jablonkagroup/rise_ai_scientists huggingface dataset:
Authors: A. Castrillo | Eugenio Fasci | Tibor Furtenbacher | Vittorio D’Agostino | M. A. Khan | Stefania Gravina | L. Gianfrani | Attila G. Császár
Source: Physical Chemistry Chemical Physics (article, 2023-01-01)
Field: Chemistry — Spectroscopy

On the <sup>12</sup>C<sub>2</sub>H<sub>2</sub> near-infrared spectrum: absolute transition frequencies and an improved spectroscopic network at the kHz accuracy level Lamb dips of twenty lines in the P, Q, and R branches of the ν<sub>1</sub> + ν<sub>3</sub> + ν<sub>4</sub><sup>1</sup> vibrational band of <sup>12</sup>C<sub>2</sub>H<sub>2</sub>, in the spectral window of 7125-7230 cm<sup>-1</sup>, have been measured using an upgraded comb-calibrated frequency-stabilized cavity ring-down spectrometer, designed for extensive sub-Doppler measurements. Due to the large number of carefully executed Lamb-dip experiments, and to the extrapolation of absolute frequencies to zero pressure in each case, the combined average uncertainty of the measured line-center positions is 15 kHz (5 × 10<sup>-7</sup> cm<sup>-1</sup>) with a 2-σ confidence level. Selection of the twenty lines was based on the theory of spectroscopic networks (SN), ensuring that a large number of transitions, measured previously by precision-spectroscopy investigations, could be connected to the <i>para</i> and <i>ortho</i> principal components of the SN of <sup>12</sup>C<sub>2</sub>H<sub>2</sub>. The assembled SN contains 331 highly precise transitions, 119 and 121 of which are in the <i>ortho</i> and <i>para</i> principal components, respectively, while the rest remain in floating components. The <i>para</i>- and <i>ortho</i>-<sup>12</sup>C<sub>2</sub>H<sub>2</sub> energy-level lists, determined during the present study, contain 82 and 80 entries, respectively, with an accuracy similar to that of the lines. Based on the newly assembled lists of <i>para</i>- and <i>ortho</i>-<sup>12</sup>C<sub>2</sub>H<sub>2</sub> empirical energy levels, a line list, called TenkHz, has been generated. The TenkHz line list contains 282 entries in the spectral range of 5898.97-7258.87 cm<sup>-1</sup>; thus far, only 149 of them have been measured directly <i>via</i> precision spectroscopy. The TenkHz line list includes 35 intense lines that are missing in the HITRAN2020 database. Extrapolation ; Spectroscopy ; Spectrometer ; Line (geometry) ; Cavity ring-down spectroscopy ; Spectral line ; Range (aeronautics) ; Energy (signal processing) ; Doppler effect ; Physics ; Atomic physics ; Analytical Chemistry (journal) ; Chemistry ; Optics ; Materials science ; Mathematics Spectroscopy and Laser Applications ; Atmospheric Ozone and Climate ; Advanced Chemical Physics Studies
Authors: Yuying Ye | Kejia Li | Yanni Ma | Xiaolei Zhang | Yanan Li | Ting Yu | Yan Wang | Mingliang Ye
Source: Molecules (article, 2023-06-20)
Field: Chemistry — Spectroscopy

The Introduction of Detergents in Thermal Proteome Profiling Requires Lowering the Applied Temperatures for Efficient Target Protein Identification Although the use of detergents in thermal proteome profiling (TPP) has become a common practice to identify membrane protein targets in complex biological samples, surprisingly, there is no proteome-wide investigation into the impacts of detergent introduction on the target identification performance of TPP. In this study, we assessed the target identification performance of TPP in the presence of a commonly used non-ionic detergent or a zwitterionic detergent using a pan-kinase inhibitor staurosporine, our results showed that the addition of either of these detergents significantly impaired the identification performance of TPP at the optimal temperature for soluble target protein identification. Further investigation showed that detergents destabilized the proteome and increased protein precipitation. By lowering the applied temperature point, the target identification performance of TPP with detergents is significantly improved and is comparable to that in the absence of detergents. Our findings provide valuable insight into how to select the appropriate temperature range when detergents are used in TPP. In addition, our results also suggest that the combination of detergent and heat may serve as a novel precipitation-inducing force that can be applied for target protein identification. Proteome ; Chemistry ; Chromatography ; Identification (biology) ; Biochemistry ; Biology Advanced Proteomics Techniques and Applications ; Protein Structure and Dynamics ; RNA and protein synthesis mechanisms
Authors: Jianming Yang | Huijun Wu | Yuying Liang | Jian Cen | Xianyong Zhang
Source: Gels (article, 2023-11-30)
Field: Chemistry — Spectroscopy

