jablonkagroup/rise_ai_scientists huggingface dataset:
Authors: C.H. Arrowsmith | Paul Workman | S Davies | H Reddy | M Caivano | P Cohen | C Arrowsmith | A Edwards | J Baell | M Walters | P Workman | I Collins | O Rossanese | J Blagg | J Lee | M Schapira | A Lin | J Mateo | M Ong | D Tan | M Gonzalez | J De Bono | R Kleiman | M Ehlers | A Antolin | B Al-Lazikani | A Carter | S Mller
Source: Nature Communications (article, 2022-07-05)
Field: Chemistry — Organic Chemistry

A conversation on using chemical probes to study protein function in cells and organisms Chemical probes are selective small-molecule modulators, usually inhibitors, of their target protein’s function, that can be used in cell or even animal studies to interrogate the functions of their target proteins. Cheryl Arrowsmith, the leader of a new initiative called Target 2035, which seeks to identify a pharmacological modulator for most human proteins by the year 2035, and Paul Workman, the Executive Director of the nonprofit Chemical Probes Portal, an online resource dedicated to chemical probes, talked to Nature Communications about chemical probes, their respective paths to leadership positions in the field, the online resources available to those interested in the topic and the promise and value of open — collaborative — science. The below material is a modified transcript of a long discussion, preserving the conversational tone, but streamlined and edited for clarity, and thus we do not attribute the particular parts to Cheryl or Paul specifically except for when they shared their personal experiences. Conversation ; Function (biology) ; Protein function ; Computational biology ; Cell biology ; Chemistry ; Computer science ; Biology ; Biochemistry ; Communication ; Psychology ; Gene Click Chemistry and Applications ; Biotin and Related Studies ; Computational Drug Discovery Methods
Authors: Denys Oliinyk | Florian Meier
Source: bioRxiv (Cold Spring Harbor Laboratory) (preprint, 2022-06-03)
Field: Chemistry — Spectroscopy

Ion mobility-resolved phosphoproteomics with dia-PASEF and short gradients Abstract Mass spectrometry-based phosphoproteomics has identified &gt;150,000 post-translational phosphorylation sites in the human proteome. To disentangle their functional relevance, complex experimental designs that require increased throughput are now coming into focus. Here, we apply dia-PASEF on a trapped ion mobility (TIMS) mass spectrometer to analyze the phosphoproteome of a human cancer cell line in short liquid chromatography gradients. At low sample amounts equivalent to ∼20 ug protein digest per analysis, we quantified over 12,000 phosphopeptides including ∼8,000 class I phosphosites in one hour without a spectral library. Decreasing the gradient time to 15 min yielded virtually identical coverage of the phosphoproteome, and with 7 min gradients we still quantified about 80% of the class I sites with a median coefficient of variation &lt;10% in quadruplicates. We attribute this in part to the increased peak capacity, which effectively compensates for the higher peptide density per time unit in shorter gradients. Our data shows a five-fold reduction in the number of co-isolated peptides with TIMS. In the most extreme case, these were positional isomers of nearby phosphosites that remained unresolved with fast chromatography. In summary, we demonstrate how key features of dia-PASEF translate to phosphoproteomics, resulting in high throughput and sensitivity. Phosphoproteomics ; Proteome ; Chemistry ; Mass spectrometry ; Chromatography ; Coefficient of variation ; Ion-mobility spectrometry ; Proteomics ; Posttranslational modification ; Throughput ; Peptide ; Phosphorylation ; Analytical Chemistry (journal) ; Computational biology ; Protein phosphorylation ; Biochemistry ; Biology ; Protein kinase A ; Computer science Advanced Proteomics Techniques and Applications ; Mass Spectrometry Techniques and Applications ; Metabolomics and Mass Spectrometry Studies
Authors: Jinxing Li | Guohui Yang | Yueyi Yuan | Qun Wu | Kuang Zhang
Source: Frontiers in Materials (article, 2022-01-07)
Field: Materials Science — Electronic, Optical and Magnetic Materials

