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Software for Genomic/Epigenomic Research
A.S.Tanas, V.V.Shkarupo, E.B.Kuznetsova, D.V.Zaletayev, V.V. Strelnikov

We present two computer programs: 1) AIMS in silico - a suggestion tool for Amplification of Intermethylated Sites experimental design and results analysis; and 2) PeakPick – a tool to view & analyse capillary electrophoregrams Our computer software is intended to standardize AIMS applications and to turn it into one of the principal approaches towards cancer methylomes studies as well as towards diagnostics in oncology, including early screening.

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Insulin Decreases Transcription of Three Proteins Associated with Lung Surfactant
Rucka, Z [a], Vanhara, P [b], Tesarova, L [a], Potesilova, M [a], Stejskal, S [a], Dolezel, J [c], Koutna, I [a]

Our project is partially focused on insulin affecting four proteins associated with lung surfactant. Small and hydrophobic SP-B and S-PC help to spread and stabilize the surfactant layer while large and hydrophilic SP-A and SP-D participate in immune responses. A549 and H441 cell lines were used. It was observed using RealTime PCR that higher doses of insulin lead to decreased transcription of SP-B, SP-C, SP-D, and both isoforms of SP-A.

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Synthesis and trafficking of the tonoplast potassium channel AtTPK1
Marie Maitrejean (1,2), Michael Wudick (2), Camilla Voelker (2), Katrin Czempinski (2), Emanuela Pedrazzini (1), Alesandro Vitale (1)

Sorting signals of tonoplast proteins and the pathway they follow through the endomembrane system are still poorly characterized. Using Brefeldin A (an inhibitor of the Golgi-mediated traffic) we showed that a Golgi-dependent pathway for tonoplast delivery may exist. Then we generated various chimeric TPK1-TPK4 fusions, exchanging various domains. We observed that the cytosolic, C-terminal domain of TPK1 is sufficient to re-direct the plasma membrane TPK4 to the tonoplast.

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Geneset-based cancer survival analysis: On the non-uniform distributiuon of p-values under the null hypothesis
Esteban Czwan, Benedikt Brors, David Kipling

Although null p-values are assumed to be uniformly distributed in gene expression experiments, the actual distribution often deviates from the assumed distribution. This can incorrectly associate the biology of a geneset with cancer prognosis in geneset-based survival studies. To assess the implications of this, a geneset-based method was developed. This method empirically approximates the distribution of null p-values and tests whether predefined sets of biologically-related genes are associate

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Reactome - a knowledgebase of human biological pathways
Esther E Schmidt, Michael Caudy, David Croft, Bernard de Bono, Phani V Garapati, Gopal Gopinath, Marc Gillespie, Robin Haw, Bijay Jassal, Steven Jupe, Alexander Kanapin, Shahana Mahajan, Lisa Matthews, Bruce May, Gavin O’Kelly, Imre Vastrik, Guanming Wu, Ewan Birney, Peter D'Eustachio, Lincoln Stein

Reactome is a manually curated knowledgebase, created and peer-reviewed by experts in their field. Its robust data model describes life processes ranging from metabolism to signal transduction and the cell cycle. As of release 28, Reactome contains 3700 human proteins in 3200 reactions. Data is cross-referenced to publicly available web-based informatics resources. Reactome features the SkyPainter tool for analysis of high-throughput datasets, and the Mart query and data retrieval tool.

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Panic attack and suicide risk: A multivariate logistic regression analysis of a national epidemiological survey
Curren Katz, Ramin Mojtabai, Leo Bierman, Kathleen Camacho, Janine Samuel, Gillian Jennings, Igor Galynker

To examine the relationship between panic attack and suicide risk, we analyzed data from a representative epidemiological survey of 43,093 adults (NESARC) using logistic regression controlling for socio-demographic and clinical variables. In depression, panic attacks are associated with increased odds of suicide attempt even after controlling for demographic and clinical variables. Furthermore, panic attacks can differentiate those who attempt suicide from those with ideation only.

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Panic attack and suicide risk: A multivariate logistic regression analysis of a national epidemiological survey
Curren Katz, Ramin Mojtabai, Leo Bierman, Kathleen Camacho, Janine Samuel, Gillian Jennings, Igor Galynker

To examine the relationship between panic attack and suicide risk, we analyzed data from a representative epidemiological survey of 43,093 adults (NESARC) using logistic regression controlling for socio-demographic and clinical variables. In depression, panic attacks are associated with increased odds of suicide attempt even after controlling for demographic and clinical variables. Furthermore, panic attacks can differentiate those who attempt suicide from those with ideation only.

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Evaluation of a Novel Approach for the Measurement of RNA Quality
Timothy Wilkes; Alison Devonshire; Carole Foy

The potential medical applications of microarrays have generated much interest, within the biomedical community. Numerous potential sources of variation have raised concerns regarding assay consistency and data quality. Previous studies have highlighted RNA integrity as having a major effect on data quality. We describe here a comparison of the performance characteristics of the Agilent (Bioanalyser) and Lab901 (Screen Tape System) platforms, and their capacity to determine sample RNA integrity.

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Evaluation of a Novel Approach for the Measurement of RNA Quality
Timothy Wilkes; Alison Devonshire; Carole Foy

The potential medical applications of microarrays have generated much interest, within the biomedical community. Numerous potential sources of variation have raised concerns regarding assay consistency and data quality. Previous studies have highlighted RNA integrity as having a major effect on data quality. We describe here a comparison of the performance characteristics of the Agilent (Bioanalyser) and Lab901 (Screen Tape System) platforms, and their capacity to determine sample RNA integrity.

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Showing Results 81 - 90 of 157
Scientific News
Spontaneous Mutations in Key Brain Gene are a Cause of Autism
In addition, there is a direct link between TBR1 and FOXP2, a well-known language-related protein, researchers report.
Protein Variant may Boost Cardiovascular Risk by Hindering Blood Vessel Repair
Researchers have found that apoE3 helps repair the lining of blood vessels.
Blood Test To Diagnose Depression
Test identifies nine blood markers tied to depression; predicts who will benefit from therapy.
Study Aims to Develop Breath Test for COPD
A new clinical iniative, lead by NYU Langone Medical Center, aims to determine a breath test’s effectiveness to identify volatile organic compounds (VOCs) in human breath that are biomarkers of chronic obstructive pulmonary disease (COPD).
Salamander Skin Peptide Promotes Wound Healing in Mice
New research suggests that the peptide tylotoin exerts the promotion of wound healing with epidermal growth factor in a murine model of a full thickness dermal wound.
Marijuana Compound May Offer Treatment for AD
Extremely low levels of the compound in marijuana known as delta-9-tetrahydrocannabinol, or THC, may slow or halt the progression of Alzheimer’s disease.
Quantitative Western Blotting Using Stain-Free Technology
Bio-Rad hosted two seminars at the EB 2014 in which KOLs discussed approaches to improve the accuracy of western blotting quantitation using Bio-Rad’s stain-free technology.
Repressing the Repressors May Drive Tissue-Specific Cancers
Stowers scientists establish Drosophila and mammalian models to study mutations found in pediatric brain tumors.
MU Researchers Discover Protein's Ability To Inhibit HIV Release
TIM-family proteins have the ability to block the release of HIV and other viruses.
Epigenetic Study Bolsters Alzheimer's Understanding
The current study found that chemical modifications to DNA within the ANK1 gene are strongly associated with measures of neuropathology in the brain.
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