EM Community Research Articles

SimpliPyTEM: An open-source Python library and app to simplify transmission electron microscopy and in situ-TEM image analysis.

Introducing SimpliPyTEM, a Python library and accompanying GUI that simplifies the post-acquisition evaluation of transmission electron microscopy (TEM) images, helping streamline the workflow. After an imaging session, a folder of image and/or video files, typically containing low contrast and large file size 32-bit images, can be quickly processed via SimpliPyTEM into high-quality, high-contrast.jpg images with suitably sized scale bars. The app can also generate HTML or PDF files containing the processed images for easy viewing and sharing. Additionally, SimpliPyTEM specifically focuses on in situ TEM videos, an emerging field of EM involving the study of dynamic processes whilst imaging. The package allows fast data processing into preview movies, averages, image series, or motion-corrected averages. The accompanying Python library offers many standard image processing methods, all simplified to a single command, plus a module to analyse particle morphology and population. This latter application is particularly useful for life sciences investigations. User-friendly tutorials and clear documentation are included to help guide users through the processing and analysis. We invite the EM community to contribute to and further develop this open-source package.

A Systematic Exploration of Kilonova Candidates from Neutron Star Mergers during the Third Gravitational-wave Observing Run

Abstract We present a comprehensive analysis of 653 optical candidate counterparts reported during the third gravitational-wave (GW) observing run. Our sample concentrates on candidates from the 15 events (published in GWTC-2, GWTC-3, or not retracted on GraceDB) that had a >1% chance of including a neutron star in order to assess their viability as true kilonovae. In particular, we leverage tools available in real time, including pre-merger detections and cross-matching with catalogs (i.e., point-source, variable-star, quasar and host-galaxy redshift data sets), to eliminate 65% of candidates in our sample. We further employ spectroscopic classifications, late-time detections, and light-curve behavior analyses and conclude that 66 candidates remain viable kilonovae. These candidates lack sufficient information to determine their classifications, and the majority would require luminosities greater than that of AT 2017gfo. Pre-merger detections in public photometric survey data and comparison of cataloged host-galaxy redshifts with the GW event distances are critical to incorporate into vetting procedures, as these tools eliminated >20% and >30% of candidates, respectively. We expect that such tools that leverage archival information will significantly reduce the strain on spectroscopic and photometric follow-up resources in future observing runs. Finally, we discuss the critical role prompt updates from GW astronomers to the EM community play in reducing the number of candidates requiring vetting.

Programmable Controls to Scattering Properties of a Radiation Array

AbstractElectromagnetic (EM) waves have been widely applied in wireless communications, radar detection, navigation, and target recognition. Radiation and scattering are two common behaviors in the EM community, but it remains a long‐standing challenge to control them in a dynamical way, especially using a single, low‐cost, and compact hardware. Here, a promising solution is proposed by combining a programmable metasurface with a radiation array, which can manipulate the scattering properties, digitally and in real‐time, and exhibit different radiation modes simultaneously. More advantageous over previous investigations with the fixed radiation‐scattering performance, a field‐programmable gate array is introduced to extend, realize, and verify the multiple functions of the meta‐microstructure (MMS). As a proof‐of‐concept, multiple functions, including polarization conversion, scattering beam manipulation, diffusion scattering, radar cross‐section reduction, EM waves radiation, and vortex beam generation, have been adequately demonstrated by the MMS prototype.

Health human resources for emergency medicine: a framework for the future.

