Linking the proteins--elucidation of proteome-scale networks using mass spectrometry

Proteomes are intricate. Typically, thousands of proteins interact through physical association and post-translational modifications (PTMs) to give rise to the emergent functions of cells. Understanding these functions requires one to study proteomes as "systems" rather than collections of individual protein molecules. The abstraction of the interacting proteome to "protein networks" has recently gained much attention, as networks are effective representations, that lose specific molecular details, but provide the ability to see the proteome as a whole. Mostly two aspects of the proteome have been represented by network models: proteome-wide physical protein-protein-binding interactions organized into Protein Interaction Networks (PINs), and proteome-wide PTM relations organized into Protein Signaling Networks (PSNs). Mass spectrometry (MS) techniques have been shown to be essential to reveal both of these aspects on a proteome-wide scale. Techniques such as affinity purification followed by MS have been used to elucidate protein-protein interactions, and MS-based quantitative phosphoproteomics is critical to understand the structure and dynamics of signaling through the proteome. We here review the current state-of-the-art MS-based analytical pipelines for the purpose to characterize proteome-scale networks.     

Benders decomposition for the uncapacitated multiple allocation hub location problem

In telecommunication and transportation systems, the uncapacitated multiple allocation hub location problem (UMAHLP) arises when we must flow commodities or information between several origin–destination pairs. Instead of establishing a direct node to node connection from an origin to its destination, the flows are concentrated with others at facilities called hubs. These flows are transported on links established between hubs, being then splitted and delivered to its final destination. Systems with this sort of topology are named hub-and-spoke (HS) systems or hub-and-spoke networks. They are designed to exploit the scale economies attainable through the shared use of high capacity links between hubs. Therefore, the problem is to find the least expensive HS network, selecting hubs and assigning traffic to them, given the demands between each origin–destination pair and the respective transportation costs. In the present paper, we present efficient Benders decomposition algorithms based on a well known formulation to tackle the UMAHLP. We have been able to solve some large instances, considered ‘out of reach’ of other exact methods in reasonable time.     

Higher incidence of Gastrospirillum sp. in swine with gastric ulcer of the pars oesophagea

Gastric ulcer in swine is characterized by an area of acid-peptic digestion, occurs usually in the pars oesophagea of the stomach, and has unknown etiopathogenesis. The present work was carried out to investigate the prevalence of the newly described spiral-shaped microorganism Gastrospirillum sp. ("Gastrospirillum suis") in stomachs of abattoir pigs with and without gastric ulcer. Stomachs were removed from 32 consecutive pigs presenting apparently normal mucosa and from 32 additional consecutive pigs presenting frank, chronic gastric ulcer of the pars oesophagea. Fragments of antral, oxyntic, cardiac and pars oesophagea regions were taken from each stomach and processed for histology and for identification of Gastrospirillum sp. in tissue sections. The microorganisms were identified mainly in the mucous layer and in gastric foveolas of the antral and oxyntic mucosa. Forty pigs (62.5%) were positive for Gastrospirillum sp.; among them, 27 (67.5%) had gastric ulcer, and 13 (32.5%) had no ulcer. Twenty-four pigs (37.5%) were negative for Gastrospirillum sp.; among them, five (20.8%) presented with gastric ulcer, and 19 (79.2%) had no ulcer. There was a significant difference between pigs with and without gastric ulcer in regard to the presence of Gastrospirillum sp. (P < 0.01). The spiral-shaped microorganism Gastrospirillum sp. that inhabits the stomach of pigs should be considered a possible factor connected with the etiopathogenesis of swine gastric ulcer.     

Cell-protection mechanism through autophagy in HGFs/<Emphasis Type="Italic">S. mitis</Emphasis> co-culture treated with Chitlac-nAg

Silver-based products have been proven to be effective in retarding and preventing bacterial growth since ancient times. In the field of restorative dentistry, the use of silver ions/nanoparticles has been explored to counteract bacterial infections, as silver can destroy bacterial cell walls by reacting with membrane proteins. However, it is also cytotoxic towards eukaryotic cells, which are capable of internalizing nanoparticles. In this work, we investigated the biological effects of Chitlac-nAg, a colloidal system based on a modified chitosan (Chitlac), administered for 24–48?h to a co-culture of primary human gingival fibroblasts and Streptococcus mitis in the presence of saliva, developed to mimic the microenvironment of the oral cavity. We sought to determine its efficiency to combat oral hygiene-related diseases without affecting eukaryotic cells. Cytotoxicity, reactive oxygen species production, apoptosis induction, nanoparticles uptake, and lysosome and autophagosome metabolism were evaluated. In vitro results show that Chitlac-nAg does not exert cytotoxic effects on human gingival fibroblasts, which seem to survive through a homoeostasis mechanism involving autophagy. That suggests that the novel biomaterial Chitlac-nAg could be a promising tool in the field of dentistry.     

