jablonkagroup/rise_ai_scientists huggingface dataset:
Authors: Nathan Turner Wamsley | Emily Wilkerson | Michael B. Major | Dennis Goldfarb
Source: bioRxiv (Cold Spring Harbor Laboratory) (article, 2026-02-18)
Field: Chemistry — Spectroscopy

Pioneer and Altimeter: Fast Analysis of DIA Proteomics Data Optimized for Narrow Isolation Windows Abstract Advances in mass spectrometry have enabled increasingly fast data-independent acquisition (DIA) experiments, producing datasets whose scale and complexity challenge existing analysis tools. Those same advances have also led to the use of narrow isolation windows, which alter MS2 spectra via fragment isotope effects and give rise to systematic deviations from spectral libraries. Here we introduce Pioneer and Altimeter, open-source tools for fast DIA analysis with explicit modeling of isolation-window effects. Altimeter predicts deisotoped fragment intensity as a continuous function of collision energy, allowing a single spectral library to be reused across datasets. Pioneer re-isotopes predicted spectra per scan and combines an intensity-aware fragment index, spectral deconvolution, and dual-window quantification for fast, spectrum-centric DIA analysis. Across instruments, experimental designs, and sample inputs, Pioneer enables high-confidence identification and precise quantification at scale, completing analyses 2–6x faster and maintaining conservative false-discovery rate control. Collision ; Fragment (logic) ; Data acquisition ; Mass spectrometry ; Scale (ratio) ; Spectral analysis ; Function (biology) ; Spectral line Advanced Proteomics Techniques and Applications ; Mass Spectrometry Techniques and Applications ; Metabolomics and Mass Spectrometry Studies
Authors: Enzo Monino | Daria Drwal | Michał Hapka | Libor Veis | Katarzyna Pernal
Source: ArXiv.org (article, 2026-03-05)
Field: Materials Science — Electronic, Optical and Magnetic Materials

Why Projection-Based DMRG-in-DFT Cannot Be Exact, Even with the Exact Exchange-Correlation Functional We establish the theoretical foundations for embedding a correlated wave function in an environment formed by Kohn-Sham orbitals. We show that introducing an approximation which equates two, in principle distinct, kinetic-energy functionals yields an embedding functional identical to the projection-based wavefunction-in-DFT formulation of Miller and co-workers. We demonstrate that this functional is inherently nonvariational: its minimum is not guaranteed to coincide with the exact ground-state energy and remains bounded from above by it. Building on this formal framework, we analyze the dominant sources of error in projection-based DMRG-in-DFT embedding with approximate exchange-correlation (xc) functionals. Using molecules with dissociating covalent bonds as a diagnostic example, we demonstrate that the primary source of error is the nonadditive exchange-correlation energy describing the nonclassical coupling between the active subsystem and its environment. Eliminating the fractional-spin error by employing a pair-density xc functional (PDFT) instead of a semilocal GGA does not remedy this deficiency, because the inaccuracy stems from self-interaction effects at the subsystem-environment interface. Embedding ; Bounded function ; Function (biology) ; Energy (signal processing) ; Wave function ; Coupling (piping) ; Spurious relationship ; Work (physics) Magnetism in coordination complexes ; Spectroscopy and Quantum Chemical Studies ; Advanced NMR Techniques and Applications
Authors: Sören Lehmkuhl | Simon Fleischer | Jing Yang | Eduard Y. Chekmenev | Thomas Theis | Stephan Appelt | Jan G. Korvink | Mazin Jouda
Source: Repository KITopen (Karlsruhe Institute of Technology) (article, 2026-01-01)
Field: Chemistry — Spectroscopy