Ultra-Thin Chiral Metasurface-Based Superoscillatory Lens The metasurface-based superoscillatory lens has been demonstrated to be effective in finely tailoring the wavefront of light to generate focal spots beyond the diffraction limit in the far-field that is capable of improving the resolution of the imaging system. In this paper, an ultra-thin (0.055 λ 0 ) metasurface-based superoscillatory lens (SOL) that can generate a sub-diffraction optical needle with a long focal depth is proposed, which is constructed by ultra-thin chiral unit cells containing two metal split-ring resonators (SRR) with a 90° twisted angle difference cladded on both sides of a 1.5 mm-thick dielectric substrate, with a high linear cross-polarized transmission coefficient around 0.9 and full phase control capability at 11 GHz. Full-wave simulation shows that SOL generates a sub-diffraction optical needle within 10.5–11.5 GHz. At the center frequency, the focal depth is 281 mm (10.3 λ 0 ) within 105–386 mm, the full width at half maximum (FWHM) is 18.5 mm (0.68 λ 0 ), about 0.7 times the diffraction limit, generally consistent with the theoretical result. The proposed ultra-thin chiral metasurface-based SOL holds great potential in integrating into practical imaging applications for its simple fabrication, high efficiency, and low-profile advantages. Optics ; Diffraction ; Materials science ; Lens (geology) ; Focal length ; Full width at half maximum ; Wavefront ; Transmission coefficient ; Diffraction efficiency ; Resonator ; Near and far field ; Optoelectronics ; Transmission (telecommunications) ; Physics Metamaterials and Metasurfaces Applications ; Advanced Antenna and Metasurface Technologies ; Antenna Design and Analysis
Authors: Yanlin Su | Bing Ye | Lian Zeng | Zekang Xiong | Tingfang Sun | Kaifang Chen | Qiuyue Ding | Weijie Su | Xirui Jing | Qing Gao | Guixiong Huang | Yizhou Wan | Xu Yang | Xiaodong Guo
Source: Membranes (article, 2022-07-20)
Field: Materials Science — Biomaterials

Small Intestinal Submucosa Biomimetic Periosteum Promotes Bone Regeneration The biomimetic periosteum could simulate the structural function of the periosteum and promote bone repair. This strategy may provide a promising method for the clinical treatment of skull bone defects. Periosteum ; Biomedical engineering ; Decellularization ; Tissue engineering ; Regeneration (biology) ; Materials science ; Bone healing ; Mesenchymal stem cell ; In vivo ; Anatomy ; Cell biology ; Medicine ; Biology Electrospun Nanofibers in Biomedical Applications ; Tissue Engineering and Regenerative Medicine ; Bone Tissue Engineering Materials
Authors: Ziyue Wang | Michael Mülleder | Ihor Batruch | Anjali Chelur | Kathrin Textoris‐Taube | Torsten Schwecke | Johannes Hartl | Jason Causon | Jose Castro-Perez | Vadim Demichev | Stephen Tate | Markus Ralser
Source: bioRxiv (Cold Spring Harbor Laboratory) (preprint, 2022-04-14)
Field: Chemistry — Spectroscopy

High-throughput proteomics of nanogram-scale samples with Zeno SWATH DIA Abstract The ability to conduct high-quality proteomic experiments in high throughput has opened new avenues in clinical research, drug discovery, and systems biology. Next to an increase in quantitative precision, recent developments in high-throughput proteomics have also gained proteomic depth, to the extent that earlier gaps between classic and high-throughput experiments have significantly narrowed. Here we introduce and benchmark Zeno SWATH, a data-independent acquisition technique that employs a linear ion trap pulsing (Zeno trap pulsing) in order to increase proteomic depth and dynamic range in proteomic experiments. Combined with the high acquisition speed, these gains in sensitivity are particularly attractive for conducting high-throughput proteomics experiments with high chromatographic flow rates and fast gradients. We demonstrate that when combined with either micro-flow- or analytical-flow-rate chromatography, Zeno SWATH increases protein identification in complex samples 5- to 10-fold when compared to current SWATH acquisition methods on the same instrument. Using 20-min micro-flow chromatography, Zeno SWATH identified &gt; 6,000 proteins from a 62.5 ng load of human cell lysate with more than 5,000 proteins consistently quantified in triplicate injections with a median CV of 6%. Using 5-min analytical-flow-rate chromatography (800 µl/min), Zeno SWATH identified 4,907 proteins from a triplicate injection of 2 µg of a human cell lysate; or more than 3,000 proteins from 250 ng tryptic digest. Zeno SWATH hence facilitates precise proteomic experiments with small sample amounts using a fast and robust high flow-rate chromatographic method, broadening the application space that requires precise proteomic experiments on a large scale. Proteomics ; Throughput ; Zeno's paradoxes ; Lysis ; Chromatography ; Volumetric flow rate ; Flow (mathematics) ; Chemistry ; Computer science ; Mechanics ; Biochemistry ; Physics ; Mathematics Advanced Proteomics Techniques and Applications ; Mass Spectrometry Techniques and Applications ; Protein purification and stability
Authors: Feng Zhang | Bin Li | Hai Yin | Ji‐ping Zou | Aiguo Ouyang
Source: Journal of Spectroscopy (article, 2022-10-14)
Field: Chemistry — Analytical Chemistry

