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At least 145 records · Page 8

Evaluation of Machine Learning and Deep Learning Algorithms for Fire Prediction in Southeast Asia

Vegetation fires are prevalent in South/Southeast Asian countries, making fire prediction crucial due to their potential environmental, economic, and social impacts. Accurate predictions of fires facilitate timely interventions, helping to mitigate uncontrolled fires that can lead to biodiversity loss and air quality issues. In this study, we utilize VIIRS satellite-derived fire data alongside six machine learning and deep learning models—Simple Persistence, Multi-Layer Perceptron (MLP), Convolutional Neural Network (CNN), Long Short-Term Memory (LSTM), CNN-LSTM, and ConvLSTM—to determine the most effective fire prediction model, using Root Mean Square Error (RMSE) as the metric. Our results indicate that the CNN model is the most reliable in regions with spatial dependencies, such as Brunei, Indonesia, Malaysia, the Philippines, Timor-Leste, and Thailand. Conversely, the ConvLSTM model excels in countries with complex spatiotemporal dynamics like Laos, Myanmar, and Vietnam. The CNN-LSTM hybrid model also performed well in Cambodia, suggesting a need for a balanced approach in areas requiring both spatial and temporal feature extraction. Furthermore, simpler models like Persistence and MLP showed limitations in capturing dynamic patterns and temporal dependencies. Our findings highlight the importance of evaluating models before implementing any decision support systems (DSS) in fire management. By tailoring models to specific regional fire data, we can enhance prediction accuracy and responsiveness, ultimately improving fire risk management in Southeast Asia and beyond.

Deep learning↗

Germplasm cryopreservation of macroalgae for aquaculture breeding and natural resource conservation: A review

The expansion of the global macroalgal aquaculture and climate change creates the need for germplasm preservation of valuable aquaculture strains and maintenance of natural biodiversity. Compared to the large number of studies in fish and shellfish species, relative few studies have been conducted on the macroalgal germplasm cryopreservation. The first cryopreservation of macroalgae to –75 °C was reported on Neopyropia tenera (formerly called Porphyra tenera) in 1964. To date, a total of 34 studies reported germplasm cryopreservation in 33 species, including Chlorophyta (7 species), Ochrophyta (14 species), and Rhodophyta (12 species). Here, the goal of this review was to summarize the published studies on macroalgal germplasm cryopreservation, compare the reported protocols for the cryopreservation process, and identify the factors affecting post-thaw viability. Overall, macroalgal germplasm cryopreservation included haploid or diploid thalli, spores, and gametes. Cryotubes (1.5-ml or 2-ml) have been widely used to package germplasm samples for cooling and storage in most studies, and the 0.5-ml straws and 5-ml cryotubes have been used in several studies. Two approaches (programmable controlled cooling and vitrification) were employed for macroalgal germplasm cryopreservation. A two-step programmable controlled cooling (e.g., from initial culture temperature to a frozen temperature, such as –40 °C, and then directly plunging into liquid nitrogen at –196 °C) was determined to be an effective cooling strategy. Vitrification, a super rapid cooling for a sample to form non-crystalline amorphous solid, was applied on macroalgal germplasm cryopreservation with sample encapsulation and dehydration. Survival of post-thaw samples varied significantly in different studies. Based on research updates, recommendations are made for future research. It is expected that this review can serve as a foundation for future germplasm banking of macroalgae for aquaculture and biodiversity preservation.

