jablonkagroup/rise_ai_scientists huggingface dataset:
Authors: Andrew R. M. Michael | B.C. do Amaral | Kallie L. Ball | Kristen H. Eiriksson | David C. Schriemer
Source: Nature Communications (article, 2024-10-02)
Field: Chemistry — Spectroscopy

Cell fixation improves performance of in situ crosslinking mass spectrometry while preserving cellular ultrastructure Crosslinking mass spectrometry (XL-MS) has the potential to map the interactome of the cell with high resolution and depth of coverage. However, current in vivo XL-MS methods are hampered by crosslinkers that demonstrate low cell permeability and require long reaction times. Consequently, interactome sampling is not high and long incubation times can distort the cell, bringing into question the validity any protein interactions identified by the method. We address these issues with a fast formaldehyde-based fixation method applied prior to the introduction of secondary crosslinkers. Using human A549 cells and a range of reagents, we show that 4% formaldehyde fixation with membrane permeabilization preserves cellular ultrastructure and simultaneously improves reaction conditions for in situ XL-MS. Protein labeling yields can be increased even for nominally membrane-permeable reagents, and surprisingly, high-concentration formaldehyde does not compete with conventional amine-reactive crosslinking reagents. Prefixation with permeabilization uncouples cellular dynamics from crosslinker dynamics, enhancing control over crosslinking yield and permitting the use of any chemical crosslinker. In situ ; Reagent ; Chemistry ; Formaldehyde ; Biophysics ; Mass spectrometry ; Interactome ; Cell ; Fixation (population genetics) ; Membrane ; Biochemistry ; Chromatography ; Biology ; Organic chemistry Mass Spectrometry Techniques and Applications ; Advanced Proteomics Techniques and Applications ; Metabolomics and Mass Spectrometry Studies
Authors: Guanmin Li | Zhong Wang | Yuliang Chen | Jae-Chun Jeon | S. Parkin
Source: Nature Communications (article, 2024-07-10)
Field: Materials Science — Polymers and Plastics

Computational elements based on coupled VO2 oscillators via tunable thermal triggering Computational technologies based on coupled oscillators are of great interest for energy efficient computing. A key to developing such technologies is the tunable control of the interaction among oscillators which today is accomplished by additional electronic components. Here we show that the synchronization of closely spaced vanadium dioxide (VO<sub>2</sub>) oscillators can be controlled via a simple thermal triggering element that itself is formed from VO<sub>2</sub>. The net energy consumed by the oscillators is lower during thermal coupling compared with the situation where they are oscillating independently. As the size of the oscillator shrinks from 6 μm to 200 nm both the energy efficiency and the oscillator frequency increases. Based on such oscillators with active tuning, we demonstrate AND, NAND, and NOR logic gates and various firing patterns that mimic the behavior of spiking neurons. Our findings demonstrate an innovative approach towards computational techniques based on networks of thermally coupled oscillators. Thermal ; Computer science ; Physics ; Topology (electrical circuits) ; Biological system ; Thermodynamics ; Biology ; Electrical engineering ; Engineering Transition Metal Oxide Nanomaterials ; Advanced Memory and Neural Computing ; Infrared Target Detection Methodologies
Authors: Rivka-Galya Nir-Harwood | G. M. Cohen | Amlan Majumdar | Richard Haight | Emanuel Ber | Lynne Gignac | Efrat Ordan | Lishai Shoham | Yair Keller | Lior Kornblum | Eilam Yalon
Source: ACS Nano (article, 2024-03-08)
Field: Materials Science — Materials Chemistry