Study on the Quantitative Assessment of Impact Damage of Yellow Peaches Using the Combined Hyperspectral Technology and Mechanical Parameters The quantitative description of the impact damage of yellow peaches is an essential basis for evaluating their quality and guiding their postharvest handling. In this study, the combined hyperspectral technology and mechanical parameters method were used to quantitatively investigate the impact damage of yellow peaches. Firstly, the mechanical parameters, which are damaged area, absorbed energy, maximum contact force, and maximum stress of yellow peaches, were obtained by the impact device. The statistical regression models between mechanical parameters and damage area were established, and the results showed that the absorbed energy and maximum contact force are the optimal parameters to characterize the impact damage of yellow peaches. Then, the raw spectra were preprocessed by three spectral pretreatment methods, which are standard normal variate (SNV), multiplicative scatter correction (MSC), and SG smoothing, respectively, and the feature wavelengths were selected by the competitive adaptive reweighted sampling (CARS), and the quantitative relationships between spectra and mechanical parameters were successfully modeled based on partial least squares regression (PLSR). The results showed that there is a strong linear correlation between the spectral data and the mechanical parameters, and the prediction performance of the SNV-CARS-PLSR model is best, and the RP and RMSEP of the damaged area, absorbed energy, maximum contact force, and maximum stress of it were 0.920 and 86.452 mm2, 0.845 and 1.303 J, 0.943 and 49.666 N, 0.660 and 0.146 MPa, respectively. In a word, this study shows that the combined hyperspectral technology and mechanical parameters method can be used to quantitatively assess the impact damage of yellow peaches, and guide the postharvest handling of fruits. Hyperspectral imaging ; Partial least squares regression ; Mathematics ; Linear regression ; Materials science ; Statistics ; Computer science ; Artificial intelligence Spectroscopy and Chemometric Analyses ; Meat and Animal Product Quality ; Bee Products Chemical Analysis
Authors: Angelica Galieni | Nicola Nicastro | A. Pentangelo | Cristiano Platani | Teodoro Cardi | Catello Pane
Source: Scientific Reports (article, 2022-03-24)
Field: Chemistry — Analytical Chemistry

Surveying soil-borne disease development on wild rocket salad crop by proximal sensing based on high-resolution hyperspectral features Wild rocket (Diplotaxis tenuifolia, Brassicaceae) is a baby-leaf vegetable crop of high economic interest, used in ready-to-eat minimally processed salads, with an appreciated taste and nutraceutical features. Disease management is key to achieving the sustainability of the entire production chain in intensive systems, where synthetic fungicides are limited or not permitted. In this context, soil-borne pathologies, much feared by growers, are becoming a real emergency. Digital screening of green beds can be implemented in order to optimize the use of sustainable means. The current study used a high-resolution hyperspectral array (spectroscopy at 350-2500 nm) to attempt to follow the progression of symptoms of Rhizoctonia, Sclerotinia, and Sclerotium disease across four different severity levels. A Random Forest machine learning model reduced dimensions of the training big dataset allowing to compute de novo vegetation indices specifically informative about canopy decay caused by all basal pathogenic attacks. Their transferability was also tested on the canopy dataset, which was useful for assessing the health status of wild rocket plants. Indeed, the progression of symptoms associated with soil-borne pathogens is closely related to the reduction of leaf absorbance of the canopy in certain ranges of visible and shortwave infrared spectral regions sensitive to reduction of chlorophyll and other pigments as well as to modifications of water content and turgor. Context (archaeology) ; Canopy ; Hyperspectral imaging ; Crop ; Environmental science ; Nutraceutical ; Agronomy ; Biology ; Botany ; Computer science ; Artificial intelligence ; Food science Spectroscopy and Chemometric Analyses ; Remote Sensing in Agriculture ; Plant Disease Management Techniques
Authors: Kuangling Guo | Yue Liu | Li Chen | Zhongchao Wei | Hongzhan Liu
Source: Nanomaterials (article, 2022-02-15)
Field: Materials Science — Electronic, Optical and Magnetic Materials

