jablonkagroup/rise_ai_scientists huggingface dataset:
Authors: Mengbo Li | Simon A. Cobbold | Gordon K. Smyth
Source: bioRxiv (Cold Spring Harbor Laboratory) (preprint, 2025-04-29)
Field: Chemistry — Spectroscopy

Quantification and differential analysis of mass spectrometry proteomics data with probabilistic recovery of information from missing values Abstract Mass spectrometry (MS) is the technology standard for expression proteomics, but statistical analysis of the resulting data is complicated by the occurrence of missing values. Missing values remain ubiquitous in MS-based proteomics data and are especially frequent in the emerging fields of single-cell and spatial proteomics. The limpa package implements new methods for quantification and differential expression analysis of MS proteomics data, including probabilistic information recovery from missing values. limpa summarises peptide-level data to estimate an expression value for every protein in every sample. Expression values that are supported by fewer detected peptides or involve more missing values are treated as less precise and are downweighted in the differential expression analysis, maximising statistical power while avoiding false discoveries. limpa produces a linear model object suitable for downstream analysis with the limma package, allowing complex experimental designs and other downstream tasks such as the gene ontology or pathway analysis. Missing data ; Mass spectrometry ; Probabilistic logic ; Proteomics ; Computer science ; Data mining ; Chromatography ; Chemistry ; Artificial intelligence ; Machine learning Advanced Proteomics Techniques and Applications ; Metabolomics and Mass Spectrometry Studies ; Gene expression and cancer classification
Authors: Kanvisit Maraphum | Kantisa Phoomwarin | Nirattisak Khongthon | Jetsada Posom
Source: Energies (article, 2025-06-26)
Field: Chemistry — Analytical Chemistry

Eliminating Effect of Moisture Content in Prediction of Lower Heating Value and Ash Content in Sugarcane Leaves Biomass Accurate assessment of biomass fuel properties is essential for quality control and fair market pricing, particularly when dealing with variable moisture content (MC) in agricultural residues. This study investigates the use of near-infrared (NIR) spectroscopy to predict the lower heating value (LHV) and ash content of sugarcane leaf pellets while minimizing the interference caused by moisture variability. Sixty-two samples were scanned using an NIR spectrometer over three week-long storage periods to get different MCs with the same sample. Additionally, variable selection methods such as a genetic algorithm (GA) and moisture-related wavelength exclusion were explored. The optimal model for LHV prediction was developed using GA-PLS regression (Method II), provided a coefficient of determination (R2) of 0.80, a root mean square error of calibration (RMSEc) of 595.80 J/g, and a ratio of performance to deviation (RPD) of 1.74, indicating fair predictive performance. The ash content model showed moderate accuracy, with a maximum R2 of 0.61 and an RPD of 1.40. These findings suggest that the variables selected via GA in Method II were not relevant to MC; as Method II provided the best result, this indicates a low impact of MC, which may influence model construction in the future. Moreover, the findings also highlight the potential of NIR spectroscopy, combined with appropriate spectral preprocessing and wavelength optimization, as a rapid, non-destructive tool for evaluating biomass quality, enabling more precise control in bioenergy production and biomass trading. Water content ; Biomass (ecology) ; Heat of combustion ; Environmental science ; Value (mathematics) ; Pulp and paper industry ; Mathematics ; Content (measure theory) ; Bioenergy ; Agronomy ; Biofuel ; Waste management ; Engineering ; Chemistry ; Statistics ; Combustion ; Biology Spectroscopy and Chemometric Analyses ; Sugarcane Cultivation and Processing ; Mineral Processing and Grinding
Authors: Bo Liu | Yunqiang Zhang | Zhu Li | Bingyan Wei | Xuetao Gan | Xin Xie
Source: Nanomaterials (article, 2025-04-07)
Field: Materials Science — Electronic, Optical and Magnetic Materials

