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Articles 4081 - 4110 of 9783

Full-Text Articles in Genetics and Genomics

Participant Perspectives On A Phase I/Ii Ocular Gene Therapy Trial (Nct02077361), Stephanie P. Brooks, Shelly Benjaminy, Tania M. Bubela Jun 2019

Participant Perspectives On A Phase I/Ii Ocular Gene Therapy Trial (Nct02077361), Stephanie P. Brooks, Shelly Benjaminy, Tania M. Bubela

Office of the Provost

Background: To learn from the experiences of potential clinical trial participants, participants in a Phase 1 ocular gene therapy trial, and their partners to improve communications and trial conduct.
Materials and methods: Primary and secondary qualitative analysis of semi-structured interviews of potential participants (n = 20), clinical trial participants (n = 2) and their partners (n = 2) in a gene therapy clinical trial for choroideremia (NCT02077361). Analysis included: 1) thematic analysis of transcribed entrance and exit semi-structured interviews with trial participants and their partners; and 2) secondary qualitative analysis of interviews with potential trial participants, …

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Effects Of Meiotic Drive On Developing Eye-Stalks In Stalk-Eyed Flies, Christopher Lepore, Olivia Smith, Heather Wood, Josephine Reinhardt Phd Jun 2019

Effects Of Meiotic Drive On Developing Eye-Stalks In Stalk-Eyed Flies, Christopher Lepore, Olivia Smith, Heather Wood, Josephine Reinhardt Phd

McNair Scholars Program

Teleopsis dalmanni, commonly known as Stalk-Eyed flies, are known for their sexually dimorphic eye-stalks which females use to pick mates. Within the Gombak-12 population, some individuals contain meiotic drive which is known to influence eye-stalk length and sex ratios. Our goal was to identify genes in developing eye tissue that play a role in causing meiotic drive. To identify these candidate genes, we determined the sex and meiotic drive status of individuals by dissecting 3rd instar larvae for their carcasses. After finding that Qiagen Puregene and Qiagen DNEasy columns DNA extraction techniques worked best—determined by using gel electrophoresis—we prepared …

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Beef Production Systems In The Nebraska Sandhills, Mckay Reed Erickson Jun 2019

Beef Production Systems In The Nebraska Sandhills, Mckay Reed Erickson

Department of Animal Science: Dissertations, Theses, and Student Research

Four studies were conducted to determine the effectiveness of improving production systems of beef cattle in the Sandhills region of Nebraska. These studies were to determine impacts of modified estrus synchronization protocols, genomic testing heifer calves for longevity, and evaluation of 2 differing calving systems (March or May) for improving biological outcome and improved production. Experiment 1 utilized 180 yearling heifers to determine the effectiveness of a second dose of prostaglandin F2α(PGF) with those females not expressing estrus after an initial 14 d MGA-PG estrus synchronization protocol. The treatment of PGF did increase estrus expression, but did not …

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Crispr/Cas9 In Yeast: A Multi-Week Laboratory Exercise For Undergraduate Students, Randi J. Ulbricht May 2019

Crispr/Cas9 In Yeast: A Multi-Week Laboratory Exercise For Undergraduate Students, Randi J. Ulbricht

Open Educational Resources

Providing undergraduate life-science students with a course-based research experience that utilizes cutting-edge technology, is tractable for students, and is manageable as an instructor is a challenge. Here, I describe a multi-week lesson plan for a laboratory-based course with the goal of editing the genome of budding yeast, Saccharomyces cerevisiae. Students apply knowledge regarding advanced topics such as: CRISPR/Cas9 gene editing, DNA repair, genetics, and cloning. The lesson requires students to master skills such as bioinformatics analysis, restriction enzyme digestion, ligation, basic microbiology skills, polymerase chain reaction, and plasmid purification. Instructors are led through the technical aspects of the protocols, …

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Novel Characterization Of The Role Of Orthologous Xap5 In Caenorhabditis Elegans, Nabor Vazquez May 2019

