Miracle-dz/UniFAR-FTUs huggingface dataset:
The Effect of Probiotics, Antibiotics, and Antipyretic Analgesics on Gut Microbiota Modification

Human gut microbial community is playing a critical role in human health and associated with different human disease. In parallel, probiotics, antibiotics, and antipyretic analgesics (AAs) were developed to improve human health or cure human diseases. We therefore examined how probiotics, antibiotics, and AAs influence to the gut microbiota. Three independent case/control studies were designed from the cross-sectional cohort data of 1,463 healthy Koreans. The composition of the gut microbiota in each case and control group was determined via 16S ribosomal RNA Illumina next-generation sequencing. The correlation between microbial taxa and the consumption of each drug was tested using zero-inflated Gaussian mixture models, with covariate adjustment of age, sex, and body mass index (BMI). Probiotics, antibiotics, and AAs consumption yielded the significant differences in the gut microbiota, represented the lower abundance of Megasphaera in probiotics, the higher abundance of Fusobacteria in antibiotics, and the higher abundance of Butyrivibrio and Verrucomicrobia in AAs, compared to each control group. The reduction of Erysipelotrichaceae family was common in three drugs consumption.
Survey of Winter Wheat (Triticum aestivum) Stubble Fields Sprayed with Herbicides After Harvest in 1986

A survey of 146 fields was conducted to investigate herbicide performance in winter wheat-producing areas of southwestern Nebraska during August and September of 1986. Only 55% of the fields received an excellent rating for weed control and stubble quality; one third rated as unacceptable. Weed control after wheat harvest was improved by planting ‘Bounty 310’, ‘Siouxland’, ‘Vona’, and ‘Centura’ winter wheat cultivars rather than ‘Mustang’, ‘Hawk’, ‘Pioneer 2656’, and ‘Wings'. Fertilizing winter wheat in the fall, planting wheat at the optimum date, high wheat stem density, using a winter wheat-corn-fallow rotation, not spraying herbicides after wheat harvest on days that it rained or air temperature exceeded 35 C, and spraying weeds when they were small also improved weed control in wheat stubble. Nine months after wheat harvest, fields treated with atrazine before July 16 had more volunteer wheat than fields treated later.
Infection with toxigenic and atoxigenic strains of Aspergillus flavus induces different transcriptional signatures in maize kernels

ABSTRACT The application of atoxigenic Aspergillus flavus strains in maize fields has been shown to be an effective strategy for controlling contamination of aflatoxins, potent carcinogens produced by the fungus. This study monitored the expression levels of 18 defense genes against toxigenic and atoxigenic A. flavus strains in developing maize kernels over a time course of 96 h after inoculation. A stronger upregulation of genes encoding pathogenesis-related proteins, oxidative stress-related proteins, transcriptional factors and lipoxygenases were observed in response to the atoxigenic strain. On the other side, this strain showed a significant enhanced growth in the later stages of infection, measured as copy number of the constitutive calmodulin gene. These results suggest that overexpression of maize-defense-associated genes observed in response to the atoxigenic strain could contribute to an aflatoxin reduction. The identification of genes significantly affecting the resistance to A. flavus or aflatoxin accumulation would accelerate the development of resistant cultivars.
Regulation of renal immunity and immunopathology by interleukin-17

