Results of international standardised beekeeper surveys of colony losses for winter 2012-2013 : analysis of winter loss rates and mixed effects modelling of risk factors for winter loss.

This article presents results of an analysis of winter losses of honey bee colonies from 19 mainly European countries, most of which implemented the standardised 2013 COLOSS questionnaire. Generalised linear mixed effects models (GLMMs) were used to investigate the effects of several factors on the risk of colony loss, including different treatments for Varroa destructor, allowing for random effects of beekeeper and region. Both winter and summer treatments were considered, and the most common combinations of treatment and timing were used to define treatment factor levels. Overall and within country colony loss rates are presented. Significant factors in the model were found to be: percentage of young queens in the colonies before winter, extent of queen problems in summer, treatment of the varroa mite, and access by foraging honey bees to oilseed rape and maize. Spatial variation at the beekeeper level is shown across geographical regions using random effects from the fitted models, both before and after allowing for the effect of the significant terms in the model. This spatial variation is considerable

Standard survey methods for estimating colony losses and explanatory risk factors in Apis mellifera

This chapter addresses survey methodology and questionnaire design for the collection of data pertaining to estimation of honey bee colony loss rates and identification of risk factors for colony loss. Sources of error in surveys are described. Advantages and disadvantages of different random and non-random sampling strategies and different modes of data collection are presented to enable the researcher to make an informed choice. We discuss survey and questionnaire methodology in some detail, for the purpose of raising awareness of issues to be considered during the survey design stage in order to minimise error and bias in the results. Aspects of survey design are illustrated using surveys in Scotland. Part of a standardized questionnaire is given as a further example, developed by the COLOSS working group for Monitoring and Diagnosis. Approaches to data analysis are described, focussing on estimation of loss rates. Dutch monitoring data from 2012 were used for an example of a statistical analysis with the public domain R software. We demonstrate the estimation of the overall proportion of losses and corresponding confidence interval using a quasi-binomial model to account for extra-binomial variation. We also illustrate generalized linear model fitting when incorporating a single risk factor, and derivation of relevant confidence intervals

Therapists’ experiences of remotely delivering cognitive-behavioural or graded-exercise interventions for fatigue: a qualitative evaluation

Objectives: Fatigue is a challenging feature of all inflammatory rheumatic diseases. LIFT (Lessening the Impact of Fatigue in inflammatory rheumatic diseases: a randomised Trial) included remotely delivered personalised exercise programme (PEP) or cognitive-behavioural approach (CBA) interventions. The aim of this nested qualitative evaluation was to understand rheumatology health professionals (therapists’) perspectives of delivering the interventions in the LIFT trial. Methods: A subgroup of therapists who had delivered the PEP and CBA interventions took part in semi-structured telephone interviews. Results: Seventeen therapists (13 women, 4 men) who delivered PEP (n = 8) or CBA (n = 9) interventions participated. Five themes were identified: In ‘The benefits of informative, structured training’, therapists described how they were able to practice their skills, and the convenience of having the LIFT manual to refer to. When ‘Getting into the swing of it’, supporting patients gave therapists the confidence to tailor the content of the manual to each patient. Clinical supervision supported therapists to gain feedback and request assistance when required. In ‘Delivering the intervention’ therapists reported that patients valued the opportunity to address their fatigue and challenge their own beliefs. ‘Challenges in delivering the LIFT intervention’ therapists struggled to work collaboratively with patients who lacked motivation or stopped engaging. Finally, ‘Lift developing clinical skills’ therapists gained confidence and professional satisfaction seeing patients’ fatigue improve. Conclusion: Findings support the value of skills training for rheumatology health professionals to deliver a remote fatigue management intervention tested in the LIFT trial. These insights can inform service provision and clinical practice Lay summary What does this mean for patients ? Fatigue can be a challenge in inflammatory rheumatic diseases (IRDs). The LIFT study (Lessening the Impact of Fatigue in inflammatory rheumatic diseases: a randomized Trial) explored interventions to support people with fatigue. These were: a cognitive-behavioural approach (CBA), a personalized exercise programme (PEP), or usual care. People with IRDs were chosen randomly to take part in seven sessions of CBA, seven sessions of PEP or usual care. All sessions (aside from the first PEP session) were delivered over the phone. The aim of this study was to explore therapists' experiences of delivering the intervention. Seventeen therapists (13 women and 4 men) took part; eight had delivered the PEP intervention, and 9 delivered the CBA intervention. Therapists who delivered LIFT told us they enjoyed the chance to practice their skills, and that the LIFT manual gave them the confidence to tailor the intervention to each patient. Clinical supervision was valued. Therapists also shared that LIFT improved their skills and they were happy to see patients' fatigue improve over time. These new results can inform clinical practice, and how services are provided

Can microprocessor knees reduce the disparity in trips and falls risks between above and below knee prosthesis users?

