jablonkagroup/rise_ai_scientists huggingface dataset:
Authors: Aniello Pelella | Arun Kumar | Kimberly Intonti | O. Durante | S. De Stefano | Xinyi Han | Zhonggui Li | Yao Guo | Filippo Giubileo | Luca Camilli | M. Passacantando | Alla Zak | Antonio Di Bartolomeo
Source: Small (article, 2024-07-12)
Field: Materials Science — Materials Chemistry

WS<sub>2</sub> Nanotube Transistor for Photodetection and Optoelectronic Memory Applications Nanotube and nanowire transistors hold great promises for future electronic and optoelectronic devices owing to their downscaling possibilities. In this work, a single multi-walled tungsten disulfide (WS<sub>2</sub>) nanotube is utilized as the channel of a back-gated field-effect transistor. The device exhibits a p-type behavior in ambient conditions, with a hole mobility µ<sub>p</sub> ≈ 1.4 cm<sup>2</sup>V<sup>-1</sup>s<sup>-1</sup> and a subthreshold swing SS ≈ 10 V dec<sup>-1</sup>. Current-voltage characterization at different temperatures reveals that the device presents two slightly different asymmetric Schottky barriers at drain and source contacts. Self-powered photoconduction driven by the photovoltaic effect is demonstrated, and a photoresponsivity R ≈ 10 mAW<sup>-1</sup> at 2 V drain bias and room temperature. Moreover, the transistor is tested for data storage applications. A two-state memory is reported, where positive and negative gate pulses drive the switching between two different current states, separated by a window of 130%. Finally, gate and light pulses are combined to demonstrate an optoelectronic memory with four well-separated states. The results herein presented are promising for data storage, Boolean logic, and neural network applications. Materials science ; Optoelectronics ; Transistor ; Photodetection ; Nanowire ; Schottky barrier ; Nanotube ; Field-effect transistor ; Nanotechnology ; Carbon nanotube field-effect transistor ; Photodetector ; Voltage ; Electrical engineering ; Carbon nanotube 2D Materials and Applications ; Advanced Memory and Neural Computing ; Nanowire Synthesis and Applications
Authors: Mostafa Kalhor | Joel Lapin | Mario Picciani | Mathias Wilhelm
Source: Molecular & Cellular Proteomics (review, 2024-06-12)
Field: Chemistry — Spectroscopy

Rescoring Peptide Spectrum Matches: Boosting Proteomics Performance by Integrating Peptide Property Predictors Into Peptide Identification Rescoring of peptide spectrum matches originating from database search engines enabled by peptide property predictors is exceeding the performance of peptide identification from traditional database search engines. In contrast to the peptide spectrum match scores calculated by traditional database search engines, rescoring peptide spectrum matches generates scores based on comparing observed and predicted peptide properties, such as fragment ion intensities and retention times. These newly generated scores enable a more efficient discrimination between correct and incorrect peptide spectrum matches. This approach was shown to lead to substantial improvements in the number of confidently identified peptides, facilitating the analysis of challenging datasets in various fields such as immunopeptidomics, metaproteomics, proteogenomics, and single-cell proteomics. In this review, we summarize the key elements leading up to the recent introduction of multiple data-driven rescoring pipelines. We provide an overview of relevant post-processing rescoring tools, introduce prominent data-driven rescoring pipelines for various applications, and highlight limitations, opportunities, and future perspectives of this approach and its impact on mass spectrometry-based proteomics. Peptide ; Boosting (machine learning) ; Proteomics ; Computer science ; Identification (biology) ; Computational biology ; Chemistry ; Artificial intelligence ; Biology ; Biochemistry ; Gene Advanced Proteomics Techniques and Applications ; Machine Learning in Bioinformatics ; vaccines and immunoinformatics approaches
Authors: Ping Liu | Siyi Lan | Duyang Gao | Dehong Hu | Zhen Chen | Ziyue Li | Guihua Jiang | Zonghai Sheng
Source: Journal of Nanobiotechnology (article, 2024-10-05)
Field: Materials Science — Biomaterials

