A standardised sampling protocol for robust assessment of reach-scale fish community diversity in wadeable New Zealand streams

The New Zealand fish fauna contains species that are affected not only by river system connectivity, but also by catchment and local-scale changes in landcover, water quality and habitat quality. Consequently, native fish have potential as multi-scale bioindicators of human pressure on stream ecosystems, yet no standardised, repeatable and scientifically defensible methods currently exist for effectively quantifying their abundance or diversity in New Zealand stream reaches. Here we report on the testing of a back-pack electrofishing method, modified from that used by the United States Environmental Protection Agency, on a wide variety of wadeable stream reaches throughout New Zealand. Seventy-three first- to third-order stream reaches were fished with a single pass over 150-345 m length. Time taken to sample a reach using single-pass electrofishing ranged from 1-8 h. Species accumulation curves indicated that, irrespective of location, continuous sampling of 150 stream metres is required to accurately describe reach-scale fish species richness using this approach. Additional species detection beyond 150 m was rare (<10%) with a single additional species detected at only two out of the 17 reaches sampled beyond this distance. A positive relationship was also evident between species detection and area fished, although stream length rather than area appeared to be the better predictor. The method tested provides a standardised and repeatable approach for regional and/or national reporting on the state of New Zealand's freshwater fish communities and trends in richness and abundance over time

Models of the SL9 Impacts II. Radiative-hydrodynamic Modeling of the Plume Splashback

We model the plume "splashback" phase of the SL9 collisions with Jupiter using the ZEUS-3D hydrodynamic code. We modified the Zeus code to include gray radiative transport, and we present validation tests. We couple the infalling mass and momentum fluxes of SL9 plume material (from paper I) to a jovian atmospheric model. A strong and complex shock structure results. The modeled shock temperatures agree well with observations, and the structure and evolution of the modeled shocks account for the appearance of high excitation molecular line emission after the peak of the continuum light curve. The splashback region cools by radial expansion as well as by radiation. The morphology of our synthetic continuum light curves agree with observations over a broad wavelength range (0.9 to 12 microns). A feature of our ballistic plume is a shell of mass at the highest velocities, which we term the "vanguard". Portions of the vanguard ejected on shallow trajectories produce a lateral shock front, whose initial expansion accounts for the "third precursors" seen in the 2-micron light curves of the larger impacts, and for hot methane emission at early times. Continued propagation of this lateral shock approximately reproduces the radii, propagation speed, and centroid positions of the large rings observed at 3-4 microns by McGregor et al. The portion of the vanguard ejected closer to the vertical falls back with high z-component velocities just after maximum light, producing CO emission and the "flare" seen at 0.9 microns. The model also produces secondary maxima ("bounces") whose amplitudes and periods are in agreement with observations.Comment: 13 pages, 9 figures (figs 3 and 4 in color), accepted for Ap.J. latex, version including full figures at: http://oobleck.tn.cornell.edu/jh/ast/papers/slplume2-20.ps.g

Genome-to-genome analysis highlights the effect of the human innate and adaptive immune systems on the hepatitis C virus

Outcomes of hepatitis C virus (HCV) infection and treatment depend on viral and host genetic factors. Here we use human genome-wide genotyping arrays and new whole-genome HCV viral sequencing technologies to perform a systematic genome-to-genome study of 542 individuals who were chronically infected with HCV, predominantly genotype 3. We show that both alleles of genes encoding human leukocyte antigen molecules and genes encoding components of the interferon lambda innate immune system drive viral polymorphism. Additionally, we show that IFNL4 genotypes determine HCV viral load through a mechanism dependent on a specific amino acid residue in the HCV NS5A protein. These findings highlight the interplay between the innate immune system and the viral genome in HCV control

The field high-amplitude SX Phe variable BL Cam: results from a multisite photometric campaign. II. Evidence of a binary - possibly triple - system

