jablonkagroup/rise_ai_scientists huggingface dataset:
Authors: Isabel J. Hoppe | Bernhard Prommegger | Andreas Uhl | Urs Lohrig | Christian G. Huber | Hans Brandstetter
Source: ChemBioChem (article, 2022-08-03)
Field: Chemistry — Spectroscopy

The Fluorescent Enzyme Cascade Detects Low Abundance Protein Modifications Suitable for the Assembly of Functionally Annotated Modificatome Databases Pathophysiological functions of proteins critically depend on both their chemical composition, including post-translational modifications, and their three-dimensional structure, commonly referred to as structure-activity relationship. Current analytical methods, like capillary electrophoresis or mass spectrometry, suffer from limitations, such as the detection of unexpected modifications at low abundance and their insensitivity to conformational changes. Building on previous enzyme-based analytical methods, we here introduce a fluorescence-based enzyme cascade (fEC), which can detect diverse chemical and conformational variations in protein samples and assemble them into digital databases. Together with complementary analytical methods an automated fEC analysis established unique modification-function relationships, which can be expanded to a proteome-wide scale, i. e. a functionally annotated modificatome. The fEC offers diverse applications, including hypersensitive biomarker detection in complex samples. Proteome ; Computational biology ; Cascade ; Database ; Mass spectrometry ; Enzyme ; Capillary electrophoresis ; Posttranslational modification ; Chemistry ; Fluorescent protein ; Fluorescence ; Biochemistry ; Biology ; Computer science ; Chromatography ; Green fluorescent protein Advanced Proteomics Techniques and Applications ; Advanced Biosensing Techniques and Applications ; Biotin and Related Studies
Authors: Aghayeva Aytan Gabil | Streatfield Stephen John | Huseynova Irada Mammad
Source: Zenodo (CERN European Organization for Nuclear Research) (article, 2022-10-22)
Field: Chemistry — Physical and Theoretical Chemistry

Study of the molecular mass of AZ-130 biomolecule and its stability at low pH The aim of this work was to determine the approximate value of the molecular mass of an exogenous biomolecule synthesized by the Bacillus vallismortis AZ-130 strain isolated from oilcontaminated soils of Azerbaijan and to determine the degree of its stability at low pH values. To achieve the goals, strain AZ-130 was cultivated for 24 hours on a shaker with constant shaking (180 rpm) at 32°C. Next, a supernatant was obtained from the culture solution, which, after the addition of trifluoroacetic acid and 10-fold concentration using 3K MWCO Amicon Ultra-15 Centrifugal Filter Devices centrifugal filter concentrators, was examined by the growth inhibition assay for the presence of activity against S. aureus ATCC 29213. Based on the obtained results, it was found that the bioactive molecule produced by the AZ-130 strain is stable at low pH values and has a molecular mass of more than 3000 Daltons. Biomolecule ; Chemistry ; Chemical physics ; Nanotechnology ; Materials science ; Biochemistry thermodynamics and calorimetric analyses
Authors: Simon Davis | Connor Scott | Janina Oetjen | Philip D. Charles | Benedikt M. Kessler | Olaf Ansorge | Román Fischer
Source: bioRxiv (Cold Spring Harbor Laboratory) (preprint, 2022-03-21)
Field: Chemistry — Spectroscopy

Deep topographic proteomics of a human brain tumour Abstract The spatial organisation of cellular protein expression profiles within tissue determines cellular function and is key to understanding disease pathology. To define molecular phenotypes in the spatial context of tissue, there is a need for unbiased, quantitative technology capable of mapping proteomes within tissue structures. Here, we present a workflow for spatially-resolved, quantitative proteomics of tissue that generates maps of protein abundance across tissue slices derived from a human atypical teratoid-rhabdoid tumour (AT/RT). We employ spatially-aware algorithms that do not require prior knowledge of the fine tissue structure to detect proteins and pathways with spatial abundance patterns. We identified PYGL, ASPH and CD45 as spatial markers for tumour boundary and reveal immune response-driven, spatially-organised protein networks of the extracellular tumour matrix. Overall, this work informs on methods for spatially resolved deep proteo-phenotyping of tissue heterogeneity, to push the boundaries of understanding tissue biology and pathology at the molecular level. Proteomics ; Proteome ; Context (archaeology) ; Computational biology ; Biology ; Extracellular matrix ; Workflow ; Phenotype ; Quantitative proteomics ; Function (biology) ; Brain tissue ; Pathology ; Neuroscience ; Computer science ; Cell biology ; Bioinformatics ; Medicine ; Genetics ; Gene Advanced Proteomics Techniques and Applications ; Single-cell and spatial transcriptomics ; Cell Adhesion Molecules Research
Authors: Valentina Gabbarini | Alessandro Puleio | Riccardo Rossi | Andrea Malizia | P. Gaudio
Source: Sensors (article, 2022-10-11)
Field: Chemistry — Analytical Chemistry

