jablonkagroup/rise_ai_scientists huggingface dataset:
Authors: Yi Di | Wenxue Li | Barbora Šalovská | Qian Ba | Zhenyi Hu | Shisheng Wang | Yansheng Liu
Source: Biophysics Reports (article, 2023-01-01)
Field: Chemistry — Spectroscopy

A basic phosphoproteomic-DIA workflow integrating precise quantification of phosphosites in systems biology Phosphorylation is one of the most important post-translational modifications (PTMs) of proteins, governing critical protein functions. Most human proteins have been shown to undergo phosphorylation, and phosphoproteomic studies have been widely applied due to recent advancements in high-resolution mass spectrometry technology. Although the experimental workflow for phosphoproteomics has been well-established, it would be useful to optimize and summarize a detailed, feasible protocol that combines phosphoproteomics and data-independent acquisition (DIA), along with follow-up data analysis procedures due to the recent instrumental and bioinformatic advances in measuring and understanding tens of thousands of site-specific phosphorylation events in a single experiment. Here, we describe an optimized Phos-DIA protocol, from sample preparation to bioinformatic analysis, along with practical considerations and experimental configurations for each step. The protocol is designed to be robust and applicable for both small-scale phosphoproteomic analysis and large-scale quantification of hundreds of samples for studies in systems biology and systems medicine. Phosphoproteomics ; Workflow ; Computational biology ; Protocol (science) ; Computer science ; Proteomics ; Systems biology ; Phosphorylation ; Posttranslational modification ; Proteome ; Protein phosphorylation ; Biology ; Biochemical engineering ; Bioinformatics ; Cell biology ; Biochemistry ; Protein kinase A ; Engineering ; Database Advanced Proteomics Techniques and Applications ; Mass Spectrometry Techniques and Applications ; Metabolomics and Mass Spectrometry Studies
Authors: Francesca Venturini | Silvan Fluri | Michael Baumgärtner
Source: Data (article, 2023-04-29)
Field: Chemistry — Analytical Chemistry

Dataset of Fluorescence EEM and UV Spectroscopy Data of Olive Oils during Ageing The dataset presented in this study encompasses fluorescence excitation–emission matrices (EEMs) and UV-spectroscopy data of 24 extra virgin olive oils (EVOOs) commercially available at supermarkets in Switzerland. To investigate the effect of thermal degradation, the samples were exposed to accelerated ageing at 60 ∘C up to 53 days. EEMs and UV absorption parameters were measured in 10 ageing steps. The dataset can be used, for example, to predict one or multiple chemical parameters or to classify samples based on their quality from fluorescence spectra. Ageing ; Fluorescence ; Fluorescence spectroscopy ; Olive oil ; Spectroscopy ; Analytical Chemistry (journal) ; Absorption (acoustics) ; Chemistry ; Ultraviolet visible spectroscopy ; Materials science ; Environmental chemistry ; Food science ; Biology ; Optics ; Organic chemistry ; Composite material ; Physics Spectroscopy and Chemometric Analyses ; Edible Oils Quality and Analysis ; Fermentation and Sensory Analysis
Authors: Shaohua Lu | Hong Lü | Tingkai Zheng | Huiming Yuan | Hongli Du | Youhe Gao | Yongtao Liu | Xuanzhen Pan | Wenlu Zhang | Shuying Fu | Zhenghua Sun | Jingjie Jin | Qing‐Yu He | Yang Chen | Gong Zhang
Source: Scientific Data (article, 2023-07-13)
Field: Chemistry — Spectroscopy

A multi-omics dataset of human transcriptome and proteome stable reference The development of high-throughput omics technology has greatly promoted the development of biomedicine. However, the poor reproducibility of omics techniques limits their application. It is necessary to use standard reference materials of complex RNAs or proteins to test and calibrate the accuracy and reproducibility of omics workflows. The transcriptome and proteome of most cell lines shift during culturing, which limits their applicability as standard samples. In this study, we demonstrated that the human hepatocellular cell line MHCC97H has a very stable transcriptome (r = 0.983~0.997) and proteome (r = 0.966~0.988 for data-dependent acquisition, r = 0.970~0.994 for data-independent acquisition) after 9 subculturing generations, which allows this steady standard sample to be consistently produced on an industrial scale in long term. Moreover, this stability was maintained across labs and platforms. In sum, our study provides omics standard reference material and reference datasets for transcriptomic and proteomics research. This helps to further standardize the workflow and data quality of omics techniques and thus promotes the application of omics technology in precision medicine. Omics ; Workflow ; Proteome ; Transcriptome ; Proteomics ; Biomedicine ; Computer science ; Computational biology ; Bioinformatics ; Biology ; Database ; Gene expression ; Genetics Advanced Proteomics Techniques and Applications ; Gene expression and cancer classification ; Molecular Biology Techniques and Applications
Authors: Yongliang Liu | Feifei Tao | Haibo Yao | Russell Kincaid
Source: Journal of Cotton Research (article, 2023-11-27)
Field: Chemistry — Analytical Chemistry

