In this thesis we introduce a new quantity which we call the dynamic fidelity susceptibility (DFS). We show that it is relevant to out-of-equilibrium dynamics in many-particle quantum systems, taking the problem of an impurity in a Bosonic Josephson junction, and the transverse field Ising model, as examples. Both of these systems feature quantum phase transitions in their ground states and understanding the dynamics near such critical points is currently an active area of research. In particular, sweeping a system through a quantum critical point at finite speed leads to non-adiabatic dynamics. A simple theoretical tool for describing such a scenario is the celebrated Kibble-Zurek theory which predicts that the number of excitations is related to the speed of sweep via the phase transition’s critical exponents at equilibrium. Another theoretical tool, useful in describing the static properties of quantum phase transitions, is the fidelity susceptibility. Our DFS generalizes the concept of fidelity susceptibility to nonequilibrium dynamics, reproducing its results in the static limit, whilst also displaying universal scaling properties, akin to those found in Kibble-Zurek theory, in the non-adiabatic regime. Furthermore, we show that the DFS is the same quantity as the time-dependent quantum Fisher information which provides a measure of multi-partite entanglement, as well as being closely related to out-of-time-order correlators (OTOCs). / Thesis / Master of Science (MSc)

Control strategies against the parasitic nematode Teladorsagia circumcincta are problematic under current sheep management systems. Infection with the parasite, particularly in young lambs, results in significant production losses therefore sustainable worm control is being sought. It has been established that variation in resistance to T. circumcincta is under genetic control and the development of resistance is an acquired characteristic and has an immunological basis. This project investigated the immunological response to infection, of lambs with predicted resistance or susceptibility to T. circumcincta. Specifically, the study aimed to identify immune response-associated genes that were differentially-expressed in resistant and susceptible lambs and attempted to identify mutations in these genes. This study was part of a long term project that aims to identify genetic marker/s to aid in marker-assisted selection (MAS) for resistance to T. circumcincta. Real time reverse transcription-quantitative polymerase chain reaction (real time RTqPCR) was performed on abomasal mucosa and lymph nodes from 55 lambs used in a previous experiment. The lambs had been either trickle-infected with 2,300 infective larvae every two days over three months (infected resistant/susceptible, n=45) or sham-dosed (non-infected control, n=10). Lambs were ranked in relation to faecal egg count (FEC) and adult worm count (AWC) at post mortem; zero or low FEC (resistant) to high FEC (susceptible). Histopathology showed only mild pathological changes in the abomasal mucosa of resistant lambs but heavy lymphocytic inflammatory infiltration in the mucosa and submucosa of infected susceptible animals. Measurements of a range of cytokine transcripts and cell markers associated with the four major CD4+ T cell subsets identified IL6, IL21, and IL23A as significantly increased by at least two-fold in abomasal lymph nodes and abomasal mucosa of susceptible lambs in comparison to resistant animals. Highly significant (P<0.02) positive correlations were found between IL6 (ρ=0.35), IL21 (ρ=0.54) and IL23A (ρ=0.38) transcript levels and AWC. Similarly, there were highly significant (P<0.01) positive correlations between FEC and IL6 (ρ=0.41), IL21 (ρ=0.65) and IL23A (ρ=0.31). In contrast, significant negative correlation (P<0.04) between IL23A with IgA antibody levels (ρ=-0.31) was found. There was also a significant positive correlation (P<0.03) of TGFB1 levels with AWC (ρ=0.42) and FEC (ρ=0.32) in the abomasal mucosa. These data suggests that susceptibility to T. circumcincta is linked to the activation of the inflammatory TH17 T cell subset and that this chronic inflammatory response was inappropriate to clear worm infection. High resolution melt analysis failed to identify single nucleotide polymorphisms in the coding regions of IL21 and IL21R. This is the first report of the involvement of TH17 response in GI worm infection in sheep. Similar gene expression studies involving the known upstream and downstream players of the TH17 response could be done.

