Changes in Diurnal Cliff-Nesting Raptor Occurrence on the Ungalik River in Western Alaska: 1977, 1979, and 2008

Diurnal cliff-nesting raptors were inventoried on the Ungalik River, Alaska, in 1977 and 1979. In 2008 we resurveyed the drainage, replicating the techniques used in 1979. The density of nesting raptors during the late nesting season has doubled in the past three decades, from six occupied territories detected in 1977 and four in 1979 to 12 in 2008. A single Peregrine Falcon (Falco peregrinus) was sighted during aerial surveys in 1977, and a pair of Peregrine Falcons was detected during a boat survey in 1979; however, nesting by these birds was not confirmed. In contrast, we detected five occupied Peregrine Falcon territories along the Ungalik River in 2008. Other changes in cliff-nesting raptor occurrence included a decrease in occupied Gyrfalcon (Falco rusticolus) territories from four in 1977 to one in 1979 and two in 2008, a decrease in Rough-legged Hawk (Buteo lagopus) nests from one in 1979 (none in 1977) to none in 2008, and increases in Golden Eagle (Aquila chrysaetos) nests, from two in 1977 and 1979 to five in 2008. Changes in the number of nests of cliff-nesting raptors in this small population may have resulted, in part, from natural variation associated with changes in weather or prey abundance. However, it is likely that the increase in nesting Peregrine Falcons is related to global population recovery. Our data indicate that factors other than available nesting sites limit cliff-nesting raptor numbers along the Ungalik River. Spatial analysis indicated that cliff-nesting raptor nests were most often on hills or cliffs that face away from the coast, which is the source of most storms.En 1977 et en 1979, des rapaces diurnes nichant en falaise ont été répertoriés sur la rivière Ungalik, en Alaska. En 2008, nous avons réalisé de nouveaux relevés dans le bassin hydrographique, en reprenant les techniques employées en 1979. La densité des nids de rapaces en fin de saison de nidification a doublé au cours des trois dernières décennies. En 1977, il y avait six territoires occupés, puis quatre en 1979, et 12 en 2008. Un seul faucon pèlerin (Falco peregrinus) a été vu durant les relevés aériens de 1977 et une paire de faucons pèlerins a été observée pendant un relevé en bateau en 1979, bien que la nidification de ces oiseaux n’ait pas été confirmée. En revanche, en 2008, nous avons observé cinq territoires de faucon pèlerin occupés le long de la rivière Ungalik. Parmi les autres changements dans l’occurrence des rapaces nichant en falaise, on compte une diminution des territoires de faucon gerfaut (Falco rusticolus) occupés, passant de quatre en 1977 à un en 1979, puis à deux, en 2008; une diminution des nids de buse pattue (Buteo lagopus), passant de un en 1979 (aucun en 1977) à aucun en 2008; une augmentation des nids d’aigle royal (Aquila chrysaetos), passant de deux en 1977 et en 1979 à cinq en 2008. Les changements caractérisant le nombre de nids de rapaces nichant en falaise dans cette petite population pourraient découler, en partie, de la variation naturelle liée aux changements climatiques ou de l’abondance des proies. Toutefois, il est probable que l’augmentation de faucons pèlerins en nidification soit liée au rétablissement de la population mondiale. Nos données indiquent que des facteurs autres que les sites de nidification disponibles limitent le nombre de rapaces diurnes nichant en falaise le long de la rivière Ungalik. Une analyse spatiale démontre que les rapaces diurnes nichant en falaise faisaient plus souvent leur nid sur les collines ou les falaises à l’opposé du littoral, d’où proviennent la plupart des tempêtes.

From sea surface to seafloor: A benthic allochthonous eDNA survey for the abyssal ocean

