Gene Regulatory Network Prediction Using Machine Learning, Deep Learning, And Hybrid Approaches,
2025
Michigan Technological University
Gene Regulatory Network Prediction Using Machine Learning, Deep Learning, And Hybrid Approaches, Sai Teja Mummadi, Md Khairul Islam, Victor Busov, Hairong Wei
Michigan Tech Publications
Construction of gene regulatory networks (GRNs) is essential for elucidating the regulatory mechanisms underlying metabolic pathways, biological processes, and complex traits. In this study, we developed and evaluated machine learning, deep learning, and hybrid approaches for constructing GRNs by integrating prior knowledge and large-scale transcriptomic data from Arabidopsis thaliana, poplar, and maize. Among these, hybrid models that combined convolutional neural networks and machine learning consistently outperformed traditional machine learning and statistical methods, achieving over 95% accuracy on the holdout test datasets. These models not only identified a greater number of known transcription factors regulating the lignin biosynthesis pathway but also …
Assessment Of The State Forest Protection Management And Community Participation In The Central Highlands, Vietnam,
2025
Faculty of E-Commerce, Tay Nguyen College, Dak Lak, Vietnam
Assessment Of The State Forest Protection Management And Community Participation In The Central Highlands, Vietnam, Do Cao Phan, Tran Thi Lan
ASEAN Journal of Community Engagement
This study focuses on state forest protection management in Central Highlands Vietnam, particularly in the Krong Bong District, Dak Lak Province, examining the role of community participation. The Central Highlands, a region rich in biodiversity and ecological significance, is severely impacted by deforestation, illegal logging, and land-use changes. This study assesses the current state of forest governance and proposes sustainable development improvement strategies. The research employs a mixed-methods approach, integrating secondary data, such as government reports and forest management reports from Krong Bong District, Đak Lak Province, as well as previous studies, with primary data collected from surveys of 96 …
Spatial Patterning And Growth Of Naturally Regenerated Eastern White Pine In A Northern Hardwood Silviculture Experiment,
2025
Michigan Technological University
Spatial Patterning And Growth Of Naturally Regenerated Eastern White Pine In A Northern Hardwood Silviculture Experiment, David A. Kromholz, Christopher R. Webster, Mike Hyslop
Michigan Tech Publications
In forests dominated by deciduous tree species, coniferous species are often disproportionately important because of their contrasting functional traits. Eastern white pine (Pinus strobus L.), once a widespread emergent canopy species, co-occurs with deciduous hardwoods in the northern Lake States, but is often uncommon in contemporary hardwood stands. To gain insights into the potential utility of hardwood management strategies for simultaneously regenerating white pine, we leveraged a northern hardwood silvicultural experiment with scattered overstory pine. Seven growing seasons post-harvest, we conducted a complete census of white pine regeneration (height ≥ 30 cm) and mapped their locations and the locations of …
Changing Aspen Stand Structure Following Large Carnivore Restoration In Yellowstone,
2025
Oregon State University
Changing Aspen Stand Structure Following Large Carnivore Restoration In Yellowstone, Luke E. Painter, Robert L. Beschta, William J. Ripple
Aspen Bibliography
Restoration of large carnivores in northern Yellowstone National Park in the late 20th century resulted in a sustained reduction of Rocky Mountain elk (Cervus canadensis) and their herbivory, facilitating new growth of quaking aspen (Populus tremuloides) saplings. In 2020–21, we examined 87 randomly selected, previously sampled aspen stands across northern Yellowstone, combining random plots with stand-wide observations. Forty-three percent of stands contained a new cohort of small trees (5–10 cm dbh), the first documented recruitment of overstory aspen trees in northern Yellowstone since the 1940s. Both aspen saplings ( ≥2 m tall) and small trees were …
Public Support For Puma Reintroduction In The Eastern United States,
2025
Panthera USA
