jablonkagroup/rise_ai_scientists huggingface dataset:
Authors: F Chakmehdouz Ghasemi | Cláudia Barata-Antunes | Yiannis Pyrris | Patrícia Ataíde | João Alves | Vítor Basto-Fernandes | Rosana Maria Abreu Alves | Ana Gonçalves | Margarida Casal | Wouter Van Genechten | Jana Nysten | Alistair J. P. Brown | Patrick Van Dijck | George Diallinas | Alexandros A. Pittis | Isabel Soares‐Silva | Sandra Paiva
Source: bioRxiv (Cold Spring Harbor Laboratory) (preprint, 2025-05-26)
Field: Chemistry — Spectroscopy

Expansion, functional diversification and gene fusion events in the Ato protein family Abstract Candida albicans , a commensal opportunistic pathogen, exhibits remarkable metabolic flexibility and adaptability to environmental changes. In glucose-limited niches, it utilizes alternative carbon sources such as carboxylic acids, which may influence its pathogenicity. In Saccharomyces cerevisiae , the uptake of monocarboxylates occurs through regulated plasma membrane (PM) transport proteins, such as Ato1 (Ady2), which belongs to the Acetate Uptake Transporter (AceTr) family. In C. albicans , these proteins are notably expanded, consisting of ten Ato-like proteins (ATO1-ATO10), whose functions remain unknown. Here, we investigated the role of Ato proteins in carboxylic acid utilization by C. albicans using in-silico and functional analysis. Our data revealed that several C. albicans Atos retain conserved AceTr motifs but possess distinct structural features, including differences in pore radius and binding sites for acetate and lactate. Expression analysis revealed that Ato1, Ato2, Ato3, and Ato6 exhibit distinct cellular localization and expression levels on the plasma membrane, depending on the presence or absence of monocarboxylates. Remarkably, deletion of ATO1 impaired Ato2 and Ato3 expression and caused ER retention of a distinct form of Ato2, suggesting a central regulatory role for Ato1 in the Ato transport system. Finally, we identified a novel Ato-related protein family in vertebrates. This family has three consecutive 6-helix transport domains and a unique C-terminal fusion with Sua5/YciO/YrdC, an enzyme involved in tRNA modification. Overall, our data suggests that the Ato protein family might play a critical role in the utilization of acetic or lactic acids in C. albicans . It also proposes potential functional redundancy among its members, which may contribute to rapid environmental adaptation and pathogenicity. Diversification (marketing strategy) ; Fusion protein ; Gene ; Genetics ; Computational biology ; Biology ; Business Advanced Proteomics Techniques and Applications ; Mass Spectrometry Techniques and Applications ; Enzyme Structure and Function
Authors: Emil Parth | Andrea Corradini | Weili Cui | Davide Romanin | C. Schuster | Clara Freytag | Lei Shi | Kazuhiro Yanagi | Matteo Calandra | Thomas Pichler
Source: Nature Communications (article, 2025-05-26)
Field: Chemistry — Organic Chemistry

Anharmonic effects control interaction of carbyne confined in carbon nanotubes shaping their vibrational properties The resonant Raman response is due to electronic and vibrational excitations. Confined carbyne is a novel one dimensional heterostructure consisting of the linear carbon chain and a hosting carbon nanotube in the bulk limit. The resonant Raman fingerprint of confined carbyne comes concomitant with several new features which can neither be assigned to the hosting tube, nor to the linear carbon chain. This identifies the tube-chain system as a true hybrid structure in which the spectrum is usually driven by modifications in the electronic excitations via charge transfer. We show that the electronic structure results from those of the two isolated systems and the spectral modifications are solely due to the anharmonic interactions between the tube and the chain. Our work establishes confined carbyne as the ideal test system to probe anharmonicity in one dimension and its implications on the resonant Raman response. Carbyne ; Anharmonicity ; Carbon nanotube ; Chemical physics ; Materials science ; Nanotechnology ; Carbon fibers ; Chemistry ; Physics ; Condensed matter physics ; Organic chemistry Fullerene Chemistry and Applications ; Diamond and Carbon-based Materials Research ; Boron and Carbon Nanomaterials Research
Authors: Juri Rappsilber | James E. Bruce | Colin Combe | Stephen D. Fried | Andrea Graziadei | Albert J. R. Heck | Claudio Iacobucci | Alexander Leitner | Karl Mechtler | Petr Novák | Francis J. O’Reilly | David C. Schriemer | Andrea Sinz | Florian Stengel | Konstantinos Thalassinos
Source: Molecular & Cellular Proteomics (article, 2025-06-26)
Field: Chemistry — Spectroscopy

