An automated framework for understanding structural variations in the binding grooves of MHC class II molecules

Background: MHC/HLA class II molecules are important components of the immune system and play a critical role in processes such as phagocytosis. Understanding peptide recognition properties of the hundreds of MHC class II alleles is essential to appreciate determinants of antigenicity and ultimately to predict epitopes. While there are several methods for epitope prediction, each differing in their success rates, there are no reports so far in the literature to systematically characterize the binding sites at the structural level and infer recognition profiles from them. Results: Here we report a new approach to compare the binding sites of MHC class II molecules using their three dimensional structures. We use a specifically tuned version of our recent algorithm, PocketMatch. We show that our methodology is useful for classification of MHC class II molecules based on similarities or differences among their binding sites. A new module has been used to define binding sites in MHC molecules. Comparison of binding sites of 103 MHC molecules, both at the whole groove and individual sub-pocket levels has been carried out, and their clustering patterns analyzed. While clusters largely agree with serotypic classification, deviations from it and several new insights are obtained from our study. We also present how differences in sub-pockets of molecules associated with a pair of autoimmune diseases, narcolepsy and rheumatoid arthritis, were captured by PocketMatch(13). Conclusion: The systematic framework for understanding structural variations in MHC class II molecules enables large scale comparison of binding grooves and sub-pockets, which is likely to have direct implications towards predicting epitopes and understanding peptide binding preferences.

Requirements for information management system in agricultural contracting

Menneinä vuosikymmeninä maatalouden työt ovat ensin koneellistuneet voimakkaasti ja sittemmin mukaan on tullut automaatio. Nykyään koneiden kokoa suurentamalla ei enää saada tuottavuutta nostettua merkittävästi, vaan työn tehostaminen täytyy tehdä olemassa olevien resurssien käyttöä tehostamalla. Tässä työssä tarkastelun kohteena on ajosilppuriketju nurmisäilörehun korjuussa. Säilörehun korjuun intensiivisyys ja koneyksiköiden runsas määrä ovat työnjohdon kannalta vaativa yhdistelmä. Työn tavoitteena oli selvittää vaatimuksia maatalouden urakoinnin tueksi kehitettävälle tiedonhallintajärjestelmälle. Tutkimusta varten haastateltiin yhteensä 12 urakoitsijaa tai yhteistyötä tekevää viljelijää. Tutkimuksen perusteella urakoitsijoilla on tarvetta tietojärjestelmille.Luonnollisesti urakoinnin laajuus ja järjestelyt vaikuttavat asiaan. Tutkimuksen perusteella keskeisimpiä vaatimuksia tiedonhallinnalle ovat: • mahdollisimman laaja, yksityiskohtainen ja automaattinen tiedon keruu tehtävästä työstä • karttapohjaisuus, kuljettajien opastus kohteisiin • asiakasrekisteri, työn tilaus sähköisesti • tarjouspyyntöpohjat, hintalaskurit • luotettavuus, tiedon säilyvyys • sovellettavuus monenlaisiin töihin • yhteensopivuus muiden järjestelmien kanssa Kehitettävän järjestelmän tulisi siis tutkimuksen perusteella sisältää seuraavia osia: helppokäyttöinen suunnittelu/asiakasrekisterityökalu, toimintoja koneiden seurantaan, opastukseen ja johtamiseen, työnaikainen tiedonkeruu sekä kerätyn tiedon käsittelytoimintoja. Kaikki käyttäjät eivät kuitenkaan tarvitse kaikkia toimintoja, joten urakoitsijan on voitava valita tarvitsemansa osat ja mahdollisesti lisätä toimintoja myöhemmin. Tiukoissa taloudellisissa ja ajallisissa raameissa toimivat urakoitsijat ovat vaativia asiakkaita, joiden käyttämän tekniikan tulee olla toimivaa ja luotettavaa. Toisaalta inhimillisiä virheitä sattuu kokeneillekin, joten hyvällä tietojärjestelmällä työstä tulee helpompaa ja tehokkaampaa.

