jablonkagroup/rise_ai_scientists huggingface dataset:
Authors: Ariel Moura Maia | Luiz Augusto Basso | Pablo Machado | Cristiano Valim Bizarro
Source: bioRxiv (Cold Spring Harbor Laboratory) (preprint, 2025-09-02)
Field: Materials Science — Biomaterials

From 2D Monolayer to 3D Spheroid: Matrigel’s Spatial and Chemical Cues Remodel the Calu-3 Proteome ABSTRACT The limited physiological relevance of conventional 2D cell cultures hampers translational research. While 3D cultures offer a superior alternative, their reliance on undefined scaffolds like Matrigel makes it difficult to distinguish cellular responses to physical architecture from those to biochemical cues. This study provides a high-resolution, label-free quantitative comparison of the Calu-3 lung adenocarcinoma proteome in 2D monolayers versus 3D Matrigel-embedded spheroids. To further dissect the specific contributions of 3D architecture versus biochemical cues from the matrix, we included an intermediate condition where a 2D monolayer was cultured in contact with Matrigel droplets (2M). After a stringent data analysis pipeline that controlled for matrix contamination, we quantified over 3,900 human proteins and revealed that 3D culture architecture is the dominant driver of proteomic remodeling. We identified 72 differentially enriched and 48 conditionally quantified proteins distinguishing the 3D spheroids from monolayers, functionally characterized by a down-regulation of cell-surface and cholesterol biosynthesis proteins and an up-regulation of proteins associated with iron clusters. While direct comparison between the two bidimensional cultures yielded no significant differences, a dedicated paired statistical analysis demonstrated that biochemical cues from Matrigel alone prompted a subtle but significant proteome-wide shift, moving the cells closer to the 3D phenotype. This study delivers a detailed blueprint of the profound proteomic reprogramming induced by 3D culture and, by isolating the matrix’s biochemical influence, provides a critical resource for rational model selection and the design of defined synthetic matrices. Spheroid ; Monolayer ; Matrigel ; Proteome ; Chemistry ; Cell biology ; Biophysics ; Biology ; Biochemistry ; In vitro Diatoms and Algae Research ; Advanced Proteomics Techniques and Applications ; Advanced Biosensing Techniques and Applications
Authors: Constance Delwarde | Joan T. Matamalas | Sarvesh Chelvanambi | Taku Kasai | Gabriel Shlayen | Diego Vinicius Santinelli Pestana | Maedeh Zamani | Elena Aïkawa | Masanori Aikawa | Sasha A. Singh
Source: bioRxiv (Cold Spring Harbor Laboratory) (preprint, 2025-08-02)
Field: Chemistry — Spectroscopy

Nanoparticle-enabled plasma proteomics of a mouse atherosclerosis model Nanoparticle-dependent proteome enrichment coupled to mass spectrometry may allow us to identify novel plasma biomarkers in Ldlr-/- mice and facilitate monitoring of candidate proteins associated with human disease mechanisms in preclinical interventional studies, thereby opening new avenues for understanding disease pathology and uncovering understudied molecular contributors. Proteomics ; Nanoparticle ; Nanotechnology ; Computational biology ; Chemistry ; Materials science ; Biology ; Biochemistry Advanced Proteomics Techniques and Applications ; Atherosclerosis and Cardiovascular Diseases ; Adipokines, Inflammation, and Metabolic Diseases
Authors: Oxana Ye. Rodionova | Alexey L. Pomerantsev
Source: Journal of Chemometrics (article, 2025-10-20)
Field: Chemistry — Analytical Chemistry

