Going the distance for protein function prediction: a new distance metric for protein interaction networks

Due to an error introduced in the production process, the x-axes in the first panels of Figure 1 and Figure 7 are not formatted correctly. The correct Figure 1 can be viewed here: http://dx.doi.org/10.1371/annotation/343bf260-f6ff-48a2-93b2-3cc79af518a9In protein-protein interaction (PPI) networks, functional similarity is often inferred based on the function of directly interacting proteins, or more generally, some notion of interaction network proximity among proteins in a local neighborhood. Prior methods typically measure proximity as the shortest-path distance in the network, but this has only a limited ability to capture fine-grained neighborhood distinctions, because most proteins are close to each other, and there are many ties in proximity. We introduce diffusion state distance (DSD), a new metric based on a graph diffusion property, designed to capture finer-grained distinctions in proximity for transfer of functional annotation in PPI networks. We present a tool that, when input a PPI network, will output the DSD distances between every pair of proteins. We show that replacing the shortest-path metric by DSD improves the performance of classical function prediction methods across the board.MC, HZ, NMD and LJC were supported in part by National Institutes of Health (NIH) R01 grant GM080330. JP was supported in part by NIH grant R01 HD058880. This material is based upon work supported by the National Science Foundation under grant numbers CNS-0905565, CNS-1018266, CNS-1012910, and CNS-1117039, and supported by the Army Research Office under grant W911NF-11-1-0227 (to MEC). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript

SRPT Scheduling for Web Servers

This note briey summarizes some results from two papers: [4] and [23]. These papers pose the following question: Is it possible to reduce the expected response time of every request at a web server, simply by changing the order in which we schedule the requests? In [4] we approach this question analytically via an M/G/1 queue. In [23] we approach the same question via implementation involving an Apache web server running on Linux

Inflammasome activation by NLRP1 and NLRC4 in patients with coronary stenosis

Objective and design: We performed an experimental, analytical and prospective study to evaluate the systemic activation of inflammasome in atherosclerosis\u2019 patients, in order to shed light into responsible mechanisms for plaque formation. Subjects: We included sixty individuals distributed into 3 groups: 2 groups based on the report from the angiography (severe lesions - SL and primary lesions - PL) and 1 group enclosing healthy individuals (HC). Methods: The expression assays of inflammasome genes NLRP1, NLRC4, CASP-1 and IL-1\u3b2 were performed using Real Time qPCR, with specific Taqman Assays. IL-1\u3b2 serum levels were analysed by commercial kit. Were applied the Shapiro-Wilk and Student's T-test as statistical tests. Statistical significance was set to p 64 0.05. Results: Upregulation of NLRP1 (+3.47 FC, p = 0.0001), NLRC4 (+7.06 FC, p = 6.792 7 10 1209) and IL-1\u3b2 (+2.43 FC, p = 0.005) was observed in all atherosclerosis patients when compared to HC. According to stenosis severity, patients with primary lesions showed upregulation of inflammasome genes NLRP1 (+2.87 FC, p = 0.0008), NLRC4 (+6.34 FC, p = 4.134 7 10-07) and IL-1\u3b2 (+3.39 FC, p = 0.0012) with respect to the HC group. No statistical difference was found in IL-1\u3b2 serum levels according the assessed groups. Conclusions: Inflammasome activation in atherosclerosis's patients can be systemic altered and may be triggered by NLRP1 and NLRC4 receptors. IL-1\u3b2 gene expression was identified in our study as an important systemic detectable marker of plaque severity

Unusual onset of a case of chronic recurrent multifocal osteomyelitis

Background: Chronic recurrent multifocal osteomyelitis (CRMO) is a rare condition that commonly affects the clavicle and pelvis. Case presentation: We report here a case a 12 years old girl with CRMO arising with recurrent episodes of left supraorbital headache, followed by the appearance of a periorbital dyschromia. Magnetic resonance imaging (MRI) of the skull and orbits revealed an important subacute inflammatory process. Few months after, the child presented a painful swelling of the left clavicle; the histological examination of the related biopsy allowed to establish the diagnosis of CRMO. Conclusion: CRMO presenting as acute headache involving neurocranium is rare; to our knowledge this is the first recognized case in the world literature. This pathological condition is frequently misdiagnosed as infection or neoplasm and needs a deep investigation for the differential diagnosis. The physical, laboratoristic and instrumental diagnostic investigations of the patient and the treatment employed are described in detail