Targeted blood-brain barrier penetration and precise imaging of infiltrative glioblastoma margins using hybrid cell membrane-coated ICG liposomes Surgical resection remains the primary treatment modality for glioblastoma (GBM); however, the infiltrative nature of GBM margins complicates achieving complete tumor removal. Additionally, the blood-brain barrier (BBB) poses a formidable challenge to effective probe delivery, thereby hindering precise imaging-guided surgery. Here, we introduce hybrid cell membrane-coated indocyanine green (ICG) liposomes (HM-Lipo-ICG) as biomimetic near-infrared (NIR) fluorescent probes for targeted BBB penetration and accurate delineation of infiltrative GBM margins. HM-Lipo-ICG encapsulates clinically approved ICG within its core and utilizes a hybrid cell membrane exterior, enabling specific targeting and enhanced BBB permeation. Quantitative assessments demonstrate that HM-Lipo-ICG achieves BBB penetration efficiency 2.8 times higher than conventional ICG liposomes. Mechanistically, CD44 receptor-mediated endocytosis facilitates BBB translocation of HM-Lipo-ICG. Furthermore, HM-Lipo-ICG enables high-contrast NIR imaging, achieving a signal-to-background ratio of 6.5 in GBM regions of an orthotopic glioma mouse model, thereby improving tumor margin detection accuracy fourfold (84.4% vs. 22.7%) compared to conventional ICG liposomes. Application of HM-Lipo-ICG facilitates fluorescence-guided precision surgery, resulting in complete resection of GBM cells. This study underscores the potential of hybrid cell membrane-coated liposomal probes in precisely visualizing and treating infiltrative GBM margins. Liposome ; Glioblastoma ; Blood–brain barrier ; Penetration (warfare) ; Biomedical engineering ; Cell ; Membrane ; Chemistry ; Biophysics ; Nanotechnology ; Materials science ; Medicine ; Cancer research ; Biology ; Central nervous system ; Biochemistry ; Internal medicine Nanoparticle-Based Drug Delivery ; Nanoplatforms for cancer theranostics ; RNA Interference and Gene Delivery
Authors: Masakazu Yamaguchi | Hiroki Saito | Satoshi Ikezawa | Kentaro Iwami
Source: Nanophotonics (article, 2024-01-19)
Field: Materials Science — Electronic, Optical and Magnetic Materials

Highly‐efficient full‐color holographic movie based on silicon nitride metasurface Metasurface holograms offer various advantages, including wide viewing angle, small volume, and high resolution. However, full-color animation of high-resolution images has been a challenging issue. In this study, a full-color dielectric metasurface holographic movie with a resolution of 2322 × 2322 was achieved by spatiotemporally multiplexing 30 frames with blue, green, and red color channels at the wavelengths of 445 nm, 532 nm, and 633 nm at the maximum reconstruction speed of 55.9 frames per second. The high average transmittance and diffraction efficiency of 92.0 % and 72.7 %, respectively, in the visible range, were achieved by adopting polarization-independent silicon nitride waveguide meta-atoms, resulting in high color reproducibility. The superposition of three wavelengths was achieved by adjusting the resolutions and positions of target images for each wavelength while maintaining the meta-atom pitch constant. The improvement in diffraction efficiency was brought about by the optimization of etching conditions to form high-aspect vertical nanopillar structures. Materials science ; Holography ; Optics ; Nanopillar ; Optoelectronics ; Silicon nitride ; Diffraction efficiency ; Wavelength ; Silicon ; Transmittance ; Diffraction ; Polarizer ; Silicon oxynitride ; Birefringence ; Grating ; Nanotechnology ; Nanostructure ; Physics Metamaterials and Metasurfaces Applications ; Advanced Antenna and Metasurface Technologies ; Antenna Design and Analysis
Authors: Allan S. Johnson | Ernest Pastor | Sergi Batlle-Porro | H. Benzidi | Tetsuo Katayama | Gilberto A. de la Peña Muñoz | Viktor Krapivin | Sunam Kim | Núria López | Mariano Trigo | Simon Wall
Source: Nature Physics (article, 2024-04-11)
Field: Materials Science — Materials Chemistry

