jablonkagroup/rise_ai_scientists huggingface dataset:
Authors: Tung X. Trinh | Rebecca Freitag | Konrad Krawczyk | Veit Schwämmle
Source: ImmunoInformatics (article, 2024-08-23)
Field: Chemistry — Spectroscopy

Data mining antibody sequences for database searching in bottom-up proteomics <h2>Abstract</h2> Mass spectrometry-based proteomics facilitates the identification and quantification of thousands of proteins but encounters challenges in measuring human antibodies due to their vast diversity. Bottom-up proteomics methods primarily rely on database searches, comparing experimental peptide values to theoretical database sequences. While the human body can produce millions of distinct antibodies, current databases, such as UniProtKB/Swiss-Prot, contain only 1095 sequences (as of January 2024), potentially hindering antibody identification via mass spectrometry. Therefore, expanding the database is crucial for discovering new antibodies. Recent genomic studies have amassed millions of human antibody sequences in the Observed Antibody Space (OAS) database, yet this data remains underutilized. Leveraging this vast collection, we conduct efficient database searches in publicly available proteomics data, focusing on SARS-CoV-2. In our study, thirty million heavy antibody sequences from 146 SARS-CoV-2 patients in the OAS database were digested <i>in silico</i> to obtain 18 million unique peptides. These peptides form the basis for new bottom-up proteomics databases. We used those databases for searching new antibody peptides in publicly available SARS-CoV-2 human plasma samples in the Proteomics Identification Database (PRIDE). This approach avoids false positives in antibody peptide identification as confirmed by searching against negative controls (brain samples) and employing different database sizes. We show that new antibody peptides were found in previous plasma samples and expect that the newly discovered antibody peptides can be further employed to develop therapeutic antibodies. The method will be broadly applicable to find characteristic antibodies for other diseases. Computer science ; Database ; Data mining ; Top-down and bottom-up design ; Data science ; Information retrieval ; Software engineering Advanced Proteomics Techniques and Applications ; Monoclonal and Polyclonal Antibodies Research ; Advanced Biosensing Techniques and Applications
Authors: Samuel S. Welborn | Chris Harris | Stephanie M. Ribet | Georgios Varnavides | Colin Ophus | Bjoern Enders | Peter Ercius
Source: arXiv (Cornell University) (preprint, 2024-07-03)
Field: Materials Science — Surfaces, Coatings and Films

Streaming Large-Scale Electron Microscopy Data to a Supercomputing Facility Data management is a critical component of modern experimental workflows. As data generation rates increase, transferring data from acquisition servers to processing servers via conventional file-based methods is becoming increasingly impractical. The 4D Camera at the National Center for Electron Microscopy (NCEM) generates data at a nominal rate of 480 Gbit/s (87,000 frames/s) producing a 700 GB dataset in fifteen seconds. To address the challenges associated with storing and processing such quantities of data, we developed a streaming workflow that utilizes a high-speed network to connect the 4D Camera's data acquisition (DAQ) system to supercomputing nodes at the National Energy Research Scientific Computing Center (NERSC), bypassing intermediate file storage entirely. In this work, we demonstrate the effectiveness of our streaming pipeline in a production setting through an hour-long experiment that generated over 10 TB of raw data, yielding high-quality datasets suitable for advanced analyses. Additionally, we compare the efficacy of this streaming workflow against the conventional file-transfer workflow by conducting a post-mortem analysis on historical data from experiments performed by real users. Our findings show that the streaming workflow significantly improves data turnaround time, enables real-time decision-making, and minimizes the potential for human error by eliminating manual user interactions. Supercomputer ; Scale (ratio) ; Computer science ; Computational science ; Computer graphics (images) ; Parallel computing ; Physics Electron and X-Ray Spectroscopy Techniques ; Advanced Electron Microscopy Techniques and Applications
Authors: S. Ryniak | Piotr Harbut
Source: Wiadomości Lekarskie (article, 2024-01-01)
Field: Chemistry — Organic Chemistry

