Sim-xl: A Powerful And User-friendly Tool For Peptide Cross-linking Analysis.

Chemical cross-linking has emerged as a powerful approach for the structural characterization of proteins and protein complexes. However, the correct identification of covalently linked (cross-linked or XL) peptides analyzed by tandem mass spectrometry is still an open challenge. Here we present SIM-XL, a software tool that can analyze data generated through commonly used cross-linkers (e.g., BS3/DSS). Our software introduces a new paradigm for search-space reduction, which ultimately accounts for its increase in speed and sensitivity. Moreover, our search engine is the first to capitalize on reporter ions for selecting tandem mass spectra derived from cross-linked peptides. It also makes available a 2D interaction map and a spectrum-annotation tool unmatched by any of its kind. We show SIM-XL to be more sensitive and faster than a competing tool when analyzing a data set obtained from the human HSP90. The software is freely available for academic use at http://patternlabforproteomics.org/sim-xl. A video demonstrating the tool is available at http://patternlabforproteomics.org/sim-xl/video. SIM-XL is the first tool to support XL data in the mzIdentML format; all data are thus available from the ProteomeXchange consortium (identifier PXD001677).

Sensitization Prevalence, Antibody Cross-Reactivity and Immunogenic Peptide Profile of Api g 2, the Non-Specific Lipid Transfer Protein 1 of Celery

Background: Celery (Apium graveolens) represents a relevant allergen source that can elicit severe reactions in the adult population. To investigate the sensitization prevalence and cross-reactivity of Api g 2 from celery stalks in a Mediterranean population and in a mouse model. Methodology: 786 non-randomized subjects from Italy were screened for IgE reactivity to rApi g 2, rArt v 3 (mugwort pollen LTP) and nPru p 3 (peach LTP) using an allergen microarray. Clinical data of 32 selected patients with reactivity to LTP under investigation were evaluated. Specific IgE titers and cross-inhibitions were performed in ELISA and allergen microarray. Balb/c mice were immunized with purified LTPs; IgG titers were determined in ELISA and mediator release was examined using RBL-2H3 cells. Simulated endolysosomal digestion was performed using microsomes obtained from human DCs. Results: IgE testing showed a sensitization prevalence of 25.6% to Api g 2, 18.6% to Art v 3, and 28.6% to Pru p 3 and frequent co-sensitization and correlating IgE-reactivity was observed. 10/32 patients suffering from LTP-related allergy reported symptoms upon consumption of celery stalks which mainly presented as OAS. Considerable IgE cross-reactivity was observed between Api g 2, Art v 3, and Pru p 3 with varying inhibition degrees of individual patients' sera. Simulating LTP mono-sensitization in a mouse model showed development of more congruent antibody specificities between Api g 2 and Art v 3. Notably, biologically relevant murine IgE cross-reactivity was restricted to the latter and diverse from Pru p 3 epitopes. Endolysosomal processing of LTP showed generation of similar clusters, which presumably represent T-cell peptides. Conclusions: Api g 2 represents a relevant celery stalk allergen in the LTP-sensitized population. The molecule displays common B cell epitopes and endolysosomal peptides that encompass T cell epitopes with pollen and plant-food derived LTP.

Integration and visualization of systems biology data in context of the genome

Background: High-density tiling arrays and new sequencing technologies are generating rapidly increasing volumes of transcriptome and protein-DNA interaction data. Visualization and exploration of this data is critical to understanding the regulatory logic encoded in the genome by which the cell dynamically affects its physiology and interacts with its environment. Results: The Gaggle Genome Browser is a cross-platform desktop program for interactively visualizing high-throughput data in the context of the genome. Important features include dynamic panning and zooming, keyword search and open interoperability through the Gaggle framework. Users may bookmark locations on the genome with descriptive annotations and share these bookmarks with other users. The program handles large sets of user-generated data using an in-process database and leverages the facilities of SQL and the R environment for importing and manipulating data. A key aspect of the Gaggle Genome Browser is interoperability. By connecting to the Gaggle framework, the genome browser joins a suite of interconnected bioinformatics tools for analysis and visualization with connectivity to major public repositories of sequences, interactions and pathways. To this flexible environment for exploring and combining data, the Gaggle Genome Browser adds the ability to visualize diverse types of data in relation to its coordinates on the genome. Conclusions: Genomic coordinates function as a common key by which disparate biological data types can be related to one another. In the Gaggle Genome Browser, heterogeneous data are joined by their location on the genome to create information-rich visualizations yielding insight into genome organization, transcription and its regulation and, ultimately, a better understanding of the mechanisms that enable the cell to dynamically respond to its environment.

