As computing power increases, vibrational circular dichroism (VCD) calculations on molecules of larger sizes and complexities become possible. At the same time, the spectra resulting from these computations become increasingly more cumbersome to analyze. Here, we describe the GUI implementation into the Amsterdam Density Functional (ADF) software package of VCDtools, a toolbox that provides a user-friendly means to analyze VCD spectra. Key features are the use of the generalized coupled oscillator analysis methods, as well as an easy visualization of the atomic electric and magnetic transition dipole moments which together provide detailed insight in the origin of the VCD intensity. Using several prototypical examples we demonstrate the functionalities of the program. In particular, we show how the spectra can be analyzed to detect differences between theory and experiment arising from large-amplitude motions or incorrect molecular structures and, most importantly, how the program can be used to prevent incorrect enantiomeric assignments.
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http://dx.doi.org/10.1021/acs.jcim.9b00956 | DOI Listing |
Motivation: Artificial intelligence (AI) applications require explainability (XAI) for FAIR, ethical deployment, whether in the clinic or in the laboratory. Richly descriptive XAI metadata representing how pre-model data were obtained, characterized, transformed, and distributed, should be available along with the data prior to training and application of AI models.
Results: The FAIRSCAPE framework generates, packages, and integrates critical pre-model XAI descriptive metadata, including deep provenance graphs and data dictionaries with feature validation on uploaded data, software, and computations, with special reference to biomedical datasets.
Sci Rep
December 2024
Department of Biomedical Engineering, Worcester Polytechnic Institute, Worcester, MA, 01605, USA.
Multicellular spheroids embedded in 3D hydrogels are prominent in vitro models for 3D cell invasion. Yet, quantification methods for spheroid cell invasion that are high-throughput, objective and accessible are still lacking. Variations in spheroid sizes and the shapes of the cells within render it difficult to objectively assess invasion extent.
View Article and Find Full Text PDFZhongguo Dang Dai Er Ke Za Zhi
December 2024
Neonatal Center, Beijing Children's Hospital, Capital Medical University, Beijing 100045 (Hei M-Y, Email: Department of Pediatrics, Third Xiangya Hospital, Central South University, Changsha 410013.
In order to guide clinical blood transfusion practices for pediatric patients, the National Health Commission has released the health standard "Guideline for pediatric transfusion" (WS/T 795-2022). Considering the physiological particularities of the neonatal period, blood transfusion practices for neonates are more complex than those for other children, the guidelines include a separate chapter dedicated to neonatal blood transfusion. This paper interprets the background and evidence for the compilation of the neonatal blood transfusion provisions, hoping to aid in the understanding and implementation of the neonatal blood transfusion section of the guidelines.
View Article and Find Full Text PDFPhytochem Anal
December 2024
College of Pharmacy, Guangxi Scientific Research Center of Traditional Chinese Medicine, Guangxi University of Chinese Medicine, Nanning, China.
Introduction: Fufang Shenqi Oral Liquid (FFSQOL) is an important Chinese medicine compound preparation with a wide range of clinical applications, which is mainly used to regulate immune function, improve cardiovascular function, and have anti-inflammatory and antibacterial effects. At present, it is of great importance to establish the quality evaluation method of FFSQOL and to investigate its quality markers (Q-markers).
Objectives: The aim of this study is to establish a quality evaluation method for FFSQOL and screen its Q-markers to provide a scientific basis for its quality control.
Bioinformatics
November 2024
Institute of Pharmaceutical and Biomedical Sciences, Johannes Gutenberg-University Mainz, Mainz, 55128, Germany.
Motivation: Oxford Nanopore Technologies recently adopted the POD5 file format for storing raw nanopore sequencing data. The information stored in these files provides detailed insights into the sequencing features and enhances the understanding of raw nanopore data. However, the process of visualizing the data can be cumbersome, especially for users without programming skills.
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