Impact of ActiGraph® cutoffs on time spent in moderate to vigorous physical activities in COPD

ActiGraphs® are often used to assess time in moderate to vigorous physical activities (MVPA) in people with COPD. Different cutoffs can be used to quantify MVPA. If they yield similar or different MVPA results is yet unknown. There are no cutoffs specifically developed, nor validated, for COPD, but Troiano and Freedson cutoffs are the most used. Recently, Santos-Lozano proposed a cutoff specific for older people, that has been used in COPD. This study aimed to explore MVPA results quantified with different cutoffs in COPD. Participants wore the ActiGraph wGT3X for 7 days and data were included if they had used it for at least 8h (7am to 10pm) for 4 days (Choi algorithm for non-wear time). MVPA was estimated using the cutoffs from Troiano, Freedson and Santos-Lozano. Differences between cutoffs were explored with Friedman Test, followed by post-hoc comparisons. 107 people with COPD (79%♂; 68±8y; FEV1pp 49±17) were included. MVPA was affected by cutoffs (χ2(2)=194.56, p<0.001). Santos-Lozano cutoff yielded the highest MVPA estimates, followed by Freedson and Troiano cutoffs (median [Interquatile Range] = 57[30-90] vs 16[4-38] vs 8[2-22] (Fig.1). All cutoffs differed significantly from each other (p<0.001). The cutoff selection affects MVPA estimates in people with COPD and may mislead the classification of these patients as physically (in)active. Future studies should develop MVPA cutoffs adapted to people with COPD.CENTR(AR): pulmões em andamento by Programa de Parcerias para o Impacto, Portugal Inovação Social through Programa Operacional Inclusão Social e Emprego (POISE-03-4639-FSE-000597). Fundação para a Ciência e a Tecnologia (SFRH/BD/148738/2019), by Fundo Social Europeu through Programa Operacional Regional Centro, and by Programa Operacional Competitividade e Internacionalização (COMPETE 2020 - POCI-01-0145-FEDER-007628; UIDB/04501/2020).publishe

Functional status and impact of the disease in people with COPD according to symptoms’ burden

Background: COPD is a heterogeneous disease. Better understanding of its trajectory, especially considering symptoms level, may help improving disease management. We described the evolution of functional status and impact of the disease in people with COPD according to symptoms level. Methods: People with COPD were assessed monthly for 6 months. Participants were grouped by the Global Initiative for Chronic Obstructive Lung Disease (GOLD) criteria in low (GOLD A & C) or high (GOLD B & D) symptom burden, based on the baseline values in the modified medical research council dyspnoea scale. Quadriceps muscle strength (QMS)–handheld dynamometry, 1-minute sit-to-stand test (1STS) and COPD assessment test (CAT) were collected. Differences within/between groups over time were explored with (non-)parametric mixed ANOVAs and Bonferroni-adjusted pairwise comparisons. Results: 87 people (85%♂, 68±9y, FEV1 51±20pp, 54% high symptoms) participated. People with low symptoms presented higher 1STS (p=0.01) and lower CAT (p<0.01). Improvements in 1STS and CAT over time (p<0.01) were found regardless of group allocation (Fig. 1). There were no group*time interaction or other significant differences. Conclusion: The pattern of progression in functional status and impact of the disease seems similar in people with COPD independently of symptoms’ burden, with improvements in CAT and 1STS over time. Reasons for this finding must be explored.publishe

Can space-for-time-substitution surveys represent zooplankton biodiversity patterns and their relationship to environmental drivers?

Space-for-Time-Substitution surveys (SFTS) are commonly used to describe zooplankton community dynamics and to determine lake ecosystem health. SFTS surveys typically combine single point observations from many lakes to evaluate the response of zooplankton community structure and dynamics (e.g., species abundance and biomass, diversity, demographics and modeled rate processes) to spatial gradients in hypothesized environmental drivers (e.g., temperature, nutrients, predation), in lieu of tracking such responses over long time scales. However, the reliability and reproducibility of SFTS zooplankton surveys have not yet been comprehensively tested against empirically-based community dynamics from longterm monitoring efforts distributed worldwide. We use a recently compiled global data set of more than 100 lake zooplankton time series to test whether SFTS surveys can accurately capture zooplankton diversity, and the hypothesized relationship with temperature, using simulated SFTS surveys of the time series data. Specifically, we asked: (1) to what degree can SFTS surveys capture observed biodiversity dynamics; (2) how does timing and duration of sampling affect detected biodiversity patterns; (3) does biodiversity ubiquitously increase with temperature across lakes, or vary by climate zone or lake type; and (4) do results from SFTS surveys produce comparable biodiversity-temperature relationship(s) to empirical data within and among lakes? Testing biodiversity-ecosystem function (BEF) relationships, and the drivers of such relationships, requires a solid data basis. Our work provides a global perspective on the design and usefulness of (long-term) zooplankton monitoring programs and how much confidence we can place in the zooplankton biodiversity patterns observed from SFTS surveys

BioTIME: A database of biodiversity time series for the Anthropocene.

