jablonkagroup/rise_ai_scientists huggingface dataset:
Authors: Tobias Schmidt | Patroklos Samaras | Viktoria Dorfer | Christian Panse | Tobias Kockmann | Leon Bichmann | Bart Van Puyvelde | Yasset Pérez‐Riverol | Eric W. Deutsch | Bernhard Küster | Mathias Wilhelm
Source: bioRxiv (Cold Spring Harbor Laboratory) (preprint, 2020-09-09)
Field: Chemistry — Spectroscopy

Universal Spectrum Explorer: A standalone (web-)application for cross-resource spectrum comparison Abstract Here we present the Universal Spectrum Explorer (USE), a web-based tool based on IPSA for cross-resource (peptide) spectrum visualization and comparison ( https://www.proteomicsdb.org/use/ ). Mass spectra under investigation can either be provided manually by the user (table format), or automatically retrieved from online repositories supporting access to spectral data via the universal spectrum identifier (USI), or requested from other resources and services implementing a newly designed REST interface. As a proof of principle, we implemented such an interface in ProteomicsDB thereby allowing the retrieval of spectra acquired within the ProteomeTools project or real-time prediction of tandem mass spectra from the deep learning framework Prosit. Annotated mirror spectrum plots can be exported from the USE as editable scalable high quality vector graphics. The USE was designed and implemented with minimal external dependencies allowing local usage and integration into other websites ( https://github.com/kusterlab/universal_spectrum_explorer ). Computer science ; Identifier ; Interface (matter) ; Table (database) ; Scalable Vector Graphics ; Resource (disambiguation) ; Scalability ; Spectrum (functional analysis) ; Proof of concept ; Visualization ; World Wide Web ; Operating system ; Data mining ; Computer network Advanced Proteomics Techniques and Applications ; Metabolomics and Mass Spectrometry Studies ; Mass Spectrometry Techniques and Applications
Authors: Abdul Talib Din | M. A. M. Piah | Abdul Rahim Abdullah | Nurbahirah Norddin | F. Abdullah
Source: Indonesian Journal of Electrical Engineering and Computer Science (article, 2020-08-04)
Field: Materials Science — Materials Chemistry

Leakage current signal parameter of various surface roughness conditions of field-aged polymer insulators This paper presents the signal parameter of leakage current based on various surface roughness degradation conditions for field-aged high voltage polymer insulators. The arithmetical mean of surface roughness is measured accordingly, and also the surface leakage current signal is captured effectively using data acquisition device via the electrical stress test. With the variation of field-aged insulators ages which include 6-year, 12-year and 18-year, they have been mechanically tested using a surface roughness tester along with electrical testing by using the standard method of inclined plane test. The surface roughness data are recorded meanwhile the leakage current signals are further analyzed using Spectrogram to extract the signal parameter. These include the instantaneous root mean squared current, the instantaneous total harmonic distortion, the instantaneous total non- harmonic distortion and the instantaneous total waveform distortion. From the results of the comparative study, it has shown that the statistical quantity of leakage current signal parameters is responding in an increasing trend with respect to the incremental of the surface roughness. Thus, the signal parameters of the leakage current are able to indicate the degradation conditions of insulator surface. Waveform ; Surface roughness ; Surface finish ; Leakage (economics) ; Acoustics ; Materials science ; Insulator (electricity) ; Root mean square ; SIGNAL (programming language) ; Total harmonic distortion ; Voltage ; Electronic engineering ; Electrical engineering ; Engineering ; Optoelectronics ; Composite material ; Computer science ; Physics High voltage insulation and dielectric phenomena ; Thermal Analysis in Power Transmission ; Power Transformer Diagnostics and Insulation
Authors: Dennis Kleimaier | Victor D. Schepkin | Cordula Nies | Eric Gottwald | Lothar R. Schad
Source: Processes (article, 2020-10-09)
Field: Materials Science — Materials Chemistry

