Article
Environmental Sciences
Rei Sonobe, Yuhei Hirono
Summary: Tea, the second most popular drink in the world after water, is consumed in different forms such as black and green teas. In response to consumer preferences, various cultivars have been developed. Leaf chlorophyll content, which is influenced by disease, nutrition, and environment, affects the appearance of dried tea leaves. Quantifying chlorophyll content can improve tea tree management.
Article
Computer Science, Artificial Intelligence
Milad Malekipirbazari, Vural Aksakalli, Waleed Shafqat, Andrew Eberhard
Summary: This study investigates the challenge of deploying feature reduction methods on datasets with massive number of instances and finds that selecting a smaller random subset of instances can achieve similar performance levels. This provides empirical evidence for drastically reducing the amount of data needed for training a classifier.
EXPERT SYSTEMS WITH APPLICATIONS
(2021)
Article
Biochemical Research Methods
Benjamin Crysup, Bruce Budowle, August E. Woerner
Summary: The study proposes using varying alignment parameters to improve alignments in the presence of varying reference structures, resulting in significantly fewer misaligned bases.
Article
Environmental Sciences
Peng Guo, Ting Li, Han Gao, Xiuwan Chen, Yifeng Cui, Yanru Huang
Summary: In this study, 56 calibration methods were explored for modeling and predicting soil nutrients using hyperspectral Vis-NIR data. The results showed that first-order derivatives based on logarithmic and inverse transformations provided better predictions for available potassium and phosphorous, while the best transformation for organic matter was SG+MSC. CARS was better than SPA in selecting effective variables, and the PLSR model outperformed the SVM models. Overall, organic matter prediction was superior, followed by available phosphorous, and then available potassium.
Article
Engineering, Biomedical
Rym Nihel Sekkal, Fethi Bereksi-Reguig, Daniel Ruiz-Fernandez, Nabil Dib, Samira Sekkal
Summary: This study compares traditional machine learning algorithms with deep learning methods, and the results show that support vector machine and random forest are just as valid as feature-based neural networks in predicting sleep stages classification, with performance similar to the state of the art.
BIOMEDICAL SIGNAL PROCESSING AND CONTROL
(2022)
Article
Cell Biology
Simona Secomandi, Guido R. Gallo, Marcella Sozzoni, Alessio Iannucci, Elena Galati, Linelle Abueg, Jennifer Balacco, Manuela Caprioli, William Chow, Claudio Ciofi, Joanna Collins, Olivier Fedrigo, Luca Ferretti, Arkarachai Fungtammasan, Bettina Haase, Kerstin Howe, Woori Kwak, Gianluca Lombardo, Patrick Masterson, Graziella Messina, Anders P. Moller, Jacquelyn Mountcastle, Timothy A. Mousseau, Joan Ferrer Obiol, Anna Olivieri, Arang Rhie, Diego Rubolini, Marielle Saclier, Roscoe Stanyon, David Stucki, Francoise Thibaud-Alquati, James Torrance, Antonio Torroni, Kristina Weber, Roberto Ambrosini, Andrea Bonisoli-Alquati, Erich D. Jarvis, Luca Gianfranceschi, Giulio Formenti
Summary: This study provides a chromosome-level reference genome and pangenome for the barn swallow, allowing for the identification of potentially conserved and accelerated genes and the inference of core and accessory genes. These resources will facilitate population genomics studies, aid in detecting candidate genes in comparative genomics studies, and reduce bias towards a single reference genome.
Article
Biochemical Research Methods
Taher Mun, Nae-Chyun Chen, Ben Langmead
Summary: LevioSAM is a tool that can translate SAM/BAM alignments from one reference genome to another using a VCF file containing population variants. It utilizes succinct data structures and efficiently scales to multiple threads, making it more than 7 times faster than traditional aligners when run with 16 threads.
Article
Chemistry, Analytical
D. Cozzolino, P. J. Williams, L. C. Hoffman
Summary: Hyperspectral imaging combines vibrational spectroscopy and imaging to provide detailed information about the chemical composition and spatial distribution of samples. Pre-processing techniques are essential to remove interferences and enhance the quality of hyperspectral images.
