Review
Computer Science, Information Systems
Fethi Fkih
Summary: This paper provides an in-depth review of similarity measures used in collaborative filtering-based recommender systems. Through experimental studies, the performance of different measures is compared, and important conclusions are drawn. Evaluation results show that different similarity measures have different suitability in user-based and item-based recommendations.
JOURNAL OF KING SAUD UNIVERSITY-COMPUTER AND INFORMATION SCIENCES
(2022)
Article
Computer Science, Artificial Intelligence
F. Ortega, J. Mayor, D. Lopez-Fernandez, R. Lara-Cabrera
Summary: CF4J 2.0 is a framework designed for research experiments based on collaborative filtering, with features like implemented algorithms, quality measures, parallel execution, and abstract classes for developers to customize. The new version focuses on simple deployment, reproducible science, hyper-parameter optimization, data analysis, and community openness as an open-source project.
KNOWLEDGE-BASED SYSTEMS
(2021)
Article
Mathematics, Applied
Jerzy Kaczorowski, Waldemar Ratajczak, Peter Nijkamp, Krzysztof Gornisiewicz
Summary: Loschian numbers are a topic of investigation in scientific fields such as spatial economics, socio-economic geography, geometry, and number theory. These numbers play a significant role in optimizing spatial interactions and achieving the best division of space between competing central places.
APPLIED MATHEMATICS AND COMPUTATION
(2024)
Article
Automation & Control Systems
Fei Song, Zhengyang Ai, Haowei Zhang, Ilsun You, Shiyong Li
Summary: In this article, a smart collaborative balancing (SCB) scheme is proposed to dynamically adjust network function orchestration and optimize workflow patterns; Mathematical models and matrix operations are utilized to ensure the capabilities of CPS in terms of bandwidth allocation and invasion defense; Experimental results demonstrate that SCB outperforms benchmarks in service reliability and malicious attack resistance.
IEEE TRANSACTIONS ON INDUSTRIAL INFORMATICS
(2021)
Article
Environmental Sciences
Matthew R. Baker, Robert Alverson, Ruth Christiansen, Keith Criddle, Danny Eilertsen, Robert J. Foy, John Gauvin, Scott E. Goodman, Leigh Habegger, Bradley P. Harris, Nicole Kimball, Anna Malek Mercer, Edward Poulsen, Matt Robinson, Jeremy Rusin, Rebecca Skinner, Claus Reedtz Sparrevohn, Kevin D. E. Stokesbury, Daryl R. Sykes
Summary: Data and insights from fishers are crucial for understanding fishery and ecosystem dynamics. Incorporating fisher and industry knowledge can improve marine science and fisheries management.
FRONTIERS IN MARINE SCIENCE
(2023)
Article
Computer Science, Artificial Intelligence
Yanjun Zhang, Guangdong Bai, Mingyang Zhong, Xue Li, Ryan K. L. Ko
Summary: Coupling learning aims to estimate and extract interactions and relationships among learning components, widely used in recommender systems. There is a high demand for privacy-preserving solutions in collaboration to prevent exposure of private data. The distributed collaborative coupling learning system ensures favorable privacy gains with a provable sensitivity bound.
IEEE INTELLIGENT SYSTEMS
(2021)
Article
Astronomy & Astrophysics
Nigel J. Mason, Perry A. Hailey, Duncan V. Mifsud, James S. Urquhart
Summary: Laboratory experiments play a crucial role in deciphering the chemistry of the interstellar medium and the formation of complex organic molecules relevant to life, but most studies have used a reductionist approach which may leave important questions unanswered. Therefore, a new systems astrochemistry approach is proposed to uncover new data and better link laboratory work to observations and models.
FRONTIERS IN ASTRONOMY AND SPACE SCIENCES
(2021)
Article
Mechanics
Aiguo Chen, Peiyun Zhang, Bolin Chen, Yong Li, Jihui Xing
Summary: Tensile fracture static tests were conducted on nine specimens of Chinese Q460C high-strength structural steel to study its ductile fracture behavior. A new model considering stress triaxiality and Lode angle was proposed to predict the ductile fracture of Q460C HSS. The model incorporated a stress softening criterion for better fracture propagation simulation. The simulation results showed good agreement with the experimental results.
ENGINEERING FRACTURE MECHANICS
(2023)
Article
Medicine, General & Internal
Patricia L. Mabry, Nicolaas P. Pronk, Christopher Amos, John S. Witte, Patrick T. Wedlock, Sarah M. Bartsch, Bruce Y. Lee
Summary: The article discusses the importance and application of systems approaches in cancer research, presenting some relevant viewpoints and recommendations.