Pro-inflammatory cytokine IL-17 has been implicated in tissue damage associated with various autoimmune diseases. IL-17 is also known to contribute in immunity against bacterial and fungal pathogens. Most research over the past decade focused on understanding how IL-17- producing cells are generated, but far less is known about the organ specific responses of IL-17. In this thesis, we delineate the specific roles for IL-17 in the kidney, an organ susceptible to both auto-inflammatory conditions and infection. With the help of murine models, we outline the IL-17-driven responses in infection and autoimmunity. We studied the role for IL-17 mediated protection in disseminated candidiasis, a fatal nosocomial infection associated with high mortality. We discovered a previously unappreciated connection between IL-17 and the kallikrein- kinin system in renal protection against disseminated candidiasis. Simultaneously, we defined the cellular and molecular events in IL-17 driven renal tissue damage in murine models of autoimmune glomerulonephritis and lupus nephritis. Our results suggest that the kidney specific role of IL-17 is in the regulation of innate immune cells associated with kidney pathology. In addition, we were the first to show that neutralization of IL-17 ameliorated renal pathology in the autoimmune glomerulonephritis model. The consequence of unchecked renal inflammation is irreversible damage in the kidney, leading to fibrosis. In the case of inflammation mediated end organ fibrosis, the role for pro-fibrotic or anti-fibrotic role for IL-17 is debatable. We focused our attention on the role for IL-17-mediates immune responses in the kidney in a mouse model of fibrosis. We uncovered a surprisingly protective, anti-fibrotic role for IL-17 in the kidney that was driven by the IL-17-Klk1 axis. In summary, our findings have advanced the understanding of IL-17 mediated immunity and immunopathology and opens up the potential to develop therapeutic strategies based on the context of the disease.
Evidence of a relationship between weight and total length of marine fish in the North-eastern Atlantic Ocean: physiological, spatial and temporal variations

Weight–Body Length relationships (WLR) of 45 fish species (37 Actinopterygii and eight Elasmobranchii) were investigated. A total of 31,167 individuals were caught and their biological parameters measured during the four quarters from 2013 to 2015, on five scientific surveys sampling the North-eastern Atlantic Ocean from the North Sea to the Bay of Biscay (ICES Divisions IVb, IVc, VIId, VIIe, VIIg, VIIh, VIIj, VIIIa and VIIIb). Among 45 tested species, all showed a significant correlation between total length (L) and total weight (W). The influence of sex on WLR was estimated for 39 species and presented a significant sexual dimorphism for 18 species. Condition factor (K) of females was always higher than for males. Moreover, a spatial effect on the WLR according to five ecoregions (the Bay of Biscay, the Celtic Sea, the Western English Channel, the Eastern English Channel and the North Sea), was significant for 18 species among 38 tested species. The temporal effect was tested according to components (year and quarter/season). The seasonality effect on WLR is more frequently significant than the year especially for the Elasmobranchii species, and can be related to the spawning season. Finally, depressiform species (skates, sharks and flatfish) are characterized by positive allometric growth, whereas there is no such clear pattern regarding roundfishes growth, whatever their body shape is.
BIODEGRADATION OF WHITE YAM (Dioscorea rotundata Poir) AND WATER YAM (Dioscorea alata L.) SLICES DRIED UNDER DIFFERENT CONDITIONS

Two varieties of yams (water yam, Dioscorea alata L. and white yam, Dioscorea rotundata Poir) were processed into chips and dried under different conditions (Sun drying, oven drying and ambient). Mycoflora of the stored yam chips were studied. Fusarium oxysporium were most abundant in the samples evaluated while other fungi which including Aspergillus niger, Rhizopus stolonifer, Fusarium solani, Botryodiplodia theobromae, Mucor sp. , Geotrichium sp. , Pichia sp. , and Candida sp. were isolated. These fungi depleted some quantities of nutrients, starch and proteins in the yams chips. Minute traces of aflatoxin were detected in the yam chips from which A. flavus was isolated. The use of dry yam chips was found to be safe for human consumption especially under controlled environment like the use of electric oven.
Evolving Genotype Phenotype Mappings as dynamical Systems

This paper investigates the evolution of Genotype Pheno-type Mappings (GPMs). Here, the GPMs are represented as dynamical systems. It is investigated to which regions of a parameterized space of GPMs evolution leads. These regions are called Regions Of Maximum Adaptability (ROMAs). These ROMAs are stable but hard to predict.
NMR-based metabolomics applications: from food to human biofluids

