SPLANG-a synthetic poisson-lognormal-based abundance and network generative model for microbial interaction inference algorithms.

Microbes are pervasive and their interaction with each other and the environment can impact fields as diverse as health and agriculture. While network inference and related algorithms that use abundance data from pyrosequencing can infer microbial interaction networks, the ambiguity surrounding the actual underlying networks hampers the validation of these algorithms. This study introduces a generative model to synthesize both the underlying interactive network and observable abundance data, serving as a test bed for the existing and future network inference algorithms.

Changes in physical activity among Canadian adults more than 6 months into the COVID-19 pandemic: a secondary analysis of the INTERACT cohort study.

Objective: To estimate the effect of (a) the COVID-19 pandemic and (b) COVID-19 restriction stringency on daily minutes of device-measured moderate-to-vigorous physical activity (MVPA).

Design: Physical activity data were collected from the INTerventions, Equity, Research and Action in Cities Team (INTERACT) cohorts in Montreal, Saskatoon and Vancouver before (May 2018 to February 2019, 'phase 1') and during the pandemic (October 2020 to February 2021, 'phase 2'). We estimated the effect of the two exposures by comparing daily MVPA measured (a) before vs during the pandemic (phase 1 vs phase 2) and (b) at different levels of COVID-19 restriction stringency during phase 2.

Comparing Contact Tracing Through Bluetooth and GPS Surveillance Data: Simulation-Driven Approach.

Background: Accurate and responsive epidemiological simulations of epidemic outbreaks inform decision-making to mitigate the impact of pandemics. These simulations must be grounded in quantities derived from measurements, among which the parameters associated with contacts between individuals are notoriously difficult to estimate. Digital contact tracing data, such as those provided by Bluetooth beaconing or GPS colocating, can provide more precise measures of contact than traditional methods based on direct observation or self-reporting.

Comparing Location Data From Smartphone and Dedicated Global Positioning System Devices: Implications for Epidemiologic Research.

In this study, we compared location data from a dedicated Global Positioning System (GPS) device with location data from smartphones. Data from the Interventions, Equity, and Action in Cities Team (INTERACT) Study, a study examining the impact of urban-form changes on health in 4 Canadian cities (Victoria, Vancouver, Saskatoon, and Montreal), were used. A total of 337 participants contributed data collected for about 6 months from the Ethica Data smartphone application (Ethica Data Inc.

Impacts of observation frequency on proximity contact data and modeled transmission dynamics.

Transmission of many communicable diseases depends on proximity contacts among humans. Modeling the dynamics of proximity contacts can help determine whether an outbreak is likely to trigger an epidemic. While the advent of commodity mobile devices has eased the collection of proximity contact data, battery capacity and associated costs impose tradeoffs between the observation frequency and scanning duration used for contact detection.

Synaptotagmin 9 Modulates Spontaneous Neurotransmitter Release in Striatal Neurons by Regulating Substance P Secretion.

Synaptotagmin 9 (SYT9) is a tandem C2 domain Ca sensor for exocytosis in neuroendocrine cells; its function in neurons remains unclear. Here, we show that, in mixed-sex cultures, SYT9 does not trigger rapid synaptic vesicle exocytosis in mouse cortical, hippocampal, or striatal neurons, unless it is massively overexpressed. In striatal neurons, loss of SYT9 reduced the frequency of spontaneous neurotransmitter release events (minis).

A theory-based model of cumulative activity.

Energy expenditure can be used to examine the health of individuals and the impact of environmental factors on physical activity. One of the more common ways to quantify energy expenditure is to process accelerometer data into some unit of measurement for this expenditure, such as Actigraph activity counts, and bin those measures into physical activity levels. However, accepted thresholds can vary between demographics, and some units of energy measurements do not currently have agreed upon thresholds.

Using combined Global Position System and accelerometer data points to examine how built environments and gentrification are associated with physical activity in four Canadian cities.