Intracellular Sodium Changes in Cancer Cells Using a Microcavity Array-Based Bioreactor System and Sodium Triple-Quantum MR Signal The sodium triple-quantum (TQ) magnetic resonance (MR) signal created by interactions of sodium ions with macromolecules has been demonstrated to be a valuable biomarker for cell viability. The aim of this study was to monitor a cellular response using the sodium TQ signal during inhibition of Na/K-ATPase in living cancer cells (HepG2). The cells were dynamically investigated after exposure to 1 mM ouabain or K+-free medium for 60 min using an MR-compatible bioreactor system. An improved TQ time proportional phase incrementation (TQTPPI) pulse sequence with almost four times TQ signal-to-noise ratio (SNR) gain allowed for conducting experiments with 12–14 × 106 cells using a 9.4 T MR scanner. During cell intervention experiments, the sodium TQ signal increased to 138.9 ± 4.1% and 183.4 ± 8.9% for 1 mM ouabain (n = 3) and K+-free medium (n = 3), respectively. During reperfusion with normal medium, the sodium TQ signal further increased to 169.2 ± 5.3% for the ouabain experiment, while it recovered to 128.5 ± 6.8% for the K+-free experiment. These sodium TQ signal increases agree with an influx of sodium ions during Na/K-ATPase inhibition and hence a reduced cell viability. The improved TQ signal detection combined with this MR-compatible bioreactor system provides a capability to investigate the cellular response of a variety of cells using the sodium TQ MR signal. Sodium ; Ouabain ; Chemistry ; Cancer cell ; Viability assay ; Nuclear magnetic resonance ; Ion ; Biophysics ; Cell ; Biochemistry ; Physics ; Cancer ; Biology ; Medicine ; Internal medicine Lanthanide and Transition Metal Complexes ; Electron Spin Resonance Studies ; Advanced MRI Techniques and Applications
Authors: Rizky Ardie Yani | Minarni Minarni | Saktioto Saktioto | Ikhsan Rahman Husein
Source: Science, Technology, and Communication Journal. (article, 2020-10-30)
Field: Chemistry — Analytical Chemistry

Volumetric Prediction of Symmetrical-Shaped Fruits by Computer Vision Computer vision in the industrial sector has the highest level of need because the work is done automatically and can speed up and save time for work productivity. Not always, work will be done manually by human workers who sometimes have obstacles in the process of taking place. The high cost causes the need for technology to simplify work so it does not materialize. A simple imaging system with computer vision is proposed in this study. Measurement of volume estimates from several samples was carried out to see the efficiency of computer vision imaging work by comparing the measurement results manually and water displacement method. Computer vision imaging is built using a CMOS camera, line laser, Raspberry Pi, Python programming language, and OpenCV. Imaging results show that computer vision has the ability to read the sample volume estimate more effectively against objects that have a symmetrical shape. The smallest error percentage of measurement of volume estimation by computer vision against manual method and the water displacement was 7.44% and 7.18% for sunkist oranges and 10.88% and 13.67% for symmetrical watermelon, respectively. Artificial intelligence ; Computer science ; Computer vision ; Computer graphics (images) Spectroscopy and Chemometric Analyses ; Smart Agriculture and AI
Authors: Benjamin J. Ravenhill | Lior Soday | Jack W. Houghton | Robin Antrobus | Michael P. Weekes
Source: bioRxiv (Cold Spring Harbor Laboratory) (preprint, 2020-02-20)
Field: Chemistry — Spectroscopy

Comprehensive cell surface proteomics defines markers of classical, intermediate and non-classical monocytes Abstract Monocytes are a critical component of the cellular innate immune system, and can be subdivided into classical, intermediate and non-classical subsets on the basis of surface CD14 and CD16 expression. Classical monocytes play the canonical role of phagocytosis, and account for the majority of circulating cells. Intermediate and non-classical cells are known to exhibit varying levels of phagocytosis and cytokine secretion, and are differentially expanded in certain pathological states. Characterisation of cell surface proteins expressed by each subset is informative not only to improve understanding of phenotype, but may also provide biological insights into function. Here we use highly multiplexed Tandem-Mass-Tag (TMT)-based mass spectrometry with selective cell surface biotinylation to characterise the classical monocyte surface proteome, then interrogate the phenotypic differences between each monocyte subset to identify novel protein markers. Proteome ; CD14 ; Proteomics ; Biology ; Monocyte ; Biotinylation ; Phagocytosis ; Cell biology ; CD16 ; Phenotype ; Cell ; Secretion ; Immune system ; Innate immune system ; Immunology ; Molecular biology ; Genetics ; Biochemistry ; Gene Advanced Proteomics Techniques and Applications ; Immune cells in cancer ; Extracellular vesicles in disease
Authors: Simone Zanotto | Martín F. Colombano | Daniel Navarro‐Urrios | G. Biasiol | Clivia M. Sotomayor-Torres | Alessandro Tredicucci | Alessandro Pitanti
Source: Frontiers in Physics (article, 2020-01-10)
Field: Materials Science — Electronic, Optical and Magnetic Materials

