COS Faculty Works

Permanent URI for this collectionhttps://hdl.handle.net/1969.6/87602

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Mathematics education researchers’ practices in interdisciplinary collaborations: Embracing different ways of knowing
(2024-03-21) Suazo-Flores, Elizabeth; Walker III, William S.; Kastberg, Signe E.; Aqazade, Mahtob; Alyami, Hanan
Mathematics education researchers (MERs) use practices unique to the mathematics education discipline to conduct their work. MERs’ practices, i.e., ways of being, interacting, and operating, define the field of mathematics education, are initially learned in doctoral preparation programs, and are encouraged and sanctioned by conferences and publications. Disciplinary practices facilitate MERs’ interactions within mathematics education. When working in interdisciplinary groups, differences in disciplinary ways of being, interacting, and operating can create challenges with completing research and other work. Since MERs’ engagement in interdisciplinary collaborations is encouraged and can result in products contributing to the evolution of the mathematics education discipline, it is important to explore what practices MERs use in interdisciplinary collaborations. We interviewed four MERs who led international interdisciplinary collaborations and used qualitative content analysis to create descriptions of practices described by MERs in their collaborations. Five practices were common between the MERs in interdisciplinary collaborations. MERs conducted interdisciplinary work by using practices that allowed them to situate themselves and others in the group (i.e., being practices), develop ideas (i.e., interacting practices), work towards common goals, and use structures to get the work done (i.e., operating practices). We argue that MERs developed new practices to position themselves and others, interact with practitioners from other disciplines, and get interdisciplinary work done. This study contributes to the evolution of the mathematics education discipline by offering five practices that can orient MERs to conducting interdisciplinary work and discussing how MERs experience interdisciplinary collaborations beyond providing mathematics education expertise.
Analysing micro- and nanoplastics with cutting-edge infrared spectroscopy techniques: A critical review
(2024-03-27) Xie, Junhao; Gowen, Aoife; Xu, Wei; Xu, Junli
The escalating prominence of micro- and nanoplastics (MNPs) as emerging anthropogenic pollutants has sparked widespread scientific and public interest. These minuscule particles pervade the global environment, permeating drinking water and food sources, prompting concerns regarding their environmental impacts and potential risks to human health. In recent years, the field of MNP research has witnessed the development and application of cutting-edge infrared (IR) spectroscopic instruments. This review focuses on the recent application of advanced IR spectroscopic techniques and relevant instrumentation to analyse MNPs. A comprehensive literature search was conducted, encompassing articles published within the past three years. The findings revealed that Fourier transform infrared (FTIR) spectroscopy stands as the most used technique, with focal plane array FTIR (FPA-FTIR) representing the cutting edge in FTIR spectroscopy. The second most popular technique is quantum cascade laser infrared (QCL-IR) spectroscopy, which has facilitated rapid analysis of plastic particles. Following closely is optical photothermal infrared (O-PTIR) spectroscopy, which can furnish submicron spatial resolution. Subsequently, there is atomic force microscopy-based infrared (AFM-IR) spectroscopy, which has made it feasible to analyse MNPs at the nanoscale level. The most advanced IR instruments identified in articles covered in this review were compared. Comparison metrics encompass substrates/filters, data quality, spatial resolution, data acquisition speed, data processing and cost. The limitations of these IR instruments were identified, and recommendations to address these limitations were proposed. The findings of this review offer valuable guidance to MNP researchers in selecting suitable instrumentation for their research experiments, thereby facilitating advancements in research aimed at enhancing our understanding of the environmental and human health risks associated with MNPs.
Insights into glacial processes from micromorphology of silt-sized sediment
(2023-06-20) Lepp, Allison P.; Miller, Lauren E.; Anderson, John B.; O'Regan, Matt; Winsborrow, Monica C.M.; Smith, James A.; Hillenbrand, Claus-Dieter; Wellner, Julia S.; Prothro, Lindsay O.; Podolskiy, Evgeny A.
