Logic Programming approaches for routing fault-free and maximally-parallel Wavelength Routed Optical Networks on Chip (Application paper)

One promising trend in digital system integration consists of boosting on-chip communication performance by means of silicon photonics, thus materializing the so-called Optical Networks-on-Chip (ONoCs). Among them, wavelength routing can be used to route a signal to destination by univocally associating a routing path to the wavelength of the optical carrier. Such wavelengths should be chosen so to minimize interferences among optical channels and to avoid routing faults. As a result, physical parameter selection of such networks requires the solution of complex constrained optimization problems. In previous work, published in the proceedings of the International Conference on Computer-Aided Design, we proposed and solved the problem of computing the maximum parallelism obtainable in the communication between any two endpoints while avoiding misrouting of optical signals. The underlying technology, only quickly mentioned in that paper, is Answer Set Programming (ASP). In this work, we detail the ASP approach we used to solve such problem. Another important design issue is to select the wavelengths of optical carriers such that they are spread across the available spectrum, in order to reduce the likelihood that, due to imperfections in the manufacturing process, unintended routing faults arise. We show how to address such problem in Constraint Logic Programming on Finite Domains (CLP(FD)). This paper is under consideration for possible publication on Theory and Practice of Logic Programming.Comment: Paper presented at the 33nd International Conference on Logic Programming (ICLP 2017), Melbourne, Australia, August 28 to September 1, 2017. 16 pages, LaTeX, 5 figure

A Bilevel Mixed Integer Linear Programming Model for Valves Location in Water Distribution Systems

The positioning of valves on the pipes of a Water Distribution System (WDS) is a core decision in the design of the isolation system of a WDS. When closed, valves permit to isolate a small portion of the network, so called a sector, which can be de-watered for maintenance purposes at the cost of a supply disruption. However, valves have a cost so their number is limited, and their position must be chosen carefully in order to minimize the worst-case supply disruption which may occur during pipe maintenance. Supply disruption is usually measured as the undelivered user demand. When a sector is isolated by closing its boundary valves, other portions of the network may become disconnected from the reservoirs as a secondary effect, and experience supply disruption as well. This induced isolation must be taken into account when computing the undelivered demand induced by a sector isolation. While sector topology can be described in terms of graph partitioning, accounting for induced undelivered demand requires network flow modeling. The aim of the problem is to locate a given number of valves at the extremes of the network pipes so that the maximum supply disruption is minimized. We present a Bilevel Mixed Integer Linear Programming (MILP) model for this problem and show how to reduce it to a single level MILP by exploiting duality. Computational results on a real case study are presented, showing the effectiveness of the approach

WoPPER: Web server for Position Related data analysis of gene Expression in Prokaryotes

The structural and conformational organization of chromosomes is crucial for gene expression regulation in eukaryotes and prokaryotes as well. Up to date, gene expression data generated using either microarray or RNA-sequencing are available for many bacterial genomes. However, differential gene expression is usually investigated with methods considering each gene independently, thus not taking into account the physical localization of genes along a bacterial chromosome. Here, we present WoPPER, a web tool integrating gene expression and genomic annotations to identify differentially expressed chromosomal regions in bacteria. RNA-sequencing or microarray-based gene expression data are provided as input, along with gene annotations. The user can select genomic annotations from an internal database including 2780 bacterial strains, or provide custom genomic annotations. The analysis produces as output the lists of positionally related genes showing a coordinated trend of differential expression. Graphical representations, including a circular plot of the analyzed chromosome, allow intuitive browsing of the results. The analysis procedure is based on our previously published R-package PREDA. The release of this tool is timely and relevant for the scientific community, as WoPPER will fill an existing gap in prokaryotic gene expression data analysis and visualization tools. WoPPER is open to all users and can be reached at the following URL: https://WoPPER.ba.itb.cnr.it

Efficacy of team work in health promotion and secondary prevention in patients admitted for cardiovascular rehabilitation