A Roadmap for Improving Reliability and Data Sharing in Crosslinking Mass Spectrometry Crosslinking mass spectrometry (MS) can uncover protein-protein interactions and provide structural information on proteins in their native cellular environments. Despite its promise, the field remains hampered by inconsistent data formats, variable approaches to error control, and insufficient interoperability with global data repositories. Recent advances, especially in false discovery rate models and pipeline benchmarking, show that crosslinking MS data can reach a reliability that matches the demand of integrative structural biology. To drive meaningful progress, however, the community must agree on error estimation, open data formats, and streamlined repository submissions. This perspective highlights these challenges, clarifies remaining barriers, and frames practical next steps. Successful field harmonization will enhance the acceptance of crosslinking MS in the broader biological community and is critical for the dependability of the data, no matter where it is produced. Mass spectrometry ; Reliability (semiconductor) ; Chemistry ; Computer science ; Chromatography ; Physics Mass Spectrometry Techniques and Applications ; Metabolomics and Mass Spectrometry Studies ; Advanced Proteomics Techniques and Applications
Authors: Chenxiao Li | Jian Yu | Shaofeng Wang | Qinglong Zhao | Qian Song | Yanlei Xu
Source: Agronomy (article, 2025-06-21)
Field: Chemistry — Analytical Chemistry

Rapid and Accurate Measurement of Major Soybean Components Using Near-Infrared Spectroscopy This study addresses the urgent need for the rapid, non-destructive assessment of key soybean components, including moisture, fat, and protein, using near-infrared (NIR) spectroscopy. This study provides technical and theoretical support for achieving the efficient and accurate detection of major soybean components and for the development of portable near-infrared (NIR) instruments. Thirty soybean samples from diverse sources were collected, and 360 spectral measurements were acquired using a 900–1700 nm NIR spectrometer after grinding and standardized sampling. To improve model robustness, preprocessing strategies such as standard normal variate (SNV), multiplicative scatter correction (MSC), and Savitzky–Golay derivatives were applied. Feature selection was conducted using competitive adaptive reweighted sampling (CARS), successive projections algorithm (SPA), and uninformative variable elimination (UVE), followed by model construction with partial least squares regression (PLSR), support vector regression (SVR), and random forest (RF). Comparative analysis revealed that the RF model consistently outperformed the others across most combinations. Specifically, the SPASNV + D1–RF combination achieved an RPD of 14.7 for moisture, CARS–SNV + D1–RF reached 5.9 for protein, and CARS–SG + D2–RF attained 12.0 for fat, all significantly surpassing alternative methods and demonstrating a strong nonlinear learning capacity and predictive precision. These findings show that integrating optimal preprocessing and feature selection strategies can markedly enhance the predictive accuracy in NIR-based soybean analyses. The RF model offers exceptional stability and performance, providing both technical reference and theoretical support for the development of portable NIR devices and practical rapid-quality assessment systems for soybeans in industrial applications. Spectroscopy ; Remote sensing ; Infrared spectroscopy ; Infrared ; Near-infrared spectroscopy ; Environmental science ; Materials science ; Analytical Chemistry (journal) ; Chemistry ; Environmental chemistry ; Optics ; Geography ; Physics ; Astronomy Spectroscopy and Chemometric Analyses ; GABA and Rice Research ; Spectroscopy Techniques in Biomedical and Chemical Research
Authors: Kien Xuan Ngo | Takashi Sumikama | Rémi Vuillemot | Han Gia Nguyen | Ngan Thi Phuong Le | Sergei Grudinin
Source: bioRxiv (Cold Spring Harbor Laboratory) (preprint, 2025-04-10)
Field: Chemistry — Physical and Theoretical Chemistry

