jablonkagroup/rise_ai_scientists huggingface dataset:
Authors: Roberta Cristina de Souza | Leonardo Meirelles da Silva | Bruna Angela Buratti | Sabrina Carra | Maicon Varella Flores | Bruna Maria Saorin Puton | Marina Rigotti | Mirian Salvador | Eloane Malvessi | Francys Kley Vieira Moreira | Clarice Steffens | Eunice Valduga | Jamile Zeni
Source: 3 Biotech (article, 2024-01-01)
Field: Materials Science — Biomaterials

Purification, bioactivity and application of maltobionic acid in active films Chitosan ; Nuclear chemistry ; Solubility ; Chemistry ; Citric acid ; Chelation ; Biochemistry ; Organic chemistry Nanocomposite Films for Food Packaging ; Medicinal Plants and Neuroprotection ; Pineapple and bromelain studies
Authors: Andrius Čeponis | Dalius Mažeika
Source: Actuators (article, 2024-11-25)
Field: Materials Science — General Materials Science

Rotary–Linear Type Piezoelectric Actuator Based on Double-Elliptical Stator This paper introduces a novel piezoelectric actuator designed for precise linear and rotational movements of a cylindrical slider-rotor. The actuator’s design features two elliptical frames interconnected by two plates, with a cylindrical contact situated on the top of the upper plate to facilitate the motion or rotation of the slider. Two piezoelectric multilayer transducers are housed within each elliptical frame and are used to excite vibrations of the elliptical frames using two harmonic signals with a phase difference of π/2 and varying excitation schemes. This excitation pattern generates elliptical motion trajectories of the contact in two orthogonal planes, enabling both linear and rotational displacements of the slider-rotor. Numerical and experimental investigations were conducted to validate the performance and accuracy of the actuator. Additionally, harmonic response and transient analysis were performed to investigate elliptical motion trajectories of the contact in perpendicular planes under various excitation schemes and frequencies. The results confirm that the rotational and linear motions of the slider-rotor can be independently controlled. The actuator achieved a maximum rotational speed of 163.1 RPM and a maximum linear speed of 41.4 mm/s, with a corresponding peak output torque and force of 236.1 mN·mm and 368.1 mN, respectively. A resolution measurements showed that the actuator can achieve an angular resolution of 1.02 mrad and a linear resolution of 53.8 µm. Actuator ; Stator ; Type (biology) ; Piezoelectricity ; Control theory (sociology) ; Mathematics ; Physics ; Acoustics ; Engineering ; Computer science ; Mechanical engineering ; Electrical engineering ; Artificial intelligence ; Geology Material Properties and Applications ; Piezoelectric Actuators and Control ; Advanced MEMS and NEMS Technologies
Authors: Riddhiman K. Garge | Valerie Lynch | Rose Fields | Silvia Casadei | S Best | Jeremy Stone | Matthew W. Snyder | Connor Kubo | Arata Wakimoto | Zukai Liu | Chris D McGann | Jay Shendure | Lea M. Starita | Nobuhiko Hamazaki | Devin K. Schweppe
Source: bioRxiv (Cold Spring Harbor Laboratory) (preprint, 2024-09-07)
Field: Chemistry — Spectroscopy

The proteomic landscape and temporal dynamics of mammalian gastruloid development Gastrulation is the highly coordinated process by which the early embryo breaks symmetry, establishes germ layers and a body plan, and sets the stage for organogenesis. As early mammalian development is challenging to study <i>in vivo,</i> stem cell-derived models have emerged as powerful surrogates, <i>e.g.</i> human and mouse gastruloids. However, although single cell RNA-seq (scRNA-seq) and high-resolution imaging have been extensively applied to characterize such <i>in vitro</i> embryo models, a paucity of measurements of protein dynamics and regulation leaves a major gap in our understanding. Here, we sought to address this by applying quantitative proteomics to human and mouse gastruloids at four key stages of their differentiation (naïve ESCs, primed ESCs, early gastruloids, late gastruloids). To the resulting data, we perform network analysis to map the dynamics of expression of macromolecular protein complexes and biochemical pathways, including identifying cooperative proteins that associate with them. With matched RNA-seq and phosphosite data from these same stages, we investigate pathway-, stage- and species-specific aspects of translational and post-translational regulation, <i>e.g.</i> finding peri-gastrulation stages of human and mice to be discordant with respect to the mitochondrial transcriptome vs. proteome, and nominating novel kinase-substrate relationships based on phosphosite dynamics. Finally, we leverage correlated dynamics to identify conserved protein networks centered around congenital disease genes. Altogether, our data (https://gastruloid.brotmanbaty.org/) and analyses showcase the potential of intersecting <i>in vitro</i> embryo models and proteomics to advance our understanding of early mammalian development in ways not possible through transcriptomics alone. Dynamics (music) ; Computational biology ; Biology ; Physics Advanced Proteomics Techniques and Applications ; Animal Genetics and Reproduction ; Pancreatic function and diabetes
Authors: E.P. Antonova
Source: Electrochemical Materials and Technologies (article, 2024-09-20)
Field: Materials Science — Materials Chemistry