Feasibility study of assessing cotton fiber maturity from near infrared hyperspectral imaging technique Abstract Background Fiber maturity is a key cotton quality property, and its variability in a sample impacts fiber processing and dyeing performance. Currently, the maturity is determined by using established protocols in laboratories under a controlled environment. There is an increasing need to measure fiber maturity using low-cost (in general less than $20 000) and small portable systems. In this study, a laboratory feasibility was performed to assess the ability of the shortwave infrared hyperspectral imaging (SWIR HSI) technique for determining the conditioned fiber maturity, and as a comparison, a bench-top commercial and expensive (in general greater than $60 000) near infrared (NIR) instrument was used. Results Although SWIR HSI and NIR represent different measurement technologies, consistent spectral characteristics were observed between the two instruments when they were used to measure the maturity of the locule fiber samples in seed cotton and of the well-defined fiber samples, respectively. Partial least squares (PLS) models were established using different spectral preprocessing parameters to predict fiber maturity. The high prediction precision was observed by a lower root mean square error of prediction (RMSEP) (&lt; 0.046), higher R p 2 (&gt; 0.518), and greater percentage (97.0%) of samples within the 95% agreement range in the entire NIR region (1 000∼2 500 nm) without the moisture band at 1 940 nm. Conclusion SWIR HSI has a good potential for assessing cotton fiber maturity in a laboratory environment. Hyperspectral imaging ; Fiber ; Maturity (psychological) ; Near-infrared spectroscopy ; Environmental science ; Remote sensing ; Mathematics ; Materials science ; Optics ; Geology ; Physics ; Composite material Spectroscopy and Chemometric Analyses ; Textile materials and evaluations ; Research in Cotton Cultivation
Authors: Andrew G. Chambers | David C. Chain | Steve M. M. Sweet | Zifeng Song | Philip Martin | Matthew J. Ellis | Claire Rooney | Yeoun Jin Kim
Source: Clinical Proteomics (article, 2023-10-25)
Field: Chemistry — Spectroscopy

Mass spectrometry quantifies target engagement for a KRASG12C inhibitor in FFPE tumor tissue This work illustrates the potential to expand mass spectrometry-based proteomics in preclinical and clinical oncology drug development through analysis of FFPE tumor biopsies. Mass spectrometry ; Chemistry ; Mass spectrometry imaging ; Ion-mobility spectrometry ; Proteomics ; Cancer research ; Chromatography ; Medicine ; Biochemistry Mass Spectrometry Techniques and Applications ; Advanced Proteomics Techniques and Applications ; Protein Structure and Dynamics
Authors: Ding Xu | Shiyun Zhang | Andrea J. Liu | Sidney R. Nagel | Ning Xu
Source: Proceedings of the National Academy of Sciences (article, 2023-08-16)
Field: Materials Science — Materials Chemistry

