jablonkagroup/rise_ai_scientists huggingface dataset:
Authors: Lennart Moritz | Maren Nicole Stillger | Ferenc Takács | Hannah Füllgraf | Martin Werner | Stefan Fichtner‐Feigl | Andreas Jud | Oliver Schilling | Melanie Christine Föll
Source: Preprints.org (preprint, 2023-02-21)
Field: Chemistry — Spectroscopy

Characterization of Spatial Heterogeneity in Metastasized Colorectal Cancer by MALDI Imaging About 50% of colorectal cancer patients develop liver metastases. Patients with metastatic colorectal cancer have 5-year survival rates below 20% despite new therapeutic regimens. Tumor heterogeneity has been linked with poor treatment response and clinical outcome, but was so far mainly studied via bulk genomic analyses. In this study we performed spatial proteomics via MALDI mass spectrometry imaging on six patient-matched CRC primary tumor and liver metastases to characterize interpatient, intertumor and intratumor hetereogeneity. We found several peptide features that were enriched in vital tumor areas of primary tumors and liver metastasis and tentatively derived from tumor cell specific proteins such as annexin A4 and prelamin A/C. Liver metastases of colorectal cancer showed higher heterogeneity between patients than primary tumors while within patients both entities show similar intratumor heterogeneity sometimes organized in zonal pattern. Together our findings give new insights into the spatial proteomic heterogeneity of primary CRC and patient-matched liver metastases. Colorectal cancer ; Medicine ; Metastasis ; Primary tumor ; Oncology ; Cancer ; Proteomics ; Internal medicine ; Cancer research ; Pathology ; Biology ; Gene Advanced Proteomics Techniques and Applications ; Mass Spectrometry Techniques and Applications ; Metabolomics and Mass Spectrometry Studies
Authors: Mitchell Buster | S. Simpfendorfer | Chris Guppy | Mike Sissons | Matthew Tighe | Richard J. Flavel
Source: Crop and Pasture Science (article, 2023-08-22)
Field: Chemistry — Analytical Chemistry

Remote detection of Fusarium crown rot in broadacre bread wheat and durum wheat through use of aerial imagery Context The cereal disease Fusarium crown rot (FCR), caused by the fungal pathogen Fusarium pseudograminearum, is a worldwide major constraint to winter cereal production, especially in Australia’s northern grain region of New South Wales and Queensland. Aims Detection of the disease is labour-intensive and often not spatially quantifiable; hence, the aim of this study was to provide methods for in-crop FCR detection on a broadacre scale. Methods A replicated field experiment across three locations in northern New South Wales explored the use of thermal and multispectral imagery and hyperspectral reflectance data for the spatial detection of FCR in three bread wheat (Triticum aestivum L.) and three durum wheat (T. durum Desf.) varieties in the presence and absence of inoculation with F. pseudograminearum. Key results Canopy temperature was 0.30–0.90°C higher in two-thirds of field sites inoculated with the pathogen during early wheat growth in a slightly wetter than normal season. Some multispectral indices including normalised difference red edge, normalised difference vegetation index, near infrared and red edge also demonstrated the ability to identify inoculated versus uninoculated treatments as early as the first node stage (GS31). Conclusions Although positive identification was achieved with remote detection, environmental conditions (i.e. soil-water availability and ambient temperature) and physiological maturity influenced the accuracy of the technology for detecting FCR infection, particularly in wetter early-season conditions. Implications Early spatial detection of FCR infection on a broadacre scale could allow producers to manage this disease spatially through better agronomic decisions. Biology ; Agronomy ; Canopy ; Crop ; Fusarium ; Growing season ; Crown (dentistry) ; Hyperspectral imaging ; Context (archaeology) ; Horticulture ; Botany ; Remote sensing ; Geography Spectroscopy and Chemometric Analyses ; Essential Oils and Antimicrobial Activity ; Remote Sensing in Agriculture
Authors: Zhao Jingxiang | Panpan Peng | Jinping Wang
Source: Open Computer Science (article, 2023-01-01)
Field: Chemistry — Analytical Chemistry

