SUPPORT FOR COLLABORATIVE AUTHORING VIA EMAIL - THE MESSIE ENVIRONMENT

MESSIE is a collaborative authoring environment to support the production of large-scale documents by teams of geographically distributed groups of authors working with hetereogenous systems. The environment allows authors to submit text at various stages of gestation (e.g. list of topics, first draft) to a shared filestore via email. All authors collaborating on a document can read each others’ contributions, and add suggestions, comments and additional material directly to the document. The system integrates automatically answered electronic mail, shared file store administration, and a version control tool in a UNIX environment. The paper describes design and implementation strategy, and reports observations and a number of changes which were made during a 4-month trial period with three collaborative authoring teams

Buprenorphine-Naloxone in the Treatment of Codeine Dependence: a Scoping Review of Clinical Case Presentations

Misuse of prescribed and over the counter (OTC) codeine containing medicines is an increasing public health concern in recent times. Studies have called for low threshold treatment services for individuals experiencing codeine dependence using buprenorphine naloxone therapy. We present a scoping review of clinical case presentation literature on the use of buprenorphine-naloxone in the treatment of codeine dependence. Seven records (four single case studies and three case series) on codeine dependence treated with buprenorphine-naloxone were included. Five themes emerged following a review of the cases for the treatment of codeine dependence with buprenorphine-naloxone. They are: (1) Patient Profiles; (2) History of Codeine Misuse; (3) Medical Problems; (4) Use of Other Substances; and (5) Buprenorphine-naloxone in the treatment of Codeine Dependence. The review highlights the complexities of patients with regards to pain, psychiatric illness, poly substance use and iatrogenic dependence, with findings encouraging in terms of patient stabilisation and recovery

Lichen response to ammonia deposition defines the footprint of a penguin rookery

Ammonia volatilized from penguin rookeries is a major nitrogen source in Antarctic coastal terrestrial ecosystems. However, the spatial extent of ammonia dispersion from rookeries and its impacts have not been quantified previously. We measured ammonia concentration in air and lichen ecophysiological response variables proximate to an Adèlie penguin rookery at Cape Hallett, northern Victoria Land. Ammonia emitted from the rookery was 15N-enriched (δ15N value +6.9) and concentrations in air ranged from 36–75 µg m−3 at the rookery centre to 0.05 µg m−3 at a distance of 15.3 km. δ15N values and rates of phosphomonoesterase (PME) activity in the lichens Usnea sphacelata and Umbilicaria decussata were strongly negatively related to distance from the rookery and PME activity was positively related to thallus N:P mass ratio. In contrast, the lichen Xanthomendoza borealis, which is largely restricted to within an area 0.5 km from the rookery perimeter, had high N, P and 15N concentrations but low PME activity suggesting that nutrient scavenging capacity is suppressed in highly eutrophicated sites. An ammonia dispersion model indicates that ammonia concentrations sufficient to significantly elevate PME activity and δ15N values (≥0.1 µg NH3 m−3) occurred over c. 40–300 km2 surrounding the rookery suggesting that penguin rookeries potentially can generate large spatial impact zones. In a general linear model NH3 concentration and lichen species identity were found to account for 72 % of variation in the putative proportion of lichen thallus N originating from penguin derived NH3. The results provide evidence of large scale impact of N transfer from a marine to an N-limited terrestrial ecosystem

Foliar δ15N values characterize soil N cycling and reflect nitrate or ammonium preference of plants along a temperate grassland gradient

The natural abundance of stable 15N isotopes in soils and plants is potentially a simple tool to assess ecosystem N dynamics. Several open questions remain, however, in particular regarding the mechanisms driving the variability of foliar δ15N values of non-N2 fixing plants within and across ecosystems. The goal of the work presented here was therefore to: (1) characterize the relationship between soil net mineralization and variability of foliar Δδ15N (δ15Nleaf − δ15Nsoil) values from 20 different plant species within and across 18 grassland sites; (2) to determine in situ if a plant’s preference for NO3− or NH4+ uptake explains variability in foliar Δδ15N among different plant species within an ecosystem; and (3) test if variability in foliar Δδ15N among species or functional group is consistent across 18 grassland sites. Δδ15N values of the 20 different plant species were positively related to soil net mineralization rates across the 18 sites. We found that within a site, foliar Δδ15N values increased with the species’ NO3− to NH4+ uptake ratios. Interestingly, the slope of this relationship differed in direction from previously published studies. Finally, the variability in foliar Δδ15N values among species was not consistent across 18 grassland sites but was significantly influenced by N mineralization rates and the abundance of a particular species in a site. Our findings improve the mechanistic understanding of the commonly observed variability in foliar Δδ15N among different plant species. In particular we were able to show that within a site, foliar δ15N values nicely reflect a plant’s N source but that the direction of the relationship between NO3− to NH4+ uptake and foliar Δδ15N values is not universal. Using a large set of data, our study highlights that foliar Δδ15N values are valuable tools to assess plant N uptake patterns and to characterize the soil N cycle across different ecosystems

