Article
Biochemistry & Molecular Biology
Caleb Ki, Jonathan Terhorst
Summary: This paper introduces VBSKY, a method for fitting Bayesian phylodynamic models to large pathogen genetic datasets. By combining recent advances in modeling, inference, and programming, VBSKY can analyze thousands of genomes in minutes and provide accurate estimates of epidemiologically relevant quantities.
MOLECULAR BIOLOGY AND EVOLUTION
(2022)
Article
Biology
Jorge F. Mejias, Xiao-Jing Wang
Summary: This article introduces a computational model based on the macaque cortex to study the distributed mechanism of neural activity in working memory. The research found that mnemonic internal states can emerge from inter-areal reverberation, leading to different attractor states. The model makes testable predictions about inhibitory bias, the role of prefrontal areas, and the resilience of distributed activity.
Article
Biotechnology & Applied Microbiology
Vanessa de Araujo Barbosa, S. Elizabeth Graham, Brian J. Smith, Ian D. Hogg, Angela McGaughran
Summary: This study compared the resolution of mitochondrial COI and nuclear SNP markers for detecting population structure among stream insects at small spatial scales. The results showed that both types of markers can provide suitable initial estimates of fine-scale population genetic differentiation in stream insects.
Article
Biochemistry & Molecular Biology
Zachery D. Zbinden, Marlis R. Douglas, Tyler K. Chafin, Michael E. Douglas
Summary: This study evaluated the genetic beta-diversity of 31 co-distributed native stream fishes in the White River Basin using SNP genotyping. The study identified general spatial patterns corresponding to river network architecture and found that a significant proportion of intraspecific genetic variation was explained by the stream hierarchy model. These findings have important implications for conservation and management in the ecosystem.
Article
Environmental Sciences
Nicole Albern, Aiko Voigt, Joaquim G. Pinto
Summary: The North Atlantic jet stream is projected to extend eastward towards Europe in winter due to climate change, with cloud-radiative changes playing a crucial role. This response is robust across various climate models and scenarios, but model uncertainties exist in the North Atlantic region. Tropical cloud-radiative changes are found to dominate the impact on the jet stream extension in one of the atmosphere models studied.
ENVIRONMENTAL RESEARCH LETTERS
(2021)
Article
Green & Sustainable Science & Technology
Che-Chih Tsao, Chia-Che Yang, Zhi-Xiang Chen
Summary: The Cross-stream Active Mooring (CSAM) is a new concept for ocean current power generation. This research examines its feasibility and stability under general sea conditions and its capability to resist storms and avoid them. Scale model tests and observations were conducted in conditions corresponding to the Kuroshio southeast of Taiwan. The results show that the CSAM model was successfully deployed as designed, maintained its formation under wave influences, and resisted a typhoon with a 10-year recurrence period.
Article
Computer Science, Information Systems
Song Chen, Fuhao Zhang, Zhiran Zhang, Siyi Yu, Agen Qiu, Shangqin Liu, Xizhi Zhao
Summary: This study proposed a method called Multi-Scale Massive Points Fast Clustering based on Hierarchical Density Spanning Tree to rapidly cluster and display elements at different spatial scales. The method introduced the concept of a hierarchical density-based spanning tree and combined it with the spatial scale and tree links of elements to propose a corresponding pruning strategy. The first experiment demonstrated the time efficiency and accuracy of the method in obtaining clustering results by adjusting parameters. The second experiment showed the feasibility and visual effect of the method on aggregation point elements.
ISPRS INTERNATIONAL JOURNAL OF GEO-INFORMATION
(2023)
Article
Ecology
Jon M. Luiken, Tony Gamble, Peter B. Berendzen
Summary: This study compared the population genomic structure of rainbow darter in river networks with different glacial histories, revealing a lasting influence of historic glaciation on the genetic structure of populations. The populations in different environments displayed distinct genetic structures, with evidence of population expansion and colonization patterns following glacial retreat. These results emphasize the importance of considering geological and climatic history as well as the life history of organisms when interpreting spatial genetic patterns.