Nondestructive detection of potato starch content based on near-infrared hyperspectral imaging technology Abstract The traditional method of determining potato starch content is not only time-consuming and labor-intensive, but also very aggressive and destructive, which also causes serious pollution to the environment. Therefore, it is necessary to study the fast, efficient, and environment-friendly detection technology. Although near-infrared technology can solve these problems well, it cannot detect potato starch because of its dot shape, invisibility, and other shortcomings. Hyperspectral imaging technology has a new technology of near-infrared, which can simultaneously detect surface defects and internal physical and chemical components. In this article, the method of nondestructive testing of potato starch using near-infrared hyperspectral technology was studied. In thisarticle, successive projection algorithm, random frog, and genetic algorithm were used to predict the content of potato starch. The experimental results in this article showed that in random frog, the root mean square error (RMSEC) of correction set and the root mean square error of prediction (RMSEP) model <m:math xmlns:m="http://www.w3.org/1998/Math/MathML"> <m:msubsup> <m:mrow> <m:mi>R</m:mi> </m:mrow> <m:mrow> <m:mtext>C</m:mtext> </m:mrow> <m:mrow> <m:mn>2</m:mn> </m:mrow> </m:msubsup> </m:math> {R}_{\text{C}}^{2} and <m:math xmlns:m="http://www.w3.org/1998/Math/MathML"> <m:msubsup> <m:mrow> <m:mi>R</m:mi> </m:mrow> <m:mrow> <m:mtext>P</m:mtext> </m:mrow> <m:mrow> <m:mn>2</m:mn> </m:mrow> </m:msubsup> </m:math> {R}_{\text{P}}^{2} have become 0.87 and 0.84, respectively, and RMSEC and RMSEP have become 0.33 and 0.30%, respectively. Therefore, the best method to select the characteristic wavelength of potato starch is the random frog algorithm. Hyperspectral imaging ; Starch ; Infrared ; Projection (relational algebra) ; Content (measure theory) ; Mathematics ; Mean squared error ; Analytical Chemistry (journal) ; Physics ; Artificial intelligence ; Materials science ; Computer science ; Algorithm ; Chemistry ; Statistics ; Food science ; Optics ; Mathematical analysis ; Environmental chemistry Spectroscopy and Chemometric Analyses ; Water Quality Monitoring and Analysis ; Advanced Chemical Sensor Technologies
Authors: Zhening Fang | Haipeng Li | Chen Yan | Shulin Sun | Shiyi Xiao | Qiong He | Lei Zhou
Source: Nanophotonics (article, 2023-02-28)
Field: Materials Science — Electronic, Optical and Magnetic Materials

Deterministic approach to design passive anomalous‐diffraction metasurfaces with nearly 100% efficiency Designing perfect anomalous reflectors is crucial for achieving many metasurface-based applications, but available design approaches for the cases of extremely large bending angles either require unrealistic gain-loss materials or rely on brute-force optimizations lacking physical guidance. Here, we propose a deterministic approach to design <i>passive</i> metasurfaces that can reflect impinging light to <i>arbitrary</i> nonspecular directions with almost 100% efficiencies. With both incident and out-going far-field waves given, we can retrieve the surface-impedance profile of the target metadevice by matching boundary conditions with <i>all</i> allowed near-field modes added self-consistently and then construct the metadevices deterministically based on passive meta-atoms exhibiting local responses. We design/fabricate two proof-of-concept microwave metadevices and experimentally demonstrate that the first one achieves anomalous reflection to a 70° angle with efficiency ∼98%, and the second one can generate multiple reflected beams with desired bending angles and power allocations. Our findings pave the way for realizing high-efficiency wave-control metadevices with desired functionalities. Computer science ; Diffraction ; Bending ; Electronic engineering ; Optics ; Physics ; Engineering Metamaterials and Metasurfaces Applications ; Advanced Antenna and Metasurface Technologies ; Antenna Design and Analysis
Authors: Qiang Zhang
Source: Scientific Reports (article, 2023-04-29)
Field: Chemistry — Spectroscopy

