Phylogeny and prediction of genetic similarity of Cronobacter and related taxa by multilocus sequence analysis (MLSA)

Multilocus sequence analysis (MLSA) based on recN, rpoA and thdF genes was done on more than 30 species of the family Enterobacteriaceae with a focus on Cronobacter and the related genus Enterobacter. The sequences provide valuable data for phylogenetic, taxonomic and diagnostic purposes. Phylogenetic analysis showed that the genus Cronobacter forms a homogenous cluster related to recently described species of Enterobacter, but distant to other species of this genus. Combining sequence information on all three genes is highly representative for the species' %GC-content used as taxonomic marker. Sequence similarity of the three genes and even of recN alone can be used to extrapolate genetic similarities between species of Enterobacteriaceae. Finally, the rpoA gene sequence, which is the easiest one to determine, provides a powerful diagnostic tool to identify and differentiate species of this family. The comparative analysis gives important insights into the phylogeny and genetic relatedness of the family Enterobacteriaceae and will serve as a basis for further studies and clarifications on the taxonomy of this large and heterogeneous family.

An analysis of the Galveston Hurricane using the 20CR data set

The Twentieth Century Reanalysis (20CR) is an atmospheric dataset consisting of 56 ensemble members, which covers the entire globe and reaches back to 1871. To assess the suitability of this dataset for studying past extremes, we analysed a prominent extreme event, namely the Galveston Hurricane, which made landfall in September 1900 in Texas, USA. The ensemble mean of 20CR shows a track of the pressure minimum with a small standard deviation among the 56 ensemble members in the area of the Gulf of Mexico. However, there are systematic differences between the assimilated “Best Track” from the International Best Track Archive for Climate Stewardship (IBTrACS) and the ensemble mean track in 20CR. East of the Strait of Florida, the tracks derived from 20CR are located systematically northeast of the assimilated track while in the Gulf of Mexico, the 20CR tracks are systematically shifted to the southwest compared to the IBTrACS position. The hurricane can also be observed in the wind field, which shows a cyclonic rotation and a relatively calm zone in the centre of the hurricane. The 20CR data reproduce the pressure gradient and cyclonic wind field. Regarding the amplitude of the wind speeds, the ensemble mean values from 20CR are significantly lower than the wind speeds known from measurements.

Synoptic Analysis of the New York March 1888 Blizzard

The meteorological circumstances that led to the Blizzard of March 1888 that hit New York are analysed in Version 2 of the “Twentieth Century Reanalysis” (20CR). The potential of this data set for studying historical extreme events has not yet been fully explored. A detailed analysis of 20CR data alongside other data sources (including historical instrumental data and weather maps) for historical extremes such as the March 1888 blizzard may give insights into the limitations of 20CR. We find that 20CR reproduces the circulation pattern as well as the temperature development very well. Regarding the absolute values of variables such as snow fall or minimum and maximum surface pressure, there is anunderestimation of the observed extremes, which may be due to the low spatial resolution of 20CR and the fact that only the ensemble mean is considered. Despite this drawback, the dataset allows us to gain new information due to its complete spatial and temporal coverage.

