TREEOME: A framework for epigenetic and transcriptomic data integration to explore regulatory interactions controlling transcription

Motivation: Predictive modelling of gene expression is a powerful framework for the in silico exploration of transcriptional regulatory interactions through the integration of high-throughput -omics data. A major limitation of previous approaches is their inability to handle conditional and synergistic interactions that emerge when collectively analysing genes subject to different regulatory mechanisms. This limitation reduces overall predictive power and thus the reliability of downstream biological inference. Results: We introduce an analytical modelling framework (TREEOME: tree of models of expression) that integrates epigenetic and transcriptomic data by separating genes into putative regulatory classes. Current predictive modelling approaches have found both DNA methylation and histone modification epigenetic data to provide little or no improvement in accuracy of prediction of transcript abundance despite, for example, distinct anti-correlation between mRNA levels and promoter-localised DNA methylation. To improve on this, in TREEOME we evaluate four possible methods of formulating gene-level DNA methylation metrics, which provide a foundation for identifying gene-level methylation events and subsequent differential analysis, whereas most previous techniques operate at the level of individual CpG dinucleotides. We demonstrate TREEOME by integrating gene-level DNA methylation (bisulfite-seq) and histone modification (ChIP-seq) data to accurately predict genome-wide mRNA transcript abundance (RNA-seq) for H1-hESC and GM12878 cell lines. Availability: TREEOME is implemented using open-source software and made available as a pre-configured bootable reference environment. All scripts and data presented in this study are available online at http://sourceforge.net/projects/budden2015treeome/.Comment: 14 pages, 6 figure

Hybrid CO₂-Ti:sapphire laser with tunable pulse duration for mid-infrared-pump terahertz-probe spectroscopy

We describe a mid-infrared pump – terahertz-probe setup based on a CO2 laser seeded with 10.6 μm wavelength pulses from an optical parametric amplifier, itself pumped by a Ti:Al2O3 laser. The output of the seeded CO2 laser produces high power pulses of nanosecond duration, which are synchronized to the femtosecond laser. These pulses can be tuned in pulse duration by slicing their front and back edges with semiconductor-plasma mirrors irradiated by replicas of the femtosecond seed laser pulses. Variable pulse lengths from 5 ps to 1.3 ns are achieved, and used in mid-infrared pump, terahertz-probe experiments with probe pulses generated and electro-optically sampled by the femtosecond laser

Strategically Enhancing Business Capabilities And Social Development In The Hispanic Community

Hurricane Katrina displaced more than one million people while destroying or badly disrupting more than 40% of Louisiana’s economic base. Thousands of small businesses ceased to exist. The socio-economic damage in the U.S. appears without precedent. The growing Hispanic population in southeast Louisiana presents a unique and distinctive socio-economic challenge. As Hispanics move into the region in large numbers seeking economic opportunities, specific needs are emerging. A variety of work and social skills must be developed and nurtured. Business skills and guidance must be offered.  These needs must be recognized and addressed to facilitate a holistic assimilation of a growing Hispanic population into southeast Louisiana and develop a strong and literate workforce.  The Hispanic Business Resources & Technology Center (HBRTC) was created by the Hispanic Chamber of Commerce of Louisiana (HCCL) in alliance with The Hispanic Apostolate Catholic Charities of the Archdiocese of New Orleans, The Jefferson Parish School System, and Southeastern Louisiana University, to address the post-Katrina crisis in the New Orleans region and to address needs of Hispanic families and businesses.  The HBRTC is the first of its kind in the State of Louisiana to specifically address the myriad needs of the developing Hispanic workforce and community in Louisiana

Enhancing Multilingual Capability Among Hispanics

Hispanics are the country’s largest and fastest growing minority, but they are not an easily identified racial or ethnic group (Pew Hispanic Center, Trends 2005). In 2000, the U.S. Census reported 32.8 million Hispanics or Latinos in the United States, representing 12% of the total population. By 2004, the Hispanic population was estimated to have grown to over 40 million, an increase of more than 23% in just four years. The largest increase in the Hispanic population is occurring in the southern United States (Pew Hispanic Center). Paralleling the growth of the Hispanic population, the Hispanic labor force will expand to nearly 10 million by 2020 (Pew Hispanic Center).  Language barriers and cultural sensitivities need to be addressed for optimal inclusion of this force in the U.S. The dramatic expansion of the Latino population in the State of Louisiana emphasizes the importance of this group, both socially and culturally.  At the same time it presents new challenges and demands a real approach for addressing the languages barriers and the cultural sensitivities inherent in such a socioeconomic shift

Uncovering degrees of workplace bullying: a comparison of Baccalaureate nursing students' experiences during clinical placement in Australia and the UK.

