Article
Environmental Sciences
Nicole K. Ward, Jennifer A. Brentrup, David C. Richardson, Kathleen C. Weathers, Paul C. Hanson, Russell J. Hewett, Cayelan C. Carey
Summary: Lake ecosystems play an important role in monitoring changes as they integrate watershed and climate stressors. The study focuses on the time-lag between stressors and lake response, and how metabolic processes in the transitional zones between streams and lakes can bridge this gap. The results show that the temperature and mixing patterns of inflow streams significantly affect the rates of GPP and R in the littoral zones of the lake.
Article
Genetics & Heredity
Sigitas Sulcius, Gediminas Alzbutas, Viktorija Jukneviciute, Eugenijus Simoliunas, Petras Venckus, Monika Simoliuniene, Ricardas Paskauskas
Summary: This study used single-cell sequencing to reveal the genomic composition and diversity of viruses infecting green sulfur bacteria in gypsum karst lake ecosystems, uncovering a range of previously undescribed viruses, with most viral gene and protein sequences showing little to no similarity with phage sequences in public databases.
Article
Computer Science, Interdisciplinary Applications
Tobias Kuhlmann Andersen, Anders Nielsen, Erik Jeppesen, Karsten Bolding, Liselotte S. Johansson, Martin Sondergaard, Dennis Trolle
Summary: This study investigates the performance of the lake model GOTM-WET in reproducing the dynamics and shifts between turbid and clear water states in Lake Arreskov. The results show that the model is capable of simulating cyanobacteria blooms and zooplankton dynamics, but has limitations in reproducing the timing of shifts between phytoplankton and submerged macrophytes dominance following fish removal.
ENVIRONMENTAL MODELLING & SOFTWARE
(2022)
Article
Biodiversity Conservation
Ruibo Wang, Yang Bai, Juha M. Alatalo, Zhangqian Yang, Zongbao Yang, Wei Yang, Guimei Guo
Summary: The study found that the ecological protection scenario (EPS) is the best-optimized urbanization path and land use pattern that can meet land use demand for urbanization while maintaining (or even improving) regional ecosystem services (ESs) levels. The major driving mechanisms underlying urbanization effects on ESs include selection of urbanization path, scale control and layout of construction land, demarcation and implementation of ecological red line and ecological protection areas.
ECOLOGICAL INDICATORS
(2021)
Review
Engineering, Biomedical
Ming Yao, Manibarathi Vaithiyanathan, Nancy L. Allbritton
Summary: Lipids are essential cellular components with diverse functions in cells. Dysfunction in lipid metabolism and signaling is linked to various diseases. Single-cell lipid assays are challenging due to the small size of cells and the large number of lipid species. However, there are several methodologies, such as mass spectrometry, Raman imaging, and fluorescence-based assays, that enable the analysis of lipids in single cells with high resolution and sensitivity.
ANNUAL REVIEW OF BIOMEDICAL ENGINEERING
(2023)
Article
Environmental Sciences
B. G. Matthias, T. R. Hrabik, J. C. Hoffman, O. T. Gorman, M. J. Seider, M. E. Sierszen, M. R. Vinson, D. L. Yule, P. M. Yurista
Summary: Ecosystem-based management relies on understanding how perturbations influence ecosystem function, with Lake Superior serving as a unique case study due to its native species-dominated food web. Research findings show Lake Superior to be relatively efficient, with non-native species representing a small proportion of total biomass and exhibiting differences in efficiency compared to native species. The study offers valuable insights into the importance of the microbial loop and provides a baseline estimate of non-native species impacts on the ecosystem for further model development.
JOURNAL OF GREAT LAKES RESEARCH
(2021)
Article
Oncology
Pei Dong, Xinyue Zhang, Yulu Peng, Yijun Zhang, Ruiqi Liu, Yilin Li, Qiwen Pan, Wensu Wei, Shengjie Guo, Zhiling Zhang, Hui Han, Fangjian Zhou, Yang Liu, Liru He
Summary: This study analyzed the genomic characteristics and microenvironment of FHRCC and the cause of heterogeneous response to immune checkpoint inhibitor (ICI)-based treatment. The results showed that FHRCC had frequent immune infiltration and ICI treatment was associated with improved overall response rate and disease control rate. However, ICI treatment could not reverse the exhaustion of CD8+ T cells in patients with progressive disease, highlighting the need for additional therapeutic strategies.
