Miracle-dz/UniFAR-FTUs huggingface dataset:
Nonlinear Dynamics of the Cosmic Neutrino Background

Nonlinear Dynamics of the Cosmic Neutrino Background Derek Inman Doctor of Philosophy Graduate Department of Physics University of Toronto 2017 At least two of the three neutrino species are known to be massive, but their exact masses are currently unknown. Cosmic neutrinos decoupled from the rest of the primordial plasma early on when the Universe was over a billion times hotter than it is today. These relic particles, which have cooled and are now non-relativistic, constitute the Cosmic Neutrino Background and permeate the Universe. While they are not observable directly, their presence can be inferred by measuring the suppression of the matter power spectrum. This suppression is a linear effect caused by the large thermal velocities of neutrinos, which prevent them from collapsing gravitationally on small scales. Unfortunately, it is difficult to measure because of degeneracies with other cosmological parameters and biases arising from the fact that we typically observe point-like galaxies rather than a continous matter field. It is therefore important to look for new effects beyond linear suppression that may be more sensitive to neutrinos. This thesis contributes to the understanding of the nonlinear dynamics of the cosmological neutrino background in the following ways: (i) the development of a new injection scheme for neutrinos in cosmological N-body simulations which circumvents many issues associated with simulating neutrinos at large redshifts, (ii) the numerical study of the relative velocity field between cold dark matter and neutrinos including its reconstruction from density fields, (iii) the theoretical description of neutrinos as a dispersive fluid and its use in modelling the nonlinear evolution of the neutrino density power spectrum, (iv) the derivation of the dipole correlation function using linear response which allows for the Fermi-Dirac velocity distribution to be properly included, and (v) the numerical study and detection of the dipole correlation function in the TianNu simulation. In totality, this thesis is a comprehensive study of neutrino density and velocity fields that may lead to a new technique for constraining neutrino properties via the dipole correlation function.
Forest Fires and Sustainability in the Boreal Forests of Canada.

The boreal forest is the largest forest region in Canada, occupying approximately 315 mill. ha. Within this forest region long-term average annual area burned is 1.3 mill. ha, with extreme fire years being common, covering up to 7 million ha in a single fire season. Only 2% to 3% of those fires that cover more than 200 ha eventually contribute about 98% of the total area burned annually. Careful examination of fire statistics seems to indicate that fire occurrence is increasing in the boreal forest. Boreal forest tree species and ecosystems are adapted to the periodic passage of fire and some would disappear as natural components of the landscape in the absence of fire. Use of fire as a management tool recognizes the natural role of fire and is applied judiciously for ecosystem maintenance and restoration in selected areas. Implications of possible anthropogenically generated climate change are examined within the context of sustainability of the boreal forest biome and the anticipated impact on fire regime and fire management.
Pharmacokinetic modeling in cancer : from functional to molecular imaging of angiogenesis

Purpose: Cancer angiogenesis can be imaged by using dynamic contrast-enhanced magnetic resonance imaging (DCE-MRI). Pharmacokinetic modeling can be used to assess vascular perfusion and permeability, but the assessment of angiogenic changes in the microvascular architecture remains challenging. This chapter presents two models enabling the characterization of the microvascular architecture by DCE-MRI. Theory: The microvascular architecture is re ected in the dispersion coe cient according to the convective dispersion equation. A solution of this equation, combined with the Tofts model, permits de ning a dispersion model for magnetic resonance imaging. A reduced dispersion model is also presented. Methods: The proposed models were evaluated for prostate cancer diagnosis. Dynamic contrast-enhanced magnetic resonance imaging was performed, and concentration-time curves were calculated in each voxel. The simultaneous generation of parametric maps related to permeability and dispersion was obtained through model tting. A preliminary validation was carried out through comparison with the histology in 15 patients referred for radical prostatectomy. Results: Cancer localization was accurate with both dispersion models, with an area under the receiver operating characteristic curve greater than 0.8. None of the compared parameters, aimed at assessing vascular permeability and perfusion, showed better results. Conclusions: A new DCE-MRI method is proposed to characterize the microvascular architecture through the assessment of intravascular dispersion, without the need for separate arterial-input-function estimation. The results are promising and encourage further research.
Comparison of population structuring in sympatric octopus species with and without a pelagic larval stage