Public Support For Puma Reintroduction In The Eastern United States, L. Mark Elbroch, Jazmin J. Murphy, Shelby C. Carlson, John A. Vucetich, Richard E.W. Berl, Lexi Galiardi, Shelby Perry, Tom Butler, Neil Carter, Joseph W. Hinton, Axel Moehrenschlager, Emily Carrollo, Rana Bayrakcismith, Jeremy T. Bruskotter
Michigan Tech Publications
Pumas (Puma concolor) are among the species identified as having the potential to enhance ecosystem function. Previous research highlights sufficient ecological habitat to support pumas in the eastern United States; however, their reintroduction requires social and institutional support as well. To this end, we conducted research to assess attitudes about puma reintroduction among key constituencies like hunters, rural residents, and young people. We sampled 2756 respondents across seven states (Massachusetts, Maine, New Hampshire, New York, Pennsylvania, Vermont, and West Virginia). Ratios of strong support (for puma reintroduction) to strong opposition across states ranged from 4:1 to 13:1, and support outweighed …
Limited Soil Water Recharge In Summer Affects Seasonal Isotopic Signatures Of Tree Xylem Water,
2025
ETH Zürich
Limited Soil Water Recharge In Summer Affects Seasonal Isotopic Signatures Of Tree Xylem Water, Marius G. Floriancic, Gregory R. Goldsmith, Harsh Beria, Scott T. Allen, James W. Kirchner
Biology, Chemistry, and Environmental Sciences Faculty Articles and Research
Recent studies have reported that xylem waters in forest trees during the summer growing season are often isotopically similar to winter, rather than summer, precipitation. Several hypotheses have been proposed to explain this observation, which can be viewed as a form of ecohydrological separation, but empirical tests spanning space and time remain limited. We hypothesise that variations in the seasonal origin of precipitation found in tree xylem waters can be explained by seasonal differences in soil water recharge. We test this hypothesis by evaluating to what extent climatic aridity can explain seasonal signals in extensive surveys of the isotope ratios …
Canopy Insect Communities Are Shaped By The Genes And Phenotypes Of Their Aspen Hosts,
2025
University of Wisconsin-Madison
Canopy Insect Communities Are Shaped By The Genes And Phenotypes Of Their Aspen Hosts, Clay J. Morrow, Jennifer Lind-Riehl, Christopher T. Cole, Kennedy Rubert-Nason, Cécile Ané, Richard L. Lindroth
Aspen Bibliography
1. Community genetics research aims to identify genetic and phenotypic mechanisms that shape communities as extended phenotypes. To date, most progress has been made identifying variation in herbivore communities associated with intraspecific variation in plants, with little focus on identifying specific genes or traits responsible for that variation. Here, we identify how extended phenotype variation of a foundation tree species, Populus tremuloides, arises from trait variation among individuals and specific genes. 2. We quantified heritability for 13 tree traits -- including phenology, defense chemistry, reproduction, and morphology -- and for 18 associated insect species (640,557 individuals). We performed genomic …
Online Citizen Science In Higher Education Courses,
2025
Michigan Technological University
Online Citizen Science In Higher Education Courses, Stacy Cotey, Amy K. Dunbar-Wallis, Yaela N. Golumbic, Pankaj Mehrotra, David A. Beamer, Heather D. Vance-Chalcraft
Michigan Tech Publications
Climate change and biodiversity loss require us to engage the next generation of scientists in addressing global ecological issues. Introducing undergraduate students to citizen science allows them to learn scientific processes and content while contributing to real-world applications. We conducted a systematic review of literature to (1) identify what types of undergraduate courses and institutions use citizen science, (2) list the projects and platforms that have been implemented in online courses in undergraduate education, (3) examine how students participated in the projects through online courses, and (4) summarize learning objectives and reported benefits of student participation. In all, 44 studies …
Integrating Belowground Recovery Into Tropical Forest Restoration Design And Monitoring,
2025
Yale University
