Article
Multidisciplinary Sciences
Nico Curti, Giuseppe Levi, Enrico Giampieri, Gastone Castellani, Daniel Remondini
Summary: One of the objectives in high-throughput genomics studies is to obtain a low-dimensional set of observables for sample classification purposes. We propose a network-based heuristic method called DNetPRO to generate feature sets. Applications on real datasets show that our method outperforms existing results or is compatible with them with a smaller number of selected features. Moreover, the resulting class-separation surfaces have a simpler geometry, allowing for clearer interpretation of the obtained features compared to nonlinear classification models.
SCIENTIFIC REPORTS
(2022)
Article
Biochemical Research Methods
Xiangtao Li, Shaochuan Li, Lei Huang, Shixiong Zhang, Ka-chun Wong
Summary: The article introduces a method called SEDIM, which automatically designs deep neural network architectures for imputing gene expression levels. It improves computational efficiency by constructing an offline surrogate model. Experimental results show that SEDIM significantly improves imputation and clustering performance, and also performs well in other contexts and platforms.
BRIEFINGS IN BIOINFORMATICS
(2022)
Article
Materials Science, Ceramics
Kewei Pan, Qing Liu, Ying Lu, Wei Wei, Zhao Ding, Shixing Wang, Yang Zhou
Summary: Carbon-based materials have received significant attention and extensive research due to their excellent electrical conductivity. Predicting the conductivity of carbon-based materials is crucial in designing and fabricating flexible carbon conductive materials for smart wearable devices before conducting experiments. To address this, ensemble data mining is employed to automatically search for relationships between factors (such as filler type, output conductivity, filling fraction, drying temperature, molding temperature, sample thickness, ultrasonic treatment time, stirring time, etc.) and the target variable (composite conductivity), providing valuable insights into the design and preparation of flexible carbon conductive materials. In this study, a uni-component carbon filler database is established, and an optimized machine learning model based on Light Gradient Boosting Machine is proposed. The importance ranking of characteristic variables in the fabrication of flexible carbon composites is demonstrated using the constructed database. The developed Light Gradient Boosting Machine model is trained on selected data to predict the optimal design strategy for flexible carbon-based conductive materials in energy storage for smart wearable devices, showing promising results in terms of effectiveness and reliability. The strategy presented in this work offers an effective approach to accelerate the research and development of flexible carbon-based conductive materials for energy storage in smart wearable devices.
CERAMICS INTERNATIONAL
(2023)
Article
Multidisciplinary Sciences
Thomas Plum, Rebecca Binzberger, Robin Thiele, Fuwei Shang, Daniel Postrach, Candice Fung, Marina Fortea, Nathalie Stakenborg, Zheng Wang, Anke Tappe-Theodor, Tanja Poth, Duncan A. A. MacLaren, Guy Boeckxstaens, Rohini Kuner, Claudia Pitzer, Hannah Monyer, Cuiyan Xin, Joseph V. Bonventre, Satoshi Tanaka, David Voehringer, Pieter Vanden Berghe, Jessica Strid, Thorsten B. Feyerabend, Hans-Reimer Rodewald
Summary: The physiological functions of mast cells are not well understood. Mast cells are involved in type 2 immunity and promote allergic diseases through the interaction with immunoglobulin E (IgE). However, allergic symptoms may also facilitate the elimination of allergens, toxins, and parasites and trigger future antigen avoidance. In this study, mast cells were found to be crucial for antigen-specific avoidance behavior in inbred mice. This behavior prevented immune activation and inflammation in the stomach and small intestine. Antigen avoidance was dependent on IgE and regulated by Th2 cytokines in the immunization phase and by IgE in the execution phase. Mucosal mast cells quickly detected the ingestion of antigens. Multiple signaling pathways between mast cells and the brain were identified. Inhibition of leukotriene synthesis impaired avoidance, but no single pathway interruption completely abolished it, suggesting complex regulation. Overall, antigen avoidance mediated by mast cells may play an important role in preventing immunopathology and repeated ingestion of toxins.
Article
Automation & Control Systems
Heonho Kim, Taewoong Ryu, Chanhee Lee, Hyeonmo Kim, Tin Truong, Philippe Fournier-Viger, Witold Pedrycz, Unil Yun
Summary: In this paper, we propose an approach called HOMI for mining high occupancy patterns on incremental databases. The experimental results demonstrate that HOMI outperforms other methods in terms of performance.