A Comparative Assessment of Different Aerogel-Insulated Building Walls for Enhanced Thermal Insulation Performance Aerogel is widely recognized as a superinsulating material with great potential for enhancing the thermal insulation performance of building walls. It can be applied in various forms such as aerogel plasters (AP), aerogel fibrous composites (AFC), and aerogel concrete (AC) in practical engineering applications. This study aims to investigate the most efficient application form for maximizing building insulation performance while minimizing the amount of aerogel used. To predict the thermal insulation performance of aerogel-insulated walls, a resistance-capacitance network model integrating the aerogels' effective thermal conductivity model was developed and was validated by comparing it with Fluent simulation software results in terms of surface temperature. Using the validated models, the thermophysical parameters, transient thermal properties, and transmission load were predicted and compared among AP, AFC, and AC walls. The results indicate that using AFC can result in approximately 50% cost savings to achieve the same thermal resistance. After adding a 20 mm thickness of aerogel to the reference wall without aerogel, the AFC wall exhibited the highest improvement in thermal insulation performance, reaching 46.0-53.5%, followed by the AP wall, and then the AC wall, aligning with considerations of microstructural perspectives, thermal resistance distributions, and thermal non-uniformity factors. Therefore, giving priority to AFC use could reduce the required amount of silica aerogel and enhance economic efficiency. These results provide valuable insights for theoretical models and the application of aerogel-insulated walls in building engineering insulation. Aerogel ; Thermal insulation ; Materials science ; Thermal conductivity ; Thermal resistance ; Composite material ; Thermal ; Thermal mass ; Thermal bridge ; Structural engineering ; Engineering Aerogels and thermal insulation ; Surface Modification and Superhydrophobicity
Authors: Aoling Li | Jianhua Li | Honghui Jia | Huigao Duan | Yueqiang Hu
Source: Nanomaterials (article, 2023-01-21)
Field: Materials Science — Surfaces, Coatings and Films

The Effect of Fabrication Error on the Performance of Mid-Infrared Metalens with Large Field-of-View Mid-infrared large field-of-view (FOV) imaging optics play a vital role in infrared imaging and detection. The metalens, which is composed of subwavelength-arrayed structures, provides a new possibility for the miniaturization of large FOV imaging systems. However, the inaccuracy during fabrication is the main obstacle to developing practical uses for metalenses. Here, we introduce the principle and method of designing a large FOV doublet metalens at the mid-infrared band. Then, the quantitative relationship between the fabrication error and the performance of the doublet metalens with a large FOV from four different fabrication errors is explored by using the finite-difference time-domain method. The simulation results show that the inclined sidewall error has the greatest impact on the focusing performance, and the interlayer alignment error deforms the focusing beam and affects the focusing performance, while the spacer thickness error has almost no impact on the performance. The contents discussed in this paper can help manufacturers determine the allowable processing error range of the large FOV doublet metalens and the priority level for optimizing the process, which is of significance. Fabrication ; Miniaturization ; Optics ; Infrared ; Field of view ; Process (computing) ; Field (mathematics) ; Materials science ; Computer science ; Physics ; Nanotechnology ; Mathematics Optical Coatings and Gratings ; Photonic and Optical Devices ; Advanced optical system design
Authors: Hong Wang | Chengxin Dai | Julianus Pfeuffer | Timo Sachsenberg | Aniel Sánchez | Mingze Bai | Yasset Pérez‐Riverol
Source: PROTEOMICS (article, 2023-07-24)
Field: Chemistry — Spectroscopy