A Weighted-LSM Method to Improve Classification and Concentration Evaluation from Laser-Induced Fluorescence Spectra The detection of biological agents using optical systems is an open field of research. Currently, different spectroscopic techniques allow to detect and classify chemical agents while a fast and accurate technique able to identify biological agents is still under investigation. Some optical techniques, such as Laser-Induced Breakdown Spectroscopy (LIBS) or Laser-Induced Fluorescence (LIF), are already used as classification methods. However, the presence of background, spectrum similarities and other confounders make these techniques not very specific. This work shows a new method to achieve better performances in terms of classification and concentration evaluations. The method is based on the Weighted Least Square Minimization method. In fact, by using ad hoc weights, the LSM looks at specific features of the spectra, resulting in higher accuracy. In order to make a systematic analysis, numerical tests have been conducted. With these tests, the authors were able to highlight the various advantages and drawbacks of the new methodology proposed. Then, the method was applied to some LIF measurements to investigate the applicability of the method to preliminary experimental cases. The results show that, by using this new weighted LSM, it is possible to achieve better classification and concentration evaluation performances. Finally, the possible application of the new method is discussed. Computer science ; Laser-induced fluorescence ; Biological system ; Laser-induced breakdown spectroscopy ; Laser ; Field (mathematics) ; Artificial intelligence ; Machine learning ; Algorithm ; Data mining ; Pattern recognition (psychology) ; Mathematics ; Optics ; Physics Spectroscopy and Chemometric Analyses ; Scientific Measurement and Uncertainty Evaluation ; Water Quality Monitoring and Analysis
Authors: Gülseren Karabay | Yavuz Şenol | Hasan Öztürk | Cansu Meşegül
Source: Fibres and Textiles in Eastern Europe (article, 2022-05-01)
Field: Materials Science — Polymers and Plastics

Artificial Neural Network-based Prediction Technique for Waterproofness of Seams Obtained by Using Fusible Threads Abstract The aim of this study was to estimate waterproofness values of seams composed of the combination of fusible threads and antiwick sewing threads through artificial neural networks (ANN). Fusible threads were used to obtain waterproof seams for the first time. Therefore, estimating the value of the waterproofness variable with the help of models created from test values can contribute to accelerating the progress of further studies. Hence, ten different samples were prepared for two fabrics, and the waterproofness values of the seams obtained were tested using a Textest FX 3000 Hydrostatic Head Tester III. For the prediction of waterproofness values of the seams, the Levenberg-Marquardt backpropagation algorithm was used for artificial neural network pattern models with sigmoid and positive linear transfer functions. Finally, the ANN model was successful in estimating the waterproofness of the seams. The highest correlation coefficient was R = 0.95081 which indicated that the prediction made by the neural network model proved to be reliable. Fusible alloy ; Artificial neural network ; Sigmoid function ; Correlation coefficient ; Backpropagation ; Engineering ; Artificial intelligence ; Computer science ; Machine learning ; Materials science Textile materials and evaluations ; Industrial Vision Systems and Defect Detection ; Surface Roughness and Optical Measurements
Authors: Xiaoyan Xu | Wei-Guang Xie | Cheng Xiang | Qian You | Xingguo Tian
Source: Research Square (preprint, 2022-10-20)
Field: Chemistry — Analytical Chemistry

Predicting the dietary fiber content of fresh-cut bamboo shoots using a visible and near-infrared hyperspectral technique Abstract The dietary fiber content in fresh-cut bamboo shoots is considered crucial for the quality of processed bamboo shoots products. This study aimed to explore the potential of applying two different hyperspectral techniques, namely visible near infrared (Vis-NIR) spectroscopy and near infrared (NIR) in the quick and non-destructive prediction of the dietary fiber content of fresh-cut bamboo shoots. The Vis-NIR and NIR hyperspectral data were collected to establish partial least square regression (PLSR) and principal component regression (PCR) calibration model for the average spectrum of fresh-cut bamboo shoots and their corresponding dietary fiber content. Subsequently, data fusion analysis, various pre-processing methods, and principal component analysis (PCA) were used to optimize the model. The results indicated that superior models were obtained based on low-level fusion data when compared with the corresponding methods based on single spectral data. The optimal SNV-PCA-PLSR model achieved a good performance with coefficient of determination of prediction ( R 2 p ) of 0.902, and root mean square errors of prediction (RMSEP) of 0.135. Therefore, hyperspectral technique combined with data fusion analysis can be a promising approach for non-invasive quality supervision of bamboo shoots products in varied processing states. Hyperspectral imaging ; Principal component analysis ; Near-infrared spectroscopy ; Partial least squares regression ; Shoot ; Bamboo shoot ; Fusion ; Bamboo ; Mathematics ; Remote sensing ; Computer science ; Horticulture ; Artificial intelligence ; Chemistry ; Botany ; Biology ; Statistics ; Optics ; Physics Spectroscopy and Chemometric Analyses ; Bamboo properties and applications ; Industrial Vision Systems and Defect Detection
Authors: Andrej Pustogow
Source: Crystals (article, 2022-12-30)
Field: Materials Science — Electronic, Optical and Magnetic Materials

