Comprehensive Determination of the Hinode/EIS Roll Angle

We present a new coalignment method for the EUV Imaging Spectrometer (EIS) on board the Hinode spacecraft. In addition to the pointing offset and spacecraft jitter, this method determines the roll angle of the instrument, which has never been systematically measured, and is therefore usually not corrected. The optimal pointing for EIS is computed by maximizing the cross-correlations of the Fe XII 195.119 \r{A} line with images from the 193 \r{A} band of the Atmospheric Imaging Assembly (AIA) on board the Solar Dynamics Observatory (SDO). By coaligning 3336 rasters with high signal-to-noise ratio, we estimate the rotation angle between EIS and AIA and explore the distribution of its values. We report an average value of (-0.387 $\pm$ 0.007)\deg. We also provide a software implementation of this method that can be used to coalign any EIS raster.Comment: Accepted for publication in Solar Physics, 11 pages, 7 figure

Uncertainty in Lung Cancer Stage for Outcome Estimation via Set-Valued Classification

Difficulty in identifying cancer stage in health care claims data has limited oncology quality of care and health outcomes research. We fit prediction algorithms for classifying lung cancer stage into three classes (stages I/II, stage III, and stage IV) using claims data, and then demonstrate a method for incorporating the classification uncertainty in outcomes estimation. Leveraging set-valued classification and split conformal inference, we show how a fixed algorithm developed in one cohort of data may be deployed in another, while rigorously accounting for uncertainty from the initial classification step. We demonstrate this process using SEER cancer registry data linked with Medicare claims data.Comment: Code available at: https://github.com/sl-bergquist/cancer_classificatio

CHIANTI - An atomic database for emission lines. XI. EUV emission lines of Fe VII, Fe VIII and Fe IX observed by Hinode/EIS

A detailed study of emission lines from Fe VII, Fe VIII and Fe IX observed by the EUV Imaging Spectrometer on board the Hinode satellite is presented. Spectra in the ranges 170-212 A and 246-292 A show strongly enhanced lines from the upper solar transition region (temperatures 5.4 <= log T <= 5.9) allowing a number of new line identifications to be made. Comparisons of Fe VII lines with predictions from a new atomic model reveal new plasma diagnostics, however there are a number of disagreements between theory and observation for emission line ratios insensitive to density and temperature, suggesting improved atomic data are required. Line ratios for Fe VIII also show discrepancies with theory, with the strong 185.21 and 186.60 lines under-estimated by 60-80 % compared to lines between 192 and 198 A. A newly-identified multiplet between 253.9 and 255.8 A offers excellent temperature diagnostic opportunities relative to the lines between 185-198 A, however the atomic model under-estimates the strength of these lines by factors 3-6. Two new line identifications are made for Fe IX at wavelengths 176.959 A and 177.594 A, while seven other lines between 186 and 200 A are suggested to be due to Fe IX but for which transition identifications can not be made. The new atomic data for Fe VII and Fe IX are demonstrated to significantly modify models for the response function of the TRACE 195 A imaging channel, affecting temperature determinations from this channel. The data will also affect the response functions for other solar EUV imaging instruments such as SOHO/EIT, STEREO/EUVI and the upcoming AIA instrument on the Solar Dynamics Observatory.Comment: 51 pages, submitted to Ap

Family integration in pulmonary rehabilitation programmes: A pilot study

Chronic Obstructive Pulmonary Disease (COPD) places a high burden on patients and their family. The World Health Organization has recommended family integration in rehabilitation interventions. However, Pulmonary Rehabilitation (PR) programmes for COPD typically focus on patients, neglecting the family. This study aimed to explore the needs and expectations of patients with COPD and respective family carers and assess their perspectives about their participation in a PR programme. Nine patients with COPD (70±8yrs; FEV169±25%pred) and their family carers (64±11yrs) were recruited in primary care. Individual interviews were conducted to explore their needs and expectations about PR programmes. Focus groups were conducted after their participation in a PR programme. Data were audio-recorded, transcribed and submitted to content analysis. Patients and carers identified the need for more information about COPD (nP=7; nC=5) and emotional support (nP=2; nC=3), and expected PR programmes to improve their skills to manage the disease (nP=9; nC=2). A PR programme with psychoeducation and exercise training was implemented, considering these findings. Participants reported that the programme helped them to cope better with the disease and patients found their carers to be less worried and living happier (n=3). The majority of carers reported self-benefits (n=6) and stressed the importance of on-going support to help themselves and their care receivers (n=2). PR programmes inclusive of carers have the potential to enhance the skills of the whole family to manage COPD and, therefore, to promote a healthy adjustment to the disease. Future research should explore the impact of PR programmes within the family unit.publishe

Stabilization arising from PGEM : a review and further developments

The aim of this paper is twofold. First, we review the recent Petrov-Galerkin enriched method (PGEM) to stabilize numerical solutions of BVP's in primal and mixed forms. Then, we extend such enrichment technique to a mixed singularly perturbed problem, namely, the generalized Stokes problem, and focus on a stabilized finite element method arising in a natural way after performing static condensation. The resulting stabilized method is shown to lead to optimal convergences, and afterward, it is numerically validated

Tbx5 is Required for Avian and Mammalian Epicardial Formation and Coronary Vasculogenesis.

