What drives the Rebound Effect in transportation? An evaluation based on a Traveling Purchaser Problem

Limiting climate change is one of the most important challenges of the 21st century. Focusing on the transport sector, encouraging the use of more energy-efficient transport modes, and improving the performance of vehicles are the main targets in the fight for GHG reductions. However, due to Rebound Effect (RE), it is proven that improvements in engine fuel efficiency result in lower cost per kilometer driven and can induce individuals to use vehicles more often or to drive longer distances. As a result, the potential energy savings from improved energy efficiency could be partially or totally offset. Therefore, we decided to examine "What drives the Rebound Effect in transportation". To answer this research question, a Traveling Purchaser Problem was evaluated. This simple real-life business application models a situation in which a company owns one or several vehicles and has to buy specific products. The goal is to select and visit a subset of suppliers to satisfy a given demand for each product while minimizing both purchasing and travel costs. In total, 510 instances of this problem with various characteristics and parameters were generated and solved using the optimization software AIMMS. The impact of five main experimentations was deeply investigated. In addition, the trends obtained from these experiments were confirmed by fitting a logistic regression and a decision tree. The results of the various experiments showed that four variables can influence the occurrence of RE in a transportation network. On the one hand, RE tended to increase with the number of potential suppliers from which the firm can choose and the number of vehicles that the company owns to procure the products. On the other hand, the exclusivity of the products to source, as well as the introduction of a distance-traveled tax, reduced the occurrence of RE. To sum up, significant conclusions could be drawn from the experiments and the results can be easily transferred to real-life business applications. Recommendations for possible future studies were also discussed.nhhma

SING: Subgraph search In Non-homogeneous Graphs

<p>Abstract</p> <p>Background</p> <p>Finding the subgraphs of a graph database that are isomorphic to a given query graph has practical applications in several fields, from cheminformatics to image understanding. Since subgraph isomorphism is a computationally hard problem, indexing techniques have been intensively exploited to speed up the process. Such systems filter out those graphs which cannot contain the query, and apply a subgraph isomorphism algorithm to each residual candidate graph. The applicability of such systems is limited to databases of small graphs, because their filtering power degrades on large graphs.</p> <p>Results</p> <p>In this paper, SING (Subgraph search In Non-homogeneous Graphs), a novel indexing system able to cope with large graphs, is presented. The method uses the notion of <it>feature</it>, which can be a small subgraph, subtree or path. Each graph in the database is annotated with the set of all its features. The key point is to make use of feature locality information. This idea is used to both improve the filtering performance and speed up the subgraph isomorphism task.</p> <p>Conclusions</p> <p>Extensive tests on chemical compounds, biological networks and synthetic graphs show that the proposed system outperforms the most popular systems in query time over databases of medium and large graphs. Other specific tests show that the proposed system is effective for single large graphs.</p

Extracellular circulating viral microRNAs: Current knowledge and perspectives

MicroRNAs (miRNAs) are small non-coding RNAs responsible of post-transcriptional regulation of gene expression through interaction with messenger RNAs (mRNAs). They are involved in important biological processes and are often dysregulated in a variety of diseases, including cancer and infections. Viruses also encode their own sets of miRNAs, which they use to control the expression of either the host's genes and/or their own. In the past few years evidence of the presence of cellular miRNAs in extracellular human body fluids such as serum, plasma, saliva, and urine has accumulated. They have been found either cofractionate with the Argonaute2 protein or in membrane-bound vesicles such as exosomes. Although little is known about the role of circulating miRNAs, it has been demonstrated that miRNAs secreted by virus-infected cells are transferred to and act in uninfected recipient cells. In this work we summarize the current knowledge on viral circulating miRNAs and provide a few examples of computational prediction of their functio

A knowledge base for the discovery of function, diagnostic potential and drug effects on cellular and extracellular miRNAs

