jablonkagroup/rise_ai_scientists huggingface dataset:
Authors: Andrew T. Rajczewski | J. Alfredo Blakeley‐Ruiz | Annaliese Meyer | Simina Vintila | Matthew R. McIlvin | Tim Van Den Bossche | Brian C. Searle | Timothy J. Griffin | Mak A. Saito | Manuel Kleiner | Pratik Jagtap
Source: PROTEOMICS (article, 2025-04-10)
Field: Chemistry — Spectroscopy

Data‐Independent Acquisition Mass Spectrometry as a Tool for Metaproteomics: Interlaboratory Comparison Using a Model Microbiome Mass spectrometry (MS)-based metaproteomics is used to identify and quantify proteins in microbiome samples, with the frequently used methodology being data-dependent acquisition mass spectrometry (DDA-MS). However, DDA-MS is limited in its ability to reproducibly identify and quantify lower abundant peptides and proteins. To address DDA-MS deficiencies, proteomics researchers have started using Data-independent acquisition mass spectrometry (DIA-MS) for reproducible detection and quantification of peptides and proteins. We sought to evaluate the reproducibility and accuracy of DIA-MS metaproteomic measurements relative to DDA-MS using a mock community of known taxonomic composition. Artificial microbial communities of known composition were analyzed independently in three laboratories using DDA- and DIA-MS acquisition methods. In this study, DIA-MS yielded more protein and peptide identifications than DDA-MS in each laboratory for the particular instruments and software parameters chosen. In addition, the protein and peptide identifications were more reproducible in all laboratories and provided an accurate quantification of proteins and taxonomic groups in the samples. We also identified some limitations of current DIA tools when applied to metaproteomic data, highlighting specific needs to improve DIA tools enabling analysis of metaproteomic datasets from complex microbiomes. Ultimately, DIA-MS represents a promising strategy for MS-based metaproteomics due to its large number of detected proteins and peptides, reproducibility, deep sequencing capabilities, and accurate quantitation. Metaproteomics ; Mass spectrometry ; Proteomics ; Computational biology ; Metagenomics ; Chromatography ; Computer science ; Chemistry ; Biology ; Biochemistry Advanced Proteomics Techniques and Applications ; Mass Spectrometry Techniques and Applications ; Metabolomics and Mass Spectrometry Studies
Authors: Daniel A. Erlanson | S.K. Burley | D. Fearon | James S. Fraser | Dale F. Kreitler | Maria Cristina Nonato | Naoki Sakai | J. Wollenhaupt | M.S. Weiss
Source: Nature Communications (review, 2025-05-05)
Field: Materials Science — Materials Chemistry

Where and how to house big data on small fragments Fragment screening by crystallography has recently skyrocketed. Multiple synchrotrons have built specialized screening platforms, established workflows, and assembled compound libraries. Crystallographic fragment screening is now widely accessible to groups that had previously not considered the approach. While hundreds of crystallographic fragment-screening campaigns have been conducted in the last few years, most of the underlying data have neither been published nor made publicly accessible. This perspective highlights the importance of establishing effective mechanisms for preserving large and often heterogeneous groups of datasets intrinsic to crystallographic fragment-screening campaigns, thereby ensuring their accessibility for advancing research and enabling applications such as training AI-based models. Big data ; Data science ; Computational biology ; Computer science ; Biology ; Data mining Enzyme Structure and Function ; Forensic and Genetic Research ; Research Data Management Practices
Authors: Qiqi Liu | Zhanxia Gao | Xiangyun Zhang | Qiannan Duan | Yue Zhang | Adam C. Midgley | Jiao Li | Ruming Liu | Mingsheng Zhu | Deling Kong | Jie Zhuang | Xinglu Huang
Source: Nature Communications (article, 2025-01-28)
Field: Materials Science — Materials Chemistry

