Here Comes Grosz

Program for the eighth annual RISD Cabaret held in Cellar at the top of the Waterman Building. Publicity, posters, cartoons and program designed by Yoon Cho, Yu-Kyung Chung,Arther Jones, Scott King, Richard Lloyd and Polly Spencer.https://digitalcommons.risd.edu/liberalarts_cabaret_programs/1007/thumbnail.jp

Acceleration of short and long DNA read mapping without loss of accuracy using suffix array

HPG Aligner applies suffix arrays for DNA read mapping. This implementation produces a highly sensitive and extremely fast mapping of DNA reads that scales up almost linearly with read length. The approach presented here is faster (over 20 for long reads) and more sensitive (over 98% in a wide range of read lengths) than the current state-of-the-art mappers. HPG Aligner is not only an optimal alternative for current sequencers but also the only solution available to cope with longer reads and growing throughputs produced by forthcoming sequencing technologies.This work is supported by BIO2011-27069 and PRI-PIBIN-2011-1289 (Spanish Ministry of Economy and Competitiveness), the HPC4G initiative (http://www.hpc4g.org) and the Bull-CIPF Chair for Computational Genomics.Tárraga, J.; Arnau, V.; Martínez, H.; Moreno, R.; Cazorla, D.; Salavert Torres, J.; Blanquer Espert, I.... (2014). Acceleration of short and long DNA read mapping without loss of accuracy using suffix array. Bioinformatics. 30(23):3396-3398. https://doi.org/10.1093/bioinformatics/btu553S339633983023Biesecker, L. G. (2010). Exome sequencing makes medical genomics a reality. Nature Genetics, 42(1), 13-14. doi:10.1038/ng0110-13Bussotti, G., Raineri, E., Erb, I., Zytnicki, M., Wilm, A., Beaudoing, E., … Notredame, C. (2011). BlastR—fast and accurate database searches for non-coding RNAs. Nucleic Acids Research, 39(16), 6886-6895. doi:10.1093/nar/gkr335Chaisson, M. J., & Tesler, G. (2012). Mapping single molecule sequencing reads using basic local alignment with successive refinement (BLASR): application and theory. BMC Bioinformatics, 13(1). doi:10.1186/1471-2105-13-238Chen, Y., Hong, J., Cui, W., Zaneveld, J., Wang, W., Gibbs, R., … Chen, R. (2013). CGAP-Align: A High Performance DNA Short Read Alignment Tool. PLoS ONE, 8(4), e61033. doi:10.1371/journal.pone.0061033Dobin, A., Davis, C. A., Schlesinger, F., Drenkow, J., Zaleski, C., Jha, S., … Gingeras, T. R. (2012). STAR: ultrafast universal RNA-seq aligner. Bioinformatics, 29(1), 15-21. doi:10.1093/bioinformatics/bts635Fonseca, N. A., Rung, J., Brazma, A., & Marioni, J. C. (2012). Tools for mapping high-throughput sequencing data. Bioinformatics, 28(24), 3169-3177. doi:10.1093/bioinformatics/bts605Langmead, B., & Salzberg, S. L. (2012). Fast gapped-read alignment with Bowtie 2. Nature Methods, 9(4), 357-359. doi:10.1038/nmeth.1923Liu, C.-M., Wong, T., Wu, E., Luo, R., Yiu, S.-M., Li, Y., … Lam, T.-W. (2012). SOAP3: ultra-fast GPU-based parallel alignment tool for short reads. Bioinformatics, 28(6), 878-879. doi:10.1093/bioinformatics/bts061Manber, U., & Myers, G. (1993). Suffix Arrays: A New Method for On-Line String Searches. SIAM Journal on Computing, 22(5), 935-948. doi:10.1137/0222058McKenna, A., Hanna, M., Banks, E., Sivachenko, A., Cibulskis, K., Kernytsky, A., … DePristo, M. A. (2010). The Genome Analysis Toolkit: A MapReduce framework for analyzing next-generation DNA sequencing data. Genome Research, 20(9), 1297-1303. doi:10.1101/gr.107524.110Raczy, C., Petrovski, R., Saunders, C. T., Chorny, I., Kruglyak, S., Margulies, E. H., … Tanner, S. W. (2013). Isaac: ultra-fast whole-genome secondary analysis on Illumina sequencing platforms. Bioinformatics, 29(16), 2041-2043. doi:10.1093/bioinformatics/btt314Rognes, T., & Seeberg, E. (2000). Six-fold speed-up of Smith-Waterman sequence database searches using parallel processing on common microprocessors. Bioinformatics, 16(8), 699-706. doi:10.1093/bioinformatics/16.8.699Smith, T. F., & Waterman, M. S. (1981). Identification of common molecular subsequences. Journal of Molecular Biology, 147(1), 195-197. doi:10.1016/0022-2836(81)90087-5Watson, M. (2014). Illuminating the future of DNA sequencing. Genome Biology, 15(2), 108. doi:10.1186/gb416

