INTEGRATE-Neo: A pipeline for personalized gene fusion neoantigen discovery

Abstract Motivation While high-throughput sequencing (HTS) has been used successfully to discover tumor-specific mutant peptides (neoantigens) from somatic missense mutations, the field currently lacks a method for identifying which gene fusions may generate neoantigens. Results We demonstrate the application of our gene fusion neoantigen discovery pipeline, called INTEGRATE-Neo, by identifying gene fusions in prostate cancers that may produce neoantigens. Availability and Implementation INTEGRATE-Neo is implemented in C ++ and Python. Full source code and installation instructions are freely available from https://github.com/ChrisMaherLab/INTEGRATE-Neo. Supplementary information Supplementary data are available at Bioinformatics online. </jats:sec

Going-Concern Opinions: Broadening the Expectations Gap

A rash of high-profile bankruptcies has led to a search for answers. Many hold auditors responsible for not detecting the potential for bankruptcy during the most recent audit. The Weiss Report, a study of several dozen bankrupt companies submitted to the U.S. Senate during its deliberations on the Sarbanes-Oxley Act, found a broad and massive failure on the part of auditors to raise yellow flags that indicate potential bankruptcy. The authors examined Weiss\u27 methodology and found that, applied to a broader group of companies, Weiss\u27 criteria would have incorrectly predicted bankruptcy for nearly half of the non-bankrupt companies studied. This failure to accurately predict undermines the credibility of the subsequently enacted legislation

To be (physically active) or not to be? That is the question! Special educational needs, physical education and leisure lifestyles

The UK’s coalition government released a statutory national curriculum in September 2014 that specified the programmes of study and attainment targets for each subject in all local authority-maintained mainstream schools in England (DfE, 2013). The aim of this short article is to debate the potential impact of the 2014 national curriculum physical education (NCPE) on the long-term participation in physical activity as an aspect of the leisure lifestyles of pupils identified as having special educational needs (SEN). Positive early learning experiences in mainstream PE are supposed to have a significant impact on the lifelong participation in physical activity as part of young people’s leisure lifestyles (Kirk, 2005), including those with SEN. While attempts to address lifelong physical activity as part of people’s leisure often focuses on young people generally, and their experiences of PE in particular, the needs of those with SEN are rarely considered by government, schools, service providers or academics. Of course, differences in national legislation, education structures, funding mechanisms, school priorities and conceptualisations of SEN will influence the PE experiences of pupils with SEN in other countries (EADSNE, 2003) and, therefore, future lifestyles. Particular light is cast in the direction of the UK’s newest NCPE given that the position of team games and competitive sport appears to have been strengthened, rather than challenged, in mainstream secondary schools despite research suggesting that (1) it is more difficult to meet the needs and capitalise on the capabilities of pupils with SEN when these activities are delivered (Fitzgerald, 2005; Morley et al., 2005; Smith, 2004); and (2) that the traditional, structured and hierarchical sport-based PE curriculum is at odds with the lifestyle activities of adults, which can influence whether young people carry on participating in physical activity into adulthood (Wheaton, 2010)

