jablonkagroup/rise_ai_scientists huggingface dataset:
Authors: Cesar B. Aparicio-Lopez | Sarah A. Timmerman | Gabriella Lorino | Tatiana Rogers | Marla Pyle | Tej B. Shrestha | Matthew T. Basel
Source: Cancers (article, 2024-09-01)
Field: Materials Science — Biomaterials

Thermosensitive Liposomes for Gemcitabine Delivery to Pancreatic Ductal Adenocarcinoma Treatment of pancreatic ductal adenocarcinoma with gemcitabine is limited by an increased desmoplasia, poor vascularization, and short plasma half-life. Heat-sensitive liposomes modified by polyethylene glycol (PEG; PEGylated liposomes) can increase plasma stability, reduce clearance, and decrease side effects. Nevertheless, translation of heat-sensitive liposomes to the clinic has been hindered by the low loading efficiency of gemcitabine and by the difficulty of inducing hyperthermia in vivo. This study was designed to investigate the effect of phospholipid content on the stability of liposomes at 37 °C and their release under hyperthermia conditions; this was accomplished by employing a two-stage heating approach. First the liposomes were heated at a fast rate, then they were transferred to a holding bath. Thermosensitive liposomes formulated with DPPC: DSPC: PEG2k (80:15:5, mole%) exhibited minimal release of carboxyfluorescein at 37 °C over 30 min, indicating stability under physiological conditions. However, upon exposure to hyperthermic conditions (43 °C and 45 °C), these liposomes demonstrated a rapid and significant release of their encapsulated content. The encapsulation efficiency for gemcitabine was calculated at 16.9%. Additionally, fluorescent analysis during the removal of unencapsulated gemcitabine revealed an increase in pH. In vitro tests with BxPC3 and KPC cell models showed that these thermosensitive liposomes induced a heat-dependent cytotoxic effect comparable to free gemcitabine at temperatures above 41 °C. This study highlights the effectiveness of the heating mechanism and cell models in understanding the current challenges in developing gemcitabine-loaded heat-sensitive liposomes. Liposome ; Gemcitabine ; Hyperthermia ; Polyethylene glycol ; In vivo ; Chemistry ; Biophysics ; Materials science ; Biochemistry ; Chemotherapy ; Medicine ; Internal medicine ; Biology Nanoparticle-Based Drug Delivery ; Pancreatic and Hepatic Oncology Research ; Nanoplatforms for cancer theranostics
Authors: Joshua Blessing Animasaun | Onuh Matthew Ijiga | Victoria Bukky Ayoola | Lawrence Anebi Enyejo
Source: International Journal of Scientific Research and Modern Technology. (article, 2024-01-30)
Field: Chemistry — Physical and Theoretical Chemistry

Impact of Solvent Polarity on Volatile and Non-Volatile Cannabinoid Recovery: A Multivariate GC-MS/LC-MS Extraction Optimization Study The increasing complexity of STEM learning tasks and the scale of digital education environments have exposed fundamental limitations in traditional automated feedback systems. Most existing approaches rely on unimodal inputs or rule-based logic, providing surface-level feedback that fails to capture underlying learner misconceptions and reasoning processes. This study proposes and evaluates a multimodal large language model–driven diagnostic feedback framework designed to deliver accurate, explainable, and instructionally aligned feedback in STEM learning platforms. The framework integrates heterogeneous learner data, including text responses, symbolic mathematics, diagrams, code submissions, and interaction traces, through modality-specific encoders and attention-based fusion strategies. Diagnostic reasoning is performed using a multimodal large language model constrained by curricular objectives and enhanced with explainability mechanisms such as rationale tracing and attention visualization. Empirical evaluation across mathematics, physics, and computer science tasks demonstrates significant improvements over baseline systems in diagnostic accuracy, learning gains, error correction rates, learner engagement, and trust. The findings indicate that multimodal LLM-driven diagnostic feedback can operationalize formative assessment principles at scale, offering a robust pathway toward more transparent, adaptive, and pedagogically meaningful AI-supported learning in STEM education. Operationalization ; Tracing ; Formative assessment ; Process (computing) ; Polarity (international relations) ; Discriminator ; Abstraction ; Multivariate statistics ; Encoder Various Chemistry Research Topics ; Forensic Toxicology and Drug Analysis ; Cannabis and Cannabinoid Research
Authors: Arora Bharti | Kulkarni Ajinkya | Markus M Andrea | Ramos-Gomes Fernanda | Bohnenberger Hanibal | Philipp Ströbel | Alves Frauke | Klein Oliver
Source: npj Imaging (article, 2024-09-23)
Field: Chemistry — Spectroscopy