Finite element analysis for prediction of bone strength

Article preview View full access options BoneKEy Reports | Review Print Email Share/bookmark Finite element analysis for prediction of bone strength Philippe K Zysset, Enrico Dall'Ara, Peter Varga & Dieter H Pahr Affiliations Corresponding author BoneKEy Reports (2013) 2, Article number: 386 (2013) doi:10.1038/bonekey.2013.120 Received 03 January 2013 Accepted 25 June 2013 Published online 07 August 2013 Article tools Citation Reprints Rights & permissions Abstract Abstract• References• Author information Finite element (FE) analysis has been applied for the past 40 years to simulate the mechanical behavior of bone. Although several validation studies have been performed on specific anatomical sites and load cases, this study aims to review the predictability of human bone strength at the three major osteoporotic fracture sites quantified in recently completed in vitro studies at our former institute. Specifically, the performance of FE analysis based on clinical computer tomography (QCT) is compared with the ones of the current densitometric standards, bone mineral content, bone mineral density (BMD) and areal BMD (aBMD). Clinical fractures were produced in monotonic axial compression of the distal radii, vertebral sections and in side loading of the proximal femora. QCT-based FE models of the three bones were developed to simulate as closely as possible the boundary conditions of each experiment. For all sites, the FE methodology exhibited the lowest errors and the highest correlations in predicting the experimental bone strength. Likely due to the improved CT image resolution, the quality of the FE prediction in the peripheral skeleton using high-resolution peripheral CT was superior to that in the axial skeleton with whole-body QCT. Because of its projective and scalar nature, the performance of aBMD in predicting bone strength depended on loading mode and was significantly inferior to FE in axial compression of radial or vertebral sections but not significantly inferior to FE in side loading of the femur. Considering the cumulated evidence from the published validation studies, it is concluded that FE models provide the most reliable surrogates of bone strength at any of the three fracture sites.

A 350 ka record of climate change from Lake El'gygytgyn, Far East Russian Arctic: refining the pattern of climate modes by means of cluster analysis

Abstract. Rock magnetic, biochemical and inorganic records of the sediment cores PG1351 and Lz1024 from Lake El’gygytgyn, Chukotka peninsula, Far East Russian Arctic, were subject to a hierarchical agglomerative cluster analysis in order to refine and extend the pattern of climate modes as defined by Melles et al. (2007). Cluster analysis of the data obtained from both cores yielded similar results, differentiating clearly between the four climate modes warm, peak warm, cold and dry, and cold and moist. In addition, two transitional phases were identified, representing the early stages of a cold phase and slightly colder conditions during a warm phase. The statistical approach can thus be used to resolve gradual changes in the sedimentary units as an indicator of available oxygen in the hypolimnion in greater detail. Based upon cluster analyses on core Lz1024, the published succession of climate modes in core PG1351, covering the last 250 ka, was modified and extended back to 350 ka. Comparison to the marine oxygen isotope (�18O) stack LR04 (Lisiecki and Raymo, 2005) and the summer insolation at 67.5� N, with the extended Lake El’gygytgyn parameter records of magnetic susceptibility (�LF), total organic carbon content (TOC) and the chemical index of alteration (CIA; Minyuk et al., 2007), revealed that all stages back to marine isotope stage (MIS) 10 and most of the substages are clearly reflected in the pattern derived from the cluster analysis.

Effect of zinc binding residues in growth hormone (GH) and altered intracellular zinc content on regulated GH secretion.

Endocrine cells store hormones in concentrated forms (aggregates) in dense-core secretory granules that are released upon appropriate stimulation. Zn(2+) binding to GH through amino acid residues His18, His21, and Glu174 are essential for GH dimerization and might mediate its aggregation and storage in secretory granules. To investigate whether GH-1 gene mutations at these positions interfere with this process, GH secretion and intracellular production were analyzed in GC cells (rat pituitary cell line) transiently expressing wt-GH and/or GH Zn mutant (GH-H18A-H21A-E174A) in forskolin-stimulated vs nonstimulated conditions. Reduced secretion of the mutant variant (alone or coexpressed with wt-GH) compared with wt-GH after forskolin stimulation was observed, whereas an increased intracellular accumulation of GH Zn mutant vs wt-GH correlates with its altered extracellular secretion. Depleting Zn(2+) from culture medium using N,N,N',N'-tetrakis(2-pyridylemethyl)ethylenediamine, a high-affinity Zn(2+) chelator, led to a significant reduction of the stimulated wt-GH secretion. Furthermore, externally added Zn(2+) to culture medium increased intracellular free Zn(2+) levels and recovered wt-GH secretion, suggesting its direct dependence on free Zn(2+) levels after forskolin stimulation. Confocal microscopy analysis of the intracellular secretory pathway of wt-GH and GH Zn mutant indicated that both variants pass through the regulated secretory pathway in a similar manner. Taken together, our data support the hypothesis that loss of affinity of GH to Zn(2+) as well as altering intracellular free Zn(2+) content may interfere with normal GH dimerization (aggregation) and storage of the mutant variant (alone or with wt-GH), which could possibly explain impaired GH secretion.