The spectral response of spontaneous EEG occipital alpha activity

University of Technology, Sydney. Faculty of Science.The desynchronisation and temporal response of the spontaneous EEG occipital alpha activity in the 8-13 Hz frequency band to a range of luminances and wavelengths from spectrally characterised illumination-sources under homogeneous viewing conditions, with and without the presence of foveal perturbations were examined. Insufficient evidence in the literature to substantiate the effect on occipital alpha to varying luminance conditions and the necessity of such knowledge for the operation of an environmental control system (ECS) provided the impetus for the work. A series of experiments were conducted in uniformly illuminated unpatterned visual fields provided by a sheet of white paper and an integrating sphere. Luminances in the range 2.6x10'5- 900 cd/m2 and peak wavelengths of 454 nm, 529 nm, 600 nm and 658 nm, for narrow band sources and white light were investigated. Results show that, (i) ECS operation based on the increased amplitude of alpha activity on eye closure is viable in the luminance range 2.6x10'4-900 cd/m2, (ii) Occipital alpha activity, in terms of maximum frequency, maximum amplitude and the frequency integrated amplitude, during the first 20 s of homogeneous visual stimulation or on fixation on a foveal perturbation in the field is equivalent to viewing in a typical patterned environment and (iii) Chromatic homogeneous stimulation effects ongoing alpha activity with respect to a wavelength dependency and a decrease in alpha amplitude on eye closure. The homogeneity of the visual field provides strong evidence of the occipital alpha wave behaviour in a such a visual field. The findings are at variance with previous reports because it is shown, (i) that the alpha amplitude in a homogeneous visual field does not increase to the amplitude observed on eye closure, (ii) that alpha behaviour is dependent on wavelength and (iii) that attenuation of alpha activity is observed on eye closure under red green and blue homogenous visual stimulation

Consultation, negotiation and compromise: The relationship between SENCos, parents and pupils with SEN

One outcome of the UK Government's commitment to inclusive educational policies was an increase in the number of pupils with special educational needs (SEN) being taught in mainstream schools. From the perspective of SENCos, this article analyses whether parents and pupils are able and willing to influence the development of SEN provision and distribution of SEN resources, both of which aim to ensure that pupils have more meaningful experiences of mainstream education. The findings of the study cast light on the power and influence of parents when it comes to SEN provision and resources, the importance of consulting parents and the ways in which parents empower SENCos to make decisions on behalf of themselves and their children. The importance of negotiating and attempting to seek a compromise with pupils was another key issue identified in the article. Ultimately, however, the power to decide where resources go and what is done with them appears to reside with SENCos

Evaluation of electric and magnetic fields distribution and SAR induced in 3D models of water containers by radiofrequency radiation using FDTD and FEM simulation techniques

In this study, two software packages using different numerical techniques FEKO 6.3 with Finite-Element Method (FEM) and XFDTD 7 with Finite Difference Time Domain Method (FDTD) were used to assess exposure of 3D models of square, rectangular, and pyramidal shaped water containers to electromagnetic waves at 300, 900, and 2400 MHz frequencies. Using the FEM simulation technique, the peak electric field of 25, 4.5, and 2 V/m at 300 MHz and 15.75, 1.5, and 1.75 V/m at 900 MHz were observed in pyramidal, rectangular, and square shaped 3D container models, respectively. The FDTD simulation method confirmed a peak electric field of 12.782, 10.907, and 10.625 V/m at 2400 MHz in the pyramidal, square, and rectangular shaped 3D models, respectively. The study demonstrated an exceptionally high level of electric field in the water in the two identical pyramid shaped 3D models analyzed using the two different simulation techniques. Both FEM and FDTD simulation techniques indicated variations in the distribution of electric, magnetic fields, and specific absorption rate of water stored inside the 3D container models. The study successfully demonstrated that shape and dimensions of 3D models significantly influence the electric and magnetic fields inside packaged materials; thus, specific absorption rates in the stored water vary according to the shape and dimensions of the packaging materials.Comment: 22 pages, 30 figures and 2 table

“Seek the Light of Love”:Philip Lamantia’s “A Simple Answer to the Enemy”: Then and Now

During the 1940s the poet Philip Lamantia transitioned away from Surrealism to “naturalistic” poetry rooted in spirituality and the mysticism that exists in extraordinary experiences. Some of the subject matter became more sensuous and sociopolitical, and an underlying theme is contempt for government and the evil perpetrated in its name. One of his most overtly political poems, “A Simple Answer to the Enemy” remains applicable today. It makes a case for dissent by laying bare the corrupt agenda of a political order that dehumanizes the public and erodes liberties. Lamantia endorses a revolutionary mindset that rejects mechanistic thinking, aggression, and greed, and encourages us to embrace a philosophy of love and the spirit of compassion