Assembly of Genetically Engineered Ionizable Protein Nanocage-based Nanozymes for Intracellular Superoxide Scavenging Nanozymes play a pivotal role in mitigating excessive oxidative stress, however, determining their specific enzyme-mimicking activities for intracellular free radical scavenging is challenging due to endo-lysosomal entrapment. In this study, we employ a genetic engineering strategy to generate ionizable ferritin nanocages (iFTn), enabling their escape from endo-lysosomes and entry into the cytoplasm. Specifically, ionizable repeated Histidine-Histidine-Glutamic acid (9H<sub>2</sub>E) sequences are genetically incorporated into the outer surface of human heavy chain FTn, followed by the assembly of various chain-like nanostructures via a two-armed polyethylene glycol (PEG). Utilizing endosome-escaping ability, we design iFTn-based tetrameric cascade nanozymes with high superoxide dismutase- and catalase-mimicking activities. The in vivo protective effects of these ionizable cascade nanozymes against cardiac oxidative injury are demonstrated in female mouse models of cardiac ischemia-reperfusion (IR). RNA-sequencing analysis highlight the crucial role of these nanozymes in modulating superoxide anions-, hydrogen peroxide- and mitochondrial functions-relevant genes in IR injured cardiac tissue. These genetically engineered ionizable protein nanocarriers provide opportunities for developing ionizable drug delivery systems. Nanocages ; Superoxide ; Intracellular ; Scavenging ; Chemistry ; Genetically engineered ; Biochemistry ; Cell biology ; Biology ; Gene ; Catalysis ; Antioxidant ; Enzyme Advanced Nanomaterials in Catalysis ; Nanoplatforms for cancer theranostics ; Electrochemical sensors and biosensors
Authors: Xiao-Qi Han | Zhenfeng Ouyang | Peng‐Jie Guo | Hao 浩 Sun 孙 | Zhiyuan Gao | Zhong-Yi Lu
Source: Chinese Physics Letters (article, 2025-03-07)
Field: Materials Science — Materials Chemistry

InvDesFlow: An AI-Driven Materials Inverse Design Workflow to Explore Possible High-Temperature Superconductors Abstract The discovery of new superconducting materials, particularly those exhibiting high critical temperature ( T c ), has been a vibrant area of study within the field of condensed matter physics. Conventional approaches primarily rely on physical intuition to search for potential superconductors within the existing databases. However, the known materials only scratch the surface of the extensive array of possibilities within the realm of materials. Here, we develop InvDesFlow, an artificial intelligence (AI)-driven materials inverse design workflow that integrates deep model pre-training and fine-tuning techniques, diffusion models, and physics-based approaches (e.g., first-principles electronic structure calculation) for the discovery of high- T c superconductors. Utilizing InvDesFlow, we have obtained 74 thermodynamically stable materials with critical temperatures predicted by the AI model to be T c ≥ 15 K based on a very small set of samples. Notably, these materials are not contained in any existing dataset. Furthermore, we analyze trends in our dataset and individual materials including B 4 CN 3 (at 5 GPa) and B 5 CN 2 (at ambient pressure) whose T c s are 24.08 K and 15.93 K, respectively. We demonstrate that AI technique can discover a set of new high- T c superconductors, outline its potential for accelerating discovery of the materials with targeted properties. Workflow ; Inverse ; Superconductivity ; Materials science ; Computer science ; Nuclear engineering ; High-temperature superconductivity ; Inverse temperature ; Engineering physics ; Condensed matter physics ; Physics ; Thermodynamics ; Engineering ; Database ; Mathematics Machine Learning in Materials Science ; Inorganic Chemistry and Materials ; Inorganic Fluorides and Related Compounds
Authors: R. Nithya | Sunaina S. Patil | Hari Prasad Dasari | Harshini Dasari | S. Nethaji
Source: Scientific Reports (article, 2025-01-07)
Field: Materials Science — Materials Chemistry