SUBSTYTUCJA EGZOGENNYCH CHOLINESTERAZ W LECZENIU CIĘŻKICH ZATRUĆ ZWIĄZKAMI FOSFOROORGANICZNYMI Zatrucia związkami fosforoorganicznymi na terenie Europy i Ameryki północnej nie zdarzają się często. Znacznie większa ich częstotliwość obserwowana jest w Azji i Afryce wschodniej zarówno w związku z używaniem tych środków chemicznych w rolnictwie (pestycydy) jak również będąc przyczyną zatruć w około 30% przypadków samobójczych. Związki fosforoorganiczne stosowanie mogą być też jako bojowe środki chemiczne z grupy środków paralityczno-drgawkowych (Sarin. Soman, Tabun, V-gaz, Nowiczok), pomimo zakazu ich użycia na mocy ustaleń konwencji Genewskiej. Najbardziej znanymi przypadkami użycia tych środków jest Halabja w Iraku, gdzie w wyniku ataku lotniczego armii irackiej zginęło około 5 000 osób a 10 000 zostało ciężko poszkodowanych. Znany jest też atak terrorystyczny na stacji metra w Tokyo (Sarin) jak też użycie środka Nowiczok na terenie Wielkiej Brytanii wobec Sergieja Skripala i później Aleksandra Nawalnego. Zatrucia związkami fosforoorganicznymi, pomimo możliwości leczenia, obarczone są wysoką śmiertelnością. W pracy tej opisujemy zakończoną sukcesem próbę kombinacji standardowego leczenia przy użyciu atropiny/toksogoniny z egzogennymi cholinesterazami podawanymi poprzez przetoczenie krwi. Pozytywny efekt tego leczenia obserwowany był u pacjentów narażonych na działanie związków fosforoorganicznych, u których aktywność endogennych cholinesteraz obniżyła się do 20%. Opisana terapia może pozwolić na uniknięcie konieczności wdrożenia wentylacji zastępczej płuc, jak też dalszym śmiertelnym powikłaniom ciężkiego zatrucia środkami fosforoorganicznymi. Philosophy Inorganic and Organometallic Chemistry ; Thermal and Kinetic Analysis
Authors: Srijika Mondal | Devi Singh | Aakanksha Tiwari
Source: Journal of Advances in Biology & Biotechnology (article, 2024-06-10)
Field: Chemistry — Analytical Chemistry

Evaluation of the Different Varieties of Lotus (Nelumbo nucifera) in Prayagraj Agro Climatic Conditions, Uttar Pradesh Lotus, an aquatic perennial flowering plant, holds significant economic and medicinal value. Lotus (Nelumbo nucifera) commonly known as sacred lotus, have significant medical value due to its wide range of bioactive compounds. This study, conducted in Prayagraj, Uttar Pradesh, evaluates the performance of six lotus varieties under local agro-climatic conditions. The Lotus varieties under investigation–Yellow Peony, Pastel Pink, Bucha, Rani Red, White Budhha and Pink cloud exhibited significant variations across all observed parameters. The research focuses on various characteristics of Lotus, including growth parameters, floral parameters, quality parameters, yield parameters and economy of the cultivation, to determine the most suitable variety for cultivation in similar climatic conditions. The variety V3: Bucha demonstrated superior performance in terms of plant height (41.31 cm), leaf length (14.94 cm), leaf width (19.68 cm), flower diameter (16.28 cm), total numbers of flowers per plant (38.13), total number of flowers per hectare (1,525,000), yield of rhizome per plant (1.74 kg), and yield of rhizome per hectare (69.73 tonnes). Additionally, V6: Pink Cloud reported longest vase-life (6.25 days), followed by V3: Bucha (5. 75 days). The variety V3: Bucha also achieved the highest gross return (4,444,500 Rs .ha-1), net return (3,437,050 Rs .ha-1), and benefit – cost ratio (4.41). Based on the findings, V3: Bucha is recommended for cultivation in the agro-climatic conditions of Prayagraj, Uttar Pradesh. Lotus ; Hectare ; Biology ; Rhizome ; Horticulture ; Yield (engineering) ; Uttar pradesh ; Nelumbo nucifera ; Botany ; Agriculture ; Ecology Chromatography in Natural Products ; Flowering Plant Growth and Cultivation ; Phytochemical Studies and Bioactivities
Source: Nanotechnology and Nanomaterials Research (article, 2024-08-21)
Field: Materials Science — Materials Chemistry