59 BASIC BIOLOGICAL SCIENCES↗

Ecologically-Informed Precision Conservation: A framework for increasing biodiversity in intensively managed agricultural landscapes with minimal sacrifice in crop production

Conservation actions are urgently needed to tackle biodiversity loss in intensively managed agricultural landscapes. Production lands are usually heterogeneous and contain low-yield areas that can be set aside for biodiversity conservation without serious yield losses. Here, we introduce Ecologically-Informed Precision Conservation, a framework that integrates yield mapping and ecological theory to select the best areas to create new set-asides while ensuring high crop yields at the farm/landscape level. Long-term yield maps can be generated using globally available satellite data and basic information on field/farm crop yield from farmers. Ecological principles are then used to select the subset of areas with the highest potential for biodiversity conservation by prioritising those that increase connectivity, maximise habitat heterogeneity and decrease landscape grain size. Here, the created non-crop habitats can be permanent and thus ensure biodiversity support over time. In addition, agricultural management efficiency can be enhanced by improving field shapes. The framework provides the basis for a practical, user-friendly tool that informs all interested stakeholders on how to rationalise existing agricultural landscapes using already-existing farming systems and available technologies. High cost-effectiveness from an economic and conservation perspective, along with the creation of heterogeneous non-crop habitats, make our framework a promising solution to re-design agricultural landscapes.

Precision agriculture↗

Application of Remote Sensing for Ex-Ante Decision Support and Evaluating Impact

Deforestation is an environmental stressor that dramatically threatens biodiversity while having adverse, deep-rooted socioeconomic impacts. Interventions to address deforestation require considerable long-term investments; therefore, assessing their impact is crucial. The UN Convention on Biological Diversity encourages establishing Protected Areas (PAs) as a strategy to conserve biodiversity, secure ecosystem services, support local livelihoods, and reduce climate change impacts. The Global Environment Facility (GEF) has supported the conservation and management of PAs, yet site accessibility and data availability present challenges in assessing PAs using traditional evaluation methods. We present a novel application of satellite Earth observations for evaluating the effectiveness and impact of PAs as a deforestation mitigation strategy. Geospatial analysis and ecological forecasting methodologies provide an efficient way to quantify land cover change, estimate above-ground carbon stock, and evaluate ecosystem services provided by the PAs ex-ante. We demonstrate the value of a geospatial approach through evaluation of GEF-supported PAs in Kenya.

Remote sensing↗

Visualizing metagenomic and metatranscriptomic data: A comprehensive review

The fields of Metagenomics and Metatranscriptomics involve the examination of complete nucleotide sequences, gene identification, and analysis of potential biological functions within diverse organisms or environmental samples. Despite the vast opportunities for discovery in metagenomics, the sheer volume and complexity of sequence data often present challenges in processing analysis and visualization. This article highlights the critical role of advanced visualization tools in enabling effective exploration, querying, and analysis of these complex datasets. Emphasizing the importance of accessibility, the article categorizes various visualizers based on their intended applications and highlights their utility in empowering bioinformaticians and non-bioinformaticians to interpret and derive insights from meta-omics data effectively.

59 BASIC BIOLOGICAL SCIENCES↗

Ground-Active Arthropod Diversity Under Energycane and Biomass Sorghum Production

Energycane and biomass sorghum are two of the most promising cellulosic energy crops in the southeastern US. Research on these two energy crops has focused mainly on biomass production, and there is a lack of knowledge on their ability to promote biodiversity and ecosystem services. This paper presents results from a comprehensive study on ground-active arthropod diversity in seven sites across five states in the southeastern US (Florida, Georgia, Louisiana, Mississippi, and Texas). Pitfall traps were deployed four times during each crop season for energycane, biomass sorghum, and a local reference conventional crop from 2020 to 2022. Arthropod abundance (individuals/(trap × day)) values were 4.9 ± 0.46, 3.7 ± 0.18, and 2.6 ± 0.16 (mean ± stderr) for conventional crops, biomass sorghum, and energycane, respectively, with a significant difference found only between conventional crops and energycane. Individuals were identified to arthropod orders, and Hill’s diversity indices were calculated based on the number of individuals in each arthropod order instead of the number of individuals in each arthropod species. Order-based arthropod richness values were 5.3, 5.2, and 4.8 for biomass sorghum, conventional crops, and energycane, with significant difference found only between biomass sorghum and energycane. There was no significant difference in the order-based Shannon diversity and Simpson diversity between the three crop types. The effective number of arthropod orders for the two energy crops decreased from 5.0 to 3.4 to 2.9 with increasing order of diversity from arthropod richness to Shannon diversity to Simpson diversity. The explained variability by environmental factors also decreased with increasing Hill’s order of diversity. The results from this study indicate no significant advantage in order-based arthropod diversity in growing biomass sorghum and energycane. This research fills a critical knowledge gap in understanding the impacts of cellulosic energy crop production on biodiversity and ecosystem services.

