Miracle-dz/UniFAR-FTUs huggingface dataset:
The gut microbiome of the critically endangered kakapo

The kakapo is one of New Zealand’s iconic endemic birds, possessing an array of characteristics that are unique among avians. The kakapo is also critically endangered, and only survives through an intensive management effort by the Department of Conservation. In order to aid in conservation practices and decision making, detailed research has been conducted previously into the ecology, physiology, genetics and breeding behaviour of the kakapo. By contrast, the interactions between kakapo and the microorganisms associated with them have remained unexplored. In order to address this lack of knowledge regarding the kakapo microbiota, cultivation-based and state-of-the-art molecular techniques were employed with the overall aim of identifying the common microbes that inhabit the kakapo gastrointestinal tract and understanding the patterns that influence them. Analysis of bacterial 16S rRNA genes revealed that the kakapo gut harbours a bacterial community of low taxonomic diversity, dominated by members of just two bacterial phyla (Proteobacteria and Firmicutes). Unexpectedly, the age of the bird played little role in shaping the kakapo microbiota, with both phylogenetic and functional data indicating no difference between age groups. By contrast, other studied factors did impact upon the microbiota, such as sampling location within the gut as well as antibiotic treatment and captivity. These analyses showed that although the kakapo microbiota is influenced by antibiotic treatment the effect is short lived, with the kakapo microbiota returning to a ‘normal’ state within weeks of release back into the wild. Genomic and metagenomic analyses reaffirmed the finding of low taxonomic diversity at broad phylogenetic levels, but showed that at fine-scale resolution (bacterial species and strains) the kakapo microbiota is much more diverse than inferred from traditional (16S rRNA-based) marker gene analysis. The functional potential of gut microbes was also examined, and was similar to that of other herbivore gut systems, despite the low taxonomic diversity. This thesis represents the first concerted effort to study the kakapo microbiota and provides a foundation of knowledge for guiding future study and management practices.
Comparison and Ranking of Metaheuristic Techniques for Optimization of PI Controllers in a Machine Drive System

Proportional integral (PI) control is still the most widely deployed controller in the industrial drives due to its simplicity and the fact that it is easy to understand and implement. Nevertheless, they are successes applied to systems with a complex behavior with a nonlinear representation, but a disadvantage is the procedure to find the optimal PI controller gains. The optimal values of PI parameters must be computed during the tuning process. However, traditional tuning techniques are based on model and do not provide optimal adjustment parameters for the PI controllers because the transient response could produce oscillations and a large overshoot. In this paper, six swarm intelligence-based algorithms (whale, moth-flame, flower pollination, dragonfly, cuckoo search, and modified flower pollination), are correctly conditioned and delimited to tune the PI controllers, the results are probed in a typical industry actuator. Also, a rigorous study is developed to evaluate the quality and reliability of these algorithms by a statistical analysis based on non-parametric test and post-hoc test. Finally, with the obtained results, some time simulations are carried out to corroborate that the nonlinear system performance is improved for high precision industrial applications subjected to endogenous and exogenous uncertainties in a wide range of operating conditions.
Applications of Biotechnology for Characterization of Plants and Pests as the Key Components of Plant Protection and Production Strategies: A Review

This is an open access article & it is licensed under a Creative Commons Attribution Non-Commercial 4.0 International (https://creativecommons.org/licenses/by-nc/4.0/) The second Sustainable Developmental Goals (SDG), among the seventeen SDG, is concerned with the pursuit of global food security and agricultural sustainability, which become the key to the success of the entire SDG. Whereas agricultural production and productivity are heavily threatened by the incidence of pests that inflict huge losses in various forms. This calls for prompt applications of biotechnology for the fast, accurate and reliable means for characterization of plant generic resources and pests as it is the pre-requisite and gateway for designing appropriate plant protection and production strategies. It is imperative that pests be identified properly so that judicious use of the literature can be made and sustainable management strategies can be implemented at the right stage. To this end, the application of biotechnology has made significant advances for reliable characterization of plant genetic resources as well as accurate diagnosis of pests, study of their genetic diversity and variability, detailed mechanisms of their transmission and evolutionary relationships. Accordingly, this review article covers the comprehensive account of the various molecular techniques, genome mapping and OMICS sciences utilized for characterization plants and pests that ultimately allow the detailed study of the biology and epidemiology of pests at any stage of their life cycle. The resulting data are eventually employed for enhancing successful implementation of sustainable plant protection and production strategies. In conclusion, the increasing projections of transboundary pests, environmental and abiotic factors together with the continuous scientific advancements and breakthroughs have made biotechnology to be an important engine of bioeconomy for generating invaluable products, processes and services.
Regulatory mechanisms of innate immune signaling in zebrafish embryos