All-optical seeding of a light-induced phase transition with correlated disorder Ultrafast manipulation of vibrational coherence provides a route to control the structure of solids. However, this strategy can only induce long-range correlations and cannot modify atomic structure locally, which is a requirement for many technological applications such as non-volatile electronics. Here we demonstrate that ultrafast lasers can generate incoherent structural fluctuations that are more efficient for material control than coherent vibrations, extending optical control to a wide range of materials. We observe that local non-equilibrium lattice distortions generated by a weak laser pulse reduce the energy barrier to switch between insulating and metallic states in vanadium dioxide. Seeding inhomogeneous structural fluctuations presents an alternative, more energy-efficient, route for controlling materials that may be applicable to all solids, including those used in data- and energy-storage devices. Controlling phase transitions in solids is crucial for many applications. Ultrafast laser pulses have now been shown to enable the energy-efficient generation of structural fluctuations in VO2 by harnessing the correlated disorder in the material. Physics ; Seeding ; Phase transition ; Phase (matter) ; Transition (genetics) ; Condensed matter physics ; Quantum mechanics ; Genetics Phase-change materials and chalcogenides ; Photonic Crystals and Applications ; Liquid Crystal Research Advancements
Authors: Michaela B. Cooley | Dana Wegierak | Reshani Perera | Eric Abenojar | Pinunta Nittayacharn | Felipe M. Berg | Youjoung Kim | Michael C. Kolios | Agata A. Exner
Source: ACS Nano (article, 2024-11-20)
Field: Materials Science — Biomaterials

Assessing Therapeutic Nanoparticle Accumulation in Tumors Using Nanobubble-Based Contrast-Enhanced Ultrasound Imaging This study explores the challenges associated with nanoparticle-based drug delivery to the tumor parenchyma, focusing on the widely utilized enhanced permeability and retention effect (EPR). While EPR has been a key strategy, its inconsistent clinical success lacks clear mechanistic understanding and is hindered by limited tools for studying relevant phenomena. This work introduces an approach that employs multiparametric dynamic contrast-enhanced ultrasound (CEUS) with a nanoscale contrast agent for noninvasive, real-time examination of tumor microenvironment characteristics. We demonstrate that CEUS imaging can: (1) evaluate tumor microenvironment features, (2) be used to help predict the distribution of doxorubicin-loaded liposomes in the tumor parenchyma, and (3) be used to predict nanotherapeutic efficacy. CEUS using nanobubbles (NBs) was carried out in two tumor types of high (LS174T) and low (U87) vascular permeability. LS174T tumors consistently showed significantly different time intensity curve (TIC) parameters, including area under the rising curve (AUC<sub>R</sub>, 2.7×) and time to peak intensity (TTP, 1.9×) compared to U87 tumors. Crucially, a recently developed decorrelation time (DT) parameter specific to NB CEUS dynamics successfully predicted the distribution of doxorubicin-loaded liposomes within the tumor parenchyma (<i>r</i> = 0.86 ± 0.13). AUC<sub>R</sub>, TTP, and DT were used to correlate imaging findings to nanotherapeutic response with 100% accuracy in SKOV-3 tumors. These findings suggest that NB-CEUS parameters can effectively discern tumor vascular permeability, serving as a biomarker for identifying tumor characteristics and predicting the responsiveness to nanoparticle-based therapies. The observed differences between LS174T and U87 tumors and the accurate prediction of nanotherapeutic efficacy in SKOV-3 tumors indicate the potential utility of this method in predicting treatment efficacy and evaluating EPR in diseases characterized by pathologically permeable vasculature. Ultimately, this research contributes valuable insights into refining drug delivery strategies and assessing the broader applicability of EPR-based approaches. Nanoparticle ; Materials science ; Nanotechnology ; Contrast (vision) ; Ultrasound ; Ultrasound imaging ; Biomedical engineering ; Medicine ; Radiology ; Computer science Nanoparticle-Based Drug Delivery ; Ultrasound and Hyperthermia Applications ; Photoacoustic and Ultrasonic Imaging
Authors: Lauren L. Porter | Irina Artsimovitch | César A. Ramírez‐Sarmiento
Source: Current Opinion in Structural Biology (article, 2024-03-26)
Field: Chemistry — Spectroscopy