Short-period high-amplitude pulsating stars of Population I ($\delta$ Sct stars) and II (SX Phe variables) exist in the lower part of the classical (Cepheid) instability strip. Most of them have very simple pulsational behaviours, only one or two radial modes being excited. Nevertheless, BL Cam is a unique object among them, being an extreme metal-deficient field high-amplitude SX Phe variable with a large number of frequencies. Based on a frequency analysis, a pulsational interpretation was previously given. aims heading (mandatory) We attempt to interpret the long-term behaviour of the residuals that were not taken into account in the previous Observed-Calculated (O-C) short-term analyses. methods heading (mandatory) An investigation of the O-C times has been carried out, using a data set based on the previous published times of light maxima, largely enriched by those obtained during an intensive multisite photometric campaign of BL Cam lasting several months. results heading (mandatory) In addition to a positive (161 $\pm$ 3) x 10$^{-9}$ yr$^{-1}$ secular relative increase in the main pulsation period of BL Cam, we detected in the O-C data short- (144.2 d) and long-term ($\sim$ 3400 d) variations, both incompatible with a scenario of stellar evolution. conclusions heading (mandatory) Interpreted as a light travel-time effect, the short-term O-C variation is indicative of a massive stellar component (0.46 to 1 M_{\sun}) with a short period orbit (144.2 d), within a distance of 0.7 AU from the primary. More observations are needed to confirm the long-term O-C variations: if they were also to be caused by a light travel-time effect, they could be interpreted in terms of a third component, in this case probably a brown dwarf star ($\geq$ 0.03 \ M_{\sun}), orbiting in $\sim$ 3400 d at a distance of 4.5 AU from the primary.Comment: 7 pages, 5 figures, accepted for publication in A&

Etiology of Severe Non-malaria Febrile Illness in Northern Tanzania: A Prospective Cohort Study.

The syndrome of fever is a commonly presenting complaint among persons seeking healthcare in low-resource areas, yet the public health community has not approached fever in a comprehensive manner. In many areas, malaria is over-diagnosed, and patients without malaria have poor outcomes. We prospectively studied a cohort of 870 pediatric and adult febrile admissions to two hospitals in northern Tanzania over the period of one year using conventional standard diagnostic tests to establish fever etiology. Malaria was the clinical diagnosis for 528 (60.7%), but was the actual cause of fever in only 14 (1.6%). By contrast, bacterial, mycobacterial, and fungal bloodstream infections accounted for 85 (9.8%), 14 (1.6%), and 25 (2.9%) febrile admissions, respectively. Acute bacterial zoonoses were identified among 118 (26.2%) of febrile admissions; 16 (13.6%) had brucellosis, 40 (33.9%) leptospirosis, 24 (20.3%) had Q fever, 36 (30.5%) had spotted fever group rickettsioses, and 2 (1.8%) had typhus group rickettsioses. In addition, 55 (7.9%) participants had a confirmed acute arbovirus infection, all due to chikungunya. No patient had a bacterial zoonosis or an arbovirus infection included in the admission differential diagnosis. Malaria was uncommon and over-diagnosed, whereas invasive infections were underappreciated. Bacterial zoonoses and arbovirus infections were highly prevalent yet overlooked. An integrated approach to the syndrome of fever in resource-limited areas is needed to improve patient outcomes and to rationally target disease control efforts

The insecticidal spider toxin SFI1 is a knottin peptide that blocks the pore of insect voltage-gated sodium channels via a large β-hairpin loop

Spider venoms contain a plethora of insecticidal peptides that act on neuronal ion channels and receptors. Because of their high specificity, potency and stability, these peptides have attracted much attention as potential environmentally friendly insecticides. Although many insecticidal spider venom peptides have been isolated, the molecular target, mode of action and structure of only a small minority have been explored. Sf1a, a 46-residue peptide isolated from the venom of the tube-web spider Segesteria florentina, is insecticidal to a wide range of insects, but nontoxic to vertebrates. In order to investigate its structure and mode of action, we developed an efficient bacterial expression system for the production of Sf1a. We determined a high-resolution solution structure of Sf1a using multidimensional 3D/4D NMR spectroscopy. This revealed that Sf1a is a knottin peptide with an unusually large beta-hairpin loop that accounts for a third of the peptide length. This loop is delimited by a fourth disulfide bond that is not commonly found in knottin peptides. We showed, through mutagenesis, that this large loop is functionally critical for insecticidal activity. Sf1a was further shown to be a selective inhibitor of insect voltage-gated sodium channels, consistent with its `depressant' paralytic phenotype in insects. However, in contrast to the majority of spider-derived sodium channel toxins that function as gating modifiers via interaction with one or more of the voltage-sensor domains, Sf1a appears to act as a pore blocker

Multimodal influences on learning walks in desert ants (Cataglyphis fortis)