Novel Characterization Of The Role Of Orthologous Xap5 In Caenorhabditis Elegans, Nabor Vazquez

Lawrence University Honors Projects

Cilia are one of the oldest and most well conserved cellular organelles. Cilia provide an essential role in cellular locomotion, fluid regulation, and are a site for signal transduction pathways involved in sensation. A new study suggests that XAP5 is a transcription factor in a unicellular organism, Chlamydomonas reinhardtii, which regulates gene expression needed for proper cilium assembly. Our study investigates the conservation of the role of XAP5 in a multicellular system, Caenorhabditis elegans. Alignments between protein, coding region, and promoter sequences for XAP5 orthologs from related species show a good conservation in DNA and protein sequences. As part of …

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Female Family Members Lack Understanding Of Indeterminate Negative Brca1/2 Test Results Shared By Probands, Deborah Himes, Deborah K. Gibbons, Wendy C. Birmingham, Renea L. Beckstrand, Amanda Gammon, Anita Y. Kinney, Margaret F. Clayton May 2019

Female Family Members Lack Understanding Of Indeterminate Negative Brca1/2 Test Results Shared By Probands, Deborah Himes, Deborah K. Gibbons, Wendy C. Birmingham, Renea L. Beckstrand, Amanda Gammon, Anita Y. Kinney, Margaret F. Clayton

Faculty Publications

Genetic test results have important implications for close family members. Indeterminate negative results are the most common outcome of BRCA1/2 mutation testing. Little is known about family members’ understanding of indeterminate negative BRCA1/2 test results. The purpose of this mixed-methods study was to investigate how daughters and sisters received and understood genetic test results as shared by their mothers or sisters. Participants included 81 women aged 40-74 with mothers or sisters previously diagnosed with breast cancer and who received indeterminate negative BRCA1/2 test results. Participants had never been diagnosed with breast cancer nor received their own genetic testing or counseling. …

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Publisher Correction: Toxoplasma Modulates Signature Pathways Of Human Epilepsy, Neurodegeneration & Cancer., Huân M Ngô, Ying Zhou, Hernan Lorenzi, Kai Wang, Taek-Kyun Kim, Yong Zhou, Kamal El Bissati, Ernest Mui, Laura Fraczek, Seesandra V Rajagopala, Craig W Roberts, Fiona L Henriquez, Alexandre Montpetit, Jenefer M Blackwell, Sarra E Jamieson, Kelsey Wheeler, Ian J Begeman, Carlos Naranjo-Galvis, Ney Alliey-Rodriguez, Roderick G Davis, Liliana Soroceanu, Charles Cobbs, Dennis A Steindler, Kenneth Boyer, A Gwendolyn Noble, Charles N Swisher, Peter T Heydemann, Peter Rabiah, Shawn Withers, Patricia Soteropoulos, Leroy Hood, Rima Mcleod May 2019

Publisher Correction: Toxoplasma Modulates Signature Pathways Of Human Epilepsy, Neurodegeneration & Cancer., Huân M Ngô, Ying Zhou, Hernan Lorenzi, Kai Wang, Taek-Kyun Kim, Yong Zhou, Kamal El Bissati, Ernest Mui, Laura Fraczek, Seesandra V Rajagopala, Craig W Roberts, Fiona L Henriquez, Alexandre Montpetit, Jenefer M Blackwell, Sarra E Jamieson, Kelsey Wheeler, Ian J Begeman, Carlos Naranjo-Galvis, Ney Alliey-Rodriguez, Roderick G Davis, Liliana Soroceanu, Charles Cobbs, Dennis A Steindler, Kenneth Boyer, A Gwendolyn Noble, Charles N Swisher, Peter T Heydemann, Peter Rabiah, Shawn Withers, Patricia Soteropoulos, Leroy Hood, Rima Mcleod

Articles, Abstracts, and Reports

A correction to this article has been published and is linked from the HTML and PDF versions of this paper. The error has been fixed in the paper.