Broadband Dynamic Polarization Conversion in Optomechanical Metasurfaces Artificial photonic materials, nanofabricated through wavelength-scale engineering, have shown astounding and promising results in harnessing, tuning and shaping photonic beams. Metamaterials have proven to be often outperforming the natural materials they take inspiration from. In particular, metallic chiral metasurfaces have demonstrated large circular and linear dichroism of light which can be used, for example, for probing different enantiomers of biological molecules. Moreover, the precise control, through designs on demand, of the output polarization state of light impinging on a metasurface, makes this kind of structures particularly relevant for polarization-based telecommunication protocols. The reduced scale of the metasurfaces makes them also appealing for integration with nanomechanical elements, adding new dynamical features to their otherwise static or quasi-static polarization properties. To this end we designed, fabricated and characterized an all-dielectric metasurface on a suspended nanomembrane. Actuating the membrane mechanical motion, we show how the metasurface reflectance response can be modified, according to the spectral region of operation, with a corresponding intensity modulation or polarization conversion. The broad mechanical resonance at atmospheric pressure, centered at about 400 kHz, makes the metasurfaces structure suitable for high-frequency operation, mainly limited by the piezo-actuator controlling the mechanical displacement, which in our experiment reached modulation frequencies exceeding 1.3 MHz. Metamaterial ; Polarization (electrochemistry) ; Photonics ; Materials science ; Optoelectronics ; Optomechanics ; Actuator ; Optics ; Broadband ; Photonic metamaterial ; Physics ; Engineering ; Electrical engineering Metamaterials and Metasurfaces Applications ; Mechanical and Optical Resonators ; Plasmonic and Surface Plasmon Research
Authors: Ziyu Tan | Wilfred Lam | Wendy Oakden | Leedan Murray | Margaret M. Koletar | Stanley K. Liu | Greg J. Stanisz
Source: Scientific Reports (article, 2020-12-04)
Field: Materials Science — Materials Chemistry

Saturation transfer properties of tumour xenografts derived from prostate cancer cell lines 22Rv1 and DU145 Histopathology is currently the most reliable tool in assessing the aggressiveness and prognosis of solid tumours. However, developing non-invasive modalities for tumour evaluation remains crucial due to the side effects and complications caused by biopsy procedures. In this study, saturation transfer MRI was used to investigate the microstructural and metabolic properties of tumour xenografts in mice derived from the prostate cancer cell lines 22Rv1 and DU145, which express different aggressiveness. The magnetization transfer (MT) and chemical exchange saturation transfer (CEST) effects, which are associated with the microstructural and metabolic properties in biological tissue, respectively, were analyzed quantitatively and compared amongst different tumour types and regions. Histopathological staining was performed as a reference. Higher cellular density and metabolism expressed in more aggressive tumours (22Rv1) were associated with larger MT and CEST effects. High collagen content in the necrotic regions might explain their higher MT effects compared to tumour regions. DU145 ; Prostate cancer ; Cancer research ; Histopathology ; Pathology ; Cancer ; Magnetization transfer ; Biopsy ; Chemistry ; Medicine ; Magnetic resonance imaging ; Internal medicine ; Radiology ; LNCaP Lanthanide and Transition Metal Complexes ; MRI in cancer diagnosis ; Advanced MRI Techniques and Applications
Authors: Mahmoud Mohammed Mohammed Sebaay | Amr A. Mattar
Source:  (article, 2020-01-13)
Field: Chemistry — Analytical Chemistry

Isoabsorptive Point Method for Simultaneous Determination of Paracetamol and Orphenadrine Citrate in Their Combined Pharmaceutical Dosage Forms A simple, specific, accurate and precise spectrophotometric method was settled for simultaneous determination of paracetamol and orphenadrine citrate in their pure form and in their pharmaceutical formulation. Isoabsorptive point technique has been used in simultaneous determination of both drugs without prior separation. Isoabsorptive point method parameters were validated according to ICH guidelines in which accuracy, precision, repeatability and robustness were found in accepted limits. Advantages and disadvantages of Isoabsorptive point were discussed and statistical comparison between the proposed method and the reference one was also performed. Repeatability ; Dosage form ; Chromatography ; Chemistry ; Mathematics Analytical Methods in Pharmaceuticals ; Analytical Chemistry and Sensors ; Pharmacological Effects and Assays
Authors: А.В. Гринек | Sergey Timofeev | С.И. Кондратьев | A. V. Khurtasenko
Source: МОРСКИЕ ИНТЕЛЛЕКТУАЛЬНЫЕ ТЕХНОЛОГИИ (article, 2020-08-13)
Field: Materials Science — General Materials Science

