73 research outputs found
The dynamic behavior of the Basilica of San Francesco of Assisi
No full textThesis (M. Eng.)--Massachusetts Institute of Technology, Dept. of Civil and Environmental Engineering, 2013.This electronic version was submitted by the student author. The certified thesis is available in the Institute Archives and Special Collections.Cataloged from student-submitted PDF version of thesis.Includes bibliographical references (p. 61-62).During the 1997 Umbria-Marche earthquake, two of the vaults of the Basilica of San Francesco in Assisi collapsed as a result of an 8.5 Mercalli-scale magnitude earthquake. The structure had endured stronger earthquakes for centuries before this earthquake, and there were likely many reasons for the collapse, such as damages accumulated from previous earthquakes. However, one of the factors that may have lead to the collapse is the modifications made to the structure over its lifetime, which could have made the basilica more susceptible to the 1997 earthquake. The basilica's roof has been subjected to three major alterations in its 760 year life. Each alteration changed the weight and stiffness properties of the roof and global dynamic behavior of the basilica. In this thesis, simple analytical models are employed to show trends in the structure's seismic response given the changes in stiffness and mass of the roof over the centuries. The findings of the analytical model suggest that the roof interventions have had the eect of decreasing the structure's fundamental period, and therefore, attracting more seismic forces to existing structural elements. The findings of this study are meant to educate preservation engineers for similar interventions in the future as well as address present day public safety issues regarding retrofitted historic structures. Keywords Basilica of San Francesco of Assisi, Historic Masonry Structures, Monumental Structures, Seismic Vulnerability, Seismic Retrofittingby Emidio Piermarini.M.Eng
RNA structure alignment by a unit-vector approach
No full textMotivation: The recent discovery of tiny RNA molecules such as μRNAs and small interfering RNA are transforming the view of RNA as a simple information transfer molecule. Similar to proteins, the native three-dimensional structure of RNA determines its biological activity. Therefore, classifying the current structural space is paramount for functionally annotating RNA molecules. The increasing numbers of RNA structures deposited in the PDB requires more accurate, automatic and benchmarked methods for RNA structure comparison. In this article, we introduce a new algorithm for RNA structure alignment based on a unit-vector approach. The algorithm has been implemented in the SARA program, which results in RNA structure pairwise alignments and their statistical significance. Results: The SARA program has been implemented to be of general applicability even when no secondary structure can be calculated from the RNA structures. A benchmark against the ARTS program using a set of 1275 non-redundant pairwise structure alignments results in ∼6% extra alignments with at least 50% structurally superposed nucleotides and base pairs. A first attempt to perform RNA automatic functional annotation based on structure alignments indicates that SARA can correctly assign the deepest SCOR classification to > 60% of the query structures. © The Author 2008. Published by Oxford University Press. All rights reserved
ContrastRank: A new method for ranking putative cancer driver genes and classification of tumor samples
No full textMotivation: The recent advance in high-throughput sequencing technologies is generating a huge amount of data that are becoming an important resource for deciphering the genotype underlying a given phenotype. Genome sequencing has been extensively applied to the study of the cancer genomes. Although a few methods have been already proposed for the detection of cancer-related genes, their automatic identification is still a challenging task. Using the genomic data made available by The Cancer Genome Atlas Consortium (TCGA), we propose a new prioritization approach based on the analysis of the distribution of putative deleterious variants in a large cohort of cancer samples. Results: In this paper, we present ContastRank, a new method for the prioritization of putative impaired genes in cancer. The method is based on the comparison of the putative defective rate of each gene in tumor versus normal and 1000 genome samples. We show that the method is able to provide a ranked list of putative impaired genes for colon, lung and prostate adenocarcinomas. The list significantly overlaps with the list of known cancer driver genes previously published. More importantly, by using our scoring approach, we can successfully discriminate between TCGA normal and tumor samples. A binary classifier based on ContrastRank score reaches an overall accuracy490% and the area under the curve (AUC) of receiver operating characteristics (ROC)>0.95 for all the three types of adenocarcinoma analyzed in this paper. In addition, using ContrastRank score, we are able to discriminate the three tumor types with a minimum overall accuracy of 77% and AUC of 0.83. Conclusions: We describe ContrastRank, a method for prioritizing putative impaired genes in cancer. The method is based on the comparison of exome sequencing data from different cohorts and can detect putative cancer driver genes. ContrastRank can also be used to estimate a global score for an individual genome about the risk of adenocarcinoma based on the genetic variants information from a whole-exome VCF (Variant Calling Format) file. We believe that the application of ContrastRank can be an important step in genomic medicine to enable genome-based diagnosis. © The Author 2014. Published by Oxford University Press. All rights reserved
Composição florística e fitossociologia de espécies arbóreas do Parque Fenológico da Embrapa Amazônia Ocidental.