An understanding of the influence of life history on dispersal capability is central to a range of disciplines within ecology and evolution. While studies have investigated this question by contrasting spatial population structuring in taxa that differ in life history, in the vast majority such comparisons differ in space and time, and therefore environmental factors may have contributed. Here, population structure of a holobenthic (i.e. direct developing) octopus, Octopus pallidus , was investigated genetically. This was compared to existing genetic data for a co-occurring merobenthic (i.e. planktonic larvae) species, Macroctopus maorum . Greater spatial genetic structuring was evident in O. pallidus than M. maorum . Patterns were consistent with isolation by distance in O. pallidus , but appeared related to oceanographic circulation systems in M. maorum , suggesting distance-dependent adult dispersal and current-mediated larval dispersal, respectively. Genetic population structuring in O. pallidus also largely corroborated inferences based on stylet microchemistry, indicating the utility of these environmental signatures. This study enables stronger predictions to be made regarding the dispersal capabilities and spatial population structuring of other cephalopods based on life history.
The influence of TGF-β signaling on precursor cells in the mouse retina

Age-related macular degeneration and glaucoma are among the most frequent causes of vision loss in the USA. Like retinitis pigmentosa or diabetic retinopathy, they cause a loss of retinal neurons, that can not be compensated by the human or mammalian retina. Fish or urodeles (salamander), in contrast, are able to not only regenerate single cells, but also complete and functioning retinae from their somatic stem cells. Based on this, many studies aim to clarify the signaling pathways that lead to regeneration in the retina or that keep the human and mammalian stem/progenitor cell populations from forming a regenerative reaction. One pathway that is part of the control mechanism of neural stem cells is the TGF-β signaling pathway. As TGF-β is known to reduce neurogenesis in the brain and in neural stem and progenitor cell cultures, we formed the hypothesis that it also has an influence on the stem/progenitor cells in the eye. Focussing on the precursor cells of the retina we were especially interested in Muller glia cells, as they present an important stem cell population in fish and birds. To demonstrate the influence of the TGF-β pathway on Muller glia in developing and lesioned adult mouse eyes, we used mice with a heterozygous deletion of the promoter region and exon I of Smad7 and of exon II of TGF-β Receptor II. With histologic and biochemical methods we could show that a deficiency of Smad7, an inhibitor of the TGF -β pathway, lead to a thickened inner and outer retina and an elevated number of Muller glia in the adult animal, caused by enhanced proliferation in newborn mice. Interestingly the stem cell marker Nestin could be shown to be elevated in Muller glia cells in adult animals as well. Additionally, we conducted NMDA lesions to provocate a proliferative reaction in the progenitor cell populations of the retina, but no effect could be shown. Experiments were also done with TGF -β receptor II deficient - and partly with TGF -β receptor II knockout mice, where a thinned retina in the adult animals could be found. We conclude that TGF-β influences proliferation during the development of the central retina, but not in the normal or injured adult retina.
Bax κ, a novel Bax splice variant from ischemic rat brain lacking an ART domain, promotes neuronal cell death

Bax is a pro‐apoptotic Bcl‐2 family protein that regulates programmed cell death through homodimerization and through heterodimerization with Bcl‐2. Bax α is encoded by six exons and undergoes alternative splicing. Bax κ, a splice variant of Bax with conserved BH1, BH2 and BH3 binding domains and a C‐terminal transmembrane domain (TM), but with an extra 446‐bp insert between exons 1 and 2 leading to loss of an N‐terminal ART domain, was identified from an ischemic rat brain cDNA library. Expression of Bax κ mRNA and protein was up‐regulated in hippocampus after cerebral ischemic injury. The increased Bax κ mRNA was distributed mainly in selectively vulnerable hippocampal CA1 neurons that are destined to die after global ischemia. Overexpression of Bax κ protein in HN33 mouse hippocampal neuronal cells induced cell death, which was partially abrogated by co‐overexpression of Bcl‐2. Moreover, co‐overexpression of Bax κ and Bax α increased HN33 cell death. The results suggest that the Bax κ may have a role in ischemic neuronal death.
DETECTION OF FUSARIUM OXYSPORUM f. sp. DIANTHI RACES IN IRAN

