Constrained Community-based Gene Regulatory Network Inference

The problem of gene regulatory network inference is a major concern of systems biology. In recent years, a novel methodology has gained momentum, called community network approach. Community networks integrate predictions from individual methods in a "metapredictor," in order to compose the advantages of different methods and soften individual limitations. This article proposes a novel methodology to integrate prediction ensembles using constraint programming, a declarative modeling and problem solving paradigm. Constraint programming naturally allows the modeling of dependencies among components of the problem as constraints, facilitating the integration and use of different forms of knowledge. The new paradigm, referred to as constrained community network, uses constraints to capture properties of the regulatory networks (e.g., topological properties) and to guide the integration of knowledge derived from different families of network predictions. The article experimentally shows the potential of this approach: The addition of biological constraints can offer significant improvements in prediction accuracy

Angiogenic T cell expansion correlates with severity of peripheral vascular damage in systemic sclerosis

The mechanisms underlying endothelial cell injury and defective vascular repair in systemic sclerosis (SSc) remain unclear. Since the recently discovered angiogenic T cells (Tang) may have an important role in the repair of damaged endothelium, this study aimed to analyze the Tang population in relation to disease-related peripheral vascular features in SSc patients. Tang (CD3+CD31+CXCR4+) were quantified by flow cytometry in peripheral blood samples from 39 SSc patients and 18 healthy controls (HC). Circulating levels of the CXCR4 ligand stromal cell-derived factor (SDF)-1α and proangiogenic factors were assessed in paired serum samples by immunoassay. Serial skin sections from SSc patients and HC were subjected to CD3/CD31 and CD3/CXCR4 double immunofluorescence. Circulating Tang were significantly increased in SSc patients with digital ulcers (DU) compared either with SSc patients without DU or with HC. Tang levels were significantly higher in SSc patients with late nailfold videocapillaroscopy (NVC) pattern than in those with early/active NVC patterns and in HC. No difference in circulating Tang was found when comparing either SSc patients without DU or patients with early/active NVC patterns and HC. In SSc peripheral blood, Tang percentage was inversely correlated to levels of SDF-1α and CD34+CD133+VEGFR-2+ endothelial progenitor cells (EPC), and positively correlated to levels of vascular endothelial growth factor and matrix metalloproteinase-9. Tang were frequently detected in SSc dermal perivascular inflammatory infiltrates. In summary, our findings demonstrate for the first time that Tang cells are selectively expanded in the circulation of SSc patients displaying severe peripheral vascular complications like DU. In SSc, Tang may represent a potentially useful biomarker reflecting peripheral vascular damage severity. Tang expansion may be an ineffective attempt to compensate the need for increased angiogenesis and EPC function. Further studies are required to clarify the function of Tang cells and investigate the mechanisms responsible for their change in SSc

Recent studies of heavy ion transfer reactions using large solid angle spectrometers

We present selected results recently obtained in the study of heavy ion transfer reactions at energies close to the Coulomb barrier by employing the large solid angle magnetic spectrometer PRISMA. We discuss the production of neutron-rich heavy nuclei via multinucleon transfer processes and the related effects of secondary processes, in particular nucleon evaporation, studied in a high resolution kinematic coincidence experiment. We also present the recent results in the studies of neutron-neutron correlations for closed shell and superfluid systems

Evidence of proton-proton correlations in the 116Sn+60Ni transfer reactions

One and two proton transfer channels have been measured in 116Sn+60Ni with the magnetic spectrometer PRISMA by making an excitation function at several bombarding energies, from above to well below the Coulomb barrier. The total kinetic energy loss distributions show the predominance of quasi-elastic processes in the sub-barrier regime. The data have been compared with calculations performed with the GRAZING program, based on semiclassical formalism, and in the Distorted Wave Born Approximation (DWBA), which provided a good theoretical description of the extracted transfer probabilities for the one proton transfers. The much larger values of the experimental two proton transfers compared with those evaluated within an independent particle transfer mechanism, indicate the presence of strong proton-proton correlations. The results complement the ones of the previously analyzed one- and two-neutron transfers, providing significant new information on the subject compared to past works

