PEDRo: A database for storing, searching and disseminating experimental proteomics data

Abstract Background Proteomics is rapidly evolving into a high-throughput technology, in which substantial and systematic studies are conducted on samples from a wide range of physiological, developmental, or pathological conditions. Reference maps from 2D gels are widely circulated. However, there is, as yet, no formally accepted standard representation to support the sharing of proteomics data, and little systematic dissemination of comprehensive proteomic data sets. Results This paper describes the design, implementation and use of a Proteome Experimental Data Repository (PEDRo), which makes comprehensive proteomics data sets available for browsing, searching and downloading. It is also serves to extend the debate on the level of detail at which proteomics data should be captured, the sorts of facilities that should be provided by proteome data management systems, and the techniques by which such facilities can be made available. Conclusions The PEDRo database provides access to a collection of comprehensive descriptions of experimental data sets in proteomics. Not only are these data sets interesting in and of themselves, they also provide a useful early validation of the PEDRo data model, which has served as a starting point for the ongoing standardisation activity through the Proteome Standards Initiative of the Human Proteome Organisation

The United Kingdom Research study into Ethnicity And COVID-19 outcomes in Healthcare workers (UK-REACH): Protocol for a prospective longitudinal cohort study of healthcare and ancillary workers in UK healthcare settings

Introduction: The COVID-19 pandemic has resulted in significant morbidity and mortality, and has devastated economies in many countries. Amongst the groups identified as being at increased risk from COVID-19 are healthcare workers (HCWs) and ethnic minority groups. Emerging evidence suggests HCWs from ethnic minority groups are at increased risk of adverse COVID-19-related physical and mental health outcomes. To date there has been no large-scale analysis of these risks in UK healthcare workers or ancillary workers in healthcare settings, stratified by ethnicity or occupation type, and adjusted for potential confounders. This paper reports the protocol for a prospective longitudinal questionnaire study of UK HCWs, as part of the UK-REACH programme (The United Kingdom Research study into Ethnicity And COVID-19 outcomes in Healthcare workers). Methods and analysis: A baseline questionnaire with follow-up questionnaires at 4 and 8 months will be administered to a national cohort of UK healthcare workers and ancillary workers in healthcare settings, and those registered with UK healthcare regulators. With consent, data will be linked to health records, and participants followed up for 25 years. Univariate associations between ethnicity and primary outcome measures (clinical COVID-19 outcomes, and physical and mental health) and key confounders/explanatory variables will be tested, followed by multivariable analyses to test for associations between ethnicity and key outcomes adjusted for the confounder/explanatory variables, with interactions included as appropriate. Using follow-up data, multilevel models will be used to model changes over time by ethnic group, facilitating understanding of absolute and relative risks in different ethnic groups, and generalisability of findings. Ethics and dissemination: The study is approved by Health Research Authority (reference 20/HRA/4718), and carries minimal risk to participants. We aim to manage the small risk of participant distress due to being asked questions on sensitive topics by clearly indicating on the participant information sheet that the questionnaire covers sensitive topics and that participants are under no obligation to answer these, or indeed any other, questions, and by providing links to support organisations. Results will be disseminated with reports to Government and papers uploaded to pre-print servers and submitted to peer reviewed journals. Registration details Trial ID: ISRCTN11811602 STRENGTHS AND LIMITATIONS OF THIS STUDY National, UK-wide, study, aiming to capture variety of healthcare worker job roles including ancillary workers in healthcare settings. Longitudinal study including three waves of questionnaire data collection, and linkage to administrative data over 25 years, with consent. Unique support from all major UK healthcare worker regulators, relevant healthcare worker organisations, and a Professional Expert Panel to increase participant uptake and the validity of findings. Potential for self-selection bias and low response rates, and the use of electronic invitations and online data collection makes it harder to reach ancillary workers without regular access to work email addresses

An ammonia spectral map of the L1495-B218 filaments in the Taurus molecular cloud. I. Physical properties of filaments and dense cores