The effects of spatial constraints on the evolution of weighted complex networks

Motivated by the empirical analysis of the air transportation system, we define a network model that includes geographical attributes along with topological and weight (traffic) properties. The introduction of geographical attributes is made by constraining the network in real space. Interestingly, the inclusion of geometrical features induces non-trivial correlations between the weights, the connectivity pattern and the actual spatial distances of vertices. The model also recovers the emergence of anomalous fluctuations in the betweenness-degree correlation function as first observed by Guimer\`a and Amaral [Eur. Phys. J. B {\bf 38}, 381 (2004)]. The presented results suggest that the interplay between weight dynamics and spatial constraints is a key ingredient in order to understand the formation of real-world weighted networks

Statistical mechanics of complex networks

Complex networks describe a wide range of systems in nature and society, much quoted examples including the cell, a network of chemicals linked by chemical reactions, or the Internet, a network of routers and computers connected by physical links. While traditionally these systems were modeled as random graphs, it is increasingly recognized that the topology and evolution of real networks is governed by robust organizing principles. Here we review the recent advances in the field of complex networks, focusing on the statistical mechanics of network topology and dynamics. After reviewing the empirical data that motivated the recent interest in networks, we discuss the main models and analytical tools, covering random graphs, small-world and scale-free networks, as well as the interplay between topology and the network's robustness against failures and attacks.Comment: 54 pages, submitted to Reviews of Modern Physic

Defining the characteristics of certified hernia centers in Italy: The Italian society of hernia and abdominal wall surgery workgroup consensus on systematic reviews of the best available evidences

Background: The terms “Hernia Center” (HC) and Hernia Surgeon” (HS) have gained more and more popularity in recent years. Nevertheless, there is lack of protocols and methods for certification of their activities and results. The Italian Society of Hernia and Abdominal Wall Surgery proposes a method for different levels of certification. Methods: The national board created a commission, with the task to define principles and structure of an accreditation program. The discussion of each topic was preceded by a Systematic Review, according to PRISMA Guidelines and Methodology. In case of lack or inadequate data from literature, the parameter was fixed trough a Commission discussion. Results: The Commission defined a certification process including: “FLC - First level Certification”: restricted to single surgeon, it is given under request and proof of a formal completion of the learning curve process for the basic procedures and an adequate year volume of operations. “Second level certification”: Referral Center for Abdominal Wall Surgery. It is a public or private structure run by at least two already certified and confirmed FLC surgeons. “Third level certification”: High Specialization Center for Abdominal Wall Surgery. It is a public or private structure, already confirmed as Referral Centers, run by at least three surgeons (two certified and confirmed with FLC and one research fellow in abdominal wall surgery). Both levels of certification have to meet the Surgical Requirements and facilities criteria fixed by the Commission. Conclusion: The creation of different types of Hernia Centers is directed to create two different entities offering the same surgical quality with separate mission: the Referral Center being more dedicated to clinical and surgical activity and High Specialization Centers being more directed to scientific tasks

ESTIMA: Extrapolating ScalabiliTy of In-Memory Applications

This paper presents ESTIMA, an easy-to-use tool for extrapolating the scalability of in-memory applications. ESTIMA is designed to perform a simple, yet important task: given the performance of an application on a small machine with a handful of cores, ESTIMA extrapolates its scalability to a larger machine with more cores, while requiring minimum input from the user. The key idea underlying ESTIMA is the use of stalled cycles (e.g. cycles that the processor spends waiting for various events, such as cache misses or waiting on a lock). ESTIMA measures stalled cycles on a few cores and extrapolates them to more cores, estimating the amount of waiting in the system. ESTIMA can be effectively used to predict the scalability of in-memory applications. For instance, using measurements of memcached and SQLite on a desktop machine, we obtain accurate predictions of their scalability on a server. Our extensive evaluation on a large number of in-memory benchmarks shows that ESTIMA has generally low prediction errors