jablonkagroup/rise_ai_scientists huggingface dataset:
Authors: Ruben Shreshta | Andrew T. Rajczewski | Katherine Do | Matthew Willets | Manuel Kleiner | Timothy J. Griffin | Pratik Jagtap
Source: bioRxiv (Cold Spring Harbor Laboratory) (preprint, 2025-08-15)
Field: Chemistry — Spectroscopy

Evaluation of Parallel Accumulation-Serial Fragmentation methods for metaproteomics using a model microbiome ABSTRACT Mass spectrometry-based metaproteomics allows for the identification and quantification of thousands of proteins from clinical and environmental samples and is rapidly gaining importance in microbiome sciences. Metaproteomics researchers can measure taxonomic and functional abundances of microbiomes, shedding light on mechanistic details of microbiome interactions with their environment. However, metaproteomic analysis suffers from limited depth of coverage due to the presence of millions of peptides at lower abundance levels. Recent advances in data-independent acquisition mass spectrometry coupled with Parallel Accumulation-Serial Fragmentation (PASEF) technology offer improved depth of coverage. PASEF technology enables simultaneous accumulation of ions from multiple co-eluting peptides by combining ion mobility separation with dynamic quadrupole isolation, allowing efficient and selective fragmentation in a single scan. This boosts ion sampling efficiency and resolves overlapping signals with high sensitivity. In this study, we assessed proteome coverage, quantitative precision, and accuracy of Data-dependent acquisition (DDA) and Data-independent acquisition (DIA) methods coupled with the PASEF method. For this, we used a ground-truth mock community containing 28 species (30 strains) from all three domains of life and bacteriophages with a 400-fold dynamic range of organism abundance. Our results showed that diaPASEF demonstrated superior performance, identifying 168% more peptide precursors, 155% more peptides, and 66% more protein groups compared to ddaPASEF. Quantitative measurements showed improved precision with diaPASEF, with 26 out of 28 organisms exhibiting coefficient of variation values below 20%, compared to 24 organisms with ddaPASEF. Both ddaPASEF and diaPASEF methods accurately quantified the 22 most abundant organisms, while measurements of low-abundance bacteriophages showed significant deviation from expected values. Our findings demonstrate that diaPASEF provides enhanced depth of coverage and quantitative reliability for metaproteomics analysis, particularly beneficial for clinical and environmental microbiome studies where deeper functional characterization is essential. This study provides valuable benchmark data to facilitate the development of advanced bioinformatic methods for quantitative metaproteomics. Microbiome ; Fragmentation (computing) ; Metaproteomics ; Computational biology ; Computer science ; Metagenomics ; Biology ; Bioinformatics ; Genetics ; Gene Advanced Proteomics Techniques and Applications ; Genomics and Phylogenetic Studies ; Microbial Community Ecology and Physiology
Authors: Heena Ninama | Shaileshkumar K. Koradia
Source: Discover Chemistry. (article, 2025-11-04)
Field: Chemistry — Analytical Chemistry