CLINICAL CANCER RESEARCH
(2022)
Review
Oncology
Shengqin Yue, Qian Wang, Jiajun Zhang, Qinyong Hu, Chao Liu
Summary: This review provides an overview of the recent advances made in understanding the heterogeneity of the cervical cancer ecosystem through single-cell sequencing studies. It highlights the potential of high-resolution single-cell dissection in driving targeted therapies and personalized medicine.
Article
Environmental Sciences
Yingchun Liu, Yande Jing, Shanmei Han
Summary: This study assessed and measured five ecosystem services in the Nansi Lake Basin and divided the region into four ecological functional zones. The results showed a decreasing spatial pattern of ecosystem services from east to west, with trade-offs and synergies observed among different services. The study provides recommendations for ecosystem management and habitat conservation in the region.
ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH
(2023)
Article
Environmental Sciences
Sachia J. Traving, John Paul Balmonte, Dan Seale, Carol Arnosti, Ronnie N. Glud, Steven J. Hallam, Mathias Middelboe
Summary: Extracellular enzyme activity is an important factor in evaluating microbial biogeochemical roles in marine ecosystems. However, understanding the enzyme activities at the single-cell level in natural communities is challenging. By studying enzyme activities at the single-cell level, we can gain insights into phenotypic heterogeneity, enzyme kinetics, and spatial-temporal distribution of enzyme producers in marine communities.
FRONTIERS IN MARINE SCIENCE
(2022)
Article
Limnology
Chaoxuan Guo, Mengyuan Zhu, Hai Xu, Yunlin Zhang, Boqiang Qin, Guangwei Zhu, Jianjun Wang
Summary: The study found that the dependency of resource use efficiency (RUE) on phytoplankton diversity has spatiotemporal patterns. The RUE of nitrogen, phosphorous, and silicate showed different temporal trends. RUE was affected by nutrients and water temperature, and was also related to phytoplankton diversity. Interestingly, there was a negative spatial dependency between RUE and phytoplankton diversity. These dependencies were related to the spatial distribution of nutrients. Furthermore, the temporal dependency of RUE on phytoplankton diversity differed in different regions, primarily driven by the temporal stability of nutrients. These findings are important for future environmental management plans.
LIMNOLOGY AND OCEANOGRAPHY
(2022)
Article
Biochemical Research Methods
Jia Liu, Hui He, Dan Xie, Yanrong Wen, Zhen Liu
Summary: Cellular heterogeneity is pervasive and crucial in biology, and single-cell analysis techniques are indispensable in understanding this heterogeneity. Low-copy-number proteins play vital roles in various cellular functions, and their quantitative analysis in single cells remains challenging. A new approach called single-cell plasmonic immunosandwich assay (scPISA) has been developed to accurately measure low-copy-number proteins in living cells by combining in vivo microextraction and plasmon-enhanced Raman scattering technology.
Article
Biochemistry & Molecular Biology
Yanhua Tian, Qingqing Li, Zhenlin Yang, Shu Zhang, Jiachen Xu, Zhijie Wang, Hua Bai, Jianchun Duan, Bo Zheng, Wen Li, Yueli Cui, Xin Wang, Rui Wan, Kailun Fei, Jia Zhong, Shugeng Gao, Jie He, Carl M. Gay, Jianjun Zhang, Jie Wang, Fuchou Tang
Summary: Single-cell sequencing technology allows for analysis of individual cells in SCLC, revealing the heterogeneity of tumor cells and their interactions with the tumor microenvironment. Non-neuroendocrine tumors show increased immune response and better responses to immune checkpoint inhibitors.
SIGNAL TRANSDUCTION AND TARGETED THERAPY
(2022)
Review
Genetics & Heredity
Katherine Williams, Kyoko Yokomori, Ali Mortazavi
Summary: Single-nucleus RNA-seq has become an important tool in muscle research, providing valuable insights into multinucleated cells and identifying disease-specific nucleus populations.