Identification of the Photoreceptor Transcriptional Co-Repressor SAMD11 as Novel Cause of Autosomal Recessive Retinitis Pigmentosa

Retinitis pigmentosa (RP), the most frequent form of inherited retinal dystrophy is characterized by progressive photoreceptor degeneration. Many genes have been implicated in RP development, but several others remain to be identified. Using a combination of homozygosity mapping, whole-exome and targeted next-generation sequencing, we found a novel homozygous nonsense mutation in SAMD11 in five individuals diagnosed with adult-onset RP from two unrelated consanguineous Spanish families. SAMD11 is ortholog to the mouse major retinal SAM domain (mr-s) protein that is implicated in CRX-mediated transcriptional regulation in the retina. Accordingly, protein-protein network analysis revealed a significant interaction of SAMD11 with CRX. Immunoblotting analysis confirmed strong expression of SAMD11 in human retina. Immunolocalization studies revealed SAMD11 was detected in the three nuclear layers of the human retina and interestingly differential expression between cone and rod photoreceptors was observed. Our study strongly implicates SAMD11 as novel cause of RP playing an important role in the pathogenesis of human degeneration of photoreceptors.This work was supported by several grants from the Spanish Centre for Biomedical Network Research on Rare Diseases (CIBERER)(06/07/0036), Instituto de Salud Carlos III (ISCIII, Spanish Ministry of Health)/FEDER, including FIS (PI013/00226) and RETICS (RD09/0076/00101 and RD12/0034/0010), Ministry of Economy and Competitiveness (MINECO), including FEDER (BFU2012-36845), and BIO2011-27069, Conselleria de Educació of the Valencia Community (PROMETEOII/2014/025), Spanish National Organization of the Blind (ONCE) and the Spanish Fighting Blindness Foundation (FUNDALUCE). M.C. was sponsored by the Miguel Servet Program for Researchers in the Spanish National Health Service (CP12/03256) and RSA by Sara Borrel Postdoctoral Program (CD12/00676), both from the ISCIII/FEDER. A.A-F. was sponsored by CIBERER, RPC is supported by Fundación Conchita Rábago (FCR), L.C is sponsored by RETICS (RD12/0034/0010) from ISCIII and L.d.S. was supported by CAPES Foundation, Ministry of Education of Brazil

Perceptions About Work/Life Balance Among DU Community Members with Young Children