New Spin on Metal-Insulator Transitions Metal-insulator transitions (MITs) constitute a core subject of fundamental condensed-matter research [...] Insulator (electricity) ; Condensed matter physics ; Metal–insulator transition ; Subject matter ; Metal ; Materials science ; Physics ; Political science ; Metallurgy ; Optoelectronics Magnetic and transport properties of perovskites and related materials ; Rare-earth and actinide compounds ; Advanced Condensed Matter Physics
Authors: Xinmin Fan | Jianxin Zhang | Sensen Li | Shun Li | Yan Wang | Fei Du | Xiaodong Huang | Yingde Li | Lujun Zhang | Chunyan Wang
Source: Frontiers in Physics (article, 2022-12-08)
Field: Materials Science — Surfaces, Coatings and Films

A method to achieve spectral beam combining based on a novel symmetric grating A symmetric grating is proposed to obtain higher output power in spectral beam combination by increasing the number of lasers and spectral utilization. The grating allows laser beams to be incident from both sides of the grating normal to achieve coaxial beam combining, so the number of beams and the combined output power are doubled compared with the traditional grating under the same spectral line-width. The grating is designed with the central wavelength of 4.65 μm, and the calculation results show that this grating is very advantageous for spectral beam combining, especially for the light waves in the range 4.55–4.71 μm, where their diffraction efficiencies are high (over 80%) and correspond to a wide and linear range of incidence angles. Meanwhile, based on the symmetric gratings we further propose a circular grating to achieve the same frequency spectral beam combining. This beam combining design will not increase the laser spectral line width while enhancing the laser power, reducing the requirements for the unit laser spectral line width, which is very meaningful in some application fields and will further enrich the research of spectral beam combining. Grating ; Optics ; Blazed grating ; Beam (structure) ; Beam diameter ; Diffraction grating ; Laser ; Spectral width ; Materials science ; Ultrasonic grating ; Wavelength ; Laser beam quality ; M squared ; Diffraction ; Physics ; Laser beams Optical Coatings and Gratings ; Photonic Crystal and Fiber Optics ; Photonic and Optical Devices
Authors: Xiang Xu | Wentao Xiao | Yiyun Cao | Zhengyong Zhang
Source: Research Square (preprint, 2022-09-01)
Field: Chemistry — Analytical Chemistry

Identification of Different Dairy Products Using Raman Spectroscopy Combined with Fused Lasso Distributionally Robust Logistic Regression <title>Abstract</title> Raman spectroscopy has been more and more widely used in the quality detection of dairy products. Due to the characteristics of high dimension and small sample size, the rapid, intelligent and accurate identification method of Raman spectroscopy is becoming one of the hot issues for researchers. In order to improve the robustness and accuracy of logistic regression identification method, a new Raman spectroscopy identification method is proposed by combining distributionally robust optimization technique and fused lasso technique with logistic regression. Raman spectroscopy of two kinds of dairy products were collected respectively for anti-jamming identification testing to verify the effectiveness of the new method. Experimental results show that the proposed method is more robust and has higher recognition accuracy than the traditional logistic regression. Logistic regression ; Lasso (programming language) ; Raman spectroscopy ; Robustness (evolution) ; Identification (biology) ; Artificial intelligence ; Multinomial logistic regression ; Pattern recognition (psychology) ; Computer science ; Statistics ; Mathematics ; Machine learning ; Chemistry ; Optics Spectroscopy and Chemometric Analyses ; Spectroscopy Techniques in Biomedical and Chemical Research ; Fault Detection and Control Systems
Authors: Wenmei HUANG | Weishuai ZHANG | Ling Weng
Source: Optics and Precision Engineering (article, 2022-01-01)
Field: Materials Science — Electronic, Optical and Magnetic Materials