While all lower limb prosthesis walkers have a high risk of tripping and/or falling, above knee prosthesis users are reported to fall more frequently. Recognising this, engineers designed microprocessor knees (MPK) to help mitigate these risks, but to what extent these devices reduce this disparity between above and below knee users is unclear. A service review was carried out in a prosthetic limb centre regarding the frequency of trips and falls in the previous four weeks. Data from unilateral, community ambulators were extracted. Ordered logistic regressions were applied to investigate whether MPKs mitigated the increased risk of trips and falls for prosthetic knee users, compared to below knee prosthesis users. Socio-demographics (sex, age), prosthesis (prosthesis type, years of use), health (comorbidities, vision, contralateral limb status, medication), and physical function (use of additional walking aids, activity level) were included as covariates. Of the 315 participants in the analysis, 57.5% reported tripping and 20.3% reported falling. Non-microprocessor prosthetic knee (non-MPK) users were shown to trip significantly more than below knee prosthesis users (OR = 1.96, 95% CI = 1.17–3.28). Other covariates showing a significant association included contralateral limb injuries (OR = 1.91, 95% CI = 1.15–3.18) and using an additional walking aid (OR = 1.99, 95% CI = 1.13–3.50). Non-MPK users were also shown to fall significantly more than below knee prosthesis users (OR = 3.34, 95% CI = 1.73–6.45), with no other covariates showing a significant association. MPK users did not show an increased frequency of trips (OR = 0.74, 95% CI = 0.33–1.64) or falls (OR = 0.34, 95% CI = 0.18–2.62), compared to below knee prosthesis users. Of those who tripped at least once in the previous four weeks, those using a non-MPK (OR = 2.73, 95% CI = 1.30–5.74) presented an increased frequency of falling. These findings provide evidence to suggest that the use of MPKs reduces the difference in falls risk between above knee and below knee prosthesis users, providing justification for their provision

Assessing the Potential Effects of Fungicides on Nontarget Gut Fungi (Trichomycetes) and Their Associated Larval Black Fly Hosts

Fungicides are moderately hydrophobic and have been detected in water and sediment, particularly in agricultural watersheds, but typically are not included in routine water quality monitoring efforts. This is despite their widespread use and frequent application to combat fungal pathogens. Although the efficacy of these compounds on fungal pathogens is well documented, little is known about their effects on nontarget fungi. This pilot study, a field survey in southwestern Idaho from April to December 2010 on four streams with varying pesticide inputs (two agricultural and two reference sites), was conducted to assess nontarget impact of fungicides on gut fungi, or trichomycetes. Tissues of larval black flies (Diptera: Simuliidae), hosts of gut fungi, were analyzed for pesticide accumulation. Fungicides were detected in hosts from streams within agricultural watersheds but were not detected in hosts from reference streams. Gut fungi from agricultural sites exhibited decreased percent infestation, density and sporulation within the gut, and black fly tissues had elevated pesticide concentrations. Differences observed between the sites demonstrate a potential effect on this symbiotic system. Future research is needed to parse out the details of the complex biotic and abiotic relationships; however, these preliminary results indicate that impacts to nontarget organisms could have far-reaching consequences within aquatic ecosystems

Understanding the impacts of novel coronavirus outbreaks on people who use drugs: A systematic review to inform practice and drug policy responses to COVID-19

People who use drugs (PWUD) experience many social and health harms and are considered at greater risk of acquiring COVID-19. Little research has examined the impact of coronaviruses either on PWUD, or on services targeted to PWUD. We report the findings of a systematic review of empirical evidence from studies which have examined the impact of coronaviruses (Severe Acute Respiratory Syndrome (SARS-CoV-1) and Middle Eastern Respiratory Syndrome (MERS-CoV) and COVID-19) on PWUD or on service responses to them. Five databases were searched (MEDLINE, PsycINFO, CINAHL, ASSIA and EMBASE) as well as COVID-19 specific databases. Inclusion criteria were studies reporting any impact of SARS, MERS or COVID-19 or any service responses to those, published between January 2000 and October 2020. Weight of Evidence judgements and quality assessment were undertaken. In total, 27 primary studies were included and grouped by seven main themes: treatment/recovery services; emergency medical settings; low-threshold services; prison setting, PWUD/substance use disorder (SUD) diagnosis; people with SUD and HIV; ‘Sexual minority’ men. Overall, research in the area was scant, and of average/poor quality. More robust research is required to inform on-going and future responses to coronavirus epidemics for PWUD.This review was funded by Scottish Government under the auspices of the Drugs Death Taskforce, Grant No DDTFRF0

LIGHT-bgcArgo-1.0: using synthetic float capabilities in E3SMv2 to assess spatiotemporal variability in ocean physics and biogeochemistry

