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Find video protocols related to scientific articles indexed in Pubmed.
Oxidative modulation of K+ channels in the central nervous system in neurodegenerative diseases and ageing.
Antioxid. Redox Signal.
PUBLISHED: 10-22-2014
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Significance. Oxidative stress and damage are well established components of neurodegenerative diseases, contributing to neuronal death during disease progression. Here, we consider key K+ channels as target proteins which can undergo oxidative modulation, describe what is understood about how this influences disease progression, and consider regulation of these channels by gasotransmitters as a means of cellular protection. Recent Advances. Oxidative regulation of the delayed rectifier Kv2.1 and the Ca2+- and voltage-sensitive BK channel are established, but recent studies contest how their redox sensitivity contributes to altered excitability, progression of neurodegenerative diseases and healthy ageing. Critical Issues. Both Kv2.1 and BK channels have recently been established as target proteins for regulation by the gasotransmitters carbon monoxide and hydrogen sulfide. Establishing the molecular basis of such regulation, and exactly how this influences excitability and vulnerability to apoptotic cell death will determine whether such regulation can be exploited for therapeutic benefit. Future Directions. Developing a more comprehensive picture of the oxidative modulation of K+ channels (and indeed other ion channels) within the CNS in health and disease will allow us to better understand processes associated with healthy ageing as well as distinct processes underlying progression of neurodegenerative diseases. Advances in the growing understanding of how gasotransmitters can regulate ion channels, including redox-sensitive K+ channels, are a research priority for this field, and will establish their usefulness in design of future approaches for the treatment of such diseases.
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Methods, safety, and early clinical outcomes of dose escalation using simultaneous integrated and sequential boosts in patients with locally advanced gynecologic malignancies.
Gynecol. Oncol.
PUBLISHED: 09-02-2014
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To evaluate the safety of dose escalated radiotherapy using a simultaneous integrated boost technique in patients with locally advanced gynecological malignancies.
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Hydrogen sulfide inhibits Cav3.2 T-type Ca2+ channels.
FASEB J.
PUBLISHED: 09-02-2014
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The importance of H2S as a physiological signaling molecule continues to develop, and ion channels are emerging as a major family of target proteins through which H2S exerts many actions. The purpose of the present study was to investigate its effects on T-type Ca(2+) channels. Using patch-clamp electrophysiology, we demonstrate that the H2S donor, NaHS (10 ?M-1 mM) selectively inhibits Cav3.2 T-type channels heterologously expressed in HEK293 cells, whereas Cav3.1 and Cav3.3 channels were unaffected. The sensitivity of Cav3.2 channels to H2S required the presence of the redox-sensitive extracellular residue H191, which is also required for tonic binding of Zn(2+) to this channel. Chelation of Zn(2+) with N,N,N',N'-tetra-2-picolylethylenediamine prevented channel inhibition by H2S and also reversed H2S inhibition when applied after H2S exposure, suggesting that H2S may act via increasing the affinity of the channel for extracellular Zn(2+) binding. Inhibition of native T-type channels in 3 cell lines correlated with expression of Cav3.2 and not Cav3.1 channels. Notably, H2S also inhibited native T-type (primarily Cav3.2) channels in sensory dorsal root ganglion neurons. Our data demonstrate a novel target for H2S regulation, the T-type Ca(2+) channel Cav3.2, and suggest that such modulation cannot account for the pronociceptive effects of this gasotransmitter.-Elies, J., Scragg, J. L., Huang, S., Dallas, M. L., Huang, D., MacDougall, D., Boyle, J. P. Gamper, N., Peers, C. Hydrogen sulfide inhibits Cav3.2 T-type Ca(2+) channels.
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Simple and accurate methods for quantifying deformation, disruption, and development in biological tissues.
J R Soc Interface
PUBLISHED: 08-29-2014
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When mechanical factors underlie growth, development, disease or healing, they often function through local regions of tissue where deformation is highly concentrated. Current optical techniques to estimate deformation can lack precision and accuracy in such regions due to challenges in distinguishing a region of concentrated deformation from an error in displacement tracking. Here, we present a simple and general technique for improving the accuracy and precision of strain estimation and an associated technique for distinguishing a concentrated deformation from a tracking error. The strain estimation technique improves accuracy relative to other state-of-the-art algorithms by directly estimating strain fields without first estimating displacements, resulting in a very simple method and low computational cost. The technique for identifying local elevation of strain enables for the first time the successful identification of the onset and consequences of local strain concentrating features such as cracks and tears in a highly strained tissue. We apply these new techniques to demonstrate a novel hypothesis in prenatal wound healing. More generally, the analytical methods we have developed provide a simple tool for quantifying the appearance and magnitude of localized deformation from a series of digital images across a broad range of disciplines.
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Smoking history predicts for increased risk of second primary lung cancer: A comprehensive analysis.
Cancer
PUBLISHED: 08-23-2014
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Tobacco use is the most important risk factor for the development of lung cancer. The objective of the current study was to determine the effect of smoking on the development of second primary lung cancers (SPLCs) and other clinical outcomes after surgery for non-small cell lung cancer (NSCLC).
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Inhibition of the cardiac Na? channel Nav1.5 by carbon monoxide.
J. Biol. Chem.
PUBLISHED: 04-09-2014
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Sublethal carbon monoxide (CO) exposure is frequently associated with myocardial arrhythmias, and our recent studies have demonstrated that these may be attributable to modulation of cardiac Na(+) channels, causing an increase in the late current and an inhibition of the peak current. Using a recombinant expression system, we demonstrate that CO inhibits peak human Nav1.5 current amplitude without activation of the late Na(+) current observed in native tissue. Inhibition was associated with a hyperpolarizing shift in the steady-state inactivation properties of the channels and was unaffected by modification of channel gating induced by anemone toxin (rATX-II). Systematic pharmacological assessment indicated that no recognized CO-sensitive intracellular signaling pathways appeared to mediate CO inhibition of Nav1.5. Inhibition was, however, markedly suppressed by inhibition of NO formation, but NO donors did not mimic or occlude channel inhibition by CO, indicating that NO alone did not account for the actions of CO. Exposure of cells to DTT immediately before CO exposure also dramatically reduced the magnitude of current inhibition. Similarly, l-cysteine and N-ethylmaleimide significantly attenuated the inhibition caused by CO. In the presence of DTT and the NO inhibitor N(?)-nitro-L-arginine methyl ester hydrochloride, the ability of CO to inhibit Nav1.5 was almost fully prevented. Our data indicate that inhibition of peak Na(+) current (which can lead to Brugada syndrome-like arrhythmias) occurs via a mechanism distinct from induction of the late current, requires NO formation, and is dependent on channel redox state.