The work presented in this thesis has provided new insights into the mechanisms involved in the regulation of innate immune responses in zebrafish embryos. Furthermore, cell-specific transcriptome profiling studies identified novel marker genes for distinguishing immune cell types, which is highly useful information to fulfill the demand for new fluorescent reporter lines and lineage-specific antibodies in the zebrafish model. We have shown that Ptpn6, a protein tyrosine phosphatase homolog of human SHP1, functions as a critical negative regulator, required for a properly balanced innate immune response and for controlling infections with bacterial pathogens. In Salmonella typhimurium infection, ptpn6 deficiency caused a general hyperinduction of pro-inflammatory genes, which was contraproductive as it impaired the infection control. In Mycobacterium marinum infection, a more specific effect of ptpn6 deficiency on matrix metalloproteinase gene expression was found as a major underlying cause of increased bacterial burden. We further concluded that Ptpn6 functions as a much stronger negative regulator than infection-inducible miRNAs of the miR-146 family, which may be involved in more subtle fine-tuning of the innate immune response. Knowledge about the distinct roles of Ptpn6 and miR-146 miRNAs has practical applicability in regard to their potential as therapeutic targets for inflammatory diseases and cancer.
Non-profit overhead and efficiency from IRS administrative data

ABSTRACT This paper investigates the efficiency of non-profit overhead spending by estimating its marginal returns on total revenue using IRS data. To explore whether using the overhead ratio as a heuristic for non-profit operational quality is justified, we compare it with administrative efficiency or the efficiency by which overhead is transformed into total revenues. We find that underinvestment on overhead may be explained by reputational concerns. Reputational concerns may be justified given a negative relationship between administrative efficiency and overhead ratio.
Microclusters of Kinked Silicon Nanowires Synthesized by a Recyclable Iodide Process for High‐Performance Lithium‐Ion Battery Anodes

Silicon shows great promise as a high‐capacity anode material for lithium‐ion batteries. Nanostructuring silicon minimizes the impact of fracturing during charging and discharging. However, synthesizing nanostructured silicon typically requires complicated procedures with high manufacturing costs. Additionally, these complicated procedures typically have poor secondary particle formation, a requirement to achieve a high tap density. Here, a cost‐effective synthesis procedure which generates nearly ideal secondary particle clusters of nanostructured silicon is developed. The cost‐effectiveness is a result of the in operando generation of silicon iodide from iodine gas and low‐grade silicon microparticle. Decomposition of silicon iodide into crystalline silicon and iodine gas enables recycling of the iodine gas, allowing for near full reutilization of iodine in the following cycles. The optimal nanostructures and microstructures of silicon synthesized by the recyclable iodide decomposition reaction enables 83.6% capacity retention over 1000 cycles. The good performance is a result of well‐maintained morphology during cycling, enabling reutilization of the solid electrolyte interphase.
Body temperature regulation in the dragonfly, Arigomphus villosipes (Odonata: Anisoptera: Gomphidae)