The renaming problem in shared memory systems: An introduction

Exploring the power of shared memory communication objects and models, and the limits of distributed computability are among the most exciting research areas of distributed computing. In that spirit, this paper focuses on a problem that has received considerable interest since its introduction in 1987, namely the renaming problem. It was the first non-trivial problem known to be solvable in an asynchronous distributed system despite process failures. Many algorithms for renaming and variants of renaming have been proposed, and sophisticated lower bounds have been proved, that have been a source of new ideas of general interest to distributed computing. It has consequently acquired a paradigm status in distributed fault-tolerant computing.In the renaming problem, processes start with unique initial names taken from a large name space, then deciding new names such that no two processes decide the same new name and the new names are from a name space that is as small as possible.This paper presents an introduction to the renaming problem in shared memory systems, for non-expert readers. It describes both algorithms and lower bounds. Also, it discusses strong connections relating renaming and other important distributed problems such as set agreement and symmetry breaking.     

Solving identity delegation problem in the e-government environment

At present, many countries allow citizens or entities to interact with the government outside the telematic environment through a legal representative who is granted powers of representation. However, if the interaction takes place through the Internet, only primitive mechanisms of representation are available, and these are mainly based on non-dynamic offline processes that do not enable quick and easy identity delegation. This paper proposes a system of dynamic delegation of identity between two generic entities that can solve the problem of delegated access to the telematic services provided by public authorities. The solution herein is based on the generation of a delegation token created from a proxy certificate that allows the delegating entity to delegate identity to another on the basis of a subset of its attributes as delegator, while also establishing in the delegation token itself restrictions on the services accessible to the delegated entity and the validity period of delegation. Further, the paper presents the mechanisms needed to either revoke a delegation token or to check whether a delegation token has been revoked. Implications for theory and practice and suggestions for future research are discussed.     

Privacy in geo-social networks: proximity notification with untrusted service providers and curious buddies

A major feature of the emerging geo-social networks is the ability to notify a user when any of his friends (also called buddies) happens to be geographically in proximity. This proximity service is usually offered by the network itself or by a third party service provider (SP) using location data acquired from the users. This paper provides a rigorous theoretical and experimental analysis of the existing solutions for the location privacy problem in proximity services. This is a serious problem for users who do not trust the SP to handle their location data and would only like to release their location information in a generalized form to participating buddies. The paper presents two new protocols providing complete privacy with respect to the SP and controllable privacy with respect to the buddies. The analytical and experimental analysis of the protocols takes into account privacy, service precision, and computation and communication costs, showing the superiority of the new protocols compared to those appeared in the literature to date. The proposed protocols have also been tested in a full system implementation of the proximity service.     

A non-intrusive estimation for high-quality Internet TV services

This paper presents a non-intrusive estimator for Internet TV services based on streaming technology. Analyzing the video packets received by the client application, the estimator is capable of selecting the most suitable encoding bitrate for the available bandwidth in the end-to-end path. The estimator has been integrated in a real client/server architecture and evaluated with different network traffic situations. The results of the performed evaluation have revealed the stability and adaptation speed as the best qualities of our proposal.     

The k-simultaneous consensus problem

This paper introduces and investigates the k-simultaneous consensus task: each process participates at the same time in k independent consensus instances until it decides in any one of them. It is shown that the k-simultaneous consensus task is equivalent to the k-set agreement task in the wait-free read/write shared memory model, and furthermore k-simultaneous consensus possesses properties that k-set does not. In particular we show that the multivalued version and the binary version of the k-simultaneous consensus task are wait-free equivalent. These equivalences are independent of the number of processes. Interestingly, this provides us with a new characterization of the k-set agreement task that is based on the fundamental binary consensus problem.