Fusarium wilt disease of carnation is one of the most im- portant diseases in all major carnation growing regions of Iran. This fungal disease is caused by Fusarium oxysporum f. sp. dianthi W.C. Snyder & H.N. Hansen. In 2011, an exten- sive sampling was carried out from carnation greenhouses in two Iranian provinces (Tehran and Markazi). Fungal iso- lates were identified as F. oxysporum based on morphological characters (Nelson et al., 1983). Pathogenicity tests were per- formed by root dipping carnation cuttings of the susceptible cv. Rendezvous. Controls were included by dipping carna- tion cuttings in sterile distilled water. All inoculated plants developed wilt symptoms after 50 days of incubation at 28 to 30°C. Fifty isolates were selected randomly for further molecular characterisation by comparison with eight F. oxy- sporum f. sp. dianthi isolates from Italy (courtesy of Professor A. Garibaldi), which were used as reference for races 1, 2, 4 and 8. F. oxysporum f. sp. dianthi races were identified by PCR amplification of transposon insertions (Chiocchetti et al., 1999). DNA was amplified using primers Ft3, R4.2, R8.1, R2.1 and IMP2 as described. Amplified fragments of 295 bp and 564 bp corresponded to races 1 (or 8, since the primers used do not allow discrimination between these two near- isogenic races) and to race 2, respectively. Of fifty isolates, 42 were identified as belonging to race 2 and two isolates were identified as race 1 (or 8). None of the tested isolates be- longed to race 4. Six isolates did not generate any amplifica- tion by using the tested primers. To the authors’ knowledge, this is first report of detection of Fusarium oxysporum f. sp. dianthi races in Iran.
Mapping the extension capability of the Goulburn Valley fresh pear network

Declining demand for canning and fresh pears, along with rising costs and diminishing returns, mean that Goulburn Valley pear growers are facing major production, market and investment decisions. Access to information and support about market opportunities, consumer preferences and quality protocols is critical for growers making reinvestment decisions; however increasing privatisation of advisory services makes it more difficult to source information. This study used social network analysis to understand how a sample of 25 pear growers use information networks to support their production and investment decision making. The findings show that growers' closest information-sharing relationships are with family members, staff and close neighbours. Fruit Growers Victoria and marketing agents are important sources of marketing information while some growers travel overseas to seek information. Industry and government organisations could strengthen the network by providing greater opportunities for growers and other stakeholders throughout the value chain to connect and share information.
Growth and production performance of threatened snakehead fish, Channa striatus (Bloch), at different stocking densities in earthen ponds

Production trials of threatened snakehead fish (Channa striatus) were carried out under different stocking densities in earthen ponds of Bangladesh. The average weight and length of the fingerlings during stocking was 17.63 ± 1.23 g and 13.21 ± 0.52 cm. Fingerlings were stocked at 5000 ha−1 in treatment-1 (T1), 6250 ha−1 in treatment-2 (T2) and 7500 ha−1 in treatment-3 (T3) respectively. Fish in all the experimental ponds were fed with supplementary feed comprising of fish meal (30%) and mustard oilcake (70%) at the rate of 3–6% of estimated body weight two times per day. In addition, trash fish were supplied at the rate of 2–3% of the estimated biomass on each alternate day. In situ water quality parameters of the pond were within the suitable range for fish culture. The growth and survival of fingerlings were significantly higher in T1 than in T2 and T3. The food conversion ratio was significantly lower (P<0.05) in T1 than in T2 and T3. The estimated gross and net production of fish was higher in T1, followed by T2 and T3. Overall, the highest growth, survival and production were obtained from T1. Therefore, it could be concluded that of 5000 fingerlings ha−1 is the most suitable stocking density for culturing C. striatus under a monoculture system in the earthen ponds for better production.
To improve haptic experiences in VR and AR, we must first improve tracking.