Environmental DNA (eDNA) metabarcoding could facilitate rapid and comprehensive biotic surveys in the deep ocean, yet many aspects of the sources and distribution of eDNA in the deep sea are still poorly understood. In order to examine the influence of the water column on benthic eDNA surveys in regions targeted for deep-sea polymetallic nodule mining, we investigated the occurrence of pelagic eDNA across: (1) two different deep-sea habitat types, abyssal plains and seamounts, (2) benthic sample types, including nodules, sediment, and seawater within the benthic boundary layer (BBL), and (3) sediment depth horizons (0–2 and 3–5 cm). Little difference was observed between seamounts and the adjacent abyssal plains in the proportion of legacy pelagic eDNA sampled in the benthos, despite >1,000 m depth difference for these habitats. In terms of both reads and amplicon sequence variants (ASVs), pelagic eDNA was minimal within sediment and nodule samples (<2%), and is unlikely to affect benthic surveys that monitor resident organisms at the deep seafloor. However, pelagic eDNA was substantial within the BBL (up to 13% ASVs, 86% reads), derived both from the high-biomass upper ocean as well as deep pelagic residents. While most pelagic metazoan eDNA found in sediments and on nodules could be sourced from the epipelagic, protist legacy eDNA sampled on these substrates appeared to originate across a range of depths in the water column. Some evidence of eDNA degradation across a vertical sediment profile was observed for protists, with higher diversity in the 0–2 cm layer and a significantly lower proportion of legacy pelagic eDNA in deeper sediments (3–5 cm). Study-wide, our estimated metazoan sampling coverage ranged from 40 to 74%, despite relatively large sample size. Future deep-sea eDNA surveys should examine oceanographic influences on eDNA transport and residence times, consider habitat heterogeneity at a range of spatial scales in the abyss, and aim to process large amounts of material per sample (with replication) in order to increase the sampling coverage in these diverse deep ocean communities.publishedVersio

Modularity Facilitates Flexible Tuning of Plastic and Evolutionary Gene Expression Responses during Early Divergence

Gene expression changes have been recognized as important drivers of adaptation to changing environmental conditions. Little is known about the relative roles of plastic and evolutionary responses in complex gene expression networks during the early stages of divergence. Large gene expression data sets coupled with in silico methods for identifying coexpressed modules now enable systems genetics approaches also in nonmodel species for better understanding of gene expression responses during early divergence. Here, we combined gene coexpression analyses with population genetics to separate plastic and population (evolutionary) effects in expression networks using small salmonid populations as a model system. We show that plastic and population effects were highly variable among the six identified modules and that the plastic effects explained larger proportion of the total eigengene expression than population effects. A more detailed analysis of the population effects using a QST - FST comparison across 16,622 annotated transcripts revealed that gene expression followed neutral expectations within modules and at the global level. Furthermore, two modules showed enrichment for genes coding for early developmental traits that have been previously identified as important phenotypic traits in thermal responses in the same model system indicating that coexpression analysis can capture expression patterns underlying ecologically important traits. We suggest that module-specific responses may facilitate the flexible tuning of expression levels to local thermal conditions. Overall, our study indicates that plasticity and neutral evolution are the main drivers of gene expression variance in the early stages of thermal adaptation in this system.Peer reviewe

Predictive validity of a brief antiretroviral adherence index: Retrospective cohort analysis under conditions of repetitive administration

<p>Abstract</p> <p>Background</p> <p>Newer antiretroviral (ARV) agents have improved pharmacokinetics, potency, and tolerability and have enabled the design of regimens with improved virologic outcomes. Successful antiretroviral therapy is dependent on patient adherence. In previous research, we validated a subset of items from the ACTG adherence battery as prognostic of virologic suppression at 6 months and correlated with adherence estimates from the Medication Event Monitoring System (MEMS). The objective of the current study was to validate the longitudinal use of the Owen Clinic adherence index in analyses of time to initial virologic suppression and maintenance of suppression.</p> <p>Results</p> <p>278 patients (naïve n = 168, experienced n = 110) met inclusion criteria. Median [range] time on the first regimen during the study period was 286 (30 – 1221) days. 217 patients (78%) achieved an undetectable plasma viral load (pVL) at median 63 days. 8.3% (18/217) of patients experienced viral rebound (pVL > 400) after initial suppression. Adherence scores varied from 0 – 25 (mean 1.06, median 0). The lowest detectable adherence score cut point using this instrument was ≥ 5 for both initial suppression and maintenance of suppression. In the final Cox model of time to first undetectable pVL, controlling for prior treatment experience and baseline viral load, the adjusted hazard ratio for time updated adherence score was 0.36_{score ≥ 5}(95% CI: 0.19–0.69) [reference: <5]. In the final generalized estimating equations (GEE) logistic regression model the adjusted odds ratio for time-updated adherence score was 0.17_{score ≥ 5}(0.05–0.66) [reference: <5].</p> <p>Conclusion</p> <p>A brief, longitudinally administered self report adherence instrument predicted both initial virologic suppression and maintenance of suppression in patients using contemporary ARV regimens. The survey can be used for identification of sub-optimal adherence with subsequent appropriate intervention.</p

An epidemiologic study of antimicrobial resistance of Staphylococcus species isolated from equine samples submitted to a diagnostic laboratory

