jablonkagroup/rise_ai_scientists huggingface dataset:
Authors: Zhu Han | Genki Terashi | Farhanaz Farheen | Tsukasa Nakamura | Daisuke Kihara
Source: Current Research in Structural Biology (review, 2025-02-02)
Field: Materials Science — Materials Chemistry

AI-based quality assessment methods for protein structure models from cryo-EM Cryogenic electron microscopy (cryo-EM) has revolutionized structural biology, with an increasing number of structures being determined by cryo-EM each year, many at higher resolutions. However, challenges remain in accurately interpreting cryo-EM maps. Inaccuracies can arise in regions of locally low resolution, where manual model building is more prone to errors. Validation scores for structure models have been developed to assess both the compatibility between map density and the structure, as well as the geometric and stereochemical properties of protein models. Recent advancements have introduced artificial intelligence (AI) into this field. These emerging AI-driven tools offer unique capabilities in the validation and refinement of cryo-EM-derived protein atomic models, potentially leading to more accurate protein structures and deeper insights into complex biological systems. Quality (philosophy) ; Quality assessment ; Protein structure prediction ; Cryo-electron microscopy ; Computer science ; Computational biology ; Chemistry ; Protein structure ; Reliability engineering ; Biology ; Engineering ; Physics ; Evaluation methods ; Biochemistry Enzyme Structure and Function ; Advanced Electron Microscopy Techniques and Applications ; Protein Structure and Dynamics
Authors: Shaoxin Zheng | Manna Gu | Guilan Feng | Mingfeng Zheng | Tianqi Zhao | X. M. Jing
Source: Photonics (article, 2025-04-16)
Field: Materials Science — Electronic, Optical and Magnetic Materials

Design of a Polarization-Insensitive and Wide-Angle Triple-Band Metamaterial Absorber This paper proposes a tri-band wide-angle polarization-insensitive absorber operating in the C-band and Ku-band, based on the design concept of metal–dielectric–metal. The absorber achieves absorption efficiencies of 99.05%, 99.3%, and 97.9% at 4.23 GHz, 7.403 GHz, and 14.813 GHz, respectively. The first two absorption frequencies are in the C-band, while the third absorption frequency is in the Ku-band, both of which are commonly used in satellite communication. The designed absorber consists of three differently sized regular hexagonal rings. To analyze the interaction mechanism between the electromagnetic wave and the absorber, we applied the theory of impedance matching and equivalent media to analyze the metamaterial properties of the absorber. In addition, the equivalent circuit model of the absorber has been analyzed. We then determined the existence of coupled electromagnetic resonances between the top and bottom surfaces by analyzing the distribution of the electric field, magnetic field, and surface currents on the absorber. By varying the polarization angle and incident angle of the incoming wave, we found that the absorber exhibits polarization insensitivity and wide-angle absorption characteristics. The TE and TM waves maintain more than 90% absorption efficiency up to incident angles of 50° and 60°, respectively. The absorber’s thickness is 1.07 mm, which is 0.0154 times the wavelength corresponding to the lowest resonant frequency (λ0), and the edge length of the subunit’s regular hexagon is 7.5 mm (0.108λ0), making the absorber sub-wavelength in scale while maintaining its compactness. The proposed absorber operates in the C-band and Ku-band, and can be applied in the field of satellite communications, achieving functions such as electromagnetic shielding and stealth. Metamaterial ; Optics ; Polarization (electrochemistry) ; Metamaterial absorber ; Optoelectronics ; Materials science ; Physics ; Tunable metamaterials Metamaterials and Metasurfaces Applications ; Advanced Antenna and Metasurface Technologies ; Antenna Design and Analysis
Authors: Yu Li | Tao Tao | Yao Xiong | Weiyu Guo | Yangbiao Liang
Source: Frontiers in Pharmacology (review, 2025-09-18)
Field: Materials Science — Biomaterials