Background: In the past fifty years, families in the USA have changed in configuration, size and dynamics. The percentage of families that do not conform to the traditional family unit (married mother and father with children) has increased as there are more single-parent families, LGBTQ families and interracial families. The proportion of unmarried or divorced families has also increased, as it has the number of married and unmarried couples that opt to not have children and, additionally, more couples are opting for adoption and foster parenting (Pew Research Center 2010). Furthermore, the percentage of households where all the adults work has increased, which impacts the amount and quality of time available for family activities and household chores (Bianchi, Robinson and Milkie 2006). These and other trends have led to the identification of “work-family balance” as an important challenge of our times, one that families have been facing for decades and that institutions are only starting to pay attention to (Hochschild 2013). Although there are many aspects of family life that are challenging to balance with workplace demands, childcare has been specifically identified as one that needs attention (Desilver 2014). Methods: Study goal: To describe the perceptions that some DU community members with children have about work-family balance with attention to challenges, difficulties and institutional responses. Study design: Descriptive, cross-sectional, qualitative study. Population and sample: We recruited 63 University of Denver students (13), staff (14) and faculty (36) who are responsible of parenting at least one child under 10 years of age. We used purposive sampling. which consists in actively finding individuals who meet the criteria. Data collection: Semi structured interviews (January 23-February 8, 2017), in person, audio recorded and transcribed within one week. Participants’ autonomy, confidentiality and anonymity were protected throughout the process. Data analysis: Thematic analysis, which consists in the systematic identification of themes in the interview transcripts, followed by their conceptual organization and hierarchization. Research team: sixty-six undergraduate students taking Cultural Anthropology (ANTH 2010) in winter 2017, four graduate teaching assistants and one course instructor. Findings: Student participants portrayed work/life balance as set of interconnected situations and relations that go from the deeply personal to the interpersonal, communal and institutional. Aiming at capturing such complexity, we organized our findings in four themes: work/life balance, family dynamics, personal challenges and support. Participants told us about their struggles when negotiating work and life responsibilities which often lead to feelings of guilt, which are mediated by their colleagues’ reactions, schedule flexibility, their job situation and the presence or absence of maternity leave. Family dynamics reflected a tension between a narrative of independence and one of dependence in raising children, highlighting the importance of social networks, both of which are also affected by immigration status and intra-household negotiations particularly, Perceptions about work/life balance among DU community members with young children Cultural Anthropology (ANTH 2010) winter 2017 4 with their partners. Personal challenges relate primarily with time management and establishing clear boundaries between work and family, which related to managing emails, organization and scheduling of activities, maintaining a financial balance, and solving transportation needs, all of which were mediated the ability parents have of controlling a flexible work schedule, an ability greatly diminished among students. Support parents need related to child care goes from the one that happens in interpersonal interactions with neighbors, friends, relatives and colleagues, to the institutionalized forms of support, where participants expressed their frustration for the insufficiency of accessible options in Denver, the lack of options at DU, and the inaccessibility of DU’s Fisher Early Learning Center. Conclusions and recommendations: Participant’s ability to control their schedules together with their financial and social capital seem to shape important differences in the ability that parents have for balancing work and life. Students, single parents and recent immigrants seem to have a combination of elements that add to the challenges. At the interpersonal level, simple acts of kindness, sympathy and empathy in the everyday interactions seem to make an important difference to parents. The perception that many of the student participants expressed about the academy not being comfortable with children, families or parents could be addressed by making it normal to talk about all these aspects of life. At the institutional level, efforts could be made at reaching out to parents, especially students and single parents, to offer them guidance and support that is already in place at DU, such as counselling and wellbeing resources, as well as orientation related to institutional policies. Policies related to maternity and paternity leave should be refined to ensure that they do not negatively affect those they are supposed to support. Convenient, affordable and sustainable on-campus child care options should be seriously considered given that they would enhance the possibilities for parents to participate in activities at DU. Events should be organized where members of the DU community have the opportunity to share not as students, staff or faculty, but as members of families

Airway Microbiota and Pathogen Abundance in Age-Stratified Cystic Fibrosis Patients