Background: Built and social environments are associated with physical activity. Global Positioning Systems (GPS) and accelerometer data can capture how people move through their environments and provide promising tools to better understand associations between environmental characteristics and physical activity. The purpose of this study is to examine the associations between GPS-derived exposure to built environment and gentrification characteristics and accelerometer-measured physical activity in a sample of adults across four cities.

Positron-emitting radiotracers spatially resolve unexpected biogeochemical relationships linked with methane oxidation in Arctic soils.

Arctic soils are marked by cryoturbic features, which impact soil-atmosphere methane (CH ) dynamics vital to global climate regulation. Cryoturbic diapirism alters C/N chemistry within frost boils by introducing soluble organic carbon and nutrients, potentially influencing microbial CH oxidation. CH oxidation in soils, however, requires a spatio-temporal convergence of ecological factors to occur.

Why machine learning (ML) has failed physical activity research and how we can improve.

Measuring physical activity is a critical issue for our understanding of the health benefits of human movement. Machine learning (ML), using accelerometer data, has become a common way to measure physical activity. ML has failed physical activity measurement research in four important ways.

Wave 1 results of the INTerventions, Research, and Action in Cities Team (INTERACT) cohort study: Examining spatio-temporal measures for urban environments and health.

Built environment interventions have the potential to improve population health and reduce health inequities. The objective of this paper is to present the first wave of the INTErventions, Research, and Action in Cities Team (INTERACT) cohort studies in Victoria, Vancouver, Saskatoon, and Montreal, Canada. We examine how our cohorts compared to Canadian census data and present summary data for our outcomes of interest (physical activity, well-being, and social connectedness).

The Effect of Season and Neighbourhood-Built Environment on Home Area Sedentary Behaviour in 9-14 Year Old Children.

There is little understanding of how the built environment shapes activity behaviours in children over different seasons. This study sought to establish how seasonal weather patterns, in a given year in a mid-western Canadian city, affect sedentary time (SED) in youth and how the relationship between season and SED are moderated by the built environment in their home neighbourhood. Families with children aged 9-14 years were recruited from the prairie city of Saskatoon, Canada.

The future of activity space and health research.

We discuss the future of activity space and health research in the context of a recently published systematic review. Our discussion outlines a number of elements for reflection among the research community. We need to think beyond activity space and reconceptualize exposure in era of high volume, high precision location data.

Intrinsic dimensionality of human behavioral activity data.

Patterns of spatial behavior dictate how we use our infrastructure, encounter other people, or are exposed to services and opportunities. Understanding these patterns through the analysis of data commonly available through commodity smartphones has become an important arena for innovation in both academia and industry. The resulting datasets can quickly become massive, indicating the need for concise understanding of the scope of the data collected.

Structural equation modeling of a winnowed soil microbiome identifies how invasive plants re-structure microbial networks.

The development of microbial networks is central to ecosystem functioning and is the hallmark of complex natural systems. Characterizing network development over time and across environmental gradients is hindered by the millions of potential interactions among community members, limiting interpretations of network evolution. We developed a feature selection approach using data winnowing that identifies the most ecologically influential microorganisms within a network undergoing change.

INTERACT: A comprehensive approach to assess urban form interventions through natural experiments.

Background: Urban form interventions can result in positive and negative impacts on physical activity, social participation, and well-being, and inequities in these outcomes. Natural experiment studies can advance our understanding of causal effects and processes related to urban form interventions. The INTErventions, Research, and Action in Cities Team (INTERACT) is a pan-Canadian collaboration of interdisciplinary scientists, urban planners, and public health decision makers advancing research on the design of healthy and sustainable cities for all.

Multiscale entropy rate analysis of complex mobile agents.

Accurate prediction of the motion of objects is a central scientific goal. For deterministic or stochastic processes, models exist which characterize motion with a high degree of reliability. For complex systems, or those where objects have a degree of agency, characterizing motion is far more challenging.

External Ion Access in the Na/K Pump: Kinetics of Na, K, and Quaternary Amine Interaction.

