The FHD/ε\boldsymbol{\varepsilon}ppsilon Epoch of Reionization Power Spectrum Pipeline

Epoch of Reionization data analysis requires unprecedented levels of accuracy in radio interferometer pipelines. We have developed an imaging power spectrum analysis to meet these requirements and generate robust 21 cm EoR measurements. In this work, we build a signal path framework to mathematically describe each step in the analysis, from data reduction in the FHD package to power spectrum generation in the $\varepsilon$ppsilon package. In particular, we focus on the distinguishing characteristics of FHD/$\varepsilon$ppsilon: highly accurate spectral calibration, extensive data verification products, and end-to-end error propagation. We present our key data analysis products in detail to facilitate understanding of the prominent systematics in image-based power spectrum analyses. As a verification to our analysis, we also highlight a full-pipeline analysis simulation to demonstrate signal preservation and lack of signal loss. This careful treatment ensures that the FHD/$\varepsilon$ppsilon power spectrum pipeline can reduce radio interferometric data to produce credible 21 cm EoR measurements.Comment: 21 pages, 10 figures, accepted by PAS

The effect of personality on collaborative task performance and interaction

Collocated, multi-user technologies, which support group-work are becoming increasingly popular. Examples include MERL's Diamondtouch and Microsoft's Surface, both of which have evolved from research prototypes to commercial products. Many applications have been developed for such technologies which support the work and entertainment needs of small groups of people. None of these applications however, have been studied in terms of the interactions and performances of their users with regards to their personality. In this paper, we address this research gap by conducting a series of user studies involving dyads working on a number of multi-user applications on the DiamondTouch tabletop device

Probing the Catalytic Roles of Arg548 and Gln552 in the Carboxyl Transferase Domain of the \u3cem\u3eRhizobium etli\u3c/em\u3e Pyruvate Carboxylase by Site-directed Mutagenesis

The roles of Arg548 and Gln552 residues in the active site of the carboxyl transferase domain of Rhizobium etli pyruvate carboxylase were investigated using site-directed mutagenesis. Mutation of Arg548 to alanine or glutamine resulted in the destabilization of the quaternary structure of the enzyme, suggesting that this residue has a structural role. Mutations R548K, Q552N, and Q552A resulted in a loss of the ability to catalyze pyruvate carboxylation, biotin-dependent decarboxylation of oxaloacetate, and the exchange of protons between pyruvate and water. These mutants retained the ability to catalyze reactions that occur at the active site of the biotin carboxylase domain, i.e., bicarbonate-dependent ATP cleavage and ADP phosphorylation by carbamoyl phosphate. The effects of oxamate on the catalysis in the biotin carboxylase domain by the R548K and Q552N mutants were similar to those on the catalysis of reactions by the wild-type enzyme. However, the presence of oxamate had no effect on the reactions catalyzed by the Q552A mutant. We propose that Arg548 and Gln552 facilitate the binding of pyruvate and the subsequent transfer of protons between pyruvate and biotin in the partial reaction catalyzed in the active site of the carboxyl transferase domain of Rhizobium etli pyruvate carboxylase

Alternative splicing and protein diversity: plants versus animals

Plants, unlike animals, exhibit a very high degree of plasticity in their growth and development and employ diverse strategies to cope with the variations during diurnal cycles and stressful conditions. Plants and animals, despite their remarkable morphological and physiological differences, share many basic cellular processes and regulatory mechanisms. Alternative splicing (AS) is one such gene regulatory mechanism that modulates gene expression in multiple ways. It is now well established that AS is prevalent in all multicellular eukaryotes including plants and humans. Emerging evidence indicates that in plants, as in animals, transcription and splicing are coupled. Here, we reviewed recent evidence in support of co-transcriptional splicing in plants and highlighted similarities and differences between plants and humans. An unsettled question in the field of AS is the extent to which splice isoforms contribute to protein diversity. To take a critical look at this question, we presented a comprehensive summary of the current status of research in this area in both plants and humans, discussed limitations with the currently used approaches and suggested improvements to current methods and alternative approaches. We end with a discussion on the potential role of epigenetic modifications and chromatin state in splicing memory in plants primed with stresses

Does co-transcriptional regulation of alternative splicing mediate plant stress responses?

