Simulating Z_{2} lattice gauge theory on a quantum computer.

The utility of quantum computers for simulating lattice gauge theories is currently limited by the noisiness of the physical hardware. Various quantum error mitigation strategies exist to reduce the statistical and systematic uncertainties in quantum simulations via improved algorithms and analysis strategies. We perform quantum simulations of Z_{2} gauge theory with matter to study the efficacy and interplay of different error mitigation methods: readout error mitigation, randomized compiling, rescaling, and dynamical decoupling. We compute Minkowski correlation functions in this confining gauge theory and extract the mass of the lightest spin-1 state from fits to their time dependence. Quantum error mitigation extends the range of times over which our correlation function calculations are accurate by a factor of 6 and is therefore essential for obtaining reliable masses.

High risk HPV testing for cervical cancer screening in a Puerto Rican population.

The Human Papillomavirus (HPV) causes cervical cancer, the fourth most common cause of death in women in the United States (US). Several major screening clinical trials have demonstrated that high risk HPV (HR-HPV) DNA primary screen is more sensitive at determining the risk of cervical intraepithelial neoplasia level 3 or higher (CIN ≥ 3) than cytology alone and is similar to co-testing. In this cross-sectional study, we characterized a Hispanic population of 18,052 women ages 21-70 years with HR-HPV DNA testing and cytology to determine the prevalence of HR-HPV in the population and determine the likelihood of high grade squamous intraepithelial lesion (HSIL). We also compared cytology, HR-HPV DNA testing, and co-testing strategies to determine sensitivity, specificity, positive predictive value, and negative predictive value for HSIL in cervical biopsies. Results show that HR-HPV had a slightly higher sensitivity (94.2% vs 92.3%) compared to cytology for all high-grade disease (CIN2/3).

Comparative analysis of onychomycosis in Puerto Rico using molecular and conventional approaches.

Onychomycosis is the most prevalent nail ailment in adults, accounting for 50% of all nail infections. Dermatophyte fungi are the primary cause, but non-dermatophyte molds (NDM) and yeasts can also cause onychomycosis. It remains important to precisely determine the fungal cause of onychomycosis since the response to current treatments may vary between fungal classes. Real-time polymerase chain reaction (qPCR) has become a widespread tool for detecting fungal organisms for diagnosis due to its sensitivity and ability to detect down to the species level. This retrospective study aims to evaluate the qPCR Onycho+ test for dermatophyte detection using remnants of toenails from a cohort of patients from Puerto Rico.  Two hundred forty-two toenail samples submitted for histological examination via Periodic acid Schiff (PAS) staining for suspected onychomycosis were analyzed by the Onycho+ test and Sanger sequencing of the internal transcribed spacer (ITS-2). Compared to the gold standard Sanger sequencing method, the Onycho+ test reported an agreement of 91.39%, a sensitivity of 100% and a specificity of 84.5% in detecting dermatophytes, superior to the histology method which had a 69.53% agreement, 85.1% sensitivity and 57.1% specificity. The distribution of fungal organisms detected in this cohort shows a dermatophyte majority but a higher-than-expected proportion of NDMs. Nails negative for the Onycho+ test and positive for histology were mostly NDMs. This study demonstrates that the clinical performance of the Onycho+ test is superior to histology in detecting dermatophytes and that a combination of Onycho+ and histology can result in a higher clinical accuracy.

DNA-based detection for onychomycosis correlates better to histopathology than does fungal culture.

Onychomycosis is a prevalent disease of the nail. Traditional methods for diagnosis include direct microscopy with potassium hydroxide (KOH microscopy) and fungal culture. Other techniques using histochemical staining have higher sensitivity, but cannot identify genus or species of the infecting agent. PCR assays are sensitive, specific, and capable of genus and species level identification. We describe a real-time PCR assay for 15 different fungi that are associated with onychomycosis. Of 425 clinical samples suspected of onychomycosis analyzed by fungal culture and PCR, 219 samples were positive for both (52% agreement). Of the 206 discordant samples, 95% were resolved in favor of PCR by DNA sequencing. On a larger data set of 2,452 samples, positivity rates for histopathology, PCR, and culture were 85%, 73%, and 54% respectively. Further, 48% of PCR positive and 51% of histopathology positive samples were negative by culture. PCR outperformed culture compared to histopathology for sensitivity (80% versus 49%), specificity (92% versus 79%), positive predictive value (94% versus 77%), and negative predictive value (76% versus 52%). These results indicate the culture method lacks the sensitivity to be a reliable assay for onychomycosis, that PCR and histopathology are highly concordant, and that PCR provides the highest degree of diagnostic accuracy available.

Mapping and sequencing of structural variation from eight human genomes.

Genetic variation among individual humans occurs on many different scales, ranging from gross alterations in the human karyotype to single nucleotide changes. Here we explore variation on an intermediate scale--particularly insertions, deletions and inversions affecting from a few thousand to a few million base pairs. We employed a clone-based method to interrogate this intermediate structural variation in eight individuals of diverse geographic ancestry. Our analysis provides a comprehensive overview of the normal pattern of structural variation present in these genomes, refining the location of 1,695 structural variants. We find that 50% were seen in more than one individual and that nearly half lay outside regions of the genome previously described as structurally variant. We discover 525 new insertion sequences that are not present in the human reference genome and show that many of these are variable in copy number between individuals. Complete sequencing of 261 structural variants reveals considerable locus complexity and provides insights into the different mutational processes that have shaped the human genome. These data provide the first high-resolution sequence map of human structural variation--a standard for genotyping platforms and a prelude to future individual genome sequencing projects.

Genome sequence of the Brown Norway rat yields insights into mammalian evolution.

The laboratory rat (Rattus norvegicus) is an indispensable tool in experimental medicine and drug development, having made inestimable contributions to human health. We report here the genome sequence of the Brown Norway (BN) rat strain. The sequence represents a high-quality 'draft' covering over 90% of the genome. The BN rat sequence is the third complete mammalian genome to be deciphered, and three-way comparisons with the human and mouse genomes resolve details of mammalian evolution. This first comprehensive analysis includes genes and proteins and their relation to human disease, repeated sequences, comparative genome-wide studies of mammalian orthologous chromosomal regions and rearrangement breakpoints, reconstruction of ancestral karyotypes and the events leading to existing species, rates of variation, and lineage-specific and lineage-independent evolutionary events such as expansion of gene families, orthology relations and protein evolution.