jablonkagroup/rise_ai_scientists huggingface dataset:
Authors: Tanzeem Fatima | Ashutosh Srivastava | Vageeshbabu S. Hanur | Min Rao
Source: Tropical Plant Research (article, 2019-08-31)
Field: Chemistry — Organic Chemistry

Approaches in development of DNA based identification system for industrially important timber species Commercial illegal trade is the largest threat to important timbers in India and industrialized countries. Timber species valued for its wood and wood products are smuggled in the adulterated form that cannot be taxonomically identified. The development of DNA marker method to identify and control the origin of tree and tree products from tropical tree species would greatly contribute to distinguish legally from illegally harvested wood. Therefore, DNA barcoding has been anticipated as a reliable technique for wood species identification that can ensure that the tree harvested and traded are the same species/origin. The availability of DNA barcodes for increasing numbers of timber species allows rapid and accurate species identification. This is the first attempt to assemble all the timber barcodes which are available as a reference for the timber species of India. This paper describes whole DNA barcoding process from collection of plant material, to extract DNA and amplification as well as sequencing the amplified region to barcode generation. DNA barcoding ; Identification (biology) ; Barcode ; Species identification ; Biology ; Tree (set theory) ; Agroforestry ; Evolutionary biology ; Ecology ; Business Wood and Agarwood Research ; Biological Stains and Phytochemicals ; Plant Pathogens and Fungal Diseases
Authors: Mathieu Lavallée‐Adam | Alexander R. Pelletier | Jolene K. Diedrich | William Low | Antônio F. M. Pinto | Salvador Martínez‐Bartolomé | Michael Petrascheck | James J. Moresco | John R. Yates
Source: bioRxiv (Cold Spring Harbor Laboratory) (preprint, 2019-01-07)
Field: Chemistry — Spectroscopy

TargetSeeker-MS: A Computational Method for Drug Target Discovery using Protein Separation Coupled to Mass Spectrometry ABSTRACT When coupled to mass spectrometry (MS), energetics-based protein separation (EBPS) techniques, such as thermal shift assay, have shown great potential to identify the targets of a drug on a proteome scale. Nevertheless, the computational analyses assessing the confidence of drug target predictions made by these methods have remained rudimentary and significantly differ depending on the protocol used to produce the data. To identify drug targets in datasets produced using different EBPS-MS techniques, we have developed a novel flexible computational approach named TargetSeeker-MS. We showed that TargetSeeker-MS reproducibly identifies known and novel drug targets in C. elegans and HEK293 samples that were treated with the fungicide benomyl and processed using two different EBPS techniques. We also validated a novel benomyl target in vitro. TargetSeeker-MS, which is available online, allows for the confident identification of targets of a drug on a proteome scale, thereby facilitating the evaluation of its clinical viability. Proteome ; Mass spectrometry ; Computational biology ; Drug ; Chemistry ; Benomyl ; Drug discovery ; Identification (biology) ; Chromatography ; Biology ; Biochemistry ; Pharmacology ; Fungicide Advanced Proteomics Techniques and Applications ; Mass Spectrometry Techniques and Applications ; Protein Structure and Dynamics
Authors: Sergey Kortov | Dmitry Shulgin | A.V. Rodnin | A. Karimova
Source: Economy of Regions (article, 2019-12-01)
Field: Materials Science — Polymers and Plastics

