Article
Computer Science, Artificial Intelligence
Junchen Ye, Weimiao Li, Zhixin Zhang, Tongyu Zhu, Leilei Sun, Bowen Du
Summary: Modeling multivariate time series has long been a topic of interest for scholars in various fields. This paper introduces MvTS, an open library based on Pytorch, which provides a unified framework for implementing and evaluating these models. Extensive experiments on public datasets demonstrate the effectiveness and universality of the models reproduced by MvTS.
KNOWLEDGE-BASED SYSTEMS
(2024)
Article
Physics, Multidisciplinary
Jonas Fankhauser, Christoph Goering, Juerg Dual
Summary: This article presents the Open-Source AcoustoFluidics Theories (OSAFT) library, a Python library for solving problems related to acoustofluidics. The library provides various theoretical models for describing acoustic scattering, acoustic streaming, and the acoustic radiation force on particles. The code is designed to be extensible, with a library of fluid and solid material models to facilitate the implementation of new theories. Comparisons between different theories are made straightforward through a unified application programming interface (API).
FRONTIERS IN PHYSICS
(2022)
Article
Materials Science, Multidisciplinary
Adrian Martinez Cendrero, Francisco Franco Martinez, William Gabriel Solorzano Requejo, Andres Diaz Lantada
Summary: The field of tissue engineering could benefit from implementing standards to enhance the repeatability and comparability of research results. An internationally accepted library of scaffold models would be valuable for comparing materials and manufacturing technologies. An open-source scaffold library has been developed, providing comprehensive blueprints and adhering to the FAIR data principles.
MATERIALS & DESIGN
(2022)
Article
Engineering, Biomedical
Patrick Foley, Micah J. Sheller, Brandon Edwards, Sarthak Pati, Walter Riviera, Mansi Sharma, Prakash Narayana Moorthy, Shih-han Wang, Jason Martin, Parsa Mirhaji, Prashant Shah, Spyridon Bakas
Summary: OpenFL is an open-source framework that enables organizations to collaborate on machine learning and deep learning projects without sharing sensitive data. It is compatible with various ML and DL frameworks and allows for easy extension.
PHYSICS IN MEDICINE AND BIOLOGY
(2022)
Article
Computer Science, Interdisciplinary Applications
Pietro Bonfa, Jonathan Frassineti, Muhammad Maikudi Isah, Ifeanyi John Onuorah, Samuele Sanna
Summary: UNDI is an open-source program for analyzing the time dependent spin polarization of an isolated muon interacting with surrounding nuclear magnetic dipoles in standard experiments. The tool, combined with ab initio estimations of the electric field gradient at the nuclei, can be a valuable complement for identifying muon sites in crystals with large nuclear magnetic moments. It allows for investigating physical properties influenced by electric field gradients, such as avoided level crossing resonance and charge ordered states, and has been shown to be efficient and effective in realistic examples.
COMPUTER PHYSICS COMMUNICATIONS
(2021)
Article
Biochemical Research Methods
Benjamin C. Orsburn
Summary: The identification of pesticide residues is crucial for environmental and food safety analysis. Liquid chromatography tandem mass spectrometry (LCMS) is commonly used for this purpose, but different instruments require user optimization to identify ideal adducts and fragment ions. The Open Pesticide Transition Library (oPestTL) is a comprehensive list of pesticide ion targets and fragments, aimed at facilitating the development of screening methods for any LCMS hardware configuration.
JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY
(2022)
Article
Oncology
Naveen Challagundla, Reena Agrawal-Rajput
Summary: A novel approach of microRNA-induced trans-differentiation of macrophages to induced neuronal cells without exogenous use of transcription factors was reported. The reprogramming involved alteration of pluripotency genes and miRs, with functional and active neurons obtained, suggesting potential clinical applications.
EXPERIMENTAL CELL RESEARCH
(2021)
Article
Reproductive Biology
Igor Tomczyk, Mikolaj Rokicki, Wioleta Sienko, Katarzyna Rozek, Anna Nalepa, Jasmin Wiench, Pawel Grzmil
Summary: The Pxt1 gene, expressed exclusively in male germ cells, encodes a small protein that induces cell death. However, the interaction between PXT1 and BAG6 prevents cell death. This study investigates whether the interaction of PXT1 and BAG6 is the sole mechanism preventing normal male germ cells from being killed by PXT1.