MICROCHEMICAL JOURNAL
(2023)
Article
Biochemical Research Methods
Nae-Chyun Chen, Luis F. Paulin, Fritz J. Sedlazeck, Sergey Koren, Adam M. Phillippy, Ben Langmead
Summary: In this study, a method called levioSAM2 is described, which performs fast and accurate lift-over between genome assemblies using a whole-genome map. By aligning reads to a high-quality reference and lifting them to an older reference, levioSAM2 improves the accuracy of variant calling on the old reference. This method enables efficient and accurate read mapping and variant calling by combining fast lift-over and selective re-mapping.
Article
Thermodynamics
Ping Jiang, Zhenkun Liu, Xinsong Niu, Lifang Zhang
Summary: Wind speed forecasting is becoming increasingly important as the use of wind energy in electricity systems grows. A combined prediction system has been proposed in this study, integrating multiple forecasting methods to provide accurate point and interval forecasts for wind speed. This system is deemed more useful for the scheduling and management of electric power systems compared to other benchmark models.
Article
Biochemistry & Molecular Biology
Krzysztof Jan Abram, Douglas McCloskey
Summary: This study assesses the impact of commonly used and newly developed data preprocessing methods on the performance of deep learning in life science data analysis. It provides a set of best practices for researchers to start downstream tasks using deep learning.
Article
Biotechnology & Applied Microbiology
Nae-Chyun Chen, Brad Solomon, Taher Mun, Sheila Iyer, Ben Langmead
Summary: This paper introduces a reference flow alignment method that improves alignment accuracy and reduces reference bias by using multiple population reference genomes. Compared to the graph aligner vg, the reference flow method achieves similar accuracy and bias avoidance with only 14% memory footprint and 5.5 times the speed.
Review
Biochemical Research Methods
Xiaoshu Zhu, Jianxin Wang, Rongruan Li, Xiaoqing Peng
Summary: In single-cell RNA-seq data analysis, gene selection methods are important for improving clustering performance. This study provides an overview of different gene selection methods, compares their performance, and finds that highly variable genes are more important for clustering. The results suggest that different gene selection methods perform differently in different scenarios.
CURRENT BIOINFORMATICS
(2023)
Article
Chemistry, Analytical
Johan Lassen, Kirstine Lykke Nielsen, Mogens Johannsen, Palle Villesen
Summary: Metabolomics field is rapidly advancing with new processing and statistical strategies being proposed. This study investigates the impact of two automated optimization tools using machine learning prediction power, showing that optimized parameters outperform default settings. Machine-learning approach is suggested for future evaluations of new optimization methods.
ANALYTICAL CHEMISTRY
(2021)
Article
Medicine, General & Internal
Maria Tamoor, Asma Naseer, Ayesha Khan, Kashif Zafar
Summary: In recent years, there has been a significant increase in the average number of skin cancer cases per year, which can be life threatening. Detecting skin diseases early through automated techniques is crucial, but it is challenging due to the presence of many image artefacts.
Article
Food Science & Technology
Martin Alewijn, Ron Wehrens, Saskia M. van Ruth
INTERNATIONAL DAIRY JOURNAL
(2018)
Article
Behavioral Sciences
Margriet Roelse, Ron Wehrens, Maurice G. L. Henquet, Renger F. Witkamp, Robert D. Hall, Maarten A. Jongsma
Article
Multidisciplinary Sciences
Guusje Bonnema, Jun Gu Lee, Wang Shuhang, David Lagarrigue, Johan Bucher, Ron Wehrens, Ric de Vos, Jules Beekwilder
Article
Multidisciplinary Sciences
Ron Wehrens, Margriet Roelse, Maurice Henquet, Marco van Lenthe, Paul W. Goedhart, Maarten A. Jongsma
Article
Chemistry, Multidisciplinary
Luuk T. C. G. van Summeren, Jan Gerretzen, Floris P. J. T. Rutjes, Tom G. Bloemberg
Summary: This experiment integrates various aspects and concepts of chemistry traditionally taught separately in undergraduate chemical education, such as organic synthesis, quantitative chemical analysis, design of experiments, optimization, statistical modeling, computer programming, and continuous-flow processes.
JOURNAL OF FLOW CHEMISTRY
(2021)
Article
Biodiversity Conservation
Rob van Treuren, Roel Hoekstra, Ron Wehrens, Theo van Hintum
GLOBAL ECOLOGY AND CONSERVATION
(2020)
Article
Nutrition & Dietetics
Diederik Esser, Juri Matualatupauw, Ric C. H. de Vos, Ron Wehrens, Jos van der Stappen, Ingrid van der Meer, Lydia A. Afman
Summary: The study examined the efficacy of Mohana Choorna, a traditional Ayurvedic herbal preparation, in preventing and treating type 2 diabetes (T2D). The results showed that four weeks' use of Mohana Choorna did not have beneficial effects on glucose homeostasis.
