Effect of Abundance and Survey Protocol on Estimates of Occupancy and Detection Probability for Northern Bobwhites

We compared estimates of occupancy of northern bobwhite (Colinus virginianus) between areas with relatively low and high abundance using single-survey and multiple-survey protocols, with and without accounting for detection probability, and investigated how time during the breeding season affected detection probability in Oklahoma, USA, in 2009–2011. Estimates of occupancy and detection probability increased as the number of survey occasions increased. Detection probability was significantly higher in the area of high abundance (P 0.001), and increased as the breeding season advanced from mid-May to late July. Accounting for detection probability increased occupancy estimates by 31% in the low-abundance area but only 1.9% in the high abundance area when using 3 survey occasions per year. Managers using occupancy to detect changes in bobwhite populations should use 4 survey occasions per year to ensure accurate estimates of both occupancy and detection probability

Northern Bobwhite and Bird Community Response to Habitat Restoration in Oklahoma

Reversing the population decline of Northern Bobwhites (Colinus virginianus, hereafter bobwhite), an economically important gamebird, in Oklahoma, is a priority for wildlife managers in the state. The Quail Habitat Restoration Initiative (QHRI) was initiated in 2008 to address this issue by doing cost-share with private landowners for the restoration of bobwhite habitat. The purpose of my study was to evaluate the effect of this program on bobwhites and other grassland bird species of conservation concern, and evaluate the key factors affecting the outcome of the program. There was very little bobwhite response to restoration treatments, and occupancy of restoration areas did not significantly increase. The main habitat factor effecting bobwhite occupancy on a sample unit was overstory canopy cover, with a secondary effect of visual obstruction. Bobwhite occupancy was also significantly affected by the amount of habitat within 1 km of the sample unit. Most restoration areas were within the appropriate landscape context for bobwhites to recolonize the site, but proper local habitat condition were only created within a few sample units and this was the limiting factor in the success of the QHRI program. Community analysis showed that bird community composition responded most strongly to overstory canopy cover and visual obstruction, and many declining grassland bird species were strongly associated with bobwhites in species groupings from cluster analysis. Bobwhites show the potential to act as an umbrella species for declining bird species that rely on early-successional habitat. Occupancy modeling showed that estimates of bobwhite occupancy may be biased low by as much as 30% if detection probability is not accounted for, especially in areas where they are uncommon. Maximizing detection probability in the study design, and accounting for it in the analysis, must be done if estimates of bobwhite occupancy are to be accurate.Department of Natural Resource Ecology and Managemen

Of detectability and camouflage: evaluating Pollard Walk rules using a common, cryptic butterfly

Abstract Estimating distribution and abundance of species depends on the probability at which individuals are detected. Butterflies are of conservation interest worldwide, but data collected with Pollard walks—the standard for national monitoring schemes—are often analyzed assuming that changes in detectability are negligible within recommended sampling criteria. The implications of this practice remain poorly understood. Here, we evaluated the effects of sampling conditions on butterfly counts from Pollard walks using the Arctic fritillary, a common but cryptic butterfly in boreal forests of Alberta, Canada. We used an open population binomial N‐mixture model to disentangle the effects of habitat suitability and phenology on abundance of Arctic fritillaries, and its detectability by sampling different conditions of temperature, wind, cloud cover, and hour of the day. Detectability varied by one order of magnitude within the criteria recommended for Pollard walks (P varying between 0.04 and 0.45), and simulations show how sampling in suboptimal conditions increases substantially the risk of false‐absence records (e.g., false‐absences are twice as likely than true‐presences when sampling 10 Arctic fritillaries at P = 0.04). Our results suggest that the risk of false‐absences is highest for species that are poorly detectable, low in abundance, and with short flight periods. Analysis with open population binomial N‐mixture models could improve estimates of abundance and distribution for rare species of conservation interest, while providing a powerful method for assessing butterfly phenology, abundance, and behavior using counts from Pollard walks, but require more intensive sampling than conventional monitoring schemes

Notch-Deficient Skin Induces a Lethal Systemic B-Lymphoproliferative Disorder by Secreting TSLP, a Sentinel for Epidermal Integrity

Epidermal keratinocytes form a highly organized stratified epithelium and sustain a competent barrier function together with dermal and hematopoietic cells. The Notch signaling pathway is a critical regulator of epidermal integrity. Here, we show that keratinocyte-specific deletion of total Notch signaling triggered a severe systemic B-lymphoproliferative disorder, causing death. RBP-j is the DNA binding partner of Notch, but both RBP-j–dependent and independent Notch signaling were necessary for proper epidermal differentiation and lipid deposition. Loss of both pathways caused a persistent defect in skin differentiation/barrier formation. In response, high levels of thymic stromal lymphopoietin (TSLP) were released into systemic circulation by Notch-deficient keratinocytes that failed to differentiate, starting in utero. Exposure to high TSLP levels during neonatal hematopoiesis resulted in drastic expansion of peripheral pre- and immature B-lymphocytes, causing B-lymphoproliferative disorder associated with major organ infiltration and subsequent death, a previously unappreciated systemic effect of TSLP. These observations demonstrate that local skin perturbations can drive a lethal systemic disease and have important implications for a wide range of humoral and autoimmune diseases with skin manifestations

Multi-platform assessment of transcriptional profiling technologies utilizing a precise probe mapping methodology