Distribution of Technological Competencies in the Field of the Antidiabetic Drugs Development in the Regions of the Russian Federation . . ) , . . ) , . . ) , . . ) ) . . . (, ; e-mail: d.b.shulgin Russian federation ; Distribution (mathematics) ; Field (mathematics) ; Medicine ; Business ; Political science ; Regional science ; Geography ; Mathematics Polymer Synthesis and Characterization ; Pharmaceutical Economics and Policy ; Regional Economic Development and Innovation
Authors: Syeda Naseem | Zeeshan Ahmed | Syed Uddin | Babar Khan | Mehwish Faiz | Un Nisa | Vidya Patil | Vsm | Jagdeep Singh Aulakh | Dvkb | G Ajay | M | K Kumar | P Prasad | Sukhvir Kaur | D | L Guang-Rong | J Christopher | Burges | D Hobson | R Carter | Y Yan | R Shanmugamani | B | Lai Pabamalie | H Premaratne | Harish S Gujjar | Dms
Source: International Journal of Recent Technology and Engineering (IJRTE) (article, 2019-11-02)
Field: Chemistry — Analytical Chemistry

An Economical Design of Automatic Rice Grading using Image Processing Product quality inspection is a crucial step in the production line of rice industries. To maintain the quality and enhance the inspection methodology, the challenge is to scrutinize rice grain individually over entire batch for escalating the yield. The conventional method used in rice industries is to examine the quality of rice grains manually. The decisions made by human quality control inspectors may be affected by external influences like fatigue, exhaustion or stress which causes non uniformity in evaluation procedure and generate the high probability of errors. The major drawback of the manual inspection comprises high labor content and expenditures. This research paper provides a cost effective design solution to overcome the described limitations by developing a system which helps in sorting rice and eliminate the manual examination. For attaining the automatic grading of rice, the image processing technique is applied which help to sort defected rice grain from the entire batch of rice grains. The system has been developed on MATLAB which helps in the inspection process and its graphical user interface provides information of rice grains in three different quality based categories which sorted on the basis of size and colors. To identify the defected grains, the multilevel threshold method of image processing has been used. The proposed design also helps to determine the quantity of defected rice grains by evaluating the quantity of discolored grains and to identify the size of the rice grain, the geometrical features extracted for each individual rice grain are used to estimate the length sort ; Sorting ; Computer science ; Grading (engineering) ; Image processing ; MATLAB ; Graphical user interface ; Grain quality ; Agricultural engineering ; Artificial intelligence ; Engineering ; Image (mathematics) ; Algorithm ; Agronomy Spectroscopy and Chemometric Analyses ; Smart Agriculture and AI
Authors: Matúš Medo | Daniel M. Aebersold | Michaela Medová
Source: BMC Bioinformatics (preprint, 2019-11-09)
Field: Chemistry — Spectroscopy

ProtRank: bypassing the imputation of missing values in differential expression analysis of proteomic data The new method for the differential expression analysis of proteomic data is available as an easy to use Python package. Missing data ; Imputation (statistics) ; Python (programming language) ; Data mining ; Computer science ; Differential (mechanical device) ; Computational biology ; Biology ; Machine learning ; Physics Advanced Proteomics Techniques and Applications ; Gene expression and cancer classification ; Bioinformatics and Genomic Networks
Authors: Ravipat Lapcharoensuk | Jirawat Phuphanutada | Patthranit Wongpromrat
Source: E3S Web of Conferences (article, 2019-01-01)
Field: Chemistry — Analytical Chemistry

