Article
Biodiversity Conservation
Norman W. H. Mason, Olivia Burge, Robbie Price, Rowan Sprague, John Dymond, Mike Watt, Tessa Roberts, Thomas Paul, Brian Richardson, Carol Rolando, Sarah Wyse, Philip E. Hulme, Pike Stahlmann-Brown, Shaun Awatere, Duane A. Peltzer
Summary: The challenge of designing and implementing long-term management strategies for chronic biological invasions lies in integrating science-based and values-based knowledge sources, as well as developing durable knowledge generation and curation platforms. This paper proposes a transdisciplinary knowledge ecology framework to address this challenge.
BIOLOGICAL INVASIONS
(2021)
Article
Environmental Sciences
Wang Shu, Peng Wang, Jun Zhao, Minjun Ding, Hua Zhang, Minghua Nie, Gaoxiang Huang
Summary: This study investigated the sources and influencing mechanisms of nitrate in a mixed land-use watershed. The findings showed the weak transformation processes of nitrate in the river and identified that nitrate concentrations were primarily influenced by exogenous inputs, such as soil nitrogen, nitrogen fertilizer, and manure & sewage. The study also found that land use and landscape metrics were important factors determining the spatial distribution and transport of nitrate.
SCIENCE OF THE TOTAL ENVIRONMENT
(2022)
Article
Biochemistry & Molecular Biology
Julian Vosseberg, Daan Stolker, Samuel H. A. von der Dunk, Berend Snel
Summary: This study uses phylogenetic analyses to infer the evolutionary history of 145 proteins in the spliceosome. The results show that an abundance of ribosome-related proteins were added to the prokaryotic-derived core, and duplications of these proteins increased the overall complexity of the spliceosome. Most of the spliceosomal complexity originated after the spread of introns in the proto-eukaryotic genome. The reconstruction of early spliceosomal evolution provides insights into the emergence of complexes with many proteins during eukaryogenesis.
MOLECULAR BIOLOGY AND EVOLUTION
(2023)
Article
Biology
Xiuhong Li, Hao Yuan, Xiaoliang Wu, Chengyi Wang, Hongbo Shi, Yingli Lv
Summary: Metabolic processes in the human body are crucial for maintaining normal life activities, and abnormal concentrations of metabolites are closely linked to disease occurrence and development. Drug usage has a significant impact on metabolism, as drug metabolites can influence efficacy, toxicity, and interactions. However, our understanding of metabolite-drug associations remains incomplete, and individual data sources are often incomplete and noisy. Thus, there is an urgent need to integrate various data sources to infer reliable metabolite-drug associations.
COMPUTERS IN BIOLOGY AND MEDICINE
(2023)
Article
Engineering, Electrical & Electronic
Jeremy Gunawardena
Summary: Learning, implemented by brains or neuronal networks, has been extensively studied in ethology, psychology, cognitive science, and neuroscience. This survey explores the possibility of learning in nonneuronal contexts such as physiology, development, and individual cells, emphasizing the importance of bridging cognitive science and systems biology for a better understanding of organisms.
PROCEEDINGS OF THE IEEE
(2022)
Article
Biochemistry & Molecular Biology
Amir Lakizadeh, Mahdi Babaei
Summary: This paper introduces a deep learning method PSECNN for predicting polypharmacy side effects, which combines various basic features of drugs for prediction. According to experimental evaluations, PSECNN outperforms existing methods in predicting polypharmacy side effects.
MOLECULAR DIVERSITY
(2022)
Review
Pharmacology & Pharmacy
Jyothsna Manikkath, J. Anand Subramony
Summary: The recent advancement of wearable technologies has opened up new opportunities in disease management, with closed-loop systems combined with transdermal drug delivery technologies providing real-time drug delivery and comprehensive disease state management.
ADVANCED DRUG DELIVERY REVIEWS
(2021)
Review
Pharmacology & Pharmacy
Amelia Palermo
Summary: Metabolomics enables the analysis of metabolites and lipids in biological systems, and can guide the discovery of lead compounds from natural sources. In combination with other omics, metabolomics can elucidate compound toxicity and mode of action. This article discusses the workflows, limitations, and future opportunities of metabolomics and big data in streamlining pharmaceutical discovery and development.