Meltwater plume deposits (MPDs) from marine sediment cores have elucidated clearly connected, yet difficult to constrain, relationships between ice-marginal landform construction, grounding-zone retreat patterns, and subglacial hydrology for several glacial systems in both hemispheres. Few attempts have been made, however, to infer coveted details of subglacial hydrology, such as flow regime, drainage style, and mode(s) of sediment transport through time from grain-scale characteristics of MPDs. Using MPD, till, and ice-proximal diamicton samples collected offshore of six modern and relict glacial systems in both hemispheres, we examine whether grain-shape distributions and microtexture assemblages (collectively, grain micromorphology) of the silt fraction are the result of subglacial meltwater action, or are indistinguishable from glacial proximal and subglacial sediments from the same region. We find that of all grains imaged (n=9,400), three-quarters can be described by one-quarter of the full range of measured shape morphometrics, indicating widespread and efficient abrasive processes in subglacial environments. Microtexture analysis reveals that while grains comprising MPDs show evidence of edge rounding more often than tills, fluvial microtextures occur in modest amounts on grain surfaces. Furthermore, MPDs retain many mechanical (i.e., glacial) textures in comparable abundances to tills. Significant alteration of MPDs from till sources is observed for systems (1) for which intensive, potentially catastrophic, meltwater drainage events in the Holocene are inferred from marine geologic records, and (2) with comparatively less mature till grains and a contribution of supraglacial melt to the bed, indicating that quantifiable grain-shape alteration of MPDs may reflect a combination of young till, high-energy flow of subglacial meltwater, persistent sediment entrainment, and/or long sediment transport distances. We encourage future works to integrate grain micromorphology into site-specific marine sediment analyses, which may distinguish periods of persistent, well-connected subglacial discharge from periods of sporadic or disorganized drainage and provide context needed to estimate sediment fluxes and characterize ice response to subglacial meltwater transmission. In addition, this work demonstrates that glacial and fluvial surface textures are retained on silts in adequate abundance for microtexture analysis.
Lower-Dimensional model of the flow and transport processes in thin domains by numerical averaging technique
(2023-12-25) Vasilyeva, Maria; Mbroh, Nana Adjoah; Mehrubeoglu, Mehrube
In this work, we present a lower-dimensional model for flow and transport problems in thin domains with rough walls. The full-order model is given for a fully resolved geometry, wherein we consider Stokes flow and a time-dependent diffusion–convection equation with inlet and outlet boundary conditions and zero-flux boundary conditions for both the flow and transport problems on domain walls. Generally, discretizations of a full-order model by classical numerical schemes result in very large discrete problems, which are computationally expensive given that sufficiently fine grids are needed for the approximation. To construct a computationally efficient numerical method, we propose a model-order-reduction numerical technique to reduce the full-order model to a lower-dimensional model. The construction of the lower-dimensional model for the flow and the transport problem is based on the finite volume method and the concept of numerical averaging. Numerical results are presented for three test geometries with varying roughness of walls and thickness of the two-dimensional domain to show the accuracy and applicability of the proposed scheme. In our numerical simulations, we use solutions obtained from the finite element method on a fine grid that can resolve the complex geometry at the grid level as the reference solution to the problem.
Commuters: A waterbird provides a new view of how species may utilize cities and wildlands
(2023-07-06) Shlepr, Katherine R; Evans, Betsy A; Gawlik, Dale E
Traditional classifications of vertebrates’ responses to urbanization fail to capture the behaviour of those that rely on both urban and wildland resources for population persistence. Here, we use the wood stork (Mycteria americana), a species that makes daily foraging trips up to 74 km away from its nest, as an example of a previously unrecognized response to urbanization. We monitored nests and sampled diets at stork colonies in south Florida (USA) during 2014–2020 to investigate how storks use urban habitats. We found that urban development now comprises up to 51.6% of the land cover within the 30-km core foraging area surrounding colonies and that storks access alternative prey types within these urban areas. Our results also showed that urban-nesting storks outperformed wildland-nesting storks when the hydrological condition of the wetlands was suboptimal for foraging. Though storks still require healthy wetlands for population persistence, urban habitat benefitted storks when hydrological patterns were not ideal for prey production in wildlands. This ‘commuter’ response to urbanization, whereby individuals opt to utilize both urban and wildland resources within short time periods, may apply to other vertebrates with large home ranges.