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Floral Dip Transformation Of Camelina Sativa L. With A Myo-Inositol Oxygenase Gene To Potentially Improve Oil Yield, Naina Narayan Rao May 2019

Floral Dip Transformation Of Camelina Sativa L. With A Myo-Inositol Oxygenase Gene To Potentially Improve Oil Yield, Naina Narayan Rao

Student Theses and Dissertations

Camelina sativa L. has potential as a winter oilseed crop to produce edible oils, livestock feed, biodiesel and jet fuel. Agrobacterium-mediated floral dip transformation of Camelina was performed to transfer the AtMIOX4 gene (Myo-inositol oxygenase from Arabidopsis thaliana) into Camelina as a means to improve agronomic characters. Three Agrobacterium strains LBA4404, GV3101 and EHA105 were used to transform Camelina sativa cultivar ‘Celine’. Recovered seeds were screened for expression of antibiotic resistance marker genes with only 2% survival of putative transgenic plants. Direct PCR analysis for the AtMIOX4 insertion was used to screen putative transgenic plants, giving an average of 10% …

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Fragile X- Associated Neuropsychiatric Disorders: A Case Report, Maria Melinda Tan, Jeanne Barbara Dy, Maria Jimena Salcedo-Arellano, Flora Tassone, Randi J. Hagerman May 2019

Fragile X- Associated Neuropsychiatric Disorders: A Case Report, Maria Melinda Tan, Jeanne Barbara Dy, Maria Jimena Salcedo-Arellano, Flora Tassone, Randi J. Hagerman

Ateneo School of Medicine and Public Health Publications

Mutations in the Fragile X Mental Retardation 1 (FMR1) gene create a spectrum of developmental disorders in children in addition to neurodegenerative problems in older populations. Two types of mutations are recognized in the FMR1 gene. The full mutation (>200 CGG repeats) in the FMR1 gene leads to Fragile X Syndrome which is the most common inherited cause of intellectual disability and autism, while the premutation (55 to 200 CGG repeats) identified among carriers leads to a range of problems linked to elevated levels of the FMR1 mRNA leading to mRNA toxicity and occasionally mildly deficient FMRP …

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Systems Pharmacogenomic Landscape Of Drug Similarities From Lincs Data: Drug Association Networks., Aliyu Musa, Shailesh Tripathi, Matthias Dehmer, Olli Yli-Harja, Stuart A Kauffman, Frank Emmert-Streib May 2019

Systems Pharmacogenomic Landscape Of Drug Similarities From Lincs Data: Drug Association Networks., Aliyu Musa, Shailesh Tripathi, Matthias Dehmer, Olli Yli-Harja, Stuart A Kauffman, Frank Emmert-Streib

Articles, Abstracts, and Reports

Modern research in the biomedical sciences is data-driven utilizing high-throughput technologies to generate big genomic data. The Library of Integrated Network-based Cellular Signatures (LINCS) is an example for a large-scale genomic data repository providing hundred thousands of high-dimensional gene expression measurements for thousands of drugs and dozens of cell lines. However, the remaining challenge is how to use these data effectively for pharmacogenomics. In this paper, we use LINCS data to construct drug association networks (DANs) representing the relationships between drugs. By using the Anatomical Therapeutic Chemical (ATC) classification of drugs we demonstrate that the DANs represent a systems pharmacogenomic …

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Hippo Signaling In Cancer: Lessons From Drosophila Models, Kirti Snigdha, Karishma Sanjay Gangwani, Gauri Vijay Lapalikar, Amit Singh, Madhuri Kango-Singh May 2019

Hippo Signaling In Cancer: Lessons From Drosophila Models, Kirti Snigdha, Karishma Sanjay Gangwani, Gauri Vijay Lapalikar, Amit Singh, Madhuri Kango-Singh