Discontinuous instabilities in disordered solids Under a sufficiently large load, a solid material will flow via rearrangements, where particles change neighbors. Such plasticity is most easily described in the athermal, quasistatic limit of zero temperature and infinitesimal loading rate, where rearrangements occur only when the system becomes mechanically unstable. For disordered solids, the instabilities marking the onset of rearrangements have long been believed to be fold instabilities, in which an energy barrier disappears and the frequency of a normal mode of vibration vanishes continuously. Here, we report that there exists another, anomalous, type of instability caused by the breaking of a "stabilizing bond," whose removal creates an unstable vibrational mode. For commonly studied systems, such as those with harmonic finite-range interparticle interactions, such "discontinuous instabilities" are not only inevitable, they often dominate the modes of failure. Stabilizing bonds are a subset of all the bonds in the system and are prevalent in disordered solids generally. Although they do not trigger discontinuous instabilities in systems with vanishing stiffness at the interaction cutoff, they are, even in those cases, local indicators of incipient mechanical failure. They therefore provide an accurate structural predictor of instabilities not only of the discontinuous type but of the fold type as well. Instability ; Quasistatic process ; Plasticity ; Physics ; Vibration ; Cutoff ; Infinitesimal ; Harmonic ; Mechanics ; Stiffness ; Classical mechanics ; Condensed matter physics ; Chemical physics ; Materials science ; Thermodynamics ; Mathematics ; Quantum mechanics Material Dynamics and Properties ; Theoretical and Computational Physics ; Granular flow and fluidized beds
Authors: Qi Wu | Yuanjin Yang | Yuechun Shi | Yang Xu | Wenlong Wang | Chao Men | Bingxiong Yang
Source: Photonics (article, 2023-11-19)
Field: Chemistry — Spectroscopy

Highly Responsive, Miniaturized Methane Telemetry Sensor Based on Open-Path TDLAS This paper proposes the design of a highly responsive, compact, non-contact methane telemetry sensor, employing the open-path tunable diode laser absorption spectroscopy (OP-TDLAS) technology. The sensor uses the dual-core structure of FPGA and ARM to achieve high-speed methane telemetry at 100 KHz repeated modulation frequency for the first time with a non-cooperate target, and a higher gas responsive time of 1.8 ms was achieved than previously reported. Moreover, the optical system (L × W × H: 68.8 × 52 × 62.7 mm) and the electronic system (L × W: 70 × 50 mm) make the sensor more compact. Methane gas samples of varying integral concentrations were examined at a distance of 20 m. The amplitude of the absorption peaks was subjected to a linear fit with the standard concentration values, resulting in a robust linear correlation coefficient (R2 = 0.998). Notably, despite the compact form factor of the methane sensor, it demonstrated commendable stability in gas concentration detection, offering a minimum detection limit of 43.14 ppm·m. Consequently, this highly responsive and compact methane sensor, with its open-path feature, is apt for integration into a variety of applications requiring such attributes. These include handheld telemetry devices, Unmanned Aerial Vehicle (UAV) gas detection systems, vehicle mounted gas detection, and laser gas radar. Methane ; Telemetry ; Tunable diode laser absorption spectroscopy ; Materials science ; Absorption (acoustics) ; Optical path ; Detection limit ; Laser ; Path length ; Optics ; Optoelectronics ; Tunable laser ; Computer science ; Analytical Chemistry (journal) ; Physics ; Wavelength ; Chemistry ; Telecommunications Spectroscopy and Laser Applications ; Atmospheric and Environmental Gas Dynamics ; Atmospheric Ozone and Climate
Authors: Zhen Qi | Jun Yan Dai | Si Ran Wang | Qun Yan Zhou | Wankai Tang | Kaicen Wang | Peng Zhang | Shuo Liu | Long Li | Qiang Cheng | Tie Jun Cui
Source: Chinese Optics Letters (article, 2023-01-01)
Field: Materials Science — Electronic, Optical and Magnetic Materials

Simultaneous wireless information and power transfer transmitting architecture based on asynchronous space-time-coding digital metasurface [Invited] Simultaneous wireless information and power transfer (SWIPT) architecture is commonly applied in wireless sensors or Internet of Things (IoT) devices, providing both wireless power sources and communication channels. However, the traditional SWIPT transmitter usually suffers from cross-talk distortion caused by the high peak-to-average power ratio of the input signal and the reduction of power amplifier efficiency. This paper proposes a SWIPT transmitting architecture based on an asynchronous space-time-coding digital metasurface (ASTCM). High-efficiency simultaneous transfer of information and power is achieved via energy distribution and information processing of the wireless monophonic signal reflected from the metasurface. We demonstrate the feasibility of the proposed method through theoretical derivations and experimental verification, which is therefore believed to have great potential in wireless communications and the IoT devices. Computer science ; Wireless ; Asynchronous communication ; Maximum power transfer theorem ; Amplifier ; Transmitter ; Information transfer ; Coding (social sciences) ; Electronic engineering ; Power (physics) ; Telecommunications ; Channel (broadcasting) ; Bandwidth (computing) ; Engineering ; Physics Metamaterials and Metasurfaces Applications ; Energy Harvesting in Wireless Networks ; Advanced Wireless Communication Technologies
Authors: Mukul K. Midha | Charu Kapil | Michal Maes | David Baxter | Seamus R. Morrone | Timothy J. Prokop | Robert L. Moritz
Source: Journal of Proteome Research (article, 2023-06-09)
Field: Chemistry — Spectroscopy