Greenness assessment and stability-indicating HPTLC method for the concurrent analysis of dapagliflozin propanediol monohydrate and bisoprolol fumarate in a novel combined oral formulation This study involved the development and validation of a precise and reliable HPTLC method for the concurrent analysis of Dapagliflozin propanediol monohydrate and bisoprolol fumarate in pharmaceutical formulations. adhering to the Q2(R2) guidelines established by the International Council for Harmonization. Chromatographic separation was achieved on HPTLC silica gel 60 F₂₅₄ plates (10.0 cm × 10.0 cm, 0.20 mm) with a mobile phase of Chloroform: Toluene: Methanol: Ammonia (1:2:6:0.1 v/v/v). Detection was performed at 224 nm. Retention factor (Rf) values for Dapagliflozin propanediol monohydrate and bisoprolol fumarate were 0.22 ± 0.003 and 0.63 ± 0.006, respectively. The method showed excellent linearity with correlation coefficients of 0.9995 and 0.9991 for Dapagliflozin (200–1200 ng/band) and bisoprolol fumarate (100–600 ng/band), respectively. The reported method demonstrated precision in both intraday and interday analyses, with the percentage relative standard deviation of the peak area remaining below 2%. and recovery studies confirmed high accuracy with values ranging from 98.21 to 100.08% for dapagliflozin and 99.19–100.15% for bisoprolol fumarate. Forced degradation studies revealed that dapagliflozin was more susceptible to acidic and oxidative hydrolysis compared to bisoprolol fumarate, with baseline-resolved degradation products observed in all stress conditions. The developed HPTLC method has potential application for the concurrent quantification of Dapagliflozin propanediol monohydrate and bisoprolol fumarate in formulation. The MoGAPI tool and its associated software constitute a significant advancement in the assessment of analytical method greenness, offering researchers a robust and user-friendly platform for the evaluation and comparison of analytical techniques. Dapagliflozin ; Bisoprolol ; Degradation (telecommunications) ; Silica gel ; Relative standard deviation Analytical Methods in Pharmaceuticals ; Diabetes Treatment and Management ; Analytical Chemistry and Chromatography
Authors: Junping Xi | Zhipeng Wang | Linkun Zhang | Li Ma | Pingying Tang
Source: Metals (article, 2025-04-27)
Field: Materials Science — Materials Chemistry

Unveiling High-Pressure Behavior of Sc3AlC MAX Phase: A Comprehensive Theoretical Study on Structural, Mechanical, Dislocation, and Electronic Properties The structural, mechanical, dislocation, and electronic properties of the Sc3AlC MAX phase under applied pressure are investigated in detail using first-principles calculations. Key parameters, including lattice parameter ratios, elastic constants, Young’s modulus, bulk modulus, shear modulus, brittle-to-ductile behavior, Poisson’s ratio, anisotropy, Cauchy pressure, yield strength, Vickers hardness, and energy factors, are systematically analyzed as a function of applied pressure. The results demonstrate that the Sc3AlC MAX phase exhibits remarkable mechanical stability within the pressure range of 0 to 60 GPa. Notably, applied pressure markedly improves its mechanical properties, such as resistance to elastic, bulk, and shear deformations. The B/G ratio suggests a tendency toward ductile behavior with increasing pressure, and the negative Cauchy pressure indicates the directional characteristics of interatomic bonding in nature. Vickers hardness and yield strength increase under pressures of 0 to 10 GPa and then decrease sharply above 50 GPa. High pressure suppresses dislocation nucleation due to the increased energy factors, along with twinning deformation. Furthermore, electronic structure analysis confirms that high pressure enhances the interatomic bonding in the Sc3AlC MAX phase, while the enhancement effect is not substantial. This study offers critical insights for designing MAX phase materials for extreme environments, advancing applications in aerospace and electronics fields. Dislocation ; Materials science ; Phase (matter) ; Condensed matter physics ; High pressure ; Statistical physics ; Thermodynamics ; Physics ; Composite material ; Quantum mechanics MXene and MAX Phase Materials ; Boron and Carbon Nanomaterials Research ; Aluminum Alloys Composites Properties
Authors: Marisa D. Meier | Mona Schoberth | Yong Li | Oleg Borisov | Burulça Uluvar | Christopher Willecke | Heike Meiselbach | Kai‐Uwe Eckardt | Oliver Schilling | Anna Köttgen | Stefan Haug
Source: medRxiv (article, 2025-12-09)
Field: Chemistry — Spectroscopy

