A sparse regulatory network of copy-number driven expression reveals putative breast cancer oncogenes

The influence of DNA cis-regulatory elements on a gene's expression has been intensively studied. However, little is known about expressions driven by trans-acting DNA hotspots. DNA hotspots harboring copy number aberrations are recognized to be important in cancer as they influence multiple genes on a global scale. The challenge in detecting trans-effects is mainly due to the computational difficulty in detecting weak and sparse trans-acting signals amidst co-occuring passenger events. We propose an integrative approach to learn a sparse interaction network of DNA copy-number regions with their downstream targets in a breast cancer dataset. Information from this network helps distinguish copy-number driven from copy-number independent expression changes on a global scale. Our result further delineates cis- and trans-effects in a breast cancer dataset, for which important oncogenes such as ESR1 and ERBB2 appear to be highly copy-number dependent. Further, our model is shown to be efficient and in terms of goodness of fit no worse than other state-of the art predictors and network reconstruction models using both simulated and real data.Comment: Accepted at IEEE International Conference on Bioinformatics & Biomedicine (BIBM 2010

ForWord: A Study on an Interactive Learning Environment in Foreign Language

With constant advances in technology, the world becomes a smaller community each day. In line with its reputation as a cultural melting pot, children of immigrants are the fastest growing student population in the United States today. It\u27s clear that the U.S. needs a strong approach in language education; one that can keep pace with our potential and our lives. Technology can be used to foster student collaboration and shared learning experiences, thereby increasing learner interest, motivation and learning outcomes. ForWord aims to use interaction design in foreign language education to meet this need. ForWord has four main goals: provide a user-friendly online learning environment, promote teacher-student interaction and collaboration, promote student-student interaction and collaboration, and increase learner interest and motivation. This project takes the form of a proof-of-concept web application. The outcome relies heavily on research, design principles, user experience and human-computer interaction theory, and the use of technology to demonstrate the overarching concepts

The Role of Extension in a University\u27s Response to a Natural Disaster

In 2014, a mudslide devastated a small community in rural northwestern Washington State, taking 43 lives. The disaster created ripple effects that affected families, economies, transportation, and employment in neighboring communities. This article provides details of the state land-grant university\u27s efforts to help affected communities recover. Aspects of this response readily replicable by other land-grant universities include outreach leadership provided by local/county-based Extension faculty; creation of a response team with depth and breadth of expertise and skills; engagement of campus-based colleges, colleagues, and students; and delivery of youth development programs in affected communities. Meaningful outcomes have been achieved, and the outreach continues

Electrolysing mud: Membraneless electrolysis of water for hydrogen production using montmorillonite-rich marine mud

This paper describes a design for a low-cost membraneless water electrolyser for the production of green hydrogen that used a viscous electrolyte of naturally abundant montmorillonite-rich marine mud in a DEFT (divergent electrode flow through) geometry with stainless steel (304) mesh electrodes. The ratio of smectite to non-swelling clays in the mud was 1:2. The electrolyte was prepared by resuspending the mud in tap-water to remove the salt, and NaOH 1 M added to enhance the ionic conductivity, as measured by both Electrochemical Impedance Spectroscopy (EIS) and by the slope of DC current/voltage curves. Successful separation and collection of the hydrogen and oxygen gas was inferred from the ratio of 2:1 in the volumes of hydrogen and oxygen collected. Both acid and alkali treatments were trialled and it was found that, whereas acid treatment flocculated the mud, adding NaOH increased the dispersion, conductivity and viscosity, and reduced clogging. The conductivity of both the 24% dry mass alkali mud and a control 4% dry mass alkali bentonite suspension increased to that of pure NaOH 1 M when repeatedly electrolysed. Hydrogen and oxygen gas was collected for 10% and 24% dry mass muds. The less viscous 10% dry mass mud showed turbulent liquid-like behaviour which led to gas mixing but the 24% mud showed stable, solid-like flow and reliable gas separation. Three components of the energy efficiency of the electrolysis process are reported and discussed – the voltage efficiency of 42%, a gas collection efficiency of 50% and the auxiliary power efficiency of 60%. The overall energy efficiency due to these three contributing efficiencies, was 13% of the Higher Heating Value of 142 MJ/kg H2 for a current density of 45 mA/cm2. This mud electrolyser may still be considered worth developing for an off-grid, low budget site with a low-power source of renewable energy

