Proteomics as the final step in the functional metagenomics study of antimicrobial resistance

peer-reviewedThe majority of clinically applied antimicrobial agents are derived from natural products generated by soil microorganisms and therefore resistance is likely to be ubiquitous in such environments. This is supported by the fact that numerous clinically important resistance mechanisms are encoded within the genomes of such bacteria. Advances in genomic sequencing have enabled the in silico identification of putative resistance genes present in these microorganisms. However, it is not sufficient to rely on the identification of putative resistance genes, we must also determine if the resultant proteins confer a resistant phenotype. This will require an analysis pipeline that extends from the extraction of environmental DNA, to the identification and analysis of potential resistance genes and their resultant proteins and phenotypes. This review focuses on the application of functional metagenomics and proteomics to study antimicrobial resistance in diverse environments.The Alimentary Pharmabiotic Centre is a research centre funded by Science Foundation Ireland (SFI). This publication has emanated from research supported in part by a research grant from Science Foundation Ireland (SFI) under Grant Number SFI/12/RC/2273 and by FP7 funded CFMATTERS (Cystic Fibrosis Microbiome-determined Antibiotic Therapy Trial in Exacerba- tions: Results Stratified, Grant Agreement no. 603038)

A Spreading Danger: Time for a New Policy towards Chechnya. CEPS Policy Briefs No. 68, 1 April 2005

The ongoing conflict in and around Chechnya is helping to feed the wider international jihadi movement, and is endangering the West as well as Russia. The next “soft target” of North Caucasian terrorism could be a Western one. Mutual recriminations over the conflict have badly damaged relations between Russia and the West. While most of the blame for this lies with Russian policies, the Western approach to the issue has often been unhelpful and irresponsible. Denunciations of Russian behaviour have not been matched by a real understanding of the Chechen conflict or a real commitment to help. In their own interest, Western countries need urgently to address the crisis in the North Caucasus. This requires them to recognize the seriousness of the threat, to open a real dialogue on cooperation with Russia rather than simply making criticisms, and to make a serious economic contribution to the region

Converting dark matter to dark radiation does not solve cosmological tensions

Tensions between cosmological parameters (in particular the local expansion rate $H_0$ and the amplitude of matter clustering $S_8$) inferred from low-redshift data and data from the cosmic microwave background (CMB) and large-scale structure (LSS) experiments have inspired many extensions to the standard cosmological model, $\Lambda$CDM. Models which simultaneously lessen both tensions are of particular interest. We consider one scenario with the potential for such a resolution, in which some fraction of the dark matter has converted into dark radiation since the release of the CMB. Such a scenario encompasses and generalizes the more standard "decaying dark matter" model, allowing additional flexibility in the rate and time at which the dark matter converts into dark radiation. In this paper, we constrain this scenario with a focus on exploring whether it can solve (or reduce) these tensions. We find that such a model is effectively ruled out by low-$\ell$ CMB data, in particular by the reduced peak-smearing due to CMB lensing and the excess Integrated Sachs--Wolfe (ISW) signal caused by the additional dark energy density required to preserve flatness after dark matter conversion into dark radiation. Thus, such a model does not have the power to reduce these tensions without further modifications. This conclusion extends and generalizes related conclusions derived for the standard decaying dark matter model.Comment: 19 pages, 8 figures. Our modified Boltzmann code is available at https://github.com/fmccarthy/class_DMDR Re-uploaded with some more details on the failure of the DMDR model (v2); Reuploaded with the version published by PRD (v3

Component-separated, CIB-cleaned thermal Sunyaev--Zel'dovich maps from Planck\textit{Planck} PR4 data with a flexible public needlet ILC pipeline

We use the full-mission $\textit{Planck}$ PR4 data to construct maps of the thermal Sunyaev$--$Zel'dovich effect (Compton-$y$ parameter) in our Universe. To do so, we implement a custom needlet internal linear combination (NILC) pipeline in a Python package, $\texttt{pyilc}$, which we make publicly available. We publicly release our Compton-$y$ maps, which we construct using various constrained ILC ("deprojection") options in order to minimize contamination from the cosmic infrared background (CIB) in the reconstructed signal. In particular, we use a moment-based deprojection which minimizes sensitivity to the assumed frequency dependence of the CIB. Our code $\texttt{pyilc}$ performs needlet or harmonic ILC on mm-wave sky maps in a flexible manner, with options to deproject various components on all or some scales. We validate our maps and compare them to the official $\textit{Planck}$ 2015 $y$-map, finding that we obtain consistent results on large scales and 10-20$\%$ lower noise on small scales. We expect that these maps will be useful for many auto- and cross-correlation analyses; in a companion paper, we use them to measure the tSZ -- CMB lensing cross-correlation. We anticipate that $\texttt{pyilc}$ will be useful both for data analysis and for pipeline validation on simulations to understand the propagation of foreground components through a full NILC pipeline.Comment: 28 pages, 15 figures. Public maps and other data products are available at https://users.flatironinstitute.org/~fmccarthy/ymaps_PR4_McCH23/ ; public code is available at https://github.com/jcolinhill/pyilc . V2: some additional notes about the effective CIB SED parameters and the halo model, also removed discussion about apodization of our maps and Planck map

Delivering research impact that is aligned to social priorities requires public participation throughout the process

The notion that increased public participation is a key component of research impact has developed and gained traction. Indeed, recent analysis has shown that public and user participation does play a key role in delivering impact. However, how does this participation work in practice? Steven Hill, Elizabeth Morrow and Fiona Ross note that the majority of public engagement focuses on the dissemination of findings. Consultation and collaboration remain uncommon, with public participation rarely extending to the framing and development of research questions. Such narrow use of participation risks missing opportunities to align impact more closely with social priorities

