University of Idaho
  • Moscow, Idaho, United States
Recent publications
Numerous toxic substances are directly and indirectly discharged by humans into water bodies, causing distress to the organisms living on it. 6PPD, an amino antioxidant from tires reacts with ozone to form 6PPD-Q, which has garnered global attention due to its lethal nature to various organisms. This review aims to provide an understanding of the sources, transformation, and fate of 6PPD-Q in water and the current knowledge on its effects on aquatic organisms. Furthermore, we discuss research gaps pertaining to the mechanisms by which 6PPD-Q acts within fish bodies. Previous studies have demonstrated the ubiquitous presence of 6PPD-Q in the environment, including air, water, and soil. Moreover, this compound has shown high lethality to certain fish species while not affecting others. Toxicological studies have revealed its impact on the nervous system, intestinal barrier function, cardiac function, equilibrium loss, and oxidative stress in various fish species. Additionally, exposure to 6PPD-Q has led to organ injury, lipid accumulation, and cytokine production in C. elegans and mice. Despite studies elucidating the lethal dose and effects of 6PPD-Q in fish species, the underlying mechanisms behind these symptoms remain unclear. Future studies should prioritize investigating the mechanisms underlying the lethality of 6PPD-Q in fish species to gain a better understanding of its potential effects on different organisms.
A workshop was held at the Massachusetts Institute of Technology (MIT) on July 25th and 26th, 2022. The objective was to develop a blueprint for educating next-generation engineers and scientists about nuclear waste management and disposal, which requires knowledge from diverse disciplines, including nuclear, chemical, civil, environmental, and geological science and engineering. The 49 participants included university professors, researchers , industry experts, and government officials from different areas. First, we have developed a list of key fundamental knowledge on waste management and disposal across the nuclear fuel cycle. In addition, we discussed strategies on how to teach students with diverse backgrounds through innovative teaching strategies as well as how to attract students into this area. Through the workshop, we identified the critical needs to (1) develop community resources for nuclear waste education; (2) synthesize historical perspectives, including past contamination and the management of general hazardous waste; (3) emphasize a complete life-cycle perspective, including proper waste management as the key component for energy sustainability; (4) teach students how to communicate about the key facts and risks to technical and non-technical audiences; and (5) accelerate the use of the state-of-art-technologies to attract and retain a young workforce. Furthermore, we aim to build a diverse, inclusive community that supports students in developing their own narratives about nuclear waste, particularly in recognizing that antagonistic views have been important to improving safety and protecting public health and the environment.
Electromagnetic transient (EMT) simulation has moved from a tool used for a few specialist applications, such as insulation coordination, to becoming a common tool for interconnection studies for inverter-based resources (IBRs). Historically, many utilities had few, if any, engineers with a background to perform EMT studies. Today, the proliferation of inverter-based generation and storage resources makes EMT simulation a critical tool for protection and planning studies.
Background A Lactobacillus-dominated vaginal microbiome provides the first line of defense against adverse genital tract health outcomes. However, there is limited understanding of the mechanisms by which the vaginal microbiome modulates protection, as prior work mostly described its composition through morphologic assessment and marker gene sequencing methods that do not capture functional information. To address this gap, we developed metagenomic community state types (mgCSTs) which use metagenomic sequences to describe and define vaginal microbiomes based on both composition and functional potential. Results MgCSTs are categories of microbiomes classified using taxonomy and the functional potential encoded in their metagenomes. MgCSTs reflect unique combinations of metagenomic subspecies (mgSs), which are assemblages of bacterial strains of the same species, within a microbiome. We demonstrate that mgCSTs are associated with demographics such as age and race, as well as vaginal pH and Gram stain assessment of vaginal smears. Importantly, these associations varied between mgCSTs predominated by the same bacterial species. A subset of mgCSTs, including three of the six predominated by Gardnerellavaginalis mgSs, as well as mgSs of L. iners, were associated with a greater likelihood of bacterial vaginosis diagnosed by Amsel clinical criteria. This L. iners mgSs, among other functional features, encoded enhanced genetic capabilities for epithelial cell attachment that could facilitate cytotoxin-mediated cell lysis. Finally, we report a mgSs and mgCST classifier for which source code is provided and may be adapted for use by the microbiome research community. Conclusions MgCSTs are a novel and easily implemented approach to reduce the dimension of complex metagenomic datasets while maintaining their functional uniqueness. MgCSTs enable the investigation of multiple strains of the same species and the functional diversity in that species. Future investigations of functional diversity may be key to unraveling the pathways by which the vaginal microbiome modulates the protection of the genital tract. Importantly, our findings support the hypothesis that functional differences between vaginal microbiomes, including those that may look compositionally similar, are critical considerations in vaginal health. Ultimately, mgCSTs may lead to novel hypotheses concerning the role of the vaginal microbiome in promoting health and disease, and identify targets for novel prognostic, diagnostic, and therapeutic strategies to improve women’s genital health. 6QiSoF_fVWyny-AcPZFxWyVideo Abstract
