Leveraging the Remake: The Role of the Arts in a Shifting Economy - 2012 Report and Recommendations

These are changing, uncertain times -- times that require new ways of thinking and engaging with both the opportunities and challenges of a more diverse, technologically driven, and entrepreneurial world. When we talk about a changing world and the role America will play in shaping the "new normal," the idea of a competitive advantage naturally arises -- moreover, how such an advantage may be achieved. Education, innovation, engineering, technology. All of these are terms that have been imbued with particular significance as we attempt to position ourselves to move into the future. At the core of all of these, however, there is something much more fundamental at play: the recognition that the way forward is through creative thinking and nontraditional problem-solving. Both of which are inherent in -- and developed through -- the arts.The 2012 National Arts Policy Roundtable convened around the idea that the arts are fundamental to navigating our shifting economy and should be recognized as such. Communities all across America are grappling with changing structures in economics, education, demographics, and more, and the arts have an important place in every locale -- urban, rural, and everything in between. Thus, the charge for the 2012 National Arts Policy Roundtable was to grapple with the question of how best to navigate "the remake" through the lens of the arts, and develop a set of actionable steps to put the arts to work in providing sustainable, creative and innovative answers

UB Knightlines Fall/Winter 2016

The UB Knightlines newsletter for fall and winter of 2016. This issue contains articles discussing winners of the UB Alumni Association's Distinguished Alumni Award, Alumni Association Scholarship winner Mendel Murray, professor Jeongkyu Lee’s Young Data Science program, president emeritus Richard Rubenstein and this book After Auschwitz, UB receiving a National Institutes of Health grant to expand research, SASD students winning third place in the Sherwin-Williams STIR Student Design Challenge, the opening of the new dorm University Hall, student Michael Asmerom a National Association of Black Accountants, professor Marsha Matto and SASD students work with couple to design beach home, faculty news, alumni news, books published by alums and faculty, and other campus and sports news

Wakeshield WSF-02 GPS Experiment

Shuttle mission STS-69 was launched on September 7, 1995, 10:09 CDT, carrying the Wake Shield Facility (WSF-02). The WSF-02 spacecraft included a set of payloads provided by the Texas Space Grant Consortium, known as TexasSat. One of the TexasSat payloads was a GPS TurboRogue receiver loaned by the University Corporation for Atmospheric Research. On September 11, the WSF-02 was unberthed from the Endeavour payload bay using the remote manipulator system. The GPS receiver was powered on prior to release and the WSF-02 remained in free-flight for three days before being retrieved on September 14. All WSF-02 GPS data, which includes dual frequency pseudorange and carrier phase, were stored in an on-board recorder for post-flight analysis, but "snap- shots" of data were transmitted for 2-3 minutes at intervals of several hours, when permitted by the telemetry band- widdl The GPS experiment goals were: (1) an evaluation of precision orbit determination in a low altitude environment (400 km) where perturbations due to atmospheric drag and the Earth's gravity field are more pronounced than for higher altitude satellites with high precision orbit requirements, such as TOPEX/POSEIDON; (2) an assessment of relative positioning using the WSF GPS receiver and the Endeavour Collins receiver; and (3) determination of atmospheric temperature profiles using GPS signals passing through the atmosphere. Analysis of snap-shot telemetry data indicate that 24 hours of continuous data were stored on board, which includes high rate (50 Hz) data for atmosphere temperature profiles. Examination of the limited number of real-time navigation solutions show that at least 7 GPS satellites were tracked simultaneously and the on-board clock corrections were at the microsec level, as expected. Furthermore, a dynamical consistency test provided a further validation of the on-board navigation solutions. Complete analysis will be conducted in post-flight using the data recorded on-board

A large scale hearing loss screen reveals an extensive unexplored genetic landscape for auditory dysfunction

The developmental and physiological complexity of the auditory system is likely reflected in the underlying set of genes involved in auditory function. In humans, over 150 non-syndromic loci have been identified, and there are more than 400 human genetic syndromes with a hearing loss component. Over 100 non-syndromic hearing loss genes have been identified in mouse and human, but we remain ignorant of the full extent of the genetic landscape involved in auditory dysfunction. As part of the International Mouse Phenotyping Consortium, we undertook a hearing loss screen in a cohort of 3006 mouse knockout strains. In total, we identify 67 candidate hearing loss genes. We detect known hearing loss genes, but the vast majority, 52, of the candidate genes were novel. Our analysis reveals a large and unexplored genetic landscape involved with auditory function