We present deep NH3 observations of the L1495-B218 filaments in the Taurus molecular cloud covering over a 3° angular range using the K-band focal plane array on the 100 m Green Bank Telescope. The L1495-B218 filaments form an interconnected, nearby, large complex extending over 8 pc. We observed NH3 (1, 1) and (2, 2) with a spectral resolution of 0.038 km s−1 and a spatial resolution of 31''. Most of the ammonia peaks coincide with intensity peaks in dust continuum maps at 350 and 500 μm. We deduced physical properties by fitting a model to the observed spectra. We find gas kinetic temperatures of 8–15 K, velocity dispersions of 0.05–0.25 km s−1, and NH3 column densities of 5 × 1012 to 1 × 1014 cm−2. The CSAR algorithm, which is a hybrid of seeded-watershed and binary dendrogram algorithms, identifies a total of 55 NH3 structures, including 39 leaves and 16 branches. The masses of the NH3 sources range from 0.05 to 9.5 ${{M}_{\odot }}$. The masses of NH3 leaves are mostly smaller than their corresponding virial mass estimated from their internal and gravitational energies, which suggests that these leaves are gravitationally unbound structures. Nine out of 39 NH3 leaves are gravitationally bound, and seven out of nine gravitationally bound NH3 leaves are associated with star formation. We also found that 12 out of 30 gravitationally unbound leaves are pressure confined. Our data suggest that a dense core may form as a pressure-confined structure, evolve to a gravitationally bound core, and undergo collapse to form a protostar

Carbon Recombination Lines from the Galactic Plane at 34.5 & 328 MHz

We present results of a search for carbon recombination lines in the Galaxy at 34.5 MHz (C$575\alpha$) made using the dipole array at Gauribidanur near Bangalore. Observations made towards 32 directions, led to detections of lines in absorption at nine positions. Followup observations at 328 MHz (C$272\alpha$) using the Ooty Radio Telescope detected these lines in emission. A VLA D-array observation of one of the positions at 330 MHz yielded no detection implying a lower limit of 10' for the angular size of the line forming region. The longitude-velocity distribution of the observed carbon lines indicate that the line forming region are located mainly between 4 kpc and 7 kpc from the Galactic centre. Combining our results with published carbon recombination line data near 76 MHz (\nocite{erickson:95} Erickson \et 1995) we obtain constraints on the physical parameters of the line forming regions. We find that if the angular size of the line forming regions is $\ge 4^{\circ}$, then the range of parameters that fit the data are: \Te $= 20-40$ K, \ne $\sim 0.1-0.3$ \cm3 and pathlengths $\sim 0.07-0.9$ pc which may correspond to thin photo-dissociated regions around molecular clouds. On the other hand, if the line forming regions are $\sim 2^{\circ}$ in extent, then warmer gas (\Te $\sim 60-300$ K) with lower electron densities (\ne $\sim 0.03-0.05$ \cm3) extending over several tens of parsecs along the line of sight and possibly associated with atomic \HI gas can fit the data. Based on the range of derived parameters, we suggest that the carbon line regions are most likely associated with photo-dissociation regions.Comment: To appear in Journal of Astrophysics & Astronomy, March 200

Early developmental pathways to childhood symptoms of attention-deficit hyperactivity disorder, anxiety and autism spectrum disorder

Background Children with autism spectrum disorder (ASD) often have co-occurring symptoms of attention-deficit/hyperactivity disorder (ADHD) and/or anxiety. It is unclear whether these disorders arise from shared or distinct developmental pathways. We explored this question by testing the specificity of early-life (infant and toddler) predictors of mid-childhood ADHD and anxiety symptoms compared to ASD symptoms. Methods Infants (n = 104) at high and low familial risk for ASD took part in research assessments at 7, 14, 24 and 38 months, and 7 years of age. Symptoms of ASD, ADHD and anxiety were measured by parent report at age 7. Activity levels and inhibitory control, also measured by parent report, in infancy and toddlerhood were used as early-life predictors of ADHD symptoms. Fearfulness and shyness measured in infancy and toddlerhood were used as early-life predictors of anxiety symptoms. Correlations and path analysis models tested associations between early-life predictors and mid-childhood ADHD and anxiety symptoms compared to mid-childhood ASD symptoms, and the influence of controlling for ASD symptoms on those associations. Results Increased activity levels and poor inhibitory control were correlated with ADHD symptoms and not ASD or anxiety; these associations were unchanged in path models controlling for risk-group and ASD symptoms. Increased fearfulness and shyness were correlated with anxiety symptoms, but also ASD symptoms. When controlling for risk-group in path analysis, the association between shyness and anxiety became nonsignificant, and when further controlling for ASD symptoms the association between fearfulness and anxiety became marginal. Conclusions The specificity of early-life predictors to ADHD symptoms suggests early developmental pathways to ADHD might be distinct from ASD. The overlap in early-life predictors of anxiety and ASD suggests that these disorders are difficult to differentiate early in life, which could reflect the presence of common developmental pathways or convergence in early behavioural manifestations of these disorders

