Allometry and growth of eight tree taxa in United Kingdom woodlands.

This work is licensed under a Creative Commons Attribution 4.0 International License. The images or other third party material in this article are included in the article’s Creative Commons license, unless indicated otherwise in the credit line; if the material is not included under the Creative Commons license, users will need to obtain permission from the license holder to reproduce the material. To view a copy of this license, visit http://creativecommons.org/licenses/by/4.0As part of a project to develop predictive ecosystem models of United Kingdom woodlands we have collated data from two United Kingdom woodlands - Wytham Woods and Alice Holt. Here we present data from 582 individual trees of eight taxa in the form of summary variables relating to the allometric relationships between trunk diameter, height, crown height, crown radius and trunk radial growth rate to the tree's light environment and diameter at breast height. In addition the raw data files containing the variables from which the summary data were obtained. Large sample sizes with longitudinal data spanning 22 years make these datasets useful for future studies concerned with the way trees change in size and shape over their life-span

Novel Block Grid Analysis (BGA) Based Algorithm for use in Determining Coefficients of Similarities Between UV Fluorescent Spectra

This paper presents a novel computational process used for determining matching coefficients for optical spectra either in real time or from a database. This simple algorithmic method is capable of outputting a set of coefficients relating to comparative matching datapoints and to a weighted similarity ratio between spectra whilst still maintaining high computational efficiency due to the minimization of floating-point calculations. The process works as effectively on signal data during real time processing or on images of spectra which may be stored in a database. A subset of the algorithm has already been used very effectively in an embedded mobile field device to determine the presence or absence of special security fluorescent emission peaks present in printing inks used in anti-counterfeiting labels. The process involves the division of test spectrum(s) signal/image into a grid of user definable blocks while applying the same grid to the test image or images. Each block is then checked to see if the signal/image passes through the block, if the signal/image passes through a block then the value of this grid block is set to 1 in a grid array. The same check is then applied to the reference signal/image(s).While it is possible to process a signal comparison without the need for data storage, useful for some embedded processes, it may be preferable to store the resultant data in simple data arrays. These arrays can then undergo simple arithmetical processing to quickly calculate a set of values representing the number of matching data points, the variation in non-matching data points and a divergence value. This check can be carried out between the test image or images and a larger number of reference images simultaneously by use of additional counters. In addition, when used with large databases of spectra this novel technique may be used to rapidly reduce a large test set to a more relevant subset which can be further analyzed using more conventional methods or by visual inspection. This grid square analysis method works as efficiently on images as it can for signal data and it is believed by the authors that the method will have applications in other image processing applications where fast and efficient comparative analysis between images is required

Unique Conference Design Showcases Small Towns, Highlights Entrepreneurs, and Strengthens Capacity

Michigan State University Extension (MSUE)’s annual conference, Connecting Entrepreneurial Communities (CEC), has served as a catalyst for entrepreneurial ecosystems across Michigan since 2012. Designed by MSUE for small towns, CEC has gained national interest as evidenced by the adoption of this conference model by four other Extension services. This article outlines the unique conference design, details the partnership between Extension and host communities, and explores conference evaluation data validating the need to continue this programming. Lessons learned and successes to date are provided to ensure readers learn the value this unique conference format has in Extension entrepreneurship programming nationally

Molecular origins of transcriptional heterogeneity in diazotrophic Klebsiella oxytoca.

Phenotypic heterogeneity in clonal bacterial batch cultures has been shown for a range of bacterial systems; however, the molecular origins of such heterogeneity and its magnitude are not well understood. Under conditions of extreme low-nitrogen stress in the model diazotroph Klebsiella oxytoca, we found remarkably high heterogeneity of nifHDK gene expression, which codes for the structural genes of nitrogenase, one key enzyme of the global nitrogen cycle. This heterogeneity limited the bulk observed nitrogen-fixing capacity of the population. Using dual-probe, single-cell RNA fluorescent in situ hybridization, we correlated nifHDK expression with that of nifLA and glnK-amtB, which code for the main upstream regulatory components. Through stochastic transcription models and mutual information analysis, we revealed likely molecular origins for heterogeneity in nitrogenase expression. In the wild type and regulatory variants, we found that nifHDK transcription was inherently bursty, but we established that noise propagation through signaling was also significant. The regulatory gene glnK had the highest discernible effect on nifHDK variance, while noise from factors outside the regulatory pathway were negligible. Understanding the basis of inherent heterogeneity of nitrogenase expression and its origins can inform biotechnology strategies seeking to enhance biological nitrogen fixation. Finally, we speculate on potential benefits of diazotrophic heterogeneity in natural soil environments

Ion-pairing chromatography and amine derivatization provide complementary approaches for the targeted LC-MS analysis of the polar metabolome.

Liquid chromatography coupled to mass spectrometry is a key metabolomics/metabonomics technology. Reversed-phase liquid chromatography (RPLC) is very widely used as a separation step, but typically has poor retention of highly polar metabolites. Here, we evaluated the combination of two alternative methods for improving retention of polar metabolites based on 6-aminoquinoloyl-N-hydroxysuccinidimyl carbamate derivatization for amine groups, and ion-pairing chromatography (IPC) using tributylamine as an ion-pairing agent to retain acids. We compared both of these methods to RPLC and also to each other, for targeted analysis using a triple-quadrupole mass spectrometer, applied to a library of ca. 500 polar metabolites. IPC and derivatization were complementary in terms of their coverage: combined, they improved the proportion of metabolites with good retention to 91%, compared to just 39% for RPLC alone. The combined method was assessed by analyzing a set of liver extracts from aged male and female mice that had been treated with the polyphenol compound ampelopsin. Not only were a number of significantly changed metabolites detected, but also it could be shown that there was a clear interaction between ampelopsin treatment and sex, in that the direction of metabolite change was opposite for males and females

Stronger or longer: Discriminating between Hawaiian and Strombolian eruption styles

The weakest explosive volcanic eruptions globally, Strombolian explosions and Hawaiian fountaining, are also the most common. Yet, despite over a hundred years of observations, no classifications have offered a convincing, quantitative way of demarcating these two styles. New observations show that the two styles are distinct in their eruptive time scale, with the duration of Hawaiian fountaining exceeding Strombolian explosions by ∼300–10,000 s. This reflects the underlying process of whether shallow-exsolved gas remains trapped in the erupting magma or is decoupled from it. We propose here a classification scheme based on the duration of events (brief explosions versus prolonged fountains) with a cutoff at 300 s that separates transient Strombolian explosions from sustained Hawaiian fountains.The authors wish to acknowledge grants from NSF (EAR-0409303, 0810332, 1145159, 1427357) and ARRA (113153 via the Hawaiian Volcano Observatory), which funded this research.This is the accepted manuscript. The final version is available at http://dx.doi.org/10.1130/G37423.

Migrations and habitat use of the smooth hammerhead shark (Sphyrna zygaena) in the Atlantic Ocean

The smooth hammerhead shark, Sphyrna zygaena, is a cosmopolitan semipelagic shark captured as bycatch in pelagic oceanic fisheries, especially pelagic longlines targeting swordfish and/or tunas. From 2012 to 2016, eight smooth hammerheads were tagged with Pop-up Satellite Archival Tags in the inter-tropical region of the Northeast Atlantic Ocean, with successful transmissions received from seven tags (total of 319 tracking days). Results confirmed the smooth hammerhead is a highly mobile species, as the longest migration ever documented for this species (> 6600 km) was recorded. An absence of a diel vertical movement behavior was noted, with the sharks spending most of their time at surface waters (0-50 m) above 23 degrees C. The operating depth of the pelagic long-line gear was measured with Minilog Temperature and Depth Recorders, and the overlap with the species vertical distribution was calculated. The overlap is taking place mainly during the night and is higher for juveniles (similar to 40% of overlap time). The novel information presented can now be used to contribute to the provision of sustainable management tools and serve as input for Ecological Risk Assessments for smooth hammerheads caught in Atlantic pelagic longline fisheries.Oceanario de Lisboa through Project "SHARK-TAG: Migrations and habitat use of the smooth hammerhead shark in the Atlantic Ocean"; Investigador-FCT from the Portuguese Foundation for Science and Technology (FCT, Fundacao para a Ciencia e Tecnologia) [Ref: IF/00253/2014]; EU European Social Fund; Programa Operacional Potencial Human

A system of metrics for the assessment and improvement of aquatic ecosystem models

In this paper, we introduce the CSPS framework for the hierarchical assessment of aquatic ecosystem models built on a range of metrics and characteristic signatures relevant to aquatic ecosystem condition. The framework is comprised of four levels: 0) conceptual validation; 1) comparison of simulated state variables with observations (‘state validation’); 2) comparison of fluxes with measured process rates (‘process validation’); and 3) assessment of system-level emergent properties, patterns and relationships (‘system validation’). Of these, only levels 0 and 1 are routinely undertaken at present. To highlight a diverse range of contexts relevant to the aquatic ecosystem modelling community, we present several case studies of improved validation approaches using the level 0–3 assessment hierarchy. We envision that the community–driven adoption of these metrics will lead to more rigorously assessed models, ultimately accelerating advances in model structure and function, and improved confidence in model predictions

Comparison of oral and vaginal metronidazole for treatment of bacterial vaginosis in pregnancy: impact on fastidious bacteria

<p>Abstract</p> <p>Background</p> <p>Bacterial vaginosis (BV) is a common condition that is associated with preterm birth and acquisition of complex communities of vaginal bacteria that include several fastidious species. Treatment of BV in pregnancy has mixed effects on the risk of preterm delivery, which some hypothesize is due to variable antibiotic efficacy for the fastidious bacteria. Both oral and intravaginal metronidazole can be used to treat bacterial vaginosis in pregnancy, but little is known about the impact of different routes of antibiotic administration on concentrations of fastidious vaginal bacteria.</p> <p>Methods</p> <p>This was a sub-study of a larger randomized trial of oral versus vaginal metronidazole for treatment of BV in pregnancy. Fifty-three women were evaluated, including 30 women who received oral metronidazole and 23 who received intravaginal metronidazole. Bacterial taxon-specific quantitative PCR assays were used to measure concentrations of bacterial vaginosis associated bacterium (BVAB) 1, 2, and 3, <it>Gardnerella vaginalis, Atopobium </it>species, <it>Leptotrichia/Sneathia </it>species, <it>Megasphaera </it>species, and <it>Lactobacillus crispatus </it>before and after antibiotic treatment.</p> <p>Results</p> <p>Concentrations of <it>Leptotrichia </it>and <it>Sneathia </it>spp. and the fastidious Clostridia-like bacterium designated BVAB1 decreased significantly with oral (p = .002, p = .02) but not vaginal therapy (p = .141, p = .126). The fastidious bacterium BVAB3 did not significantly decrease with either treatment. Concentrations of <it>Atopobium </it>spp., reportedly resistant to metronidazole <it>in vitro</it>, dropped significantly with oral (p = .002) and vaginal (p = .001) treatment. There was no significant difference in the magnitude of change in bacterial concentrations between oral and vaginal treatment arms for any of the bacterial species. <it>Lactobacillus crispatus </it>concentrations did not change.</p> <p>Conclusion</p> <p>Both oral and vaginal metronidazole therapy in pregnant women result in a significant decrease in concentrations of most BV-associated anaerobic bacteria, with the exception that <it>Leptotrichia, Sneathia </it>and BVAB1 do not significantly decrease with vaginal metronidazole therapy. These data suggest that the route of antibiotic administration has a minor impact on bacterial eradication in pregnant women with BV.</p> <p>Trail Registration</p> <p>This trial is registered with ClinicalTrials.gov, number NCT00153517</p