jablonkagroup/rise_ai_scientists huggingface dataset:
Authors: Schwarzmüller, Luisa
Source: heiDOK (Heidelberg University) (article, 2025-01-01)
Field: Chemistry — Spectroscopy

Phosphoproteomic Characterization of Colorectal Cancer for Precision Oncology Colorectal cancer (CRC) is the third most common cancer worldwide and a leading cause of cancer-related mortality. Despite advances in molecular stratification and the integration of genomic and transcriptomic data into clinical decision-making, treatment options for patients with metastatic CRC remain limited, and therapeutic resistance is common. A key challenge in precision oncology is the inability of DNA and RNA profiling alone to capture the functional state of cancer cells, particularly the activity of signaling pathways that govern cell behavior. To address this gap, this thesis presents a phosphoproteomic characterization of CRC within the framework of the DKFZ/NCT/DKTK-MASTER precision oncology program. I developed and optimized workflows for protein extraction, clean-up, digestion, and phosphopeptide enrichment from fresh-frozen clinical tissue samples using a high-throughput liquid handling robotic platform. These protocols enabled consistent and scalable preparation of patient samples with minimal hands-on time, while maintaining high proteome and phosphoproteome coverage. In parallel, I fine-tuned mass spectrometry acquisition and data analysis strategies to control false discovery rates and improve quantification accuracy, even in samples with low phosphosite abundance. The resulting dataset revealed substantial heterogeneity in kinase signaling activity among CRC patients. By inferring kinase activation states from phosphosite profiles, I identified three kinase-based patient subgroups with distinct biological and clinical features, including differences in immune infiltration. These subtypes did not overlap with established transcriptomic classifications, highlighting the unique value of phosphoproteomic data in uncovering functional tumor phenotypes. Importantly, I demonstrate that genomic alterations such as gene amplifications (e.g., ERBB2, CDH17) do not consistently translate to elevated protein expression or activity. This disconnect suggests that relying solely on DNA or RNA data for therapeutic stratification may lead to suboptimal treatment choices. Moreover, comparison of tumor tissues with patient-derived organoids (PDOs) revealed marked divergence in proteomic signatures, calling into question the fidelity of PDOs as preclinical models, particularly in the absence of the tumor microenvironment. Overall, this work provides both technical and conceptual advances for integrating phosphoproteomics into precision oncology workflows. It underscores the need to consider protein-level information when making clinical decisions and sets the stage for future studies evaluating proteome-informed treatment strategies in CRC and beyond. Colorectal cancer ; Transcriptome ; Precision medicine ; Proteome ; Proteomics ; Precision oncology ; Cancer ; Gene expression profiling ; Kinome Advanced Proteomics Techniques and Applications ; Cancer Genomics and Diagnostics ; Single-cell and spatial transcriptomics
Authors: Zh.T. Kambarova | Serik S. Kassymov
Source: Eastern-European Journal of Enterprise Technologies (article, 2025-10-31)
Field: Materials Science — Surfaces, Coatings and Films