Metabolomics is the scientific discipline that identifies and quantifies endogenous and exogenous metabolites in different biological samples. Metabolites are crucial components of a biological system and they are highly informative about its functional state, due to their closeness to the organism’s phenotype. This approach finds an increasing number of applications in many areas including medical, pharmaceutical, food and environmental sciences. The combined use of NMR spectroscopy and chemometrics techniques, is able to provide the metabolic “fingerprint” of the various samples. This PhD project focused on the analysis of various samples covering a wide range of fields, namely, food and nutraceutical sciences, cell metabolomics and medicine using a metabolomics approach. Indeed, the first part of the thesis describes two exploratory studies performed on Algerian extra virgin olive oil and apple juice from ancient Danish apple cultivars. Both studies revealed variety-related peculiarities that would have been difficult to detect by means of traditional analysis. The second part of the project includes four metabolomics studies performed on samples of biological origin. In particular, the first study is related to a recent emerging field: cell metabolomics. Indeed, tumour cells (HTC116) were treated with novel anticancer drugs in order to understand their in vitro action. The aim of this study was also the development of a reliable experimental protocol for an efficient harvesting, quenching and extraction of cellular metabolites of human adherent cancer cell lines. The second and the third studies concern the evaluation of the effects of functional food ingredients, namely β-glucans and phytosterols, on in vivo animal models. In particular, the hypocholesterolemic action of β-glucans was investigated by analysing rat plasma and faecal samples. This study confirmed the role of barley β-glucans in increasing faecal bile acids excretion in hypercholesterolemic rats and showed, for the first time, a modulation of the primary and secondary bile acid excretion, depending on the molecular weight of the β-glucan employed. In the other study, the effects of phytosterols on a murine colitis model, was investigated. NMR measurements on the liver metabolome revealed the role of these plant sterols in restoring the homeostatic equilibrium of the living system. Thus, in both cases, the results suggest the appropriate use of these nutraceutical products. The last study explores the differences in the follicular fluid metabolome of hyper- and normoinsulinemic women affected with Polycystic Ovary Syndrome (PCOS). The study provides preliminary but interesting relationships between serum hormones and metabolites in follicular fluids.
The High-resolution Timeline of Expression of Ribosomal Protein Genes in Yeast

The yeast ribosome is a complex molecular machine built from four rRNAs and over 70 r-proteins. Ribosome biogenesis involves ordered incorporation of ribosomal proteins, accompanied by and association and dissociation of other proteins specific to different stages of the process. By model-based analysis of temporal profiles of gene expression in a metabolically regulated system, we obtained an accurate, high-resolution estimation of the time of expression of genes coding for proteins involved in ribosome biogenesis. The ribosomal proteins are expressed in a sequence that spans approximately 25-minutes under metabolically regulated conditions. The genes coding for proteins incorporated into the mature ribosome are expressed significantly later than those that are not incorporated, but are otherwise involved in ribosome biogenesis, localization and assembly, rRNA processing and translational initiation. The relative expression time of proteins localized within specified neighborhood is significantly correlated with the distance to the centroid of the mature ribosome: protein localized closer to the center of mass of the entire complex tend to be expressed earlier than the protein localized further from the center. The timeline of gene expression also agrees with the known dependencies between recruitment of specific proteins into the mature ribosome. These findings are consistent in two independent experiments. We have further identified regulatory elements correlated with the time of regulation, including a possible dependence of expression time on the position of the RAP1 binding site within the 5’UTR.
The role of bioenergy and biochemicals in CO2 mitigation through the energy system – a scenario analysis for the Netherlands

Bioenergy as well as bioenergy with carbon capture and storage are key options to embark on cost‐efficient trajectories that realize climate targets. Most studies have not yet assessed the influence on these trajectories of emerging bioeconomy sectors such as biochemicals and renewable jet fuels (RJFs). To support a systems transition, there is also need to demonstrate the impact on the energy system of technology development, biomass and fossil fuel prices. We aim to close this gap by assessing least‐cost pathways to 2030 for a number of scenarios applied to the energy system of the Netherlands, using a cost‐minimization model. The type and magnitude of biomass deployment are highly influenced by technology development, fossil fuel prices and ambitions to mitigate climate change. Across all scenarios, biomass consumption ranges between 180 and 760 PJ and national emissions between 82 and 178 Mt CO2. High technology development leads to additional 100–270 PJ of biomass consumption and 8–20 Mt CO2 emission reduction compared to low technology development counterparts. In high technology development scenarios, additional emission reduction is primarily achieved by bioenergy and carbon capture and storage. Traditional sectors, namely industrial biomass heat and biofuels, supply 61–87% of bioenergy, while wind turbines are the main supplier of renewable electricity. Low technology pathways show lower biochemical output by 50–75%, do not supply RJFs and do not utilize additional biomass compared to high technology development. In most scenarios the emission reduction targets for the Netherlands are not met, as additional reduction of 10–45 Mt CO2 is needed. Stronger climate policy is required, especially in view of fluctuating fossil fuel prices, which are shown to be a key determinant of bioeconomy development. Nonetheless, high technology development is a no‐regrets option to realize deep emission reduction as it also ensures stable growth for the bioeconomy even under unfavourable conditions.
Regulation of mitochondrial fission by ceramide-induced Bcl-2-related ovarian killer in preeclampsia