Assessing Reproducibility of Inherited Variants Detected With Short-Read Whole Genome Sequencing

Background: Reproducible detection of inherited variants with whole genome sequencing (WGS) is vital for the implementation of precision medicine and is a complicated process in which each step affects variant call quality. Systematically assessing reproducibility of inherited variants with WGS and impact of each step in the process is needed for understanding and improving quality of inherited variants from WGS. Results: To dissect the impact of factors involved in detection of inherited variants with WGS, we sequence triplicates of eight DNA samples representing two populations on three short-read sequencing platforms using three library kits in six labs and call variants with 56 combinations of aligners and callers. We find that bioinformatics pipelines (callers and aligners) have a larger impact on variant reproducibility than WGS platform or library preparation. Single-nucleotide variants (SNVs), particularly outside difficult-to-map regions, are more reproducible than small insertions and deletions (indels), which are least reproducible when \u3e 5 bp. Increasing sequencing coverage improves indel reproducibility but has limited impact on SNVs above 30×. Conclusions: Our findings highlight sources of variability in variant detection and the need for improvement of bioinformatics pipelines in the era of precision medicine with WGS

Assessing reproducibility of inherited variants detected with short-read whole genome sequencing

Background: Reproducible detection of inherited variants with whole genome sequencing (WGS) is vital for the implementation of precision medicine and is a complicated process in which each step affects variant call quality. Systematically assessing reproducibility of inherited variants with WGS and impact of each step in the process is needed for understanding and improving quality of inherited variants from WGS. Results: To dissect the impact of factors involved in detection of inherited variants with WGS, we sequence triplicates of eight DNA samples representing two populations on three short-read sequencing platforms using three library kits in six labs and call variants with 56 combinations of aligners and callers. We find that bioinformatics pipelines (callers and aligners) have a larger impact on variant reproducibility than WGS platform or library preparation. Single-nucleotide variants (SNVs), particularly outside difficult-to-map regions, are more reproducible than small insertions and deletions (indels), which are least reproducible when > 5 bp. Increasing sequencing coverage improves indel reproducibility but has limited impact on SNVs above 30x. Conclusions: Our findings highlight sources of variability in variant detection and the need for improvement of bioinformatics pipelines in the era of precision medicine with WGS.Peer reviewe

Identification of Clinically Relevant Protein Targets in Prostate Cancer with 2D-DIGE Coupled Mass Spectrometry and Systems Biology Network Platform

Prostate cancer (PCa) is the most common type of cancer found in men and among the leading causes of cancer death in the western world. In the present study, we compared the individual protein expression patterns from histologically characterized PCa and the surrounding benign tissue obtained by manual micro dissection using highly sensitive two-dimensional differential gel electrophoresis (2D-DIGE) coupled with mass spectrometry. Proteomic data revealed 118 protein spots to be differentially expressed in cancer (n = 24) compared to benign (n = 21) prostate tissue. These spots were analysed by MALDI-TOF-MS/MS and 79 different proteins were identified. Using principal component analysis we could clearly separate tumor and normal tissue and two distinct tumor groups based on the protein expression pattern. By using a systems biology approach, we could map many of these proteins both into major pathways involved in PCa progression as well as into a group of potential diagnostic and/or prognostic markers. Due to complexity of the highly interconnected shortest pathway network, the functional sub networks revealed some of the potential candidate biomarker proteins for further validation. By using a systems biology approach, our study revealed novel proteins and molecular networks with altered expression in PCa. Further functional validation of individual proteins is ongoing and might provide new insights in PCa progression potentially leading to the design of novel diagnostic and therapeutic strategies

Identification of genetic elements in metabolism by high-throughput mouse phenotyping.

Metabolic diseases are a worldwide problem but the underlying genetic factors and their relevance to metabolic disease remain incompletely understood. Genome-wide research is needed to characterize so-far unannotated mammalian metabolic genes. Here, we generate and analyze metabolic phenotypic data of 2016 knockout mouse strains under the aegis of the International Mouse Phenotyping Consortium (IMPC) and find 974 gene knockouts with strong metabolic phenotypes. 429 of those had no previous link to metabolism and 51 genes remain functionally completely unannotated. We compared human orthologues of these uncharacterized genes in five GWAS consortia and indeed 23 candidate genes are associated with metabolic disease. We further identify common regulatory elements in promoters of candidate genes. As each regulatory element is composed of several transcription factor binding sites, our data reveal an extensive metabolic phenotype-associated network of co-regulated genes. Our systematic mouse phenotype analysis thus paves the way for full functional annotation of the genome