Ants are excellent navigators using multimodal information for navigation. To accurately localise the nest at the end of a foraging journey, visual cues, wind direction and also olfactory cues need to be learnt. Learning walks are performed at the start of an ant’s foraging career or when the appearance of the nest surrounding has changed. We investigated here whether the structure of such learning walks in the desert ant Cataglyphis fortis takes into account wind direction in conjunction with the learning of new visual information. Ants learnt to travel back and forth between their nest and a feeder, and we then introduced a black cylinder near their nest to induce learning walks in regular foragers. By doing this across days with different wind directions, we were able to probe how ants balance different sensory modalities. We found that (1) the ants’ outwards headings are influenced by the wind direction with their routes deflected such that they will arrive downwind of their target, (2) a novel object along the route induces learning walks in experienced ants and (3) the structure of learning walks is shaped by the wind direction rather than the position of the visual cue

Skeletal muscle metabolomics and blood biochemistry analysis reveal metabolic changes associated with dietary amino acid supplementation in dairy calves

The effects of different amino acid (AA) supplementations of milk protein-based milk replacers in pre-ruminant calves from 3 days to 7 weeks of age were studied. Animals were divided into 4 groups: Ctrl) Control group fed with milk protein-based milk replacer without supplementation; GP) supplementation with 0.1% glycine and 0.3% proline; FY) supplementation with 0.2% phenylalanine and 0.2% tyrosine; MKT) supplementation with 0.62% lysine, 0.22% methionine and 0.61% threonine. For statistical analysis, t-test was used to compare AA-supplemented animals to the Ctrl group. At week 7, body weight and average daily gain (ADG) were measured and blood samples and skeletal muscle biopsies were taken. Blood biochemistry analytes related to energy metabolism were determined and it was shown that MKT group had higher serum creatinine and higher plasma concentration of three supplemented AAs as well as arginine compared with the Ctrl group. GP group had similar glycine/proline plasma concentration compared with the other groups while in FY group only plasma phenylalanine concentration was higher compared with Control. Although the AA supplementations in the GP and FY groups did not affect average daily gain and metabolic health profile from serum, the metabolome analysis from skeletal muscle biopsy revealed several differences between the GP-FY groups and the Ctrl-MKT groups, suggesting a metabolic adaptation especially in GP and FY groupsinfo:eu-repo/semantics/publishedVersio

Singular regional brightening events on Titan as seen by Cassini/VIMS

Titan, the largest satellite of Saturn, is the only satellite in the solar system with a dense atmosphere. The close and continuous observations of Titan by the Cassini spacecraft, in orbit around Saturn since July 2004, bring us evidences that Titan tropo-sphere and low stratosphere experience an exotic, but complete meteorological cycle similar to the Earth hy-drological cycle, with hydrocarbons evaporation, con-densation in clouds, and rainfall. Cassini monitoring campaigns also demonstrate that Titan’s cloud cover-age and climate vary with latitude. Titan’s tropics, with globally weak meteorological activity and widespread dune fields, seem to be slightly more arid than the poles, where extensive and numerous liquid reservoirs and sustained cloud activity were discovered. Only a few tropospheric clouds have been observed at Titan’s tropics during the southern summer [2-4]. As equinox was approaching (in August 2009), they oc-curred more frequently and appeared to grow in strength and size [5-7]

Evidence for the η_b(1S) Meson in Radiative Υ(2S) Decay

We have performed a search for the η_b(1S) meson in the radiative decay of the Υ(2S) resonance using a sample of 91.6 × 10^6 Υ(2S) events recorded with the BABAR detector at the PEP-II B factory at the SLAC National Accelerator Laboratory. We observe a peak in the photon energy spectrum at E_γ = 609.3^(+4.6)_(-4.5)(stat)±1.9(syst) MeV, corresponding to an η_b(1S) mass of 9394.2^(+4.8)_(-4.9)(stat) ± 2.0(syst) MeV/c^2. The branching fraction for the decay Υ(2S) → γη_b(1S) is determined to be [3.9 ± 1.1(stat)^(+1.1)_(-0.9)(syst)] × 10^(-4). We find the ratio of branching fractions B[Υ(2S) → γη_b(1S)]/B[Υ(3S) → γη_b(1S)]= 0.82 ± 0.24(stat)^(+0.20)_(-0.19)(syst)