Biology Faculty Publications

Hippo pathway was initially identified through genetic screens for genes regulating organ size in fruitflies. Recent studies have highlighted the role of Hippo signaling as a key regulator of homeostasis, and in tumorigenesis. Hippo pathway is comprised of genes that act as tumor suppressor genes like hippo (hpo) and warts (wts), and oncogenes like yorkie (yki). YAP and TAZ are two related mammalian homologs of Drosophila Yki that act as effectors of the Hippo pathway. Hippo signaling deficiency can cause YAP- or TAZ-dependent oncogene addiction for cancer cells. YAP and TAZ are often activated …

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Toward A Comprehensive View Of Cancer Immune Responsiveness: A Synopsis From The Sitc Workshop., Davide Bedognetti, Michele Ceccarelli, Lorenzo Galluzzi, Rongze Lu, Karolina Palucka, Josue Samayoa, Stefani Spranger, Sarah Warren, Kwok-Kin Wong, Elad Ziv, Diego Chowell, Lisa M Coussens, Daniel D De Carvalho, David G Denardo, Jérôme Galon, Howard L Kaufman, Tomas Kirchhoff, Michael T Lotze, Jason J Luke, Andy J Minn, Katerina Politi, Leonard D Shultz, Richard Simon, Vésteinn Thórsson, Joanne B Weidhaas, Maria Libera Ascierto, Paolo Antonio Ascierto, James M Barnes, Valentin Barsan, Praveen K Bommareddy, Adrian Bot, Sarah E Church, Gennaro Ciliberto, Andrea De Maria, Dobrin Draganov, Winson S Ho, Heather M Mcgee, Anne Monette, Joseph F Murphy, Paola Nisticò, Wungki Park, Maulik Patel, Michael Quigley, Laszlo Radvanyi, Harry Raftopoulos, Nils-Petter Rudqvist, Alexandra Snyder, Randy F Sweis, Sara Valpione, Lisa H Butterfield, Mary L Disis, Bernard A Fox, Alessandra Cesano, Francesco M Marincola May 2019

Toward A Comprehensive View Of Cancer Immune Responsiveness: A Synopsis From The Sitc Workshop., Davide Bedognetti, Michele Ceccarelli, Lorenzo Galluzzi, Rongze Lu, Karolina Palucka, Josue Samayoa, Stefani Spranger, Sarah Warren, Kwok-Kin Wong, Elad Ziv, Diego Chowell, Lisa M Coussens, Daniel D De Carvalho, David G Denardo, Jérôme Galon, Howard L Kaufman, Tomas Kirchhoff, Michael T Lotze, Jason J Luke, Andy J Minn, Katerina Politi, Leonard D Shultz, Richard Simon, Vésteinn Thórsson, Joanne B Weidhaas, Maria Libera Ascierto, Paolo Antonio Ascierto, James M Barnes, Valentin Barsan, Praveen K Bommareddy, Adrian Bot, Sarah E Church, Gennaro Ciliberto, Andrea De Maria, Dobrin Draganov, Winson S Ho, Heather M Mcgee, Anne Monette, Joseph F Murphy, Paola Nisticò, Wungki Park, Maulik Patel, Michael Quigley, Laszlo Radvanyi, Harry Raftopoulos, Nils-Petter Rudqvist, Alexandra Snyder, Randy F Sweis, Sara Valpione, Lisa H Butterfield, Mary L Disis, Bernard A Fox, Alessandra Cesano, Francesco M Marincola

Articles, Abstracts, and Reports

Tumor immunology has changed the landscape of cancer treatment. Yet, not all patients benefit as cancer immune responsiveness (CIR) remains a limitation in a considerable proportion of cases. The multifactorial determinants of CIR include the genetic makeup of the patient, the genomic instability central to cancer development, the evolutionary emergence of cancer phenotypes under the influence of immune editing, and external modifiers such as demographics, environment, treatment potency, co-morbidities and cancer-independent alterations including immune homeostasis and polymorphisms in the major and minor histocompatibility molecules, cytokines, and chemokines. Based on the premise that cancer is fundamentally a disorder of the genes …