Fusion Hindrance and Pauli Blocking in 58Ni + 64Ni

58Ni +64Ni is the first case where the influence of positive Q-value transfer channels on sub-barrier fusion was evidenced, in a very well known experiment by Beckerman et al., by comparing with the two systems 58Ni + 58Ni and 64Ni+64Ni. Subsequent measurements on 64Ni + 64Ni showed that fusion hindrance is clearly present in this case. On the other hand, no indication of hindrance can be observed for 58Ni + 64Ni down to the measured level of 0.1 mb. In the present experiment the excitation function has been extended by two orders of magnitude downward. The cross sections for 58Ni + 64Ni continue decreasing very smoothly below the barrier, down to '1 µb. The logarithmic slope of the excitation function increases slowly, showing a tendency to saturate at the lowest energies. No maximum of the astrophysical S -factor is observed. Coupled-channels (CC) calculations using a Woods-Saxon potential and includinginelastic excitations only, underestimate the sub-barrier cross sections by a large amount. Good agreement is found by adding two-neutron transfer couplings to a schematical level. This behaviour is quite different from what already observed for 64Ni+ 64Ni (no positive Q-value transfer channels available), where a clear low-energy maximum of the S -factorappears, and whose excitation function is overestimated by a standard Woods-Saxon CC calculation. No hindrance effect is observed in 58Ni+ 64Ni in the measured energy range. This trend at deep sub-barrier energies reinforces the recent suggestion that the availability of several states following transfer with Q>0, effectively counterbalances the Pauli repulsion that, in general, is predicted to reduce tunneling probability inside the Coulomb barrier

Study of the neutron-rich region in the vicinity of 208Pb via multinucleon transfer reactions

The multinucleon transfer reaction mechanism was employed to populate isotopes around the doubly- magic 208 Pb nucleus. We used an unstable 94 Rb beam on 208 Pb targets of different thickness. Transfer channels were studied via the fragment-γ and γ-γ coincidences, by using MINIBALL γ spectrometer coupled to a particle detector. Gamma transitions associated to the different Pb isotopes, populated by the neutron transfers, are discussed in terms of excitation energy and spin. Fragment angular distributions were extracted, andcompared with the reaction model

Light and heavy fragments mass correlation in the 197Au+130Te transfer reaction

We studied multinucleon transfer (MNT) processes in the 197Au+130Te at Elab=1.07 GeV system coupling the PRISMA magnetic spectrometer to NOSE, an ancillary particle detector. We constructed a mass correlation matrix associating to each light fragment identified in PRISMA the corresponding mass distribution of the heavy partner detected in NOSE and, through the comparison with Monte Carlo simulations, we could infer about the role of neutron evaporation in multinucleon transfer reactions for the population of neutron-rich heavy nuclei

Multinucleon transfer reactions and proton transfer channels

Transfer reactions have always been of great importance for nuclear structure and reaction mechanism studies. So far, in multinucleon transfer studies, proton pickup channels have been completely identified in atomic and mass numbers at energies close to the Coulomb barrier only in few cases. We measured the multinucleon transfer reactions in the 40Ar+208Pb system near the Coulomb barrier, by employing the PRISMA magnetic spectrometer. By using the most neutron-rich stable 40Ar beam we could populate, besidesneutron pickup and proton stripping channels, also neutron stripping and proton pickup channels. Comparison ofcross sections between different systems with the 208Pb target and with projectiles going from neutron-poor to neutron-rich nuclei, as well as between the data and GRAZING calculations, was carried out.Finally, recent results concerning the measurement of the excitation function from the Coulomb barrier to far below for the 92Mo+54Fe system, where both proton stripping and pickup channels were populated with similar strength, will be discussed