H/D isotope effects in the electrical conductivity of LaScO <sub>3</sub> -based solid state proton-conducting electrolyte Electrical conductivity of a solid proton-conducting electrolyte with the composition of La0.9Sr0.1ScO3 is studied depending on temperature and oxygen partial pressure in the atmospheres, humidified with H2O and D2O. Isotope H/D effect in the electrical conductivity is observed at the temperatures below 700 °C in air conditions. For reductive atmosphere, the isotope effect is pronounced for the whole investigated temperature range. Based on the pO2-dependencies of electrical conductivity, the transport numbers of ions and electron holes are determined. The ionic transport numbers in the H2O-containing atmosphere are found to be higher than the corresponding values for the D2O-containing atmosphere for all investigated conditions. The possible role of protons (deuterons) in the oxygen ion transport is pointed out. The kinetic isotope effect is found to be predominant in the conditions under study. Electrolyte ; Proton ; Conductivity ; Solid-state ; Isotope ; Electrical resistivity and conductivity ; Materials science ; Chemistry ; Inorganic chemistry ; Analytical Chemistry (journal) ; Physics ; Physical chemistry ; Environmental chemistry ; Nuclear physics ; Electrode Advancements in Solid Oxide Fuel Cells ; Catalysis and Oxidation Reactions ; Solid-state spectroscopy and crystallography
Authors: Yu Zheng | Weiting Peng | Xu-Peng Wen | Qiquan Wan
Source: Heliyon (article, 2024-06-01)
Field: Chemistry — Spectroscopy

Protein interactome analysis of ATP1B1 in alveolar epithelial cells using Co-Immunoprecipitation mass spectrometry and parallel reaction monitoring assay Our study provides new insights into the role of ATP1B1 in alveolar epithelial cells and indicates that six proteins, in particular HSP90AB1, may be key proteins interacting with and regulating ATP1B1, which might be potential targets for the treatment of acute respiratory distress syndrome. Interactome ; Immunoprecipitation ; Mass spectrometry ; Chemistry ; Proteomics ; Gas chromatography–mass spectrometry ; Chromatography ; Molecular biology ; Computational biology ; Cell biology ; Biochemistry ; Biology ; Gene Mass Spectrometry Techniques and Applications ; Metabolomics and Mass Spectrometry Studies ; Protein Structure and Dynamics
Authors: Amit Nain | Akshat Joshi | Souvik Debnath | Saswat Choudhury | Jobin Thomas | Jitendra Satija | Chih‐Ching Huang | Kaushik Chatterjee
Source: ChemRxiv (preprint, 2024-03-12)
Field: Materials Science — Biomaterials

4D printed nanoengineered super bioactive hydrogel scaffold with programmable deformation for potential bifurcated vascular channel construction Four-dimensional (4D) printing of hydrogel enabled the fabrication of complex scaffold geometries out of static parts. Although current 4D fabrication strategies are promising for creating vascular parts such as tubes, developing branched networks or tubular junctions is still challenging. Here, for the first time, a 4D printing approach is employed to fabricate T-shaped perfusable bifurcation using an extrusion-based multi-material 3D printing process. An alginate/methylcellulose-based dual-component hydrogel system (with defined swelling behavior) is nanoengineered with carbonized alginate (~100 nm) to introduce anti-oxidative, anti-inflammatory, and anti-thrombotic properties and shape-shifting properties. A computational model to predict shape deformations in the printed hydrogels with defined infill angles was designed and further validated experimentally. Shape deformations of the 3D-printed flat sheets were achieved by ionic cross-linking. An undisrupted perfusion of a dye solution through a T-junction with minimal leakage mimicking blood flow through vessels is also demonstrated. Moreover, human umbilical vein endothelial and fibroblast cells seeded with printed constructs show intact morphology and excellent cell viability. Overall, developed strategy paves the way for manufacturing self-actuated vascular bifurcations with remarkable anti-thrombotic properties to potentially treat coronary artery diseases. Scaffold ; 3d printed ; Deformation (meteorology) ; Channel (broadcasting) ; Materials science ; Nanotechnology ; Biomedical engineering ; Composite material ; Computer science ; Engineering ; Telecommunications Electrospun Nanofibers in Biomedical Applications ; Tissue Engineering and Regenerative Medicine ; 3D Printing in Biomedical Research
Authors: Alessandro De Vita | Roberto Sant | Vincent Polewczyk | G. van der Laan | N. B. Brookes | Tai Kong | R. J. Cava | G. Rossi | Giovanni Vinai | G. Panaccione
Source: Nano Letters (article, 2024-01-29)
Field: Materials Science — Materials Chemistry

