jablonkagroup/rise_ai_scientists huggingface dataset:
Authors: Annie Ha | Amanda Khoo | Vladimir Ignatchenko | Shahbaz Khan | Matthew Waas | Danny Vesprini | Stanley K. Liu | Julius O. Nyalwidhe | O. John Semmes | Paul C. Boutros | Thomas Kislinger
Source: Journal of Proteome Research (article, 2024-04-05)
Field: Chemistry — Spectroscopy

Comprehensive Prostate Fluid-Based Spectral Libraries for Enhanced Protein Detection in Urine Biofluids contain molecules in circulation and from nearby organs that can be indicative of disease states. Characterizing the proteome of biofluids with DIA-MS is an emerging area of interest for biomarker discovery; yet, there is limited consensus on DIA-MS data analysis approaches for analyzing large numbers of biofluids. To evaluate various DIA-MS workflows, we collected urine from a clinically heterogeneous cohort of prostate cancer patients and acquired data in DDA and DIA scan modes. We then searched the DIA data against urine spectral libraries generated using common library generation approaches or a library-free method. We show that DIA-MS doubles the sample throughput compared to standard DDA-MS with minimal losses to peptide detection. We further demonstrate that using a sample-specific spectral library generated from individual urines maximizes peptide detection compared to a library-free approach, a pan-human library, or libraries generated from pooled, fractionated urines. Adding urine subproteomes, such as the urinary extracellular vesicular proteome, to the urine spectral library further improves the detection of prostate proteins in unfractionated urine. Altogether, we present an optimized DIA-MS workflow and provide several high-quality, comprehensive prostate cancer urine spectral libraries that can streamline future biomarker discovery studies of prostate cancer using DIA-MS. Biomarker discovery ; Urine ; Prostate cancer ; Biomarker ; Proteome ; Prostate ; Computational biology ; Computer science ; Cancer ; Chemistry ; Proteomics ; Bioinformatics ; Medicine ; Internal medicine ; Biology ; Biochemistry ; Gene Advanced Proteomics Techniques and Applications ; Mass Spectrometry Techniques and Applications ; Prostate Cancer Treatment and Research
Authors: Khaled Aliqab | Ammar Armghan | Meshari Alsharari
Source: Scientific Reports (article, 2024-08-19)
Field: Materials Science — Electronic, Optical and Magnetic Materials

Polarization insensitive and wideband terahertz absorber using high-impedance resistive material of RuO2 This paper introduces a novel, cost-effective solution designed to achieve large absorption bandwidth within the THz spectrum employing a miniaturized, single-layer metamaterial structure. The designed structure features a single circular ring composed of an ohmic resistive sheet with notably higher sheet resistance than traditional metallic resonators. This distinctive design is implemented on a lossy dielectric polyimide substrate with a backing of metallic gold. Our developed absorbing structure demonstrates the capability to achieve a substantial absorption bandwidth ranging from 3.78 to 4.25 THz, maintaining a consistent absorption rate of over 90%. Moreover, we conducted an analysis to assess its absorption performance under various sheet resistance values within the top layer. Additionally, we characterized its angular stability and polarization insensitivity through oblique incident and polarization angle analysis. Finally, an RLC circuital and interference theory approach is adopted to justify its simulated results. The proposed absorber shows potential for a broad spectrum of applications, encompassing communication, imaging, and diverse integrated circuits operating within the THz band. Materials science ; Resistive touchscreen ; Wideband ; Terahertz radiation ; Optoelectronics ; Metamaterial absorber ; Metamaterial ; Resonator ; Sheet resistance ; Polarization (electrochemistry) ; Bandwidth (computing) ; Dielectric ; Optics ; Electrical impedance ; Equivalent circuit ; Voltage ; Layer (electronics) ; Telecommunications ; Computer science ; Tunable metamaterials ; Electrical engineering ; Nanotechnology ; Physics Metamaterials and Metasurfaces Applications ; Advanced Antenna and Metasurface Technologies ; Antenna Design and Analysis
Authors: Shiho Kamakura | Gust Bilcke | Shinya Sato
Source: Journal of Phycology (article, 2024-03-06)
Field: Materials Science — Biomaterials