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Heme oxygenase-1 regulates cell proliferation via carbon monoxide-mediated inhibition of T-type Ca(2+) channels.
Pflugers Arch.
PUBLISHED: 02-05-2014
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Induction of the antioxidant enzyme heme oxygenase-1 (HO-1) affords cellular protection and suppresses proliferation of vascular smooth muscle cells (VSMCs) associated with a variety of pathological cardiovascular conditions including myocardial infarction and vascular injury. However, the underlying mechanisms are not fully understood. Over-expression of Cav3.2 T-type Ca(2+) channels in HEK293 cells raised basal [Ca(2+)]i and increased proliferation as compared with non-transfected cells. Proliferation and [Ca(2+)]i levels were reduced to levels seen in non-transfected cells either by induction of HO-1 or exposure of cells to the HO-1 product, carbon monoxide (CO) (applied as the CO releasing molecule, CORM-3). In the aortic VSMC line A7r5, proliferation was also inhibited by induction of HO-1 or by exposure of cells to CO, and patch-clamp recordings indicated that CO inhibited T-type (as well as L-type) Ca(2+) currents in these cells. Finally, in human saphenous vein smooth muscle cells, proliferation was reduced by T-type channel inhibition or by HO-1 induction or CO exposure. The effects of T-type channel blockade and HO-1 induction were non-additive. Collectively, these data indicate that HO-1 regulates proliferation via CO-mediated inhibition of T-type Ca(2+) channels. This signalling pathway provides a novel means by which proliferation of VSMCs (and other cells) may be regulated therapeutically.
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National Breast and Cervical Cancer Early Detection Program partnerships in action.
Cancer
PUBLISHED: 01-31-2014
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Since the inception of the Centers for Disease Control and Prevention (CDC) National Breast and Cervical Cancer Early Detection Program (NBCCEDP) in 1990, partnerships have played a significant role in providing breast and cervical cancer screening and early detection to uninsured and underinsured women. The state, tribal, and territorial NBCCEDP grantees have shared resources and responsibilities with a variety of partners (eg, community-based organizations, government agencies, tribes, health care systems, companies, professional organizations) to achieve common goals. National partners, such as the American Cancer Society, Susan G. Komen for the Cure, and the Avon Foundation for Women, have provided funding, lobbied for national and state funding, supported outreach and education activities, and provided treatment referral services for the programs. This article provides an overview of grantee partnerships to illustrate the effects, successes, and challenges of these partnerships and how they have affected the populations served by the program.
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Body mass index, dose to organs at risk during vaginal brachytherapy, and the role of three-dimensional CT-based treatment planning.
Brachytherapy
PUBLISHED: 01-16-2014
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To assess the effect of body mass index (BMI) on dose to organs at risk (OARs) during high-dose-rate vaginal brachytherapy and evaluate the role of three-dimensional dose evaluation during treatment planning.
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Evaluation of Outcomes in Patients With Carcinoma of the Cervix Treated With Concurrent Radiation and Cisplatin Versus Cisplatin/5-FU Compared With Radiation Alone.
Am. J. Clin. Oncol.
PUBLISHED: 09-12-2013
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The objective of this study was to compare outcomes for patients with cervical cancer treated with radiation concurrently with cisplatin, cisplatin/5-fluorouracil (5-FU), or without chemotherapy.
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Carbon monoxide inhibition of Cav3.2 T-type Ca2+ channels reveals tonic modulation by thioredoxin.
FASEB J.
PUBLISHED: 05-13-2013
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T-type Ca(2+) channels play diverse roles in tissues such as sensory neurons, vascular smooth muscle, and cancers, where increased expression of the cytoprotective enzyme, heme oxygenase-1 (HO-1) is often found. Here, we report regulation of T-type Ca(2+) channels by carbon monoxide (CO) a HO-1 by-product. CO (applied as CORM-2) caused a concentration-dependent, poorly reversible inhibition of all T-type channel isoforms (Cav3.1-3.3, IC50 ?3 ?M) expressed in HEK293 cells, and native T-type channels in NG108-15 cells and primary rat sensory neurons. No recognized CO-sensitive signaling pathway could account for the CO inhibition of Cav3.2. Instead, CO sensitivity was mediated by an extracellular redox-sensitive site, which was also highly sensitive to thioredoxin (Trx). Trx depletion (using auranofin, 2-5 ?M) reduced Cav3.2 currents and their CO sensitivity by >50% but increased sensitivity to dithiothreitol ?3-fold. By contrast, Cav3.1 and Cav3.3 channels, and their sensitivity to CO, were unaffected in identical experiments. Our data propose a novel signaling pathway in which Trx acts as a tonic, endogenous regulator of Cav3.2 channels, while HO-1-derived CO disrupts this regulation, causing channel inhibition. CO modulation of T-type channels has widespread implications for diverse physiological and pathophysiological mechanisms, such as excitability, contractility, and proliferation.
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Anaphylaxis in America: The prevalence and characteristics of anaphylaxis in the United States.
J. Allergy Clin. Immunol.
PUBLISHED: 04-20-2013
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Although anaphylaxis is recognized as an important life-threatening condition, data are limited regarding its prevalence and characteristics in the general population.
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VennPlex--a novel Venn diagram program for comparing and visualizing datasets with differentially regulated datapoints.
PLoS ONE
PUBLISHED: 01-07-2013
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With the development of increasingly large and complex genomic and proteomic data sets, an enhancement in the complexity of available Venn diagram analytical programs is becoming increasingly important. Current freely available Venn diagram programs often fail to represent extra complexity among datasets, such as regulation pattern differences between different groups. Here we describe the development of VennPlex, a program that illustrates the often diverse numerical interactions among multiple, high-complexity datasets, using up to four data sets. VennPlex includes versatile output features, where grouped data points in specific regions can be easily exported into a spreadsheet. This program is able to facilitate the analysis of two to four gene sets and their corresponding expression values in a user-friendly manner. To demonstrate its unique experimental utility we applied VennPlex to a complex paradigm, i.e. a comparison of the effect of multiple oxygen tension environments (1-20% ambient oxygen) upon gene transcription of primary rat astrocytes. VennPlex accurately dissects complex data sets reliably into easily identifiable groups for straightforward analysis and data output. This program, which is an improvement over currently available Venn diagram programs, is able to rapidly extract important datasets that represent the variety of expression patterns available within the data sets, showing potential applications in fields like genomics, proteomics, and bioinformatics.
