jablonkagroup/rise_ai_scientists huggingface dataset:
Authors: Tamsin J. Samuels | Elizabeth J. Torley | Valeriia Nadmitova | Emily L Naden | P Blair | Frankjel A. Hernandez Frometa | Felipe Karam Teixeira
Source: Development (article, 2025-02-18)
Field: Materials Science — Biomaterials

Destabilisation of <i>bam</i> transcripts terminates the mitotic phase of <i>Drosophila</i> female germline differentiation The tight control of the mitotic phase of differentiation is crucial to prevent tumourigenesis while securing tissue homeostasis. In the Drosophila female germline, differentiation involves precisely four mitotic divisions, and accumulating evidence suggests that bag of marbles (bam), the initiator of differentiation, is also involved in controlling the number of divisions. To test this hypothesis, we depleted Bam from differentiating cells and found a reduced number of mitotic divisions. We examined the regulation of Bam using RNA imaging methods and found that the bam 3' UTR conveys instability to the transcript in the eight-cell cyst and early 16-cell cyst. We show that the RNA-binding protein Rbp9 is responsible for timing bam mRNA decay. Rbp9 itself is part of a sequential cascade of RNA-binding proteins activated downstream of Bam, and we show that it is regulated through a change in transcription start site, driven by Rbfox1. Altogether, we propose a model in which Bam expression at the beginning of differentiation initiates a series of events that eventually terminates the Bam expression domain. Biology ; Germline ; Mitosis ; Cell biology ; Cellular differentiation ; RNA-binding protein ; Genetics ; RNA ; Messenger RNA ; Gene Silk-based biomaterials and applications ; RNA Research and Splicing
Authors: Ismael Sánchez-Calderón | Félix Lizalde-Arroyo | Judith Martín‐de León | Miguel Ángel Rodríguez‐Pérez | Victoria Bernardo
Source: Construction and Building Materials (article, 2025-02-28)
Field: Chemistry — Spectroscopy

Improvement of the thermal conductivity of micronized nanocellular poly(methyl-methacrylate) (PMMA) by adding infrared blockers Micronized nanocellular polymers show great potential to be used as core materials for vacuum insulation panels due to their reduced thermal conductivity under vacuum. However, as a result of their nanocellular structure, these materials are characterized by thermal radiation contributions higher than 4 mW/(m·K). This work studies how to further enhance their thermal insulation behavior by adding infrared blockers to reduce thermal radiation. Three different opacifiers (titanium(IV) oxide, graphene nanoplatelets, and silicon carbide) are used in different contents (2.5, 5, 10, 15, and 20 wt%). The obtained powders are characterized to determine the apparent density, the particle size distribution, and the thermal conductivity. The addition of infrared blockers leads to an increase in apparent density which is also related to the opacifier’s particle size. For each infrared blocker, there is an optimum concentration to achieve the minimum thermal conductivity. Finally, compacted panels are produced to analyze their behavior as VIP cores by measuring thermal conductivity under vacuum conditions. A minimum thermal conductivity of 9.6 mW/(m·K) is obtained for the compacted panel containing 10 wt% of silicon carbide, a reduction of 2 mW/(m·K) regarding the sample without opacifier. • Analysis of the addition of different infrared blockers to micronized nanocellular poly(methyl-methacrylate) (PMMA). • Titanium oxide, graphite nanoplatelets, and silicon carbide are used as infrared blockers in different contents. • The size of the infrared blockers particles affects the packaging and the final density. • Thermal conductivities lower than 10 mW/(m·K) are obtained at vacuum when infrared blockers are introduced. Thermal conductivity ; Materials science ; Methyl methacrylate ; Infrared ; Composite material ; Thermal ; Methacrylate ; Conductivity ; Chemical engineering ; Polymer ; Chemistry ; Copolymer ; Thermodynamics ; Optics Aerogels and thermal insulation ; Additive Manufacturing and 3D Printing Technologies ; Polymer Foaming and Composites
Authors: Ryotaro Yoneyama | Ryota Ushiyama | Tomoya Maruyama | Reiko Sato | Mamiko Tsugane | Masahiro Takinoue | Hiroaki Suzuki
Source: RSC Applied Interfaces (article, 2025-01-01)
Field: Materials Science — Materials Chemistry