MALDI imaging combined with two-photon microscopy reveals local differences in the heterogeneity of colorectal cancer Colorectal cancer (CRC) remains a leading cause of cancer-related mortality worldwide, accentuated by its heterogeneity and complex tumour microenvironment (TME). The role of TME on tumour pathophysiology is pivotal, especially the influence of components of the extracellular matrix (ECM), such as collagen. We introduce a novel multimodal imaging strategy to unravel the complex spatial heterogeneity of CRC by integrating the imaging features from two-photon laser scanning microscopy (2PLSM) and histology with proteomics signatures from matrix-assisted laser desorption ionization-mass spectrometry imaging (MALDI MSI). Our study is the first to correlate the structural coherence of collagen fibres and the nuclei distribution profile of tumour tissue with the peptide signatures, offering insights into the proteomic landscape of CRC within regions of high nuclei distribution (HND), as well as chaotic and organised regions of collagen. We use this approach to distinguish the patient tissues originating from left-sided colorectal cancer (LSCC) and from right-sided colorectal cancer (RSCC). This discriminative signature highlights the role of high nuclei distribution and collagen architecture in tumour progression. Complementary m/z values of several proteins associated to components of ECM, such as plectin, vinculin, vimentin, and myosin, have shown differentially intensity distributions between LSCC and RSCC. Our findings demonstrate the potential of combining structural information with peptide features to identify molecular signatures in different tumour regions and retrieve new insights into CRC pathophysiology. Extracellular matrix ; Colorectal cancer ; Pathology ; Plectin ; Proteomics ; Biology ; Tumor microenvironment ; Mass spectrometry imaging ; Vinculin ; Cancer research ; Cancer ; Computational biology ; Cell biology ; Chemistry ; Intermediate filament ; Medicine ; Cell ; Mass spectrometry ; Genetics ; Signal transduction ; Focal adhesion ; Gene Advanced Proteomics Techniques and Applications ; Molecular Biology Techniques and Applications ; Bacterial Identification and Susceptibility Testing
Authors: Fanny Kozak | Dörte Brandis | Christopher Pötzl | Ludovica M. Epasto | Daniela Reichinger | Dominik Obrist | Herwig Peterlik | Anton A. Polyansky | Bojan Žagrović | Fabian Daus | Armin Geyer | Christian F. W. Becker | Dennis Kurzbach
Source: Advanced Science (article, 2024-06-14)
Field: Materials Science — Biomaterials

An Atomistic View on the Mechanism of Diatom Peptide‐Guided Biomimetic Silica Formation Deciphering nature's remarkable way of encoding functions in its biominerals holds the potential to enable the rational development of nature-inspired materials with tailored properties. However, the complex processes that convert solution-state precursors into solid biomaterials remain largely unknown. In this study, an unconventional approach is presented to characterize these precursors for the diatom-derived peptides R5 and synthetic Silaffin-1A<sub>1</sub> (synSil-1A<sub>1</sub>). These molecules can form defined supramolecular assemblies in solution, which act as templates for solid silica structures. Using a tailored structural biology toolbox, the structure-function relationships of these self-assemblies are unveiled. NMR-derived constraints are employed to enable a recently developed fractal-cluster formalism and then reveal the architecture of the peptide assemblies in atomistic detail. Finally, by monitoring the self-assembly activities during silica formation at simultaneous high temporal and residue resolution using real-time spectroscopy, the mechanism is elucidated underlying template-driven silica formation. Thus, it is demonstrated how to exercise morphology control over bioinorganic solids by manipulating the template architectures. It is found that the morphology of the templates is translated into the shape of bioinorganic particles via a mechanism that includes silica nucleation on the solution-state complexes' surfaces followed by complete surface coating and particle precipitation. Diatom ; Mechanism (biology) ; Nanotechnology ; Rational design ; Materials science ; Peptide ; Chemistry ; Biology ; Physics ; Biochemistry ; Ecology Diatoms and Algae Research ; Paleontology and Stratigraphy of Fossils ; Calcium Carbonate Crystallization and Inhibition
Authors: Zhilin Gao | Wenqian Wang | Hongjia Wang | LI Ruiyan
Source: Horticulturae (article, 2024-04-04)
Field: Chemistry — Analytical Chemistry

