Search for Technicolor Particles Produced in Association with a W Boson at CDF

We present a search for the technicolor particles $\rho_{T}$ and $\pi_{T}$ in the process $p\bar{p} \to \rho_{T} \to W\pi_{T}$ at a center of mass energy of $\sqrt{s}=1.96 \mathrm{TeV}$. The search uses a data sample corresponding to approximately $1.9 \mathrm{fb}^{-1}$ of integrated luminosity accumulated by the CDF II detector at the Fermilab Tevatron. The event signature we consider is $W\to \ell\nu$ and $\pi_{T} \to b\bar{b}, b\bar{c}$ or $b\bar{u}$ depending on the $\pi_{T}$ charge. We select events with a single high-$p_T$ electron or muon, large missing transverse energy, and two jets. Jets corresponding to bottom quarks are identified with multiple $b$-tagging algorithms. The observed number of events and the invariant mass distributions are consistent with the standard model background expectations, and we exclude a region at 95% confidence level in the $\rho_T$-$\pi_T$ mass plane. As a result, a large fraction of the region $m(\rho_T) = 180$ - $250 \mathrm{GeV}/c^2$ and $m(\pi_T) = 95$ - $145 \mathrm{GeV}/c^2$ is excluded.

Measurement of the kT Distribution of Particles in Jets Produced in pp̅ Collisions at √s=1.96 TeV

We present a measurement of the transverse momentum with respect to the jet axis (kt) of particles in jets produced in pp̅ collisions at √s=1.96  TeV. Results are obtained for charged particles in a cone of 0.5 radians around the jet axis in events with dijet invariant masses between 66 and 737  GeV/c2. The experimental data are compared to theoretical predictions obtained for fragmentation partons within the framework of resummed perturbative QCD using the modified leading log and next-to-modified leading log approximations. The comparison shows that trends in data are successfully described by the theoretical predictions, indicating that the perturbative QCD stage of jet fragmentation is dominant in shaping basic jet characteristics.

Phospholipid cytochrome c interactions

The ability of the peripherally associated membrane protein cytochrome c (cyt c) to bind phospholipids in vitro was studied using fluorescence spectroscopy and large unilamellar liposomes. Previous work has shown that cyt c can bind phospholipids using two distinct mecha- nisms and sites, the A-site and the C-site. This binding is mediated by electrostatic or hydrophobic interactions, respectively. Here, we focus on the mechanism underlying these interactions. A chemically modified cyt c mutant Nle91 was used to study the ATP-binding site, which is located near the evolutionarily invariant Arg 91 on the protein surface. This site was also demonstrated to mediate phospholipid binding, possibly by functioning as a phospholipid binding site. Circular dichroism spectroscopy, time resolved fluorescence spectroscopy of zinc- porphyrin modified [Zn2+-heme] cyt c and liposome binding studies of the Nle91 mutant were used to demonstrate that ATP induces a conformational change in membrane- bound cyt c. The ATP-induced conformational changes were mediated by Arg 91 and were most pronounced in cyt c bound to phospholipids via the C-site. It has been previously reported that the hydrophobic interaction between phospho- lipids and cyt c (C-site) includes the binding of a phospholipid acyl chain inside the protein. In this mechanism, which is known as extended phospholipid anchorage, the sn-2 acyl chain of a membrane phospholipid protrudes out of the membrane surface and is able to bind in a hydrophobic cavity in cyt c. Direct evidence for this type of bind- ing mechanism was obtained by studying cyt c/lipid interaction using fluorescent [Zn2+- heme] cyt c and fluorescence quenching of brominated fatty acids and phospholipids. Under certain conditions, cyt c can form fibrillar protein-lipid aggregates with neg- atively charged phospholipids. These aggregates resemble amyloid fibrils, which are involved in the pathogenesis of many diseases. Congo red staining of these fibers con- firmed the presence of amyloid structures. A set of phospholipid-binding proteins was also found to form similar aggregates, suggesting that phospholipid-induced amyloid formation could be a general mechanism of amyloidogenesis.

