Localization and lattice fermions

I review how the phenomenology of localization applies to fermions in lattice gauge theory, present measurements of the localization length and other quantities, and discuss the consequences for things like the overlap kernel.Comment: Talk given at the Workshop on Computational Hadron Physics, Nicosia, Cyprus, September 2005. 6 pp., 3 fig

Effective Lagrangian for strongly coupled domain wall fermions

We derive the effective Lagrangian for mesons in lattice gauge theory with domain-wall fermions in the strong-coupling and large-N_c limits. We use the formalism of supergroups to deal with the Pauli-Villars fields, needed to regulate the contributions of the heavy fermions. We calculate the spectrum of pseudo-Goldstone bosons and show that domain wall fermions are doubled and massive in this regime. Since we take the extent and lattice spacing of the fifth dimension to infinity and zero respectively, our conclusions apply also to overlap fermions.Comment: 26 pp. RevTeX and 3 figures; corrected error in symmetry breaking scheme and added comments to discussio

Screening for prostate cancer: systematic review and meta-analysis of randomised controlled trials

Objective To examine the evidence on the benefits and harms of screening for prostate cancer

DNA deaminases induce break-associated mutation showers with implication of APOBEC3B and 3A in breast cancer kataegis.

Breast cancer genomes have revealed a novel form of mutation showers (kataegis) in which multiple same-strand substitutions at C:G pairs spaced one to several hundred nucleotides apart are clustered over kilobase-sized regions, often associated with sites of DNA rearrangement. We show kataegis can result from AID/APOBEC-catalysed cytidine deamination in the vicinity of DNA breaks, likely through action on single-stranded DNA exposed during resection. Cancer-like kataegis can be recapitulated by expression of AID/APOBEC family deaminases in yeast where it largely depends on uracil excision, which generates an abasic site for strand breakage. Localized kataegis can also be nucleated by an I-SceI-induced break. Genome-wide patterns of APOBEC3-catalyzed deamination in yeast reveal APOBEC3B and 3A as the deaminases whose mutational signatures are most similar to those of breast cancer kataegic mutations. Together with expression and functional assays, the results implicate APOBEC3B/A in breast cancer hypermutation and give insight into the mechanism of kataegis. DOI:http://dx.doi.org/10.7554/eLife.00534.001

Hamiltonian domain wall fermions at strong coupling

We apply strong-coupling perturbation theory to gauge theories containing domain-wall fermions in Shamir's surface version. We construct the effective Hamiltonian for the color-singlet degrees of freedom that constitute the low-lying spectrum at strong coupling. We show that the effective theory is identical to that derived from naive, doubled fermions with a mass term, and hence that domain-wall fermions at strong coupling suffer both doubling and explicit breaking of chiral symmetry. Since we employ a continuous fifth dimension whose extent tends to infinity, our result applies to overlap fermions as well.Comment: Revtex, 21 pp. Some changes in Introduction, dealing with consistency with previous wor

Lattice gauge theory with baryons at strong coupling

We study the effective Hamiltonian for strong-coupling lattice QCD in the case of non-zero baryon density. In leading order the effective Hamiltonian is a generalized antiferromagnet. For naive fermions, the symmetry is U(4N_f) and the spins belong to a representation that depends on the local baryon number. Next-nearest-neighbor (nnn) terms in the Hamiltonian break the symmetry to U(N_f) x U(N_f). We transform the quantum problem to a Euclidean sigma model which we analyze in a 1/N_c expansion. In the vacuum sector we recover spontaneous breaking of chiral symmetry for the nearest-neighbor and nnn theories. For non-zero baryon density we study the nearest-neighbor theory only, and show that the pattern of spontaneous symmetry breaking depends on the baryon density.Comment: 31 pages, 5 EPS figures. Corrected Eq. (6.1

Structural and Thermodynamic Approach to Peptide Immunogenicity

In the conventional paradigm of humoral immunity, B cells recognize their cognate antigen target in its native form. However, it is well known that relatively unstable peptides bearing only partial structural resemblance to the native protein can trigger antibodies recognizing higher-order structures found in the native protein. On the basis of sound thermodynamic principles, this work reveals that stability of immunogenic proteinlike motifs is a critical parameter rationalizing the diverse humoral immune responses induced by different linear peptide epitopes. In this paradigm, peptides with a minimal amount of stability (ΔGX<0 kcal/mol) around a proteinlike motif (X) are capable of inducing antibodies with similar affinity for both peptide and native protein, more weakly stable peptides (ΔGX>0 kcal/mol) trigger antibodies recognizing full protein but not peptide, and unstable peptides (ΔGX>8 kcal/mol) fail to generate antibodies against either peptide or protein. Immunization experiments involving peptides derived from the autoantigen histidyl-tRNA synthetase verify that selected peptides with varying relative stabilities predicted by molecular dynamics simulations induce antibody responses consistent with this theory. Collectively, these studies provide insight pertinent to the structural basis of immunogenicity and, at the same time, validate this form of thermodynamic and molecular modeling as an approach to probe the development/evolution of humoral immune responses

Search for a Technicolor omega_T Particle in Events with a Photon and a b-quark Jet at CDF

If the Technicolor omega_T particle exists, a likely decay mode is omega_T -> gamma pi_T, followed by pi_T -> bb-bar, yielding the signature gamma bb-bar. We have searched 85 pb^-1 of data collected by the CDF experiment at the Fermilab Tevatron for events with a photon and two jets, where one of the jets must contain a secondary vertex implying the presence of a b quark. We find no excess of events above standard model expectations. We express the result of an exclusion region in the M_omega_T - M_pi_T mass plane.Comment: 14 pages, 2 figures. Available from the CDF server (PS with figs): http://www-cdf.fnal.gov/physics/pub98/cdf4674_omega_t_prl_4.ps FERMILAB-PUB-98/321-

Observation of Hadronic W Decays in t-tbar Events with the Collider Detector at Fermilab

We observe hadronic W decays in t-tbar -> W (-> l nu) + >= 4 jet events using a 109 pb-1 data sample of p-pbar collisions at sqrt{s} = 1.8 TeV collected with the Collider Detector at Fermilab (CDF). A peak in the dijet invariant mass distribution is obtained that is consistent with W decay and inconsistent with the background prediction by 3.3 standard deviations. From this peak we measure the W mass to be 77.2 +- 4.6 (stat+syst) GeV/c^2. This result demonstrates the presence of two W bosons in t-tbar candidates in the W (-> l nu) + >= 4 jet channel.Comment: 20 pages, 4 figures, submitted to PR

Measurement of the B0 anti-B0 oscillation frequency using l- D*+ pairs and lepton flavor tags

The oscillation frequency Delta-md of B0 anti-B0 mixing is measured using the partially reconstructed semileptonic decay anti-B0 -> l- nubar D*+ X. The data sample was collected with the CDF detector at the Fermilab Tevatron collider during 1992 - 1995 by triggering on the existence of two lepton candidates in an event, and corresponds to about 110 pb-1 of pbar p collisions at sqrt(s) = 1.8 TeV. We estimate the proper decay time of the anti-B0 meson from the measured decay length and reconstructed momentum of the l- D*+ system. The charge of the lepton in the final state identifies the flavor of the anti-B0 meson at its decay. The second lepton in the event is used to infer the flavor of the anti-B0 meson at production. We measure the oscillation frequency to be Delta-md = 0.516 +/- 0.099 +0.029 -0.035 ps-1, where the first uncertainty is statistical and the second is systematic.Comment: 30 pages, 7 figures. Submitted to Physical Review