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Identification Of Snp-Containing Regulatory Motifs In The Myelodysplastic Syndromes Model Using Snp Arrays Ad Gene Expression Arrays, Jing Fan, Jennifer G. Dy, Chung-Che Chang, Xiaoboo Zhou Jan 2013

Identification Of Snp-Containing Regulatory Motifs In The Myelodysplastic Syndromes Model Using Snp Arrays Ad Gene Expression Arrays, Jing Fan, Jennifer G. Dy, Chung-Che Chang, Xiaoboo Zhou

Faculty Bibliography 2010s

Myelodysplastic syndromes have increased in frequency and incidence in the American population, but patient prognosis has not significantly improved over the last decade. Such improvements could be realized if biomarkers for accurate diagnosis and prognostic stratification were successfully identified. In this study, we propose a method that associates two state-of-the-art array technologies-single nucleotide polymor-phism (SNP) array and gene expression array-with gene motifs considered transcription factor-binding sites (TFBS). We are particularly interested in SNP-containing motifs introduced by genetic variation and mutation as TFBS. The potential regulation of SNP-containing motifs affects only when certain mutations occur. These motifs can be identified from …

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Seasonality Influences Cuticle Melanization And Immune Defense In A Cricket: Support For A Temperature-Dependent Immune Investment Hypothesis In Insects, Kenneth M. Fedorka, Emily K. Copeland, Wade E. Winterhalter Jan 2013

Seasonality Influences Cuticle Melanization And Immune Defense In A Cricket: Support For A Temperature-Dependent Immune Investment Hypothesis In Insects, Kenneth M. Fedorka, Emily K. Copeland, Wade E. Winterhalter

Faculty Bibliography 2010s

To improve thermoregulation in colder environments, insects are expected to darken their cuticles with melanin via the phenoloxidase cascade, a phenomenon predicted by the thermal melanin hypothesis. However, the phenoloxidase cascade also plays a significant role in insect immunity, leading to the additional hypothesis that the thermal environment indirectly shapes immune function via direct selection on cuticle color. Support for the latter hypothesis comes from the cricket Allonemobius socius, where cuticle darkness and immune-related phenoloxidase activity increase with latitude. However, thermal environments vary seasonally as well as geographically, suggesting that seasonal plasticity in immunity may also exist. Although seasonal fluctuations …

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Skeletal Muscles Of Ambulant Children With Duchenne Muscular Dystrophy: Validation Of Multicenter Study Of Evaluation With Mr Imaging And Mr Spectroscopy, Sean C. Forbes, Glenn A. Walter, William D. Rooney, Dah-Jyuu Wang, Soren Devos, Jim Pollaro, William Triplett, Donovan J. Lott, Rebecca J. Willcocks, Claudia Senesac, Michael J. Daniels, Barry J. Byrne, Barry Russman, Richard S. Finkel, James S. Meyer, H. Lee Sweeney, Krista Vandenborne Jan 2013

Skeletal Muscles Of Ambulant Children With Duchenne Muscular Dystrophy: Validation Of Multicenter Study Of Evaluation With Mr Imaging And Mr Spectroscopy, Sean C. Forbes, Glenn A. Walter, William D. Rooney, Dah-Jyuu Wang, Soren Devos, Jim Pollaro, William Triplett, Donovan J. Lott, Rebecca J. Willcocks, Claudia Senesac, Michael J. Daniels, Barry J. Byrne, Barry Russman, Richard S. Finkel, James S. Meyer, H. Lee Sweeney, Krista Vandenborne

Faculty Bibliography 2010s

Purpose: To validate a multicenter protocol that examines lower extremity skeletal muscles of children with Duchenne muscular dystrophy (DMD) by using magnetic resonance (MR) imaging and MR spectroscopy in terms of reproducibility of these measurements within and across centers. Materials and Methods: This HIPAA-compliant study was approved by the institutional review boards of all participating centers, and informed consent was obtained from each participant or a guardian. Standardized procedures with MR operator training and quality assurance assessments were implemented, and data were acquired at three centers by using different 3-T MR imaging instruments. Measures of maximal cross-sectional area (CSA(max)), transverse …