Plants display exquisite control over gene expression to elicit appropriate responses under normal and stress conditions. Alternative splicing (AS) of pre-mRNAs, a process that generates two or more transcripts from multi-exon genes, adds another layer of regulation to fine-tune condition-specific gene expression in animals and plants. However, exactly how plants control splice isoform ratios and the timing of this regulation in response to environmental signals remains elusive. In mammals, recent evidence indicate that epigenetic and epitranscriptome changes, such as DNA methylation, chromatin modifications and RNA methylation, regulate RNA polymerase II processivity, co-transcriptional splicing, and stability and translation efficiency of splice isoforms. In plants, the role of epigenetic modifications in regulating transcription rate and mRNA abundance under stress is beginning to emerge. However, the mechanisms by which epigenetic and epitranscriptomic modifications regulate AS and translation efficiency require further research. Dynamic changes in the chromatin landscape in response to stress may provide a scaffold around which gene expression, AS and translation are orchestrated. Finally, we discuss CRISPR/Cas-based strategies for engineering chromatin architecture to manipulate AS patterns (or splice isoforms levels) to obtain insight into the epigenetic regulation of AS

Astrochemical Modeling of Propargyl Radical Chemistry in TMC-1

Recent detections of aromatic species in dark molecular clouds suggest formation pathways may be efficient at very low temperatures and pressures, yet current astrochemical models are unable to account for their derived abundances, which can often deviate from model predictions by several orders of magnitude. The propargyl radical, a highly abundant species in the dark molecular cloud TMC- 1, is an important aromatic precursor in combustion flames and possibly interstellar environments. We performed astrochemical modeling of TMC-1 using the three-phase gas-grain code NAUTILUS and an updated chemical network, focused on refining the chemistry of the propargyl radical and related species. The abundance of the propargyl radical has been increased by half an order of magnitude compared to the previous GOTHAM network. This brings it closer in line with observations, but it remains underestimated by two orders of magnitude compared to its observed value. Predicted abundances for the chemically related C4H3N isomers within an order of magnitude of observed values corroborate the high efficiency of CN addition to closed-shell hydrocarbons under dark molecular cloud conditions. The results of our modeling provide insight into the chemical processes of the propargyl radical in dark molecular clouds and highlight the importance of resonance-stabilized radicals in PAH formation.Comment: 31 pages and 17 figures (including the appendix), accepted for publication in The Astrophysical Journa

Theresa May’s disjunctive premiership: Choice and constraint in political time

Theresa May’s premiership is widely acknowledged to have been a failure, but political commentators and the scholarly literature have, thus far, tended to focus on May’s misuse of her agency. This article argues that May’s premiership presents a particularly powerful example of the need to disentangle structure and agency when assessing prime ministerial performance. Drawing upon the work of Stephen Skowronek, it sets out a framework of evaluating prime ministerial agency in ‘political time’. This is then used to show how the conditions and circumstances in which May governed limited the feasibility, increased the costs, and compromised the effectiveness of her actions in office. We argue that this confirms that May was a victim of circumstances as much as a victim of her own agency

"If We Want to Get Men in, Then We Need to Ask Men What They Want": Pathways to Effective Health Programing for Men.

In Ireland, men’s health is becoming a priority. In line with global trends, indicators of poor mental health (including rates of depression and suicide) are increasing alongside rates of unemployment and social isolation. Despite the growing awareness of men’s health as a national priority, and development of the first National Men’s Health Policy in the world, there is still a concern about men’s non-engagement with health services. Health and community services often struggle to appropriately accommodate men, and men commonly avoid health spaces. A growing body of literature suggests that a persistent lack of support or resources for service providers contributes to their inability to identify and meet men’s unique health needs. This study aims to provide further insight into the ways in which this gap between men and health services can be closed. Semi-structured, qualitative interviews were conducted with nine project partners (n=9) of a successful men’s health program in Dublin. Interviews captured reflections on what processes or strategies contribute to effective men’s health programs. Findings suggest that gender-specific strategies – especially related to community- engagement and capacity building - are necessary in creating health programs that both promote men’s health and enable men to safely and comfortably participate. Moreover, including men in all aspects of the planning stages helps to ensure that programs are accessible and acceptable for men. It is envisaged that these findings will be operationalized into a user-driven resource to illustrate evidence-informed strategies and guiding principles that could be used by practitioners hoping to engage with me

Comparison Between Wolfe, Boyd, BI-RADS and Tabár Based Mammographic Risk Assessment

Abstract. Mammographic risk assessment provides an indication of the likelihood of women developing breast cancer. Anumber ofmammographic image based classification methods have been developed, such as Wolfe, Boyd, BI-RADS and Tabár based assessment. We provide a comparative study of these four approaches. Results on the full MIAS database are presented, which indicate strong correlation (Spearman’s> 0.9) between Wolfe, Boyd andBI-RADSbased classification, whilst the correlation with Tabár based classification is less straight forward (Spearman’s < 0.5, but low correlations mainly caused by one of the classes).