Optical Properties of High-Frequency Radio Sources from the Australia Telescope 20 GHz (AT20G) Survey

Our current understanding of radio-loud AGN comes predominantly from studies at frequencies of 5 GHz and below. With the recent completion of the Australia Telescope 20 GHz (AT20G) survey, we can now gain insight into the high-frequency radio properties of AGN. This paper presents supplementary information on the AT20G sources in the form of optical counterparts and redshifts. Optical counterparts were identified using the SuperCOSMOS database and redshifts were found from either the 6dF Galaxy survey or the literature. We also report 144 new redshifts. For AT20G sources outside the Galactic plane, 78.5% have optical identifications and 30.9% have redshift information. The optical identification rate also increases with increasing flux density. Targets which had optical spectra available were examined to obtain a spectral classification. There appear to be two distinct AT20G populations; the high luminosity quasars that are generally associated with point-source optical counterparts and exhibit strong emission lines in the optical spectrum, and the lower luminosity radio galaxies that are generally associated with passive galaxies in both the optical images and spectroscopic properties. It is suggested that these different populations can be associated with different accretion modes (cold-mode or hot-mode). We find that the cold-mode sources have a steeper spectral index and produce more luminous radio lobes, but generally reside in smaller host galaxies than their hot-mode counterparts. This can be attributed to the fact that they are accreting material more efficiently. Lastly, we compare the AT20G survey with the S-cubed semi-empirical (S3-SEX) models and conclude that the S3-SEX models need refining to correctly model the compact cores of AGN. The AT20G survey provides the ideal sample to do this.Comment: Accepted for publication in MNRA

Multidetector CT improving surgical outcomes in breast cancer (MISO-BC) : a randomised controlled trial

Background: Early diagnosis of malignant axillary nodes in breast cancer guides the extent of axillary surgery: patients with known axillary malignancy receive a more extensive single operation at the same time as surgery to their breast. A multicentre randomised controlled trial assessed whether a Computed Tomography (CT) scan of the axilla could more accurately diagnose malignant axillary lymph node involvement in patients with newly diagnosed breast cancer when compared to usual care. Methods: Patients with newly diagnosed breast cancer (identified via screening and symptomatic pathways) at two NHS Trusts in the North East of England were recruited and randomised in equal numbers. Both groups received routine diagnostic and surgical care. In addition, one group received a CT scan of their axilla on the same side as the breast cancer. The primary endpoint was the need to undergo a second axillary surgical procedure. Findings: The trial recruited 297 patients of whom 291 contributed to findings. The proportion of patients undergoing a second operation was similar (CT vs UC: 19.4% vs. 19.7%; CT-UC: −0.3%, 95%CI: = −9.5% to 8.9%, χ2 [1]: p = 1.00). Patients in the two groups were similar before treatment, had similar types and grade of cancer, experienced similar patterns of post-operative complications and reported similar experiences of care. Interpretation: CT scan-guided care did not result in a change in the number of patients requiring a second operation; similar numbers of patients needed further axillary surgery in both groups. New diagnostic imaging technologies regularly enter NHS centres. It is important these are evaluated rigorously before becoming routine care

WHIRLY1 functions in the nucleus to regulate barley leaf development and associated metabolite profiles

The WHIRLY (WHY) DNA/RNA binding proteins fulfil multiple but poorly characterised functions in leaf development. Here, we show that WHY1 transcript levels were highest in the bases of 7-day old barley leaves. Immunogold labelling revealed that the WHY1 protein was more abundant in the nuclei than the proplastids of the leaf bases. To identify transcripts associated with leaf development we conducted hierarchical clustering of differentially abundant transcripts along the developmental gradient of wild-type leaves. Similarly, metabolite profiling was employed to identify metabolites exhibiting a developmental gradient. A comparative analysis of transcripts and metabolites in barley lines (W1–1 and W1–7) lacking WHY1, which show delayed greening compared with the wild type revealed that the transcript profile of leaf development was largely unchanged in W1–1 and W1–7 leaves. However, there were differences in levels of several transcripts encoding transcription factors associated with chloroplast development. These include a barley homologue of the Arabidopsis GATA transcription factor that regulates stomatal development, greening and chloroplast development, NAC1; two transcripts with similarity to Arabidopsis GLK1 and two transcripts encoding ARF transcriptions factors with functions in leaf morphogenesis and development. Chloroplast proteins were less abundant in the W1–1 and W1–7 leaves than the wild type. The levels of tricarboxylic acid cycle metabolites and GABA were significantly lower in WHY1 knockdown leaves than the wild type. This study provides evidence that WHY1 is localised in the nuclei of leaf bases, contributing the regulation of nuclear-encoded transcripts that regulate chloroplast development