Characterization of the Urine Proteome Using the Olink Explore 3072 Platform Abstract Urinary proteins are valuable biomarkers for physiological processes and early detection and monitoring of systemic and kidney diseases. However, comprehensive quantification and characterization of the urine proteome using high-throughput platforms remains limited. Using an affinity-based assay for large-scale proteomics, the Olink Explore 3072 platform, we quantified 2,868 proteins in urine samples from 1,268 participants of the German Chronic Kidney Disease (GCKD) study. Protein detectability in urine, defined as the percentage of samples with measurements above the limit of detection, showed a bimodal distribution: 659 (23%) proteins had high (&gt;80%) and 1,336 proteins (47%) had low (&lt;20%) detectability. Over 95% of highly detectable proteins were confirmed as present in urine by mass spectrometry. They were enriched for extracellular, exosomal, and cell-surface localization, and showed tissue-specific expression in hepatocytes, immune cells, and proximal tubule cells. Significant associations of protein levels with sex (921 proteins), BMI (367 proteins) and age (157 proteins) showed plausible relationships such as prostate-specific antigen and male sex. Unsupervised correlation analysis of protein levels detected multiple biologically meaningful protein clusters, reflecting shared cellular compartments (e.g., lysosomal origin), tissue of origin (e.g., liver), and molecular interactions (e.g., receptor-ligand or chaperone-transporter complexes). In conclusion, the Olink Explore 3072 platform is well-suited for large-scale urine proteomics and identifies biologically plausible representations of ongoing processes in health and disease. Our comprehensive characterization provides a valuable resource for biomarker discovery and future targeted studies of urine proteins. Translational Statement Urinary proteins reflect kidney-specific and systemic processes, with the potential to serve as disease biomarkers. We demonstrate that the Olink Proximity Extension Assay enables high-throughput urine proteome screening with sufficient specificity to identify biologically plausible protein signatures and demographic associations. By providing comprehensive data on protein detectability, variability, and clinical associations, our study serves as a reference resource for designing targeted proteomic investigations, facilitating the development of urine-based biomarker panels for different purposes, potentially including early detection of impaired kidney function, monitoring kidney disease progression, and predicting treatment response. Proteome ; Urine ; Biomarker ; Proteomics ; Immune system ; Biomarker discovery ; Kidney ; Kidney disease Advanced Proteomics Techniques and Applications ; vaccines and immunoinformatics approaches ; Advanced Biosensing Techniques and Applications
Authors: R. Schulz | Ruohong Li | Julius Wessolek | Maryam Mostamand | P. Kunz | J. Lassen
Source: ArXiv.org (preprint, 2025-04-22)
Field: Chemistry — Spectroscopy

Two-step laser resonant ionization spectroscopy of chromium At TRIUMF's off-line laser ion source test stand, stepwise resonant laser ionization spectroscopy of chromium (Cr) was carried out, to find an efficient ionization scheme suitable for titanium sapphire (Ti:Sa) laser systems. With three different first-excitation transitions, 357.971 nm, 359.451 nm, and 360.636 nm, automated continuous laser-frequency scans using a frequency-doubled, grating-tuned Ti:Sa laser were performed. Rydberg series as well as autoionizing(AI) states were observed. From these results, the ionization potential (IP) of Cr was determined as 54575.49(2)$_\text{stat}$(2)$_\text{sys}$ cm$^{-1}$, which is one order of magnitude more precise than the previously reported 54575.6(3) cm$^{-1}$ in NIST database. The ionization scheme using the observed AI resonance, with 357.971 nm as the first step and 373.935 nm as the second step was subsequently deployed to the online delivery of radioactive Cr isotope beams for precision mass measurements. The online yields of $^{50-59}$Cr have been measured at TRIUMF-ISAC. Laser ; Ionization ; Atmospheric-pressure laser ionization ; Chromium ; Spectroscopy ; Mass spectrometry ; Ambient ionization ; Thermal ionization ; Ion source Mass Spectrometry Techniques and Applications ; Analytical chemistry methods development ; Ion-surface interactions and analysis
Authors: Amanda Suárez-Fernández | Judit Bestilleiro-Marquez | Gonzalo Sanchez-Duffhues | Ignacio Ortea
Source: bioRxiv (Cold Spring Harbor Laboratory) (preprint, 2025-10-02)
Field: Chemistry — Spectroscopy