Integrating Belowground Recovery Into Tropical Forest Restoration Design And Monitoring, Lauren Toro, Leland K. Werden, Shalom D. Addo-Danso, Kelly M. Andersen, Sarah Batterman, Matilde M. Bragadini, Pooja Choksi, Rebecca J. Cole, Liza S. Comita, Daniela Cusack, Daisy H. Dent, Lee H. Dietterich, Joshua B. Fisher, Katrin Fleischer, Lucia Fuchslueger, Nohemi Huanca-Nunez, Janey R. Lienau, Lindsay A. Mcculloch, Ember M. Morrissey, Jennifer S. Powers, Mareli Sánchez-Juliá, Oscar Valverde-Barrantes, Anita Weissflog, Michelle Y. Wong
Biology, Chemistry, and Environmental Sciences Faculty Articles and Research
There is growing recognition that tropical forest restoration is key for sequestering carbon and enhancing ecosystem resilience. Soils, roots, and soil biota are central to ecosystem function and services, but belowground recovery is largely overlooked in restoration monitoring frameworks. Here, we outline current understanding of the links between above- and belowground recovery in tropical forests by examining how belowground properties before and after intervention influence recovery; by evaluating whether aboveground recovery can serve as a proxy for belowground dynamics; and by proposing a blueprint for monitoring dynamic soil physical (bulk density, aggregate stability), chemical (organic matter or carbon, pH), and …
Aspen Impedes Wildfire Spread In Southwestern United States Landscapes,
2025
Western Colorado University
Aspen Impedes Wildfire Spread In Southwestern United States Landscapes, Matthew P. Harris, Jonathan D. Coop, Jared A. Balik, Jessika R. Mcfarland, Sean A. Parks, Camille S. Stevens-Rumann
Aspen Bibliography
Aspen (Populus tremuloides) forests are generally thought to impede fire spread, yet the extent of this effect is not well quantified in relation to other vegetation types. We examined the influence of aspen cover on interpolated daily fire spread rates, the relative abundance of aspen at fire perimeters versus burn interiors, and whether these relationships shifted under more fire-conducive atmospheric conditions. Our study incorporated 314 fires occurring between 2001 and 2020 in the southwestern United States and a suite of gridded vegetation, topography, and fire weather predictor variables. We found that aspen slows fire progression: as aspen cover …
Assessment Of Spatial Autocorrelation And Scalability In Fine-Scale Wildfire Random Forest Prediction Models,
2025
California Institute of Technology
Assessment Of Spatial Autocorrelation And Scalability In Fine-Scale Wildfire Random Forest Prediction Models, Madeleine Pascolini-Campbell, Joshua B. Fisher, Kerry Cawse-Nicholson, Christine M. Lee, Natasha Stavros
Biology, Chemistry, and Environmental Sciences Faculty Articles and Research
Wildfire prediction models that can be applied across diverse regions at fine scales (< 100 m) are critical for wildfire management. Remote sensing offers a path forward by providing heterogeneous and dynamic measurements of fuel load, type, and flammability. Machine learning methods such as random forests provide an empirical framework that are high-accuracy, computationally efficient, interpretable and able to model complex ecological relationships. Here we use high resolution (70 m, every 3–5 days) remote sensing observations of evapotranspiration and evaporative stress index, which represent plant water stress, from Ecosystem Spaceborne Thermal Radiometer on Space Station (ECOSTRESS), as well as topography and weather data, to predict burn severity and occurrence for 8 large wildfires that burned 3715 km2 from 2021 and 2022 in New Mexico, USA. These fires ranged from low to high burn intensity, and covered a diverse range of ecoregions (deserts, grasslands, forests), plant species, and topographies. We used a single model to predict the burn severity of all wildfires one week before occurrence. The prediction accuracy was greatest when using all predictors (ECOSTRESS, weather, topography) (R2 = 0.77). We assessed the role of spatial autocorrelation in driving model performance by: (1) increasing the sample spacing of our dataset, (2) …
The Influence Of Human Presence And Footprint On Animal Space Use In Us National Parks,
2025
The University of British Columbia
The Influence Of Human Presence And Footprint On Animal Space Use In Us National Parks, Kaitlyn M. Gaynor, Forest P. Hayes, Kezia Manlove, Nathan Galloway, John F. Benson, Michael J. Cherry, Rolf O. Peterson, Sarah Hoy, John Vucetich, Et Al.
