Article
Computer Science, Information Systems
Ting Guo, Jiye Liang, Guo-Sen Xie
Summary: This paper proposes a model called GIRL, which enhances the discrimination of region features through interactive region learning among a group of images, and achieves knowledge transfer between seen and unseen classes. Experimental results demonstrate the superior performance of the GIRL model over other methods on multiple datasets.
INFORMATION SCIENCES
(2023)
Editorial Material
Biochemical Research Methods
Michael B. Sheets, Joshua T. Atkinson, Mark P. Styczynski, Emily R. Aurand
Summary: As engineering biology continues to have increasing impacts, it is crucial to introduce the field early on in an accessible manner. However, teaching engineering biology faces challenges such as limited representation in widely used scientific textbooks or curricula, as well as its interdisciplinary nature. To address this, we have developed an adaptable curriculum module that provides a versatile slide deck designed by engineering biology experts to cover the fundamental principles and applications of the field. Free and accessible through a public website, this module can be used independently or integrated into existing curricula, aiming to enhance the ease of teaching current engineering biology topics and promote public engagement with the field.
ACS SYNTHETIC BIOLOGY
(2023)
Article
Environmental Sciences
Mateus Habermann, Elcio Hideiti Shiguemori, Vincent Fremont
Summary: A hyperspectral image provides detailed information about a scene, but the high dimensionality in the feature space can lead to unreliable classification results. This paper proposes a new dimensionality reduction algorithm that uses an unsupervised band selection technique based on clustering. The algorithm iteratively selects bands based on the parameters of a separating hyperplane, achieving the best separation in the feature space. The proposed method outperformed five other state-of-the-art frameworks in 60% of the experiments, demonstrating its effectiveness.
Article
Biochemical Research Methods
An-Phi Nguyen, Stefania Vasilaki, Maria Rodriguez Martinez
Summary: Interpretability is crucial for machine learning models in critical scenarios. We propose FLAN, a structurally constrained deep neural network that processes each input feature separately, allowing users to estimate the effect of each feature independently.
BRIEFINGS IN BIOINFORMATICS
(2023)
Article
Automation & Control Systems
Dominik Kahl, Andreas Weber, Maik Kschischo
Summary: Understanding the dynamics of complex systems is crucial in various fields, but unexpected behavior and system failures can be challenging to comprehend. Localizing error sources in the system and reconstructing their dynamics require informative measured outputs. Criteria and methods have been proposed to achieve this goal.
IEEE TRANSACTIONS ON CONTROL OF NETWORK SYSTEMS
(2021)
Article
Environmental Sciences
Lijian Zhou, Erya Xu, Siyuan Hao, Yuanxin Ye, Kun Zhao
Summary: In this paper, a Data-wise spAtial regioNal Consistency re-Enhancement (DANCE) method is proposed to address the issue of wrong classifications at the edge of regions in hyperspectral image classification. The proposed method enhances the intra-class correlation and filters the non-smooth region edge to improve the performance of feature-wise approaches. Experimental results demonstrate the effectiveness of the proposed method.
Editorial Material
Microbiology
Christopher E. Lawson
Summary: The commentary discusses the development of microbial communities in biotechnology applications over the past century, and how systems biology and genetic engineering tools have helped us better understand and manipulate the functions of microbiomes. It also emphasizes the integration of synthetic biology, automation, and machine learning technologies to accelerate microbiome engineering to meet future sustainability challenges.
Article
Computer Science, Interdisciplinary Applications
Melanie Mouchet, Jean Michel Letang, Jerome Lesaint, Simon Rit
Summary: This article investigates the use of data consistency conditions (DCC) for CT reconstruction in a helical acquisition with a cylindrical detector. The study evaluates the ability of DCC to detect breathing motion and proposes a method to normalize the inconsistency caused by motion.
IEEE TRANSACTIONS ON MEDICAL IMAGING
(2023)
Article
Engineering, Electrical & Electronic
Sebastian Baba, Andrzej Gieraltowski, Marek Jasinski, Frede Blaabjerg, Amir Sajjad Bahman, Marcin Zelechowski
Summary: This article discusses the implementation of a cost-effective and industrial-friendly laboratory setup for active power cycling testing of SiC power MOSFETs, as well as the application of reliability design methodology in high-performance power supply design processes.