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Dietary Restriction Enhances Circadian Amplitude And Delays Visual Decline By A Clock-Driven Increase In Phototransduction, Geoff Meyerhof May 2019

Dietary Restriction Enhances Circadian Amplitude And Delays Visual Decline By A Clock-Driven Increase In Phototransduction, Geoff Meyerhof

Natural Sciences and Mathematics | Biological Sciences Master's Theses

Aging is accompanied by a progressive loss of circadian rhythms. Lifespan-extending dietary paradigms such as dietary restriction (DR) enhance circadian amplitude and appear to extend lifespan in a clock-dependent fashion. However, the mechanisms by which DR amplifies circadian rhythms and why circadian rhythms decline with age have yet to be fully elucidated. Here we find that DR amplifies circadian amplitude by enhancing light sensitivity in the eye. We performed a circadian mRNA microarray in flies (Drosophila melanogaster) reared on DR or a high nutrient diet and found that DR increases the number of circadian transcripts and selectively amplifies the …

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New Targeted Treatments For Fragile X Syndrome, Dragana Protic, Maria J. Salcedo-Arellano, Jeanne Barbara Dy, Laura A. Potter, Randi J. Hagerman May 2019

New Targeted Treatments For Fragile X Syndrome, Dragana Protic, Maria J. Salcedo-Arellano, Jeanne Barbara Dy, Laura A. Potter, Randi J. Hagerman

Ateneo School of Medicine and Public Health Publications

Fragile X Syndrome (FXS) is the most common cause of inherited intellectual disability with prevalence rates estimated to be 1:5,000 in males and 1:8,000 in females. The increase of >200 Cytosine Guanine Guanine (CGG) repeats in the 5' untranslated region of the Fragile X Mental Retardation 1 (FMR1) gene results in transcriptional silencing on the FMR1 gene with a subsequent reduction or absence of fragile X mental retardation protein (FMRP), an RNA binding protein involved in the maturation and elimination of synapses. In addition to intellectual disability, common features of FXS are behavioral problems, autism, language deficits and atypical physical …

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Effect Of Cooled Perches On The Efficacy Of An Induced Molt In White Leghorn Laying Hens Previously Exposed To Heat Stress, J Y. Hu, P Y. Hester, Y Xiong, R S. Gates, M M. Makagon, H W. Cheng May 2019

Effect Of Cooled Perches On The Efficacy Of An Induced Molt In White Leghorn Laying Hens Previously Exposed To Heat Stress, J Y. Hu, P Y. Hester, Y Xiong, R S. Gates, M M. Makagon, H W. Cheng

Department of Animal Science: Faculty Publications

This study examined the effect of water chilled perches on hen production and physiological responses to induced molt during elevated temperatures. A total of 288White Leghorns at 82 wk of age were housed in 36 cages of 6 banks. Each bank was assigned to 1 of 3 treatments: cooled perches, air perches, and no perches. The hens were subjected to 2 heat episodes during their first laying cycle at week 21 to 35 and week 73 to 80, respectively. The hens were subjected to a 28 D nonfasted molting regimen starting at 85 wk of age. Cyclic heat of 32◦C …

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Applications Of Sirna For Cancer Gene Therapy, Christopher Nicholas Cultrara May 2019

Applications Of Sirna For Cancer Gene Therapy, Christopher Nicholas Cultrara

Seton Hall University Dissertations and Theses (ETDs)

Gene therapy is a potent and versatile nano-medicine strategy in the treatment of cancer. Of the many tools currently used in this application, short-interfering RNA (siRNA) are among the most commonly employed due to their ability to silence oncogenic mRNA with high precision through the RNA interference (RNAi) pathway potentially leading to cancer cell death. Our work revolves around silencing the Glucose-Regulated Proteins (GRPs) whose expressions are upregulated in cancerous tissues and are implicated in the proliferative, pro-survival, and anti-apoptotic pathways that govern tumor biology. Here we present a variety of applications to improve the potency and functionality of GRP-targeting …