Yang, Yubin↗

KBase Narrative - Atacama Trench & Sn Clemente 2018 cruise Metagenomes -Decontamination through Metagenomic Fractionation and analysis of Metabolic Potential-

Deep-sea microbiomes sampled with traditional or pressure-retaining instrumentation A fundamental property of life in the sea is that with increasing depth must come increased adaptation to elevated hydrostatic pressures. This project aims to assess technology for the accurate characterization of microbial biodiversity and biochemistry at greater depths, and validate its use in some of the deepest and least-explored waters in the Ocean: Hadal Trench. Compared to the 0.1 megapascal (MPa) of surface waters, organisms inhabiting at the average depth of the Ocean (3800 m) have to deal with pressures of 38 MPa (5,500 psi). The effects of these high pressure have been most thoroughly investigated in microorganisms, where it has been found to affect membrane integrity and transport, cytoskeletal assembly and both DNA and protein synthesis. We will explore the diversity and activity of microorganisms from 2000 m to >8,000 m depths within the highly productive water column of hadal trenches, comparing seawater samples obtained with and without substantial pressure changes during recovery. A pressure retaining device was used to sample the microbial communities of the watercolumn with reduced decompression during retreival (Peoples et. al., 2019). References: Peoples LM, Norenberg M, Price D, McGoldrick M, Novotny M, Bochdansky A, Bartlett DH. A full-ocean-depth rated modular lander and pressure-retaining sampler capable of collecting hadal-endemic microbes under in situ conditions. Deep Sea Research Part I: Oceanographic Research Papers. 2019 Jan 1;143:50-7.

Plominsky, Alvaro M.↗

KBase Narrative - Atacama Trench & Sn Clemente 2018 cruise Metagenomes -Sequence quality filtration & Assembly-

Deep-sea microbiomes sampled with traditional or pressure-retaining instrumentation A fundamental property of life in the sea is that with increasing depth must come increased adaptation to elevated hydrostatic pressures. This project aims to assess technology for the accurate characterization of microbial biodiversity and biochemistry at greater depths, and validate its use in some of the deepest and least-explored waters in the Ocean: Hadal Trench. Compared to the 0.1 megapascal (MPa) of surface waters, organisms inhabiting at the average depth of the Ocean (3800 m) have to deal with pressures of 38 MPa (5,500 psi). The effects of these high pressure have been most thoroughly investigated in microorganisms, where it has been found to affect membrane integrity and transport, cytoskeletal assembly and both DNA and protein synthesis. We will explore the diversity and activity of microorganisms from 2000 m to >8,000 m depths within the highly productive water column of hadal trenches, comparing seawater samples obtained with and without substantial pressure changes during recovery. A pressure retaining device was used to sample the microbial communities of the watercolumn with reduced decompression during retreival (Peoples et. al., 2019). References: Peoples LM, Norenberg M, Price D, McGoldrick M, Novotny M, Bochdansky A, Bartlett DH. A full-ocean-depth rated modular lander and pressure-retaining sampler capable of collecting hadal-endemic microbes under in situ conditions. Deep Sea Research Part I: Oceanographic Research Papers. 2019 Jan 1;143:50-7.