ECOLOGY AND EVOLUTION
(2021)
Article
Computer Science, Information Systems
Yangyang Jiang, Yepeng Guan
Summary: This paper proposes a cluster reputation-based hierarchical consensus model (CRHCM) to address the limited scalability and inadequate consideration of dynamic node behavior in current consensus protocols. The model introduces a reputation system that updates node reputations based on both current and historical behaviors during the consensus process. Node reputation fluctuations are assessed using a discrete Markov chain, enabling the identification of abnormal nodes and improving overall node reliability. Furthermore, a hierarchical structure is proposed to improve scalability and reduce communication complexity by assigning nodes to upper or lower layers based on reputation and fluctuation levels. Experimental and theoretical evaluations demonstrate the effectiveness of CRHCM, which achieves a balanced distribution of reputation values among all nodes and exhibits high scalability. It outperforms some other state-of-the-arts.
PEER-TO-PEER NETWORKING AND APPLICATIONS
(2023)
Article
Parasitology
Tim Maes, Zoe De Corte, Carl Vangestel, Massimiliano Virgilio, Nathalie Smitz, Felicite F. Djuikwo-Teukeng, Maria Ioanna Papadaki, Tine Huyse
Summary: This study used high-throughput sequencing to investigate the population genetic structure of the hermaphroditic snail Bulinus truncatus. The results showed low genetic diversity and significant genetic differentiation between populations at both regional and inter-regional scales. The study also demonstrated the potential of high-throughput sequencing techniques in studying the role of snail species in parasite transmission.
PARASITES & VECTORS
(2022)
Article
Environmental Sciences
Kyongho Son, Yilin Fang, Jesus D. Gomez-Velez, Kyuhyun Byun, Xingyuan Chen
Summary: A basin-scale river corridor model was developed to identify the dominant factors associated with the spatial variation of denitrification in the hyporheic zone (HZ) of river corridors. The modeling results suggest that hydrologic variability, substrate availability influenced by land use, and hyporheic exchange flux are the main factors influencing HZ denitrification at the basin scale.
WATER RESOURCES RESEARCH
(2022)
Review
Cell Biology
Hui San Chin, Nai Yang Fu
Summary: The protein Mcl-1 plays a crucial role in cell survival, with its essential functions revealed through genetically engineered mouse models. Understanding its physiological roles in different tissues and developmental stages has implications for the treatment of various diseases, including cancer.
FRONTIERS IN CELL AND DEVELOPMENTAL BIOLOGY
(2021)
Article
Meteorology & Atmospheric Sciences
Jiyeong Kim, Sarah M. Kang, Shang-Ping Xie, Baoqiang Xiang, Doyeon Kim, Xiao-Tong Zheng, Hai Wang
Summary: This study investigates the effect of ocean dynamics on the tropical climate response to localized radiative cooling over three northern extratropical land regions. The results show that ocean dynamics can modulate the spatial pattern of climate response and its effect depends on the extratropical forcing location.
Article
Virology
Zekai Zhao, Lin Cao, Zixian Sun, Wenqiang Liu, Xiangmin Li, Kui Fang, Xianfei Shang, Junjie Hu, Huanchun Chen, Zhiyong Lou, Ping Qian
Summary: Two novel SVV mutants, SVV-S177A and SVV-S177A/P60S, modified based on structural biology and reverse genetics, significantly prolonged the median overall survival (mOS) from 11 days to 23 days in the NSCLC-bearing athymic mouse model, providing a direction for improving the oncolysis effect of SVV.
JOURNAL OF VIROLOGY
(2023)
Article
Business, Finance
Jose E. Gomez-Gonzalez, Jorge Hirs-Garzon, Jorge M. Uribe
Summary: This study reveals the interdependence of capital structure choices of US corporations over time. Macroeconomic factors are found to be crucial in making these decisions. Firms first determine the proportion of debt in new funding, and based on this, decide on debt term and earnings retention policy.
NORTH AMERICAN JOURNAL OF ECONOMICS AND FINANCE
(2022)
Article
Ecology
David S. Green, Marie E. Martin, Roger A. Powell, Eric L. McGregor, Mourad W. Gabriel, Kristine L. Pilgrim, Michael K. Schwartz, Sean M. Matthews
Summary: The historical suppression of forest fires and increasing droughts due to climate change are predicted to result in larger and more intense wildfires in western North America and other regions. Understanding the impact of wildfires on forest-dependent species and species interactions is crucial for conservation and management decisions.
Article
Biodiversity Conservation
Kellie J. Carim, Lisa A. Eby, Loren M. Miller, Holly McLellan, Virgil Dupuis, Michael K. Schwartz
Summary: The spread of aquatic invasive species is typically a result of both natural and human mediated dispersal. This study used genetic information to understand the invasion history and dynamics of northern pike in the Columbia River basin. The results showed that the initial introduction of northern pike was due to human transport, and subsequent reproduction and natural dispersal led to the downstream expansion of the species. These findings emphasize the importance of a holistic approach to invasive species suppression.