Transcriptional responses to salinity‐induced changes in cell wall morphology of the euryhaline diatom <i>Pleurosira laevis</i> Diatoms are unicellular algae with morphologically diverse silica cell walls, which are called frustules. The mechanism of frustule morphogenesis has attracted attention in biology and nanomaterials engineering. However, the genetic regulation of the morphology remains unclear. We therefore used transcriptome sequencing to search for genes involved in frustule morphology in the centric diatom Pleurosira laevis, which exhibits morphological plasticity between flat and domed valve faces in salinity 2 and 7, respectively. We observed differential expression of transposable elements (TEs) and transporters, likely due to osmotic response. Up-regulation of mechanosensitive ion channels and down-regulation of Ca<sup>2+</sup>-ATPases in cells with flat valves suggested that cytosolic Ca<sup>2+</sup> levels were changed between the morphologies. Calcium signaling could be a mechanism for detecting osmotic pressure changes and triggering morphological shifts. We also observed an up-regulation of ARPC1 and annexin, involved in the regulation of actin filament dynamics known to affect frustule morphology, as well as the up-regulation of genes encoding frustule-related proteins such as BacSETs and frustulin. Taken together, we propose a model in which salinity-induced morphogenetic changes are driven by upstream responses, such as the regulation of cytosolic Ca<sup>2+</sup> levels, and downstream responses, such as Ca<sup>2+</sup>-dependent regulation of actin dynamics and frustule-related proteins. This study highlights the sensitivity of euryhaline diatoms to environmental salinity and the role of active cellular processes in controlling gross valve morphology under different osmotic pressures. Frustule ; Biology ; Euryhaline ; Cell biology ; Diatom ; Hydrostatic pressure ; Botany ; Salinity ; Ecology Diatoms and Algae Research ; Protist diversity and phylogeny ; Microbial Community Ecology and Physiology
Authors: Karl Kristian Krull | Syed Azmal Ali | Jeroen Krijgsveld
Source: Nature Communications (article, 2024-09-26)
Field: Chemistry — Spectroscopy

Enhanced feature matching in single-cell proteomics characterizes IFN-γ response and co-existence of cell states Proteome analysis by data-independent acquisition (DIA) has become a powerful approach to obtain deep proteome coverage, and has gained recent traction for label-free analysis of single cells. However, optimal experimental design for DIA-based single-cell proteomics has not been fully explored, and performance metrics of subsequent data analysis tools remain to be evaluated. Therefore, we here formalize and comprehensively evaluate a DIA data analysis strategy that exploits the co-analysis of low-input samples with a so-called matching enhancer (ME) of higher input, to increase sensitivity, proteome coverage, and data completeness. We assess the matching specificity of DIA-ME by a two-proteome model, and demonstrate that false discovery and false transfer are maintained at low levels when using DIA-NN software, while preserving quantification accuracy. We apply DIA-ME to investigate the proteome response of U-2 OS cells to interferon gamma (IFN-γ) in single cells, and recapitulate the time-resolved induction of IFN-γ response proteins as observed in bulk material. Moreover, we uncover co- and anti-correlating patterns of protein expression within the same cell, indicating mutually exclusive protein modules and the co-existence of different cell states. Collectively our data show that DIA-ME is a powerful, scalable, and easy-to-implement strategy for single-cell proteomics. Proteome ; Proteomics ; Computer science ; Computational biology ; Single-cell analysis ; Scalability ; Matching (statistics) ; Cell ; Biology ; Bioinformatics ; Mathematics ; Genetics Advanced Proteomics Techniques and Applications ; Single-cell and spatial transcriptomics ; Receptor Mechanisms and Signaling
Authors: X. Li | Yuan Zhao | Renpan Lu | Sun Xiao | Zhao Yang | Hai He | Yan Hui Liu | G. Du
Source: Nanophotonics (article, 2024-10-22)
Field: Materials Science — Electronic, Optical and Magnetic Materials

