Article
Cell Biology
Federico Plazzi, Guglielmo Puccio, Marco Passamonti
Summary: The study introduces an improved tool, HERMES index, for measuring and quantifying molecular changes in mitochondrial genomes. By analyzing complete mitochondrial genomes in molecular phylogenetic studies, HERMES can identify clades or species with unique molecular characteristics, helping to reveal phylogenetic and ecological patterns. The software presented in the study can handle linear, circular, and multi-chromosome genomes, extending HERMES' scope to the entire domain of eukaryotes.
Article
Geochemistry & Geophysics
Soung Sub Lee
Summary: This article presents an optimization method for satellite constellations in a specific area considering observation priority and weight for dispersed targets. The proposed method solves the limitations of the Walker technique by applying various optimization problems based on satellite target access. The optimized constellation design uses a dynamic model, geometric analysis, and an access matrix for multiple targets, significantly reducing revisit performance compared to the Walker constellation and suggesting an optimized design technique.
IEEE TRANSACTIONS ON GEOSCIENCE AND REMOTE SENSING
(2023)
Article
Biochemistry & Molecular Biology
Maria Pilar Giner, Stefan Christen, Simona Bartova, Mikhail Makarov, Marie E. Migaud, Carles Canto, Sofia Moco
Summary: NAD(+) and its reduced form NADH are essential coenzymes in hundreds of metabolic reactions, serving as substrates for key enzymes. Analyzing the NAD(+) metabolome using liquid chromatography-tandem mass spectrometry can provide insights into NAD(+) biology and its implications for health and disease.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2021)
Article
Computer Science, Hardware & Architecture
Hui-Ning Pei, Meng Wu, Xue-Qin Huang, Man Ding, Xin-Xin Zhang
Summary: In this paper, a method of generating digital camouflage image based on several background images is proposed. The K-harmonic means (KHM) clustering algorithm is introduced to extract color features from several background images. The digital camouflage image is generated using the regular hexagon as the basic unit and the lowest horizontal line algorithm. The results show that the generated digital camouflage image effectively conceals maneuvering targets and has a good camouflage effect.
Article
Geochemistry & Geophysics
Danyelle da Silva, Edwin Fagua Duarte, Wagner Almeida, Mauro Ferreira, Francisco Alirio Moura, Joao Medeiros de Araujo
Summary: The target-oriented methodology of full-waveform inversion using patched Green's function technique in frequency-domain wave propagator reduces computational time without compromising accuracy, making it suitable for wave propagation in spatially variable media. By dividing the computational domain into target and non-target areas, precise calculations are performed separately, resulting in identical results to conventional FWI but in reduced time based on target size.
Article
Microbiology
Fernanda Rosa, Katelin S. Matazel, Ahmed A. Elolimy, Sean H. Adams, Anne Bowlin, Keith D. Williams, Lars Bode, Laxmi Yeruva
Summary: This study investigated the impact of human milk (HM) feeding compared to cow's milk formula (MF) feeding on small intestinal and circulatory metabolome patterns, revealing differences in metabolite levels and associated microbial genera at different stages of development.
Article
Engineering, Environmental
Fengming Hou, Wei Wei, Yihang Li, Zhipeng Guo, Xiaoke Zhang, Jin Li, Ang Wei
Summary: By target-oriented functionalization, carbon nitride was successfully modified as a round-the-clock antimicrobial photocatalyst for high-efficient water disinfection and bacteriostasis. The modified photocatalyst demonstrated excellent disinfection efficacy against pathogenic microorganisms and continuous inhibition of microbial proliferation.
CHEMICAL ENGINEERING JOURNAL
(2023)
Article
Plant Sciences
Lerato Nephali, Paul Steenkamp, Karl Burgess, Johan Huyser, Margaretha Brand, Justin J. J. van der Hooft, Fidele Tugizimana
Summary: By using metabolome mining tools, this study revealed the chemical space of Bacillus strains and their consortium, providing valuable insights for the innovative design and use of PGPR-based biostimulants.
FRONTIERS IN PLANT SCIENCE
(2022)
Article
Chemistry, Multidisciplinary
Farah Syazana Dzulkefli, Abdul Halim Abdul Latiff, Hazwan Syahmi Hashim, Amir Mustaqim Majdi, Herurisa Rusmanugroho, Junxiao Li
Summary: This paper presents a target-oriented imaging workflow that combines seismic redatuming with Kirchhoff migration to reduce computational cost and improve the accuracy and quality of migrated images. The developed methodology was tested using a sub-salt SEG Advanced Modeling (SEAM) model and field data in East Malaysia, demonstrating its capability to generate better quality and instant migrated images within the designated region.