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Nasal allergies in the Asian-Pacific population: results from the Allergies in Asia-Pacific Survey.
Am J Rhinol Allergy
PUBLISHED: 12-22-2011
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The Allergies in Asia-Pacific Survey describes the symptoms, impact, and treatment of allergic rhinitis (AR) across Australia, China, Hong Kong, Malaysia, Singapore, Taiwan, Vietnam, and the Philippines. The Allergies in Asia-Pacific Survey was undertaken to further clarify the prevalence of physician-diagnosed nasal allergies (NAs), impact on quality-of-life (QOL), existing treatment paradigms and gaps, and NA medications currently used in treatment.
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Interfaces to PeptideAtlas: a case study of standard data access systems.
Brief. Bioinformatics
PUBLISHED: 11-22-2011
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Access to public data sets is important to the scientific community as a resource to develop new experiments or validate new data. Projects such as the PeptideAtlas, Ensembl and The Cancer Genome Atlas (TCGA) offer both access to public data and a repository to share their own data. Access to these data sets is often provided through a web page form and a web service API. Access technologies based on web protocols (e.g. http) have been in use for over a decade and are widely adopted across the industry for a variety of functions (e.g. search, commercial transactions, and social media). Each architecture adapts these technologies to provide users with tools to access and share data. Both commonly used web service technologies (e.g. REST and SOAP), and custom-built solutions over HTTP are utilized in providing access to research data. Providing multiple access points ensures that the community can access the data in the simplest and most effective manner for their particular needs. This article examines three common access mechanisms for web accessible data: BioMart, caBIG, and Google Data Sources. These are illustrated by implementing each over the PeptideAtlas repository and reviewed for their suitability based on specific usages common to research. BioMart, Google Data Sources, and caBIG are each suitable for certain uses. The tradeoffs made in the development of the technology are dependent on the uses each was designed for (e.g. security versus speed). This means that an understanding of specific requirements and tradeoffs is necessary before selecting the access technology.
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Regional skeletal muscle remodeling and mitochondrial dysfunction in right ventricular heart failure.
Am. J. Physiol. Heart Circ. Physiol.
PUBLISHED: 10-28-2011
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Exercise intolerance is a cardinal symptom of right ventricular heart failure (RV HF) and skeletal muscle adaptations play a role in this limitation. We determined regional remodeling of muscle structure and mitochondrial function in a rat model of RV HF induced by monocrotaline injection (MCT; 60 mg·kg(-1); n = 11). Serial sections of the plantaris were stained for fiber type, succinate dehydrogenase (SDH) activity and capillaries. Mitochondrial function was assessed in permeabilized fibers using respirometry, and isolated complex activity by blue native gel electrophoresis (BN PAGE). All measurements were compared with saline-injected control animals (CON; n = 12). Overall fiber cross-sectional area was smaller in MCT than CON: 1,843 ± 114 vs. 2,322 ± 120 ?m(2) (P = 0.009). Capillary-to-fiber ratio was lower in MCT in the oxidative plantaris region (1.65 ± 0.09 vs. 1.93 ± 0.07; P = 0.03), but not in the glycolytic region. SDH activity (P = 0.048) and maximal respiratory rate (P = 0.012) were each ?15% lower in all fibers in MCT. ADP sensitivity was reduced in both skeletal muscle regions in MCT (P = 0.032), but normalized by rotenone. A 20% lower complex I/IV activity in MCT was confirmed by BN PAGE. MCT-treatment was associated with lower mitochondrial volume density (lower SDH activity), quality (lower complex I activity), and fewer capillaries per fiber area in oxidative skeletal muscle. These features are consistent with structural and functional remodeling of the determinants of oxygen supply potential and utilization that may contribute to exercise intolerance and reduced quality of life in patients with RV HF.
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Implementation of a protocol to reduce occurrence of retained sponges after vaginal delivery.
Mil Med
PUBLISHED: 06-28-2011
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Retained sponges (gossypiboma) following vaginal delivery are an uncommon occurrence. Although significant morbidity from such an event is unlikely, there are many reported adverse effects, including symptoms of malodorous discharge, loss of confidence in providers and the medical system, and legal claims.
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SAMQA: error classification and validation of high-throughput sequenced read data.
BMC Genomics
PUBLISHED: 05-11-2011
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The advances in high-throughput sequencing technologies and growth in data sizes has highlighted the need for scalable tools to perform quality assurance testing. These tests are necessary to ensure that data is of a minimum necessary standard for use in downstream analysis. In this paper we present the SAMQA tool to rapidly and robustly identify errors in population-scale sequence data.
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Ocular and systemic findings in a survey of aniridia subjects.
J AAPOS
PUBLISHED: 05-03-2011
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To determine the prevalence of ocular and systemic abnormalities in a group of subjects with aniridia.
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Multiple oxygen tension environments reveal diverse patterns of transcriptional regulation in primary astrocytes.
PLoS ONE
PUBLISHED: 03-01-2011
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The central nervous system normally functions at O(2) levels which would be regarded as hypoxic by most other tissues. However, most in vitro studies of neurons and astrocytes are conducted under hyperoxic conditions without consideration of O(2)-dependent cellular adaptation. We analyzed the reactivity of astrocytes to 1, 4 and 9% O(2) tensions compared to the cell culture standard of 20% O(2), to investigate their ability to sense and translate this O(2) information to transcriptional activity. Variance of ambient O(2) tension for rat astrocytes resulted in profound changes in ribosomal activity, cytoskeletal and energy-regulatory mechanisms and cytokine-related signaling. Clustering of transcriptional regulation patterns revealed four distinct response pattern groups that directionally pivoted around the 4% O(2) tension, or demonstrated coherent ascending/decreasing gene expression patterns in response to diverse oxygen tensions. Immune response and cell cycle/cancer-related signaling pathway transcriptomic subsets were significantly activated with increasing hypoxia, whilst hemostatic and cardiovascular signaling mechanisms were attenuated with increasing hypoxia. Our data indicate that variant O(2) tensions induce specific and physiologically-focused transcript regulation patterns that may underpin important physiological mechanisms that connect higher neurological activity to astrocytic function and ambient oxygen environments. These strongly defined patterns demonstrate a strong bias for physiological transcript programs to pivot around the 4% O(2) tension, while uni-modal programs that do not, appear more related to pathological actions. The functional interaction of these transcriptional programs may serve to regulate the dynamic vascular responsivity of the central nervous system during periods of stress or heightened activity.
