jablonkagroup/rise_ai_scientists huggingface dataset:
Authors: Zhaoyang Xie | Chi Li | Krishna Murali | Haoyi Yu | Changxu Liu | Yiqing Lu | Stefan Maier | Madhu Bhaskaran | Haoran Ren
Source: arXiv (Cornell University) (preprint, 2024-10-03)
Field: Materials Science — Materials Chemistry

Ultrathin BIC metasurfaces based on ultralow-loss Sb2Se3 phase-change material Phase-change materials (PCMs) are increasingly recognised as promising platforms for tunable photonic devices due to their ability to modulate optical properties through solid-state phase transitions. Ultrathin and low-loss PCMs are highly valued for their fast and more effective phase transitions and applications in reconfigurable photonic chips, metasurfaces, optical modulators, sensors, photonic memories, and neuromorphic computing. However, conventional PCMs such as GST, GSST, VO2, and In3SbTe2, despite optimisation for tunable meta-optics, suffer from high intrinsic losses in the near-infrared (NIR) region, limiting their potential for high quality factor (Q-factor) resonant metasurfaces. Here we present the design and fabrication of tunable bound states in the continuum (BIC) metasurfaces using the ultralow-loss PCM Sb2Se3. Our BIC metasurfaces, only 25 nm thick, achieve high modulation depth and broad resonance tuning in the NIR with high Q-factors up to 130, without the need for additional materials. Experimentally, we employ these BIC metasurfaces to modulate photoluminescence in rare earth-doped upconversion nanoparticles, reducing the excitation power for multiphoton photoluminescence and enabling emission polarisation manipulation. This work offers a promising platform for developing active resonant metasurfaces in the NIR region, with broad applications including super resolution imaging, optical modulation, ultrafast switches, harmonic generation, colour filtering, and optical sensing. Materials science ; Phase change ; Phase (matter) ; Nanotechnology ; Engineering physics ; Physics Phase-change materials and chalcogenides ; Chalcogenide Semiconductor Thin Films ; 2D Materials and Applications
Authors: Nisha | Prachi Chaudhary
Source: Journal of Integrated Science and Technology (article, 2024-09-26)
Field: Chemistry — Analytical Chemistry

Classification of Celiac disease using ensemble SMOTE-RF approach There are emerging challenges in the medical field as artificial intelligence is being introduced for automated detection of different diseases including celiac disease (CD). Manual interpretation is time time-consuming task performed by endoscopists whereas experience plays a key role in figuring out the abnormal region. The endoscopy images are processed with automated detection as their results are promising in terms of presence and non-presence of the disease. Initially, fastNLmeans denoising enabled pre-processing with Synthetic Minority Oversampling Technique (SMOTE) is utilized for mitigating the effect of the noise and for increasing the minority class images. For effective automatic classification, segmentation is a crucial step in image processing. Then, the Sobel operator with Multilevel Otsu thresholding is used as a segmentation step to reduce the complexity of the image. Image spatial features are extracted using a hybrid approach of discrete wavelet transform and high-order spectra (HOS). Thereafter, the Balanced random forest classifier is implemented to classify images as normal and abnormal. This model achieves remarkable performance with an accuracy of 89.41%, precision of 94.23%, recall of 89.09%, and F1 score of 91.58%. This approach validates the results with the help of endoscopists to prove its efficacy. These results outperform by imparting a high value of precision and F1 score. Computer science ; Artificial intelligence ; Disease ; Pattern recognition (psychology) ; Medicine ; Machine learning ; Internal medicine Spectroscopy and Chemometric Analyses ; Freezing and Crystallization Processes ; Gene expression and cancer classification
Authors: Natalia H. Rogoża | Magdalena A. Krupa | Paweł Krupa | Adam K. Sieradzan
Source: Molecules (article, 2024-04-23)
Field: Materials Science — Materials Chemistry