Drift of Schottky Barrier Height in Phase Change Materials Phase-change memory (PCM) devices have great potential as multilevel memory cells and artificial synapses for neuromorphic computing hardware. However, their practical use is hampered by resistance drift, a phenomenon commonly attributed to structural relaxation or electronic mechanisms primarily in the context of bulk effects. In this study, we reevaluate the electrical manifestation of resistance drift in sub-100 nm Ge<sub>2</sub>Sb<sub>2</sub>Te<sub>5</sub> (GST) PCM devices, focusing on the contributions of bulk vs interface effects. We employ a combination of measurement techniques to elucidate the current transport mechanism and the electrical manifestation of resistance drift. Our steady-state temperature-dependent measurements reveal that resistance in these devices is predominantly influenced by their electrical contacts, with conduction occurring through thermionic emission (Schottky) at the contacts. Additionally, temporal current-voltage characterization allows us to link the resistance drift to a time-dependent increase in the Schottky barrier height. These findings provide valuable insights, pinpointing the primary contributor to resistance drift in PCM devices: the Schottky barrier height for hole injection at the interface. This underscores the significance of contacts (interface) in the electrical manifestation of drift in PCM devices. Thermionic emission ; Materials science ; Schottky barrier ; Schottky diode ; Optoelectronics ; Context (archaeology) ; Phase-change memory ; Neuromorphic engineering ; Thermal conduction ; Nanotechnology ; Engineering physics ; Electron ; Physics ; Computer science ; Composite material Phase-change materials and chalcogenides ; Advanced Memory and Neural Computing ; Transition Metal Oxide Nanomaterials
Authors: Iman Tahmasbian | Matthew N. McMillan | Jonathan Kok | Anthony J. Courtney
Source: Reviews in Fish Biology and Fisheries (article, 2024-01-04)
Field: Chemistry — Analytical Chemistry

Underwater hyperspectral imaging technology has potential to differentiate and monitor scallop populations Abstract Accurate and low-impact monitoring of scallop abundance is critical for stock assessment, especially in sensitive habitats. The possibility of using low-impact hyperspectral imaging (HSI) for differentiating scallop species in the marine environment was investigated. Live saucer ( Ylistrum balloti ) and mud ( Ylistrum pleuronectes ) scallops (N = 31) were scanned inside a sea simulator using a visible to near infrared (400–1000 nm) line-scanner HSI camera. Partial least square discriminant analysis (PLS-DA) was trained to distinguish between the species using their spectral signatures. Important wavelengths were identified and new models were developed using these wavelengths to reduce the model complexity and potentially increase the imaging speed when applied under at-sea conditions. The PLS-DA model distinguished between saucer and mud scallops using any area of the left valve that was exposed above the sediments, with 90.73% accuracy when all 462 available wavelengths were used. Using the subset of important wavelengths (N = 13) reduced the classification accuracy to 84%. Overall, our results showed that HSI has potential for detecting, distinguishing and counting commercially important saucer scallops for low-impact monitoring and resource management, and to complement RGB imaging that relies solely on morphological properties. Graphical abstract Hyperspectral imaging ; Scallop ; Underwater ; Benthic zone ; Biology ; Wavelength ; Remote sensing ; Fishery ; Oceanography ; Geology ; Optics ; Physics Spectroscopy and Chemometric Analyses ; Identification and Quantification in Food ; Isotope Analysis in Ecology
Authors: Srinivasan Rajaram | Thirugnanam Subbiah | A. Felix Sahayaraj | Jenish Iyyadurai
Source:  (article, 2024-02-04)
Field: Materials Science — Polymers and Plastics

Transforming Agricultural Waste into Sustainable Composite Materials: Mechanical Properties of Tamarindus Fruit Fiber (TFF)-Reinforced Polylactic Acid Composites Natural fiber-based polymer composite has great potential and is in high demand due to its high specific strength, low carcinogenic nature and economic market value. Tamarindus Fruit Fiber (TFF) has low density, high tensile strength and is easily available. It is one of the industrial waste materials. Polylactic acid (PLA) possesses an entangled coherence with fiber, since it is more compatible. A sample was prepared by integrating TFF as fiber and PLA as the binding agent. The fiber variations in all samples were 10 to 50 wt.% step by 10 wt.%. A pure PLA sample was also fabricated for the purpose of comparison. Mechanical properties such as tensile strength, flexural strength, impact and hardness have been evaluated. It was revealed that TFF reinforcement increased the mechanical properties of the samples. The highest mechanical properties were observed in Sample S5, which had 40 wt.% TFF and 60 wt.% PLA. Fracture failure was found using fractographic analysis. In conclusion, this study demonstrates the potential of utilizing TFF as an agricultural waste product for enhancing the mechanical properties of biodegradable polymer composites. These sustainable compositions of materials have been used for many applications in various industries, including packaging, automotive, and construction, while also providing an environmentally friendly solution for agricultural waste products. Polylactic acid ; Composite material ; Materials science ; Composite number ; Agricultural waste ; Fiber ; Waste management ; Polymer ; Engineering Natural Fiber Reinforced Composites
Authors: Bo‐Wen Shen | Leena R. Pade | Péter Nemes
Source: Journal of Proteome Research (article, 2024-09-26)
Field: Chemistry — Spectroscopy