Multifunctional PLGA nanosystems: enabling integrated diagnostic and therapeutic strategies In the past decades, biodegradable polymers have been widely used in pharmaceutical and medical engineering materials. Poly (lactic-co-glycolic acid) (PLGA) copolymer, renowned for its exceptional biocompatibility, inherent non-toxicity, and superior encapsulation and film-forming capabilities, has been widely acknowledged as one of the foremost candidate materials among next-generation biodegradable polymers with remarkable application potential. PLGA nanoparticles exhibit demonstrated versatility in accommodating hydrophobic or hydrophilic substances, which can be either encapsulated within their core matrix or adsorbed onto the surface. This includes chemical drugs, nucleic acids, peptides, and proteins. Upon entering the systemic circulation, the size-tunable characteristics of PLGA nanoparticles synergize with surface ligand-receptor interactions to confer dual-targeting capabilities: passive targeting through enhanced permeability and retention (EPR) effects, and active targeting <i>via</i> specific molecular recognition at pathological sites. Moreover, the integration of multimodal imaging capabilities into PLGA-based nanoparticles enables <i>in vivo</i> imaging-guided drug delivery, which paves the way for more precise and enhanced approaches to disease diagnosis and therapeutic intervention. This review systematically examines the fabrication strategies, structural variants of PLGA-based nanostructures, and their applications in both diagnostic and therapeutic domains of biomedicine. PLGA ; Nanoparticle ; Drug delivery ; Nanomedicine ; Biodegradable polymer ; Polymer Nanoparticle-Based Drug Delivery ; Nanoplatforms for cancer theranostics ; Graphene and Nanomaterials Applications
Authors: Alexandra Gennaris | Van Son Nguyen | Laurie Thouvenel | Naemi Csoma | Didier Vertommen | Bogdan I. Iorga | Han Remaut | Jean‐François Collet
Source: Cell Reports (article, 2025-03-23)
Field: Chemistry — Spectroscopy

Optimal functioning of the Lpt bridge depends on a ternary complex between the lipocalin YedD and the LptDE translocon The outer membrane is an efficient permeability barrier that protects gram-negative bacteria against external assaults, including many antibiotics. The unique permeability features of the outer membrane are due to the presence of lipopolysaccharide (LPS) molecules in its outer leaflet. LPS transport relies on the essential lipopolysaccharide transport (Lpt) pathway, which forms a bridge from the inner to the outer membrane. The LptDE translocon inserts LPS into the outer leaflet. Here, we identify the lipocalin YedD as a component of the translocon. Cryoelectron microscopy of the YedD-LptDE complex reveals that YedD binds LptD at a critical interface between its β-barrel and periplasmic β-taco domain. The YedD-LptDE complex is functionally relevant: under conditions where the connectivity of the β-taco and Lpt bridge is compromised, the absence of YedD decreases cell viability and causes LPS accumulation in the inner membrane. Our findings establish YedD as an Lpt component required for optimal LPS transport. Ternary operation ; Translocon ; Bridge (graph theory) ; Lipocalin ; Computer science ; Chemistry ; Medicine ; Internal medicine ; Biochemistry ; Gene ; Chromosomal translocation Molecular Sensors and Ion Detection ; Neuroscience and Neuropharmacology Research ; Lanthanide and Transition Metal Complexes
Authors: Sasmita Bal | Namrata Rani
Source: Discover Applied Sciences (article, 2025-07-17)
Field: Chemistry — Spectroscopy

Next generation building materials for energy efficiency and climate responsive design Abstract The growing demand for sustainable construction, driven by climate change and urban expansion, highlights the urgent need for next generation building materials that enhance energy efficiency while supporting environmental goals. Traditional materials often fall short in addressing dynamic thermal loads, resource efficiency, and occupant comfort. This review investigates recent advancements in energy-efficient and climate responsive building materials, focusing on their insulation properties, thermal regulation, durability, and ecological impact. The objective is to assess the performance, benefits, and limitations of materials such as phase change materials (PCMs), aerogels, vacuum insulation panels, nanocomposites, and bio-based alternatives including straw, cork, and recycled steel. Based on findings from experimental, numerical, and analytical studies, these materials demonstrate significant potential to reduce energy consumption, improve indoor thermal comfort, and contribute to low-carbon construction practices. However, challenges such as high upfront costs, scalability issues, and lack of standardized performance metrics remain. The review recommends prioritizing life-cycle performance assessments, cost-effective production, and integration into building codes to support practical deployment. This work provides actionable insights for architects, engineers, and policymakers aiming to implement energy smart and climate-resilient design strategies through advanced material selection. Efficient energy use ; Software deployment ; Life-cycle assessment ; Resource efficiency ; Work (physics) ; Architectural engineering ; Energy consumption ; Sustainability ; Resource (disambiguation) ; Thermal insulation ; Environmental economics ; Computer science ; Environmental science ; Systems engineering ; Engineering ; Production (economics) ; Mechanical engineering ; Materials science Aerogels and thermal insulation ; Phase Change Materials Research ; Building Energy and Comfort Optimization
Authors: Hunter B. Andrews | Lyndsey Hendriks | Sawyer Irvine | Daniel R. Dunlap | Benjamin T. Manard
Source: Journal of Analytical Atomic Spectrometry (article, 2025-01-01)
Field: Chemistry — Spectroscopy