Rapid RASER MRI Conventional Magnetic Resonance Imaging (MRI) relies on high-power Radio-Frequency (RF) pulses to excite nuclear spins and in turn generate NMR signals. These pulses require large high-power RF-amplifiers and cause heat deposition in the tissue, which must be minimized for safety, presenting a growing problem when moving toward ever-higher field MRI. An alternative to RF-pulse excitation is self-excitation of nuclear spins using Radiofrequency Amplification by Stimulated Emission of Radiation (RASER), where the nuclear spins undergo spontaneous transition, without RF excitation, from an over-populated state to a ground state. Here, the feasibility of recording rapid proton RASER MRI images of pyrazine at low concentration (120 mM) with large matrix (128x128 pixels) in as little as 78 ms is demonstrated at 500 MHz (11.7 T). We also recorded a time-series of images using a single bolus hyperpolarized pyrazine highlighting the feasibility of dynamic tracking. The demonstrated approach allows recording MRI scans without transmit-receive electronics of the MRI scanner, which is highly desirable for portable MRI as well as the emerging field of hyperpolarized MRI using, e.g., HP protons, $^{129}$Xe gas or HP $^{13}$C labeled biomolecules as molecular tracers and imaging agents Spins ; Excitation ; Magnetic resonance spectroscopic imaging ; Magnetic resonance imaging ; Hyperpolarization (physics) ; Nuclear imaging ; Proton Advanced NMR Techniques and Applications ; Advanced MRI Techniques and Applications ; Atomic and Subatomic Physics Research
Authors: Clément Prunier | Thomas Jeannin | Jérôme Rousseau | Pauline Butaud | Vincent Placet
Source: Journal of Materials Science (article, 2026-03-17)
Field: Materials Science — Polymers and Plastics

Improving plywood performances through hybridisation with plant fibres composites: a comparative analysis of quasi-static properties, failure kinetics and fatigue behaviour Abstract This study explores the hybridisation of wood veneers with plant fibre-reinforced thermoplastic composites. Beech and Douglas fir plywood are made using environmentally friendly adhesives, polylactic acid (PLA) and recycled maleic anhydride-grafted polypropylene (rMAPP). Hybridised plywood is produced by incorporating flax fibres at specific locations within the lay-up. The mechanical performances of these hybrid laminates are assessed through 3-point bending tests. The results show that hybridisation enhances bending modulus and strength in nearly all tested configurations: the bending modulus increased by up to 24% in beech and 31 in Douglas fir, whereas bending strength gains reached up to 27 and 79%, respectively. Predictions based on classical laminate theory align closely with experimental data, validating its use for estimating the elastic properties of hybrid laminates. Additionally, the failure kinetics reveal that hybridisation enables stress redistribution within the composite layers, leading to improved bending strength even when outer veneers are damaged. A fatigue study under cyclic bending loads further demonstrates that hybridisation can double the fatigue strength of Douglas fir plywood over 1 million cycles compared to its non-hybrid counterpart. These findings highlight the potential of hybrid laminates to improve the mechanical performance and durability of wood-based composites for structural applications. Graphical abstract Flexural strength ; Bending ; Flexural modulus ; Composite number ; Thermoplastic ; Polypropylene ; Wood-plastic composite ; Durability Natural Fiber Reinforced Composites ; Wood Treatment and Properties ; Bamboo properties and applications
Authors: Yingsong Zheng | Longfeng Lv | Y L Zou | Bo Cheng | Hanxiao Shao | Guofeng Song | Kunpeng Zhai
Source: Micromachines (article, 2026-01-28)
Field: Materials Science — Electronic, Optical and Magnetic Materials

High-Extinction-Ratio Chiral Mid-Wave Infrared Photodetector Using Trapezoidal Si Pillars Although the polarization state, as a key physical dimension of light, plays an irreplaceable role in many frontier fields such as quantum communication and chiral sensing, traditional photodetectors are limited by the inherent optical isotropy of materials and thus are unable to directly distinguish circular polarization information. This paper numerically reports a miniature circular polarization photodetector based on chiral metasurfaces, which achieves an excellent extinction ratio of up to 31 dB through the collaborative regulation of geometric displacement manipulation and tilt angle operation. This device utilizes the symmetry-breaking effect to construct significantly different transmission spectral responses between left circularly polarized light (LCP) and right circularly polarized light (RCP). Our research not only provides a high-performance implementation solution for on-chip polarization detection but also opens up new paths for the future development of quantum optics, integrated sensing, and ultra-compact polarization optical systems. Photodetector ; Circular polarization ; Extinction ratio ; Polarization (electrochemistry) ; Optical communication ; Isotropy ; Quantum ; Polarization rotator Metamaterials and Metasurfaces Applications ; Plasmonic and Surface Plasmon Research ; Photonic Crystals and Applications
Authors: James W. Meadows | Sharon J. Cooper | Mark A. Miller | M. N. Wilson
Source: Journal of Chemical Theory and Computation (article, 2026-04-06)
Field: Materials Science — Materials Chemistry