Data-Independent Acquisition Shortens the Analytical Window of Single-Cell Proteomics to Fifteen Minutes in Capillary Electrophoresis Mass Spectrometry Separation in single-cell mass spectrometry (MS) improves molecular coverage and quantification; however, it also elongates measurements, thus limiting analytical throughput to study large populations of cells. Here, we advance the speed of bottom-up proteomics by capillary electrophoresis (CE) high-resolution mass spectrometry (MS) for single-cell proteomics. We adjust the applied electrophoresis potential to readily control the duration of electrophoresis. On the HeLa proteome standard, shorter separation times curbed proteome detection using data-dependent acquisition (DDA) but not data-independent acquisition (DIA) on an Orbitrap analyzer. This DIA method identified 1161 proteins vs 401 proteins by the reference DDA within a 15 min effective separation from single HeLa-cell-equivalent (∼200 pg) proteome digests. Label-free quantification found these exclusively DIA-identified proteins in the lower domain of the concentration range, revealing sensitivity improvement. The approach also significantly advanced the reproducibility of quantification, where ∼76% of the DIA-quantified proteins had <20% coefficient of variation vs ∼43% by DDA. As a proof of principle, the method allowed us to quantify 1242 proteins in subcellular niches in a single, neural-tissue fated cell in the live <i>Xenopus laevis</i> (frog) embryo, including many canonical components of organelles. DIA integration enhanced throughput by ∼2-4 fold and sensitivity by a factor of ∼3 in single-cell (subcellular) CE-MS proteomics. Mass spectrometry ; Chromatography ; Proteomics ; Capillary electrophoresis ; Capillary electrophoresis–mass spectrometry ; Chemistry ; Window (computing) ; Data acquisition ; Analytical Chemistry (journal) ; Computer science ; Biochemistry ; Electrospray ionization ; World Wide Web Advanced Proteomics Techniques and Applications ; Single-cell and spatial transcriptomics ; Biosensors and Analytical Detection
Authors: Leijinyu Zhou | Hongbo Wu | Tingting Jing | Tianhao Li | Jinsheng Li | Lijuan Kong | Lina Zhou
Source: Agronomy (article, 2024-02-22)
Field: Chemistry — Analytical Chemistry

Estimation of Relative Chlorophyll Content in Lettuce (Lactuca sativa L.) Leaves under Cadmium Stress Using Visible—Near-Infrared Reflectance and Machine-Learning Models Chlorophyll content is a crucial assessment parameter in the growth monitoring of lettuce, particularly in cases when it is affected by disease. Accurate estimation of chlorophyll content is beneficial for early detection and prevention of diseases and holds significant importance in practical production. To construct a model for estimating the chlorophyll content in lettuce leaves under cadmium stress, this study utilized lettuce as the experimental material. The visible–near-infrared reflectance spectra of lettuce leaves, as well as the relative chlorophyll content of the leaves, were detected and analyzed under different concentrations of cadmium stress. Subsequently, an inversion model for estimating the relative chlorophyll content in lettuce leaves was established. First, to determine the optimal spectral preprocessing method, eight techniques are utilized: Savitzky–Golay smoothing (SG), multiplicative scatter correction (MSC), standard normal variable transformation (SNV), mean normalization (MN), baseline offset (B), detrending (D), gap derivatives—first derivative (FD), and gap derivatives—second derivative (SD). These methods are used to preprocess the spectra and establish a partial least squares regression (PLSR) monitoring model. The optimal spectral preprocessing method is then selected. Next, the feature bands are extracted from the preprocessed spectral data using the correlation coefficient method. Finally, the selected feature bands will be combined with support vector regression (SVR) to establish a chlorophyll content estimation model using a training-to-testing set ratio of 4:1. The results showed that the PLSR model established after preprocessing with detrending (D) had the highest accuracy, with the coefficient of determination (Rv2) and root mean squared error (RMSEv) values of 0.87 and 1.16, respectively. The feature bands selected by the correlation coefficient method were used to establish SVR models for estimating the chlorophyll content of lettuce leaves under cadmium stress, with the highest accuracy being achieved by the genetic algorithm (GA)–SVR model. It can be seen that near-infrared spectroscopy technology provides a scientific basis for rapid, nondestructive, and accurate detection of lettuce diseases and stress. Lactuca ; Cadmium ; Reflectivity ; Infrared ; Chlorophyll ; Stress (linguistics) ; Remote sensing ; Horticulture ; Environmental science ; Botany ; Chemistry ; Biology ; Geology ; Optics ; Physics Spectroscopy and Chemometric Analyses ; Leaf Properties and Growth Measurement ; Remote Sensing in Agriculture
Authors: Pei Zeng | Yuting Zhou | Chonghao Zhang | Jie Yao | Meiyan Pan | Yifei Fu | Hao Chen | Guanying Chen | Qian Zhao | Xun Guan | Mengjie Zheng
Source: Scientific Reports (article, 2024-10-28)
Field: Materials Science — Electronic, Optical and Magnetic Materials

