Sampled Household Views on Various Aspects of Selected Rural Services in Haakon, Grant, and Brookings Counties, South Dakota

Sufficient and relevant information on existing levels of rural area services is a necessary for public and private suppliers if effective and efficient decisions are to be made concerning the creation of, addition to, or adequacy of various rural services. The primary purpose of this thesis is to obtain information on the adequacy of selected rural services from the perspective of the consuming household

“We Can Do Better”: Parents’ Experiences of the Diagnostic Process of Their Child’s Intellectual and Developmental Disability

The main purpose of this study was to examine parents’ experiences of the diagnostic process of their child’s intellectual and developmental disability. Research over the past thirty years has demonstrated that most parents are not satisfied with the diagnostic process, and has suggested best practices for professionals. The hope for this study was that parents’ experiences have improved since the last research was done and that best practices are being followed. Parents in the Twin Cities metro area of Minnesota were interviewed regarding their experience of the diagnostic process. The results indicated that parents are still dissatisfied with the process and raised a number of concerns, some of which were unique to this research. Suggestions and implications for practice based on these results are presented

ORDINARY AND GENERALIZED STOCHASTIC DOMINANCE: A PRIMER

Research Methods/ Statistical Methods,

Cofactor Genomics: A Sequencing Service Company Emerges from the Technology Development Laboratory

Jump Starting Technologies, Patent Issues, and Translational Medicine Poster SessionCofactor Genomics is based in St. Louis, MO and provides sequencing and analysis services to academic and industry clients. We are a small company committed to changing the service sequencing paradigm by offering our customers front-to-back solutions; experimental design, next-generation sequencing, and advanced analytics for their work. Cofactor Genomics was founded by individuals with one-of-a-kind experience in Next-Generation sequencing technology development. The Cofactor Genomics executive team spent a collective 35 years working in the Technology Development Group at The Genome Center at Washington University in St. Louis, Missouri. From early 2004 to late 2008, their primary responsibilities within the group were to investigate, evaluate and develop both wet-lab and computational applications for emerging Next-Generation sequencing technology platforms. Their experience began with beta testing the 454 Life Sciences (now Roche) GS 20, continued with beta testing the first serial numbered instrument from Solexa (now Illumina), and culminated with beta testing the Applied Biosystems (now Life Technologies) SOLiD instrument. Our individual experiences were unique within the realm of next-generation sequencing technology, thus extremely complimentary for a consolidation and commercialization of skill sets; Matt Hickenbotham became a renowned expert in library construction and Next-Gen instrumentation, Jon Armstrong emerged as an expert in targeted and reduced representation genomic sequencing, and Ryan Richt and Dr. Jarret Glasscock were two of the first individuals in the world to characterize the data generated by these instruments. It is this early-access wet-lab and computational experience with these disruptive sequencing technologies that provided the foundation for operations at Cofactor Genomics. Cofactor Genomics has been in operation for 2 years and has already established a proven track record of capability, versatility, remarkably consistent high quality data generation, and delivering custom data analysis solutions. We constructed 268 different sequencing libraries in our first year spanning nearly every sequencing application and multiple Next-Gen instrument platforms. This feat would be impossible for any firm other than Cofactor to complete in such a short time frame, much to the credit of our highly skilled and talented team. We pooled our talents to form a company offering customers end-to-end sequencing solutions that ultimately allow them to concentrate on what they do best, breakthrough research

Gallus GBrowse: a unified genomic database for the chicken

Gallus GBrowse (http://birdbase.net/cgi-bin/gbrowse/gallus/) provides online access to genomic and other information about the chicken, Gallus gallus. The information provided by this resource includes predicted genes and Gene Ontology (GO) terms, links to Gallus In Situ Hybridization Analysis (GEISHA), Unigene and Reactome, the genomic positions of chicken genetic markers, SNPs and microarray probes, and mappings from turkey, condor and zebra finch DNA and EST sequences to the chicken genome. We also provide a BLAT server (http://birdbase.net/cgi-bin/webBlat) for matching user-provided sequences to the chicken genome. These tools make the Gallus GBrowse server a valuable resource for researchers seeking genomic information regarding the chicken and other avian species

Bringing Agriculture into the GATT: Assessing the Benefits of Trade Liberalization

International Relations/Trade,

Analysis of the prostate cancer cell line LNCaP transcriptome using a sequencing-by-synthesis approach

BACKGROUND: High throughput sequencing-by-synthesis is an emerging technology that allows the rapid production of millions of bases of data. Although the sequence reads are short, they can readily be used for re-sequencing. By re-sequencing the mRNA products of a cell, one may rapidly discover polymorphisms and splice variants particular to that cell. RESULTS: We present the utility of massively parallel sequencing by synthesis for profiling the transcriptome of a human prostate cancer cell-line, LNCaP, that has been treated with the synthetic androgen, R1881. Through the generation of approximately 20 megabases (MB) of EST data, we detect transcription from over 10,000 gene loci, 25 previously undescribed alternative splicing events involving known exons, and over 1,500 high quality single nucleotide discrepancies with the reference human sequence. Further, we map nearly 10,000 ESTs to positions on the genome where no transcription is currently predicted to occur. We also characterize various obstacles with using sequencing by synthesis for transcriptome analysis and propose solutions to these problems. CONCLUSION: The use of high-throughput sequencing-by-synthesis methods for transcript profiling allows the specific and sensitive detection of many of a cell's transcripts, and also allows the discovery of high quality base discrepancies, and alternative splice variants. Thus, this technology may provide an effective means of understanding various disease states, discovering novel targets for disease treatment, and discovery of novel transcripts

Next-generation transcriptome sequencing of the premenopausal breast epithelium using specimens from a normal human breast tissue bank

Introduction Our efforts to prevent and treat breast cancer are significantly impeded by a lack of knowledge of the biology and developmental genetics of the normal mammary gland. In order to provide the specimens that will facilitate such an understanding, The Susan G. Komen for the Cure Tissue Bank at the IU Simon Cancer Center (KTB) was established. The KTB is, to our knowledge, the only biorepository in the world prospectively established to collect normal, healthy breast tissue from volunteer donors. As a first initiative toward a molecular understanding of the biology and developmental genetics of the normal mammary gland, the effect of the menstrual cycle and hormonal contraceptives on DNA expression in the normal breast epithelium was examined. Methods Using normal breast tissue from 20 premenopausal donors to KTB, the changes in the mRNA of the normal breast epithelium as a function of phase of the menstrual cycle and hormonal contraception were assayed using next-generation whole transcriptome sequencing (RNA-Seq). Results In total, 255 genes representing 1.4% of all genes were deemed to have statistically significant differential expression between the two phases of the menstrual cycle. The overwhelming majority (221; 87%) of the genes have higher expression during the luteal phase. These data provide important insights into the processes occurring during each phase of the menstrual cycle. There was only a single gene significantly differentially expressed when comparing the epithelium of women using hormonal contraception to those in the luteal phase. Conclusions We have taken advantage of a unique research resource, the KTB, to complete the first-ever next-generation transcriptome sequencing of the epithelial compartment of 20 normal human breast specimens. This work has produced a comprehensive catalog of the differences in the expression of protein-coding genes as a function of the phase of the menstrual cycle. These data constitute the beginning of a reference data set of the normal mammary gland, which can be consulted for comparison with data developed from malignant specimens, or to mine the effects of the hormonal flux that occurs during the menstrual cycle