M.Sc. / Tuberculosis, of which the causative agent is Mycobacterium tuberculosis, presents itself as a serious health problem globally, especially in Africa. Susceptibility to this infectious disease is influenced by the virulence of the strain of mycobacteria, environmental factors, and genetic variation within the host. The Vitamin D Receptor gene or VDR has been identified as a candidate gene for TB susceptibility. This gene codes for the VDR protein that mediates the biological actions of the active form of vitamin D. Vitamin D has been shown to impair growth of Mycobacterium tuberculosis in human monocytes and macrophages. Vitamin D also provides a link between Toll-like receptor activation and the antibacterial responses of innate immunity in its production of cathelicidin. The VDR protein is a transcription factor that mediates the effects of the active form of vitamin D. Vitamin D has an immunomodulatory role and variations in the VDR gene may result in variations in the functioning of the VDR protein, and hence variations in response to infection. The VDR gene includes the largely non-coding 5’ regulatory region exons 1a-1f and the coding exons 2-9. As a result of increased awareness of the heritability of gene expression and reports of disease associations with VDR promoter region variants, the focus of the research described in this dissertation was the regulatory region of the VDR gene. Polymorphisms that occur within the regulatory region were viii investigated, as were the effects these polymorphisms may have on gene expression, influencing host susceptibility to tuberculosis, with an emphasis on African populations. VDR polymorphisms have been shown to be involved in susceptibility to tuberculosis, particularly the FokI SNP in exon 2, BsmI and ApaI in intron 8 and the synonomous TaqI in exon 9. However, results have been inconsistent. SNPs shown to be associated with TB may serve as markers of truly functional SNP with which they are in linkage disequilibrium (LD). The majority of these association studies involve single nucleotide polymorphisms (SNPs) found in the introns or are silent mutations in the coding exons. Variations in the 5’ regulatory region have been shown to affect gene expression, in particular if they influence the binding sites of transcription factors.

Theresa.J.Ochoa@uth.tmc.edu / Article / BACKGROUND: Diarrheagenic Escherichia coli strains are being recognized as important pediatric enteropathogens worldwide. However, it is unclear whether there are differences in age-related susceptibility to specific strains, especially among infants. METHODS: We conducted a passive surveillance cohort study of diarrhea that involved 1034 children aged 2-12 months in Lima, Peru. Control stool samples were collected from randomly selected children without diarrhea. All samples were analyzed for common enteric pathogens and for diarrheagenic E. coli with use of multiplex real-time polymerase chain reaction. RESULTS: The most frequently isolated pathogens in 1065 diarrheal episodes were diarrheagenic E. coli strains (31%), including enteroaggregative (15.1%) and enteropathogenic E. coli (7.6%). Diarrheagenic E. coli, Campylobacter species, and rotavirus were more frequently isolated from infants aged >or=6 months. Among older infants, diffusely adherent E. coli and enterotoxigenic E. coli were more frequently isolated from diarrheal samples than from control samples (P <.05). Children aged >or=6 months who were infected with enterotoxigenic E. coli had a 4.56-fold increased risk of diarrhea (95% confidence interval, 1.20-17.28), compared with younger children. Persistent diarrhea was more common in infants aged <6 months (13.5% vs 3.6%; P <.001). Among children with diarrheagenic E. coli-positive samples, coinfections with other pathogens were more common in children with diarrhea than in control children (40.1% vs 15.6%; P <.001). CONCLUSIONS: Diarrheagenic E. coli strains were more frequently isolated in samples from older infants. In this setting with high frequency of pathogen exposure and high frequency of breastfeeding, we hypothesize that the major age-related differences result from decreased exposure to milk-related protective factors and from increased exposure to contaminated food and water.

The objective of the work reported in this paper is one of a two-fold nature. The first objective is to develop a disk-plate sensitivity test that is more rapid than that of existing methods. The second requisite is that the materials, techniques, interpretation, and reporting of results be the sane as those required for the disk-plate method described in the Difco Manual.