Article
Plant Sciences
Manya Afonso, Hubert Fonteijn, Felipe Schadeck Fiorentin, Dick Lensink, Marcel Mooij, Nanne Faber, Gerrit Polder, Ron Wehrens
FRONTIERS IN PLANT SCIENCE
(2020)
Article
Multidisciplinary Sciences
Sue Marr, Jos A. Hageman, Ron Wehrens, Nicole M. van Dam, Helge Bruelheide, Steffen Neumann
Summary: This study investigates the seasonal variation and responses to the environment in plant secondary metabolite profiles, utilizing trait and mass spectrometry data of thirteen grassland species collected at different time points in the growing season. The comprehensive data set allows for the exploration of environmental dynamics across diverse neighborhoods reflected in metabolomic profiles.
Article
Food Science & Technology
Jurriaan J. Mes, Diederik Esser, Els Oosterink, Ronald T. M. van den Dool, Jasper Engel, Govardus A. H. de Jong, Ron Wehrens, Ingrid M. van der Meer
Summary: A human intervention trial comparing amino acid uptake of Lemna protein concentrate (LPC) to whey protein concentrate (WPC) showed that LPC led to a lower postprandial increase in amino acids compared to WPC, with significant interindividual variation. The study suggests that LPC's effects in the human body can vary greatly, and provides new estimates for research purposes.
INTERNATIONAL JOURNAL OF FOOD SCIENCES AND NUTRITION
(2022)
Article
Agronomy
Hubert Fonteijn, Manya Afonso, Dick Lensink, Marcel Mooij, Nanne Faber, Arjan Vroegop, Gerrit Polder, Ron Wehrens
Summary: High-throughput phenotyping is becoming increasingly important in agriculture, used by breeders and growers for estimating genetic value and predicting yield. Image analysis plays a crucial role in most phenotyping applications, with recent advances in robotics, image registration, and image segmentation improving the feasibility of fully integrated automatic phenotyping systems. However, challenges remain in developing complete phenotyping systems for routine use in production environments.
Article
Agronomy
Daniela Bustos-Korts, Martin P. Boer, Jamie Layton, Anke Gehringer, Tom Tang, Ron Wehrens, Charlie Messina, Abelardo J. de la Vega, Fred A. van Eeuwijk
Summary: This study evaluates self-organizing maps (SOM) to identify adaptation zones and visualize genotypic responses to multiple environments. The results show that grouping trial locations into adaptation zones can enhance the selection of well-adapted varieties. The study demonstrates the potential of SOM-based strategies in analyzing genotype-by-environment interactions.
THEORETICAL AND APPLIED GENETICS
(2022)
Article
Nutrition & Dietetics
Meeke Ummels, Lonneke JanssenDuijghuijsen, Jurriaan J. Mes, Claire van der Aa, Ron Wehrens, Diederik Esser
Summary: This study aimed to evaluate the nutritional value of upcycled barley/rice proteins (BRP) extracted from brewers' spent grain (BSG) and compare it with pea proteins (PP). The results showed that the amino acid uptake of BRP was comparable to PP, indicating the potential for optimizing protein quality for overall health.
Article
Food Science & Technology
Diederik Esser, Ron Wehrens, Kaatje Lenaerts, Jasper Engel, Ronald T. M. van den Dool, Shanna Bastiaan-Net, Jurriaan J. Mes, Harry J. Wichers
Summary: Important considerations in the choice of future sustainable protein sources include tolerance, nutritional quality, and potential health benefits. This study evaluated two sustainable protein sources and found that they can be consumed in high quantities without causing gastrointestinal complaints or gut barrier dysfunction. They also provide essential amino acids, but one of the protein sources may lead to an increase in blood pressure.
CURRENT RESEARCH IN FOOD SCIENCE
(2023)
Article
Computer Science, Interdisciplinary Applications
Ron Wehrens, Johannes Kruisselbrink
JOURNAL OF STATISTICAL SOFTWARE
(2018)
Article
Chemistry, Analytical
Yujia Ying, Huilin Li
Summary: Enzymes play a crucial role as biological catalysts in accelerating biochemical reactions in living organisms. This study proposes a convenient method for monitoring enzymatic catalytic processes using native top-down mass spectrometry. By exploring the heterogeneity of the chymotrypsin sample and using tandem mass spectrometry, the researchers were able to monitor covalent and noncovalent enzymatic complexes, substrates, and products during catalysis. The results demonstrate that this method has the potential to be a promising tool for characterizing biocatalysts.
