Toward the prediction of class I and II mouse major histocompatibility complex-peptide-binding affinity:in silico bioinformatic step-by-step guide using quantitative structure-activity relationships

Quantitative structure-activity relationship (QSAR) analysis is a cornerstone of modern informatics. Predictive computational models of peptide-major histocompatibility complex (MHC)-binding affinity based on QSAR technology have now become important components of modern computational immunovaccinology. Historically, such approaches have been built around semiqualitative, classification methods, but these are now giving way to quantitative regression methods. We review three methods--a 2D-QSAR additive-partial least squares (PLS) and a 3D-QSAR comparative molecular similarity index analysis (CoMSIA) method--which can identify the sequence dependence of peptide-binding specificity for various class I MHC alleles from the reported binding affinities (IC50) of peptide sets. The third method is an iterative self-consistent (ISC) PLS-based additive method, which is a recently developed extension to the additive method for the affinity prediction of class II peptides. The QSAR methods presented here have established themselves as immunoinformatic techniques complementary to existing methodology, useful in the quantitative prediction of binding affinity: current methods for the in silico identification of T-cell epitopes (which form the basis of many vaccines, diagnostics, and reagents) rely on the accurate computational prediction of peptide-MHC affinity. We have reviewed various human and mouse class I and class II allele models. Studied alleles comprise HLA-A*0101, HLA-A*0201, HLA-A*0202, HLA-A*0203, HLA-A*0206, HLA-A*0301, HLA-A*1101, HLA-A*3101, HLA-A*6801, HLA-A*6802, HLA-B*3501, H2-K(k), H2-K(b), H2-D(b) HLA-DRB1*0101, HLA-DRB1*0401, HLA-DRB1*0701, I-A(b), I-A(d), I-A(k), I-A(S), I-E(d), and I-E(k). In this chapter we show a step-by-step guide into predicting the reliability and the resulting models to represent an advance on existing methods. The peptides used in this study are available from the AntiJen database (http://www.jenner.ac.uk/AntiJen). The PLS method is available commercially in the SYBYL molecular modeling software package. The resulting models, which can be used for accurate T-cell epitope prediction, will be made are freely available online at the URL http://www.jenner.ac.uk/MHCPred.

New horizons in mouse immunoinformatics:reliable in silico prediction of mouse class I histocompatibility major complex peptide binding affinity

Quantitative structure–activity relationship (QSAR) analysis is a main cornerstone of modern informatic disciplines. Predictive computational models, based on QSAR technology, of peptide-major histocompatibility complex (MHC) binding affinity have now become a vital component of modern day computational immunovaccinology. Historically, such approaches have been built around semi-qualitative, classification methods, but these are now giving way to quantitative regression methods. The additive method, an established immunoinformatics technique for the quantitative prediction of peptide–protein affinity, was used here to identify the sequence dependence of peptide binding specificity for three mouse class I MHC alleles: H2–Db, H2–Kb and H2–Kk. As we show, in terms of reliability the resulting models represent a significant advance on existing methods. They can be used for the accurate prediction of T-cell epitopes and are freely available online (http://www.jenner.ac.uk/MHCPred).

Access Rights Inheritance in Information Systems Controlled by Metadata

All information systems have to be protected. As the number of information objects and the number of users increase the task of information system’s protection becomes more difficult. One of the most difficult problems is access rights assignment. This paper describes the graph model of access rights inheritance. This model takes into account relations and dependences between different objects and between different users. The model can be implemented in the information systems controlled by the metadata, describing information objects and connections between them, such as the systems based on CASE-technology METAS.