SimHS-AFMfit-MD: An Integrative Approach to Deciphering Alpha-Actinin Atomic Conformational Dynamics Abstract Many molecular systems, such as intrinsically disordered proteins and flexible multi-domain complexes, are highly dynamic and often inaccessible to conventional X-ray crystallography or cryo-EM due to their conformational heterogeneity and flexibility. As a result, resolving their atomic-level dynamics remains a significant challenge. In this study, we present SimHS-AFMfit-MD, an integrative framework that combines high-speed atomic force microscopy (HS-AFM), molecular dynamics (MD) simulations, and AFMfit-based structural modeling to reconstruct dynamic protein conformations at atomic resolution. Using alpha-actinin, an actin crosslinking protein, as a challenging test system, we show that AFMfit guided by nonlinear normal mode analysis (AFMfit-NMA) enables accurate structural fitting, while guiding AFMfit with MD trajectories (AFMfit-MD) further enhances the flexible fitting performance, achieving closer agreement with unbiased all-atom MD simulation results. This strategy allows us to convert thousands of three-dimensional HS-AFM images into atomic-scale conformational ensembles, revealing the twisting and bending transitions underlying Ca²⁺-bound and Ca²⁺-unbound alpha-actinin. Together, our results establish a hybrid computational–experimental approach that bridges the spatial and, to some extent, temporal resolution gaps between simulation and imaging, paving the way for real-time visualization of protein conformational dynamics at the atomic scale. Graphic Abstract Actinin ; Actin ; Biophysics ; Alpha (finance) ; Function (biology) ; Chemistry ; Dynamics (music) ; Cell biology ; Physics ; Biochemistry ; Biology ; Cytoskeleton ; Cell ; Medicine thermodynamics and calorimetric analyses ; Metabolomics and Mass Spectrometry Studies ; Protein Structure and Dynamics
Authors: Alice Maiocchi | Martina Pedrini | Veronica Ferrari | Ágata Sofia Assunção Carreira | Vincenzo Maria D’Amore | Federica Santoro | Anna Di Porzio | Michela Bosetti | Riccardo Cristofani | Alessandra Silvani | Diego Brancaccio | Luciana Marinelli | Francesco Saverio Di Leva | Alessandro Provenzani | Angelo Poletti | Pierfausto Seneci
Source: European Journal of Medicinal Chemistry (article, 2025-05-08)
Field: Chemistry — Organic Chemistry

Design, synthesis and characterization of aryl bis-guanyl hydrazones as RNA binders of C9orf72 G4C2 extended repeats Expanded G<sub>4</sub>C<sub>2</sub> repeats derived from mutations of the C9orf72 gene are causative factors in amyotrophic lateral sclerosis (ALS) and frontotemporal dementia (FTD) patients, leading to multiple pathological events. Bis thiophene para dinicotinimidamide 2a was reported to preferentially stabilize G-quadruplex G<sub>4</sub>C<sub>2</sub> RNA structures at sub-micromolar concentrations. We replaced its amidine groups with BBB-compliant guanyl hydrazones, and carried out scaffold variations to improve water solubility. An eight-membered array was built around bis-thiophene- (4b-6a), bis-oxazole- (7b), diphenylurea diamide- (8b) and phenyldioxy ditriazolephenyl scaffolds (9a,b). Biological profiling of the array identified 4b as a promising, drug-like hit, active in cellular assays on ALS patient-derived cells. Chemistry ; Aryl ; Characterization (materials science) ; Stereochemistry ; RNA ; Combinatorial chemistry ; Biochemistry ; Nanotechnology ; Organic chemistry ; Gene Synthesis of heterocyclic compounds ; Chemical Synthesis and Analysis ; Click Chemistry and Applications
Authors: Wenxiang Zhang | Liao Pan | Xueyu Cheng | Lixin Lu
Source: Packaging Technology and Science (article, 2025-02-05)
Field: Chemistry — Analytical Chemistry

Nondestructive TVB‐N Detection in Packaged Beef Using Hyperspectral Imaging ABSTRACT Hyperspectral imaging (HSI) technology has shown potential in monitoring fresh meat. It is necessary to investigate the rapid detection technology of packaged fresh meat in order to ensure food quality and safety. In this study, hyperspectral images of beef in the presence of packaging film were collected, and the spectra were optimized using spectral pretreatment, band selection and film radiation correction methods to predict the total volatile basic nitrogen (TVB‐N) of beef in the presence of packaging film. The results of the competitive adaptive reweighted sampling (CARS) combined with least squares support vector machines (CARS‐LSSVM) model constructed by using the corrected reflectance spectra were = 0.8687, RMSEP = 3.1970 mg/100 g, which is higher than that obtained before the correction ( was 0.8168, and RMSEP was 3.0449 mg/100 g). The results reveal that HSI with radiation correction has the potential in monitoring the TVB‐N content of beef through packaging film. Hyperspectral imaging ; Materials science ; Nondestructive testing ; Remote sensing ; Geology ; Physics Spectroscopy and Chemometric Analyses ; Water Quality Monitoring and Analysis ; Advanced Chemical Sensor Technologies
Authors: Eslam B. Elkaeed | Hazem Elkady | Ahmed M. Khattab | Reda G. Yousef | Hanan Al-Ghulikah | Dalal Z. Husein | Ibrahim M. Ibrahim | Mohamed A. Elkady | Ahmed M. Metwaly | Ibrahim H. Eissa
Source: PLoS ONE (article, 2025-01-27)
Field: Chemistry — Organic Chemistry