Rationale: Holt-Oram syndrome (HOS) is an autosomal dominant heart-hand syndrome caused by mutations in the TBX5 gene. Overexpression of Tbx5 in the chick proepicardial organ (PEO) impaired coronary blood vessel formation. However, the potential activity of Tbx5 in the epicardium itself, and Tbx5\u27s role in mammalian coronary vasculogenesis, remains largely unknown. Objective: To evaluate the consequences of altered Tbx5 gene dosage during PEO and epicardial development in the embryonic chick and mouse. Methods and Results: Retroviral-mediated knockdown or upregulation of Tbx5 expression in the embryonic chick PEO as well as proepicardial-specific deletion of Tbx5 in the embryonic mouse (Tbx5(epi-/-)) impaired normal PEO cell development, inhibited epicardial and coronary blood vessel formation and altered developmental gene expression. The generation of epicardial-derived cells (EPDCs) and their migration into the myocardium was impaired between embryonic day (E) 13.5-15.5 in mutant hearts due to delayed epicardial attachment to the myocardium and subepicardial accumulation of EPDCs. This caused defective coronary vasculogenesis associated with impaired vascular smooth muscle cell recruitment, and reduced invasion of cardiac fibroblasts and endothelial cells into myocardium. In contrast to wildtype hearts that exhibited an elaborate ventricular vascular network, Tbx5(epi-/-) hearts displayed a marked decrease in vascular density that was associated with myocardial hypoxia as exemplified by HIF1α upregulation and increased binding of Hypoxyprobe-1. Tbx5(epi-/-) mice with such myocardial hypoxia exhibited reduced exercise capacity compared to wildtype mice. Conclusions: Our findings support a conserved Tbx5 dose-dependent requirement for both proepicardial and epicardial progenitor cell development in chick and mouse coronary vascular formation

TeV-scale seesaw from a multi-Higgs model

We suggest new simple model of generating tiny neutrino masses through a TeV-scale seesaw mechanism without requiring tiny Yukawa couplings. This model is a simple extension of the standard model by introducing extra one Higgs singlet, and one Higgs doublet with a tiny vacuum expectation value. Experimental constraints, electroweak precision data and no large flavor changing neutral currents, are satisfied since the extra doublet only has a Yukawa interaction with lepton doublets and right-handed neutrinos, and their masses are heavy of order a TeV-scale. Since active light neutrinos are Majorana particles, this model predicts a neutrinoless double beta decay.Comment: 21 pages, 8 figure

VIPERdb: a relational database for structural virology

VIPERdb () is a database for icosahedral virus capsid structures. Our aim is to provide a comprehensive resource specific to the needs of the structural virology community, with an emphasis on the description and comparison of derived data from structural and energetic analyses of capsids. A relational database implementation based on a schema for macromolecular structure makes the data highly accessible to the user, allowing detailed queries at the atomic level. Together with curation practices that maintain data uniformity, this will facilitate structural bioinformatics studies of virus capsids. User friendly search, visualization and educational tools on the website allow both structural and derived data to be examined easily and extensively. Links to relevant literature, sequence and taxonomy databases are provided for each entry

Transient genome-wide interactions of the master transcription factor NLP7 initiate a rapid nitrogen-response cascade

Dynamic reprogramming of gene regulatory networks (GRNs) enables organisms to rapidly respond to environmental perturbation. However, the underlying transient interactions between transcription factors (TFs) and genome-wide targets typically elude biochemical detection. Here, we capture both stable and transient TF-target interactions genome-wide within minutes after controlled TF nuclear import using time-series chromatin immunoprecipitation (ChIP-seq) and/or DNA adenine methyltransferase identification (DamID-seq). The transient TF-target interactions captured uncover the early mode-of-action of NIN-LIKE PROTEIN 7 (NLP7), a master regulator of the nitrogen signaling pathway in plants. These transient NLP7 targets captured in root cells using temporal TF perturbation account for 50% of NLP7-regulated genes not detectably bound by NLP7 in planta. Rapid and transient NLP7 binding activates early nitrogen response TFs, which we validate to amplify the NLP7-initiated transcriptional cascade. Our approaches to capture transient TF-target interactions genome-wide can be applied to validate dynamic GRN models for any pathway or organism of interest. Conventional methods cannot reveal transient transcription factors (TFs) and targets interactions. Here, Alvarez et al. capture both stable and transient TF-target interactions by time-series ChIP-seq and/or DamID-seq in a cell-based TF perturbation system and show NLP7 as a master TF to initiate a rapid nitrogen-response cascade