Selection of Spectral Parameters and Optimization of Estimation Models for Soil Total Nitrogen Content during Fertilization Period in Apple Orchards The rapid and accurate diagnosis of nitrogen content in apple orchard soil is of great significance for the rational application of nitrogen fertilizer in orchards to improve apple yield and quality. An apple orchard in Shuangquan Town, Changqing District, Jinan City, Shandong Province, was taken as the experimental area. The optimal method for extracting spectral characteristic bands and screening spectral characteristic indices (SCIs) of soil total nitrogen (TN) for independent and comprehensive fertilization periods was explored. Independent and comprehensive soil TN content estimation models were constructed and optimized for each and the entire fertilization period, respectively. The results show that compared with the correlation coefficient method, stepwise multiple linear regression (SMLR) performs better in extracting hyperspectral characteristic bands of soil TN content. It helps to achieve a higher modeling accuracy, smaller root mean square error (RMSE), and is more conducive to avoiding the influence of multicollinearity of model variables. The sensitive areas of soil TN content in the SCI do not undergo significant changes due to different fertilization periods. Among them, the ratio spectral indices (RSIs) are in the range of 800–900 nm, 1900–1950 nm, and 2200–2300 nm, while the sensitive areas of the difference spectral index (DI) and Normalized difference spectral index (NDSI) are in the range of 1900–1950 nm and 2200–2300 nm. The combination of SCI and characteristic bands significantly improves the prediction accuracy of soil TN estimation models. The independent and comprehensive estimation models for each fertilization period based on the BP (back propagation) neural network optimized by the Mind Evolution Algorithm (MEA-BPNN) can achieve a more stable and accurate estimation of soil TN. Finally, using soil spectral characteristic bands selected through continuum removal (CR) transformation and SMLR, combined with SCI, the model based on the MEA-BPNN (CR-SCI-MEA-BPNN) has the best prediction performance. The modeling determination coefficients R2 for each fertilization period reached 0.94, 0.95, 0.92, and 0.94, respectively, with RMSE of 0.0032, 0.0024, 0.0035, and 0.0027. The R2 and RMSE of the modeling and validation set of the entire fertilization period comprehensive model are 0.899, 0.0038, and 0.89, 0.0041, respectively. The results of this article provide technical support for promoting the timely monitoring of soil TN content and guiding rational fertilization in apple orchards. Orchard ; Mean squared error ; Human fertilization ; Soil science ; Nitrogen ; Coefficient of determination ; Environmental science ; Soil test ; Mathematics ; Soil water ; Agronomy ; Statistics ; Chemistry ; Biology Spectroscopy and Chemometric Analyses ; Remote Sensing in Agriculture ; Horticultural and Viticultural Research
Authors: Hossein Shamsi | Reza Yari | Ali Salehzadeh
Source: Scientific Reports (article, 2024-05-04)
Field: Materials Science — Biomaterials