Analysis of the vcgC gene in Vibrio vulnificus isolates from the Texas Coastal Bend region of the Gulf of Mexico
(2023-05-12) Buck, Gregory W; Brumfield, LarReshia I; Giagnocavo, Stephanie Dudics; Perkins, Danielle S; Tortosa, Alvaro Ortola; Okuyemi, Tolulope B; Carbaugh, Joshua S; Planas Costas, Githzette M; Ramirez, Gabriel D
Vibrio vulnificus is a gram-negative, halophilic bacterium normally found in temperate marine and estuarine waters. The organism may enter wounds in the skin and cause sepsis or necrotizing fasciitis; the latter condition has a 50-60% mortality rate and may result in death or disfigurement within 4-6 days. Persons exposed to coastal flood waters during hurricanes may be at risk for this organism. The virulence-correlated gene, vcgC, is specific for clinical isolates of V. vulnificus, but the function of this locus remains unknown. This study used Polymerase Chain Reaction (PCR) and novel primers for vcgC not previously described to specifically identify V. vulnificus isolates from the Texas Coastal Bend region that may result in serious infections. Of the 28 isolates, four isolates could not be revived multiple times; crude lysates of the remaining 24 Vibrio vulnificus cultures were analyzed by PCR, and 19 were found to have amplicons of 428bp for vcgC. This study confirms the presence of the vcgC gene in V. vulnificus isolates from the Texas Coastal Bend region of the Gulf of Mexico.
A meta-analysis of disturbance caused by drones on nesting birds
(2023) Cantu de Leija, Antonio; Mirzadi, Rostam E.; Randall, Jessica M.; Portmann, Maxwell D.; Mueller, Erin J.; Gawlik, Dale E.
The use of drones for monitoring nesting birds is rapidly increasing given their affordability and efficiency in bird detection and quantification across habitats. Reports of disturbance caused by drones on different bird species have been mixed, with no consensus on the degree to which different factors affect disturbance responses. Given the lack of systematic assessments of disturbance from drones on nesting birds, we conducted a formal meta-analysis to quantify the degree of disturbance caused by multi-rotor drones on nesting birds, with a particular focus on the effects of altitude of flights and species nesting traits. Seventeen studies met our criteria for inclusion in the analysis, from which we extracted 31 effect sizes in the form of log-odds ratio. Drones showed a small disturbance effect (-1.54; 95% CI: -2.83, -0.26) on nesting birds overall, but heterogeneity was large. Drone flights > 50 m showed no evidence of disturbance on nesting birds. Conversely, flights at lower altitudes (≤ 50 m) showed stronger evidence of disturbance effects, with the largest odds of disturbance observed on ground solitary and non-ground solitary nesters. Only ground colonial nesters showed no evidence of disturbance regardless of the drone altitude. We conclude that the use of drones can be an efficient and safe means of surveying nesting birds if altitude and nesting traits are considered in survey protocols. RESUMEN. El uso de drones para monitorear las aves que anidan está aumentando rápidamente dada su asequibilidad y eficiencia en la detección y cuantificación de aves en todos los hábitats. Los informes de perturbaciones causadas por drones en diferentes especies de aves han sido mixtos, sin consenso sobre el grado en que los diferentes factores afectan las respuestas de perturbación. Dada la falta de evaluaciones sistemáticas de la perturbación de los drones en las aves que anidan, realizamos un metanálisis formal para cuantificar el grado de perturbación causada por drones multirotor en las aves que anidan, haciendo foco en particular en los efectos de la altitud de los vuelos y los rasgos de anidación de las especies. Diecisiete estudios cumplieron los criterios de inclusión en el análisis, de los cuales se extrajeron 31 tamaños del efecto en forma de relación logarítmica de probabilidades. Los drones mostraron un pequeño efecto de perturbación (-1,54; IC del 95%: -2,83, -0,26) en las aves que anidan en general, pero la heterogeneidad fue grande. Los vuelos de drones > 50 m no mostraron evidencia de perturbación en las aves que anidan. Por el contrario, los vuelos a altitudes más bajas (≤ 50m) mostraron una mayor evidencia de efectos de perturbación, con las mayores probabilidades de perturbación observadas en anidadores solitarios y no terrestres. Solo los anidadores coloniales terrestres no mostraron evidencia de perturbación, independientemente de la altitud del dron. Concluimos que el uso de drones puede ser un medio eficiente y seguro para inspeccionar las aves que anidan si la altitud y los rasgos de anidación se consideran en los protocolos de monitoreo.