Assessment and Optimization of Force Fields for Glycine Polymorphism and Solution Properties Molecular dynamics studies of glycine crystal growth require a force field that accurately reproduces both solution- and crystal-phase properties for all three ambient-pressure polymorphs. However, many studies use force fields validated only for α-glycine, which often yield poor crystal properties. Here, we extensively evaluate 18 force field variants (10 OPLS and 8 GAFF) and recalibrate the parameters of the best-performing models using multiobjective Bayesian optimization. Crystal lattice energies and densities are computed for α-, β-, and γ-glycine, and the mechanical stability of these polymorphs is tested over a range of temperatures. Solution densities and concentration-dependent self-diffusion coefficients are calculated in conjunction with three water models. Using alchemical hydration free energy calculations, we also obtain solvation and solution enthalpies. Optimization of the nonbonded parameters in OPLS force field variants improves the prediction of crystal properties for all polymorphs simultaneously. We present a force field that correctly reproduces the relative polymorph stability, remains mechanically stable beyond ambient temperatures, and gives excellent agreement with experimental lattice energies, crystal densities, and solution enthalpies. This optimized model is expected to provide accurate insight into the mechanisms controlling glycine polymorphism in complex environments. Moreover, the optimization framework developed here provides a general approach for improving force fields of other molecular crystals. Force field (fiction) ; Lattice energy ; Crystal structure prediction ; Molecular dynamics ; Crystal (programming language) ; Solvation ; Energy minimization ; Polymorphism (computer science) ; Crystal structure Crystallization and Solubility Studies ; Crystallography and molecular interactions ; Enzyme Structure and Function
Authors: George Dwapanyin | Edward I. Appleton | Stella Corsetti | Charles Descoins | Xavier Poitou | Kishan Dholakia | Graham D. Bruce
Source: arXiv (Cornell University) (article, 2026-02-25)
Field: Chemistry — Analytical Chemistry

Through-bottle spectroscopy as a tool for quality control and anti-counterfeiting of Brandy and Cognac Counterfeiting of premium spirits poses significant economic and health risks, that could be tackled by robust, accurate, portable and non-destructive through-bottle measurements. Here, we demonstrate the capability of focus-matched inverse spatially offset spectroscopy, combining fluorescence and Raman signals, for authenticating Cognac and Brandy. The technique accurately identifies age classification, bottling year, spoilage due to elevated storage temperatures, and distinguishes between Cognac brands. Critically, our method effectively differentiates genuine Cognacs from counterfeit products, correctly identifying 98% of counterfeit samples. This shows the promise of through-bottle spectroscopy as a powerful tool for supply chain integrity and consumer protection in the high-value spirits market. Bottling line ; Counterfeit ; Quality (philosophy) ; Wine ; Food spoilage ; Spectroscopy ; Raman spectroscopy ; Analytical Chemistry (journal) Spectroscopy and Chemometric Analyses ; Spectroscopy Techniques in Biomedical and Chemical Research ; Pharmaceutical Quality and Counterfeiting
Authors: Asier González | Meriç Ataman | Aleksei Mironov | Niels Schlusser | Muskan Pandey | Alexander Schmidt | Mairene Coto‐Llerena | Salvatore Piscuoglio | Nitish Mittal | Mihaela Zavolan
Source: bioRxiv (Cold Spring Harbor Laboratory) (article, 2026-02-12)
Field: Chemistry — Spectroscopy

Ribosome profiling reveals extensive translational alterations in steatohepatitis-associated hepatocellular carcinoma Abstract Hepatocellular carcinoma (HCC) is one the most lethal cancer types. While infections with hepatitis B or hepatitis C viruses remain the primary risk factors for HCC development worldwide, metabolic disease-associated steatohepatitis has become the fastest growing etiology of HCC, particularly in the West. Our study characterizes, for the first time, the remodeling of the translation landscape in steatohepatitis-associated HCC using ribosome profiling and mass spectrometry techniques. In striking contrast with the transcriptional alterations, which do not show strong dependence on associated co-morbidity, translational alterations are broader in the steatohepatitis compared to the viral background. These alterations affect hundreds of genes, whose products are often involved in subcellular protein localization. By quantifying the relationship between the ribosome occupancy of upstream or downstream open reading frames (uORFs or dORFs) and coding regions (CDSs), we provide evidence of uORFs attenuating the translation efficiency of CDSs in HCC. We also identify numerous novel translated regions, including from RNAs currently annotated as non-coding, some yielding peptides that can be reproducibly identified in mass spectrometry datasets. Our study thus provides novel molecular data on HCC with a focus on the steatohepatitis etiology, reveals unexpectedly extensive translational control in this co-morbidity, and gives multiple hints and candidate targets for follow-up experiments. Steatohepatitis ; Ribosome profiling ; Hepatocellular carcinoma ; Translation (biology) ; Ribosome ; Eukaryotic translation ; Open reading frame ; Proteomics ; Reading frame Advanced Proteomics Techniques and Applications ; RNA and protein synthesis mechanisms ; Metabolomics and Mass Spectrometry Studies
Authors: S. Bhuvaneswari | R. Muthuganesan | R. Radha
Source: arXiv (Cornell University) (article, 2026-01-01)
Field: Materials Science — Electronic, Optical and Magnetic Materials