Plominsky, Alvaro M.↗

VLM4Bio: A Benchmark Dataset to Evaluate Pretrained Vision-Language Models for Trait Discovery from Biological Images

Images are increasingly becoming the currency for documenting biodiversity on the planet, providing novel opportunities for accelerating scientific discoveries in the field of organismal biology, especially with the advent of large vision-language models (VLMs). We ask if pre-trained VLMs can aid scientists in answering a range of biologically relevant questions without any additional fine-tuning. In this paper, we evaluate the effectiveness of 12 state-of-the-art (SOTA) VLMs in the field of organismal biology using a novel dataset, VLM4Bio, consisting of 469K question8 answer pairs involving 30K images from three groups of organisms: fishes, birds, and butterflies, covering five biologically relevant tasks. We also explore the effects of applying prompting techniques and tests for reasoning hallucination on the performance of VLMs, shedding new light on the capabilities of current SOTA VLMs in answering biologically relevant questions using images

Maruf, M [Virginia Tech, Blacksburg]↗

Discovering Innovations in Stress Tolerance through Comparative Gene Regulatory Network Analysis and Cell-Type Specific Expression Maps (Final Technical Report with Cover Page)

Through this grant, we developed a comparative framework to elucidate the mechanisms behind variations in environmental stress responses among a diverse group of species within the Brassicaceae family. Our focus was on the differences in physiological and transcriptomic responses to abscisic acid (ABA), a hormone associated with water stress. We examined the differential growth responses of four Brassicaceae species, finding that most exhibited reduced root growth correlated with smaller meristem size. In contrast, Schrenkiella parvula showed accelerated growth due to increased root cell elongation. We employed RNA sequencing to analyze the transcriptional responses to ABA across these species, and innovative bioinformatics techniques were used to pinpoint biological pathways with significant divergence. Additionally, we utilized DAP-seq to map the gene regulatory networks associated with ABAresponsive transcription factors, revealing that variations in the regulation of growth hormone biosynthesis play a critical role in the distinct ABA effects on root growth among the species. This research sets a new standard for comparative physiology by integrating comparative genomics and transcriptomics to uncover pathway divergences.

59 BASIC BIOLOGICAL SCIENCES↗

Producing cultivated meat cuts that match traditional meat in quality and affordability (CRADA Final Report)

Novel Farms, Inc., as a participant of the Cyclotron Road Lab-Embedded Entrepreneurship Program, investigated the performance of various animal cell lines and animal cell media formulations using its proprietary scaffolds as a growth substratum towards the development of economically-feasible cultivated meat production. As an alternative to conventionally farmed animal meat, cultivated meat production has the potential to yield a marginal carbon footprint while providing sustainable and cruelty-free animal protein. The prohibitively high cost of the growth factors necessary in animal cell culture media constitutes the primary barrier that hinders the economically viable production of cultivated meat products. Furthermore, scaffolding is required to create structured meat products, but current options are unsuitable for cost-effective large-scale production of cultivated meat. Novel Farms has developed a proprietary technology to produce scaffolding that has the potential to reduce production costs while providing an ideal 3D surface for cell growth. Developing cost-efficient methods for cultivated meat production will be vital in satisfying the growing demand for animal protein while avoiding the deforestation, carbon emissions, biodiversity loss and other negative outcomes of industrial animal farming.

59 BASIC BIOLOGICAL SCIENCES↗

Detecting multi‐scale riverine topographic variability and its influence on Chinook salmon habitat selection