Classification of saline water for irrigated agriculture using near infrared spectroscopy coupled with pattern recognition techniques This research aimed to create near infrared (NIR) spectroscopy models for the classification of saline water with a pattern recognition technique. A total of 112 water samples were collected from the Tha Chin river basin in Thailand. Water samples with salinity less than 0.2 g/l were identified as suitable for agriculture, while water samples with salinity higher than 0.2 g/l were found to be unsuitable. The NIR spectra of water samples were recorded using a Fourier transform (FT) NIR spectrometer in the wavenumber of 12,500–4,000 cm -1 . The salinity of each water sample was analysed by electrical conductivity meter. Identification models were established with 5 supervised pattern recognition techniques including k-nearest neighbour (k-NN), support vector machine (SVM), artificial neural network (ANN), soft independent modelling of class analogies (SIMCA), and partial least squares-discriminant analysis (PLS-DA). The performance of the NIR model was carried out with a split-test method. About 80% of spectra (90 spectra) were randomly selected to develop the classification models. After model development, the NIR spectroscopy models were used to classify the categories of the remaining samples (22 samples). The ANN model showed the highest performance for classifying saline water with precision, recall, F-measure and accuracy of 84.6%, 100.0%, 91.7% and 90.9%, respectively. Other techniques presented satisfactory classification results with accuracy greater than 68.2%. This point indicated that NIR spectroscopy coupled with the pattern recognition technique could be applied to classify saline water for agricultural use according to salinity level in natural resources. Saline water ; Linear discriminant analysis ; Artificial intelligence ; Pattern recognition (psychology) ; Salinity ; Partial least squares regression ; Spectroscopy ; Near-infrared spectroscopy ; Mathematics ; Analytical Chemistry (journal) ; Computer science ; Chemistry ; Statistics ; Chromatography ; Geology ; Physics Spectroscopy and Chemometric Analyses ; Water Quality Monitoring and Analysis ; Water Quality Monitoring Technologies
Authors: Byong Chon Park | Min Jeong Kwak
Source: Microscopy and Microanalysis (article, 2019-08-01)
Field: Materials Science — Surfaces, Coatings and Films

Investigation of Digital Imaging Processing in Determining Nano-Particle Size Distribution Based on Scanning Electron Microscopic Image Journal Article Investigation of Digital Imaging Processing in Determining Nano-Particle Size Distribution Based on Scanning Electron Microscopic Image Get access Byong Chon Park, Byong Chon Park Center for Nanometrology, Korea Research Institute of Standards and Science (KRISS), Daejeon, Rep. of Korea Corresponding author: bcpark@kriss.re.kr Search for other works by this author on: Oxford Academic Google Scholar Min Jeong Kwak Min Jeong Kwak Center for Nano-Bio Measurement, Korea Research Institute of Standards and Science (KRISS) Search for other works by this author on: Oxford Academic Google Scholar Microscopy and Microanalysis, Volume 25, Issue S2, 1 August 2019, Pages 2654–2655, https://doi.org/10.1017/S1431927619014004 Published: 01 August 2019 Suite ; Nanometrology ; Nano- ; Library science ; Nanotechnology ; Computer graphics (images) ; Physics ; Engineering ; Optics ; Materials science ; Engineering physics ; Computer science ; Geography ; Atomic force microscopy ; Archaeology ; Chemical engineering Electron and X-Ray Spectroscopy Techniques ; Advanced Electron Microscopy Techniques and Applications ; Non-Destructive Testing Techniques
Authors: Mariem Ben Ameur | Jean-Luc Rebière | Abderrahim El Mahi | Moez Beyaoui | Moez Abdennadher | Mohamed Haddar
Source: MATEC Web of Conferences (article, 2019-01-01)
Field: Materials Science — Polymers and Plastics

Damage mechanisms assessment of hybrid carbon/flax fibre composites using acoustic emission The purpose of the present experimental study is to describe the damage mechanisms occurring in epoxy matrix composites reinforced with hybrid carbon-flax fibres. The samples tested were consist of unidirectional carbon and flax fibre plies with different stacking sequences. Composite laminates were manufactured by hand lay-up process. The specimens were tested under uniaxial tensile loading. The tests carried out were monitored by the acoustic emission (AE) technique. The results obtained during the monotonic tensile tests were analyzed in order to identify the damage mechanisms evolutions. The recorded events were classified with the k-means algorithm which is a statistical multivariable analysis. In addition, it was an unsupervised classification according to temporal descriptors. The percentage of each damage mechanism to the global failure was evaluated by the hits number and the acoustic energy activity. The AE technique was correlated with scanning electron microscopy (SEM) observations to identify the typical damage mechanisms. Acoustic emission ; Composite material ; Ultimate tensile strength ; Materials science ; Epoxy ; Composite number ; Scanning electron microscope ; Carbon fibers Natural Fiber Reinforced Composites ; Mechanical Behavior of Composites ; Fiber-reinforced polymer composites
Authors: A. S. Shcherbakov | Vladimir Alexandrovich Frolov
Source: Computer Science Research Notes (article, 2019-01-01)
Field: Materials Science — Materials Chemistry