Metamorphic proteins and how to find them In the last two decades, our existing notion that most foldable proteins have a unique native state has been challenged by the discovery of metamorphic proteins, which reversibly interconvert between multiple, sometimes highly dissimilar, native states. As the number of known metamorphic proteins increases, several computational and experimental strategies have emerged for gaining insights about their refolding processes and identifying unknown metamorphic proteins amongst the known proteome. In this review, we describe the current advances in biophysically and functionally ascertaining the structural interconversions of metamorphic proteins and how coevolution can be harnessed to identify novel metamorphic proteins from sequence information. We also discuss the challenges and ongoing efforts in using artificial intelligence-based protein structure prediction methods to discover metamorphic proteins and predict their corresponding three-dimensional structures. Metamorphic rock ; Computational biology ; Proteome ; Coevolution ; Biology ; Sequence (biology) ; Computer science ; Evolutionary biology ; Bioinformatics ; Genetics ; Paleontology Advanced Proteomics Techniques and Applications ; Machine Learning in Bioinformatics ; Protein Structure and Dynamics
Authors: Xuemei Zhang | Boris A. Vinatzer | Li Song
Source: Scientific Reports (article, 2024-11-12)
Field: Chemistry — Analytical Chemistry

Hyperspectral imaging analysis for early detection of tomato bacterial leaf spot disease Recent advancements in hyperspectral imaging (HSI) for early disease detection have shown promising results, yet there is a lack of validated high-resolution (spatial and spectral) HSI data representing the responses of plants at different stages of leaf disease progression. To address these gaps, we used bacterial leaf spot (Xanthomonas perforans) of tomato as a model system. Hyperspectral images of tomato leaves, validated against in planta pathogen populations for seven consecutive days, were analyzed to reveal differences between infected and healthy leaves. Machine learning models were trained using leaf-level full spectra data, leaf-level Vegetation index (VI) data, and pixel-level full spectra data at four disease progression stages. The results suggest that HSI can detect disease on tomato leaves at pre-symptomatic stages and differentiate bacterial disease spots from abiotic leaf spots. Using VI data as features for machine learning improved overall classification performance by 26-37% compared to the direct use of raw data. Critical wavelength bands and VIs varied across disease progression stages, suggesting that pre-symptomatic disease detection relied more on changes in leaf water content (1400 nm) and plant defense hormone-mediated responses (750 nm) rather than changes in leaf pigments or internal structure (800-900 nm), which may become more crucial during symptomatic stages. In conclusion, this study provides valuable insights into the dynamics of bacterial spot disease, revealing the potential benefits of leaf structure segmentation and VI group pattern analysis in HSI studies for the early detection of leaf diseases. Hyperspectral imaging ; Leaf spot ; Remote sensing ; Computer science ; Biology ; Artificial intelligence ; Botany ; Geography Spectroscopy and Chemometric Analyses ; Leaf Properties and Growth Measurement ; Smart Agriculture and AI
Authors: Gil I. Olgenblum | Brent O. Hutcheson | Gary J. Pielak | Daniel Harries
Source: Chemical Reviews (review, 2024-04-18)
Field: Materials Science — Materials Chemistry

