Distribution and Community Characteristics of Staging Shorebirds on the Northern Coast of Alaska

Avian studies conducted in the 1970s on Alaska’s Arctic Coastal Plain (ACP) indicated that coastal littoral habitats are important to Arctic-breeding shorebirds for staging prior to fall migration. However, relatively little recent, broad-scale, or quantitative information exists on shorebird use of staging areas in this region. To locate possible shorebird concentration areas in the littoral zone of the ACP, we conducted aerial surveys from the southwest end of Kasegaluk Lagoon on the Chukchi Sea to Demarcation Point on the Beaufort Sea during the summers of 2005–07. These surveys identified persistent within- and between-year concentrations of staging shorebirds at Peard Bay, Point Barrow/Elson Lagoon, Cape Simpson, and Smith Bay to Cape Halkett. Among river deltas in the Beaufort Sea, the Sagavanirktok and Kongakut deltas had large concentrations of staging shorebirds. We also collected data on shorebird community characteristics, staging phenology, and habitat use in 2005 and 2006 by conducting land-based surveys at six camps: Kasegaluk Lagoon, Peard Bay, Point Barrow/Elson Lagoon, Colville Delta, Sagavanirktok Delta, and Okpilak Delta. The shorebird community was more even and diverse (evenness E and Shannon Weiner H’) along the Beaufort Sea compared to the Chukchi Sea and in 2005 versus 2006. Staging phenology varied by species and location and differed for several species from that reported in previous studies. Our results suggest the existence of three foraging habitat guilds among the shorebird species observed in this study: gravel beach, mudflat, and salt marsh/pond edge. A comparison to data collected in the mid-1970s suggests that these foraging associations are conserved through time. Results from this research will be useful to land managers for monitoring the effects of changing environmental conditions and human activity on shorebirds and their habitats in Arctic Alaska.Des études aviaires réalisées dans les années 1970 sur la plaine côtière de l’Arctique en Alaska ont permis de constater que les habitats du littoral côtier revêtent de l’importance pour les oiseaux de rivage nicheurs de l’Arctique en halte migratoire avant la migration d’automne. Cependant, relativement peu d’information récente, à grande échelle ou quantitative existe à propos de l’utilisation que font les oiseaux de rivage des haltes migratoires de cette région. Afin de localiser des zones de concentration possibles d’oiseaux de rivage dans la région littorale de la plaine côtière de l’Arctique, nous avons effectué des levés aériens du sud-ouest de la lagune Kasegaluk dans la mer des Tchouktches jusqu’à Demarcation Point dans la mer de Beaufort au cours des étés allant de 2005 à 2007. Ces levés ont permis de repérer des concentrations durables d’oiseaux de rivage en halte migratoire au cours d’une même année ainsi que d’une année à l’autre à la baie Peard, à pointe Barrow et à la lagune Elson, au cap Simpson de même que de la baie Smith jusqu’au cap Halkett. Parmi les deltas de rivières de la mer de Beaufort, les deltas Sagavanirktok et Kongakut comptaient de fortes concentrations d’oiseaux de rivage en halte migratoire. Nous avons également recueilli des données sur les caractéristiques des populations d’oiseaux de rivage, sur la phénologie des haltes migratoires de même que sur l’utilisation des habitats en 2005 et en 2006 au moyen de levés terrestres effectués à six camps, soit celui de la lagune Kasegaluk, de la baie Peard, de la pointe Barrow et de la lagune Elson, du delta Colville, du delta Sagavanirktok et du delta Okpilak. La population d’oiseaux de rivage était plus homogène et diverse (homogénéité E et Shannon Weiner H’) le long de la mer de Beaufort comparativement à la mer des Tchouktches, ainsi qu’en 2005 par rapport à 2006. La phénologie en halte migratoire variait selon les espèces et les emplacements, et différait pour plusieurs espèces de celles signalées dans le cadre d’études ultérieures. Nos résultats laissent croire à l’existence de trois guildes d’habitats de fourrage chez les espèces d’oiseaux de rivage observées dans cette étude : plage de gravier, vasière et marais salant ou bordure d’étang. La comparaison des données recueillies au milieu des années 1970 laisse entendre que ces associations de fourrage se sont conservées au fil du temps. Les résultats découlant de cette recherche seront utiles aux gestionnaires de terres dans le cadre de la surveillance des effets des conditions environnementales changeantes et de l’activité humaine sur les oiseaux de rivage et leurs habitats de l’Arctique alaskien

