Modeling uncertainty in mountain pine beetle management systems

This study attempts to introduce elements of data uncertainty into the Shore and Safranyik model for approximating risk and susceptibility ratings for Mountain Pine Beetle attack in the Morice Forest District of British Columbia, Canada. Data uncertainty is introduced into the modeling procedure by introducing attribute uncertainty and spatial (boundary) vagueness into representations of Forest Inventory Polygon data, an essential component of the Shore and Safranyik modeling system, for the purposes of assessing the effects of uncertainty on the results of the Shore and Safranyik susceptibility modeling procedure. Introducing uncertainty into the forest inventory data is done by introducing spatial vagueness to the discrete forest polygon data (accomplished using a geostatistical approach) as well as attribute uncertainty through a neighbourhood-based weighting algorithm, resulting in a forest inventory representation which incorporates both spatial and attribute uncertainty and can be incorporated into the Shore and Safranyik modeling procedure. The impacts of data uncertainty are assessed by comparing the results of the Shore and Safranyik model derived using representations of forest data which incorporates uncertainty, versus the use of traditional or discrete data inputs

Validation of the Mental Health Checklist (MHCL) during COVID-19 lockdown

The COVID-19 pandemic resulted in unprecedented disruption to everyday life, including widespread social distancing and self-quarantining aimed at reducing the virus spread. The Mental Health Checklist (MHCL) is a measure developed to assess psychological health during extended periods of isolation and confinement, and has shown strong psychometric properties in community samples and during Antarctic missions. This study validated the MHCL in a sample of 359 U.S. and U.K adults during the peak of the COVID-19 lockdown. Confirmatory factor analysis (CFA) tested model fit, and convergent validity analyses were conducted to compare the MHCL with validated measures of depression, anxiety and stress, as well as insomnia. The MHCL exhibited good model fit for most CFA indices, and showed strong convergent validity with other measures of psychological well-being. Findings suggest that the MHCL is useful for assessing mental health in a variety of environments and conditions

Polyclonal B Cell Differentiation and Loss of Gastrointestinal Tract Germinal Centers in the Earliest Stages of HIV-1 Infection

BACKGROUND: The antibody response to HIV-1 does not appear in the plasma until approximately 2–5 weeks after transmission, and neutralizing antibodies to autologous HIV-1 generally do not become detectable until 12 weeks or more after transmission. Moreover, levels of HIV-1–specific antibodies decline on antiretroviral treatment. The mechanisms of this delay in the appearance of anti-HIV-1 antibodies and of their subsequent rapid decline are not known. While the effect of HIV-1 on depletion of gut CD4(+) T cells in acute HIV-1 infection is well described, we studied blood and tissue B cells soon after infection to determine the effect of early HIV-1 on these cells. METHODS AND FINDINGS: In human participants, we analyzed B cells in blood as early as 17 days after HIV-1 infection, and in terminal ileum inductive and effector microenvironments beginning at 47 days after infection. We found that HIV-1 infection rapidly induced polyclonal activation and terminal differentiation of B cells in blood and in gut-associated lymphoid tissue (GALT) B cells. The specificities of antibodies produced by GALT memory B cells in acute HIV-1 infection (AHI) included not only HIV-1–specific antibodies, but also influenza-specific and autoreactive antibodies, indicating very early onset of HIV-1–induced polyclonal B cell activation. Follicular damage or germinal center loss in terminal ileum Peyer's patches was seen with 88% of follicles exhibiting B or T cell apoptosis and follicular lysis. CONCLUSIONS: Early induction of polyclonal B cell differentiation, coupled with follicular damage and germinal center loss soon after HIV-1 infection, may explain both the high rate of decline in HIV-1–induced antibody responses and the delay in plasma antibody responses to HIV-1. Please see later in the article for Editors' Summar

Expanding the diversity of mycobacteriophages: insights into genome architecture and evolution.

Mycobacteriophages are viruses that infect mycobacterial hosts such as Mycobacterium smegmatis and Mycobacterium tuberculosis. All mycobacteriophages characterized to date are dsDNA tailed phages, and have either siphoviral or myoviral morphotypes. However, their genetic diversity is considerable, and although sixty-two genomes have been sequenced and comparatively analyzed, these likely represent only a small portion of the diversity of the mycobacteriophage population at large. Here we report the isolation, sequencing and comparative genomic analysis of 18 new mycobacteriophages isolated from geographically distinct locations within the United States. Although no clear correlation between location and genome type can be discerned, these genomes expand our knowledge of mycobacteriophage diversity and enhance our understanding of the roles of mobile elements in viral evolution. Expansion of the number of mycobacteriophages grouped within Cluster A provides insights into the basis of immune specificity in these temperate phages, and we also describe a novel example of apparent immunity theft. The isolation and genomic analysis of bacteriophages by freshman college students provides an example of an authentic research experience for novice scientists

Expanding the Diversity of Mycobacteriophages: Insights into Genome Architecture and Evolution

Mycobacteriophages are viruses that infect mycobacterial hosts such as Mycobacterium smegmatis and Mycobacterium tuberculosis. All mycobacteriophages characterized to date are dsDNA tailed phages, and have either siphoviral or myoviral morphotypes. However, their genetic diversity is considerable, and although sixty-two genomes have been sequenced and comparatively analyzed, these likely represent only a small portion of the diversity of the mycobacteriophage population at large. Here we report the isolation, sequencing and comparative genomic analysis of 18 new mycobacteriophages isolated from geographically distinct locations within the United States. Although no clear correlation between location and genome type can be discerned, these genomes expand our knowledge of mycobacteriophage diversity and enhance our understanding of the roles of mobile elements in viral evolution. Expansion of the number of mycobacteriophages grouped within Cluster A provides insights into the basis of immune specificity in these temperate phages, and we also describe a novel example of apparent immunity theft. The isolation and genomic analysis of bacteriophages by freshman college students provides an example of an authentic research experience for novice scientists

Trust in scientists and their role in society across 67 countries

Scientific information is crucial for evidence-based decision-making. Public trust in science can help decision-makers act based on the best available evidence, especially during crises such as climate change or the COVID-19 pandemic. However, in recent years the epistemic authority of science has been challenged, causing concerns about low public trust in scientists. Here we interrogated these concerns with a pre-registered 67-country survey of 71,417 respondents on all inhabited continents and find that in most countries, a majority of the public trust scientists and think that scientists should be more engaged in policymaking. We further show that there is a discrepancy between the public’s perceived and desired priorities of scientific research. Moreover, we find variations between and within countries, which we explain with individual-and country-level variables,including political orientation. While these results do not show widespread lack of trust in scientists, we cannot discount the concern that lack of trust in scientists by even a small minority may affect considerations of scientific evidence in policymaking. These findings have implications for scientists and policymakers seeking to maintain and increase trust in scientists