Dynamic Radiosity In this paper we propose a novel radiosity implementation which we called dynamic radiosity. By storing and updating local form-factor matrix of the patches closest to the observer we have solved 2 main problems of radiosity algorithm: (1) quadratic complexity of the algorithm and thus difficulty of applying it to a large-scale scenes, and (2) the possibility of changing geometry on the fly (dynamic geometry). Radiosity (computer graphics) ; Computer science ; Computer graphics (images) Nuclear Materials and Properties ; Gas Dynamics and Kinetic Theory ; Radiative Heat Transfer Studies
Authors: Luis Enrique Colmenares Guillén | Maya Carillo Ruiz | Victor Giovanni Morales Murillo | José Gustavo López y López
Source: Ingeniería Investigación y Tecnología (article, 2019-04-01)
Field: Chemistry — Organic Chemistry

Validación de un algoritmo de clasificación para la identificación de interacciones farmacológicas La interacción farmacológica es la modificación del efecto de un fármaco por la acción de otro fármaco. En México, se ha incrementado año con año el número de reacciones no deseadas de medicamentos provocadas por interacciones farmacológicas. En este artículo se realizó un análisis de los diccionarios médicos iDoctus México, PLM México y Vademécum. Con este análisis, se desarrolló un corpus con 540 interacciones farmacológicas que pueden presentarse en los medicamentos más frecuentes del Hospital Universitario de Puebla. Se generó un modelo de clasificación en la plataforma Weka utilizando un algoritmo Naïve Bayes que predice la posibilidad de una interacción farmacológica, clasificada en leve, moderada o grave. Se realizaron las pruebas con el algoritmo Naïve Bayes utilizando el método de validación cruzada con 10 pliegues. Posteriormente, las pruebas de validación, se compararon con el resultado obtenido con el algoritmo Random Forest, utilizando nuevamente el método de validación cruzada con 10 pliegues. Los resultados en el algoritmo Naïve Bayes son en precisión 79.1%, en recuerdo 75.7% y en F-measure 74.8%. En el algoritmo Random Forest son en precisión 51.7%, en recuerdo 51.7% y en F-measure 50.7%. Finalmente, los resultados obtenidos beneficiarían a la farmacovigilancia para aproximarse a predecir nuevas interacciones farmacológicas antes de la comercialización de un medicamento. Humanities ; Mathematics ; Philosophy Advanced Synthetic Organic Chemistry ; Computational Drug Discovery Methods ; Biomedical Text Mining and Ontologies
Authors: Amna Elsadig Elsafi Abodlaa | Dalia Mursi | Mona Abdelrahman Mohamed Khaier | Mai Abdul RahmanMasri | Nazik Elmalaika Husain | Hind Abdelaziz Elnasri
Source: International Journal of Genetics and Genomics (article, 2019-01-01)
Field: Chemistry — Organic Chemistry