Search for High-Mass Resonances Decaying to Dimuons at CDF

We present a search for high-mass neutral resonances using dimuon data corresponding to an integrated luminosity of 2.3 fb$^{-1}$ collected in {$p\bar p$} collisions at {$\sqrt{s}$ = 1.96 TeV} by the CDF II detector at the Fermilab Tevatron. No significant excess above the standard model expectation is observed in the dimuon invariant-mass spectrum. We set 95% confidence level upper limits on $\sigma \cdot BR (p \bar{p} \to X \to \mu \bar{\mu})$, where $X$ is a boson with spin 0, 1, or 2. Using these cross section limits, we determine lower mass limits on sneutrinos in R-parity-violating supersymmetric models, $Z'$ bosons, and Kaluza-Klein gravitons in the Randall-Sundrum model.

First Measurement of the tt̅ Differential Cross Section dσ/dMtt̅ in pp̅ Collisions at √s=1.96 TeV

We present a measurement of the $\ttbar$ differential cross section with respect to the $\ttbar$ invariant mass, dSigma/dMttbar, in $\ppbar$ collisions at $\sqrt{s}=1.96$ TeV using an integrated luminosity of $2.7\invfb$ collected by the CDF II experiment. The $\ttbar$ invariant mass spectrum is sensitive to a variety of exotic particles decaying into $\ttbar$ pairs. The result is consistent with the standard model expectation, as modeled by \texttt{PYTHIA} with \texttt{CTEQ5L} parton distribution functions.

Measurement of the kT Distribution of Particles in Jets Produced in pp̅ Collisions at √s=1.96 TeV

We present a measurement of the transverse momentum with respect to the jet axis ($k_{T}$) of particles in jets produced in $p\bar p$ collisions at $\sqrt{s}=1.96$ TeV. Results are obtained for charged particles within a cone of opening angle 0.5 radians around the jet axis in events with dijet invariant masses between 66 and 737 GeV/c$^{2}$. The experimental data are compared to theoretical predictions obtained for fragmentation partons within the framework of resummed perturbative QCD using the modified leading log and next-to-modified leading log approximations. The comparison shows that trends in data are successfully described by the theoretical predictions, indicating that the perturbative QCD stage of jet fragmentation is dominant in shaping basic jet characteristics.

First simultaneous measurement of the top quark mass in the lepton+jets and dilepton channels at CDF

We present a measurement of the mass of the top quark using data corresponding to an integrated luminosity of 1.9fb^-1 of ppbar collisions collected at sqrt{s}=1.96 TeV with the CDF II detector at Fermilab's Tevatron. This is the first measurement of the top quark mass using top-antitop pair candidate events in the lepton + jets and dilepton decay channels simultaneously. We reconstruct two observables in each channel and use a non-parametric kernel density estimation technique to derive two-dimensional probability density functions from simulated signal and background samples. The observables are the top quark mass and the invariant mass of two jets from the W decay in the lepton + jets channel, and the top quark mass and the scalar sum of transverse energy of the event in the dilepton channel. We perform a simultaneous fit for the top quark mass and the jet energy scale, which is constrained in situ by the hadronic W boson mass. Using 332 lepton + jets candidate events and 144 dilepton candidate events, we measure the top quark mass to be mtop=171.9 +/- 1.7 (stat. + JES) +/- 1.1 (syst.) GeV/c^2 = 171.9 +/- 2.0 GeV/c^2.

Search for narrow resonances lighter than ϒ mesons

We report a search for narrow resonances, produced in $p\bar{p}$ collisions at $\sqrt{s}=1.96$ TeV, that decay into muon pairs with invariant mass between 6.3 and 9.0 GeV/c^2. The data, collected with the CDF~II detector at the Fermilab Tevatron collider, correspond to an integrated luminosity of 630 pb$^{-1}$. We use the dimuon invariant mass distribution to set 90% upper credible limits of about 1% to the ratio of the production cross section times muonic branching fraction of possible narrow resonances to that of the $\Upsilon(1{\rm S})$ meson.