Since their advent over 2 decades ago, autonomous Argo floats have revolutionized the field of oceanography, and, more recently, the addition of biogeochemical and biological sensors to these floats has greatly improved our understanding of carbon, nutrient, and oxygen cycling in the ocean. While Argo floats offer unprecedented horizontal, vertical, and temporal coverage of the global ocean, uncertainties remain about whether Argo sampling frequency and density capture the true spatiotemporal variability in physical, biogeochemical, and biological properties. As the true distributions of, e.g., temperature or oxygen are unknown, these uncertainties remain difficult to address with Argo floats alone. Numerical models with synthetic observing systems offer one potential avenue to address these uncertainties. Here, we implement synthetic biogeochemical Argo floats into the Energy Exascale Earth System Model version 2 (E3SMv2), which build on the Lagrangian In Situ Global High-Performance Particle Tracking (LIGHT) module in E3SMv2 (E3SMv2-LIGHT-bgcArgo-1.0). Since the synthetic floats sample the model fields at model run time, the end user defines the sampling protocol ahead of any model simulation, including the number and distribution of synthetic floats to be deployed, their sampling frequency, and the prognostic or diagnostic model fields to be sampled. Using a 6-year proof-of-concept simulation, we illustrate the utility of the synthetic floats in different case studies. In particular, we quantify the impact of (i) sampling density on the float-derived detection of deep-ocean change in temperature or oxygen and on float-derived estimates of phytoplankton phenology, (ii) sampling frequency and sea-ice cover on float trajectory lengths and hence float-derived estimates of current velocities, and (iii) short-term variability in ecosystem stressors on estimates of their seasonal variability

Genomic landscape of extended-spectrum β-lactamase resistance in Escherichia coli from an urban African setting

Objectives: Efforts to treat Escherichia coli infections are increasingly being compromised by the rapid, global spread of antimicrobial resistance (AMR). Whilst AMR in E. coli has been extensively investigated in resource-rich settings, in sub-Saharan Africa molecular patterns of AMR are not well described. In this study, we have begun to explore the population structure and molecular determinants of AMR amongst E. coli isolates from Malawi. Methods: Ninety-four E. coli isolates from patients admitted to Queen’s Hospital, Malawi, were whole-genome sequenced. The isolates were selected on the basis of diversity of phenotypic resistance profiles and clinical source of isolation (blood, CSF and rectal swab). Sequence data were analysed using comparative genomics and phylogenetics. Results: Our results revealed the presence of five clades, which were strongly associated with E. coli phylogroups A, B1, B2, D and F. We identified 43 multilocus STs, of which ST131 (14.9%) and ST12 (9.6%) were the most common. We identified 25 AMR genes. The most common ESBL gene was blaCTX-M-15 and it was present in all five phylogroups and 11 STs, and most commonly detected in ST391 (4/4 isolates), ST648 (3/3 isolates) and ST131 [3/14 (21.4%) isolates]. Conclusions: This study has revealed a high diversity of lineages associated with AMR, including ESBL and fluoroquinolone resistance, in Malawi. The data highlight the value of longitudinal bacteraemia surveillance coupled with detailed molecular epidemiology in all settings, including low-income settings, in describing the global epidemiology of ESBL resistance

Global gene expression analysis of human erythroid progenitors

This article is available open access through the publisher’s website. Copyright @ 2011 American Society of Hematology. This article has an erratum: http://bloodjournal.hematologylibrary.org/content/118/26/6993.3.Understanding the pattern of gene expression during erythropoiesis is crucial for a synthesis of erythroid developmental biology. Here, we isolated 4 distinct populations at successive erythropoietin-dependent stages of erythropoiesis, including the terminal, pyknotic stage. The transcriptome was determined using Affymetrix arrays. First, we demonstrated the importance of using defined cell populations to identify lineage and temporally specific patterns of gene expression. Cells sorted by surface expression profile not only express significantly fewer genes than unsorted cells but also demonstrate significantly greater differences in the expression levels of particular genes between stages than unsorted cells. Second, using standard software, we identified more than 1000 transcripts not previously observed to be differentially expressed during erythroid maturation, 13 of which are highly significantly terminally regulated, including RFXAP and SMARCA4. Third, using matched filtering, we identified 12 transcripts not previously reported to be continuously up-regulated in maturing human primary erythroblasts. Finally, using transcription factor binding site analysis, we identified potential transcription factors that may regulate gene expression during terminal erythropoiesis. Our stringent lists of differentially regulated and continuously expressed transcripts containing many genes with undiscovered functions in erythroblasts are a resource for future functional studies of erythropoiesis. Our Human Erythroid Maturation database is available at https://cellline.molbiol.ox.ac.uk/eryth/index.html.National Health Service Blood and Transplant, National Institute for Health Research Biomedical Research Center Program, and National Institute for Health Research