Prediction of Structural and Functional Effects of Single Nucleotide Polymorphisms in &amp;lt;i&amp;gt;NAT2&amp;lt;/i&amp;gt;gene, a Computational Analysis N-acetyltransferase 2 (encoded by <i>NAT2</i>) is a phase II enzyme that detoxifies and metabolizes xenobiotics and drugs components. It is a critical enzyme in clinical pharmacology. It has remarkable genetic polymorphisms, which is associated with the risk of developing cancer due to the change of normally fast acetylation of substrates to slow acetylation. This study assessed single nucleotide polymorphisms (SNPs) in the coding region and (3ʹUTR) of <i>NAT2</i>. Computational approaches were used in this study for functional and structural effects of <i>NAT2</i> gene. SNPs. Were retrieved from NCBI SNPsdatabase. TheNAT2 protein sequence and amino acid change were used as an input to the SIFT, PolyPhen-2, PhD-SNP, SNPs& GO, SNPAnalyzer, I-Mutant 3.0 and PMut to determine the deleterious and SNPs conditions. Other software for predication of the structural change were Mutation3D, Chimera and Project HOPE. GeneMANIA software was used to show gene –gene interaction. PolymiRTs was used to investigate the disruption or creation of SNPs of miRNA region. In Homosapiens182 were nonsynonymous SNPs (nsSNPs), 60 synonymous SNPs, 48 3ʹUTRSNPs and 19 5ʹUTR SNPs. A total, 65 of thosensSNPs were predicted to be highly damaging with 3-6 score rates when analyzed with six software. Re-computation of results with I-Mutant 3.0 showed adecrease in the effective stability of the protein due to 55 nsSNPs. Consequent structural changes were shown using Project HOPE and Chimera. <i>NAT2</i> is a highly polymorphic gene; the majority of deleterious <i>NAT2</i>SNPs are nsSNPs that alter the physiochemical and structural properties of the protein, possibly leading to the loss or distortion of the protein's ability to detoxify and metabolize xenobiotic and aromatic amine compounds. There were three SNPs at the 3ʹUTR that changed the miRNA binding sites, which might affect the gene regulation. Single-nucleotide polymorphism ; Gene ; Genetics ; SNP genotyping ; Biology ; Nonsynonymous substitution ; SNP ; Coding region ; Genome ; Genotype Synthesis and Characterization of Heterocyclic Compounds ; DNA and Nucleic Acid Chemistry
Authors: Navinder J. Singh | S. Roy | Praveen Kumar | M. M. Kimothi | S. Mamatha
Source: The international archives of the photogrammetry, remote sensing and spatial information sciences/International archives of the photogrammetry, remote sensing and spatial information sciences (article, 2019-07-26)
Field: Chemistry — Inorganic Chemistry

COMPARISON OF DIFFERENT CLASSIFICATION TECHNIQUES TO IDENTIFY COCONUT GROWING AREAS IN KOZIKHODE DISTRICT, KERALA Abstract. This study was envisaged to map the coconut growing areas in Kerala state of India, using multidate NDVI obtained from sentinel 2A MSI data, having spatial resolution as 10 m. 95% Cloud free satellite images were taken for classification and date of pass considered for the study were 16th February, 2017 and 18th December, 2017 for Kozhikode district of Kerala. In this study bio-window of coconut plantation was identified using NDVI images of two dates. It was observed that interclass variations were more prominent in February image. Forest, dense and moderately dense coconut plantations have significantly different NDVI values in February image whereas in December image all three features have similar values. Hence, February image was classified using three classification methods i.e. ISODATA, maximum likelihood and random forest classification to assess which method is better to distinguish coconut plantation from other classes. Random Forest classification technique was found to be more accurate in identifying coconut plantation. Area was also estimated for Kozhikode district and compared with the government statistics. Google Earth was taken as reference to identify coconut plantation as it has a unique star shaped canopy, which is clearly visible in high-resolution imagery. Normalized Difference Vegetation Index ; Remote sensing ; Geography ; Multispectral image ; Random forest ; Satellite imagery ; Canopy ; Forestry ; Environmental science ; Computer science ; Ecology ; Artificial intelligence ; Biology ; Climate change Coconut Research and Applications ; Remote Sensing and LiDAR Applications
Authors: Carlos Marinho
Source: RIUnB Institutional Repository (University of Brasília) (article, 2019-08-08)
Field: Chemistry — Analytical Chemistry

