jablonkagroup/rise_ai_scientists huggingface dataset:
Authors: Maria Fumanal | Joaquim Jornet-Somoza | Sergi Vela | Juan J. Novoa | Jordi Ribas‐Ariño | Mercè Deumal
Source: Journal of Materials Chemistry C (article, 2021-01-01)
Field: Materials Science — Electronic, Optical and Magnetic Materials

Pitfalls on evaluating pair exchange interactions for modelling molecule-based magnetism Human know-how is crucial to cross-examine and challenge computations before trusting any result for modelling magnetic properties in molecule-based materials. Magnetism ; Materials science ; Molecule ; Computation ; Nanotechnology ; Chemical physics ; Computer science ; Condensed matter physics ; Physics ; Quantum mechanics Magnetism in coordination complexes ; Advanced NMR Techniques and Applications ; Lanthanide and Transition Metal Complexes
Authors: Andrés C. Rodríguez | Rodrigo Caye Daudt | Stefano D’Aronco | Konrad Schindler | Jan Dirk Wegner
Source: Remote Sensing (article, 2021-10-26)
Field: Chemistry — Inorganic Chemistry

Robust Damage Estimation of Typhoon Goni on Coconut Crops with Sentinel-2 Imagery Typhoon Goni crossed several provinces in the Philippines where agriculture has high socioeconomic importance, including the top-3 provinces in terms of planted coconut trees. We have used a computational model to infer coconut tree density from satellite images before and after the typhoon’s passage, and in this way estimate the number of damaged trees. Our area of study around the typhoon’s path covers 15.7 Mha, and includes 47 of the 87 provinces in the Philippines. In validation areas our model predicts coconut tree density with a Mean Absolute Error of 5.9 Trees/ha. In Camarines Sur we estimated that 3.5 M of the 4.6 M existing coconut trees were damaged by the typhoon. Overall we estimated that 14.1 M coconut trees were affected by the typhoon inside our area of study. Our validation images confirm that trees are rarely uprooted and damages are largely due to reduced canopy cover of standing trees. On validation areas, our model was able to detect affected coconut trees with 88.6% accuracy, 75% precision and 90% recall. Our method delivers spatially fine-grained change maps for coconut plantations in the area of study, including unchanged, damaged and new trees. Beyond immediate damage assessment, gradual changes in coconut density may serve as a proxy for future changes in yield. Typhoon ; Canopy ; Satellite imagery ; Forestry ; Environmental science ; Agroforestry ; Mathematics ; Geography ; Remote sensing ; Meteorology ; Biology ; Ecology Coconut Research and Applications ; Pacific and Southeast Asian Studies ; Remote Sensing in Agriculture
Authors: Rahul Joshi | Ritu Joshi | Hanim Zuhrotul Amanah | Mohammad Akbar Faqeerzada | J. Kumar | Geonwoo Kim | Insuck Baek | Eun-Sung Park | Rudiati Evi Masithoh | Byoung–Kwan Cho
Source: Korean Journal of Agricultural Science (article, 2021-06-01)
Field: Chemistry — Analytical Chemistry

Quantitative analysis of glycerol concentration in red wine using Fourier transform infrared spectroscopy and chemometrics analysis Glycerol is a non-volatile compound with no aromatic properties that contributes significantly to the quality of wine by providing sweetness and richness of taste.In addition, it is also the third most significant byproduct of alcoholic fermentation in terms of quantity after ethanol and carbon dioxide.In this study, Fourier transform infrared (FT-IR) spectroscopy was employed as a fast non-destructive method in conjugation with multivariate regression analysis to build a model for the quantitative analysis of glycerol concentration in wine samples.The samples were prepared by using three varieties of red wine samples (i.e., Shiraz, Merlot, and Barbaresco) that were adulterated with glycerol in concentration ranges from 0.1 to 15% (vv -1 ), and subjected to analysis together with pure wine samples.A net analyte signal (NAS)-based methodology, called hybrid linear analysis in the literature (HLA/GO), was applied for predicting glycerol concentrations in the collected FT-IR spectral data.Calibration and validation sets were designed to evaluate the performance of the multivariate method.The obtained results exhibited a high coefficient of determination (R 2 ) of 0.987 and a low root mean square error (RMSE) of 0.563% for the calibration set, and a R 2 of 0.984 and a RMSE of 0.626% for the validation set.Further, the model was validated in terms of sensitivity, selectivity, and limits of detection and quantification, and the results confirmed that this model can be used in most applications, as well as for quality assurance. Chemometrics ; Fourier transform infrared spectroscopy ; Fourier transform spectroscopy ; Fourier transform ; Analytical Chemistry (journal) ; Wine ; Infrared ; Spectroscopy ; Chemistry ; Chromatography ; Mathematics ; Optics ; Physics ; Food science Spectroscopy and Chemometric Analyses
Authors: Mengyao Lu | Qiang Zhou | Tianen Chen | Junhui Li | Shuwen Jiang | Qin Gao | Cong Wang | Dong Chen
Source: Journal of Spectroscopy (article, 2021-12-02)
Field: Chemistry — Analytical Chemistry