Antimicrobial resistance limits traditional treatment options and increases costs. It is therefore important to estimate the magnitude of the problem so as to provide empirical data to guide control efforts. The aim of this study was to investigate the burden and patterns of antimicrobial resistance (AMR) among equine Staphylococcussamples submitted to the University of Kentucky Veterinary Diagnostic Laboratory (UKVDL) from 1993 to 2009. Retrospective data of 1711 equine Staphylococcus samples submitted to the UKVDL during the time period 1993 to 2009 were included in the study. Antimicrobial susceptibility testing, that included 16 drugs, were performed using cultures followed by the Kirby-Bauer disk diffusion susceptibility test. The proportion of resistant isolates by animal breed, species of organism, sample source, and time period were computed. Chi-square and Cochran-Armitage trend tests were used to identify significant associations and temporal trends, respectively. Logistic regression models were used to investigate predictors of AMR and multidrug resistance (MDR)

An Epidemiologic Study of Antimicrobial Resistance of \u3cem\u3eStaphylococcus\u3c/em\u3e Species Isolated from Equine Samples Submitted to a Diagnostic Laboratory

Background Antimicrobial resistance limits traditional treatment options and increases costs. It is therefore important to estimate the magnitude of the problem so as to provide empirical data to guide control efforts. The aim of this study was to investigate the burden and patterns of antimicrobial resistance (AMR) among equine Staphylococcus samples submitted to the University of Kentucky Veterinary Diagnostic Laboratory (UKVDL) from 1993 to 2009. Retrospective data of 1711 equine Staphylococcus samples submitted to the UKVDL during the time period 1993 to 2009 were included in the study. Antimicrobial susceptibility testing, that included 16 drugs, were performed using cultures followed by the Kirby-Bauer disk diffusion susceptibility test. The proportion of resistant isolates by animal breed, species of organism, sample source, and time period were computed. Chi-square and Cochran-Armitage trend tests were used to identify significant associations and temporal trends, respectively. Logistic regression models were used to investigate predictors of AMR and multidrug resistance (MDR). Results A total of 66.3% of the isolates were resistant to at least one antimicrobial, most of which were Staphylococcus aureus (77.1%), while 25.0% were MDR. The highest level of resistance was to penicillins (52.9%). Among drug classes, isolates had the highest rate of AMR to at least one type of β-lactams (49.2%), followed by aminoglycosides (30.2%). Significant (p \u3c 0.05) associations were observed between odds of AMR and horse breed, species of organism and year. Similarly, significant (p \u3c 0.05) associations were identified between odds of MDR and breed and age. While some isolates had resistance to up to 12 antimicrobials, AMR profiles featuring single antimicrobials such as penicillin were more common than those with multiple antimicrobials. Conclusion Demographic factors were significant predictors of AMR and MDR. The fact that some isolates had resistance to up to 12 of the 16 antimicrobials assessed is quite concerning. To address the high levels of AMR and MDR observed in this study, future studies will need to focus on antimicrobial prescription practices and education of both practitioners and animal owners on judicious use of antimicrobials to slow down the development of resistance

Improved method for quantification of regional cardiac function in mice using phase-contrast MRI

Phase-contrast magnetic resonance imaging is a technique that allows for characterization of regional cardiac function and for measuring transmural myocardial velocities in human hearts with high temporal and spatial resolution. The application of this technique (also known as tissue phase mapping) to murine hearts has been very limited so far. The aim of our study was to implement and to optimize tissue phase mapping for a comprehensive assessment of murine transmural wall motion. Baseline values for regional motion patterns in mouse hearts, based on the clinically used American Heart Association's 17-segment model, were established, and a detailed motion analysis of mouse heart for the entire cardiac cycle (including epicardial and endocardial motion patterns) is provided. Black-blood contrast was found to be essential to obtain reproducible velocity encoding. Tissue phase mapping of the mouse heart permits the detailed assessment of regional myocardial velocities. While a proof-of-principle application in a murine ischemia–reperfusion model was performed, future studies are warranted to assess its potential for the investigation of systolic and diastolic functions in genetically and surgically manipulated mouse models of human heart disease. Magn Reson Med, 2012. © 2011 Wiley Periodicals, Inc

Temporal trends and predictors of antimicrobial resistance among Staphylococcus spp. isolated from canine specimens submitted to a diagnostic laboratory