TOFHunter—unlocking rapid untargeted screening of inductively coupled plasma–time-of-flight–mass spectrometry data This study provides an overview of a newly developed program written in Python, TOFHunter, which permits the rapid and untargeted screening of inductively coupled plasma (ICP)-time-of-flight (TOF)-mass spectrometry (MS) datasets. Inductively coupled plasma mass spectrometry ; Mass spectrometry ; Chemistry ; Python (programming language) ; Time of flight ; Inductively coupled plasma ; Analytical Chemistry (journal) ; Chromatography ; Plasma ; Computer science ; Physics ; Nuclear physics Mass Spectrometry Techniques and Applications ; Analytical chemistry methods development ; Laser-induced spectroscopy and plasma
Authors: Simona Lupșor | Gabriela Stanciu | Radu Emilian Cristache | Emilia Pǎnuş | Cristiana Rădulescu | Radu Lucian Olteanu | Claudia Lavinia Buruleanu | Raluca Maria Ştirbescu
Source: Plants (article, 2025-06-22)
Field: Materials Science — Biomaterials

Phytochemical Evaluation and Antioxidant-Antimicrobial Potential of Lilium spp. Bulbs: Therapeutic and Dermatocosmetic Applications <i>Lilium</i> spp. bulbs are traditionally valued for their medicinal properties, yet their phytochemical profile and biomedical potential remain underexplored. This study aims to assess the antioxidant, antimicrobial, and dermatocosmetic potential of ethanolic macerates from five <i>Lilium</i> spp. cultivars. Bulb macerates were obtained using 70% and 96% ethanol and evaluated for total phenolic content (TPC), total flavonoid content (TFC), condensed tannins (CTC), mineral composition, and antioxidant activity (DPPH assay). Spectroscopic (FTIR) and antimicrobial analyses were also performed. Macerates from <i>Lilium</i> "Dark Secret" (LD-70) and <i>Lilium asiaticum</i> "White" (LA-70) exhibited the highest levels of TPC (225 and 162.5 mg GAE/100 g f.w.), TFC (26.12 and 21.75 mg QE/100 g f.w.), and antioxidant activity (81.5 and 58.75 mg GAE/100 g f.w.). FTIR confirmed the phenolic composition, while mineral analysis revealed a high potassium content and negligible toxic metals. Selective antimicrobial activity was observed against <i>Escherichia coli</i>, <i>Pseudomonas aeruginosa</i>, and <i>Candida albicans</i>, particularly for LD-70 and LA-70 macerates. Based on these findings, stable hydrogel formulations incorporating LD-70 and LA-70 were developed, showing favorable pH, rheology, and sustained antioxidant activity over 60 days. These findings support the integration of <i>Lilium</i>-derived macerates into dermatocosmetic formulations targeting skin protection and microbial defense. Phytochemical ; Antimicrobial ; Traditional medicine ; Lilium ; Antioxidant ; Biology ; Botany ; Medicine ; Microbiology ; Biochemistry Phytochemistry and Bioactive Compounds ; Phytochemical Studies and Bioactivities ; Phytochemistry and biological activities of Ficus species
Authors: Qiong Yao | Pan Pan | Xiaoming Zheng | Guomin Zhou | Jianhua Zhang
Source: Frontiers in Plant Science (article, 2025-06-02)
Field: Chemistry — Analytical Chemistry

ST-YOLO: a deep learning based intelligent identification model for salt tolerance of wild rice seedlings The experimental results show that the improved model significantly improves in precision compared with the current mainstream model, and the model evaluates the salt tolerance level of wild rice varieties, and screens out a total of 2 varieties that are extremely salt tolerant and 7 varieties that are salt tolerant, which meets the real-time requirements, and has a certain reference value for the practical application. Identification (biology) ; Biology ; Rice plant ; Salt (chemistry) ; Botany ; Artificial intelligence ; Computer science ; Agronomy ; Chemistry Spectroscopy and Chemometric Analyses ; GABA and Rice Research ; Leaf Properties and Growth Measurement
Authors: Gianmaria Viciconte | Paolo Guida | Tadd Truscott | William L. Roberts
Source: Physics of Fluids (article, 2025-01-01)
Field: Materials Science — Materials Chemistry

