The Evolution of Hetergeneous "Clumpy Jets": A Parameter Study

We investigate the role discrete clumps embedded in an astrophysical jet play on the jet's morphology and line emission characteristics. By varying clumps' size, density, position, and velocity, we cover a range of parameter space motivated by observations of objects such as the Herbig Haro object HH~34. We here extend the results presented in Yirak et al. 2009, including how analysis of individual observations may lead to spurious sinusoidal variation whose parameters vary widely over time, owing chiefly to interacts between clumps. The goodness of the fits, while poor in all simulations, are best when clump-clump collisions are minimal. Our results indicate that a large velocity dispersion leads to a clump-clump collision-dominated flow which disrupts the jet beam. Finally, we present synthetic emission images of H-$\alpha$ and [SII] and note an excess of [SII] emission along the jet length as compared to observations. This suggests that observed beams undergo earlier processing, if they are present at all.Comment: 18 pages, 7 figures. Submitted to the Astrophysical Journa

Genetic strategies for improving crop yields.

The current trajectory for crop yields is insufficient to nourish the world's population by 20501. Greater and more consistent crop production must be achieved against a backdrop of climatic stress that limits yields, owing to shifts in pests and pathogens, precipitation, heat-waves and other weather extremes. Here we consider the potential of plant sciences to address post-Green Revolution challenges in agriculture and explore emerging strategies for enhancing sustainable crop production and resilience in a changing climate. Accelerated crop improvement must leverage naturally evolved traits and transformative engineering driven by mechanistic understanding, to yield the resilient production systems that are needed to ensure future harvests

Semantic Web Applications and Tools for Life Sciences, 2008 – Introduction

BACKGROUND: Semantically-enriched browsing has enhanced the browsing experience by providing contextualized dynamically generated Web content, and quicker access to searched-for information. However, adoption of Semantic Web technologies is limited and user perception from the non-IT domain sceptical. Furthermore, little attention has been given to evaluating semantic browsers with real users to demonstrate the enhancements and obtain valuable feedback. The Sealife project investigates semantic browsing and its application to the life science domain. Sealife's main objective is to develop the notion of context-based information integration by extending three existing Semantic Web browsers (SWBs) to link the existing Web to the eScience infrastructure. METHODS: This paper describes a user-centred evaluation framework that was developed to evaluate the Sealife SWBs that elicited feedback on users' perceptions on ease of use and information findability. Three sources of data: i) web server logs; ii) user questionnaires; and iii) semi-structured interviews were analysed and comparisons made between each browser and a control system. RESULTS: It was found that the evaluation framework used successfully elicited users' perceptions of the three distinct SWBs. The results indicate that the browser with the most mature and polished interface was rated higher for usability, and semantic links were used by the users of all three browsers. CONCLUSION: Confirmation or contradiction of our original hypotheses with relation to SWBs is detailed along with observations of implementation issues

A user-centred evaluation framework for the Sealife semantic web browsers

BACKGROUND: Semantically-enriched browsing has enhanced the browsing experience by providing contextualized dynamically generated Web content, and quicker access to searched-for information. However, adoption of Semantic Web technologies is limited and user perception from the non-IT domain sceptical. Furthermore, little attention has been given to evaluating semantic browsers with real users to demonstrate the enhancements and obtain valuable feedback. The Sealife project investigates semantic browsing and its application to the life science domain. Sealife's main objective is to develop the notion of context-based information integration by extending three existing Semantic Web browsers (SWBs) to link the existing Web to the eScience infrastructure. METHODS: This paper describes a user-centred evaluation framework that was developed to evaluate the Sealife SWBs that elicited feedback on users' perceptions on ease of use and information findability. Three sources of data: i) web server logs; ii) user questionnaires; and iii) semi-structured interviews were analysed and comparisons made between each browser and a control system. RESULTS: It was found that the evaluation framework used successfully elicited users' perceptions of the three distinct SWBs. The results indicate that the browser with the most mature and polished interface was rated higher for usability, and semantic links were used by the users of all three browsers. CONCLUSION: Confirmation or contradiction of our original hypotheses with relation to SWBs is detailed along with observations of implementation issues

Human PXR Forms a Tryptophan Zipper-Mediated Homodimer †

The human nuclear receptor pregnane X receptor (PXR) responds to a wide variety of potentially harmful chemicals and coordinates the expression of genes central to xenobiotic and endobiotic metabolism. Structural studies reveal that the PXR ligand binding domain (LBD) uses a novel sequence insert to form a homodimer unique to the nuclear receptor superfamily. Terminal β-strands from each monomeric LBD interact in an ideal antiparallel fashion to bury potentially exposed surface β-strands, generating a ten-stranded intermolecular β-sheet. Conserved tryptophan and tyrosine residues lock across the dimer interface and provide the first tryptophan-zipper (Trp-Zip) interaction observed in a native protein. We show using analytical ultracentrifugation that the PXR LBD forms a homodimer in solution. We further find that removal of the interlocking aromatic residues eliminates dimer formation but does not affect PXR's ability to interact with DNA, RXRα, or ligands. Disruption of the homodimer significantly reduces receptor activity in transient transfection experiments, however, and effectively eliminates the receptor's recruitment of the transcriptional coactivator SRC-1 both in vitro and in vivo. Taken together, these results suggest that the unique Trp-Zip-mediated PXR homodimer plays a role in the function of this nuclear xenobiotic receptor