No full textEste trabalho objetiva contribuir para o maior conhecimento acerca da composição florística e estrutura fitossociológica de espécies arbóreas do parque fenológico da Embrapa Amazônia Ocidental, visando subsidiar ações futuras de seleção de árvores matrizes para estudos fenológicos e implantação de áreas de coleta de sementes
Bioinformatics challenges for personalized medicine
No full textMotivation: Widespread availability of low-cost, full genome sequencing will introduce new challenges for bioinformatics. Results: This review outlines recent developments in sequencing technologies and genome analysis methods for application in personalized medicine. New methods are needed in four areas to realize the potential of personalized medicine: (i) processing large-scale robust genomic data; (ii) interpreting the functional effect and the impact of genomic variation; (iii) integrating systems data to relate complex genetic interactions with phenotypes; and (iv) translating these discoveries into medical practice. © The Author(s) 2011. Published by Oxford University Press
Displaced Myonuclei in Cachexia Suggest the Occurrence of Altered Innervation
No full textAn idiopathic myopathy characterized by central nuclei in muscle fibers(Mazzotti, 2016), a hallmark of muscle regeneration, has been observed in cancer patients. In cancer cachexia skeletal muscle is incapable of regeneration (He, 2013), consequently, this observation remains unaccounted for. In C26‐tumor bearing, cachectic mice, we observed muscle fiberswith cen-tral nuclei in the absence of molecular markers of bona fideregeneration. These clustered, non‐peripheral nuclei were present in NCAM-expressing muscle fibers.Since NCAM expres-sion is upregulated in denervated myofiers, we searched for additional makers of denerva-tion, including AchRs, MUSK, and HDAC. This last one being also consistently upregulated in cachectic muscles, correlated with an increase of central myonuclei. This held true in the musculature of patients sufferingfrom gastrointestinal cancer, where a progressive increase in the number of central myonuclei was observed in weight stable and in cachectic patients, com-pared to healthy subjects. Based on all of the above, the presence of central myonuclei in can-cer patients and animal models of cachexia is consistent with motor neuron loss or NMJ per-turbation and could underlie a previously neglected phenomenon of denervation, rather than representing myofiberdamage and regeneration in cachexia. Motoneuron loss and gliosis typi-cally occur in association with neuromuscular regressive changes during ageing in mice, how-ever there are only two, contradictory reports on altered innervation in cachexia (Boehm, 2020; Daou, 2020). Based on all the above, we propose that, similarly to aging, denervation depend-ent myofiberatrophy contributes to muscle wasting in cancer cachexia
Displaced myonuclei in cancer cachexia suggest altered innervation
No full textIntroduction. Central nuclei are considered a hallmark of skeletal muscle fiber regeneration and a sign of myopathy. We and others have previously observed central myonuclei in both pre-cachectic patients and animal models of cancer cachexia, in striking contrast with the reduced regenerative potential characterizing cachectic muscles. Methods. To elucidate the mechanisms underlying these divergent observations we further characterised the nature of central nuclei, and the muscle fiber involved, in both pre- and cachectic cancer patients, as well as in C26-tumor bearing mice. Muscle with different physiological properties, the Rectus abdominis and the Tibialis anterior, were analysed in search of denervation and regeneration markers. Results. We observed rare though measurable, non-peripheral myonuclei. The latter consisted of two distinct population: bona fide central nuclei and nuclei that are neither central nor subsarcolemmal, which we named «displaced» myonuclei. Displaced and central nuclei were detected in all types of muscle fibers. However, displaced myonuclei were the only ones to vary between control and cachectic muscles, suggesting a link with the pathological condition. Non-peripheral myonuclei were observed in the absence of muscle regeneration molecular markers, such as embryonic or fetal myosin expression. The analysis of longitudinal sections revealed that displaced myonuclei are clustered as it occurs upon denervation, and that the number of nuclear clusters increases in cachexia, coincident with N-CAM upregulation, another denervation marker. Additional denervation markers were upregulated in both human and murine cachectic muscles. Conclusions. We observed a novel phenomenon in cancer patients and animal models of cachexia: the presence of displaced nuclei consistent with motor neuron loss or NMJ perturbation. This phenomenon could underlay a previously neglected phenomenon of denervation rather that myofiber damage and regeneration in cachexia. Like in aging, denervation-dependent myofiber atrophy could contribute to the atrophic process leading to muscle wasting
Book of Abstracts: 2022 Poster Sessions. 9th Annual Conference of the Marie Curie Alumni Association, March 25-27, 2022, Lisbon, Portugal
No full textThis book collects the posters and their abstracts presented at the Annual Conference of the Marie Curie Alumni Association which took place in Lisbon (Portugal) and online on 26-27 March 2022.
Proposals that passed selection were categorised and divided into different areas approximately corresponding to the MSCA panels, which were integrated by two topics of great relevance for the MCAA. Since the conference was organised as a hybrid event, authors had the possibility to either present in person or online. The presential panel included posters from all the areas. As for the online panels, some topics were merged into a single panel or spread over two panels for better organisation. The final distribution was the following:
Presential
Engineering
Chemistry & Physics
Social Sciences & Humanities
Life Sciences
Environmental Sustainability, Economics, Sustainable Research Practice
Humanities and Arts, Career Development, Sustainable Research Practice
Each panel corresponds to a macro-section of this book. Within each macro-section, a poster page includes an abstract, an image of the poster, and information about the author(s) and their organisation(s).
Cite as: G. M. Greco, G. Emidio, P. E. Tomatis, A. Avasthi (Eds). (2022). Book of Abstracts: 2022 Poster Sessions. 9th Annual Conference of the Marie Curie Alumni Association, March 25-27, 2022, Lisbon, Portugal. Brussels: Marie Curie Alumni Association. ISBN 978-94-6433-602-3. http://dx.doi.org/10.5281/zenodo.660882
Above-ground carbon estimated throughout Ikonos II Satellite in upland forest on Central Amazon.
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