Formation dynamics of patchy/Janus DNA condensates in monodisperse giant vesicles generated using microfluidics The one-step formation of uniform patchy or Janus-type DNA condensates within monodisperse giant vesicles was demonstrated for homogeneous production of artificial cells with hierarchical structures. Janus ; Microfluidics ; Dispersity ; Dynamics (music) ; Nanotechnology ; Vesicle ; Chemical physics ; Biophysics ; Chemistry ; Materials science ; Physics ; Biology ; Polymer chemistry ; Membrane Pickering emulsions and particle stabilization ; Particle Dynamics in Fluid Flows ; Innovative Microfluidic and Catalytic Techniques Innovation
Authors: Vatsal Vaghasia | Rakesh Chaudhari | Sakshum Khanna | J.J. Modi | Jay Vora
Source: Journal of Manufacturing and Materials Processing (article, 2025-07-11)
Field: Materials Science — Materials Chemistry

Experimental Investigations on Microstructure and Mechanical Properties of L-Shaped Structure Fabricated by WAAM Process of NiTi SMA In the present study, an L-shaped multi-walled structure of NiTi shape memory alloy (SMA) was fabricated by using the wire arc additive manufacturing (WAAM) method on a titanium substrate. The present study aims to investigate the fabricated structure for microstructure, macrostructure, and mechanical properties. The 40 layers of L-shaped structure were successfully fabricated at optimized parameters of wire feed speed at 6 m/min, travel speed at 12 mm/s, and voltage at 20 V. The macrographs demonstrated the continuous bonding among the layers with complete fusion. The microstructure in the area between the two middle layers has exhibited a mixture of columnar grains (both coarse and fine), interspersed with dendritic colonies. The microstructure in the topmost layers has exhibited finer colonial structures in relatively greater numbers. The microhardness (MH) test has shown the average values of 283.2 ± 3.67 HV and 371.1 ± 5.81 HV at the bottom and topmost layers, respectively. A tensile test was conducted for specimens extracted from deposition and build directions, which showed consistent mechanical behavior. For the deposition direction, the average ultimate tensile strength (UTS) and elongation (EL) were obtained as 831 ± 22.91 MPa and 14.32 ± 0.55%, respectively, while the build direction has shown average UTS and EL values of 774 ± 6.56 MPa and 14.16 ± 0.21%, respectively. The elongation exceeding 10% in all samples suggests that the fabricated structure demonstrates properties comparable to those of wrought metal. Fractography of all tensile specimens has shown good ductility and toughness. Lastly, a differential scanning calorimetry test was carried out to assess the retention of shape memory effect for the fabricated structure. The authors believe that the findings of this work will be valuable for various industrial applications. Materials science ; Microstructure ; Ultimate tensile strength ; Indentation hardness ; Composite material ; Fractography ; Elongation ; Tensile testing ; Toughness ; Nickel titanium ; Ductility (Earth science) ; Shape-memory alloy Shape Memory Alloy Transformations ; Additive Manufacturing Materials and Processes ; Additive Manufacturing and 3D Printing Technologies
Authors: Florian Foitzik | Massimiliano Bartolomei | José Campos‐Martínez | Fernando Pirani | Stefan Bergmeister | Lisa Ganner | Ianessa Stromberg | Fábio Zappa | Masoomeh Mahmoodi‐Darian | Tomás González‐Lezana | Elisabeth Gruber
Source: Small Structures (article, 2025-06-12)
Field: Materials Science — Materials Chemistry

Formation of Large Ordered Helium Solvation Shells Around Multiply Charged Species: He<sub><i>N</i></sub>Ho<sup>2+</sup> and He<sub><i>N</i></sub>Bi<sup>2+</sup> In this article, the results of a combined experimental and theoretical investigation which provides evidence of the existence of large well‐ordered structures of helium atoms in He N Ho 2+ and He N Bi 2+ clusters. In particular, we observe up to four shells of helium surrounding the metallic dication for He 74 Ho 2+ in a sequence from inside to outside of: an icosahedron; a dodecahedron; an icosahedron and finally an icosidodecahedron. While these results confirm our previous study for He N Ca 2+ , for He N Bi 2+ , the mass spectra exhibit different magic numbers ( N = 14, 38, 52 and 90). Evaporation energies calculated by means of classical minimization and Monte Carlo simulations confirm the existence of Mozartkugel‐like structures compatible with the features observed experimentally. Thus, He 90 Bi 2+ , the largest of these clusters ever observed exhibiting ordered solvation arrangements, would be formed by the following sequence of concentric ordered structures: a bicapped hexagonal antiprism (BHA) with the first 14 He atoms; a tetradecahedron with 24 atoms, another BHA and, finally, the last 38 He atoms form a pentagonal icositetrahedron. The formation of these large ordered shells seems the result of a delicate balance between the He–Bi 2+ and He–He equilibrium distances besides a sufficiently strong He–Bi 2+ interaction potential. Helium ; Isotopes of helium ; Atomic physics ; Helium-4 ; Solvation ; Helium-3 ; Physics ; Charged particle ; Ion ; Quantum mechanics Hydrogen Storage and Materials ; Quantum, superfluid, helium dynamics ; Advanced Chemical Physics Studies
Authors: Francesca Blasi | Maria Rachele Ceccarini | Stefano Bistarelli | Francesco Galli | Lina Cossignani | Desirée Bartolini | Federica Ianni
Source: Foods (article, 2025-06-15)
Field: Chemistry — Organic Chemistry