When designing phylogeographic investigations researchers can choose to collect many different types of molecular markers, including mitochondrial genes or genomes, SNPs from reduced representation protocols, large sequence capture data sets, and even whole genomes. Given that the statistical power and accuracy of various analyses are expected to differ depending on both the type of marker and the amount of data collected, an exploration of the variance across methodological results as a function of marker type should provide valuable information to researchers. Here we collect mitochondrial Cytochrome b sequences, whole mitochondrial genomes, single nucleotide polymorphisms (SNP)s isolated using a genotype by sequencing (GBS) protocol, sequences from ultraconserved elements, and low-coverage nuclear genomes from the North American water vole ( Microtus richardsoni ). We estimate genetic distances, population genetic structure, and historical demography using data from each of these datasets and compare the results across markers. As anticipated, the results exhibit differences across marker types, particularly in terms of the resolution offered by different analyses. A cost-benefit analysis indicates that SNPs collected using a GBS protocol are the most cost-effective molecular marker, with inferences that mirror those collected from the whole genome data at a fraction of the cost per sample.
Video games have the potential to help teach evolutionary biology, but most commercial games misrepresent evolutionary principles by allowing player choice to dictate evolutionary trajectories. Our game studio aims to incorporate scientifically accurate evolutionary models into gameplay mechanics. In our previous games Darwin’s Demons and Project Hastur, we designed digital genomes and implemented evolutionary models to create enemy populations that adapt to player strategies. However, accurately simulating evolution can sometimes conflict with crafting an enjoyable game. Here we examine balancing scientific realism with fun in the game design process. Using experimental data from Project Hastur, we show enemies evolve increased size and sensory abilities to counter player defenses, demonstrating the game mechanic’s adaptive capabilities. We discuss how mutation rates, population sizes, generation times and other parameters can be adjusted to balance accuracy and enjoyment, with the goal of creating engaging games that reinforce and demonstrate, rather than misrepresent, evolutionary principles.
The aim of this trial was to investigate the effects of apple polyphenols (AP) and taurine (TA) on the growth performance, tissue morphology, and lipid and glucose metabolism in rice field eel fed diets with high oxidized fish oil (OFO). A 10-week feeding experiment was conducted using juveniles (initial body weight 16.66 ± 0.02 g) fed five different diets. Three diets were formulated with various levels of OFO at 9.5, 600, and 800 meq·kg−1 and named as Control, POV600, and POV800 diet, respectively. The other two diets were POV600 and POV800 supplemented with 0.5% AP and 0.2% TA, respectively. Compared to the Control group, only the eels fed POV800 exhibited an increase in weight gain and specific growth rate along with a reduction in feed conversion ratio. AP and TA did not affect growth performance; juveniles fed AP, however, showed a decrease in liver weight. Both POV600 and POV800 decreased nuclei number and increased vacuoles size in the liver. POV800 damaged the intestinal structure integrity and reduced goblet cells number. AP repaired the liver damage on nuclei number and vacuoles size in fish fed with POV600 diet, while TA mitigated intestinal histopathological damage on intact structure and goblet cells number. The mRNA expression level of liver ampkα in fish fed AP was upregulated, while dietary TA upregulated the mRNA expression levels of liver ampkα and accα. In the muscle, POV600 downregulated mRNA expression levels of accα, cpt1, and lipin, whereas POV800 upregulated mRNA expression levels of accα, pparα, and lipin. Dietary AP and TA could counteract the effects of POV600 and POV800 diet on muscle lipid metabolism. Both POV600 and POV800 diets upregulated mRNA expression levels of liver pck1 and gsk3α. AP and TA both downregulated mRNA expression level of liver pck1, while only TA downregulated the expression of liver gsk3α. AP increased the mRNA expression level of gsk3α in muscle. In summary, inclusion of AP and TA did not affect growth performance but showed a potential to alleviate liver or intestinal damages induced by a high OFO diet. Dietary AP and TA were also found to regulate mRNA expression of genes related to lipid and glucose metabolism.