KFTKGA: Knowledge Flow Tracer and Growth Analyzer for Community Learning

The advances in building learning technology now have to emphasize on the aspect of the individual learning besides the popular focus on the technology per se. Unlike the common research where a great deal has been on finding ways to build, manage, classify, categorize and search knowledge on the server, there is an interest in our work to look at the knowledge development at the individual’s learning. We build the technology that resides behind the knowledge sharing platform where learning and sharing activities of an individual take place. The system that we built, KFTGA (Knowledge Flow Tracer and Growth Analyzer), demonstrates the capability of identifying the topics and subjects that an individual is engaged with during the knowledge sharing session and measuring the knowledge growth of the individual learning on a specific subject on a given time space.

Optical trapping with superfocused high-M2 laser diode beam

Many applications of high-power laser diodes demand tight focusing. This is often not possible due to the multimode nature of semiconductor laser radiation possessing beam propagation parameter M2 values in double-digits. We propose a method of 'interference' superfocusing of high-M2 diode laser beams with a technique developed for the generation of Bessel beams based on the employment of an axicon fabricated on the tip of a 100 μm diameter optical fiber with highprecision direct laser writing. Using axicons with apex angle 140º and rounded tip area as small as 10 μm diameter, we demonstrate 2-4 μm diameter focused laser 'needle' beams with approximately 20 μm propagation length generated from multimode diode laser with beam propagation parameter M2=18 and emission wavelength of 960 nm. This is a few-fold reduction compared to the minimal focal spot size of 11 μm that could be achieved if focused by an 'ideal' lens of unity numerical aperture. The same technique using a 160º axicon allowed us to demonstrate few-μm-wide laser 'needle' beams with nearly 100 μm propagation length with which to demonstrate optical trapping of 5-6 μm rat blood red cells in a water-heparin solution. Our results indicate the good potential of superfocused diode laser beams for applications relating to optical trapping and manipulation of microscopic objects including living biological objects with aspirations towards subsequent novel lab-on-chip configurations.

A simulating software of fetal phonocardiographic signals

A valuable alternative to traditional diagnostic tool to record fetal heart rate, to monitor the general fetal wellbeing, is fetal phonocardiography, a passive and low cost acoustic recording of fetal heart sounds. In this paper, it is presented a simulating software of fetal phonocardiographic signals relative to different fetal physiological states and recording conditions (for example different kinds and levels of noise). This software can be useful to test and assess fetal heart rate extraction algorithms from fetal phonocardiographic recordings and as a teaching tool for demonstration to medical students and others. © 2010 IEEE.

Foveation time measure in Congenital Nystagmus through second order approximation of the slow phases

Congenital Nystagmus (CN) is an ocular-motor disorder characterised by involuntary, conjugated ocular oscillations, and its pathogenesis is still unknown. The pathology is de fined as "congenital" from the onset time of its arise which could be at birth or in the first months of life. Visual acuity in CN subjects is often diminished due to nystagmus continuous oscillations, mainly on the horizontal plane, which disturb image fixation on the retina. However, during short periods in which eye velocity slows down while the target image is placed onto the fovea (called foveation intervals) the image of a given target can still be stable, allowing a subject to reach a higher visual acuity. In CN subjects, visual acuity is usually assessed both using typical measurement techniques (e.g. Landolt C test) and with eye movement recording in different gaze positions. The offline study of eye movement recordings allows physicians to analyse nystagmus main features such as waveform shape, amplitude and frequency and to compute estimated visual acuity predictors. This analytical functions estimates the best corrected visual acuity using foveation time and foveation position variability, hence a reliable estimation of this two parameters is a fundamental factor in assessing visual acuity. This work aims to enhance the foveation time estimation in CN eye movement recording, computing a second order approximation of the slow phase components of nystag-mus oscillations. About 19 infraredoculographic eye-movement recordings from 10 CN subjects were acquired and the visual acuity assessed with an acuity predictor was compared to the one measured in primary position. Results suggest that visual acuity measurements based on foveation time estimation obtained from interpolated data are closer to value obtained during Landolt C tests. © 2010 IEEE.