Condylar displacement between centric relation and maximum intercuspation in symptomatic and asymptomatic individuals

Objective: To measure condylar displacement between centric relation (CR) and maximum intercuspation (MIC) in symptomatic and asymptomatic subjects. Materials and Methods: The sample comprised 70 non-deprogrammed individuals, divided equally into two groups, one symptomatic and the other asymptomatic, grouped according to the research diagnostic criteria for temporomandibular disorders (RDC/TMD). Condylar displacement was measured in three dimensions with the condylar position indicator (CPI) device. Dahlberg's index, intraclass correlation coefficient, repeated measures analysis of variance, analysis of variance, and generalized estimating equations were used for statistical analysis. Results: A greater magnitude of difference was observed on the vertical plane on the left side in both symptomatic and asymptomatic individuals (P = .033). The symptomatic group presented higher measurements on the transverse plane (P = .015). The percentage of displacement in the mesial direction was significantly higher in the asymptomatic group than in the symptomatic one (P = .049). Both groups presented a significantly higher percentage of mesial direction on the right side than on the left (P = .036). The presence of bilateral condylar displacement (left and right sides) in an inferior and distal direction was significantly greater in symptomatic individuals (P = .012). However, no statistical difference was noted between genders. Conclusion: Statistically significant differences between CR and MIC were quantifiable at the condylar level in asymptomatic and symptomatic individuals. (Angle Orthod. 2010;80:835-842.)

Pressure of massless hot scalar theory in the boundary effective theory framework

We use the boundary effective theory approach to thermal field theory in order to calculate the pressure of a system of massless scalar fields with quartic interaction. The method naturally separates the infrared physics, and is essentially nonperturbative. To lowest order, the main ingredient is the solution of the free Euler-Lagrange equation with nontrivial (time) boundary conditions. We derive a resummed pressure, which is in good agreement with recent calculations found in the literature, following a very direct and compact procedure.

Process oriented framework to support PLM implementation

Product lifecycle management (PLM) innovates as it defines both the product as a central element to aggregate enterprise information and the lifecycle as a new time dimension for information integration and analysis. Because of its potential benefits to shorten innovation lead-times and to reduce costs, PLM has attracted a lot of attention at industry and at research. However, the current PLM implementation stage at most organisations still does not apply the lifecycle management concepts thoroughly. In order to close the existing realisation gap, this article presents a process oriented framework to support effective PLM implementation. The framework central point consists of a set of lifecycle oriented business process reference models which links the necessary fundamental concepts, enterprise knowledge and software solutions to effectively deploy PLM. (c) 2007 Elsevier B.V. All rights reserved.

Reducing Urban Transport Energy Dependence: A New Urban Development Framework and GIS-Based Tool

High urban transport energy consumption is directly influenced by transport energy dependence. Dramatic reductions in urban transport energy dependence or consumption are not yet being widely observed despite the variety of urban planning tools currently available. A new urban development framework is presented to tackle this issue that makes use of a recently developed and successfully trialed GIS-based tool, the Transport Energy Specification (TES). The TES was simulated on a neighborhood in Sao Carlos, Brazil. In the simulation, energy dependence was reduced by a factor of 8 through activity location or infrastructure modifications to the built environment.

Learning Profile Identification Based on the Analysis of the User Context of Interaction

One of the e-learning environment goal is to attend the individual needs of students during the learning process. The adaptation of contents, activities and tools into different visualization or in a variety of content types is an important feature of this environment, bringing to the user the sensation that there are suitable workplaces to his profile in the same system. Nevertheless, it is important the investigation of student behaviour aspects, considering the context where the interaction happens, to achieve an efficient personalization process. The paper goal is to present an approach to identify the student learning profile analyzing the context of interaction. Besides this, the learning profile could be analyzed in different dimensions allows the system to deal with the different focus of the learning.

Role of price and enforcement in water allocation: Insights from Game Theory

As many countries are moving toward water sector reforms, practical issues of how water management institutions can better effect allocation, regulation, and enforcement of water rights have emerged. The problem of nonavailability of water to tailenders on an irrigation system in developing countries, due to unlicensed upstream diversions is well documented. The reliability of access or equivalently the uncertainty associated with water availability at their diversion point becomes a parameter that is likely to influence the application by users for water licenses, as well as their willingness to pay for licensed use. The ability of a water agency to reduce this uncertainty through effective water rights enforcement is related to the fiscal ability of the agency to monitor and enforce licensed use. In this paper, this interplay across the users and the agency is explored, considering the hydraulic structure or sequence of water use and parameters that define the users and the agency`s economics. The potential for free rider behavior by the users, as well as their proposals for licensed use are derived conditional on this setting. The analyses presented are developed in the framework of the theory of ""Law and Economics,`` with user interactions modeled as a game theoretic enterprise. The state of Ceara, Brazil, is used loosely as an example setting, with parameter values for the experiments indexed to be approximately those relevant for current decisions. The potential for using the ideas in participatory decision making is discussed. This paper is an initial attempt to develop a conceptual framework for analyzing such situations but with a focus on the reservoir-canal system water rights enforcement.