Measurement and optimization control of output characteristics of high frequency magnetostrictive transducer é«é¢ç£è´ä¼¸ç¼©æ¢è½å¨çè°æ¯ç¶æåè¾åºç¹æ§åçµç£æ¿å±æ¡ä»¶ãåç­ç¨åº¦ä»¥åè´è½½ç¶åµç­å¤ç§å ç´ å ±åå½±åãä¸ºäºæåé«é¢ç£è´ä¼¸ç¼©æ¢è½å¨çè¾åºæ§è½ï¼æ¬ææ·±å ¥ç ç©¶äºå·¥ä½æ¸©åº¦åè´è½½ååå¯¹æ¢è½å¨è°æ¯é¢çåæä½³åç½®ç£åºçå½±åè§å¾å¹¶è®¾è®¡äºé­ç¯æ§å¶ç³»ç»ãé¦å ï¼ä¾æ®æ¢è½å¨é»æåå¾åè¾åºå éåº¦ç¹æ§ï¼å¯¹ä¸åæ¸©åº¦åè´è½½ä¸ç£è´ä¼¸ç¼©æ¢è½å¨çè°æ¯é¢çä¸æä½³åç½®ç£åºè¿è¡äºå®éªæµè¯ä»¥åç°å ¶ååè§å¾ï¼ç¶åï¼åºäºæµè¯æ°æ®å»ºç«äºååä¼ æ­ï¼Back Propagationï¼BPï¼ç¥ç»ç½ç»é¢æµæ¨¡åå¹¶éç¨éä¼ ç®æ³åç²å­ç¾¤ç®æ³å¯¹BPç¥ç»ç½ç»è¿è¡ä¼åä»¥è¡¨å¾æ¸©åº¦åè´è½½ä¸è°æ¯é¢çåæä½³åç½®çµæµä¹é´çéçº¿æ§å ³ç³»ï¼æåï¼æ­å»ºäºç£è´ä¼¸ç¼©æ¢è½å¨çé­ç¯æ§å¶ç³»ç»å¹¶å©ç¨é¢æµæ¨¡åçé¢æµç»æå®æ¶è°æ´é­ç¯æ§å¶å¨çåèå¼ä»¥å®ç°è°æ¯é¢çåæä½³åç½®ç£åºçèªå¨è¿½è¸ªï¼å®éªç»æè¯æäºè¯¥æ§å¶ç³»ç»ä¼åæ¢è½å¨è¾åºç¹æ§çæææ§ï¼ä¸åå·¥åµä¸å¯ä½¿æ¢è½å¨çè¾åºå éåº¦å¹ å¼å¹³åæé«25.65%ã Transducer ; Magnetostriction ; Acoustics ; Materials science ; Control (management) ; Control theory (sociology) ; Computer science ; Physics ; Magnetic field Magnetic Properties and Applications ; Magnetic Bearings and Levitation Dynamics ; Magneto-Optical Properties and Applications
Authors: Jimy Oblitas | Yuleyci Cieza | Wilson Castro
Source: Proceedings of the 20th LACCEI International Multi-Conference for Engineering, Education and Technology: “Education, Research and Leadership in Post-pandemic Engineering: Resilient, Inclusive and Sustainable Actions” (article, 2022-01-01)
Field: Chemistry — Analytical Chemistry

Determination of semolina adulteration by NIR spectroscopy T he objective was to implement a semolina percentage recognition system using near-infrared spectroscopy (NIR) and multivariate data analysis. For this purpose, 6 samples were an aly zed with different percentages of semolina (20, 4 0, 6 0, 80 an d 100 %) . Samples were repeated 20 times. T he observed NI R sp ect r um was absorbance in the range of 1100 and 2500 nm. In order to reduce the data, the analysis of main components was used by testing 24 classification models, from which the one that reached the highest level of precision was the Linear Support Vector Machine (SVM) algorithm, reaching 98.8%, achieving fairly satisfactory discriminatio n with values of PC1 (99.7%), PC2 (0.3%) and PC3 (0.1%), reachin g a total cumulative variation of the contribution of th e f ir st 3 P Cs of 99.9%. Partial Least Regression (PLS) models applied to NIR-spectra showed R2 between 0.9388. T hese values demonstrated that NIR spectroscopy can be used for the identification and quantif ication of fiber added to semolina. Spectroscopy ; Materials science ; Near-infrared spectroscopy ; Chemistry ; Chromatography ; Optics ; Physics Spectroscopy and Chemometric Analyses ; Spectroscopy Techniques in Biomedical and Chemical Research
Authors: Mark V. Ivanov | Julia A. Bubis | Vladimir Gorshkov | Irina A. Tarasova | Lev I. Levitsky | Elizaveta M. Solovyeva | Anastasiya V. Lipatova | Frank Kjeldsen | Mikhail V. Gorshkov
Source: bioRxiv (Cold Spring Harbor Laboratory) (preprint, 2022-05-13)
Field: Chemistry — Spectroscopy

