Miracle-dz/UniFAR-FTUs huggingface dataset:
Detection of Pathogenic Waterborne Parasites in Treated Wastewater of Rada'a City -Yemen

Purpose: The aim of this study is to detect the presence of waterborne parasites in the treated wastewater in Rada'a city. Study Design: An Experimental Research Design. Materials and Methods: Waterborne parasites in the collected samples were concentrated using formol ether and zinc sulphate techniques and then microscopically analyzed to identify protozoa and helminth eggs. Fifteen treated sewage samples were randomly collected from different positions of wastewater treatment plant in three different months of 2019 (May, June and August) with three replications. Each sample was collected in one-litre volume and recorded as original sample. Parasite analysis was done using the McMaster worm egg counting slides with chamber size of 0.3 mm. Results: In this study, Giardia lamblia was found in a high percentage in comparison to other parasites, followed by Entamoeba histolytica, Entamoeba coli. The majority of parasite eggs in the treated wastewater samples were related to Hookworm and Ascaris lumbricoide followed by Taenia saginat and Enterobius vermicularis. Furthermore, Cryptosprodium oocyst and Fasciola hepatica eggs were rarely detected. Conclusion: The observed pattern of contamination demonstrated that the quantity of parasites in sewage after treatment exceeded the permitted levels and it is necessary to modify the treatment process of wastewater to prevent the possible spread of parasitic contamination.
Computations Reveal a Rich Mechanistic Variation of Demethylation of N-Methylated DNA/RNA Nucleotides by FTO

The fat-mass and obesity-associated (FTO) protein employs an iron(IV) oxo species to demethylate N-methylated nucleic acids. Herein, we use atomistic-theoretical calculations to study the demethylation of the N-methylated DNA/RNA bases 6-methylated adenine (m6A), 3-methylated thymine (m3T), and 3-methylated uracil (m3U). The mechanisms involve in-enzyme hydroxylation of the methyl group, followed by hydrolysis of the oxidized intermediates in aqueous solution to demethylate the bases. The in-enzyme reactions have been studied using quantum mechanical/molecular mechanical (QM/MM) calculations, while the hydrolytic reactions occurring outside the enzyme have been explored with hybrid cluster-continuum (HCC) calculations. When the results obtained with these different methods are combined, the calculated barrier for the overall transformation is consistent with the experimental free energy barrier for the major route of m6A demethylation: in this pathway, adenine’s N1 site acts as an internal base catalyst i.
Activité antifongique d'extraits de Thymelaea lythroides sur trois champignons pathogènes du riz

Les racines, ecorces, feuilles, fleurs et fruits de Thymelaea lythroides, plante medicinale repandue dans la foret de la Mamora dans la region du Gharb au Maroc, ont ete extraits par quatre solvants : ether de petrole, chloroforme, acetate d'ethyle et methanol. Les extraits presentent une activite antifongique variable sur Curvularia lunata, Helminthosporium oryzae et Pyricularia oryzae, champignons pathogenes du Riz. La sporulation apparait plus inhibee que la croissance mycelienne.
Identification of novel protein band (s) distinguishing hulled v.s hullless varieties in barley (Hordeum vulgare L.) and its characterization

Barley (Hordeum vulgare) is one of the cereal crops among top five major crops of the world which is widely used for food, feed stock, malting, brewing and distilling industry. It belongs to the Poaceae family. The barley is cultivated as a Rabi crop in India with sowing being under taken from OctoberDecember and harvesting from March-May. Our aim was to quantify the protein of the hulled and hullless barley varieties and identify the novel protein band in hulled barley varieties. The range of seed grain protein in both hulled and hullless barley varieties were found 49.63 mg/gm. to 105.63 mg/gm. Maximum protein was found in Dolma i.e., 105.63 mg/gm, which minimum protein was found in NDB 1173 i.e., 49.63 mg/gm. Variation in presence or absence and the relative mobility of some electrophoretic band was also observed among the hulled and hullless barley genotype. The highest variation in the electrophoretic profile of seed storage protein was observed around at 70 kDa and 20 to 40 kDa range of band. All the Twelve barley genotypes hulled and hullless also differed in intensity of bands as well as in number of protein bands. To raise antibody against identified protein, rabbit was selected for immunization. A subcutaneous method was used for making protein titer for production of antibody.
A Sequential Study of Cell Divisions and Expansion Patterns on a Single Developing Shoot Apex of Vinca major