Development of a new branded UK food composition database for an online dietary assessment tool

The current UK food composition tables are limited, containing ~3300 mostly generic food and drink items. To reflect the wide range of food products available to British consumers and to potentially improve accuracy of dietary assessment, a large UK specific electronic food composition database (FCDB) has been developed. A mapping exercise has been conducted that matched micronutrient data from generic food codes to “Back of Pack” data from branded food products using a semi-automated process. After cleaning and processing, version 1.0 of the new FCDB contains 40,274 generic and branded items with associated 120 macronutrient and micronutrient data and 5669 items with portion images. Over 50% of food and drink items were individually mapped to within 10% agreement with the generic food item for energy. Several quality checking procedures were applied after mapping including; identifying foods above and below the expected range for a particular nutrient within that food group and cross-checking the mapping of items such as concentrated and raw/dried products. The new electronic FCDB has substantially increased the size of the current, publically available, UK food tables. The FCDB has been incorporated into myfood24, a new fully automated online dietary assessment tool and, a smartphone application for weight loss

Anatomy ontologies and potential users: bridging the gap.

MOTIVATION: To evaluate how well current anatomical ontologies fit the way real-world users apply anatomy terms in their data annotations. METHODS: Annotations from three diverse multi-species public-domain datasets provided a set of use cases for matching anatomical terms in two major anatomical ontologies (the Foundational Model of Anatomy and Uberon), using two lexical-matching applications (Zooma and Ontology Mapper). RESULTS: Approximately 1500 terms were identified; Uberon/Zooma mappings provided 286 matches, compared to the control and Ontology Mapper returned 319 matches. For the Foundational Model of Anatomy, Zooma returned 312 matches, and Ontology Mapper returned 397. CONCLUSIONS: Our results indicate that for our datasets the anatomical entities or concepts are embedded in user-generated complex terms, and while lexical mapping works, anatomy ontologies do not provide the majority of terms users supply when annotating data. Provision of searchable cross-products for compositional terms is a key requirement for using ontologies.RIGHTS : This article is licensed under the BioMed Central licence at http://www.biomedcentral.com/about/license which is similar to the 'Creative Commons Attribution Licence'. In brief you may : copy, distribute, and display the work; make derivative works; or make commercial use of the work - under the following conditions: the original author must be given credit; for any reuse or distribution, it must be made clear to others what the license terms of this work are

maxdLoad2 and maxdBrowse: standards-compliant tools for microarray experimental annotation, data management and dissemination

BACKGROUND: maxdLoad2 is a relational database schema and Java(® )application for microarray experimental annotation and storage. It is compliant with all standards for microarray meta-data capture; including the specification of what data should be recorded, extensive use of standard ontologies and support for data exchange formats. The output from maxdLoad2 is of a form acceptable for submission to the ArrayExpress microarray repository at the European Bioinformatics Institute. maxdBrowse is a PHP web-application that makes contents of maxdLoad2 databases accessible via web-browser, the command-line and web-service environments. It thus acts as both a dissemination and data-mining tool. RESULTS: maxdLoad2 presents an easy-to-use interface to an underlying relational database and provides a full complement of facilities for browsing, searching and editing. There is a tree-based visualization of data connectivity and the ability to explore the links between any pair of data elements, irrespective of how many intermediate links lie between them. Its principle novel features are: • the flexibility of the meta-data that can be captured, • the tools provided for importing data from spreadsheets and other tabular representations, • the tools provided for the automatic creation of structured documents, • the ability to browse and access the data via web and web-services interfaces. Within maxdLoad2 it is very straightforward to customise the meta-data that is being captured or change the definitions of the meta-data. These meta-data definitions are stored within the database itself allowing client software to connect properly to a modified database without having to be specially configured. The meta-data definitions (configuration file) can also be centralized allowing changes made in response to revisions of standards or terminologies to be propagated to clients without user intervention. maxdBrowse is hosted on a web-server and presents multiple interfaces to the contents of maxd databases. maxdBrowse emulates many of the browse and search features available in the maxdLoad2 application via a web-browser. This allows users who are not familiar with maxdLoad2 to browse and export microarray data from the database for their own analysis. The same browse and search features are also available via command-line and SOAP server interfaces. This both enables scripting of data export for use embedded in data repositories and analysis environments, and allows access to the maxd databases via web-service architectures. CONCLUSION: maxdLoad2 and maxdBrowse are portable and compatible with all common operating systems and major database servers. They provide a powerful, flexible package for annotation of microarray experiments and a convenient dissemination environment. They are available for download and open sourced under the Artistic License

