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Recent years have seen an exponential increase in the variety of healthcare data captured across numerous sources. However, mechanisms to leverage these data sources to support scientific investigation have remained limited. In 2013 the Pediatric Heart Network (PHN), funded by the National Heart, Lung, and Blood Institute, developed the Integrated CARdiac Data and Outcomes (iCARD) Collaborative with the goals of leveraging available data sources to aid in efficiently planning and conducting PHN studies; supporting integration of PHN data with other sources to foster novel research otherwise not possible; and mentoring young investigators in these areas. This review describes lessons learned through the development of iCARD, initial efforts and scientific output, challenges, and future directions. This information can aid in the use and optimisation of data integration methodologies across other research networks and organisations.
Using existing data from clinical registries to support clinical trials and other prospective studies has the potential to improve research efficiency. However, little has been reported about staff experiences and lessons learned from implementation of this method in pediatric cardiology.
We describe the process of using existing registry data in the Pediatric Heart Network Residual Lesion Score Study, report stakeholders’ perspectives, and provide recommendations to guide future studies using this methodology.
The Residual Lesion Score Study, a 17-site prospective, observational study, piloted the use of existing local surgical registry data (collected for submission to the Society of Thoracic Surgeons-Congenital Heart Surgery Database) to supplement manual data collection. A survey regarding processes and perceptions was administered to study site and data coordinating center staff.
Survey response rate was 98% (54/55). Overall, 57% perceived that using registry data saved research staff time in the current study, and 74% perceived that it would save time in future studies; 55% noted significant upfront time in developing a methodology for extracting registry data. Survey recommendations included simplifying data extraction processes and tailoring to the needs of the study, understanding registry characteristics to maximise data quality and security, and involving all stakeholders in design and implementation processes.
Use of existing registry data was perceived to save time and promote efficiency. Consideration must be given to the upfront investment of time and resources needed. Ongoing efforts focussed on automating and centralising data management may aid in further optimising this methodology for future studies.
White mold caused by the fungus, Sclerotinia sclerotiorum is a devastating disease of soybean (Glycine max) and other leguminous crops, including dry bean (Phaseolus vulgaris). Previous research has demonstrated that no-till planting soybean into rolled–crimped cereal rye residue can enhance weed management, improve soil health and reduce labor requirements in organic production. However, there are limited data on the effects of cereal rye residue on white mold suppression in no-till planted soybean and dry bean. Two field trials were conducted in 2016–2017 (Year 1) and repeated in 2017–2018 (Year 2) to evaluate the potential of cereal rye cover crop residue to suppress white mold in these crops. In each trial (soybean and dry bean), the experimental design was a randomized complete block with two treatments: (1) rolled–crimped cereal rye residue and (2) no cover crop control. Treatment effects on plant population, biomass and yield components varied between the main crops. Compared with the control treatment, cereal rye residue reduced the incidence of white mold in soybean in both years and in dry bean in Year 2. The reduction in white mold in cereal rye residue plots was due to a combination of (1) decreased sclerotial germination (no stipes formed) and (2) increased nonfunctional sclerotial germination defined here as sclerotia that germinated but produced stipes without the expanded cup where asci containing ascospores are formed. Weed density and biomass were lower in cereal rye residue plots in soybean and dry bean, except in Year 1 in soybean when weed biomass was low in both treatments. Our findings indicate that cereal rye residue could help organic and conventional farmers manage white mold in no-till planted soybean and dry bean. Germination of sclerotia resulting in nonfunctional apothecia could potentially exhaust soilborne inoculum in the upper soil profile and reduce infections in subsequent crops.
Downy brome (Bromus tectorum L.) is a common impediment to ecological restoration, because its seedbank remains viable after repeated treatment with herbicides. Soil solarization has been used in ecological restoration to control seedbanks of invasive plants. Here we test the efficacy of soil solarization to reduce B. tectorum cover and establish native plants at a site in B. tectorum’s core invasive range with a long history of disturbance and infestation. Solarization raised soil temperatures by as much as 13 C and reduced B. tectorum densities by approximately 20-fold. In 30 plots solarized for 0 to 101 d, B. tectorum emerged in inverse abundance to treatment duration. Broadleaf weeds were less abundant than B. tectorum before treatment, and diminished under solarization, but their response to solarization was weaker than B. tectorum’s, and they emerged in greater numbers than B. tectorum 2 to 3 yr after treatment. When seeded after solarization, a native perennial bunchgrass, squirreltail [Elymus elymoides (Raf.) Swezey], did not differ in abundance between solarized and control plots. Solarization may facilitate B. tectorum control on a small scale without jeopardizing the establishment of native plants, but only if treatment durations are long and subsequent management of broadleaf weeds and remnant B. tectorum is planned.