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Microrna Profiling And Engineering Of Cho Cell Lines Stably Expressing Difficult-To-Express Lysosomal Protein, Ifeanyi Amadi May 2019

Microrna Profiling And Engineering Of Cho Cell Lines Stably Expressing Difficult-To-Express Lysosomal Protein, Ifeanyi Amadi

KGI Theses and Dissertations

Difficult-to-express (DTE) recombinant proteins like multi-specific proteins, DTE monoclonal antibodies and lysosomal enzymes, have seen difficulties in manufacturability using Chinese hamster ovary (CHO) cells and other mammalian cells as production platforms. CHO cells are preferably used for protein production because of their innate ability to secrete human-like recombinant proteins with post-translational modification, resistance to viral infection and familiarity with drug regulators. However, despite huge progress made in engineering CHO cells for high volumetric productivity, expression of DTE proteins like recombinant lysosomal sulfatase represent one of the poorly understood proteins. Furthermore, there are growing interest in the use of microRNAs (miRNAs) …

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Frogs Hiding In Plain Sight: Phylogenetic Systematics Of Myanmar’S Occidozyga Species Complex, And The Identification Of A Novel Species, Allison Bogisich May 2019

Frogs Hiding In Plain Sight: Phylogenetic Systematics Of Myanmar’S Occidozyga Species Complex, And The Identification Of A Novel Species, Allison Bogisich

Master's Theses

Different species can be difficult to distinguish from one another when they are morphologically similar. Such cryptic species are the reason many anuran species go undetected. For this study, the taxonomic identity of the Occidozyga complex across Myanmar was investigated. An integrated approach was used combining molecular, morphological and phylogeographic data to better assess its taxonomy. Results indicate the presence of three new candidate species within Occidozyga, and three evolutionarily significant unit (ESU) lineages. Two mitochondrial gene fragments (16S, COI) and one nuclear gene fragment (Rhodopsin) were examined from DNA isolated from forty-seven preserved specimens from the California Academy …

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Phylogenetic Inference Of Multiscale Selection Pressures Using A Continuous State Birth-Death Process, Marco Hamins-Puertolas, David Rasmussen May 2019

Phylogenetic Inference Of Multiscale Selection Pressures Using A Continuous State Birth-Death Process, Marco Hamins-Puertolas, David Rasmussen

Biology and Medicine Through Mathematics Conference

No abstract provided.

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Mapping A New Disease Resistance Locus In An F1 Progeny Derived From Two Grape Wild Relatives, Gaurab Bhattarai May 2019

Mapping A New Disease Resistance Locus In An F1 Progeny Derived From Two Grape Wild Relatives, Gaurab Bhattarai

Graduate Theses/Dissertations

Linkage maps and quantitative trait loci (QTL) analysis have become essential tools for the positional cloning of agronomically important genes and for marker-assisted breeding. In this study, two North American grape species, Vitis rupestris and Vitis riparia, and their 294 F1 progeny were used to construct parental linkage maps and to perform QTL analysis for downy mildew resistance. Single nucleotide polymorphism (SNP) discovery was accomplished using genotyping-by-sequencing (GBS) and resulted in 348,888 SNPs. Of these, 11,063 informative SNP markers (3.17% of the original SNP dataset) were derived after filtering for various quality parameters and missing data. A two-way …

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Computations Of Top-Down Attention By Modulating V1 Dynamics, David Berga, Xavier Otazu May 2019

Computations Of Top-Down Attention By Modulating V1 Dynamics, David Berga, Xavier Otazu