Bacterial communities in the airways of cystic fibrosis (CF) patients are, as in other ecological niches, influenced by autogenic and allogenic factors. However, our understanding of microbial colonization in younger versus older CF airways and the association with pulmonary function is rudimentary at best. Using a phylogenetic microarray, we examine the airway microbiota in age stratified CF patients ranging from neonates (9 months) to adults (72 years). From a cohort of clinically stable patients, we demonstrate that older CF patients who exhibit poorer pulmonary function possess more uneven, phylogenetically-clustered airway communities, compared to younger patients. Using longitudinal samples collected form a subset of these patients a pattern of initial bacterial community diversification was observed in younger patients compared with a progressive loss of diversity over time in older patients. We describe in detail the distinct bacterial community profiles associated with young and old CF patients with a particular focus on the differences between respective “early” and “late” colonizing organisms. Finally we assess the influence of Cystic Fibrosis Transmembrane Regulator (CFTR) mutation on bacterial abundance and identify genotype-specific communities involving members of the Pseudomonadaceae, Xanthomonadaceae, Moraxellaceae and Enterobacteriaceae amongst others. Data presented here provides insights into the CF airway microbiota, including initial diversification events in younger patients and establishment of specialized communities of pathogens associated with poor pulmonary function in older patient populations

Characteristics of therapeutic alliance in musculoskeletal physiotherapy and occupational therapy practice: A scoping review of the literature

© 2017 The Author(s). Background: Most conventional treatment for musculoskeletal conditions continue to show moderate effects, prompting calls for ways to increase effectiveness, including drawing from strategies used across other health conditions. Therapeutic alliance refers to the relational processes at play in treatment which can act in combination or independently of specific interventions. Current evidence guiding the use of therapeutic alliance in health care arises largely from psychotherapy and medicine literature. The objective of this review was to map out the available literature on therapeutic alliance conceptual frameworks, themes, measures and determinants in musculoskeletal rehabilitation across physiotherapy and occupational therapy disciplines. Methods: A scoping review of the literature published in English since inception to July 2015 was conducted using Medline, EMBASE, PsychINFO, PEDro, SportDISCUS, AMED, OTSeeker, AMED and the grey literature. A key search term strategy was employed using physiotherapy , occupational therapy , therapeutic alliance , and musculoskeletal to identify relevant studies. All searches were performed between December 2014 and July 2015 with an updated search on January 2017. Two investigators screened article title, abstract and full text review for articles meeting the inclusion criteria and extracted therapeutic alliance data and details of each study. Results: One hundred and thirty articles met the inclusion criteria including quantitative (33%), qualitative (39%), mixed methods (7%) and reviews and discussions (23%) and most data came from the USA (23%). Randomized trials and systematic reviews were 4.6 and 2.3% respectively. Low back pain condition (22%) and primary care (30.7%) were the most reported condition and setting respectively. One theory, 9 frameworks, 26 models, 8 themes and 42 subthemes of therapeutic alliance were identified. Twenty-six measures were identified; the Working Alliance Inventory (WAI) was the most utilized measure (13%). Most of the therapeutic alliance themes extracted were from patient perspectives. The relationship between adherence and therapeutic alliance was examined by 26 articles of which 57% showed some correlation between therapeutic alliance and adherence. Age moderated the relationship between therapeutic alliance and adherence with younger individuals and an autonomy support environment reporting improved adherence. Prioritized goals, autonomy support and motivation were facilitators of therapeutic alliance. Conclusion: Therapeutic Alliance has been studied in a limited extent in the rehabilitation literature with conflicting frameworks and findings. Potential benefits described for enhancing therapeutic alliance might include better exercise adherence. Several knowledge gaps have been identified with a potential for generating future research priorities for therapeutic alliance in musculoskeletal rehabilitation