Potential of CoMn2O4 spinel as soot oxidation catalyst and its kinetics thereof Efficient catalysts for soot oxidation are critical for mitigating environmental pollution. In this study, CoMn<sub>2</sub>O<sub>4</sub> spinel catalysts were synthesised using reverse co-precipitation and co-precipitation methods to evaluate their performance in soot oxidation and kinetic behaviour. All samples exhibited a tetragonal phase (XRD) and spherical morphology with rough surfaces (SEM). Raman spectroscopy confirmed structural disorder and oxygen vacancies, while XPS analysis revealed the presence of low-valence Mn ions, facilitating oxygen vacancy formation critical for soot oxidation. Additionally, the co-existence of Co and Mn ions contributed to a synergistic effect, enhancing the catalytic properties of the spinel structure. The reverse co-precipitation method produced a catalyst with a higher concentration of oxygen vacancies and active oxygen species among the samples. This sample demonstrated superior catalytic performance, achieving a T<sub>50%</sub> of 424 °C, low activation energy (153 kJ/mol) and pre-exponential factor (25 min<sup>- 1</sup>). Soot TPR analysis highlighted the role of catalyst reducibility, while thermogravimetric analysis revealed that activation energy and pre-exponential factors were influenced by surface composition. These findings provide valuable insights into the design of efficient catalysts for soot oxidation, emphasising the importance of synthesis methods and surface characteristics. Catalysis ; Spinel ; Soot ; X-ray photoelectron spectroscopy ; Materials science ; Chemical engineering ; Activation energy ; Oxygen ; Tetragonal crystal system ; Kinetics ; Thermogravimetric analysis ; Inorganic chemistry ; Chemistry ; Phase (matter) ; Physical chemistry ; Metallurgy ; Combustion ; Organic chemistry Catalytic Processes in Materials Science ; Catalysis and Oxidation Reactions ; Thermal and Kinetic Analysis
Authors: Jafar Abdi | Golshan Mazloom | Yeojoon Yoon
Source: Scientific Reports (article, 2025-05-12)
Field: Materials Science — Materials Chemistry

Surface modification of MXene using cationic CTAB surfactant for adsorptive elimination of cefazolin antibiotic from water The increasing prevalence of pharmaceutical contaminants in aquatic ecosystems has raised significant environmental concerns, necessitating the development of efficient removal strategies. In this study, Ti<sub>3</sub>C<sub>2</sub>T<sub>x</sub> MXene was synthesized and modified with cetyltrimethylammonium bromide (CTAB) to enhance its adsorption performance for cefazolin (CFZ), a widely used cephalosporin antibiotic. The structural and physicochemical properties of the modified MXene were comprehensively characterized using FESEM, EDS, FTIR, XRD, BET, and zeta potential analyses. Adsorption experiments were conducted under various operational conditions, including pH, contact time, adsorbent dosage, and initial CFZ concentration. The results revealed that CTAB modification significantly improved the adsorption capacity by increasing interlayer spacing and enhancing the accessibility of active adsorption sites. The optimized adsorbent (MC-0.9) exhibited a maximum CFZ removal efficiency of 96.3% and an adsorption capacity of 481.5 mg/g under optimal conditions: an adsorbent dosage of 0.1 g/L, a solution pH of 5, a contact time of 60 min, and an initial CFZ concentration of 50 mg/L. Kinetic and isotherm modeling indicated that the batch adsorption process followed the pseudo-second-order kinetic model and fitted well with the Langmuir isotherm, suggesting monolayer adsorption. Additionally, the presence of co-existing anions adversely affected adsorption efficiency, following the order CO<sub>3</sub><sup>2-</sup> > Cl<sup>-</sup> > SO<sub>4</sub><sup>2</sup><sup>-</sup> > NO<sub>3</sub><sup>-</sup>. The adsorption mechanism was primarily governed by electrostatic interactions, π-cation interactions, and hydrogen bonding. Furthermore, the CTAB-modified MXene demonstrated robust recyclability, maintaining high efficiency over four consecutive cycles, highlighting its potential as a promising adsorbent for the removal of pharmaceutical pollutants from wastewater. Adsorption ; Langmuir adsorption model ; Bromide ; Cefazolin ; Pulmonary surfactant ; Chemistry ; Zeta potential ; Chemical engineering ; Cationic polymerization ; Nuclear chemistry ; Inorganic chemistry ; Organic chemistry ; Nanoparticle ; Antibiotics MXene and MAX Phase Materials ; Advanced biosensing and bioanalysis techniques ; Graphene and Nanomaterials Applications
Authors: N. Errahmany | M. Nounah | S. Yaqouti | Aziza Nounah | R. Touir | El Hassan El Kafssaoui
Source: Next research. (article, 2025-01-14)
Field: Chemistry — Organic Chemistry

