Preface to the Special Issue on Immersive Environments: Challenges, Research and New Developments

Immersion could be defined as a subjective impression of participating in a comprehensive, realistic experience [1]. However, immersion should not be treated as a unique property, as it is achieved from a complex interaction of representational fidelity and learner interaction, holding a dependency on other aspects of the environment [2, 3]. The use of immersive environments which create a feeling of ?presence? naturally allows for more complex social interactions and designed experiences [4]. A particular use of these technologies is in educational settings, where they can enhance learning experiences, foster participation, collaboration, creativity and engagement; creating huge opportunities for integration and research. Effective immersive learning experiences can be created with multiple media using myriad techniques and employing a wealth of knowledge that spans many disciplines. This includes but is not limited to computer science, user experience and media design, the learning sciences, architecture, game development, artificial intelligence, biology, medicine, and thousands of disciplinary and occupational content areas wherein immersive learning and training may be relevant. The Immersive Learning Research Network (iLRN) is ?an international organization of developers, educators, and research professionals collaborating to develop the scientific, technical, and applied potential of immersive learning? [5]. The vision of the network is to develop a comprehensive research and outreach agenda that encompasses the breadth and scope of learning potentialities, affordances and challenges of immersive learning environments. The first international conference iLRN 2015 held in Prague, Czech Republic, attracted a number of high-quality contributions. As a follow-up, this special issue was organised as an open call to seek a wider set of contributions from the research community, including extended versions of iLRN 2015 best papers

Link between supercurrent diode and anomalous Josephson effect revealed by gate-controlled interferometry

In Josephson diodes the asymmetry between positive and negative current branch of the current-phase relation leads to a polarity-dependent critical current and Josephson inductance. The supercurrent nonreciprocity can be described as a consequence of the anomalous Josephson effect -- a $\varphi_0$-shift of the current-phase relation -- in multichannel ballistic junctions with strong spin-orbit interaction. In this work, we simultaneously investigate $\varphi_0$-shift and supercurrent diode efficiency on the same Josephson junction by means of a superconducting quantum interferometer. By electrostatic gating, we reveal a direct link between $\varphi_0$-shift and diode effect. Our findings show that the supercurrent diode effect mainly results from magnetochiral anisotropy induced by spin-orbit interaction in combination with a Zeeman field.Comment: 15 pages, 8 figure

Sign reversal of the AC and DC supercurrent diode effect and 0-π\pi-like transitions in ballistic Josephson junctions

The recent discovery of intrinsic supercurrent diode effect, and its prompt observation in a rich variety of systems, has shown that nonreciprocal supercurrents naturally emerge when both space- and time-inversion symmetries are broken. In Josephson junctions, nonreciprocal supercurrent can be conveniently described in terms of spin-split Andreev states. Here, we demonstrate a sign reversal of the supercurrent diode effect, in both its AC and DC manifestations. In particular, the AC diode effect -- i.e., the asymmetry of the Josephson inductance as a function of the supercurrent -- allows us to probe the current-phase relation near equilibrium. Using a minimal theoretical model, we can then link the sign reversal of the AC diode effect to the so-called 0-$\pi$-like transition, a predicted, but still elusive feature of multi-channel junctions. Our results demonstrate the potential of inductance measurements as sensitive probes of the fundamental properties of unconventional Josephson junctions.Comment: 13 pages, 6 figure

Endometrial stromal cells of women with recurrent miscarriage fail to discriminate between high- and low-quality human embryos

