jablonkagroup/rise_ai_scientists huggingface dataset:
Authors: Xiaoqing He | Shiyu Ying | Yi Xu | Zhuo Gao | Yi Wu | Yu Wu | Mengbo Wu
Source: The Plant Journal (article, 2025-08-01)
Field: Materials Science — Materials Chemistry

Nanoselenium application improves post‐harvest fruit quality and disease resistance in tomato Fruits constitute a vital component of a nutritious diet but are highly perishable, contributing substantially to food waste. Consequently, identifying safe and edible biological agents to enhance product quality and extend shelf life is of critical importance. In this study, we demonstrate that exogenous pre-harvest foliar application with nanoselenium (nano-Se) in tomato enhances fruit quality, prolongs fruit shelf life, and enhances the resistance of tomato fruit to Botrytis cinerea infection. Transcriptomic analysis revealed coordinated upregulation of genes associated with quality maintenance and modulation of phytohormone-related pathways. Notably, nano-Se treatment induced expression patterns of ripening-related genes that resembled those triggered by ethylene (ET) but were antagonistic to the effects of 1-MCP. We further demonstrated that although SlMYC2 knockout increased susceptibility to B. cinerea, nano-Se application restored resistance in a manner independent of the SlMYC2-associated jasmonic acid signaling pathway, implicating ET as the primary regulatory mechanism. Collectively, these findings support nano-Se as a promising biostimulant for reducing post-harvest losses while preserving the nutritional and sensory quality of tomato fruits. Jasmonic acid ; Botrytis cinerea ; Biology ; Ripening ; Postharvest ; Plant disease resistance ; Shelf life ; Horticulture ; Transcriptome ; Biotechnology ; Gene ; Botany ; Food science ; Gene expression ; Biochemistry Nanoparticles: synthesis and applications ; Postharvest Quality and Shelf Life Management ; Plant Stress Responses and Tolerance
Authors: Marta Štindlová | Václav Peroutka | Kamila Zdeňková | Simona Lencová
Source: Folia Microbiologica (article, 2025-07-28)
Field: Materials Science — Biomaterials

Assessing metabolic activity of yeast biofilm-forming cells on nanofibrous materials using MTT assay Nanofibrous materials (NMs), widely used in medical and food industry applications, are highly susceptible to colonisation by microorganisms, including yeasts. Although yeasts can form dense biofilms, methods for studying their metabolic activity remain limited. This study is the first to apply the MTT assay, a standardised method for assessing cell metabolic activity, to evaluate the metabolic activity of yeast biofilm-forming cells on electrospun NMs. First, the biofilm formation of Candida albicans and Saccharomyces cerevisiae on NMs electrospun from polycaprolactone (PCL), polylactic acid (PLA), and polyamide (PA) was examined. Then, key parameters of the MTT assay were systematically evaluated: (i) the addition of glucose to the MTT solution, (ii) the presence of menadione in the MTT solution, and (iii) the incubation time with the MTT solution. The addition of glucose was not proven necessary; however, in some cases, it may help distinguish the number of metabolically active cells. Based on this study, we recommend incubation with an MTT solution containing menadione for 2 h. To verify the protocol, colony-forming unit (CFU) enumeration was employed as a reference method. As differences between the results of these two methods were observed, the MTT assay should be complemented by other standardised methods. Nevertheless, the refined protocol offers a solid basis for investigating interactions between NMs and yeasts. MTT assay ; Biofilm ; Yeast ; Chemistry ; Microbiology ; Metabolic activity ; Menadione ; Biochemistry ; Biology ; In vitro ; Bacteria Electrospun Nanofibers in Biomedical Applications ; Nanocomposite Films for Food Packaging
Authors: Kaleolani S. Ogura | Sirisak Singsen | Dmitri Leo Mesoza Cordova | Jinyu Liu | Griffin M. Milligan | Diana Lopez | Tyler A. Kerr | Joseph W. Ziller | Rahul Rao | Luis A. Jauregui | Elizabeth Lee | Maxx Q. Arguilla
Source: Matter (article, 2025-12-08)
Field: Materials Science — Materials Chemistry