Impact of Extra-Virgin Olive Oil Storage Conditions on Phenolic Content and Wound-Healing Properties Storage conditions significantly impact the quality and functional properties of extra-virgin olive oil (EVOO). This study investigated the impact of light and dark storage on the nutritional quality of Umbrian EVOO and its effectiveness in tissue repair. The research aimed to simulate real-world conditions occurring during transport, retail, and domestic storage. Light exposure accelerated EVOO oxidation, significantly affecting peroxide levels (ranging from 5.19 to 24.30 meq O<sub>2</sub>/kg of oil), total antioxidant capacity (measured spectrophotometrically, collectively ranging from 399.47 to 684.63 mg TE/kg of oil), and phenolic compound concentrations, particularly secoiridoids, lignans, and flavonoids (measured by HPLC, collectively ranging from 41.92 to 169.74 mg/kg of oil). Statistically significant differences (<i>p</i> < 0.01) were recorded between the control sample and the others in almost all cases, after storage. For instance, both light and dark exposure over a 24-month period resulted in a marked reduction (<i>p</i> < 0.01) in oleocanthal, pinoresinol, luteolin, and apigenin. Pigment levels were also affected, representing a rapid and cost-effective indicator of product oxidative degradation. The loss of phenolic compounds (especially oleacein and oleocanthal, which showed the most significant reductions of approximately 75% and 60%, respectively), impaired the EVOO's wound-healing properties, affecting key tissue regeneration processes such as keratinocyte migration, hyaluronic acid synthesis, and angiogenesis. Notably, oleocanthal and oleacein, present at higher concentrations in fresh extracts, emerged as the primary contributors to the observed dermal effects and wound-healing processes, demonstrating a significant highest efficacy (<i>p</i> < 0.0001) in promoting wound closure. These findings underscore the critical role of EVOO storage in preserving its sensory properties and labile components with tissue repair and regeneration functions. Olive oil ; Food science ; Wound healing ; Chemistry ; Biology Edible Oils Quality and Analysis ; Phytochemicals and Antioxidant Activities ; Nuts composition and effects
Authors: Joel C. Corbin | Alireza Moallemi | Daniel Poitras | Timothy A. Sipkens | J. Norooz Oliaee
Source: Aerosol Science and Technology (article, 2025-03-07)
Field: Chemistry — Spectroscopy

Self-calibrating aerosol absorption measurements using co-located TDLAS and tunable-wavelength photothermal interferometry Photothermal spectroscopy, and photothermal interferometry (PTI) in particular, has the potential to provide reference measurements of aerosol absorption coefficients βabn. Such βabn measurements represent a fundamental property of aerosols such as black carbon and brown carbon, the accurate knowledge of which is essential for understanding their climate forcing: βabn can be used in calculating the imaginary refractive index, absorption function, or mass absorption cross-section of a sample. Furthermore, βabn is commonly expressed in units of equivalent black carbon mass (eBC) in the many photoacoustic or filter-based instruments that are used for air-quality monitoring and emissions testing of on-road, airborne, and marine transportation. Here, we propose the use of tunable-laser PTI (TL-PTI) as a self-calibrating reference technique for quantifying βabn. In TL-PTI, a wavelength-tunable laser is used to quantify the narrow absorption lines of a gas via direct absorption spectroscopy, providing a reference βabn,ref in units of Mm⁻¹. The A-band absorption lines of ambient oxygen at about 760 nm provide a convenient reference. The PTI signal is then calibrated to this βabn,ref. This gas-PTI signal can then be “switched off” by tuning the laser wavelength away from the absorption lines, so that only particulate PTI signals remain in the background-subtracted signal. The PTI signal is directly related to light absorption for both aerosols and gases, since the PTI pump-laser modulation is slower than the thermalization timescales of both. We demonstrate the accuracy of our PTI prototype by retrieving the refractive index of nigrosine dye. Aerosol ; Photothermal therapy ; Absorption (acoustics) ; Wavelength ; Interferometry ; Optics ; Materials science ; Chemistry ; Analytical Chemistry (journal) ; Remote sensing ; Optoelectronics ; Chromatography ; Physics Spectroscopy and Laser Applications ; Atmospheric aerosols and clouds ; Atmospheric and Environmental Gas Dynamics
Authors: T.H.B. Demont | S.K.F. Stoter | C. Diddens | E.H. van Brummelen
Source: Computer Methods in Applied Mechanics and Engineering (article, 2025-11-08)
Field: Materials Science — Materials Chemistry