Micro-blogging adoption in the enterprise: an empirical analysis

Given the increasing interest in using social software for company-internal communication and collaboration, this paper examines drivers and inhibitors of micro-blogging adoption at the workplace. While nearly one in two companies is currently planning to introduce social software, there is no empirically validated research on employees’ adoption. In this paper, we build on previous focus group results and test our research model in an empirical study using Structural Equation Modeling. Based on our findings, we derive recommendations on how to foster adoption. We suggest that micro-blogging should be presented to employees as an efficient means of communication, personal brand building, and knowledge management. In order to particularly promote content contribution, privacy concerns should be eased by setting clear rules on who has access to postings and for how long they will be archived.

Carbon dioxide and climate impulse response functions for the computation of greenhouse gas metrics: a multi-model analysis

The responses of carbon dioxide (CO2) and other climate variables to an emission pulse of CO2 into the atmosphere are often used to compute the Global Warming Potential (GWP) and Global Temperature change Potential (GTP), to characterize the response timescales of Earth System models, and to build reduced-form models. In this carbon cycle-climate model intercomparison project, which spans the full model hierarchy, we quantify responses to emission pulses of different magnitudes injected under different conditions. The CO2 response shows the known rapid decline in the first few decades followed by a millennium-scale tail. For a 100 Gt-C emission pulse added to a constant CO2 concentration of 389 ppm, 25 ± 9% is still found in the atmosphere after 1000 yr; the ocean has absorbed 59 ± 12% and the land the remainder (16 ± 14%). The response in global mean surface air temperature is an increase by 0.20 ± 0.12 °C within the first twenty years; thereafter and until year 1000, temperature decreases only slightly, whereas ocean heat content and sea level continue to rise. Our best estimate for the Absolute Global Warming Potential, given by the time-integrated response in CO2 at year 100 multiplied by its radiative efficiency, is 92.5 × 10−15 yr W m−2 per kg-CO2. This value very likely (5 to 95% confidence) lies within the range of (68 to 117) × 10−15 yr W m−2 per kg-CO2. Estimates for time-integrated response in CO2 published in the IPCC First, Second, and Fourth Assessment and our multi-model best estimate all agree within 15% during the first 100 yr. The integrated CO2 response, normalized by the pulse size, is lower for pre-industrial conditions, compared to present day, and lower for smaller pulses than larger pulses. In contrast, the response in temperature, sea level and ocean heat content is less sensitive to these choices. Although, choices in pulse size, background concentration, and model lead to uncertainties, the most important and subjective choice to determine AGWP of CO2 and GWP is the time horizon.

Decreased generation of procoagulant platelets detected by flow cytometric analysis in patients with bleeding diathesis