DirectMS1Quant: ultrafast quantitative proteomics with MS/MS-free mass spectrometry Abstract Recently, we presented the DirectMS1 method of ultrafast proteome-wide analysis based on minute-long LC gradients and MS1-only mass spectra acquisition. Currently, the method provides the depth of human cell proteome coverage of 2500 proteins at 1% false discovery rate (FDR) when using 5-min LC gradients and 7.3 min runtime in total. While the standard MS/MS approaches provide 4000 to 5000 protein identifications within a couple of hours of instrumentation time, we advocate here that the higher number of identified proteins does not always translate into better quantitation quality of the proteome analysis. To further elaborate on this issue we performed one-by-one comparison of quantitation results obtained using DirectMS1 with three popular MS/MS-based quantitation methods: label-free quantification (LFQ), tandem mass tag (TMT), both based on data dependent acquisition (DDA), and data independent acquisition (DIA). For the comparison we performed a series of proteome-wide analysis of well-characterized (ground truth) and biological relevant samples, including a mix of UPS1 proteins spiked at different concentrations into E. coli digest used as a background and a set of glioblastoma cell lines. MS1-only data was analyzed using a novel quantitation workflow called DirectMS1Quant developed in this work. The results obtained in this study demonstrated comparable quantitation efficiency of 5 min DirectMS1 with both TMT and DIA methods utilizing 10 to 20-fold longer instrumentation time. Proteome ; Mass spectrometry ; Tandem mass spectrometry ; Quantitative proteomics ; Chemistry ; Proteomics ; Chromatography ; Tandem mass tag ; Label-free quantification ; Instrumentation (computer programming) ; Computational biology ; Shotgun proteomics ; Workflow ; Analytical Chemistry (journal) ; Computer science ; Biology ; Biochemistry ; Database Advanced Proteomics Techniques and Applications ; Mass Spectrometry Techniques and Applications ; Metabolomics and Mass Spectrometry Studies
Authors: Yi Ai | Ruoyu Luo | Deqiang Yang | Jiong Ma | Yao Yu | Hong Lü
Source: Frontiers in Bioengineering and Biotechnology (article, 2022-09-02)
Field: Chemistry — Spectroscopy

Fluorescence lifetime imaging of NAD(P)H upon oxidative stress in Kluyveromyces marxianus <i>K. marxianus</i> is a promising cell factory for producing heterologous proteins. Oxidative stresses were raised during overexpression of heterologous proteins, leading to the shift of the redox state. How to measure the redox state of live <i>K. marxianus</i> cells without perturbing their growth remains a big challenge. Here, a fluorescence lifetime imaging (FLIM)-based method was developed in live <i>K. marxianus</i> cells. During the early exponential growth, <i>K. marxianus</i> cells exhibited an increased mean fluorescence lifetime (τ-mean) of NAD(P)H compared with <i>Saccharomyces cerevisiae</i> cells, which was consistent with the preference for respiration in <i>K. marxianus</i> cells and that for fermentation in <i>S. cerevisiae</i> cells. Upon oxidative stresses induced by high temperature or H<sub>2</sub>O<sub>2</sub>, <i>K. marxianus</i> cells exhibited an increased τ-mean in company with decreased intracellular NAD(P)H/NAD(P)<sup>+</sup>, suggesting a correlation between an increased τ-mean and a more oxidized redox state. The relationship between τ-mean and the expression level of a heterologous protein was investigated. There was no difference between the τ-means of <i>K. marxianus</i> strains which were not producing a heterologous protein. The τ-mean of a strain yielding a high level of a heterologous protein was higher than that of a low-yielding strain. The results suggested the potential application of FLIM in the non-invasive screen of high-yielding cells. Kluyveromyces marxianus ; Oxidative stress ; NAD+ kinase ; Kluyveromyces ; Fluorescence ; Chemistry ; Oxidative phosphorylation ; Biochemistry ; Yeast ; Saccharomyces cerevisiae ; Enzyme ; Physics Mass Spectrometry Techniques and Applications ; Advanced Proteomics Techniques and Applications ; Photosynthetic Processes and Mechanisms