Method of controlling geometric accuracy for ship shafts В статье представлен способ контроля параметров геометрической точности элементов гребных валов: радиального биения поперечного сечения, отклонения реального профиля вала от цилиндрической формы. Целью работы являлось научное обоснование способа контроля и реализация методики контроля. Разработан алгоритм и схема измерений погрешности формы и положения оси составных валов гребного валопровода на основе существующих авторских решений по контролю точности формы крупногабаритных цилиндрических изделий, в том числе с нестационарной осью вращения. Разработана оригинальная конструкция устройства для контроля геометрических параметров и изготовлена экспериментальная установка и лабораторный образец на базе датчиков отечественного производителя. Алгоритм и методика протестированы с помощью имитационной трехмерной модели. На основе предложенной схемы может быть построено мобильное измерительное оборудование с ручным или автоматизированным измерением - контрольно-измерительная машина. Программно-аппаратная реализация такого оборудования также может основываться на разработанных алгоритмах определения геометрических параметров. The article presents a method for controlling the parameters of geometric accuracy of elements of propeller shafts. The purpose of the work was scientific justification of the control method and methodology implementation. These parameters include the cross section radial runout and the real shaft profile deviations from the cylindrical shape. The author's solutions in the field of controlling the accuracy of the large-sized cylindrical parts shape are obtained. An algorithm and a scheme for measuring the error in the shape and the shaft elements axis position are developed. The presented engineering solutions are applicable to shafts with a non-stationary axis of rotation. The original design of the device for monitoring geometric parameters was developed and an experimental installation and laboratory sample were made based on domestic manufacturer sensors. The algorithm and methodology were tested using a three-dimensional simulation model. On the basis of the proposed circuitry, a mobile measuring equipment with manual or automated measurement can be built - a control and measuring machine. Software and hardware implementation of such equipment can also be based on the developed algorithms for determining geometric parameters. Position (finance) ; Rotation (mathematics) ; Software ; Propeller ; Field (mathematics) ; Computer science ; Basis (linear algebra) ; Engineering ; Mechanical engineering ; Simulation ; Marine engineering ; Artificial intelligence ; Mathematics ; Geometry Material Properties and Applications ; Engineering Diagnostics and Reliability ; Engineering Technology and Methodologies
Authors: Bambang Sugiarto | Elli A. Gojali | Herlan Herlan | Puji Lestari
Source: Journal of Computer Science and Informatics Engineering (J-Cosine) (article, 2020-06-30)
Field: Chemistry — Organic Chemistry

A Smartphone-Based of Wood Identification Using Image Feature Extraction Each wood species has their special characteristics which can be differentiated based on their anatomical structures through wood identification. One of the methods is by detecting macroscopic wood image using computer vision. This method is more rapid and accurate to identify wood species compared to the conventional method. In previous work, we have developed a computer vision technique for wood identification by combining Histogram of Oriented Gradient (HOG) and Support Vector Machine (SVM). As smartphone usage increasing worldwide, capturing wood structures using this smart device is very easy to do and can replace the use of digital microscopes. This paper propose a technique for extraction the wood species on smartphone using HOG method as well as the classification method using SVM on android smartphone. SVM was used to classify the extracted wood textures from the HOG features. In our experiments, wood images of 7 wood species were used i.e Mimusops_-elengi, Melanorrhoea wallichii, Acer niveum, Cratoxylon formosum, Agathis endertii, Dyera costulata and Knema glauca. Each species has a total of 100 training images and 100 testing images. The highest accuracy is obtained by Melanorrhoea wallichii and Agathis endertii species with 84.00% score. The Agathis endertii species has the highest sensitivity and the value reaches 86%. Moreover, the Melanorrhoea wallichii species has a highest score for specificity and precision Support vector machine ; Artificial intelligence ; Pattern recognition (psychology) ; Histogram ; Feature extraction ; Identification (biology) ; Computer science ; Computer vision ; Mathematics ; Botany ; Biology ; Image (mathematics) Wood and Agarwood Research ; Industrial Vision Systems and Defect Detection ; Plant Pathogens and Fungal Diseases
Authors: Ronghui Lou | Pan Tang | Kang Ding | Shanshan Li | Cuiping Tian | Yunxia Li | Suwen Zhao | Yaoyang Zhang | Wenqing Shui
Source: bioRxiv (Cold Spring Harbor Laboratory) (preprint, 2020-01-17)
Field: Chemistry — Spectroscopy