Quantum correlation and coherence in a mononuclear nickel-based molecular Magnet We investigate the behaviors of thermal entanglement, quantum correlation beyond entanglement namely, measurement-induced nonlocality (MIN) and coherence in a nickel radical molecular magnet (Et3NH)[Ni(hfac)2L], whose spin-spin interactions are well described by the Heisenberg model. Using experimentally estimated coupling parameters, we compute the thermal state of the system and analyze the dependence of quantum resources on temperature and magnetic field. The results indicate that the quantum resources of the nickel-radical molecular magnet persist even at room temperature. We show that while negativity (the entanglement measure) rapidly vanishes with increasing temperature and magnetic field, measurement-induced nonlocality and quantum coherence remain comparatively more stable and persist in regions where entanglement is absent. These results highlight the significance of nonclassical correlations beyond entanglement in thermally activated spin systems and suggest that such molecular magnets could serve as viable platforms for quantum information processing in realistic conditions. Quantum nonlocality ; Quantum entanglement ; Coherence (philosophical gambling strategy) ; Quantum correlation ; Quantum discord ; Quantum ; Magnet ; Molecular magnets ; Negativity effect Magnetism in coordination complexes ; Organic and Molecular Conductors Research ; Advanced NMR Techniques and Applications
Authors: Devin M. Mulvey | Katsu Ogawa | Alyssa V. B. Santos | Henri C Santos | Patrick W. Schneider | Scott Simpson
Source: ChemRxiv (article, 2026-01-23)
Field: Materials Science — Materials Chemistry

Revisiting a Common Cobalt Chloride Equilibrium Experiment with Generative Artificial Intelligence We have developed and implemented a first-year undergraduate laboratory experiment at St. Bonaventure University that augments a well-established thermodynamics lab on the spectrophotometric determination of the equilibrium of cobalt(II) chloride hexahydrate with generative artificial intelligence (GenAI). Students utilized free ChatGPT accounts as a support tool in their analysis of laboratory data and iteratively refined their answers to chemical questions. Overall, the inclusion of GenAI in student workflow did not appear to negatively impact student performance, but there were instances where it struggled to produce correct answers for tasks. Descriptive analysis of student responses, chat logs, and instructor discussions suggests that students were resilient to incorrect GenAI output. This laboratory experiment is designed such that it can be easily adopted by faculty with an interest in exploring the use of GenAI in chemistry curricula. Generative grammar ; Workflow ; Inclusion (mineral) ; Experimental data ; Cobalt chloride Machine Learning in Materials Science ; Artificial Intelligence in Healthcare and Education ; Various Chemistry Research Topics
Authors: Sungwoo Park | Yeonghee Jeong | Sohyeon Jang | Cho-Hee Yang | Jun-Sik Chu | Homan Kang | Seung-min Park | Hyejin Lisa Chang | Bong-Hyun Jun
Source: Preprints.org (preprint, 2026-01-16)
Field: Materials Science — Electronic, Optical and Magnetic Materials