Image analysis reveals environmental influences on the seagrass-epiphyte dynamic relationship for Thalassia testudinum in the northwestern Gulf of Mexico
(2023-01-16) Huang, Chi; Piñón, Carissa; Mehrubeoglu, Mehrube; Cammarata, Kirk
Spatiotemporal patterns in seagrass-epiphyte dynamics for Thalassia testudinum in the northwestern Gulf of Mexico were evaluated through biomass measurements and scanned-image based metrics to investigate the potentially harmful impact of excessive epiphyte accumulations on seagrass condition. Image analysis with Spectral Angle Mapper algorithms distinguished epiphyte and uncovered seagrass leaf pixels to generate a normalized metric of leaf area coverage (epiphyte pixels/total leaf pixels). Imaging metrics were compared to biomass based metrics seasonally, among three locations with different environmental conditions (depth, salinity, temperature and nutrient levels inferred from sediment porewater measurements) near Redfish Bay, Texas, USA. Image analysis, in conjunction with biomass measures, provides enhanced insight into the seagrass-epiphyte dynamic relationship and how it varies with environmental conditions. Compared with the biomass and morphological measures, image analysis may be more informative as an indicator of environmental changes. Variation in linear regressions of epiphyte biomass vs. epiphyte area (pixels) suggested changes in the thickness and/or density of accumulated epiphytes across environmental contexts and seasons. Two different epiphyte colonization patterns were presented based on the correlation between the normalized metrics of epiphyte load and epiphyte leaf coverage. The epiphyte load was highest at low temperatures and locations with elevated DIN:P ratio in sediment porewater. Conversely, the mean leaf coverage by epiphytes stayed relatively constant (±10%) across seasons but differed by location (25% ~55% in this case), suggesting that leaf growth in this study is regulated to maintain the proportion of uncolonized leaf surface and that epiphyte coverage plays a role in its regulation.
Economic pressures of COVID-19 lockdowns result in increased timber extraction within a critically endangered region: A case study from the Pacific Forest of Ecuador
(2022-11-22) Tleimat, Jacquelyn M.; Fritts, Sarah R.; Brunner, Rebecca M.; Rodriguez, David; Lynch, Ryan L.; McCracken, Shawn F.
Although the COVID-19 lockdowns in 2020 had some environmental benefits, the pandemic's impact on the global economy has also had conservation repercussions, especially in biodiverse nations. Ecuador, which is heavily reliant on petroleum, agricultural exports, and ecotourism, experienced a rise in poverty in response to pandemic shutdowns. In this study, we sought to quantify levels of illegal timber extraction and poaching before and after the start of COVID-19 lockdowns throughout two protected areas (Reserva Jama Coaque [JCR] and Bosque Seco Lalo Loor [BSLL]) in the endangered Pacific Forest of Ecuador. We analyzed chainsaw and gunshot acoustic data recorded from devices installed in the forest canopy from December 2019 to March 2020 and October 2020 to March 2021. Results from generalized linear mixed effects models indicated less chainsaw activity before lockdowns (βpost. lockdown = 0.568 ± 0.266 SE, p-value = .030), although increased average rainfall also seemed to negatively affect chainsaw activity (βavg.rainfall = −0.002 ± 0.0006 SE, pvalue = .003). Gunshots were too infrequent to conduct statistical models; however, 87% of gunshots were detected during the ‘lockdown’ period. Observational data collected by rangers from these protected areas also noted an increase in poaching activities beginning mid to late 2020 and persisting into 2021. These results add to the steadily growing literature indicating an increase in environmental crime, particularly in biodiverse nations, catalyzed by COVID-19-related economic hardships. Identifying areas where environmental crime increased during pandemic lockdowns is vital to address both socioeconomic drivers and enforcement deficiencies to prevent further biodiversity loss and disease outbreaks and to promote ecosystem resilience. Our study also demonstrates the utility of passive acoustic monitoring to detect illegal resource extraction patterns, which can inform strategies such as game theory modeling for ranger patrol circuits and placement of real-time acoustic detection technologies to monitor and mitigate environmental crimes.
Seagrass response to wastewater inputs: Implementation of a seagrass monitoring program in two Texas estuaries
(2011-02-25) Cammarata, Kirk
The study protocol followed a recent proposal by Dunton and Pulich to the Seagrass Monitoring Work Group (Landscape Monitoring and Biological Indicators for Seagrass Conservation in Texas Coastal Waters, draft, Dunton et al. 2007) and included three components: 1) landscape monitoring using high resolution color aerial photography, 2) seagrass condition and water quality indicators, and 3) seagrass epiphyte fluorescence analysis. Findings from the third objective are presented here.