Article
Biochemical Research Methods
Stefano Grasso, Valentina Dabene, Margriet M. W. B. Hendriks, Priscilla Zwartjens, Rene Pellaux, Martin Held, Sven Panke, Jan Maarten van Dijl, Andreas Meyer, Tjeerd van Rij
Summary: The passage of proteins across biological membranes via the Sec pathway is a universally conserved process with critical functions. Estimating the impact of physicochemical signal peptide features on protein secretion levels was achieved through a high-throughput assay and machine learning model. The results allow for quantifying feature importance and predicting protein secretion levels, providing a versatile tool for signal peptide design and evaluation.
ACS SYNTHETIC BIOLOGY
(2023)
Article
Computer Science, Information Systems
Hossein Estiri, Zachary H. Strasser, Shawn N. Murphy
Summary: This study aimed to develop a high-throughput phenotyping method leveraging temporal sequential patterns from electronic health records. Using temporal sequences for phenotyping resulted in superior classification performance compared to standard representations, and transitive sequences offered more accurate phenotype characterization.
JOURNAL OF THE AMERICAN MEDICAL INFORMATICS ASSOCIATION
(2021)
Article
Computer Science, Information Systems
Alon Geva, Molei Liu, Vidul A. Panickan, Paul Avillach, Tianxi Cai, Kenneth D. Mandl
Summary: The study demonstrates that Multimodal Automated Phenotyping (MAP) performs well in pediatric setting and shows similar performance in comparison to adult hospital system. The performance of MAP in pediatric sample is comparable to six specific phenotypes validated in adult biobank.
JOURNAL OF THE AMERICAN MEDICAL INFORMATICS ASSOCIATION
(2021)
Article
Genetics & Heredity
Yongbing Zhao, Jinfeng Shao, Yan W. Asmann
Summary: Explainable artificial intelligence aims to interpret how machine learning models make decisions. This study comprehensively evaluated multiple explainers for predicting tissue types from transcriptomic data and proposed optimization strategies to improve reproducibility and interpretability of results. The work provides novel insights and guidance for exploring biological mechanisms using explainable machine learning models.
GENOMICS PROTEOMICS & BIOINFORMATICS
(2022)
Article
Materials Science, Multidisciplinary
Kenneth S. Vecchio, Olivia F. Dippo, Kevin R. Kaufmann, Xiao Liu
Summary: This article presents a high-throughput rapid experimental alloy development method that integrates a closed-loop material screening process and artificial intelligence agent technology. It achieves a unified framework for computational identification, experimental preparation, and high-throughput analysis, preventing institutional knowledge loss and enabling the use of new experimental data in new design objectives.
Article
Computer Science, Hardware & Architecture
Marc Carrascosa-Zamacois, Giovanni Geraci, Edward Knightly, Boris Bellalta
Summary: In this article, the real-world capability of the multi-link operation (MLO) framework, one of the key features in IEEE 802.11be, is investigated using a large dataset of 5 GHz spectrum occupancy measurements. The study shows that MLO achieves higher throughput gains over single-link operation (SLO) in ultra-dense and crowded scenarios by leveraging multiple intermittent transmission opportunities. However, in asymmetrically occupied links, MLO may increase latency due to suboptimal packet mapping and interruption on the busier link. The benefits of MLO for latency-sensitive applications are quantified using real-time traffic generated by a cloud gaming application.
IEEE-ACM TRANSACTIONS ON NETWORKING
(2023)
Article
Engineering, Chemical
Jonathan A. Ouimet, Xinhong Liu, David J. Brown, Elvis A. Eugene, Tylar Popps, Zachary W. Muetzel, Alexander W. Dowling, William A. Phillip
Summary: This study emphasizes the importance of improved characterization techniques in advancing membrane processes. By developing a diafiltration apparatus guided by data science, membrane performance can be rapidly characterized over a broad range of feed solution compositions. The synergy between data analytics and instrumentation, including an inline conductivity probe, allows for accurate determination of membrane transport coefficients and identification of governing phenomena.
JOURNAL OF MEMBRANE SCIENCE
(2022)
Article
Construction & Building Technology
Joaquin Osorio-Arjona, Jiri Horak, Radek Svoboda, Yolanda Garcia-Ruiz
Summary: This study investigates the value of social networks as a data source for detecting spatial distribution of problems within public transit networks. By analyzing Twitter data from the Madrid Metro account, it identifies that mid-income workers mainly tweet when traveling to workplaces, focusing on issues like punctuality and breakdowns in transfer stations or central areas. The spatial distribution is affected by the density of points of interest in destination areas.