‘You have got to stick to your times’: Care workers and managers’ experiences of working in extra care housing

Extra care housing (ECH) has been lauded as an innovative model of housing with care for older people that promotes and supports independent living. The study used a qualitative design to explore how care is delivered in four extra care settings in England over 20 months during 2016-2017. This paper reports findings from semi-structured interviews with 20 care workers and seven managers. The article argues that, despite being heralded as a new model, care workers in ECH face similar organisational pressures as those working in more conventional settings and, in turn, the care which they are able to provide to residents mimics traditional forms of care

Modulation of EEG theta by naturalistic social content is not altered in infants with family history of autism

Theta oscillations (spectral power and connectivity) are sensitive to the social content of an experience in typically developing infants, providing a possible marker of early social brain development. Autism is a neurodevelopmental condition affecting early social behaviour, but links to underlying social brain function remain unclear. We explored whether modulations of theta spectral power and connectivity by naturalistic social content in infancy are related to family history for autism. Fourteen-month-old infants with (family history; FH; N = 75) and without (no family history; NFH; N = 26) a first-degree relative with autism watched social and non-social videos during EEG recording. We calculated theta (4–5 Hz) spectral power and connectivity modulations (social–non-social) and associated them with outcomes at 36 months. We replicated previous findings of increased theta power and connectivity during social compared to non-social videos. Theta modulations with social content were similar between groups, for both power and connectivity. Together, these findings suggest that neural responses to naturalistic social stimuli may not be strongly altered in 14-month-old infants with family history of autism

A Bronze Age Round Barrow Cemetery, Pit Alignments, Iron Age Burials, Iron Age Copper Working, and Later Activity at Four Crosses, Llandysilio, Powys.

Excavation undertaken at the Upper Severn valley round barrow cemetery at Four Crosses, Llandysilio between 2004 and 2006 has increased the known barrows and ring-ditches to some 26 monuments, and revealed additional burials. Based on limited dating evidence, and the data from earlier excavations, the majority of the barrows are thought to be constructed in the Bronze Age. The barrows are part of a larger linear cemetery and the landscape setting and wider significance of this linear barrow cemetery are explored within this report. Dating suggests two barrows were later, Iron Age additions. The excavation also investigated Iron Age and undated pit alignments, Middle Iron Age copper working and a small Romano-British inhumation cemetery and field systems. Much of this evidence reflects the continuing importance of the site for ritual and funerary activity

Submillimeter absorption from SH+, a new widespread interstellar radical, 13CH+ and HCl

We have used the Atacama Pathfinder Experiment 12 m telescope (APEX) to carry out an absorption study of submillimeter wavelength rotational ground-state lines of H35Cl, H37Cl, 13CH+, and, for the first time, of the SH+ radical (sulfoniumylidene or sulfanylium). We detected the quartet of ground-state hyperfine structure lines of SH+ near 683 GHz with the CHAMP+ array receiver against the strong continuum source Sagittarius B2, which is located close to the center of our Galaxy. In addition to absorption from various kinematic components of Galactic center gas, we also see absorption at the radial velocities belonging to intervening spiral arms. This demonstrates that SH+ is a ubiquitous component of the diffuse interstellar medium. We do not find clear evidence for other SH+ lines we searched for, which is partially due to blending with lines from other molecules. In addition to SH+, we observed absorption from H35Cl, H37Cl, and 13CH+. The observed submillimeter absorption is compared in detail with absorption in 3 mm transitions of H13CO+ and c-C3H2 and the CO J = 1-0 and 3-2 transitions.Comment: 17 pages, 9 figure