Experimental and theoretical screening of core gold nanoparticles and their binding mechanism to an anticancer drug, 2-Thiouracil
(2023-12-24) Lorenzana-Vazquez, Genesis; Adams, Daniel G.; Reyna, Lauren G.; Melendez, Enrique; Pavel, Ioana E.
This study demonstrated the capability of two readily available optical spectroscopy tools, namely UV-Vis absorption spectrophotometry and Raman/surface-enhanced Raman spectroscopy, to select in a rapid and noninvasive manner the most homogenous gold nanoparticle (AuNP) models and to identify their chemical binding mechanism to 2-thiouracil (2-TU). 2-TU is an anticancer drug of great promise in the antiproliferative and photothermal therapies of cancer. The citrate-capped AuNPs emerged as the most stable as well as time- and cost-effective AuNP model out of the three widely used colloidal nanocores (citrate-, borohydride-citrate-, and sodium dodecyl sulfate (SDS)- capped AuNPs) that were examined. 2-TU chemically attached to the relatively monodispersed AuNPs via a chemisorption mechanism. The 2-TU-AuNPs complex formed through the covalent bonding of the S atom of 2-TU to the nanosurface in a vertical orientation. The spectroscopic results were then confirmed with the help of density functional theory (DFT) calculations and other physicochemical characterization tools for nanomaterials such as transmission electron microscopy (TEM), dynamic light scattering (DLS), and zeta potential. Overall, the purified 2-TU-AuNPs were found to be spherical, had an average diameter of 25 ± 2 nm, a narrow size distribution (1–30 nm), a sharp localized surface plasmon resonance (LSPR) peak at 525 nm, and a negative surface charge (−14 mV).
Long-term vertical-land-motion investigation with space and terrestrial geodetic techniques near San Leon, Texas, USA
(2023-11-22) Qiao, Xiaojun; Chu, Tianxing; Tissot, Philippe; Holland, Seneca
Monitoring vertical land motion (VLM) along coastlines, which influences the dynamics of sea level changes in relation to the land, is a challenging task due to its inherent high spatiotemporal variability and limited availability of observations. This study aimed to investigate the rates, patterns, and drivers of land subsidence near the coastal town of San Leon, TX, United States, since the 1990s, utilizing a range of space and terrestrial geodetic techniques. These techniques included interferometric synthetic aperture radar (InSAR), global navigation satellite systems (GNSS), tide gauge (TG), and satellite radar altimetry (SRA). The small baseline subset (SBAS) InSAR method was adopted to process 254 images from three synthetic aperture radar (SAR) sensors, i.e., ERS-2 between 1995 and 1999, ALOS-1 PALSAR between 2006 and 2011, and Sentinel-1 between 2016 and 2020. The results from InSAR subsidence maps were verified by comparing with high-accuracy vertical positioning observations at ten continuously operating GNSS (cGNSS) stations. Within the study area, a special attention was given to the Eagle Point TG station where sea level has been significantly rising relative to the sinking land. Long-term time series of land subsidence at Eagle Point obtained from sea-level difference between TG and SRA observations were confirmed and compared against InSAR and the cGNSS station observations recorded in close proximity. Gaussian Process regression (GPR) was then employed to model the VLM processes at Eagle Point using: (1) the combined results of InSAR and sea-level difference (i.e., GPR 1), and (2) the InSAR results alone (i.e., GPR 2). A 0.9 mm/yr divergence was found between GPR 1 and GPR 2 models, indicating the potential to accurately estimate long-term VLM with InSAR standalone measurements even if multi-year observation gaps intermittently occur, especially for inland areas where measurement data from other geodetic techniques, such as GNSS, TG, and SRA, are not available. Further investigations suggest that land subsidence around Eagle Point since 1998 was related to anthropogenic activities such as hydrocarbon pumping from oil and gas wells that were situated in close proximity to the TG station.
