PyFolding: An open-source software package for graphing, simulation and analysis of the biophysical properties of proteins

For many years, curve fitting software has been heavily utilized to fit simple models to various types of biophysical data. Although such software packages are easy to use for simple functions, they are often expensive and present substantial impediments to applying more complex models or for the analysis of large datasets. One field that is relient on such data analysis is the thermodynamics and kinetics of protein folding. Over the past decade, increasingly sophisticated analytical models have been generated, but without simple tools to enable routine analysis. Consequently, users have needed to generate their own tools or otherwise find willing collaborators. Here we present PyFolding, a free, open source, and extensible Python framework for graphing, analysis and simulation of the biophysical properties of proteins. To demonstrate the utility of PyFolding, we have used it to analyze and model experimental protein folding and thermodynamic data. Examples include: (i) multi-phase kinetic folding fitted to linked equations, (ii) global fitting of multiple datasets and (iii) analysis of repeat protein thermodynamics with Ising model variants. Moreover, we demonstrate how Pyfolding is easily extensible to novel functionality beyond applications in protein folding via the addition of new models. Example scripts to perform these and other operations are supplied with the software, and we encourage users to contribute notebooks and models to create a community resource. Finally, we show that PyFolding can be used in conjunction with Jupyter notebooks as an easy way to share methods and analysis for publication and amongst research teams.L.S.I. acknowledges the support of a Senior Fellowship from the UK Medical Research Foundation. A.P.-R. was supported by a Biotechnology and Biological Sciences Research Council Doctoral Training Programme scholarship and an Oliver Gatty Studentship. E.R.G.M. and L.S.I. laboratories acknowledge support from a Leverhulme Trust project grant

Transition to professional social work practice: The first three years

This article presents the findings of a longitudinal research project that followed the employ-ment outcomes of one cohort of Bachelor of Social Work graduates for three years. Prior to graduation, students receive professional preparation that develops their ability to critically engage with theory and practice. Following graduation, newly qualified social workers require quality induction, supervision and other workload management strategies to support the transition to social work practice. The development of this study was fuelled by political criticism of social work education. Additionally, there was a desire to track the employment outcomes of the graduates and understand what supported their transition to competent professional practice. The findings fit within a five-year longitudinal research project that follows three separate graduate cohorts each for three years to seek and compare participants’ experiences for their first three years post-qualification. An anonymous, semi-structured, on-line survey was used to provide both quantitative and qualitative data. By the second year of practice, these respond-ents were taking on the workload of an experienced social work practitioner with widely varied levels of support. By the end of their third year in practice, they reported that they had found little opportunity to apply their critical analytical academic skills to consider the wider social system in practice. Further, the graduates’ confidence in their cultural competencies also gradually decreased over the three-year period

Transition to Professional Social Work Practice: The First Three Years

This article presents the findings of a longitudinal research project that followed the employ-ment outcomes of one cohort of Bachelor of Social Work graduates for three years. Prior to graduation, students receive professional preparation that develops their ability to critically engage with theory and practice. Following graduation, newly qualified social workers require quality induction, supervision and other workload management strategies to support the transition to social work practice. The development of this study was fuelled by political criticism of social work education. Additionally, there was a desire to track the employment outcomes of the graduates and understand what supported their transition to competent professional practice. The findings fit within a five-year longitudinal research project that follows three separate graduate cohorts each for three years to seek and compare participants’ experiences for their first three years post-qualification. An anonymous, semi-structured, on-line survey was used to provide both quantitative and qualitative data. By the second year of practice, these respond-ents were taking on the workload of an experienced social work practitioner with widely varied levels of support. By the end of their third year in practice, they reported that they had found little opportunity to apply their critical analytical academic skills to consider the wider social system in practice. Further, the graduates’ confidence in their cultural competencies also gradually decreased over the three-year period

Tephrochronology of core PRAD 1-2 from the Adriatic Sea: insights into Italian explosive volcanism for the period 200-80ka

Core PRAD 1-2, located on the western flank of the Mid-Adriatic Deep, was investigated for tephra content within the part of the sequence assigned on biostratigraphic and sapropel-layer stratigraphy to MIS 5 and 6 (ca. 80–200 ka BP). A total of 11 discrete tephra layers are identified, 8 visible and 3 cryptotephra layers. 235 geochemical measurements obtained from individual glass shards using WDS-EPMA enabled 8 of the 11 tephras to be correlated to known eruption events, 5 of which are represented in the Lago Grande di Monticchio (LGdM) regional tephra archive sequence. Three of these layers are recognised ultra-distally for the first time, extending their known distributions approximately 210 km further north. The results provide an independent basis for establishing an age-depth profile for the MIS 5–6 interval in the PRAD 1-2 marine record. This approach allowed age estimates to be interpolated for the tephra layers that could not be correlated to known events. It also provides an independent test of, and support for, the broad synchroneity of sapropel-equivalent (S-E) events in the Adriatic Sea with the better-developed sapropel layers of the eastern Mediterranean, proposed by Piva et al. (2008a)