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The role of radiation therapy in uterine-confined endometrial carcinoma.
Pract Radiat Oncol
PUBLISHED: 02-19-2011
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The treatment of endometrial cancer begins with surgery, including total abdominal hysterectomy, bilateral salpingo-oophorectomy, peritoneal lavage, and a consideration for lymph node evaluation. Selection of adjuvant therapy is based on an approximation of the risk of recurrence with features such as stage, tumor histology, lymphovascular space invasion, and patient age. The role of adjuvant radiation therapy in patients with intermediate risk of recurrence is a matter of ongoing controversy. Several randomized trials indicate that adjuvant radiation therapy improves loco-regional control. However, the ideal form of radiation therapy in these patients continues to be under debate.
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EPEPT: a web service for enhanced P-value estimation in permutation tests.
BMC Bioinformatics
PUBLISHED: 01-20-2011
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In computational biology, permutation tests have become a widely used tool to assess the statistical significance of an event under investigation. However, the common way of computing the P-value, which expresses the statistical significance, requires a very large number of permutations when small (and thus interesting) P-values are to be accurately estimated. This is computationally expensive and often infeasible. Recently, we proposed an alternative estimator, which requires far fewer permutations compared to the standard empirical approach while still reliably estimating small P-values.
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Carbon monoxide protects against oxidant-induced apoptosis via inhibition of Kv2.1.
FASEB J.
PUBLISHED: 01-19-2011
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Oxidative stress induces neuronal apoptosis and is implicated in cerebral ischemia, head trauma, and age-related neurodegenerative diseases. An early step in this process is the loss of intracellular K(+) via K(+) channels, and evidence indicates that K(v)2.1 is of particular importance in this regard, being rapidly inserted into the plasma membrane in response to apoptotic stimuli. An additional feature of neuronal oxidative stress is the up-regulation of the inducible enzyme heme oxygenase-1 (HO-1), which catabolizes heme to generate biliverdin, Fe(2+), and carbon monoxide (CO). CO provides neuronal protection against stresses such as stroke and excitotoxicity, although the underlying mechanisms are not yet elucidated. Here, we demonstrate that CO reversibly inhibits K(v)2.1. Channel inhibition by CO involves reactive oxygen species and protein kinase G activity. Overexpression of K(v)2.1 in HEK293 cells increases their vulnerability to oxidant-induced apoptosis, and this is reversed by CO. In hippocampal neurons, CO selectively inhibits K(v)2.1, reverses the dramatic oxidant-induced increase in K(+) current density, and provides marked protection against oxidant-induced apoptosis. Our results provide a novel mechanism to account for the neuroprotective effects of CO against oxidative apoptosis, which has potential for therapeutic exploitation to provide neuronal protection in situations of oxidative stress.
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Residents educational needs during transition into radiation oncology residency.
J Am Coll Radiol
PUBLISHED: 01-07-2011
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The aim of this study was to assess current practices, strengths, and deficiencies in the orientation process for incoming radiation oncology (RO) residents.
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Increased accumulation of sulfur in lake sediments of the high arctic.
Environ. Sci. Technol.
PUBLISHED: 10-27-2010
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We report a synchronous increase in accumulation of reduced inorganic sulfur since c. 1980 in sediment cores from eight of nine lakes studied in the Canadian Arctic and Svalbard (Norway). Sediment incubations and detailed analyses of sediment profiles from two of the lakes indicate that increases in sulfur accumulation may be due ultimately to a changing climate. Warming-induced lengthening of the ice-free season is resulting in well-documented increases in algal production and sedimentation of the resulting detrital matter. Algal detritus is a rich source of labile carbon, which in these sediments stimulates dissimilatory sulfate reduction. The sulfide produced is stored in sediment (as acid volatile sulfide), converted to other forms of sulfur, or reoxidized to sulfate and lost to the water column. An acceleration of the sulfur cycle in Arctic lakes could have profound effects on important biogeochemical processes, such as carbon burial and mercury methylation.
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SEQADAPT: an adaptable system for the tracking, storage and analysis of high throughput sequencing experiments.
BMC Bioinformatics
PUBLISHED: 07-14-2010
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High throughput sequencing has become an increasingly important tool for biological research. However, the existing software systems for managing and processing these data have not provided the flexible infrastructure that research requires.
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Nasal allergies in the Latin American population: results from the Allergies in Latin America survey.
Allergy Asthma Proc
PUBLISHED: 06-16-2010
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Allergies in Latin America is the first cross-national survey that describes the symptoms, impact, and treatment of nasal allergies (NAs) in individuals >or=4 years old in Latin America (LA). In total, 22,012 households across the Latin American countries of Argentina, Brazil, Chile, Colombia, Ecuador, Mexico, Peru, and Venezuela were screened for children, adolescents, and adults with a diagnosis of NA and either symptoms or treatment in the past 12 months. A total of 1088 adults and 457 children and adolescents were included and the sample was probability based to ensure valid statistical inference to the population. Approximately 7% of the LA population was diagnosed with NAs with two of three respondents stating that their allergies were seasonal or intermittent in nature. A general practice physician or otolaryngologist diagnosed the majority of individuals surveyed. Nasal congestion was the most common and bothersome symptom of NAs. Sufferers indicated that their symptoms affected productivity and sleep and had a negative impact on quality of life. Two-thirds of patients reported taking some type of medication for their NAs, with a roughly equal percentage of patients reporting taking over-the-counter versus prescription medications. Changing medications was most commonly done in those reporting inadequate efficacy. The most common reasons cited for dissatisfaction with current medications were related to inadequate effectiveness, effectiveness wearing off with chronic use, failure to provide 24-hour relief, and bothersome side effects (e.g., unpleasant taste and retrograde drainage into the esophagus). Findings from this cross-national survey on NAs have confirmed a high prevalence of physician-diagnosed NAs and a considerable negative impact on daily quality of life and work productivity as well as substantial disease management challenges in LA. Through identification of disease impact on the LA population and further defining treatment gaps, clinicians in LA may better understand and treat NAs, thus leading to improvements in overall patient satisfaction and quality of life.