Abstract Quantifying geomorphic conditions that impact riverine ecosystems is critical in river management due to degraded riverine habitat, changing flow and thermal conditions, and increasing anthropogenic pressure. Geomorphic complexity at different scales directly impacts habitat heterogeneity and affects aquatic biodiversity resilience. Here we showed that the combination of continuous spatial survey at high resolution, topobathymetric light detection and ranging (LiDAR), and continuous wavelet analysis can help identify and characterize that complexity. We used a continuous wavelet analysis on 1‐m resolution topobathymetry in three rivers in the Salmon River Basin, Idaho (USA), to identify different scales of topographic variability and the potential effects of this variability on salmonid redd site selection. On each river, wavelet scales characterized the topographic variability by portraying repeating patterns in the longitudinal profile. We found three major representative spatial wavelet scales of topographic variability in each river: a small wavelet scale associated with local morphology such as pools and riffles, a mid‐wavelet scale that identified larger channel unit features, and a large wavelet scale related to valley‐scale controls. The small wavelet scale was used to identify pools and riffles along the entire lengths of each river as well as areas with differing riffle‐pool development. Areas along the rivers with high local topographic variability (high wavelet power) at all wavelet scales contained the largest features (i.e., deepest or longest pools) in the systems. By comparing the wavelet power for each wavelet scale to Chinook salmon redd locations, we found that higher small‐scale wavelet power, which is related to pool‐riffle topography, is important for redd site selection. The continuous wavelet methodology objectively identified scales of topographic variability present in these rivers, performed efficient channel‐unit identification, and provided geomorphic assessment without laborious field surveys.

Duffin, Jenna↗

Biodiversity and Ecology of Amphibians and Reptiles of the Kennedy Space Center: 1998 Close-Out Report to NASA

Since 1992, there have been researchers have been studying the population ecology and conservation biology of the amphibians and reptiles of the Kennedy Space Center (KSC) This research is an outgrowth of my Master's work in the late 1970's under Lew Ehrhart at UCF. The primary emphasis of our studies are (1) examination of long-term changes in the abundance of amphibians and reptile populations, (2) occurrence and effects of Upper Respiratory Tract Disease (URTD) in gopher tortoises (Gopherus polyphemus), and (3) ecological studies of selected species.

Sigel, Richard A.↗

Transcriptomic and functional analyses uncover a conserved effector driving genotype-dependent virulence in the Sphaerulina musiva-Populus trichocarpa interaction

The introduction of invasive microbes compromises the structure, biodiversity, and function of naïve ecosystems. Sphaerulina musiva, a hemibiotrophic pathogen that causes leaf spot and stem cankers in Populus species, exemplifies an invasive fungal pathogen spread by human activities. However, the genetic mechanisms of pathogenicity and virulence are poorly understood, impeding mitigation strategies. We utilized RNA sequencing to identify fungal effectors linked to stem canker formation, informing the development of future strategies for effective disease management. Our analysis revealed 70 genes differentially expressed at 2 weeks and 110 genes at 3 weeks between inoculated trees and controls. Notably, the gene with the highest expression at 2 weeks and the second highest at 3 weeks was homologous to Extracellular protein 2 (Ecp2). Complementary genome-wide association studies linked sequence polymorphisms in this locus to phenotypic variation in disease severity. Infiltration of S. musiva Ecp2 into Populus trichocarpa leaves induced necrosis in susceptible genotypes. Gene disruption using a CRISPR-Cas9 RNP system resulted in a genotype-dependent reduction of stem canker and disease severity. Tracing the evolutionary history of this effector across the fungal kingdom, we uncovered clade-specific gene-family expansions and orthologs in new species. These findings raise questions about the function and adaptive significance of these gene families in fungal lifestyles. Our study provides the first tractable target for breeding resistant poplar genotypes, addressing the challenges of managing S. musiva and uncovering mechanisms that drive its virulence, and provides deeper insights into the evolutionary dynamics of a conserved small-secreted protein with a diversity of functions.

Sondreli, Kelsey L [Oregon State University]↗

Soil disturbance and invasion magnify CO 2 effects on grassland productivity, reducing diversity