FRONTIERS IN GENETICS
(2022)
Article
Engineering, Civil
Xiang Wang, Guo Chen, Xiaoai Dai, Jingjing Zhao, Xian Liu, Yu Gao, Junmin Zhang, Yongjun Chen, Xiaozhen Li, Wenyi Qin, Peng Wang
Summary: This study constructed a systematic GLOF hazard management process chain for moraine-dammed lakes by integrating various methods. The findings showed that two moraine-dammed lakes in southwestern Tibet were continuing to expand and at risk of GLOF. Modeling and simulation provided important data and results related to GLOF.
WATER RESOURCES MANAGEMENT
(2022)
Article
Environmental Sciences
Ahmed Taha, Mauricio Paton, Farrukh Ahmad, Jorge Rodriguez
Summary: This study developed a mechanistic biokinetic model to provide a theoretical accurate description for treating water contaminated with nitrate. The model successfully described the complex processes and the impact of design parameters on system performance, especially the effects of changing applied voltage and hydraulic retention time.
Article
Computer Science, Interdisciplinary Applications
Charuleka Varadharajan, Valerie C. Hendrix, Danielle S. Christianson, Madison Burrus, Catherine Wong, Susan S. Hubbard, Deborah A. Agarwal
Summary: BASIN-3D is a data integration framework designed to dynamically retrieve and transform heterogeneous data from different sources into a common format. Users can adopt a standardized approach for data retrieval and avoid customizations for the data type or source, supporting both web-based tools and data analytics.
COMPUTERS & GEOSCIENCES
(2022)
Article
Engineering, Environmental
B. Faybishenko, R. Versteeg, G. Pastorello, D. Dwivedi, C. Varadharajan, D. Agarwal
Summary: The representativeness and quality of collected meteorological data are crucial for the accuracy and precision of climate, hydrological, and biogeochemical analyses. A comprehensive QA/QC statistical framework was developed with three major phases: data exploration, QA of datasets, and development of time series, suitable for both real-time and post-data-collection analysis of meteorological datasets.
STOCHASTIC ENVIRONMENTAL RESEARCH AND RISK ASSESSMENT
(2022)
Article
Multidisciplinary Sciences
Harsh Maan, Maxim Itkin, Sergey Malitsky, Jonathan Friedman, Ilana Kolodkin-Gal
Summary: Microbial communities use various complex strategies, such as antibiotic production, to compete against competitors sharing their niche. This study demonstrates that antibiotics produced by Bacillus subtilis act synergistically to effectively eliminate phylogenetically distinct competitors, and their production is regulated by the global regulator ComA.
NATURE COMMUNICATIONS
(2022)
Article
Water Resources
Charuleka Varadharajan, Alison P. Appling, Bhavna Arora, Danielle S. Christianson, Valerie C. Hendrix, Vipin Kumar, Aranildo R. Lima, Juliane Mueller, Samantha Oliver, Mohammed Ombadi, Talita Perciano, Jeffrey M. Sadler, Helen Weierbach, Jared D. Willard, Zexuan Xu, Jacob Zwart
Summary: The global decline in water quality in rivers and streams has created an urgent need for new watershed management strategies. Machine learning can aid in developing more accurate, computationally tractable, and scalable models for analyzing and predicting river water quality. When combined with decades of process understanding, machine learning has the potential to address water quality problems effectively.
HYDROLOGICAL PROCESSES
(2022)
Article
Engineering, Environmental
Mohammed Ombadi, Charuleka Varadharajan
Summary: This study examines the effects of floods on salinity by analyzing long-term observational records of daily streamflow and specific conductance in 259 monitoring sites across the United States. The results show that salinity changes during flood events exhibit large variability, with dilution being the prevailing mechanism. The analysis also reveals that the antecedent conditions of salinity prior to the flood are the most important factor in explaining intra-site variability.
Article
Public, Environmental & Occupational Health
Scott W. Olesen, Eric Trabert
Summary: This article focuses on the importance of collaboration between decision-makers and modelers in effectively applying infectious disease modeling to public health decision-making. It proposes a set of guiding principles to improve the working relationships between decision-makers and modelers, aiming to enhance the utility of infectious disease modeling in public health decision-making.