Biosynthesized BiFe2O4@Ag nanoparticles mediated Scenedesmus obliquus induce apoptosis in AGS gastric cancer cell line The use of magnetic metal nanoparticles has been considered in cancer treatment studies. In this study, BiFe<sub>2</sub>O<sub>4</sub>@Ag nanoparticles were synthesized biologically by Scenedesmus obliquus for the first time and their anticancer mechanism in a gastric cancer cell line was characterized. The physicochemical properties of the nanoparticles were evaluated by fourier transform infrared spectroscopy (FT-IR), X-ray diffraction (XRD), energy-dispersive X-ray spectroscopy (EDS), scanning electron microscopy (SEM), transmission electron microscopy (TEM), dynamic Light Scattering (DLS), and zeta potential analyses. Cell viability and nuclear damage were investigated by the MTT and Hoechst staining assays, respectively. Flow cytometry analysis was performed to determine the frequency of the necrotic and apoptotic cells as well as cell cycle analysis of the nanoparticles-treated cells. Physicochemical characterization showed that the synthesized particles were spherical, without impurities, in a size range of 38-83 nm, with DLS size and zeta potential of 295.7 nm and -27.7 mV, respectively. BiFe<sub>2</sub>O<sub>4</sub>@Ag nanoparticles were considerably more toxic for the gastric cancer cells (AGS cell line) than HEK293 normal cells with IC<sub>50</sub> of 67 and 117 µg/ml, respectively. Treatment of AGS cells with the nanoparticles led to a remarkable increase in the percentage of late apoptosis (38.5 folds) and cell necrosis (13.4 folds) and caused cell cycle arrest, mainly at the S phase. Also, nuclear fragmentation and apoptotic bodies were observed in the gastric cancer cells treated with the nanoparticles. This study represents BiFe<sub>2</sub>O<sub>4</sub>@Ag as a novel anticancer candidate against gastric cancer that can induce cell apoptosis through DNA damage and inhibition of cell cycle progression. Apoptosis ; Zeta potential ; Dynamic light scattering ; Viability assay ; Nanoparticle ; Flow cytometry ; Cell cycle ; DNA fragmentation ; Materials science ; Fragmentation (computing) ; Chemistry ; Nuclear chemistry ; Biophysics ; Molecular biology ; Nanotechnology ; Biology ; Biochemistry ; Programmed cell death Nanoparticle-Based Drug Delivery ; Nanoparticles: synthesis and applications ; Nanoplatforms for cancer theranostics
Authors: Xiaoyu Tian | Fang Qin | Xiaorui Zhang | Shanshan Yu | Chunxia Dai | Xingyi Huang
Source: Foods (article, 2024-11-10)
Field: Chemistry — Analytical Chemistry

Visualization of Moisture Content, Reducing Sugars, and Chewiness in Bread During Oral Processing Based on Hyperspectral Imaging Technology This study evaluated the differences in oral processing and texture perception of breads with varying compositions. The research investigated the dynamic changes in moisture content (MC), reducing sugars (RSs), and chewiness of the bolus formed from white bread (B0) and 50% whole-wheat bread (B50) during oral processing. Hyperspectral imaging (HSI) combined with chemometric methods was used to establish quantitative prediction models for MC, RSs, and chewiness, and to create visual distribution maps of these parameters. The results showed that B0 had a higher moisture content and a faster hydration rate than B50 during the initial stages of oral processing, indicating greater hydrophilicity and ease of saliva wetting. Additionally, the uniformity of moisture distribution in the bolus of B0 was higher than that of B50. B50 exhibited significantly lower RSs content and poorer distribution uniformity compared to B0. The primary differences in chewiness between the two types of bread were observed during the early stages of oral processing, with B50 requiring more chewing effort initially. This study demonstrated that HSI technology can effectively monitor and elucidate the compositional changes in food particles during oral processing, providing new insights into bread texture perception and offering a scientific basis for improving bread processing and texture. Chewiness ; Food science ; Hyperspectral imaging ; Moisture ; Water content ; Chemistry ; Computer science ; Artificial intelligence Spectroscopy and Chemometric Analyses ; Food composition and properties ; Sensory Analysis and Statistical Methods
Authors: Saurabh Rai | Ankit Gupta
Source: Scientific Reports (article, 2024-09-17)
Field: Materials Science — Materials Chemistry