Tissue‐based absolute quantification using large‐scale TMT and LFQ experiments Relative and absolute intensity-based protein quantification across cell lines, tissue atlases and tumour datasets is increasingly available in public datasets. These atlases enable researchers to explore fundamental biological questions, such as protein existence, expression location, quantity and correlation with RNA expression. Most studies provide MS1 feature-based label-free quantitative (LFQ) datasets; however, growing numbers of isobaric tandem mass tags (TMT) datasets remain unexplored. Here, we compare traditional intensity-based absolute quantification (iBAQ) proteome abundance ranking to an analogous method using reporter ion proteome abundance ranking with data from an experiment where LFQ and TMT were measured on the same samples. This new TMT method substitutes reporter ion intensities for MS1 feature intensities in the iBAQ framework. Additionally, we compared LFQ-iBAQ values to TMT-iBAQ values from two independent large-scale tissue atlas datasets (one LFQ and one TMT) using robust bottom-up proteomic identification, normalisation and quantitation workflows. Proteome ; Quantitative proteomics ; Ranking (information retrieval) ; Computational biology ; Isobaric labeling ; Tandem mass tag ; Proteomics ; Pattern recognition (psychology) ; Biology ; Computer science ; Artificial intelligence ; Bioinformatics ; Genetics Advanced Proteomics Techniques and Applications ; Molecular Biology Techniques and Applications ; Cell Image Analysis Techniques
Authors: Daniel Paech | Nina Weckesser | Vanessa L. Franke | Johannes Breitling | Steffen Görke | Katerina Deike‐Hofmann | Antje Wick | Moritz Scherer | Andreas Unterberg | Wolfgang Wick | Martin Bendszus | Peter Bachert | Mark E. Ladd | Heinz‐Peter Schlemmer | Andreas Korzowski
Source: Radiology Imaging Cancer (article, 2023-12-22)
Field: Materials Science — Materials Chemistry

Whole-Brain Intracellular pH Mapping of Gliomas Using High-Resolution <sup>31</sup>P MR Spectroscopic Imaging at 7.0 T Malignant tumors commonly exhibit a reversed pH gradient compared with normal tissue, with a more acidic extracellular pH and an alkaline intracellular pH (pH<sub>i</sub>). In this prospective study, pH<sub>i</sub> values in gliomas were quantified using high-resolution phosphorous 31 (<sup>31</sup>P) spectroscopic MRI at 7.0 T and were used to correlate pH<sub>i</sub> alterations with histopathologic findings. A total of 12 participants (mean age, 58 years ± 18 [SD]; seven male, five female) with histopathologically proven, newly diagnosed glioma were included between September 2018 and November 2019. The <sup>31</sup>P spectroscopic MRI scans were acquired using a double-resonant <sup>31</sup>P/<sup>1</sup>H phased-array head coil together with a three-dimensional (3D) <sup>31</sup>P chemical shift imaging sequence (5.7-mL voxel volume) performed with a 7.0-T whole-body system. The 3D volumetric segmentations were performed for the whole-tumor volumes (WTVs); tumor subcompartments of necrosis, gadolinium enhancement, and nonenhancing T2 (NCE T2) hyperintensity; and normal-appearing white matter (NAWM), and pH<sub>i</sub> values were compared. Spearman correlation was used to assess association between pH<sub>i</sub> and the proliferation index Ki-67. For all study participants, mean pH<sub>i</sub> values were higher in the WTV (7.057 ± 0.024) compared with NAWM (7.006 ± 0.012; <i>P</i> < .001). In eight participants with high-grade gliomas, pH<sub>i</sub> was increased in all tumor subcompartments (necrosis, 7.075 ± 0.033; gadolinium enhancement, 7.075 ± 0.024; NCE T2 hyperintensity, 7.043 ± 0.015) compared with NAWM (7.004 ± 0.014; all <i>P</i> < .01). The pH<sub>i</sub> values of WTV positively correlated with Ki-67 (<i>R</i><sup>2</sup> = 0.74, <i>r</i> = 0.78, <i>P</i> = .001). In conclusion, <sup>31</sup>P spectroscopic MRI at 7.0 T enabled high-resolution quantification of pH<sub>i</sub> in gliomas, with pH<sub>i</sub> alteration associated with the Ki-67 proliferation index, and may aid in diagnosis and treatment monitoring. <b>Keywords:</b> <sup>31</sup>P MRSI, pH, Glioma, Glioblastoma, Ultra-High-Field MRI, Imaging Biomarker, 7 Tesla <i>Supplemental material is available for this article.</i> © RSNA, 2023. Nuclear medicine ; White matter ; Glioma ; Gadolinium ; Hyperintensity ; Magnetic resonance imaging ; Medicine ; Extracellular ; Nuclear magnetic resonance ; Chemistry ; Pathology ; Radiology ; Physics ; Cancer research Lanthanide and Transition Metal Complexes ; Advanced MRI Techniques and Applications ; Advanced NMR Techniques and Applications
Authors: Yannek Nowatzky | Philipp Benner | Knut Reinert | Thilo Muth
Source: Bioinformatics (article, 2023-06-01)
Field: Chemistry — Spectroscopy