Nanostructures/TiN layer/Al2O3 layer/TiN substrate configuration-based high-performance refractory metasurface solar absorber Metasurface solar absorber serves as a kind of important component for green energy devices to convert solar electromagnetic waves into thermal energy. In this work, we design a new solar light absorber configuration that incorporates the titanium nitride substrate, aluminum oxide layer, titanium nitride layer, and the topmost refractory nanostructures. The metasurface absorber based on this configuration can achieve an average spectral absorption of over 91% and a total solar radiation absorption of 91.5% at ultra-wide wavelengths of 300-2500 nm. It is discovered that the excellent performance of the proposed metasurface absorber is attributed to the synergistic effects of surface plasmonic effect and Fabry-Pérot (FP) cavity resonance by comprehensive analysis of the simulated field distributions. Furthermore, the effect of geometrical parameter of the proposed configuration on absorber performance is studied, indicating the proposed configuration possesses a large fabrication tolerance. Moreover, the proposed configuration is not sensitive to the polarization direction and the angle of incident light. It is also found that the use of other refractory metal materials and other shapes as the topmost absorbent nanostructures also have good results with this configuration. This work can offer a universal platform for constructing and guiding the design of refractory metasurface solar absorbers. Tin ; Layer (electronics) ; Nanostructure ; Materials science ; Refractory (planetary science) ; Substrate (aquarium) ; Optoelectronics ; Nanotechnology ; Composite material ; Metallurgy ; Biology Metamaterials and Metasurfaces Applications ; Energy Harvesting in Wireless Networks ; Advanced Antenna and Metasurface Technologies
Authors: Henri Lösel | Navid Shakiba | René Bachmann | Soeren Wenck | Phat Le Tan | Marina Creydt | Stephan Seifert | Thomas Hackl | Markus Fischer
Source: Food Analytical Methods (article, 2024-01-30)
Field: Chemistry — Analytical Chemistry

Rapid testing in the food industry: the potential of Fourier transform near-infrared (FT-NIR) spectroscopy and spatially offset Raman spectroscopy (SORS) to detect raw material defects in hazelnuts (Corylus avellana L.) Abstract The detection of raw material defects, e.g., due to incorrect or excessively long storage, is an important issue in incoming goods inspections in the food industry. Fast and easy-to-use analytical methods for evaluating the usability of raw materials are particularly important. In this study, the applicability of Fourier transform near-infrared (FT-NIR) spectroscopy and spatially offset Raman spectroscopy (SORS) for the detection of raw material defects was evaluated. For this purpose, six hazelnut batches stored at different temperatures, humidity levels, and storage times were used as examples in this pilot study. Classification models of samples before and after the different physical treatments show that the resulting changes can be detected by FT-NIR spectroscopy and SORS at elevated temperature and humidity. When one of the storage parameters is increased, FT-NIR spectroscopy is also useful for detecting differences between sample groups. In contrast, SORS cannot distinguish between pre- and post-stored samples when only one of the storage parameters is increased, making SORS unsuitable for incoming inspection of nuts. FT-NIR spectroscopy analysis is also a fast application, because freeze-drying of the sample material prior to analysis is not required as the results before and after freeze-drying are comparable. Combining the FT-NIR spectroscopy and SORS data in a low-level data fusion improved the classification models for samples stored at low storage temperatures, suggesting that the two methods provide complementary information. In summary, analyzing nuts with FT-NIR spectroscopy and SORS, as shown for hazelnuts, has the potential to identify abnormal samples during incoming goods inspections. Fourier transform infrared spectroscopy ; Raman spectroscopy ; Chemistry ; Near-infrared spectroscopy ; Spectroscopy ; Fourier transform spectroscopy ; Analytical Chemistry (journal) ; Fourier transform ; Offset (computer science) ; Infrared spectroscopy ; Infrared ; Chromatography ; Optics ; Organic chemistry ; Physics ; Computer science Spectroscopy and Chemometric Analyses ; Spectroscopy Techniques in Biomedical and Chemical Research ; Essential Oils and Antimicrobial Activity
Authors: Siobhán Kelly | Jia‐Lynn Tham | Kate McKeever | Eugène Dillon | David O’Connell | Dimitri Scholz | Jeremy C. Simpson | Kevin E. O’Connor | Tanja Narančić | Gerard Cagney
Source: Molecular & Cellular Proteomics (article, 2024-04-10)
Field: Materials Science — Biomaterials