Dynamic response of sandwich functionally graded nanoplate under thermal environments and elastic foundations using dynamic stiffness method The present paper introduces the development of dynamic stiffness method for analyzing small-scale sandwich functionally graded nanoplates resting on elastic foundation in thermal environments. The mathematical formulation is based on classical plate theory in conjunction with nonlocal elasticity theory. The governing equation is derived using Hamilton's principle. The dynamic stiffness matrix is obtained through the application of the Levy displacement approach and assembled to form the global stiffness matrix. The final matrix is solved for natural frequency of the plates using the Wittrick-Williams algorithm. The proposed methodology is validated against existing literature, demonstrating a strong agreement. Various parametric studies explore the effects of thermal environments, volume fraction index, sandwich configurations, elastic foundation characteristics, nonlocal parameter and boundary conditions. The results show the versatility of the proposed approach in addressing small scaled complex engineering structures. This research significantly contributes to the understanding and analysis of sandwich functionally graded nanoplates, providing valuable insights for applications in aerospace, structural systems, sensors, actuators, and energy harvesting devices. Stiffness ; Thermal ; Materials science ; Composite material ; Structural engineering ; Computer science ; Engineering ; Physics ; Thermodynamics Nonlocal and gradient elasticity in micro/nano structures ; Composite Structure Analysis and Optimization ; Structural Behavior of Reinforced Concrete
Authors: Koichiro Adachi | Makiko Shimizu | Fumiaki Shono | Kimito Funatsu | Hiroshi Yamazaki
Source: The Journal of Toxicological Sciences (article, 2024-01-01)
Field: Chemistry — Spectroscopy

Octanol/water partition coefficients estimated using retention times in reverse-phase liquid chromatography and calculated &lt;i&gt;in silico&lt;/i&gt; as one of the determinant factors for pharmacokinetic parameter estimations of general chemical substances The octanol/water partition coefficient P (logP) is a hydrophobicity index and is one of the determining factors for the pharmacokinetics of orally administered substances because it influences membrane permeability. To illustrate the wide-ranging variety of compounds in the chemical space, a two-dimensional data plot consisting of 25 blocks was previously proposed based on a substance's in silico chemical descriptors. The logP values of approximately 200 diverse chemicals (test plus reference compounds covering all 25 blocks of the chemical space) were estimated experimentally using retention times in reverse-phase liquid chromatography; these values were compared with those of authentic reference compounds with established logP values (available for 17 of 60 reference substances in the Organization for Economic Co-operation and Development Test Guideline 117). The logP values of 140 of 165 chemicals successfully estimated using four different mobile phase conditions (pH 2, 4, 7, and 10 for molecular forms) correlated significantly with those calculated using the in silico packages ChemDraw and ACD/Percepta (r > 0.72). Although substances that neighbored authentic compounds in the chemical space had precisely correlated logP values estimated experimentally and in silico, some compounds that were more distant from authentic substances showed lower logP values than those estimated in silico. These results indicate that additional authentic reference materials with wider ranging chemical diversity and their logP values from reverse-phase liquid chromatography should be included in the international test guidance to promote simple and reliable estimation of octanol/water partition coefficients, which are important determinant factors for the pharmacokinetics of general chemicals. Partition coefficient ; In silico ; Chemistry ; Octanol ; Chromatography ; Chemical space ; Physiologically based pharmacokinetic modelling ; Molecular descriptor ; Pharmacokinetics ; Quantitative structure–activity relationship ; Stereochemistry ; Bioinformatics ; Drug discovery Analytical Chemistry and Chromatography ; Analytical Methods in Pharmaceuticals ; Computational Drug Discovery Methods
Authors: Yun Chiang | Frido Welker | Matthew J. Collins
Source: Open Research Europe (article, 2024-04-15)
Field: Chemistry — Spectroscopy

Spectra without stories: reporting 94% dark and unidentified ancient proteomes We report that typically 94% of the published ancient spectra remain unidentified. This phenomenon may be caused by multiple factors, notably the limitations of database searching and the selection of user-defined reference data with advanced modification patterns. These 'spectra without stories' highlight the need for widespread data sharing to facilitate methodological development and minimise the loss of often irreplaceable ancient materials. Testing and validating alternative search strategies, such as open searching and de novo sequencing, may also improve overall identification rates. Hence, lessons learnt in palaeoproteomics may benefit other fields grappling with challenging data. Proteome ; History ; Biology ; Bioinformatics Advanced Proteomics Techniques and Applications ; Genomics and Phylogenetic Studies ; Cell Image Analysis Techniques