Multifunctional Optical Vortex Beam Generator via Cross-Phase Based on Metasurface We propose a multifunctional optical vortex beam (OVB) generator via cross-phase based on a metasurface. Accordingly, we separately investigate the two different propagation characteristics of OVB modulated by the low-order cross-phase (LOCP) and the high-order cross-phase (HOCP) in a self-selected area. When LOCP modulation is added to OVB, topological charges can be measured for any order of OVB. Moreover, we achieve the rotation tunable performance successfully by adding the rotation component. Then, we realize the function of polygonal beam generation and singularities regulation with the HOCP. The order of the HOCP is exactly equal to the number of a polygon OVB's sides. The waist radius and usable width of the beam lengthens as the distance of the self-selected area increases. When the conversion rate is doubled, the distance between singularities widens by about 0.5 μm. The proposed OVB generator provides a simple strategy for detecting the value of topological charges and achieving OVB shaping and singularity manipulation simultaneously. We hope this can open new horizons for promoting the development of photon manipulation, optical communication, and vortex beam modulation. Optical vortex ; Beam (structure) ; Phase (matter) ; Topology (electrical circuits) ; Modulation (music) ; Optics ; Physics ; Mathematics Metamaterials and Metasurfaces Applications ; Orbital Angular Momentum in Optics ; Advanced Antenna and Metasurface Technologies
Authors: Justyna Ośko | Adrian Szewczyk | Paulina Berk | Magdalena Prokopowicz | Małgorzata Grembecka
Source: Foods (article, 2022-11-10)
Field: Chemistry — Analytical Chemistry

Assessment of the Mineral Composition and the Selected Physicochemical Parameters of Dietary Supplements Containing Green Tea Extracts Our aim was to assess the mineral composition as well as the physicochemical quality of green tea-based dietary supplements (capsules and tablets) with respect to average weight, size and shape, friability, breaking force and disintegration time. Products were analysed by flame atomic absorption spectrometry for Ca, K, Mg, Na, Cr, Cu, Fe, Zn, Mn, Pb and Cd. Approximately 60% of the analysed supplements met the requirements of European and Polish regulations. The dietary supplements passed weight variation tests, but not all products had compliant capsule sizes. One product in tablet form failed the friability test, and eleven dietary supplements in tablet form failed the disintegration test. The supplements were characterised by a varied elemental composition, with the highest values found for Ca, Fe, Zn and Mn. The recommended daily allowance realisation for Fe and Zn in two dietary supplements (capsule form) exceeded 100%. As a result of the estimation of the monthly intake of toxic metals, it was concluded that the tested products do not pose a risk to consumer health. Significant relationships (p < 0.001) were found for K, Mg, Na, Cu, Fe, Mn and Zn. The application of factor and cluster analyses allowed the verification of the similarity of green tea extracts contained in dietary supplements to the natural raw material, green tea leaves, used as a reference material. Friability ; Chemistry ; Food science ; Composition (language) ; Raw material ; Dietary Reference Intake ; Dietary supplement ; Starch ; Nutrient ; Biochemistry Heavy Metals in Plants ; Tea Polyphenols and Effects ; Complementary and Alternative Medicine Studies
Authors: Mohammad Al Ktash | Mona Stefanakis | Frank Wackenhut | Volker Jehle | Edwin Ostertag | Karsten Rebner | Marc Brecht
Source: Sensors (article, 2022-12-28)
Field: Chemistry — Analytical Chemistry

Prediction of Honeydew Contaminations on Cotton Samples by In-Line UV Hyperspectral Imaging UV hyperspectral imaging (225 nm-410 nm) was used to identify and quantify the honeydew content of real cotton samples. Honeydew contamination causes losses of millions of dollars annually. This study presents the implementation and application of UV hyperspectral imaging as a non-destructive, high-resolution, and fast imaging modality. For this novel approach, a reference sample set, which consists of sugar and protein solutions that were adapted to honeydew, was set-up. In total, 21 samples with different amounts of added sugars/proteins were measured to calculate multivariate models at each pixel of a hyperspectral image to predict and classify the amount of sugar and honeydew. The principal component analysis models (PCA) enabled a general differentiation between different concentrations of sugar and honeydew. A partial least squares regression (PLS-R) model was built based on the cotton samples soaked in different sugar and protein concentrations. The result showed a reliable performance with <i>R</i><sup>2</sup><sub>cv</sub> = 0.80 and low RMSECV = 0.01 g for the validation. The PLS-R reference model was able to predict the honeydew content laterally resolved in grams on real cotton samples for each pixel with light, strong, and very strong honeydew contaminations. Therefore, inline UV hyperspectral imaging combined with chemometric models can be an effective tool in the future for the quality control of industrial processing of cotton fibers. Honeydew ; Hyperspectral imaging ; Partial least squares regression ; Sugar ; Principal component analysis ; Pixel ; Multivariate statistics ; Biological system ; Environmental science ; Mathematics ; Chemistry ; Artificial intelligence ; Computer science ; Food science ; Botany ; Biology ; Statistics Spectroscopy and Chemometric Analyses ; Bee Products Chemical Analysis ; Meat and Animal Product Quality
Authors: Haohan Ding | David I. Wilson | Wei Yu | Brent R. Young
Source: Foods (article, 2022-05-23)
Field: Materials Science — Polymers and Plastics