Telomerase Activation to Reverse Immunosenescence in Elderly Patients With Acute Coronary Syndrome: Protocol for a Randomized Pilot Trial

Background: Inflammation plays a key role in the pathophysiology of coronary heart disease (CHD) and its acute manifestation, acute coronary syndrome (ACS). Aging is associated with a decline of the immune system, a process known as immunosenescence. This is characterized by an increase in highly proinflammatory T cells that are involved in CHD progression, plaque destabilization, and myocardial ischemia–reperfusion injury. Telomere dysfunction has been implicated in immunosenescence of T lymphocytes. Telomerase is the enzyme responsible for maintaining telomeres during cell divisions. It has a protective effect on cells under oxidative stress and helps regulate flow-mediated dilation in microvasculature. Objective: The TACTIC (Telomerase ACTivator to reverse Immunosenescence in Acute Coronary Syndrome) trial will investigate whether a telomerase activator, TA-65MD, can reduce the proportion of senescent T cells in patients with ACS with confirmed CHD. It will also assess the effect of TA-65MD on decreasing telomere shortening, reducing oxidative stress, and improving endothelial function. Methods: The study was designed as a single-center, randomized, double-blind, parallel-group, placebo-controlled phase II trial. Recruitment started in January 2019. A total of 90 patients, aged 65 years or older, with treated ACS who have had CHD confirmed by angiography will be enrolled. They will be randomized to one of two groups: TA-65MD oral therapy (8 mg twice daily) or placebo taken for 12 months. The primary outcome is the effect on immunosenescence determined by a decrease in the proportion of CD8+ TEMRA (T effector memory cells re-expressing CD45RA [CD45 expressing exon A]) cells at 12 months. Secondary outcomes include leukocyte telomere length, endothelial function, cardiac function as measured by echocardiography and NT-proBNP (N-terminal fragment of the prohormone brain-type natriuretic peptide), systemic inflammation, oxidative stress, and telomerase activity. Results: The study received National Health Service (NHS) ethics approval on August 9, 2018; Medicines and Healthcare products Regulatory Agency approval on October 19, 2018; and NHS Health Research Authority approval on October 22, 2018. The trial began recruiting participants in January 2019 and completed recruitment in March 2020; the trial is due to report results in 2021. Conclusions: This pilot trial in older patients with CHD will explore outcomes not previously investigated outside in vitro or preclinical models. The robust design ensures that bias has been minimized. Should the results indicate reduced frequency of immunosenescent CD8+ T cells as well as improvements in telomere length and endothelial function, we will plan a larger, multicenter trial in patients to determine if TA-65MD is beneficial in the treatment of CHD in elderly patients

Prehabilitation in elective patients undergoing cardiac surgery: a randomised control trial (THE PrEPS TRIAL) – a study protocol