Full‐space trifunctional metasurface with independent control of amplitude and phase for circularly polarized waves Flexible and diverse manipulation of electromagnetic (EM) waves in half space (reflection or transmission) has facilitated strong aspiration toward full-space wave control. However, it remains challenging to achieve independent amplitude and phase control, which seriously hinder the real-world applications. Herein, an innovative strategy of trifunctional metasurface is proposed to independently and simultaneously manipulate the amplitude and phase of circular polarized waves in full space. The multifunctional design is composed of double-layer anisotropic metasurface sandwiched with a bandpass frequency selective surface, with a frequency-direction multiplexed paradigm for on-demand control of both amplitude and phase across three independent channels. To validate the concept, a multifunctional metadevice is designed and verified by simulations and experiments, showcasing arbitrary near-field and far-field power modulation in full space. Lateral and axial bifocal metalenses with desired intensity distribution are designed in two reflection channels at 9 GHz, while multibeam generator with desired spatial scatterings and power allocations is designed in transmissive channel at 13 GHz. The finding paves the way for attaining multifunctional metadevices with amplitude and phase modulation in full space, which have potential applications in high-quality imaging and high-capacity communication systems. Phase control ; Amplitude ; Optics ; Phase (matter) ; Metamaterial ; Circular polarization ; Physics ; Polarization (electrochemistry) ; Materials science ; Chemistry ; Quantum mechanics Metamaterials and Metasurfaces Applications ; Advanced Antenna and Metasurface Technologies ; Antenna Design and Analysis
Authors: Jin Shang | Yinqiao Wang | Deng Pan | Yuliang Jin | Jie Zhang
Source: Proceedings of the National Academy of Sciences (article, 2024-08-08)
Field: Materials Science — Materials Chemistry

The yielding of granular matter is marginally stable and critical Amorphous materials undergo a transition from liquid-like to solid-like states through processes like rapid quenching or densification. Under external loads, they exhibit yielding, with minimal structural changes compared to crystals. However, these universal characteristics are rarely explored comprehensively in a single granular experiment due to the added complexity of inherent friction. The discernible differences between static configurations before and after yielding are largely unaddressed, and a comprehensive examination from both statistical physics and mechanical perspectives is lacking. To address these gaps, we conducted experiments using photoelastic disks, simultaneously tracking particles and measuring forces. Our findings reveal that the yielding transition demonstrates critical behavior from a statistical physics standpoint and marginal stability from a mechanical perspective, akin to the isotropic jamming transition. This criticality differs significantly from spinodal criticality in frictionless amorphous solids, highlighting unique characteristics of granular yielding. Furthermore, our analysis confirms the marginal stability of granular yielding by assessing the contact number and evaluating the balance between weak forces and small gaps. These factors serve as structural indicators for configurations before and after yielding. Our results not only contribute to advancing our understanding of the fundamental physics of granular materials but also bear significant implications for practical applications in various fields. Granular matter ; Jamming ; Spinodal ; Criticality ; Marginal stability ; Granular material ; Statistical physics ; Isotropy ; Materials science ; Amorphous solid ; Stability (learning theory) ; Condensed matter physics ; Physics ; Mechanics ; Nanotechnology ; Instability ; Computer science ; Chemistry ; Composite material ; Crystallography ; Optics Material Dynamics and Properties ; Granular flow and fluidized beds ; Adhesion, Friction, and Surface Interactions
Authors: Xianjin Liu | Zhanying Ma | Dasen Zhang | Qiwen Bao | Zhenzhen Liu | Jun‐Jun Xiao
Source: Advanced Optical Materials (article, 2024-06-27)
Field: Materials Science — Electronic, Optical and Magnetic Materials

Hypermultiplexed Off‐Chip Hologram by On‐Chip Integrated Metasurface Abstract The waveguide‐integrated metasurface introduces a novel photonic chip capable of converting guided modes into free‐space light. This enables functions such as off‐chip beam focusing, steering, and imaging. The challenge lies in achieving hyper‐multiplexing across diverse parameters, including guided‐wave mode type, direction, polarization, and notably, multiple wavelengths. Here, a comprehensive end‐to‐end inverse design framework is introduced, rooted in a physical model, for the multifunctional design of on‐chip metasurfaces. This framework allows for metasurface optimization through a target‐field‐driven iteration process. A hypermultiplexed on‐chip metasurface capable of generating red‐green‐blue holograms at multiple target planes is demonstrated, with both independent and cooperative control over guided‐wave direction. Significantly, the proposed method streamlines the design process utilizing only the positions of meta‐atoms as the design variable. Nine independent holographic channels are demonstrated through a combination of wavelength and distance multiplexing. Moreover, by incorporating the excitation direction into the design, the metasurface produces a total of 36 distinct holograms. The robustness of these results against fabrication discrepancies is validated through 3D full‐wave electromagnetic simulations, aligning well with advanced manufacturing techniques. The research presents a universal design framework for the development of multifunctional on‐chip metasurfaces, opening up new avenues for a wide range of applications. Holography ; Chip ; Multiplexing ; Optics ; Robustness (evolution) ; Materials science ; Photonics ; Optoelectronics ; Beam steering ; Computer science ; Physics ; Beam (structure) ; Telecommunications Metamaterials and Metasurfaces Applications ; Advanced Antenna and Metasurface Technologies ; Orbital Angular Momentum in Optics
Authors: Karolina Andrzejczyk | Sabrina Abou Kamar | Anne-Mar van Ommen | Elisa Dal Canto | Teun B. Petersen | Gideon Valstar | K. Martijn Akkerhuis | Maarten J. Cramer | Victor A. Umans | Frans H. Rutten | Arco J. Teske | Eric Boersma | Roxana Menken | Bas M. van Dalen | Leonard Hofstra | Marianne C. Verhaar | Jasper J. Brugts | Folkert W. Asselbergs | Hester M. den Ruijter | Isabella Kardys
Source: Scientific Reports (article, 2024-06-27)
Field: Chemistry — Spectroscopy