Quinoxaline derivatives as corrosion inhibitors: Development of predictive machine using partial least squares and random forest (PLS/RF) models based on quantitative structure-activity relationship (QSAR) Quantitative structure–activity relationship ; Partial least squares regression ; Random forest ; Quinoxaline ; Chemistry ; Biological system ; Artificial intelligence ; Computer science ; Machine learning ; Organic chemistry ; Stereochemistry ; Biology Synthesis and Biological Evaluation ; Corrosion Behavior and Inhibition ; Chemistry and Chemical Engineering
Authors: Samira Husen Alamudi | Yong‐An Lee
Source: RSC Advances (review, 2025-01-01)
Field: Chemistry — Spectroscopy

Design strategies for organelle-selective fluorescent probes: where to start? Monitoring physiological changes within cells is crucial for understanding their biological aspects and pathological activities. Fluorescent probes serve as powerful tools for this purpose, offering advantageous characteristics over genetically encoded probes. While numerous organelle-selective probes have been developed in the past decades, several challenges persist. This review explores the strategies and key factors contributing to the successful rationale design of these probes. We systematically discuss the typical mode of cellular uptake generally adopted by fluorescent probes and provide a detailed examination of the key factors to consider in design rationale from two perspectives: the properties of the target organelle and the physicochemical properties of the probe itself. Additionally, recent examples of organelle-targeted probes are presented, along with a discussion of the current challenges faced by fluorescent probes in the field. Organelle ; Fluorescence ; Key (lock) ; Nanotechnology ; Chemistry ; Computer science ; Cell biology ; Biophysics ; Biology ; Materials science ; Physics Molecular Sensors and Ion Detection ; Photochromic and Fluorescence Chemistry ; Click Chemistry and Applications
Authors: Jan Tauchen | Lukáš Huml | Michal Jurášek | Joe M. Regenstein | Fatih Özoğul
Source: Frontiers in Pharmacology (review, 2025-07-22)
Field: Chemistry — Organic Chemistry

Synthetic and semi-synthetic antioxidants in medicine and food industry: a review Oxidative stress is recognized as both a causative and contributing factor in many human diseases. As a result, significant research has been devoted to the development of synthetic and semi-synthetic antioxidants (ATs). This review summarizes the therapeutic potential of synthetic ATs, explores their possible clinical applications, and highlights novel structural modifications aimed at improving their pharmacological properties. Additionally, it presents ideas for refining current antioxidant testing methodologies. Despite the ongoing research, the therapeutic efficacy of synthetic ATs remains ambiguous for several reasons. These include the following: therapeutic benefits resulting from non-antioxidant mechanisms, insufficient dosage to elicit an antioxidant effect, poor oral bioavailability, a narrow therapeutic index, or toxicity that precludes clinical use. Nevertheless, some compounds, such as ebselen, edaravone, MitoQ10, and potentially N-acetylcysteine, have shown promising results. However, further studies are needed to confirm their efficacy and clarify whether their therapeutic effects are truly mediated through antioxidant mechanisms. Dietary antioxidants have achieved relatively higher clinical success, although their toxicity has also led to the withdrawal of some agents. One emerging therapeutic strategy involves inhibition of NADPH oxidase (NOX) enzymatic activity, with compounds such as ebselen, S17834, and GKT137831 showing potential across various disease models. Efforts to enhance antioxidant properties through molecular modifications, using advanced technologies such as prodrug strategies, nanotechnology, polymer complexation, targeted delivery systems, or conversion into inhalable formulations, have yielded variable success. Still, confirming the clinical relevance of newly developed antioxidants will require a paradigm shift in the testing approaches. Future studies must better define the molecular context of antioxidant action, including the following: which biomolecules are being protected, the specific radical species targeted, the tissue and subcellular distribution of the antioxidant, and how levels of endogenous antioxidants and reactive oxygen species (ROS) change post-administration (e.g., within the mitochondria). Despite extensive research, only a few synthetic antioxidants, such as edaravone, are currently used in clinical practice. Currently, no new antioxidant drugs are expected to receive regulatory approval in the near future. Ebselen ; Context (archaeology) ; Pharmacology ; Antioxidant ; Medicine ; Prodrug ; Biotechnology ; Chemistry ; Biology ; Biochemistry ; Glutathione peroxidase ; Superoxide dismutase Free Radicals and Antioxidants ; Vitamin C and Antioxidants Research ; Biochemical Acid Research Studies
Authors: Pengfei Dang | Jinlong Hu | Yuehui Xian | Cheng Li | Yumei Zhou | Xiangdong Ding | Jun Sun | Dezhen Xue
Source: Advanced Materials (article, 2025-01-06)
Field: Materials Science — Materials Chemistry