During the growth of a single developing vegetative apex of Vinca major, both the orientation and frequency of cell divisions, and the pattern of cell expansion, were observed using a non-destructive replica technique. Micrographs taken at daily intervals illustrate that the central region of the apical dome remains relatively inactive, except for a phase of cell division which occurs after 2 d of growth. The majority of growth takes place at the proximal regions of the dome from which develop the successive pairs of leaves
Comparison of Chemical Composition and Immune-enhancing Activity of the Four Lines of Korean Native Chickens

ABSTRAT This study was conducted to compare the general composition and immunomodulatory activity of breast and thigh meats from four lines of Korean native chickens: Yeonsan Ogye, Hyunin Black, Hwangbong, and Hoengseong Yakdak. White Leghorn was used as a control. Fifteen male chickens (three chickens in each line) were grown under the same conditions and slaughtered at 13 weeks old. The four lines of Korean native chickens, regardless of the part, had higher contents of crude fat ( p <0.05) than White Leghorn. The cholesterol contents were significantly higher in Hyunin Black and significantly lower in Hoengseong Yakdak than those of other chickens ( p <0.05). The immunomodulatory effect, assessed by macrophage cell proliferation and nitric oxide production, was only observed in the breast meat of the four lines of Korean native chickens. The phagocytic activity of macrophage cells was significantly augmented by the breast meat of Hyunin Black and Hoengseong Yakdak. Furthermore, the mRNA expressions of pro-inflammatory cytokines, such as IL-4, IL-10 and IFN-γ, was significantly suppressed by Korean native chickens compared with White Leghorn. These results suggested that the four lines of Korean native chickens exhibited greater immune-enhancing activity than White Leghorn.
Phenotypic and Genetic Variation of Milk Fat Components Incorporating Mid-Infrared Technology

PHENOTYPIC AND GENETIC VARIATION OF MILK FAT COMPONENTS INCORPORATING MID-INFRARED TECHNOLOGY Allison L. Fleming Advisors: University of Guelph, 2016 Dr. Filippo Miglior Dr. Flavio S. Schenkel Milk fat influences the economic, nutritional, flavour, and physico-chemical properties of milk and milk products. Genetic selection for fat components is therefore of interest. This would require an efficient means of phenotyping these traits routinely, on a large scale. The purpose of this study was to assess the ability to predict milk fat components using mid-infrared (MIR) spectroscopy and to examine the phenotypic and genetic variation of these traits. Individual cow milk samples from multiple breeds and herds were collected during routine milk recording multiple times throughout the lactation and the MIR spectra obtained. Milk samples were further analyzed for average milk fat globule (MFG) size and fatty acid profile using gold standard methodologies. Partial least squares regression models were employed to develop equations to predict the milk fat component traits from the MIR spectra of milk samples. Genetic parameters were estimated in Holsteins for both the measured and predicted MFG size and predicted fatty acids, along with their genetic correlations with milk production traits using multi-trait animal models. Milk fatty acid contents could be predicted with variable accuracy depending on the calibration set used and the concentration of the fatty acid in milk. In first-parity Holsteins, the predicted groups of fatty acids were found to have genetic correlations of similar magnitude with
ON MULTICOMPONENT FLOWS: MECHANICAL MODELING AND FINITE ELEMENT SIMULATIONS

