phyr: Anrpackage for phylogenetic species-distribution modelling in ecological communities

Model-based approaches are increasingly popular in ecological studies. A good example of this trend is the use of joint species distribution models to ask questions about ecological communities. However, most current applications of model-based methods do not include phylogenies despite the well-known importance of phylogenetic relationships in shaping species distributions and community composition. In part, this is due to a lack of accessible tools allowing ecologists to fit phylogenetic species distribution models easily. To fill this gap, therpackagephyr(pronounced fire) implements a suite of metrics, comparative methods and mixed models that use phylogenies to understand and predict community composition and other ecological and evolutionary phenomena. Thephyrworkhorse functions are implemented in C++ making all calculations and model estimations fast. phyrcan fit a variety of models such as phylogenetic joint-species distribution models, spatiotemporal-phylogenetic autocorrelation models, and phylogenetic trait-based bipartite network models.phyralso estimates phylogenetically independent trait correlations with measurement error to test for adaptive syndromes and performs fast calculations of common alpha and beta phylogenetic diversity metrics. Allphyrmethods are united under Brownian motion or Ornstein-Uhlenbeck models of evolution, and phylogenetic terms are modelled as phylogenetic covariance matrices. The functions and model formula syntax we propose inphyrprovide an easy-to-use collection of tools that we hope will ignite the use of phylogenies to address a variety of ecological questions

TRPV1 channels in human skeletal muscle feed arteries: implications for vascular function

New Findings What is the central question of this study? We sought to determine whether human skeletal muscle feed arteries (SFMAs) express TRPV1 channels and what role they play in modulating vascular function. What is the main finding and its importance? Human SMFAs do express functional TRPV1 channels that modulate vascular function, specifically opposing α-adrenergic receptor-mediated vasocontraction and potentiating vasorelaxation, in an endothelium-dependent manner, as evidenced by the α1-receptor-mediated responses. Thus, the vasodilatory role of TRPV1 channels, and their ligand capsaicin, could be a potential therapeutic target for improving vascular function. Additionally, given the ‘sympatholytic’ effect of TRPV1 activation and known endogenous activators (anandamide, reactive oxygen species, H+, etc.), TRPV1 channels might contribute to functional sympatholysis during exercise. To examine the role of the transient receptor potential vanilloid type 1 (TRPV1) ion channel in the vascular function of human skeletal muscle feed arteries (SMFAs) and whether activation of this heat-sensitive receptor could be involved in modulating vascular function, SMFAs from 16 humans (63 ± 5 years old, range 41–89 years) were studied using wire myography with capsaicin (TRPV1 agonist) and without (control). Specifically, phenylephrine (α1-adrenergic receptor agonist), dexmedetomidine (α2-adrenergic receptor agonist), ACh and sodium nitroprusside concentration–response curves were established to assess the role of TRPV1 channels in α-receptor-mediated vasocontraction as well as endothelium-dependent and -independent vasorelaxation, respectively. Compared with control conditions, capsaicin significantly attenuated maximal vasocontraction in response to phenylephrine [control, 52 ± 8% length–tensionmax (LTmax) and capsaicin, 21 ± 5%LTmax] and dexmedetomidine (control, 29 ± 12%LTmax and capsaicin, 2 ± 3%LTmax), while robustly enhancing maximal vasorelaxation with ACh (control, 78 ± 8% vasorelaxation and capsaicin, 108 ± 13% vasorelaxation) and less clearly enhancing the sodium nitroprusside response. Denudation of the endothelium greatly attenuated the maximal ACh-induced vasorelaxation equally in the control and capsaicin conditions (∼17% vasorelaxation) and abolished the attenuating effect of capsaicin on the maximal phenylephrine response (denuded + capsaicin, 61 ± 20%LTmax). Immunohistochemistry identified a relatively high density of TRPV1 channels in the endothelium compared with the smooth muscle of the SMFAs, but because of the far greater volume of smooth muscle, total TRPV1 protein content was not significantly attenuated by denudation. Thus, SMFAs ubiquitously express functional TRPV1 channels, which alter vascular function, in terms of α1-receptors, in a predominantly endothelium-dependent manner, conceivably contributing to the functional sympatholysis and unveiling a therapeutic target

In vitro susceptibilities of Bartonella henselae, B. quintana, B. elizabethae, Rickettsia rickettsii, R. conorii, R. akari, and R. prowazekii to macrolide antibiotics as determined by immunofluorescent-antibody analysis of infected Vero cell monolayers.

The in vitro susceptibilities of Bartonella (Rochalimaea) henselae, B. quintana, B. elizabethae, Rickettsia akari, R. conorii, R. prowazekii, and R. rickettsii to different concentrations of azithromycin, clarithromycin, dirithromycin, erythromycin, and roxithromycin in Vero cell cultures were evaluated. Bartonella and Rickettsia spp. were allowed to initiate infection of the antibiotic-free Vero cell monolayers, which were maintained in 16-chamber microscope slides in the absence of antibiotics at 32 degrees C in a CO2-enriched atmosphere. The monolayers were then incubated for 3 h to allow for initial host cell intracellular penetration by infecting species. After inoculation, inocula were replaced and tested with media containing 12 different concentrations of each antibiotic in replicate (10 wells of each antibiotic dilution) for each species, and the monolayers were reincubated. Tetracycline served as the control. Growth status of Bartonella spp. and Rickettsia spp. was determined by evaluation of immunofluorescent staining bacilli. Five days later, when antibiotic-free, control-infected cell monolayers demonstrated significant fluorescence, media were removed for all cell monolayers, the monolayers were fixed, and all specimens were stained with standard indirect immunofluorescent antibody reagents. Fluorescent foci were enumerated by counting such foci on random fields visualized with an epifluorescence microscope. The extent of antibiotic-induced focus inhibition was recorded for each dilution of antibiotic and compared with that of an antibiotic-negative control. Effective antibiotic dilution endpoints for inhibition of Bartonella and Rickettsia proliferation, as judged by absence of increase of significant fluorescence (as compared with no-growth controls), were enumerated by determining the number of cell culture chambers at various antibiotic dilutions that were negative or positive for significant Bartonella- or Rickettsia-specific fluorescence. All of the macrolide agents tested were readily active against all three Bartonella organisms, and azithromycin, clarithromycin, and roxithromycin may have potential in the treatment of Rickettsia infections. Animal model-based clinical trials are warranted to define the specific treatment role of the newer macrolide antibiotics

