Physics at the B Factories

We review recent progress at the two $e^+ e^-$ B factories. The first measurement of CP violation and the prospects for measuring all the angles of the unitarity triangle are discussed.Comment: To appear in the Proceedings of From the Smallest to the Largest Distances, a conference in honor of Tranh Thanh Van in Moscow, Russi

The effect of electromechanical coupling on the strain in AlGaN/GaN heterojunction field effect transistors

The strain in AlGaN/GaN heterojunction field-effect transistors (HFETs) is examined theoretically in the context of the fully-coupled equation of state for piezoelectric materials. Using a simple analytical model, it is shown that, in the absence of a two-dimensional electron gas (2DEG), the out-of-plane strain obtained without electromechanical coupling is in error by about 30% for an Al fraction of 0.3. This result has consequences for the calculation of quantities that depend directly on the strain tensor. These quantities include the eigenstates and electrostatic potential in AlGaN/GaN heterostructures. It is shown that for an HFET, the electromechanical coupling is screened by the 2DEG. Results for the electromechanical model, including the 2DEG, indicate that the standard (decoupled) strain model is a reasonable approximation for HFET calculataions. The analytical results are supported by a self-consistent Schr\"odinger-Poisson calculation that includes the fully-coupled equation of state together with the charge-balance equation.Comment: 6 figures, revte

GOexpress: an R/Bioconductor package for the identification and visualisation of robust gene ontology signatures through supervised learning of gene expression data

Background: Identification of gene expression profiles that differentiate experimental groups is critical for discovery and analysis of key molecular pathways and also for selection of robust diagnostic or prognostic biomarkers. While integration of differential expression statistics has been used to refine gene set enrichment analyses, such approaches are typically limited to single gene lists resulting from simple two-group comparisons or time-series analyses. In contrast, functional class scoring and machine learning approaches provide powerful alternative methods to leverage molecular measurements for pathway analyses, and to compare continuous and multi-level categorical factors. Results: We introduce GOexpress, a software package for scoring and summarising the capacity of gene ontology features to simultaneously classify samples from multiple experimental groups. GOexpress integrates normalised gene expression data (e.g., from microarray and RNA-seq experiments) and phenotypic information of individual samples with gene ontology annotations to derive a ranking of genes and gene ontology terms using a supervised learning approach. The default random forest algorithm allows interactions between all experimental factors, and competitive scoring of expressed genes to evaluate their relative importance in classifying predefined groups of samples. Conclusions: GOexpress enables rapid identification and visualisation of ontology-related gene panels that robustly classify groups of samples and supports both categorical (e.g., infection status, treatment) and continuous (e.g., time-series, drug concentrations) experimental factors. The use of standard Bioconductor extension packages and publicly available gene ontology annotations facilitates straightforward integration of GOexpress within existing computational biology pipelines.Department of Agriculture, Food and the MarineEuropean Commission - Seventh Framework Programme (FP7)Science Foundation IrelandUniversity College Dubli

A Firefly-inspired method for protein structure prediction in lattice models

We introduce a Firefly-inspired algorithmic approach for protein structure prediction over two different lattice models in three-dimensional space. In particular, we consider three-dimensional cubic and three-dimensional face-centred-cubic (FCC) lattices. The underlying energy models are the Hydrophobic-Polar (H-P) model, the Miyazawa–Jernigan (M-J) model and a related matrix model. The implementation of our approach is tested on ten H-P benchmark problems of a length of 48 and ten M-J benchmark problems of a length ranging from 48 until 61. The key complexity parameter we investigate is the total number of objective function valuations required to achieve the optimum energy values for the H-P model or competitive results in comparison to published values for the M-J model. For H-P instances and cubic lattices, where data for comparison are available, we obtain an average speed-up over eight instances of 2.1, leaving out two extreme values (otherwise, 8.8). For six M-J instances, data for comparison are available for cubic lattices and runs with a population size of 100, where, a priori, the minimum free energy is a termination criterion. The average speed-up over four instances is 1.2 (leaving out two extreme values, otherwise 1.1), which is achieved for a population size of only eight instances. The present study is a test case with initial results for ad hoc parameter settings, with the aim of justifying future research on larger instances within lattice model settings, eventually leading to the ultimate goal of implementations for off-lattice models