MANAGEMENT OF BIOLOGICAL INVASIONS
(2022)
Article
Biochemistry & Molecular Biology
John A. Kronenberger, Taylor M. Wilcox, Daniel H. Mason, Thomas W. Franklin, Kevin S. McKelvey, Michael K. Young, Michael K. Schwartz
Summary: Environmental DNA (eDNA) sampling is a sensitive and cost-effective technique for wildlife monitoring. This study used SYBR Green and TaqMan hydrolysis probes to test 10 qPCR assays and trained random forest classifiers to predict amplification. The models achieved high accuracy in cross-validation and independent tests, making it easier for practitioners to develop specific assays.
MOLECULAR ECOLOGY RESOURCES
(2022)
Article
Fisheries
Michael K. Young, Daniel J. Isaak, David Nagel, Dona L. Horan, Kellie J. Carim, Thomas W. Franklin, Victoria A. Zeller, Brett Roper, Michael K. Schwartz
Summary: One of the most challenging tasks for aquatic ecologists is to precisely delineate the range of species, especially those that are broadly distributed, require specialized sampling methods, and may be simultaneously declining and increasing in different portions of their range. In this study, the distribution of Pacific lamprey in the upper Snake River basin was determined through a two-stage environmental DNA survey. The results showed that Pacific lamprey mainly occupied river main stems and stocked tributaries, with weaker detections in downstream and warm channels and near their headwaters. Furthermore, there was no evidence of indigenous populations in natural habitats.
JOURNAL OF FISH BIOLOGY
(2022)
Article
Multidisciplinary Sciences
Sara J. Oyler-McCance, Todd B. Cross, Jeffery R. Row, Michael K. Schwartz, Dave E. Naugle, Jennifer A. Fike, Kristopher Winiarski, Brad C. Fedy
Summary: Characterizing genetic structure across a species' range is crucial for management and conservation. In this study, using the Greater Sage-grouse as an example, the authors propose strategies to overcome the challenges in characterizing genetic structure of wide-ranging species. They identify genetic differentiation centers and highlight the importance of maintaining genetic diversity and connectivity.
Article
Ecology
Andrew J. Shirk, Gavin M. Jones, Zhiqiang Yang, Raymond J. Davis, Joseph L. Ganey, R. J. Gutierrez, Sean P. Healey, Shaula J. Hedwall, Serra J. Hoagland, Ron Maes, Karl Malcolm, Kevin S. McKelvey, Carly Vynne, Jamie S. Sanderlin, Michael K. Schwartz, Mark E. Seamans, Ho Yi Wan, Samuel A. Cushman
Summary: This study introduces a framework for automatically monitoring and assessing species habitats. Using this framework, an automated habitat monitoring system for the Mexican spotted owl was developed and linked to federal agency adaptive management plans. The system demonstrated high accuracy in monitoring the owl's habitat over a 35-year period. It highlights the necessity for continuous monitoring and the benefits of an automated workflow in managing species in dynamic landscapes.
Correction
Ecology
Gavin M. Jones, Andrew J. Shirk, Zhiqiang Yang, Raymond J. Davis, Joseph L. Ganey, R. J. Gutierrez, Sean P. Healey, Shaula J. Hedwall, Serra J. Hoagland, Ron Maes, Karl Malcolm, Kevin S. McKelvey, Jamie S. Sanderlin, Michael K. Schwartz, Mark E. Seamans, Ho Yi Wan, Samuel A. Cushman
Article
Ecology
Gavin M. Jones, Andrew J. Shirk, Zhiqiang Yang, Raymond J. Davis, Joseph L. Ganey, R. J. Gutierrez, Sean P. Healey, Shaula J. Hedwall, Serra J. Hoagland, Ron Maes, Karl Malcolm, Kevin S. McKelvey, Jamie S. Sanderlin, Michael K. Schwartz, Mark E. Seamans, Ho Yi Wan, Samuel A. Cushman
Summary: Understanding habitat dynamics is crucial for effective conservation. This study developed a dynamic model of Mexican spotted owl habitat using an automated habitat monitoring system. The study explored environmental correlates, spatial non-stationarity in habitat selection, long-term trends, and the impact of wildfires on habitat changes. The results showed that topography and climate had a significant influence on the owl's habitat, with a decline in total habitat area over the past 35 years, and wildfires accounting for a portion of the habitat loss.