Background The aetiology of recurrent miscarriage (RM) remains largely unexplained. Women with RM have a shorter time to pregnancy interval than normally fertile women, which may be due to more frequent implantation of non-viable embryos. We hypothesized that human endometrial stromal cells (H-EnSCs) of women with RM discriminate less effectively between high-and low-quality human embryos and migrate more readily towards trophoblast spheroids than H-EnSCs of normally fertile women. Methodology/Principal Findings Monolayers of decidualized H-EnSCs were generated from endometrial biopsies of 6 women with RM and 6 fertile controls. Cell-free migration zones were created and the effect of the presence of a high-quality (day 5 blastocyst, n = 13), a low-quality (day 5 blastocyst with three pronuclei or underdeveloped embryo, n = 12) or AC-1M88 trophoblast cell line spheroid on H-ESC migratory activity was analyzed after 18 hours. In the absence of a spheroid or embryo, migration of H-EnSCs from fertile or RM women was similar. In the presence of a low-quality embryo in the zone, the migration of H-EnSCs of control women was inhibited compared to the basal migration in the absence of an embryo (P<0.05) and compared to the migration in the presence of high-quality embryo (p<0.01). Interestingly, the migratory response H-EnSCs of women with RM did not differ between high- and low-quality embryos. Furthermore, in the presence of a spheroid their migration was enhanced compared to the H-EnSCs of controls (p<0.001). Conclusions H-EnSCs of fertile women discriminate between high- and low-quality embryos whereas H-EnSCs of women with RM fail to do so. H-EnSCs of RM women have a higher migratory response to trophoblast spheroids. Future studies will focus on the mechanisms by which low-quality embryos inhibit the migration of H-EnSCs and how this is deregulated in women with RM

The role of ICT in supporting disruptive innovation: a multi-site qualitative study of nurse practitioners in emergency departments

<p>Abstract</p> <p>Background</p> <p>The disruptive potential of the Nurse Practitioner (NP) is evident in their ability to offer services traditionally provided by primary care practitioners and their provision of a health promotion model of care in response to changing health trends. No study has qualitatively investigated the role of the Emergency NP in Australia, nor the impact of Information and Communication Technology (ICT) on this disruptive workforce innovation. This study aimed to investigate ways in which Nurse Practitioners (NP) have incorporated the use of ICT as a mechanism to support their new clinical role within Emergency Departments.</p> <p>Methods</p> <p>A cross-sectional qualitative study was undertaken in the Emergency Departments (EDs) of two large Australian metropolitan public teaching hospitals. Semi-structured, in-depth interviews were conducted with five nurse practitioners, four senior physicians and five senior nurses. Transcribed interviews were analysed using a grounded theory approach to develop themes in relation to the conceptualisation of the ED nurse practitioner role and the influences of ICT upon the role. Member checking of results was achieved by revisiting the sites to clarify findings with participants and further explore emergent themes.</p> <p>Results</p> <p>The role of the ENP was distinguished from those of Emergency nurses and physicians by two elements: advanced practice and holistic care, respectively. ICT supported the advanced practice dimension of the NP role in two ways: availability and completeness of electronic patient information enhanced timeliness and quality of diagnostic and therapeutic decision-making, expediting patient access to appropriate care. The ubiquity of patient data sourced from a central database supported and improved quality of communication between health professionals within and across sites, with wider diffusion of the Electronic Medical Record holding the potential to further facilitate team-based, holistic care.</p> <p>Conclusions</p> <p>ICT is a facilitator through which the disruptive impact of NPs can be extended. However, integration of ICT into work practices without detracting from provider-patient interaction is crucial to ensure utilisation of such interventions and realisation of potential benefits.</p

Pan-Cancer Analysis of lncRNA Regulation Supports Their Targeting of Cancer Genes in Each Tumor Context

Long noncoding RNAs (lncRNAs) are commonly dys-regulated in tumors, but only a handful are known toplay pathophysiological roles in cancer. We inferredlncRNAs that dysregulate cancer pathways, onco-genes, and tumor suppressors (cancer genes) bymodeling their effects on the activity of transcriptionfactors, RNA-binding proteins, and microRNAs in5,185 TCGA tumors and 1,019 ENCODE assays.Our predictions included hundreds of candidateonco- and tumor-suppressor lncRNAs (cancerlncRNAs) whose somatic alterations account for thedysregulation of dozens of cancer genes and path-ways in each of 14 tumor contexts. To demonstrateproof of concept, we showed that perturbations tar-geting OIP5-AS1 (an inferred tumor suppressor) andTUG1 and WT1-AS (inferred onco-lncRNAs) dysre-gulated cancer genes and altered proliferation ofbreast and gynecologic cancer cells. Our analysis in-dicates that, although most lncRNAs are dysregu-lated in a tumor-specific manner, some, includingOIP5-AS1, TUG1, NEAT1, MEG3, and TSIX, synergis-tically dysregulate cancer pathways in multiple tumorcontexts