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Gap junction-mediated spontaneous Ca(2+) waves in differentiated cholinergic SN56 cells.
Biochem. Biophys. Res. Commun.
PUBLISHED: 05-25-2010
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Neuronal gap junctions are receiving increasing attention as a physiological means of intercellular communication, yet our understanding of them is poorly developed when compared to synaptic communication. Using microfluorimetry, we demonstrate that differentiation of SN56 cells (hybridoma cells derived from murine septal neurones) leads to the spontaneous generation of Ca(2+) waves. These waves were unaffected by tetrodotoxin (1microM), but blocked by removal of extracellular Ca(2+), or addition of non-specific Ca(2+) channel inhibitors (Cd(2+) (0.1mM) or Ni(2+) (1mM)). Combined application of antagonists of NMDA receptors (AP5; 100microM), AMPA/kainate receptors (NBQX; 20microM), nicotinic AChR receptors (hexamethonium; 100microM) or inotropic purinoceptors (brilliant blue; 100nM) was also without effect. However, Ca(2+) waves were fully prevented by carbenoxolone (200microM), halothane (3mM) or niflumic acid (100microM), three structurally diverse inhibitors of gap junctions, and mRNA for connexin 36 was detected by PCR. Whole-cell patch-clamp recordings revealed spontaneous inward currents in voltage-clamped cells which we inhibited by Cd(2+), Ni(2+) or niflumic acid. Our data suggest that differentiated SN56 cells generated spontaneous Ca(2+) waves which are propagated by intercellular gap junctions. We propose that this system can be exploited conveniently for the development of neuronal gap junction modulators.
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Porphyrin-nanosensor conjugates. New tools for the measurement of intracellular response to reactive oxygen species.
Photochem. Photobiol. Sci.
PUBLISHED: 05-12-2010
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Reactive oxygen species (ROS) have for some time been implicated in the onset and progression of medical conditions including cancer, ageing, heart disease and Alzheimers disease. Recently, it has been postulated that ROS play a much more subtle role in intracellular signalling mechanisms as second messengers. Given the importance of these species in influencing cellular processes, it is surprising that tools for studying intracellular levels of ROS are extremely limited and devices for studying the cells response to internally generated ROS are virtually non-existent. In order to study the response of cells to intracellular ROS we have designed a nano-scale device that can both generate ROS and simultaneously monitor the cells reaction as a function of changes in the important signalling ion, calcium. Here we report the synthesis, characterisation, and calibration of a new ROS nano-probe and demonstrate its ability to detect cellular response to elevated levels of intracellular ROS.
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QTIPS: a novel method of unsupervised determination of isotopic amino acid distribution in SILAC experiments.
J. Am. Soc. Mass Spectrom.
PUBLISHED: 04-02-2010
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Stable incorporation of labeled amino acids in cell culture is a simple approach to label proteins in vivo for mass spectrometric quantification. Full incorporation of isotopically heavy amino acids facilitates accurate quantification of proteins from different cultures, yet analysis methods for determination of incorporation are cumbersome and time-consuming. We present QTIPS, Quantification by Total Identified Peptides for SILAC, a straightforward, accurate method to determine the level of heavy amino acid incorporation throughout a population of peptides detected by mass spectrometry. Using QTIPS, we show that the incorporation of heavy amino acids in bakers yeast is unaffected by the use of prototrophic strains, indicating that auxotrophy is not a requirement for SILAC experiments in this organism. This method has general utility for multiple applications where isotopic labeling is used for quantification in mass spectrometry.
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mspecLINE: bridging knowledge of human disease with the proteome.
BMC Med Genomics
PUBLISHED: 03-10-2010
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Public proteomics databases such as PeptideAtlas contain peptides and proteins identified in mass spectrometry experiments. However, these databases lack information about human disease for researchers studying disease-related proteins. We have developed mspecLINE, a tool that combines knowledge about human disease in MEDLINE with empirical data about the detectable human proteome in PeptideAtlas. mspecLINE associates diseases with proteins by calculating the semantic distance between annotated terms from a controlled biomedical vocabulary. We used an established semantic distance measure that is based on the co-occurrence of disease and protein terms in the MEDLINE bibliographic database.
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The Ahmed Glaucoma Valve in patients with and without neovascular glaucoma.
J. Glaucoma
PUBLISHED: 02-19-2010
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To evaluate the results of Ahmed Glaucoma Valve surgery in neovascular glaucoma and control patients.
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Genome-wide analysis of effectors of peroxisome biogenesis.
PLoS ONE
PUBLISHED: 02-17-2010
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Peroxisomes are intracellular organelles that house a number of diverse metabolic processes, notably those required for beta-oxidation of fatty acids. Peroxisomes biogenesis can be induced by the presence of peroxisome proliferators, including fatty acids, which activate complex cellular programs that underlie the induction process. Here, we used multi-parameter quantitative phenotype analyses of an arrayed mutant collection of yeast cells induced to proliferate peroxisomes, to establish a comprehensive inventory of genes required for peroxisome induction and function. The assays employed include growth in the presence of fatty acids, and confocal imaging and flow cytometry through the induction process. In addition to the classical phenotypes associated with loss of peroxisomal functions, these studies identified 169 genes required for robust signaling, transcription, normal peroxisomal development and morphologies, and transmission of peroxisomes to daughter cells. These gene products are localized throughout the cell, and many have indirect connections to peroxisome function. By integration with extant data sets, we present a total of 211 genes linked to peroxisome biogenesis and highlight the complex networks through which information flows during peroxisome biogenesis and function.
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Hypoxia and neurodegeneration.
Ann. N. Y. Acad. Sci.
PUBLISHED: 10-23-2009
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Periods of chronic hypoxia, which can arise from numerous cardiorespiratory disorders, predispose individuals to the development of dementias, particularly Alzheimers disease (AD). AD is characterized in part by the increased production of amyloid beta peptide (Abeta), which forms the extracellular plaques by which the disease can be identified post mortem. Numerous studies have now shown that hypoxia, even in vitro, can increase production of Abeta in different cell types. Evidence has been produced to indicate hypoxia alters both expression of the Abeta precursor, APP, and also the expression of the secretase enzymes, which cleave Abeta from APP. Other studies implicate reduced Abeta degradation as a possible means by which hypoxia increases Abeta levels. Such variability may be attributable to cell-specific responses to hypoxia. Further evidence indicates that some, but not all of the cellular adaptations to chronic hypoxia (including alteration of Ca(2+) homeostasis) require Abeta formation. However, other aspects of hypoxic remodeling of cell function appear to occur independently of this process. The molecular and cellular responses to hypoxia contribute to our understanding of the clinical association of hypoxia and increased incidence of AD. However, it remains to be determined whether inhibition of one or more of the effects of hypoxia may be of benefit in arresting the development of this neurodegenerative disease.