Mitochondrial fission (MF) is regulated by the dynamin-related protein 1 (DRP1), and its excess is implicated in a number of human diseases. Preeclampsia (PE) is a hypertensive disorder of pregnancy associated with elevated placental ceramide (CER), a bioactive sphingolipid implicated in cell death. We hypothesize that increased CER, as found in PE, increase MF. We have found that PE placentae have increased expression of DRP1, and the mitochondrial compartment is enriched in CERs. JEG3 and primary isolated cytotrophoblast cells treated with CERs have increased pDRP1 expression and recruitment to the mitochondria. CER also increases pro-death Bcl-2 related ovarian killer (BOK) recruitment to the mitochondria in JEG3 cells, where it increases DRP1 expression. pDRP1 and BOK are recruited to the mitochondria associated ER membranes in primary cytotrophoblast cells treated with CER. In conclusion, increased CER augments MF via a mechanism involving BOK, and this may contribute to increased cell death in PE.
Toxicity of aflatoxin B1 on laying Japanese quails (Coturnix coturnix japonica)

ABSTRACT This study was performed to evaluate the efficacy of a herbal mycotoxin binder to overcome the adverse effects of 1.5 mg/kg of aflatoxin fed to laying quails. Results showed that addition of aflatoxin altered the performance indices of quails in terms of feed intake, FCR, egg production, and egg weight. Intestinal morphology of quails was also manipulated by inclusion of aflatoxin into the diet. The immunity of quails fed aflatoxin declined significantly. However, it could increase the population of harmful bacteria collected from the ileum of quails. The results of this study established that using herbal mycotoxin binder could bypass these adverse effects significantly and can be used in laying quails as a suitable binder when mycotoxin is present in their feed.
Estimating gains from genetic tests of somatic emblings of interior spruce

To assess the growth of somatic emblings versus seedlings and to estimate genetic parameters and gain that would accrue from a clonal testing and selection program, seedlings and 3 13 enibling clones froni 1 1 fullsib families of interior spruce (Yiccu glmc~r (Moench) Voss and l? crzgclr~~ur~izii Parry and their hybrid coniplex) were assessed at two test sites in British Colunlbia. Seedlings were 11'%1 taller than emblings after 7 years, however, when height at planting (age-one) was accounted for, the difference between the two stocktypes was reduced to 8 'XI (I, = 0.0414). Height-age trajectories between stocktypes were similar. Repeatabilities ibr height at age-7 were strong for clones ( A ; = 0.71; lr+ = 0.69) and families ( h i = 0.80). Variation was relatively high among clones (CV, 'XI = 14.6 ' X ; CVc/,,, /;, = 13.3 'XI), but low among families (CV, 'XI = 5.9). Genetic gains in excess of the seed orchard alternative were estimated for selection scenarios involving hypothetical tests containing between 200 and 2000 clones from 40 families. Gain for direct selection for height at age-7 was large: 21.5 'XI for niass clonal selection if the tallest 20 of 200 clones were selected, increasing to 32.8 ' X I if 20 of 2000 clones were selected. Substantial relatedness among the tallest clones was avoided by using 2-stage (family and clone-withinfi-lmily) selection, however, gains were about 4 ' X I less (e.g., 17.0 'X, and 28.9 'XI for tests of 200 and 2000 clones respectively) than for unrestricted (niass clonal) selection. Gain estimates are contingent on improved propagation methods being able to produce seedlings and emblings that possess equivalent growth rates. These results indicate that testing and deployn~ent of enibling clones can produce significant gains beyond that expected froni seed orchards, however several technical and economic issues remain to be addressed.
Vegetation zoning in relation to site and soil properties : A case study in the Darling Range, south-western Australia