Current research prototypes provide haptic experiences unthinkable with current commercial devices. As haptic feedback is complex and multi-faceted a significant research effort has been put into developing elaborate feedback devices. We believe that haptics must be considered as a coupled input/output system. Looking at commercial VR / AR systems it appears as if the work on the output side has far outpaced the work on the input side. We therefore argue that the next step in improved haptic touch and communication systems lies not in better output technologies, but in better input and position tracking technologies. In this position paper we provide context to this claim, explain how our backgrounds put us in a uniquely suited position to explore this topic further and present some discussion points which we wish to consider in our future work.
Relationship Between Protein Oxidation Markers and Oxidative Stress Biomarkers

There is a general agreement (belief) that lipids are the pivotal element in inflammatory disease. One of the most studied topics is the connection between lipid oxidation and cardiovascular disease. In a very recent review, the introductory paragraphs states, after resuming the elements of the inflammatory response starting with stimulated endothelium displaying adhesive molecules for circulating leucocytes, lipid oxidation products formed by virtually every vascular cell type participate in orchestrating these processes and the inflammatory process is actively limited by activation of a resolution phase, often via generation of structurally specific oxidized lipids whose function is to orchestrate resolution of inflammation (McIntyre & Hazen 2010). Most of the knowledge involving lipid oxidation comes from “in vitro” studies and on supplementation trials with antioxidants like vitamins and anti-inflammatory drugs. Vitamins E and C are considered dietary antioxidants although mostly ex vivo measurements of lipid peroxidation have been performed (Hillstrom et al. 2003; Heinecke 2001). Quantifying “in vivo” lipid oxidation is not easy and several biomarkers of lipid peroxidation has been used like F2-isoprostanes, considered the most accurate way to measure oxidative stress “in vivo”, and as a risk factor for atherosclerosis and other diseases (Lawson et al. 1999). The secondary products of lipid peroxidation (LPO) the reactive carbonyl compounds, modify biologically essential molecules such as proteins and DNA bases (Yuan et al. 2006). Thus lipid oxidation processes in biological tissues may be more complicated since they contain a plethora of carbohydrates, proteins and lipids forming a complex matrix. In tissues, lipid oxidation can cause protein oxidation due to close interactions between lipids and proteins. LPO “in vivo” has been implicated as the underlying mechanisms in numerous disorders and diseases such as cardiovascular diseases, cancer, neurological disorders, and aging. Thus, when oxidative stress biomarkers are evaluated protein oxidation deserves consideration.
Direct Binding of Toll-Like Receptor 2 to Zymosan, and Zymosan-Induced NF-κB Activation and TNF-α Secretion Are Down-Regulated by Lung Collectin Surfactant Protein A1

The lung collectin surfactant protein A (SP-A) has been implicated in the regulation of pulmonary host defense and inflammation. Zymosan induces proinflammatory cytokines in immune cells. Toll-like receptor (TLR)2 has been shown to be involved in zymosan-induced signaling. We first investigated the interaction of TLR2 with zymosan. Zymosan cosedimented the soluble form of rTLR2 possessing the putative extracellular domain (sTLR2). sTLR2 directly bound to zymosan with an apparent binding constant of 48 nM. We next examined whether SP-A modulated zymosan-induced cellular responses. SP-A significantly attenuated zymosan-induced TNF-α secretion in RAW264.7 cells and alveolar macrophages in a concentration-dependent manner. Although zymosan failed to cosediment SP-A, SP-A significantly reduced zymosan-elicited NF-κB activation in TLR2-transfected human embryonic kidney 293 cells. Because we have shown that SP-A binds to sTLR2, we also examined whether SP-A affected the binding of sTLR2 to zymosan. SP-A significantly attenuated the direct binding of sTLR2 to zymosan in a concentration-dependent fashion. From these results, we conclude that 1) TLR2 directly binds zymosan, 2) SP-A can alter zymosan-TLR2 interaction, and 3) SP-A down-regulates TLR2-mediated signaling and TNF-α secretion stimulated by zymosan. This study supports an important role of SP-A in controlling pulmonary inflammation caused by microbial pathogens.
Artistic design of visual multimedia content