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alpha-Synuclein modulation of Ca2+ signaling in human neuroblastoma (SH-SY5Y) cells.
J. Neurochem.
PUBLISHED: 10-05-2009
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Parkinsons disease (PD) is characterized in part by the presence of alpha-synuclein (alpha-syn) rich intracellular inclusions (Lewy bodies). Mutations and multiplication of the alpha-synuclein gene (SNCA) are associated with familial PD. Since Ca2+ dyshomeostasis may play an important role in the pathogenesis of PD, we used fluorimetry in fura-2 loaded SH-SY5Y cells to monitor Ca2+ homeostasis in cells stably transfected with either wild-type alpha-syn, the A53T mutant form, the S129D phosphomimetic mutant or with empty vector (which served as control). Voltage-gated Ca2+ influx evoked by exposure of cells to 50 mM K+ was enhanced in cells expressing all three forms of alpha-syn, an effect which was due specifically to increased Ca2+ entry via L-type Ca2+ channels. Mobilization of Ca2+ by muscarine was not strikingly modified by any of the alpha-syn forms, but they all reduced capacitative Ca2+ entry following store depletion caused either by muscarine or thapsigargin. Emptying of stores with cyclopiazonic acid caused similar rises of [Ca2+](i) in all cells tested (with the exception of the S129D mutant), and mitochondrial Ca2+ content was unaffected by any form of alpha-synuclein. However, only WT alpha-syn transfected cells displayed significantly impaired viability. Our findings suggest that alpha-syn regulates Ca2+ entry pathways and, consequently, that abnormal alpha-syn levels may promote neuronal damage through dysregulation of Ca2+ homeostasis.
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Use of intravenous immunoglobulin and adjunctive therapies in the treatment of primary immunodeficiencies: A working group report of and study by the Primary Immunodeficiency Committee of the American Academy of Allergy Asthma and Immunology.
Clin. Immunol.
PUBLISHED: 09-09-2009
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There are an expanding number of primary immunodeficiency diseases (PIDDs), each associated with unique diagnostic and therapeutic complexities. Limited data, however, exist supporting specific therapeutic interventions. Thus, a survey of PIDD management was administered to allergists/immunologists in the United States to identify current perspectives and practices. Among 405 respondents, the majority of key management practices identified were consistent with existing data and guidelines, including the provision of immunoglobulin therapy, immunoglobulin dosing and selective avoidance of live viral vaccines. Practices for which there are little specific data or evidence-based guidance were also examined, including evaluation of IgG trough levels for patients receiving immunoglobulin, use of prophylactic antibiotics and recommendations for complementary/alternative medicine. Here, variability applied to PIDD patients was identified. Differences between practitioners clinically focused upon PIDD and general allergists/immunologists were also identified. Thus, a need for expanded clinical research in PIDD to optimize management and potentially improve outcomes was defined.
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Implications of the growing use of wireless telephones for health care opinion polls.
Health Serv Res
PUBLISHED: 07-27-2009
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To assess the effect of wireless telephone substitution in a survey of health care reform opinions.
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Cytoscape: a community-based framework for network modeling.
Methods Mol. Biol.
PUBLISHED: 07-15-2009
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Cytoscape is a general network visualization, data integration, and analysis software package. Its development and use has been focused on the modeling requirements of systems biology, though it has been used in other fields. Cytoscapes flexibility has encouraged many users to adopt it and adapt it to their own research by using the plugin framework offered to specialize data analysis, data integration, or visualization. Plugins represent collections of community-contributed functionality and can be used to dynamically extend Cytoscape functionality. This community of users and developers has worked together since Cytoscapes initial release to improve the basic project through contributions to the core code and public offerings of plugin modules. This chapter discusses what Cytoscape does, why it was developed, and the extensions numerous groups have made available to the public. It also describes the development of a plugin used to investigate a particular research question in systems biology and walks through an example analysis using Cytoscape.
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Modulation of Ca(2+) signalling in human vascular endothelial cells by hydrogen sulfide.
Atherosclerosis
PUBLISHED: 06-24-2009
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Hydrogen sulfide (H(2)S) is now recognised as an important endogenous antihypertensive molecule and is synthesised in the vasculature primarily by endothelial cystathionine gamma lyase. Activity of this enzyme, and the production of other vasoactive substances by the endothelium, are subject to modulation by changes of [Ca(2+)](i). Here, we have used microfluorimetry to investigate whether H(2)S can regulate human endothelial [Ca(2+)](i). H(2)S (applied via the donor NaHS, 5-500 microM) caused concentration-dependent rises of [Ca(2+)](i) which were attributable to release from an ATP- and 4-CEP sensitive intracellular pool. Rises of [Ca(2+)](i) evoked by H(2)S were essentially abolished by prior pool depletion. In the absence of external Ca(2+), H(2)S slowed the decay phase of responses to cyclopiazonic acid, but this could not be attributed to the inhibition of Ca(2+) extrusion since the effects of H(2)S were at least additive with the Na(+)/Ca(2+) exchange inhibitors bepridil and SEA 0400 and the Ca(2+) ATPase inhibitor, carboxyeosin. In some but not all the cells, re-exposure to extracellular Ca(2+) following the addition and removal of H(2)S activated capacitative Ca(2+) entry (CCE), and H(2)S increased ATP-evoked (but not thapsigargin-evoked) CCE. Effects of H(2)S were not mediated by energy depletion or production of cyclic ADP ribose. Our data indicate that H(2)S can modulate endothelial [Ca(2+)](i) via multiple mechanisms, and such effects are likely to contribute to this gasotransmitters beneficial actions.
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The role of adjuvant radiation in endometrial cancer.
Oncology (Williston Park, N.Y.)