Study of interdiffusion and growth of topologically closed packed phases in the Co-Nb system

Interdiffusion study of the Co-Nb system is conducted to determine the diffusion parameters in different phases. The integrated diffusion coefficients at different temperatures are calculated for the Nb2Co7 phase, which has very narrow composition range. The interdiffusion coefficients at different compositions in the NbCo2 Laves phase are determined. The interdiffusion coefficient in this phase decreases with increasing Nb content to the stoichiometric composition. Further, the average interdiffusion coefficient in the N6Co7-mu phase is determined. The activation energies for diffusion in different phases are calculated, providing valuable information regarding the diffusion mechanism. In addition, an experiment using Kirkendall markers is conducted to calculate the relative mobilities of the species.

Reduced ML-Decoding Complexity, Full-Rate STBCs for 4 Transmit Antenna Systems

For an n(t) transmit, n(r) receive antenna system (n(t) x nr system), a full-rate space time block code (STBC) transmits min(n(t), n(r)) complex symbols per channel use. In this paper, a scheme to obtain a full-rate STBC for 4 transmit antennas and any n(r), with reduced ML-decoding complexity is presented. The weight matrices of the proposed STBC are obtained from the unitary matrix representations of a Clifford Algebra. By puncturing the symbols of the STBC, full rate designs can be obtained for n(r) < 4. For any value of n(r), the proposed design offers the least ML-decoding complexity among known codes. The proposed design is comparable in error performance to the well known Perfect code for 4 transmit antennas while offering lower ML-decoding complexity. Further, when n(r) < 4, the proposed design has higher ergodic capacity than the punctured Perfect code. Simulation results which corroborate these claims are presented.

A Low-Complexity, Full-Rate, Full-Diversity 2 x 2 STBC with Golden Code's Coding Gain

This paper presents a low-ML-decoding-complexity, full-rate, full-diversity space-time block code (STBC) for a 2 transmit antenna, 2 receive antenna multiple-input multiple-output (MIMO) system, with coding gain equal to that of the best and well known Golden code for any QAM constellation. Recently, two codes have been proposed (by Paredes, Gershman and Alkhansari and by Sezginer and Sari), which enjoy a lower decoding complexity relative to the Golden code, but have lesser coding gain. The 2 x 2 STBC presented in this paper has lesser decoding complexity for non-square QAM constellations, compared with that of the Golden code, while having the same decoding complexity for square QAM constellations. Compared with the Paredes-Gershman-Alkhansari and Sezginer-Sari codes, the proposed code has the same decoding complexity for non-rectangular QAM constellations. Simulation results, which compare the codeword error rate (CER) performance, are presented.

Performability of automated manufacturing systems with centralized material handling

We present a framework for performance evaluation of manufacturing systems subject to failure and repair. In particular, we determine the mean and variance of accumulated production over a specified time frame and show the usefulness of these results in system design and in evaluating operational policies for manufacturing systems. We extend this analysis for lead time as well. A detailed performability study is carried out for the generic model of a manufacturing system with centralized material handling. Several numerical results are presented, and the relevance of performability analysis in resolving system design issues is highlighted. Specific problems addressed include computing the distribution of total production over a shift period, determining the shift length necessary to deliver a given production target with a desired probability, and obtaining the distribution of Manufacturing Lead Time, all in the face of potential subsystem failures.

A Low-Complexity, Full-Rate, Full-Diversity 2x2 STBC with Golden Code's Coding Gain

This paper presents a low-ML-decoding-complexity, full-rate, full-diversity space-time block code (STBC) for a 2 transmit antenna, 2 receive antenna multiple-input multipleoutput (MIMO) system, with coding gain equal to that of the best and well known Golden code for any QAM constellation.Recently, two codes have been proposed (by Paredes, Gershman and Alkhansari and by Sezginer and Sari), which enjoy a lower decoding complexity relative to the Golden code, but have lesser coding gain. The 2 × 2 STBC presented in this paper has lesser decoding complexity for non-square QAM constellations,compared with that of the Golden code, while having the same decoding complexity for square QAM constellations. