jablonkagroup/rise_ai_scientists huggingface dataset:
Authors: Aswini Panigrahi | Allison L. Hunt | Diego M. Assis | Matthew Willetts | Bhaskar Kallakury | Bruce J. Davidson | Thomas P. Conrads | Radoslav Goldman
Source: bioRxiv (Cold Spring Harbor Laboratory) (preprint, 2024-08-10)
Field: Chemistry — Spectroscopy

dia-PASEF Proteomics of Tumor and Stroma LMD Enriched from Archived HNSCC Samples We employed laser microdissection to selectively harvest tumor cells and stroma from the microenvironment of formalin-fixed, paraffin-embedded head and neck squamous cell carcinoma (HNSCC) tissues. The captured HNSCC tissue fractions were analyzed by quantitative mass spectrometry-based proteomics using a data independent analysis approach. In paired samples, we achieved excellent proteome coverage having quantified 6,668 proteins with a median quantitative coefficient of variation under 10%. We observed significant differences in relevant functional pathways between the spatially resolved tumor and stroma regions. Our results identified extracellular matrix (ECM) as a major component enriched in the stroma, including many cancer associated fibroblast signature proteins in this compartment. We demonstrate the potential for comparative deep proteome analysis from very low starting input in a scalable format that is useful to decipher the alterations in tumor and the stromal microenvironment. Correlating such results with clinical features or disease progression will likely enable identification of novel targets for disease classification and interventions. Laser capture microdissection ; Stroma ; Stromal cell ; Tumor microenvironment ; Microdissection ; Proteomics ; Proteome ; Extracellular matrix ; Head and neck squamous-cell carcinoma ; Quantitative proteomics ; Biology ; Cancer research ; Cancer-Associated Fibroblasts ; Computational biology ; Cancer ; Bioinformatics ; Cell biology ; Tumor cells ; Head and neck cancer ; Immunohistochemistry ; Biochemistry ; Immunology ; Gene ; Genetics ; Gene expression Advanced Proteomics Techniques and Applications ; Molecular Biology Techniques and Applications ; RNA modifications and cancer
Authors: Rashid Nazir | Muniza Saeed | Hifza Noor Lodhi | Ghulam Mustafa | Seher Naeem | Zunnera Rashid
Source: Life and Science (article, 2024-11-22)
Field: Chemistry — Organic Chemistry

Antioxidant Effect of Extra Virgin Olive Oil and Apple Cider Vinegar in Type 2 Diabetic Rat Model Objective: Comparison between the antioxidant effects of extra virgin olive oil and apple cider vinegar in ratsinduced with diabetes mellitus type 2.Study Design: Randomized controlled trial.Place and Duration of Study: This Study was conducted in Postgraduate Medical Institute, Animal House,Lahore, Pakistan from May 2021 to June 2021.Methods: In this study, 40 male Sprague Dawley rats were divided into 4 groups i.e., Group I was NC (negativecontrol), Group II PC (positive control), Group III EVOO (Extra virgin olive oil) and Group IV (Apple cider vinegar),each group having 10 rats. Diabetes was induced in all rats except the rats of NC group at the start of the study by intraperitoneal administration of injection nicotinamide, followed by injection Streptozosin (STZ) after 15minutes. Group III was given 1ml/100gBW/ day EVOO and Group IV was given 2ml/kg BW/day diluted ACV withdistilled water in 1:5 orally for 4 weeks. Sampling was done after 4 weeks for determination of oxidative stressmarkers Malonaldehyde, Superoxide dismutase and Total antioxidant status in serum.Results: Intake of EVOO and ACV showed reduction in serum Malonaldehyde levels as compared to positivecontrol group with P-values 0.000 and 0.014 respectively. Serum superoxide dismutase activity and Totalantioxidant status were lowest in the positive control group while both the treatment groups showedsignificant enhancement in these parameters as compared to positive control group with P-value = 0.000.Conclusion: Both extra virgin olive oil and apple cider vinegar have antioxidant effects in type 2 diabetic rats.However, Extra virgin olive oil is more potent. How to cite this: Nazir R, Saeed M, Lodhi HN, Mustafa G, Naeem S, Chaudry ZR. Antioxidant Effect of Extra Virgin Olive Oil and Apple Cider Vinegar in Type 2 Diabetic Rat Model. Life and Science. 2024; 5(4): 559-564. doi: http://doi.org/10.37185/LnS.1.1.780 Antioxidant ; Olive oil ; Food science ; Chemistry ; Traditional medicine ; Horticulture ; Biology ; Biochemistry ; Medicine Edible Oils Quality and Analysis
Authors: Marta Radaelli | Elisa Scalabrin | Marco Roman | Gabriella Buffa | Irene Griffante | Diego Streliotto | Gabriele Capodaglio
Source: Preprints.org (preprint, 2024-06-07)
Field: Chemistry — Analytical Chemistry

Characterization of Ancient Cereals Cultivated by Intensive and Organic Procedures for Elements Content According to their nutritional value, their ability to adapt to the various environmental conditions, and their versatility, cereals are among the most cultivated plants in the world. However, the ongoing climate changes subject crops to important environmental stress that for some varieties leads to high production losses. Therefore, selection of species and varieties more versatile and adaptable to different environmental conditions can be important. However, the characteristics of some cereals are not completely known, this is a priority before to improve their cultivation. The aim of this study is to characterize select species of potential suitable for local environmental conditions, nutritional value. Environmental stress ; Selection (genetic algorithm) ; Production (economics) ; Value (mathematics) ; Biotechnology ; Environmental science ; Agricultural engineering ; Biology ; Agronomy ; Mathematics ; Environmental protection ; Engineering ; Computer science ; Statistics Heavy Metals in Plants ; Plant Micronutrient Interactions and Effects ; Food composition and properties
Authors: Ilhama A. Zarbaliyeva | Hajar T. Nabiyeva | Amina N. Alimova | Ayaz M. Mammadov | Narmin Rzayeva
Source:  (article, 2024-12-12)
Field: Chemistry — Organic Chemistry

SYNTHESIS AND ANALYSIS OF SALTS BASED ON OLEIC ACID AND DIETHYLETRIAMINE Being an ever-renewing process, education is influenced by the conditions of the historical epoch and the tasks that society sets for it.Accordingly, in a changing world, education faces the problem of obsolescence of theoretical concepts and methodological approaches.The increase in the speed of development of society and the economy, the activation of the mobility of the population in the labor market led to the transformation of the needs of the population in training, necessitating the practical implementation of the conceptual installation "education through life".The article states the importance of the principle of continuity in the education system, in which the state, companies and employees are interested. Oleic acid ; Computer science ; Chemistry ; Biochemistry Chemical Synthesis and Reactions ; Analytical Chemistry and Chromatography
Authors: Jamilyam Ismailova | Ayaulym Baibekova | Dinara Delikesheva | Aibek Abdukarimov | Alfiya Khussainova
Source: Eastern-European Journal of Enterprise Technologies (article, 2024-02-28)
Field: Chemistry — Analytical Chemistry

Pressure-volume-temperature analysis of Caspian oil to improve the analytical delumping procedure Compositional modeling of the reservoir isn’t complete without calculations of phase equilibrium and is a complex process involving many calculations. In nature, hydrocarbons don’t occur as separate components, they’re mainly mixtures. When modeling the reservoir composition for phase equilibrium calculations, in order to reduce computational costs, in practice, hydrocarbon mixtures are grouped into pseudo-components. The number of grouped pseudo-components varies from 4 to 10. This grouping process is called lumping. However, when crude oil comes to the surface, it’s important to know its detailed composition, since mixtures grouped into pseudo-components don’t allow you to know this. In this regard, modeling of the detailed composition of hydrocarbons is the main tool for understanding the detailed phase separation and design of surface facilities. In practice, this process is called delumping. In the case of this process, the detailed composition of the fluid is presented and the amount reaches up to 36 components, sometimes more. The delumping process, due to the precise separation of heavy plus fractions into carbons with single ordinal numbers (C7, C8, etc.), makes it possible to clearly recognize non-zero BIP’s in the equation of state. The new analytical approach has not previously been applied to the oils of the Caspian region, so this approach has an important role for the oil industry in the Caspian region. Analytical delumping in this paper was done to improve the PVT modeling. This paper presents the results of PVT research of Caspian oil and presents a comparison of analytical and numerical methods of delumping. As a result of the study, it was found that the analytical approach is in excellent agreement with experimental data and data from software such as PVTsim Volume (thermodynamics) ; Petroleum engineering ; Environmental science ; Thermodynamics ; Geology ; Physics Petroleum Processing and Analysis ; Mass Spectrometry Techniques and Applications ; Fluid Dynamics and Mixing
Authors: S R Padma
Source: Journal of Experimental Agriculture International (article, 2024-11-02)
Field: Chemistry — Inorganic Chemistry

Coconut Growers: Challenges Faced and Solutions Proposed Aim: To analyse the challenges faced by the coconut growers and suggestion to overcome. Research Design: Ex-post facto research design. Sample: Coconut growers of Coimbatore district, Simple random sampling. Methodology: A structured interview schedule was developed to collect the data from 200 respondents. An Ex-post facto research was employed and Simple random sampling technique was used to select the 200 coconut growers. Results: Ninety-eight percent of respondents voiced concerns about their insufficient understanding of various plant protection aspects, including chemicals, spray frequency, symptoms, and application methods. Ninety-two and a half percent of respondents are worried about the toxicity of plan protection to both cattle and humans. Additionally, the lack of nearby repair facilities (89%) and the belief that traditional methods are more effective (87%) add to the difficulties encountered by farmers. Ensuring Fair Market Prices for Produce" ranked highest (88%), showing that farmers prioritize stable prices to secure their income and reduce risks. "Technical Guidance on Coconut Farming" (76%) and "Timely Availability of Quality Inputs at Subsidized Rates" (75%) were also important, indicating the need for ongoing support and reliable inputs from the government. Business ; Agricultural science ; Computer science ; Agricultural engineering ; Engineering ; Environmental science Coconut Research and Applications
Authors: Piera Grisolia | Antonio De Falco | Rossella Tufano | Clara Iannarone | Alfonso Fiorelli | Pier Vitale Nuzzo | Stefano Forte | Raffaella Giuffrida | Michele Caraglia | Michele Ceccarelli
Source: The Journal of Liquid Biopsy (article, 2024-11-01)
Field: Materials Science — Materials Chemistry

Advanced CNA-informed fragmentomics enhances cross-cohort tumor detection measured (n8 GD1, n6 GD2, n17 GD3.) GD2 and GD3 species were confirmed using ganglioside-specific fragment moieties.4 species of GD3 and 3 species of GD2 are significantly elevated in OC, with several other species showing an increased trend.We also observed a significant decrease in GD1 (36:1), with several other GD1 species showing a decreased trend, in OC.We further identified a significant increase in the ratio of GD2 (36:1) to GD1 (36:1) for both early-and late-stage OC.Receiver operating characteristic (ROC) curve analysis found the ratio of GD2 (36:1) to GD1 (36:1) distinguishes normal from OC subjects with an area under curve (AUC) of 92% (95CI 86-98%), as well as early-stage and late-stage cancers with AUCs of 86% and 94%, respectively.Our study has identified an altered ganglioside signature in OC serum, with elevated levels of GD3 and GD2 and decreased levels of GD1.Additionally, the ratio of GD2 (36:1) to GD1 (36:1) acts as a sensitive and specific diagnostic signature for distinguishing early-and late-stage OC from healthy patients.Future studies will validate these findings and investigate this signature in a population with signs and symptoms of OC.Our goal is to create a robust statistical model that effectively differentiates non-cancer subgroups from OC with high sensitivity and specificity. Cohort ; Medicine ; Internal medicine Machine Learning in Materials Science
Authors: P Jamuna | K R Vijayalatha | A. Nithya Devi | V. Jegadeeswari | K. Geetha | J. Suresh
Source: Plant Science Today (article, 2024-12-02)
Field: Materials Science — Biomaterials

Effect of lipid-polysaccharide edible coatings on enhancing shelf life and quality of guava (Arka Kiran) The physicochemical properties of guava (Arka Kiran) fruits were examined in relation to pre- and post-harvest treatments, both individually and in combination, using various edible compounds, including hexanal, chitosan, and salicylic acid. The fruits were treated with different concentrations of hexanal (2%), chitosan (1%), and salicylic acid (500 ppm) and assessed for various physico–chemical parameters. In the storage study, guava fruits treated with these edible compounds were stored under both ambient conditions (30°C ± 1°C) and cold storage conditions (10 ± 2°C). The fruits treated with 2% hexanal demonstrated the most significant improvements in quality-related parameters under cold storage and ambient conditions. The combination of pre-harvest spray and post-harvest treatments using 2% hexanal in cold storage significantly delayed physiological weight loss (24.55%), preserved total soluble solids (10.25 ºBrix), and maintained ascorbic acid content (135.05µg) by the 18th day of the storage period. Furthermore, pre-and post-harvest treatment with chitosan under cold storage conditions significantly enhanced the retention of antioxidant activity and phenolic content in guava fruit. Overall, the treatment with 2% hexanal proved to be the most effective in regulating physicochemical changes and improving the storage quality of guava fruits. Shelf life ; Polysaccharide ; Food science ; Quality (philosophy) ; Chemistry ; Biology ; Biotechnology ; Biochemistry ; Physics Nanocomposite Films for Food Packaging ; Postharvest Quality and Shelf Life Management ; Psidium guajava Extracts and Applications
Authors: Rajshree Gupta
Source: International Journal of Science and Research (IJSR) (article, 2024-04-05)
Field: Chemistry — Analytical Chemistry

A Comparative Analysis on Examining Heavy Metal Effects on Seedling Growth (Root and Shoot Length) in Raphanus Sativus Cultivar Pusa Rashmi Seedlings The study investigates the impact of copper, cadmium, lead, nickel, and zinc on the growth of Raphanus sativus cv Pusa rashmi, a prominent radish variety. Through controlled experiments with varying metal concentrations, this research observes their effects on seedling growth over ten days. Higher concentrations of these metals significantly reduce both shoot and root lengths in the radish seedlings. Cadmium and lead notably hinder shoot growth, while all metals inhibit root length, particularly at higher concentrations. Comparison with control groups highlights substantial growth reduction in metal -treated seedlings. Interestingly, Raphanus sativus cv Pusa rashmi shows relative resistance to heavy metal toxicity at lower concentrations of copper and nickel. These findings shed light on the nuanced impact of heavy metals on plant growth, suggesting a complex interplay involving enzyme function, hormonal regulation, and cellular alterations. Ultimately, this research enriches our understanding of how heavy metal pollution impedes radish plant growth, offering insights into the intricate mechanisms involved in these inhibitory effects. Raphanus ; Seedling ; Pusa ; Cultivar ; Shoot ; Horticulture ; Biology ; Botany Heavy Metals in Plants ; Agricultural Science and Fertilization ; Leaf Properties and Growth Measurement
Authors: Eyyüp Çavdar | Kubilay Karaboyun | Yakup İriağaç
Source: Revista da Associação Médica Brasileira (review, 2024-01-01)
Field: Materials Science — Biomaterials

Nanotechnology in oncology: a mini review Medical physics ; Medicine ; Oncology ; Internal medicine Nanoparticle-Based Drug Delivery ; Graphene and Nanomaterials Applications ; Nanoplatforms for cancer theranostics
Authors: Khabirov F.F. | Vokhmin V.S. | Idrisov А.V.
Source: RUSSIAN ELECTRONIC SCIENTIFIC JOURNAL (article, 2024-01-01)
Field: Materials Science — Materials Chemistry

MATHEMATICAL MODELING OF THE OPERATION OF THE THERMOELECTRIC GENERATOR AND PHOTOVOLTAIC CONVERTER IN THE MATLAB SIMULATION BLOCK MODELING ENVIRONMENT Alternative energy in connection with new scientific and technological discoveries gives an opportunity to increase energy efficiency and opens wide opportunities for the energy industry. Based on this, the paper describes the development of a mathematical model for the operation of photovoltaic converter and thermoelectric generator. The design of thermoelectric generator was developed to jointly produce electrical energy together with photovoltaic converter. A mathematical model in MATLAB-Simulink simulation software was adopted to investigate the output voltage and current characteristics. Modeling of thermoelectric generator with eight thermoelectric modules in series connection, and one photovoltaic converter was carried out. The characteristics of which were selected on the basis of literature review, including the required temperature values of the equipment. On the developed virtual mathematical model of photovoltaic converter and thermoelectric generator with simulation of thermal modes, we took experimental characteristics of current, voltage and power at parallel connection of photovoltaic converter and thermoelectric generator (TEG). According to the results of the study of the developed virtual mathematical model, it was found that the best energy effect of the developed design will be observed when the optimal temperature difference between the walls of the TEG is observed. The series connection of thermoelectric elements allows to increase the output voltage. The proposed design of TEG together with a photovoltaic converter, taking into account further improvements, can be used as an autonomous energy source for agricultural enterprises of agro-industrial complex. MATLAB ; Photovoltaic system ; Block (permutation group theory) ; Modeling and simulation ; Thermoelectric generator ; Generator (circuit theory) ; Computer science ; Thermoelectric effect ; Electronic engineering ; Electrical engineering ; Simulation ; Engineering ; Power (physics) ; Physics ; Mathematics ; Thermodynamics Advanced Thermoelectric Materials and Devices ; Advanced Materials and Semiconductor Technologies ; Energy and Environmental Sustainability
Authors: Somar Khalil | Michel Plisnier
Source: bioRxiv (Cold Spring Harbor Laboratory) (preprint, 2024-11-03)
Field: Chemistry — Spectroscopy

