Permanent draft genome sequences for two variants of Frankia sp. strain CpI1, the first Frankia strain isolated from root nodules of Comptonia peregrina

Frankia stains CpI1-S and CpI1-P are members of Frankia lineage Ia that are able to reinfect plants of the Betulaceae and Myricaceae families. Here, we report two 7.6-Mbp draft genome sequences with 6,396 and 6,373 candidate protein-coding genes for CpI1-S and CpI1-P, respectively

Exploring the sensitivities of crenulate-bay shorelines to wave climates using a new vector-based one-line model

We use a new exploratory model that simulates the evolution of sandy coastlines over decadal to centennial timescales to examine the behavior of crenulate-shaped bays forced by differing directional wave climates. The model represents the coastline as a vector in a Cartesian reference frame, and the shoreface evolves relative to its local orientation, allowing simulation of coasts with high planform-curvature. Shoreline change is driven by gradients in alongshore transport following newly developed algorithms that facilitate dealing with high planform-curvature coastlines. We simulated the evolution of bays from a straight coast between two fixed headlands with no external sediment inputs to an equilibrium condition (zero net alongshore sediment flux) under an ensemble of directional wave climate conditions. We find that planform bay relief increases with obliquity of the mean wave direction, and decreases with the spread of wave directions. Varying bay size over 2 orders of magnitude (0.1–16 km), the model predicts bay shape to be independent of bay size. The time taken for modeled bays to attain equilibrium was found to scale with the square of the distance between headlands, so that, all else being equal, small bays are likely to respond to and recover from perturbations more rapidly (over just a few years) compared to large bays (hundreds of years). Empirical expressions predicting bay shape may be misleading if used to predict their behavior over planning timescales

Complex coastlines responding to climate change: do shoreline shapes reflect present forcing or “remember” the distant past?

A range of planform morphologies emerge along sandy coastlines as a function of offshore wave climate. It has been implicitly assumed that the morphological response time is rapid compared to the timescales of wave climate change, meaning that coastal morphologies simply reflect the extant wave climate. This assumption has been explored by focussing on the response of two distinctive morphological coastlines – flying spits and cuspate capes – to changing wave climates, using a coastline evolution model. Results indicate that antecedent conditions are important in determining the evolution of morphologies, and that sandy coastlines can demonstrate hysteresis behaviour. In particular, antecedent morphology is particularly important in the evolution of flying spits, with characteristic timescales of morphological adjustment on the order of centuries for large spits. Characteristic timescales vary with the square of aspect ratios of capes and spits; for spits, these timescales are an order of magnitude longer than for capes (centuries vs. decades). When wave climates change more slowly than the relevant characteristic timescales, coastlines are able to adjust in a quasi-equilibrium manner. Our results have important implications for the management of sandy coastlines where decisions may be implicitly and incorrectly based on the assumption that present-day coastlines are in equilibrium with current conditions

Stochastic Opinion Formation in Scale-Free Networks

The dynamics of opinion formation in large groups of people is a complex non-linear phenomenon whose investigation is just at the beginning. Both collective behaviour and personal view play an important role in this mechanism. In the present work we mimic the dynamics of opinion formation of a group of agents, represented by two state $\pm 1$, as a stochastic response of each of them to the opinion of his/her neighbours in the social network and to feedback from the average opinion of the whole. In the light of recent studies, a scale-free Barab\'asi-Albert network has been selected to simulate the topology of the interactions. A turbulent-like dynamics, characterized by an intermittent behaviour, is observed for a certain range of the model parameters. The problem of uncertainty in decision taking is also addressed both from a topological point of view, using random and targeted removal of agents from the network, and by implementing a three state model, where the third state, zero, is related to the information available to each agent. Finally, the results of the model are tested against the best known network of social interactions: the stock market. A time series of daily closures of the Dow Jones index has been used as an indicator of the possible applicability of our model in the financial context. Good qualitative agreement is found.Comment: 24 pages and 13 figures, Physical Review E, in pres

Gastroenteritis and Transmission of Helicobacter pylori Infection in Households1

In northern California homes, exposure to gastroenteritis in an H. pylori–infected contact markedly increased H. pylori infection

Endocast morphology of Homo naledi from the Dinaledi Chamber, South Africa

Hominin cranial remains from the Dinaledi Chamber, South Africa, represent multiple individuals of the species Homo naledi. This species exhibits a small endocranial volume comparable to Australopithecus, combined with several aspects of external cranial anatomy similar to larger-brained species of Homo such as Homo habilis and Homo erectus. Here, we describe the endocast anatomy of this recently discovered species. Despite the small size of the H. naledi endocasts, they share several aspects of structure in common with other species of Homo, not found in other hominins or great apes, notably in the organization of the inferior frontal and lateral orbital gyri. The presence of such structural innovations in a small-brained hominin may have relevance to behavioral evolution within the genus Homo