PSD modifications of FHRV due to CTG storage rate

Cardiotocographic data provide physicians information about foetal development and, through assessment of specific parameters (like accelerations, uterine contractions, ...), permit to assess conditions such as foetal distress. An incorrect evaluation of foetal status can be of course very dangerous. In the last decades, to improve interpretation of cardiotocographic recordings, great interest has been dedicated to FHRV spectral analysis. It is worth reminding that FHR is intrinsically an uneven series and that to obtain evenly sampled series, many commercial cardiotocographs use a zero-order interpolation (storage rate of CTG data equal to 4 Hz). This is not suitable for frequency analyses because interpolation introduces alterations in the FHR power spectrum. In particular, this interpolation process can produce artifacts and an attenuation of the high-frequency components of the PSD that, for example, affects the estimation of the sympatho-vagal balance (SVB - computed as low-frequency/high-frequency ratio), which represents an important clinical parameter. In order to estimate the frequency spectrum alterations due to zero-order interpolation and other CTG storage rates, in this work, we simulated uneven FHR series with set characteristics, their evenly spaced versions (with different storage rates) and computed SVB values by PSD. For PSD estimation, we chose the Lomb method, as suggested by other authors in application to uneven HR series. ©2009 IEEE.

Whole body vibration training:analysis and characterization

The aim of this work is to contribute to the analysis and characterization of training with whole body vibration (WBV) and the resultant neuromuscular response. WBV aims to mechanically activate muscle by eliciting stretch reflexes. Generally, surface electromyography is utilized to assess muscular response elicited by vibrations. However, EMG analysis could potentially bring to erroneous conclusions if not accurately filtered. Tiny and lightweight MEMS accelerometers were found helpful in monitoring muscle motion. Displacements were estimated integrating twice the acceleration data after gravity and small postural subject adjustments contribution removal. Results showed the relevant presence of motion artifacts on EMG recordings, the high correlation between muscle motion and EMG activity and how resonance frequencies and dumping factors depended on subject and his positioning onto the vibrating platform. Stimulations at the resonant frequency maximize muscles lengthening and in turn, muscle spindle solicitation , which may produce more muscle activation. Local mechanical stimulus characterization (Le, muscle motion analysis) could be meaningful in discovering proper muscle stimulation and may contribute to suggest appropriate and effective WBV exercise protocols. ©2009 IEEE.

Digital learning, discourse and ideology

In recent decades, digital technologies have seen widespread use across global society and adoption at all levels of education. Digital learning might therefore simply be described as learning that is facilitated by digital technologies, but to discuss digital learning only in this way obscures important complexities linked to language, culture, politics, and the economy. To talk or write about learning as if it were directly facilitated by technology of any kind, places a strong focus on what technology has, or seems to be, achieving. At the same time, this marginalizes, or reduces the visibility of, human roles within the academia and beyond (Hayes and Jandrić 2014).

Protection issue discussion of DC network development:circuit breaker or fault-tolerant converter

This paper provides a discussion on future direct current (DC) network development in terms of system protection under DC-side fault scenarios. The argument between appropriate DC circuit breaker and new DC fault-tolerant converters is discussed after a review on DC technology development and bottleneck issues that require proper solutions. The overcurrent/cost curve of power-electronic DC circuit breakers (CB) superimposed to voltage-source converter (VSC) systems is derived and compared with other possible fault-tolerant power conversion options. This in-advance planning of protection capability is essential for the future development of DC networks.

Improving energy efficiency in a wireless sensor network by combining cooperative MIMO with data aggregation

In wireless sensor networks where nodes are powered by batteries, it is critical to prolong the network lifetime by minimizing the energy consumption of each node. In this paper, the cooperative multiple-input-multiple-output (MIMO) and data-aggregation techniques are jointly adopted to reduce the energy consumption per bit in wireless sensor networks by reducing the amount of data for transmission and better using network resources through cooperative communication. For this purpose, we derive a new energy model that considers the correlation between data generated by nodes and the distance between them for a cluster-based sensor network by employing the combined techniques. Using this model, the effect of the cluster size on the average energy consumption per node can be analyzed. It is shown that the energy efficiency of the network can significantly be enhanced in cooperative MIMO systems with data aggregation, compared with either cooperative MIMO systems without data aggregation or data-aggregation systems without cooperative MIMO, if sensor nodes are properly clusterized. Both centralized and distributed data-aggregation schemes for the cooperating nodes to exchange and compress their data are also proposed and appraised, which lead to diverse impacts of data correlation on the energy performance of the integrated cooperative MIMO and data-aggregation systems.