A general description of the cavitation threshold in acoustic systems Traditionally, the cavitation threshold is defined by some combination of vapor pressure and surface tension. However, these formulations present a large discrepancy with experimental data for cases where cavitation is induced by acoustic waves. The present study aims to identify a more suitable cavitation threshold for such cases. The method adopted in this work consists of a combination of visualizations with a high-speed camera and direct measurements using a hydrophone. The data collected confirmed that vapor pressure is not a proper indicator of cavitation occurrence for an acoustic system characterized by high frequencies. The main reason behind the inability of vapor pressure to predict incipient cavitation in acoustic systems is that they evolve very quickly toward strong gradients in pressure, and the quasi-static assumptions used by traditional models are not valid. Instead, the system evolves toward a metastable state [Brennen, Cavitation and Bubble Dynamics, 2013], where the liquid exhibits an elastic behavior and can withstand negative pressures. A new cavitation number is defined to properly describe the phenomenology of acoustic cavitation. However, to provide a complete description of the cavitation threshold, future experiments, in a wide range of acoustic frequencies, are still necessary. An acoustic analogy is also proposed for the description, with the same framework, of an impulsive cavitation phenomenon. Cavitation ; Physics ; Acoustics ; Bubble ; Mechanics ; Sonochemistry ; Metastability ; Hydrophone ; Sound pressure Ultrasound and Cavitation Phenomena ; Cavitation Phenomena in Pumps ; Flow Measurement and Analysis
Authors: Carlos Miguel Peraza-Alemán | Silvia Arazuri Garín | Carmen Jarén | José Ignacio Ruíz de Galarreta | Leire Barandalla | Ainara López-Maestresalas
Source: Computers and Electronics in Agriculture (article, 2025-03-29)
Field: Chemistry — Analytical Chemistry

Predicting the spatial distribution of reducing sugars using near-infrared hyperspectral imaging and chemometrics: a study in multiple potato genotypes • Hyperspectral imaging successfully predicted reducing sugars in potato genotypes. • PLS and SVM regression methods showed similar prediction performance. • Variable selection algorithms effectively preserved the accuracy of the models. • CARS-PLSR and iPLS-SVMR models were validated at pixel level. • A visual screening of reducing sugars on the surface of potato slices was provided. The determination of reducing sugars in potatoes is important due to their impact on product quality during industrial processing. The significant variability of these compounds between genotypes presents a challenge to the development of accurate predictive models. This study evaluated the potential of near-infrared hyperspectral imaging (NIR-HSI) for the prediction of reducing sugars in potatoes. For this, a wide range of genotypes (n = 92) from two seasons (2020–2021) was selected. Partial Least Squares Regression (PLSR) and Support Vector Machine Regression (SVMR) methods were used to build the prediction models. Furthermore, interval PLS (iPLS), recursive weighted PLS (rPLS), Genetic Algorithm (GA) and Competitive Adaptive Reweighted Sampling (CARS) were used for relevant wavelength identification to develop less computationally complex models. The best full spectrum model (SNV-PLSR) achieved coefficient of determination and root mean square error values of 0.88 and 0.053 % and 0.86 and 0.057 %, for calibration and external validation, respectively. Variable selection algorithms successfully reduced the dimensionality of the data without compromising the performance of the models. Robust predicted models were built with only 2.65 % (CARS-PLSR) and 3.57 % (iPLS-SVMR) of the total wavelengths. Finally, a pixel-wise prediction was performed on the validation set and chemical images were built to visualise the spatial distribution of reducing sugars. This study demonstrated that NIR-HSI is a feasible technique for predicting reducing sugars in several potato genotypes. Hyperspectral imaging ; Chemometrics ; Chemical imaging ; Remote sensing ; Spatial distribution ; Near-infrared spectroscopy ; Environmental science ; Pattern recognition (psychology) ; Artificial intelligence ; Chemistry ; Computer science ; Biology ; Chromatography ; Geography Spectroscopy and Chemometric Analyses ; Potato Plant Research ; Spectroscopy Techniques in Biomedical and Chemical Research
Authors: Huanhuan Gao | Yi Zhu | Dongxue Wang | Zongxiang Nie | He Wang | Guibin Wang | Shuang Liang | Yuting Xie | Yingying Sun | Wenhao Jiang | Zhen Dong | Liqin Qian | Xufei Wang | Mengdi Liang | Min Chen | Houqi Fang | Qiufang Zeng | Jiao Tian | Zeyu Sun | Juan Xue | Shan Li | Chen Chen | Xiang Liu | Xiaolei Lyu | Zhenchang Guo | Yingzi Qi | Ruoyu Wu | Xiaoxian Du | Tingde Tong | Fengchun Kong | Liming Han | Minghui Wang | Yang Zhao | Xinhua Dai | Fuchu He | Tiannan Guo
Source: Nature Communications (article, 2025-01-21)
Field: Chemistry — Spectroscopy