Top quark mass measurement in the tt̅ all hadronic channel using a matrix element technique in pp̅ collisions at √s=1.96 TeV

We present a measurement of the top quark mass in the all-hadronic channel (\tt $\to$ \bb$q_{1}\bar{q_{2}}q_{3}\bar{q_{4}}$) using 943 pb$^{-1}$ of \ppbar collisions at $\sqrt {s} = 1.96$ TeV collected at the CDF II detector at Fermilab (CDF). We apply the standard model production and decay matrix-element (ME) to $\ttbar$ candidate events. We calculate per-event probability densities according to the ME calculation and construct template models of signal and background. The scale of the jet energy is calibrated using additional templates formed with the invariant mass of pairs of jets. These templates form an overall likelihood function that depends on the top quark mass and on the jet energy scale (JES). We estimate both by maximizing this function. Given 72 observed events, we measure a top quark mass of 171.1 $\pm$ 3.7 (stat.+JES) $\pm$ 2.1 (syst.) GeV/$c^{2}$. The combined uncertainty on the top quark mass is 4.3 GeV/$c^{2}$.

Search for new color-octet vector particle decaying to t tbar in p pbar collisions at sqrt{s} = 1.96 TeV

We present the result of a search for a massive color-octet vector particle, (e.g. a massive gluon) decaying to a pair of top quarks in proton-antiproton collisions with a center-of-mass energy of 1.96 TeV. This search is based on 1.9 fb$^{-1}$ of data collected using the CDF detector during Run II of the Tevatron at Fermilab. We study $t\bar{t}$ events in the lepton+jets channel with at least one $b$-tagged jet. A massive gluon is characterized by its mass, decay width, and the strength of its coupling to quarks. These parameters are determined according to the observed invariant mass distribution of top quark pairs. We set limits on the massive gluon coupling strength for masses between 400 and 800 GeV$/c^2$ and width-to-mass ratios between 0.05 and 0.50. The coupling strength of the hypothetical massive gluon to quarks is consistent with zero within the explored parameter space.

Generalizations and Models in Ecology : Lawlikeness, Invariance, Stability, and Robustness

The question at issue in this dissertation is the epistemic role played by ecological generalizations and models. I investigate and analyze such properties of generalizations as lawlikeness, invariance, and stability, and I ask which of these properties are relevant in the context of scientific explanations. I will claim that there are generalizable and reliable causal explanations in ecology by generalizations, which are invariant and stable. An invariant generalization continues to hold or be valid under a special change called an intervention that changes the value of its variables. Whether a generalization remains invariant during its interventions is the criterion that determines whether it is explanatory. A generalization can be invariant and explanatory regardless of its lawlike status. Stability deals with a generality that has to do with holding of a generalization in possible background conditions. The more stable a generalization, the less dependent it is on background conditions to remain true. Although it is invariance rather than stability of generalizations that furnishes us with explanatory generalizations, there is an important function that stability has in this context of explanations, namely, stability furnishes us with extrapolability and reliability of scientific explanations. I also discuss non-empirical investigations of models that I call robustness and sensitivity analyses. I call sensitivity analyses investigations in which one model is studied with regard to its stability conditions by making changes and variations to the values of the model s parameters. As a general definition of robustness analyses I propose investigations of variations in modeling assumptions of different models of the same phenomenon in which the focus is on whether they produce similar or convergent results or not. Robustness and sensitivity analyses are powerful tools for studying the conditions and assumptions where models break down and they are especially powerful in pointing out reasons as to why they do this. They show which conditions or assumptions the results of models depend on. Key words: ecology, generalizations, invariance, lawlikeness, philosophy of science, robustness, explanation, models, stability

Task-dependent activations of human auditory cortex during pitch discrimination and pitch memory tasks

"The functional organization of auditory cortex (AC) is still poorly understood. Previous studies suggest segregation of auditory processing streams for spatial and nonspatial information located in the posterior and anterior AC, respectively (Rauschecker and Tian, 2000; Arnott et al., 2004; Lomber and Malhotra, 2008). Furthermore, previous studies have shown that active listening tasks strongly modulate AC activations (Petkov et al., 2004; Fritz et al., 2005; Polley et al., 2006). However, the task dependence of AC activations has not been systematically investigated. In the present study, we applied high-resolution functional magnetic resonance imaging of the AC and adjacent areas to compare activations during pitch discrimination and n-back pitch memory tasks that were varied parametrically in difficulty. We found that anterior AC activations were increased during discrimination but not during memory tasks, while activations in the inferior parietal lobule posterior to the AC were enhanced during memory tasks but not during discrimination. We also found that wide areas of the anterior AC and anterior insula were strongly deactivated during the pitch memory tasks. While these results are consistent with the proposition that the anterior and posterior AC belong to functionally separate auditory processing streams, our results show that this division is present also between tasks using spatially invariant sounds. Together, our results indicate that activations of human AC are strongly dependent on the characteristics of the behavioral task."