A 10-year Metocean dataset for Laguna Madre, Texas, including for the study of extreme cold events
(2023-11-28) White, Miranda C.; Vicens-Miquel, Marina; Tissot, Philippe; Krell, Evan
Coastal observations along the Texas coast are valuable for many stakeholders in diverse domains. However, the management of the collected data has been limited, creating gaps in hydrological and atmospheric datasets. Among these, water and air temperature measurements are particularly crucial for water temperature predictions, especially during freeze events. These events can pose a serious threat to endangered sea turtles and economically valuable fish, which can succumb to hypothermic stunning, making them vulnerable to cold-related illness or death. Reliable and complete water and air temperature measurements are needed to provide accurate predictions of when cold-stunning events occur. To address these concerns, the focus of this paper is to describe the method used to create a complete 10-year dataset that is representative of the upper Laguna Madre, TX using multiple stations and various gap-filling methods. The raw datasets consist of a decade’s worth of air and water temperature measurements within the Upper Laguna Madre from 2012 to 2022 extracted from the archives of the Texas Coastal Ocean Observation Network and the National Park Service. Large portions of data from the multiple stations were missing from the raw datasets, therefore a systematic gap-filling approach was designed and applied to create a near-continuous dataset. The proposed imputation method consists of three steps, starting with a short gap interpolation method, followed by a long gap-filling process using nearby stations, and finalized by a second short gap interpolation method. This systematic data imputation approach was evaluated by creating random artificial gaps within the original datasets, filling them using the proposed data imputation method, and assessing the viability of the proposed methods using various performance metrics. The evaluation results help to ensure the reliability of the newly imputed dataset and the effectiveness of the data imputation method. The newly created dataset is a valuable resource that transcends the local cold-stunning issue, offering viable utility for analyzing temporal variability of air and water temperatures, exploring temperature interdependencies, reducing forecasting uncertainties, and refining natural resource and weather advisory decision-making processes. The cleaned dataset with minimal gaps (<2%) is ready and convenient for artificial intelligence and machine learning applications.
Diurnal precipitation features over complex terrains along the Yangtze River in China based on long-term TRMM and GPM radar products
(7/7/2023) Zhu, Suxing; Liu, Chuntao; Cao, Jie; Lavigne, Thomas
Based on the 20-year high-resolution precipitation data from TRMM and GPM radar products, diurnal features over complex terrains along the Yangtze River (YR) are investigated. Using the Fast Fourier Transform (FFT) method, the first (diurnal) and second (semi-diurnal) harmonic amplitude and phase of precipitation amount (PA), precipitation frequency (PF), and intensity (PI) are analyzed. The diurnal amplitudes of PA and PF have a decreasing trend from the west to the east with the decreasing altitude of large-scale terrain, while the semi-diurnal amplitudes of PA and PI depict the bimodal precipitation cycle over highlands. For the eastward propagation of PA, PF is capable of depicting the propagation from the upper to the middle reaches of YR, while PI shows the eastward propagation from the middle to the lower reaches of YR during nighttime and presents sensitivity to highlands and lowlands. According to the contribution of different-sized precipitation systems to PI over the highlands and lowlands, the small (6000 km2 ) contribute the most, but the medium ones (200â€“6000 km2 ) show a slightly larger contribution over the highlands than over the lowlands. The propagation of each scaled precipitation system along the YR is further analyzed. We found that small precipitation systems mainly happen in the afternoon without obvious propagation. Medium ones peak 2â€“4 h later than the small ones, with two eastward propagation directions at night from the middle reaches of YR to the east. The large ones are mainly located in lowlands at night, with two propagation routes in the morning over the middle and lower reaches of YR. Such a relay of the propagation of the medium and large precipitation systems explains the eastward movement of PI along the YR, which merits future dynamic studies.
Multiscale model reduction with local online correction for polymer flooding process in heterogeneous porous media
(7/13/2023) Vasilyeva, Maria; Spiridonov, Denis
In this work, we consider a polymer flooding process in heterogeneous media. A system of equations for pressure, water saturation, and polymer concentration describes a mathematical model. For the construction of the fine grid approximation, we use a finite volume method with an explicit time approximation for the transports and implicit time approximation for the flow processes. We employ a loose coupling approach where we first perform an implicit pressure solve using a coarser time step. Subsequently, we execute the transport solution with a minor time step, taking into consideration the constraints imposed by the stability of the explicit approximation. We propose a coupled and splitted multiscale method with an online local correction step to construct a coarse grid approximation of the flow equation. We construct multiscale basis functions on the offline stage for a given heterogeneous field; then, we use it to define the projection/prolongation matrix and construct a coarse grid approximation. For an accurate approximation of the nonlinear pressure equation, we propose an online step with calculations of the local corrections based on the current residual. The splitted multiscale approach is presented to decoupled equations into two parts related to the first basis and all other basis functions. The presented technique provides an accurate solution for the nonlinear velocity field, leading to accurate, explicit calculations of the saturation and concentration equations. Numerical results are presented for two-dimensional model problems with different polymer injection regimes for two heterogeneity fields.
