On the use of photobleaching to reduce fluorescence background in Raman spectroscopy to improve the reliability of pigment identification on painted textiles

Subjecting a specimen of red lead watercolour paint on silk to photobleaching was demonstrated to be a simple means by which to engineer a reduction in the magnitude of the fluorescent background that was approximately exponential with time, with a corresponding improvement in the signal to noise ratio of the Raman spectrum, thus rendering the characteristic peaks more easily visible and allowing more confident identification of the pigment. However, relative heights of the Raman peaks obtained from the sample were seen to alter progressively as a result of irradiation, indicating that some component of the sample was undergoing degradation that may result in longer-term damage to a fragile historic artefact. It was also shown that crystals of the lead monoxide pigment massicot were present in the samples ofred lead on a painted silk artefact dating from 1750. It is concluded that this was either due to deliberate mixing of pigments by the artist, contrary to historic records, or as a result of the roasting techniques used to create red lead pigments at the time and not due to thermal degradation of the pigment during Raman analysis

Effects of heat on new and aged polyamide 6,6 textiles during pest eradication

AbstractSubjecting artefacts to raised (58 °C) or lowered (−30 °C) temperatures in order to combat the problem of pest infestations is common practice within the museum and heritage sector. However, concerns have been raised by the conservation profession about applying temperature based pest treatments to polyamide 6,6, due to the changes in thermal properties known to occur over the range of temperatures in question.Unaged and artificially aged polyamide 6,6 fibres were subjected to creep/recovery experiments using dynamic mechanical analysis at temperatures ranging from 58 °C to −30 °C. These experiments were carried out on loaded samples to determine whether textile material would suffer deterioration if treated whilst hanging under load, for example on a mannequin. Samples were analysed before and after loading by attenuated total reflectance Fourier-transform infrared spectroscopy, differential scanning calorimetry and tensile testing to investigate the chemical and physical alterations in the polyamide 6,6 fabric subject to treatment.Samples loaded at room temperature exhibited permanent contraction, attributed to strain induced crystallization. For both the unaged and aged samples at elevated temperatures the samples underwent permanent deformation. Samples treated at sub-ambient temperatures recovered to their original length during the recovery section of the creep test, although some structural alterations were evident during subsequent analysis. The results suggest that the low temperature treatments of polyamide artefacts, particularly in the presence of stress, are preferable

Aggressive behavioural interactions between swans (Cygnus spp.) and other waterbirds during winter: A webcam-based study

This is the final version. Available on open access from BMC via the DOI in this recordAvailability of data and materials: The datasets generated and analysed during the current study are available from the corresponding author upon reasonable request.Background: Our understanding of any impacts of swans on other waterbirds (including other swans), and potential effects on waterbird community structure, remain limited by a paucity of fundamental behavioural and ecological data, including which species swans interact aggressively with and how frequently such interactions occur. Methods: Behavioural observations of aggression by swans and other waterbirds in winters 2018/2019 and 2019/2020, were carried out via live-streaming webcams at two wintering sites in the UK. All occurrence sampling was used to identify all aggressive interactions between conspecific or heterospecifics individuals, whilst focal observations were used to record the total time spent by swans on aggressive interactions with other swans. Binomial tests were then used to assess whether the proportion of intraspecific aggressive interactions of each species differed from 0.5 (which would indicate equal numbers of intraspecific and interspecific interactions). Zero-inflated generalized linear mixed effects models (ZIGLMMs) were used to assess between-individual variation in the total time spent by swans on aggressive interactions with other swans. Results: All three swan species were most frequently aggressive towards, and received most aggression from, their conspecifics. Our 10-min focal observations showed that Whooper (Cygnus cygnus) and Bewick's Swans (C. columbianus bewickii) spent 13.8 ± 4.7 s (means ± 95% CI) and 1.4 ± 0.3 s, respectively, on aggression with other swans. These durations were equivalent to 2.3% and 0.2% of the Whooper and Bewick's Swan time-activity budgets, respectively. Model selection indicated that the time spent in aggressive interactions with other swans was best-explained by the number of other swans present for Whooper Swans, and an interactive effect of time of day and winter of observation for Bewick's Swans. However, the relationship between swan numbers and Whooper Swan aggression times was not strong (R 2 = 19.3%). Conclusions: Whilst swans do exhibit some aggression towards smaller waterbirds, the majority of aggression by swans is directed towards other swans. Aggression focused on conspecifics likely reflects greater overlap in resource use, and hence higher potential for competition, between individuals of the same species. Our study provides an example of how questions relating to avian behaviour can be addressed using methods of remote data collection such as live-streaming webcams.Wildfowl & Wetlands TrustUniversity of Exete

oPOSSUM: identification of over-represented transcription factor binding sites in co-expressed genes