Comparative Analysis of MS/MS Search Algorithms in Label-Free Shotgun Proteomics for Monitoring Host-Cell Proteins Using Trapped Ion Mobility and ddaPASEF ABSTRACT Host cell proteins (HCPs) are critical quality attributes that can impact the safety, efficacy, and quality of biotherapeutics. Label-free shotgun proteomics is a vital approach for HCP monitoring, yet the choice of tandem mass spectrometry (MS/MS) search algorithms directly influences identification depth and quantification reliability. In this study, six prominent MS/MS search tools—Mascot, MaxQuant, SpectroMine, FragPipe, Byos, and PEAKS—were systematically benchmarked for their performance on complex samples spiked with isotopically labeled proteins from Chinese hamster ovary cells, using trapped ion mobility spectrometry and parallel accumulation-serial fragmentation in data-dependent acquisition mode. Key performance metrics, including peptide and protein identifications, data extraction precision, fold-change (FC) accuracy, linearity, and measurement trueness, were evaluated. A Bayesian modeling framework with Hamiltonian Monte Carlo sampling was employed to robustly estimate FC means and variances, alongside local false discovery rates through posterior probability calibration. Bayesian decision theory, implemented via expected utility maximization, was used to balance accuracy against posterior uncertainty, providing a probabilistic assessment of each tool’s performance. Through this cumulative analysis, variability across tools was observed: some excelled in identification sensitivity and protein coverage, others in quantitative accuracy with minimal bias, and a few offered balanced performance across metrics. This study establishes a rigorous, data-driven framework for tool benchmarking, delivering insights for selecting MS/MS tools suited to HCP monitoring in biopharmaceutical development. Graphical abstract Shotgun proteomics ; Shotgun ; Ion-mobility spectrometry ; Host (biology) ; Proteomics ; Computer science ; Computational biology ; Chemistry ; Chromatography ; Mass spectrometry ; Biology ; Biochemistry ; Genetics ; Gene Advanced Proteomics Techniques and Applications ; Mass Spectrometry Techniques and Applications ; Metabolomics and Mass Spectrometry Studies
Authors: Callum Wiseman | Marwa Ben Yaala Chalisa Gier | L. Marot | Christopher McCormick | Sheila Rowan | S. Reid
Source: arXiv (Cornell University) (preprint, 2024-06-11)
Field: Materials Science — Materials Chemistry

Ion Energy Tuning for Enhanced sp3 Carbon Fraction in Electron Cyclotron Resonance Ion Beam Deposited Diamond-Like Carbon Coatings: a Computational and Experimental Approach A novel high-energy electron cyclotron resonance (ECR) ion beam deposition (IBD) technique was used to fabricate DLC films at different ion beam energies. The ratios of sp2/sp3 bonding in the DLC coatings were determined by Raman spectroscopy and XPS, with the confirmation of being hydrogen-free due to the lack of photoluminescence (PL) background in the Raman spectra. The results indicate that the sp3 percentage ranges from 45% - 85% for the ECR-IBD fabricated DLC films in this study. Monte-Carlo based SRIM simulation was used to extract the energy and angular distribution of the sputtered particles from the carbon target and correlate it to the highest sp3 fraction in the manufactured ECR-IBD DLCs. This study demonstrates a method of depositing DLC thin films under ambient conditions (room temperature with no post-annealing or additional bias voltage applied) which produces high-sp3 coatings (higher than those traditionally reported for other sputtering methods) suitable for applications where high quality DLC coatings are required. Ion ; Diamond-like carbon ; Electron cyclotron resonance ; Carbon fibers ; Materials science ; Diamond ; Ion beam deposition ; Atomic physics ; Ion beam ; Electron ; Ion beam analysis ; Ion cyclotron resonance ; Cyclotron ; Optoelectronics ; Thin film ; Nanotechnology ; Chemistry ; Physics ; Composite material ; Nuclear physics Diamond and Carbon-based Materials Research ; Ion-surface interactions and analysis ; Metal and Thin Film Mechanics