Michigan Tech Publications
Given the importance of protected areas for biodiversity, the growth of visitation to many areas has raised concerns about the effects of humans on wildlife. In 2020, the COVID-19 pandemic led to temporary closure of national parks in the United States, offering a pseudonatural experiment to tease apart the effects of permanent infrastructure and transient human presence on animals. We compiled GPS tracking data from 229 individuals of 10 mammal species in 14 parks and used third-order hierarchical resource selection functions to evaluate the influence of the human footprint on animal space use in 2019 and 2020. Averaged across all …
Catching A Fever: A Comparison Of Vachellia Xanthophloea Populations In The Limpopo And Luvuvhu River Floodplains Of The Makuleke Contractual Park,
2025
University of Nebraska-Lincoln
Catching A Fever: A Comparison Of Vachellia Xanthophloea Populations In The Limpopo And Luvuvhu River Floodplains Of The Makuleke Contractual Park, Kianie B. David
School of Natural Resources: Dissertations, Theses, and Student Research
This study investigates patterns of stand structure regeneration, growth characteristics, and coarse woody debris (CWD) patterns in Vachellia xanthophloea (fever tree) stands within the Makuleke Contractual Park (MCP), a semi-arid savanna system in northern Kruger National Park (KNP), South Africa. Fieldwork was conducted across two stand types: a monospecific fever tree stand in Rietbok Vlei and a mixed-species stand in the Western Nhlangaluwe Floodplain where fever tree is established with Faidherbia albida (ana tree). Data were collected from 20 total 1/4-acre (1,011 m2) circular plots between both stands in 2024 and 2025, including seedling root collar diameter (RCD), …
Exploring The Composition Of Forest Collaboratives In Northeastern Oregon,
2025
US Forest Service
Exploring The Composition Of Forest Collaboratives In Northeastern Oregon, Lee K. Cervany, Rebecca J. Mclain, Kristen Wright
National Policy Consensus Center Publications
Community-based collaboration has been touted as an effective model for forest governance because it promotes democratized decision-making and stakeholder engagement to address landscape-scale problems. Forest collaboratives are assumed to be heterogeneous, consisting of stakeholders with a diverse range of interests. Few studies have systematically explored variables associated with collaborative composition. We identify six elements of collaborative composition for investigation: size, stakeholder diversity, balance, locality–diversity, core attendance, and cross-participation. This exploratory study examines five forest collaborative groups in eastern Oregon (USA). We analyzed meeting minutes over an 18-month period to track attendance and evaluate who shows up and at what frequency. …
Assessing The Influence Of Afforestation On Soil Quality And Soil Organic Carbon: A Case Study In Rashaya District, Lebanon,
2025
Department of Biological Sciences, Faculty of Science, Beirut Arab University, Debbyeh, Lebanon
Assessing The Influence Of Afforestation On Soil Quality And Soil Organic Carbon: A Case Study In Rashaya District, Lebanon, Mohammad Saleh, Wael Mostafa, Safaa Baydoun, Hisham Salman, Jamilah Borjac
BAU Journal - Science and Technology
Afforestation is a promising strategy for improving soil quality and enhancing carbon sequestration, contributing to climate change mitigation efforts. This study assessed the impact of afforestation on soil parameters in two afforested areas and one natural forest, compared with adjacent non-forested sites in Rashaya al-Wadi, Lebanon. Soil samples (0–30 cm depth) were analyzed for texture, pH, electrical conductivity (EC), soil organic matter (SOM), soil organic carbon (SOC), organic nitrogen (ON), mineral nitrogen (MN), and available phosphorus (AP) using ISO and standardized protocols at the Lebanese Agricultural Research Institute (LARI). The findings indicate that afforestation significantly increased SOM, SOC, and ON, …
Bite By Bite: How Ungulate Browsing Shapes North America's Forest Future,
2025
Transilvania University of Brasov
Bite By Bite: How Ungulate Browsing Shapes North America's Forest Future, Darius Hardalau, Vladut Stefanescu, Mindaugas Bakševičius, Michael Manton, Charles Ruffner, Gediminas Brazaitis, Georgeta Ionescu, Ovidiu Ionescu
Aspen Bibliography