Targeted transcript profiling studies can identify sets of co-expressed genes; however, identification of the underlying functional mechanism(s) is a significant challenge. Established methods for the analysis of gene annotations, particularly those based on the Gene Ontology, can identify functional linkages between genes. Similar methods for the identification of over-represented transcription factor binding sites (TFBSs) have been successful in yeast, but extension to human genomics has largely proved ineffective. Creation of a system for the efficient identification of common regulatory mechanisms in a subset of co-expressed human genes promises to break a roadblock in functional genomics research. We have developed an integrated system that searches for evidence of co-regulation by one or more transcription factors (TFs). oPOSSUM combines a pre-computed database of conserved TFBSs in human and mouse promoters with statistical methods for identification of sites over-represented in a set of co-expressed genes. The algorithm successfully identified mediating TFs in control sets of tissue-specific genes and in sets of co-expressed genes from three transcript profiling studies. Simulation studies indicate that oPOSSUM produces few false positives using empirically defined thresholds and can tolerate up to 50% noise in a set of co-expressed genes

Designing the social Internet of Things

Copyright © 2017 by the Association for Computing Machinery, Inc. (ACM). What role do people have in the Internet of Things? Compared to the impressive body of research that is currently tackling the technical issues of the Internet of Things, social aspects of agency, engagement, participation, and ethics, are receiving less attention. The goal of this 'Designing the Social Internet of Things' workshop is to contribute by shedding light on these aspects. We invite prospective participants to take a humanistic standpoint, explore people's relations with 'things' first, and then build on such relations so as to support socially relevant goals of engagement, relatedness, participation, and creativity

Treasure codes: augmenting learning from physical museum exhibits through treasure hunting

Previous studies have highlighted the difficulty that designers face in creating mobile museum guides to enhance small group experiences. In this paper, we report a study exploring the potential of mobile visual recognition technology (Artcodes) to improve users’ experiences in a visitor centre. A prototype mobile guide in the form of a treasure hunt was developed and evaluated by means of a field study comparing this technology with the existing personal guided tour. The results reveal a preference for the mobile guide amongst participants and show significant learning gains from pre-test to post-test compared with the pre-existing personal tour. Our observational analyses indicate how the mobile guide can be used to improve visitors’ learning experiences by supporting active discovery and by balancing physical and digital interactions. We further expand the concept of design trajectories to consider micro-scaffolding as a way of understanding and designing future public technologies

Numerical Solution of Differential Equations by the Parker-Sochacki Method

A tutorial is presented which demonstrates the theory and usage of the Parker-Sochacki method of numerically solving systems of differential equations. Solutions are demonstrated for the case of projectile motion in air, and for the classical Newtonian N-body problem with mutual gravitational attraction.Comment: Added in July 2010: This tutorial has been posted since 1998 on a university web site, but has now been cited and praised in one or more refereed journals. I am therefore submitting it to the Cornell arXiv so that it may be read in response to its citations. See "Spiking neural network simulation: numerical integration with the Parker-Sochacki method:" J. Comput Neurosci, Robert D. Stewart & Wyeth Bair and http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2717378

Studying the functional conservation of cis-regulatory modules and their transcriptional output