In June of 2016, the Collaborative Working Group (CWG) on the Future of Emergency Medicine presented its final report at the Canadian Association of Emergency Physicians (CAEP) annual meeting in Quebec City. The CWG report made a number of recommendations concerning physician Human Health Resource (HHR) shortfalls in emergency medicine, specific changes for both the Royal College of Physicians and Surgeons of Canada (FRCPC) and the College of Family Physicians of Canada (CCFP-EM) training programs, HHR needs in rural and remote hospitals, future collaboration of the CCFP-EM and FRCPC programs, and directions for future research. All recommendations were endorsed by CAEP, the Royal College of Physicians and Surgeons of Canada (RCPSC), and the College of Family Physicians of Canada (CFPC). The CWG report was published in CJEM and has served as a basis for ongoing discussion in the emergency medicine community in Canada. The CWG identified an estimated shortfall of 478 emergency physicians in Canada in 2016, rising to 1071 by 2020 and 1518 by 2025 assuming no expansion of EM residency training capacity. In 2017, the CAEP board struck a new committee, The Future of Emergency Medicine in Canada (FEMC), to advocate with appropriate stakeholders to implement the CWG recommendations and to continue with this important work. FEMC led a workshop at CAEP 2018 in Calgary to develop a regional approach to HHR advocacy, recognizing different realities in each province and region. There was wide representation at this workshop and a rich and passionate discussion among those present. This paper represents the output of the workshop and will guide subsequent deliberations by FEMC. FEMC has set the following three goals as we work toward the overarching purpose to improve timely access to high quality emergency care: (1) to define and describe categories of emergency departments (EDs) in Canada, (2) define the full time equivalents required by category of ED in Canada, and (3) recommend the ideal combination of training and certification for emergency physicians in Canada. A fourth goal supports the other three goals: (4) urge further consideration and implementation of the CWG-EM recommendations related to coordination and optimization of the current two training programs. We believe that goals 1 and 2 can largely be accomplished by the CAEP annual meeting in 2020, and goal 3 by the CAEP annual meeting in 2021. Goal 4 is ongoing with both the RCPSC and the CFPC. We urge the EM community across Canada to engage with our committee to support improved access and EM care for all Canadians.

Web-based volume slicer for 3D electron-microscopy data from EMDB.

We describe the functionality and design of the Volume slicer – a web-based slice viewer for EMDB entries. This tool uniquely provides the facility to view slices from 3D EM reconstructions along the three orthogonal axes and to rapidly switch between them and navigate through the volume. We have employed multiple rounds of user-experience testing with members of the EM community to ensure that the interface is easy and intuitive to use and the information provided is relevant. The impetus to develop the Volume slicer has been calls from the EM community to provide web-based interactive visualisation of 2D slice data. This would be useful for quick initial checks of the quality of a reconstruction. Again in response to calls from the community, we plan to further develop the Volume slicer into a fully-fledged Volume browser that provides integrated visualisation of EMDB and PDB entries from the molecular to the cellular scale.