MotivationThe BioTIME database contains raw data on species identities and abundances in ecological assemblages through time. These data enable users to calculate temporal trends in biodiversity within and amongst assemblages using a broad range of metrics. BioTIME is being developed as a community-led open-source database of biodiversity time series. Our goal is to accelerate and facilitate quantitative analysis of temporal patterns of biodiversity in the Anthropocene.Main types of variables includedThe database contains 8,777,413 species abundance records, from assemblages consistently sampled for a minimum of 2 years, which need not necessarily be consecutive. In addition, the database contains metadata relating to sampling methodology and contextual information about each record.Spatial location and grainBioTIME is a global database of 547,161 unique sampling locations spanning the marine, freshwater and terrestrial realms. Grain size varies across datasets from 0.0000000158 km2 (158 cm2) to 100 km2 (1,000,000,000,000 cm2).Time period and grainBioTIME records span from 1874 to 2016. The minimal temporal grain across all datasets in BioTIME is a year.Major taxa and level of measurementBioTIME includes data from 44,440 species across the plant and animal kingdoms, ranging from plants, plankton and terrestrial invertebrates to small and large vertebrates.Software format.csv and .SQL

Rainfall and sentinel chicken seroconversions predict human cases of Murray Valley encephalitis in the north of Western Australia

Background Murray Valley encephalitis virus (MVEV) is a flavivirus that occurs in Australia and New Guinea. While clinical cases are uncommon, MVEV can cause severe encephalitis with high mortality. Sentinel chicken surveillance is used at many sites around Australia to provide an early warning system for risk of human infection in areas that have low population density and geographical remoteness. MVEV in Western Australia occurs in areas of low population density and geographical remoteness, resulting in logistical challenges with surveillance systems and few human cases. While epidemiological data has suggested an association between rainfall and MVEV activity in outbreak years, it has not been quantified, and the association between rainfall and sporadic cases is less clear. In this study we analysed 22 years of sentinel chicken and human case data from Western Australia in order to evaluate the effectiveness of sentinel chicken surveillance for MVEV and assess the association between rainfall and MVEV activity. Methods Sentinel chicken seroconversion, human case and rainfall data from the Kimberley and Pilbara regions of Western Australia from 1990 to 2011 were analysed using negative binomial regression. Sentinel chicken seroconversion and human cases were used as dependent variables in the model. The model was then tested against sentinel chicken and rainfall data from 2012 and 2013.Results Sentinel chicken seroconversion preceded all human cases except two in March 1993. Rainfall in the prior three months was significantly associated with both sentinel chicken seroconversion and human cases across the regions of interest. Sentinel chicken seroconversion was also predictive of human cases in the models. The model predicted sentinel chicken seroconversion in the Kimberley but not in the Pilbara, where seroconversions early in 2012 were not predicted. The latter may be due to localised MVEV activity in isolated foci at dams, which do not reflect broader virus activity in the region. Conclusions We showed that rainfall and sentinel chickens provide a useful early warning of MVEV risk to humans across endemic and epidemic areas, and that a combination of the two indicators improves the ability to assess MVEV risk and inform risk management measures

Data Descriptor : A European Multi Lake Survey dataset of environmental variables, phytoplankton pigments and cyanotoxins

Under ongoing climate change and increasing anthropogenic activity, which continuously challenge ecosystem resilience, an in-depth understanding of ecological processes is urgently needed. Lakes, as providers of numerous ecosystem services, face multiple stressors that threaten their functioning. Harmful cyanobacterial blooms are a persistent problem resulting from nutrient pollution and climate-change induced stressors, like poor transparency, increased water temperature and enhanced stratification. Consistency in data collection and analysis methods is necessary to achieve fully comparable datasets and for statistical validity, avoiding issues linked to disparate data sources. The European Multi Lake Survey (EMLS) in summer 2015 was an initiative among scientists from 27 countries to collect and analyse lake physical, chemical and biological variables in a fully standardized manner. This database includes in-situ lake variables along with nutrient, pigment and cyanotoxin data of 369 lakes in Europe, which were centrally analysed in dedicated laboratories. Publishing the EMLS methods and dataset might inspire similar initiatives to study across large geographic areas that will contribute to better understanding lake responses in a changing environment.Peer reviewe

Signature-Tagged Mutagenesis in a Chicken Infection Model Leads to the Identification of a Novel Avian Pathogenic Escherichia coli Fimbrial Adhesin

The extraintestinal pathogen, avian pathogenic E. coli (APEC), known to cause systemic infections in chickens, is responsible for large economic losses in the poultry industry worldwide. In order to identify genes involved in the early essential stages of pathogenesis, namely adhesion and colonization, Signature-tagged mutagenesis (STM) was applied to a previously established lung colonization model of infection by generating and screening a total of 1,800 mutants of an APEC strain IMT5155 (O2:K1:H5; Sequence type complex 95). The study led to the identification of new genes of interest, including two adhesins, one of which coded for a novel APEC fimbrial adhesin (Yqi) not described for its role in APEC pathogenesis to date. Its gene product has been temporarily designated ExPEC Adhesin I (EA/I) until the adhesin-specific receptor is identified. Deletion of the ExPEC adhesin I gene resulted in reduced colonization ability by APEC strain IMT5155 both in vitro and in vivo. Furthermore, complementation of the adhesin gene restored its ability to colonize epithelial cells in vitro. The ExPEC adhesin I protein was successfully expressed in vitro. Electron microscopy of an afimbriate strain E. coli AAEC189 over-expressed with the putative EA/I gene cluster revealed short fimbrial-like appendages protruding out of the bacterial outer membrane. We observed that this adhesin coding gene yqi is prevalent among extraintestinal pathogenic E. coli (ExPEC) isolates, including APEC (54.4%), uropathogenic E. coli (UPEC) (65.9%) and newborn meningitic E. coli (NMEC) (60.0%), and absent in all of the 153 intestinal pathogenic E. coli strains tested, thereby validating the designation of the adhesin as ExPEC Adhesin I. In addition, prevalence of EA/I was most frequently associated with the B2 group of the EcoR classification and ST95 complex of the multi locus sequence typing (MLST) scheme, with evidence of a positive selection within this highly pathogenic complex. This is the first report of the newly identified and functionally characterized ExPEC adhesin I and its significant role during APEC infection in chickens