Broadband and Wide Field-of-View Refractive and Meta-Optics Hybrid Imaging System for Mid-Wave Infrared We propose a wide field-of-view (FOV) refractive and meta-optics hybrid imaging system designed for the mid-wave infrared spectrum (3-5 μm) to address the challenge of high-quality imaging in wide FOV applications. The system consists of only three refractive lenses and two metasurfaces (one functioning as a circular polarizer and the other as a phase element), with a total length of 29 mm. Through a detailed analysis of modulation transfer function curves and spot diagrams, the system achieves 178° FOV while maintaining exceptional imaging performance across a temperature range of -40 °C to 60 °C. The system demonstrates the potential for extending applications to other wavelengths and scenarios, thereby contributing to the advancement of high-performance compact optical systems. Polarizer ; Optics ; Broadband ; Optical transfer function ; Field of view ; Infrared ; Phase (matter) ; Physics ; Materials science Metamaterials and Metasurfaces Applications ; Optical Wireless Communication Technologies ; Photonic and Optical Devices
Authors: Ettore Settanni | Jagjit Singh Srai
Source: Quality & Quantity (preprint, 2025-07-26)
Field: Chemistry — Analytical Chemistry

It’s a long way to the top (if you wanna biplot): a back-to-basics perspective on the implementation of principal component biplots in R Principal Component Analysis and biplots are so well-established and readily implemented that it is just too tempting to take for granted their internal workings. In this note we compare how PCA and biplots are implemented in the R language for statistical computing, leveraging a software-agnostic understanding of computational building-blocks that both techniques have in common. We do so with a view to illustrating discrepancies that users might find elusive, as these arise from seemingly innocuous computational choices made under the hood. Wider implications are derived from a simplified case based on real-world clinical trial supply chains data. By getting back to basics, the proposed evaluation grid elevates aspects that are usually disregarded, including relationships that should hold if the computational rationale underpinning each technique is followed correctly. Strikingly, what is expected from these equivalences rarely follows without caveats from the output of specific implementations alone. Principal component analysis ; Biplot ; Implementation ; Component (thermodynamics) ; Computer science ; Principal (computer security) ; Artificial intelligence ; Software engineering ; Biology ; Physics Spectroscopy and Chemometric Analyses ; Meat and Animal Product Quality
Authors: Ute Distler | Han Byul Yoo | Oliver Kardell | D. Hein | Malte Sielaff | Marc Scherer | Anna Maria Józefowicz | Christian Leps | David Gómez-Zepeda | Christine von Toerne | Juliane Merl‐Pham | Teresa K. Barth | Johanna Tüshaus | Pieter Giesbertz | Torsten Müller | Georg Kliewer | Karim Aljakouch | Barbara Helm | Horst Unger | Dario L. Frey | Dominic Helm | Luisa Schwarzmüller | Oliver Popp | Di Qin | Susanne I. Wudy | Ludwig Sinn | Julia Mergner | Christina Ludwig | Axel Imhof | Bernhard Küster | Stefan F. Lichtenthaler | Jeroen Krijgsveld | Ursula Klingmüller | Philipp Mertins | Fabian Coscia | Markus Ralser | Michael Mülleder | Stefanie M. Hauck | Stefan Tenzer
Source: Nature Communications (article, 2025-10-02)
Field: Chemistry — Spectroscopy

Multicenter evaluation of label-free quantification in human plasma on a high dynamic range benchmark set Human plasma is routinely collected during clinical care and constitutes a rich source of biomarkers for diagnostics and patient stratification. Liquid chromatography-mass spectrometry (LC-MS)-based proteomics is a key method for plasma biomarker discovery, but the high dynamic range of plasma proteins poses significant challenges for MS analysis and data processing. To benchmark the quantitative performance of neat plasma analysis, we introduce a multispecies sample set based on a human tryptic plasma digest containing varying low level spike-ins of yeast and E. coli tryptic proteome digests, termed PYE. By analysing the sample set on state-of-the-art LC-MS platforms across twelve different sites in data-dependent (DDA) and data-independent acquisition (DIA) modes, we provide a data resource comprising a total of 1116 individual LC-MS runs. Centralized data analysis shows that DIA methods outperform DDA-based approaches regarding identifications, data completeness, accuracy, and precision. DIA achieves excellent technical reproducibility, as demonstrated by coefficients of variation (CVs) between 3.3% and 9.8% at protein level. Comparative analysis of different setups clearly shows a high overlap in identified proteins and proves that accurate and precise quantitative measurements are feasible across multiple sites, even in a complex matrix such as plasma, using state-of-the-art instrumentation. The collected dataset, including the PYE sample set and strategy presented, serves as a valuable resource for optimizing the accuracy and reproducibility of LC-MS and bioinformatic workflows for clinical plasma proteome analysis. Human plasma ; Proteome ; Benchmark (surveying) ; Data set ; Set (abstract data type) ; Workflow ; Quantitative proteomics ; Proteomics ; Sample (material) Advanced Proteomics Techniques and Applications ; Mass Spectrometry Techniques and Applications ; Metabolomics and Mass Spectrometry Studies
Authors: Babu Naik Gugulothu | Sanjay Lakshminarayanan | Madhu Palati | Suresh Haleyur Lakshmegowda | Mahipal Bukya
Source: Engineering Research Express (article, 2025-01-03)
Field: Materials Science — Materials Chemistry