Identifying plasma proteomic signatures from health to heart failure, across the ejection fraction spectrum Circulating proteins may provide insights into the varying biological mechanisms involved in heart failure (HF) with preserved ejection fraction (HFpEF) and reduced ejection fraction (HFrEF). We aimed to identify specific proteomic patterns for HF, by comparing proteomic profiles across the ejection fraction spectrum. We investigated 4210 circulating proteins in 739 patients with normal (Stage A/Healthy) or elevated (Stage B) filling pressures, HFpEF, or ischemic HFrEF (iHFrEF). We found 2122 differentially expressed proteins between iHFrEF-Stage A/Healthy, 1462 between iHFrEF-HFpEF and 52 between HFpEF-Stage A/Healthy. Of these 52 proteins, 50 were also found in iHFrEF vs. Stage A/Healthy, leaving SLITRK6 and NELL2 expressed in lower levels only in HFpEF. Moreover, 108 proteins, linked to regulation of cell fate commitment, differed only between iHFrEF-HFpEF. Proteomics across the HF spectrum reveals overlap in differentially expressed proteins compared to stage A/Healthy. Multiple proteins are unique for distinguishing iHFrEF from HFpEF, supporting the capacity of proteomics to discern between these conditions. Ejection fraction ; Fraction (chemistry) ; Heart failure ; Heart failure with preserved ejection fraction ; Spectrum (functional analysis) ; Computational biology ; Cardiology ; Medicine ; Chemistry ; Biology ; Physics ; Chromatography Advanced Proteomics Techniques and Applications ; Cardiovascular Function and Risk Factors ; Cardiovascular and exercise physiology
Authors: Mary Rachel Nalehua | Joseph Zaia
Source: Analytical and Bioanalytical Chemistry (article, 2024-02-15)
Field: Chemistry — Spectroscopy

A critical evaluation of ultrasensitive single-cell proteomics strategies Throughput ; Proteome ; Proteomics ; Computer science ; Computational biology ; Mass spectrometry ; Instrumentation (computer programming) ; Single-cell analysis ; Chemistry ; Cell ; Bioinformatics ; Biology ; Chromatography ; Biochemistry Advanced Proteomics Techniques and Applications ; Mass Spectrometry Techniques and Applications ; Single-cell and spatial transcriptomics
Authors: Yuesong Zhou | Changsheng Zheng
Source: Polymer Composites (article, 2024-02-13)
Field: Materials Science — Materials Chemistry