In this paper, we describe, using multivariate analysis, the distribution of plant species at three valley-floor sites in the Northern Jarrah Forest, south-western Australia. At each site, plant species are distributed along a topographic gradient in communities that broadly parallel the valley floor, resulting in a conspicuously zoned vegetation pattern. Soils are arranged in a similar pattern, with a clear distinction between upland sandy soils, sandy loams on the footslope and silty loams on the flat valley floor, as reflected by changes in field texture, gravel content, electrical conductivity (EC) and major element concentrations. We found that the predominant influences on plant distribution were waterlogging and gradient, indicating a direct relationship between vegetation and topography. However, the relationship between vegetation and soil was less pronounced. There were moderate correlations between species distribution and the soil properties Texture, Gravel Content and Electrical Conductivity, and weak correlations with soil concentrations of Fe, C and Mn. We speculate that soil properties at these sites developed in response to the same seasonal conditions of desiccation and waterlogging that currently control plant distribution, albeit at substantially different timescales. Thus, the relationship between vegetation and soil is an indirect one, reflecting the dominant influence of hydrology on the distributions of both plants and soil.
Computational modeling of spontaneous behavior changes and infectious disease spread

This dissertation is dedicated to all who contributed to the success of it. iii ACKNOWLEDGEMENTS This journey which began as a dream and has now become a reality would not have been possible without the grace of God, the support of my family, professors and mentors, and friends. To my family, especially my mother, thank you for your innumerable prayers and for inspiring and encouraging me to pursue my dreams even when the light on the path was dim. Thank you for believing in me and supporting me emotionally and financially. Thank you for reminding me to be the best that I can be and to finish the race. I would like to give special thanks to my dissertation committee. First and foremost, my profound gratitude goes to my advisor, Dr. Peter Brecke, for his time, his careful attention to detail, and encouraging me to finish this dissertation. Words are inadequate to describe the tremendous support I received from him. I am thankful for his untiring support, encouragement, and guidance throughout this journey. I am also thankful for the support and encouragement I received from Dr. Without all your valuable feedbacks and encouragements, I would not have made it. To my friends, thank you for supporting me through this entire process. Thank you for listening and offering me advice when needed. Thank you for your thoughts, well-wishes, and constant prayers throughout this whole process. Above all, I owe all my gratitude to the Lord God Almighty who has brought me thus far and who is still taking me even farther; all that I am and ever hope to be, I owe it all to Thee.
Prospecting soil bacteria from subtropical Brazil for hydrolases production

Abstract Eighteen bacterial strains were isolated from soil of an urban area located in a transition zone between the Atlantic Forest and Pampa biomes, in southern Brazil. These strains were screened for cellulolytic, lipolytic and proteolytic potentials. Eleven isolates (61%) were able to produce cellulolytic enzymes on carboxymethylcellulose (CMC) agar plates, 14 isolates (78%) were proteolytic on skim milk agar plates, and all isolates demonstrated lipolytic/esterolytic potential on tributyrin agar (TBA) plates. From the 18 bacteria, nine (50%) were shown to produce the three investigated enzyme activities. Selected isolates were then evaluated for growth and enzyme production at different conditions of temperature and pH on CMC agar, TBA, and feather meal agar plates. As a general trend, growth and hydrolysis zones were observed at pH 6.0–9.0 and 30–37∘C. Sequencing of 16S rRNA gene fragments indicated that 10 isolates belonged to the genus Bacillus, three to Lysinibacillus genus, and the remaining isolates were representatives of Serratia, Phyllobacterium, Paenibacillus, Acinetobacter, and Curtobacterium. The isolate Bacillus sp. CL18 displayed competence for feather degradation when cultured in mineral medium (30∘C, pH 7.0) containing a single feather as the only organic substrate. Results from bioprospection indicate the functional versatility of the bacterial isolates, which might be of significance from both ecological and biotechnological perspectives.