Evidence of Temperature-Dependent Interplay between Spin and Orbital Moment in van der Waals Ferromagnet VI<sub>3</sub> van der Waals materials provide a versatile toolbox for the emergence of new quantum phenomena and fabrication of functional heterostructures. Among them, the trihalide VI<sub>3</sub> stands out for its unique magnetic and structural landscape. Here we investigate the spin and orbital magnetic degrees of freedom in the layered ferromagnet VI<sub>3</sub> by means of temperature-dependent X-ray absorption spectroscopy and X-ray magnetic circular and linear dichroism. We detect localized electronic states and reduced magnetic dimensionality, due to electronic correlations. We furthermore provide experimental evidence of (a) an unquenched orbital magnetic moment (up to 0.66(7) μ<sub>B</sub>/V atom) in the ferromagnetic state and (b) an instability of the orbital moment in the proximity of the spin reorientation transition. Our results support a coherent picture where electronic correlations give rise to a strong magnetic anisotropy and a large orbital moment and establish VI<sub>3</sub> as a prime candidate for the study of orbital quantum effects. Condensed matter physics ; Ferromagnetism ; Magnetic moment ; van der Waals force ; Magnetic circular dichroism ; Chemistry ; Electronic structure ; Spin (aerodynamics) ; Physics ; Quantum mechanics ; Spectral line 2D Materials and Applications ; Advanced Condensed Matter Physics ; Perovskite Materials and Applications
Authors: Junhu Kan | Liyun Nie | Zenglu Mi | Xiaojin Liu | Daping Xu | Luke R. Tembrock | Zhiqiang Wu | Zhou Hong
Source: Forestry Research (article, 2024-01-01)
Field: Chemistry — Organic Chemistry

Insights into &lt;i&gt;Aquilaria&lt;/i&gt; phylogenetics through comparative plastomic resources The plastid is an essential organelle for its role in photosynthesis and energy production and its genomic information is always employed as important evolutionary markers to explore the relationship among species. Agarwood (<i>Aquilaria</i>), prized for its aromatic blend, finds extensive use in various cultures as incense and perfume. Despite its high economic importance, the phylogenetic status among <i>Aquilaria</i> based on plastomes remains ambiguous due to the lack of available plastomic resources. To bridge this knowledge gap, 22 <i>Aquilaria</i> plastomes were newly sequenced, similar variation patterns in this genus were determined, including a shared 16 bp extension of the <i>rps19</i> gene and seven highly variable regions. The analysis highlighted the highest prevalence of the A/T motif among simple sequence repeats in these plastomes. Further phylogenetic analysis revealed <i>Aquilaria</i>'s phylogenetic implications with an expanded dataset. This comprehensive plastomic resource not only enhances our understanding of <i>Aquilaria</i> evolution but also presents potential molecular markers for DNA barcoding. Phylogenetics ; Biology ; Genetics Wood and Agarwood Research ; Identification and Quantification in Food ; Medicinal Plants and Neuroprotection
Authors: Bernhard Brutscher
Source: Magnetic Resonance (article, 2024-09-12)
Field: Chemistry — Spectroscopy