Integrated in silico and in vitro exploration of the anti-VEGFR-2 activities of a semisynthetic xanthine alkaloid inhibiting breast cancer This study presents T-1-NBAB, a new compound derived from the natural xanthine alkaloid theobromine, aimed at inhibiting VEGFR-2, a crucial protein in angiogenesis. T-1-NBAB's potential to interacts with and inhibit the VEGFR-2 was indicated using in silico techniques like molecular docking, MD simulations, MM-GBSA, PLIP, essential dynamics, and bi-dimensional projection experiments. DFT experiments was utilized also to study the structural and electrostatic properties of T-1-NBAB. Computational analysis was performed to predict the ADME-Tox profiles of T-1-NBAB. After semisynthesis, the in vitro results showed that T-1-NBAB effectively inhibits VEGFR-2, with an IC50 of 0.115 μM, compared to sorafenib's 0.0591 μM. In vitro tests also demonstrated significant activity of T-1-NBAB against breast cancer cell lines MCF7 and T47D, with IC50 values of 16.88 μM and 61.17 μM, respectively, and high selectivity. Importantly, T-1-NBAB induced early and late apoptosis in MCF7 cells, indicating its potential as a strong anticancer agent. Additionally, T-1-NBAB reduced the migration and healing abilities of MCF7 cells, suggesting it could be a promising anti-angiogenic agent. Overall, these findings suggest that T-1-NBAB is a promising lead compound for further research as a potential treatment for breast cancer. In silico ; In vitro ; Chemistry ; ADME ; Xanthine ; Angiogenesis ; Alkaloid ; Sorafenib ; Pharmacology ; Cancer cell ; Semisynthesis ; Cancer research ; Stereochemistry ; Cancer ; Biochemistry ; Biology ; Enzyme ; Genetics Synthesis and biological activity ; Angiogenesis and VEGF in Cancer ; Click Chemistry and Applications
Authors: Hao‐Cheng Thong | Fang‐Zhou Yao | Xianxian Cai | Ze Xu | Mao‐Hua Zhang | Huazhang Zhang | Ben Xu | Yan Wei | Shidong Wang | Ke Wang
Source: npj Computational Materials (article, 2025-04-04)
Field: Materials Science — Materials Chemistry

Increased Curie temperature in lithium substituted ferroelectric niobate perovskite via soft polar mode enhancement The functionality of ferroelectrics is often constrained by their Curie temperature, above which depolarization occurs. Lithium (Li) is the only experimentally known substitute that can increase the Curie temperature in ferroelectric niobate-based perovskites, yet the mechanism remains unresolved. Here, the unique phenomenon in Li-substituted KNbO3 is investigated using first-principles density functional theory. Theoretical calculations show that Li substitution at the A-site of perovskite introduces compressive chemical pressure, reducing Nb–O hybridization and associated ferroelectric instability. However, the large off-center displacement of the Li cation compensates for this reduction and further enhances the soft polar mode, thereby raising the Curie temperature. In addition, the stability of the tetragonal phase over the orthorhombic phase is predicted upon Li substitution, which reasonably explains the experimental observation of a decreased orthorhombic-to-tetragonal phase transition temperature. Finally, a metastable anti-phase polar state in which the Li cation displaces oppositely to the Nb cation is revealed, which could also contribute to the variation of phase transition temperatures. These findings provide critical insights into the atomic-scale mechanisms governing Curie temperature enhancement in ferroelectrics and pave the way for designing advanced ferroelectric materials with improved thermal stability and functional performance. Curie temperature ; Materials science ; Lithium niobate ; Ferroelectricity ; Perovskite (structure) ; Polar ; Mode (computer interface) ; Curie ; Lithium (medication) ; Soft modes ; Condensed matter physics ; Optoelectronics ; Crystallography ; Chemistry ; Ferromagnetism ; Dielectric ; Physics ; Psychology Ferroelectric and Piezoelectric Materials ; Multiferroics and related materials ; Acoustic Wave Resonator Technologies
Authors: Dayang Yu | Jiming Zhu | Xingsheng Li | An He | Huaiqian Liu | Changjiang Chen | Yong Liu
Source: Geomechanics and Geophysics for Geo-Energy and Geo-Resources (article, 2025-06-12)
Field: Chemistry — Spectroscopy