IEEE TRANSACTIONS ON POWER ELECTRONICS
(2021)
Article
Computer Science, Interdisciplinary Applications
Alexis Cousin, Josselin Garnier, Martin Guiton, Miguel Munoz Zuniga
Summary: In this paper, we study a time-dependent reliability-based design optimization problem with constraints involving the maximum and/or the integral of a random process over a time interval. We propose a two-step procedure to solve the problem, which involves reformulating the original constraints using ergodic theory and extreme value theory, and then solving the reformulated problem using a new method called AK-ECO.
STRUCTURAL AND MULTIDISCIPLINARY OPTIMIZATION
(2022)
Review
Biotechnology & Applied Microbiology
Christopher E. Lawson, Jose Manuel Marti, Tijana Radivojevic, Sai Vamshi R. Jonnalagadda, Reinhard Gentz, Nathan J. Hillson, Sean Peisert, Joonhoon Kim, Blake A. Simmons, Christopher J. Petzold, Steven W. Singer, Aindrila Mukhopadhyay, Deepti Tanjore, Joshua G. Dunn, Hector Garcia Martin
Summary: The review introduces how machine learning can make metabolic engineering more predictable, provides examples and advice, discusses various applications, and examines future prospects.
METABOLIC ENGINEERING
(2021)
Article
Chemistry, Multidisciplinary
Michaela Petaroudi, Aleixandre Rodrigo-Navarro, Oana Dobre, Matthew J. Dalby, Manuel Salmeron-Sanchez
Summary: Living interfaces are a novel class of active materials that allow precise control over cell behavior. This study presents a biointerface between engineered bacteria and mammalian cells, which successfully regulates the stemness markers of human mesenchymal stem cells.
ADVANCED FUNCTIONAL MATERIALS
(2022)
Article
Neurosciences
Iman Beheshti, Olivier Potvin, Simon Duchesne
Summary: The study introduced a patch-wise technique for estimating brain age from T1w MRI data, and demonstrated its longitudinal reliability on a unique dataset. The results showed high prediction accuracy and no significant difference between manufacturers, suggesting the technique can be used for longitudinal multi-centric studies.
HUMAN BRAIN MAPPING
(2021)
Review
Biotechnology & Applied Microbiology
Javad Aminian-Dehkordi, Shadi Rahimi, Mehdi Golzar-Ahmadi, Amritpal Singh, Javiera Lopez, Rodrigo Ledesma-Amaro, Ivan Mijakovic
Summary: Synthetic biology offers new solutions for environmental protection by developing remediation systems using genetically engineered microbes and plants, and utilizing computational methods for design and application to detect and respond to specific pollutants.
BIOTECHNOLOGY ADVANCES
(2023)
Article
Multidisciplinary Sciences
Mingji Li, Xiaolu Zheng, Sudhanshu Shanker, Thapakorn Jaroentomeechai, Tyler D. Moeller, Sophia W. Hulbert, Ilkay Kocer, Josef Byrne, Emily C. Cox, Qin Fu, Sheng Zhang, Jason W. Labonte, Jeffrey J. Gray, Matthew P. DeLisa
Summary: The shotgun scanning glycomutagenesis strategy allows for rapid determination of glycosylatable sites in proteins and systematic investigation of the effects of glycan conjugation on protein structure and function. Experiment results show that stability and activity of many glycovariants are significantly altered by N-linked glycans, depending on the precise location of the modification.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2021)
Review
Genetics & Heredity
Citlalli Mejia-Almonte, Stephen J. W. Busby, Joseph T. Wade, Jacques van Helden, Adam P. Arkin, Gary D. Stormo, Karen Eilbeck, Bernhard O. Palsson, James E. Galagan, Julio Collado-Vides
NATURE REVIEWS GENETICS
(2020)
Review
Biotechnology & Applied Microbiology
Matthew J. McNulty, Yongao (Mary) Xiong, Kevin Yates, Kalimuthu Karuppanan, Jacob M. Hilzinger, Aaron J. Berliner, Jesse Delzio, Adam P. Arkin, Nancy E. Lane, Somen Nandi, Karen A. McDonald
Summary: This article highlights the assumption in space missions that the risk of spacecraft malfunction outweighs human system failure, but this assumption breaks down in longer duration exploration missions. It suggests using plants to produce pharmaceuticals to mitigate the risks in current space medical systems.