Construction of an electron-optical scheme for electrostatic quasi-spherical deflector-type energy analyzer This study investigates electrostatic spherical deflector-type energy analyzers designed to analyze energy of charged particle beams. The research aims to eliminate quadratic angular aberrations characteristic of classical spherical deflector-type energy analyzers, which limit the quality of angular focusing and the energy resolution of the instruments. An electron-optical scheme of an electrostatic quasi-spherical deflector-type energy analyzer has been proposed, whose field is synthesized using a multipole approach. The electrostatic field of the energy analyzer is a superposition of an axisymmetric hexapole and a spherical field. Analytical calculations have shown that by choosing the coefficient that determines the weighting contribution of the axisymmetric hexapole, it is possible to completely compensate for second-order angular aberrations and significantly improve the focusing properties of the quasi-spherical energy analyzer. The profile of the deflecting electrodes of the energy analyzer has been determined, providing the necessary spatial distribution of the deflecting field potential to achieve the specified electron-optical parameters. Numerical simulation of the electron-optical scheme of the quasi-spherical energy analyzer and calculation of the trajectories of charged particles were carried out using the "Focus" numerical program. The electron-optical scheme of the energy analyzer implements a second-order angular focusing mode of the "axis-ring" type. The instrumental function of the scheme has been constructed. The relative energy resolution and luminosity of the energy analyzer were estimated. The numerical results show that the relative energy resolution of the energy analyzer is 1.6% at a luminosity of 17.5% of 2π, which confirms effectiveness of the proposed scheme. The proposed electron-optical scheme could be used to design real structures of new high-resolution spectrometers intended for the analysis of charged particle beams. Spectrum analyzer ; Multipole expansion ; Energy (signal processing) ; Angular resolution (graph drawing) ; Superposition principle ; Rotational energy ; Field (mathematics) ; Resolution (logic) Electron and X-Ray Spectroscopy Techniques ; Advanced Electron Microscopy Techniques and Applications ; X-ray Spectroscopy and Fluorescence Analysis
Authors: Davi Marques de Farias | Gabriel N. Meloni | Thiago R. L. C. Paixão
Source: Advanced Materials Technologies (article, 2025-09-10)
Field: Chemistry — Electrochemistry

Tunable Mass Transport and Enhanced Electrochemical Performance of CO <sub>2</sub> Laser Engraved Electrodes Abstract This work introduces a novel approach to laser‐engraved electrochemical sensors by exploring vectorized CO 2 laser engraving. Vectorized engraving reduces the interaction between the laser and the precursor material, decreasing uneven carbonization and enhancing charge transfer kinetics. The vectorized engraved patterns allow control over mass transport regimes. The final optimized electrode layout is a spiral, mimicking a disk electrode. Experimental and simulated evaluations have shown that diffusion can be modulated by adjusting the spiral spacing of the lines, leading to radial or planar diffusion. Comparative studies reveal that vector‐engraved electrodes outperform raster‐mode devices in current density (271 vs. 115–175 µA cm −2 ) and closely match commercial platinum electrodes (deviation 〈7%). Proof‐of‐concept detection of levofloxacin confirms improved sensitivity without the need for post‐fabrication treatments. Interestingly, the interdigitated electrodes incorporate the tunable mass transport features of the vectorized engraving method into numerical simulations to predict and optimize electrode design and electrochemical performance. This work establishes an alternative pathway for developing versatile, next‐generation sensor platforms, overcoming the limitations of traditional laser engraving protocols. Engraving ; Electrode ; Electrochemistry ; Laser ; Carbonization ; Planar ; Mass transport Electrochemical Analysis and Applications ; Analytical Chemistry and Sensors ; Molecular Junctions and Nanostructures
Authors: Stefano Marchetti | Francesco Di Maio | E. Wismer Samantha | Katrina M. Groth | Enrico Zio
Source:  (article, 2025-01-01)
Field: Materials Science — Materials Chemistry

Preliminary Hazard Analysis for Hydrogen Production by Coupled High Temperature Electrolysis Facilities and Nuclear Power Plants Coupling of High Temperature Electrolysis Facilities (HTEFs) and Nuclear Power Plants (NPPs) is a promising solution for large-scale clean hydrogen production.A preliminary hazards analysis of the system of systems made of HTEF and NPP is presented with reference to a preliminary design in which steam and electricity are supplied by the NPP to the HTEF.The outcomes of the analysis point at the fact that hydrogen leakage, steam leakage and overcurrent events on the HTEF side may contribute to an increase in the risk at the NPP side, in terms of higher probability of Loss Of Offsite Power (LOOP), Main Steam Line Break (MSLB) and Loss of Heat Sink (LHS). Nuclear power ; Production (economics) ; Hydrogen production ; Hydrogen ; Hazard ; Electrolysis Nuclear Materials and Properties ; Nuclear reactor physics and engineering ; Advanced Power Generation Technologies
Authors: Shaojie Wu | Yan Gao | Zilong Tan
Source: Journal of Engineering Research and Reports (article, 2025-01-16)
Field: Materials Science — Materials Chemistry