Background: A clinically relevant bleeding diathesis is a frequent diagnostic challenge, which sometimes remains unexplained despite extensive investigations. The aim of our work was to evaluate the diagnostic utility of functional platelet testing by flow cytometry in this context. Methods: In case of negative results after standard laboratory work-up, flow cytometric analysis (FCA) of platelet function was done. We performed analysis of surface glycoproteins (GP) Ibα, IIb, IIIa; P-selectin expression and PAC-1 binding after graded doses of ADP, collagen and thrombin; content/secretion of dense granules; ability to generate procoagulant platelets. Results: Out of 437 patients investigated with standard tests between January 2007 and December 2011, we identified 67 (15.3%) with high bleeding scores and non-diagnostic standard laboratory work-up including platelet aggregation studies. Among these patients FCA revealed some potentially causative platelet defects: decreased dense-granule content/secretion (n=13); decreased alpha-granule secretion induced by ADP (n=10), convulxin (n=4) or thrombin (n=3); decreased fibrinogen-receptor activation induced by ADP (n=11), convulxin (n=11) or thrombin (n=8); decreased generation of COAT-platelets, i.e. highly procoagulant platelets induced by simultaneous activation with collagen and thrombin (n=16). Conclusion: Our work confirms that storage pool defects are frequent in patients with a bleeding diathesis and normal coagulation and platelet aggregations studies. Additionally, flow cytometric analysis is able to identify discrete platelet activation defects. In particular, we show for the first time that a relevant proportion of these patients has an isolated impaired ability to generate COAT-platelets - a conceptually new defect in platelet procoagulant activity, that is missed by conventional laboratory work-up. © 2014 Clinical Cytometry Society.

The Global Digital Divide as Impeded Access to Content

The paper seeks a re-conceptualization of the global digital divide debate. It critically explores the predominant notion, its evolution and measurement, as well as the policies that have been advanced to bridge the digital divide. Acknowledging the complexity of this inequality, the paper aims at analyzing the disparities beyond the connectivity and the skills barriers. Without understating the first two digital divides, it is argued that as the Internet becomes more sophisticated and more integrated into economic, social and cultural processes, a ‘third’ generation of divides becomes critical. These divides are drawn not at the entry to the net but within the net itself, and limit access to content. The increasing barriers to content, although of diverse nature, all relate to some governance characteristics inherent in cyberspace, such as global spillover of local decisions, regulation through code or proliferation of self- and co-regulatory models. It is maintained that as the practice of intervention intensifies in cyberspace, multiple and far-reaching points of control outside formal legal institutions are created, which threaten the availability of public goods and make the pursuit of public objectives difficult. This is an aspect that is rarely addressed in the global digital divide discussions, even in comprehensive analysis and political initiatives such as the World Summit on the Information Society. Yet, the conceptualization of the digital divide as impeded access to content may be key in terms of ensuring real participation and catering for the long-term implications of digital technologies.

Taxon-specific δ13C analysis of chitinous invertebrate remains in sediments from Strandsjön, Sweden

Taxon-specific stable carbon isotope (δ13C) analysis of chitinous remains of invertebrates can provide valuable information about the carbon sources used by invertebrates living in specific habitats of lake ecosystems (for example, sediments, water column, or aquatic vegetation). This is complementary to δ13C of sedimentary organic matter (SOM), which provides an integrated signal of organic matter produced in a lake and its catchment, and of diagenetic processes within sediments. In a sediment record from Strandsjön (Sweden) covering the past circa 140 years, we analyzed SOM geochemistry (δ13C, C:Natomic, organic carbon content) and δ13C of chitinous invertebrate remains in order to examine whether taxon-specific δ13C records could be developed for different invertebrate groups and whether these analyses provide insights into past changes of organic carbon sources for lacustrine invertebrates available in benthic and planktonic compartments of the lake. Invertebrate taxa included benthic chironomids (Chironomus, Chironomini excluding Chironomus, Tanytarsini, and Tanypodinae), filter-feeders on suspended particulate organic matter (Daphnia, Plumatella and Cristatella mucedo), and Rhabdocoela. δ13C of chironomid remains indicated periodic availability of 13C-depleted carbon sources in the benthic environment of the lake as δ13C values of the different chironomid taxa fluctuated simultaneously between -34.7 and -30.5‰ (VPDB). Daphnia and Bryozoa showed parallel changes in their δ13C values which did not coincide with variations in δ13C of chironomids, though, and a 2-3‰ decrease since circa AD 1960. The decrease in δ13C of Daphnia and Bryozoa could indicate a decrease in phytoplankton δ13C as a result of lower lake productivity, which is in accordance with historical information about the lake that suggests a shift to less eutrophic conditions after AD 1960. In contrast, Rhabdocoela cocoons were characterized by relatively high δ13C values (-30.4 to -28.2‰) that did not show a strong temporal trend, which could be related to the predatory feeding mode and wide prey spectrum of this organism group. The taxon-specific δ13C analyses of invertebrate remains indicated that different carbon sources were available for the benthic chironomid larvae than for the filter-feeding Daphnia and bryozoans. Our results therefore demonstrate that taxon-specific analysis of δ13C of organic invertebrate remains can provide complementary information to measurements on bulk SOM and that δ13C of invertebrate remains may allow the reconstruction of past changes in carbon sources and their δ13C in different habitats of lake ecosystems.