Ungulate browsing represents a contemporary issue for forest development, influencing forest regeneration, composition, and management practices across the world, especially in North America. This review synthesizes findings from 101 studies conducted between 1980 and 2025 to examine patterns of herbivory damage through browsing by moose, elk, white-tailed deer, black-tailed deer, and bison. Despite regional variation, high ungulate density consistently emerges as the primary factor driving browsing intensity and ecological and economic impact, leading to decreased social acceptance of coexistence with ungulates. This review highlights the selective suppression of palatable species such as balsam fir, red oak, and white cedar, leading …
Annotated Checklist And Distribution Of The Jewel Beetles (Coleoptera: Buprestidae) Of Idaho,
2025
University of Idaho
Annotated Checklist And Distribution Of The Jewel Beetles (Coleoptera: Buprestidae) Of Idaho, Luc Leblanc, Emma L. Eakins
Insecta Mundi
An annotated checklist of the 102 species of Buprestidae (Coleoptera) known to be present in the state of Idaho is provided, with photographs and detailed distribution maps for each species. The checklist is based on label data from 7,506 museum specimens, 21 observations obtained from iNaturalist.org and Bug-Guide.net, and 63 distribution records from published literature. Buprestis consularis Gory is a new record for Idaho, formerly reported as Buprestis nutalli Kirby, which is not known to occur in the state. Obscure past records of Anthaxia retifera LeConte and Melanophila occidentalis Obenberger published in the literature are regarded as dubious and are …
Living Heritage, Resilience And Ethically Informed Infrastructures In Malawi,
2025
CUNY Lehman College
Living Heritage, Resilience And Ethically Informed Infrastructures In Malawi, Martha B. Lerski, Frank Puluputu Mwale
Publications and Research
Rooted in a rural community’s needs, this paper explores how historically, and ethically informed infrastructures can support community engagement towards identification, documentation, and dissemination of local, traditional, and indigenous knowledge relating to climate change. The paper examines climate adaptation and sustainability issues through the lenses of community organizing and Library & Information Science best practices. It draws on a growing body of literature identifying a role for expanded epistemological and subject discipline perspectives. While the impacts of climate on material culture are increasingly recognized, intangible, and biocultural heritage have not received as much attention. Living heritage traditions and knowledge systems …
Deep Reinforcement Learning-Driven Decision Support System Design For Precision Agriculture: Optimizing Farming And Resource Use, Qingshan Bai
Turkish Journal of Agriculture and Forestry
This study focuses on enhancing the efficiency of agricultural decision support systems by integrating deep reinforcement learning techniques to optimize the path planning of agricultural vehicles. By decomposing the system into dynamics, action, strategy, reward, and discount factor components, a robust framework is established. A value-based reinforcement learning algorithm is introduced, enriched with policy gradient (PG) methodology to enable continuous and adaptive state-to-action decision-making process. A deep neural network (DNN) was used to approximate the state-action value function, resulting in the innovative DNN-PG-Q-learning algorithm. This algorithm leverages an empirical playback pool to enable efficient and intelligent path planning for agricultural …
Accurate Crop Yield Prediction Via Temporal Convolutional Network And Variational Autoencoder,
2025
TÜBİTAK
Accurate Crop Yield Prediction Via Temporal Convolutional Network And Variational Autoencoder, Lei Liu, Xiaoling Song
Turkish Journal of Agriculture and Forestry
With the advancement of technology, smart agriculture assumes a pivotal role in enhancing the efficiency and sustainability of agricultural production. Nevertheless, accurately forecasting crop yields and understanding their determining factors often faces limitations inherent in conventional data processing techniques. To address this challenge, this study proposes a TCN-VAE framework, amalgamating temporal convolutional networks (TCNs) and variational autoencoders (VAEs), to tackle the crop yield prediction task in smart agricultural systems. The framework intricately models four principal categories of features—meteorological conditions, soil conditions, agricultural management, and environmental conditions—via TCN and compensates for missing data using VAE, thereby achieving a comprehensive analysis and …