Observation of a multimode plasma response and its relationship to density pumpout and edge-localized mode suppression

Density pumpout and edge-localized mode (ELM) suppression by applied n=2 magnetic fields in low-collisionality DIII-D plasmas are shown to be correlated with the magnitude of the plasma response driven on the high-field side (HFS) of the magnetic axis but not the low-field side (LFS) midplane. These distinct responses are a direct measurement of a multimodal magnetic plasma response, with each structure preferentially excited by a different n=2 applied spectrum and preferentially detected on the LFS or HFS. Ideal and resistive magneto-hydrodynamic (MHD) calculations find that the LFS measurement is primarily sensitive to the excitation of stable kink modes, while the HFS measurement is primarily sensitive to resonant currents (whether fully shielding or partially penetrated). The resonant currents are themselves strongly modified by kink excitation, with the optimal applied field pitch for pumpout and ELM suppression significantly differing from equilibrium field alignment.This material is based upon work supported by the U.S. Department of Energy, Office of Science, Office of Fusion Energy Sciences, using the DIII-D National Fusion Facility, a DOE Office of Science user facility, under Awards No. DE-FC02-04ER54698, No. DE-AC02-09CH11466, No. DE-FG02-04ER54761, No. DE-AC05-06OR23100, No. DE-SC0001961, and No. DE-AC05-00OR22725. S. R. H. was supported by AINSE and ANSTO

Distribution of Breeding Shorebirds on the Arctic Coastal Plain of Alaska

Available information on the distribution of breeding shorebirds across the Arctic Coastal Plain of Alaska is dated, fragmented, and limited in scope. Herein, we describe the distribution of 19 shorebird species from data gathered at 407 study plots between 1998 and 2004. This information was collected using a single-visit rapid area search technique during territory establishment and early incubation periods, a time when social displays and vocalizations make the birds highly detectable. We describe the presence or absence of each species, as well as overall numbers of species, providing a regional perspective on shorebird distribution. We compare and contrast our shorebird distribution maps to those of prior studies and describe prominent patterns of shorebird distribution. Our examination of how shorebird distribution and numbers of species varied both latitudinally and longitudinally across the Arctic Coastal Plain of Alaska indicated that most shorebird species occur more frequently in the Beaufort Coastal Plain ecoregion (i.e., closer to the coast) than in the Brooks Foothills ecoregion (i.e., farther inland). Furthermore, the occurrence of several species indicated substantial longitudinal directionality. Species richness at surveyed sites was highest in the western portion of the Beaufort Coastal Plain ecoregion. The broad-scale distribution information we present here is valuable for evaluating potential effects of human development and climate change on Arctic-breeding shorebird populations.Les renseignements qui existent en matière de répartition des oiseaux de rivage en reproduction sur la plaine côtière de l’Arctique en Alaska sont anciens, fragmentés et restreints. Ici, nous décrivons la répartition de 19 espèces d’oiseaux de rivage à partir de données recueillies à 407 lieux de recherche entre 1998 et 2004. Cette information a été recueillie grâce à une technique de recherche consistant en une seule visite rapide durant les périodes d’établissement du territoire et de début d’incubation, périodes pendant lesquelles les comportements sociaux et les vocalisations permettent de bien repérer les oiseaux. Nous décrivons la présence ou l’absence de chaque espèce, de même que le nombre général d’espèces, ce qui procure une perspective régionale de la répartition des oiseaux de rivage. Nous comparons et contrastons nos cartes de répartition des oiseaux de rivage à celles d’études antérieures, en plus de décrire les tendances les plus marquées en matière de répartition des oiseaux de rivage. Notre examen de la variation latitudinale et longitudinale en matière de répartition et de nombre d’espèces d’oiseaux de rivage à l’échelle de la plaine côtière arctique de l’Alaska nous a permis de constater que la plupart des espèces d’oiseaux de rivage se manifestaient plus souvent dans la région écologique de la plaine côtière de Beaufort (c’est-à-dire plus proche de la côte) que dans la région écologique des contreforts de Brooks (c’est-à-dire plus à l’intérieur des terres). Par ailleurs, l’occurrence de plusieurs espèces indiquait une directionalité longitudinale substantielle. La richesse des espèces aux sites à l’étude était à son meilleur dans la partie ouest de la région écologique de la plaine côtière de Beaufort. Les renseignements sur la répartition à grande échelle que nous présentons ici jouent un rôle dans l’évaluation des effets éventuels des travaux de mise en valeur par l’être humain et du changement climatique sur les populations d’oiseaux de rivage en reproduction de l’Arctique

