Fitting statistical distributions to sea duck count data: Implications for survey design and abundance estimation

Determining appropriate statistical distributions for modeling animal count data is important for accurate estimation of abundance, distribution, and trends. In the case of sea ducks along the U.S. Atlantic coast, managers want to estimate local and regional abundance to detect and track population declines, to define areas of high and low use, and to predict the impact of future habitat change on populations. In this paper, we used a modified marked point process to model survey data that recorded flock sizes of Common eiders, Long-tailed ducks, and Black, Surf, and White-winged scoters. The data come from an experimental aerial survey, conducted by the United States Fish & Wildlife Service (USFWS) Division of Migratory Bird Management, during which east-west transects were flown along the Atlantic Coast from Maine to Florida during the winters of 2009–2011. To model the number of flocks per transect (the points), we compared the fit of four statistical distributions (zero-inflated Poisson, zero-inflated geometric, zero-inflated negative binomial and negative binomial) to data on the number of species-specific sea duck flocks that were recorded for each transect flown. To model the flock sizes (the marks), we compared the fit of flock size data for each species to seven statistical distributions: positive Poisson, positive negative binomial, positive geometric, logarithmic, discretized lognormal, zeta and Yule–Simon. Akaike’s Information Criterion and Vuong’s closeness tests indicated that the negative binomial and discretized lognormal were the best distributions for all species for the points and marks, respectively. These findings have important implications for estimating sea duck abundances as the discretized lognormal is a more skewed distribution than the Poisson and negative binomial, which are frequently used to model avian counts; the lognormal is also less heavy-tailed than the power law distributions (e.g., zeta and Yule–Simon), which are becoming increasingly popular for group size modeling. Choosing appropriate statistical distributions for modeling flock size data is fundamental to accurately estimating population summaries, determining required survey effort, and assessing and propagating uncertainty through decision-making processes

Characterization of Cre recombinase models for the study of adipose tissue

The study of adipose tissue in vivo has been significantly advanced through the use of genetic mouse models. While the aP2-CreBI and aP2-CreSalk lines have been widely used to target adipose tissue, the specificity of these lines for adipocytes has recently been questioned. Here we characterize Cre recombinase activity in multiple cell populations of the major adipose tissue depots of these and other Cre lines using the membrane-Tomato/membrane-GFP (mT/mG) dual fluorescent reporter. We find that the aP2-CreBI and aP2-CreSalk lines lack specificity for adipocytes within adipose tissue, and that the aP2-CreBI line does not efficiently target adipocytes in white adipose depots. Alternatively, the Adiponectin-CreERT line shows high efficiency and specificity for adipocytes, while the PdgfRα-CreERUCL and PdgfRα-CreERJHU lines do not efficiently target adipocyte precursor cells in the major adipose depots. Instead, we show that the PdgfRα-Cre line is preferable for studies targeting adipocyte precursor cells in vivo

Novel characteristics identified in two cases of feline Cow Pox Virus infection

Case series summary This case series discusses novel characteristics identified in two cases of cowpox. One presented with upper airway signs, and was identified to have a focal laryngeal lesion. The other had central neurological signs at the terminal stages, with intracytoplasmic inclusion bodies identified within the cerebral hemispheres on histopathology. Relevance and novel information Currently, cowpox would be an unlikely consideration in patients with neurological signs or upper respiratory noise. These cases both document novel presentations of cowpox infection, which clinicians should be aware of and consider as differential diagnoses in patients with these atypical presentations

Tracking the X-ray Polarization of the Black Hole Transient Swift J1727.8-1613 during a State Transition

We report on a campaign on the bright black hole X-ray binary Swift J1727.8$-$1613 centered around five observations by the Imaging X-ray Polarimetry Explorer (IXPE). This is the first time it has been possible to trace the evolution of the X-ray polarization of a black hole X-ray binary across a hard to soft state transition. The 2--8 keV polarization degree slowly decreased from $\sim$4\% to $\sim$3\% across the five observations, but remained in the North-South direction throughout. Using the Australia Telescope Compact Array (ATCA), we measure the intrinsic 7.25 GHz radio polarization to align in the same direction. Assuming the radio polarization aligns with the jet direction (which can be tested in the future with resolved jet images), this implies that the X-ray corona is extended in the disk plane, rather than along the jet axis, for the entire hard intermediate state. This in turn implies that the long ($\gtrsim$10 ms) soft lags that we measure with the Neutron star Interior Composition ExploreR (NICER) are dominated by processes other than pure light-crossing delays. Moreover, we find that the evolution of the soft lag amplitude with spectral state differs from the common trend seen for other sources, implying that Swift J1727.8$-$1613 is a member of a hitherto under-sampled sub-population.Comment: Submitted to ApJ. 20 pages, 8 figure

The genome of the water strider Gerris buenoi reveals expansions of gene repertoires associated with adaptations to life on the water.