Virtual Reconstruction is a powerful tool broadly suited to a diverse array of archaeological heritage applications. In practice, however, reconstruction has largely focused on grand and monumental sites. Here we present two case studies–one from southern Oklahoma, the other from western Nebraska–to explore the use of this technology for more common heritage applications. The goal of this article is to advertise the dilemma we faced with communicating information on ephemeral sites and how we, as nonspecialists, solved the issue using affordable and accessible digital tools. Our workflow makes use of common tools (GIS) and open source software and online tutorials provide step by step instruction to support its replication. In presenting our experiences and the results of these efforts, we hope to spur similar applications in the use of Virtual Reconstruction to communicate information on archaeological heritage more broadly.
The book brings together papers covering the most recent scientific research from the top endophyte researchers in the world. It presents the state of the art in our knowledge and technical capacity and explores future directions of this work. It is highly relevant and timely because of the need to improve global food security and its sustainability, and also to provide novel bioactive molecules for medicine. There is also a need to protect forestry in a changing and growing world. Endophytes offer a huge potential to reduce environmentally damaging agricultural inputs such as fertilisers and pesticides. They are also a largely overlooked group of organisms where much basic science remains to be undertaken. For example, new molecular tools of DNA profiling using high throughput environmental sequencing are allowing the exploration of a previously largely unknown resource. There is a pressing need to convert scientific research on endophytes into practical application. This book describes how that will be achieved.
In some environments, the survival and production of ryegrass and fescue is heavily reliant on its mutualistic association with Epichloë endophytes. Epichloë endophytes produce a range of bioactive alkaloids, or secondary metabolites that can be effective in deterring insect pests, although some have also been shown to be toxic to grazing animals. These endophytes are being used in grassland farming systems in Australia, New Zealand, USA and some parts of South America. However, to achieve this outcome there has been considerable investment into developing a research pipeline for delivery of animal-safe endophyte strains that are still capable of deterring insect pests and providing protection against abiotic stresses. The pipeline starts with the discovery and isolation of endophytes from wild populations of ryegrass and fescue, characterisation of the known alkaloids they produce, use of genetic markers to determine the relationship between known well-characterised strains and new strains entering the collection, determination of their bioactivity against insect pests of economic significance, understanding issues of compatibility of a strain of interest with the elite germplasm into which it has been inoculated, determining ease of transmission to subsequent seed generations, and ensuring there will be no or minimal animal health and welfare issues associated with using the strain in grazing systems.
A study to detect the diversity of endophytic Actinobacteria from Australian rice was conducted using culture-dependent and culture-independent methods. Rice samples were collected from the rice growing area near Yanco, New South Wales, Australia. Isolation of the endophytic Actinobacteria was done over two consecutive growing seasons. The results demonstrated that most isolates were obtained from plants 10 weeks and older, and only a few were found in younger plants. Microbispora spp. were the most commonly isolated endophytic Actinobacteria (94%) with Streptomyces spp. and other genera present at lower numbers (6%). The culture-dependent method findings were confirmed by T-RFLP profile analysis. Restriction digests using HhaI and RsaI also showed an abundance of terminal restriction fragments (TRFs) profiles related to the genus Microbispora. Furthermore, other biological properties of the endophytic Actinobacteria isolates were also determined. Four isolates, Saccharothrix OSH21, Saccharopolyspora OSR26, Streptomyces OSR46 and Microbispora OSR61, were found to suppress the growth of the pathogenic fungus Rhizoctonia solani. Moreover, these isolates might be able to promote plant growth by producing indole acetic acid or to solubilise phosphate making this nutrient available for plant uptake.