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Nitration Of Hsp90 Induces Cell Death, Maria Clara Franco, Yaozu Ye, Christian A. Refakis, Jessica L. Feldman, Audrey L. Stokes, Raquel M. Melero Fernandez De Mera, Nicklaus A. Sparrow, Noel Y. Callingasan, Mahmoud Kiaei, Timonthy W. Rhoads, Thong C. Ma, Martin Grumet, Stephen Barnes, M. Flint Beal, Joseph S. Beckman, Ryan Mehl, Alvaro G. Estevez Jan 2013

Nitration Of Hsp90 Induces Cell Death, Maria Clara Franco, Yaozu Ye, Christian A. Refakis, Jessica L. Feldman, Audrey L. Stokes, Raquel M. Melero Fernandez De Mera, Nicklaus A. Sparrow, Noel Y. Callingasan, Mahmoud Kiaei, Timonthy W. Rhoads, Thong C. Ma, Martin Grumet, Stephen Barnes, M. Flint Beal, Joseph S. Beckman, Ryan Mehl, Alvaro G. Estevez

Faculty Bibliography 2010s

Oxidative stress is a widely recognized cause of cell death associated with neurodegeneration, inflammation, and aging. Tyrosine nitration in these conditions has been reported extensively, but whether tyrosine nitration is a marker or plays a role in the cell-death processes was unknown. Here, we show that nitration of a single tyrosine residue on a small proportion of 90-kDa heat-shock protein (Hsp90), is sufficient to induce motor neuron death by the P2X7 receptor-dependent activation of the Fas pathway. Nitrotyrosine at position 33 or 56 stimulates a toxic gain of function that turns Hsp90 into a toxic protein. Using an antibody that …

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Incorporating Phylogenetic-Based Covarying Mutations Into Rnaalifold For Rna Consensus Structure Prediction, Ping Ge, Shaojie Zhang Jan 2013

Incorporating Phylogenetic-Based Covarying Mutations Into Rnaalifold For Rna Consensus Structure Prediction, Ping Ge, Shaojie Zhang

Faculty Bibliography 2010s

Background: RNAalifold, a popular computational method for RNA consensus structure prediction, incorporates covarying mutations into a thermodynamic model to fold the aligned RNA sequences. When quantifying covariance, it evaluates conserved signals of two aligned columns with base-pairing rules. This scoring scheme performs better than some other approaches, such as mutual information. However it ignores the phylogenetic history of the aligned sequences, which is an important criterion to evaluate the level of sequence covariance. Results: In this article, in order to improve the accuracy of consensus structure folding, we propose a novel approach named PhyloRNAalifold. It incorporates the number of covarying …

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Tryptophan-Mediated Charge-Resonance Stabilization In The Bis-Fe(Iv) Redox State Of Maug, Jiafeng Geng, Kednerlin Dornevil, Victor L. Davidson, Aimin Liu Jan 2013

Tryptophan-Mediated Charge-Resonance Stabilization In The Bis-Fe(Iv) Redox State Of Maug, Jiafeng Geng, Kednerlin Dornevil, Victor L. Davidson, Aimin Liu

Faculty Bibliography 2010s

The diheme enzyme MauG catalyzes posttranslational modifications of a methylamine dehydrogenase precursor protein to generate a tryptophan tryptophylquinone cofactor. The MauG-catalyzed reaction proceeds via a bis-Fe(IV) intermediate in which one heme is present as Fe(IV)=O and the other as Fe(IV) with axial histidine and tyrosine ligation. Herein, a unique near-infrared absorption feature exhibited specifically in bis-Fe(IV) MauG is described, and evidence is presented that it results from a charge-resonance-transition phenomenon. As the two hemes are physically separated by 14.5 angstrom, a hole-hopping mechanism is proposed in which a tryptophan residue located between the hemes is reversibly oxidized and reduced to …

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Nanoceria: A Rare-Earth Nanoparticle As A Novel Anti-Angiogenic Therapeutic Agent In Ovarian Cancer, Shailendra Giri, Ajay Karakoti, Rondell P. Graham, Jacie L. Maguire, Christopher M. Reilly, Sudipta Seal, Ramandeep Rattan, Viji Shridhar Jan 2013

Nanoceria: A Rare-Earth Nanoparticle As A Novel Anti-Angiogenic Therapeutic Agent In Ovarian Cancer, Shailendra Giri, Ajay Karakoti, Rondell P. Graham, Jacie L. Maguire, Christopher M. Reilly, Sudipta Seal, Ramandeep Rattan, Viji Shridhar