Introduction: Prehabilitation prior to surgery has been shown to reduce postoperative complications, reduce length of hospital stay and improve quality of life after cancer and limb reconstruction surgery. However, there are minimal data on the impact of prehabilitation in patients undergoing cardiac surgery, despite the fact these patients are generally older and have more comorbidities and frailty. This trial will assess the feasibility and impact of a prehabilitation intervention consisting of exercise and inspiratory muscle training on preoperative functional exercise capacity in adult patients awaiting elective cardiac surgery, and determine any impact on clinical outcomes after surgery. Methods and analysis: PrEPS is a randomised controlled single-centre trial recruiting 180 participants undergoing elective cardiac surgery. Participants will be randomised in a 1:1 ratio to standard presurgical care or standard care plus a prehabilitation intervention. The primary outcome will be change in functional exercise capacity measured as change in the 6 min walk test distance from baseline. Secondary outcomes will evaluate the impact of prehabilitation on preoperative and postoperative outcomes including; respiratory function, health-related quality of life, anxiety and depression, frailty, and postoperative complications and resource use. This trial will evaluate if a prehabilitation intervention can improve preoperative physical function, inspiratory muscle function, frailty and quality of life prior to surgery in elective patients awaiting cardiac surgery, and impact postoperative outcomes. Ethics and dissemination: A favourable opinion was given by the Sheffield Research Ethics Committee in 2019. Trial findings will be disseminated to patients, clinicians, commissioning groups and through peer-reviewed publication

Preventing cardiotoxicity in patients with breast cancer and lymphoma: protocol for a multicentre randomised controlled trial (PROACT)

Introduction: Anthracyclines are included in chemotherapy regimens to treat several different types of cancer and are extremely effective. However, it is recognised that a significant side effect is cardiotoxicity; anthracyclines can cause irreversible damage to cardiac cells and ultimately impaired cardiac function and heart failure, which may only be evident years after exposure. The PROACT trial will establish the effectiveness of the ACE inhibitor enalapril maleate (enalapril) in preventing cardiotoxicity in patients with breast cancer and non-Hodgkin’s lymphoma (NHL) receiving anthracycline-based chemotherapy. Methods and analysis: PROACT is a prospective, randomised, open-label, blinded end-point, superiority trial which will recruit adult patients being treated for breast cancer and NHL at NHS hospitals throughout England. The trial aims to recruit 106 participants, who will be randomised to standard care (high-dose anthracycline-based chemotherapy) plus enalapril (intervention) or standard care alone (control). Patients randomised to the intervention arm will receive enalapril (starting at 2.5 mg two times per day and titrating up to a maximum dose of 10 mg two times per day), commencing treatment at least 2 days prior to starting chemotherapy and finishing 3 weeks after their last anthracycline dose. The primary outcome is the presence or absence of cardiac troponin T release at any time during anthracycline treatment, and 1 month after the last dose of anthracycline. Secondary outcomes will focus on cardiac function measured using echocardiogram assessment, adherence to enalapril and side effects. Ethics and dissemination: A favourable opinion was given following research ethics committee review by West Midlands—Edgbaston REC, Ref: 17/WM/0248. Trial findings will be disseminated through engagement with patients, the oncology and cardiology communities, NHS management and commissioning groups and through peer-reviewed publication

Quality metrics for the evaluation of Rapid Response Systems: Proceedings from the third international consensus conference on Rapid Response Systems.

BACKGROUND: Clinically significant deterioration of patients admitted to general wards is a recognized complication of hospital care. Rapid Response Systems (RRS) aim to reduce the number of avoidable adverse events. The authors aimed to develop a core quality metric for the evaluation of RRS. METHODS: We conducted an international consensus process. Participants included patients, carers, clinicians, research scientists, and members of the International Society for Rapid Response Systems with representatives from Europe, Australia, Africa, Asia and the US. Scoping reviews of the literature identified potential metrics. We used a modified Delphi methodology to arrive at a list of candidate indicators that were reviewed for feasibility and applicability across a broad range of healthcare systems including low and middle-income countries. The writing group refined recommendations and further characterized measurement tools. RESULTS: Consensus emerged that core outcomes for reporting for quality improvement should include ten metrics related to structure, process and outcome for RRS with outcomes following the domains of the quadruple aim. The conference recommended that hospitals should collect data on cardiac arrests and their potential predictability, timeliness of escalation, critical care interventions and presence of written treatment goals for patients remaining on general wards. Unit level reporting should include the presence of patient activated rapid response and metrics of organizational culture. We suggest two exploratory cost metrics to underpin urgently needed research in this area. CONCLUSION: A consensus process was used to develop ten metrics for better understanding the course and care of deteriorating ward patients. Others are proposed for further development