Climate change, disturbance, and plant invasion threaten grassland ecosystems, but their combined and interactive effects are poorly understood. Here, in this study, we examine how the combination of disturbance and plant invasion influences the sensitivity of mixed-grass prairie to elevated carbon dioxide (eCO 2 ) and warming. We established subplots of intact prairie and disturbed/invaded prairie within a free-air CO 2 enrichment (to 600 ppmv) by infrared warming (+1.5°C day, 3°C night) experiment and followed plant and soil responses for 5 years. Elevated CO 2 initially led to moderate increases in biomass and plant diversity in both intact and disturbed/invaded prairie, but these effects shifted due to strong eCO 2 responses of the invasive forb Centaurea diffusa. In the final 3 years, biomass responses to eCO 2 in disturbed/invaded prairie were 10 times as large as those in intact prairie (+186% vs. +18%), resulting in reduced rather than increased plant diversity (-17% vs. +10%). At the same time, warming interacted with disturbance/invasion and year, reducing the rate of topsoil carbon recovery following disturbance. The strength of these interactions demonstrates the need to incorporate disturbance into predictions of climate change effects. In contrast to expectations from studies in intact ecosystems, eCO 2 may threaten plant diversity in ecosystems subject to soil disturbance and invasion.

54 ENVIRONMENTAL SCIENCES↗

Triton Field Trials - Changes in Habitats, a Literature Review of Monitoring Technologies

Marine energy devices are installed in highly dynamic environments and have the potential to affect benthic and pelagic habitats around them. Regulatory bodies often require baseline characterization and/or post-installation monitoring to determine whether changes in these habitats are being observed. However, a great diversity of technologies is available for surveying and sampling marine habitats. Selecting the most suitable instrument to identify and measure changes in habitats at marine energy sites can become a daunting task. We conducted a thorough review of journal articles, survey reports, and grey literature to extract information about the technologies used, the data collection and processing methods, and the performance and effectiveness of these instruments. We examined documents related to marine energy development, offshore wind farms, oil and gas offshore sites, and other marine industries around the world over the last 20 years, as well as national and international guidelines for surveying habitats around offshore activities. A total of 120 different technologies were identified across six main habitat categories: seafloor, sediment, infauna, epifauna, pelagic, and biofouling. The technologies were organized into 12 broad technology classes: acoustic, corer, dredge, grab, hook and line, net and trawl, plate, remote sensing, scrape samples, trap, visual, and others. Visual was the most common and the most diverse technology class, with applications across all six habitat categories. Sampling designs varied considerably among the reviewed studies but transect was the predominant design for surveying seafloor, epifauna, and pelagic habitats. The most common data analyses were univariate and multivariate statistical analyses aimed at calculating and comparing biodiversity indices, characterizing faunal assemblages or sediment classes, or modeling the distribution of animals related to abiotic parameters. Technologies and sampling methods adaptable and designed to work efficiently in energetic environments have greater success at marine energy sites. In addition, sampling designs and statistical analyses should be carefully thought through to identify differences in faunal assemblages and spatiotemporal changes in habitats.

16 TIDAL AND WAVE POWER↗

Restoring Soil Fertility on Degraded Lands to Meet Food, Fuel, and Climate Security Needs via Perennialization

A continuously growing pressure to increase food, fiber, and fuel production to meet worldwide demand and achieve zero hunger has put severe pressure on soil resources. Abandoned, degraded, and marginal lands with significant agricultural constraints—many still used for agricultural production—result from inappropriately intensive management, insufficient attention to soil conservation, and climate change. Continued use for agricultural production will often require ever more external inputs such as fertilizers and herbicides, further exacerbating soil degradation and impeding nutrient recycling and retention. Growing evidence suggests that degraded lands have a large potential for restoration, perhaps most effectively via perennial cropping systems that can simultaneously provide additional ecosystem services. Here we synthesize the advantages of and potentials for using perennial vegetation to restore soil fertility on degraded croplands, by summarizing the principal mechanisms underpinning soil carbon stabilization and nitrogen and phosphorus availability and retention. We illustrate restoration potentials with example systems that deliver climate mitigation (cellulosic bioenergy), animal production (intensive rotational grazing), and biodiversity conservation (natural ecological succession). Perennialization has substantial promise for restoring fertility to degraded croplands, helping to meet future food security needs.

54 ENVIRONMENTAL SCIENCES↗