Faculty Bibliography 2010s

Ovarian cancer (OvCa) is the fifth most common cause of death from all cancers among women in United Sates and the leading cause of death from gynecological malignancies. While most OvCa patients initially respond to surgical debulking and chemotherapy, 75% of patients later succumb to the disease. Thus, there is an urgent need to test novel therapeutic agents to counteract the high mortality rate associated with OvCa. In this context, we have developed and engineered Nanoceria (NCe), nanoparticles of cerium oxide, possessing anti-oxidant properties, to be used as a therapeutic agent in OvCa. We show for the first time that …

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Helicobacter Pylori Infection And Light Chain Gammopathy, José A. Girón, Shawn L. Shah Jan 2013

Helicobacter Pylori Infection And Light Chain Gammopathy, José A. Girón, Shawn L. Shah

Faculty Bibliography 2010s

Objective. Helicobacter pylori provokes a host of immune alterations upon colonizing the gastric mucosa. Design. We report 22 individuals with confirmed Helicobacter pylori infection who were also managed for the concurrent elevation of immunoglobulin free light chain (kappa and lambda) levels. Result. Of the 22 patients, 15 patients (68.2%) had elevated free light chain levels: 6 patients (40%) had only kappa chain elevation, 2 patients (13.3%) had only lambda chain elevation, and 7 patients (46.7%) had both kappa and lambda chain elevation. Twenty out of the 22 patients (90.9%) were microbiologically confirmed cured with 3 patients being lost to follow-up …

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Shockwave Based Nonlinear Optical Manipulation In Densely Scattering Opaque Suspensions, Elad Greenfield, Jonathan Nemirovsky, Ramy El-Ganainy, Demetri N. Christodoulides, Mordechai Segev Jan 2013

Shockwave Based Nonlinear Optical Manipulation In Densely Scattering Opaque Suspensions, Elad Greenfield, Jonathan Nemirovsky, Ramy El-Ganainy, Demetri N. Christodoulides, Mordechai Segev

Faculty Bibliography 2010s

Optical manipulation of particulate-loaded, highly scattering (opaque) suspensions is considered impossible. Here we demonstrate theoretically and experimentally optical manipulation of the local properties of such opaque suspensions. We show that the optical forces exerted by multiply-scattered light give rise to dense shock fronts of particle concentration, propagating deep inside the opaque suspensions, where the optical field is completely diffuse. We exploit these waves to demonstrate a plethora of optofluidic manipulations, ranging from optical transport and concentration of large populations of nanoparticles, to light-induced 'writing' of concentrated spots in the suspensions and light-induced phase-transition from suspension to gel in localized volumes …

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Assessment Of Biosorption Activated Media Under Roadside Swales For The Removal Of Phosphorus From Stormwater, Andrew Hood, Manoj Chopra, Martin Wanielista Jan 2013

Assessment Of Biosorption Activated Media Under Roadside Swales For The Removal Of Phosphorus From Stormwater, Andrew Hood, Manoj Chopra, Martin Wanielista

Faculty Bibliography 2010s

Stormwater runoff from highways is a source of pollution to surface water bodies and groundwater. Excess loadings of phosphorus in stormwater discharged to surface water bodies can result in eutrophication. Treatment of stormwater for phosphorus is necessary in order to sustain ecological and economical benefits related to aquatic resources. If phosphorus is removed, the water can be sustained for other uses, such as irrigation and industrial applications. The data presented in this paper is used to evaluate the treatment performance of a roadside biosorption activated media system with regards to the removal of total phosphorus and soluble reactive phosphorus from …

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An Identity-Based Key-Insulated Encryption With Message Linkages For Peer-To-Peer Communication Network, Chien-Lung Hsu, Han-Yu Lin Jan 2013

An Identity-Based Key-Insulated Encryption With Message Linkages For Peer-To-Peer Communication Network, Chien-Lung Hsu, Han-Yu Lin

Faculty Bibliography 2010s

Key exposure is a major threat to secure cryptosystems. To mitigate the impact caused by key-compromise attacks, a key-insulated cryptographic mechanism is a better alternative. For securing the large message communication in peer-to-peer networks, in this paper, we propose the first novel identity-based key-insulated encryption (IB-KIE) scheme with message linkages. Our scheme has the properties of unbounded time periods and random-access key-updates. In the proposed scheme, each client can periodically update his private key while the corresponding public one remains unchanged. The essential security assumption of our proposed scheme is based on the well-known bilinear Diffie-Hellman problem (BDHP). To ensure …