Integrating Explicit and Implicit Fullerene Models into UNRES Force Field for Protein Interaction Studies Fullerenes, particularly C<sub>60</sub>, exhibit unique properties that make them promising candidates for various applications, including drug delivery and nanomedicine. However, their interactions with biomolecules, especially proteins, remain not fully understood. This study implements both explicit and implicit C<sub>60</sub> models into the UNRES coarse-grained force field, enabling the investigation of fullerene-protein interactions without the need for restraints to stabilize protein structures. The UNRES force field offers computational efficiency, allowing for longer timescale simulations while maintaining accuracy. Five model proteins were studied: FK506 binding protein, HIV-1 protease, intestinal fatty acid binding protein, PCB-binding protein, and hen egg-white lysozyme. Molecular dynamics simulations were performed with and without C<sub>60</sub> to assess protein stability and investigate the impact of fullerene interactions. Analysis of contact probabilities reveals distinct interaction patterns for each protein. FK506 binding protein (1FKF) shows specific binding sites, while intestinal fatty acid binding protein (1ICN) and uteroglobin (1UTR) exhibit more generalized interactions. The explicit C<sub>60</sub> model shows good agreement with all-atom simulations in predicting protein flexibility, the position of C<sub>60</sub> in the binding pocket, and the estimation of effective binding energies. The integration of explicit and implicit C<sub>60</sub> models into the UNRES force field, coupled with recent advances in coarse-grained modeling and multiscale approaches, provides a powerful framework for investigating protein-nanoparticle interactions at biologically relevant scales without the need to use restraints stabilizing the protein, thus allowing for large conformational changes to occur. These computational tools, in synergy with experimental techniques, can aid in understanding the mechanisms and consequences of nanoparticle-biomolecule interactions, guiding the design of nanomaterials for biomedical applications. Force field (fiction) ; Fullerene ; Field (mathematics) ; Computer science ; Physics ; Mathematics ; Artificial intelligence ; Quantum mechanics ; Pure mathematics Carbon Nanotubes in Composites ; Fullerene Chemistry and Applications ; ATP Synthase and ATPases Research
Authors: Tamara Ruiz-Calleja | Alberto Jiménez‐Suárez | Rocío Calderón‐Villajos | Silvia G Prolongo
Source: Textile Research Journal (article, 2024-03-14)
Field: Materials Science — Polymers and Plastics

Characterization of conductive particle dispersion in textile coatings through Joule’s effect monitoring analysis Achieving proper dispersion of pigments, dyes, or other additives, such as microcapsules or nanoparticles, within printing pastes or textile coatings is crucial for obtaining a homogeneous result. In certain specialized applications, such as coloration technology, it is possible to use colorimetry tools, visual examination, and even artificial vision to identify defects. However, none of these techniques comprehensively map the specific additive distribution. This paper proposes a novel approach: monitoring the distribution of conductive particles (graphene nanoplatelets, referred to as GNPs) within an acrylic coating paste using the Joule’s effect. Four different dispersion systems (ultrasound mixer, blender, toroidal agitation, and three-roll mill) are employed. Thermographic images provide an accurate view of how conductive particles are distributed. This complements data from numerical values, such as the maximum and average temperatures recorded for each sample. In certain cases, relying solely on numerical values can be inadequate or insufficient, hence the novelty of this article emphasizing the significance of using the Joule’s effect to assess the distribution of conductive particles. Concerning the mixing systems, optimal dispersion of GNPs in distilled water is most effectively achieved using an ultrasound mixer, with enhanced uniformity as dispersion time increases. For mixing the components of the coating paste, the toroidal agitation method yields the best result. Employing the three-roll mill is discouraged for this application due to its propensity to induce phase separation. Textile ; Materials science ; Dispersion (optics) ; Characterization (materials science) ; Particle (ecology) ; Composite material ; Electrical conductor ; Joule (programming language) ; Joule heating ; Electrically conductive ; Nanotechnology ; Engineering ; Electrical engineering ; Optics Textile materials and evaluations ; Material Properties and Processing ; Advanced Sensor and Energy Harvesting Materials
Authors: Nikolaos Loukeris | Iordanis Eletheriadis
Source: Preprints.org (preprint, 2024-06-18)
Field: Chemistry — Organic Chemistry

Optimal Investments in the Portfolia Yield Reactives (PYR)‡ We evolve our past models PYR, Loukeris, et al. (2016) to provide a competitive system whose infiltration of categorical information and fundamentals into advanced higher moments, supports a more objective Portfolio Selection, aided by Intelligent Computing. The system of Portfolia Yield Reactives (PYR) searches for hidden prototypes into big data of accounting and financial statements, restricting malicious patterns such as hoax, noise, manipulation, incorporated to a novel optimal portfolio selection method. Yield (engineering) ; Business ; Materials science ; Metallurgy Chemistry and Stereochemistry Studies
Authors: Vasyl Martsenyuk | О. О. Солдаткін | Aleksandra Kłos-Witkowska | А. С. Сверстюк | Ksenya Berketa
Source: Frontiers in Bioengineering and Biotechnology (article, 2024-07-16)
Field: Chemistry — Physical and Theoretical Chemistry