Article
Engineering, Industrial
Chao Liu, Leopold Le Roux, Carolin Korner, Olivier Tabaste, Franck Lacan, Samuel Bigot
Summary: Metal Additive Manufacturing (AM) has gained attention due to its advantages, but the complex relationships limit its widespread use. To facilitate its development, this paper proposes a Digital Twin-enabled collaborative data management framework, which has been validated through practical implementation.
JOURNAL OF MANUFACTURING SYSTEMS
(2022)
Article
Biochemical Research Methods
Nathan Braniff, Taylor Pearce, Zixuan Lu, Michael Astwood, William S. R. Forrest, Cody Receno, Brian Ingalls
Summary: Modeling in systems and synthetic biology relies on accurate parameter estimates and predictions, which can be optimized by optimal experimental design techniques. The NLoed software package, a Python library, provides access to OED methods with emphasis on experimental design for systems biology research.
ACS SYNTHETIC BIOLOGY
(2022)
Article
Computer Science, Artificial Intelligence
Hao Liu, Mang Ye, Yan Wang, Sanyuan Zhao, Ping Li, Jianbing Shen
Summary: This article presents a new adaptive metric distillation approach that significantly improves the backbone features of student networks and achieves better classification results. Previous knowledge distillation methods focused on transferring knowledge across classifier logits or feature structure, neglecting the excessive sample relations in the feature space. The proposed collaborative adaptive metric distillation (CAMD) optimizes the relationship between key pairs, adapts the metric for student embeddings using teacher embeddings as supervision, and employs a collaborative scheme for knowledge aggregation. Extensive experiments show that CAMD outperforms other cutting-edge distillers and sets a new state-of-the-art in both classification and retrieval tasks.
IEEE TRANSACTIONS ON NEURAL NETWORKS AND LEARNING SYSTEMS
(2023)
Article
Multidisciplinary Sciences
Kishore Vasan, Jevin D. West
Summary: The study finds that collaboration among funders in clinical science can accelerate the success of clinically relevant research. Communities of funders are formed by national boundaries and funding objectives. Funders generally achieve higher success when collaborating rather than solo-funding.
ROYAL SOCIETY OPEN SCIENCE
(2021)
Article
Automation & Control Systems
Byeori Kim, Minseong Choi, Taek-Young Youn, Jeong Hyun Yi, Haehyun Cho
Summary: Recently, there has been a shift towards using collaborative cloud-based office suites like Microsoft Office 365 instead of traditional office applications. These cloud-based systems allow simultaneous collaboration on the same document stored in a cloud server, enabling effective teamwork. However, security concerns arise with cloud collaboration, particularly regarding the encryption and protection of data. This study proposes a new AES operation mode called DL-ECB, which allows for modifications, insertions, and deletions of ciphertext based on changes in plaintext, enabling the use of encrypted data in collaborative cloud-based platforms. The prototype of the DL-ECB mode is implemented and evaluated to demonstrate its ability to preserve data confidentiality, integrity, and auditability in collaborative cloud systems.
INTELLIGENT AUTOMATION AND SOFT COMPUTING
(2023)
Article
Automation & Control Systems
Ruochen Tai, Liyong Lin, Yuting Zhu, Rong Su
Summary: This paper proposes a new framework for modeling networked discrete-event systems with channel delays and losses. The framework allows users to realize different mechanisms and potentially generate more permissive controllers. Two sets of new formulations are established to capture the temporal relationships between channel inputs and outputs. The framework could serve as an analysis tool and building block for future theoretical explorations and practical implementations of networked DES control.
Article
Microbiology
Robbie M. Martin, Eric R. Gann, Alex R. Truchon, Gregory L. Boyer, Steven W. Wilhelm
Summary: Pseudanabaena spp. are filamentous cyanobacteria commonly found in temperate lakes. They can occasionally form harmful algal blooms, and a high-quality genome of a toxic crimson cyanobacterial bloom in Lake Salubria, NY was presented.
MICROBIOLOGY RESOURCE ANNOUNCEMENTS
(2022)
Article
Environmental Sciences
Kylie Langlois, Jackie L. Collier
Summary: On-site wastewater treatment systems (OWTSs) can use nitrogen-removing biofilters (NRBs) to promote specific microbial communities for effective treatment. The study found that the microbial communities in different layers of the NRBs were distinct, indicating the influence of environmental selection. The relative abundance and diversity of functional groups and genera also varied between the layers, highlighting the importance of niche processes in designing efficient OWTSs.