Accessible and fast single-cell proteomics by DIA integrating Tecan UNO cell dispensing platform, Vanquish Neo LC and Exploris 480 MS Abstract Recent technological advancements in high-sensitivity LC-MS platforms and MS acquisition strategies have addressed key analytical challenges in single-cell proteomics (SCP), paving the way for SCP to become a transformative tool in biology and medicine. Techniques such as MS2 DIA and HRMS1 DIA exploit wide isolation windows and high-resolution MS1 and MS2 spectra to maximize protein identifications, even from low-abundance signals. In parallel, improved data processing algorithms reduce missing values and enhance the reliability of SCP data. These advancements are complemented by automated cell isolation technologies, which ensure precise single-cell handling with minimal sample loss, and in some implementations enable integrated, automated downstream sample preparation steps. Despite this progress, practical, end-to-end best practices for MS-based SCP remain an active area of optimization. Severe sample limitation, adsorption-related losses, the need for robust quantification across hundreds to thousands of single cells, and the lack of comprehensive protocols that systematically integrate and compare critical workflow variables complicate method selection and SCP implementation. In this context, this study builds on recent LC-MS based SCP advancements by presenting a complete, optimized, minimum user operation SCP workflow that integrates the Tecan UNO cell dispensing platform, a Vanquish Neo LC system, and an Orbitrap Exploris 480 mass spectrometer, applied to human primary cells. The workflow is designed to minimize data/cell loss, ensure high reproducibility, and maximize identifications. We evaluate key parameters, including acquisition schemes and LC gradient and column, and distill practical recommendations. The resulting protocol provides a foundation for an easy and accessible routine SCP application in biology and medicine. Workflow ; Automation ; Sample (material) ; Key (lock) ; Exploit ; Data acquisition ; Reliability (semiconductor) ; Isolation (microbiology) Advanced Proteomics Techniques and Applications
Authors: Nicoleta Matei | Semaghiul Birghilă | Simona Dobrinaș | Alina Soceanu | Viorica Popescu | Roxana Zaharia
Source: Applied Sciences (article, 2025-06-03)
Field: Chemistry — Analytical Chemistry

Physicochemical Properties, Trace Elements, and Health Risk Assessment of Edible Vegetable Oils Consumed in Romania The concentrations of trace elements (Cd, Pb, Cu, Cr, Ni, Co, and Mn) and physicochemical parameters of eight types of edible vegetable oils (obtained from a local market in Romania) were determined using graphite furnace atomic absorption spectrometry (GF-AAS) and Association of Official Analytical Chemists (AOAC) standard methods. The values of the physicochemical parameters show that most of the oils analyzed were within the limits established by the Codex Standards for Edible Oils, with a few exceptions (walnut oil acidity 2.080 mg/g; iodine value 72.7 g/100 g). The concentration of metals such as Cr, Ni, Co, Mn, and Cd were found to be within acceptable limits set by FAO/OMS (2002) in the edible vegetable oils, except for Cu (blend oil 0.627 mg/kg; organic extra virgin oil 0.312 mg/kg) and Pb (rice oil 0.217 mg/kg). The results obtained after health risk assessments and incremental lifetime cancer risk calculations showed that their values do not pose a health hazard, but continuous monitoring can provide data on the quality of edible vegetable oils for local consumers. A statistical test at the 0.1 probability level (p &lt; 0.1) was used to determine the degree of association between pairs of the variables. The data corresponding to the correlation coefficients for physicochemical parameters and different metals show significant and insignificant positive/negative correlations. Health risk ; Food science ; Health risk assessment ; Environmental science ; Environmental health ; Chemistry ; Medicine Heavy Metals in Plants ; Edible Oils Quality and Analysis ; Nutritional Studies and Diet
Authors: Jun‐Jie Wu | Xiaoming Zhang | Tongrui Li | Chunsheng Wang | C. H. Wang | Yan Feng | Xiang Ma | Zhe Sun | Yalin Lu | Guolin Zheng | Feng Liu | Bin Xiang
Source: Nano Research (article, 2025-07-18)
Field: Materials Science — Materials Chemistry