State of the California current 2013-14: El niño looming

In 2013, the California current was dominated by strong coastal upwelling and high productivity. Indices of total cumulative upwelling for particular coastal locations reached some of the highest values on record. Chlorophyll a levels were high throughout spring and summer. Catches of upwelling-related fish species were also high. After a moderate drop in upwelling during fall 2013, the California current system underwent a major change in phase. Three major basin-scale indicators, the PDO, the NPGO, and the ENSO-MEI, all changed phase at some point during the winter of 2013/14. The PDO changed to positive values, indicative of warmer waters in the North Pacific; the NPGO to negative values, indicative of lower productivity along the coast; and the MEI to positive values, indicative of an oncoming El Niño. Whereas the majority of the California Current system appears to have transitioned to an El Niño state by August 2014, based on decreases in upwelling and chlorophyll a concentration, and increases in SST, there still remained pockets of moderate upwelling, cold water, and high chlorophyll a biomass at various central coast locations, unlike patterns seen during the more major El Niños (e.g., the 97-98 event). Catches of rockfish, market squid, euphausiids, and juvenile sanddab remained high along the central coast, whereas catches of sardine and anchovy were low throughout the CCS. 2014 appears to be heading towards a moderate El Niño state, with some remaining patchy regions of upwellingdriven productivity along the coast. Superimposed on this pattern, three major regions have experienced possibly non-El Niño-related warming since winter: the Bering Sea, the Gulf of Alaska, and offshore of southern California. It is unclear how this warming may interact with the predicted El Niño, but the result will likely be reduced growth or reproduction for many key fisheries species

Automated analysis of XANES: A feasibility study of Au reference compounds

With the advent of high-throughput and imaging core level spectroscopies (including X-ray absorption spectroscopy, XAS, as well as electron energy loss spectroscopy, EELS), automated data processing, visualisation and analytics will become a necessity. As a first step towards these objectives we examined the possibilities and limitations of a simple automated XANES peak fitting procedure written in MATLAB, for the parametrisation of XANES features, including ionisation potentials as well as the energies and intensities of electronic transitions. Using a series of Au L3-edge XANES reference spectra we show that most of the relevant information can be captured through a small number of rules applied to constrain the fits. Uncertainty in this strategy arises mostly when the ionisation potential (IP) overlaps with weak electronic transitions or features in the continuum beyond the IP, which can result in ambiguity through multiple equally good fits

State of the California current 2012-13: No such thing as an “average” year

This report reviews the state of the California Current System (CCS) between winter 2012 and spring 2013, and includes observations from Washington State to Baja California. During 2012, large-scale climate modes indicated the CCS remained in a cool, productive phase present since 2007. The upwelling season was delayed north of 42°N, but regions to the south, especially 33° to 36°N, experienced average to above average upwelling that persisted throughout the summer. Contrary to the indication of high production suggested by the climate indices, chlorophyll observed from surveys and remote sensing was below average along much of the coast. As well, some members of the forage assemblages along the coast experienced low abundances in 2012 surveys. Specifically, the concentrations of all lifestages observed directly or from egg densities of Pacific sardine, Sardinops sagax, and northern anchovy, Engraulis mordax, were less than previous years’ survey estimates. However, 2013 surveys and observations indicate an increase in abundance of northern anchovy. During winter 2011/2012, the increased presence of northern copepod species off northern California was consistent with stronger southward transport. Krill and small-fraction zooplankton abundances, where examined, were generally above average. North of 42°N, salps returned to typical abundances in 2012 after greater observed concentrations in 2010 and 2011. In contrast, salp abundance off central and southern California increased after a period of southward transport during winter 2011/2012. Reproductive success of piscivorous Brandt’s cormorant, Phalacrocorax penicillatus, was reduced while planktivorous Cassin’s auklet, Ptychoramphus aleuticus was elevated. Differences between the productivity of these two seabirds may be related to the available forage assemblage observed in the surveys. California sea lion pups from San Miguel Island were undernourished resulting in a pup mortality event perhaps in response to changes in forage availability. Limited biological data were available for spring 2013, but strong winter upwelling coastwide indicated an early spring transition, with the strong upwelling persisting into early summer

Evaluation of satisfaction with care in a midwifery unit and an obstetric unit: a randomized controlled trial of low-risk women

Publisher's version, source: http://doi.org/10.1186/s12884-016-0932-x.BACKGROUND Satisfaction with birth care is part of quality assessment of care. The aim of this study was to investigate possible differences in satisfaction with intrapartum care among low-risk women, randomized to a midwifery unit or to an obstetric unit within the same hospital. METHODS Randomized controlled trial conducted at the Department of Obstetrics and Gynecology, Østfold Hospital Trust, Norway. A total of 485 women with no expressed preference for level of birth care, assessed to be at low-risk at onset of spontaneous labor were included. To assess the overall satisfaction with intrapartum care, the Labour and Delivery Satisfaction Index (LADSI) questionnaire, was sent to the participants 6 months after birth. To assess women’s experience with intrapartum transfer, four additional items were added. In addition, we tested the effects of the following aspects on satisfaction; obstetrician involved, intrapartum transfer from the midwifery unit to the obstetric unit during labor, mode of delivery and epidural analgesia. RESULTS Women randomized to the midwifery unit were significantly more satisfied with intrapartum care than those randomized to the obstetric unit (183 versus 176 of maximum 204 scoring points, mean difference 7.2, p = 0.002). No difference was found between the units for women who had an obstetrician involved during labor or delivery and who answered four additional questions on this aspect (mean item score 4.0 at the midwifery unit vs 4.3 at the obstetric unit, p = 0.3). Intrapartum transfer from the midwifery unit to an obstetric unit, operative delivery and epidurals influenced the level of overall satisfaction in a negative direction regardless of allocated unit (p < 0.001). CONCLUSION Low-risk women with no expressed preference for level of birth care were more satisfied if allocated to the midwifery unit compared to the obstetric unit. TRIAL REGISTRATION The trial is registered at www.​clinicaltrials.​gov NCT00857129. Initially released 03/05/2009