ANALYTICA CHIMICA ACTA
(2024)
Article
Chemistry, Analytical
Kang Yang, Shuaibo Shi, Jinyu Wu, Shaolong Han, Shengdi Tai, Shishen Zhang, Kun Zhang
Summary: H2O and D2O are important analogues closely related to various industries and monitoring fields. This study successfully distinguishes and detects H2O and D2O by designing a novel eu(III)-macrocycle with dual emitters, Eu-2a, and conducting fluorescence titration experiments.
ANALYTICA CHIMICA ACTA
(2024)
Article
Chemistry, Analytical
Julia Kuligowski, Alvaro Perez-Rubio, Marta Moreno-Torres, Polina Soluyanova, Judith Perez-Rojas, Ivan Rienda, David Perez-Guaita, Eugenia Pareja, Ramon Trullenque-Juan, Jose Castell, Marcha Verheijen, Florian Caiment, Ramiro Jover, Guillermo Quintas
Summary: This study introduces a novel variable selection approach called cluster PLS (c-PLS) to assess the joint impact of variable groups selected based on biological characteristics on the predictive performance of a multivariate model. The usefulness of c-PLS is shown using miRNomic and metabolomic datasets obtained from the analysis of liver tissue biopsies.
ANALYTICA CHIMICA ACTA
(2024)
Article
Chemistry, Analytical
Meixue Lai, Lijie Zhong, Siyi Liu, Yitian Tang, Tingting Han, Huali Deng, Yu Bao, Yingming Ma, Wei Wang, Li Niu, Shiyu Gan
Summary: This study presents a method for constructing wearable sweat electrolyte sensors using carbon fiber-based solid-contact ion-selective electrodes (SC-ISEs). By using carbon fibers extracted from commercial cloth as electrode material, the cost and reproducibility issues of flexible SC-ISEs were addressed. The results showed that the carbon fiber-based SC-ISEs exhibited reversible voltammetric and stable impedance performances, and had high reproducibility of standard potentials between normal and bending states.
ANALYTICA CHIMICA ACTA
(2024)
Article
Chemistry, Analytical
Ke Yang, Ying Liu, Min Deng, Peipei Wang, Dan Cheng, Songjiao Li, Longwei He
Summary: A near-infrared fluorescent probe has been developed to accurately measure the levels of peroxynitrite (ONOO-) in the endoplasmic reticulum (ER) in acute lung injury (ALI). The probe demonstrated rapid response, high selectivity, good sensitivity, and enhanced fluorescence intensity in response to ONOO-. It was successfully used to detect changes in ONOO- levels and showed significant increases in an ALI cell model and an ALI mouse model.
ANALYTICA CHIMICA ACTA
(2024)
Article
Chemistry, Analytical
Yanping Wang, Yuemei Chen, Kejun Li, Jinrong Zhou, Xin Yuan, Mei Zhang, Ke Huang
Summary: In this work, a portable analytical system based on point discharge chemical vapor generation atomic emission spectrometry (PD-CVG-AES) coupling with gold filament enrichment was designed. The highly sensitive analysis of Hg2+ indirectly realized the detection of ascorbic acid (AA). The measurement is based on the fact that Ag+ can decrease the concentration of Hg2+ by forming Ag-Hg amalgam in the presence of the reductant SnCl2, while AA can pre-reduce Ag+ to Ag0, leading to the generation of silver nanoparticles (Ag NPs). The developed novel analytical strategy broadens the application of microplasma-based AES and offers a higher level of sensitivity compared to current AA detection techniques.
ANALYTICA CHIMICA ACTA
(2024)
Article
Chemistry, Analytical
Yundi Huang, Bo Song, Kaiwen Chen, Deshu Kong, Jingli Yuan
Summary: This study developed two lysosome-targetable background-free TGL probes for efficient and accurate detection of 1O2, which can be used for monitoring endogenous 1O2 concentrations in lysosomes and discriminating variability induced by different photosensitizers. Furthermore, a smart luminescent sensor film was successfully prepared for on-site 1O2 production detection during PDT processes, offering a promising clinical monitoring tool for skin diseases.