Scambio, a novel guanine nucleotide exchange factor for Rho

BACKGROUND: Small GTPases of the Rho family are critical regulators of various cellular functions including actin cytoskeleton organization, activation of kinase cascades and mitogenesis. For this reason, a major objective has been to understand the mechanisms of Rho GTPase regulation. Here, we examine the function of a novel protein, Scambio, which shares homology with the DH-PH domains of several known guanine nucleotide exchange factors for Rho family members. RESULTS: Scambio is located on human chromosome 14q11.1, encodes a protein of around 181 kDa, and is highly expressed in both heart and skeletal muscle. In contrast to most DH-PH-domain containing proteins, it binds the activated, GTP-bound forms of Rac and Cdc42. However, it fails to associate with V14RhoA. Immunofluorescence studies indicate that Scambio and activated Rac3 colocalize in membrane ruffles at the cell periphery. In accordance with these findings, Scambio does not activate either Rac or Cdc42 but rather, stimulates guanine nucleotide exchange on RhoA and its close relative, RhoC. CONCLUSION: Scambio associates with Rac in its activated conformation and functions as a guanine nucleotide exchange factor for Rho

Syntaxin 3b is a t-SNARE specific for ribbon synapses of the retina.

Previous studies have demonstrated that ribbon synapses in the retina do not contain the t-SNARE (target-soluble N-ethylmaleimide-sensitive factor attachment protein receptor) syntaxin 1A that is found in conventional synapses of the nervous system. In contrast, ribbon synapses of the retina contain the related isoform syntaxin 3. In addition to its localization in ribbon synapses, syntaxin 3 is also found in nonneuronal cells, where it has been implicated in the trafficking of transport vesicles to the apical plasma membrane of polarized cells. The syntaxin 3 gene codes for four different splice forms, syntaxins 3A, 3B, 3C, and 3D. We demonstrate here by using analysis of EST databases, RT-PCR, in situ hybridization, and Northern blot analysis that cells in the mouse retina express only syntaxin 3B. In contrast, nonneuronal tissues, such as kidney, express only syntaxin 3A. The two major syntaxin isoforms (3A and 3B) have an identical N-terminal domain but differ in the C-terminal half of the SNARE domain and the C-terminal transmembrane domain. These two domains are thought to be directly involved in synaptic vesicle fusion. The interaction of syntaxin 1A and syntaxin 3B with other synaptic proteins was examined. We found that both proteins bind Munc18/N-sec1 with similar affinity. In contrast, syntaxin 3B had a much lower binding affinity for the t-SNARE SNAP25 compared with syntaxin 1A. By using an in vitro fusion assay, we could demonstrate that vesicles containing syntaxin 3B and SNAP25 could fuse with vesicles containing synaptobrevin2/VAMP2, demonstrating that syntaxin 3B can function as a t-SNARE

Comparison of manual and semi-automated delineation of regions of interest for radioligand PET imaging analysis

BACKGROUND As imaging centers produce higher resolution research scans, the number of man-hours required to process regional data has become a major concern. Comparison of automated vs. manual methodology has not been reported for functional imaging. We explored validation of using automation to delineate regions of interest on positron emission tomography (PET) scans. The purpose of this study was to ascertain improvements in image processing time and reproducibility of a semi-automated brain region extraction (SABRE) method over manual delineation of regions of interest (ROIs). METHODS We compared 2 sets of partial volume corrected serotonin 1a receptor binding potentials (BPs) resulting from manual vs. semi-automated methods. BPs were obtained from subjects meeting consensus criteria for frontotemporal degeneration and from age- and gender-matched healthy controls. Two trained raters provided each set of data to conduct comparisons of inter-rater mean image processing time, rank order of BPs for 9 PET scans, intra- and inter-rater intraclass correlation coefficients (ICC), repeatability coefficients (RC), percentages of the average parameter value (RM%), and effect sizes of either method. RESULTS SABRE saved approximately 3 hours of processing time per PET subject over manual delineation (p 0.8) for both methods. RC and RM% were lower for the manual method across all ROIs, indicating less intra-rater variance across PET subjects' BPs. CONCLUSION SABRE demonstrated significant time savings and no significant difference in reproducibility over manual methods, justifying the use of SABRE in serotonin 1a receptor radioligand PET imaging analysis. This implies that semi-automated ROI delineation is a valid methodology for future PET imaging analysis

An Annotated Bibliography of Financial Therapy Research: 2010 to 2018

The purpose of this paper is to expand upon Mentzer, Britt, Samuelson, and Herrera’s (2010) annotated bibliography of research conducted in the field of financial therapy prior to 2010 and provide readers with a current overview of financial therapy research published since that time. Annotated bibliographies are categorized by topics and future research in each area is suggested. In addition, two tables were developed to provide readers a snapshot of the current landscape of financial therapy. The first table provides a list of journals of published articles featuring financial therapy or related topics. The second table provides an overview of types of research, population studies, key topics, as well as highlighting whether theory and financial therapy are overtly referred to within the article