CRITICAL REVIEWS IN BIOTECHNOLOGY
(2021)
Article
Genetics & Heredity
Morgan N. Price, Adam M. Deutschbauer, Adam P. Arkin
Summary: The study investigated the roles and mechanisms of different families of methionine synthases in methionine synthesis, identifying four folate-independent methionine synthase families. Some of these families co-occur with corrinoid proteins, while another family interacts with oxygen for activity.
Article
Biochemical Research Methods
Lauren M. Lui, Torben N. Nielsen, Adam P. Arkin
Summary: This study presents a semi-automated method called Jorg for circularizing small bacterial, archaeal, and viral genomes from metagenomics data. The method successfully circularized 36 bacterial genomes and two megaphage genomes, highlighting the utility of circularizing genomes in discovering new biological patterns.
PLOS COMPUTATIONAL BIOLOGY
(2021)
Article
Geosciences, Multidisciplinary
Charles J. Paradis, John Miller, Ji-Won Moon, Sarah J. Spencer, Lauren M. Lui, Joy D. Van Nostrand, Daliang Ning, Andrew D. Steen, Larry D. McKay, Adam P. Arkin, Jizhong Zhou, Eric J. Alm, Terry C. Hazen
Summary: Microbial-mediated nitrate removal from groundwater is dependent on the presence of a carbon-bearing electron donor. The sustained ability of a microbial community to remove nitrate can occur without repeated exposure to an electron donor, potentially involving enzymatic and/or genetic mechanisms.
Article
Astronomy & Astrophysics
Aaron J. Berliner, Jacob M. Hilzinger, Anthony J. Abel, Matthew J. McNulty, George Makrygiorgos, Nils J. H. Averesch, Soumyajit Sen Gupta, Alexander Benvenuti, Daniel F. Caddell, Stefano Cestellos-Blanco, Anna Doloman, Skyler Friedline, Davian Ho, Wenyu Gu, Avery Hill, Paul Kusuma, Isaac Lipsky, Mia Mirkovic, Jorge Luis Meraz, Vincent Pane, Kyle B. Sander, Fengzhe Shi, Jeffrey M. Skerker, Alexander Styer, Kyle Valgardson, Kelly Wetmore, Sung-Geun Woo, Yongao Xiong, Kevin Yates, Cindy Zhang, Shuyang Zhen, Bruce Bugbee, Douglas S. Clark, Devin Coleman-Derr, Ali Mesbah, Somen Nandi, Robert M. Waymouth, Peidong Yang, Craig S. Criddle, Karen A. McDonald, Lance C. Seefeldt, Amor A. Menezes, Adam P. Arkin
Summary: The passage discusses the potential use of biotechnologies in a crewed mission to Mars, emphasizing the need for an integrated biomanufacturing plant. It outlines the goals and constraints guiding the design of such a plant, including modules for microbial resource utilization and production of necessary materials.
FRONTIERS IN ASTRONOMY AND SPACE SCIENCES
(2021)
Article
Microbiology
Matthew J. McNulty, Aaron J. Berliner, Patrick G. Negulescu, Liber McKee, Olivia Hart, Kevin Yates, Adam P. Arkin, Somen Nandi, Karen A. McDonald
Summary: This study examines the use of bioregenerative technology for pharmaceutical production to address medical treatment vulnerabilities in longer-duration space exploration missions. By evaluating different pharmaceutical purification processing strategies and technologies, key areas for future development of pharmaceutical life support technology and improvement of assessment frameworks were identified.
FRONTIERS IN MICROBIOLOGY
(2021)
Article
Microbiology
Fangchao Song, Jennifer V. Kuehl, Arjun Chandran, Adam P. Arkin
Summary: In this study, a direct PCR method was evaluated as a cost-effective and time-saving alternative to traditional DNA extraction methods for analyzing microbial communities. The direct PCR method showed comparable efficiency to the conventional DNeasy PowerSoil protocol, with higher efficiency for extracting gDNA from Gram-negative strains. This method is significantly less expensive and faster, making it a potential solution for high-throughput large-scale bacterial community analysis.