Research on real time measurement model and measurement system for gas concentration in extraction drilling Accurate and real-time monitoring of methane concentration at extraction boreholes is critical for intelligent gas management in coal seams. Although tunable diode laser absorption spectroscopy (TDLAS) offers high sensitivity and rapid response, its performance is limited under complex underground conditions due to low signal-to-noise ratios and lack of effective environmental compensation, leading to reduced detection accuracy at low concentrations. This study develops an enhanced TDLAS-based detection system that integrates wavelength modulation spectroscopy (WMS) with a centroid-weighted Lagrange interpolation algorithm. The system accounts for fluctuations in borehole gas composition, pressure, and temperature, enabling dynamic compensation for spectral distortion and improved measurement reliability. Experimental validation using 0.5% and 4.5% CH₄ standard gases yielded the following key findings:(1) Methane concentration accuracy is highly dependent on line strength and spectral shape, both sensitive to temperature and pressure. (2) The Lorentzian profile was selected as the optimal line shape for pressure-broadened conditions, and the proposed interpolation algorithm effectively compensates for dual-variable spectral shifts. (3) The system achieves a maximum measurement error below 0.5%, demonstrating strong robustness and precision in variable environments. This work provides a compact, accurate, and environment-adaptive solution for methane monitoring at borehole outlets and supports the development of intelligent gas sensing systems in coal mining applications. Drilling ; Extraction (chemistry) ; Petroleum engineering ; Computer science ; Process engineering ; Chromatography ; Engineering ; Chemistry ; Mechanical engineering Spectroscopy and Laser Applications ; Atmospheric and Environmental Gas Dynamics ; Laser Design and Applications
Authors: Yanis Taïbi | Ali Charbal | Jean-Christophe Brachet | Elodie Rouesne | Sergio Sao‐Joao | Szilvia Kalácska | Morgan Rusinowicz | Guillaume Kermouche
Source: Journal of Nuclear Materials (article, 2025-08-13)
Field: Materials Science — Materials Chemistry

High temperature chromium coating cracking investigation during tensile tests monitored by acoustic emission The present study focuses on in-situ measurements of crack initiation and propagation in first-generation PVD-HiPIMS chromium coatings on M5 Framatome 1 1 M5 Framatome is a trademark or a registered trademark of Framatome or its affiliates in the USA or other countries. cladding substrates using an acoustic emission (AE) device and a tensile test machine. A key novelty of this work is the implementation of a temperature-controlled cracking monitoring system adapted to the cladding geometry under tensile loading. Post-mortem examinations (after different interrupted tensile tests) provide an evaluation of the in-situ method for determining the crack initiation threshold and crack density evolution. The critical strain to crack initiation increases exponentially from 0.4 % at room temperature to 3 % at 350 °C. Above 410 °C, the coating no longer exhibits brittle cracking until reaching high macroscopic imposed strain (up to 30-50 %). Additionally, the crack density decreases more or less linearly with the increasing testing temperature. At higher temperatures, the coating becomes highly ductile, consistently with the increased plasticity of pure chromium. SEM observations of the coating cross-section confirm that cracks do not propagate beyond the coating and that no delamination occurs. Thus, after rapidly reaching crack density saturation, the residual uncracked chromium coating exhibits significant plasticity and widening of the existing Cr cracks while providing slight mechanical reinforcement to the Zr-based cladding up to at least 400 °C. Acoustic emission ; Cracking ; Materials science ; Coating ; Ultimate tensile strength ; Composite material ; Chromium ; Tensile testing ; Metallurgy Nuclear Materials and Properties ; Advanced materials and composites ; Fusion materials and technologies