The Role of Nanomedicine in Welfare of Humankind Nanomedicine, the application of nanotechnology in the medical field, has emerged as a transformative force in healthcare, offering innovative solutions to some of the most pressing health challenges facing humanity today. Nanomedicine ; Welfare ; Human welfare ; Engineering ethics ; Nanotechnology ; Political science ; Environmental ethics ; Engineering ; Materials science ; Philosophy Nanoparticles: synthesis and applications
Authors: Paul‐Albert Schneide | Michael Armstrong | Neal B. Gallagher | Rasmus Bro
Source: arXiv (Cornell University) (preprint, 2024-12-02)
Field: Chemistry — Spectroscopy

Unlocking new capabilities in the analysis of GC$\times$GC-TOFMS data with shift-invariant multi-linearity This paper introduces a novel deconvolution algorithm, shift-invariant multi-linearity (SIML), which significantly enhances the analysis of data from a comprehensive two-dimensional gas chromatograph coupled to a mass spectrometric detector (GC$\times$GC-TOFMS). Designed to address the challenges posed by retention time shifts and high noise levels, SIML incorporates wavelet-based smoothing and Fourier-Transform based shift-correction within the multivariate curve resolution-alternating least squares (MCR-ALS) framework. We benchmarked the SIML algorithm against traditional methods such as MCR-ALS and Parallel Factor Analysis 2 with flexible coupling (PARAFAC2$\times$N) using both simulated and real GC$\times$GC-TOFMS datasets. Our results demonstrate that SIML provides unique solutions with significantly improved robustness, particularly in low signal-to-noise ratio scenarios, where it maintains high accuracy in estimating mass spectra and concentrations. The enhanced reliability of quantitative analyses afforded by SIML underscores its potential for broad application in complex matrix analyses across environmental science, food chemistry, and biological research. Linearity ; Invariant (physics) ; Chromatography ; Chemistry ; Pattern recognition (psychology) ; Mathematics ; Analytical Chemistry (journal) ; Computer science ; Artificial intelligence ; Engineering ; Electronic engineering ; Mathematical physics Advanced NMR Techniques and Applications ; Cardiovascular Health and Disease Prevention ; Metabolomics and Mass Spectrometry Studies
Authors: Aidarkhan Kaimov | Talgat Kaiym | Suleimen Kaimov | Abylay Kaimov | Nazym Kanagatova
Source: Eastern-European Journal of Enterprise Technologies (article, 2024-10-25)
Field: Materials Science — Materials Chemistry