Pan-cancer Alterations of the MYC Oncogene and Its Proximal Network across the Cancer Genome Atlas

Although theMYConcogene has been implicated incancer, a systematic assessment of alterations ofMYC, related transcription factors, and co-regulatoryproteins, forming the proximal MYC network (PMN),across human cancers is lacking. Using computa-tional approaches, we define genomic and proteo-mic features associated with MYC and the PMNacross the 33 cancers of The Cancer Genome Atlas.Pan-cancer, 28% of all samples had at least one ofthe MYC paralogs amplified. In contrast, the MYCantagonists MGA and MNT were the most frequentlymutated or deleted members, proposing a roleas tumor suppressors.MYCalterations were mutu-ally exclusive withPIK3CA,PTEN,APC,orBRAFalterations, suggesting that MYC is a distinct onco-genic driver. Expression analysis revealed MYC-associated pathways in tumor subtypes, such asimmune response and growth factor signaling; chro-matin, translation, and DNA replication/repair wereconserved pan-cancer. This analysis reveals insightsinto MYC biology and is a reference for biomarkersand therapeutics for cancers with alterations ofMYC or the PMN

Genomic, Pathway Network, and Immunologic Features Distinguishing Squamous Carcinomas

This integrated, multiplatform PanCancer Atlas study co-mapped and identified distinguishing molecular features of squamous cell carcinomas (SCCs) from five sites associated with smokin

Spatial Organization and Molecular Correlation of Tumor-Infiltrating Lymphocytes Using Deep Learning on Pathology Images

Beyond sample curation and basic pathologic characterization, the digitized H&E-stained images of TCGA samples remain underutilized. To highlight this resource, we present mappings of tumorinfiltrating lymphocytes (TILs) based on H&E images from 13 TCGA tumor types. These TIL maps are derived through computational staining using a convolutional neural network trained to classify patches of images. Affinity propagation revealed local spatial structure in TIL patterns and correlation with overall survival. TIL map structural patterns were grouped using standard histopathological parameters. These patterns are enriched in particular T cell subpopulations derived from molecular measures. TIL densities and spatial structure were differentially enriched among tumor types, immune subtypes, and tumor molecular subtypes, implying that spatial infiltrate state could reflect particular tumor cell aberration states. Obtaining spatial lymphocytic patterns linked to the rich genomic characterization of TCGA samples demonstrates one use for the TCGA image archives with insights into the tumor-immune microenvironment

A tale of two 'opens': intersections between Free and Open Source Software and Open Scholarship

There is no clear-cut boundary between Free and Open Source Software and Open Scholarship, and the histories, practices, and fundamental principles between the two remain complex. In this study, we critically appraise the intersections and differences between the two movements. Based on our thematic comparison here, we conclude several key things. First, there is substantial scope for new communities of practice to form within scholarly communities that place sharing and collaboration/open participation at their focus. Second, Both the principles and practices of FOSS can be more deeply ingrained within scholarship, asserting a balance between pragmatism and social ideology. Third, at the present, Open Scholarship risks being subverted and compromised by commercial players. Fourth, the shift and acceleration towards a system of Open Scholarship will be greatly enhanced by a concurrent shift in recognising a broader range of practices and outputs beyond traditional peer review and research articles. In order to achieve this, we propose the formulation of a new type of institutional mandate. We believe that there is substantial need for research funders to invest in sustainable open scholarly infrastructure, and the communities that support them, to avoid the capture and enclosure of key research services that would prevent optimal researcher behaviours. Such a shift could ultimately lead to a healthier scientific culture, and a system where competition is replaced by collaboration, resources (including time and people) are shared and acknowledged more efficiently, and the research becomes inherently more rigorous, verified, and reproducible