Assessing the Impact of Non-Differential Genotyping Errors on Rare Variant Tests of Association

Background/Aims: We aim to quantify the effect of non-differential genotyping errors on the power of rare variant tests and identify those situations when genotyping errors are most harmful. Methods: We simulated genotype and phenotype data for a range of sample sizes, minor allele frequencies, disease relative risks and numbers of rare variants. Genotype errors were then simulated using five different error models covering a wide range of error rates. Results: Even at very low error rates, misclassifying a common homozygote as a heterozygote translates into a substantial loss of power, a result that is exacerbated even further as the minor allele frequency decreases. While the power loss from heterozygote to common homozygote errors tends to be smaller for a given error rate, in practice heterozygote to homozygote errors are more frequent and, thus, will have measurable impact on power. Conclusion: Error rates from genotype-calling technology for next-generation sequencing data suggest that substantial power loss may be seen when applying current rare variant tests of association to called genotypes

Citizen Science as a REAL Environment for Authentic Scientific Inquiry

Citizen science projects can serve as constructivist learning environments for programming focused on science, technology, engineering, and math (STEM) for youth. Attributes of rich environments for active learning (REALs) provide a framework for design of Extension STEM learning environments. Guiding principles and design strategies for the University of Minnesota Extension\u27s Driven to Discover: Enabling Authentic Inquiry through Citizen Science project demonstrate how education and investigations grounded in real-world citizen science projects can capitalize on REAL environments to generate meaningful STEM learning. Positive evaluation results support the efficacy of the design for enhancing youth science identity and practice

Counting Arithmetical Structures on Paths and Cycles

Let G be a finite, connected graph. An arithmetical structure on G is a pair of positive integer vectors d, r such that (diag (d) - A) r=0 , where A is the adjacency matrix of G. We investigate the combinatorics of arithmetical structures on path and cycle graphs, as well as the associated critical groups (the torsion part of the cokernels of the matrices (diag (d) - A)). For paths, we prove that arithmetical structures are enumerated by the Catalan numbers, and we obtain refined enumeration results related to ballot sequences. For cycles, we prove that arithmetical structures are enumerated by the binomial coefficients ((2n-1)/(n-1)) , and we obtain refined enumeration results related to multisets. In addition, we determine the critical groups for all arithmetical structures on paths and cycles

Counting Arithmetical Structures on Paths and Cycles

Let G be a finite, connected graph. An arithmetical structure on G is a pair of positive integer vectors d, r such that (diag (d) - A) r=0 , where A is the adjacency matrix of G. We investigate the combinatorics of arithmetical structures on path and cycle graphs, as well as the associated critical groups (the torsion part of the cokernels of the matrices (diag (d) - A)). For paths, we prove that arithmetical structures are enumerated by the Catalan numbers, and we obtain refined enumeration results related to ballot sequences. For cycles, we prove that arithmetical structures are enumerated by the binomial coefficients ((2n-1)/(n-1)) , and we obtain refined enumeration results related to multisets. In addition, we determine the critical groups for all arithmetical structures on paths and cycles

A world wide web informational reference source for viral ocular disease

This World Wide Web page is a quick reference source for anyone wishing to research ocular viral disease. Doctors and medical students will find the web site helpful to aid in the diagnosis and treatment of ocular viral disease. Topics within the site are cross-linked and presented in subjective, objective, assessment, plan format (SOAP). Photographs are included as are references for further study

Deleterious mutations predicted in the sorghum (\u3ci\u3eSorghum bicolor\u3c/i\u3e) \u3ci\u3eMaturity\u3c/i\u3e (\u3ci\u3eMa\u3c/i\u3e) and \u3ci\u3eDwarf\u3c/i\u3e (\u3ci\u3eDw\u3c/i\u3e) genes from whole‑genome resequencing