APPLIED SCIENCES-BASEL
(2023)
Article
Computer Science, Artificial Intelligence
Ganggang Dong, Hongwei Liu
Summary: In recent years, there has been a resurgence in neural networks for learning high-level representations. However, the limited availability of radar images with label information restricts the fitting power of deep architectures. Moreover, the presence of speckles, which are multiplicative noise with statistical specificity, makes image interpretation difficult. To address these issues, this paper proposes a new hierarchical receptive neural network that encodes and refines features using signal-wise receptive modules and patch-wise receptive units.
PATTERN RECOGNITION
(2022)
Article
Biochemistry & Molecular Biology
Jamie M. Newton, Emma L. Betts, Lyto Yiangou, Jose Ortega Roldan, Anastasios D. Tsaousis, Gary S. Thompson
Summary: Blastocystis is an opportunistic parasite commonly found in the intestines of humans and other animals, but there is limited knowledge about its biology. Analyzing its metabolites can reveal its role in health and disease. Using methanol as an extraction solvent and bead bashing as a lysis technique, carrying out the procedure at room temperature provides a consistent and efficient method to extract metabolites from Blastocystis for NMR analysis.
Article
Biochemistry & Molecular Biology
Xiaoshan Sun, Zhen Jia, Yuqing Zhang, Xinjie Zhao, Chunxia Zhao, Xin Lu, Guowang Xu
Summary: Direct infusion nanoelectrospray high-resolution mass spectrometry (DI-nESI-HRMS) is a promising tool for high-throughput metabolomics analysis. To overcome the limitations of metabolite assignment, a serum metabolome characterization method using a reaction network combined with mass accuracy and isotopic patterns filter was proposed. The approach was validated and compared to database search, showing improved coverage and accuracy rates. The method was then applied to a case study in diabetes metabolomics.
Article
Engineering, Electrical & Electronic
Xiaojie Ma, Kefeng Ji, Boli Xiong, Linbin Zhang, Sijia Feng, Gangyao Kuang
Summary: This article proposes a lightweight detector named Light-YOLOv4 through model compression, significantly reducing model size and improving detection speed while maintaining detection accuracy. Experiments on edge devices show that Light-YOLOv4 reduces model size, parameter size, and FLOPs by 98.63%, 98.66%, and 91.30% respectively compared to YOLOv4, with a 4.2x increase in detection speed and only slight decrease in detection accuracy.
IEEE JOURNAL OF SELECTED TOPICS IN APPLIED EARTH OBSERVATIONS AND REMOTE SENSING
(2021)
Article
Geochemistry & Geophysics
Yanqin Xu, Xiaoling Zhang, Shunjun Wei, Jun Shi, Tianjiao Zeng, Tianwen Zhang
Summary: A target-oriented Bayesian compressive sensing imaging method with region-adaptive extractor (TO-BCS-RAE) is proposed for mmW automotive radar imaging. It combines the prior probability distributions and inherent continuity of the target scattering points to suppress background clutter and enhance the smooth structure of targets. Experimental results demonstrate that the proposed method outperforms conventional BP, OMP, and ISTA methods in terms of imaging quality.
IEEE TRANSACTIONS ON GEOSCIENCE AND REMOTE SENSING
(2023)
Review
Biochemistry & Molecular Biology
Jean-Francois Haince, Philippe Joubert, Horacio Bach, Rashid Ahmed Bux, Paramjit S. Tappia, Bram Ramjiawan
Summary: The five-year survival rate of lung cancer patients is low due to late-stage diagnosis, emphasizing the importance of early detection. This review discusses various early detection methods such as chest X-rays, bronchoscopy, sputum analysis, and low-dose computed tomography (LDCT). It also highlights the potential of metabolomic fingerprinting as a cost-effective and accessible blood-based test for early-stage lung cancer screening.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2022)
Article
Biochemical Research Methods
Andrea M. Brunner, Philip Lossl, Paul P. Geurink, Huib Ovaa, P. Albanese, A. F. Maarten Altelaar, Albert J. R. Heck, Richard A. Scheltema
Summary: Top-down proteomics combined with bioinformatics approaches can improve the localization and quantification of protein modifications, even for positional isomers with the same number of modifications at different sites. This method shows promising results in characterizing multiple modified proteins and estimating the stoichiometry of phosphorylated sites.
MOLECULAR & CELLULAR PROTEOMICS
(2021)
Editorial Material
Biochemical Research Methods
Evelyn Rampler, Erin S. Baker, Kaylie Kirkwood, Michaela Schwaiger-Haber, Maggie Tam, Marissa A. Jones, Melissa Sherman
EXPERT REVIEW OF PROTEOMICS
(2022)
Article
Biochemistry & Molecular Biology
Johannes Rainer, Andrea Vicini, Liesa Salzer, Jan Stanstrup, Josep M. Badia, Steffen Neumann, Michael A. Stravs, Vinicius Verri Hernandes, Laurent Gatto, Sebastian Gibb, Michael Witting
Summary: Liquid chromatography-mass spectrometry (LC-MS)-based untargeted metabolomics experiments require customized annotation workflows. We present an ecosystem of R packages that provide a modular infrastructure for annotating untargeted metabolomics data, including initial annotation and reference library comparison. The system supports various data formats and offers highly customizable functionality for most untargeted LC-MS data.