A practical case study on effect of moisture ingress in power cables and methods to reduce equipment failure Abstract Over the past few years, there has been a rise in the quantity of underground cables used in power transmission and distribution networks in many urban areas worldwide. Technological and economic considerations, along with space constraints, are responsible for this increase. As the number of cables increases, utilities face challenges in effectively maintaining and testing their condition. Particularly, the maintenance of medium-voltage cables, such as three-core 33 kV cables, is becoming increasingly challenging. One of the biggest problems with medium-voltage cables is their preference when the load is closer to the substation. Because the cables are closer to the source, the probability of the end termination kit failing is higher, leading to short-line faults (SLF). Short-line faults subject the connected switchgear and transformers to severe electrical, thermal, and mechanical stresses. Cable faults can cause equipment failure, resulting in external flashovers, which in turn raise the temperature and ultimately lead to insulator failure. Low external temperatures can increase moisture content in the environment, leading to equipment failure. This paper investigates switchgear failures in 132/33 KV substations caused by cable faults and ambient temperature and presents methods to mitigate switchgear and instrument transformer failures caused by cable faults. Over time, the proposed methods have led to a decrease in the number of failures. In recent years, protocols such as IEC61850, MODBUS, IEC60870-4, and others have transformed conventional substations into automated substations. We propose a low-cost, practically feasible solution using the GOOSE technique in the IEC61850 protocol to prevent the flashover of the circuit breakers, following a detailed investigation. Switchgear ; Reliability engineering ; Transformer ; Engineering ; Arc flash ; Electrical engineering ; Power transmission ; Voltage ; Automotive engineering ; Power (physics) High voltage insulation and dielectric phenomena ; Electrical Fault Detection and Protection ; Thermal Analysis in Power Transmission
Authors: Juho Park | Ju‐Young Kim | Sunghyun Nam | Min Seok Jang
Source: Advanced Optical Materials (article, 2025-05-15)
Field: Materials Science — Electronic, Optical and Magnetic Materials

High‐Efficiency Multi‐Level Beam Switching with Single‐Gate Tunable Metasurfaces Based on Graphene Abstract The growing demand for ultra‐fast telecommunications, autonomous driving, and futuristic technologies highlights the crucial role of active beam steering at the nanoscale. This is essential for applications like LiDAR, beam‐forming, and holographic displays, especially as devices reduce in form factor. Although a device with active beam‐switching capability is a potential candidate for realizing those applications, there are only a few works to realize beam switching in reconfigurable metasurfaces with active tuning materials. In this paper, a multi‐level beam‐switching dielectric metasurface is theoretically presented with a graphene layer for active tuning, addressing challenges associated with achieving high directivity and diffraction efficiency, and doing so while using a single‐gate setup. For two‐level switching, the directivities reached above 95%, and the diffraction efficiencies are ≈50% at the operation wavelength λ 0 = 8 µm. Through quasi‐normal mode expansion, the physics of the beam‐switching metasurface inverse‐designed by the adjoint method is illustrated, highlighting the role of resonant modes and their response to charge carrier tuning. Under the same design scheme, characteristics of a three‐level and four‐level beam‐switching device is designed and reported, suggesting a possibility of generalizing to multi‐level beam switching. Materials science ; Beam steering ; Beam (structure) ; Optoelectronics ; Optical switch ; Graphene ; Optics ; Diffraction ; Nanotechnology ; Physics Metamaterials and Metasurfaces Applications ; Advanced Antenna and Metasurface Technologies ; Antenna Design and Analysis
Authors: Ananth Prakash | Andrew Collins | Liora Haim-Vilmovsky | Silvie Fexová | Andrew R. Jones | Juan Antonio Vizcaíno
Source: Journal of Proteome Research (article, 2025-01-07)
Field: Chemistry — Spectroscopy