Article
Genetics & Heredity
Morgan Price, Adam O. Deutschbauer, Adam Arkin
Summary: To discover novel catabolic enzymes and transporters, the researchers combined high-throughput genetic data from 29 bacteria with an automated tool. They used GapMind to annotate the uptake and catabolism of compounds in bacterial and archaeal genomes, and systematically examined the gaps in predicted pathways. They identified new pathways or enzymes for the utilization of various compounds and annotated numerous enzymes and transporters.
Article
Astronomy & Astrophysics
Anthony J. Abel, Aaron J. Berliner, Mia Mirkovic, William D. Collins, Adam P. Arkin, Douglas S. Clark
Summary: Studies have shown that photovoltaics-based power systems can provide sufficient and practical energy for manned outposts on Mars. The analysis suggests that these systems would require a relatively low carry-along mass and outperform alternatives over a significant portion of the planet's surface.
FRONTIERS IN ASTRONOMY AND SPACE SCIENCES
(2022)
Article
Multidisciplinary Sciences
Joao A. A. Ascensao, Kelly M. M. Wetmore, Benjamin H. H. Good, Adam P. P. Arkin, Oskar Hallatschek
Summary: Ascensao et al. engineered knockout libraries of a nascent bacterial community and found that ecological and epistatic patterns combine to shape adaptive landscapes, despite idiosyncratic behavior of individual knockouts. The study also revealed that fitness effects are correlated with evolutionary outcomes for certain conditions, indicating shifting patterns of adaptation.
NATURE COMMUNICATIONS
(2023)
Article
Biochemistry & Molecular Biology
Benjamin A. Adler, Karthik Chamakura, Heloise Carion, Jonathan Krog, Adam M. Deutschbauer, Ry Young, Vivek K. Mutalik, Adam P. Arkin
Summary: This study used a high-throughput genetic screen to identify genome-wide host suppressors of diverse single-gene lysis factors (Sgls). In addition to validating known mechanisms, the researchers discovered that the Sgl of PP7, a Pseudomonas aeruginosa ssRNA phage, targets MurJ, the flippase responsible for lipid II export, which was previously shown to be the target of the Sgl of coliphage M. These unrelated Sgls, which are predicted to have opposite membrane topology, represent a case of convergent evolution. Furthermore, the genetic screens revealed a common set of multicopy suppressors for uncharacterized Sgls, suggesting a shared or similar mechanism of action.
NATURE CHEMICAL BIOLOGY
(2023)
Article
Biochemistry & Molecular Biology
David B. Bernstein, Batu Akkas, Morgan N. Price, Adam P. Arkin
Summary: The accuracy of four consecutive E. coli GEMs was quantified using mutant fitness data, and the utility of the area under a precision-recall curve as an accuracy metric was demonstrated. Errors in the latest model were identified, including the availability of certain vitamins/cofactors to mutants and inaccurate predictions from isoenzyme gene-protein-reaction mapping. Machine learning identified metabolic fluxes through hydrogen ion exchange and specific central metabolism branch points as important determinants of model accuracy.
MOLECULAR SYSTEMS BIOLOGY
(2023)
Article
Ecology
Hans K. Carlson, Denish Piya, Madeline L. Moore, Roniya T. Magar, Nathalie H. Elisabeth, Adam M. Deutschbauer, Adam P. Arkin, Vivek K. Mutalik
Summary: Lytic phages can have significant impacts on microbial ecosystem function, but the conditions under which phage predation modulates terrestrial systems are uncertain. Ionic strength and carbon composition play important roles in phage infection, but limited data exist on their thresholds and variability in environmental conditions. This study provides insights on the ion thresholds for phage infection and the influence of carbon source variability on phage predation on microbiome function.
ISME COMMUNICATIONS
(2023)
Article
Biology
Pavel S. Novichkov, John-Marc Chandonia, Adam P. Arkin
Summary: In this article, a platform called CORAL is introduced, which greatly facilitates adherence to the FAIR principles. CORAL achieves interoperability and reusability of heterogeneous datasets by requiring data generators to extensively document the context for all data and maintaining that context throughout the entire analysis pipeline. Additionally, CORAL provides web and Jupyter notebook interfaces for data uploading, exploration, and analysis.