ANALYTICA CHIMICA ACTA
(2024)
Article
Chemistry, Analytical
Wei Lang, Jia-Mei Qin, Qian-Yong Cao
Summary: A novel polymer-based probe P1 was successfully synthesized for fluorescently ratiometric sensing of H2S with high selectivity and sensitivity. A smartphone sensing platform was constructed to conduct visual quantitative detection of H2S. P1 can be employed in evaluating the level fluctuations of H2S in living cells, testing water samples/wine samples, and monitoring food freshness.
ANALYTICA CHIMICA ACTA
(2024)
Article
Chemistry, Analytical
Yuanyuan Qin, Shuda Liu, Shuyun Meng, Dong Liu, Tianyan You
Summary: The study developed a split aptamer-based sandwich-type ratiometric biosensor for the detection of 17 beta-estradiol (E2) using photoelectrochemical and electrochemical assays. The biosensor utilized split aptamer fragments to recognize E2 and trigger a hybridization chain reaction, resulting in the production of double-stranded DNA labeled with CdTe quantum dots. This DNA complex was able to sensitize CdTe quantum dots and generate response signals for E2 detection. The developed biosensor demonstrated high sensitivity and accuracy with two linear ranges and low detection limits.
ANALYTICA CHIMICA ACTA
(2024)
Article
Chemistry, Analytical
Siriwan Teepoo, Jongjit Jantra, Khaunnapa Panapong, David Taiwo Ajayi
Summary: A novel immunochromatographic assay based on hyperbranched Au plasmonic blackbodies with a smartphone readout was developed for rapid and sensitive detection of leucomalachite green residues in fish and shrimp products.
ANALYTICA CHIMICA ACTA
(2024)
Article
Chemistry, Analytical
Andrea L. Larraga-Urdaz, Borja Moreira-Alvarez, Jorge Ruiz Encinar, Jose M. Costa-Fernandez, Maria Luisa Fernandez-Sanchez
Summary: A major challenge in the 21st century is the development of point-of-care diagnostic tools. In this study, a highly sensitive and simple bioassay using AuNPs and MNAzymes was developed for rapid detection and quantification of miRNA-4739. The proposed strategy shows potential for breast cancer diagnosis.
ANALYTICA CHIMICA ACTA
(2024)
Article
Chemistry, Analytical
Xiaohan Zhao, Anyu Wang, Lingzi Zhai, Jiuhe Gao, Sizhe Lyu, Yingshan Jiang, Tian Zhong, Ying Xiao, Xi Yu
Summary: A novel method using polystyrene-coated magnetic nanoparticles for extracting monohydroxy polycyclic aromatic hydrocarbons from urine samples was investigated. The proposed method is simple, sensitive, and efficient, with desirable sensitivity for analyzing low-abundance metabolites in large volumes of complex urine samples.
ANALYTICA CHIMICA ACTA
(2024)
Article
Chemistry, Analytical
Ke Quan, Yuqing Zeng, Wenke Zhang, Fengfeng Li, Mengjiao Li, Zhihe Qing, Linlin Wu
Summary: In this study, a visual and reusable biosensor was developed for detecting substrates that are closely associated with human physiological health. The immobilized oxidase showed higher stability and sensitivity under harsh conditions, enabling reliable detection of substrates in complex fluids.
ANALYTICA CHIMICA ACTA
(2024)
Article
Chemistry, Analytical
Dongjuan Wang, Xiuqian Ding, Jinling Xie, Juan Wang, Guanhao Li, Xin Zhou
Summary: In this study, a three-in-one sensor was developed for real-time detection of biogenic amines (BAs) with high sensitivity and selectivity. The sensor showed multimodal responses and could be used to fabricate portable devices for on-site non-destructive assessment of food spoilage indicators.
ANALYTICA CHIMICA ACTA
(2024)
Article
Chemistry, Analytical
Jinting Meng, Zihao Xu, Shasha Zheng, Hongqun Yang, Tianfu Wang, Hong Wang, Yingwei Zhang
Summary: This study demonstrates the development of a cascade signal amplification system using a multi-pedal DNA walker and strand displacement reactions for the electrochemical detection of miRNA-155. The biosensor exhibited high sensitivity, selectivity, and the potential for clinical applications.
ANALYTICA CHIMICA ACTA
(2024)