Evidence of population-level impacts and resiliency for Gulf of Mexico shelf taxa following the Deepwater Horizon oil spill
(2023-08-02) Patterson III, William F.; Robinson, Kelly Lynn; Barnett, Beverly K.; Campbell, Matthew D.; Chagaris, David C.; Chanton, Jeffrey P.; Daly, Kendra L.; Hanisko, David S.; Hernandez Jr., Frank J.; Murawski, Steven A.; Pollack, Adam G.; Portnoy, David S.; Pulster, Erin L.
The goal of this paper was to review the evidence of population-level impacts of the Deepwater Horizon Oil Spill (DWH) on Gulf of Mexico (GOM) continental shelf taxa, as well as evidence of resiliency following the DWH. There is considerable environmental and biological evidence that GOM shelf taxa were exposed to and suffered direct and indirect impacts of the DWH. Numerous assessments, from mesocosm studies to analysis of biopsied tissue or tissue samples from necropsied animals, revealed a constellation of physiological effects related to DWH impacts on GOM biota, some of which clearly or likely resulted in mortality. While the estimated concentrations of hydrocarbons in shelf waters and sediments were orders of magnitude lower than measured in inshore or deep GOM environments, the level of mortality observed or predicted was substantial for many shelf taxa. In some cases, such as for zooplankton, community shifts following the spill were ephemeral, likely reflecting high rates of population turnover and productivity. In other taxa, such as GOM reef fishes, impacts of the spill are confounded with other stressors, such as fishing mortality or the appearance and rapid population growth of invasive lionfish (Pterois spp.). In yet others, such as cetaceans, modeling efforts to predict population-level effects of the DWH made conservative assumptions given the species’ protected status, which post-DWH population assessments either failed to detect or population increases were estimated. A persistent theme that emerged was the lack of precise population-level data or assessments prior to the DWH for many taxa, but even when data or assessments did exist, examining evidence of population resiliency was confounded by other stressors impacting GOM biota. Unless efforts are made to increase the resolution of the data or precision of population assessments, difficulties will likely remain in estimating the scale of population-level effects or resiliency in the case of future large-scale environmental catastrophes.
Long range gene flow beyond predictions from oceanographic transport in a tropical marine foundation species
(2023-06-05) Tavares, Ana I.; Assis, Jorge; Larkin, Patrick D.; Creed, Joel C.; Magalhaes, Karine; Horta, Paulo; Engelen, Aschwin; Cardoso, Noelo; Barbosa, Castro; Pontes, Samuel; Regalla, Aissa; Almada, Carmen; Ferreira, Rogerio; Abdoul, Ba Mamadou; Ebaye, Sidina; Bourweiss, Mohammed; Van-Dunem dos Santos, Carmen; Patricio, Ana R.; Teodosio, Alexandra; Santos, Rui; Pearson, Gareth A.; Serrao, Ester A.
The transport of passively dispersed organisms across tropical margins remains poorly understood. Hypotheses of oceanographic transportation potential lack testing with large scale empirical data. To address this gap, we used the seagrass species, Halodule wrightii, which is unique in spanning the entire tropical Atlantic. We tested the hypothesis that genetic differentiation estimated across its large-scale biogeographic range can be predicted by simulated oceanographic transport. The alternative hypothesis posits that dispersal is independent of ocean currents, such as transport by grazers. We compared empirical genetic estimates and modelled predictions of dispersal along the distribution of H. wrightii. We genotyped eight microsatellite loci on 19 populations distributed across Atlantic Africa, Gulf of Mexico, Caribbean, Brazil and developed a biophysical model with high-resolution ocean currents. Genetic data revealed low gene flow and highest differentiation between (1) the Gulf of Mexico and two other regions: (2) Caribbean-Brazil and (3) Atlantic Africa. These two were more genetically similar despite separation by an ocean. The biophysical model indicated low or no probability of passive dispersal among populations and did not match the empirical genetic data. The results support the alternative hypothesis of a role for active dispersal vectors like grazers.