Elastocaloric Thermal Battery: Ultrahigh Heat‐Storage Capacity Based on Generative Learning‐Designed Phase‐Change Alloys An elastocaloric thermal battery based on generative learning-designed phase-change alloys is developed to facilitate the efficient recycling of low-temperature waste heat. This battery stores thermal energy as latent heat in a phase-change alloy and releases it on demand through applied stress at ambient temperature. Alloy compositions and corresponding processing parameters, tailored to desired transformation characteristics, are efficiently discovered through a generative learning-enabled inverse design framework, which converts the hand-drawn target heat flow curve into tangible compositional and processing designs. The designed battery achieves an ultrahigh figure of merit for heat storage capacity, surpassing existing thermal batteries, and boasts a work-to-heat efficiency exceeding 9. This opens up exciting possibilities for manipulating thermal energy in diverse applications such as low-temperature waste heat recycling, solar thermal collection, and heat management in electric vehicles and data center facilities. The inverse design framework promises to expedite the development of various materials with tailored property curves. Materials science ; Thermal energy storage ; Phase change ; Heat capacity ; Phase-change material ; Latent heat ; Battery (electricity) ; Thermal ; Engineering physics ; Thermodynamics Advanced Thermoelectric Materials and Devices ; Phase Change Materials Research ; Advanced Battery Materials and Technologies
Authors: Meng He | Yanmei Lin | Yujia Huang | Yunhui Fang | Xiaopeng Xiong
Source: Molecules (review, 2025-04-04)
Field: Materials Science — Biomaterials

Research Progress of the Preparation of Cellulose Ethers and Their Applications: A Short Review Cellulose ethers (CEs), synthesized through the etherification of cellulose, have emerged as indispensable "green additives" in our modern industries, earning the moniker of industrial "monosodium glutamate" due to their unparalleled multifunctionality. Unlike traditional petroleum-based modifiers, CEs offer a unique combination of renewability, low toxicity, and tunable properties (e.g., water retention, thickening, and stimuli-responsiveness), making them pivotal for advancing sustainable construction practices. This review presents an overview of the preparation methods of various CEs and the applications of CEs especially in concrete and mortars as well as corresponding mechanisms. We systematically analyze the preparation methodologies (homogeneous vs. heterogeneous processes) and highlight the effect of molecular determinants (degree of substitution, molecular weight, functional groups) on the performances of CEs. CEs can enhance the workability and other properties of concrete and mortars primarily by acting as water-retaining and thickening agents to mitigate rapid water loss, improve hydration efficiency and cohesion. The effects of CEs on the delay of hydration and microstructure of concrete and mortars are also analyzed and highlighted. Beyond construction, we reviewed the current and emerging CE applications in biomedicine, tissue-engineering, petroleum industry and food engineering, highlighting their cross-disciplinary potential. This review provides some insights into the structure-property-application relationships of CEs and their brief historical developments, offering guidance for optimizing their utilizations especially in sustainable construction practices. Thickening ; Cellulose ; Petroleum industry ; Cohesion (chemistry) ; Materials science ; Nanotechnology ; Biochemical engineering ; Environmental science ; Chemistry ; Polymer science ; Engineering ; Chemical engineering ; Organic chemistry ; Environmental engineering Advanced Cellulose Research Studies ; Surface Modification and Superhydrophobicity ; Innovations in Concrete and Construction Materials