MODVIS Workshop

The human visual system processes information defining what is visually conspicuous (saliency) to our perception, guiding eye movements towards certain objects depending on scene context and its feature characteristics. However, attention has been known to be biased by top-down influences (relevance), which define voluntary eye movements driven by goal-directed behavior and memory. We propose a unified model of the visual cortex able to predict, among other effects, top-down visual attention and saccadic eye movements. First, we simulate activations of early mechanisms of the visual system (RGC/LGN), by processing distinct image chromatic opponencies with Gabor-like filters. Second, we use a cortical …

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Clinical Utility Of Exon Deletion/Duplication Microarray Testing - A Children’S Mercy Kansas City Two-Year Experience, Binu Porath May 2019

Clinical Utility Of Exon Deletion/Duplication Microarray Testing - A Children’S Mercy Kansas City Two-Year Experience, Binu Porath

Research Days

No abstract provided.

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Topology And Dynamics Of Gene Regulatory Networks: A Meta-Analysis, Claus Kadelka May 2019

Topology And Dynamics Of Gene Regulatory Networks: A Meta-Analysis, Claus Kadelka

Biology and Medicine Through Mathematics Conference

No abstract provided.

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The Genetic Information Nondiscrimination Act At Age 10: Gina’S Controversial Assertion That Data Transparency Protects Privacy And Civil Rights, Barbara J. Evans May 2019

The Genetic Information Nondiscrimination Act At Age 10: Gina’S Controversial Assertion That Data Transparency Protects Privacy And Civil Rights, Barbara J. Evans

William & Mary Law Review

The genomic testing industry is an edifice built on data transparency: transparent and often unconsented sharing of our genetic information with researchers to fuel scientific discovery, transparent sharing of our test results to help regulators infer whether the tests are safe and effective, and transparent sharing of our health information to help treat other patients on the premise that we gain reciprocity of advantage when each person’s health care is informed by the best available data about all of us. Transparency undeniably confers many social benefits but creates risks to the civil rights of the people whose genetic information is …

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Simplicity Diffexpress: A Bespoke Cloud-Based Interface For Rna-Seq Differential Expression Modeling And Analysis, Cintia C. Palu, Marcelo Ribeiro-Alves, Yanxin Wu, Brendan Lawlor, Pavel V. Baranov, Brian Kelly, Paul Walsh May 2019

Simplicity Diffexpress: A Bespoke Cloud-Based Interface For Rna-Seq Differential Expression Modeling And Analysis, Cintia C. Palu, Marcelo Ribeiro-Alves, Yanxin Wu, Brendan Lawlor, Pavel V. Baranov, Brian Kelly, Paul Walsh

Department of Computer Science Publications

One of the key challenges for transcriptomics-based research is not only the processing of large data but also modeling the complexity of features that are sources of variation across samples, which is required for an accurate statistical analysis. Therefore, our goal is to foster access for wet lab researchers to bioinformatics tools, in order to enhance their ability to explore biological aspects and validate hypotheses with robust analysis. In this context, user-friendly interfaces can enable researchers to apply computational biology methods without requiring bioinformatics expertise. Such bespoke platforms can improve the quality of the findings by allowing the researcher to …

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Differential Effects Of Influenza Virus Na, Ha Head, And Ha Stalk Antibodies On Peripheral Blood Leukocyte Gene Expression During Human Infection., Kathie-Anne Walters, Ruoqing Zhu, Michael Welge, Kelsey Scherler, Jae-Keun Park, Zainab Rahil, Hao Wang, Loretta Auvil, Colleen Bushell, Min Young Lee, David Baxter, Tyler Bristol, Luz Angela Rosas, Adriana Cervantes-Medina, Lindsay Czajkowski, Alison Han, Matthew J Memoli, Jeffery K Taubenberger, John C Kash May 2019