On the consistency of dynamic wetting boundary conditions for the Navier–Stokes–Cahn–Hilliard equations We investigate the limiting behavior of the Navier–Stokes–Cahn–Hilliard model for binary-fluid flows as the diffuse-interface thickness passes to zero, in the presence of fluid–fluid–solid contact lines. Allowing for motion of such contact lines relative to the solid substrate is required to adequately model multi-phase and multi-species fluid transport past and through solid media. Even though diffuse-interface models provide an inherent slip mechanism through the mobility-induced diffusion, this slip vanishes as the interface thickness and mobility parameter tend to zero in the so-called sharp-interface limit. The objective of this work is to present and analyze dynamic wetting and generalized Navier boundary conditions for diffuse-interface models that are consistent in the sharp-interface limit. We concentrate our analysis on the prototypical binary-fluid Couette-flow problems. To verify the consistency of the diffuse-interface model in the limit of vanishing interface thickness, we provide reference limit solutions of a corresponding sharp-interface model. For parameter values both at and away from the critical viscosity ratio, we present and compare the results of both the diffuse- and sharp-interface models. As a corollary of the close agreement between the diffuse-interface and sharp-interface results, the presented results can serve as a benchmark for future investigations. Boundary value problem ; Slip (aerodynamics) ; Consistency (knowledge bases) ; Limit (mathematics) ; Corollary ; Wetting ; Work (physics) Solidification and crystal growth phenomena ; Fluid Dynamics and Thin Films ; Block Copolymer Self-Assembly
Authors: Wenyang Zhang | Yanjiao Wang | Wenyan Li | Shaowen Wu | Yuanyuan Chen | M Ye | Wenjie Huang | Alisdair R. Fernie | Shijuan Yan
Source: aBIOTECH (article, 2025-07-15)
Field: Chemistry — Spectroscopy

A novel proteomics workflow for simultaneous analysis of protein phosphorylation and S-nitrosylation The online version contains supplementary material available at 10.1007/s42994-025-00227-2. S-Nitrosylation ; Proteomics ; Workflow ; Phosphorylation ; Computational biology ; Chemistry ; Computer science ; Biology ; Biochemistry ; Database ; Cysteine Advanced Proteomics Techniques and Applications ; Mass Spectrometry Techniques and Applications ; Enzyme Structure and Function
Authors: Wenjing Ding | Ruochen Xin | Yang Deng | Gang Wang | Junhua Gao | Hongtao Cao | Shiwei Tang
Source: Scientific Reports (article, 2025-10-16)
Field: Materials Science — Electronic, Optical and Magnetic Materials

Nanoporous-structured metasurface refractive index sensor employing quasi-bound states in the continuum Bound states in the continuum represent a unique optical phenomenon characterized by extremely high-quality factors and low energy losses, offering great potential for high-sensitivity sensing applications. In this study, we investigated the optical properties of nanoporous silica substrates (NSS) and nanoporous silicon dimer (NSD) structures with varying porosity percentages in different refractive index environments. The results demonstrate that the combined architecture achieves high refractive index sensitivity ([Formula: see text]) and an exceptionally high figure of merit ([Formula: see text]). The lower refractive index of the NSS accelerates the decay of localized quasi-bound states in the continuum evanescent modes into the substrate, channeling the field into the surrounding medium, while the NSD further boosts local field intensity. The nanoporous medium structure design presented in this work offers a new strategy for developing high-performance refractive index sensors, deepening our understanding of nanoporous materials for optical sensing, and updating valuable theoretical and technical support for the practical sensor design. Nanoporous ; Refractive index ; Figure of merit ; Porosity ; Porous silicon ; High-refractive-index polymer ; Silicon ; Field (mathematics) Metamaterials and Metasurfaces Applications ; Plasmonic and Surface Plasmon Research ; Photonic Crystals and Applications
Authors: Din Baruch | Ioannis Tsirkas | Ehud Sass | Benjamin Dubreuil | Yeynit Asraf | Amir Aharoni | Maya Schuldiner | Ofir Klein
Source: Journal of Cell Science (article, 2025-07-24)
Field: Chemistry — Spectroscopy