Impact resistance performance and structural optimization of lightweight composite target plate Abstract The finite element model of a 7.62 mm armor‐piercing incendiary bomb penetrating lightweight composite target is established. The structure of the target plate is composed of boron carbide ceramic/carbon fiber laminate/aramid fiber laminate/damping material. The reasonable distribution position of damping material is explored by designing the material structure and geometric parameters. Genetic algorithm is used to optimize the structure of the lightweight composite target plate, and the feasibility of the optimization results is verified through experiments. The results show that under the same surface density, the energy absorption value of the target plate with a certain thickness of back layer damping is 1.36% higher than that of the target plate without damping. And the damping material on the back layer can act as a buffer layer to reduce blunt trauma caused by bullets to the human body. The surface density of the optimized lightweight composite target plate is reduced by 21.6% under the same protection capability. This work provides a theoretical foundation for the impact resistance design and optimization of lightweight composite target plates. Highlights Impact resistance performance of lightweight composite target plate is investigated. The impacting analytical model of the structure is established. The validity of the optimized impacting analytical model is verified by numerical simulation. Materials science ; Composite material ; Composite number ; Impact resistance ; Composite plate ; Resistance (ecology) ; Structural engineering ; Engineering High-Velocity Impact and Material Behavior ; Energetic Materials and Combustion ; Mechanical Behavior of Composites
Authors: Thanh Son Pham | Haiyu Zheng | Liang‐Yao Chen | Bui Xuan Khuyen | YoungPak Lee
Source: Scientific Reports (article, 2024-05-03)
Field: Materials Science — Electronic, Optical and Magnetic Materials

Wide-incident-angle, polarization-independent broadband-absorption metastructure without external resistive elements by using a trapezoidal structure The absorption of electromagnetic waves in a broadband frequency range with polarization insensitivity and incidence-angle independence is greatly needed in modern technology applications. Many structures based on metamaterials have been suggested for addressing these requirements; these structures were complex multilayer structures or used special materials or external electric components, such as resistive ones. In this paper, we present a metasurface structure that was fabricated simply by employing the standard printed-circuit-board technique but provides a high absorption above 90% in a broadband frequency range from 12.35 to 14.65 GHz. The metasurface consisted of structural unit cells of 4 symmetric substructures assembled with a metallic bar pattern, which induced broadband absorption by using a planar resistive interaction in the pattern without a real resistive component. The analysis, simulation, and measurement results showed that the metasurface was also polarization insensitive and still maintained an absorption above 90% at incident angles up to 45°. The suggested metasurface plays a role in the fundamental design and can also be used to design absorbers at different frequency ranges. Furthermore, further enhancement of the absorption performance is achieved by improved design and fabrication. Resistive touchscreen ; Metamaterial ; Broadband ; Materials science ; Polarization (electrochemistry) ; Absorption (acoustics) ; Optics ; Planar ; Optoelectronics ; Printed circuit board ; Fabrication ; Computer science ; Physics ; Electrical engineering ; Engineering ; Chemistry Metamaterials and Metasurfaces Applications ; Advanced Antenna and Metasurface Technologies ; Antenna Design and Analysis
Authors: Cristina Martínez-Ruedas | J.M. Flores-Arias | Isabel M. Moreno-Garcia | Matías Liñán-Reyes | F.J. Bellido-Outeiriño
Source: Preprints.org (preprint, 2024-03-25)
Field: Chemistry — Analytical Chemistry

A Cyber-Physical System Based on Digital Twin and 3D SCADA for Real-Time Monitoring of Olive Oil Mills. Cyber-physical Systems involve the creation, continuous updating and monitoring of virtual replicas that closely mirror their physical counterparts. These virtual representations are fed by real-time data from sensors, Internet of Things (IoT) devices and other sources, enabling a dynamic and accurate reflection of the state of the physical system. This emphasizes the importance of data synchronization, visualization and interaction within virtual environments as a means to improve decision-making, training, maintenance and overall operational efficiency. This paper presents a novel approach to a cyber-physical system to harness the power of Industry 4.0, Digital Twin technology, Virtual Reality (VR) and 3D SCADA in the context of monitoring and optimizing an olive mill. In conclusion, this paper presents a methodology that leverages digital twins and virtual reality to create an immersive, data-driven simulation and monitoring system for an olive mill. The proposed CPS takes data from the physical environment through the existing sensors and measurement elements in the olive mill, concentrates them and exposes them to the virtual environment through the Open Platform Communication United Architecture (OPC-UA) protocol, thus establishing a bidirectional and real-time communication. Furthermore, in the proposed virtual environment, the digital twin is interfaced with the 3D SCADA system, allowing it to create virtual models of the process. This innovative approach has the potential to revolutionize the olive oil industry by improving operational efficiency, product quality and sustainability, while optimizing maintenance practices. SCADA ; Olive oil ; Cyber-physical system ; Computer science ; Real-time computing ; Embedded system ; Engineering ; Petroleum engineering ; Computer security ; Operating system ; Electrical engineering ; Chemistry Spectroscopy and Chemometric Analyses