Multiclass Partial Least Squares Discriminant Analysis: Taking New Ways—A Perspective ABSTRACT An overview of various prospective PLS‐DA strategies is presented. PLS‐DA is considered not only as a discrimination method per se but also as a method for extracting low‐dimensional features suitable for discriminating high‐dimensional data, which makes it similar to PCA. Unlike PCA, PLS‐DA extracts two sets of features: the matrix of predicted dummy responses ( Y ) and the matrix of PLS scores ( T ). Both sets are then used as input to hard (deterministic) and soft (probabilistic) discriminators, providing a wide selection of combinations. Moreover, the features can be enriched by using additional information provided by the PLS model. A total of 18 different strategies are considered, including 8 based on Y ‐features and 10 based on T ‐features. Two data sets are used to illustrate the theory, yielding the following results. Both the T ‐ and the Y ‐based approaches are comparable; additional information is ineffective. The cons and pros of each strategy are discussed. Partial least squares regression ; Pattern recognition (psychology) ; Perspective (graphical) ; Selection (genetic algorithm) ; Linear discriminant analysis ; Matrix (chemical analysis) Spectroscopy and Chemometric Analyses ; Fault Detection and Control Systems ; Spectroscopy Techniques in Biomedical and Chemical Research
Authors: A. Fouda | Amany Khalil | Brigita Kolčavová Sirková | Abdelhamid R.R. Aboalasaad
Source: Autex Research Journal (article, 2025-01-01)
Field: Materials Science — Polymers and Plastics

Effect of construction parameters on faux fur knitted fabric properties Abstract Fur is the soft, thick hair that covers the skin of certain animals, and is often used in clothing, while the cut pile loop (faux fur) knitted fabrics are produced to simulate the natural fur. The production process of these fabrics was explained in detail, and the effects of fabric construction parameters (ground loop length ( L ), ground count ( G ), and pile yarn count ( F )) on the geometrical, thermal, and abrasion resistance properties were investigated. The faux fur knitted fabric samples were produced at three levels of ground loop length (3.3, 3.5, and 3.7 mm), two different ground count (100 and 150 den), and three levels of pile yarn’s count (200, 300, and 400 den). The Tien Yang circular knitting machine settings, feeders, cams and yarns’ arrangements were illustrated. It can be concluded from the evaluated results that the fabric construction parameters had significant effects on the faux fur fabric’s properties. By increasing the pile yarn count from 200 to 400 den; the fabric weight, thickness, thermal resistance, and weight loss due to abrasion were increased approximately 75, 78, 56, and 61%, respectively. Composite material ; Materials science ; Polymer science Textile materials and evaluations ; Dyeing and Modifying Textile Fibers ; Material Properties and Processing
Authors: Atoyebi Olumoyewa D. | Tuyi Banwo S. | Alabi Adeola S. | Olusanya Oluwafemi
Source: NIPES Journal of Science and Technology Research (article, 2025-11-11)
Field: Materials Science — Polymers and Plastics

Effects of Oil Palm Fibre Additives on the Density and Compressive Strength of Aerated Concrete The popularity in the usage of concrete has prompted research to discover methods of reducing its weight, improving insulating properties, and making it cheaper. Utilising waste goods as recycled materials is one of the best ways to reduce pollution, which is a goal shared by most nations today. This can introduce novel materials for public use in addition to developing sustainable environmental management. Using a water/cement ratio of 0.65 and a mix ratio of 1:2 with an aerating agent of 0.5% of the concrete weight, the compressive strength development of aerated concrete cubes reinforced with Oil Palm Fibre (OPF) cured in water was examined at various ages. OPF was added to the mortar at weight percentages of 0.5%, 0.7%, and 1%. With compressive strengths of 5.05 N/mm2, 6.35 N/mm2, and 6.6 N/mm2, respectively, the tests' results indicated that the ideal Oil Palm Fibre level is 0.75% at 7, 14, and 28 days. These values are greater than those for the control mortar mix, whose compressive strengths were 0.3 N/mm2, 0.35 N/mm2, and 0.75 N/mm2 after 7, 14, and 28 days, respectively. According to these findings, the best amount of Oil Palm Fibre to add to aerated concrete to maximise compressive strength is 0.75 percent. When it comes to concrete repair and retrofit, this amount of oil palm fibre added to aerated concrete might effectively replace concrete Compressive strength ; Aeration ; Mortar ; Palm oil ; Autoclaved aerated concrete ; Cement Natural Fiber Reinforced Composites ; Innovative concrete reinforcement materials ; Concrete and Cement Materials Research
Authors: Matthias Hollmann | Arne Walter | Frank Duschek
Source: Journal of Instrumentation (article, 2025-07-01)
Field: Chemistry — Spectroscopy