Mzion enables deep and precise identification of peptides in data-dependent acquisition proteomics Sensitive and reliable identification of proteins and peptides pertains the basis of proteomics. We introduce Mzion, a new database search tool for data-dependent acquisition (DDA) proteomics. Our tool utilizes an intensity tally strategy and achieves generally a higher performance in terms of depth and precision across 20 datasets, ranging from large-scale to single-cell proteomics. Compared to several other search engines, Mzion matches on average 20% more peptide spectra at tryptic enzymatic specificity and 80% more at no enzymatic specificity from six large-scale, global datasets. Mzion also identifies more phosphopeptide spectra that can be explained by fewer proteins, demonstrated by six large-scale, local datasets corresponding to the global data. Our findings highlight the potential of Mzion for improving proteomic analysis and advancing our understanding of protein biology. Proteomics ; Computer science ; Identification (biology) ; Computational biology ; Quantitative proteomics ; Phosphopeptide ; Scale (ratio) ; Data mining ; Bioinformatics ; Peptide ; Chemistry ; Biology ; Biochemistry ; Physics Advanced Proteomics Techniques and Applications ; Machine Learning in Bioinformatics ; Mass Spectrometry Techniques and Applications
Authors: József Lázár | Péter Antal‐Szalmás | István Kurucz | Annamária Ferenczi | Mihály Józsi | Ilona Tornyi | Mónika Müller | János Tibor Fekete | John Lamont | Peter Fitzgerald | Anna Gall-Debreceni | János Kádas | András Vida | Nadège Tardieu | Yann Kieffer | A Jullien | Mariana Guergova-Kuras | William M. Hempel | András Kovács | Tamás Kardos | Nóra Bittner | Eszter Csánky | Mária Szilasi | György Losonczy | Klára Szondy | Gabriella Gálffy | Edit Csada | Klara Szalontai | Attila Somfay | David Malka | Paul Cottu | Krisztina Bogos | László Takács
Source: Molecular & Cellular Proteomics (article, 2023-05-20)
Field: Chemistry — Spectroscopy

Large-Scale Plasma Proteome Epitome Profiling is an Efficient Tool for the Discovery of Cancer Biomarkers Current proteomic technologies focus on the quantification of protein levels, while little effort is dedicated to the development of system approaches to simultaneously monitor proteome variability and abundance. Protein variants may display different immunogenic epitopes detectable by monoclonal antibodies. Epitope variability results from alternative splicing, posttranslational modifications, processing, degradation, and complex formation and possesses dynamically changing availability of interacting surface structures that frequently serve as reachable epitopes and often carry different functions. Thus, it is highly likely that the presence of some of the accessible epitopes correlates with function under physiological and pathological conditions. To enable the exploration of the impact of protein variation on the immunogenic epitome first, here, we present a robust and analytically validated PEP technology for characterizing immunogenic epitopes of the plasma. To this end, we prepared mAb libraries directed against the normalized human plasma proteome as a complex natural immunogen. Antibody producing hybridomas were selected and cloned. Monoclonal antibodies react with single epitopes, thus profiling with the libraries is expected to profile many epitopes which we define by the mimotopes, as we present here. Screening blood plasma samples from control subjects (n = 558) and cancer patients (n = 598) for merely 69 native epitopes displayed by 20 abundant plasma proteins resulted in distinct cancer-specific epitope panels that showed high accuracy (AUC 0.826-0.966) and specificity for lung, breast, and colon cancer. Deeper profiling (≈290 epitopes of approximately 100 proteins) showed unexpected granularity of the epitope-level expression data and detected neutral and lung cancer-associated epitopes of individual proteins. Biomarker epitope panels selected from a pool of 21 epitopes of 12 proteins were validated in independent clinical cohorts. The results demonstrate the value of PEP as a rich and thus far unexplored source of protein biomarkers with diagnostic potential. Epitope ; Monoclonal antibody ; Proteome ; Computational biology ; Biology ; Epitope mapping ; Antibody ; Immunology ; Bioinformatics Advanced Proteomics Techniques and Applications ; Glycosylation and Glycoproteins Research ; vaccines and immunoinformatics approaches
Authors: Soumia Dine Elhennani | Zouaoui R. Harrat | Mohammed Chatbi | Asma Belbachir | Baghdad Krour | Ercan Işık | Ehsan Harirchian | Mohamed Bouremana | Mohamed Bachir Bouiadjra
Source: Materials (article, 2023-08-27)
Field: Materials Science — Materials Chemistry

