Is soft breaking of BRST symmetry consistent?

A definition of soft breaking of BRST symmetry in the field-antifield formalism is proposed, valid for general gauge theories and arbitrary gauge fixing. The Ward identities for the generating functionals of Green's functions are derived, and their gauge dependence is investigated. We discuss the Gribov-Zwanziger action for the one-parameter family of R_xi gauges. It is argued that gauge theories with a soft breaking of BRST symmetry are inconsistent.Comment: 1+16 pages; v2: example of section 5 changed to R_xi gauges; v3: small corrections to section 5, one reference added, published versio

Carbon related defects in irradiated silicon revisited

Electronic structure calculations employing hybrid functionals are used to gain insight into the interaction of carbon (C) atoms, oxygen (O) interstitials, and self-interstitials in silicon (Si). We calculate the formation energies of the C related defects C(i)(Si(I)), C(i)O(i), C(i)C(s), and C(i)O(i)(Si(I)) with respect to the Fermi energy for all possible charge states. The C(i)(Si(I))(2+) state dominates in almost the whole Fermi energy range. The unpaired electron in the C(i)O(i)(+) state is mainly localized on the C interstitial so that spin polarization is able to lower the total energy. The three known atomic configurations of the C(i)C(s) pair are reproduced and it is demonstrated that hybrid functionals yield an improved energetic order for both the A and B-types as compared to previous theoretical studies. Different structures of the C(i)O(i)(Si(I)) cluster result for positive charge states in dramatically distinct electronic states around the Fermi energy and formation energies

BRST Quantization of Unimodular Gravity

We study the quantization of two versions of unimodular gravity, namely fully diffeomorphism-invariant unimodular gravity and unimodular gravity with fixed metric determinant, utilizing standard path integral approach. We derive the BRST symmetry of effective actions corresponding to several relevant gauge conditions. We observe that for some gauge conditions, the restricted gauge structure may complicate the formulation and effective actions, in particular, if the chosen gauge conditions involve the canonical momentum conjugate to the induced metric on the spatial hypersurface. The BRST symmetry is extended further to the finite field-dependent BRST transformation, in order to establish the mapping between different gauge conditions in each of the two versions of unimodular gravity.Peer reviewe

PEDIA: prioritization of exome data by image analysis

Purpose Phenotype information is crucial for the interpretation of genomic variants. So far it has only been accessible for bioinformatics workflows after encoding into clinical terms by expert dysmorphologists. Methods Here, we introduce an approach driven by artificial intelligence that uses portrait photographs for the interpretation of clinical exome data. We measured the value added by computer-assisted image analysis to the diagnostic yield on a cohort consisting of 679 individuals with 105 different monogenic disorders. For each case in the cohort we compiled frontal photos, clinical features, and the disease-causing variants, and simulated multiple exomes of different ethnic backgrounds. Results The additional use of similarity scores from computer-assisted analysis of frontal photos improved the top 1 accuracy rate by more than 20–89% and the top 10 accuracy rate by more than 5–99% for the disease-causing gene. Conclusion Image analysis by deep-learning algorithms can be used to quantify the phenotypic similarity (PP4 criterion of the American College of Medical Genetics and Genomics guidelines) and to advance the performance of bioinformatics pipelines for exome analysis

The Mitochondrial Genome of Baylisascaris procyonis

BACKGROUND: Baylisascaris procyonis (Nematoda: Ascaridida), an intestinal nematode of raccoons, is emerging as an important helminthic zoonosis due to serious or fatal larval migrans in animals and humans. Despite its significant veterinary and public health impact, the epidemiology, molecular ecology and population genetics of this parasite remain largely unexplored. Mitochondrial (mt) genomes can provide a foundation for investigations in these areas and assist in the diagnosis and control of B. procyonis. In this study, the first complete mt genome sequence of B. procyonis was determined using a polymerase chain reaction (PCR)-based primer-walking strategy. METHODOLOGY/PRINCIPAL FINDINGS: The circular mt genome (14781 bp) of B. procyonis contained 12 protein-coding, 22 transfer RNA and 2 ribosomal RNA genes congruent with other chromadorean nematodes. Interestingly, the B. procyonis mtDNA featured an extremely long AT-rich region (1375 bp) and a high number of intergenic spacers (17), making it unique compared with other secernentean nematodes characterized to date. Additionally, the entire genome displayed notable levels of AT skew and GC skew. Based on pairwise comparisons and sliding window analysis of mt genes among the available 11 Ascaridida mtDNAs, new primer pairs were designed to amplify specific short fragments of the genes cytb (548 bp fragment) and rrnL (200 bp fragment) in the B. procyonis mtDNA, and tested as possible alternatives to existing mt molecular beacons for Ascaridida. Finally, phylogenetic analysis of mtDNAs provided novel estimates of the interrelationships of Baylisasaris and Ascaridida. CONCLUSIONS/SIGNIFICANCE: The complete mt genome sequence of B. procyonis sequenced here should contribute to molecular diagnostic methods, epidemiological investigations and ecological studies of B. procyonis and other related ascaridoids. The information will be important in refining the phylogenetic relationships within the order Ascaridida and enriching the resource of markers for systematic, population genetic and evolutionary biological studies of parasitic nematodes of socio-economic importance

Syndromics: A Bioinformatics Approach for Neurotrauma Research

Substantial scientific progress has been made in the past 50 years in delineating many of the biological mechanisms involved in the primary and secondary injuries following trauma to the spinal cord and brain. These advances have highlighted numerous potential therapeutic approaches that may help restore function after injury. Despite these advances, bench-to-bedside translation has remained elusive. Translational testing of novel therapies requires standardized measures of function for comparison across different laboratories, paradigms, and species. Although numerous functional assessments have been developed in animal models, it remains unclear how to best integrate this information to describe the complete translational “syndrome” produced by neurotrauma. The present paper describes a multivariate statistical framework for integrating diverse neurotrauma data and reviews the few papers to date that have taken an information-intensive approach for basic neurotrauma research. We argue that these papers can be described as the seminal works of a new field that we call “syndromics”, which aim to apply informatics tools to disease models to characterize the full set of mechanistic inter-relationships from multi-scale data. In the future, centralized databases of raw neurotrauma data will enable better syndromic approaches and aid future translational research, leading to more efficient testing regimens and more clinically relevant findings