Electromechanical coupling in free-standing AlGaN/GaN planar structures

The strain and electric fields present in free-standing AlGaN/GaN slabs are examined theoretically within the framework of fully-coupled continuum elastic and dielectric models. Simultaneous solutions for the electric field and strain components are obtained by minimizing the electric enthalpy. We apply constraints appropriate to pseudomorphic semiconductor epitaxial layers and obtain closed-form analytic expressions that take into account the wurtzite crystal anisotropy. It is shown that in the absence of free charges, the calculated strain and electric fields are substantially differently from those obtained using the standard model without electromechanical coupling. It is also shown, however, that when a two-dimensional electron gas is present at the AlGaN/GaN interface, a condition that is the basis for heterojunction field-effect transistors, the electromechanical coupling is screened and the decoupled model is once again a good approximation. Specific cases of these calculations corresponding to transistor and superlattice structures are discussed.Comment: revte

Differences in Dopamine Function in Fibromyalgia

poster abstractObjective: Fibromyalgia (FM) is a debilitating pain disorder that affects 2% of the population. Many of the drugs prescribed to fibromyalgia sufferers are highly addictive, have limited clinical efficacy, and do not treat the cognitive symptoms of fibromyalgia. The neurobiological substrates of fibromyalgia are unknown, but there is evidence for involvement of altered dopaminergic transmission in pain disorders. Given that dopamine is essential for proper cognitive function, it is possible that fibromyalgia symptoms are partly mediated by abnormal dopaminergic functioning. However, the in vivo dopamine system in fibromyalgia patients has not been assessed. Thus, the objective of the current study was to ascertain how the dopamine system in fibromyalgia differs from healthy controls. Methods: [18F]-Fallypride (FAL) PET scanning was used to assess DA changes during a working memory task relative to a baseline task. Twelve patients with FM and twelve controls completed study procedures. Subjects received one FAL PET scan during a 2-back working-memory condition and one during a 0-back (attentional control) task. Results: Fibromyalgia subjects had higher baseline FAL binding potential (BPND) in the right amygdala and ventral pallidum relative to controls. FM subjects had lower baseline FAL BPND in frontal, temporal, and cingulate cortices. Voxel-wise paired t-tests were used to infer increases or decreases in FAL BPND (indicative of decreases or increases in dopamine, respectively) during 2-back performance. Fibromyalgia subjects had significant dopamine release in the ACC, left insula, OFC, and bilateral hippocampus during the 2-back task. Conversely, decreases in DA were detected in the posterior parietal cortex and vmPFC. In controls, dopamine appeared to decrease in the posterior parietal lobe, left hippocampus, and vmPFC during the 2-back task. No significant DA release was detected in controls. Self-reported pain ratings in fibromyalgia subjects were significantly associated with baseline FAL BPND in the ACC, bilateral ventral pallidum, amygdalae, and PAG. Conclusion: These data suggest that in fibromyalgia, abnormalities in dopamine function may be associated with both working memory and pain perception. Further studies are needed to further explore the potential associations between dopamine and cognitive performance and pain perception in FM

Effects of Possible ΔB=−ΔQ\Delta B =- \Delta Q Transitions in Neutral BB Meson Decays}

We explore the possibility that the existing data on like-sign dileptons at the $\Upsilon (4S)$ resonance consist of events arising from $B_{d}^0 -\bar B_{d}^0$ mixing and also from $\Delta B = - \Delta Q$ transitions. The consequences of these nonstandard transitions for certain time-asymmetries which are likely to be measured at the $B$ factories are studied.Comment: {\LARGE \bf 10 pages, no figures, process using latex, TIFR/TH/93-5

Highlights from Five Years at the B Factories

The highlights and conflicts at the B Factories are briefly reviewed. $CP$ violation was established in 2001 in $B^0 \to J/\psi K_S$ and related modes, which has now become a precision measurement of CP violation in $B^0$-$\bar B^0$ mixing. However, the situation for the $B^0 \to \pi^+\pi^-$ and charmless $b\to s$ modes, which probe also CP violation in the {\it decay} amplitude, are not quite settled yet. They could be hinting at presence of both strong (CP conserving) and new physics (CP violating) phases. We critically assess the developments and discuss some related discrepancies and highlights, such as observation of direct CP violation, and make a projection towards the next few years.Comment: 16 pages, 5 figures, to appear as Brief Review in Mod. Phys. Lett.

Transport signatures of quasiparticle poisoning in a Majorana island

We investigate effects of quasiparticle poisoning in a Majorana island with strong tunnel coupling to normal-metal leads. In addition to the main Coulomb blockade diamonds, "shadow" diamonds appear, shifted by 1e in gate voltage, consistent with transport through an excited (poisoned) state of the island. Comparison to a simple model yields an estimate of parity lifetime for the strongly coupled island (~ 1 {\mu}s) and sets a bound for a weakly coupled island (> 10 {\mu}s). Fluctuations in the gate-voltage spacing of Coulomb peaks at high field, reflecting Majorana hybridization, are enhanced by the reduced lever arm at strong coupling. In energy units, fluctuations are consistent with previous measurements.Comment: includes supplementary materia