Az egyensúlyi ráták unicitása és a bérráta pozitivitása a Neumann-modell általánosításaiban (Uniqueness of equilibrium rates and the positive value of the wage rate in generalizations from the Neumann model)

Cikkünk arról a paradox jelenségről szól, hogy a fogyasztást explicit módon megjelenítő Neumann-modell egyensúlyi megoldásaiban a munkabért meghatározó létszükségleti termékek ára esetenként nulla lehet, és emiatt a reálbér egyensúlyi értéke is nulla lesz. Ez a jelenség mindig bekövetkezik az olyan dekomponálható gazdaságok esetén, amelyekben eltérő növekedési és profitrátájú, alternatív egyensúlyi megoldások léteznek. A jelenség sokkal áttekinthetőbb formában tárgyalható a modell Leontief-eljárásra épülő egyszerűbb változatában is, amit ki is használunk. Megmutatjuk, hogy a legnagyobbnál alacsonyabb szintű növekedési tényezőjű megoldások közgazdasági szempontból értelmetlenek, és így érdektelenek. Ezzel voltaképpen egyrészt azt mutatjuk meg, hogy Neumann kiváló intuíciója jól működött, amikor ragaszkodott modellje egyértelmű megoldásához, másrészt pedig azt is, hogy ehhez nincs szükség a gazdaság dekomponálhatóságának feltételezésére. A vizsgált téma szorosan kapcsolódik az általános profitráta meghatározásának - Sraffa által modern formába öntött - Ricardo-féle elemzéséhez, illetve a neoklasszikus növekedéselmélet nevezetes bér-profit, illetve felhalmozás-fogyasztás átváltási határgörbéihez, ami jelzi a téma elméleti és elmélettörténeti érdekességét is. / === / In the Marx-Neumann version of the Neumann model introduced by Morishima, the use of commodities is split between production and consumption, and wages are determined as the cost of necessary consumption. In such a version it may occur that the equilibrium prices of all goods necessary for consumption are zero, so that the equilibrium wage rate becomes zero too. In fact such a paradoxical case will always arise when the economy is decomposable and the equilibrium not unique in terms of growth and interest rate. It can be shown that a zero equilibrium wage rate will appear in all equilibrium solutions where growth and interest rate are less than maximal. This is another proof of Neumann's genius and intuition, for he arrived at the uniqueness of equilibrium via an assumption that implied that the economy was indecomposable, a condition relaxed later by Kemeny, Morgenstern and Thompson. This situation occurs also in similar models based on Leontief technology and such versions of the Marx-Neumann model make the roots of the problem more apparent. Analysis of them also yields an interesting corollary to Ricardo's corn rate of profit: the real cause of the awkwardness is bad specification of the model: luxury commodities are introduced without there being a final demand for them, and production of them becomes a waste of resources. Bad model specification shows up as a consumption coefficient incompatible with the given technology in the more general model with joint production and technological choice. For the paradoxical situation implies the level of consumption could be raised and/or the intensity of labour diminished without lowering the equilibrium rate of the growth and interest. This entails wasteful use of resources and indicates again that the equilibrium conditions are improperly specified. It is shown that the conditions for equilibrium can and should be redefined for the Marx-Neumann model without assuming an indecomposable economy, in a way that ensures the existence of an equilibrium unique in terms of the growth and interest rate coupled with a positive value for the wage rate, so confirming Neumann's intuition. The proposed solution relates closely to findings of Bromek in a paper correcting Morishima's generalization of wage/profit and consumption/investment frontiers.