Self-assembled SnS/TaS <sub>2</sub> superconducting superlattice with non-trivial band topology Intrinsic topological superconductors have garnered significant attention for their potential to harbor novel quantum phenomena. However, the limited availability of suitable material systems has hindered progress in this field. Here, we present the synthesis and characterization of high-quality self-assembled SnS/TaS<sub>2</sub> (SnTaS<sub>3</sub>) superlattice, which exhibits superconductivity alongside non-trivial band topology. Temperature-dependent magnetization susceptibility and electrical transport results confirm SnTaS<sub>3</sub> as a type-II superconductor with a critical transition temperature <em>T</em><sub>c</sub> of 3 K. Interestingly, this superconductivity can be turned off via an innovative solid proton gate technique, and a new superconducting state with a <em>T</em><sub>c</sub> of ~2.3 K emerges when the gating voltage reaches -9.47 V. Heat capacity measurements reveal strong electronic correlations within this material, which is further supported by angle-resolved photoemission spectroscopy and first-principles calculations, underscoring the effect of topological flat bands and Van Hove singularity. Our research introduces a promising self-assembled material platform, adeptly positioned to delve into the quest for topological superconductors. Superlattice ; Superconductivity ; Condensed matter physics ; Topology (electrical circuits) ; Physics ; Materials science ; Mathematics ; Combinatorics 2D Materials and Applications ; Chalcogenide Semiconductor Thin Films ; Quantum Dots Synthesis And Properties
Authors: Hideki Maki | Fukumatsu Iwahashi | Yoshie Ohke | Ryo Fujimoto | Masanori Yamasaki
Source: Breeding Research (article, 2025-04-14)
Field: Chemistry — Analytical Chemistry

Development of a non-destructive evaluation system for photosynthetic product contents in rice seedlings using hyperspectral imaging 作物の品種育成で必要不可欠となっている表現型計測には多大な時間と労力が割かれていることから，その効率化が求められている．ハイパースペクトル（HS）カメラを利用したイメージング技術は，植物の内部状態を非破壊で解析できるだけでなく，目的とする情報の分布を可視化できる点が大きな魅力である．本手法の強みを活かし，植物における化学的ならびに生理的特性の解析を高速かつ簡便にすることを本研究の目的とし，その一例としてイネ幼苗の光合成産物含量の非破壊評価系の確立を試みた．日本型イネ品種「コシヒカリ」およびインド型イネ品種「IR64」の幼苗を様々な光条件で栽培し，HSカメラで撮影した画像から植物部分のHS反射率データを抽出した．撮影後のイネ幼苗は部位別に採集し，光合成産物（ショ糖およびデンプン）の含量をLC-MSの分析値から算出した．全体で葉身198点および葉鞘198点のデータを分割し，学習データと検証データとした．HS反射率データを説明変数，ショ糖含量およびデンプン含量を目的変数として，部分的最小二乗回帰（Partial Least Squares Regression: PLS）によって部位別に予測モデルを作成し，決定係数（R2）などを算出した．同一個体を経時的に撮影したHS反射率データに，作成したショ糖含量の予測モデル（葉身：R2 = 0.58，葉鞘：R2 = 0.73）とデンプン含量の予測モデル（葉身：R2 = 0.89，葉鞘：R2 = 0.68）を適用し，画素単位のショ糖含量およびデンプン含量の分布を推定したところ，連続的な光条件下で各含量が徐々に増加する様子を可視化できた．また，各含量の実測値では，先んじて葉身で増加し，遅れて葉鞘での増加が認められ，可視化画像においても同様の傾向が確認された．以上の結果から，HSイメージングを用いることで，イネの幼苗における個体レベルの光合成産物含量の差異や変化を非破壊で可視化できることが示された． Hyperspectral imaging ; Photosynthesis ; Product (mathematics) ; Horticulture ; Agricultural engineering ; Agronomy ; Botany ; Biology ; Mathematics ; Computer science ; Engineering ; Artificial intelligence Spectroscopy and Chemometric Analyses
Authors: Sopheap Sam | Sreypich Say | Kosuke Yamazaki | Hiroshi Nakatsugawa
Source: Institutional Repositories DataBase (IRDB) (article, 2025-11-12)
Field: Materials Science — Materials Chemistry