α1-Adrenergic responsiveness in human skeletal muscle feed arteries: the impact of reducing extracellular pH

What is the central question of this study? In human arteries involved in the regulation of muscle blood flow, there is a lack of data about whether acidosis alters vascular sensitivity to vasoactive agents, as well as altering endothelium dependent vasorelaxation. Little is known about the interaction of metabolites and vascular function in human skeletal muscle feed arteries. • What is the main finding and its importance? Increasing acidosis attenuated the response and sensitivity of the arteries to phenylephrine; this effect was selective to the receptor over smooth muscle. Acidosis did not alter endothelium dependent vasorelaxation. Impaired vasoconstriction coupled with intact vasorelaxation, promotes decreased vascular tone with exposure to acidosis, and may contribute to sympatholysis during exercise

Business interrelationships of the Tillamook County economy : a study for analysis of economic change

Published October 1978. Facts and recommendations in this publication may no longer be valid. Please look for up-to-date information in the OSU Extension Catalog: http://extension.oregonstate.edu/catalo

Oseltamivir-Resistant Influenza Viruses A (H1N1), Norway, 2007–08

Resistance was not associated with oseltamivir use or more severe disease

The Tillamook County economy : a working model for evaluating economic change

Published March 1977. Facts and recommendations in this publication may no longer be valid. Please look for up-to-date information in the OSU Extension Catalog: http://extension.oregonstate.edu/catalo

Differential power of placebo across major psychiatric disorders: a preliminary meta-analysis and machine learning study

The placebo effect across psychiatric disorders is still not well understood. In the present study, we conducted meta-analyses including meta-regression, and machine learning analyses to investigate whether the power of placebo effect depends on the types of psychiatric disorders. We included 108 clinical trials (32,035 participants) investigating pharmacological intervention effects on major depressive disorder (MDD), bipolar disorder (BD) and schizophrenia (SCZ). We developed measures based on clinical rating scales and Clinical Global Impression scores to compare placebo effects across these disorders. We performed meta-analysis including meta-regression using sample-size weighted bootstrapping techniques, and machine learning analysis to identify the disorder type included in a trial based on the placebo response. Consistently through multiple measures and analyses, we found differential placebo effects across the three disorders, and found lower placebo effect in SCZ compared to mood disorders. The differential placebo effects could also distinguish the condition involved in each trial between SCZ and mood disorders with machine learning. Our study indicates differential placebo effect across MDD, BD, and SCZ, which is important for future neurobiological studies of placebo effects across psychiatric disorders and may lead to potential therapeutic applications of placebo on disorders more responsive to placebo compared to other conditions

Interactive effects of video, priming, and music on emotions and the needs underlying intrinsic motivation

Objectives: Emotions can enhance motivation towards a particular goal (Brehm, 1999), while activation of human motivation does not necessarily involve conscious processes (Bargh, 1990). The main purpose of the present study was to explore the impact of video, priming, and music on a range of emotion- and motivation-related variables, while the secondary purpose was to conduct a cross-cultural comparison. Design: A randomized controlled design was employed to address the interactive effects of video, priming, and music on emotions and motivation with reference to the circumplex theory of emotion. Methods: Participants comprised a convenience sample of 210 volunteers (English, n = 128; M = 20.0, SD = 4.7 years; Male, n = 65; Female, n = 63; Greek, n = 82, M = 23.3, SD = 2.4 years; Male, n = 59; Female, n = 23). A control condition and five experimental conditions were presented to participants in a counterbalanced order. The needs underlying intrinsic motivation were accessed using the Activity Feeling-state Scales (AFS; Reeve & Sickenius, 1994), while emotional states were assessed using adjectives from the Circumplex Model of Affect (Russell, 1980). Results: Findings showed that music had positive effects on emotional states and the psychological needs underlying intrinsic motivation. They also highlighted the positive effects of priming as a psychological intervention – particularly when presented through video and coupled with music. Conclusions: The study presents the state-of-the-art for the use of video, priming, and music in sport and includes recommendations for sport psychology practitioners and researchers

Quantifying the effects of climate change and water abstraction on a population of barramundi (Lates calcarifer), a diadromous estuarine finfish

Many aquatic species are linked to environmental drivers such as temperature and salinity through processes such as spawning, recruitment and growth. Information is needed on how fished species may respond to altered environmental drivers under climate change so that adaptive management strategies can be developed. Barramundi (Lates calcarifer) is a highly prized species of the Indo-West Pacific, whose recruitment and growth is driven by river discharge. We developed a monthly age- and length-structured population model for barramundi. Monte Carlo Markov Chain simulations were used to explore the population's response to altered river discharges under modelled total licenced water abstraction and projected climate change, derived and downscaled from Global Climate Model A1FI. Mean values of exploitable biomass, annual catch, maximum sustainable yield and spawning stock size were significantly reduced under scenarios where river discharge was reduced; despite including uncertainty. These results suggest that the upstream use of water resources and climate change have potential to significantly reduce downstream barramundi stock sizes and harvests and may undermine the inherent resilience of estuarine-dependent fisheries. © 2012 CSIRO