Na/K pumps build essential ion gradients across the plasmalemma of animal cells by coupling the extrusion of three Na, with the import of two K and the hydrolysis of one ATP molecule. The mechanisms of selectivity and competition between Na, K, and inhibitory amines remain unclear. We measured the effects of external tetrapropylammonium (TPA) and ethylenediamine (EDA) on three different Na/K pump transport modes in voltage-clamped Xenopus oocytes: 1) outward pump current (I), 2) passive inward H current at negative voltages without Na or K (I), and 3) transient charge movement reporting the voltage-dependent extracellular binding/release of Na (Q).

How many days are enough?: capturing routine human mobility.

Wedding mobile phone sensor technology and human spatial behaviour has great potential. The ubiquity of Global Positioning Systems (GPS) technology has made gathering data about human mobility simpler, more precise, and with higher fidelity, providing minute-by-minute records of the locations of cohorts from dozens of participants. While this data provides a strong basis for Geographic Information Science research, it also constitutes an invasion of the participants' privacy and can provide more information than researchers require to answer their questions.

A glossary for big data in population and public health: discussion and commentary on terminology and research methods.

The volume and velocity of data are growing rapidly and big data analytics are being applied to these data in many fields. Population and public health researchers may be unfamiliar with the terminology and statistical methods used in big data. This creates a barrier to the application of big data analytics.

Ethical implications of location and accelerometer measurement in health research studies with mobile sensing devices.

Quantification of individual behaviours using mobile sensing devices, including physical activity and spatial location, is a rapidly growing field in both academic research and the corporate world. In this case study, we summarize the literature examining the ethical aspects of mobile sensing and argue that a robust discussion about the ethical implications of mobile sensing for research purposes has not occurred sufficiently in the literature. Based on our literature summary and guided by basic ethical principles set out in Canadian, US, and International Ethics documents we propose four areas where further discussion should occur: consent, privacy and confidentiality, mitigating risk, and consideration of vulnerable populations.

Building Research Capacity: Results of a Feasibility Study Using a Novel mHealth Epidemiological Data Collection System Within a Gestational Diabetes Population.

Public health researchers have traditionally relied on individual self-reporting when collecting much epidemiological surveillance data. Data acquisition can be costly, difficult to acquire, and the data often notoriously unreliable. An interesting option for the collection of individual health (or indicators of individual health) data is the personal smartphone.

Intracellular Requirements for Passive Proton Transport through the Na,K-ATPase.

The Na,K-ATPase (NKA or Na/K pump) hydrolyzes one ATP to exchange three intracellular Na+ (Na) for two extracellular K+ (K) across the plasma membrane by cycling through a set of reversible transitions between phosphorylated and dephosphorylated conformations, alternately opening ion-binding sites externally (E2) or internally (E1). With subsaturating [Na] and [K], the phosphorylated E2P conformation passively imports protons generating an inward current (I), which may be exacerbated in NKA-subunit mutations associated with human disease. To elucidate the mechanisms of I, we studied the effects of intracellular ligands (transported ions, nucleotides, and beryllium fluoride) on I and, for comparison, on transient currents measured at normal Na (Q).

A Theoretical Basis for Entropy-Scaling Effects in Human Mobility Patterns.

Characterizing how people move through space has been an important component of many disciplines. With the advent of automated data collection through GPS and other location sensing systems, researchers have the opportunity to examine human mobility at spatio-temporal resolution heretofore impossible. However, the copious and complex data collected through these logging systems can be difficult for humans to fully exploit, leading many researchers to propose novel metrics for encapsulating movement patterns in succinct and useful ways.

Design and methods of a social network isolation study for reducing respiratory infection transmission: The eX-FLU cluster randomized trial.

Background: Social networks are increasingly recognized as important points of intervention, yet relatively few intervention studies of respiratory infection transmission have utilized a network design. Here we describe the design, methods, and social network structure of a randomized intervention for isolating respiratory infection cases in a university setting over a 10-week period.

Methodology/principal Findings: 590 students in six residence halls enrolled in the eX-FLU study during a chain-referral recruitment process from September 2012-January 2013.