Regulation of thoracic muscle temperature has been investigated in a number of dragonfly species but is poorly known in the large and diverse family, Gomphidae. Moreover, temperatures of other body regions have been recorded in very few ectothermic insects. In addition, correlations among multiple components of thermoregulatory behavior have rarely been examined quantitatively. Here I examine thermoregulation in Arigomphus villosipes, a medium-sized gomphid common at the shores of lakes and ponds in the northeastern USA. Measurements of the temperatures of the thorax (Tth), head (Th) and abdomen (Tab), using standard "grab and jab" techniques, indicate that both Tth and Th are relatively independent of air temperature (Ta). It is not clear whether Tth and Th are independently regulated, although some data suggest that they might be. Arigomphus villosipes can warm its thoracic musculature endothermically to maintain high Tth during cool Ta in conditions of low solar radiation intensity. However, regulation is principally behavioral, involving variation in body and wing postures and perhaps in perch substrate choice. Certain of these behaviors are closely associated to form suites of behavior that together are adapted to enhance or inhibit heating, while others are constrained by trade-offs with other functional demands. The former have a significant demonstrable effect on Tth. These combinations of behaviors results in a well-developed capacity for thermoregulation, allowing the insects to expand their activity periods and choice of perches, and probably improving male performance during competitive chases of females prior to mating.
Interfacial instability of thin films in soft microfluidic configurations actuated by electro-osmotic flow

We analyze the interfacial instability of a thin ﬁlm conﬁned between a rigid surface and a pre-stretched elastic sheet, triggered by non-uniform electro-osmotic ﬂow. We derive a nonlinear viscous − elastic equation governing the deformation of the elastic sheet, describing the balance between viscous resistance, the dielectric and electro-osmotic eﬀects, and the restoring eﬀect of elasticity. Our theoretical analysis, validated by numerical simulations, shows several distinct modes of instability depending on the electro-osmotic pattern, controlled by a non-dimensional parameter representing the ratio of electro-osmotic to elastic forces. We consider several limiting cases and present approximate asymptotic expressions predicting the electric ﬁeld required for triggering of the instability. Through dynamic numerical simulations of the governing equation, we study the hysteresis of the system and show that the instability can result in an asymmetric deformation pattern, even for symmetric actuation. Finally, we validate our theoretical model with ﬁnite-element simulations of the two-way coupled Navier equations for the elastic solid, the unsteady Stokes equations for the ﬂuid, and the Laplace equation for the electric potential, showing very good agreement. The mechanism illustrated in this work, together with the provided analysis, may be useful in toward the implementation of instability-based soft actuators for lab-on-a-chip and soft-robotic applications.
Virus-like particles as a novel platform for delivery of protective Burkholderia antigens

18 Acknowledgments . 20 List of abbreviations . 21 Chapter 1: General Introduction . 25 1.1 Burkholderia . 25 1.2 Burkholderia pseudomallei and melioidosis . 25 1.2. 1 Diagnosis and treatment . 27 1.2. 2 Burkholderia pseudomallei intracellular infection and mechanisms of virulence . 28 1.3 Burkholderia mallei and glanders . 30 1.4 Burkholderia cepacia . 31 1.5 Burkholderia thailandensis . 31 1.6 Bacterial polysaccharides . 32 1.6. 1 B. pseudomallei and B. mallei capsular polysaccharide . 32 1.7 Vaccines . 38 1.7. 1 Barriers to vaccine development . 39 1.7. 2 Economics of vaccine development . 41 1.7. 3 Biodefense vaccines . 42 1.7. 4 Animal models . 43 1.7. 5 Live attenuated vaccines . 44 1.7. 6 Inactivated vaccines . 45 1.7. 7 Subunit vaccines and toxoids . 46 1.8 Vaccine immunology . 55 1.8. 1 Th1/Th2 response . 56 1.8. 2 Immune response to polysaccharides . 56
Holocene records of eolian dust deposition from high‐elevation lakes in the Uinta Mountains, Utah, USA