Persistent metallicity and systematic vacancies in tellurium-based quasi-one-dimensional Chevrel-type single crystals Vacancy defect ; Anisotropy ; Characterization (materials science) ; Dirac (video compression format) ; Crystal (programming language) ; Crystal structure 2D Materials and Applications ; Topological Materials and Phenomena ; Iron-based superconductors research
Authors: Zhen Zhang | K. D. Belashchenko | Vladimir Antropov
Source: arXiv (Cornell University) (preprint, 2025-01-08)
Field: Materials Science — Materials Chemistry

High-Throughput Studies of Novel Magnetic Materials in Borides Borides are a versatile material family with various properties for valuable applications. Conventional magnetism, such as ferromagnetism and antiferromagnetism in borides, have been extensively studied. However, research on unconventional magnetism in borides where quantum effects are dominant is scarce. Here, we implement a high-throughput workflow combining first-principles calculations, materials prediction, and magnetic properties calculations to discover novel magnetism and magnetic materials in borides. Successfully applying the workflow, we report three families of novel magnetic borides, including two families of borides exhibiting quantum magnetism. One is a family of dimerized quantum magnets among YCrB$_4$-type borides, which provides a rare platform for studying the spin-gap quantum critical point. The other is a family of altermagnets among FeMo$_2$B$_2$-type borides, extending the magnetic orderings exhibited by borides beyond conventional ferromagnetism and antiferromagnetism. We also predict a family of magnetic laminate transition metal borides, known as the MAB phases, in the AlFe$_2$B$_2$-type family, which provide pure-phase or alloying candidates for studying magnetocaloric materials and the associated magnetic transitions. The workflow is expected to be used in further studies of novel magnetism and magnetic materials. Throughput ; Business ; Computer science ; Telecommunications Boron and Carbon Nanomaterials Research ; Rare-earth and actinide compounds ; Diamond and Carbon-based Materials Research
Authors: Phumin Simpalipan | Sittiporn Pattaradilokrat | Vorthon Sawaswong | Korawich Uthayopas | Kittima Phutthawong | Pongchai Harnyuttanakorn
Source: ScienceAsia (article, 2025-01-01)
Field: Chemistry — Organic Chemistry

Genetic analysis of glutathione synthetase of Plasmodium falciparum, a potential candidate for antimalarial drug development Glutathione synthetase (GS) is an enzyme involved in the synthesis of glutathione, a molecule protecting the parasite from heme-induced cell damage and potentially affecting antimalarial drug responses.Currently, the design of in silico assay for chemical screen is impeded due to the lack of complete gene sequences from endemic populations of malaria parasites.This study aimed to investigate the genetic diversity of the gs gene in P. falciparum populations in Thailand and worldwide.The catalog of the gs gene of P. falciparum was generated, consisting of sequences of 223 P. falciparum isolates from 15 countries.Population genetic analyses were conducted using the sequences of gs in the database to reveal the allelic and nucleotide diversity.In addition, the neutrality tests were performed to determine the evidence of natural selection.The analysis of the gs sequences in the database identified 55 unique haplotypes, characterized by 41 SNPs and 1 indel mutation.The most common gs haplotype was the gs1 which was found in all P. falciparum populations.Sequence analysis also revealed low genetic diversity at the gs locus, likely due to negative selection.In conclusion, the present study establishes the catalog of P. falciparum gs gene and provides basic genetic diversity information for antimalarial drug design and for monitoring the effects of antimalarial drugs on parasite populations. Plasmodium falciparum ; Glutathione ; Drug ; Biology ; Drug development ; Malaria ; Computational biology ; Pharmacology ; Biochemistry ; Enzyme ; Immunology Synthesis and Characterization of Heterocyclic Compounds ; Synthesis and biological activity
Authors: Jiawei Chen | Yang Lü | Wei Zhang | Yili Liu | Yongqi Wei | Li Wang | Mingfeng Jiang | Biao Li
Source: Animal Bioscience (article, 2025-09-30)
Field: Chemistry — Spectroscopy