Qualitative Discrimination of Intact Tobacco Leaves Based on Near-Infrared Technology To explore the application of near-infrared (NIR) technology to the quality analysis of raw intact tobacco leaves, a nondestructive discrimination method based on NIR spectroscopy is proposed. A “multiregion + multipoint” NIR spectrum acquisition method is developed, allowing 18 NIR diffuse reflectance spectra to be collected from an intact tobacco leaf. The spectral characteristics and spectral preprocessing methods of intact tobacco leaves are analyzed, and then different spectra (independent or average spectra) and different algorithms (discriminant partial least-squares (DPLS) and Fisher’s discriminant algorithms) are used to construct discriminant models for verifying the feasibility of intact leaf modeling and determining the optimal model conditions. Qualitative discrimination models based on the position, green-variegated (GV), and the grade of intact tobacco leaves are then constructed using the NIR spectra. In the application and verification stage, a multiclassification voting mechanism is used to fuse the results of multiple spectra from a single tobacco leaf to obtain the final discrimination result for that leaf. The results show that the position-GV discrimination model constructed using independent spectra and the DPLS algorithm and the grade discrimination model constructed using independent spectra and Fisher’s algorithm achieve optimal results with intact leaf NIR wavenumbers from 5006–8988 cm−1 and the first-derivative and standard normal variate transformation preprocessing method. Finally, when applied to new tobacco leaves, the position-GV model and the grade model achieve discrimination accuracies of 95.18% and 92.77%, respectively. This demonstrates that the two models have satisfactory qualitative discrimination ability for intact tobacco leaves. This study has established a feasible method for the nondestructive qualitative discrimination of the position, GV, and grade of intact tobacco leaves based on NIR technology. Linear discriminant analysis ; Preprocessor ; Mathematics ; Pattern recognition (psychology) ; Near-infrared spectroscopy ; Position (finance) ; Artificial intelligence ; Spectral line ; Transformation (genetics) ; Computer science ; Biological system ; Chemistry ; Biology ; Physics ; Optics Spectroscopy and Chemometric Analyses ; Water Quality Monitoring and Analysis ; Spectroscopy Techniques in Biomedical and Chemical Research
Authors: Siti Saadah | Fakhira Zahra Z | Hasna Haifa Z
Source: Journal of Computer Science and Informatics Engineering (J-Cosine) (article, 2021-06-25)
Field: Chemistry — Analytical Chemistry

Support Vector Regression (SVR) Dalam Memprediksi Harga Minyak Kelapa Sawit di Indonesia dan Nilai Tukar Mata Uang EUR/USD Support Vector Machine merupakan algoritma pembelajaran mesin yang banyak digunakan untuk melakukan prediksi. Salah satunya dengan menggunakan vector kernel radial basis. Dengan karakteristik regresi pada kernel RBF maka metode ini berhasil melakukan prediksi untuk permasalahan seasoning. Mengacu kepada hal tersebut, maka pada penelitian ini akan digunakan pendekatan RBF untuk prediksi forex exchange rate atau minyak kelapa sawit. Karakteristik dua data ini jauh memiliki kesamaan, yakni cenderung ke arah trend seasonal. Mengingat pentingnya dilakukan prediksi untuk kedua studi kasus tersebut, maka kedua permasalahan ini dikaji pada penelitian ini untuk diuji menggunakan algoritma SVR. Hasil yang diperoleh menunjukkan bahwa presentase akurasi untuk exchange rate yaitu 99.97%. Sementara, akurasi pada saat memprediksi minyak kelapa sawit yaitu pada kisaran 98%. Computer science Spectroscopy and Chemometric Analyses ; Oil Palm Production and Sustainability ; Natural Products and Biological Research
Authors: Guilherme Corrêa Soares | Mikko Hokka
Source: Metals (article, 2021-12-23)
Field: Materials Science — Materials Chemistry