Plant Products for Pharmacology: Application of Enzymes in Their Transformations

Different plant products have been subjected to detailed investigations due to their increasing importance for improving human health. Plants are sources of many groups of natural products, of which large number of new compounds has already displayed their high impact in human medicine. This review deals with the natural products which may be found dissolved in lipid phase (phytosterols, vitamins etc.). Often subsequent convenient transformation of natural products may further improve the pharmacological properties of new potential medicaments based on natural products. To respect basic principles of sustainable and green procedures, enzymes are often employed as efficient natural catalysts in such plant product transformations. Transformations of lipids and other natural products under the conditions of enzyme catalysis show increasing importance in environmentally safe and sustainable production of pharmacologically important compounds. In this review, attention is focused on lipases, efficient and convenient biocatalysts for the enantio- and regioselective formation / hydrolysis of ester bond in a wide variety of both natural and unnatural substrates, including plant products, eg. plant oils and other natural lipid phase compounds. The application of enzymes for preparation of acylglycerols and transformation of other natural products provides big advantage in comparison with employing of conventional chemical methods: Increased selectivity, higher product purity and quality, energy conservation, elimination of heavy metal catalysts, and sustainability of the employed processes, which are catalyzed by enzymes. Two general procedures are used in the transformation of lipid-like natural products: (a) Hydrolysis/alcoholysis of triacylglycerols and (b) esterification of glycerol. The reactions can be performed under conventional conditions or in supercritical fluids/ionic liquids. Enzyme-catalyzed reactions in supercritical fluids combine the advantages of biocatalysts (substrate specificity under mild reaction conditions) and supercritical fluids (high mass-transfer rate, easy separation of reaction products from the solvent, environmental benefits based on excluding organic solvents from the production process)

Evaluating the Effects of SARS-CoV-2 Spike Mutation D614G on Transmissibility and Pathogenicity.

Global dispersal and increasing frequency of the SARS-CoV-2 spike protein variant D614G are suggestive of a selective advantage but may also be due to a random founder effect. We investigate the hypothesis for positive selection of spike D614G in the United Kingdom using more than 25,000 whole genome SARS-CoV-2 sequences. Despite the availability of a large dataset, well represented by both spike 614 variants, not all approaches showed a conclusive signal of positive selection. Population genetic analysis indicates that 614G increases in frequency relative to 614D in a manner consistent with a selective advantage. We do not find any indication that patients infected with the spike 614G variant have higher COVID-19 mortality or clinical severity, but 614G is associated with higher viral load and younger age of patients. Significant differences in growth and size of 614G phylogenetic clusters indicate a need for continued study of this variant

Impact of COVID-19 on cardiovascular testing in the United States versus the rest of the world

Objectives: This study sought to quantify and compare the decline in volumes of cardiovascular procedures between the United States and non-US institutions during the early phase of the coronavirus disease-2019 (COVID-19) pandemic. Background: The COVID-19 pandemic has disrupted the care of many non-COVID-19 illnesses. Reductions in diagnostic cardiovascular testing around the world have led to concerns over the implications of reduced testing for cardiovascular disease (CVD) morbidity and mortality. Methods: Data were submitted to the INCAPS-COVID (International Atomic Energy Agency Non-Invasive Cardiology Protocols Study of COVID-19), a multinational registry comprising 909 institutions in 108 countries (including 155 facilities in 40 U.S. states), assessing the impact of the COVID-19 pandemic on volumes of diagnostic cardiovascular procedures. Data were obtained for April 2020 and compared with volumes of baseline procedures from March 2019. We compared laboratory characteristics, practices, and procedure volumes between U.S. and non-U.S. facilities and between U.S. geographic regions and identified factors associated with volume reduction in the United States. Results: Reductions in the volumes of procedures in the United States were similar to those in non-U.S. facilities (68% vs. 63%, respectively; p = 0.237), although U.S. facilities reported greater reductions in invasive coronary angiography (69% vs. 53%, respectively; p < 0.001). Significantly more U.S. facilities reported increased use of telehealth and patient screening measures than non-U.S. facilities, such as temperature checks, symptom screenings, and COVID-19 testing. Reductions in volumes of procedures differed between U.S. regions, with larger declines observed in the Northeast (76%) and Midwest (74%) than in the South (62%) and West (44%). Prevalence of COVID-19, staff redeployments, outpatient centers, and urban centers were associated with greater reductions in volume in U.S. facilities in a multivariable analysis. Conclusions: We observed marked reductions in U.S. cardiovascular testing in the early phase of the pandemic and significant variability between U.S. regions. The association between reductions of volumes and COVID-19 prevalence in the United States highlighted the need for proactive efforts to maintain access to cardiovascular testing in areas most affected by outbreaks of COVID-19 infection