Justification of an innovative system for the complete burial of solid, high-level radioactive waste (HLW) in spent open-pit mines The object of research is the spent open-pit mines themselves where the proposed system could be applied. The primary reason for this studying is the following circumstance: up to the present time period, in all countries of the world, no methods of HLW disposal in a storage facility has been identified that is absolutely safe for any length of time, taking into account the impact of catastrophic natural emergencies and man-made emergencies. The research was conducted to address the problem of safely managing and storing HLW, leveraging the unique characteristics of spent open-pit mines, such as their large volume and geological stability, to prevent environmental contamination and ensure long-term safety. In the article has been justified a novel approach to the burial of sarcophagus containers with solid HLW in exhausted mining pits and studied the usabilities of the basalt sarcofagous container. Robust materials and advanced robotic systems proposed in the article aims to address the challenges associated with long-term radioactive waste disposal effectively. The robotic systems transfer the basalt container with HLW, ensuring personnel safety by minimizing human presence near radioactive materials. In the article have been established the distribution of temperature into the multi-layered composite structure of the basalt sarcophagous with HLW from 300 °C into the inner space to 50 °C onto on the its outer suffer where the thickness of each layers (from inner to outer radius) was respectively: for lead matrix: from r1=0.1 m to r2=0.2 m; for clay layer: from r2=0.2 m to r3=0.3 m; for basalt block: from r3=0.3 m to r4=0.4 m. The findings on temperature distribution are crucial as they directly affect the performance and longevity of the basalt containment system High-level waste ; Radioactive waste ; Waste management ; Municipal solid waste ; Environmental science ; Engineering Graphite, nuclear technology, radiation studies ; Nuclear and radioactivity studies
Authors: François Dubois
Source: arXiv (Cornell University) (preprint, 2024-11-20)
Field: Chemistry — Physical and Theoretical Chemistry

On Macroscopic Intricate States The present contribution is in the field of quantum modelling of macroscopic phenomena. The focus is on one enigmatic aspect of quantum physics, namely the Einstein-Podolsky-Rosen paradox and entanglement. After a review of the state of the art concerning macroscopic quantum effects and quantum interaction, this contribution proposes a link between embryology and acupuncture in the framework of macroscopic intricate states induced by quantum mechanics. Statistical physics ; Theoretical physics ; Physics Advanced Physical and Chemical Molecular Interactions
Authors: Hadi Mokhtari | Sedigheh Razi | Saeed Rahimi | Pouya Haghighat | Atefeh Abedi | Elham Behrouzpour
Source: PubMed (article, 2024-01-01)
Field: Chemistry — Analytical Chemistry

Evaluation of Canal Transportation and Centering Ability of RaCe and Af f-one Systems by Cone-beam Computed Tomography: An <i>in Vitro</i> Study. The two studied rotary systems did not exhibit significant differences in root canal transportation and preservation of root canal centrality in the apical, middle, and coronal thirds. Cone beam computed tomography ; Computed tomography ; Cone (formal languages) ; Race (biology) ; Beam (structure) ; Medicine ; Geology ; Optics ; Computer science ; Physics ; Radiology Analytical chemistry methods development ; Integrated Circuits and Semiconductor Failure Analysis
Authors: Séhi Zokagon Sylvain | Kouakou Konan Elie | Konan Kouamé Firmin | Brahima Koné | Albert Yao‐Kouamé
Source: International Journal of Plant & Soil Science (article, 2024-12-16)
Field: Materials Science — Biomaterials

Determination of Kaolin Optimum Dose to Inhibit Iron Toxic Effect on Rice Plant in Lowland Rice Cultivation In tropical areas, lowland rice cultivation with or without water control is often faced with iron toxicity constraint. This problem causes a drop of the rice grain yield when the iron concentration in soil solution is more than 300 ppm. To resolve iron toxicity problem, drainage and fertilizers as industrial silicon applying have been recommended. However, the used of industrial silicon is not adopted by the farmers because of his high cost and his accessibility. Kaolin contains 54.7% of SiO2 the aim of this research is to explore the potential of kaolin as a natural substitute of industrial silicon. A pot test was carried in 900 ppm iron toxicity condition. of Fe2+ the condition out for two successive rice cultivation cycles by applying 900ppm of Fe2+. Five kaolin treatments were analyzed (T0 = 0, T1 = 366, T2 = 735, T3 = 1097 and T4 = 1465 kg kaolin ha-1) in a complete randomized block design with 5 repetitions. The dose of 366 kg ha-1 reduced the symptoms of iron toxicity on rice plant. kaolin applying improved the grain yield of rice (0 tha-1 to 1.8 tha-1). The dose of 1465 kg kaolin ha-1 gave the best grain yield (1.08 t ha-1). The response of rice to kaolin doses was an equation RDG = 0.98 ×Dose more linear than quadratic and the dose of 1465 kg kaolin ha-1 was recommended as the optimal dose in the conditions of 900 ppm Fe2+. Randomized block design ; Silicon ; Grain yield ; Yield (engineering) ; Mathematics ; Agronomy ; Toxicity ; Toxicology ; Chemistry ; Horticulture ; Animal science ; Biology ; Materials science ; Metallurgy Clay minerals and soil interactions ; Silicon Effects in Agriculture ; Aluminum toxicity and tolerance in plants and animals
Authors: Oleksandr Manoilenko | Volodymyr Dvorzhak | ВАСИЛЬ ГОРОБЕЦЬ | Igor Panasiuk | Dmytro Bezuhlyi
Source: Eastern-European Journal of Enterprise Technologies (article, 2024-12-20)
Field: Materials Science — Polymers and Plastics