JOURNAL OF ENVIRONMENTAL QUALITY
(2023)
Review
Environmental Sciences
Brittany N. Zepernick, Steven W. Wilhelm, George S. Bullerjahn, Hans W. Paerl
Summary: This article discusses the problem of the freshwater-marine continuum, which refers to the effects of nutrients and toxic cyanobacterial blooms spreading through water bodies. Historically, marine and freshwater research have been conducted independently, failing to address the exchange of nutrients and biology between these systems.
ENVIRONMENTAL MICROBIOLOGY REPORTS
(2023)
Article
Microbiology
Brittany N. Zepernick, Alexander R. Truchon, Eric R. Gann, Steven W. Wilhelm
Summary: In this study, we present the assembled and annotated genome of the freshwater diatom Fragilaria crotonensis SAG 28.96. The nuclear genome, with a size of 61.85 Mb, was assembled into 879 contigs and has a GC content of 47.40%. It contains 26,015 predicted genes and exhibits a completeness of 81%.
MICROBIOLOGY RESOURCE ANNOUNCEMENTS
(2022)
Editorial Material
Multidisciplinary Sciences
Ferdi L. Hellweger, Charlotte Schampera, Robbie M. Martin, Falk Eigemann, Derek J. Smith, Gregory J. Dick, Steven W. Wilhelm
Summary: In response to the criticism by Huisman et al., this article demonstrates that their claims are based on incomplete evidence, misinterpretation of data, or do not actually refute our model. While our model, like any ecosystem models, has its simplifications and uncertainties, it outperforms existing approaches that ignore biology and cannot predict toxin concentration.
Article
Multidisciplinary Sciences
David Geller-McGrath, Paraskevi Mara, Gordon T. T. Taylor, Elizabeth Suter, Virginia Edgcomb, Maria Pachiadaki
Summary: By using metagenomics and metatranscriptomics, the researchers identified diverse biosynthetic gene clusters (BGCs) in free-living and particle-associated microbial communities in the stratified water column of the Cariaco Basin, Venezuela. They discovered 565 bacterial and archaeal metagenome-assembled genomes (MAGs) and 1154 BGCs. Their findings suggest that variations in water redox potential and microbial lifestyle are associated with differences in the predicted composition and production of secondary metabolites. This study highlights the potential of genome mining for the discovery of biotechnologically important compounds.
NATURE COMMUNICATIONS
(2023)
Article
Microbiology
Xiuping Liu, Lu Lyu, Jiaqian Li, Biswarup Sen, Mohan Bai, Jason E. Stajich, Jackie L. Collier, Guangyi Wang
Summary: This study reports high-quality genomes of two newly isolated Labyrinthulomycetes strains and investigates their ecological functions from the perspective of organic matter degradation using comparative genomics and biochemical assays. The results show that Labyrinthulomycetes may occupy multiple ecological niches in marine ecosystems and can actively participate in marine biochemical cycles as decomposers. The study also emphasizes the dual roles of endoglucanase in the process of cellulose degradation.
MICROBIOLOGY SPECTRUM
(2023)
Article
Evolutionary Biology
Mariana Rius, Joshua S. Rest, Gina Filloramo, Anna M. G. Novak Vanclova, John M. Archibald, Jackie L. Collier
Summary: In this study, the essential role of the crtIBY gene in carotenoid biosynthesis in the marine protist Aurantiochytrium limacinum ATCC MYA-1381 was demonstrated. The related protein domains were found in other heterotrophic protists, suggesting a horizontal gene transfer event. This reveals a novel origin of eukaryotic (apo)carotenogenesis through parallel evolution in divergent protist lineages.
GENOME BIOLOGY AND EVOLUTION
(2023)
Article
Limnology
Robbie M. Martin, Maddie K. Denney, Helena L. Pound, Justin D. Chaffin, George S. Bullerjahn, R. Michael L. McKay, Arthur Zastepa, Katarina A. Jones, Hector F. Castro, Shawn R. Campagna, Steven W. Wilhelm
Summary: Phosphorus availability plays a crucial role in primary production and cyanobacterial blooms in lakes. Phospholipid substitution by sulfolipids has been established as an indicator of phosphorus stress in marine phytoplankton. This study shows that sulfatequinovosyldiacylglycerol (SQDG) to phosphatidylglycerol (PG) ratio can serve as a biomarker for phosphorus stress in freshwater phytoplankton communities, providing valuable insights into nutrient history and phosphorus scarcity.