Exploring the publications in three major orthodontic journals: a comparative analysis of two 5-year periods.

OBJECTIVE To analyze the types of articles and authorship characteristics of three orthodontic journals--American Journal of Orthodontics and Dentofacial Orthopedics (AJODO), The Angle Orthodontist (AO), and European Journal of Orthodontics (EJO)--published between 2008 and 2012 and to assess the differences in content within this period and an earlier period of 1998 to 2002. MATERIALS AND METHODS Each journal's content was accessed through the web edition. From each article, the following parameters were recorded: article type, number of authors, number of affiliations, source of article (referring to the first author's affiliation), and geographic origin. Descriptive statistics were performed and selected parameters were analyzed with the Pearson chi-square or Fisher exact test for independence at the .05 level of significance. RESULTS Review of differences between the two periods showed that the number of publications was almost double. The percentages of multi-authored articles increased. Fewer studies derived from the United States/Canada and European Union countries. Increases for articles from non-European Union countries, Asia, and other countries were found. Characteristics of the second period showed that the EJO and AO published more research articles, whereas the AJODO regularly published case reports and other articles. Approximately 75% of all studies derived from orthodontic departments. CONCLUSIONS The publications from 1998-2002 and 2008-2012 were significantly different both in terms of numbers and characteristics. Within 2008-2012 there were notable differences between the three journals concerning the type and origin of the publications.

Global phylogenomic analysis of nonencapsulated Streptococcus pneumoniae reveals a deep-branching classic lineage that is distinct from multiple sporadic lineages.

The surrounding capsule of Streptococcus pneumoniae has been identified as a major virulence factor and is targeted by pneumococcal conjugate vaccines (PCV). However, nonencapsulated Streptococcus pneumoniae (Non-Ec-Sp) have also been isolated globally, mainly in carriage studies. It is unknown if Non-Ec-Sp evolve sporadically, if they have high antibiotic non-susceptiblity rates and a unique, specific gene content. Here, whole genome sequencing of 131 Non-Ec-Sp isolates sourced from 17 different locations around the world was performed. Results revealed a deep-branching classic lineage that is distinct from multiple sporadic lineages. The sporadic lineages clustered with a previously sequenced, global collection of encapsulated S. pneumoniae (Ec-Sp) isolates while the classic lineage is comprised mainly of the frequently identified multi-locus sequences types ST344 (n=39) and ST448 (n=40). All ST344 and nine ST448 isolates had high non-susceptiblity rates to β-lactams and other antimicrobials. Analysis of the accessory genome reveals that the classic Non-Ec-Sp contained an increased number of mobile elements, than Ec-Sp and sporadic Non-Ec-Sp. Performing adherence assays to human epithelial cells for selected classic and sporadic Non-Ec-Sp revealed that the presence of a integrative conjugative element (ICE) results in increased adherence to human epithelial cells (P=0.005). In contrast, sporadic Non-Ec-Sp lacking the ICE had greater growth in vitro possibly resulting in improved fitness. In conclusion, Non-Ec-Sp isolates from the classic lineage have evolved separately. They have spread globally, are well adapted to nasopharyngeal carriage and are able to coexist with Ec-Sp. Due to continued use of pneumococcal conjugate vaccines, Non-Ec-Sp may become more prevalent.