Background: Bullying in health workplaces has a negative impact on individual nurses, their families, multidisciplinary teams, patient care and the profession. Aim: This paper compares the experiences of bully and harassment of Australian and UK baccalaureate nursing students during clinical placement. Method: A secondary analysis was conducted on two primary cross-sectional studies of bullying experiences of Australian and UK nursing students. Data were collected using the SEBDCP questionnaire and analysed using descriptive and inferential statistics. The total sample consisted of 833 Australian and 561 UK students Results: Australian nursing students experienced a higher rate of bullying (50.1%) than UK students (35.5%). Across both cohorts (Aust 53%, UK 68%). students identified other nurses as the main perpetrators and few bullied students chose to report the episode/s (Aust 28.5%, UK 19.4%). The main reason given for not reporting was fear of being victimised (Aust 53.6%, UK 54.5%). Sadly, a number felt ‘it is part of the job’ (UK: 21.6%, Aust: 23.9%). Conclusions: It is clear that a culture of bullying in nursing persists internationally. Nursing students are vulnerable and often experience and/or witness bullying episodes during clinical placement, leading them to question their future in the ‘caring’ profession of nursing. Bullying behaviour requires a zero tolerance by the nursing profession and education providers need to develop clear policies and implement procedures that protect students as the future nursing workforce

Australian women's prediagnostic values and influencing sociodemographic variables relating to treatment choices for early breast cancer treatment

Women are often asked by their doctors to choose their preferred treatment for early breast cancer. Evidence shows that many women are distressed and confused about how to make this treatment decision and frequently seek help from nurses. Very little is known about women's value-centred decision-making in relation to selecting treatment for breast cancer and for nurses it is difficult to know how to assist these women with this process. In this study, 377 women participated prior to undergoing routine mammography screening and the data were collected using the Pre-Decision Portfolio Questionnaire (PDPQ) by Pierce 1. The partipants identified that expected treatment outcomes were the most important factor in choosing early breast cancer treatment. The majority reported that it was very important that a treatment would reduce the chances the cancer would return (95.6%), increase the length of their life (82.1%) and lead them to being healthy (80.4%). In addition, the participants indicated that it was important, or very important, that the emotional consequences of the treatment did "not make you depressed" (88.6%) or "sad" (90.4%) and should "keep you from worrying" (97%) and "give you peace of mind" (98.6%). Other factors, such as treatment's side effects, were identified as less important. Age, employment, education and having a family history of breast cancer were found to be significant influencing variables on the values of the participants. It was concluded that assessing and understanding the treatment values of women can help nurses focus on areas of importance to the woman and lead to informed decision-making when they are choosing treatment for early breast cancer

Impacts Of The Aggregate Economic And Financial Conditions On Output In An Emerging Economy

This study formulates the theoretical model based on the money market equilibrium, the goods market equilibrium, and an augmented aggregate supply function. The sample ranges from 1996.Q1 to 2009.Q3 and has 55 observations. Applying the generalized autoregressive conditional heteroskedasticity (GARCH) model, this paper finds that Brazil’s real GDP is positively impacted by real M2 money supply, the real stock price, world output and the expected inflation rate and is negatively influenced by the government deficit as a percent of GDP, the real BRL/USD exchange rate and the U.S. Treasury bill rate. The first and third quarters exhibit seasonal effects. Therefore, expansionary monetary policy is more effective than deficit-financed expansionary fiscal policy, and pursuing real appreciation, promoting a robust stock market, and maintaining a strong world economy will benefit the Brazilian economy