Viewpoint

FigureFigureJournal clubs have served as a way for the local medical community to appraise and dissect medical literature for more than two centuries. (Postgrad Med J 1987;63[740]:475.) The first journal clubs date back to the early 1800s, and involved cards, smoky rooms, and late-night discussion. Sir William Osler organized a formal meeting at McGill University in 1875, and since then, residents and attendings have discussed classic and new research in settings ranging from resident conferences to local bars. The traditional format of a local journal club is undoubtedly successful, but it has significant constraints. Only physicians in attendance gain from the discussion. Even fantastic local clubs have little global impact, and documentation for knowledge translation and recall is often absent. Online tools offer opportunities for local emergency medicine journal clubs to reimagine their place within the global EM community, increase engagement, and enhance knowledge translation. Many journal clubs struggle to achieve maximum attendance because of busy resident and attending schedules. An innovative solution to this dilemma has been demonstrated by the Global EM Journal Club Series hosted by Academic Life in Emergency Medicine. (www.ALiEM.com; Ann Emerg Med 2014;63[4]:490.) The blog picks a journal article to discuss and allows its followers to contribute talking points on Twitter using the hashtag #ALiEMJC until a specific closing date. They then host a discussion of experts on Google+, with an accompanying blog post that includes a summary of the Twitter discussion. The Global EMJC Series using social media eliminates attendance stress by allowing everyone to contribute through Twitter and comments on the blog asynchronously. This setup, however, can make the contributions difficult to navigate because some comments are made on the video Google+ hangout while others are hidden within the Twitter summary. This format also lacks integration with local existing clubs that may not read the scheduled paper during the assigned time frame. The emergency medicine journal club at Washington University in St. Louis has enhanced recall and knowledge translation through online documentation. Recording a session makes a journal club much more valuable for members because they can later review discussions and teaching points. Many residency programs accomplish this goal privately by distributing minutes via emails to members. Documentation provides a permanent source for reviewing findings and recalling discussions, but the content is static. New literature cannot be added to older journal reviews, and these reviews are typically impossible to locate on a busy shift. WikEM's Journal Club offers a novel approach to an accessible, dynamic journal club with ongoing discussion and contributions. (www.WikEM.org.) By using a wiki exactly like Wikipedia, any member from any journal club at any time can contribute knowledge gained from local discussion. The system augments the already-existing residency-sponsored in-person meetings. The material is highly integrated with core emergency medicine content linked between pages, and all content is expandable for future contributions. More importantly, the format allows local groups to set their own club schedule while also contributing relevant material to the wiki for the benefit of the global EM community. Because WikEM.org is open access and user-generated, any journal club blog post, paper, online calculator, or podcast can be referenced and linked to a discussion to curate the best related content. Pages never close or disappear, allowing participants to build on historical knowledge, validate previous studies, or refute old evidence. Most importantly, all of the content is available offline on a mobile device using the WikEM app. Journal club discussions directly translate into bedside knowledge because of this tool. Just as we use new meaningful technologies for patient care, it is imperative that we also bring Osler's journal club into the 21st century by making it more accessible and dynamic with online resources. Share this article on Twitter and Facebook. Access the links in EMN by reading this on our website or in our free iPad app, both available at www.EM-News.com. Comments? Write to us at [email protected].

Strong differences in Quercus robur-associated ectomycorrhizal fungal communities along a forest-city soil sealing gradient

Abstract Ectomycorrhizal fungi (EM) that associate with tree roots in a symbiotic relationship may be crucial in mediating tree health in urban environments, but research on the effects of urbanization on EM communities is very limited so far. Here, we compared EM communities of adult pedunculate oaks ( Quercus robur ) between urban and forest environments, and assessed the effect of soil sealing around the trees on their EM community composition and EM diversity. We sampled 32 oak individuals across 4 sampling classes (Street, Lane, Park and Forest), and we characterized their EM communities using 454 amplicon pyrosequencing. The EM communities were not nested but they were significantly different between all sampling classes, with a very strong community differentiation between forest and urban trees. There were indications that EM richness declined with increasing sealed soil surface, with a significant effect of sampling class on estimated EM richness and diversity. We also identified indicator EM of the different sampling classes. The most important soil factor affecting EM community composition was pH, followed by plant available phosphorus, total nitrogen content and organic matter. Our results may have important implications when developing EM inocula for managing tree health in urban environments.

Hot off the press: Assessing older adult fall risk in the emergency department.

Editor’s note: Academic Emergency Medicine (AEM) is collaborating with the Skeptics Guide to EmergencyMedicine (SGEM) to summarize and critically appraise the current emergency medicine literature using evi-dence-based medicine principles. For this new “Hot Off the Press” series, we will select original researchmanuscripts published in AEM to be featured on the SGEM site and discussed by study authors and theonline EM community of medical students, residents, and practicing physicians. What follows is a summaryof a selected article, the immediate postpublication synthesis in the SGEM podcast, commentary by the firstauthor, and the subsequent discussion on the SGEM blog and on social media. Through this series, we hopeto enhance the value, accessibility, and application of important, clinically relevant EM research.BACKGROUND

Improving the quality of emergency medicine care by developing a quality requirement framework: a study from The Netherlands