DISASTER MEDICINE AND PUBLIC HEALTH PREPAREDNESS
(2023)
Article
Biochemistry & Molecular Biology
Daphne S. Sun, Stephen M. Kissler, Sanjat Kanjilal, Scott W. Olesen, Marc Lipsitch, Yonatan H. Grad
Summary: Understanding the relationship between antibiotic use and resistance is crucial for guiding effective strategies to limit resistance spread. Research findings showed that the use-resistance relationship varied across different pathogens and antibiotics, with resistance peaking in the winter and spring. These findings challenge the simple model of antibiotic use independently selecting for resistance and highlight the importance of considering differences between pathogens and antibiotics when developing stewardship strategies.
Article
Environmental Sciences
Helen Weierbach, Aranildo R. Lima, Jared D. Willard, Valerie C. Hendrix, Danielle S. Christianson, Michaelle Lubich, Charuleka Varadharajan
Summary: Stream temperature (T-s) is an important water quality parameter that affects ecosystem health and human water use. Accurate predictions of T-s using machine learning models can inform water management decisions, with air temperature identified as the primary driver of monthly T-s.
Article
Biology
Amichai Baichman-Kass, Tingting Song, Jonathan Friedman
Summary: Microorganisms in diverse communities are influenced by interspecific interactions, and the joint effects of multiple species on a single species remain largely unknown. In a study, thousands of bacterial communities were assayed, revealing that the joint effects of multiple species on a focal species are often dominated by the strongest individual-species effect. This finding is significant for understanding the introduction of species into occupied environments and has implications in fields such as medicine, agriculture, and ecology.
Article
Multidisciplinary Sciences
Mohammed Ombadi, Mark D. Risser, Alan M. Rhoades, Charuleka Varadharajan
Summary: The intensity of extreme precipitation events is projected to increase in a warmer climate, posing challenges to water sustainability. This study shows that the increase in rainfall extremes in high-elevation regions is double the rate expected from increases in atmospheric water vapour due to a shift from snow to rain. The findings highlight the vulnerability of high-altitude regions to extreme-rainfall-related hazards and the need for climate adaptation plans.
Article
Biochemical Research Methods
Ahmed Taha, Mauricio Paton, David Penas, Julio Banga, Jorge Rodriguez
Summary: In this study, a method is developed to evaluate the feasibility of alternative metabolic pathways in microbes by optimizing the energy yield and driving forces of metabolic intermediates. The method uses thermodynamic principles and multi-objective optimization to consider different pathway variants. Other constraints, such as the balance of conserved components, are also taken into account. The method transforms the maximum energy yield problem into a multi-objective mixed-integer linear optimization problem and solves it using the epsilon-constraint method. The methodology is applied to analyze different pathways in propionate oxidation and CO2 fixation by microbes.
PLOS COMPUTATIONAL BIOLOGY
(2023)
Review
Microbiology
Christian Kost, Kiran Raosaheb Patil, Jonathan Friedman, Sarahi L. Garcia, Markus Ralser
Summary: Microbial communities are shaped by ecological and environmental interactions, where antagonistic and synergistic interactions play important roles in driving their structure and dynamics.
NATURE MICROBIOLOGY
(2023)
Article
Engineering, Environmental
Tomas Allegue, Ramis Rafay, Sanjana Chandran, Shady A. Amin, S. Jane Fowler, Jorge Rodriguez
Summary: This preliminary study aims to improve the valerate yields achievable in a lab-scale granular mixed culture fermentation. The results show that exogenous addition of lactate can significantly increase the valerate production and decrease the propionate concentration.
JOURNAL OF ENVIRONMENTAL CHEMICAL ENGINEERING
(2022)
Article
Mathematical & Computational Biology
Mauricio Paton, Farida Al-Hosani, Anderson E. Stanciole, Bashir Aden, Andrey Timoshkin, Amrit Sadani, Omar Najim, Cybill A. Cherian, Juan M. Acuna, Jorge Rodriguez
Summary: The impact of the COVID-19 pandemic on large events is significant. A study on the potential impact of international arrivals due to Expo 2020 in the United Arab Emirates reveals that the number of infected arrivals is the major factor causing a surge in cases, while the vaccination status of visitors has a minor impact.
INFECTIOUS DISEASE MODELLING
(2022)