DRUG DISCOVERY TODAY
(2023)
Article
Biochemical Research Methods
Betul Guvenc Paltun, Hiroshi Mamitsuka, Samuel Kaski
Summary: Predicting the response of cancer cell lines to specific drugs is a central problem in personalized medicine. Choosing informative data sources and methods that can efficiently incorporate multiple sources is a challenging part of successful analysis in personalized medicine.
BRIEFINGS IN BIOINFORMATICS
(2021)
Article
Multidisciplinary Sciences
M. D. Fraser, H. E. Vallin, J. R. T. Davies, G. E. Rowlands, X. Chang
Summary: The study showed that incorporating narcissus pseudonarcissus into grazed permanent pasture had no negative effects on the health or performance of sheep, and there was no consistent impact of fertilizer rates on galanthamine yields. There was no significant difference in overall galanthamine yield between cutting the pseudonarcissus biennially and annually.
SCIENTIFIC REPORTS
(2021)
Review
Toxicology
Amy L. Schofield, Joseph P. Brown, Jack Brown, Ania Wilczynska, Catherine Bell, Warren E. Glaab, Matthias Hackl, Lawrence Howell, Stephen Lee, James W. Dear, Mika Remes, Paul Reeves, Eunice Zhang, Jens Allmer, Alan Norris, Francesco Falciani, Louise Y. Takeshita, Shiva Seyed Forootan, Robert Sutton, B. Kevin Park, Chris Goldring
Summary: miRNAs are short non-coding RNA molecules that have been shown to be dysregulated and released in different organ systems. Circulating miRs are proposed as useful biomarkers for various disease states, potentially replacing existing traditional biomarkers. However, pre-analytical and analytical challenges need to be addressed before their clinical use can be realized.
ARCHIVES OF TOXICOLOGY
(2021)
Review
Chemistry, Analytical
Ping Zhu, Yulan Tian, Yating Chen, Wei Chen, Ping Wang, Liping Du, Chunsheng Wu
Summary: The mammalian olfactory system is able to distinguish thousands of odorant molecules at trace levels. Optogenetics offers a new technical approach utilizing light to illuminate specific parts of the olfactory system, aiding in revealing olfactory mechanisms. Recent advances in olfactory optogenetics focus on elucidating chemical sensing mechanisms, with current challenges and future development trends discussed.
Review
Immunology
Charles D. Murin, Pavlo Gilchuk, James E. Crowe, Andrew B. Ward
Summary: This review describes how structural biology has revealed the molecular basis of broad ebolavirus neutralization, and discusses the history of monoclonal antibody therapeutics for ebolaviruses, as well as key structural studies that have advanced our understanding of ebolavirus glycoprotein structures and antibody-mediated neutralization.
FRONTIERS IN IMMUNOLOGY
(2022)
Article
Biochemistry & Molecular Biology
Jessica L. Binder, Joel Berendzen, Amy O. Stevens, Yi He, Jian Wang, Nikolay Dokholyan, Tudor Oprea
Summary: This paper investigates the use of confidence scores to evaluate the accuracy of AlphaFold protein models for drug discovery. It proposes criteria for useful models and residues and presents findings on the effects of disorder and sequence divergence on accuracy.
CURRENT OPINION IN STRUCTURAL BIOLOGY
(2022)
Review
Computer Science, Information Systems
Yuli Sudriani, Viktor Sebestyen, Janos Abonyi
Summary: This study evaluates the existing water monitoring systems based on the latest approach and analyzes the factors affecting the placement of sensors at sampling locations. By reviewing more than 300 papers published between 2011 and 2022, it summarizes the advancement and trends of various water monitoring systems as well as the suitability of sensor placement in the area. The study highlights the urgency of an integrative approach with regard to water monitoring systems, including water quality model and water quantity model. A framework is proposed to incorporate all water monitoring approaches, sampling techniques, and predictive models to provide comprehensive information about environmental assessment. It was observed that the urgency of model-based approaches as verification and fusion of data assembly has the ability to improve the performances of the systems. Furthermore, integrated systems with the inclusion of a separate modeling approach through integrated, semi-mechanistic models, data science, and artificial intelligence are recommended in the future.