Abstract. The study of multicomponent systems finds a large scope of applications in engineering problems. They involve multiphase problems, as porous media and gas-liquid interfaces; and single-phase problems, as gas and liquid mixtures. The main goal of this paper is the application of a finite element method to simulate flow problems involving incompressible mixtures. A mixture theory supported by continuum mechanics was employed to present the development of a mechanical modeling for multicomponent flows. This theory is based on classic conservation postulates, which were written for multicomponent systems. The mechanical modeling was summarized in a set of equations in terms of velocity, pressure and mass fraction fields. Those equations were approximated by a stabilized finite element method, for the classical Galerkin method does not have the ability of solving some flows of practical interest. That happens because: first, Galerkin approximation involves a mixed formulation where the compatibility of pressure and velocity subspaces is critical and demands the use of non-conventional finite elements; and second, it suffers from the asymmetric nature of advective terms – a numerical difficulty in the approximation of advective-dominated problems. The stabilized Galerkin/least-squares method (GLS) was able to overcome the numerical difficulties mentioned above. In this study the GLS formulation was applied to approximate generalized newtonian binary mixtures. Some results were compared with other authors showing good agreement. Those problems involved geometric and material non-linearities employing Carreau fluid model, opening the spectra for industrial applications in areas such as food, polymer, biological and environmental engineering.
Lecane tenuiseta rotifers improves activated sludge settleability in laboratory scale SBR system at 13°C and 20°C

Two experiments at different temperatures were conducted in five laboratory‐scale bioreactors with enhanced nutrient removal simulating the work of sequencing batch reactors (SBRs). The process was operated in three 8‐hour cycles. The oxygen concentration, pH and temperature were controlled and maintained at 1 mg of O2/L, 7 and 13°C, respectively, throughout the first two weeks and at 20°C for the next 10 days. The introduction of Lecane tenuiseta improved the settling properties of the activated sludge dominated by Microthrix parvicella at both temperatures tested. L. tenuiseta rotifers led to a reduction in filamentous bacteria abundance and did not negatively affect the chemical parameters of the effluent. For each temperature, there were no differences in COD, Ntot, N‐NH4 or P‐PO4 values between the treatment and control bioreactors. The results have shown that the application of L. tenuiseta is a promising biological tool for bulking prevention especially in a cold season.
Length, Nodes Underground, and Orientation of Transplants in Relation to Yields of Sweet Potato

Total marketable root yield was greater with 40- to 45-cm rather than 20- to 25-cm lengths of ‘Red Jewel’ sweet potato [Ipomoea batatas (L.) Lam. ] transplants. U.S. #1 root yield from 20- to 25-cm ‘Red Jewel’ transplants was increased when they were oriented vertically, but there was no difference in the percentage of U.S. #1 root yield under these conditions. Orientation did not influence significantly U.S. #1 root yield from 40- to 45-cm ‘Red Jewel’ transplants, but the percentage of U.S. #1 roots increased due to horizontal orientation. When ‘Red Jewel’ transplants were oriented vertically, their length did not affect U.S. #1 root yields. With horizontal orientation, U.S. #1 root yield of 40- to 45-cm ‘Red Jewel’ transplants increased. Yield of U.S. #1 roots of ‘Georgia Jet’ was not affected by transplant length or orientation but was reduced when 5 or 6 nodes were planted underground.
The role of Ikaros in Foxo1-driven gene expression in CD4 T cells

The existence of a robust, mature CD4 T cell population is essential in orchestration of an immune response. CD4 T cell activation is a result of antigenic stimulation of a unique cell pool that is normally resting. Termed “naïve”, these CD4 T cells lack effector function and are maintained long term in the periphery. Expression of key cell surface receptors and transcription factors dictates their ability to survive, home and differentiate into effector subsets. However, transcriptional regulation of these processes in naïve CD4 T cells is only partly characterized. Ikaros has been identified as a transcriptional activator and repressor of T cell lineage fate decisions and polarization into T helper cell subsets. In this dissertation, a role for Ikaros in regulation of naïve CD4 T cells is revealed as in its absence, cells exhibit decreased survivability, impaired migration to lymph nodes and failure to develop into induced regulatory T cells (iTreg). Defects are linked to decreased expression of IL7Rα, CD62L and Foxp3, respectively, all identified as targets of a transcription factor important in naïve CD4 T cell homeostasis, Foxo1. Analogous consequences on T cell survival, homing and differentiation have been reported for Foxo1deficient T cells.
Autoimmune kidney damage correlates with autoantibody specificity and inflammatory mononuclear cell phenotype in the CD45 mutant mouse model of lupus