Protecting Proteins from Desiccation Stress Using Molecular Glasses and Gels Faced with desiccation stress, many organisms deploy strategies to maintain the integrity of their cellular components. Amorphous glassy media composed of small molecular solutes or protein gels present general strategies for protecting against drying. We review these strategies and the proposed molecular mechanisms to explain protein protection in a vitreous matrix under conditions of low hydration. We also describe efforts to exploit similar strategies in technological applications for protecting proteins in dry or highly desiccated states. Finally, we outline open questions and possibilities for future explorations. Desiccation ; Chemistry ; Drought stress ; Nanotechnology ; Biochemical engineering ; Biophysics ; Botany Material Dynamics and Properties ; Hemoglobin structure and function ; Photochemistry and Electron Transfer Studies
Authors: Zeyu Chen | Yiling Huang | Zhaoxuan Zhang | Wei Zheng | Xuemei Song | Yaran Niu | Yi Zeng
Source: Journal of Advanced Ceramics (article, 2024-04-25)
Field: Materials Science — Ceramics and Composites

Investigation of improving the thermophysical properties and corrosion resistance of RE <sub>2</sub>SiO <sub>5</sub>/RE <sub>2</sub>Si <sub>2</sub>O <sub>7</sub> multiphase silicates by component design with RE doping In this research, a novel method for regulating components in RE<sub>2</sub>SiO<sub>5</sub>/RE<sub>2</sub>Si<sub>2</sub>O<sub>7</sub> multiphase silicates was developed, combining the benefits of suitable thermal expansion coefficient (CTE) and outstanding corrosion resistance against calcium-magnesium-alumino-silicate (CMAS). This approach enhanced the overall thermophysical properties. Additionally, the results from the CMAS corrosion resistance test indicated that (Lu<sub>1/3</sub>Yb<sub>1/3</sub>Tm<sub>1/3</sub>)<sub>2</sub>SiO<sub>5</sub>/(Lu<sub>1/3</sub>Yb<sub>1/3</sub>Tm<sub>1/3</sub>)<sub>2</sub>Si<sub>2</sub>O<sub>7</sub> and (Lu<sub>1/4</sub>Yb<sub>1/4</sub>Tm<sub>1/4</sub>Er<sub>1/4</sub>)<sub>2</sub>SiO<sub>5</sub>/(Lu<sub>1/4</sub>Yb<sub>1/4</sub>Tm<sub>1/4</sub>Er<sub>1/4</sub>)<sub>2</sub>Si<sub>2</sub>O<sub>7</sub> exhibited exceptional resistance to CMAS penetration, even at temperatures up to 1500 ℃. To comprehend the corrosion mechanism of CMAS on these silicates, we introduced a reaction-diffusion model, which involved observing interface changes between the corrosion product layer and the silicate block. This was achieved using Electron Back Scatter Diffraction (EBSD). These findings lay a theoretical basis for selecting rare earth elements in RE<sub>2</sub>SiO<sub>5</sub>/RE<sub>2</sub>Si<sub>2</sub>O<sub>7</sub> multiphase silicates based on the radius of different rare earth cations. Materials science ; Corrosion ; Analytical Chemistry (journal) ; Mineralogy ; Metallurgy ; Chemistry Advanced ceramic materials synthesis ; Nuclear materials and radiation effects ; Glass properties and applications
Authors: Muneeb Ullah | Uzma Azeem Awan | Haider Ali | Abdul Wahab | Shahid Ullah Khan | Muhammad Naeem | Muhammad Ruslin | Apon Zaenal Mustopa | Nurhasni Hasan
Source: Journal of Nanotheranostics (article, 2024-12-28)
Field: Materials Science — Materials Chemistry

