jablonkagroup/rise_ai_scientists huggingface dataset:
Authors: Aleksander M. Haack | Konstantinos Kalogeropoulos
Source: PROTEOMICS (article, 2025-11-01)
Field: Chemistry — Spectroscopy

Data Processing and Analysis in Positional Proteomics Proteolytic cleavage is an irreversible post-translational modification (PTM), and dysregulation of protease activity is often a hallmark in disease. Aberrant proteolysis can alter protein abundance or function, disturbing cellular state and resulting in disease-specific biomarkers or therapeutic targets. Positional proteomics facilitates global identification and precise quantification of position-specific peptides, such as those located N- or C-terminal in the protein sequence. These techniques enable the study of both natural and neo-protein termini, as well as associated PTMs. Despite its importance, proteolysis remains understudied due to experimental challenges and complex data processing. In this review, we outline key strategies for data analysis and processing in positional proteomics, emphasizing how identification, quantification, and interpretation of proteolytic cleavage sites differ from standard proteomics data analysis pipelines. We discuss differences in common approaches for terminomics-focused workflows, comparing N- versus C-terminomics, as well as different labeling strategies and acquisition methods. Additionally, we highlight considerations for proper normalization approaches, specifically the need to normalize cleavage abundances relative to protein and protease abundance. We explain the importance of integrating structural data, solvent accessibility, and tissue expression profiles during data analysis to better evaluate the biological significance of experimental results. Proteomics ; Proteolysis ; Normalization (sociology) ; Protease ; Quantitative proteomics ; Proteome ; Protein expression ; Cleavage (geology) Advanced Proteomics Techniques and Applications ; Biomedical Text Mining and Ontologies ; Machine Learning in Bioinformatics
Authors: Limin Wang | Zi Long | Tao Gu | Feng Ju | Huajun Zhen | Hui Luan | Guangli Xiu | Zhihe Tang
Source: Sustainability (article, 2025-09-24)
Field: Chemistry — Analytical Chemistry

Emerging Pollutants as Chemical Additives in the Petroleum Industry: A Review of Functional Uses, Environmental Challenges and Sustainable Control Strategies Emerging pollutants (EPs) associated with the petroleum industry present considerable challenges to environmental management and sustainable development. To support sustainable development and improve the control of EPs in the petroleum industry, this review systematically examines the functional uses of EPs as chemical additives across the entire petroleum supply chain—from extraction and transportation to refining and product blending. It also summarizes the environmental emissions, health impacts, mitigation strategies, and current regulatory frameworks of EPs. In addition, some challenges have been found, namely unclear data on EPs in chemical additives, insufficient attention to high-risk areas, undefined health risks of mixing EPs, lack of green assessment of alternative technologies, and regional policy disparities, which collectively hinder the effective prevention and management ofEPs. In response, we propose future perspectives including enhanced screening and substitution of high-EP-risk additives, development of source-specific fingerprinting techniques, expanded monitoring of mixed contaminants and understudied regions, accelerated deployment of green technologies, and strengthened global cooperation under sustainability-oriented governance frameworks. This study underscores the necessity of integrated, science-based approaches to align petroleum industry practices with global sustainability goals. This review underscores the critical need for a proactive and integrated approach toward the sustainable development of the petroleum industry through the control of and reduction in EPs. Sustainability ; Sustainable development ; Oil refinery ; Petroleum ; Pollutant ; Control (management) ; Corporate governance Petroleum Processing and Analysis ; Toxic Organic Pollutants Impact ; Microbial bioremediation and biosurfactants
Authors: Zhongfan Luo | Fanmin Kong | Hao Su | Ang Xiao | Dong Wang | Peng Jiang | Jingjing Chen | Danyang Cao | Jiahua Zhu | Xiaohua Lü | Liwen Mu
Source: Journal of Applied Polymer Science (article, 2025-05-22)
Field: Materials Science — Polymers and Plastics

