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Search Results: 1 - 10 of 6169 matches for " Fabio Rinaldi "
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Ranking relations between diseases, drugs and genes for a curation task
Clematide Simon,Rinaldi Fabio
Journal of Biomedical Semantics , 2012, DOI: 10.1186/2041-1480-3-s3-s5
Abstract: Background One of the key pieces of information which biomedical text mining systems are expected to extract from the literature are interactions among different types of biomedical entities (proteins, genes, diseases, drugs, etc.). Several large resources of curated relations between biomedical entities are currently available, such as the Pharmacogenomics Knowledge Base (PharmGKB) or the Comparative Toxicogenomics Database (CTD). Biomedical text mining systems, and in particular those which deal with the extraction of relationships among entities, could make better use of the wealth of already curated material. Results We propose a simple and effective method based on logistic regression (also known as maximum entropy modeling) for an optimized ranking of relation candidates utilizing curated abstracts. Furthermore, we examine the effects and difficulties of using widely available metadata (i.e. MeSH terms and chemical substance index terms) for relation extraction. Cross-validation experiments result in an improvement of the ranking quality in terms of AUCiP/R by 39% (PharmGKB) and 116% (CTD) against a frequency-based baseline of 0.39 (PharmGKB) and 0.21 (CTD). For the TAP-10 metrics, we achieve an improvement of 53% (PharmGKB) and 134% (CTD) against the same baseline system (0.21 PharmGKB and 0.15 CTD). Conclusions Our experiments with the PharmGKB and the CTD database show a strong positive effect for the ranking of relation candidates utilizing the vast amount of curated relations covered by currently available knowledge databases. The tasks of concept identification and candidate relation generation profit from the adaptation to previously curated material. This presents an effective and practical method suitable for conservative extension and re-validation of biomedical relations from texts that has been successfully used for curation experiments with the PharmGKB and CTD database.
Temperature Measurement in WTE Boilers Using Suction Pyrometers
Fabio Rinaldi,Behzad Najafi
Sensors , 2013, DOI: 10.3390/s131115633
Abstract: The temperature of the flue-gas in the post combustion zone of a waste to energy (WTE) plant has to be maintained within a fairly narrow range of values, the minimum of which is prescribed by the European Waste Directive 2000/76/CE, whereas the maximum value must be such as to ensure the preservation of the materials and the energy efficiency of the plant. A high degree of accuracy in measuring and controlling the aforementioned temperature is therefore required. In almost the totality of WTE plants this measurement process is carried out by using practical industrial thermometers, such as bare thermocouples and infrared radiation (IR) pyrometers, even if affected by different physical contributions which can make the gas temperature measurements incorrect. The objective of this paper is to analyze errors and uncertainties that can arise when using a bare thermocouple or an IR pyrometer in a WTE plant and to provide a method for the in situ calibration of these industrial sensors through the use of suction pyrometers. The paper describes principle of operation, design, and uncertainty contributions of suction pyrometers, it also provides the best estimation of the flue-gas temperature in the post combustion zone of a WTE plant and the estimation of its expanded uncertainty.
Efficiency Analysis of Independent and Centralized Heating Systems for Residential Buildings in Northern Italy
Matteo Zago,Andrea Casalegno,Renzo Marchesi,Fabio Rinaldi
Energies , 2011, DOI: 10.3390/en4112115
Abstract: The primary energy consumption in residential buildings is determined by the envelope thermal characteristics, air change, outside climatic data, users’ behaviour and the adopted heating system and its control. The new Italian regulations strongly suggest the installation of centralized boilers in renovated buildings with more than four apartments. This work aims to investigate the differences in primary energy consumption and efficiency among several independent and centralized heating systems installed in Northern Italy. The analysis is carried out through the following approach: firstly building heating loads are evaluated using the software TRNSYS ? and, then, heating system performances are estimated through a simplified model based on the European Standard EN 15316. Several heating systems have been analyzed, evaluating: independent and centralized configurations, condensing and traditional boilers, radiator and radiant floor emitters and solar plant integration. The heating systems are applied to four buildings dating back to 2010, 2006, 1960s and 1930s. All the combinations of heating systems and buildings are analyzed in detail, evaluating efficiency and primary energy consumption. In most of the cases the choice between centralized and independent heating systems has minor effects on primary energy consumption, less than 3%: the introduction of condensing technology and the integration with solar heating plant can reduce energy consumption by 11% and 29%, respectively.
Treatises and Ars construendi: Teaching’s Method Theory and Practice of Critical History’s Application Based on Teacher-Student Relationships  [PDF]
Carlos Alberto Cacciavillani, Simona Rinaldi
Open Journal of Social Sciences (JSS) , 2016, DOI: 10.4236/jss.2016.49016
Abstract: The topic of this lecture is the results’ description obtained during many years of teaching. We shall illustrate how students use the same analytical techniques to study two different aspects: 1) Architectural Treatises are first studied separately and then in a comparative way. The purpose of this graphic analysis is to reach a new interpretation of them through the realization of original graphics; 2) The Roman Ars construendi: architectural techniques and buildings’ typologies used by the Romans are investigated in the archaeological sites, where the reading of buildings’ stratification in different historical periods becomes an important teaching tool.