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Feature Issue Introduction: Mid-Ir Photonic Materials, Juejun Hu, Jerry Meyer, Kathleen Richardson, Lawrence Shah Jan 2013

Feature Issue Introduction: Mid-Ir Photonic Materials, Juejun Hu, Jerry Meyer, Kathleen Richardson, Lawrence Shah

Faculty Bibliography 2010s

The mid-infrared (mid-IR, 2.5 to 10 mu m wavelengths) is a strategically important spectral band for an array of applications such as thermal imaging, chem/bio sensing, spectroscopy, infrared countermeasures, and free space communications. Mid-IR photonics have emerged as an active area of investigation in recent years, largely spurred by the rapid progress of cascade laser sources, uncooled detectors, and specialty mid-IR optical fibers. The 26 papers of this feature issue focus on the leading enabling material technologies for mid-IR photonics, and encompass recent advances in both active (lasers and detectors) and passive (fibers and waveguides) components. Linear and nonlinear photon-matter …

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In-Fiber Production Of Polymeric Particles For Biosensing And Encapsulation, Joshua J. Kaufman, Richard Ottman, Guangming Tao, Soroush Shabahang, Esmaeil-Hooman Banaei, Xiangdong Liang, Steven G. Johnson, Yoel Fink, Ratna Chakrabarti, Ayman F. Abouraddy Jan 2013

In-Fiber Production Of Polymeric Particles For Biosensing And Encapsulation, Joshua J. Kaufman, Richard Ottman, Guangming Tao, Soroush Shabahang, Esmaeil-Hooman Banaei, Xiangdong Liang, Steven G. Johnson, Yoel Fink, Ratna Chakrabarti, Ayman F. Abouraddy

Faculty Bibliography 2010s

Polymeric micro- and nanoparticles are becoming a mainstay in biomedicine, medical diagnostics, and therapeutics, where they are used in implementing sensing mechanisms, as imaging contrast agents, and in drug delivery. Current approaches to the fabrication of such particles are typically finely tuned to specific monomer or polymer species, size ranges, and structures. We present a general scalable methodology for fabricating uniformly sized spherical polymeric particles from a wide range of polymers produced with complex internal architectures and continuously tunable diameters extending from the millimeter scale down to 50 nm. Controllable access to such a wide range of sizes enables broad …

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On A Calderon Problem In Frequency Differential Electrical Impedance Tomography, Sungwhan Kim, Alexandru Tamasan Jan 2013

On A Calderon Problem In Frequency Differential Electrical Impedance Tomography, Sungwhan Kim, Alexandru Tamasan

Faculty Bibliography 2010s

Recent research in electrical impedance tomography produced images of biological tissue from frequency differential boundary voltages and corresponding currents. Physically one is to recover the electrical conductivity sigma and permittivity c from the frequency differential boundary data. Let gamma = sigma+iota omega is an element of denote the complex admittivity, Lambda(gamma) be the corresponding Dirichlet-to-Neumann map, and d Lambda(gamma)/d omega|omega=0 be its frequency differential at omega = 0. If sigma is an element of C-1,C-1 ((Omega) over bar) is constant near the boundary and is an element of is an element of C-0(1,1) (Omega), we show that d Lambda(gamma)/d omega|omega=0 …

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Social Insects Dominate Eastern Us Temperate Hardwood Forest Macroinvertebrate Communities In Warmer Regions, Joshua R. King, Robert J. Warren, Mark A. Bradford Jan 2013

Social Insects Dominate Eastern Us Temperate Hardwood Forest Macroinvertebrate Communities In Warmer Regions, Joshua R. King, Robert J. Warren, Mark A. Bradford

Faculty Bibliography 2010s

Earthworms, termites, and ants are common macroinvertebrates in terrestrial environments, although for most ecosystems data on their abundance and biomass is sparse. Quantifying their areal abundance is a critical first step in understanding their functional importance. We intensively sampled dead wood, litter, and soil in eastern US temperate hardwood forests at four sites, which span much of the latitudinal range of this ecosystem, to estimate the abundance and biomass m(-2) of individuals in macroinvertebrate communities. Macroinvertebrates, other than ants and termites, differed only slightly among sites in total abundance and biomass and they were similar in ordinal composition. Termites and …