Article
Ecology
Gretchen H. Roffler, Kristine L. Pilgrim, Katherine E. Zarn, Michael K. Schwartz, Taal Levi
Summary: Wolves focus on natal den sites during the pup-rearing season, where the survival of their pups depends on food provided by adult pack members. The availability of prey is influenced by habitat quality within the wolves' home range. A study conducted in Southeast Alaska's Prince of Wales Island examined the relationship between prey species, habitat characteristics, wolf diet, and litter size.
ECOLOGY AND EVOLUTION
(2023)
Article
Biodiversity Conservation
Kristine L. Pilgrim, Rebecca E. Green, Kathryn L. Purcell, Taylor M. Wilcox, Eric L. McGregor, Larissa E. Gleason, Samuel K. Wasser, Michael K. Schwartz
Summary: A recent climate-induced tree mortality in California has resulted in significant landscape changes in the southern Sierra Nevada. The mortality event has affected the habitat of the fisher, a species of concern in the region. Analysis of fisher scats showed changes in diet composition, with a decrease in mammalian prey and an increase in Ribes plants following the tree mortality event.
JOURNAL FOR NATURE CONSERVATION
(2023)
Article
Multidisciplinary Sciences
Todd B. Cross, Jason D. Tack, David E. Naugle, Michael K. Schwartz, Kevin E. Doherty, Sara J. Oyler-McCance, Ronald D. Pritchert, Bradley C. Fedy
Summary: Conserving genetic connectivity is crucial for species survival, especially for imperilled species. This study integrates network and functional connectivity models to identify population centres and pathways important for maintaining genetic connectivity in the greater sage-grouse population. The spatial action maps generated from this process prioritize areas important for range-wide genetic connectivity. Comparing these maps to impedances such as cultivation and woodland expansion provides valuable information for future management and tracking conservation efforts.
ROYAL SOCIETY OPEN SCIENCE
(2023)
Article
Biodiversity Conservation
L. M. Elbroch, S. H. Williams, O. Ohrens, K. Pilgrim, A. Moeller, S. Arroyo-Arce, M. Parker, D. Goic, H. Robinson, M. K. Schwartz
Summary: Determining the abundance of cryptic carnivores is essential for conservation management and coexistence strategies. This study compares two methods, one using camera traps and the other using genetic data extracted from scats, to estimate the population of pumas in a UNESCO Biosphere Reserve in Chile. The results show the variation in estimates depending on the analysis start time and length of the sampling window, and present a refined iterative sampling approach to stabilize density estimates.
ANIMAL CONSERVATION
(2023)
Article
Evolutionary Biology
Joanna W. Elmore, Taylor M. Wilcox, Alex E. Dutcher, Yuki Reiss, Michael K. Schwartz
Summary: Predation is a crucial factor to consider when studying the impact of invasive species on ecosystems. However, observing and understanding predation can be challenging. This study used DNA metabarcoding to analyze the digestive tracts of invasive Barn Owls and identified multiple species of seabirds as their prey. Traditional morphological assessment detected only a small proportion of seabirds in owl stomach contents, highlighting the effectiveness of molecular methods.
JOURNAL OF HEREDITY
(2023)
Article
Biodiversity Conservation
Thomas W. Franklin, Joseph C. Dysthe, Helen Neville, Michael K. Young, Kevin M. McKelvey, Michael K. Schwartz
Summary: Lahontan cutthroat trout and Paiute cutthroat trout are rare and remote species, making traditional sampling difficult. A sensitive eDNA assay has been developed to detect both species, enhancing the ability to describe their distributions.
WESTERN NORTH AMERICAN NATURALIST
(2022)
Article
Biodiversity Conservation
Michael K. Young, Rebecca Smith, Kristine L. Pilgrim, Daniel J. Isaak, Kevin S. McKelvey, Sharon Parkes, Jacob Egge, Michael K. Schwartz
Summary: The taxonomy of sculpins in western North America remains unresolved. This study used molecular approaches to identify candidate species and assess their distribution. Results indicated the presence of 43 candidate species and established a benchmark for understanding sculpin diversity in the region.
WESTERN NORTH AMERICAN NATURALIST
(2022)