Operational stability study of lactate biosensors: modeling, parameter identification, and stability analysis Qalitative examination of the model elucidates the influence of delay on dynamic behavior. We observe a transition from stable focus to limit cycle and period-doubling phenomena with increasing delay values, as evidenced by phase plots and bifurcation diagrams employing Poincaré sections. Additionally, we identify limitations in model applicability, notably the loss of solution positivity with growing delays, underscoring the necessity for cautious interpretation when employing delayed exponential function formulations. This comprehensive study provides valuable insights into the design and operational characteristics of lactate biosensors, offering a robust framework for understanding and optimizing their performance in diverse settings. Linearization ; Stability (learning theory) ; Computer science ; Bifurcation ; Polynomial ; Control theory (sociology) ; Exponential stability ; Nonlinear system ; Mathematical optimization ; Mathematics ; Physics ; Artificial intelligence thermodynamics and calorimetric analyses ; Molecular Junctions and Nanostructures ; Receptor Mechanisms and Signaling
Authors: David Mrdjenovich | Kristin A. Persson
Source: Physical Review Materials (article, 2024-03-13)
Field: Materials Science — Materials Chemistry

Crystallographic map: A general lattice and basis formalism enabling efficient and discretized exploration of crystallographic phase space Three-dimensional lattices are fundamental to solid-state physics. The description of a lattice with an atomic basis constitutes the necessary information to predict solid phase properties and evolution. Here, we present an algorithm for systematically exploring crystallographic phase space. Coupled with ab initio techniques, such as density functional theory, this algorithm offers an approach for exploring and tuning materials behavior, with a broad range of potential applications: particularly martensitic phase transformations and materials stability. Materials science ; Lattice (music) ; Formalism (music) ; Ab initio ; Discretization ; Basis (linear algebra) ; Crystal structure ; Solid-state ; Crystallography ; Condensed matter physics ; Statistical physics ; Physics ; Geometry ; Quantum mechanics ; Engineering physics ; Mathematics ; Chemistry ; Mathematical analysis Machine Learning in Materials Science ; Microstructure and mechanical properties ; High-pressure geophysics and materials
Authors: Fumiaki Ito | Ziyuan Li | Leonid Minakhin | Htet A. Khant | Richard T. Pomerantz | Xiaojiang S. Chen
Source: bioRxiv (Cold Spring Harbor Laboratory) (preprint, 2024-06-07)
Field: Materials Science — Materials Chemistry

Structural Basis for Polθ-Helicase DNA Binding and Microhomology-Mediated End-Joining DNA double-strand breaks (DSBs) present a critical threat to genomic integrity, often precipitating genomic instability and oncogenesis. Repair of DSBs predominantly occurs through homologous recombination (HR) and non-homologous end joining (NHEJ). In HR-deficient cells, DNA polymerase theta (Polθ) becomes critical for DSB repair via microhomology-mediated end joining (MMEJ), also termed theta-mediated end joining (TMEJ). Thus, Polθ is synthetically lethal with BRCA1/2 and other HR factors, underscoring its potential as a therapeutic target in HR-deficient cancers. However, the molecular mechanisms governing Polθ-mediated MMEJ remain poorly understood. Here we present a series of cryo-electron microscopy structures of the Polθ helicase domain (Polθ-hel) in complex with DNA containing 3'-overhang. The structures reveal the sequential conformations adopted by Polθ-hel during the critical phases of DNA binding, microhomology searching, and microhomology annealing. The stepwise conformational changes within the Polθ-hel subdomains and its functional dimeric state are pivotal for aligning the 3'-overhangs, facilitating the microhomology search and subsequent annealing necessary for DSB repair via MMEJ. Our findings illustrate the essential molecular switches within Polθ-hel that orchestrate the MMEJ process in DSB repair, laying the groundwork for the development of targeted therapies against the Polθ-hel. Helicase ; Genetics ; DNA ; Basis (linear algebra) ; Computational biology ; Biology ; Computer science ; Mathematics ; Gene Enzyme Structure and Function ; Protein Structure and Dynamics ; RNA and protein synthesis mechanisms
Authors: Selvam Paramasivan | Mohamed Ashick | Kevin J. Dudley | Nana Satake | Paul C. Mills | Paweł Sadowski | Shivashankar H. Nagaraj
Source: PROTEOMICS (article, 2024-03-11)
Field: Chemistry — Spectroscopy