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Putrescine Importer Plap Contributes To Swarming Motility And Urothelial Cell Invasion In Proteus Mirabilis, Shin Kurihara, Yumi Sakai, Hideyuki Suzuki, Aaron Muth, Otto Phanstiel Iv, Philip N. Rather Jan 2013

Putrescine Importer Plap Contributes To Swarming Motility And Urothelial Cell Invasion In Proteus Mirabilis, Shin Kurihara, Yumi Sakai, Hideyuki Suzuki, Aaron Muth, Otto Phanstiel Iv, Philip N. Rather

Faculty Bibliography 2010s

Previously, we reported that the speA gene, encoding arginine decarboxylase, is required for swarming in the urinary tract pathogen Proteus mirabilis. In addition, this previous study suggested that putrescine may act as a cell-to-cell signaling molecule (Sturgill, G., and Rather, P. N. (2004) Mol. Microbiol. 51, 437-446). In this new study, PlaP, a putative putrescine importer, was characterized in P. mirabilis. In a wild-type background, a plaP null mutation resulted in a modest swarming defect and slightly decreased levels of intracellular putrescine. In a P. mirabilis speA mutant with greatly reduced levels of intracellular putrescine, plaP was required for the …

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Oral Delivery Of Bioencapsulated Exendin-4 Expressed In Chloroplasts Lowers Blood Glucose Level In Mice And Stimulates Insulin Secretion In Beta-Tc6 Cells, Kwang-Chul Kwon, Ramya Nityanandam, James S. New, Henry Daniell Jan 2013

Oral Delivery Of Bioencapsulated Exendin-4 Expressed In Chloroplasts Lowers Blood Glucose Level In Mice And Stimulates Insulin Secretion In Beta-Tc6 Cells, Kwang-Chul Kwon, Ramya Nityanandam, James S. New, Henry Daniell

Faculty Bibliography 2010s

Glucagon-like peptide (GLP-1) increases insulin secretion but is rapidly degraded (half-life: 2min in circulation). GLP-1 analogue, exenatide (Byetta) has a longer half-life (3.34h) with potent insulinotropic effects but requires cold storage, daily abdominal injections with short shelf life. Because patients with diabetes take > 60000 injections in their life time, alternative delivery methods are highly desired. Exenatide is ideal for oral delivery because insulinotropism is glucose dependent, with reduced risk of hypoglycaemia even at higher doses. Therefore, exendin-4 (EX4) was expressed as a cholera toxin B subunit (CTB)fusion protein in tobacco chloroplasts to facilitate bioencapsulation within plant cells and transmucosal delivery …

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Release Of Proteins From Intact Chloroplasts Induced By Reactive Oxygen Species During Biotic And Abiotic Stress, Kwang-Chul Kwon, Dheeraj Verma, Shuangxia Jin, Nameirakpam D. Singh, Henry Daniell Jan 2013

Release Of Proteins From Intact Chloroplasts Induced By Reactive Oxygen Species During Biotic And Abiotic Stress, Kwang-Chul Kwon, Dheeraj Verma, Shuangxia Jin, Nameirakpam D. Singh, Henry Daniell

Faculty Bibliography 2010s

Plastids sustain life on this planet by providing food, feed, essential biomolecules and oxygen. Such diverse metabolic and biosynthetic functions require efficient communication between plastids and the nucleus. However, specific factors, especially large molecules, released from plastids that regulate nuclear genes have not yet been fully elucidated. When tobacco and lettuce transplastomic plants expressing GFP within chloroplasts, were challenged with Erwinia carotovora (biotic stress) or paraquat (abiotic stress), GFP was released into the cytoplasm. During this process GFP moves gradually towards the envelope, creating a central red zone of chlorophyll fluorescence. GFP was then gradually released from intact chloroplasts into …

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Low Cost Tuberculosis Vaccine Antigens In Capsules: Expression In Chloroplasts, Bio-Encapsulation, Stability And Functional Evaluation In Vitro, Priya Saikumar Lakshmi, Dheeraj Verma, Xiangdong Yang, Bethany Lloyd, Hnery Daniell Jan 2013

Low Cost Tuberculosis Vaccine Antigens In Capsules: Expression In Chloroplasts, Bio-Encapsulation, Stability And Functional Evaluation In Vitro, Priya Saikumar Lakshmi, Dheeraj Verma, Xiangdong Yang, Bethany Lloyd, Hnery Daniell