Buckling and Free Vibration Analyses of Various Nanoparticle Reinforced Concrete Beams Resting on Multi-Parameter Elastic Foundations Given their considerable specific surface area and amorphous characteristics, nanoparticles exhibit excellent pozzolanic activity, and when undergoing a reaction with calcium hydroxide, this leads to the generation of a denser matrix by promoting the formation of a greater amount of C-S-H gel, thereby enhancing the strength and durability of the concrete and fortifying the overall structure. Indeed, the present study investigates a comparative study of the buckling and free vibration analyses of concrete beams reinforced with various types of nanoparticles. For its simplicity and accuracy, a higher-order shear deformation theory will be used to analytically model the reinforced concrete beam. Furthermore, the powerful Eshelby's model is used to derive the equivalent nanocomposite properties. The soil medium is simulated with Pasternak elastic foundation, including a shear layer, and Winkler's spring, interlinked with a Kerr foundation. The motion equations are derived using Hamilton's principle. Moreover, based on Navier's analytical methods, the closed-form solutions of simply supported beams have been obtained. Different parameters, such as type and volume percent of nanoparticles, geometrical parameters, choice of theory and soil medium, on the buckling and dynamic behavior of the beam, are exercised and shown. The major findings of this work indicate that the use of nanoparticles in concretes increases better mechanical resistance and amplifies the natural frequencies. In addition, the elastic foundation has a significant impact on the buckling and vibration performances of concrete beams. Buckling ; Materials science ; Structural engineering ; Vibration ; Reinforced concrete ; Composite material ; Engineering ; Physics ; Acoustics Structural mechanics and materials ; Structural Behavior of Reinforced Concrete ; Composite Structure Analysis and Optimization
Authors: Kevin M. Roccapriore | Matthew G. Boebinger | Julian Klein | Mads Weile | Frances M. Ross | Maxim Ziatdinov | Raymond R. Unocic | Sergei V. Kalinin
Source: Microscopy and Microanalysis (article, 2023-07-22)
Field: Materials Science — Materials Chemistry

AI-enabled Automation of Atomic Manipulation and Characterization in the STEM Journal Article AI-enabled Automation of Atomic Manipulation and Characterization in the STEM Get access Kevin M Roccapriore, Kevin M Roccapriore Center for Nanophase Materials Sciences, Oak Ridge National Laboratory, Oak Ridge, TN, USA Corresponding author: roccapriorkm@ornl.gov Search for other works by this author on: Oxford Academic Google Scholar Matthew G Boebinger, Matthew G Boebinger Center for Nanophase Materials Sciences, Oak Ridge National Laboratory, Oak Ridge, TN, USA Search for other works by this author on: Oxford Academic Google Scholar Julian Klein, Julian Klein Department of Materials Science and Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA Search for other works by this author on: Oxford Academic Google Scholar Mads Weile, Mads Weile Center for Visualizing Catalytic Processes, Technical University of Denmark, Copenhagen, Denmark Search for other works by this author on: Oxford Academic Google Scholar Frances Ross, Frances Ross Department of Materials Science and Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA Search for other works by this author on: Oxford Academic Google Scholar Maxim Ziatdinov, Maxim Ziatdinov Center for Nanophase Materials Sciences, Oak Ridge National Laboratory, Oak Ridge, TN, USAComputational Sciences and Engineering Division, Oak Ridge National Laboratory, Oak Ridge, TN, USA Search for other works by this author on: Oxford Academic Google Scholar Raymond R Unocic, Raymond R Unocic Center for Nanophase Materials Sciences, Oak Ridge National Laboratory, Oak Ridge, TN, USA Search for other works by this author on: Oxford Academic Google Scholar Sergei V Kalinin Sergei V Kalinin Department of Materials Science and Engineering, University of Tennessee, Knoxville, TN, USA Search for other works by this author on: Oxford Academic Google Scholar Microscopy and Microanalysis, Volume 29, Issue Supplement_1, 1 August 2023, Pages 1366–1367, https://doi.org/10.1093/micmic/ozad067.702 Published: 22 July 2023 Oak Ridge National Laboratory ; Ridge ; Library science ; Art history ; Engineering physics ; Engineering ; History ; Computer science ; Geography ; Cartography ; Physics Electronic and Structural Properties of Oxides ; Advanced Electron Microscopy Techniques and Applications ; Electron and X-Ray Spectroscopy Techniques
Authors: Ahmed A. Abdel Aziz | Ali Abdelsallam | Abdelhamid Gaafar | Mahmoud A. Abdalla
Source: Journal of Instrumentation (article, 2023-03-01)
Field: Materials Science — Electronic, Optical and Magnetic Materials