Yaws: A Second (and Maybe Last?) Chance for Eradication
Andrea Rinaldi
PLOS Neglected Tropical Diseases , 2008, DOI: 10.1371/journal.pntd.0000275
Abstract:
The Global Campaign to Eliminate Leprosy
Andrea Rinaldi
PLOS Medicine , 2005, DOI: 10.1371/journal.pmed.0020341
Abstract:
Counting tillers
Andrea Rinaldi
Genome Biology , 2003, DOI: 10.1186/gb-spotlight-20030410-02
Abstract: Li et al. screened rice plant collections for mutants with altered tiller numbers. Genetic analysis with reciprocal crosses between tiller mutants and wild-type plants revealed that mutants possess a recessive mutation in a single locus, termed Monoculm 1 (MOC1). The MOC1 gene was then mapped to the long arm of chromosome 6, and encoded a nuclear-localized protein of 441 amino-acid residues. Tiller mutants transformed with up to three copies of the MOC1 gene produced 2-3 fold more tillers than wild-type plants, confirming the role of the gene in branching control. High-tillering transformed plants were also observed to be shorter than wild-type plants, indicating that MOC1 affects both rice tillering and plant height - another economically important trait.Although MOC1 seems to be a key regulator of rice tillering, this is expected to be a complex process which involves the finely-tuned expression of many genes. The identification of the other parties is likely to benefit from the recent completion of several drafts of the rice genome, produced by the International Rice Genome Sequencing Project and other sequencing programs.
tmRNA to the rescue
Andrea Rinaldi
Genome Biology , 2003, DOI: 10.1186/gb-spotlight-20030404-01
Abstract: Valle et al. used purified Thermus thermophilus extracts and prepared a stalled ribosome with a docked tmRNA. They added the protein synthesis elongation factor Tu (EF-Tu), SmpB, a small protein required for tmRNA-mediated peptide tagging activity, and kirromycin, an antibiotic that traps ribosome rescue at an early stage. The cryo-EM image of the complex yielded novel details of tmRNA entry into the ribosome, revealing that tmRNA initially binds the ribosome and EF-Tu in a manner similar to canonical tRNAs. SmpB acted by facilitating the contacts between tmRNA and the stalled ribosome, and tmRNA pseudoknots played a role in the presentation of the molecule to the ribosome, helping to orient the alanyl-tRNA like domain and the open reading frame."Predictably, the cryo-EM images presented by Valle et al. only whet our appetite for higher-resolution structural information about each stage of ribosome rescue", note Sean Moore and colleagues from the Massachusetts Institute of Technology, Cambridge, MA, USA, in an accompanying Perspectives article.
Maternal impact of chromatin reorganization
Andrea Rinaldi
Genome Biology , 2003, DOI: 10.1186/gb-spotlight-20030425-01
Abstract: Using Xenopus NPM2 as a template, Burns et al. isolated the murine NPM2 ortholog. In situ hybridization showed that expression of the NPM2 protein was limited to growing oocytes. To study the NPM2 activity, they used embryonic stem cell technology to generate homozygous NPM2-null mice. Although Xenopus NPM2 decondenses sperm DNA, the same process seems to proceed without NPM2 in mice, as NPM2-null males were fertile and normal. In contrast, NPM2 knockout females were found to be subfertile or infertile. Analysis of fertilization and post-fertilization events in vitro and in vivo revealed impaired early embryo development, mostly due to failure of the one-cell to two-cell transition. Examining oocytes and eggs from NPM2-null females, they detected gross defects, including an absence of coalesced nucleolar structures and loss of heterochromatin and deacetylated histone H3 that normally circumscribe nucleoli in oocytes and early zygotes, respectively.NPM2 is one of a family of oocyte-derived proteins for which a role in zygote development has been demonstrated. "In the future it will be important to define the functional domains of NPM2… and to assess whether NPM2-gene mutations may cause infertility in women," conclude the authors.
Gill-specific glutamine synthetase
Andrea Rinaldi
Genome Biology , 2003, DOI: 10.1186/gb-spotlight-20030327-01
Abstract: Walsh et al. focused on nitrogen metabolism in the toadfish because it can facultatively excrete nitrogen as ammonia (ammonotely) or as urea (ureotely). They assessed GS enzymatic activity and scrutinized mRNA in several key tissues for general and nitrogen metabolism throughout the animal. Analysis of the PCR-derived sequences of the extracted mRNA revealed - in addition to the GS cDNA previously cloned from liver - the presence of a second GS gene, exclusively expressed in gill tissue. The two proteins showed a relatively low sequence similarity; the closest relative amongst sequenced GSs was from Xenopus laevis.These findings indicate toadfish GS gene duplication and diversification and confirm recent observations that the rainbow trout has at least four GS-encoding genes with differing levels of tissue expression and different metabolic pathways.Walsh et al. suggest that gill GS traps toxic ammonia in this organ. This is analogous to the toadfish switching to ureotely - it excretes urea in pulses from the gills, simultaneously shutting down the leakage ammonia that accumulates. The authors speculate that toadfish gill GS has a function that is closer to that of strictly ureotelic terrestrial animals i.e. avid ammonia scavenging. This could also help explain the similarity between the fish and frog genes.
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