Integrated Peptidogenomics Decoding Yak Non-Conventional Peptides: Functional Mapping and Biopotential Mining of Genetic Resources In conclusion, this study demonstrates that a substantial portion of the yak genome can be translated into molecules with biological functions which is highly significant for functional genome research, and these unique hidden molecules will provide basic data for future biomedical development and plateau disease treatment. Genome ; Decoding methods ; YAK ; Human genome ; Genetic data Advanced Proteomics Techniques and Applications
Authors: Peter Bellotti | Zuliang Chen | Charles David Warren | Jacob B. Geri
Source: Analytical Chemistry (article, 2025-07-21)
Field: Chemistry — Spectroscopy

Gas Phase Separation of Modified Peptides for Activity-Based Protein Profiling Profiling the reactivity of the proteome with amino-acid level resolution requires the identification and quantification of reacted peptides in the presence of abundant unmodified peptides. Affinity-based approaches use solid sorbents such as streptavidin beads to enrich modified peptides in a solution but are step-intensive and suffer from analyte losses. Here, we describe timShift, a gas phase, in-spectrometer approach for enhanced reactive amino acid profiling, which exploits modification-induced alteration of peptide physical properties. A dicationic, aerodynamic, cysteine-reactive reagent increases the ion mobility of labeled peptides, physically separating them from unmodified 1<sup>+</sup> and 2<sup>+</sup> peptide ions and enabling their targeted sequencing and quantification in whole proteomes. Using these reagents, we profiled >8,200 reactive cysteine sites, demonstrated higher sensitivity versus desthiobiotin/streptavidin enrichment at low protein input, and performed activity-based protein profiling of covalent fragments and selective electrophiles in a 96-well plate format. Chemistry ; Chromatography ; Profiling (computer programming) ; Gas phase ; Organic chemistry Mass Spectrometry Techniques and Applications ; Advanced Proteomics Techniques and Applications ; Analytical Chemistry and Chromatography
Authors: Yaji P. Maseshin Yaji P. Maseshin | Gundu D. Terfa | G. B. Nyior | Ikpambese K. Kumaden
Source: International Journal of Engineering Applied Sciences and Technology (article, 2025-09-01)
Field: Chemistry — Organic Chemistry

EVALUATION OF INHIBITIVE PROPERTIESOF ORGANIC NANO-PARTICLES OBTAINED FROM THE BARKS OF FICUS THONNINGII BLENDED WITH HYPTIS SUAVEOLENS EXTRACT AS CORROSION INHIBITOR ON MILD STEEL IN 1M H2SO4 SOLUTION Globally, researchers are looking for low-cost and good-performance solutions to prevent and reduce corrosion. Over the years traditional (chemical) corrosion inhibitors have been used to prevent corrosion. Although these inhibitors have good efficiency, their use has been limited due to high cost, toxicity, non-biodegradability, and health hazards. This study, evaluated the inhibitive properties of nanoparticles obtained from the barks of Ficusthonningii (FT) blended with Hyptis Suaveolens L Poit (HSLP) extract as corrosion inhibitor on mild steel. Leave extracts of HSLP and nano particles prepared from the stem barks of FT were used as corrosion inhibitor for mild steel in 1m H2SO4 using weight loss technique. The study was conducted at room and elevated temperatures of 313, 323, 333 and 343K. The test period was varied from 48 to 336 hours at 48 hours interval, at room temperature and 3 hours at each elevated temperature.The experiments were performed with extract concentrations of 0.1, 0.2, 0.3, 0.4 and 0.5 g/L. with 0.5 g of nano particles from barks of FT blended with HSLP in each concentration. Weight loss measurements were used to compute the corrosion rate and inhibition efficiencies in the various concentrations. The results showed that the corrosion rates increased with time of immersion in the absence of inhibitor but decreased with inhibitor concentration and in the blends of the HSLP/FT nano particles at room and elevated temperatures, while inhibition efficiency increased with increase in inhibitor concentration and in the blends of the HSLP/FT nano particles at room temperature but decreased with temperature rise. Inhibition efficiencies of 93.54 and 96.01% at 0.5 g/L were obtained for HSLP and HSLP/FT respectively at room temperature. At elevated temperatures of 313K to 343K inhibition efficiencies reduced to a minimum of 70% at 0.5 g/L and temperature of 343K implying desorption of inhibitor at higher temperatures. Based on the results obtained, the study concluded that, the extract and blends with nano particles of FT acted as good inhibitors for mild steel corrosion in acidic medium with inhibition efficiencies above 70%. hence, these inhibitors can be used for corrosion control and prevention. Corrosion ; Corrosion inhibitor ; Nanoparticle ; Bark (sound) Inorganic and Organometallic Chemistry
Authors: Sang‐Hyo Kweon | Kota Kasatani | Isaku Kanno
Source: SSRN Electronic Journal (preprint, 2025-01-01)
Field: Materials Science — Materials Chemistry