Article
Computer Science, Information Systems
Ethan Eddy, Evan Campbell, Angkoon Phinyomark, Scott Bateman, Erik Scheme
Summary: The article introduces an open-source Python library, LibEMG, which can be used for offline EMG analysis and online EMG-based interaction development. By eliminating the barriers that require substantial domain expertise, the library provides researchers with an accessible tool to accelerate research and improve reproducibility. By combining expertise from the prosthetics and human-computer interaction communities, it aims to facilitate the exploration of myoelectric control technology.
Article
Computer Science, Information Systems
Valeri Mladenov
Summary: In this paper, a unified and open linear technology simulation program with integrated circuit emphasis (LTSPICE) memristor library is proposed, which can be freely used and expanded. The library includes existing standard memristor models and enhanced models based on transition metal oxides. LTSPICE is a widely used and free software with very good convergence, suitable for analysis and design of electronic schemes.
Article
Food Science & Technology
Nurullah Gunay, Serpil Taheri, Mehmet Memis, Zeynep Yilmaz Sukranli, Taner Sahin, Seniz Demiryurek, Nahide Ekici Gunay, Yusuf Ertugrul Aslan, Abdullah Tuncay Demiryurek
Summary: The aims of this study were to identify the miRNAs involved in methanol poisoning and determine the male and female-specific miRNA expression patterns in mice. Methanol was orally administered to induce mild and severe poisoning, and miRNA expression levels were measured at different time points. The study found potential biomarkers for different tissues and differences in miRNA expression between male and female mice.
FOOD AND CHEMICAL TOXICOLOGY
(2023)
Article
Multidisciplinary Sciences
Ashkan Hassanzadeh, Sonia Valdivielso, Enric Vazquez-Sune, Rotman Criollo, Merce Corbella
Summary: Isocompy is an open source Python library that uses machine learning algorithms and user-defined variables to estimate isotopic compositions. It provides functionalities such as dataset preprocessing, outlier detection, statistical analysis, feature selection, model validation and calibration, and postprocessing. Isocompy can handle discontinuous inputs in time and space, and generates extensive output reports, figures, and maps for the comprehension of stable water isotope studies.
SCIENTIFIC REPORTS
(2023)
Article
Public, Environmental & Occupational Health
Elliott J. Price, Jiri Palat, Katerina Coufalikova, Petr Kukucka, Garry Codling, Chiara Maria Vitale, Stepan Koudelka, Jana Klanova
Summary: A retention-indexed HR-[EI+]-MS library for environmental chemicals has been constructed using GC-Orbitrap MS analysis of authentic compounds. The library, which is freely available, currently contains over 350 compounds from 56 compound classes, including legacy and emerging contaminants, providing a valuable resource for full-scan chemical exposure studies.
FRONTIERS IN PUBLIC HEALTH
(2021)
Article
Biochemical Research Methods
Issar Arab, William E. Fondrie, Kris Laukens, Wout Bittremieux
Summary: A key analysis task in mass spectrometry proteomics is matching tandem mass spectra to peptides using sequence database searching or spectral library searching. Machine learning is an increasingly popular postprocessing approach that improves identification of confident spectra. This study integrates semisupervised machine learning into the ANN-SoLo tool, an efficient spectral library search engine optimized for open modification searching. The machine learning approach boosts the identification of spectra in both standard and open searching, and provides insights into spectrum characteristics.
JOURNAL OF PROTEOME RESEARCH
(2023)
Article
Biochemistry & Molecular Biology
Feng Zhao, Shiyu Ma, Yuling Zhou, Bailing Wei, Zhen Hao, Xiaolin Cui, Lina Xing, Gang Liu, Lingling Jin, Tonghui Ma, Lei Shi
Summary: miRNA-223 plays a critical role in hepatic cholesterol homeostasis and regulation of biliary cholesterol secretion and gallstone formation. The study demonstrated that miRNA-223 KO, Delta Hepa, and KD mice showed accelerated gallstone formation with elevated cholesterol levels in liver tissues and bile. Key biliary cholesterol transporters ABCG5 and ABCG8 were identified as direct targets of miRNA-223 in gallstone formation.
INTERNATIONAL JOURNAL OF BIOLOGICAL SCIENCES
(2021)