PRESERVE: adding variable flip-angle excitation to transverse relaxation-optimized NMR spectroscopy We introduce the "Polarization Restoring Excitation SEquence foR Versatile Experiments" (PRESERVE) pulse sequence element, allowing variable flip-angle adjustment in 2D <mml:math xmlns:mml="http://www.w3.org/1998/Math/MathML"><mml:msup><mml:mi></mml:mi> <mml:mn>1</mml:mn></mml:msup> </mml:math> H- <mml:math xmlns:mml="http://www.w3.org/1998/Math/MathML"><mml:msup><mml:mi></mml:mi> <mml:mn>15</mml:mn></mml:msup> </mml:math> N and <mml:math xmlns:mml="http://www.w3.org/1998/Math/MathML"><mml:msup><mml:mi></mml:mi> <mml:mn>1</mml:mn></mml:msup> </mml:math> H- <mml:math xmlns:mml="http://www.w3.org/1998/Math/MathML"><mml:msup><mml:mi></mml:mi> <mml:mn>13</mml:mn></mml:msup> </mml:math> C transverse-relaxation-optimized-spectroscopy (TROSY)-type correlation experiments. PRESERVE-TROSY exploits a remarkable array of up to nine orthogonal coherence-transfer pathways, showcasing the remarkable potential of spin manipulations achievable through the design and optimization of nuclear magnetic resonance (NMR) pulse sequences. Flip angle ; Pulse sequence ; Excitation ; Polarization (electrochemistry) ; Nuclear magnetic resonance spectroscopy ; Nuclear magnetic resonance ; Coherence (philosophical gambling strategy) ; Relaxation (psychology) ; Spectroscopy ; Transverse plane ; Pulse (music) ; Physics ; Materials science ; Molecular physics ; Chemistry ; Optics ; Magnetic resonance imaging ; Physical chemistry ; Quantum mechanics Advanced NMR Techniques and Applications ; NMR spectroscopy and applications ; Advanced MRI Techniques and Applications
Authors: Xiong Li | Lisha Jiang | Heng‐Ning Deng | Yu Qi | Wen‐Bin Ju | Xiao-Juan Chen | Yu Feng | Bo Xu
Source: Horticulture Research (article, 2024-12-17)
Field: Chemistry — Organic Chemistry

High-resolution genome assembly and population genetic study of the endangered maple <i>Acer pentaphyllum</i> (Sapindaceae): implications for conservation strategies <i>Acer pentaphyllum</i> Diels (Sapindaceae), a highly threatened maple endemic to the dry-hot valleys of the Yalong River in western Sichuan, China, represents a valuable resource for horticulture and conservation. This study presents the first chromosomal-scale genome assembly of <i>A. pentaphyllum</i> (~626 Mb, 2<i>n</i> = 26), constructed using PacBio HiFi and Hi-C sequencing technologies. Comparative genomic analyses revealed significant recent genomic changes through rapid amplification of transposable elements, particularly long terminal repeat retrotransposons, coinciding with the dramatic climate change during recent uplift of the Hengduan Mountains. Genes involved in photosynthesis, plant hormone signal transduction, and plant-pathogen interaction showed expansion and/or positive selection, potentially reflecting adaptation to the species' unique dry-hot valley habitat. Population genomic analysis of 227 individuals from 28 populations revealed low genetic diversity (1.04 ± 0.97 × 10<sup>-3</sup>) compared to other woody species. Phylogeographic patterns suggest an unexpected upstream colonization along the Yalong River, while Quaternary climate fluctuations drove its continuous lineage diversification and population contraction. Assessment of genetic diversity, inbreeding, and genetic load across populations revealed concerning levels of inbreeding and accumulation of deleterious mutations in small, isolated populations, particularly those at range edges (TKX, CDG, TES). Based on these results, we propose conservation strategies, including the identification of management units and recommendations for genetic rescue. These findings not only facilitate the conservation of <i>A. pentaphyllum</i> but also serve as a valuable resource for future horticultural development and as a model for similar studies on other endangered plant species adapted to extreme environments. Biology ; Endangered species ; Sapindaceae ; Aceraceae ; Population ; Maple ; Evolutionary biology ; Ecology ; Demography ; Habitat Plant-Derived Bioactive Compounds ; Genetic diversity and population structure ; Plant Taxonomy and Phylogenetics
Authors: Gabriel Asher | Mimoun Cadosh Delmar | J. M. Campbell | Jack Geremia | Timothy Kassis
Source: ChemRxiv (preprint, 2024-06-06)
Field: Chemistry — Spectroscopy

LSM1-MS2: A Foundation Model for MS/MS, Encompassing Chemical Property Predictions, Search and de novo Generation We present LSM1-MS2, a pre-trained self-supervised foundation model designed for tandem mass spectrometry (MS/MS) utilizing a transformer architecture with custom tokenization for masked MS2 peak reconstruction. Our model is fine-tuned on smaller, labeled datasets for tasks such as compound property prediction, spectral matching, and de novo molecular generation. LSM1-MS2 demonstrates superior performance compared to traditional supervised models, achieving high accuracy with minimal labeled data. It outperforms conventional methods in database lookups and molecular query retrievals and shows promising results in the opening field of de novo molecular generation. The model's efficiency in spectral lookup tasks, with significantly reduced evaluation times, underscores its potential for large-scale applications. Our findings highlight the transformative capability of self-supervised pre-training in enhancing the predictive power of models for mass spectrometry, particularly in data-limited scenarios. The success of LSM1-MS2 in property prediction, database spectral lookup, and molecular generation paves the way for its application in metabolomics and drug discovery, facilitating robust and scalable analysis with reduced data requirements. Foundation (evidence) ; Property (philosophy) ; Geography ; Philosophy ; Epistemology ; Archaeology Advanced Proteomics Techniques and Applications ; Analytical Chemistry and Chromatography ; Metabolomics and Mass Spectrometry Studies
Authors: Sławomir Jarosz | Zbigniew Pakulski
Source: Advances in carbohydrate chemistry and biochemistry (review, 2024-01-01)
Field: Chemistry — Organic Chemistry