In sorghum [Sorghum bicolor (L.) Moench] the Maturity (Ma1, Ma2, Ma3, Ma4, Ma5, Ma6) and Dwarf (Dw1, Dw2, Dw3, Dw4) loci, encode genes controlling flowering time and plant height, respectively, which are critical for designing sorghum ideotypes for a maturity timeframe and a harvest method. Publicly available whole-genome resequencing data from 860 sorghum accessions was analyzed in silico to identify genomic variants at 8 of these loci (Ma1, Ma2, Ma3, Ma5, Ma6, Dw1, Dw2, Dw3) to identify novel loss of function alleles and previously characterized ones in sorghum germplasm. From~ 33 million SNPs and~ 4.4 million InDels, 1445 gene variants were identified within these 8 genes then evaluated for predicted effect on the corresponding encoded proteins, which included newly identified mutations (4 nonsense, 15 frameshift, 28 missense). Likewise, most accessions analyzed contained predicted loss of function alleles (425 ma1, 22 ma2, 40 ma3, 74 ma5, 414 ma6, 289 dw1, 268 dw2 and 45 dw3) at multiple loci, but 146 and 463 accessions had no predicted ma or dw mutant alleles, respectively. The ma and dw alleles within these sorghum accessions represent a valuable source for manipulating flowering time and plant height to develop the full range of sorghum types: grain, sweet and forage/biomass

Emergency Department Clinicians’ Attitudes Toward Opioid Use Disorder and Emergency Department-initiated Buprenorphine Treatment: A Mixed-Methods Study

Introduction: Emergency department (ED) visits related to opioid use disorder (OUD) have increased nearly twofold over the last decade. Treatment with buprenorphine has been demonstrated to decrease opioid-related overdose deaths. In this study, we aimed to better understand ED clinicians’ attitudes toward the initiation of buprenorphine treatment in the ED.Methods: We performed a mixed-methods study consisting of a survey of 174 ED clinicians (attending physicians, residents, and physician assistants) and semi-structured interviews with 17 attending emergency physicians at a tertiary-care academic hospital.Results: A total of 93 ED clinicians (53% of those contacted) completed the survey. While 80% of respondents agreed that buprenorphine should be administered in the ED for patients requesting treatment, only 44% felt that they were prepared to discuss medication for addiction treatment. Compared to clinicians with fewer than five years of practice, those with greater experience were less likely to approve of ED-initiated buprenorphine. In our qualitative analysis, physicians had differing perspectives on the role that the ED should play in treating OUD. Most physicians felt that a buprenorphine-based intervention in the ED would be feasible with institutional support, including training opportunities, protocol support within the electronic health record, counseling and support staff, and a robust referral system for outpatient follow-up.Conclusion: ED clinicians’ perception of buprenorphine varied by years of practice and training level. Most ED clinicians did not feel prepared to initiate buprenorphine in the ED. Qualitative interviews identified several addressable barriers to ED-initiated buprenorphine

Terrain Park Injuries

Background: This study examined demographics, injury pattern, and hospital outcome in patients injured in winter resort terrain parks.Methods: The study included patients >12 years of age who presented to a regional trauma center with an acute injury sustained at a winter resort. Emergency department (ED) research assistants collected patient injury and helmet use information using a prospectively designed questionnaire. ED and hospital data were obtained from trauma registry and hospital records.Results: Seventy-two patients were injured in a terrain park, and 263 patients were injured on non-terrain park slopes. Patients injured in terrain parks were more likely to be male [68/72 (94%) vs. 176/263 (67%), p<0.0001], younger in age [23 ± 7 vs. 36 ± 17, p<0.0001], live locally [47/72 (65%) vs. 124/263 (47%), p=0.006], use a snowboard [50/72 (69%) vs. 91/263 (35%), p<0.0001], hold a season pass [46/66 (70%) vs. 98/253 (39%), p<0.0001], and sustain an upper extremity injury [29/72 (40%) vs. 52/263 (20%), p<0.001] when compared to patients injured on non-terrain park slopes. There were no differences between the groups in terms of EMS transport to hospital, helmet use, admission rate, hospital length of stay, and patients requiring specialty consultation in the ED.Conclusions: Patients injured in terrain parks represent a unique demographic within winter resort patrons. Injury severity appears to be similar to those patients injured on non-terrain park slopes.[West J Emerg Med. 2009;10(4):257-262.