Rheological Property‐Based Optimization of Spinning Temperature to Enhance the Performance of Ultra‐High‐Molecular‐Weight Polyethylene Fibers ABSTRACT In this work, the effect of spinning temperatures (165°C, 170°C, 175°C, and 180°C) on the rheological properties of ultra‐high‐molecular‐weight polyethylene (UHMWPE) gel was investigated, and its subsequent direct effect on the performance of UHMWPE fibers was analyzed, including modulus, morphology, structure, and mechanical properties. The experimental results indicate that the structural viscosity index can be used as a rapid and effective screening tool in evaluating the properties of UHMWPE fibers. When the structural viscosity index reaches a relatively smaller value of 12.584 at 170°C, the linear density, tensile strength, tensile modulus, and breaking elongation of UHMWPE fibers are better, achieving values of 52.33 dtex, 31.88 cN/dtex, 1022.49 cN/dtex, and 3.34%, respectively. Moreover, AFM analysis further confirms that UHMWPE fibers spun at 170°C exhibit a smoother surface with a roughness of 0.57 nm and a relatively high contact modulus of 61.94 MPa. These findings provide valuable insights for tailoring rheological properties to enhance subsequent applications, including spinning, adhesive, and 3D printing. Materials science ; Composite material ; Spinning ; Rheology ; Ultimate tensile strength ; Modulus ; Ultra-high-molecular-weight polyethylene ; Polyethylene ; Viscosity ; Elongation ; Intrinsic viscosity ; Polymer Polymer crystallization and properties ; Polymer Foaming and Composites ; Advanced Sensor and Energy Harvesting Materials
Authors: Carina Karner | Emanuela Bianchi
Source: ACS Nano (article, 2025-01-28)
Field: Materials Science — Materials Chemistry

Partially Bonded Crystals: A Pathway to Porosity and Polymorphism In recent years, experimental and theoretical investigations have shown that anisotropic colloids can self-organize into ordered porous monolayers, where the interplay of localized bonding sites, so-called patches, with the particle's shape is responsible for driving the systems away from close-packing and toward porosity. Until now it has been assumed that patchy particles have to be fully bonded with their neighboring particles for crystals to form, and that, if full bonding cannot be achieved due to the choice of patch placement, disordered assemblies will form instead. In contrast, we show that by deliberately displacing the patches such that full bonding is disfavored, a different route to porous crystalline monolayers emerges, where geometric frustration and partial bonding are decisive process. The resulting dangling bonds lead to the emergence of effectively chiral units which then act as building blocks for energetically equivalent crystal polymorphs. Materials science ; Porosity ; Polymorphism (computer science) ; Crystallography ; Composite material ; Nanotechnology ; Chemical engineering ; Chemistry ; Genetics ; Biology ; Gene ; Genotype ; Engineering Pickering emulsions and particle stabilization ; Surfactants and Colloidal Systems ; Cultural Heritage Materials Analysis
Authors: Assiya Atif | Soukaina Ameur | Houssine Ait Sir
Source: Current Chemistry Letters (article, 2025-01-01)
Field: Chemistry — Organic Chemistry

Synthesis, characterization and in silico evaluation of 2,5-bis(2-(trifluoromethyl)-1H-benzimidazol-5-yl)-1,3,4-oxadiazole: Reactivity, ADME/toxicity, and docking against therapeutic targets This study presents the synthesis and characterization of a novel 1,3,4-oxadiazole derivative compound, 2,5-bis(2-(trifluoromethyl)-1H-benzimidazol-5-yl)-1,3,4-oxadiazole, using 1H NMR, 13C NMR, mass spectrometry and FTIR-ATR infrared spectroscopy. Reactivity, ADME/toxicity and docking to therapeutic targets were investigated revealed that 2,5-bis(2-(trifluoromethyl)-1H-benzimidazol-5-yl)-1,3,4-oxadiazole (BTBO) exhibits excellent intestinal absorption, limited solubility and CNS penetration, and restained clearance. It interacts with key cytochromes and transporters, suggesting possible drug–drug interactions. Toxicity evaluations indicated mutagenic potential and moderate oral toxicity, with no hepatotoxicity or skin sensitization. Molecular docking demonstrated strong binding affinities to targets in six therapeutic areas, often outshining reference ligands, supporting its auspicious pharmacokinetic and therapeutic potential. In silico ; Docking (animal) ; Binding affinities ; In vitro ; Pharmacokinetics ; Mass spectrometry ; Molecular model Synthesis and biological activity ; Synthesis and Characterization of Heterocyclic Compounds
Authors: Robert Rauschen | Dean Thomas | Leroy Cronin
Source: Angewandte Chemie International Edition (article, 2025-11-20)
Field: Chemistry — Spectroscopy