Carbon Dots: New Rising Stars in the Carbon Family for Diagnosis and Biomedical Applications Carbon dots (CDs) are a class of carbon-based nanomaterials undergoing rapid development with broad potential applications across diverse biomedical fields. These materials are highly attractive for diagnostics, therapeutics, and nanomedicine due to their remarkable optical and physicochemical properties, including photoluminescence, biocompatibility, and aqueous dispersibility. CDs can be synthesized using various techniques, ranging from top-down to bottom-up approaches. Among these, biogenic synthesis, utilizing natural sources and waste materials, presents an eco-friendly and sustainable alternative. CDs have exhibited considerable promise in diagnostics, especially with bioimaging and biosensing, providing both high sensitivity and precise identification. CDs are presently being investigated in the pharmaceutical sector for their potential applications in cancer and infection treatment, as well as in photodynamic and thermal therapies. The advancement of CD composites, through enhanced functionality and broader application, facilitates novel research in nanomedicine. This article highlights the advantages of CDs, focusing on their structural properties, classification, and versatility in synthesis methods. Furthermore, the safety and toxicity profiles of CDs are critically analyzed. In conclusion, the innocuity, adaptability, and multifunctionality of CDs position them as a cornerstone in the advancement of nanotechnology and biomedical applications. With their broad applicability and promising potential, CDs stand poised to drive significant innovation across diagnostics, therapeutics, and other domains, heralding a new era in nanomedicine and sustainable material development. Stars ; Carbon fibers ; Nanotechnology ; Astrophysics ; Materials science ; Astronomy ; Physics Carbon and Quantum Dots Applications ; Nanocluster Synthesis and Applications ; Graphene and Nanomaterials Applications
Authors: Agnieszka Czylkowska | Monika Pitucha | Anita Raducka | Ewelina Fornal | Edyta Kordialik‐Bogacka | Sylwia Ścieszka | Marek Smoluch | Franciszek Burdan | Mateusz Jędrzejec | Paweł Szymański
Source: Molecules (article, 2024-12-31)
Field: Chemistry — Organic Chemistry

Thiosemicarbazone-Based Compounds: A Promising Scaffold for Developing Antibacterial, Antioxidant, and Anticancer Therapeutics This paper presents the synthesis and characterization of new thiosemicarbazone derivatives with potential applications as antibacterial, antioxidant and anticancer agents. Six thiosemicarbazone derivatives (L-L5) were synthesized by reacting an appropriate thiosemicarbazide derivative with 2-pyridinecarboxaldehyde. The structures of the obtained compounds were confirmed using mass spectrometry, infrared spectroscopy, and NMR spectroscopy. Antibacterial activity was evaluated by using the microdilution method, determining the minimum inhibitory concentration (MIC) against a panel of Gram-positive and Gram-negative bacteria. Compound L1 showed the most potent antibacterial activity, especially against <i>Bacillus cereus</i> (MIC 10 mg/L). Molecular docking to topoisomerase II and transcriptional regulator PrfA suggests that the studied compounds can effectively bind to molecular targets recognized in anticancer and antibacterial therapies. An assessment of physicochemical properties (ADME) indicates favorable parameters of the compounds as potential drugs. Compounds L and L2 showed the highest antioxidant activity, surpassing the activity of the Trolox standard. Cytotoxicity against A549 lung cancer cells was evaluated by the MTT assay. Compound L4 exhibited the strongest inhibitory effect on cancer cell survival. The obtained results indicate that the synthesized thiosemicarbazide derivatives, especially L1, L2, and L4, are promising compounds with potential applications as antibacterial and anticancer drugs. Chemistry ; Semicarbazone ; Antibacterial activity ; Broth microdilution ; ADME ; MTT assay ; Antioxidant ; Cytotoxicity ; Bacillus cereus ; Combinatorial chemistry ; Stereochemistry ; Minimum inhibitory concentration ; Antimicrobial ; Biochemistry ; Bacteria ; Organic chemistry ; In vitro ; Biology Synthesis and biological activity ; Cancer therapeutics and mechanisms ; Computational Drug Discovery Methods