SNANA: A Public Software Package for Supernova Analysis

We describe a general analysis package for supernova (SN) light curves, called SNANA, that contains a simulation, light curve fitter, and cosmology fitter. The software is designed with the primary goal of using SNe Ia as distance indicators for the determination of cosmological parameters, but it can also be used to study efficiencies for analyses of SN rates, estimate contamination from non-Ia SNe, and optimize future surveys. Several SN models are available within the same software architecture, allowing technical features such as K-corrections to be consistently used among multiple models, and thus making it easier to make detailed comparisons between models. New and improved light-curve models can be easily added. The software works with arbitrary surveys and telescopes and has already been used by several collaborations, leading to more robust and easy-to-use code. This software is not intended as a final product release, but rather it is designed to undergo continual improvements from the community as more is learned about SNe. Below we give an overview of the SNANA capabilities, as well as some of its limitations. Interested users can find software downloads and more detailed information from the manuals at http://www.sdss.org/supernova/SNANA.html .Comment: Accepted for publication in PAS

Ruler Arrays Reveal Haploid Genomic Structural Variation

Despite the known relevance of genomic structural variants to pathogen behavior, cancer, development, and evolution, certain repeat based structural variants may evade detection by existing high-throughput techniques. Here, we present ruler arrays, a technique to detect genomic structural variants including insertions and deletions (indels), duplications, and translocations. A ruler array exploits DNA polymerase’s processivity to detect physical distances between defined genomic sequences regardless of the intervening sequence. The method combines a sample preparation protocol, tiling genomic microarrays, and a new computational analysis. The analysis of ruler array data from two genomic samples enables the identification of structural variation between the samples. In an empirical test between two closely related haploid strains of yeast ruler arrays detected 78% of the structural variants larger than 100 bp.United States. National Institutes of Health (Grant R01GM069676

‘Not everybody walks around and thinks “That’s an example of othering or stigmatisation”’: identity, pedagogic rights and the acquisition of undergraduate sociology-based social science knowledge

This article places itself in conversation with literature about how the experience and outcomes of university education are structured by intersections between social class, ethnicity, gender, age and type of university attended. It addresses undergraduate students’ acquisition of sociological knowledge in four diverse university settings. Basil Bernstein’s concepts of pedagogic identity, pedagogic rights, classification and framing are employed to analyse curriculum and interviews with 31 students over the period of their undergraduate degree. The nature of a sociology-based disciplinary identity is described and illustrated, and it is shown how the formation of this identity gives access to pedagogic rights and the acquisition of valuable capabilities. Addressing the question of whether pedagogic rights are distributed unequally in a stratified university system, it was found that they were not distributed, as might be expected, according to institutional hierarchy. It is argued that the acquisition of university sociological knowledge can disrupt social inequality

Initial validation of the Spanish Childhood Trauma Questionnaire-short form: Factor structure, reliability and association with parenting

The present study examines the internal consistency and factor structure of the Spanish version of the Childhood Trauma Questionnaire-Short Form (CTQ-SF) and the association between the CTQ-SF subscales and parenting style. Cronbach's α and confirmatory factor analyses (CFA) were performed in a female clinical sample (n = 185). Kendall's ι correlations were calculated between the maltreatment and parenting scales in a subsample of 109 patients. The Spanish CTQ-SF showed adequate psychometric properties and a good fit of the 5-factor structure. The neglect and abuse scales were negatively associated with parental care and positively associated with overprotection scales. The results of this study provide initial support for the reliability and validity of the Spanish CTQ-SF

Driving performance in older adults: Current measures, findings, and implications for roadway safety

BACKGROUND AND OBJECTIVES: Over 10,000 people a day turn 65 in the United States. For many older adults, driving represents an essential component of independence and is one of the most important factors in overall mobility. Recent survey studies in older adults suggest that up to 60% of older adult drivers with mild cognitive impairment, and up to 30% with dementia, continue to drive. The purpose of this review is to provide a comprehensive and detailed resource on the topics of cognition and driving for clinicians, researchers, and policymakers working on efforts related to older adult drivers. RESEARCH DESIGN AND METHODS: Publications on PubMed and Medline and discussions with experts working in geriatrics, technology, driving policy, psychology, and diverse aspects of driving performance were utilized to inform the current review. RESULTS: Research indicates that there is a complex and inverse correlation between multiple cognitive measures, driving performance, and risky driving behaviors. The fragmented nature of available peer-reviewed literature, and a reliance on correlative data, do not currently allow for the identification of the temporal and reciprocal nature of the interplay between cognition and driving endpoints. DISCUSSION AND IMPLICATIONS: There are currently no widely accepted definitions, conceptual models, or uniform set of analyses for conducting geriatric research that is focused on driving. Establishing conventions for conducting research that harmonizes the fields of geriatrics, cognition, and driving research is critical for the development of the evidence base that will inform clinical practice and road safety policy