Utilizing Similarity Measures to Map Chemical Reactivity The development of fully autonomous chemical synthesis platforms requires robust, real-time assessment of reactivity that does not rely on prior mechanistic knowledge. Existing methods often depend on predefined reaction models or chemical intuition, limiting their generalizability and adaptability. To address this challenge, we introduce a chemically agnostic approach that quantifies reactivity dynamics by applying similarity metrics to the full informational content of in-situ spectroscopic data. Using NMR, UV/Vis, IR, and EPR spectroscopy, we demonstrate that spectral similarity trajectories can reliably indicate reaction progress, detect kinetic features such as autocatalysis, and resolve complex behaviours including oscillations. Across diverse reaction classes, this method enabled estimated end-point detection and kinetic profiling without reaction-specific tuning. For example, the formation of lophine was followed by NMR at different reaction temperatures revealing Arrhenius-type kinetics. In a different experiment, the Belousov Zhabotinsky reaction was monitored by UV/Vis and the chemical oscillation with a periodicity of 7.25 s was captured. These results establish a generalizable framework for real-time, data-driven reactivity monitoring, representing a critical step toward autonomous synthesis guided by multidimensional spectroscopic feedback. Generalizability theory ; Similarity (geometry) ; Reactivity (psychology) ; Limiting ; Chemical reaction ; Kinetic energy Molecular spectroscopy and chirality ; Cyclization and Aryne Chemistry ; Machine Learning in Materials Science
Authors: Qingan Meng | Junjie Zhou | Jie Pang | Luofeng Wang | Kaicheng Yang | Zhangcan Li | Jiayu Xie
Source: Biomimetics (review, 2025-05-08)
Field: Materials Science — Surfaces, Coatings and Films

Directional Liquid Transport on Biomimetic Surface with Wedge-Shaped Pattern: Mechanism, Construction, and Applications Natural organisms have evolved highly sophisticated mechanisms for managing water across a broad range of environmental conditions, from arid to highly humid regions. Among these mechanisms, directional liquid transport (DLT) is particularly noteworthy, as it relies on structural designs that facilitate the spontaneous movement of liquids along predefined pathways without the need for external energy sources. The increasing interest in DLT systems is primarily driven by their potential applications in fields such as microfluidics, water harvesting, and biomedical engineering. The focus on DLT is motivated by its ability to inspire efficient, energy-independent liquid transport technologies, which hold significant promise for both fundamental research and practical applications. Notably, wedge-shaped DLT systems have emerged as a particularly promising area of study due to their advantages in terms of manufacturability, liquid collection efficiency, and scalability-attributes that are essential for industrial deployment. This review seeks to explore natural wedge-based DLT systems, providing an in-depth analysis of their underlying principles and their potential for engineering replication. The discussion includes examples from nature, such as desert beetles and spider silk, and explores the theoretical mechanisms governing these systems, including the role of surface energy gradients and Laplace pressure. Additionally, the review highlights advanced fabrication techniques, such as photolithography and laser micromachining, which are crucial for the development of these systems in practical applications. Nanotechnology ; Computer science ; Microfluidics ; Scalability ; Mechanical engineering ; Systems engineering ; Materials science ; Engineering Surface Modification and Superhydrophobicity ; Adhesion, Friction, and Surface Interactions ; Fluid Dynamics and Heat Transfer
Authors: Ryo Toyama | S. Tsuda | Yuma Iwasaki | Thang Dinh Phan | Susumu Yamamoto | Hiroyuki Yamane | Koichiro Yaji | Yuya Sakuraba
Source: Science and Technology of Advanced Materials (article, 2025-01-07)
Field: Materials Science — Electronic, Optical and Magnetic Materials