Differential Effects Of Influenza Virus Na, Ha Head, And Ha Stalk Antibodies On Peripheral Blood Leukocyte Gene Expression During Human Infection., Kathie-Anne Walters, Ruoqing Zhu, Michael Welge, Kelsey Scherler, Jae-Keun Park, Zainab Rahil, Hao Wang, Loretta Auvil, Colleen Bushell, Min Young Lee, David Baxter, Tyler Bristol, Luz Angela Rosas, Adriana Cervantes-Medina, Lindsay Czajkowski, Alison Han, Matthew J Memoli, Jeffery K Taubenberger, John C Kash

Articles, Abstracts, and Reports

In this study, we examined the relationships between anti-influenza virus serum antibody titers, clinical disease, and peripheral blood leukocyte (PBL) global gene expression during presymptomatic, acute, and convalescent illness in 83 participants infected with 2009 pandemic H1N1 virus in a human influenza challenge model. Using traditional statistical and logistic regression modeling approaches, profiles of differentially expressed genes that correlated with active viral shedding, predicted length of viral shedding, and predicted illness severity were identified. These analyses further demonstrated that challenge participants fell into three peripheral blood leukocyte gene expression phenotypes that significantly correlated with different clinical outcomes and prechallenge serum …

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A Biological Function Based Biomarker Panel Optimization Process., Min Young Lee, Taek-Kyun Kim, Kathie-Anne Walters, Kai Wang May 2019

A Biological Function Based Biomarker Panel Optimization Process., Min Young Lee, Taek-Kyun Kim, Kathie-Anne Walters, Kai Wang

Articles, Abstracts, and Reports

Implementation of multi-gene biomarker panels identified from high throughput data, including microarray or next generation sequencing, need to be adapted to a platform suitable in a clinical setting such as quantitative polymerase chain reaction. However, technical challenges when transitioning from one measurement platform to another, such as inconsistent measurement results can affect panel development. We describe a process to overcome the challenges by replacing poor performing genes during platform transition and reducing the number of features without impacting classification performance. This approach assumes that a diagnostic panel reflects the effect of dysregulated biological processes associated with a disease, and genes …

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Defining Microbiome Health Through A Host Lens., Sean M Gibbons May 2019

Defining Microbiome Health Through A Host Lens., Sean M Gibbons

Articles, Abstracts, and Reports

We are walking ecosystems, inoculated at birth with a unique set of microbes that are integral to the functioning of our bodies. The physiology of our commensal microbiota is intertwined with our metabolism, immune function, and mental state. The specifics of this entanglement remain largely unknown and are somewhat unique to individuals, and when any one piece of this complex system breaks, our health can suffer. There appear to be many ways to build a healthy, functional microbiome and several distinct ways in which it can break. Despite the hundreds of associations with human disease, there are only a handful …

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A Discrepancy Between The Human Reference Genome (Grch37) And Transcriptome (Refseq) Results In The Incorrect Annotation Of A Clinically-Relevant Sequence Variant In Recql4, Lisa A. Lansdon May 2019

A Discrepancy Between The Human Reference Genome (Grch37) And Transcriptome (Refseq) Results In The Incorrect Annotation Of A Clinically-Relevant Sequence Variant In Recql4, Lisa A. Lansdon

Research Days

No abstract provided.

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Clinical Implications Of Evolutionary Modeling Of Cancer Progression, Kelsey Heiland May 2019

Clinical Implications Of Evolutionary Modeling Of Cancer Progression, Kelsey Heiland

Biology: Student Scholarship & Creative Works

Evolutionary theory of cancer was developed in 1976 by cancer research Peter Nowell and has illuminated the path toward increasing safety and efficacy of clinical treatment strategies. Major foundations that makeup the complexity in Darwinian framework of cancer includes clonal evolution, clonal expansion, and competition. Due to these characteristics, virtually all types of cancer have evolutionary capabilities to reject or adapt and become resistant to pharmaceutical therapies. Despite compelling evidence of these process, evolutionary modeling of cancer continues to be underutilized in clinical settings. Contributions to this include the complex adaptive mechanisms that tools fail to detect or are unable …

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