SLoMo: automated site localization of modifications from ETD/ECD mass spectra

Recently, software has become available to automate localization of phosphorylation sites from CID data and to assign associated confidence scores. We present an algorithm, SLoMo (Site Localization of Modifications), which extends this capability to ETD/ECD mass spectra. Furthermore, SLoMo caters for both high and low resolution data and allows for site-localization of any UniMod post-translational modification. SLoMo accepts input data from a variety of formats (e.g., Sequest, OMSSA). We validate SLoMo with high and low resolution ETD, ECD, and CID data

Good CoP or Bad CoP? What makes a Community of Practice successful; Learning from experience at Flinders University

Published version of the paper reproduced here with permission from the publisher.This paper details the current state of play of an institutional learning and teaching community of practice initiative at Flinders University. The majority of Flinders University CoPs are cross-institutional and focussed on key learning and teaching challenges. Flinders University CoPs are voluntarily facilitated by staff and each CoP’s knowledge creation and outcomes are driven by members, with the University providing a framework and support for their activities without institutional expectations. In this paper, through four firsthand case studies, the authors reflect on the CoPs that they facilitate and consider how the CoPs are progressing by exploring lessons learnt, success factors and potential for future success. The paper commences with a brief review of relevant literature. Four case studies are then introduced and explored. The paper argues that considerable social learning and collective identity formation has been achieved, but that obstacles remain to future success

Large scale localization of protein phosphorylation by use of electron capture dissociation mass spectrometry.

We used on-line electron capture dissociation (ECD) for the large scale identification and localization of sites of phosphorylation. Each FT-ICR ECD event was paired with a linear ion trap collision-induced dissociation (CID) event, allowing a direct comparison of the relative merits of ECD and CID for phosphopeptide identification and site localization. Linear ion trap CID was shown to be most efficient for phosphopeptide identification, whereas FT-ICR ECD was superior for localization of sites of phosphorylation. The combination of confident CID and ECD identification and confident CID and ECD localization is particularly valuable in cases where a phosphopeptide is identified just once within a phosphoproteomics experiment

Weight-management in children living with asthma:a qualitative study of the experiences of paediatric healthcare professionals

OBJECTIVE: Weight loss has been found to improve the symptoms of asthma in children who are overweight. However, many paediatric weight management programmes do not address the challenges associated with living with asthma. The aim of this study was to explore the views and experiences of paediatric healthcare professionals concerning weight management advice and support offered to families of children living with asthma. METHODS: In-depth individual interviews with 10 healthcare professionals who work with a paediatric asthma population (n = 4 Respiratory Consultants, 3 Respiratory Nurses, 3 General Paediatricians). Data were analysed using a Framework approach. RESULTS: Healthcare professionals highlighted that families' perceptions of weight, their approach to physical activity and nutrition, the family's social context and perceptions of asthma and asthma treatment all influence weight management in children living with asthma. Initiating weight management conversations and referring to weight management support were perceived as challenging. It was thought that tailoring weight management to the needs of children living with asthma and locating support within the community were important to the success of a family-centred intervention. CONCLUSIONS: The results highlight the added complexity of responding to excessive weight in a paediatric population with asthma. Training and referral guidance for healthcare professionals may help overcome weight management support challenges. Addressing family beliefs about the factors influencing paediatric asthma and exploring families' motivations for behaviour change may enhance engagement with weight management

Phimai is the New Black: Assessing the Standardisation of Kiln Fired Phimai Black Ceramics from the Iron Age Site of Non Ban Jak, Northeast Thailand