Construction Technology and Quality Control of Reinforced Concrete Beam and Column Joints Reinforced concrete beam-column joints are critical components in building structures, and their construction quality directly affects the safety and stability of the entire building. This paper first introduces the construction characteristics and challenges of reinforced concrete beam-column joints, then elaborates on the construction techniques and quality control measures, and finally analyzes the precautions in the construction of reinforced concrete beam-column joints. The aim is to provide valuable references and insights for relevant engineering projects. Column (typography) ; Quality (philosophy) ; Structural engineering ; Beam (structure) ; Control (management) ; Reinforced concrete ; Engineering ; Materials science ; Computer science ; Artificial intelligence ; Physics Structural mechanics and materials ; Geodetic Measurements and Engineering Structures
Authors: Dmitry V. Davydov | Maksim O. Karpechkin | N. B. Morozova | Varvara A. Khokhlova | Nadezhda V. Perova | Anna O. Nemechkina
Source: Ophthalmology Reports (article, 2025-12-30)
Field: Materials Science — Biomaterials

Effects of heterogeneous collagen-based formulation on growth and metastasis of B16-F1 melanoma in mice: an experimental, cohort, controlled study BACKGROUND: Defects after melanoma resection require effective and minimally invasive methods for their management to be developed. Current techniques have several limitations and do not always provide a satisfactory aesthetic outcome. Thus, new techniques, including gel injection, should be developed. Рeterogeneous collagen-based formulation is one of the promising options. It has shown its effectiveness in enhancement of wound healing; however, there is no data on its interaction with tumor cells. AIM: The study aimed to assess the interaction and effect of heterogeneous collagen-based formulation on B16-F1 melanoma in an experiment. METHODS: The experiment was conducted on laboratory animals (mice) divided into groups to receive injections of heterogeneous collagen-based formulation and 0.9% sodium chloride solution. Laboratory animals were monitored for 20 days, weight and tumor size were measured regularly. The animals were sacrificed, and the primary tumor, lymph nodes, and lungs were sampled for histological examination. RESULTS: An analysis of the growth rate, metastasis to the lymph nodes and lungs revealed no significant difference between the study and control groups. Tumor histology also did not differ; however, the examination found the injected heterogeneous collagen-based formulation in several samples from unoperated animals. CONCLUSION: The B16-F1 melanoma model showed no effect of the heterogeneous collagen-based formulation on primary tumor growth and metastasis. This result suggests that this material is potentially safe, which is an important step in the search and development of new oncological reconstructions techniques. Melanoma ; Metastasis ; Lymph ; Histology ; Primary tumor ; Resection Collagen: Extraction and Characterization ; Wound Healing and Treatments ; Surgical Sutures and Adhesives
Authors: Xing Fan | Yuanpeng Zhu | Yan Jia | Pengzhen Du | Weini Wang | Junmei Liu | Zhijun Lv | Ronghao Liu | Xiaobin Li
Source: Frontiers in Plant Science (article, 2025-11-03)
Field: Materials Science — Biomaterials