Faculty Bibliography 2010s

Tuberculosis (TB) caused by Mycobacterium tuberculosis is one of the leading fatal infectious diseases. The development of TB vaccines has been recognized as a major public health priority by the World Health Organization. In this study, three candidate antigens, ESAT-6 (6kDa early secretory antigenic target) and Mtb72F (a fusion polyprotein from two TB antigens, Mtb32 and Mtb39) fused with cholera toxin B-subunit (CTB) and LipY (a cell wall protein) were expressed in tobacco and/or lettuce chloroplasts to facilitate bioencapsulation/oral delivery. Site-specific transgene integration into the chloroplast genome was confirmed by Southern blot analysis. In transplastomic leaves, CTB fusion proteins existed …

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New Insights Into The Synergism Of Nucleoside Analogs With Radiotherapy, Michael W. Lee, William B. Parker, Bo Xu Jan 2013

New Insights Into The Synergism Of Nucleoside Analogs With Radiotherapy, Michael W. Lee, William B. Parker, Bo Xu

Faculty Bibliography 2010s

Nucleoside analogs have been frequently used in combination with radiotherapy in the clinical setting, as it has long been understood that inhibition of DNA repair pathways is an important means by which many nucleoside analogs synergize. Recent advances in our understanding of the structure and function of deoxycytidine kinase (dCK), a critical enzyme required for the anti-tumor activity for many nucleoside analogs, have clarified the mechanistic role this kinase plays in chemo- and radio-sensitization. A heretofore unrecognized role of dCK in the DNA damage response and cell cycle machinery has helped explain the synergistic effect of these agents with radiotherapy. …

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Evolvability Is Inevitable: Increasing Evolvability Without The Pressure To Adapt, Joel Lehman, Kenneth O. Stanley Jan 2013

Evolvability Is Inevitable: Increasing Evolvability Without The Pressure To Adapt, Joel Lehman, Kenneth O. Stanley

Faculty Bibliography 2010s

Why evolvability appears to have increased over evolutionary time is an important unresolved biological question. Unlike most candidate explanations, this paper proposes that increasing evolvability can result without any pressure to adapt. The insight is that if evolvability is heritable, then an unbiased drifting process across genotypes can still create a distribution of phenotypes biased towards evolvability, because evolvable organisms diffuse more quickly through the space of possible phenotypes. Furthermore, because phenotypic divergence often correlates with founding niches, niche founders may on average be more evolvable, which through population growth provides a genotypic bias towards evolvability. Interestingly, the combination of …

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"Normative Content" And Health Inequity Enculturation: A Logic Model Of Men's Health Advocacy, James E. Leone, Michael J. Rovito Jan 2013

"Normative Content" And Health Inequity Enculturation: A Logic Model Of Men's Health Advocacy, James E. Leone, Michael J. Rovito

Faculty Bibliography 2010s

Epidemiologic studies and related literature consistently report that males have fewer years of life expectancy than females. Moreover, males experience fewer quality years of life in that they tend to live with greater rates of morbidity such as heart disease, cancer, and diabetes among other conditions. Causal evidence traditionally highlights the role of biology in determining the life course for males. However, emerging literature suggests that social determinants of health play a more central role in male morbidity and mortality, and thus contribute to health inequities between the sexes. The purpose of this article is to explore core concepts of …

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Genome-Wide Methylated Cpg Island Profiles Of Melanoma Cells Reveal A Melanoma Coregulation Network, Jian-Liang Li, Joseph Mazar, Cuncong Zhong, Geoffrey J. Faulkner, Subramaniam S. Govindarajan, Zhan Zhang, Marcel E. Dinger, Gavin Meredith, Christopher Adams, Shaojie Zhang, John S. Mattick, Animesh Ray, Ranjan J. Perera Jan 2013

Genome-Wide Methylated Cpg Island Profiles Of Melanoma Cells Reveal A Melanoma Coregulation Network, Jian-Liang Li, Joseph Mazar, Cuncong Zhong, Geoffrey J. Faulkner, Subramaniam S. Govindarajan, Zhan Zhang, Marcel E. Dinger, Gavin Meredith, Christopher Adams, Shaojie Zhang, John S. Mattick, Animesh Ray, Ranjan J. Perera