BACKGROUND: Having conquered water surfaces worldwide, the semi-aquatic bugs occupy ponds, streams, lakes, mangroves, and even open oceans. The diversity of this group has inspired a range of scientific studies from ecology and evolution to developmental genetics and hydrodynamics of fluid locomotion. However, the lack of a representative water strider genome hinders our ability to more thoroughly investigate the molecular mechanisms underlying the processes of adaptation and diversification within this group. RESULTS: Here we report the sequencing and manual annotation of the Gerris buenoi (G. buenoi) genome; the first water strider genome to be sequenced thus far. The size of the G. buenoi genome is approximately 1,000 Mb, and this sequencing effort has recovered 20,949 predicted protein-coding genes. Manual annotation uncovered a number of local (tandem and proximal) gene duplications and expansions of gene families known for their importance in a variety of processes associated with morphological and physiological adaptations to a water surface lifestyle. These expansions may affect key processes associated with growth, vision, desiccation resistance, detoxification, olfaction and epigenetic regulation. Strikingly, the G. buenoi genome contains three insulin receptors, suggesting key changes in the rewiring and function of the insulin pathway. Other genomic changes affecting with opsin genes may be associated with wavelength sensitivity shifts in opsins, which is likely to be key in facilitating specific adaptations in vision for diverse water habitats. CONCLUSIONS: Our findings suggest that local gene duplications might have played an important role during the evolution of water striders. Along with these findings, the sequencing of the G. buenoi genome now provides us the opportunity to pursue exciting research opportunities to further understand the genomic underpinnings of traits associated with the extreme body plan and life history of water striders

The genome of the water strider Gerris buenoi reveals expansions of gene repertoires associated with adaptations to life on the water

Background: Having conquered water surfaces worldwide, the semi-aquatic bugs occupy ponds, streams, lakes, mangroves, and even open oceans. The diversity of this group has inspired a range of scientific studies from ecology and evolution to developmental genetics and hydrodynamics of fluid locomotion. However, the lack of a representative water strider genome hinders our ability to more thoroughly investigate the molecular mechanisms underlying the processes of adaptation and diversification within this group. Results: Here we report the sequencing and manual annotation of the Gerris buenoi (G. buenoi) genome; the first water strider genome to be sequenced thus far. The size of the G. buenoi genome is approximately 1,000Mb, and this sequencing effort has recovered 20,949 predicted protein-coding genes. Manual annotation uncovered a number of local (tandem and proximal) gene duplications and expansions of gene families known for their importance in a variety of processes associated with morphological and physiological adaptations to a water surface lifestyle. These expansions may affect key processes associated with growth, vision, desiccation resistance, detoxification, olfaction and epigenetic regulation. Strikingly, the G. buenoi genome contains three insulin receptors, suggesting key changes in the rewiring and function of the insulin pathway. Other genomic changes affecting with opsin genes may be associated with wavelength sensitivity shifts in opsins, which is likely to be key in facilitating specific adaptations in vision for diverse water habitats. Conclusions: Our findings suggest that local gene duplications might have played an important role during the evolution of water striders. Along with these findings, the sequencing of the G. buenoi genome now provides us the opportunity to pursue exciting research opportunities to further understand the genomic underpinnings of traits associated with the extreme body plan and life history of water striders

Molecular evolutionary trends and feeding ecology diversification in the Hemiptera, anchored by the milkweed bug genome.

BACKGROUND: The Hemiptera (aphids, cicadas, and true bugs) are a key insect order, with high diversity for feeding ecology and excellent experimental tractability for molecular genetics. Building upon recent sequencing of hemipteran pests such as phloem-feeding aphids and blood-feeding bed bugs, we present the genome sequence and comparative analyses centered on the milkweed bug Oncopeltus fasciatus, a seed feeder of the family Lygaeidae. RESULTS: The 926-Mb Oncopeltus genome is well represented by the current assembly and official gene set. We use our genomic and RNA-seq data not only to characterize the protein-coding gene repertoire and perform isoform-specific RNAi, but also to elucidate patterns of molecular evolution and physiology. We find ongoing, lineage-specific expansion and diversification of repressive C2H2 zinc finger proteins. The discovery of intron gain and turnover specific to the Hemiptera also prompted the evaluation of lineage and genome size as predictors of gene structure evolution. Furthermore, we identify enzymatic gains and losses that correlate with feeding biology, particularly for reductions associated with derived, fluid nutrition feeding. CONCLUSIONS: With the milkweed bug, we now have a critical mass of sequenced species for a hemimetabolous insect order and close outgroup to the Holometabola, substantially improving the diversity of insect genomics. We thereby define commonalities among the Hemiptera and delve into how hemipteran genomes reflect distinct feeding ecologies. Given Oncopeltus's strength as an experimental model, these new sequence resources bolster the foundation for molecular research and highlight technical considerations for the analysis of medium-sized invertebrate genomes

