117 research outputs found

    Management of non-native tree species in forests of the Alpine space

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    This guide was prepared within the framework of the project ALPTREES (code ASP791), which is co-funded by the European Commission through the INTERREG Alpine Space financial mechanism. The INTERREG Alpine Space programme is a European transnational cooperation programme for the Alpine region. It provides a framework for facilitating cooperation between key economic, social, and environmental players in seven Alpine countries, as well as between various institutional levels. The programme is financed through the European Regional Development Fund (ERDF) as well as through national public and private co-funding in the Partner States

    Final Report of the AFIT Quality Initiative External Discovery Committee

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    This report summarizes the findings of the Air Force Institute of Technology’s (AFIT’s) Quality Initiative - External Discovery Team. The overarching purpose of the Quality Initiative is to create a detailed, executable investment strategy for modernizing AFIT’s instructional capabilities across five thrust areas. These activities were completed over the course of one year, beginning in June of 2016 and concluding in June of 2017. The data gathered were evaluated and several recommendations for further review were decided upon by the External Discovery Team. The following report briefly covers those recommendations and provides sources from which the recommendations were gleaned. These recommendations are meant to serve as a baseline for ways in which AFIT could begin to program resources to help improve teaching and instruction across the institution as a whole. The data presented here are meant to serve as a compliment to the Internal Discovery Team’s report that focuses on data and feedback gathered from institutions internal to AFIT

    Transnational strategy on the sustainable management and responsible use of non-native trees in the Alpine Space

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    Abstract Non-native tree species – defined as those species intentionally or unintentionally introduced by humans – have long been a part of the Alpine Space, providing numerous benefits, but also posing a potential threat to native biodiversity and related ecosystem services. Compared to the urban space where non-native trees comprise most tree species, the number of non-native trees in forests and plantations is relatively low. To evaluate potential risks and benefits of non-native trees in the Alpine Space, a transnational strategy for the responsible use and management of non-native trees is needed. The goals of the strategy are to tailor management practices for a sustainable and responsible use or admixture of non-native trees, to reduce the risks connected with the invasive potential of some non-native tree species, to help forests and urban areas to adapt to climate change, and to improve coordination and cooperation regarding best practices between different regions of the Alpine Space. A proposal was developed in a four-step process including expert-based assessment, stakeholder mapping, an extensive data review, and a public consultation. For implementing the strategy fully, strong collaboration among diverse stakeholders is anticipated and robust governance and an adequate long-term and fair funding scheme is needed

    RNA secondary structure prediction from multi-aligned sequences

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    It has been well accepted that the RNA secondary structures of most functional non-coding RNAs (ncRNAs) are closely related to their functions and are conserved during evolution. Hence, prediction of conserved secondary structures from evolutionarily related sequences is one important task in RNA bioinformatics; the methods are useful not only to further functional analyses of ncRNAs but also to improve the accuracy of secondary structure predictions and to find novel functional RNAs from the genome. In this review, I focus on common secondary structure prediction from a given aligned RNA sequence, in which one secondary structure whose length is equal to that of the input alignment is predicted. I systematically review and classify existing tools and algorithms for the problem, by utilizing the information employed in the tools and by adopting a unified viewpoint based on maximum expected gain (MEG) estimators. I believe that this classification will allow a deeper understanding of each tool and provide users with useful information for selecting tools for common secondary structure predictions.Comment: A preprint of an invited review manuscript that will be published in a chapter of the book `Methods in Molecular Biology'. Note that this version of the manuscript may differ from the published versio

    Role of 3′UTRs in the Translation of mRNAs Regulated by Oncogenic eIF4E—A Computational Inference

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    Eukaryotic cap-dependent mRNA translation is mediated by the initiation factor eIF4E, which binds mRNAs and stimulates efficient translation initiation. eIF4E is often overexpressed in human cancers. To elucidate the molecular signature of eIF4E target mRNAs, we analyzed sequence and structural properties of two independently derived polyribosome recruited mRNA datasets. These datasets originate from studies of mRNAs that are actively being translated in response to cells over-expressing eIF4E or cells with an activated oncogenic AKT: eIF4E signaling pathway, respectively. Comparison of eIF4E target mRNAs to mRNAs insensitive to eIF4E-regulation has revealed surprising features in mRNA secondary structure, length and microRNA-binding properties. Fold-changes (the relative change in recruitment of an mRNA to actively translating polyribosomal complexes in response to eIF4E overexpression or AKT upregulation) are positively correlated with mRNA G+C content and negatively correlated with total and 3′UTR length of the mRNAs. A machine learning approach for predicting the fold change was created. Interesting tendencies of secondary structure stability are found near the start codon and at the beginning of the 3′UTR region. Highly upregulated mRNAs show negative selection (site avoidance) for binding sites of several microRNAs. These results are consistent with the emerging model of regulation of mRNA translation through a dynamic balance between translation initiation at the 5′UTR and microRNA binding at the 3′UTR