This paper explores the adult learning theory related to Profound Learning (PL). A discussion of the ways in which PL is linked to Formative Design processes and traditional teaching/learning models is presented. PL is defined, including PL practices, components, and an image of application of PL to Formative Design processes. A linkage between PL, Formative Design, design thinking, and community is briefly made before reviewing already accomplished research.
A primary explosive is an ideal chemical substance for performing ignition in military and commercial applications. For over 150 years, nearly all of the developed primary explosives have suffered from various issues, such as troublesome syntheses, high toxicity, poor stability or/and weak ignition performance. Now we report an interesting example of a primary explosive with double perovskite framework, {(C6H14N2)2[Na(NH4)(IO4)6]}n (DPPE-1), which was synthesized using a simple green one-pot method in an aqueous solution at room temperature. DPPE-1 is free of heavy metals, toxic organic components, and doesn’t involve any explosive precursors. It exhibits good stability towards air, moisture, sunlight, and heat and has acceptable mechanical sensitivities. It affords ignition performance on par with the most powerful primary explosives reported to date. DPPE-1 promises to meet the challenges existing with current primary explosives, and this work could trigger more extensive applications of perovskite.
In males of many vertebrate species, sexual selection has led to the evolution of sexually dimorphic traits, which are often developmentally controlled by androgen signaling involving androgen response elements (AREs). Evolutionary changes in the number and genomic locations of AREs can modify patterns of receptor regulation and potentially alter gene expression. Here, we use recently sequenced primate genomes to evaluate the hypothesis that the strength of sexual selection is related to the genome-wide number of AREs in a diversifying lineage. In humans, we find a higher incidence of AREs near male-biased genes and androgen-responsive genes when compared with randomly selected genes from the genome. In a set of primates, we find that gains or losses of AREs proximal to genes are correlated with changes in male expression levels and the degree of sex-biased expression of those genes. In a larger set of primates, we find that an increase in one indicator of sexual selection, canine size sexual dimorphism, is correlated with genome-wide ARE counts. Our results suggest that the responsiveness of the genome to androgens in humans and their close relatives has been shaped by sexual selection that arises from competition among males for mating access to females.
Tutoring and training clinical practitioners are the corner stones of quality healthcare systems. While formal education and training give medical students the basis of human physiology, anatomy, health, and medicine, internships and hospital mentorships offer more hands-on practice, real life experiences and clinical insights to become a successful young physician. A digital tutoring and assessment system can aid in the training and learning process immensely. While there are several clinical tutoring and e-learning systems around, most do not support community contributed learning challenges to introduce new learning experiences. In this paper, we introduce a new clinical e-learning and tutoring system, called ClinLearning, for online training and assessment of medical students. In this system, we allow inclusion of partitioned EHRs for focused training, and submission and inclusion of challenging real life case scenarios for the recommendation of interventions. We highlight ClinLearning’s promises and discuss potential research opportunities.
An understanding of the molecular basis of musculoskeletal pain is necessary for the development of therapeutics, their management, and possible personalization. One-in-three Americans use OTC pain killers, and one tenth use prescription drugs to manage pain. The CDC also estimates that about 20% Americans suffer from chronic pain. As the experience of acute or chronic pain varies due to individual genetics and physiology, it is imperative that researchers continue to find novel therapeutics to treat or manage symptoms. In this paper, our goal is to develop a seed knowledgebased computational platform, called BioNursery, that will allow biologists to computationally hypothesize, define and test molecular mechanisms underlying pain. In our knowledge ecosystem, we accumulate curated information from users about the relationships among biological databases, analysis tools, and database contents to generate biological analyses modules, called \(\pi \)-graphs, or process graphs. We propose a mapping function from a natural language description of a hypothesized molecular model to a computational workflow for testing in BioNursery. We use a crowd computing feedback and curation system, called Explorer, to improve proposed computational models for molecular mechanism discovery, and growing the knowledge ecosystem.