PUBLISHED: 05-30-2009
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Endometrial cancer treatment ideally begins with a staging procedure including abdominopelvic washing, total abdominal hysterectomy, bilateral salpingo-oophorectomy, and lymph node evaluation. Recommendations for postoperative adjuvant radiotherapy are determined by recurrence risk. Patients who have undergone staging and have early stage I disease and an absence of high-risk features for recurrence generally are treated with surgery alone. Intermediate-risk patients--those with high-risk stage I disease and some stage II patients--may benefit from adjuvant radiation therapy. Several randomized trials show that radiation therapy improves locoregional control among intermediate-risk patients. The optimal type of radiation therapy, whether vaginal brachytherapy or whole-pelvic radiation therapy, remains undetermined, though treatment decision can be guided by risk factors not encompassed by the current staging system. Patients with high-risk stage II disease and stage III disease generally receive external-beam radiotherapy, often in combination with chemotherapy. Chemotherapy alone in advanced-stage patients is a consideration, given the results of the Gynecologic Oncology Group (GOG)-122 trial.
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Effects of the HEET garment in the prevention of hypothermia in a porcine model.
J. Surg. Res.
PUBLISHED: 05-19-2009
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Hypothermia is a common battlefield trauma occurrence. This study compared the effectiveness of the hypothermia, environmental, exposure, and trauma (HEET) garment (Trident Industries, Beaufort, SC) with and without thermal inserts with a control group of two wool blankets in the prevention of hypothermia in a treated hypovolemic porcine model.
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Burden of allergic rhinitis: results from the Pediatric Allergies in America survey.
J. Allergy Clin. Immunol.
PUBLISHED: 04-29-2009
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Allergic rhinitis (AR), a chronic inflammatory disease of the upper airway, is one of the most common chronic diseases in the United States and is estimated to affect up to 60 million people. Pediatric Allergies in America is the largest and most comprehensive survey to date of pediatric patients and parents of patients with allergy, as well as health care providers (HCPs), regarding AR in children and its treatment. The goals of the survey were to determine the prevalence of AR in the US pediatric population and to collect information on what effect the condition has on patients in terms of symptom burden, quality of life, productivity, disease management, and pharmacologic treatment. This national survey screened 35,757 households to identify 500 children with HCP-diagnosed nasal allergies and 504 children without nasal allergies who were between the ages of 4 and 17 years. Parents of young children, as well as children 10 to 17 years of age, were questioned about the condition and its treatment. In parallel, 501 HCPs were interviewed. This survey has captured previously unavailable data on the prevalence of nasal allergies and their most common and most bothersome symptoms, on the effect of nasal allergies on the quality of life of children, and on medication use, including both over-the-counter and prescription medications, and has identified factors affecting satisfaction with treatment. The Pediatric Allergies in America survey also identifies distinct areas for improvement in the management of AR in children. In fact, based on the results of this survey, it appears that HCPs overestimate patients and parents satisfaction with disease management and the benefit of medications used for the treatment of nasal allergies in children. Findings from this national survey have identified important challenges to the management of AR, suggesting that its burden on children in the United States has been significantly underestimated.
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Adaptable data management for systems biology investigations.
BMC Bioinformatics
PUBLISHED: 03-06-2009
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Within research each experiment is different, the focus changes and the data is generated from a continually evolving barrage of technologies. There is a continual introduction of new techniques whose usage ranges from in-house protocols through to high-throughput instrumentation. To support these requirements data management systems are needed that can be rapidly built and readily adapted for new usage.
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Hydra: a scalable proteomic search engine which utilizes the Hadoop distributed computing framework.
BMC Bioinformatics
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For shotgun mass spectrometry based proteomics the most computationally expensive step is in matching the spectra against an increasingly large database of sequences and their post-translational modifications with known masses. Each mass spectrometer can generate data at an astonishingly high rate, and the scope of what is searched for is continually increasing. Therefore solutions for improving our ability to perform these searches are needed.
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Fastbreak: a tool for analysis and visualization of structural variations in genomic data.
EURASIP J Bioinform Syst Biol
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Genomic studies are now being undertaken on thousands of samples requiring new computational tools that can rapidly analyze data to identify clinically important features. Inferring structural variations in cancer genomes from mate-paired reads is a combinatorially difficult problem. We introduce Fastbreak, a fast and scalable toolkit that enables the analysis and visualization of large amounts of data from projects such as The Cancer Genome Atlas.
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Burden of allergic rhinitis: allergies in America, Latin America, and Asia-Pacific adult surveys.
Allergy Asthma Proc
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Allergic rhinitis (AR; also nasal allergies or "hay fever") is a chronic upper airway inflammatory disease that affects ?60 million adults and children in the United States. The duration and severity of AR symptoms contribute to a substantial burden on patients quality of life (QoL), sleep, work productivity, and activity. This study was designed to examine symptoms, QoL, productivity, comorbidities, disease management, and pharmacologic treatment of AR in United States and ex-U.S. sufferers. Allergies in America was a comprehensive telephone-based survey of 2500 adults with AR. These data are compared and contrasted with findings from the Pediatric Allergies in America, Allergies in Latin America, and Allergies in Asia-Pacific telephone surveys. The prevalence of physician-diagnosed AR was 14% in U.S. adults, 7% in Latin America adults, and 9% in Asia-Pacific adults. Nasal congestion is the most common and bothersome symptom for adults. Approximately two-thirds of adults rely on medication to relieve intolerable AR symptoms. Incomplete relief, slow onset, <24-hour relief, and reduced efficacy with sustained use were commonly reported with AR medications, including intranasal corticosteroids. One in seven U.S. adults reported achieving little to no relief with AR medications. Bothersome adverse effects of AR medications included drowsiness, a drying feeling, medication dripping down the throat, and bad taste. Perception of inadequate efficacy was the leading cause of medication discontinuation or change and contributed to treatment dissatisfaction. These findings support the assertion that AR burden has been substantially underestimated and identify several important challenges to successful management of AR.
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Carbon monoxide induces cardiac arrhythmia via induction of the late Na+ current.
Am. J. Respir. Crit. Care Med.
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Clinical reports describe life-threatening cardiac arrhythmias after environmental exposure to carbon monoxide (CO) or accidental CO poisoning. Numerous case studies describe disruption of repolarization and prolongation of the QT interval, yet the mechanisms underlying CO-induced arrhythmias are unknown.
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Carbon monoxide mediates the anti-apoptotic effects of heme oxygenase-1 in medulloblastoma DAOY cells via K+ channel inhibition.