31st Annual Meeting and Associated Programs of the Society for Immunotherapy of Cancer (SITC 2016) : part two

Background The immunological escape of tumors represents one of the main ob- stacles to the treatment of malignancies. The blockade of PD-1 or CTLA-4 receptors represented a milestone in the history of immunotherapy. However, immune checkpoint inhibitors seem to be effective in specific cohorts of patients. It has been proposed that their efficacy relies on the presence of an immunological response. Thus, we hypothesized that disruption of the PD-L1/PD-1 axis would synergize with our oncolytic vaccine platform PeptiCRAd. Methods We used murine B16OVA in vivo tumor models and flow cytometry analysis to investigate the immunological background. Results First, we found that high-burden B16OVA tumors were refractory to combination immunotherapy. However, with a more aggressive schedule, tumors with a lower burden were more susceptible to the combination of PeptiCRAd and PD-L1 blockade. The therapy signifi- cantly increased the median survival of mice (Fig. 7). Interestingly, the reduced growth of contralaterally injected B16F10 cells sug- gested the presence of a long lasting immunological memory also against non-targeted antigens. Concerning the functional state of tumor infiltrating lymphocytes (TILs), we found that all the immune therapies would enhance the percentage of activated (PD-1pos TIM- 3neg) T lymphocytes and reduce the amount of exhausted (PD-1pos TIM-3pos) cells compared to placebo. As expected, we found that PeptiCRAd monotherapy could increase the number of antigen spe- cific CD8+ T cells compared to other treatments. However, only the combination with PD-L1 blockade could significantly increase the ra- tio between activated and exhausted pentamer positive cells (p= 0.0058), suggesting that by disrupting the PD-1/PD-L1 axis we could decrease the amount of dysfunctional antigen specific T cells. We ob- served that the anatomical location deeply influenced the state of CD4+ and CD8+ T lymphocytes. In fact, TIM-3 expression was in- creased by 2 fold on TILs compared to splenic and lymphoid T cells. In the CD8+ compartment, the expression of PD-1 on the surface seemed to be restricted to the tumor micro-environment, while CD4 + T cells had a high expression of PD-1 also in lymphoid organs. Interestingly, we found that the levels of PD-1 were significantly higher on CD8+ T cells than on CD4+ T cells into the tumor micro- environment (p < 0.0001). Conclusions In conclusion, we demonstrated that the efficacy of immune check- point inhibitors might be strongly enhanced by their combination with cancer vaccines. PeptiCRAd was able to increase the number of antigen-specific T cells and PD-L1 blockade prevented their exhaus- tion, resulting in long-lasting immunological memory and increased median survival

Sykepleieres holdninger til pasienter med HIV/AIDS

Hensikt Oppgavens hensikt var å finne hvilke faktorer som påvirket sykepleieres holdninger i møte med pasienter diagnostiserte med HIV/AIDS. Dette for å finne ut hvorfor enkelte sykepleiere møter pasienter med HIV/AIDS med positive holdninger, mens andre med negative. Metode Det ble utført en systematisk litteraturstudie for å få svar på problemstillingen. Flere databaser ble benyttet for å finne forskning som svarte på denne. I oppgaven ble det benyttet to metastudier, to kvalitative og fire kvantitative studier. Resultat Gjennom forskningen ble det funnet at villighet, kunnskap og trivsel på jobb var sentrale faktorer som påvirket sykepleiernes holdning i møte med pasienter med HIV/AIDS. Sykepleierens holdning avgjorde om møtet med pasienten førte til en positiv eller negativ opplevelse for pasienten. Konklusjon Det finnes flere faktorer som påvirker sykepleieres holdninger i møte med pasienter med HIV/AIDS. Likevel kan sykepleiere endre eller holde tilbake egne personlige holdninger i møte med pasienter som har andre verdier eller livsstil enn dem selv