Rainfall-induced landslides are sudden, widespread, and prone to cause significant loss of life and property. To explore the heterogeneity and changes in slope stability under extreme rainfall conditions, we took Yongtai County, Fuzhou City, as the study area, and focused on the impact of rainfall on slope stability during the "7·9" extreme rainstorm event in 2016. Regional data on topography, geotechnical engineering, hydrogeology, and precipitation were collected through field sampling, site monitoring, and public datasets. The collected data, after preprocessing, were used to build the TRIGRS (transient rainfall infiltration and grid-based regional slope stability) model for evaluating the regional slope stabilities during the event. Finally, the local spatial and temporal effects of rainfall on slope stability were analyzed by using the STWR (spatiotemporal weighted regression) model. Results show that: (1) Most areas in Yongtai County was safe during the event (most of the factor of safety (FS) were higher than 1.5), but as the duration of rainfall increased, the FS of some grids in the study area continued to decline, the unsafety areas were gradually expanding, and some areas were still at risk of landslides. (2) The spatial variation of slope stability in Yongtai County was great, with characteristics of low in the center and high in the east and west. High-risk areas were concentrated in the northwest of Qingliang Town, and the south of Songkou Town. Southeast of Dayang Town and Baiyun Town. (3) The impacts of rainfall on slope stability were spatiotemporally heterogeneous. In terms of time, rainfall negatively impacted slope stability and continued to show an enhancing trend as the duration of rainfall increased. In terms of space, the affected area showed an expanding trend as the rainfall continued, expanding from the towns of Hongxing, Fukou, and the northeastern part of Geling to the towns of Songkou, southeastern Wutong, eastern Chengfeng, and southern Chixi, etc. Overall, our study fills the insufficiency of the spatiotemporal heterogeneity analysis on the impact of rainfall on slope stability of landslides, which can provide some reference for shallow landslide risk management and disaster early warning.
Values and motivations can shape natural resource management decision-making as individuals set conservation goals based on diverse, unique backgrounds, histories, and experiences. Recent literature points to the need to understand, evaluate, and articulate practitioner values to make explicit how experiences shape their work. Our research responds to calls to explore a diverse range of values and motivations among conservation practitioners. We used a qualitative approach grounded in phenomenology to advance an in-depth understanding of how conservation and stewardship practitioners experience, acknowledge, and make sense of conservation decision-making in Maine, USA. We interviewed 21 conservation and stewardship practitioners. Our results indicate the presence of complex value systems, including strong biospheric, altruistic, eudaimonic, as well as egoistic values. These values interact and intersect with motivations for participants’ careers in conservation in unique ways, driving participant actions and decision-making. Within Maine specifically, our results highlight the many areas for convergence of broad values among seemingly diverse groups that can inform opportunities for collaboration. Participants expressed various pathways to careers in conservation, where their work enables them to make a meaningful contribution to the environment and society. However in situations where personal and organizational values are misaligned, the role of organizational transparency, employee empowerment, and agency are key. Our results have implications for conservation groups seeking to achieve high employee satisfaction, as well as researchers, policymakers, and practitioners who hope to inspire individuals to take on conservation careers to create sustainable and transformative action for the future. Fostering early experiences in place, including interactions with the non-human world and local community, are important for influencing and reinforcing values and motivations for conservation action.
A common explanation for Hillary Clinton’s loss in the 2016 presidential election was that she catered to minorities at the expense of the broader electorate. How does such a loss narrative influence voters' interpretation of subsequent elections? In a conjoint experiment, white and Black Democratic respondents were randomly exposed to a vignette that ascribed Democrats’ 2016 losses to their focus on identity politics. This narrative had an asymmetric effect on attitudes toward the 2020 election based on both race and gender. While it had no impact on white men’s or Black women’s understanding of why the Democrats lost the last presidential election or their candidate preferences for the next, it had a substantial impact on the electoral attitudes of white women and a moderate impact on those of Black men. Specifically, it shifted their support away from candidates committed to gender and racial equity and toward those emphasizing broad economic policies. The identity politics loss narrative thus may have acted as a self-fulfilling prophecy that advantaged white male candidates in the 2020 election.
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3,887 members
Leslie Baker
  • Department of Geological Sciences
Kenneth E Wallen
  • Department of Natural Resources and Society
Christian Joseph Cumagun
  • College of Agricultural and Life Sciences
Saket Chandra
  • Department of Plant, Soil and Entomological Sciences
Moscow, Idaho, United States