This thesis set out to ascertain the nature of the Phimai Black ceramic tradition at the site of Non Ban Jak, Northeast Thailand. The research was undertaken to assess the degree of visual standardisation through a form-plus-fabric analysis of ceramics over time and through multiple contexts across the site. This in turn led to an investigation into the nature of social organisation surrounding pottery production at Non Ban Jak. Excavations at Non Ban Jak have revealed extensive residential quarters, burial chambers, and ceramic kilns. Along with a large ceramic assemblage, accurately dated context, and the evidence of production onsite, models concerning sourcing, cultural transmission, the nature of production, and previous models pertaining to Phimai Black could be assessed. In one exploratory model, it was hypothesised that the ceramic tradition originated as an elite good that was widely exchanged, resulting in local imitation and standardisation in production and form across multiple sites. Through this research it can be seen that Phimai Black moved from elite ware to common ware, its production carried out by independent specialists who lived with, and catered for, the community. Burial offerings in terms of the Phimai Black tradition were concluded to be highly standardised at Non Ban Jak. Regardless of status and wealth, it was the social norm to use certain ceramics for burial, this is seen in the sets of ceramics reserved for different age groups. Individual grief and status associated with the deceased was not necessarily expressed in ceramic offerings, but mainly in offerings such as gold, carnelian, and bronze ornaments. Social significance surrounding infant interment was prominent on site, these people would have put much social value on infant passing, as the most elaborate vessels were chosen. The purpose of the Phimai Black ceramic tradition was to symbolise a community-wide goal to associate the deceased with an identity that reflected Iron Age communities across the Mun Valley. Phimai Black through time is seen to be made with a specific clay, showing that originally there was a set of ideals associated with these ceramics, linking to the emulation/imitation hypothesis. While vessel forms gradually transcended clay borders throughout the Iron Age, the standardisation of form highlights an effort to hold onto past beliefs, and to the identity of the wider community

C.R.I.S.T.A.L. Concurrent Repository & Information System for Tracking Assembly and production Lifecycles: A data capture and production management tool for the assembly and construction of the CMS ECAL detector

The CMS experiment will comprise several very large high resolution detectors for physics. Each detector may be constructed of well over a million parts and will be produced and assembled during the next decade by specialised centres distributed world-wide. Each constituent part of each detector must be accurately measured and tested locally prior to its ultimate assembly and integration in the experimental area at CERN. The CRISTAL project (Concurrent Repository and Information System for Tracking Assembly and production Lifecycles) [1] aims to monitor and control the quality of the production and assembly process to aid in optimising the performance of the physics detectors and to reject unacceptable constituent parts as early as possible in the construction lifecycle. During assembly CRISTAL will capture all the information required for subsequent detector calibration. Distributed instances of Object databases linked via CORBA [2] and with WWW/Java-based query processing are the main technology aspects of CRISTAL.The CMS experiment will comprise several very large high resolution detectors for physics. Each detector may be constructed of well over a million parts and will be produced and assembled during the next decade by specialised centres distributed world-wide. Each constituent part of each detector must be accurately measured and tested locally prior to its ultimate assembly and integration in the experimental area at CERN. The CRISTAL project (Concurrent Repository and Information System for Tracking Assembly and production Lifecycles) [1] aims to monitor and control the quality of the production and assembly process to aid in optimising the performance of the physics detectors and to reject unacceptable constituent parts as early as possible in the construction lifecycle. During assembly CRISTAL will capture all the information required for subsequent detector calibration. Distributed instances of Object databases linked via CORBA [2] and with WWW/Java-based query processing are the main technology aspects of CRISTAL

‘It’s not in my job description’: An exploration of trainee clinical psychologists’ attitudes towards research and perceptions of DClinPsy research culture

© 2023 The British Psychological Society. This is the accepted manuscript version of an article which has been published in final form at https://doi.org/10.53841/bpscpf.2023.1.366.20This project aimed to investigate attitudes towards research and perceived research culture among trainee clinicalpsychologists across the UK. This was achieved by exploring factors such as: research training environment,research attitudes, research self-efficacy, and professional identity. An online survey was completed by 44 traineeclinical psychologists who started training in 2020. The findings showed that UK trainee clinical psychologistsdid not perceive a strong research training environment, they did not hold strong attitudes towards research,or have positive research self-efficacy as indicated in previous research. It is of some concern that the role ofresearcher, as part of the identity of a clinical psychologist, was not seen to be instrumental by most trainees.Important differences in the results of this research compared to previous published literature are discussed, inaddition to a consideration of the implications of these findings for training and the post-qualification role ofclinical psychologists.Peer reviewe