Layer Configuration-Driven Phase Engineering of Sol-Gel Epitaxial Pb(Zr,Ti)O3 Thin Films for High Piezoelectricity on Silicon Substrate Silicon ; Materials science ; Substrate (aquarium) ; Piezoelectricity ; Epitaxy ; Layer (electronics) ; Phase (matter) ; Thin film ; Optoelectronics ; Sol-gel ; Chemical engineering ; Nanotechnology ; Composite material ; Chemistry ; Organic chemistry ; Engineering Ferroelectric and Piezoelectric Materials ; Liquid Crystal Research Advancements ; Synthesis and properties of polymers
Authors: Caroline S. Pereira | Sandrine Coquille | Céline Brochier‐Armanet | Fabio Sterpone | Dominique Madern
Source: Journal of Molecular Biology (article, 2025-11-20)
Field: Materials Science — Materials Chemistry

Unraveling the Link Between Thermal Adaptation and Latent Allostery in Malate Dehydrogenase From Methanococcales Malate dehydrogenase (MalDH) (EC.1.1.1.37) is an enzyme engaged in the central metabolism of cells, catalyzing the interconversion between oxaloacetate and malate using NADH or NADPH as coenzyme. These enzymes are particularly interesting models for studying how proteins adapt to physical and chemical environmental constraints. In this study, we investigated the molecular mechanisms that have enabled MalDHs to adapt to changes in temperature, using Methanococcales archaea as a model organism. We solved the crystal structure of ancestral MalDHs in these archaea. Structural comparison with present-day MalDHs such as those from Methanocaldococcus infernus (M. inf) and Methanocaldococcus jannaschii (M. jan), highlights the role salt-bridges in thermal adaptation. We also found that present-day MalDHs from M. inf and M. jan, show structural features that resemble the extended or compact states typical of allosteric lactate dehydrogenases. To test hypotheses about a possible link between thermal adaptation and the emergence of allosteric regulation, we characterized structurally two M. jan MalDH mesophilic-like mutants. Molecular dynamics simulations using the Wt M. jan and mutant MalDHs were used to rationalize the experimental data. The results indicate that uncompetent and competent catalytic site configurations are in an equilibrium that depends on temperature conditions. At low temperature the Wt M. jan MalDH select non-competent conformers, whereas high temperature favors active conformers. In contrast, the M. jan MalDH mutants explore competent conformers for catalysis at a lowest temperature, a phenomenon that fits well with their biochemical behavior. Our work reveals that thermal adaptation and evolution of allostery are strongly linked via the modulation of the protein conformational landscape. Allosteric regulation ; Malate dehydrogenase ; Conformational isomerism ; Allosteric enzyme ; Dehydrogenase ; Enzyme ; Mutant ; Adaptation (eye) ; Citrate synthase Enzyme Structure and Function ; Microbial metabolism and enzyme function ; Protein Structure and Dynamics
Authors: Diana Rivera Valentin | Marian Lakey | P Araque Arroyo | Yolanda García García | Fabiola Rodriguez | Yalimar Rivera | M. Patricia Rivera | Pablo Vivas | Yaritza Inostroza‐Nieves
Source: Journal of Biological Chemistry (article, 2025-05-01)
Field: Materials Science — Biomaterials