Comprehensive Proteomics Analysis of Polyhydroxyalkanoate (PHA) Biology in Pseudomonas putida KT2440: The Outer Membrane Lipoprotein OprL is a Newly Identified Phasin Pseudomonas putida KT2440 is an important bioplastic-producing industrial microorganism capable of synthesizing the polymeric carbon-rich storage material, polyhydroxyalkanoate (PHA). PHA is sequestered in discrete PHA granules, or carbonosomes, and accumulates under conditions of stress, for example, low levels of available nitrogen. The pha locus responsible for PHA metabolism encodes both anabolic and catabolic enzymes, a transcription factor, and carbonosome-localized proteins termed phasins. The functions of phasins are incompletely understood but genetic disruption of their function causes PHA-related phenotypes. To improve our understanding of these proteins, we investigated the PHA pathways of P.putida KT2440 using three types of experiments. First, we profiled cells grown in nitrogen-limited and nitrogen-excess media using global expression proteomics, identifying sets of proteins found to coordinately increase or decrease within clustered pathways. Next, we analyzed the protein composition of isolated carbonosomes, identifying two new putative components. We carried out physical interaction screens focused on PHA-related proteins, generating a protein-protein network comprising 434 connected proteins. Finally, we confirmed that the outer membrane protein OprL (the Pal component of the Pal-Tol system) localizes to the carbonosome and shows a PHA-related phenotype and therefore is a novel phasin. The combined datasets represent a valuable overview of the protein components of the PHA system in P.putida highlighting the complex nature of regulatory interactions responsive to nutrient stress. Pseudomonas putida ; Polyhydroxyalkanoates ; Biology ; Biochemistry ; Proteomics ; Catabolism ; Bacterial outer membrane ; Phenotype ; Function (biology) ; Enzyme ; Cell biology ; Gene ; Bacteria ; Genetics ; Escherichia coli biodegradable polymer synthesis and properties ; Enzyme Production and Characterization ; Biofuel production and bioconversion
Authors: Arfan Ali | Abdul Rauf Bhatti | Akhtar Rasool | Fazal Rehman | Muhammad Amjad Khan | Ahmed Ali | Abdulkerim Sherefa
Source: Scientific Reports (article, 2024-08-31)
Field: Materials Science — Materials Chemistry

Performance analysis of high voltage disc insulators with different profiles in clean and polluted environments using flashover, withstand voltage tests and finite element analysis Severe pollution-induced flashovers on insulators present a pressing challenge to power system safety. The frequent failure of high-voltage insulators, particularly in the polluted environments of Pakistan, poses a critical concern. This paper investigates the impact of insulator profile on reducing pollution flashovers, testing two designs as per IEC standard 60383 and simulated using the Finite Element Method in COMSOL Multiphysics®. The test results revealed that deep under-ribs insulators exhibited a 5.008% reduction in flashover voltage, while alternating shed insulators experienced a 3.233% decrease in polluted conditions compared to clean conditions. Notably, under both clean and polluted conditions, alternating shed insulators consistently outperformed deep under-ribs insulators, with a 25.377% higher flashover voltage in clean conditions and a 27.400% superiority in polluted conditions. Computational analysis through the Finite Element Method in COMSOL Multiphysics shows a consistent pattern in potential distribution with increasing insulator count, but the presence of a pollution layer introduces spikes in the electric field distribution, validating experimental results. These findings highlight the superior performance of alternating shed insulators, especially in polluted environments. Multiphysics ; Insulator (electricity) ; Arc flash ; Finite element method ; Voltage ; High voltage ; Materials science ; Electric field ; Structural engineering ; Environmental science ; Engineering ; Composite material ; Electrical engineering ; Physics High voltage insulation and dielectric phenomena ; Power Transformer Diagnostics and Insulation ; Lightning and Electromagnetic Phenomena