Vacuum Insulated Probe Heated Electrospray Ionization Source Enhances Microflow Rate Chromatography Signals in the Bruker timsTOF Mass Spectrometer By far the largest contribution to ion detectability in liquid chromatography-driven mass spectrometry-based proteomics is the efficient generation of peptide molecular ions by the electrospray source. To maximize the transfer of peptides from the liquid to gaseous phase and allow molecular ions to enter the mass spectrometer at microspray flow rates, an efficient electrospray process is required. Here we describe the superior performance of newly design vacuum insulated probe heated electrospray ionization (VIP-HESI) source coupled to a Bruker timsTOF PRO mass spectrometer operated in microspray mode. VIP-HESI significantly improves chromatography signals in comparison to electrospray ionization (ESI) and nanospray ionization using the captivespray (CS) source and provides increased protein detection with higher quantitative precision, enhancing reproducibility of sample injection amounts. Protein quantitation of human K562 lymphoblast samples displayed excellent chromatographic retention time reproducibility (<10% coefficient of variation (CV)) with no signal degradation over extended periods of time, and a mouse plasma proteome analysis identified 12% more plasma protein groups allowing large-scale analysis to proceed with confidence (1,267 proteins at 0.4% CV). We show that the Slice-PASEF VIP-HESI mode is sensitive in identifying low amounts of peptide without losing quantitative precision. We demonstrate that VIP-HESI coupled with microflow rate chromatography achieves a higher depth of coverage and run-to-run reproducibility for a broad range of proteomic applications. Data and spectral libraries are available via ProteomeXchange (PXD040497). Mass spectrometry ; Electrospray ionization ; Chemistry ; Electrospray ; Chromatography ; Reproducibility ; Analytical Chemistry (journal) ; Ionization ; Ion source ; Ion Mass Spectrometry Techniques and Applications ; Advanced Proteomics Techniques and Applications ; Analytical Chemistry and Chromatography
Authors: Oliver Kardell | Christine von Toerne | Juliane Merl‐Pham | Ann‐Christine König | Marcel Blindert | Teresa K. Barth | Julia Mergner | Christina Ludwig | Johanna Tüshaus | Stephan Eckert | Stephan A. Müller | Stephan Breimann | Pieter Giesbertz | Alexander Bernhardt | Lisa Schweizer | Vincent Albrecht | Daniel Teupser | Axel Imhof | Bernhard Küster | Stefan F. Lichtenthaler | Matthias Mann | Jürgen Cox | Stefanie M. Hauck
Source: Journal of Proteome Research (article, 2023-11-28)
Field: Chemistry — Spectroscopy

Multicenter Collaborative Study to Optimize Mass Spectrometry Workflows of Clinical Specimens The foundation for integrating mass spectrometry (MS)-based proteomics into systems medicine is the development of standardized start-to-finish and fit-for-purpose workflows for clinical specimens. An essential step in this pursuit is to highlight the common ground in a diverse landscape of different sample preparation techniques and liquid chromatography-mass spectrometry (LC-MS) setups. With the aim to benchmark and improve the current best practices among the proteomics MS laboratories of the CLINSPECT-M consortium, we performed two consecutive round-robin studies with full freedom to operate in terms of sample preparation and MS measurements. The six study partners were provided with two clinically relevant sample matrices: plasma and cerebrospinal fluid (CSF). In the first round, each laboratory applied their current best practice protocol for the respective matrix. Based on the achieved results and following a transparent exchange of all lab-specific protocols within the consortium, each laboratory could advance their methods before measuring the same samples in the second acquisition round. Both time points are compared with respect to identifications (IDs), data completeness, and precision, as well as reproducibility. As a result, the individual performances of participating study centers were improved in the second measurement, emphasizing the effect and importance of the expert-driven exchange of best practices for direct practical improvements. Workflow ; Protocol (science) ; Sample (material) ; Mass spectrometry ; Computer science ; Benchmark (surveying) ; Chromatography ; Medicine ; Chemistry ; Pathology ; Database Advanced Proteomics Techniques and Applications ; Mass Spectrometry Techniques and Applications ; Metabolomics and Mass Spectrometry Studies
Authors: J. Erb | David Shrekenhamer | Timothy Sleasman | Thomas M. Antonsen | Steven M. Anlage
Source: Acta Physica Polonica A (article, 2023-12-01)
Field: Materials Science — Electronic, Optical and Magnetic Materials