VPBrowse: Genome‐based representation of MS/MS spectra to quantify 10,000 bovine proteins SWATH is a data acquisition strategy acclaimed for generating quantitatively accurate and consistent measurements of proteins across multiple samples. Its utility for proteomics studies in nonlaboratory animals, however, is currently compromised by the lack of sufficiently comprehensive and reliable public libraries, either experimental or predicted, and relevant platforms that support their sharing and utilization in an intuitive manner. Here we describe the development of the Veterinary Proteome Browser, VPBrowse (http://browser.proteo.cloud/), an on-line platform for genome-based representation of the Bos taurus proteome, which is equipped with an interactive database and tools for searching, visualization, and building quantitative mass spectrometry assays. In its current version (VPBrowse 1.0), it contains high-quality fragmentation spectra acquired on QToF instrument for over 36,000 proteotypic peptides, the experimental evidence for over 10,000 proteins. Data can be downloaded in different formats to enable analysis using popular software packages for SWATH data processing whilst normalization to iRT scale ensures compatibility with diverse chromatography systems. When applied to published blood plasma dataset from the biomarker discovery study, the resource supported label-free quantification of additional proteins not reported by the authors previously including PSMA4, a tissue leakage protein and a promising candidate biomarker of animal's response to dehorning-related injury. Proteome ; Computer science ; Proteomics ; Genome ; Computational biology ; Normalization (sociology) ; Visualization ; Biomarker discovery ; Profiling (computer programming) ; Data mining ; Bioinformatics ; Biology ; Genetics Advanced Proteomics Techniques and Applications ; Identification and Quantification in Food ; Mass Spectrometry Techniques and Applications
Authors: Lin Yang | Yan Cheng | Yanlong Jia | Zhenfu Cao | Zerui Zhuang | Xiaolei Zhang | Jitian Guan | Rongzhi Cai | Yan Lin | Renhua Wu
Source: ACS Chemical Neuroscience (article, 2024-11-30)
Field: Materials Science — Materials Chemistry

Visualization of Unconjugated Bilirubin In Vivo with a Novel Approach Using Chemical Exchange Saturation Transfer Magnetic Resonance Imaging in a Rat Model Unconjugated bilirubin (UCB) visualization is valuable for early bilirubin encephalopathy (BE) diagnosis and management. UCB neurotoxicity is a challenge, necessitating improved imaging modalities for precise localization and characterization. This study developed a noninvasive method for UCB imaging in the brain using chemical exchange saturation transfer (CEST) magnetic resonance imaging, which visualizes UCB distribution through amide-bulk water proton exchange, a process termed bilirubin CEST (Bil-CEST) imaging. Bil-CEST imaging parameters were initially optimized; the exchange rate of the amide protons of UCB was calculated. Bil-CEST imaging characteristics and specificity were assessed using in vitro images of UCB solutions under different conditions and images of other brain metabolites. Bil-CEST maps of the rat brain were collected at the baseline and dynamically, postinjection of the UCB solution or vehicle into lateral ventricles of Sprague-Dawley rats. The model was validated using a water maze and pathological staining. In vitro, the Bil-CEST effect was observed at approximately 5.5 ppm downfield from bulk water. This effect was proportional to the UCB concentration and B1 amplitude. In vivo, Bil-CEST imaging revealed a progressive enhancement following a lateral ventricular UCB injection. Conversely, no significant imaging changes were observed in the vehicle group. Compared with the vehicle group, the UCB group had more hippocampal neuronal apoptosis and worse cognitive function. These findings highlight the utility of Bil-CEST in direct UCB imaging, indicating its potential as a clinically valuable biomarker for BE diagnosis and management. Magnetic resonance imaging ; In vivo ; Nuclear magnetic resonance ; Chemistry ; Saturation (graph theory) ; Biophysics ; Visualization ; Medicine ; Biology ; Radiology ; Computer science ; Physics ; Artificial intelligence ; Mathematics Lanthanide and Transition Metal Complexes ; Neonatal Health and Biochemistry ; Advanced MRI Techniques and Applications
Authors: Bo Cheng | Yuxiao Zou | Guofeng Song
Source: Heliyon (article, 2024-11-01)
Field: Materials Science — Electronic, Optical and Magnetic Materials