Psychoimmunological effects of dioscorea in ovariectomized rats: role of anxiety level

<p>Abstract</p> <p>Background</p> <p>Anxiety levels in rats are correlated with interleukin-2 (IL-2) levels in the brain. The aim of the present study was to investigate the effects of dioscorea (wild yam), a Chinese medicine, on emotional behavior and IL-2 levels in the brain of ovariectomized (OVX) rats.</p> <p>Methods</p> <p>One month after ovariectomy, female Wistar rats were screened in the elevated plus-maze (EPM) test to measure anxiety levels and divided into low anxiety (LA) and high anxiety (HA) groups, which were then given dioscorea (250, 750, or 1500 mg/kg/day) by oral gavage for 27 days and were tested in the EPM on day 23 of administration and in the forced swim test (FST) on days 24 and 25, then 3 days later, the brain was removed and IL-2 levels measured.</p> <p>Results</p> <p>Compared to sham-operated rats, anxiety behavior in the EPM was increased in half of the OVX rats. After chronic dioscorea treatment, a decrease in anxiety and IL-2 levels was observed in the HA OVX rats. Despair behavior in the FST was inhibited by the highest dosage of dioscorea.</p> <p>Conclusion</p> <p>These results show that OVX-induced anxiety and changes in neuroimmunological function in the cortex are reversed by dioscorea treatment. Furthermore, individual differences need to be taken into account when psychoneuroimmunological issues are measured and the EPM is a useful tool for determining anxiety levels when examining anxiety-related issues.</p

Recovering complete and draft population genomes from metagenome datasets

Assembly of metagenomic sequence data into microbial genomes is of fundamental value to improving our understanding of microbial ecology and metabolism by elucidating the functional potential of hard-to-culture microorganisms. Here, we provide a synthesis of available methods to bin metagenomic contigs into species-level groups and highlight how genetic diversity, sequencing depth, and coverage influence binning success. Despite the computational cost on application to deeply sequenced complex metagenomes (e.g., soil), covarying patterns of contig coverage across multiple datasets significantly improves the binning process. We also discuss and compare current genome validation methods and reveal how these methods tackle the problem of chimeric genome bins i.e., sequences from multiple species. Finally, we explore how population genome assembly can be used to uncover biogeographic trends and to characterize the effect of in situ functional constraints on the genome-wide evolution

Mitochondrial phylogeography of baboons (Papio spp.) – Indication for introgressive hybridization?

<p>Abstract</p> <p>Background</p> <p>Baboons of the genus <it>Papio </it>are distributed over wide ranges of Africa and even colonized parts of the Arabian Peninsula. Traditionally, five phenotypically distinct species are recognized, but recent molecular studies were not able to resolve their phylogenetic relationships. Moreover, these studies revealed para- and polyphyletic (hereafter paraphyletic) mitochondrial clades for baboons from eastern Africa, and it was hypothesized that introgressive hybridization might have contributed substantially to their evolutionary history. To further elucidate the phylogenetic relationships among baboons, we extended earlier studies by analysing the complete mitochondrial cytochrome <it>b </it>gene and the 'Brown region' from 67 specimens collected at 53 sites, which represent all species and which cover most of the baboons' range.</p> <p>Results</p> <p>Based on phylogenetic tree reconstructions seven well supported major haplogroups were detected, which reflect geographic populations and discordance between mitochondrial phylogeny and baboon morphology. Our divergence age estimates indicate an initial separation into southern and northern baboon clades 2.09 (1.54–2.71) million years ago (mya). We found deep divergences between haplogroups within several species (~2 mya, northern and southern yellow baboons, western and eastern olive baboons and northern and southern chacma baboons), but also recent divergence ages among species (< 0.7 mya, yellow, olive and hamadryas baboons in eastern Africa).</p> <p>Conclusion</p> <p>Our study confirms earlier findings for eastern Africa, but shows that baboon species from other parts of the continent are also mitochondrially paraphyletic. The phylogenetic patterns suggest a complex evolutionary history with multiple phases of isolation and reconnection of populations. Most likely all these biogeographic events were triggered by multiple cycles of expansion and retreat of savannah biomes during Pleistocene glacial and inter-glacial periods. During contact phases of populations reticulate events (i.e. introgressive hybridization) were highly likely, similar to ongoing hybridization, which is observed between East African baboon populations. Defining the extent of the introgressive hybridization will require further molecular studies that incorporate additional sampling sites and nuclear loci.</p