Synchronized Full-Field Strain and Temperature Measurements of Commercially Pure Titanium under Tension at Elevated Temperatures and High Strain Rates Understanding the mechanical behavior of materials at extreme conditions, such as high temperatures, high strain rates, and very large strains, is fundamental for applications where these conditions are possible. Although tensile testing has been used to investigate material behavior under high strain rates and elevated temperatures, it disregards the occurrence of localized strains and increasing temperatures during deformation. The objective of this work is to combine synchronized full-field techniques and an electrical resistive heating system to investigate the thermomechanical behavior of commercially pure titanium under tensile loading at high temperatures and high strain rates. An electrical resistive heating system was used to heat dog-bone samples up to 1120 °C, which were then tested with a tensile Split Hopkinson Pressure Bar at strain rates up to 1600 s−1. These tests were monitored by two high-speed optical cameras and an infrared camera to acquire synchronized full-field strain and temperature data. The displacement and strain noise floor, and the stereo reconstruction error increased with temperature, while the temperature noise floor decreased at elevated temperatures. A substantial decrease in mechanical strength and an increase in ductility were observed with an increase in testing temperature. The localized strains during necking were much higher at elevated temperatures, while adiabatic heating was much lower or non-existent at elevated temperatures. Materials science ; Necking ; Split-Hopkinson pressure bar ; Composite material ; Ultimate tensile strength ; Strain rate ; Strain (injury) ; Deformation (meteorology) ; Temperature measurement ; Tensile testing ; Titanium ; Ductility (Earth science) ; Metallurgy ; Creep ; Thermodynamics High-Velocity Impact and Material Behavior ; High-pressure geophysics and materials ; Nuclear Materials and Properties
Authors: Omid Khalaj | Hana Jirková | Karolína Burdová | Adam Stehlík | Ludmila Kučerová | Jiří Vrtáček | Jiří Svoboda
Source: Metals (article, 2021-01-28)
Field: Materials Science — Materials Chemistry

Hot Rolling vs. Forging: Newly Developed Fe-Al-O Based OPH Alloy Two oxide precipitation hardened (OPH) Fe-Al-O-based steels were prepared by mechanical alloying. In addition to the variant using yttria nano-precipitates to improve the mechanical properties, a variant using only alumina precipitates for strengthening was also prepared. Therefore, a more economically acceptable variant of these steels was developed. Hot consolidation is a significant production step for achieving the required mechanical properties. Hot consolidation was performed by either hot rolling or forging. The heat treatment was subsequently performed on both variants (0.85Fe–0.11Al–0.03Y2O3–0.01Y and 0.87Fe–0.11Al–0.02O2) of the alloys to support secondary recrystallization. The paper describes the influence of the consolidation method on grain size, material recrystallization, and mechanical properties. The difference in the consolidation method was reflected in the grain size after the heat treatment, where the material consolidated by hot rolling reached a grain size of almost 200 μm, while after forging the maximum grain size was around 30 μm. A higher ultimate tensile strength was achieved with forged states, both with and without the heat treatment. Materials science ; Forging ; Metallurgy ; Recrystallization (geology) ; Grain size ; Ultimate tensile strength ; Consolidation (business) ; Alloy ; Grain growth ; Oxide Fusion materials and technologies ; Advanced materials and composites ; Microstructure and Mechanical Properties of Steels
Authors: Kumaran Baskaran | Colin W. Wilburn | Jonathan R. Wedell | Leonardus M. I. Koharudin | Eldon L. Ulrich | Adam D. Schuyler | Hamid R. Eghbalnia | Angela M. Gronenborn | Jeffrey C. Hoch
Source: Magnetic Resonance (article, 2021-10-25)
Field: Chemistry — Spectroscopy