Faculty Bibliography 2010s

Metastatic melanoma is a malignant cancer with generally poor prognosis, with no targeted chemotherapy. To identify epigenetic changes related to melanoma, we have determined genome-wide methylated CpG island distributions by next-generation sequencing. Melanoma chromosomes tend to be differentially methylated over short CpG island tracts. CpG islands in the upstream regulatory regions of many coding and noncoding RNA genes, including, for example, TERC, which encodes the telomerase RNA, exhibit extensive hypermethylation, whereas several repeated elements, such as LINE 2, and several LTR elements, are hypomethylated in advanced stage melanoma cell lines. By using CpG island demethylation profiles, and by integrating these …

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Si-Cmos Compatible Materials And Devices For Mid-Ir Microphotonics, Pao Tai Lin, Vivek Singh, Jianfei Weng, Hongtao Lin, Juejun Hu, Kathleen Richardson, J. David Musgraves, Igor Luzinov, Joel Hensley, Lionel C. Kimberling, Anu Agarwal Jan 2013

Si-Cmos Compatible Materials And Devices For Mid-Ir Microphotonics, Pao Tai Lin, Vivek Singh, Jianfei Weng, Hongtao Lin, Juejun Hu, Kathleen Richardson, J. David Musgraves, Igor Luzinov, Joel Hensley, Lionel C. Kimberling, Anu Agarwal

Faculty Bibliography 2010s

CMOS compatible mid-Infrared (mid-IR) microphotonics including (1) broadband SOUP (Silicon on Oxide Undercladding Pedestal) waveguides; and (2) mid-IR transparent chalcogenide glass (ChGs) waveguides monolithically integrated with a PbTe thin film photodetector; are demonstrated. Using a pedestal undercladding geometry we obtain an optical loss for our Si waveguide which is 10 dB/cm lower compared to other waveguides using planar SiO2 cladding at lambda = 5 mu m, and a fundamental mode is seen over a broad mid-IR spectral range. To realize a fully integrated mid-IR on-chip system, in parallel, we develop PbTe thin film detectors that can be deposited on various …

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Fusionq: A Novel Approach For Gene Fusion Detection And Quantification From Paired-End Rna-Seq, Chenglin Liu, Jinwen Ma, Chung-Che "Jeff" Chang, Xiaobo Zhou Jan 2013

Fusionq: A Novel Approach For Gene Fusion Detection And Quantification From Paired-End Rna-Seq, Chenglin Liu, Jinwen Ma, Chung-Che "Jeff" Chang, Xiaobo Zhou

Faculty Bibliography 2010s

Background: Gene fusions, which result from abnormal chromosome rearrangements, are a pathogenic factor in cancer development. The emerging RNA-Seq technology enables us to detect gene fusions and profile their features. Results: In this paper, we proposed a novel fusion detection tool, FusionQ, based on paired-end RNA-Seq data. This tool can detect gene fusions, construct the structures of chimerical transcripts, and estimate their abundances. To confirm the read alignment on both sides of a fusion point, we employed a new approach, "residual sequence extension", which extended the short segments of the reads by aggregating their overlapping reads. We also proposed a …

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Assessing The Performance Of A Northern Gulf Of Mexico Tidal Model Using Satellite Imagery, Stephen C. Medeiros, Scott C. Hagen, Naira Chaouch, Jesse Feyen, Marouane Temimi, John F. Weishampel, Yuji Funakoshi, Reza Khanbilvardi Jan 2013

Assessing The Performance Of A Northern Gulf Of Mexico Tidal Model Using Satellite Imagery, Stephen C. Medeiros, Scott C. Hagen, Naira Chaouch, Jesse Feyen, Marouane Temimi, John F. Weishampel, Yuji Funakoshi, Reza Khanbilvardi

Faculty Bibliography 2010s

Tidal harmonic analysis simulations along with simulations spanning four specific historical time periods in 2003 and 2004 were conducted to test the performance of a northern Gulf of Mexico tidal model. A recently developed method for detecting inundated areas based on integrated remotely sensed data (i.e., Radarsat-1, aerial imagery, LiDAR, Landsat 7 ETM+) was applied to assess the performance of the tidal model. The analysis demonstrates the applicability of the method and its agreement with traditional performance assessment techniques such as harmonic resynthesis and water level time series analysis. Based on the flooded/non-flooded coastal areas estimated by the integrated remotely …