The heterogeneity of systemic inflammation in bronchiectasis

BACKGROUND: Systemic inflammation in bronchiectasis is poorly studied in relation to aetiology and severity. We hypothesized that molecular patterns of inflammation may define particular aetiology and severity groups in bronchiectasis. METHOD: We assayed blood concentrations of 31 proteins from 90 bronchiectasis patients (derivation cohort) and conducted PCA to examine relationships between these markers, disease aetiology and severity. Key results were validated in two separate cohorts of 97 and 79 patients from other centres. RESULTS: There was significant heterogeneity in protein concentrations across the derivation population. Increasing severity of bronchiectasis (BSI) was associated with increasing fibrinogen (rho = 0.34, p = 0.001 -validated in a second cohort), and higher fibrinogen was associated with worse lung function, Pseudomonas colonisation and impaired health-status. There were generally similar patterns of inflammation in patients with idiopathic and post-infectious disease. However, patients with primary immunodeficiency had exaggerated IL-17 responses, validated in a second cohort (n = 79, immunodeficient 12.82 pg/ml versus idiopathic/post-infectious 4.95 pg/ml, p = 0.001), and thus IL-17 discriminated primary immunodeficiency from other aetiologies (AUC 0.769 (95%CI 0.661-0.877)). CONCLUSION: Bronchiectasis is associated with heterogeneity of systemic inflammatory proteins not adequately explained by differences in disease aetiology or severity. More severe disease is associated with enhanced acute-phase responses. Plasma fibrinogen was associated with bronchiectasis severity in two cohorts, Pseudomonas colonisation and health status, and offers potential as a useful biomarker

A core outcome set for localised prostate cancer effectiveness trials

Objective: To develop a core outcome set (COS) applicable for effectiveness trials of all interventions for localised prostate cancer. Background: Many treatments exist for localised prostate cancer, although it is unclear which offers the optimal therapeutic ratio. This is confounded by inconsistencies in the selection, definition, measurement and reporting of outcomes in clinical trials. Subjects and methods: A list of 79 outcomes was derived from a systematic review of published localised prostate cancer effectiveness studies and semi-structured interviews with 15 prostate cancer patients. A two-stage consensus process involving 118 patients and 56 international healthcare professionals (HCPs) (cancer specialist nurses, urological surgeons and oncologists) was undertaken, consisting of a three-round Delphi survey followed by a face-to-face consensus panel meeting of 13 HCPs and 8 patients. Results: The final COS included 19 outcomes. Twelve apply to all interventions: death from prostate cancer, death from any cause, local disease recurrence, distant disease recurrence/metastases, disease progression, need for salvage therapy, overall quality of life, stress urinary incontinence, urinary function, bowel function, faecal incontinence, sexual function. Seven were intervention-specific: perioperative deaths (surgery), positive surgical margin (surgery), thromboembolic disease (surgery), bothersome or symptomatic urethral or anastomotic stricture (surgery), need for curative treatment (active surveillance), treatment failure (ablative therapy), and side effects of hormonal therapy (hormone therapy). The UK-centric participants may limit the generalisability to other countries, but trialists should reason why the COS would not be applicable. The default position should not be that a COS developed in one country will automatically not be applicable elsewhere. Conclusion: We have established a COS for trials of effectiveness in localised prostate cancer, applicable across all interventions which should be measured in all localised prostate cancer effectiveness trials

Studies in vitro with ICI 174, 864, [D-Pen2, D-Pen5]-enkephalin (DPDPE) and [D-Ala2, NMePhe4, Gly-ol]-enkephalin (DAGO)

The interactions of a proposed, selective delta receptor antagonist (ICI 174, 864) and selective agonists at mu and delta receptors, [D-Ala2, NMePhe4, Gly-ol]-enkephalin (DAGO) and [D-Pen2, D-Pen5]-enkephalin (DPDPE), respectively, have been studied using the electrically-stimulated mouse isolated vas deferens (MVD) and the guinea-pig isolated ileum (GPI). Incubation of increasing concentrations of ICI 174, 864 (10, 30, 100 and 300 nM) produced a dose-related and parallel rightward displacement of the DPDPE dose-response curve in the MVD. In contrast, ICI 174, 864 (300-3000 nM) failed to affect the DAGO dose-response curve in the same tissue. Analysis of the DPDPE-ICI 174, 864 interaction in the MVD using the pA2 method revealed a Schild plot slope of -0.68 suggesting the involvement of more than one population of receptors. ICI 174, 864 (300 nM) failed to antagonize DPDPE in the GPI at doses up to 30 uM. These results suggest that (a) ICI 174, 864 acts as a selective delta antagonist in the MVD; (b) DPDPE interacts with mu receptors in the MVD but only at very high concentrations, and (c) delta receptors appear not to be of functional importance in the GPI.Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/25769/1/0000330.pd

The “Ebb and Flow” of Documentation: Does the Transition Between Two Electronic Medical Records Systems Affect Emergency Department Efficiency?

Background: Electronic Medical Record (EMR) systems are electronic databases for compiling patient records. As healthcare networks expand, it is critical for providers to have access to patient data more broadly. As a result individual healthcare facilities must adjust to enterprise wide EMRs. Objective: This study examined the operational effects of transitioning from an Emergency Department (ED) specific EMR to an enterprise wide EMR by evaluating throughput metrics in a community ED. Methods: During a 6-month transition period (July-December 2017) in a community-based, academic ED located in North Central West Virginia, length of stay (LOS) and the following operational metrics were analyzed: door-to-provider times, door to disposition time, average LOS, left without treatment (LWOT) rates, and total ED volumes. These metrics were compared with the prior year’s same 6-month period to account for seasonal variability in patient pathology or ED volumes. Results: Overall, there was a statistically significant increase in the LOS measures, including door-to-provider time (p=0.0003), door to disposition time (p Conclusion: An ED-specific EMR to enterprise wide EMR transition in a community ED had a negative effect on the overall efficiency of the emergency department