Integrated View of Baseline Protein Expression in Human Tissues Using Public Data Independent Acquisition Data Sets The PRIDE database is the largest public data repository of mass spectrometry-based proteomics data and currently stores more than 40,000 data sets covering a wide range of organisms, experimental techniques, and biological conditions. During the past few years, PRIDE has seen a significant increase in the amount of submitted data-independent acquisition (DIA) proteomics data sets. This provides an excellent opportunity for large-scale data reanalysis and reuse. We have reanalyzed 15 public label-free DIA data sets across various healthy human tissues to provide a state-of-the-art view of the human proteome in baseline conditions (without any perturbations). We computed baseline protein abundances and compared them across various tissues, samples, and data sets. Our second aim was to compare protein abundances obtained here from the results of previous analyses using human baseline data-dependent acquisition (DDA) data sets. We observed a good correlation across some tissues, especially in the liver and colon, but weak correlations were found in others, such as the lung and pancreas. The reanalyzed results including protein abundance values and curated metadata are made available to view and download from the resource Expression Atlas. Metadata ; Human Protein Atlas ; Proteomics ; Proteome ; Baseline (sea) ; Computer science ; Data acquisition ; Protein expression ; Biology ; Computational biology ; Bioinformatics ; World Wide Web ; Biochemistry Advanced Proteomics Techniques and Applications ; Mass Spectrometry Techniques and Applications ; Metabolomics and Mass Spectrometry Studies
Authors: Florian Harking | Ulises H. Guzmán | Julia Kraegenbring | Hamish Stewart | Konstantin Aizikov | Heiner Koch | Kyle L. Fort | Alexander Harder | Jesper V. Olsen
Source: Journal of Proteome Research (article, 2025-06-30)
Field: Chemistry — Spectroscopy

Enhancing Tandem MS Sensitivity and Peptide Identification via Ion Preaccumulation in an Orbitrap Mass Spectrometer High-throughput mass spectrometry-based proteomics has gained increasing interest for both academic and industrial applications. As implementation of faster gradients has facilitated higher sample throughput, mass spectrometers must adapt to shorter analysis times by enhancing the scanning speed and sensitivity. For Orbitrap mass spectrometers, faster scan rates are constrained by the need for sufficient ion accumulation time, particularly given the limitations on the duty cycle at high repetition rates, and transient length, which determines analyzer sensitivity and resolving power. In this context, implementing alternative ion scheduling and better ion signal-processing strategies is needed to unleash the speed of these instruments. Here, we introduce a new scanning strategy termed preaccumulation, which enables the storage of ions in the bent flatapole in parallel to the operation of the C-trap/IRM, leading to a significant improvement in ion beam utilization and enabling for the first time scanning speeds of ∼70 Hz on hybrid Orbitrap instruments. The combination of preaccumulation and increased scan speeds notably enhances peptide and protein group identifications for short LC gradients and improves sensitivity for high-throughput applications. These benefits were further amplified when coupled with the full mass range phase-constrained spectrum deconvolution method (ΦSDM), especially for fast, lower-resolution Orbitrap measurements with short LC gradients. Overall, we demonstrate that preaccumulation of ions in the bent flatapole offers distinct advantages, particularly for conditions with reduced signal input. Since no hardware changes are required, this approach is highly attractive for Orbitrap mass spectrometers operated with fast MS/MS acquisition methods. Orbitrap ; Tandem mass spectrometry ; Mass spectrometry ; Chemistry ; Hybrid mass spectrometer ; Chromatography ; Top-down proteomics ; Tandem mass tag ; Tandem ; Protein mass spectrometry ; Peptide ; Selected reaction monitoring ; Analytical Chemistry (journal) ; Proteomics ; Quantitative proteomics ; Materials science ; Biochemistry Advanced Proteomics Techniques and Applications ; Mass Spectrometry Techniques and Applications ; Metabolomics and Mass Spectrometry Studies
Authors: Vincent Nieboer | Jakob Wohlert | Peter Olsén | Karin Odelius
Source: Faraday Discussions (article, 2025-09-17)
Field: Materials Science — Biomaterials