Article
Physiology
Laura Brugnara, Ana Isabel Garcia, Serafin Murillo, Josep Ribalta, Guerau Fernandez, Susanna Marquez, Miguel Angel Rodriguez, Maria Vinaixa, Nuria Amigo, Xavier Correig, Susana Kalko, Jaume Pomes, Anna Novials
Summary: The aim of this study was to investigate the relationship between muscle carnosine and type 1 diabetes, as well as how it is influenced by physical activity. The results showed that patients with type 1 diabetes had higher levels of muscle carnosine, which were influenced by physical activity, clinical characteristics, and lipoprotein subfractions.
EUROPEAN JOURNAL OF APPLIED PHYSIOLOGY
(2022)
Article
Engineering, Environmental
Peer H. A. Timmers, T. Slootweg, A. Knezev, M. van der Schans, L. Zandvliet, A. Reus, D. Vughs, L. Heijnen, T. Knol, J. El Majjaoui, P. van der Wielen, P. J. Stuyfzand, K. Lekkerkerker-Teunissen
JOURNAL OF HAZARDOUS MATERIALS
(2022)
Article
Biochemistry & Molecular Biology
Yahui Wang, Ethan Stancliffe, Ronald Fowle-Grider, Rencheng Wang, Cheng Wang, Michaela Schwaiger-Haber, Leah P. Shriver, Gary J. Patti
Summary: This study found that the lactate excretion in proliferating cells is correlated with the activity of mitochondrial NADH shuttles, rather than proliferation itself. Proliferating cells primarily transform glucose to lactate when glycolysis outpaces the mitochondrial NADH shuttles.
Article
Environmental Sciences
Ruud Steenbeek, Erik Emke, Dennis Vughs, Joao Matias, Tim Boogaerts, Sara Castiglioni, Marina Campos-Manas, Adrian Covaci, Pim de Voogt, Thomas ter Laak, Felix Hernandez, Noelia Salgueiro-Gonzalez, Wim G. Meijer, Mario J. Dias, Susana Simoes, Alexander L. N. van Nuijs, Lubertus Bijlsma, Frederic Been
Summary: This study assessed crack cocaine use on a broad scale, both temporal and in cities across Europe, using wastewater-based epidemiology. The results highlight the importance of monitoring community loads of crack cocaine use.
SCIENCE OF THE TOTAL ENVIRONMENT
(2022)
Article
Geriatrics & Gerontology
Paola Sebastiani, Zeyuan Song, Dylan Ellis, Qu Tian, Michaela Schwaiger-Haber, Ethan Stancliffe, Michael S. Lustgarten, Cory C. Funk, Priyanka Baloni, Cong-Hui Yao, Shakchhi Joshi, Megan M. Marron, Anastasia Gurinovich, Mengze Li, Anastasia Leshchyk, Qingyan Xiang, Stacy L. Andersen, Mary F. Feitosa, Svetlana Ukraintseva, Mette Soerensen, Oliver Fiehn, Jose M. Ordovas, Marcia Haigis, Stefano Monti, Nir Barzilai, Sofiya Milman, Luigi Ferrucci, Noa Rappaport, Gary J. Patti, Thomas T. Perls
Summary: By conducting a meta-analysis of five studies, this research identified a signature of 19 metabolites significantly associated with the e2 allele of the APOE gene. These metabolites were primarily glycerolipids and glycerophospholipids, which were higher in carriers of the e2 allele. Additionally, one organic acid metabolite was also found to be associated with the e2 allele. However, no significant associations were found with metabolites in the e4 allele group.
Article
Chemistry, Analytical
Ethan Stancliffe, Michaela Schwaiger-Haber, Miriam Sindelar, Matthew J. Murphy, Mette Soerensen, Gary J. Patti
Summary: The success of precision medicine relies on collecting large-scale data from populations. This study presents an untargeted metabolomics workflow for large-scale projects and uses a reference sample and computational approaches for data processing, resulting in distinct features associated with geographic location.
ANALYTICAL CHEMISTRY
(2022)
Article
Medicine, General & Internal
Marina Canyelles, Antonio Perez, Alexandra Junza, Inka Minambres, Oscar Yanes, Helena Sarda, Noemi Rotllan, Josep Julve, Jose Luis Sanchez-Quesada, Mireia Tondo, Joan Carles Escola-Gil, Francisco Blanco-Vaca
Summary: This study evaluated the effects of glycemic control and bariatric surgery on TMAO and γ BB in newly diagnosed T2D patients and morbidly obese subjects, showing that neither glycemic control nor bariatric surgery improved the circulating concentrations of TMAO in these populations.