A hazai vállalatok elektronikus beszerzés iránti nyitottsága = E-procurement Responsiveness of the Hungarian Companies’

A Versenyképesség Kutató Központ 2004-ben a „Versenyben a világgal 1995-97.” kutatási program és az 1999-es vállalati versenyképességi kérdőíves felmérés hagyományait folytatva, valamint azok tapasztalataira építve egy hároméves kutatási programot kezdett el „Versenyben a világgal 2004-2006 − Gazdasági versenyképességünk vállalati nézőpontból” címmel. A kérdőíves felmérés nyomán létrejött adatbázist elemeztük hasonló témában 2005-ben. A korábbi eredményeken okulva, a kérdőív-elemzés kiterjesztésével azt kívántuk felmérni, hogy az elektronikus beszerzés iránti nyitottság növekedett-e hazánkban, illetve milyen egyéb összefüggések fedezhetők fel a beszerzési szervezet, a beszerzés vállalati kapcsolatai, valamint az elektronikus beszerzés értelmezésében az egyes válaszadóknál. A kutatás továbbra is eltér a hagyományos megoldásoktól, azaz nem kívánja vizsgálni a hazai vállalati honlapok elterjedtségét, azonban a korábbiaktól eltérően több információ-technológiával kapcsolatos információt kíván a válaszadóktól. A cél, tehát belső vállalati folyamatok, vevő-szállító kapcsolatok, az informatikai háttér elektronikus beszerzéssel való kapcsolatának feltárása és következtetéseink levonása volt annak érdekében, hogy megtudjuk milyen hatékonyságnövelési lehetőséget hordoz az elektronikus beszerzés és a hazai információs társadalmi fejlettség figyelembe vételével mennyire nyitottak erre a beszerzők és a pályázók egyaránt. Az elektronikus beszerzés és versenyképesség kapcsolata különösen a 2000-es éves eleje óta foglalkoztatja a kutatókat. Vita az elektronikus beszerzés beszerzési költségre gyakorolt hatásában, valamint a kormányzati politika által gyakorolt hatás jellegében van, melyet a közbeszerzés mint speciálisan szabályozott beszerzési tevékenység és az e-beszerzés kapcsolatára fejt ki. A vállalatok versenyképességének és az elektronikus beszerzés folyamatosan bővülő és fejlődő eszközrendszerének kapcsolata azonban nem kérdéses, ezt kutatási eredményeink is megerősítik. _________ The Competitiveness Research Center based on the experience of the „ In Global Competition 1995-1997” research programme and continuing the company competitiveness survey (1999) has begun a three-year research programme with the following title: „In Global Competition 2004-2006” Our economic competitiveness, company point of view”. We had analyzed a database generated on the basis of a questionnaire survey with a similar theme in 2005. Drawing the lessons from earlier researches and expanding the questionnaire examination, we now seek to find out how far receptiveness to electronic procurement has increased in Hungary and what other relations can be observed in responses concerning the interpretation of procurement organizations, the corporate aspects of procurement and electronic procurement. The new research project continues to differ from traditional solutions insofar as it does not intend to examine the currency of corporate web pages, but, in contrast to earlier practice, it does want responders to provide information on IT technology. The objectives are thus to understand how electronic procurement relates to corporate processes, purchaser-supplier relations and IT base, and to see what opportunities of increasing efficiency there are in electronic procurement and how far procurers and bidders are open to this at the level of information society development in Hungary. Researchers have focused on the relation between electronic procurement and competitiveness since the early 2000s. What is debated is how electronic procurement influences procurement costs, and how government policies influence the relation between public procurement as a specially regulated procurement activity and electronic procurement. The relation between corporate competitiveness and the continually increasing means of electronic procurement is beyond doubt, evidenced by our research findings.