BackgroundIn The Netherlands, mainly inexperienced physicians work in the ED on all shifts, including the evening and night shifts, when no direct supervision is available. In 2004 a report of the Dutch Health Care Inspectorate revealed that quality of care at Emergency Departments (EDs) was highly variable. Based on this report and international studies showing significant potential for quality improvement, stakeholders felt the need to improve the quality of EM care. Based on the literature, a baseline measurement and a panel of experts, The Netherlands recently developed a nationwide quality requirement framework (QRF) for EM. This article describes the content of and path to this QRF.MethodsTo conduct a baseline measurement, the panel needed to identify measurable entities related to EM care at EDs. This was done by formulating both qualitative and partly quantitative questions related to the following competence areas: triage system, training of personnel (physicians and nurses), facilities and supervision of physicians.27 out of 104 Dutch EDs were sampled via a cross-sectional study design, using an online survey and standardized follow-up interview in which the answers of the survey were reviewed.ResultsIn the QRF, EM care is divided into a basic level of EM care and six competence certification areas (CCAs): (acute) abdominal aortic aneurysm, acute coronary syndrome, acute psychiatric behavioral disorder, cerebral vascular accident, pediatric critical care and infants with low birth weight. For the basic level of EM care and for every CCA minimum prerequisites for medical devices and training of personnel are established. The factors selected for the QRF can be regarded as minimum quality standards for EM care. A major finding of this study was that in The Netherlands, none of the 27 sampled EDs demonstrated compliance with these factors.ConclusionOur study shows that Dutch EDs fall short of what the expert consensus panelists considered minimum prerequisites for adequate EM care. The process of systematic enquiry allowed this information to come to light for the first time, which resulted in the implementation of a QRF for Dutch ED personnel, that is intended improve quality of EM care over time. This is an important development for the worldwide EM community as the QRF shows a way to generate interim standards to improve the chances of appropriate delivery of EM care when the gold standard of providing fully qualified EPs is not initially achievable.

Investigations on the synthesis of uniform linear antenna array using biogeography-based optimisation techniques

This paper presents the use of biogeography-based optimisation (BBO) algorithm for uniform linear antenna array (ULA) synthesis using amplitude only control method. BBO is a new evolutionary algorithm (EA) proposed by Dan Simon in the year 2008. The first objective of this paper is to optimise the excitation magnitude of array elements to minimise the maximum side lobe levels. Second objective is to place nulls at specific directions for the optimised pattern by optimising a weight parameter. We review classic BBO and modified biogeography-based optimisation (M-BBO) with two migration models namely linear and sinusoidal. Several simulation experiments are conducted on ULA using BBO techniques to minimise the maximum side lobe level (SLL) imposed with broad nulls. We compare the results of simulation case studies of classic BBO and M-BBO with other EAs such as ACO, GA and StudGA. Best performance is achieved using BBO techniques compared to other EAs for our design problem. The major aim of our investigation is to expose BBO to the EM community and demonstrate its great potential in antenna array design optimisation problem.

Community composition of bacterial biofilms on two submerged macrophytes and an artificial substrate in a pre-alpine lake