Evaluation of molecular hydrogen detection from distance by Raman scattering Abstract The growing importance of hydrogen in the context of industrial decarbonisation is intrinsically tied with hydrogen safety and highlights the need for effective and secure detection methods. This study assesses the fundamental feasibility of remote hydrogen leak detection in outdoor environments, with the view on monitoring large scale production and storage facilities. Therefore, a Raman LIDAR approach is evaluated for the remote detection of hydrogen. In addition to its real-time detection capabilities in a closed containment at distances up to 100 m, the leaks from an opened valve are studied, both in the absence and presence of back scattering hard targets behind the hydrogen source. It is demonstrated that hydrogen leaks can be detected effectively in the presence of elastically scattered light from objects near the leak, provided that both signals can be distinguished in time. Signal count rates are used to calculate necessary integration times, based on the Poisson distribution depending on laser power and repetition rates, distance from the sample to the detector, and the amount of hydrogen to be detected. Raman scattering ; Hydrogen molecule ; Raman spectroscopy ; Hydrogen ; X-ray Raman scattering ; Scattering ; Materials science ; Optics ; Atomic physics ; Physics ; Quantum mechanics Spectroscopy and Laser Applications ; Gas Sensing Nanomaterials and Sensors ; Advanced Chemical Sensor Technologies
Authors: Olaf Witkowski | Alyssa Adams | Lana Sinapayen | Manuel Baltieri | Mahdi Khosravy
Source: ALIFE (article, 2025-10-01)
Field: Chemistry — Physical and Theoretical Chemistry

ALIFE 2025 Preface received a total of 195 full paper submissions, 12 summary submissions, and 83 late-breaking abstract submissions.In addition, there were 59 submissions to the Community Art and Demo show.All full papers and summaries were reviewed in a rigorous double-blind process by the Program Committee.Senior Program Committee members performed topic-wide meta-reviews to recommend acceptance and rejection decisions.Of these, 91 papers were accepted (67 oral presentations and 24 posters).Eight summaries were accepted.All accepted full papers are included in these proceedings.Summaries are not included here but appear in the Companion Proceedings, which is shared on the conference website for everyone to view and enjoy.Late-breaking abstracts did not undergo double-blind review.Seventy-eight were accepted and presented at the conference.Fourteen Process (computing) ; MEDLINE Various Chemistry Research Topics ; Architecture and Computational Design ; History and advancements in chemistry
Authors: Bo Wan
Source: Applied and Computational Engineering (article, 2025-07-30)
Field: Materials Science — Materials Chemistry

Logical Reasoning Capabilities of Large Language Models: A Comparative Evaluation on GPQA Dataset Recent advancements in Large Language Models (LLMs) have significantly enhanced their logical reasoning capabilities, presenting new opportunities for applications in scientific reasoning tasks. This study systematically evaluates and compares the logical reasoning performance of five prominent LLMs—GPT-4o, OpenAI-o3, OpenAI-o3 pro, DeepSeek V3, and DeepSeek R1—using the GPQA dataset, a standardized collection of science-related multiple-choice questions spanning biology, chemistry, and physics. Three dimensions were analyzed: overall accuracy, response time, and performance across difficulty levels.Results indicate that all tested models outperformed human experts in overall accuracy. Particularly, models utilizing deep-thinking (Chain-of-Thought) mechanisms consistently surpassed those without, underscoring the effectiveness of advanced reasoning strategies. Domain-specific analyses revealed superior performance on structured computational tasks in physics but relatively weaker performance in chemistry questions involving complex organic inference. Notably, increased processing time (as observed with OpenAI-o3 pro) did not proportionally enhance accuracy. Detailed analysis suggests this discrepancy was due not to resource constraints but to inefficiencies in the model’s reasoning or exploratory pathways, as it frequently expended additional time retrieving descriptive but non-essential background information. Further investigation into these reasoning bottlenecks is necessary to better understand and overcome these limitations, providing valuable insights for future research and model improvements. Computer science ; Natural language processing ; Artificial intelligence Machine Learning in Materials Science ; Topic Modeling ; Natural Language Processing Techniques
Authors: Milen Chanev | Zlatomir Dimitrov
Source: Aerospace Research in Bulgaria (article, 2025-01-01)
Field: Chemistry — Analytical Chemistry