Predictors of invertebrate biomass and rate of advancement of invertebrate phenology across eight sites in the North American Arctic

Average annual temperatures in the Arctic increased by 2–3 °C during the second half of the twentieth century. Because shorebirds initiate northward migration to Arctic nesting sites based on cues at distant wintering grounds, climate-driven changes in the phenology of Arctic invertebrates may lead to a mismatch between the nutritional demands of shorebirds and the invertebrate prey essential for egg formation and subsequent chick survival. To explore the environmental drivers afecting invertebrate availability, we modeled the biomass of invertebrates captured in modifed Malaise-pitfall traps over three summers at eight Arctic Shorebird Demographics Network sites as a function of accumulated degree-days and other weather variables. To assess climate-driven changes in invertebrate phenology, we used data from the nearest long-term weather stations to hindcast invertebrate availability over 63 summers, 1950–2012. Our results confrmed the importance of both accumulated and daily temperatures as predictors of invertebrate availability while also showing that wind speed negatively afected invertebrate availability at the majority of sites. Additionally, our results suggest that seasonal prey avail ability for Arctic shorebirds is occurring earlier and that the potential for trophic mismatch is greatest at the northernmost sites, where hindcast invertebrate phenology advanced by approximately 1–2.5 days per decade. Phenological mismatch could have long-term population-level efects on shorebird species that are unable to adjust their breeding schedules to the increasingly earlier invertebrate phenologies.publishedVersio

Closest string with outliers

Background: Given n strings s1, …, sn each of length ℓ and a nonnegative integer d, the CLOSEST STRING problem asks to find a center string s such that none of the input strings has Hamming distance greater than d from s. Finding a common pattern in many – but not necessarily all – input strings is an important task that plays a role in many applications in bioinformatics. Results: Although the closest string model is robust to the oversampling of strings in the input, it is severely affected by the existence of outliers. We propose a refined model, the CLOSEST STRING WITH OUTLIERS (CSWO) problem, to overcome this limitation. This new model asks for a center string s that is within Hamming distance d to at least n – k of the n input strings, where k is a parameter describing the maximum number of outliers. A CSWO solution not only provides the center string as a representative for the set of strings but also reveals the outliers of the set. We provide fixed parameter algorithms for CSWO when d and k are parameters, for both bounded and unbounded alphabets. We also show that when the alphabet is unbounded the problem is W[1]-hard with respect to n – k, ℓ, and d. Conclusions: Our refined model abstractly models finding common patterns in several but not all input strings

Functional divergence in the role of N-linked glycosylation in smoothened signaling

The G protein-coupled receptor (GPCR) Smoothened (Smo) is the requisite signal transducer of the evolutionarily conserved Hedgehog (Hh) pathway. Although aspects of Smo signaling are conserved from Drosophila to vertebrates, significant differences have evolved. These include changes in its active sub-cellular localization, and the ability of vertebrate Smo to induce distinct G protein-dependent and independent signals in response to ligand. Whereas the canonical Smo signal to Gli transcriptional effectors occurs in a G protein-independent manner, its non-canonical signal employs Gαi. Whether vertebrate Smo can selectively bias its signal between these routes is not yet known. N-linked glycosylation is a post-translational modification that can influence GPCR trafficking, ligand responsiveness and signal output. Smo proteins in Drosophila and vertebrate systems harbor N-linked glycans, but their role in Smo signaling has not been established. Herein, we present a comprehensive analysis of Drosophila and murine Smo glycosylation that supports a functional divergence in the contribution of N-linked glycans to signaling. Of the seven predicted glycan acceptor sites in Drosophila Smo, one is essential. Loss of N-glycosylation at this site disrupted Smo trafficking and attenuated its signaling capability. In stark contrast, we found that all four predicted N-glycosylation sites on murine Smo were dispensable for proper trafficking, agonist binding and canonical signal induction. However, the under-glycosylated protein was compromised in its ability to induce a non-canonical signal through Gαi, providing for the first time evidence that Smo can bias its signal and that a post-translational modification can impact this process. As such, we postulate a profound shift in N-glycan function from affecting Smo ER exit in flies to influencing its signal output in mice