Author(s): Hai, Si-Han Virginia | Advisor(s): Tang, Qizhi | Abstract: Systemic lupus erythematosus is a complex autoimmune disease with a multi-step pathogenesis that is caused by both environmental and genetic factors. The mechanisms that govern the transition from autoreactivity (presence of autoantibodies) to autoimmunity (end-organ damage) and that determine disease severity remain incompletely understood. Here, we leverage a mouse model where the phenotypic consequences of the same activating point mutation E613R in the phosphatase CD45 depend on genetic background. While both BALB/c and (B6-129) F1 CD45E613R mice develop high titer anti-double stranded (ds) DNA antibodies, only F1 mice develop glomerulonephritis (GN) and die prematurely. Surprisingly, similar immune complex deposition is seen in glomeruli of both strains. We find that genetic background dependent differences in the autoantibody repertoire and renal effector cell populations correlate with development of renal pathology in only F1 CD45E613R mice. Whereas BALB/c CD45E613R mice develop anti-dsDNA antibodies, F1 CD45E613R mice develop a broader autoantibody repertoire that recognizes both DNA- and RNA-containing antigens and that induces a more pro-inflammatory phenotype when cultured with a macrophage cell line. Consistent with this, inflammatory renal mononuclear cells are preferentially expanded in young F1 CD45E613R kidneys prior to disease onset and infiltrate glomeruli over time. This correlates with elevated MCP-1, RANTES, and BAFF levels and functional studies demonstrating F1 CD45E613R macrophages are skewed towards a more pro-inflammatory phenotype. Together, our findings demonstrate that genetic background influences both autoantibody profiles and renal immune cell subsets and provide new insights into mechanisms governing the transition from autoreactivity to autoimmunity in lupus nephritis.
NON-MIGRATORY MOVEMENTS OF DUNLINS ON THEIR CALIFORNIA WINTERING GROUNDS

In 1991-1992, we tracked 150 marked Dunlins (C&i&s alpina) from two central California coastal sites to ascertain if they made winter-time movements to inland areas and examined census data from these and other coastal sites to document the possible extent and frequency of these movements. Between December 1991 and January 1992, Dunlin numbers at four central California coastal sites decreased by 44-84% during periods of heavy rain. Subsequently, six or seven of the marked Dunlins from one of these sites were located inland, up to 140 km away. The sudden disappearance of more than 40% of the wintering Dunlins from this coastal area in 10 of 21 years suggests that such movements may be fairly frequent. Median (October-March) numbers of Dunlins at this site during the 21 years were negatively correlated with local rainfall, suggesting a relationship between winter storm activity and the level of use of coastal sites. It remains to be determined whether deteriorating conditions in coastal wetlands or the increased availability of inland habitats related to winter storms is responsible for reducing Dunlin winter-time use of coastal sites. Received 28 March 1994, accepted 6 Sept. 1994. Although much has been learned about the distribution and abundance of shorebirds in the Pacific Flyway in recent years (Page et al. 1992), how different sectors of the flyway are linked together remains poorly understood, particularly for wintering shorebirds. Small scale movements of shorebirds are known to occur in winter, often in response to specific weather conditions. Eurasian Curlews (Numenius arquatu) move between coastal mudflats and agricultural fields up to 30 km away, depending on weather (Bainbridge and Minton 1978, Townshend 1981) and perhaps moon phase (Hale 1980). Freezing weather in Europe forces Lapwings (Vanellus vane&s) and Greater Golden-Plovers (Pluvialis apricaria) from inland fields to coastal estuaries (Hale 1980). Local movements of 2-10 km between estuaries and fields in response to rain, snow, or ice have been documented for Redshanks (Tringa totanus), Dunlins (Culidris ulpina), Black-bellied Plovers (Pluvialis squuturola), Killdeers (Churud- rius vociferus), Marbled Godwits (Limosu fedoa), Least Sandpipers (Cal-
Optimization of the touchscreen paired-associate learning (PAL) task for mice and its dorsal hippocampal dependency