SUSTAINABLE CITIES AND SOCIETY
(2021)
Article
Materials Science, Multidisciplinary
Alena Vishina, O. Eriksson, H. C. Herper
Summary: A high-throughput and data-mining search has been conducted to find rare-earth-free permanent magnets using materials containing a 3d and p-element of the Periodic Table. Three promising compounds, Fe 2 C, Mn2MoB4, and Mn2WB4, have been investigated in detail and suggested as potential candidates for applications as permanent magnets. Doping protocols have also been explored for these systems.
MATERIALS RESEARCH LETTERS
(2023)
Article
Ecology
Pratik Rajan Gupte, Christine E. Beardsworth, Orr Spiegel, Emmanuel Lourie, Sivan Toledo, Ran Nathan, Allert Bijleveld
Summary: Cleaning modern, high-throughput animal tracking data is crucial to reduce location errors and improve data quality for subsequent analyses. Developing automated pre-processing pipelines that balance ease of use with computational efficiency is essential for handling large datasets and enhancing reproducibility in movement ecology research. The use of standardized methods and tools like the atlastools R package can lead to better inferences and exploration of animal space use patterns.
JOURNAL OF ANIMAL ECOLOGY
(2022)
Review
Biochemistry & Molecular Biology
Sabeeha S. Merchant, Stefan Schmollinger, Daniela Strenkert, Jeffrey L. Moseley, Crysten E. Blaby-Haas
BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR CELL RESEARCH
(2020)
Review
Plant Sciences
Nicolas Grosjean, Crysten E. Blaby-Haas
Article
Biochemistry & Molecular Biology
Fatima Foflonker, Crysten E. Blaby-Haas
Summary: This study utilizes comparative genomics to identify evolutionarily conserved gene pairs in green algae and reveals novel functional clusters, indicating the potential existence of new biosynthetic pathways in green algae.
MOLECULAR BIOLOGY AND EVOLUTION
(2021)
Editorial Material
Multidisciplinary Sciences
Crysten E. Blaby-Haas
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2021)
Article
Multidisciplinary Sciences
Sean D. Gallaher, Rory J. Craig, Iniyan Ganesan, Samuel O. Purvine, Sean R. McCorkle, Jane Grimwood, Daniela Strenkert, Lital Davidi, Melissa S. Roth, Tim L. Jeffers, Mary S. Lipton, Krishna K. Niyogi, Jeremy Schmutz, Steven M. Theg, Crysten E. Blaby-Haas, Sabeeha S. Merchant
Summary: The common belief that polycistronic gene expression is rare in eukaryotes has been challenged by the discovery of hundreds of examples in green algae using the Iso-Seq technology. Various approaches confirmed that multiple proteins are translated from a shared transcript at numerous loci, with transcription starting exclusively at upstream genes and ending after downstream genes. The conservation of this mechanism in different green algae species suggests it may be evolutionarily ancient and biologically significant.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2021)
Article
Microbiology
Yavuz Ozturk, Crysten E. Blaby-Haas, Noel Daum, Andreea Andrei, Juna Rauch, Fevzi Daldal, Hans-Georg Koch
Summary: Copper is an essential cofactor for redox enzymes, with tightly controlled mechanisms to deliver it for cuproenzyme biogenesis while protecting cells from its toxicity. Many Gram-negative bacteria contain multicopper oxidases for periplasmic copper detoxification, highlighting the importance of copper homeostasis in biological systems.
FRONTIERS IN MICROBIOLOGY
(2021)
Article
Biology
Benjamin Cole, Dominique Bergmann, Crysten E. Blaby-Haas, Ian K. Blaby, Kristofer E. Bouchard, Siobhan M. Brady, Doina Ciobanu, Devin Coleman-Derr, Samuel Leiboff, Jenny C. Mortimer, Tatsuya Nobori, Seung Y. Rhee, Jeremy Schmutz, Blake A. Simmons, Anup K. Singh, Neelima Sinha, John P. Vogel, Ronan C. O'Malley, Axel Visel, Diane E. Dickel
Summary: This Perspective discusses the opportunities and challenges brought by single-cell technologies in the fields of energy and environmental science, emphasizing the need to develop better and more comprehensive single-cell technologies, analysis and visualization tools, as well as tissue preparation methods. It also calls for the establishment of a centralized, open-access database to store plant single-cell data and to balance the need for deep characterization of select model species while still capturing the diversity in the plant kingdom.
COMMUNICATIONS BIOLOGY
(2021)
Review
Plant Sciences
Claus Schwechheimer, Peter Michael Schroeder, Crysten E. Blaby-Haas
Summary: This review summarizes the current knowledge of plant GATA factors, including their roles in photosynthesis and chloroplast development. Through phylogenomic analysis, the evolutionary origin of plant GATA classes in the green lineage and their relationship to animal and fungal GATAs are explored.