High-throughput evaluation of half-metallicity of Co <sub>2</sub> MnSi Heusler alloys using composition-spread films and spin-integrated hard X-ray photoelectron spectroscopy We demonstrate high-throughput evaluation of the half-metallicity of Co<sub>2</sub>MnSi Heusler alloys by spin-integrated hard X-ray photoelectron spectroscopy (HAXPES) of composition-spread films performed with high-brilliance synchrotron radiation at NanoTerasu, which identifies the optimum composition showing the best half-metallicity. Co<sub>75-<i>x</i></sub> Mn <sub><i>x</i></sub> Si<sub>25</sub> composition-spread thin films for <i>x</i> = 10-40% with a thickness of 30 nm are fabricated on MgO(100) substrates using combinatorial sputtering technique. The <i>L</i>2<sub>1</sub>-ordering and (001)-oriented epitaxial growth of Co<sub>2</sub>MnSi are confirmed by X-ray diffraction for <i>x</i> = 18-40%. The valence band HAXPES spectra exhibit a systematic compositional dependence and the smallest photoemission intensity at the Fermi level (<i>E</i> <sub>F</sub>) for a slightly Mn-rich composition of <i>x</i> = 27%. The density of states (DOS) for <i>L</i>2<sub>1</sub>-ordered Co<sub>2</sub>MnSi with different Mn compositions obtained from first-principles calculation also show the smallest total DOS at <i>E</i> <sub>F</sub> for <i>x</i> = 27% because of the formation of a clear half-metallic gap in the minority spin channel and the less localized <i>d</i>-states in the majority spin channel, indicating the best half-metallic nature of this composition. Our experimental results demonstrate that high-throughput evaluation of half-metallicity is possible even with spin-integrated HAXPES by capturing systematic changes in the electronic structures through the measurements on the composition-spread film. Moreover, the anisotropic magnetoresistance (AMR) of the composition-spread film is measured for electric current directions along the [110] and [100] of Co<sub>2</sub>MnSi. Previous studies indicated that a larger negative AMR ratio is a signature of a higher spin polarization. The largest negative AMR ratio is observed for <i>x</i> = 27% for both current directions, which also supports the best half-metallicity for this off-stoichiometric composition. X-ray photoelectron spectroscopy ; Materials science ; X-ray spectroscopy ; Spectroscopy ; Spin (aerodynamics) ; Condensed matter physics ; Throughput ; Composition (language) ; Nuclear magnetic resonance ; Physics Heusler alloys: electronic and magnetic properties ; MXene and MAX Phase Materials ; Chalcogenide Semiconductor Thin Films
Authors: Md. Maruf Billah | Muhammed Nur Talha Kilic | Md Mahmudul Hasan | Zekeriya Ender Eğer | Yuwei Mao | Kewei Wang | Alok Choudhary | Ankit Agrawal | Veera Sundararaghavan | Pınar Acar
Source: Integrating materials and manufacturing innovation (article, 2025-06-23)
Field: Materials Science — Materials Chemistry

MicroProcSim: A Software for Simulation of Microstructure Evolution The online version of this article (10.1007/s40192-025-00405-6) contains an Editor's Video Summary, which is available to authorized users. Texture (cosmology) ; Software ; Deformation (meteorology) ; Computer science ; Process (computing) ; Microstructure ; Computational science ; Replicate ; Finite element method ; Materials science ; Orientation (vector space) ; Geometry ; Artificial intelligence ; Structural engineering ; Composite material ; Engineering ; Mathematics Microstructure and mechanical properties ; Microstructure and Mechanical Properties of Steels ; Aluminum Alloy Microstructure Properties
Authors: Paresh Tank | Shruti Vora | Fatima D'Souza | Shashank S. Kamble | Neelamegam Rameshkumar
Source: Trends in biotechnology (review, 2025-08-22)
Field: Chemistry — Spectroscopy