Assessing and Quantifying the Surface Texture of Milk Powder Using Image Processing Milk powders produced from similar spray dryers have different visual appearances, while the surface appearance of the powder is a key quality attribute because the smoothness of the milk powder also affects flowability and handling properties. Traditionally quantifying this nuanced visual metric was undertaken using sensory panelists, which is both subjective and time consuming. Therefore, it is advantageous to develop an on-line quick and robust appearance assessment tool. The aim of this work is to develop a classification model which can classify the milk powder samples into different surface smoothness groups. This work proposes a strategy for quantifying the relative roughness of commercial milk powder from 3D images. Photogrammetry equipment together with the software RealityCapture were used to build 3D models of milk powder samples, and a surface normal analysis which compares the area of the triangle formed by the 3 adjacent surface normals or compares the angle between the adjacent surface normals was used to quantify the surface smoothness of the milk powder samples. It was found that the area of the triangle of the smooth-surface milk powder cone is smaller than the area of the triangle of the rough-surface milk powder cone, and the angle between the adjacent surface normals of the rough-surface milk powder cone is larger than the angle between the adjacent surface normals of the smooth-surface milk powder cone, which proved that the proposed area metrics and angle metrics can be used as tools to quantify the smoothness of milk powder samples. Finally, the result of the support vector machine (SVM) classifier proved that image processing can be used as a preliminary tool for classifying milk powder into different surface texture groups. Smoothness ; Surface roughness ; Materials science ; Surface (topology) ; Surface finish ; Texture (cosmology) ; Metric (unit) ; Cone (formal languages) ; Mathematics ; Geometry ; Artificial intelligence ; Composite material ; Computer science ; Image (mathematics) ; Algorithm ; Mathematical analysis Textile materials and evaluations ; Microencapsulation and Drying Processes ; Surface Roughness and Optical Measurements
Authors: Mohamed A. Eltaher | A. Wagih | Ammar A. Melaibari | Ghazi Alsoruji | Mohamed A. Attia
Source: Polymers (article, 2022-03-17)
Field: Materials Science — Ceramics and Composites

Elastoplastic Indentation Response of Sigmoid/Power Functionally Graded Ceramics Structures Due to the applicability of new advanced functionally graded materials (FGMs) in numerous tribological systems, this manuscript aims to present computational and empirical indentation models to investigate the elastoplastic response of FG substrate under an indention process with spherical rigid punch. The spatial variation of the ceramic volume fraction through the specimen thickness is portrayed using the power law and sigmoid functions. The effective properties of two-constituent FGM are evaluated by employing a modified Tamura-Tomota-Ozawa (TTO) model. Bilinear hardening behavior is considered in the analysis. The finite element procedure is developed to predict the contact pressure, horizontal displacement, vertical deformation, and permanent deformation of FG structure under the rigid cylindrical indentation. The empirical forms for permanent deformation were evaluated and assigned. Model validation with experimental works was considered. The convergence of the mesh and solution procedure was checked. Numerical studies were performed to illustrate the influence of gradation function, gradation index, and indentation parameters on the contact pressure, von Mises stresses, horizontal/vertical displacements, and permanent plastic deformation. The present model can help engineers and designers in the selection of an optimum gradation function and gradation index based on their applications. Materials science ; Sigmoid function ; Indentation ; Composite material ; Ceramic ; Structural engineering ; Computer science ; Engineering ; Artificial intelligence Advanced ceramic materials synthesis ; Numerical methods in engineering ; Aluminum Alloys Composites Properties