Assessing the impact of sewing machine thread take-up mechanism parameters on the magnitude and nature of thread take-up The subject of this study is the needle thread take-up mechanisms (NTТM) of modern chain stitch sewing machines of classes 400 and 600. The principal issue with these mechanisms is the complexity of their adjustment because of the large number of adjustable parameters and the need for clear recommendations for proper setup, which negatively affects their performance. The research involved analyzing the impact of NTTM’s kinematic parameters and various thread path configurations in machines. The study revealed new patterns that allow for more precise thread take-up regulation, enabling better synchronization of the actual thread take-up with the required amount, thereby improving stitch quality and increasing sewing process productivity. Accurate thread take-up adjustment prevents excessive or insufficient thread tension, a common issue when sewing materials with variable thickness or stitch length. The results can be used to adjust sewing machines and automate the tuning of technological processes by changing the adjustment parameters with variations in technological parameters. This is particularly important in producing 3D textile structures for reinforcing composite molds, where adjusting for average material thickness can cause thread tension issues when the current thickness changes. The practical application of these results will ensure stable sewing quality based on stitch parameters, which is relevant for automating machine settings and working with materials of varying thicknesses. The proposed recommendations will improve the manufacturing process and increase equipment efficiency Thread (computing) ; Computer science ; Sewing machine ; Engineering drawing ; Mechanical engineering ; Engineering ; Operating system Textile materials and evaluations ; Additive Manufacturing and 3D Printing Technologies ; Advanced Theoretical and Applied Studies in Material Sciences and Geometry
Authors: Ludyane Nascimento Costa | Rogério Soares de Melo | Ana Glória Fonseca | Anna Clara Silva Pismel | Jorge Ferreira | Aline Aparecida Carvalho França | Vítor Alexandre Nunes de Carvalho
Source: Caderno Pedagógico (article, 2024-11-14)
Field: Chemistry — Analytical Chemistry