Performance analysis of a single-user MISO ultra-wideband time reversal system with DFE

This paper presents an analysis of the performance of a baseband multiple-input single-output (MISO) time reversal ultra-wideband system (TR-UWB) incorporating a symbol spaced decision feedback equalizer (DFE). A semi-analytical performance analysis based on a Gaussian approach is considered, which matched well with simulation results, even for the DFE case. The channel model adopted is based on the IEEE 802.15.3a model, considering correlated shadowing across antenna elements. In order to provide a more realistic analysis, channel estimation errors are considered for the design of the TR filter. A guideline for the choice of equalizer length is provided. The results show that the system`s performance improves with an increase in the number of transmit antennas and when a symbol spaced equalizer is used with a relatively small number of taps compared to the number of resolvable paths in the channel impulse response. Moreover, it is possible to conclude that due to the time reversal scheme, the error propagation in the DFE does not play a role in the system`s performance.

Distributed power control algorithm for multiple access systems based on Verhulst model

In this paper the continuous Verhulst dynamic model is used to synthesize a new distributed power control algorithm (DPCA) for use in direct sequence code division multiple access (DS-CDMA) systems. The Verhulst model was initially designed to describe the population growth of biological species under food and physical space restrictions. The discretization of the corresponding differential equation is accomplished via the Euler numeric integration (ENI) method. Analytical convergence conditions for the proposed DPCA are also established. Several properties of the proposed recursive algorithm, such as Euclidean distance from optimum vector after convergence, convergence speed, normalized mean squared error (NSE), average power consumption per user, performance under dynamics channels, and implementation complexity aspects, are analyzed through simulations. The simulation results are compared with two other DPCAs: the classic algorithm derived by Foschini and Miljanic and the sigmoidal of Uykan and Koivo. Under estimated errors conditions, the proposed DPCA exhibits smaller discrepancy from the optimum power vector solution and better convergence (under fixed and adaptive convergence factor) than the classic and sigmoidal DPCAs. (C) 2010 Elsevier GmbH. All rights reserved.

Jointly multi-user detection and channel estimation with genetic algorithm

This work aims at proposing the use of the evolutionary computation methodology in order to jointly solve the multiuser channel estimation (MuChE) and detection problems at its maximum-likelihood, both related to the direct sequence code division multiple access (DS/CDMA). The effectiveness of the proposed heuristic approach is proven by comparing performance and complexity merit figures with that obtained by traditional methods found in literature. Simulation results considering genetic algorithm (GA) applied to multipath, DS/CDMA and MuChE and multi-user detection (MuD) show that the proposed genetic algorithm multi-user channel estimation (GAMuChE) yields a normalized mean square error estimation (nMSE) inferior to 11%, under slowly varying multipath fading channels, large range of Doppler frequencies and medium system load, it exhibits lower complexity when compared to both maximum likelihood multi-user channel estimation (MLMuChE) and gradient descent method (GrdDsc). A near-optimum multi-user detector (MuD) based on the genetic algorithm (GAMuD), also proposed in this work, provides a significant reduction in the computational complexity when compared to the optimum multi-user detector (OMuD). In addition, the complexity of the GAMuChE and GAMuD algorithms were (jointly) analyzed in terms of number of operations necessary to reach the convergence, and compared to other jointly MuChE and MuD strategies. The joint GAMuChE-GAMuD scheme can be regarded as a promising alternative for implementing third-generation (3G) and fourth-generation (4G) wireless systems in the near future. Copyright (C) 2010 John Wiley & Sons, Ltd.

A Computational Framework for Institutional Agency

This paper provides a computational framework, based on Defeasible Logic, to capture some aspects of institutional agency. Our background is Kanger-Lindahl-P\"orn account of organised interaction, which describes this interaction within a multi-modal logical setting. This work focuses in particular on the notions of counts-as link and on those of attempt and of personal and direct action to realise states of affairs. We show how standard Defeasible Logic can be extended to represent these concepts: the resulting system preserves some basic properties commonly attributed to them. In addition, the framework enjoys nice computational properties, as it turns out that the extension of any theory can be computed in time linear to the size of the theory itself.

The BCD transient recorder revisited: firmware for the ISA-to-USB bridging card and software for the graphical user interface

This report describes recent updates to the custom-built data-acquisition hardware operated by the Center for Hypersonics. In 2006, an ISA-to-USB bridging card was developed as part of Luke Hillyard's final-year thesis. This card allows the hardware to be connected to any recent personal computers via a (USB or RS232) serial port and it provides a number of simple text-based commands for control of the hardware. A graphical user interface program was also updated to help the experimenter manage the data acquisition functions. Sampled data is stored in text files that have been compressed with the gzip for mat. To simplify the later archiving or transport of the data, all files specific to a shot are stored in a single directory. This includes a text file for the run description, the signal configuration file and the individual sampled-data files, one for each signal that was recorded.