Ultrahigh-reflectivity chiral mirrors based on the metasurface of the quarter-waveplate A study is conducted on a GaAs-based high-contrast subwavelength chiral metasurface (HCCM) designed for 1064 nm. The metasurface integrates a high-contrast subwavelength grating (HCG) for TM mode modulation, a SiO<sub>2</sub> support layer, and a compact quarter-waveplate (QWP) to convert linearly polarized light to circularly polarized light. The HCG achieves ultra-high reflectivity at 1064 nm, attributed to the large refractive index contrast between the Si grating and SiO2 layer. The designed HCCM has a reflectivity of more than 99 % for the TM mode and less than 80 % for the TE waves in the wavelength range of 1050 nm-1085nm, and it can also excite the circularly polarized light with an absolute error of less than 0.03 at the transmitting end in the case of the 1064 nm TM wavelength. These results suggest that circular dichroic metasurfaces could offer a promising approach for photonic manipulation in circular polarization VCSELs, potentially reducing the manufacturing challenges and costs associated with traditional methods. Waveplate ; Quarter (Canadian coin) ; Optics ; Reflectivity ; Materials science ; Optoelectronics ; Physics ; Engineering physics ; History ; Laser ; Archaeology Metamaterials and Metasurfaces Applications ; Advanced Antenna and Metasurface Technologies ; Optical Coatings and Gratings
Authors: Zewen Zhuo | Ilya Belevich | Ville Leinonen | Jokitalo Eija | Tarja Malm | Alejandra Sierra | Jussi Tohka
Source: arXiv (Cornell University) (preprint, 2024-11-04)
Field: Materials Science — Materials Chemistry

Segment Anything for Dendrites from Electron Microscopy Segmentation of cellular structures in electron microscopy (EM) images is fundamental to analyzing the morphology of neurons and glial cells in the healthy and diseased brain tissue. Current neuronal segmentation applications are based on convolutional neural networks (CNNs) and do not effectively capture global relationships within images. Here, we present DendriteSAM, a vision foundation model based on Segment Anything, for interactive and automatic segmentation of dendrites in EM images. The model is trained on high-resolution EM data from healthy rat hippocampus and is tested on diseased rat and human data. Our evaluation results demonstrate better mask quality compared to the original and other fine-tuned models, leveraging the features learned during training. This study introduces the first implementation of vision foundation models in dendrite segmentation, paving the path for computer-assisted diagnosis of neuronal anomalies. Electron microscope ; Microscopy ; Electron ; Materials science ; Nanotechnology ; Optics ; Physics ; Nuclear physics Solidification and crystal growth phenomena
Authors: Hesham H. El-Feky | Talaat Y. Mohammed | Alaa S. Amin | Mohammed A. Kassem
Source: Analytical Methods in Environmental Chemistry Journal (article, 2024-01-20)
Field: Chemistry — Analytical Chemistry

Rapid extraction and separation of mercury in water and food samples based on micelles and azo-thiazoles complexation before determination by UV-Vis spectrophotometry A simple and sensitive procedure has been established for analyzing mercury (II) ions spectrophotometrically in the presence of micellar medium using three azo-thiazoles complexing reagents: 2-amino-6-(thiazole-2-yldiazenyl)-3-pyridinol (C8H7N5OS), 8-hydroxy-7-(thiazole-2-yldiazenyl) quinoline-5-sulfonic acid (C12H8N4O4S2), and 1-hydroxy-4-(thiazole-2-yldiazenyl)-2-naphthoic acid (C14H9N3O3S). H1 NMR spectra validated the three azo thiazoles synthesized material. Tween 80 (polysorbate 80) and cetyltrimethylammonium bromide (C19H42BrN as molecular biology) are micellar mediums to enhance sensitivity. Absorbances were measured for Hg (II) complexation with R1, R2, and R3 at λmax of 617, 633, and 554 nm, respectively. The UV-Vis spectrophotometer showed calibration curves in the 0.2-15 mg L-1. The molar absorptivity, Sandell's sensitivity, detection, and quantification limits (LOD, LOQ) were determined. The interferences of various ions were investigated, and a statistical assessment of the results was performed. The methods have been applied for trace determination of mercury (II) in food and environmental water samples. For food samples, all samples were digested before complexation with the azo-thiazoles material at optimized pH before determination by UV-Vis spectrophotometry. Chemistry ; Spectrophotometry ; Mercury (programming language) ; Detection limit ; Bromide ; Molar absorptivity ; Chromatography ; Reagent ; Metal ions in aqueous solution ; Micelle ; Nuclear chemistry ; Aqueous solution ; Ion ; Inorganic chemistry ; Organic chemistry Analytical chemistry methods development ; Electrochemical Analysis and Applications ; Analytical Chemistry and Sensors