Creation and validation of a proteome-wide yeast library for protein detection and analysis A significant challenge in cell biology is to uncover the function of uncharacterized proteins. Surprisingly, a quarter of the proteome is still poorly understood even in the most well-studied model organisms. Systematic methodologies, including the use of tagged protein collections, have emerged as a powerful approach to address this gap. Despite the availability of proteome-wide collections featuring various fused proteins, the impact of different tags on protein function highlights the need for diversifying the tags used for functional genomic studies. To rise to this challenge, we created a proteome-wide collection of yeast strains in which proteins are N-terminally tagged with the broadly utilized and compact hemagglutinin (HA) epitope. We showcase the potential uses of our library for systematically evaluating protein size, abundance and localization using an in vivo labeling approach. Our characterization underscores the potential utility of a proteome-wide HA-tagged library in revealing novel aspects of cell biology, providing an additional powerful tool for functional genomics. Biology ; Proteome ; Computational biology ; Proteomics ; Function (biology) ; Human proteome project ; Yeast ; Genomics ; Functional genomics ; Genetics ; Genome ; Gene Advanced Proteomics Techniques and Applications ; Advanced Biosensing Techniques and Applications ; Genomics and Phylogenetic Studies
Authors: Loïc Moczko | Sven Reichardt | Aditya Singh | Xin Zhang | Elise Jouaiti | Luis Enrique Parra López | Joanna Wolff | Aditi Raman Moghe | Étienne Lorchat | Rajendra Singh | Kenji Watanabe | Takashi Taniguchi | Hicham Majjad | Michelangelo Romeo | A. Gloppe | Ludger Wirtz | Stéphane Berciaud
Source: Physical Review X (article, 2025-05-07)
Field: Materials Science — Materials Chemistry

Symmetry-Dependent Dielectric Screening of Optical Phonons in Monolayer Graphene Quantized lattice vibrations (i.e., phonons) in solids are robust and unambiguous fingerprints of crystal structures and of their symmetry properties. In metals and semimetals, strong electron-phonon coupling may lead to so-called Kohn anomalies in the phonon dispersion, providing an image of the Fermi surface in a nonelectronic observable. Kohn anomalies become prominent in low-dimensional systems, in particular, in graphene, where they appear as sharp kinks in the in-plane optical phonon branches. However, in spite of intense research efforts on electron-phonon coupling in graphene and related van der Waals heterostructures, little is known regarding the links between the symmetry properties of optical phonons at and near Kohn anomalies and their sensitivity towards the local environment. Here, using inelastic light scattering (Raman) spectroscopy, we investigate a set of custom-designed graphene-based van der Waals heterostructures, wherein dielectric screening is finely controlled at the atomic-layer level. We demonstrate experimentally and explain theoretically that, depending exclusively on their symmetry properties, the two main Raman lines of graphene react differently to the surrounding environment. While the 2D line, which is due to near-zone-edge optical phonons, undergoes changes due to the neighboring dielectric environment, the in-plane, zone-center optical phonons are symmetry protected from the influence of the latter. These results shed new light on the unique electron-phonon coupling properties in graphene and related systems and provide invaluable guidelines to characterize dielectric screening in van der Waals heterostructures and moiré superlattices. Graphene ; Phonon ; Monolayer ; Condensed matter physics ; Dielectric ; Symmetry (geometry) ; Materials science ; Physics ; Quantum mechanics ; Nanotechnology ; Mathematics Graphene research and applications ; 2D Materials and Applications ; Thermal properties of materials
Authors: Yaozu Han | Biwen Wang | Alberto Agnolin | Gaurav Dugar | Frans van der Kloet | Christopher Sauer | Paul Igor Costea | Max Fabian Felle | Mathis Appelbaum | Leendert W. Hamoen
Source: Microbial Cell Factories (article, 2025-01-27)
Field: Materials Science — Materials Chemistry

Ribosome pausing in amylase producing Bacillus subtilis during long fermentation Expression of the α-amylase gene amyM in B. subtilis is accompanied by several ribosome pausing events. Since these sites can neither be predicted based on codon specificity nor on secondary protein structures, we speculate that secondary mRNA structures are responsible for these translation pausing sites. The detailed information of ribosome pausing sites in amyM provide novel information that can be used in future codon optimization studies aimed at improving the production of this amylase by B. subtilis. Bacillus subtilis ; Amylase ; Fermentation ; Ribosome ; Biology ; Food science ; Bacillales ; Microbiology ; Biochemistry ; Chemistry ; Biotechnology ; Bacteria ; Enzyme ; RNA ; Genetics ; Gene Enzyme Structure and Function ; RNA and protein synthesis mechanisms ; Enzyme Production and Characterization