AME Aquatic Microbial Ecology Contact the journal Facebook Twitter RSS Mailing List Subscribe to our mailing list via Mailchimp HomeLatest VolumeAbout the JournalEditorsSpecials AME 58:79-94 (2009) - DOI: https://doi.org/10.3354/ame01353 Community composition of bacterial biofilms on two submerged macrophytes and an artificial substrate in a pre-alpine lake Melanie Hempel1,*, Hans-Peter Grossart2, Elisabeth M. Gross1 1Limnological Institute, Department of Biology, University of Konstanz, PO Box 659, 78457 Konstanz, Germany 2Leibniz Institute of Freshwater Ecology and Inland Fisheries (IGB), Department of Limnology of Stratified Lakes, Alte Fischerhuette 2, 16775 Stechlin, Germany *Email: hempelmelanie@web.de ABSTRACT: We compared the heterotrophic community composition of bacterial biofilms on the submerged macrophytes Myriophyllum spicatum and Potamogeton perfoliatus and on an artificial surface in Lower Lake Constance (Germany) on spatial (plant age) and temporal scales using denaturing gradient gel electrophoresis (DGGE) and fluorescence in situ hybridization (FISH). M. spicatum contains polyphenolic allelochemicals that inhibit algae, cyanobacteria, and heterotrophic bacteria, and possibly influence the community composition, whereas P. perfoliatus does not. In 2005, the community composition of bacterial biofilms on apices and leaves of M. spicatum differed significantly. In 2006, the biofilm communities on the apices or leaves of M. spicatum and P. perfoliatus and the artificial surface did not differ significantly, although all except one apex sample of M. spicatum formed a distinct cluster based on DGGE banding patterns. On all surfaces, members of the Cytophaga-Flavobacter-Bacteroidetes (CFB) group (16 to 22%), Alphaproteobacteria (19%), and Betaproteobacteria (7 to 31%) were abundant; Actinobacteria and Planctomycetes occurred less frequently. Sequences of DNA fragments excised from DGGE gels were mainly affiliated with yet uncultured clones originating from various freshwater habitats. Several sequences were from bacteria capable of degrading phenolic and aromatic compounds. The chemical composition of the 2 plant species and of the different parts of M. spicatum differed up to an order of magnitude. Differences in the biofilm community composition mainly depended on environmental factors (water level, conductivity, temperature, pH) and the plant chemical composition, especially the carbon and total phenolic content. Our results suggest that the biofilm community on M. spicatum apices is related to specific bacterial functions in this microenvironment. KEY WORDS: Myriophyllum spicatum . Potamogeton perfoliatus . DGGE . FISH . Phenolic compounds . Biofilms . Macrophytes Full text in pdf format Supplementary material PreviousNextCite this article as: Hempel M, Grossart HP, Gross EM (2009) Community composition of bacterial biofilms on two submerged macrophytes and an artificial substrate in a pre-alpine lake. Aquat Microb Ecol 58:79-94. https://doi.org/10.3354/ame01353Export citation RSS - Facebook - Tweet - linkedIn Cited by Published in AME Vol. 58, No. 1. Online publication date: December 08, 2009 Print ISSN: 0948-3055; Online ISSN: 1616-1564 Copyright © 2009 Inter-Research.

EM Community Should Increase Residency Positions

EM Community Should Increase Residency Positions

Characterization of beech ectomycorrhizae formed by species of the Pachyphloeus–Amylascus lineage

The hypogeous genus Pachyphloeus forms a common phylogenetic lineage with the epigeous Scabropezia and the hypogeous Amylascus, within the Pezizaceae (Ascomycota). Though the ectomycorrhiza- (EM) forming ability of this group was proposed previously, no detailed description has been published up to now, except for the characterization of EM related to P. virecens. During our several-year-long survey on the EM community of a beech forest reserve in Hungary, we found ten EM specimens belonging to the Pachyphloeus-Amylascus lineage. All of them share common morphological and anatomical characters. The densely ramifying whitish-yellow to light-brown mycorrhizal systems are pyramidal with short, stout ends. The EM surface is densely wooly with white or brown, curly hyphae. All mantle layers are pseudoparenchymatous angular, covered by a thick-walled hyphal network. Frequent emanating hyphae are densely septate without clamps. The EM can be sorted into three different morphotypes (Mt) according to their color, specific morphometric traits (cell-wall thickness, diameter of emanating hyphae, septal distance), and certain anatomical characters (structure of the surface net). Molecular identification was accomplished by the phylogenetic analysis of the ITS and LSU regions of the nrDNA, what proved that the sequences clustered into three clades corresponding to the three Mt. With the aid of fruitbody-derived sequences, obtained from GenBank, one of the Mt can be identified as Pachyphloeus melanoxanthus and another one as Pachyphloeus citrinus. The third Mt, together with another unidentified EM sequence of the GenBank, forms a distinct branch, which is a sister group to the Pachyphloeus-Scabropezia-Amylascus lineage. In addition to presenting the first detailed anatomical and molecular comparison of the EM related to P. melanoxanthus and P. citrinus, we call the attention to the need for further microscopical investigations amended by molecular taxonomical analyses.