Article
Biochemistry & Molecular Biology
Xiangfeng Niu, Ethan Stancliffe, Susan J. Gelman, Lingjue Wang, Michaela Schwaiger-Haber, Joe L. Rowles, Leah P. Shriver, Gary J. Patti
Summary: In this study, an approach to resolve the fluxes of NADPH in the cytosol and mitochondria was introduced using deuterium tracing. It was found that challenges in the cytosol affected NADPH fluxes in the cytosol, while challenges in the mitochondria affected NADPH fluxes in the mitochondria. This work highlights the value of using proline labeling as a reporter system for studying compartmentalized metabolism and reveals independent regulation of NADPH homeostasis in the cytosol and mitochondria, without evidence for NADPH shuttle activity.
NATURE CHEMICAL BIOLOGY
(2023)
Article
Multidisciplinary Sciences
Michaela Schwaiger-Haber, Ethan Stancliffe, Dhanalakshmi S. Anbukumar, Blake Sells, Jia Yi, Kevin Cho, Kayla Adkins-Travis, Milan G. Chheda, Leah P. Shriver, Gary J. Patti
Summary: Tumors are heterogeneous and consist of various cell types in different microenvironments. The integration of mass spectrometry imaging (MSI), stable isotope labeling, and isotopologue spectral analysis enables the mapping of metabolite distributions and metabolic fluxes in the brains of mice with GL261 glioma. This approach reveals alterations in anabolic pathways, specifically an increase in de novo fatty acid synthesis and elongation fluxes in the glioma compared to surrounding healthy tissue.
NATURE COMMUNICATIONS
(2023)
Article
Biology
Alejandro Sola-Garcia, Maria Angeles Caliz-Molina, Isabel Espadas, Michael Petr, Concepcion Panadero-Moron, Daniel Gonzalez-Moran, Maria Eugenia Martin-Vazquez, Alvaro Jesus Narbona-Perez, Livia Lopez-Noriega, Guillermo Martinez-Corrales, Raul Lopez-Fernandez-Sobrino, Lina M. Carmona-Marin, Enrique Martinez-Force, Oscar Yanes, Maria Vinaixa, Daniel Lopez-Lopez, Jose Carlos Reyes, Joaquin Dopazo, Franz Martin, Benoit R. Gauthier, Morten Scheibye-Knudsen, Vivian Capilla-Gonzalez, Alejandro Martin-Montalvo
Summary: A multiomic approach reveals that long-term exposure to the Acly inhibitor SB-204990 can modulate molecular mechanisms associated with aging. ATP-citrate lyase has a crucial role in cellular metabolism, integrating the protein, carbohydrate, and lipid metabolism. In vivo studies using untargeted metabolomics, transcriptomics, and proteomics show that SB-204990 regulates energy metabolism, mitochondrial function, mTOR signaling, and folate cycle, and can prevent the development of metabolic abnormalities associated with an unhealthy diet.
COMMUNICATIONS BIOLOGY
(2023)
Article
Biochemistry & Molecular Biology
Laia Bertran, Jordi Capellades, Sonia Abello, Joan Duran-Bertran, Carmen Aguilar, Salome Martinez, Fatima Sabench, Xavier Correig, Oscar Yanes, Teresa Auguet, Cristobal Richart
Summary: This study explores the importance of metabolomic analysis in nonalcoholic steatohepatitis (NASH) associated with obesity. The analysis of blood metabolites in morbidly obese women showed significant differences in lipid metabolites and derivatives between NASH and normal liver patients. These findings may contribute to identifying the main metabolic pathways related to NASH and could potentially be used as biomarkers in the diagnosis and follow-up of the disease.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
Article
Biochemistry & Molecular Biology
Teresa Auguet, Laia Bertran, Jordi Capellades, Sonia Abello, Carmen Aguilar, Fatima Sabench, Daniel del Castillo, Xavier Correig, Oscar Yanes, Cristobal Richart
Summary: This study aimed to identify differences between metabolically healthy obese individuals and those with metabolic disorders by conducting a metabolomics analysis in women. The findings showed that women with morbid obesity had higher levels of choline and acylglycerols, and lower levels of bile acids, steroids, ceramides, glycosphingolipids, lysophosphatidylcholines, and lysophosphatidylethanolamines compared to the normal weight group. In women with morbid obesity and type 2 diabetes mellitus, increased levels of glutamate, propionyl-carnitine, bile acids, ceramides, lysophosphatidylcholine 14:0, phosphatidylinositols, and phosphoethanolamines were found, along with lower levels of Phe-Ile/Leu. These metabolites may serve as new factors for further study on the pathogenesis of obesity and associated type 2 diabetes mellitus in women.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
