Regulatory networks and connected components of the neutral space

The functioning of a living cell is largely determined by the structure of its regulatory network, comprising non-linear interactions between regulatory genes. An important factor for the stability and evolvability of such regulatory systems is neutrality - typically a large number of alternative network structures give rise to the necessary dynamics. Here we study the discretized regulatory dynamics of the yeast cell cycle [Li et al., PNAS, 2004] and the set of networks capable of reproducing it, which we call functional. Among these, the empirical yeast wildtype network is close to optimal with respect to sparse wiring. Under point mutations, which establish or delete single interactions, the neutral space of functional networks is fragmented into 4.7 * 10^8 components. One of the smaller ones contains the wildtype network. On average, functional networks reachable from the wildtype by mutations are sparser, have higher noise resilience and fewer fixed point attractors as compared with networks outside of this wildtype component.Comment: 6 pages, 5 figure

Linear Complexity Lossy Compressor for Binary Redundant Memoryless Sources

A lossy compression algorithm for binary redundant memoryless sources is presented. The proposed scheme is based on sparse graph codes. By introducing a nonlinear function, redundant memoryless sequences can be compressed. We propose a linear complexity compressor based on the extended belief propagation, into which an inertia term is heuristically introduced, and show that it has near-optimal performance for moderate block lengths.Comment: 4 pages, 1 figur

Material Availability: A Study of Academic Library Performance

This article reports the findings of a study modeled after Saracevic, Shaw, and Kantor\u27s efforts to identify and quantify the causes of users\u27 failures to identify and locate library materials. The researchers analyzed patron-reported and librarian-observed subject and known-item searches and found an overall success rate of only 54 percent. The problems that led to the 46 percent failure rate were analyzed by source and type of failure, and subjective observations concerning problems encountered by patrons were recorded. Recommendations are made for reducing library malfunctions and circulation, patron, and acquisition errors

On the origin of the Boson peak in globular proteins

We study the Boson Peak phenomenology experimentally observed in globular proteins by means of elastic network models. These models are suitable for an analytic treatment in the framework of Euclidean Random Matrix theory, whose predictions can be numerically tested on real proteins structures. We find that the emergence of the Boson Peak is strictly related to an intrinsic mechanical instability of the protein, in close similarity to what is thought to happen in glasses. The biological implications of this conclusion are also discussed by focusing on a representative case study.Comment: Proceedings of the X International Workshop on Disordered Systems, Molveno (2006

Experiences of patients with Poland syndrome of diagnosis and care in Italy: A pilot survey

Background: Poland Syndrome (PS) is a rare congenital malformation involving functional and aesthetic impairments. Early diagnosis and timely therapeutic approaches play an important role in improving the quality of life of patients and kindred. This study aims to explore healthcare experiences of the diagnosis of patients affected by PS and to investigate the factors associated with diagnostic delay in Italy. Results: Seventy-two patients affected by PS were asked to fill in a self-administered questionnaire on: a) diagnostic path; b) perceived quality of care received after diagnosis; c) knowledge of the rights and the socio-economic hardships related to their disease; d) evaluation of the integration of various professional skills involved in the diagnostic and therapeutic approach; e) perception of the social support provided by the Italian Association of Poland Syndrome (AISP). The average age at diagnosis was around 14 years; diagnosis was made at birth in only 31.58% of cases. Although typical symptomatology had appeared on average at an early age (4 months), only 23 patients (40.35%) received an early diagnosis (within the first year of life). Just over half of the patients (n = 30) were diagnosed in their region of origin, while 27 were diagnosed elsewhere. Furthermore, 12.28% were self-diagnoses. Among the patients who were diagnosed outside their region, 15 (88.24%) stated they had foregone some visits or treatments owing to costs and/or organizational issues. Conclusions: An analysis of the patients' experiences highlights several gaps and a lack of homogeneity in the diagnostic and therapeutic follow-up of PS patients in Italy. A specific national diagnostic and therapeutic path is essential to guarantee patients complete and appropriate health services, compliant with the ethical principles of non-discrimination, justice and empathy. Implementation of an effective information and research network and empowerment of patients' associations are necessary conditions to encourage clinical collaboration and improve the quality of life of people living with rare diseases

Study of MicroPattern Gaseous detectors with novel nanodiamond based photocathodes for single photon detection in EIC RICH

Identification of high momentum hadrons at the future EIC is crucial, gaseous RICH detectors are therefore viable option. Compact collider setups impose to construct RICHes with small radiator length, hence significantly limiting the number of detected photons. More photons can be detected in the far UV region, using a windowless RICH approach. QE of CsI degrades under strong irradiation and air contamination. Nanodiamond based photocathodes (PCs) are being developed as an alternative to CsI. Recent development of layers of hydrogenated nanodiamond powders as an alternative photosensitive material and their performance, when coupled to the THick Gaseous Electron Multipliers (THGEM)-based detectors, are the objects of an ongoing R\&D. We report about the initial phase of our studies.Comment: 3 pages, 5 figures, RICH2018 conference proceedin

The effect of scale-free topology on the robustness and evolvability of genetic regulatory networks

We investigate how scale-free (SF) and Erdos-Renyi (ER) topologies affect the interplay between evolvability and robustness of model gene regulatory networks with Boolean threshold dynamics. In agreement with Oikonomou and Cluzel (2006) we find that networks with SFin topologies, that is SF topology for incoming nodes and ER topology for outgoing nodes, are significantly more evolvable towards specific oscillatory targets than networks with ER topology for both incoming and outgoing nodes. Similar results are found for networks with SFboth and SFout topologies. The functionality of the SFout topology, which most closely resembles the structure of biological gene networks (Babu et al., 2004), is compared to the ER topology in further detail through an extension to multiple target outputs, with either an oscillatory or a non-oscillatory nature. For multiple oscillatory targets of the same length, the differences between SFout and ER networks are enhanced, but for non-oscillatory targets both types of networks show fairly similar evolvability. We find that SF networks generate oscillations much more easily than ER networks do, and this may explain why SF networks are more evolvable than ER networks are for oscillatory phenotypes. In spite of their greater evolvability, we find that networks with SFout topologies are also more robust to mutations than ER networks. Furthermore, the SFout topologies are more robust to changes in initial conditions (environmental robustness). For both topologies, we find that once a population of networks has reached the target state, further neutral evolution can lead to an increase in both the mutational robustness and the environmental robustness to changes in initial conditions.Comment: 16 pages, 15 figure