16 Feb 2024

Assessing the Genetic Diversity of Nymphoides peltata in the Native and Adventive Range Using Microsatellite Markers

Abstract: Nymphoides peltata (yellow floatingheart), native to Eurasia, is an invasive plant in the USA, where it grows in relatively isolated but widespread populations. The species is capable of sexual reproduction by seed and asexual reproduction through fragmentation. Although N. peltata is recognized as a noxious weed, little is known about its geographic region of origin or its dispersal mechanisms and relative amount of genetic variation in its adventive range. We conducted a genetic analysis of N. peltata by studying 68 localities across the native range and 47 localities in the adventive range, using microsatellite markers to determine genetic variability within and among populations, and to infer regions in the native range from which invasive plants originated. A large number of sites in the USA were genetically identical to one another, and there were two predominant multilocus allele phenotypes that were distributed in the northern and southern latitudes, respectively. Additional USA sites were similar to one of the predominant genetic profiles, with greater genetic diversity in southern populations. The genetically identical sites are consistent with asexual spread, potentially via anthropogenic mechanisms. Plants across the USA range were observed to produce viable seeds, and some genetic variation could be explained by sexual reproduction. All USA plants were more similar to plants in Europe than they were to plants in Asia, indicating that the plants likely were introduced originally from Europe. The existence of two genetic clusters and their similarity to plants in different parts of Europe constitute evidence for at least two N. peltata introductions into the USA.

16 Feb 2024

Deep Learning Methods for Omics Data Imputation

Abstract: One common problem in omics data analysis is missing values, which can arise due to various reasons, such as poor tissue quality and insufficient sample volumes. Instead of discarding missing values and related data, imputation approaches offer an alternative means of handling missing data. However, the imputation of missing omics data is a non-trivial task. Difficulties mainly come from high dimensionality, non-linear or non-monotonic relationships within features, technical variations introduced by sampling methods, sample heterogeneity, and the non-random missingness mechanism. Several advanced imputation methods, including deep learning-based methods, have been proposed to address these challenges. Due to its capability of modeling complex patterns and relationships in large and high-dimensional datasets, many researchers have adopted deep learning models to impute missing omics data. This review provides a comprehensive overview of the currently available deep learning-based methods for omics imputation from the perspective of deep generative model architectures such as autoencoder, variational autoencoder, generative adversarial networks, and Transformer, with an emphasis on multi-omics data imputation. In addition, this review also discusses the opportunities that deep learning brings and the challenges that it might face in this field.

16 Feb 2024

A Comprehensive Review on Wood Chip Moisture Content Assessment and Prediction

Abstract: Wood chips are the primary sources of raw materials for numerous industries, including pelleting mills, biorefineries, pulp-and-paper industries, and biomass-based power generation facilities. Unfortunately, when wood chips are utilized as a renewable and environmentally friendly resource, industries are constantly challenged by the consistency of the wood chip qualities (e.g., moisture/ash contents, size distributions) - a historically recognized problem on a global scale. Among other wood chip quality attributes, the moisture content is considered the most pressing one as it directly impacts the energy content, storage stability, and handling properties of the raw and finished products. Therefore, accurate wood chip moisture content prediction can help optimize the drying process and reduce energy consumption. In this review, a survey was conducted on various techniques and models employed for predicting wood chip moisture content. The advantages and limitations of these approaches, as well as their potential applications and future directions were also discussed. This review aims to provide a comprehensive overview of the current state-of-the-art in wood chip moisture content prediction and to highlight the challenges and opportunities for further research and development in this field.

14 Feb 2024

Hydraulic Sorting of Dredged Sediment in a Pipeline: An Evaluation of the Sediment Distribution Pipe

Abstract: The US Army Corps of Engineers (USACE) recently established a goal to beneficially use 70% of material dredged from the nation’s navigable waterways by the year 2030. Most of the sediments dredged by the USACE are heterogeneous mixtures of mud and sand, which can limit beneficial use of dredged material (BUDM) applications. Innovative technologies that can sort material during the dredging process are needed to help increase BUDM practices. This investigation sought to evaluate the ability of a sediment distribution pipe (SDP) to sort particles during transport in a pipeline. Field demonstrations were conducted during dredged material placements at Sturgeon Island, New Jersey. Velocity within the pipeline was found to be inadequate for efficient hydraulic sorting of fines (<75 μm) and produced inconclusive results. Small scale laboratory SDP experiments found that effluent from the SDP holes had an altered sediment texture compared to the initial slurry and that hydraulic sorting was occurring within the pipeline. However, outflow from the SDP holes was inconsistent, and typically >90% of the sediment mass was discharged out the end of the pipeline. Sorting efficiency of the SDP could not be accurately assessed in the current experimental configuration.

9 Feb 2024

Overview of Microscale Analytical Methods for the Quantitative Detection of Bioaccumulative Contaminants in Small Tissue Masses

Abstract: For many bioaccumulation studies, generation of large sample masses of exposed organisms is challenging or even prohibitive. Therefore, the use of smaller sample masses for analysis without compromising data quality or quantitative level achieved is desirable. To this end, a variety of microanalytical procedures have been developed that used 1 g or less of tissue to address specific experimental challenges. However, these methods have not been systematically evaluated or published. The present work evaluates the current state of the microanalytical methods reported and identifies additional needs that would benefit US Army Corps of Engineers (USACE) research and navigation dredging programs. Discussions with commercial laboratories revealed that they typically do not accept small sample masses and require individual sample masses ranging from 10 to 20 g wet weight of tissue per analysis. If they do analyze a small mass sample, they routinely do not modify their standard process, resulting in detection and reporting limits orders of magnitude higher; therefore, essentially useless nondetect data are generated for regulatory decisions. To address the lack of commercial availability of microanalytical methods, we recommend pursuing method development and subsequent validation of microscale extraction and analysis of a variety of common contaminant compounds in tissue matrices.