Abstract 1180 Development of Liposome-Based Therapeutics to Modulate Microglial Activation for Neurodegenerative Disease Treatment BACKGROUND: Microglia, the resident immune cells of the central nervous system (CNS), play a key role in immune defense and inflammatory responses in the brain. As primary modulators of neuroinflammation, microglia release proinflammatory cytokines, nitric oxide (NO), and reactive oxygen species (ROS) in response to various stimuli. While essential for immune response, these inflammatory processes contribute to the progression of neurodegenerative diseases such as Alzheimer's disease (AD) and Parkinson's disease (PD). Liposome ; Disease ; Neuroscience ; Microglia ; Pharmacology ; Medicine ; Neuroprotection ; Chemistry ; Biology ; Immunology ; Inflammation ; Biochemistry ; Internal medicine Nanoparticle-Based Drug Delivery
Authors: Thi Ngoc Anh Mai | Md. Shakhawath Hossain | Nhat Minh Nguyen | Yongliang Chen | Chaohao Chen | Xiaoxue Xu | Quang Thang Trịnh | Toan Dinh | Toan Trong Tran
Source: ArXiv.org (preprint, 2025-01-22)
Field: Materials Science — Materials Chemistry

Quantum Emitters in Hexagonal Boron Nitride: Principles, Engineering and Applications Solid-state quantum emitters, molecular-sized complexes releasing a single photon at a time, have garnered much attention owing to their use as a key building block in various quantum technologies. Among these, quantum emitters in hexagonal boron nitride (hBN) have emerged as front runners with superior attributes compared to other competing platforms. These attributes are attainable thanks to the robust, two-dimensional lattice of the material formed by the extremely strong B-N bonds. This review discusses the fundamental properties of quantum emitters in hBN and highlights recent progress in the field. The focus is on the fabrication and engineering of these quantum emitters facilitated by state-of-the-art equipment. Strategies to integrate the quantum emitters with dielectric and plasmonic cavities to enhance their optical properties are summarized. The latest developments in new classes of spin-active defects, their predicted structural configurations, and the proposed suitable quantum applications are examined. Despite the current challenges, quantum emitters in hBN have steadily become a promising platform for applications in quantum information science. Hexagonal boron nitride ; Boron nitride ; Nitride ; Materials science ; Hexagonal crystal system ; Nanotechnology ; Boron ; Engineering physics ; Optoelectronics ; Engineering ; Physics ; Chemistry ; Crystallography ; Graphene Boron and Carbon Nanomaterials Research ; Diamond and Carbon-based Materials Research ; Graphene research and applications
Authors: Xinyue Jing | Minxuan Chen | Xinli Ma | Xinrui Xu | Ning Wang | Kunpeng Niu | Xiaohan Chen | Yihao Wang | Jiayi Zhu | Jianguo Hou | Zhichao Wang
Source: Solids (article, 2025-09-01)
Field: Materials Science — Materials Chemistry