Change in hematologic indices over time in pediatric inflammatory bowel disease treated with azathioprine

Azathioprine leads to changes in mean corpuscular volume (MCV) and white blood cell (WBC) indices reflecting efficacy or toxicity. Understanding the interactions between bone marrow stem cells and azathioprine could highlight abnormal response patterns as forerunners for hematologic malig-nancies. This study gives a statistical description of factors influencing the relationship between MCV and WBC in children with inflammatory bowel disease treated with azathioprine. We found that leukopenia preceded macro¬cytosis. Macrocytosis is therefore not a good predictor of leukopenia. Further studies will be necessary to determine the subgroup of patients at increased risk of malignancies based on bone marrow response

PROMIS Pain Interference Is Superior vs Numeric Pain Rating Scale for Pain Assessment in Foot and Ankle Patients

Background: The Numeric Pain Rating Scale (NPRS) is a popular method to assess pain. Recently, the Patient-Reported Outcomes Measurement Information System (PROMIS) has been suggested to be more accurate in measuring pain. This study aimed to compare NPRS and PROMIS Pain Interference (PI) scores in a population of foot and ankle patients to determine which method demonstrated a stronger correlation with preoperative and postoperative function, as measured by PROMIS Physical Function (PF). Methods: Prospective PROMIS PF and PI and NPRS data were obtained for 8 common elective foot and ankle surgical procedures. Data were collected preoperatively and postoperatively at a follow-up visit at least 6 months after surgery. Spearman correlation coefficients were calculated to determine the relationship among NPRS (0-10) and PROMIS domains (PI, PF) pre- and postoperatively. A total of 500 patients fit our inclusion criteria. Results: PROMIS PF demonstrated a stronger correlation to PROMIS PI in both the pre- and postoperative settings (preoperative: ρ = −0.66; postoperative: ρ = −0.69) compared with the NPRS (preoperative: ρ = −0.32; postoperative: ρ = −0.33). Similar results were found when data were grouped by Current Procedural Terminology (CPT) code. Conclusion: PROMIS PI was a superior tool to gauge a patient’s preoperative level of pain and functional ability. This information may assist surgeons and patients in setting postoperative functional expectations and pain management. Level of Evidence: Level II, prognosti

New CRISPR Mutagenesis Strategies Reveal Variation in Repair Mechanisms among Fungi

We have created new vectors for clustered regularly interspaced short palindromic repeat (CRISPR) mutagenesis in Candida albicans, Saccharomyces cerevisiae, Candida glabrata, and Naumovozyma castellii These new vectors permit a comparison of the requirements for CRISPR mutagenesis in each of these species and reveal different dependencies for repair of the Cas9 double-stranded break. Both C. albicans and S. cerevisiae rely heavily on homology-directed repair, whereas C. glabrata and N. castellii use both homology-directed and nonhomologous end-joining pathways. The high efficiency of these vectors permits the creation of unmarked deletions in each of these species and the recycling of the dominant selection marker for serial mutagenesis in prototrophs. A further refinement, represented by the "Unified" Solo vectors, incorporates Cas9, guide RNA, and repair template into a single vector, thus enabling the creation of vector libraries for pooled screens. To facilitate the design of such libraries, we have identified guide sequences for each of these species with updated guide selection algorithms.IMPORTANCE CRISPR-mediated genome engineering technologies have revolutionized genetic studies in a wide range of organisms. Here we describe new vectors and guide sequences for CRISPR mutagenesis in the important human fungal pathogens C. albicans and C. glabrata, as well as in the related yeasts S. cerevisiae and N. castellii The design of these vectors enables efficient serial mutagenesis in each of these species by leaving few, if any, exogenous sequences in the genome. In addition, we describe strategies for the creation of unmarked deletions in each of these species and vector designs that permit the creation of vector libraries for pooled screens. These tools and strategies promise to advance genetic engineering of these medically and industrially important species.National Institutes of Health (U.S.) (Grant GM035010)National Institutes of Health (U.S.) (Grant GM118135)National Institutes of Health (U.S.) (Grant R15AI130950

Classicality of quantum information processing

The ultimate goal of the classicality programme is to quantify the amount of quantumness of certain processes. Here, classicality is studied for a restricted type of process: quantum information processing (QIP). Under special conditions, one can force some qubits of a quantum computer into a classical state without affecting the outcome of the computation. The minimal set of conditions is described and its structure is studied. Some implications of this formalism are the increase of noise robustness, a proof of the quantumness of mixed state quantum computing and a step forward in understanding the very foundation of QIP.Comment: Minor changes, published in Phys. Rev. A 65, 42319 (2002