7 Feb 2024

Ecological Modeling of Microbial Community Composition under Variable Temperatures

Abstract: Soil microorganisms interact with one another within soil pores and respond to external conditions such as temperature. Data on microbial community composition and potential function are commonly generated in studies of soils. However, these data do not provide direct insight into the drivers of community composition and can be difficult to interpret outside the context of ecological theory. In this study, we explore the effect of abiotic environmental variation on microbial species diversity. Using a modified version of the Lotka-Volterra Competition Model with temperature-dependent growth rates, we show that environmentally relevant temperature variability may expand the set of temperature-tolerance phenotype pairs that can coexist as two-species communities compared to constant temperatures. These results highlight a potential role of temperature variation in influencing microbial diversity. This in turn suggests a need to incorporate temperature into predictive models of microbial communities in soil and other environments. We recommend future work to parameterize the model applied in this study with empirical data from environments of interest, and to validate the model predictions using field observations and experimental manipulations.

6 Feb 2024

USACE Freshwater Harmful Algal Bloom Research and Development Initiative

Abstract: Harmful Algal Blooms (HABs) represent a significant and costly threat to our nation’s economy and natural resources. This report outlines the US Army Corps of Engineers, Engineer Research and Development Center’s (USACE-ERDC’s) approach to deliver scalable technologies for prevention, early detection, and management of HABs to reduce HAB event frequency, severity, and duration.

6 Feb 2024

Dynamic Tensile Behavior of Laser-Directed Energy Deposition and Additive Friction Stir-Deposited AerMet 100

Abstract: Quasi-static and high-rate tensile experiments were used to examine the strain rate sensitivity of laser-directed energy deposition (L-DED)- and additive friction stir deposition (AFSD)-formed AerMet 100 ultrahigh-strength steel-additive manufactured builds. Electron backscattered diffraction (EBSD) revealed similar as-deposited grain sizes between the two AM processes at approximately 24 µm and 17 µm for the L-DED and AFSD samples, respectively. The strain hardening rate, θ, revealed little change in the overall hardening observed in the L-DED and AFSD materials, with a consistent hardening in the quasi-static samples and three identifiable regions in that of the high-rate tested materials. The L-DED deposited materials displayed average ultimate tensile strength values of 1835 and 2902 MPa for the 0.001 s−1 and 2500 s−1 strain rates, respectively and the AFSD deposited materials displayed ultimate tensile strength values of 1928 and 3080 MPa for the 0.001 s−1 and 2500 s−1 strain rates, respectively. Overall, the strength for both processes displayed a positive strain rate sensitivity, with increases in strength of ~1000 MPa for both processes. Fractography revealed significant solidification voids in the laser DED material and poor layer adhesion in the AFSD material.

2 Feb 2024

Extreme Cold Weather Airfield Damage Repair Testing at Goose Bay Air Base, Canada

Abstract: Rapid Airfield Damage Recovery (RADR) technologies have proven successful in temperate and subfreezing temperatures but have not been evaluated in extreme cold weather temperatures near 0°F. To address this capability gap, laboratory-scale and full-scale testing was conducted at these temperatures. Methods developed for moderate climates were adapted and demonstrated alongside methods that used snow harvested on-site as compacted backfill. After only a few days of training, seven experimental repairs were conducted by Canadian airmen at Goose Bay Air Base in Labrador, Canada, and load tested with a single-wheel C-17 load cart. Existing RADR technologies performed adequately despite the freezing temperatures, with the main tactic, techniques, and procedures modification being an increased cure time for the rapid-setting concrete surface material. Compacted snow-water slurry methods also performed well, demonstrating their ability to withstand over 500 passes of single-wheel C-17 traffic after sufficient freezing time.

2 Feb 2024

The Influence of Mesoscale Atmospheric Convection on Local Infrasound Propagation

Abstract: Infrasound—that is, acoustic waves with frequencies below the threshold of human hearing—has historically been used to detect and locate distant explosive events over global ranges (≥1,000 km). Simulations over these ranges have traditionally relied on large-scale, synoptic meteorological information. However, infrasound propagation over shorter, local ranges (0–100 km) may be affected by smaller, mesoscale meteorological features. To identify the effects of these mesoscale meteorological features on local infrasound propagation, simulations were conducted using the Weather Research and Forecasting (WRF) meteorological model to approximate the meteorological conditions associated with a series of historical, small-scale explosive test events that occurred at the Big Black Test Site in Bovina, Mississippi. These meteorological conditions were then incorporated into a full-wave acoustic model to generate meteorology-informed predictions of infrasound propagation. A series of WRF simulations was conducted with varying degrees of horizontal resolution—1, 3, and 15 km—to investigate the spatial sensitivity of these infrasound predictions. The results illustrate that convective precipitation events demonstrate potentially observable effects on local infrasound propagation due to strong, heterogeneous gradients in temperature and wind associated with the convective events themselves. Therefore, to accurately predict infrasound propagation on local scales, it may be necessary to use convection-permitting meteorological models with a horizontal resolution ≤4 km at locations and times that support mesoscale convective activity.