More than ring-strain: revisiting the definition of enthalpy in ring-opening polymerization The thermodynamics of ring-opening polymerization (ROP) are central when predicting the chemical recyclability of aliphatic polyesters and polycarbonates. Conceptually, the enthalpy of polymerization, , is widely understood as a measure of ring-strain for a given monomer. However, the ring-strain is commonly larger than , generating the question of how the release of ring-strain energy during ring-opening transforms. In this work, we propose that is the sum of the energy released by the ring-strain and the energy absorbed by the polymer conformations . Owing to the similar ring-strain, but vastly different values, δ-valerolactone, δ-caprolactone, δ-octalactone, and δ-decalactone were used as model compounds to evaluate the energy cost of polymer conformational freedom. Polymer conformation, measured by <sup>13</sup>C NMR, DSC, and molecular dynamics, results are in good agreement with the hypothesis and can explain previous literature observations <i>i.e.</i> positive for systems with ring-strain, substituent effects, and solvent effects, that are difficult to understand when only using the analogy of ring-strain and . We believe that our results provide a deeper understanding of the underlying thermodynamics and their interpretation in ROP. Polymerization ; Enthalpy ; Polymer ; Substituent ; Interpretation (philosophy) ; Polyester ; Solvent ; Standard enthalpy of reaction biodegradable polymer synthesis and properties ; Advanced Polymer Synthesis and Characterization ; Polymer crystallization and properties
Authors: Markus M. Hoffmann | T. N. SMITH | Gerd Buntkowsky
Source: Molecules (article, 2025-06-04)
Field: Chemistry — Spectroscopy

The Interplay of Inter- and Intramolecular Hydrogen Bonding in Ether Alcohols Related to n-Octanol n-Octanol and related ether alcohols are studied via molecular dynamics (MD) simulations using the two classical all-atom force fields OPLS-AA and CHARMM. The ether alcohols studied possess one ether functionality separated by varying n carbon atoms from the hydroxy group to elucidate how the positioning of the ether functionality affects intra- and intermolecular hydrogen bonding and, in turn, the physical properties of the studied alcohols. Important general trends observed from simulations with both force fields include the following: Intramolecular hydrogen bonding is majorly present in 3-butoxypropanol and 4-propoxybutanol (n = 3 and 4) while being only marginally present for 5-ethoxypentanol and 6-methoxyhexanol (n = 5 and 6) and absent in 1-hexyloxymethanol and 2-pentyloxyethanol (n = 1 and 2). The intramolecular hydrogen bonds formed by 3-butoxypropanol and 4-propoxybutanol are among the most stable ones of all present hydrogen bonds. Intermolecular hydrogen bonding is stronger between hydroxy groups (OH-OH) than between hydroxy and ether groups (OH-OE). An increased temperature causes a reduction in intermolecular OH-OH and OH-OE hydrogen bonding but a slight increase in intramolecular hydrogen bonding. A reduction in end-to-end distances at a higher temperature is also observed for all studied alcohols, which is likely a reflection of increased dihedral bond rotations. Hydrogen bonding extends mostly between just two molecules while hydrogen bonding networks are rare but do exist, involving, in some instances, up to 30 hydrogen bonds. Regardless of force field and temperature, the obtained radial distribution functions (RDFs) mostly show the same features at same distances that only vary in their intensity. 1-hexyloxymethanol forms a very specific and stable intermolecular double OH-OE hydrogen-bonded dimer. Similar double-hydrogen-bonded dimers can be found for the ether alcohols but are only significantly present for 2-pentyloxyethanol. Overall, the main difference between OPLS-AA and CHARMM is their quantitative prediction of the present hydrogen bonding speciation largely due to the stiffer dihedral potentials in OPLS-AA compared to the CHARMM force field. The simulations indicate that (a) the variations in densities are correlated to the reduced packing efficiency caused by intramolecular hydrogen bonding, (b) self-diffusion correlates with the stability of the intermolecular hydrogen bonds, and (c) the presence of hydrogen-bonded networks, although small in numbers, affect the viscosity. Intramolecular force ; Hydrogen bond ; Intermolecular force ; Chemistry ; Ether ; Low-barrier hydrogen bond ; Dihedral angle ; Crystallography ; Molecule ; Hydrogen ; Computational chemistry ; Stereochemistry ; Organic chemistry Molecular spectroscopy and chirality ; Crystallography and molecular interactions ; Analytical Chemistry and Chromatography