Multiplexed Detection of Cancer Biomarker Using a Dual-Mode Colorimetric-SERS Lateral Flow Immunoassay Based on Elongated Rod Ag Nanoshell (ERNS) SERS Tags Early detection of cancer biomarkers in blood is critical for improving patient outcomes; however, conventional immunoassays often rely on complex instrumentation and are not well suited for point-of-care testing or multiplexed analysis. Herein, we present a dual-mode colorimetric–surface-enhanced Raman scattering (SERS) lateral flow immunoassay (LFIA) platform for multiplexed detection of cancer biomarkers, employing elongated rod-shaped silver nanoshells (ERNSs) as SERS nanotags. The ERNS features a rough Ag shell with internally incorporated Raman labeling compounds (RLCs), enabling plasmonic extinction for visual readout and strong SERS signals for quantitative analysis while preserving the external metal surfaces for efficient antibody conjugation. Leveraging these advantages, a multiplex LFIA capable of simultaneously detecting prostate-specific antigen (PSA) and carbohydrate antigen 19-9 (CA19-9) on a single strip was successfully demonstrated. Visual inspection enabled rapid discrimination of samples at or near clinically relevant cut-off levels, while Raman analysis achieved limits of detection of 8.0 × 10-3 ng/mL for PSA and 5.4 × 10-2 U/mL for CA19-9, corresponding to approximately 500-fold and 685-fold lower concentrations than their respective clinical thresholds. This ERNS-based colorimetric–SERS LFIA integrates rapid screening and highly sensitive quantification within a single platform and offers a versatile nanoprobe design strategy for multiplex biomarker detection and liquid biopsy–based point-of-care diagnostics. Multiplex ; Nanoshell ; Multiplexing ; Nanoprobe ; Immunoassay ; Detection limit ; Cancer biomarkers ; Raman scattering Gold and Silver Nanoparticles Synthesis and Applications ; Biosensors and Analytical Detection ; Innovative Microfluidic and Catalytic Techniques Innovation
Authors: T. W. Kim | Minseo Lee | Sanghyun Cheong | Chunghwa Song | Han‐Cheol Ryu
Source: Journal of Sensor and Actuator Networks (article, 2026-02-26)
Field: Chemistry — Analytical Chemistry

Image-Based Quantification of Boundary Uncertainty for Reliable Soymilk Solid Content Measurement Soymilk solid content (%) is a critical quality indicator that is directly related to product classification and regulatory compliance in food manufacturing. However, conventional optical refractometer-based measurements often suffer from blurred scale boundaries and subjective reading errors, leading to poor reproducibility under varying illumination conditions. This study proposes an image-based signal analysis framework that quantitatively interprets blurred liquid-scale boundaries by analyzing pixel intensity profiles, their gradients, and effective boundary widths. Instead of relying on human visual judgment, the proposed method characterizes boundary uncertainty using Gaussian-smoothed intensity signals and derivative-based feature extraction. Quantitative validation against ground-truth concentration values over 150 images demonstrates an overall mean absolute error (MAE) of 1.90 and a root mean squared error (RMSE) of 3.85. Illumination conditions yielding stable, single-peak derivative responses achieve an overall MAE of 0.23, whereas severe illumination conditions associated with unstable or distorted derivative patterns result in substantially higher errors (MAE = 8.57, RMSE = 8.60). These results quantitatively confirm that derivative-based boundary signal stability is directly linked to measurement accuracy. By transforming visual ambiguity into quantifiable signal features, this work provides a practical and reproducible alternative to subjective refractometer readings and offers a foundation for reliability-aware optical concentration measurement systems in industrial environments. Mean squared error ; SIGNAL (programming language) ; Boundary (topology) ; Measurement uncertainty ; Stability (learning theory) ; Feature (linguistics) ; Intensity (physics) ; Pattern recognition (psychology) ; Ambiguity Spectroscopy and Chemometric Analyses ; Material Properties and Processing ; Surface Roughness and Optical Measurements
Authors: Qian Feng | Jia‐Yi Wang | Jianliang Wang | Xuelian Chen | Mengqin Xu | Haoxiang Wang
Source: Frontiers in Oncology (article, 2026-03-20)
Field: Materials Science — Materials Chemistry

Association between amide proton transfer-weighted imaging biomarkers and Gleason score in prostate cancer: a study on differential diagnosis from benign prostatic hyperplasia APTw imaging correlates with tumor aggressiveness and provides excellent diagnostic performance for differentiating PCa from BPH. Crucially, it offers incremental diagnostic value to the standard PI-RADS v2.1 assessment and demonstrates robust utility in challenging clinical scenarios, such as the PSA gray zone, thereby serving as a valuable non-invasive biomarker for risk stratification. Hyperplasia ; Prostate ; Prostate cancer ; Differential diagnosis ; Receiver operating characteristic ; Prostate-specific antigen ; Area under the curve ; Correlation Lanthanide and Transition Metal Complexes ; Prostate Cancer Diagnosis and Treatment ; MRI in cancer diagnosis