Advanced mass spectrometry techniques for monitoring biopharmaceutical host cell proteins Residual host cell proteins (HCPs) in biologic drug products can compromise safety or stability and must be carefully monitored. While traditional immunoassays remain essential, they often lack specificity or coverage. Mass spectrometry (MS) offers a complementary approach by enabling direct identification and quantification of individual HCPs throughout development. This review highlights recent advances in MS technologies and workflows relevant to HCP detection, including new data acquisition strategies, software tools, and artificial intelligence applications. We also discuss regulatory perspectives and considerations for implementing MS in controlled environments. By integrating analytical innovations with risk-based strategies, MS-based approaches are becoming key components of modern biopharmaceutical quality control. Biopharmaceutical ; Mass spectrometry ; Computational biology ; Chemistry ; Host (biology) ; Proteomics ; Chromatography ; Biotechnology ; Biology ; Biochemistry ; Gene ; Genetics Mass Spectrometry Techniques and Applications ; Protein purification and stability ; Viral Infectious Diseases and Gene Expression in Insects
Authors: Josué Ismael García-Ramírez | Marcos Luna-Cervantes | Irma Yadira Izaguirre-Hernández | J. Hernández-Torres | Enrique Juárez‐Aguilar | Pablo Thomas-Dupont | J.M. Remes-Troche | L. Zamora‐Peredo
Source: Biosensors (article, 2025-09-22)
Field: Materials Science — Electronic, Optical and Magnetic Materials

SERS-Based Immunoassay for α-Fetoprotein Biomarker Detection Using an Au-Ag Nanostars Platform Spiky Au-Ag nanostars offer intense plasmonic enhancement due to their sharp-tipped morphology, enabling powerful surface-enhanced Raman scattering (SERS). Here, we report a liquid-phase SERS platform that addresses current limitations in cancer biomarker detection, such as low sensitivity and dependence on Raman reporters. Nanostar concentration was tuned by simple centrifugation (10, 30, and 60 min), and their SERS performance was evaluated using methylene blue (MB) and mercaptopropionic acid (MPA) as probe molecules. Signal intensity scaled with nanostar content, enabling sensitive detection. Optimized nanostars were functionalized with MPA, 1-Ethyl-3-(3-dimethylamino1-Ethyl-3-(3dimethylaminopropyl1) carbodiimide (EDC), and N-Hydroxy succinimide (NHS) for covalent attachment of monoclonal anti-α-fetoprotein antibodies (AFP-Ab), facilitating the detection of AFP antigens across 167-38 ng/mL (antibody) and 500-0 ng/mL (antigen) ranges. The limit of detection (LOD) for the antigens was determined to be 16.73 ng/mL. Unlike conventional SERS systems, this aqueous, surfactant-free platform exploits the intrinsic vibrational modes of AFP, enabling sensitive and rapid biomarker detection with strong potential for early cancer diagnostics. Immunoassay ; Detection limit ; Biomarker ; Raman scattering ; Plasmon ; Monoclonal antibody ; Raman spectroscopy ; Cancer biomarkers ; Cancer detection Gold and Silver Nanoparticles Synthesis and Applications ; Advanced biosensing and bioanalysis techniques ; Biosensors and Analytical Detection
Authors: Elham Lori Zoudani | Prabuddha De Saram | S. Feih | Hoang Huy Vu | Nam‐Trung Nguyen | Navid Kashaninejad
Source: Small Structures (article, 2025-11-16)
Field: Materials Science — Surfaces, Coatings and Films

Micropatterned Surfaces with Unidirectional Wetting Properties for Liquid Transport Interest in micropatterned surfaces with unidirectional wetting properties has grown significantly due to their unique ability to enable controlled liquid manipulation. This property is essential for diverse applications, including microfluidics, water harvesting, and self‐cleaning systems, where directional droplet motion promotes efficient removal of contaminants and reduces surface fouling. Despite extensive research on anisotropic wetting, a comprehensive framework encompassing design considerations, fabrication methods, and practical challenges for unidirectional liquid transport remains underdeveloped. This review paper addresses this gap by presenting a holistic overview of micropatterned anisotropic surfaces and their wetting behaviors in unidirectional fluid handling. Key mechanisms of liquid transport, ranging from passive modes such as gravity and wettability gradient to active modes involving external stimuli, are discussed. This review critically evaluates surface fabrication techniques, highlighting their advantages and limitations. By critically analyzing recent advances and identifying key structure–function relationships, this review offers design principles and emerging fabrication strategies that can accelerate the development of next‐generation micropatterned surfaces for directional liquid transport in microfluidics, diagnostics, and surface engineering. Wetting ; Fabrication ; Anisotropy ; Key (lock) ; Surface (topology) ; Wetting transition ; Liquid metal Surface Modification and Superhydrophobicity ; Electrowetting and Microfluidic Technologies ; Innovative Microfluidic and Catalytic Techniques Innovation