Anomalous amide proton chemical shifts as signatures of hydrogen bonding to aromatic sidechains Hydrogen bonding between an amide group and the p-<mml:math xmlns:mml="http://www.w3.org/1998/Math/MathML"><mml:mi>π</mml:mi></mml:math> cloud of an aromatic ring was first identified in a protein in the 1980s. Subsequent surveys of high-resolution X-ray crystal structures found multiple instances, but their preponderance was determined to be infrequent. Hydrogen atoms participating in a hydrogen bond to the p-<mml:math xmlns:mml="http://www.w3.org/1998/Math/MathML"><mml:mi>π</mml:mi></mml:math> cloud of an aromatic ring are expected to experience an upfield chemical shift arising from a shielding ring current shift. We surveyed the Biological Magnetic Resonance Data Bank for amide hydrogens exhibiting unusual shifts as well as corroborating nuclear Overhauser effects between the amide protons and ring protons. We found evidence that Trp residues are more likely to be involved in p-<mml:math xmlns:mml="http://www.w3.org/1998/Math/MathML"><mml:mi>π</mml:mi></mml:math> hydrogen bonds than other aromatic amino acids, whereas His residues are more likely to be involved in in-plane hydrogen bonds, with a ring nitrogen acting as the hydrogen acceptor. The p-<mml:math xmlns:mml="http://www.w3.org/1998/Math/MathML"><mml:mi>π</mml:mi></mml:math> hydrogen bonds may be more abundant than previously believed. The inclusion in NMR structure refinement protocols of shift effects in amide protons from aromatic sidechains, or explicit hydrogen bond restraints between amides and aromatic rings, could improve the local accuracy of sidechain orientations in solution NMR protein structures, but their impact on global accuracy is likely be limited. Hydrogen bond ; Amide ; Chemistry ; Ring (chemistry) ; Chemical shift ; Aromaticity ; Crystallography ; Hydrogen ; Low-barrier hydrogen bond ; Proton NMR ; Stereochemistry ; Molecule ; Organic chemistry ; Physical chemistry Molecular spectroscopy and chirality ; Protein Structure and Dynamics ; Advanced NMR Techniques and Applications
Authors: Tom Altenburg | Thilo Muth | Patrick van Zalm | Hanno Steen | Bernhard Y. Renard
Source: bioRxiv (Cold Spring Harbor Laboratory) (preprint, 2021-12-03)
Field: Chemistry — Spectroscopy

Foundation Model Enables Interpretable Open and Error-Tolerant Searching for Mass Spectrometry-Based Proteomics Abstract Mass spectrometry-based proteomics allows to study all proteins of a sample on a molecular level. However, mass spectra are noisy and contain complex patterns, making them inherently challenging to analyze with purely algorithmic approaches. In terms of the protein sequence landscape, most recent bottom-up MS-based proteomics studies consider either a diverse pool of post-translational modifications, employ large databases – as in metaproteomics or proteogenomics, study multiple isoforms of proteins, include unspecific cleavage sites or even combinations thereof. All this makes peptide and protein identifications challenging due to sheer size of the search space. To cope with this two-sided challenge, i.e. the complexity of real spectra and the search space size, we present a foundation model, called yHydra, that jointly embeds spectra and peptides. This allows us to implement various downstream tasks and search modes in Euclidean space. In particular, we implement an open search which allows to query multiple ten-thousands of spectra against millions of peptides. Furthermore, we implement an error-tolerant search for identifying additional proteoforms that are not included in off-the-shelf reference proteomes. Our foundation model provides meaningful embeddings, as we interpret learned peptide embeddings in comparison to the peptide’s physico-chemical properties. yHydra’s open search, assigns delta masses to each identification which allows to unrestrictedly characterize post-translational modifications. The error-tolerant mode of yHydra can be used as post-processing to existing search engines or as a standalone. yHydra is evaluated on several real life data sets for the identification of modified protein sequences and shows up to 25% increase in protein identification at constant false discovery rate compared to the current state-of-the-art. Availability (under MIT license) https://gitlab.com/dacs-hpi/yHydra Contact bernhard.renard@hpi.de Mass spectrometry ; Proteomics ; Mass spectrum ; Embedding ; Chemistry ; Computer science ; Chromatography ; Artificial intelligence ; Biochemistry Advanced Proteomics Techniques and Applications ; Mass Spectrometry Techniques and Applications ; Metabolomics and Mass Spectrometry Studies
Authors: Erhan Kilinc | A.M.T. Bell | Paul A. Bingham | Russell J. Hand
Source: Journal of the American Ceramic Society (article, 2021-03-16)
Field: Materials Science — Ceramics and Composites