Improved age estimates for key Late Quaternary European tephra horizons in the RESET lattice

The research project 'Response of Humans to Abrupt Environmental Transitions' (RESET) used tephra layers to tie together and synchronise the chronologies of stratigraphic records at archaeological and environmental sites. With the increasing importance of tephra as chronological markers in sedimentary sequences, both in this project and more generally, comes a requirement to have good estimates for the absolute age of these volcanic horizons. This paper summarises the chronology of the key tephra in the RESET tephra lattice in the time range 10-60 ka BP, from the existing literature, from papers produced as part of the RESET project, and reanalysis conducted for this paper. The paper outlines the chronological ap- proach taken to the dating of tephra within the RESET project, and the basis for further work, as part of the INTIMATE (INTegrating Ice core MArine and TEr- restrial records) initiative. For each of the tephra layers in the lattice, the existing literature is discussed and, where relevant date estimates updated using the latest radiocarbon calibration curves (IntCal13 and Marine13) and methods. Maps show the approximate extent of tephra finds, giving a visual indication of the coverage of the lattice in different time-periods.</p

Transition to professional social work practice: the initial year

This paper presents the findings of the first year of a three-year longitudinal study of new graduate social workers from a Bachelor of Social Work (BSW) program in Aotearoa New Zealand. We compare work outcomes and graduates’ perceptions of their readiness for practice against the New Zealand Social Workers Registration Board’s (SWRB’s) 10 core competencies. This study’s impetus came from an increase in the professionally accepted minimum qualification benchmark, recent political commentary on the preparedness of social work graduates, and associated roles of the SWRB and Aotearoa New Zealand Association of Social Work (ANZASW). The aim of this longitudinal research is to track paid and unpaid work outcomes and identify the support needs of social work graduates as they transition from students into professional practitioners. An on-line questionnaire offered graduates the opportunity to comment annually on their professional progress. The respondents all found paid employment as social workers in that first year and identified transitional challenges. Supports to ease this transition included supervision, mentoring, collegiality, coaching, case-load protection (both volume and complexity), continuing professional development, and professional networking. Concluding that the first year of practice is a highly demanding one, we highlight the need for new graduates to have reduced case-loads and additional levels of support. This article is highly relevant for the profession in Aotearoa New Zealand and elsewhere, particularly for countries such as Australia where there is no legislated registration process for social workers

Establishing tephrostratigraphic frameworks to aid the study of abrupt climatic and glacial transitions: a case study of the Last Glacial-Interglacial Transition in the British Isles (c. 16-8 ka BP)

Distally dispersed tephra layers have become an important tool in the investigation of palaeoenvironmental and archaeological records across the globe. They offer possibilities for the synchronisation and improved chronological control in those records to which they can be traced and hence contribute to an improved understanding of the pattern and timing of environmental and archaeological change during periods of rapid climatic adjustment. However, their use as robust isochronous markers for synchronising records is frequently compromised by uncertainties relating to stratigraphical context, precise chronology and chemical composition. Here we collate and review the tephrostratigraphical information dating to the Last Glacial-Interglacial Transition (LGIT; c. 16-8 ka BP) in the British Isles based on published and unpublished records obtained from 54 sites. Based on details of their stratigraphic position, chronology and chemical composition, we propose that 26 individual eruption events may be represented in this collective record which spans the LGIT. The great majority of these eruptives can be traced in origin to Iceland, but we also report on the recent discoveries of ultra-distal tephra from the North American Cascades range, including for the first time the Mount St Helens J Tephra at a site in southern Ireland. These particular ultra-distal discoveries have resulted from a reinterpretation of older data, demonstrating the potential importance of ‘unknown’ analyses in older tephra datasets. The outcome of this review is a comprehensive but provisional tephrostratigraphic framework for the LGIT in the British Isles, which helps to focus future research on parts of the scheme that are in need of further development or testing. The results, therefore, make an important contribution to the wider European tephrostratigraphic framework, while adding new discoveries of transcontinental isochronous tephra markers

Methodologies for Housing Justice Resource Guide

This Resource Guide is the outcome of a Summer Institute on Methodologies for Housing Justice convened by the Institute on Inequality and Democracy at UCLA Luskin as part of the Housing Justice in Unequal Cities Network, which is supported by the National Science Foundation (BCS 1758774). Held in Los Angeles in August 2019, the Summer Institute brought together participants from cities around the world. As is the case with the overall scope and purpose of the Housing Justice in Unequal Cities Network, it created a shared terrain of scholarship for movement-based and university-based scholars. Dissatisfied with the canonical methods that are in use in housing studies and guided by housing justice movements that are active research communities, the Summer Institute was premised on the assertion that methodology is political. Methodology is rooted in arguments about the world and involves relations of power and knowledge. The method itself – be it countermapping or people’s diaries – does not ensure an ethics of solidarity and a purpose of justice. Such goals&nbsp;require methodologies for liberation. Thus, as is evident in this Resource Guide, our endeavor foregrounds innovative methods that are being used by researchers across academia and activism and explicitly situates such methods in an orientation towards housing justice