Mistle: bringing spectral library predictions to metaproteomics with an efficient search index Mistle is freely available on GitHub at https://github.com/BAMeScience/Mistle. Search engine indexing ; Database search engine ; Computer science ; Workflow ; Sequence database ; Search engine ; Proteogenomics ; Search algorithm ; Data mining ; Information retrieval ; Database index ; Nearest neighbor search ; Index (typography) ; Database ; Algorithm ; World Wide Web ; Genomics Advanced Proteomics Techniques and Applications ; Mass Spectrometry Techniques and Applications ; Metabolomics and Mass Spectrometry Studies
Authors: Nina Demeulemeester | Marie Gébelin | Lucas Caldi Gomes | Paul Lingor | Christine Carapito | Lennart Martens | Lieven Clement
Source: Molecular & Cellular Proteomics (article, 2023-12-26)
Field: Chemistry — Spectroscopy

msqrob2PTM: Differential Abundance and Differential Usage Analysis of MS-Based Proteomics Data at the Posttranslational Modification and Peptidoform Level In the era of open-modification search engines, more posttranslational modifications than ever can be detected by LC-MS/MS-based proteomics. This development can switch proteomics research into a higher gear, as PTMs are key in many cellular pathways important in cell proliferation, migration, metastasis, and aging. However, despite these advances in modification identification, statistical methods for PTM-level quantification and differential analysis have yet to catch up. This absence can partly be explained by statistical challenges inherent to the data, such as the confounding of PTM intensities with its parent protein abundance. Therefore, we have developed msqrob2PTM, a new workflow in the msqrob2 universe capable of differential abundance analysis at the PTM and at the peptidoform level. The latter is important for validating PTMs found as significantly differential. Indeed, as our method can deal with multiple PTMs per peptidoform, there is a possibility that significant PTMs stem from one significant peptidoform carrying another PTM, hinting that it might be the other PTM driving the perceived differential abundance. Our workflows can flag both differential peptidoform abundance (DPA) and differential peptidoform usage (DPU). This enables a distinction between direct assessment of differential abundance of peptidoforms (DPA) and differences in the relative usage of peptidoforms corrected for corresponding protein abundances (DPU). For DPA, we directly model the log2-transformed peptidoform intensities, while for DPU, we correct for parent protein abundance by an intermediate normalization step which calculates the log2-ratio of the peptidoform intensities to their summarized parent protein intensities. We demonstrated the utility and performance of msqrob2PTM by applying it to datasets with known ground truth, as well as to biological PTM-rich datasets. Our results show that msqrob2PTM is on par with, or surpassing the performance of, the current state-of-the-art methods. Moreover, msqrob2PTM is currently unique in providing output at the peptidoform level. Abundance (ecology) ; Proteomics ; Posttranslational modification ; Differential (mechanical device) ; Computer science ; Computational biology ; Biology ; Chemistry ; Physics ; Biochemistry ; Ecology ; Enzyme Advanced Proteomics Techniques and Applications ; Genomics and Phylogenetic Studies ; Bioinformatics and Genomic Networks
Authors: José Antonio Badri | Jordi‐Roger Riba | A. García | Santi Trujillo | Albert Marzàbal
Source: International Journal of Electrical Power & Energy Systems (article, 2023-08-25)
Field: Materials Science — Electronic, Optical and Magnetic Materials

Transformer modelling considering power losses using an inverse Jiles-Atherton approach Power transformers are devices with non-linear behavior due to the saturation of the ferromagnetic core. When modelling such devices, the saturation effect must be taken into account because it greatly affects their performance and efficiency. In this paper, an electromagnetic model for power transformers is proposed and experimentally validated using an electrical T-model coupled with a reluctance network to model the magnetic part. The electrical circuit and the reluctance network are linked by two B–H approaches. The B–H relationships are modelled by the full hysteresis cycle based on the inverse Jiles-Atherton theory and by the initial magnetization curve. The results obtained with the inverse Jiles-Atherton theory model reproduce the magnetic core behavior with more accuracy than the one based on the initial magnetization curve, especially at low load conditions where saturation plays a more prominent role on the no-load current. The proposed model can be applied to other magnetic devices such as inductors for power electronic applications or electromechanical relays, among others. Transformer ; Inductor ; Magnetic core ; Ferrite core ; Magnetic reluctance ; Inverse ; Magnetic circuit ; Electrical engineering ; Current transformer ; Magnetization ; Electronic engineering ; Control theory (sociology) ; Engineering ; Computer science ; Voltage ; Physics ; Magnetic field ; Electromagnetic coil ; Mathematics ; Magnet Magnetic Properties and Applications ; Electric Motor Design and Analysis ; Magnetic properties of thin films
Authors: Zhiyuan Du | Madhav Gupta | Feng Xu | Kai Zhang | Jiahua Zhang | Yan Zhou | Yiyao Liu | Zhenyu Wang | Jörg Wrachtrup | Ngai Wong | Can Li | Zhiqin Chu
Source: Advanced Science (article, 2023-11-08)
Field: Materials Science — Materials Chemistry