Radiocarbon‐dated sediment cores from subalpine lakes were used to investigate post‐glacial dust deposition in the Uinta Mountains (Utah, USA). Lake sediments were geochemically characterized with ICP‐OES, ICP‐MS and XRF core scanning. Collections from passive samplers constrain the properties of modern dust, and samples of regolith constrain properties of the local material within the watershed. Ca and Eu are more abundant in dust, whereas Ti and Zr are more abundant in local regolith. As a result, the Ca/Ti and Eu/Zr ratios are indices for the dust content of lake sediment. In all records, the dust index rises in the early Holocene as watersheds became stabilized with vegetation, reducing the influx of local material. After this point, values remained above average through the middle Holocene, consistent with an increased dust content in the sediment. Dust index values drop in the late Holocene in most lakes, suggesting a decrease in dust abundance. Generally synchronous shifts in dust index values in cores from lakes in different parts of this mountain range are evidence of enhanced dust deposition in this region during the middle Holocene, and are consistent with a variety of records for increased aridity in the south‐western USA at this time.
Elucidating The Role Of Type I Interferon Signaling In Adipocyte Biology

Brown and beige adipose tissues represent promising therapeutic targets for combating the rapidly growing obesity pandemic. The goal of this thesis work was to better understand the signaling pathways that affect brown and beige adipose function. First, we investigated pathways regulated by PRDM16, a critical transcription factor for brown and beige fat development. We found that PRDM16 represses type I Interferon (IFN) responses in both preadipocytes and mature adipocytes to promote thermogenic and mitochondrial function. Type I IFN signaling is a critical antiviral pathway, which was previously unexplored in the context of brown fat biology. We found that brown adipocyte character and mitochondrial function were disrupted by ectopic IFN signaling and that increased PRDM16 expression could reverse these negative effects. Additionally, we showed that PRDM16 is required to protect brown fat function from type I IFN signaling in vivo. Utilizing multiple transcriptional assays, we determined that PRDM16 blocks IFN regulatory factor 1 (IRF1)-mediated activation of ISGs by competitively binding ISG promoter regions. Adipose inflammation has been implicated in the progression of obesity and insulin resistance. Next, we aimed to determine the role of type I IFN in diet-induced obesity. We found that ISGs are activated in multiple tissues of mice early in the course of high-fat diet (HFD) feeding. Blocking IFN responses using an IFN alpha receptor knockout mouse led to protection from diet-induced obesity and insulin resistance. Additionally, HFD-induced type I IFN decreased energy expenditure, potentially due to mitochondrial dysfunction in the subcutaneous adipose depot. Together this work demonstrates for the first time the negative effects of type I IFN in adipose tissue that may contribute to obesity and insulin resistance. Degree Type Dissertation Degree Name Doctor of Philosophy (PhD) Graduate Group Cell & Molecular Biology First Advisor Patrick Seale
Effects of invasion at two trophic levels on diet, body condition, and population size structure of Hawaiian red shrimp

We examined the degree to which invasion by non-native, nitrogen (N)-fixing riparian trees and poeciliid fish alters diet of a common grazer/detritivore in brackish ponds on the dry coast of Hawai‛i Island. Because this shrimp, Halocaridina rubra (ʻōpaeʻula), displays a preference for autotrophic components of epilithon, we hypothesized that tree canopy would reduce their body condition and abundance, but that this would be moderated by nutrient quality of leaf litter (high-quality, non-native, nitrogen-fixing tree vs. low-quality, endemic non-nitrogen-fixing tree). We hypothesized that poeciliid invasion would reduce population size and body condition of H. rubra by direct predation and by inducing reductions in feeding rate. Analysis of stable isotopes (δD, δ13C, and δ15N) showed that direct consumption of leaf litter detritus supplemented H. rubra diet in ponds with canopy cover. In addition, epilithon in ponds with canopy cover was isotopically more similar to leaf litter than epilithon in ponds without canopy cover, and our evidence suggests this may be due to contributions of allochthonous nutrient sources to epilithon assemblages. However, canopy cover, whether native or invasive, did not decrease epilithon growth rates and had little effect on shrimp body condition or population size. In contrast, poeciliid invasion reduced daylight grazing on the benthos, and caused a reduction in body condition among larger shrimp. Our results indicate that primary succession by invasive trees may shift food web linkages in these ponds from autotrophic to heterotrophic support, without negative impacts on native grazer/detritivore communities. We suggest that poeciliid invasions have sub-lethal effects on H. rubra as well as their direct predation effects, with potential long-term implications for the ecosystem function of anchialine ponds and other coastal systems.
Lifestyle medicine: A pragmatic approach to chronic disease management