Background: MicroRNAs (miRNAs) are small noncoding RNAs that play an important role in the regulation of various biological processes through their interaction with cellular mRNAs. A significant amount of miRNAs has been found in extracellular human body fluids (e.g. plasma and serum) and some circulating miRNAs in the blood have been successfully revealed as biomarkers for diseases including cardiovascular diseases and cancer. Released miRNAs do not necessarily reflect the abundance of miRNAs in the cell of origin. It is claimed that release of miRNAs from cells into blood and ductal fluids is selective and that the selection of released miRNAs may correlate with malignancy. Moreover, miRNAs play a significant role in pharmacogenomics by down-regulating genes that are important for drug function. In particular, the use of drugs should be taken into consideration while analyzing plasma miRNA levels as drug treatment. This may impair their employment as biomarkers. Description: We enriched our manually curated extracellular/circulating microRNAs database, miRandola, by providing (i) a systematic comparison of expression profiles of cellular and extracellular miRNAs, (ii) a miRNA targets enrichment analysis procedure, (iii) information on drugs and their effect on miRNA expression, obtained by applying a natural language processing algorithm to abstracts obtained from PubMed. Conclusions: This allows users to improve the knowledge about the function, diagnostic potential, and the drug effects on cellular and circulating miRNAs

Comparison between off-resonance and electron Bernstein waves heating regime in a microwave discharge ion sourcea)

A microwave discharge ion source (MDIS) operating at the Laboratori Nazionali del Sud of INFN, Catania has been used to compare the traditional electron cyclotron resonance (ECR) heating with an innovative mechanisms of plasma ignition based on the electrostatic Bernstein waves (EBW). EBW are obtained via the inner plasma electromagnetic-to-electrostatic wave conversion and they are absorbed by the plasma at cyclotron resonance harmonics. The heating of plasma by means of EBW at particular frequencies enabled us to reach densities much larger than the cutoff ones. Evidences of EBW generation and absorption together with X-ray emissions due to high energy electrons will be shown. A characterization of the discharge heating process in MDISs as a generalization of the ECR heating mechanism by means of ray tracing will be shown in order to highlight the fundamental physical differences between ECR and EBW heating

Sequence similarity is more relevant than species specificity in probabilistic backtranslation

BACKGROUND: Backtranslation is the process of decoding a sequence of amino acids into the corresponding codons. All synthetic gene design systems include a backtranslation module. The degeneracy of the genetic code makes backtranslation potentially ambiguous since most amino acids are encoded by multiple codons. The common approach to overcome this difficulty is based on imitation of codon usage within the target species. RESULTS: This paper describes EasyBack, a new parameter-free, fully-automated software for backtranslation using Hidden Markov Models. EasyBack is not based on imitation of codon usage within the target species, but instead uses a sequence-similarity criterion. The model is trained with a set of proteins with known cDNA coding sequences, constructed from the input protein by querying the NCBI databases with BLAST. Unlike existing software, the proposed method allows the quality of prediction to be estimated. When tested on a group of proteins that show different degrees of sequence conservation, EasyBack outperforms other published methods in terms of precision. CONCLUSION: The prediction quality of a protein backtranslation methis markedly increased by replacing the criterion of most used codon in the same species with a Hidden Markov Model trained with a set of most similar sequences from all species. Moreover, the proposed method allows the quality of prediction to be estimated probabilistically

miRandola 2017: a curated knowledge base of non-invasive biomarkers

miRandola (http://mirandola.iit.cnr.it/) is a database of extracellular non-coding RNAs (ncRNAs) that was initially published in 2012, foreseeing the relevance of ncRNAs as non-invasive biomarkers. An increasing amount of experimental evidence shows that ncRNAs are frequently dysregulated in diseases. Further, ncRNAs have been discovered in different extracellular forms, such as exosomes, which circulate in human body fluids. Thus, miRandola 2017 is an effort to update and collect the accumulating information on extracellular ncRNAs that is spread across scientific publications and different databases. Data are manually curated from 314 articles that describe miRNAs, long non-coding RNAs and circular RNAs. Fourteen organisms are now included in the database, and associations of ncRNAs with 25 drugs, 47 sample types and 197 diseases. miRandola also classifies extracellular RNAs based on their extracellular form: Argonaute2 protein, exosome, microvesicle, microparticle, membrane vesicle, high density lipoprotein and circulating. We also implemented a new web interface to improve the user experience