: The article is dedicated to the development of an approach to the design of visual information content of an exposition for museum equipment. It considers the importance of designing informative visual imagery. The proposed techniques for solving the issue of images in the absence of complete archaeological and historical data imply the use of stylization. Various ways and approaches to the solution of the content styling issue are provided. Successful application of the design techniques is illustrated by experimental data.
Turtle carotid circulation: a character analysis case study

The bony canals permeating the turtle skull associated with the cranial circulation have long been considered integral to an understanding of extinct and extant turtle systematics. Recent phylogenetic analyses, employing a variety of data sets, suggest alternatives to the traditional arrangement of crown turtles. Of particular note is the recent failure of investigations employing molecular techniques to retrieve a monophyletic Trionychoidea, a clade supported largely by shared circulatory features. These alternative phylogenies may also have implications for extinct forms. The turtle cranial arterial circulation therefore represents an ideal system upon which to conduct a detailed, multipronged analysis of a systematically influential character. In the present study, the theoretical underpinnings of character analysis are critically evaluated, and a new interpretation of circulatory variation in turtles is offered, including a revised phylogenetic character suite. This assessment indicates an autapomorphic circulatory pattern in Trionychia, whereas Trionychoidea is not supported. © 2008 The Linnean Society of London, Biological Journal of the Linnean Society, 2008, 93, 239–256.
E-selectin as anti-inflammatory drug target : expression, purification and charactrization for structural studies : assay development for antaginists evaluation

E-, P- and L-selectin belong to the C-type lectin family of cell adhesion molecules that initiate inflammatory response. Infammation per se is a physiologocal defense mechanism, but excessive leukcyte extravasation leads to numerous pathoIogical and disease states, as well as metastatic cancer spread. Leukocyte tethering and rolling toward inflammatory site start with the interaction of selectins and the carbohydrate epitope of their glycoprotein ligands, sialyl Lewisx. Therefore inhibitors of selectin-ligand interaction are of high pharmaceutical interest as potent anti-inflammatory agents. Tetrasaccharide sialyl Lewisx serves as a lead strucure in chemical and computational search for selectin antagonists. Structural NMR and X-ray studies indicated binding mode of sialyl Lewisx with E-, and P-selectin, but improved structural studies with the second and third generation antagonists is missing. We expressed recombinant human E-, P- and L-selectin/IgG as secreted proteins in mammalian expression system and purified them to homogniety. Acitivity of the proteins was confirmed with blocking monoclonal antibodies and ligand binding confirmed by NMR. Bioassays were developed in cell-free and cell-based formats with E-selectin/IgG to evaluate inhibitory potencies of in-house synthesized selectin antagonists. Due to variation and instabilities on day-to-day and batch-to-batch basis, assays were used only for preliminary antagonists screen. To enhance further structural studies, we developed a new system for the expression of truncated form of human E-selectin (lectin and EGF-like domains). Initialy we tried to express these two domains in E.coli, but refolding of expressed inclusion bodies was inefficient. Therefore lectin and EGF-like domains of human E-selectin were expressed as secreted form in baculovirus-infeced insect cells with a flag-epitope on its C-terminus. Expressed protein (LecEGFFlag) was monomeric in solution, correctly folded and active, as confirmed in the reaction with monoclonal blocking antibodies, and NMR studies. Protein was expressed in two distinct glycosylation forms, with apparent molecular weigts of 19.96 kDa and 21.15 kDa. In addition, we developed for the first time a cell-free assay with truncated form of Eselectin (aforementioned LecEGFFlag) for the evaluation of of E-selectin inhibitors. In a proof-of-concept manner, three different E-selectin antagonists were tested and obtained IC50 values were in close agreement with published results. Reproducibility and stability of the assay on day-to-day and batch-to batch basis make it suitable not only for the preliminary screening, but also to quantify inhibitory potencies of E-selectin antagonists. Developed system is suitable for expression and similar characterization of P- and Lselectin as well.