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Effect Of Sodium Bicarbonate And Beta-Alanine Supplementation On Maximal Sprint Swimming, Antti A. Mero, Petri Hirvonen, Janne Saarela, Juha J. Hulmi, Jay R. Hoffman, Jeffrey R. Stout Jan 2013

Effect Of Sodium Bicarbonate And Beta-Alanine Supplementation On Maximal Sprint Swimming, Antti A. Mero, Petri Hirvonen, Janne Saarela, Juha J. Hulmi, Jay R. Hoffman, Jeffrey R. Stout

Faculty Bibliography 2010s

Background: This study examined the effect of simultaneous supplementation of extracellular buffer sodium bicarbonate (SB) and intracellular buffer beta-alanine (BA) on maximal sprint swimming. Methods: Thirteen competitive male swimmers completed 4 different treatments (placebo [PL], SB, BA + PL, and BA + SB) in a crossover procedure. PL or SB supplementation (0.3 g/kg body weight) was ingested 60 min before two maximal 100-m freestyle swims that were performed with a passive recovery of 12-min between each swim. Because of the known long washout period for carnosine, four weeks of BA supplementation (4.8 g per day) was started after the first …

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The Use Of Structured Imagery And Dispositional Measurement To Assess Situational Use Of Mindfulness Skills, Jonathan C. Mitchell, Patricia A. Bach, Jeffrey E. Cassisi Jan 2013

The Use Of Structured Imagery And Dispositional Measurement To Assess Situational Use Of Mindfulness Skills, Jonathan C. Mitchell, Patricia A. Bach, Jeffrey E. Cassisi

Faculty Bibliography 2010s

The recent proliferation of studies on mindfulness produced varying theoretical models, each based in part on how mindfulness is assessed. These models agree, however, that mindfulness encompasses moment-to-moment or situational experiences. Incongruence between dispositional and situational assessment would be problematic for theory and empirical research. In particular, it remains to be established whether situational measurement is an accurate method for mindfulness assessment and whether dispositional measures are able to accurately detect mindfulness skills in various situations. The association between dispositional and situational mindfulness processes (i.e., situational attention awareness and emotion acceptance) was examined in two studies. In Study 1 (N …

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Erythropoietin Is A Jak2 And Erk1/2 Effector That Can Promote Renal Tumor Cell Proliferation Under Hypoxic Conditions, Makito Miyake, Steve Goodison, Adrienne Lawton, Ge Zhang, Evan Gomes-Giacoia, Charles J. Rosser Jan 2013

Erythropoietin Is A Jak2 And Erk1/2 Effector That Can Promote Renal Tumor Cell Proliferation Under Hypoxic Conditions, Makito Miyake, Steve Goodison, Adrienne Lawton, Ge Zhang, Evan Gomes-Giacoia, Charles J. Rosser

Faculty Bibliography 2010s

Background: Erythropoietin (EPO) provides an alternative to transfusion for increasing red blood cell mass and treating anemia in cancer patients. However, recent studies have reported increased adverse events and/or reduced survival in patients receiving both EPO and chemotherapy, potentially related to EPO-induced cancer progression. Additional preclinical studies that elucidate the possible mechanism underlying EPO cellular growth stimulation are needed. Methods: Using commercial tissue microarray (TMA) of a variety of cancers and benign tissues, EPO and EPO receptor immunohistochemical staining was performed. Furthermore using a panel of human renal cells (Caki-1, 786-O, 769-P, RPTEC), in vitro and in vivo experiments were …

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The Role Of Chemokine Receptor Cxcr4 In Breast Cancer Metastasis, Debarati Mukherjee, Jihe Zhao Jan 2013

The Role Of Chemokine Receptor Cxcr4 In Breast Cancer Metastasis, Debarati Mukherjee, Jihe Zhao

Faculty Bibliography 2010s

Breast cancer is one of the leading causes of cancer related deaths worldwide. Breast cancer-related mortality is associated with the development of metastatic potential of primary tumor lesions. The chemokine receptor CXCR4 has been found to be a prognostic marker in various types of cancer, including breast cancer. Recent advances in the field of cancer biology has pointed to the critical role that CXCR4 receptor and its ligand CXCL12 play in the metastasis of various types of cancer, including breast cancer. Breast tumors preferentially metastasize to the lung, bones and lymph nodes, all of which represent organs that secrete high …

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