    Predicting RNA secondary structure by the comparative approach: how to select the homologous sequences

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    <p>Abstract</p> <p>Background</p> <p>The secondary structure of an RNA must be known before the relationship between its structure and function can be determined. One way to predict the secondary structure of an RNA is to identify covarying residues that maintain the pairings (Watson-Crick, Wobble and non-canonical pairings). This "comparative approach" consists of identifying mutations from homologous sequence alignments. The sequences must covary enough for compensatory mutations to be revealed, but comparison is difficult if they are too different. Thus the choice of homologous sequences is critical. While many possible combinations of homologous sequences may be used for prediction, only a few will give good structure predictions. This can be due to poor quality alignment in stems or to the variability of certain sequences. This problem of sequence selection is currently unsolved.</p> <p>Results</p> <p>This paper describes an algorithm, <it>SSCA</it>, which measures the suitability of sequences for the comparative approach. It is based on evolutionary models with structure constraints, particularly those on sequence variations and stem alignment. We propose three models, based on different constraints on sequence alignments. We show the results of the <it>SSCA </it>algorithm for predicting the secondary structure of several RNAs. <it>SSCA </it>enabled us to choose sets of homologous sequences that gave better predictions than arbitrarily chosen sets of homologous sequences.</p> <p>Conclusion</p> <p><it>SSCA </it>is an algorithm for selecting combinations of RNA homologous sequences suitable for secondary structure predictions with the comparative approach.</p

    Effects of total laryngectomy on olfactory function, health-related quality of life, and communication: a 3-year follow-up study

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    <p>Abstract</p> <p>Background</p> <p>As total laryngectomy results in loss of airflow through the nose, one of the adverse effects for a majority of patients is the reduced or complete loss of olfactory function. However, with the introduction of a new method, the Nasal Airflow-Inducing Maneuver (NAIM), an important technique is available for laryngectomized patients to regain the ability to smell. The purpose of the present study was to assess changes in olfaction, health-related quality of life (HRQL) and communication 3 years after NAIM rehabilitation.</p> <p>Methods</p> <p>18 patients (15 men and 3 women; mean age, 71 years) who had undergone laryngectomy and NAIM rehabilitation were followed longitudinally for 3 years. For comparison an age and gender matched control group with laryngeal cancer treated with radical radiotherapy was included. Olfactory function was assessed using the Questionnaire on Odor, Taste and Appetite and the Scandinavian Odor Identification Test. HRQL was assessed by: 1) the European Organization for Research and Treatment for cancer quality of life questionnaires; and 2) the Hospital Anxiety and Depression Scale. Communication was assessed by the Swedish Self-Evaluation of Communication Experiences after Laryngeal Cancer. Descriptive statistics with 95% confidence interval were calculated according to standard procedure. Changes over time as well as tests between pairs of study patients and control patients were analyzed with the Fisher nonparametric permutation test for matched pairs.</p> <p>Results</p> <p>Thirty-six months after rehabilitation 14 of 18 laryngectomized patients (78%) were smellers. There were, with one exception (sleep disturbances), no clinically or statistically significant differences between the study and the control group considering HRQL and mental distress. However, statistical differences (p < 0.001) were found between the study and the control group concerning changes in communication.</p> <p>Conclusion</p> <p>Olfactory training with NAIM should be integrated into the multidisciplinary rehabilitation program after total laryngectomy. Our study shows that patients who were successfully rehabilitated concerning olfaction and communication had an overall good HRQL and no mental distress. Moreover, the EORTC questionnaires should be complemented with more specific questionnaires when evaluating olfaction and communication in laryngectomized patients.</p

    Transnational strategy on the sustainable management and responsible use of non-native trees in the Alpine Space

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    Non-native tree species – defined as those species intentionally or unintentionally introduced by humans – have longbeen a part of the Alpine Space, providing numerous benefits, but also posing a potential threat to native biodiversityand related ecosystem services. Compared to the urban space where non-native trees comprise most tree species,the number of non-native trees in forests and plantations is relatively low. To evaluate potential risks and benefits ofnon-native trees in the Alpine Space, a transnational strategy for the responsible use and management of non-nativetrees is needed. The goals of the strategy are to tailor management practices for a sustainable and responsible useor admixture of non-native trees, to reduce the risks connected with the invasive potential of some non-native treespecies, to help forests and urban areas to adapt to climate change, and to improve coordination and cooperationregarding best practices between different regions of the Alpine Space. A proposal was developed in a four-stepprocess including expert-based assessment, stakeholder mapping, an extensive data review, and a public consulta-tion. For implementing the strategy fully, strong collaboration among diverse stakeholders is anticipated and robustgovernance and an adequate long-term and fair funding scheme is needed
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