LIMNOLOGY AND OCEANOGRAPHY
(2023)
Article
Limnology
Jane C. Y. Wong, John A. Raven, Montserrat Aldunate, Sebastian Silva, Juan Diego Gaitan-Espitia, Cristian A. Vargas, Osvaldo Ulloa, Peter von Dassow
Summary: Phytoplankton play a crucial role in marine biogeochemistry and ecosystems, but their response to deoxygenation is not well-studied. A review of available information on phytoplankton in oxygen minimum zones (OMZs) reveals that surface phytoplankton disappear and are replaced by unique cyanobacteria lineages below the oxycline. Several factors, including top-down grazing, respiratory demand, and irradiance, cannot fully explain this vertical structure, suggesting a potential dependence on O2-dependent pathways.
LIMNOLOGY AND OCEANOGRAPHY
(2023)
Article
Microbiology
Naomi E. Gilbert, Gary R. LeCleir, Helena L. Pound, Robert F. Strzepek, Michael J. Ellwood, Benjamin S. Twining, Simon Roux, Philip W. Boyd, Steven W. Wilhelm
Summary: Viruses can impact the abundance, evolution, and metabolism of microorganisms in the ocean, playing a critical role in biogeochemistry and carbon cycles. This study investigates the diversity and activity of giant viruses in the subpolar Southern Ocean and finds that these viruses exhibit depth-dependent structuring and metabolic reprogramming of their hosts under different physicochemical conditions. Additionally, the study shows that iron availability affects the activity of giant viruses. These findings enhance our understanding of how the water column and environmental factors shape the viral community in the Southern Ocean.
Article
Marine & Freshwater Biology
Gwendolyn F. Stark, Robbie M. Martin, Laura E. Smith, Bofan Wei, Ferdi L. Hellweger, George S. Bullerjahn, R. Michael L. Mckay, Gregory L. Boyer, Steven W. Wilhelm
Summary: The increase in microcystin quota per cell in Microcystis aeruginosa PCC 7806 provides a fitness advantage during growth at lower temperatures, while a non-toxigenic mutant strain employs compensatory mechanisms to defend against reactive oxygen species without the presence of microcystin.
Article
Multidisciplinary Sciences
Nicola M. Moloney, Konstantin Barylyuk, Eelco Tromer, Oliver M. Crook, Lisa M. Breckels, Kathryn S. Lilley, Ross F. Waller, Paula MacGregor
Summary: This study maps the spatial proteomes of two African trypanosome species, Trypanosoma brucei and Trypanosoma congolense, providing insights into the molecular basis for diversity within and between these pathogen species. Comparative analysis reveals key routes of parasitic adaptation to different biological niches.
NATURE COMMUNICATIONS
(2023)
Article
Microbiology
Daniel J. Wieczynski, Kristin M. Yoshimura, Elizabeth R. Denison, Stefan Geisen, Jennifer M. DeBruyn, A. Jonathan Shaw, David J. Weston, Dale A. Pelletier, Steven W. Wilhelm, Jean P. Gibert
Summary: We provide a roadmap for understanding the impact of viral infections within microbial food webs on ecosystem carbon and nutrient cycling in the context of global warming. Microorganisms play a crucial role in carbon and nutrient cycles and act as a link between ecosystems and climate. However, viral infections within complex microbial food webs pose a significant challenge in predicting and understanding ecosystem responses to warming. We highlight the need for further research on virus-microbe-temperature interactions and their effects on ecosystem functioning in the face of climate change.
FEMS MICROBIOLOGY ECOLOGY
(2023)
Article
Environmental Sciences
Paraskevi Mara, Robert K. Nelson, Christopher M. Reddy, Andreas Teske, Virginia P. Edgcomb
Summary: Based on geochemical and chromatographic analyses of sediment cores, this study reveals that hopane and sterane biomarkers in hydrothermal sediments of Guaymas Basin are carried to surficial sediments by hydrothermal fluids. The sediment cores from Guyamas sites with distinct temperature and geochemistry profiles show evidence of biodegradation and hydrocarbon alteration. The composition of hopane and sterane biomarkers in different sites reflects temperature-related differences in geochemical and microbial hydrocarbon alterations. This study also highlights the compressed changes in surficial sediments compared to traditional microbial biodegradation patterns observed in subsurface oil reservoirs.
COMMUNICATIONS EARTH & ENVIRONMENT
(2022)