A qualitative exploration of patient and healthcare-professional perspectives on barriers and facilitators to foot self-care behaviours in diabetes

INTRODUCTION: Diabetic foot ulcers contribute significantly to morbidity and mortality associated with diabetes, but are preventable with good foot self-care. This study sought to explore the perspectives of patients and healthcare professionals (HCPs) on barriers and/or facilitators to foot self-care behaviors in diabetes and areas of consensus and/or tension between patient and HCP perspectives. RESEARCH DESIGN AND METHODS: This was a sequential, qualitative study that used a hermeneutic phenomenological approach. Phase I involved nine in-depth, semi-structured patient interviews. Phase II involved seven in-depth semi-structured interviews with HCPs (podiatrists, diabetes nurses, foot health practitioners (FHPs) and general practitioners (GPs)). In phase III, findings from phases I and II were brought back to two patient interview groups (five patients in total) to try and identify any areas of consensus and tension between HCP and patient perspectives. RESULTS: Patient and HCP perspectives had several areas of alignment: concerns over consequences of diabetes complications; the importance of patient education and frustrations around aspects of health service delivery. There were also some notable tensions identified: mixed messaging from HCPs around whose responsibility patient foot health is; and who patients should initially consult following the development of a foot problem. Overall, patients expressed that motivation to undertake good foot self-care behaviors was generated from their lived experiences, and was enhanced when this aligned with the information they received from HCPs. HCPs appeared to attribute lack of patient motivation to lack of knowledge, which was not raised by patients. CONCLUSIONS: This study has identified points of misalignment between the views of patients and practitioners that may help to explain why adherence to foot self-care among patients with diabetes is low. Our results suggest that better outcomes may stem from HCPs focusing on supporting autonomous motivation for self-care and enhancing the rationale through referencing patients’ own experience rather than focussing on increasing patient knowledge. Renewed focus on consistency of messaging by HCPs around the roles and responsibilities relating to foot health in diabetes, and the benefit of foot-specific training being provided to non-foot specialist HCPs may also help to improve uptake and adherence to foot self-care behaviors in diabetes

A whole of institution approach to supporting learning, teaching and assessment

This paper overviews a whole of institution approach recently implemented at James Cook University (JCU) to supporting staff and students in terms of identified learning, teaching and assessment priorities. It reports on collaborations established between academic and professional staff, across targeted Bachelor courses, with a view to enhancing course coherence, blended learning and assessment practices, and within-curriculum development of English language and numeracy skills, as well as student and professional identity. These collaborations see academic staff work with academic developers, educational designers, learning advisors and careers staff to design curriculum and assessment strategies that are responsive to the needs of highly diverse student cohorts. Assessment redesign is informed by student achievement, retention, progression and satisfaction data, as well as curriculum mapping data pertaining to coverage of course learning outcomes and range of assessment types across year levels and whole of course. The whole of institution approach has been recently detailed in two key documents: the JCU Learning and Teaching Blueprint 2014-2016 and the Access, Participation and Success Plan, 2015-2017. Within these strategic documents and key policies, such as the Learning, Teaching and Assessment Policy and the English Language and Numeracy Policy, the promotion of diagnostic and formative assessment, especially in the first year, and expansion of more authentic and technology-enabled assessment practices are identified as key strategies to support student engagement, learning and success. This paper will draw upon cases of assessment redesign, external evaluator reports and self-reflections to review some of the tools, processes and outcomes of the 2014 and 2015 collaborations

The Ballpark podcast Extra Innings: Dr Fiona Hill on Putin, the War in Ukraine, and European security

On 15 June 2022, The Phelan US Centre’s Chris Gilson and Mohid Malik spoke to Dr Fiona Hill of the Brookings Institution in Washington D.C. about Russia’s invasion of Ukraine in February 2022 and the ramifications for the future of NATO and the European security framework. They also discuss future possibilities of engaging with Russia and the role that non-European states may play in this process

Coming to grips with student mobility and policy implications: a case study from regional Queensland

In 2008, in what could be considered a significant shift in Australian education policy, Rudd and Gillard stated that,"'business as usual' in Australian schools will not, by itself, substantially lift educational outcomes, particularly in low SES communities" (2008, p.26). They highlighted the need for schools to not only "commit to excellence in teaching and learning within the classroom, but . . . be prepared to address the range of external factors that impact on students' ability to engage in learning"(ibid). This paper summarises some of the issues exposed through a collaborative research project with schools related to one set of external factors in lower socio-economic communities - student mobility or movement of students between schools. Taking a policy research perspective, informed by Dale(1989), Rist (2005) and Ball (1994), the paper examines the relationship between 'wider policies of the state' in particular marketisation and considers how mobility plays out in school sites, specifically school sites marked by poverty. The paper firstly presents an overview of the issues related to the measurement of mobility outlining the various ways stability within school populations has been measured. The paper argues for a measurement tool that reflects both the transactional pressure student mobility creates for schools and teachers but also the complexity conferred by poverty, suggesting that current metrics effectively mask issues of mobility within such communities. The paper then presents research findings on the work of schools and teachers in relation to mobile students. Through a detailed analysis of this work, actions are located as serving the interests of the state - technical transactions related to the Education (General Provisions) Act 2006, practical requirements related to inducting students to a new school and, most importantly, critical actions related to student learning and support needs. The use of this framework to examine the work of teachers exposes the 'complex interplay of interests' (Ball, 1997) that require visibility within any policy reform. Using Rist's (2005) notion of research as having an 'enlightenment function' the paper argues that sustained collaborative research with schools can expose the complexities of such phenomena as student mobility. In the context of renewed commitment to 'needs based funding', the paper concludes with suggested directions to support individual case management of mobile students within a social justice framework and a call for the reconsideration of the role of the state in order to reduce mobility in low SES communities