The roadmap for sucrose – a very inexpensive raw product Chemistry ; Product (mathematics) ; Raw material ; Organic chemistry ; Mathematics Carbohydrate Chemistry and Synthesis ; Enzyme Production and Characterization ; Glycosylation and Glycoproteins Research
Authors: Keren Iudanov | Noy B. Nechmad | Albert Poater | N. Gabriel Lemcoff
Source: Angewandte Chemie International Edition (article, 2024-09-21)
Field: Chemistry — Organic Chemistry

Selective Cross‐Metathesis Versus Ring‐Closing Metathesis of Terpenes, Taking the Path Less Travelled A diiodo ruthenium olefin metathesis pre-catalyst was employed to achieve remarkably selective cross-metathesis reactions of prenylated 1,6-dienes, effectively overcoming the entropically favored intramolecular ring-closing metathesis. This reaction was investigated using Density Functional Theory (DFT) computations and fine-tuned through the application of a Design of Experiments (DoE) approach. The potential of this innovative process was demonstrated through the unprecedented functionalization of various terpene natural products via cross-metathesis, resulting in the synthesis of new derivatives in a single step. Ring-closing metathesis ; Metathesis ; Intramolecular force ; Ruthenium ; Olefin metathesis ; Salt metathesis reaction ; Ring-opening metathesis polymerisation ; Chemistry ; Catalysis ; Combinatorial chemistry ; Organic chemistry ; Polymerization Synthetic Organic Chemistry Methods ; Chemical Synthesis and Analysis ; Asymmetric Synthesis and Catalysis
Authors: Markus J. Buehler
Source: arXiv (Cornell University) (preprint, 2024-05-29)
Field: Materials Science — Biomaterials

Cephalo: Multi-Modal Vision-Language Models for Bio-Inspired Materials Analysis and Design We present Cephalo, a series of multimodal vision large language models (V-LLMs) designed for materials science applications, integrating visual and linguistic data for enhanced understanding. A key innovation of Cephalo is its advanced dataset generation method. Cephalo is trained on integrated image and text data from thousands of scientific papers and science-focused Wikipedia data demonstrates can interpret complex visual scenes, generate precise language descriptions, and answer queries about images effectively. The combination of a vision encoder with an autoregressive transformer supports multimodal natural language understanding, which can be coupled with other generative methods to create an image-to-text-to-3D pipeline. To develop more capable models from smaller ones, we report both mixture-of-expert methods and model merging. We examine the models in diverse use cases that incorporate biological materials, fracture and engineering analysis, protein biophysics, and bio-inspired design based on insect behavior. Generative applications include bio-inspired designs, including pollen-inspired architected materials, as well as the synthesis of bio-inspired material microstructures from a photograph of a solar eclipse. Additional model fine-tuning with a series of molecular dynamics results demonstrate Cephalo's enhanced capabilities to accurately predict statistical features of stress and atomic energy distributions, as well as crack dynamics and damage in materials. Modal ; Computer science ; Artificial intelligence ; Natural language processing ; Materials science Diatoms and Algae Research
Authors: Mizuho Yabushita | Ryota Osuga | Yoshinao Nakagawa | Satoshi Suganuma | Kiyotaka Nakajima | Keiichi Tomishige
Source: CrystEngComm (article, 2024-01-01)
Field: Chemistry — Inorganic Chemistry

Overview of intentional formation of paired heteroatom sites in zeolite frameworks Intentional placement of two heteroatoms in close proximity in zeolite frameworks is an important task for developing fine-tuned catalysts and ion exchangers and has been achieved via three different strategies. Heteroatom ; Zeolite ; Chemistry ; Materials science ; Organic chemistry ; Catalysis Zeolite Catalysis and Synthesis ; Catalysis and Hydrodesulfurization Studies ; Mesoporous Materials and Catalysis