STUDY THE APPLICABILITY OF SENTINEL-2 OPTICAL DATA, AS WELL AS BENEFITS FROM THE SENTINEL-1 SAR DATA, FOR PREDICTING THE YIELD OF ORGANIC BARLEY The barley crop is widely used in the economic life of humanity and is characterized by great ecological plasticity. It is a good competitor to other cereals, which is why it is extremely suitable for growing in organic farming. The multispectral data obtained from the COPERNICUS Sentinel-2 satellites has proven in numerous scientific works its applicability to support crop monitoring. In that way, that data is invaluable in optimizing the production processes. In this study, a comparison was made between satellite data products derived from the COPERNICUS Sentinel-2 optical and Sentinel-1 SAR data, as well as studying their statistical relationship with the yield of the organically grown barley. The spatial resolution of all products is 10 m. The utilization of both satellite data types for monitoring and forecasting the yield of organically grown barley has been verified. The BBCH-41 phase was found to be the most suitable for the utilization of Sentinel-2 optical data to generate a different set of vegetation indices for yield prediction. In that phase, most of the tested vegetation indices showed successful yield prediction. The most relevant is the Green Chlorophyll Vegetation Index (GCVI; r = 0.80), which has the highest correlation with the yield. Considering SAR data, the backscatter in co- and cross-pol were derived in terms of Sigma-Nought. The Radar Vegetation Index in dual-pol (dRVI) was also calculated. As reported in other studies, a correlation is observed between dRVI and vegetation indices (e.g., NDVI). Whole output SAR products are sensitive to the geometrical properties of the crop and represent in various extent the phenological development of the organic barley. In this regard, SAR data complements optical data and provides reliable information on crop conditions during periods of high cloud cover. Bearing in mind that very often these periods coincide with phenological phases that are critical in crop development. Yield (engineering) ; Remote sensing ; Environmental science ; 3D optical data storage ; Geology ; Computer science ; Materials science Spectroscopy and Chemometric Analyses
Authors: Cecilia Spedalieri | Janina Kneipp
Source: Analysis & Sensing (article, 2025-06-06)
Field: Materials Science — Electronic, Optical and Magnetic Materials

Surface Enhanced Raman Scattering of a Lysosomal Fluorescent Dye Knowledge about the molecular structure and interactions of intracellular dyes is important to understand their function and possible effects in the biological environment. Here we discuss vibrational spectra of LysoSensor (LSG), a fluorescent marker for the acidic lysosomal compartment in cells. Raman spectra of the molecule at concentrations typically applied in experiments with cell cultures were obtained by surface‐enhanced Raman scattering (SERS) experiments at varying pH values, using biocompatible gold nanoprobes also used in live cell SERS. The signals in the SERS spectrum of LSG were assigned based on spectra collected from its aromatic constituents benzimidazole and naphthalimide under the same conditions. The data indicate a strong pH dependence of the spectra of benzimidazole that is less pronounced in the vibrational signature of the LSG molecule. Despite excitation of the SERS off‐resonance with the dye molecule, spectra obtained with the biocompatible wavelength of 785 nm have better sensitivity towards pH‐dependent structural changes, due to favorable electromagnetic enhancement of vibrational modes, than when using excitation at 633 nm. The characterization based on SERS will help to understand the interactions of LSG with the cellular environment and with other probes, which will be useful for the design of efficient labels for bioanalysis. Fluorescence ; Raman scattering ; Surface (topology) ; Materials science ; Raman spectroscopy ; Photochemistry ; Nanotechnology ; Chemistry ; Biophysics ; Optics ; Physics ; Biology Gold and Silver Nanoparticles Synthesis and Applications ; Spectroscopy Techniques in Biomedical and Chemical Research ; Protein Interaction Studies and Fluorescence Analysis
Authors: Martin Petrun | Ermin Rahmanović
Source: Materials (article, 2025-05-03)
Field: Materials Science — Electronic, Optical and Magnetic Materials