Multi-environment meta-analysis reveals the mechanism of action of potassium-solubilizing microorganisms on crop yields The availability of soil potassium plays a critical role in yield increases. Potassium-solubilizing microorganisms (KSM) offer a promising biological solution to improve potassium availability, but their efficacy across diverse global environments remains uncertain. Through a global meta-analysis of 102 studies (846 paired observations), we systematically evaluated the effects of KSM application on crop yields across five key dimensions: microorganism types, soil factors, crop classifications, field management, and stress types. KSM inoculation significantly increased soil available potassium (+28.9%), crop yield (+23.4%), and key growth indices, such as root length (+29.50%) and leaf area (+44.7%). This study identified <i>Aspergillus</i> spp. as the most suitable microorganism, and revealed that KSM efficacy is highly dependent on context: yield responses were greatest in clay loam soils, vegetable crops, and greenhouse conditions. Structural equation modeling indicated that microbial abundance, climate, soil available potassium, and plant growth (root length and leaf area) are key direct and indirect drivers of yield enhancement. The results indicate that the application of KSM is an effective strategy to increase crop yields in various environments. By identifying the optimal conditions for KSM application, the identification of optimal application parameters, derived from cross-study analysis, provides a robust strategy for leveraging microbial communities to boost soil potassium availability and nutrient efficiency, thereby contributing to the transition toward more sustainable and climate-resilient agriculture. Crop ; Microorganism ; Loam ; Yield (engineering) ; Potassium ; Crop yield ; Nutrient ; Soil water Clay minerals and soil interactions ; Soil Carbon and Nitrogen Dynamics ; Plant-Microbe Interactions and Immunity
Authors: Tanvirul Islam | Alfi Shahriar | Md. Sazzad Hossain
Source:  (article, 2025-12-20)
Field: Materials Science — Biomaterials

Improving Sigma Level in Wet Blue Leather Processing: Context of Bangladesh Tannery Industry The expansion of economic growth in Bangladesh results in making the leather industry an emerging foreign exchange earner. Although the supply of raw skin is high and the availability of labor is cheap, the industry is not showing it’s full capacity within which it can perform. It happens due to non-structured and less productivity based production system. This study will observe the problem by focusing on a tannery which is situated in BSCIC in Savar that works with Wet-Blue Leather. The general objective of this study is to develop a continuous quality improvement model and combine Lean and Six Sigma concepts to reduce defects and increase the sigma level. The study is comprised of primary and scondary data by using Snowball sampling. The primary data includes, process mapping, defect types, cause and effects, as well as secondary data includes, firm records, defect prevalence and lead times. It constructs DMAIC structure (Define, Measure, Analyze, Improve, Control) with Lean tools such as, SIPOC, Value Stream Mapping, Pareto analysis, Ishikawa diagram and Control Charts. The finding shows that the causes of defects are mainly shortage of manpower, equipment, raw material, improper technique and process, lack of organizational practices. Therefore, the implementation of the systematic and continuous improvement framework raised sigma level from 1.82 to 1.98 and also proposed a future Value Stream Mapping. Although the improvement isn’t large enough, it will pave the way to create a great practice in the tannery industry. Context (archaeology) ; Six Sigma ; Quality (philosophy) Collagen: Extraction and Characterization ; Chromium effects and bioremediation ; Edible Oils Quality and Analysis
Authors: Luis M Minier
Source:  (article, 2025-12-09)
Field: Chemistry — Spectroscopy

QuantoniumOS: A Hybrid Computational Framework for Quantum Resonance Simulation with Validated Unitary Transform and Post-Quantum Cryptographic Primitives This paper presents QuantoniumOS, a hybrid computational framework introducing the closed-form Phi-Resonance Fourier Transform (Phi-RFT), a novel unitary transformation defined as Ψ = DφCσF where F is the unitary DFT, Cσ applies quadratic chirp phase modulation, and Dφ applies golden-ratio phase modulation via the sequence {k/φ}. Using parameters σ = 1.0 and β = 1.0, we prove unitarity through algebraic factorization, demonstrate O(n log n) computational complexity matching FFT, and establish that the Phi-RFT lies outside the Linear Canonical Transform family due to its non-quadratic phase structure (RMS residual 1.817 rad). The transform exactly diagonalizes a commutative algebra of twisted convolution operators. Empirical validation confirms machineprecision unitarity errors: Frobenius norm ∥Ψ †Ψ − I∥F ranging from 6.42 × 10−16 (n=8) to 1.06 × 10−14 (n=512). Sparsity comparisons on standard test signals (chirp, ECG, seismic, speech) show competitive performance with mean rank 2.1 across transforms. The framework includes a 48-round Feistel cipher with measured diffusion metrics: key avalanche 0.506, key sensitivity 0.494, and Shannon entropy 7.87 bits. Hardware validation through SystemVerilog FPGA implementation demonstrates real-time transform capability with 100% verification pass rate across all engine modes. Source code is available at https://github.com/mandcony/quantoniumos. Unitary transformation ; Discrete Fourier transform (general) ; Residual ; Computational complexity theory ; Fast Fourier transform ; Quantum Fourier transform ; Unitary state ; Algebra over a field ; Fourier transform Advanced NMR Techniques and Applications ; Fractal and DNA sequence analysis ; Electron Spin Resonance Studies
Authors: А. В. Разуваев
Source: Tractors and Agricultural Machinery (article, 2025-09-07)
Field: Materials Science — Materials Chemistry