MariClus: Your one-stop platform for information on marine natural products, their gene clusters and producing organisms
(2023-08-15) Hermans, Cedric; Lieven De Mol, Maarten; Mispelaere, Marieke; De Rop, Anne-Sofie; Rombaut, Jeltien; Nusayr, Tesneem; Creamer, Rebecca; De Maeseneire, Sofie L.; Soetaert, Wim K.; Hulpiau, Paco
Background: The marine environment hosts the vast majority of living species and marine microbes that produce natural products with great potential in providing lead compounds for drug development. With over 70% of Earth’s surface covered in water and the high interaction rate associated with liquid environments, this has resulted in many marine natural product discoveries. Our improved understanding of the biosynthesis of these molecules, encoded by gene clusters, along with increased genomic information will aid us in uncovering even more novel compounds. Results: We introduce MariClus (https://www.mariclus.com), an online user-friendly platform for mining and visualizing marine gene clusters. The first version contains information on clusters and the predicted molecules for over 500 marine-related prokaryotes. The user-friendly interface allows scientists to easily search by species, cluster type or molecule and visualize the information in table format or graphical representation. Conclusions: This new online portal simplifies the exploration and comparison of gene clusters in marine species for scientists and assists in characterizing the bioactive molecules they produce. MariClus integrates data from public sources, like GenBank, MIBiG and PubChem, with genome mining results from antiSMASH. This allows users to access and analyze various aspects of marine natural product biosynthesis and diversity.
Indicators to monitor the status of the tree of life
(2023-06-28) Gumbs, Rikki; Chaudhary, Abhishek; Daru, Barnabas H.; Faith, Daniel P.; Forest, Felix; Gray, Claudia L.; Kowalska, Aida; Lee, Who-Seung; Pellens, Roseli; Pipins, Sebastian; Pollock, Laura J.; Rosindell, James; Scherson, Rosa A.; Owen, Nisha R.
Following the failure to fully achieve any of the 20 Aichi biodiversity targets, the future of biodiversity rests in the balance. The Convention on Biological Diversity’s Kunming–Montreal Global Biodiversity Framework (GBF) presents the opportunity to preserve nature’s contributions to people (NCPs) for current and future generations by conserving biodiversity and averting extinctions. There is a need to safeguard the tree of life—the unique and shared evolutionary history of life on Earth—to maintain the benefits it bestows into the future. Two indicators have been adopted within the GBF to monitor progress toward safeguarding the tree of life: the phylogenetic diversity (PD) indicator and the evolutionarily distinct and globally endangered (EDGE) index. We applied both to the world’s mammals, birds, and cycads to show their utility at the global and national scale. The PD indicator can be used to monitor the overall conservation status of large parts of the evolutionary tree of life, a measure of biodiversity’s capacity to maintain NCPs for future generations. The EDGE index is used to monitor the performance of efforts to conserve the most distinctive species. The risk to PD of birds, cycads, and mammals increased, and mammals exhibited the greatest relative increase in threatened PD over time. These trends appeared robust to the choice of extinction risk weighting. EDGE species had predominantly worsening extinction risk. A greater proportion of EDGE mammals(12%) had increased extinction risk compared with threatened mammals in general (7%).
Nanosilver: An old antibacterial agent with great promise in the fight against antibiotic resistance
(2023-07-31) Kaiser, Kyra G.; Delattre, Victoire; Frost, Victoria J.; Buck, Gregory W.; Phu, Julianne V.; Fernandez, Timea G.; Pavel, Ioana E.
Antibiotic resistance in bacteria is a major problem worldwide that costs 55 billion USD annually for extended hospitalization, resource utilization, and additional treatment expenditures in the United States. This review examines the roles and forms of silver (e.g., bulk Ag, silver salts (AgNO3), and colloidal Ag) from antiquity to the present, and its eventual incorporation as silver nanoparticles (AgNPs) in numerous antibacterial consumer products and biomedical applications. The AgNP fabrication methods, physicochemical properties, and antibacterial mechanisms in Gram-positive and Gram-negative bacterial models are covered. The emphasis is on the problematic ESKAPE pathogens and the antibiotic-resistant pathogens of the greatest human health concern according to the World Health Organization. This review delineates the differences between each bacterial model, the role of the physicochemical properties of AgNPs in the interaction with pathogens, and the subsequent damage of AgNPs and Ag+ released by AgNPs on structural cellular components. In closing, the processes of antibiotic resistance attainment and how novel AgNP–antibiotic conjugates may synergistically reduce the growth of antibiotic-resistant pathogens are presented in light of promising examples, where antibiotic efficacy alone is decreased.

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