Prevalence of Influenza A viruses in wild migratory birds in Alaska: Patterns of variation in detection at a crossroads of intercontinental flyways

<p>Abstract</p> <p>Background</p> <p>The global spread of the highly pathogenic avian influenza H5N1 virus has stimulated interest in a better understanding of the mechanisms of H5N1 dispersal, including the potential role of migratory birds as carriers. Although wild birds have been found dead during H5N1 outbreaks, evidence suggests that others have survived natural infections, and recent studies have shown several species of ducks capable of surviving experimental inoculations of H5N1 and shedding virus. To investigate the possibility of migratory birds as a means of H5N1 dispersal into North America, we monitored for the virus in a surveillance program based on the risk that wild birds may carry the virus from Asia.</p> <p>Results</p> <p>Of 16,797 birds sampled in Alaska between May 2006 and March 2007, low pathogenic avian influenza viruses were detected in 1.7% by rRT-PCR but no highly pathogenic viruses were found. Our data suggest that prevalence varied among sampling locations, species (highest in waterfowl, lowest in passerines), ages (juveniles higher than adults), sexes (males higher than females), date (highest in autumn), and analytical technique (rRT-PCR prevalence = 1.7%; virus isolation prevalence = 1.5%).</p> <p>Conclusion</p> <p>The prevalence of low pathogenic avian influenza viruses isolated from wild birds depends on biological, temporal, and geographical factors, as well as testing methods. Future studies should control for, or sample across, these sources of variation to allow direct comparison of prevalence rates.</p

Initial Genomics of the Human Nucleolus

We report for the first time the genomics of a nuclear compartment of the eukaryotic cell. 454 sequencing and microarray analysis revealed the pattern of nucleolus-associated chromatin domains (NADs) in the linear human genome and identified different gene families and certain satellite repeats as the major building blocks of NADs, which constitute about 4% of the genome. Bioinformatic evaluation showed that NAD–localized genes take part in specific biological processes, like the response to other organisms, odor perception, and tissue development. 3D FISH and immunofluorescence experiments illustrated the spatial distribution of NAD–specific chromatin within interphase nuclei and its alteration upon transcriptional changes. Altogether, our findings describe the nature of DNA sequences associated with the human nucleolus and provide insights into the function of the nucleolus in genome organization and establishment of nuclear architecture

Respiratory hospitalizations and respiratory syncytial virus prophylaxis in special populations

Palivizumab utilization, compliance, and outcomes were examined in infants with preexisting medical diseases within the Canadian Registry Database (CARESS) to aid in developing guidelines for potential “at-risk” infants in the future. Infants who received ≥1 dose of palivizumab during the 2006–2010 respiratory syncytial virus (RSV) seasons at 29 sites were recruited and utilization, compliance, and outcomes related to respiratory infection/illness (RI) events were collected monthly. Hazard ratios (HRs) and 95% confidence intervals (CIs) were calculated for premature infants ≤35 completed weeks gestational age (GA) who met standard approval criteria (group 1) compared to those with medical disorders (group 2) using Cox proportional hazards regression models with adjustment for potential confounding factors. Of 7,339 registry infants, 4,880 were in group 1 and 952 in group 2, which included those with Down syndrome (20.3%), upper airway anomalies (18.7%), pulmonary diseases (13.3%), and cystic fibrosis (12.3%). Group 2 were older at enrolment (10.2 ± 9.2 vs. 3.5 ± 3.1 months, p < 0.0005), had higher GA (35.9 ± 6.0 vs. 31.0 ± 5.4 weeks, p < 0.0005), and were less compliant with treatment intervals (69.4% vs. 72.6%, p = 0.048). A greater proportion of group 2 infants were hospitalized for RI (9.0% vs. 4.2%, p < 0.0005) and RSV (2.4% vs. 1.3%, p = 0.003) (unadjusted). Being in group 2 was associated with an increased risk of RI (HR = 2.0, 95%CI 1.5–2.5, p < 0.0005), but not RSV hospitalization (HR = 1.6, 95%CI 0.9–2.8, p = 0.106). In infants receiving palivizumab, those with underlying medical disorders, though not currently approved for prophylaxis, are at higher risk for RI events compared with preterm infants. However, risk of RSV hospitalizations is similar