Cogeneration plants and specific features of their operation with the consumer The paper considers relevance of the issue of development of all sectors of the national economy, including such an important industry as agriculture. The development of the agricultural industry is associated in some cases with some of its specific features, which involve the necessity (sometimes historically developed) to have autonomous and remote objects of agricultural production. At the same time, production facilities and housing of service specialists are forced to be located at some distance from the sources of central (or main) electricity and heat supply. To achieve the stated objective of this study, it is necessary to estimate the building's (consumer's) heat loss, which will be equal to the heat required for its heating. This required analyzing the heat balance data for the planned engine-generator system and the possibility of recovering secondary heat from the engine-generator in the exhaust gas, coolant, and oil recovery system, taking into account its simultaneous generation of electrical energy. Based on the experimental heat balance data presented in the technical literature, it was found that the value generated from secondary heat in the engine-generator recovery system depends on the amount of electrical energy generated for the same consumer. Based on the analysis, specific conclusions are made for the implementation of cogeneration plants at various facilities, both for investors and for manufacturers of cogeneration plants based on internal combustion engines. Cogeneration ; Electricity ; Production (economics) ; Heat recovery ventilation ; Electricity generation ; Service (business) ; Balance (ability) ; Combustion Metallurgy and Material Science ; Flexible and Reconfigurable Manufacturing Systems ; Energy Efficiency and Management
Authors: Vikram Rathore | Paul Blair | Gustav Robertson | Martin Jonson | Peter Andersson
Source: Frontiers in Energy Research (article, 2025-10-30)
Field: Materials Science — Materials Chemistry

Study of the impact of load-following operation on light water reactor fuel performance using the TRANSURANUS code Small modular reactors (SMRs) are gaining popularity due to several economic and safety benefits, along with their desirable load-following capability, which allows them to complement intermittent renewable energy sources. However, the impact of load-following operation on fuel performance remains underexplored. This study uses the fuel performance code, TRANSURANUS, to assess the effects of such operations on pressurized water reactor (PWR) fuel performance, given the design similarities between many SMRs and large light water reactors (LWRs). Hypothetical load-following operations were simulated using varying linear heat rate levels, neutron flux, and coolant flow rate, in accordance with a parameterized load-following operation. Most fuel performance parameters remained below safety limits. However, in some cases, the pellet–cladding interaction–stress corrosion cracking (PCI–SCC) model (SPAKOR) predicted cladding cracks and failures that were not observed during regular reference operation. A sensitivity analysis of load-following parameters indicated minimal deviations in fuel performance, apart from the PCI–SCC-related issues. Light-water reactor ; Cladding (metalworking) ; Coolant ; Loss-of-coolant accident ; Modular design ; Sensitivity (control systems) ; Renewable energy ; Pressurized water reactor Nuclear Materials and Properties ; Nuclear reactor physics and engineering ; Nuclear Engineering Thermal-Hydraulics