Parameter Estimation for the Basic Zirka-Moroz History-Dependent Hysteresis Model for Electrical Steels History-dependent hysteresis models can potentially describe magnetization curves of all orders accurately. This property is essential for modeling magnetization and power loss in magnetic components subjected to distorted excitation waveforms, which result in complex magnetization patterns such as offset minor loops. The basic Zirka-Moroz history-dependent hysteresis model offers a good balance between the model's complexity and accuracy. However, estimating the model's parameters can be challenging. This research provides insight into the parameter estimation procedure for the discussed hysteresis model. Based on the measured first-order reversal curves, the fundamental two-step parameter estimation procedure was employed and analyzed for two non-oriented and one grain-oriented electrical steel types used widely in contemporary electric drives and electromagnetic devices. For each sample evaluated, two sets of parameters were estimated and compared to the reference parameters recommended for non-oriented electrical steels. The performed analysis is essential for gaining a comprehensive understanding of the capabilities, challenges, requirements, and limitations associated with estimating the parameters and performance of the analyzed model for specific electrical steel types. Hysteresis ; Magnetization ; Magnetic hysteresis ; Electrical steel ; Estimation theory ; Excitation ; Offset (computer science) ; Waveform ; Mathematical model ; Materials science ; Computer science ; Voltage ; Mathematics ; Algorithm ; Physics ; Statistics ; Magnetic field ; Engineering ; Condensed matter physics ; Electrical engineering Magnetic Properties and Applications ; Electric Motor Design and Analysis ; Magnetic properties of thin films
Authors: Linze Li | Andrew A. Li | Ning Lü | Jiashun Jin
Source: Microscopy and Microanalysis (article, 2025-07-01)
Field: Materials Science — Surfaces, Coatings and Films

Scanning Transmission Electron Microscopy-Based Grain Mapping via Non-Negative Matrix Factorization Processing Materials science ; Transmission electron microscopy ; Scanning transmission electron microscopy ; Scanning electron microscope ; Matrix (chemical analysis) ; Nanotechnology ; Composite material Electron and X-Ray Spectroscopy Techniques ; Advanced Electron Microscopy Techniques and Applications ; Force Microscopy Techniques and Applications
Authors: Jinshan Li
Source: Materials and Solidification (article, 2025-06-01)
Field: Materials Science — Materials Chemistry

Inaugural Editorial for <i>Materials and Solidification</i> With great pleasure, we announce the official launch of Materials and Solidification, an international, peer-reviewed academic journal dedicated to publishing original research, reviews, and perspectives in the fields of materials science and solidification phenomena.Solidification lies at the heart of modern materials processing.From casting and crystal growth to additive manufacturing and rapid quenching, the understanding and control of solidification processes are fundamental to the design of advanced materials with tailored microstructures and properties.Moreover, new computational tools, multiscale simulations, in situ characterizations, and interdisciplinary approaches have revolutionized how we study and manipulate solidification behavior. Materials science ; Engineering physics ; Engineering Solidification and crystal growth phenomena ; Metallurgical and Alloy Processes ; Machine Learning in Materials Science
Authors: David Z. He | S.H. Liu | Veronica Gomez‐Godinez | Zachary Wang | Chengbiao Wu | Linda Shi
Source: Proceedings of the World Congress on Electrical Engineering and Computer Systems and Science (article, 2025-08-01)
Field: Materials Science — Biomaterials

Using Robotic Laser Ablation System to Study Cellular Stress Responses Laser ablation is an established process for analyzing cellular responses to damage.By utilizing the specificity and visualization capabilities of a femtosecond laser in conjunction with fluorescent dyes and image analysis applications, this contemporary laser ablation methodology is a promising process for emulating and analyzing cellular reactions affected by degenerative diseases and other diseases characterized by cellular stress responses.In this study, we evaluated the methodology using two cell types: primary mouse cortical neurons and myocardial cells.We used Quantitative Phase Imaging to analyze the changes in the thickness of PC12 cells, HEK293 cells, and collagen tissue.In mouse primary cortical neurons, laser ablation was applied to assess axonal responses under varying glucose concentrations.In myocardial cells, laser ablation was used alongside nucleic acid dyes to evaluate cellular reactions to neighboring cell death.Although definitive results have yet to be reached, the laser ablation model is thus a viable approach for simulating and analyzing cellular degeneration. Ablation ; Laser ablation ; Stress (linguistics) ; Computer science ; Laser ; Materials science ; Engineering ; Optics ; Aerospace engineering ; Physics Electrospun Nanofibers in Biomedical Applications ; Laser Applications in Dentistry and Medicine