Search for High-Mass e+e- Resonances in pp̅ Collisions at √s=1.96 TeV

A search for high-mass resonances in the $e^+e^-$ final state is presented based on 2.5 fb$^{-1}$ of $\sqrt{s}=$1.96 TeV $p\bar{p}$ collision data from the CDF II detector at the Fermilab Tevatron. The largest excess over the standard model prediction is at an $e^+e^-$ invariant mass of 240 GeV/$c^2$. The probability of observing such an excess arising from fluctuations in the standard model anywhere in the mass range of 150--1,000 GeV/$c^2$ is 0.6% (equivalent to 2.5 $\sigma$). We exclude the standard model coupling $Z'$ and the Randall-Sundrum graviton for $k/\overline{M}_{Pl}=0.1$ with masses below 963 and 848 GeV/$c^2$ at the 95% credibility level, respectively.

Gauge Field Theories, Quantum Space-Time and Some Applications

In this thesis, the possibility of extending the Quantization Condition of Dirac for Magnetic Monopoles to noncommutative space-time is investigated. The three publications that this thesis is based on are all in direct link to this investigation. Noncommutative solitons have been found within certain noncommutative field theories, but it is not known whether they possesses only topological charge or also magnetic charge. This is a consequence of that the noncommutative topological charge need not coincide with the noncommutative magnetic charge, although they are equivalent in the commutative context. The aim of this work is to begin to fill this gap of knowledge. The method of investigation is perturbative and leaves open the question of whether a nonperturbative source for the magnetic monopole can be constructed, although some aspects of such a generalization are indicated. The main result is that while the noncommutative Aharonov-Bohm effect can be formulated in a gauge invariant way, the quantization condition of Dirac is not satisfied in the case of a perturbative source for the point-like magnetic monopole.

Innate Immune Recognition of RNA-virus infection in human macrophages

Innate immunity and host defence are rapidly evoked by structurally invariant molecular motifs common to microbial world, called pathogen associated molecular patterns (PAMPs). In addition to PAMPs, endogenous molecules released in response to inflammation and tissue damage, danger associated molecular patterns (DAMPs), are required for eliciting the response. The most important PAMPs of viruses are viral nucleic acids, their genome or its replication intermediates, whereas the identity and characteristics of virus infection-induced DAMPs are poorly defined. PAMPs and DAMPs engage a limited set of germ-line encoded pattern recognition receptors (PRRs) in immune and non-immune cells. Membrane-bound Toll-like receptors (TLRs), cytoplasmic retinoic acid inducible gene-I (RIG-I)-like receptors (RLRs) and nucleotide-binding oligomerization domain-like receptor (NLRs) are important PRRs involved in the recognition of the molecular signatures of viral infection, such as double-stranded ribonucleic acids (dsRNAs). Engagement of PRRs results in local and systemic innate immune responses which, when activated against viruses, evoke secretion of antiviral and pro-inflammatory cytokines, and programmed cell death i.e., apoptosis of the virus-infected cell. Macrophages are the central effector cells of innate immunity. They produce significant amounts of antiviral cytokines, called interferons (IFNs), and pro-inflammatory cytokines, such as interleukin (IL)-1β and IL-18. IL-1β and IL-18 are synthesized as inactive precursors, pro-IL-1β and pro-IL-18, that are processed by caspase-1 in a cytoplasmic multiprotein complex, called the inflammasome. After processing, these cytokines are biologically active and will be secreted. The signals and secretory routes that activate inflammasomes and the secretion of IL-1β and IL-18 during virus infections are poorly characterized. The main goal of this thesis was to characterize influenza A virus-induced innate immune responses and host-virus interactions in human primary macrophages during an infection. Methodologically, various techniques of cellular and molecular biology, as well as proteomic tools combined with bioinformatics, were utilized. Overall, the thesis provides interesting insights into inflammatory and antiviral innate immune responses, and has characterized host-virus interactions during influenza A virus-infection in human primary macrophages.