Electric Field-Enhanced SPR Sensors with AuNPs and CQDs for Rapid and Low-Detection-Limit Detection of Co2+ As a vital transition metal species, cobalt ions (Co2+) play a critical role in industrial and medical fields. However, uncontrolled release into ecosystems via industrial effluents presents significant environmental risks. To address this, a prism-coupled surface plasmon resonance (SPR) sensor chip was developed which enables simultaneous high sensitivity, wide detection range, and rapid detection of Co2+ under ultra-low detection limit conditions. By depositing a 50 nm Au film and AuNPs on a glass substrate, and integrating carboxyl-functionalized carbon quantum dots (CQDs), the chip achieved the detection range of 10−20 mol/L to 10−4 mol/L, and the response time was reduced from 21 min to 11 min under optimal electric field conditions (1.2 V, 0.15 mol/L electrolyte concentration). The sensor exhibits high selectivity, repeatability, and stability. It can be integrated with optofluidic technology to enable high-throughput microfluidic analysis, thereby facilitating further advancements in related research. Detection limit ; Limit (mathematics) ; Nanotechnology ; Field (mathematics) ; Materials science ; Electric field ; Optoelectronics ; Analytical Chemistry (journal) ; Chemistry ; Chromatography ; Physics ; Mathematics Carbon and Quantum Dots Applications ; Advanced biosensing and bioanalysis techniques ; Gas Sensing Nanomaterials and Sensors
Authors: Michel Brück | Michael Daume | Lennart Randau | José Vicente Gomes‐Filho
Source: bioRxiv (Cold Spring Harbor Laboratory) (preprint, 2025-08-02)
Field: Materials Science — Materials Chemistry

A Multi-Layered Transcriptomic Analysis Sheds Light on Antisense Transcription, RNA Processing, and SmAP Interactions in <i>Sulfolobus acidocaldarius</i> ABSTRACT The archaeal domain contains organisms that are well-adapted to extreme conditions and changes in their habitat. Post-transcriptional regulation plays a key role in environmental adaptation, including rapid molecular responses to stress conditions. To understand the importance of RNA-based post-transcriptional regulation for these processes, a comprehensive analysis of the presence and processing of regulatory RNAs, as well as their interactions with other RNAs and proteins, is indispensable. Here, we combine the analysis of several RNA sequencing approaches to reveal the presence of a set of novel non-coding RNAs (ncRNAs), their expression in various conditions, processing, and molecular interactions in the transcriptome of Sulfolobus acidocaldarius , a model organism for Archaea. We expand its annotation by 160 intergenic ncRNAs (sRNAs) and 990 antisense RNAs (asRNAs), add the location and motifs of over 6000 transcript processing sites, and determine the interaction of transcripts with Sm-like archaeal proteins (SmAPs). We determined the correlation between the expression patterns of asRNAs and their cognate mRNAs, suggesting transcript-based regulation patterns in gene expression, particularly in response to changing environmental conditions. Additionally, we observed differential binding preferences of SmAP1 and SmAP2 towards mRNA and ncRNAs, suggesting a distribution of regulating roles of these chaperones. Finally, we provide an overview of our post-transcriptional data analysis results, optimized for custom exploration, in the form of a web-based transcriptome atlas ( https://vicentebr.github.io/Sulfolobus_atlas/ ). IMPORTANCE Post-transcriptional regulation is a key control layer in gene expression. Yet, resources integrating asRNAs, RNA processing sites, and RNA-protein interactions are scarce for archaeal organisms. Here we combine multiple RNA-seq strategies and RIP-seq to expand the Sulfolobus acidocaldarius transcriptome with 990 asRNAs, thousands of transcript processing sites, and the interactomes of the essential RNA chaperones SmAP1 and SmAP2. Integrating the novel generated data for the re-analysis of heat-shock transcriptomics and proteomics reveals locus-specific antisense mechanisms that might help to explain the weak correlation between cellular RNA and protein levels reported previously. Moreover, our publicly accessible web atlas provides a community platform to explore these datasets and assist in the formulation of new hypotheses about archaeal RNA regulation. Sulfolobus acidocaldarius ; Transcription (linguistics) ; Transcriptome ; RNA ; Biology ; Computational biology ; Sulfolobus ; Genetics ; Gene ; Cell biology ; Archaea ; Gene expression Enzyme Structure and Function ; Genomics and Phylogenetic Studies ; Enzyme Production and Characterization