Object-oriented CEM programming

The essence of object-oriented software technology and its application to CEM have been discussed. OOP is a promising technology for implementing a unified simulation framework for CEM. A well-designed object-oriented CEM package can encapsulate features common to all CEM techniques and support development of new modeling algorithms via object inheritance and polymorphism. Such a package would be a useful modeling tool for the CEM community. As of the writing of this article, there is no coordinated open-source initiative for creating a unified object-oriented CEM package. Availability of such a package would foster new channels of collaboration in the EM community. This would enable future students, engineers, and researchers to better focus their efforts in engineering design and algorithm innovation. The IEEE MTT Society could play an important role in realizing this proposed object-oriented CEM package.

Energetic Materials: Crystallization, Characterization and Insensitive Plastic Bonded Explosives

AbstractThe product quality of energetic materials is predominantly determined by the crystallization process applied to produce these materials. It has been demonstrated in the past that the higher the product quality of the solid energetic ingredients, the less sensitive a plastic bonded explosive containing these energetic materials becomes. The application of submicron or nanometric energetic materials is generally considered to further decrease the sensitiveness of explosives. In order to assess the product quality of energetic materials, a range of analytical techniques is available. Recent attempts within the Reduced‐sensitivity RDX Round Robin (R4) have provided the EM community a better insight into these analytical techniques and in some cases a correlation between product quality and shock initiation of plastic bonded explosives containing (RS‐)RDX was identified, which would provide a possibility to discriminate between conventional and reduced sensitivity grades.

The Good, the Bad, and the Ugly: Demonstrating Basic Circuit Layout and Measurement Concepts [Education Column

Circuit prototyping and layout are facts of life for many of us in the EM community. Whether we are designing amplifiers, phase shifters, or filters, or trying to diagnose a difficult electromagnetic compatibility problem, the physical construction of high-frequency circuits is a major concern. The topic of circuit layout is often overlooked in the typical undergraduate curriculum. Proper measurement practices are also important, since a poor testing configuration can lead to misleading data. This issue's column will demonstrate one way to introduce the importance of good circuit layout and measurement practices into introductory level courses.

SIGNATURE: A single-particle selection system for molecular electron microscopy

SIGNATURE is a particle selection system for molecular electron microscopy. It applies a hierarchical screening procedure to identify molecular particles in EM micrographs. The user interface of the program provides versatile functions to facilitate image data visualization, particle annotation and particle quality inspection. The system design emphasizes both functionality and usability. This software has been released to the EM community and has been successfully applied to macromolecular structural analyses.

Status of the Rayleigh scattering method in three-dimensional electromagnetic modeling

The Rayleigh scattering method offers distinct advantages in geophysical modeling over differencing or integral formulations but an inherent error in the Rayleigh hypothesis has severely limited its wider application. The method can be numerically implemented to be very fast and topographic and subsurface geometries can be described simply by digitized surface and interface values. This contrasts with gridding throughout a volume as used in finite difference and finite element methods. However, the error in the Rayleigh method prevents the modeling of steep topography and very high subsurface slopes such as the vertical sides of prismatic bodies. The inherent Rayleigh error, or famous Rayleigh ansatz (approximation), exists because the formulation assumes that scattering above a rough surface is described by a superposition of upward-scattered plane waves or plane wavelets only. This does not allow multiple scattering with downward components that should occur in topographic depressions. Manifestations of this omission are non-convergence behavior, numerical instabilities, and incorrect results. Valid results are obtained for plane wave EM sources normally incidence on buried 2-D and 3-D structures having interface slopes as high as 50-60°. In the far-field, above the topography, the surface slope limit can be extended to over 74° by adapted-regularization. In the near-field, on 2-D topography, surface slopes of only 26° are properly modeled for the TM (transverse magnetic) mode. Since the physics of 3-D scattering can be dominated by TM-like (galvanic) effects, near-field Rayleigh EM scattering from 3-D topography is probably limited to slopes of about this value unless regularization schemes are used. Regularization and the identification and reduction of specific numerical instabilities are considered the keys to extending the Rayleigh method to general 3-D EM modeling. New ways of extending the validity of the Rayleigh scattering method justify more interest in the geophysical EM community especially in 3-D subsurface and airborne (i.e., far-field) modeling.