WCN26-181 HEAT STROKE AND KIDNEY INJURY: A GROWING CONCERN AMIDST CLIMATE CHANGE to 3.2 in Syria).Average pediatric kidney transplant share was about 8.5% of total kidney transplants (ranging from 3.2 in Iraq to 20% in Algeria).The deceased kidney transplant program is currently available in only 8 of the 18 Middle Eastern countries included in this study.However, a deceased program is active in some Middle East countries (ie, Iran, Turkey, Kingdom of Saudi Arabia, Kuwait, and United Arab Emirates).Of note, Turkey had the highest kidney transplant rate per million populations per year (39.7),Syria had the highest pediatric kidney transplant rate per million populations per year (3.2), and Iran had the highest deceased donor kidney transplant percent of the total kidney transplants (64.2%).In the Middle East, Iran alone performed 63.5% (888/1399) of all deceased donor kidney transplants and 63.9% (106/166) of all deceased donor pediatric kidney transplants.Algeria had the highest pediatric kidney transplant share of the total transplants (20%).Low health spending, poorly developed infrastructures, delayed referral of children with chronic kidney disease, comorbidities, lack of technical expertise, inadequate pediatric dialysis programs, extended dialysis time, organ shortage, commercial transplantation, and posttransplant infections are the main pre-and posttransplant challenges.The communitygovernment partnership model from the Sindh Institute of Urology and Transplantation in Karachi Pakistan showed that pediatric renal replacement therapy and transplant can be successfully established in a developing country.Conclusion: Although pediatric kidney transplant is active in many parts of the Middle East, it is still inactive in others, mostly relying on living donors.The lack of deceased donor programs in most Middle Eastern countries is a main issue to be addressed to adequately responding to the increasing demand for organs.I have no potential conflict of interest to disclose.I did not use generative AI and AI-assisted technologies in the writing process. Climate change ; Stroke (engine) ; Heat wave ; Kidney ; Heat exhaustion Nuclear Materials and Properties ; Engineering and Material Science Research ; Nuclear Engineering Thermal-Hydraulics