J. Biol. Chem.
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Tumor cell survival and proliferation is attributable in part to suppression of apoptotic pathways, yet the mechanisms by which cancer cells resist apoptosis are not fully understood. Many cancer cells constitutively express heme oxygenase-1 (HO-1), which catabolizes heme to generate biliverdin, Fe(2+), and carbon monoxide (CO). These breakdown products may play a role in the ability of cancer cells to suppress apoptotic signals. K(+) channels also play a crucial role in apoptosis, permitting K(+) efflux which is required to initiate caspase activation. Here, we demonstrate that HO-1 is constitutively expressed in human medulloblastoma tissue, and can be induced in the medulloblastoma cell line DAOY either chemically or by hypoxia. Induction of HO-1 markedly increases the resistance of DAOY cells to oxidant-induced apoptosis. This effect was mimicked by exogenous application of the heme degradation product CO. Furthermore we demonstrate the presence of the pro-apoptotic K(+) channel, Kv2.1, in both human medulloblastoma tissue and DAOY cells. CO inhibited the voltage-gated K(+) currents in DAOY cells, and largely reversed the oxidant-induced increase in K(+) channel activity. p38 MAPK inhibition prevented the oxidant-induced increase of K(+) channel activity in DAOY cells, and enhanced their resistance to apoptosis. Our findings suggest that CO-mediated inhibition of K(+) channels represents an important mechanism by which HO-1 can increase the resistance to apoptosis of medulloblastoma cells, and support the idea that HO-1 inhibition may enhance the effectiveness of current chemo- and radiotherapies.
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Reactive oxygen species are second messengers of neurokinin signaling in peripheral sensory neurons.
Proc. Natl. Acad. Sci. U.S.A.
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Substance P (SP) is a prominent neuromodulator, which is produced and released by peripheral damage-sensing (nociceptive) neurons; these neurons also express SP receptors. However, the mechanisms of peripheral SP signaling are poorly understood. We report a signaling pathway of SP in nociceptive neurons: Acting predominantly through NK1 receptors and G(i/o) proteins, SP stimulates increased release of reactive oxygen species from the mitochondrial electron transport chain. Reactive oxygen species, functioning as second messengers, induce oxidative modification and augment M-type potassium channels, thereby suppressing excitability. This signaling cascade requires activation of phospholipase C but is largely uncoupled from the inositol 1,4,5-trisphosphate sensitive Ca(2+) stores. In rats SP causes sensitization of TRPV1 and produces thermal hyperalgesia. However, the lack of coupling between SP signaling and inositol 1,4,5-trisphosphate sensitive Ca(2+) stores, together with the augmenting effect on M channels, renders the SP pathway ineffective to excite nociceptors acutely and produce spontaneous pain. Our study describes a mechanism for neurokinin signaling in sensory neurons and provides evidence that spontaneous pain and hyperalgesia can have distinct underlying mechanisms within a single nociceptive neuron.
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Methods for visual mining of genomic and proteomic data atlases.
BMC Bioinformatics
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As the volume, complexity and diversity of the information that scientists work with on a daily basis continues to rise, so too does the requirement for new analytic software. The analytic software must solve the dichotomy that exists between the need to allow for a high level of scientific reasoning, and the requirement to have an intuitive and easy to use tool which does not require specialist, and often arduous, training to use. Information visualization provides a solution to this problem, as it allows for direct manipulation and interaction with diverse and complex data. The challenge addressing bioinformatics researches is how to apply this knowledge to data sets that are continually growing in a field that is rapidly changing.
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Peroxynitrite mediates disruption of Ca2+ homeostasis by carbon monoxide via Ca2+ ATPase degradation.
Antioxid. Redox Signal.
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Sublethal carbon monoxide poisoning causes prolonged neurological damage involving oxidative stress. Given the central role of Ca(2+) homeostasis and its vulnerability to stress, we investigated whether CO disrupts neuronal Ca(2+) homeostasis.
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Cellular consequences of the expression of Alzheimers disease-causing presenilin 1 mutations in human neuroblastoma (SH-SY5Y) cells.
Brain Res.
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Mutations in the presenilin 1 (PS1) gene lead to early-onset Alzheimers disease with the S170F mutation causing the earliest reported age of onset. Expression of this, and other PS1 mutations, in SH-SY5Y cells resulted in significant loss of cellular viability compared to control cells. Basal Ca2+ concentrations in PS1 mutants were never lower than controls and prolonged incubation in Ca2+ -free solutions did not deplete Ca2+ stores, demonstrating there was no difference in Ca2+ leak from endoplasmic reticulum (ER) stores in PS1 mutants. Peak muscarine-evoked rises of [Ca2+]i were variable, but the integrals were not significantly different, suggesting, while kinetics of Ca2+ store release might be affected in PS1 mutants, store size was similar. However, when Ca2+ -ATPase activity was irreversibly inhibited with thapsigargin, the S170F and ?E9 cells showed larger capacitative calcium entry indicating a direct effect on Ca2+ influx pathways. There was no significant effect of any of the mutations on mitochondrial respiration. Amyloid ?(A?(1-40)) secretion was reduced, and A?(1-42) secretion increased in the S170F cells resulting in a very large increase in the A?42/40 ratio. This, rather than any potential disruption of ER Ca2+ stores, is likely to explain the extreme pathology of this mutant.
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Mining PeptideAtlas for biomarkers and therapeutics in human disease.
Curr. Pharm. Des.
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Mass spectrometry information has long offered the potential of discovering biomarkers that would enable clinicians to diagnose disease, and treat it with targeted therapies. PeptideAtlas currently provides access to large-scale spectra data and identification information. This data, and the generation of targeted peptide information, represents the first step in the process of locating disease biomarkers. Reaching the goal of clinical proteomics requires that this data be integrated with additional information from disease literature and genomic studies. Here we describe PeptideAtlas and associated methods for mining the data, as well as the software tools necessary to support large-scale integration and mining.
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What is Visualize?

JoVE Visualize is a tool created to match the last 5 years of PubMed publications to methods in JoVE's video library.

How does it work?

We use abstracts found on PubMed and match them to JoVE videos to create a list of 10 to 30 related methods videos.

Video X seems to be unrelated to Abstract Y...

In developing our video relationships, we compare around 5 million PubMed articles to our library of over 4,500 methods videos. In some cases the language used in the PubMed abstracts makes matching that content to a JoVE video difficult. In other cases, there happens not to be any content in our video library that is relevant to the topic of a given abstract. In these cases, our algorithms are trying their best to display videos with relevant content, which can sometimes result in matched videos with only a slight relation.