BACKGROUND: The arrival of RNA-seq as a high-throughput method competitive to the established microarray technologies has necessarily driven a need for comparative evaluation. To date, cross-platform comparisons of these technologies have been relatively few in number of platforms analyzed and were typically gene name annotation oriented. Here, we present a more extensive and yet precise assessment to elucidate differences and similarities in performance of numerous aspects including dynamic range, fidelity of raw signal and fold-change with sample titration, and concordance with qRT-PCR (TaqMan). To ensure that these results were not confounded by incompatible comparisons, we introduce the concept of probe mapping directed “transcript pattern”. A transcript pattern identifies probe(set)s across platforms that target a common set of transcripts for a specific gene. Thus, three levels of data were examined: entire data sets, data derived from a subset of 15,442 RefSeq genes common across platforms, and data derived from the transcript pattern defined subset of 7,034 RefSeq genes. RESULTS: In general, there were substantial core similarities between all 6 platforms evaluated; but, to varying degrees, the two RNA-seq protocols outperformed three of the four microarray platforms in most categories. Notably, a fourth microarray platform, Agilent with a modified protocol, was comparable, or marginally superior, to the RNA-seq protocols within these same assessments, especially in regards to fold-change evaluation. Furthermore, these 3 platforms (Agilent and two RNA-seq methods) demonstrated over 80 % fold-change concordance with the gold standard qRT-PCR (TaqMan). CONCLUSIONS: This study suggests that microarrays can perform on nearly equal footing with RNA-seq, in certain key features, specifically when the dynamic range is comparable. Furthermore, the concept of a transcript pattern has been introduced that may minimize potential confounding factors of multi-platform comparison and may be useful for similar evaluations. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (doi:10.1186/s12864-015-1913-6) contains supplementary material, which is available to authorized users

Randomised, double-blind, multicentre, mixed-methods, dose-escalation feasibility trial of mirtazapine for better treatment of severe breathlessness in advanced lung disease (BETTER-B feasibility)

© Author(s) (or their employer(s)) 2020. Re-use permitted under CC BY. Published by BMJ. New treatments are required for severe breathlessness in advanced disease. We conducted a randomised feasibility trial of mirtazapine over 28 days in adults with a modified medical research council breathlessness scale score ≥3. Sixty-four patients were randomised (409 screened), achieving our primary feasibility endpoint of recruitment. Most patients had COPD or interstitial lung disease; 52 (81%) completed the trial. There were no differences between placebo and mirtazapine in tolerability or safety, and blinding was maintained. Worst breathlessness ratings at day 28 (primary clinical activity endpoint) were, 7.1 (SD 2.3, placebo) and 6.3 (SD 1.8, mirtazapine). A phase III trial of mirtazapine is indicated. Trial registration: ISRCTN 32236160; European Clinical Trials Database (EudraCT no: 2015-004064-11)

Transformed non‐Hodgkin lymphoma in the rituximab era: analysis of the NCCN outcomes database

Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/100290/1/bjh12570.pd

Reducing Suffering During Conflict: The Interface Between Buddhism And International Humanitarian Law

This article stems from a project launched by the International Committee of the Red Cross (ICRC) in 2017 to examine the degree to which Buddhism might complement or enhance international humanitarian law (IHL), also known as ‘the law of war’ or ‘the law of armed conflict’. Given that Buddhist teachings discourage violence, scholarship has critiqued Buddhists’ involvement in armed conflict rather than considered how Buddhism might contribute to regulating the conduct of hostilities once war has broken out. Yet the Buddhist aim to reduce suffering is particularly relevant during armed conflict, and the empirical realism of early Buddhist texts shows that early Buddhist communities were very much aware of its grim reality. The article investigates the evidence for this empirical realism before exploring a range of concepts, doctrines and practices from within Buddhism that are pertinent to the recognition and implementation of IHL principles and the conduct of war. While IHL lays down explicit rules to follow during war, Buddhism emphasises broader ethical principles to be applied, so as not to dilute its ideal of non-violence. At a deeper level, it addresses the intention or motivation of parties to armed conflict, and possesses psychological insights and resources to help change their behaviour

Forecasting the response of Earth's surface to future climatic and land use changes: a review of methods and research needs

In the future, Earth will be warmer, precipitation events will be more extreme, global mean sea level will rise, and many arid and semiarid regions will be drier. Human modifications of landscapes will also occur at an accelerated rate as developed areas increase in size and population density. We now have gridded global forecasts, being continually improved, of the climatic and land use changes (C&LUC) that are likely to occur in the coming decades. However, besides a few exceptions, consensus forecasts do not exist for how these C&LUC will likely impact Earth-surface processes and hazards. In some cases, we have the tools to forecast the geomorphic responses to likely future C&LUC. Fully exploiting these models and utilizing these tools will require close collaboration among Earth-surface scientists and Earth-system modelers. This paper assesses the state-of-the-art tools and data that are being used or could be used to forecast changes in the state of Earth's surface as a result of likely future C&LUC. We also propose strategies for filling key knowledge gaps, emphasizing where additional basic research and/or collaboration across disciplines are necessary. The main body of the paper addresses cross-cutting issues, including the importance of nonlinear/threshold-dominated interactions among topography, vegetation, and sediment transport, as well as the importance of alternate stable states and extreme, rare events for understanding and forecasting Earth-surface response to C&LUC. Five supplements delve into different scales or process zones (global-scale assessments and fluvial, aeolian, glacial/periglacial, and coastal process zones) in detail

Tracing the role of human civilization in the globalization of plant pathogens

Acknowledgments. We apologize to all those colleagues whose work was not cited because of space restrictions.Peer reviewedPostprin