Background Resistance to commonly used antimicrobials is a growing concern in both human and veterinary medicine. Understanding the temporal changes in the burden of the problem and identifying its determinants is important for guiding control efforts. Therefore, the objective of this study was to investigate temporal patterns and predictors of antimicrobial resistance among Staphylococcus spp. isolated from canine specimens submitted to the University of Kentucky Veterinary Diagnostic Laboratory (UKVDL) between 1993 and 2009. Methods Retrospective data of 4,972 Staphylococcus isolates assessed for antimicrobial susceptibility using the disk diffusion method at the UKVDL between 1993 and 2009 were included in the study. Temporal trends were assessed for each antimicrobial using the Cochran-Armitage trend test. Logistic regression models were used to investigate predictors of antimicrobial resistance (AMR) and multidrug resistance (MDR). Results A total of 68.2% (3,388/4,972) Staphylococcus isolates were S. intermedius group (SIG), 18.2% (907/4,972) were coagulase-negative staphylococci (CoNS), 7.6% (375/4,972) were S. aureus, 5.8% (290/4,972) were S. hyicus, and S. schleiferi subsp. coagulans comprised 0.2% (12/4,972) of the isolates. The overall percentage of AMR and MDR were 77.2% and 25.6%, respectively. The highest levels of AMR were seen in CoNS (81.3%; 737/907), S. aureus(80.5%; 302/375), and SIG (77.6%; 2,629/3388). The lowest levels of AMR were observed in S. hyicus (57.9%; 168/290) and S. schleiferi subsp. coagulans (33.3%; 4/12). Overall, AMR and MDR showed significant (p Conclusions Although not unexpected nor alarming, the high levels of AMR to a number of antimicrobial agents and the increasing temporal trends are concerning. Therefore, continued monitoring of AMR among Staphylococcus spp. is warranted. Future studies will need to identify local factors responsible for the observed geographic differences in risk of both AMR and MDR

Temporal trends and predictors of antimicrobial resistance among Staphylococcus spp. isolated from canine specimens submitted to a diagnostic laboratory

Background Resistance to commonly used antimicrobials is a growing concern in both human and veterinary medicine. Understanding the temporal changes in the burden of the problem and identifying its determinants is important for guiding control efforts. Therefore, the objective of this study was to investigate temporal patterns and predictors of antimicrobial resistance among Staphylococcus spp. isolated from canine specimens submitted to the University of Kentucky Veterinary Diagnostic Laboratory (UKVDL) between 1993 and 2009. Methods Retrospective data of 4,972 Staphylococcus isolates assessed for antimicrobial susceptibility using the disk diffusion method at the UKVDL between 1993 and 2009 were included in the study. Temporal trends were assessed for each antimicrobial using the Cochran-Armitage trend test. Logistic regression models were used to investigate predictors of antimicrobial resistance (AMR) and multidrug resistance (MDR). Results A total of 68.2% (3,388/4,972) Staphylococcus isolates were S. intermedius group (SIG), 18.2% (907/4,972) were coagulase-negative staphylococci (CoNS), 7.6% (375/4,972) were S. aureus, 5.8% (290/4,972) were S. hyicus, and S. schleiferi subsp. coagulans comprised 0.2% (12/4,972) of the isolates. The overall percentage of AMR and MDR were 77.2% and 25.6%, respectively. The highest levels of AMR were seen in CoNS (81.3%; 737/907), S. aureus(80.5%; 302/375), and SIG (77.6%; 2,629/3388). The lowest levels of AMR were observed in S. hyicus (57.9%; 168/290) and S. schleiferi subsp. coagulans (33.3%; 4/12). Overall, AMR and MDR showed significant (p\u3c0.001) decreasing temporal trends. Significant temporal trends (both increasing and decreasing) were observed among 12 of the 16 antimicrobials covering 6 of the 9 drug classes assessed. Thus, significant increasing temporal trends in resistance were observed to β-lactams (p\u3c0.001) (oxacillin, amoxicillin-clavulanate, cephalothin, and penicillin (p = 0.024)), aminoglycosides (p\u3c0.001) (gentamicin, and neomycin), bacitracin (p\u3c0.001), and enrofloxacin (p\u3c0.001). In contrast, sulfonamide (p\u3c0.001) (sulfadiazin) and tetracycline (p = 0.010) resistant isolates showed significant decreasing temporal trends in AMR. Staphylococcus spp., geographic region, and specimen source were significant predictors of both AMR and MDR. Conclusions Although not unexpected nor alarming, the high levels of AMR to a number of antimicrobial agents and the increasing temporal trends are concerning. Therefore, continued monitoring of AMR among Staphylococcus spp. is warranted. Future studies will need to identify local factors responsible for the observed geographic differences in risk of both AMR and MDR