A hybrid spectral library combining DIA-MS data and a targeted virtual library substantially deepens the proteome coverage Abstract Data-independent acquisition mass spectrometry (DIA-MS) is a rapidly evolving technique that enables relatively deep proteomic profiling with superior quantification reproducibility. DIA data mining predominantly relies on a spectral library of sufficient proteome coverage that, in most cases, is built on data-dependent acquisition-based analysis of the same sample. To expand the proteome coverage for a pre-determined protein family, we report herein on the construction of a hybrid spectral library that supplements a DIA experiment-derived library with a protein family-targeted virtual library predicted by deep learning. Leveraging this DIA hybrid library substantially deepens the coverage of three transmembrane protein families (G protein coupled receptors; ion channels; and transporters) in mouse brain tissues with increases in protein identification of 37-87%, and peptide identification of 58-161%. Moreover, of the 412 novel GPCR peptides exclusively identified with the DIA hybrid library strategy, 53.6% were validated as present in mouse brain tissues based on orthogonal experimental measurement. Proteome ; Computational biology ; Mass spectrometry ; Identification (biology) ; Transmembrane protein ; Computer science ; Peptide library ; Chemistry ; Biology ; Bioinformatics ; Receptor ; Gene ; Peptide sequence ; Genetics ; Chromatography Mass Spectrometry Techniques and Applications ; Advanced Proteomics Techniques and Applications ; Receptor Mechanisms and Signaling
Authors: Chi‐Lin Yu | Hsin‐Chin Chen | Zih-Yun Yang | Tai‐Li Chou
Source: Behavior Research Methods (article, 2020-02-05)
Field: Chemistry — Analytical Chemistry

Multi-time-point analysis: A time course analysis with functional near-infrared spectroscopy Generalizability theory ; Univariate ; Computer science ; Time point ; Set (abstract data type) ; Artificial intelligence ; Machine learning ; Functional near-infrared spectroscopy ; Data set ; Point (geometry) ; Data mining ; Pattern recognition (psychology) ; Statistics ; Mathematics ; Psychology ; Multivariate statistics Spectroscopy and Chemometric Analyses ; Optical Imaging and Spectroscopy Techniques ; Advanced Chemical Sensor Technologies
Authors: Ade Irvan Tauvana | Widodo Widodo
Source: Turbo Jurnal Program Studi Teknik Mesin (article, 2020-06-16)
Field: Materials Science — Materials Chemistry

Analisis pemotongan logam ST-37 dengan mesin potong menggunakan gas oxy-LPG This gas cutting machine is an ST-37 metal cutting tool in a semi-automatic way using Liquified Potroleum Gas (LPG) and Oxygen gas materials. LPG gas is used with a composition of propane 80% and Isobutane 20%. In the process of cutting metal based on several parameters, namely: metal thickness, oxygen gas pressure, and LPG gas and cutting speed. Before cutting down the metal, the preparation stage is done by conditioning the test equipment and work equipment used to collect test data. The method used in this research is to select the type of metal and cutting equipment then do the recording and taking test data. Further analysis and examination are carried out as follows: visual inspection of the results of cutting and flame shape, a better composition results from testing in accordance with applicable rules such as pressure, plate thickness, and time of cutting. 80% and 20% LPG gas composition at gas working pressure: 0.2 kg / cm2, oxygen pressure: 2.5 kg / cm2, cutting distance of 2 mm. The results of this test are overall in good condition and no defects occur. Keywords: LPG Gas cutting, Propane, Isobutane, Cutting speed, oxygen. Isobutane ; Propane ; Materials science ; Oxygen ; Work (physics) ; Gas composition ; Automotive engineering ; Mechanical engineering ; Composite material ; Chemistry ; Engineering ; Physics Material Selection and Properties