Fractal metasurface for THz applications with polarization and incidence angle insensitivity Abstract A Fractal metasurface-based absorber is designed to obtain a wideband absorption in THz frequency band. The developed absorber has a broadband absorption over more than 600 GHz bandwidth, from 0.6 THz to 1.2 THz, with a minimum absorption percentage of 70% and total absorption from 1 to 1.1 THz. The proposed fractal structure is investigated using a Modified Split Ring Resonator (MSRR). The absorption coefficient of the proposed fractal metasurface is compared with the modified initially SRR metasurface. The results indicate that by using fractal design, the metasurface operating band is summed up, resulting in a wide bandwidth. The absorption coefficient of the proposed fractal metasurface is studied using two different simulation software programs to ensure the obtained results, with a high agreement between the results of them. The designed metasurface has a similar absorption response for the different polarization of the incident wave. The impedance of the designed metasurface indicates that, for the operating band, the fractal metasurface has a surface impedance of around 377 Ω, indicating a good matching between the designed metasurface and air. Different incidence and polarization angles are studied with results showing its insensitivity to both of them. The designed metasurface is compared with previously published works, showing wider bandwidth, higher absorption, and incidence and polarization insensitivity. The proposed metasurface absorber can be used for biomedical applications. Fractal ; Wideband ; Optics ; Polarization (electrochemistry) ; Metamaterial absorber ; Terahertz radiation ; Materials science ; Broadband ; Bandwidth (computing) ; Resonator ; Attenuation coefficient ; Fractal antenna ; Impedance matching ; Molar absorptivity ; Finite-difference time-domain method ; Metamaterial ; Optoelectronics ; Physics ; Electrical impedance ; Tunable metamaterials ; Telecommunications ; Radiation pattern ; Computer science ; Chemistry Metamaterials and Metasurfaces Applications ; Antenna Design and Analysis ; Advanced Antenna and Metasurface Technologies
Authors: Raghvenda Kumar Singh | Ashish Gupta | Akash Yadav | Nishchay Gupta | Utkarsh Tyagi
Source: International Journal of Antennas and Propagation (article, 2023-09-05)
Field: Materials Science — Electronic, Optical and Magnetic Materials

An Ultrathin Polarization Free Asterick-Shaped Metamaterial Absorber with Quad-Band Characteristics In this paper, a quad-band absorber is proposed and developed, which is exhibiting ultrathin and polarization insensitive behaviour. It has been designed to be operated in S, C, and Ku bands with absorptions peaks at more than 95%. The proposed absorber is implemented on a FR4 glass epoxy laminate with an equivalent electrical thickness of 0.0108 λ0, where λ0 is the wavelength corresponding to the lowest frequency of operation. This confirms the ultrathin nature of the structure. The absorption performance of the proposed structure has been characterized under normal and oblique incidences followed by their experimental verification. Presented results demonstrate highly polarization-independent behavior of the proposed absorber due to its symmetric geometry. Also, the electromagnetic field distributions have been studied to acquire better insight of the absorption mechanism corresponding to distinct elements present in the structure. It is characterized in terms of its behavior as metamaterial, which ensures the miniaturization. The proposed absorber is suitable to be used in applications like radar cross section reduction, stealth technology, radio frequency identification, and electromagnetic compatibility. Metamaterial absorber ; Metamaterial ; Miniaturization ; Materials science ; Polarization (electrochemistry) ; Frequency band ; Wavelength ; Optics ; Absorption band ; Radar ; Radar cross-section ; Optoelectronics ; Physics ; Tunable metamaterials ; Engineering ; Electrical engineering ; Telecommunications ; Nanotechnology ; Chemistry ; Scattering Metamaterials and Metasurfaces Applications ; Advanced Antenna and Metasurface Technologies ; Antenna Design and Analysis