iDIA-QC: AI-empowered data-independent acquisition mass spectrometry-based quality control Quality control (QC) in mass spectrometry (MS)-based proteomics is mainly based on data-dependent acquisition (DDA) analysis of standard samples. Here, we collect 2754 files acquired by data independent acquisition (DIA) and paired 2638 DDA files from mouse liver digests using 21 mass spectrometers across nine laboratories over 31 months. Our data demonstrate that DIA-based LC-MS/MS-related consensus QC metrics exhibit higher sensitivity compared to DDA-based QC metrics in detecting changes in LC-MS status. We then prioritize 15 metrics and invite 21 experts to manually assess the quality of 2754 DIA files based on those metrics. We develop an AI model for DIA-based QC using 2110 training files. It achieves AUCs of 0.91 (LC) and 0.97 (MS) in the first validation dataset (n = 528), and 0.78 (LC) and 0.94 (MS) in an independent validation dataset (n = 116). Finally, we develop an offline software called iDIA-QC for convenient adoption of this methodology. Mass spectrometry ; Computer science ; Quality (philosophy) ; Control (management) ; Data quality ; Data mining ; Computational biology ; Chemistry ; Chromatography ; Artificial intelligence ; Physics ; Biology ; Engineering ; Operations management Mass Spectrometry Techniques and Applications ; Advanced Proteomics Techniques and Applications ; Metabolomics and Mass Spectrometry Studies
Authors: Jascha A. Lau | Martin DeWitt | Peter R. Franke | John F. Stanton | Daniel M. Neumark
Source: The Journal of Physical Chemistry A (article, 2025-02-03)
Field: Chemistry — Spectroscopy

High-Resolution Photoelectron Spectroscopy of NO <sub>3</sub> <sup>–</sup> Vibrationally Excited Along Its ν <sub>3</sub> Mode The nitrate (NO<sub>3</sub>) radical has long been the subject of both experimental and theoretical studies due to its complex electronic structure resulting from vibronic interactions between its <i>X̃</i><sup>2</sup><i>A</i><sub>2</sub><sup>'</sup> and <i>B̃</i><sup>2</sup><i>E</i><sup>'</sup> states. In particular, the definite assignment of the fundamental of its degenerate stretching vibration (ν<sub>3</sub>) is still under debate. Here, we report high-resolution photoelectron spectra of vibrationally pre-excited NO<sub>3</sub><sup>-</sup> using the recently developed IR-cryo-SEVI technique. The anions are excited through infrared (IR) excitation near 1350 cm<sup>-1</sup>, accessing the ν<sub>3</sub> and 2ν<sub>3</sub>(<i>e</i>') vibrational levels with band centers at 1350.5 and ∼2700 cm<sup>-1</sup>, respectively. The IR-cryo-SEVI spectrum for 2ν<sub>3</sub> pre-excitation shows clear evidence for an intense 3<sub>2</sub><sup>1</sup> transition. From the position of this feature (30031 cm<sup>-1</sup>), the electron affinity of NO<sub>3</sub> also determined in this work (31680 cm<sup>-1</sup>), and the IR excitation energy, we obtain a fundamental frequency of 1051 cm<sup>-1</sup> for the ν<sub>3</sub> fundamental of the NO<sub>3</sub> radical. This assignment and other features in the IR-cryo-SEVI spectra are supported by spectral simulations based on a vibronic Köppel-Domcke-Cederbaum Hamiltonian. The simulations also show that nearly all features in the IR-cryo-SEVI spectra arise because of pseudo-Jahn-Teller coupling between the <i>X̃</i> and <i>B̃</i> states of NO<sub>3</sub>. The results and analysis presented here settle a long-standing controversy regarding the ν<sub>3</sub> frequency of NO<sub>3</sub>. Excited state ; Atomic physics ; X-ray photoelectron spectroscopy ; Spectroscopy ; Mode (computer interface) ; High resolution ; Physics ; Nuclear magnetic resonance Spectroscopy and Laser Applications ; Advanced Chemical Physics Studies ; Atmospheric chemistry and aerosols