Strategies to improve the thermoelectric performance of iron silicide-based materials Iron silicide (β-FeSi2) has attracted considerable interest as a sustainable thermoelectric material due to its abundance, non-toxicity, and environmental compatibility. Their conduction flexibility allows a wide range of dopants to tune transport behavior, creating opportunities for improved performance. However, dopant solubility limits and the formation of secondary phases remain key challenges. In this article, we highlight recent advances in strategies to enhance the thermoelectric performance of β-FeSi2-based materials and discuss the interplay between phase evolution, electrical, and thermal transport. We also outline prospects that may unlock further improvements, offering pathways toward higher thermoelectric efficiency in this material system. Impact Statement This review covers the observation of structural transition and strategies to enhance electrical and thermoelectric properties of metal-doped iron silicides, providing insights for future research to improve material performance. Thermoelectric effect ; Work (physics) ; Thermoelectric materials ; Thermoelectric cooling ; Field (mathematics) Advanced Thermoelectric Materials and Devices ; Semiconductor materials and interfaces ; Heusler alloys: electronic and magnetic properties
Authors: Dwi Ardiana Setyawardhani | Tri Hardian Satiawardana
Source: Discover Chemical Engineering (article, 2025-11-05)
Field: Chemistry — Organic Chemistry

Innovative approach to vegetable oil production and refining technology in Indonesia: a review Indonesia, as one of the world’s largest producers of vegetable oil, consistently develops oil production technology, including the extraction and refining process. This study reviews recent innovations in vegetable oil extraction and refining technologies across Indonesia, emphasizing industrial scalability, efficiency, and sustainability. Key extraction methods include mechanical pressing, solvent extraction, and advanced techniques such as microwave- and ultrasound-assisted extraction. Refining stages—degumming, neutralization, bleaching, and deodorization—have seen technological advancements including enzymatic and membrane-based degumming, bio-adsorbent-based FFAs removal, and regeneration of spent bleaching earth. New methods like microwave-assisted extraction (MAE) and the use of natural adsorbents from waste materials are being used to improve oil quality, reduce harmful compounds, and make the process more efficient and eco-friendly. These innovations aim to improve oil yield, purity, and functional quality while minimizing environmental impacts. The review consolidates data from 40 recent studies and highlights the potential of integrating these technologies to elevate Indonesia’s vegetable oil industry toward higher quality, eco-friendly, and economically viable production. While significant development has been made in extraction and purification using biosorbents, improvements in degumming and deodorization are still limited. Refining (metallurgy) ; Vegetable oil ; Extraction (chemistry) ; Production (economics) ; Process (computing) ; Oil refinery ; Solvent extraction Edible Oils Quality and Analysis ; Biodiesel Production and Applications ; Food Drying and Modeling
Authors: María Belén Buenaño | Carmen Ulloa Ulloa | Javier Francisco‐Ortega | Alan W. Meerow | Nora H. Oleas
Source: BMC Plant Biology (article, 2025-01-24)
Field: Chemistry — Organic Chemistry

Population genetic structure of Phaedranassa cinerea Ravenna (Amaryllidaceae) and conservation implications Phaedranassa cinerea shows lower genetic diversity than related species, with the most variation within populations. We identified two to four genetic groups, suggesting recent divergence along the ridges of the western Andes. The findings suggest that conservation efforts should focus on securing genetic exchange between populations to preserve the genetic diversity of P. cinerea. Biology ; Ravenna ; Amaryllidaceae ; Population ; Population structure ; Botany ; Demography ; Engineering Chemical synthesis and alkaloids ; Plant and animal studies ; Flowering Plant Growth and Cultivation