Control of the Scattering Properties of Complex Systems by Means of Tunable Metasurfaces We demonstrate the ability to control the scattering properties of a two-dimensional wave-chaotic microwave billiard through the use of tunable metasurfaces located on the interior walls of the billiard. The complex reflection coefficient of the metasurfaces can be varied by applying a DC voltage bias to varactor diodes on the mushroom-shaped resonant patches, and this proves to be very effective at perturbing the eigenmodes of the cavity. Placing multiple metasurfaces inside the cavity allows us to engineer desired scattering conditions, such as coherent perfect absorption, by actively manipulating the poles and zeros of the scattering matrix through the application of multiple voltage biases. We demonstrate the ability to create on-demand coherent perfect absorption conditions at a specific frequency, and document the near-null of output power as a function of four independent parameters tuned through the coherent perfect absorption point. A remarkably low output-to-input power ratio Pout/Pin= 3.71 x 10-8 is achieved near the coherent perfect absorption point at 8.54 GHz. Scattering ; Dynamical billiards ; Optics ; Varicap ; Physics ; Absorption (acoustics) ; Microwave ; Matrix (chemical analysis) ; Materials science ; Quantum mechanics ; Capacitance Metamaterials and Metasurfaces Applications ; Advanced Antenna and Metasurface Technologies ; Antenna Design and Analysis
Authors: Tahir Çetin Akıncı | Ömer AKGÜN | Musa Yılmaz | Alfredo A. Martinez‐Morales
Source: IEEE Access (article, 2023-01-01)
Field: Materials Science — Electronic, Optical and Magnetic Materials

High Order Spectral Analysis of Ferroresonance Phenomena in Electric Power Systems This study presents a comprehensive investigation of ferroresonance, a dangerous electrical phenomenon that poses significant financial risks. Using real electrical transmission line parameters, we simulated synthetic ferroresonance scenarios on a model and analyzed the resulting data using high-order spectral analysis methods, including the Wigner-Ville method, Welch method, frequency-power analysis, and spectral methods. Our analysis revealed changes in frequency and power before and after ferroresonance, with third and fourth-order cumulants being calculated. We confirmed the accuracy of the power transmission line’s base frequency and power before the ferroresonance event and determined the frequency and power values before and after ferroresonance with frequency-power analysis. Our cumulative analysis results showed symmetrical results that are consistent with the properties of ferroresonance. Additionally, we found that the Wigner Ville method’s high-resolution results were significantly more effective than conventional methods. Our study’s findings provide valuable insights into ferroresonance’s behavior and may inform the development of more effective prevention and mitigation strategies. Ferroresonance in electricity networks ; Electric power system ; Transmission line ; Electric power transmission ; Spectral analysis ; Power (physics) ; Computer science ; Control theory (sociology) ; Engineering ; Physics ; Electrical engineering ; Telecommunications ; Artificial intelligence Magnetic Properties and Applications ; Power Transformer Diagnostics and Insulation ; Magneto-Optical Properties and Applications
Authors: Yu Zhang | Qianfan Liu | Jing Chen | Chengxu Sun | Shenghuang Lin | Hongxing Cao | Zhaolin Xiao | Mengxing Huang
Source: Plant Methods (article, 2023-03-09)
Field: Chemistry — Inorganic Chemistry

Developing non-invasive 3D quantificational imaging for intelligent coconut analysis system with X-ray The evaluation results show that the 3D quantitative imaging model has high accuracy in capturing the internal development process of coconut fruits. The system can effectively assist growers in internal developmental observations and in structural data acquisition from coconut, thus providing decision-making support for improving the cultivation conditions of coconuts. Cocos nucifera ; Process (computing) ; Computer science ; Point cloud ; Coconut oil ; RGB color model ; Artificial intelligence ; Environmental science ; Mathematics ; Horticulture ; Biology ; Food science Coconut Research and Applications ; Agricultural and Environmental Management