ANNUAL REVIEW OF PLANT BIOLOGY
(2022)
Article
Cell Biology
Miriam Pasquini, Nicolas Grosjean, Kim K. Hixson, Carrie D. Nicora, Estella F. Yee, Mary Lipton, Ian K. Blaby, John D. Haley, Crysten E. Blaby-Haas
Summary: The evolution of zinc as a protein cofactor altered the functional landscape of biology, but dependency on zinc also created an Achilles' heel, necessitating adaptive mechanisms to ensure zinc availability to proteins. Evidence for a conserved family of putative metal transferases was presented, which interact with zinc-dependent proteins. In vitro experiments showed that these transferases can transfer zinc or cobalt to apo-proteins.
Editorial Material
Ecology
Crysten E. Blaby-Haas
Summary: Whole-genome sequencing and comparative omics analyses reveal recent and parallel adaptive evolution paths involving expansions in zinc-binding proteins in the genomes of diverse cold-adapted algae.
NATURE ECOLOGY & EVOLUTION
(2022)
Article
Biochemistry & Molecular Biology
Rory J. Craig, Sean D. Gallaher, Shengqiang Shu, Patrice A. Salome, Jerry W. Jenkins, Crysten E. Blaby-Haas, Samuel O. Purvine, Samuel O'Donnell, Kerrie Barry, Jane Grimwood, Daniela Strenkert, Janette Kropat, Chris Daum, Yuko Yoshinaga, David M. Goodstein, Olivier Vallon, Jeremy Schmutz, Sabeeha S. Merchant
Summary: The article presents a major update to the Chlamydomonas reference genome and structural annotations, revealing large genomic changes in laboratory culture. The authors improved assembly quality and annotations, generated chromosome-level assemblies for two laboratory strains, and validated their results through linkage analyses. They also updated gene symbols and textual annotation of functionally characterized genes, and discovered genomic instability in the classical reference strain. The resources presented in this article will pave the way for further research in Chlamydomonas genomics.
Article
Multidisciplinary Sciences
Bahia Khalfaoui-Hassani, Crysten E. Blaby-Haas, Andreia Verissimo, Fevzi Daldal
Summary: Heme-copper oxygen reductases are crucial membrane-bound complexes in cellular respiration. This study identified potential MFS transporters as missing copper transporters and found their importance in the biogenesis of E. coli bo(3)-Qox.
Article
Multidisciplinary Sciences
Lital Davidi, Sean D. Gallaher, Eyal Ben-David, Samuel O. Purvine, Thomas L. Fillmore, Carrie D. Nicora, Rory J. Craig, Stefan Schmollinger, Sanja Roje, Crysten E. Blaby-Haas, Robert P. Auber, Jennifer H. Wisecaver, Sabeeha S. Merchant
Summary: This article investigates the adaptation mechanisms of two marine algae species under iron-deficient conditions. The study reveals multiple iron uptake routes in these species and their ability to adjust protein expression and structure to cope with iron deficiency.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2023)
Article
Plant Sciences
Lifang Zhang, Janeen Braynen, Audrey Fahey, Kriti Chopra, Paolo Cifani, Dimiru Tadesse, Michael Regulski, Fangle Hu, Hubertus J. J. van Dam, Meng Xie, Doreen Ware, Crysten E. Blaby-Haas
Summary: Metal homeostasis is important for maintaining metal availability within cells, and low bioavailability of essential metal nutrients can negatively affect crop health and yield. Understanding the function of metallochaperones in plants provides an opportunity to improve metal-use efficiency and develop plant food with higher concentrations of bioavailable metals.
FRONTIERS IN PLANT SCIENCE
(2023)
Article
Biochemistry & Molecular Biology
Leticia Pollo-Oliveira, Nick K. Davis, Intekhab Hossain, Peiying Ho, Yifeng Yuan, Pedro Salguero Garcia, Cecile Pereira, Shane R. Byrne, Jiapeng Leng, Melody Sze, Crysten E. Blaby-Haas, Agnieszka Sekowska, Alvaro Montoya, Thomas Begley, Antoine Danchin, Daniel P. Aalberts, Alexander Angerhofer, John Hunt, Ana Conesa, Peter C. Dedon, Valerie de Crecy-Lagard
Summary: This study reveals the physiological effects of Q deficiency in Escherichia coli, including increased resistance to nickel and cobalt, increased sensitivity to cadmium, and triggering of an atypical oxidative stress response.