Effects of composition and phase relations on mechanical properties and crystallization of silicate glasses Abstract Crystallization, mechanical properties, and workability are all important for the commercialization and optimization of silicate glass compositions. However, the inter‐relations of these properties as a function of glass composition have received little investigation. Soda‐lime‐silica glasses with Na 2 O‐MgO‐CaO‐Al 2 O 3 ‐SiO 2 compositions relevant to commercial glass manufacture were experimentally studied and multiple liquidus temperature and viscosity models were used to complement the experimental results. Liquidus temperatures of the fabricated glasses were measured by the temperature gradient technique, and Rietveld refinements were applied to X‐Ray powder diffraction (XRD) data for devitrified glasses, enabling quantitative determination of the crystalline and amorphous fractions and the nature of the crystals. Structural properties were investigated by Raman spectroscopy. Acoustic echography, micro‐Vicker's indentation, and single‐edge‐notched bend testing methods were used to measure Young's moduli, hardness, and fracture toughness, respectively. It is shown that it is possible to design lower‐melting soda‐lime‐silica glass compositions without compromising their mechanical and crystallization properties. Unlike Young's modulus, brittleness is highly responsive to the composition in soda‐lime‐silica glasses, and notably low brittleness values can be obtained in glasses with compositions in the wollastonite primary phase field: an effect that is more pronounced in the silica primary phase field. The measured bulk crystal fractions of the glasses subjected to devitrification at the lowest possible industrial conditioning temperatures indicate that soda‐lime‐silica glass melts can be conditioned close to their liquidus temperatures within the compositional ranges of the primary phase fields of cristobalite, wollastonite, or their combinations. Materials science ; Liquidus ; Crystallization ; Devitrification ; Phase (matter) ; Mineralogy ; Soda-lime glass ; Borosilicate glass ; Soda lime ; Glass recycling ; Cristobalite ; Composite material ; Quartz ; Chemical engineering ; Alloy ; Chemistry Glass properties and applications ; Cultural Heritage Materials Analysis ; Mineralogy and Gemology Studies
Authors: Hoang Van Chuyen | Jong‐Bang Eun
Source: Food Research (article, 2021-11-07)
Field: Chemistry — Analytical Chemistry

Effects of different extraction methods on the extraction yield, degradation ofbixin and formation of harmful volatile compounds in the extracts from annattoseeds Annatto is one of the most common natural colorants used in the food industry. However, the degradation of bixin (principle colour component) during the manufacturing and storage of annatto leads to the formation of undesirable volatile compounds which are harmful to human health. The aim of this study was to reduce the amount of undesirable volatile compounds while remain a sufficient extraction yield of bixin in annatto extracts. Bixin from annatto seeds was extracted using soybean oil at 120°C, sodium hydroxide solution at 50°C and acetone with a Soxhlet extractor. The extraction yield and the degradation of bixin in annatto extracts during the extraction processes were investigated and the formation of harmful volatile compounds including toluene and m-xylene in the extracts was analysed using a gas chromatography (GC) system equipped with a flame ionization detector (FID). The extraction with acetone resulted in the highest bixin yield, followed by extraction with sodium hydroxide. Bixin extraction yield of the extraction with soybean oil was the lowest and decreased gradually after 40 mins of the extraction. Losses of bixin by the extractions with acetone and sodium hydroxide were low while the extraction with soybean oil caused significant degradation of bixin. All three methods produced negligible amounts of toluene. However, the concentration of m-xylene in the acetone extracts was very high and remained unchanged during the extraction while sodium hydroxide extract contained a low level of this compound. Thus, the extraction method using sodium hydroxide solution is recommended for recovering pigment from annatto seeds to minimize the risk of harmful volatile compounds in annatto products. Extraction (chemistry) ; Acetone ; Sodium hydroxide ; Chemistry ; Chromatography ; Toluene ; Yield (engineering) ; Xylene ; Sodium ; Organic chemistry ; Materials science Dye analysis and toxicity
Authors: Glen van Ginkel | Lukáš Pravda | Jose M Dana | Mihály Váradi | Peter M. Keller | Stephen Anyango | Sameer Velankar
Source: BMC Bioinformatics (article, 2021-07-23)
Field: Materials Science — Materials Chemistry

PDBeCIF: an open-source mmCIF/CIF parsing and processing package PDBeCIF is an efficient and lightweight Python 2.6+/3+ package with no external dependencies. It can be readily integrated with 3rd party libraries as well as adopted for broad scientific analyses. Computer science ; Python (programming language) ; Parsing ; Documentation ; File format ; Programming language ; Exploit ; Source code ; World Wide Web ; Database Enzyme Structure and Function ; Protein Structure and Dynamics ; Advanced Proteomics Techniques and Applications