The object of the study was to evaluate the immediate efficacy of periodical educational meetings organized in Cardiovascular Rehabilitation Department aimed to improve knowledge about cardiovascular pathology, risk factors and correct life style. Methods: from October 2008 a multiprofessional group organized educational meetings for patients and their relatives, using two questionnaires to explore patients’ level of knowledge, before and after the meeting. Results: 124 patients (90 males) answered the questionnaire 1, while questionnaire 2 was completed by 93 subjects (70 males). From the answers to questionnaire 1, a significant improvement of knowledge about coronary anatomy and cardiovascular therapy emerged. Indeed, 99% of patients vs 81% before the meeting (p=0.001) understood the coronary artery function, 69% vs 44% (p=0,0001) of participants was familiar with coronary angioplasty, 81% vs. 64% (p=0,003) demonstrated to understand the coronary artery bypass and finally 85% vs. 52% (p=0,0001) were able to distinguish mechanical from biological prosthesis. From answers to questionnaire 2, a trend in favour to an improvement of knowledge regarding coronary risk factors and correct life style emerged. Younger patients (<70 ys) had a higher baseline level knowledge (p=0,003 and p=0.001 group 1 and 2, respectively) compared to older subjects, but in the latter a trend in favour of enhanced knowledge (p=0.06) after the educational meetings emerged. Conclusions: educational meetings are significantly correlated with an improvement of patients’ knowledge regarding cardiovascular pathology and treatments independently from patients’ age

Modulation of gut microbiota dysbioses in type 2 diabetic patients by macrobiotic Ma-Pi 2 diet

The study was carried out with internal funding

Diversity of Bifidobacteria within the Infant Gut Microbiota

Background The human gastrointestinal tract (GIT) represents one of the most densely populated microbial ecosystems studied to date. Although this microbial consortium has been recognized to have a crucial impact on human health, its precise composition is still subject to intense investigation. Among the GIT microbiota, bifidobacteria represent an important commensal group, being among the first microbial colonizers of the gut. However, the prevalence and diversity of members of the genus Bifidobacterium in the infant intestinal microbiota has not yet been fully characterized, while some inconsistencies exist in literature regarding the abundance of this genus. Methods/Principal Findings In the current report, we assessed the complexity of the infant intestinal bifidobacterial population by analysis of pyrosequencing data of PCR amplicons derived from two hypervariable regions of the 16 S rRNA gene. Eleven faecal samples were collected from healthy infants of different geographical origins (Italy, Spain or Ireland), feeding type (breast milk or formula) and mode of delivery (vaginal or caesarean delivery), while in four cases, faecal samples of corresponding mothers were also analyzed. Conclusions In contrast to several previously published culture-independent studies, our analysis revealed a predominance of bifidobacteria in the infant gut as well as a profile of co-occurrence of bifidobacterial species in the infant’s intestine

Neutrophils Driving Unconventional T Cells Mediate Resistance against Murine Sarcomas and Selected Human Tumors

Neutrophils are a component of the tumor microenvironment and have been predominantly associated with cancer progression. Using a genetic approach complemented by adoptive transfer, we found that neutrophils are essential for resistance against primary 3-methylcholantrene-induced carcinogenesis. Neutrophils were essential for the activation of an interferon-γ-dependent pathway of immune resistance, associated with polarization of a subset of CD4- CD8- unconventional αβ T cells (UTCαβ). Bulk and single-cell RNA sequencing (scRNA-seq) analyses unveiled the innate-like features and diversity of UTCαβ associated with neutrophil-dependent anti-sarcoma immunity. In selected human tumors, including undifferentiated pleomorphic sarcoma, CSF3R expression, a neutrophil signature and neutrophil infiltration were associated with a type 1 immune response and better clinical outcome. Thus, neutrophils driving UTCαβ polarization and type 1 immunity are essential for resistance against murine sarcomas and selected human tumors

An ASP approach for the valves positioning optimization in a water distribution system

Positioning of valves is a real-life issue in Water Distribution System (WDS) design and, currently, it is usually addressed by hydraulic engineers either by hand or by means of genetic algorithms, that give no assurance of optimality. Since a given valves placement identifies a sectorization of the WDS in several isolable portions, the valves positioning problem can be seen as a variant of the well known graph partitioning problem, which is a hard combinatorial problem. Cattafi et al. (2011, TPLP, 11, 731–747) showed recently that Computational Logic can provide technologies and techniques that can be exploited to model and achieve the optimal partition of the water network (i.e. the optimal positioning of valves). In particular, the authors tackled the optimization of the valves positioning through a two player game model, giving a Constraint Logic Programming formalization to solve it effectively. The aim of this article, instead, is to investigate the potential of Answer Set Programming in this practical application; evaluation is in terms both of language expressivity and solving efficiency. Results are discussed for different ASP models and a comparison with the CLP(FD) technique shown by Cattafi et al. (2011, TPLP, 11, 731–747) will be given