The fortuitous discovery of penicillin from Penicillium chrysogenum heralded the golden era of antibiotics. Since then, fungi have significantly contributed to the welfare of humans by producing bioactive compounds which have been used as antibacterial, anticancer, antioxidant and immunomodulatory agents. However, in recent years, microorganisms associated with plants have emerged as fountainheads of bioactive molecules with high therapeutic potential. In general terms, endophytes are an extremely diverse and ubiquitous group of microorganisms that resides within the living internal tissues of a host plant in a non-invasive manner. Endophytes communicate with their host plant through metabolic interactions which enables them to produce signal molecules with interesting biological activities. Further, the genetic recombination of endophytes with the host plant enables them to mimic the biological properties of the host and produce analogous bioactive compounds. Thus, they start producing the host plant phytochemicals when cultured independently. The endless need for potent drugs has prompted researchers to explore alternative avenues for finding novel bioactive molecules, and endophytes appear to be a plausible target for drug discovery. This chapter reviews the current research trends with these promising organisms.
There are increasing efforts aiming to utilise endophytes as biological control agents (BCAs) to improve crop production. However, reliability remains a major practical constraint for the development of novel BCAs. Many organisms are adapted to their specific habitat; it is optimistic to expect that a new organism added can find a niche or even out-compete those adapted and already present. Our approach for isolating novel BCAs for specific plant diseases is therefore to look in healthy plants in a habitat where disease is a problem, since we predict that it is more likely to find competitive strains among those present and adapted. In vitro inhibitory activities often do not correlate with in planta efficacy, especially since endophytes rely on intimate plant contact. They can, however, be useful to indicate modes of action. We therefore screen for in planta biological activity as early as possible in the process in order to minimise the risk of discarding valuable strains. Finally, some fungi are endophytic in one situation and pathogenic in another (the mutualism–parasitism continuum). This depends on their biology, environmental conditions, the formulation of inoculum, the health, developmental stage and cultivar of the host plant, and the structure of the plant microbiome.
Endophytes are any microbes that can live within plants. We divide them into three major functional groups: endosyms (endosymbionts), endopaths (pathogens) and endosympaths (those that exist in both forms along a mutualism–parasitism continuum). Within these groups, endophytologists recognise harmful pathogenic microbes and a diverse range of beneficial/commensal microbes, including bacteria and archaea, such as diazotrophs, and fungi, such as the vertically transmitted clavicipitaceous endophytes, the generally horizontally transmitted class 2 fungal endophytes, mycorrhizal fungi and dark septate endophytes. This chapter introduces the science of endophyte biology and its application for a world population that is projected to grow to over 9 billion by 2050. It explores the potential of endophytes for improved agricultural and silvicultural sustainability including: yield improvement and nutrition; biocontrol of pests and diseases; and abiotic stress resistance in the context of climate change. It outlines how bioprospectors are using endophytes as sources of novel metabolites for the pharmaceutical and biochemical industries, and describes how endophytes can be used in vitro to elicit the increased production of known secondary metabolites from plants.
The need for hollow microneedle arrays is important for both drug delivery and wearable sensor applications; however, their fabrication poses many challenges. Hollow metal microneedle arrays residing on a flexible metal foil substrate were created by combining additive manufacturing, micromolding, and electroplating approaches in a process we refer to as electromolding. A solid microneedle with inward facing ledge was fabricated with a two photon polymerization (2PP) system utilizing laser direct write (LDW) and then molded with polydimethylsiloxane. These molds were then coated with a seed layer of Ti/Au and subsequently electroplated with pulsed deposition to create hollow microneedles. An inward facing ledge provided a physical blocking platform to restrict deposition of the metal seed layer for creation of the microneedle bore. Various ledge sizes were tested and showed that the resulting seed layer void could be controlled via the ledge length. Mechanical properties of the PDMS mold was adjusted via the precursor ratio to create a more ductile mold that eliminated tip damage to the microneedles upon removal from the molds. Master structures were capable of being molded numerous times and molds were able to be reused. SEM/EDX analysis showed that trace amounts of the PDMS mold were transferred to the metal microneedle upon removal. The microneedle substrate showed a degree of flexibility that withstood over 100 cycles of bending from side to side without damaging. Microneedles were tested for their fracture strength and were capable of puncturing porcine skin and injecting a dye.