Widefield Diamond Quantum Sensing with Neuromorphic Vision Sensors Despite increasing interest in developing ultrasensitive widefield diamond magnetometry for various applications, achieving high temporal resolution and sensitivity simultaneously remains a key challenge. This is largely due to the transfer and processing of massive amounts of data from the frame-based sensor to capture the widefield fluorescence intensity of spin defects in diamonds. In this study, a neuromorphic vision sensor to encode the changes of fluorescence intensity into spikes in the optically detected magnetic resonance (ODMR) measurements is adopted, closely resembling the operation of the human vision system, which leads to highly compressed data volume and reduced latency. It also results in a vast dynamic range, high temporal resolution, and exceptional signal-to-background ratio. After a thorough theoretical evaluation, the experiment with an off-the-shelf event camera demonstrated a 13× improvement in temporal resolution with comparable precision of detecting ODMR resonance frequencies compared with the state-of-the-art highly specialized frame-based approach. It is successfully deploy this technology in monitoring dynamically modulated laser heating of gold nanoparticles coated on a diamond surface, a recognizably difficult task using existing approaches. The current development provides new insights for high-precision and low-latency widefield quantum sensing, with possibilities for integration with emerging memory devices to realize more intelligent quantum sensors. Neuromorphic engineering ; Computer science ; Temporal resolution ; Materials science ; Quantum sensor ; Optoelectronics ; Quantum ; Nanotechnology ; Physics ; Optics ; Artificial intelligence ; Quantum computer Diamond and Carbon-based Materials Research ; Electronic and Structural Properties of Oxides ; Advanced Memory and Neural Computing
Authors: Mariusz Borkowski | Piotr Batys | Oleg M. Demchuk | Przemyslaw B. Kowalczuk | Jan Zawała
Source: Industrial & Engineering Chemistry Research (article, 2023-08-17)
Field: Chemistry — Organic Chemistry

Amino-Acids Surfactants and <i>n</i>-Octanol Mixtures─Sustainable, Efficient, and Dynamically Triggered Foaming Systems Surfactants with amino-acid heads (AASs), namely N-lauroyl-l-alanine (C12-ALA), N-lauroyl-l-leucine (C12-LEU), and N-lauroyl-l phenylalanine (C12-PHE) were mixed with n-octanol (C8OH) and thoroughly investigated via surface tension and foamability experiments. Significant differences between the selected AAS were observed. Moreover, the results obtained under equilibrium and dynamic conditions were remarkably different in terms of surface activity. The surface tension measurements (equilibrium conditions) indicated that the C12-ALA/C8OH mixture exhibits the highest synergistic effect. For the C12-LEU/C8OH system, a moderate synergism was observed, while for C12-PHE/C8OH, the effect was antagonistic. In contrast, in foamability experiments (dynamic conditions), all of the studied AAS/C8OH mixtures exhibited a spectacular synergistic effect at a wide concentration range. The observed effect was referred to as convection-activated surface activity of AAS/C8OH mixtures. The obtained experimental results were interpreted on the molecular level via all-atom detail molecular dynamics simulations (MD). The observed phenomenon was connected with the hydrogen bond-mediated aggregate formation in the bulk solution. Such aggregates act as reservoirs of surfactant molecules for supplementation of the adsorption coverage at the freshly formed liquid/gas interface. Additionally, the differences between the specific AAS were explained via the interplay of AAS–AAS and AAS-C8OH hydrogen bond affinities. The presented results showed an interesting example of a foaming system in which the surface activity can be controlled in situ via convection. This finding also significantly expands the range of potentially interesting molecules that can be used as efficient foaming additives and impacts the current understanding of the role of hydrogen bonding in designing of tuneable surfactant mixtures. Surface tension ; Chemistry ; Adsorption ; Pulmonary surfactant ; Octanol ; Hydrogen bond ; Amino acid ; Molecule ; Phenylalanine ; Intramolecular force ; Alanine ; Chemical engineering ; Chromatography ; Organic chemistry ; Thermodynamics ; Partition coefficient Surfactants and Colloidal Systems ; Pickering emulsions and particle stabilization ; Proteins in Food Systems