Desenvolvimento do classificador Pixel Explorer (PEX), para a discretização de alvos em imagens multiespectrais Tese (Doutorado em Ciências Ambientais)—Universidade de Brasília, Faculdade UnB - Planaltina, Programa de Pós-Graduação em Ciências Ambientais, Planaltina, 2019. Computer science Spectroscopy and Chemometric Analyses ; Water Quality Monitoring and Analysis
Authors: Xiaomi Yuan | Fa Zhou | Fang Long | Ruilin Man | Jianhan Huang
Source: Environmental Technology (article, 2019-09-24)
Field: Materials Science — Materials Chemistry

Polar modified dendritic post-cross-linked polymer for Cu<sup>2+</sup> adsorption The polar modified dendritic post-cross-linked polymer, namely HCPD was synthesized and used for adsorptive removal of Cu<sup>2+</sup> from aqueous solution. The results showed that 5.12 mmol/g of amino and 2.25 mmol/g of carbonyl groups were uploaded on the polymer and these groups were significantly beneficial for Cu<sup>2+</sup> removal. The maximum capacity reached 157.8 mg/g at 313 K and increased as the temperature increased. The Langmuir model characterized the equilibrium data well and a chemical interaction was involved with the enthalpy change of 49.50 kJ/mol. The pseudo-second-order kinetic model described the kinetic data well and the intra-particle diffusion model was appropriate for characterizing the kinetic adsorption. HCPD could be easily regenerated and the regenerated polymers were effectively recycled for five times without significant loss of the equilibrium capacity. Moreover, Fourier-transform infrared (FT-IR) and X-ray photoelectron spectroscopy (XPS) results revealed that the chelating coordination of the amino and carbonyl groups with Cu<sup>2+</sup> was the main driving force for the adsorption. Adsorption ; Chemistry ; Aqueous solution ; Polymer ; X-ray photoelectron spectroscopy ; Fourier transform infrared spectroscopy ; Enthalpy ; Langmuir adsorption model ; Diffusion ; Kinetic energy ; Langmuir ; Nuclear chemistry ; Polymer chemistry ; Physical chemistry ; Chemical engineering ; Organic chemistry ; Thermodynamics Covalent Organic Framework Applications ; Metal-Organic Frameworks: Synthesis and Applications ; Adsorption and biosorption for pollutant removal
Authors: Hongwei Mei | Xiyuan Guan | Fanghui Yin | Jun Zhou | Liming Wang
Source:  (article, 2019-10-01)
Field: Materials Science — Materials Chemistry

Research on Infiltration Characteristics of Moisture in the Polyurethane Perfusion Post Insulator Moisture is an important factor that decreases the insulation performance of polyurethane perfusion post insulator. It is still not clear how much this impact is. Therefore, the infiltration characteristics of moisture in the polyurethane perfusion post insulator are investigated. In this paper, in order to observe the porous structure of polyurethane material systematically, the polyurethane materials were observed by optical microscope, scanning electron microscope and digital microscope. Then, through the moisture absorption test of polyurethane material, the moisture absorption process in polyurethane material was analyzed based on the Fick diffusion model and the Langmuir diffusion model. Finally, the Infiltration characteristics of moisture in the polyurethane perfusion post insulator are obtained by analyzing the moisture seepage test of the post insulator model. The results show that the porous structure of the interface is denser than the internal porous structure. The moisture absorption process of polyurethane material is compatible with the Langmuir diffusion model. The moisture will penetrate quickly through the interface. These results were conducted to provide the theoretical basis for the study of the effect of moisture on the insulation performance of polyurethane perfusion post insulator. Polyurethane ; Materials science ; Moisture ; Composite material ; Insulator (electricity) ; Scanning electron microscope ; Water content ; Infiltration (HVAC) ; Porosity ; Absorption of water ; Geotechnical engineering High voltage insulation and dielectric phenomena ; Enhanced Oil Recovery Techniques ; Electrical and Bioimpedance Tomography