ABSTRACT Two versions of the touchscreen paired-associate learning (PAL) task have been developed for rodents: same PAL (sPAL) and different PAL (dPAL). These tasks are very important in studying murine models of Alzheimer’s disease and schizophrenia, and have also been used to test object-location memory in various studies. However, the relatively long time needed for the tasks (approx. 50 days for mice) limits their widespread use. By giving training that was more intensive with a higher number of trials, we shortened the time required for learning saturation in sPAL and dPAL to about one-third of the time required for the generally used protocol. Furthermore, by applying a reduced number of objects and trial types for sPAL, we developed a simplified version of sPAL, termed 2-object sPAL, in which mice could reach the fully learned level in 6 days. Our pharmacological experiments indicate that the dorsal hippocampal CA1 region is crucial for the performance of the two PAL tasks with the new protocols and the new 2-object sPAL. This work has significantly enhanced the usefulness of the touchscreen PAL tasks to increase the speed of learning, but they remain highly hippocampus-dependent object-location memory tasks.
Signal Divergence and Speciation in a Hispaniolan Anolis Lizard

My dissertation research investigates the processes underlying signal divergence and speciation in Anolis lizards. To investigate this, I study the striking geographic variation in Anolis distichus dewlaps across Hispaniola; a signal important to sexual selection and species recognition in anoles. In Chapter 1, I test whether variation in A. distichus dewlap color, pattern and size is a result of adaptive signal divergence to heterogeneous environments. Using phylogenetic comparative analyses of environmental and phenotypic data, I show a strong correlation between divergence in dewlap phenotype and environmental variation across Hispaniola. The repeated pattern of dewlap divergence and environmental variation provides strong evidence for adaptive dewlap divergence. In Chapter 2, I test a critical assumption of natural selection and adaptation by investigating whether dewlap color is inherited. I conduct a common garden breeding experiment with A. distichus populations exhibiting different dewlap phenotypes, and follow this with a carotenoid supplementation experiment to investigate the contribution of dietary pigments to dewlap color variation. I find that several aspects of dewlap color and pattern are highly heritable, and dewlaps exhibit no change with carotenoid
Evaluación de la toxicidad de cianofítas sobre el microcrustáceo Artemia Cyanophytes toxicity evaluation on Artemia micro crustacean

Toxicity of three strains of autochthonous cyanophytes: Microcystis, Limnothrix and Oscillatoria was evaluated in bioassays by triplicate until 48 hours of exposition on Artemia, by using different concentrations of hydrosoluble fractions and with a thermic treatment; and liposoluble fractions extracted from harvested biomass of each cyanophyte culture in seawater to proportions of 1:2, 1:5, 1:10 and 1:25 (fraction : seawater). A high toxicity was detected in the hydrosoluble fraction in function of the concentration; also, it was demonstrated
Performance Evaluation of Crumb Rubber Asphalt Modified with Silicone-Based Warm Mix Additives

This research was conducted to elucidate better understanding of the performance of crumb rubber asphalt modified with silicone-based warm mix additives. Two different silicone-based warm mix asphalt (WMA) additives (herein Tego XP and Addibit) were used to prepare crumb rubber modified (CRM) warm mix asphalt binders. The viscosity of these CRM binders was measured at different temperatures and shearing rates. Furthermore, softening point and penetration tests, Multiple Stress Creep Recovery (MSCR), Time Sweep (TS), Atomic Force Microscopy (AFM), Frequency sweep (FS), and Fourier Transform Infrared (FTIR) tests were also conducted on prepared samples. Based on these robust and rigorous laboratory experiments, it was established that viscosity of CRM binders was reduced by addition of Tego XP and Addibit WMA additives. However, WMA additives had different influence on rheological properties of the binder. CRM binder with Tego XP improved resistance to rutting of the binders but would degrade the fatigue performance. On the contrary, viscoelastic continuum damage (VECD) model results and those of phase angle approach revealed that the binder with Addibit improved resistance to fatigue cracking of the binders but had no adverse effects on high temperature rutting performance. FTIR test results established a presence of polydimethylsiloxane (PDMS) in CRM binders with Tego XP and Addibit. PDMS is a well-known hydrophobic organic and inorganic polymer that is water repellent; therefore, binders containing these silicone-based warm mix additives could be beneficial in resisting moisture damage in asphalt binders and mixtures. Morphology of CRM binders with and without WMA revealed good distribution of the rubber particles in asphalt binder matrix. Further addition of WMA increased surface roughness of the binder, which can be correlated to changes in microstructure properties of the binder. Therefore, the study concluded that addition of Tego XP and Addibit reduces viscosity and improves mechanical properties of the asphalt binder.