<p>Abstract</p> <p>Background</p> <p><it>Cis</it>-regulatory modules (CRMs) are distinct, genomic regions surrounding the target gene that can independently activate the promoter to drive transcription. The activation of a CRM is controlled by the binding of a certain combination of transcription factors (TFs). It would be of great benefit if the transcriptional output mediated by a specific CRM could be predicted. Of equal benefit would be identifying <it>in silico </it>a specific CRM as the driver of the expression in a specific tissue or situation. We extend a recently developed biochemical modeling approach to manage both prediction tasks. Given a set of TFs, their protein concentrations, and the positions and binding strengths of each of the TFs in a putative CRM, the model predicts the transcriptional output of the gene. Our approach predicts the location of the regulating CRM by using predicted TF binding sites in regions near the gene as input to the model and searching for the region that yields a predicted transcription rate most closely matching the known rate.</p> <p>Results</p> <p>Here we show the ability of the model on the example of one of the CRMs regulating the <it>eve </it>gene, MSE2. A model trained on the MSE2 in <it>D. melanogaster </it>was applied to the surrounding sequence of the <it>eve </it>gene in seven other <it>Drosophila </it>species. The model successfully predicts the correct MSE2 location and output in six out of eight <it>Drosophila </it>species we examine.</p> <p>Conclusion</p> <p>The model is able to generalize from <it>D. melanogaster </it>to other <it>Drosophila </it>species and accurately predicts the location and transcriptional output of MSE2 in those species. However, we also show that the current model is not specific enough to function as a genome-wide CRM scanner, because it incorrectly predicts other genomic regions to be MSE2s.</p

Discovery and Expansion of Gene Modules by Seeking Isolated Groups in a Random Graph Process

BACKGROUND: A central problem in systems biology research is the identification and extension of biological modules-groups of genes or proteins participating in a common cellular process or physical complex. As a result, there is a persistent need for practical, principled methods to infer the modular organization of genes from genome-scale data. RESULTS: We introduce a novel approach for the identification of modules based on the persistence of isolated gene groups within an evolving graph process. First, the underlying genomic data is summarized in the form of ranked gene-gene relationships, thereby accommodating studies that quantify the relevant biological relationship directly or indirectly. Then, the observed gene-gene relationship ranks are viewed as the outcome of a random graph process and candidate modules are given by the identifiable subgraphs that arise during this process. An isolation index is computed for each module, which quantifies the statistical significance of its survival time. CONCLUSIONS: The Miso (module isolation) method predicts gene modules from genomic data and the associated isolation index provides a module-specific measure of confidence. Improving on existing alternative, such as graph clustering and the global pruning of dendrograms, this index offers two intuitively appealing features: (1) the score is module-specific; and (2) different choices of threshold correlate logically with the resulting performance, i.e. a stringent cutoff yields high quality predictions, but low sensitivity. Through the analysis of yeast phenotype data, the Miso method is shown to outperform existing alternatives, in terms of the specificity and sensitivity of its predictions

Provision of obstetrics and gynaecology services during the COVID-19 pandemic:a survey of junior doctors in the UK National Health Service

Objective: The COVID-19 pandemic is disrupting health services worldwide. We aimed to evaluate the provision of obstetrics and gynaecology services in the UK during the acute-phase of the COVID-19 pandemic. Design: Interview-based national survey. Setting: Women’s healthcare units in the National Health Service. Population: Junior doctors in obstetrics and gynaecology. Methods: Participants were interviewed by members of the UKARCOG trainees’ collaborative between 28th March and 7th of April 2020. We used a quantitative analysis for closed-ended questions and a thematic framework analysis for open comments. Results: We received responses from 148/155 units (95%), majority of the participants were in years 3-7 of training (121/148, 82%). Most completed specific training drills for managing obstetric and gynaecological emergencies in women with COVID-19 (89/148, 60.1%) and two-persons donning and doffing of Personal Protective Equipment (PPE) (96/148, 64.9%). The majority of surveyed units implemented COVID-19 specific protocols (130/148, 87.8%), offered adequate PPE (135/148, 91.2%) and operated dedicated COVID-19 emergency theatres (105/148, 70.8%). Most units reduced face-to-face antenatal clinics (117/148, 79.1%), and suspended elective gynaecology services (131/148, 88.5%). The two-week referral pathway for oncology gynaecology was not affected in half of the units (76/148, 51.4%), while half reported a planned reduction in oncology operating (82/148, 55.4%). Conclusion: The provision of obstetrics and gynaecology services in the UK during the acute phase of the COVID-19 pandemic seems to be in line with current guidelines, but strategic planning is needed to restore routine gynaecology services and ensure safe access to maternity care on the longterm