Reator fotoquímico: montagem e aplicação fotocatalítica na degradação de poluentes orgânicos O avanço das atividades industriais e da produção agrícola tem desencadeado a geração de poluentes orgânicos que possuem alto índice de toxicidade, sendo esses classificados como poluentes emergentes. O descarte e o tratamento inadequado destes poluentes geram diversas consequências negativas ao meio ambiente, podendo alterar as propriedades físicas, químicas e biológicas das águas naturais e, assim, comprometer a qualidade da água destinada para o abastecimento populacional. Diante da problemática apresentada, este trabalho reporta a construção de um reator fotoquímico que utiliza a fotocatálise para a degradação das moléculas tóxicas presentes nos mais variados resíduos gerados. A partir de pesquisas realizadas, montou-se um sistema fotocatalítico de simples manuseio e eficiente no processo de degradação de moléculas orgânicas, dando ênfase à corantes, fármacos e poluentes comumente gerados na região de Barra do Corda, bem como nas cidades vizinhas, tais como os defensivos agrícolas de uso extensivo nas lavouras maranhenses. Para a construção do reator fotoquímico foram utilizados lâmpadas de emissão eletromagnética na faixa do ultravioleta (UV-C), um sistema de ventilação que utiliza coolers, contando também com termômetro que possibilita medir a temperatura interna e externa da caixa, trazendo segurança e praticidade ao operador durante as aplicações. Para testar a eficiência da caixa fotocatalítica, realizou-se a degradação do corante azul de metileno a partir de nanoestruturas de Cu-NTTi (nanotubos de titânio trocados com cobre), obtendo-se uma taxa de degradação de 97% e comprovando o funcionamento eficiente do reator construído. Chemistry Dye analysis and toxicity ; Water Quality and Pollution Assessment ; Water Quality Monitoring and Analysis
Authors: Rostyslav O. Serha | Andrey A. Voronov | David Schmoll | Rebecca Klingbeil | Sebastian Knauer | Sabri Koraltan | Ekaterina Pribytova | Morris Lindner | Timmy Reimann | Carsten Dubs | Claas Abert | Roman Verba | Michal Urbánek | Dieter Suess | Andrii V. Chumak
Source: arXiv (Cornell University) (preprint, 2024-12-03)
Field: Materials Science — Surfaces, Coatings and Films

Damping Enhancement in YIG at Millikelvin Temperatures due to GGG Substrate Quantum magnonics aims to exploit the quantum mechanical properties of magnons for nanoscale quantum information technologies. Ferrimagnetic yttrium iron garnet (YIG), which offers the longest magnon lifetimes, is a key material typically grown on gadolinium gallium garnet (GGG) substrates for structural compatibility. However, the increased magnetic damping in YIG/GGG systems below 50$\,$K poses a challenge for quantum applications. Here, we study the damping in a 97$\,$nm-thick YIG film on a 500$\,μ$m-thick GGG substrate at temperatures down to 30$\,$mK using ferromagnetic resonance (FMR) spectroscopy. We show that the dominant physical mechanism for the observed tenfold increase in FMR linewidth at millikelvin temperatures is the non-uniform bias magnetic field generated by the partially magnetized paramagnetic GGG substrate. Numerical simulations and analytical theory show that the GGG-driven linewidth enhancement can reach up to 6.7 times. In addition, at low temperatures and frequencies above 18$\,$GHz, the FMR linewidth deviates from the viscous Gilbert-damping model. These results allow the partial elimination of the damping mechanisms attributed to GGG, which is necessary for the advancement of solid-state quantum technologies. Materials science ; Substrate (aquarium) ; Optoelectronics ; Condensed matter physics ; Composite material ; Physics ; Geology Optical Coatings and Gratings ; Photonic and Optical Devices ; Magneto-Optical Properties and Applications
Authors: Trevor Kling | Dong-yeop Na | Mahdi Hosseini
Source: arXiv (Cornell University) (preprint, 2024-08-26)
Field: Materials Science — Surfaces, Coatings and Films

Modeling Atomistically Assembled Diffractive Optics in Solids We develop a model describing long-range atom-atom interactions in a two-dimensional periodic or a-periodic lattice of optical centers considering spectral and spatial broadening effects. Using both analytical and numerical Green's function techniques, we develop a mathematical framework to describe effective atom-atom interactions and collective behaviors in the presence of disorder. This framework is applicable to a broad range of quantum systems with arbitrary lattice geometries, including cold atoms, solid-state photonics, and superconducting platforms. The model can be used, for example, to scalably design quantum optical elements, e.g. a quantum lens, harnessing atomistic engineering (e.g. via ion implantation) of collective interactions in materials to enhance quantum properties at scale. Physics Optical Coatings and Gratings ; Photonic Crystals and Applications ; Advanced optical system design