Bird cherry-oat aphid (Rhopalosiphum padi L.) is an important pest on spring-sown cereals. The aphid reduces yield and can act as a vector of barley yellow dwarf virus. R. padi does not give visible symptoms, but heavy infestation can reduce the yield substantially. R. padi is one of the most important pests of barley, which has the fourth rank among the cereals in global production. In order to overcome this problem, the plants are treated with pesticides. However, some of the pesticides are no longer permitted to use due to their negative environmental effects. Another problem is that the aphids develop resistance against them. Therefore, a new approach is to identify genetic factors that could be used in breeding host plants for resistance. There are many examples of successful plant breeding for resistance to aphids, but in the case of R. padi and barley, no resistant cultivar is commercially available. The aim of this thesis was to identify and characterise aphid resistance and susceptibility factors in barley. This was done using two major approaches. Firstly, constitutive and aphid-induced gene expression was studied in a large number of barley genotypes with known levels of resistance. Secondly, two cDNAs putatively adding to aphid resistance were transformed to Arabidopsis and barley and the effect of transformation on aphid performance and behaviour was evaluated.      The study of constitutive transcript abundance in 23 barley genotypes gave suggestive evidence that two genes might be related to aphid resistance; a thionin and a proteinase inhibitor gene, and that a lipoxygenase gene might be related to aphid susceptibility.The study of both constitutive and aphid-induced transcript abundances of three glucanase genes, gave support to the idea that two of them might be susceptibility factors. The cDNA of the proteinase inhibitor mentioned above was expressed in Arabidopsis, under control of either a constitutive or a phloem-specific promoter and the effects were evaluated using the green peach aphid, Myzus persicae Sulzer. This aphid is a generalist, feeding on many different plant species, both monocot (such as barley) and dicot (such as Arabidopsis).  The results showed lower settling and fecundity on some of the transgenic lines as compared to on controls.        In conclusion, the thesis suggests a role in resistance against R. padi in barley for two genes encoding a thionin and a proteinase inhibitor. It has also given support for a role in susceptibility against R. padi of genes encoding a lipoxygenase and two glucanases. The work further shows that a cDNA from barley, selected based on the interaction between a monocot plant and an essentially monocot specialist aphid, affected the resistance of the dicot Arabidopsis against a generalist aphid. / <p>At the time of the doctoral defense, the following papers were unpublished and had a status as follows: Paper 3: Manuscript. Paper 4: Manuscript.</p>

Fusarium Ear Blight (FEB) is a globally important floral disease of cereal crops such as wheat, maize and barley. The predominant causal agents of FEB disease of wheat in the UK are Fusarium culmorum and F. graminearum. Wheat infecting isolates of both of these fungal species infect the floral and silique tissues of the model plant Arabidopsis thaliana, providing a tractable model for analysis of factors determining plant susceptibility or resistance to Fusarium infection. The effect of F. culmorum infection on the metabolic composition (metabolome) of Arabidopsis pedicel tissue following silique inoculation was investigated in a collection of mutants with altered defence responses to F. culmorum and/or other plant pathogens, using a 1¬H-NMR/ESI-MS (+/-) triple fingerprinting approach. These mutants showed differing metabolomic fingerprints in the absence of F. culmorum infection, as well as differences in accumulation or depletion of metabolites in response to F. culmorum colonisation. A number of metabolites were also identified which were induced by F. culmorum infection irrespective of plant genotype. Quantitative differences in compound accumulation were also observed between genotypes in the Columbia and Landsberg erecta accessions following F. culmorum infection. One of the genotypes investigated was eds11, which has enhanced susceptibility to F. culmorum floral infection. Mapping of the mutation responsible for the eds11 phenotype was initiated using an isogenic mapping by sequencing approach. This resulted in a list of potential candidates for the EDS11 gene. Additional Arabidopsis mutants were investigated for altered defence responses to F. culmorum floral infection. Multiple mutant alleles of the Arabidopsis homoserine kinase gene DMR1 were found to have enhanced resistance to F. culmorum silique infection and rosette leaf colonisation, associated with accumulation of homoserine in siliques and delayed leaf senescence. Exogenous homoserine application enhanced resistance in wild type and dmr1 plants. Collectively, these findings form a novel contribution to current knowledge of the Fusarium-Arabidopsis interaction. This may have applications for improvement of FEB resistance in cereals.

In the present work I study temperature dependence of magnetic penetration depth in superconductors which allows us to determine the symetry of the order parameter, important for theoretical models. In conventional superconductors we talk about s-symetry. Energy gap is isotropic and as a consequence of this fact penetration depth grows exponencialy with the temperature. On the other hand, in unconventional superconductors with d-symetry we find the power dependence on the temperature. Anyway the exponent depends on impurities and structure of the material and the influence of these parametrs is not completely clear at the moment.