MiRandola 2017: A curated knowledge base of non-invasive biomarkers

miRandola (http://mirandola.iit.cnr.it/) is a database of extracellular non-coding RNAs (ncRNAs) that was initially published in 2012, foreseeing the relevance of ncRNAs as non-invasive biomarkers. An increasing amount of experimental evidence shows that ncRNAs are frequently dysregulated in diseases. Further, ncRNAs have been discovered in different extracellular forms, such as exosomes, which circulate in human body fluids. Thus, miRandola 2017 is an effort to update and collect the accumulating information on extracellular ncRNAs that is spread across scientific publications and different databases. Data are manually curated from 314 articles that describe miRNAs, long non-coding RNAs and circular RNAs. Fourteen organisms are now included in the database, and associations of ncRNAs with 25 drugs, 47 sample types and 197 diseases. miRandola also classifies extracellular RNAs based on their extracellular form: Argonaute2 protein, exosome, microvesicle, microparticle, membrane vesicle, high density lipoprotein and circulating. We also implemented a new web interface to improve the user experience

Involvement of GTA protein NC2β in Neuroblastoma pathogenesis suggests that it physiologically participates in the regulation of cell proliferation

<p>Abstract</p> <p>Background</p> <p>The General Transcription Apparatus (GTA) comprises more than one hundred proteins, including RNA Polymerases, GTFs, TAFs, Mediator, and cofactors such as heterodimeric NC2. This complexity contrasts with the simple mechanical role that these proteins are believed to perform and suggests a still uncharacterized participation to important biological functions, such as the control of cell proliferation.</p> <p>Results</p> <p>To verify our hypothesis, we analyzed the involvement in Neuroblastoma (NB) pathogenesis of GTA genes localized at 1p, one of NB critical regions: through RT-PCR of fifty eight NB biopsies, we demonstrated the statistically significant reduction of the mRNA for NC2β (localized at 1p22.1) in 74% of samples (p = 0.0039). Transcripts from TAF13 and TAF12 (mapping at 1p13.3 and 1p35.3, respectively) were also reduced, whereas we didn't detect any quantitative alteration of the mRNAs from GTF2B and NC2α (localized at 1p22-p21 and 11q13.3, respectively). We confirmed these data by comparing tumour and constitutional DNA: most NB samples with diminished levels of NC2β mRNA had also genomic deletions at the corresponding locus.</p> <p>Conclusion</p> <p>Our data show that NC2β is specifically involved in NB pathogenesis and may be considered a new NB biomarker: accordingly, we suggest that NC2β, and possibly other GTA members, are physiologically involved in the control of cell proliferation. Finally, our studies unearth complex selective mechanisms within NB cells.</p

Cellular and molecular effects of protons: apoptosis induction and potential implications for cancer therapy.

Due to their ballistic precision, apoptosis induction by protons could be a strategy to specifically eliminate neoplastic cells. To characterize the cellular and molecular effects of these hadrons, we performed dose-response and time-course experiments by exposing different cell lines (PC3, Ca301D, MCF7) to increasing doses of protons and examining them with FACS, RT-PCR, and electron spin resonance (ESR). Irradiation with a dose of 10 Gy of a 26,7 Mev proton beam altered cell structures such as membranes, caused DNA double strand breaks, and significantly increased intracellular levels of hydroxyl ions, are active oxygen species (ROS). This modified the transcriptome of irradiated cells, activated the mitochondrial (intrinsic) pathway of apoptosis, and resulted in cycle arrest at the G2/M boundary. The number of necrotic cells within the irradiated cell population did not significantly increase with respect to the controls. The effects of irradiation with 20 Gy were qualitatively as well as quantitatively similar, but exposure to 40 Gy caused massive necrosis. Similar experiments with photons demonstrated that they induce apoptosis in a significantly lower number of cells and in a temporally delayed manner. These data advance our knowledge on the cellular and molecular effects of proton irradiation and could be useful for improving current hadrontherapy protocols