This article gives a generic outline of lifestyle medicine as an evidence-based specialty and how to develop a portfolio career in this new and exciting field. It also discusses the current disease burden associated with non-communicable diseases. Lifestyle medicine is defined by the American College of Lifestyle Medicine as ‘the use of a whole food, plant-predominant dietary lifestyle, regular physical activity, restorative sleep, stress management, avoidance of risky substances and positive social connection as a primary therapeutic modality for treatment and reversal of chronic disease’.
Mobilization and Transformation of Mercury Across a Dammed Boreal River Are Linked to Carbon Processing and Hydrology

Reservoirs are known to accelerate the mobilization and cycling of mercury and carbon as a result of flooding of terrestrial organic matter, which can lead to environmental concerns at local and broader spatial scales. We explored the covariation of mercury (Hg) and carbon (C) functional pools in natural and recently dammed portions of the aquatic network of the Romaine River watershed in Northern Quebec, Canada, to understand how the fate of these elements varies across systems with contrasting hydrology and environmental conditions. We found that total Hg (THg) concentrations in surface waters were relatively constant along the network, whereas both the concentrations and proportions of MeHg tended to increase in reservoirs compared to surrounding nonflooded systems, and along the cascade of reservoirs. Whereas THg was related to total and terrestrial pools of dissolved organic carbon (DOC), MeHg was weakly related to DOC but strongly linked to surface concentrations of CO2, as well as to concentrations of iron and manganese. The latter are proxies of cumulative organic matter processing within the network, presumably in anoxic portions of shallow bays, deep reservoir waters, and river sediments, as well as in prior seasons (e.g., under ice). Our results suggest that these deep boreal reservoirs acted more as transformation sites for Hg that was already present than as mobilizers of new Hg, and that under ice metabolism plays a role in MeHg production in these systems as we found strong dichotomies in MeHg patterns between spring and summer.
Stoichiometric N:P flexibility and mycorrhizal symbiosis favour plant resistance against drought

Drought induces changes in the nitrogen (N) and phosphorus (P) cycle but most plant species have limited flexibility to take up nutrients under such variable or unbalanced N and P availability. Both the degree of flexibility in plant N:P ratio and of root symbiosis with arbuscular mycorrhizal fungi might control plant resistance to drought‐induced changes in nutrient availability, but this has not been directly tested. Here, we examined the role of plant N:P stoichiometric status and mycorrhizal symbiosis in the drought‐resistance of dominant and subordinate species in a semi‐natural grassland. We reduced water availability using rainout shelters (control vs. drought) and measured how plant biomass responded for the dominant and subordinate species. We then selected a dominant (Paspalum dilatatum) and a subordinate species (Cynodon dactylon), for which we investigated the N:P stoichiometric status, mycorrhizal root colonization and water‐use efficiency. The biomass of all dominant plant species, but not subordinate species, decreased under drought. Drought increased soil available nitrogen, and thus increased soil N:P ratio, due to decreasing plant N uptake. The dominant P. dilatatum showed a high degree of plant N:P homeostasis and a considerable reduction in biomass under drought. At the opposite, the more flexible subordinate species C. dactylon increased its N uptake and water‐use efficiency, apparently due to stronger symbiosis with mycorrhizae, and maintained its biomass. Synthesis. We conclude that the maintenance of N:P homeostasis in dominant species, possibly because of a large root nutrient foraging capacity, becomes inefficient when water stress limits N mobility in the soil. By contrast, we demonstrate that higher stoichiometric N:P flexibility coupled with stronger mutualistic association with mycorrhizae allow subordinate species to better withstand drought perturbations. Using a stoichiometric approach in a field experiment, our study provides for the first time clear and novel understandings of the mechanisms involved in drought‐resistance within the plant‐mycorrhizae‐soil system.