Se determinó la susceptibilidad antimicrobiana de 95 cepas de Salmonella sp aisladas a partir de muestras remitidas al laboratorio de microbiología pertenecientes al Laboratorio Bioservice, ante 18 antimicrobianos durante el periodo de diciembre 2012 a noviembre del 2014. La prueba de susceptibilidad antimicrobiana determinó que el 93.7% mostraron resistencia a Sulfametoxazol, el 82.1% a Eritromicina, el 71.6% a Sulfametoxazol/Trimetropim, el 50.5% a Ácido Nalidíxico y Furazolidona, el 37.9% a Ampicilina y Tetraciclina, 31.6% a Kanamicina, el 28.4%% a Gentamicina, 25.3% a Cloranfenicol, 20% a Ceftriaxona, 12.6% a Colistina y Fosfomicina, 7.4% a Amikacina y Cefoxitina, 6.3% a Amoxicilina/Ácido clavulánico, 4.2% Ciprofloxacina y 2.1% a Estreptomicina. Demostrando que una mayor resistencia ante la familia de las Sulfanilamidas, siendo las cepas de Salmonellas Enteritidis (93.55%) y Salmonella Infantis (100%), las que presentaran mayor resistencia ante Sulfametoxazol. Cabe resaltar que, las Salmonella Typhimurium (82.35%) y Salmonella sp (94.44%), obtuvieron mayor resistencia a la combinación Sulfametoxazol y trimetroprim.The antimicrobial susceptibility of 95 strains of Salmonella sp, isolated from samples submitted to the laboratory of microbiology belonging to the Bio- service Laboratory, against 18 antimicrobials during the period from December 2012 to November 2014, was determined. The antimicrobial susceptibility test determined that 93.7% showed resistance To Sulfamethoxazole, 82.1% to Erythromycin, 71.6% to Sulfamethoxazole / Trimetropim, 50.5% to Nalidixic Acid and Furazolidone, 37.9% to Ampicillin and Tetracycline, 31.6% to Kanamycin, 28.4% to Gentamicin, 25.3% to Chloramphenicol, 20% to Ceftriaxone, 12.6% to Colistin and Fosfomycin, 7.4% to Amikacin and Cefoxitin, 6.3% to Amoxicillin / Clavulanic acid, 4.2% to Ciprofloxacin and 2.1% to Streptomycin. Showing a greater resistance to the Sulfanilamide’s family, considering the strains of Salmonella Enteritidis (93.55%) and Salmonella Infantis (100%) the ones which were more resistant to Sulfamethoxazole. It should be noted that Salmonella Typhimurium (82.35%) and Salmonella sp (94.44%), obtained greater resistance to the combination of Sulfamethoxazole and trimethoprim.

Thesis advisor: Michael J. Graf / In this work I present a characterization of spin dynamics in LiY1-xHoxF4 over a wide region of frequency - temperature - magnetic field - concentration phase space to probe the onset of magnetic correlations. Specifically, measurements were made of the T = 1.8 K magnetic field and frequency dependence of AC susceptibility, and temperature and field dependence of the longitudinal field positive muon spin relaxation (μSR) for LiY1-xHoxF4 with x = 0.0017, 0.0085, 0.0408, and 0.0855. To determine the concentration range over which the spin dynamics are determined primarily by the Ho3+-μ interaction rather than by the F-μ interaction I characterize the dynamics associated with the formation of the (F-μ-F)−complex by comparing data with Monte Carlo simulations. Numerical simulations of the susceptibility for the x = 0.0017 and 0.0085 are fit to my data and show that Ho-Ho cross-relaxation processes become important at higher concentration, signaling the crossover from single-ion to correlated behavior. The muon spin depolarization is simulated using the parameters extracted from the susceptibility, and the simulations agree well with data for these two samples. It is found that the susceptibility and μSR data for samples with x = 0.0408 and 0.0855 cannot be described within a single-ion picture, possibly due to the onset of collective phenomena. An unusual peak is also discovered in the magnetic field dependence of the muon relaxation rate in the temperature interval 10 – 20 K, and ascribed to a modification of the Ho3+ fluctuation rate due to a field induced shift of the energy splitting between the ground and first excited doublet crystal field states relative to a peak in the phonon density of states centered near 63 cm-1. / Thesis (PhD) — Boston College, 2012. / Submitted to: Boston College. Graduate School of Arts and Sciences. / Discipline: Physics.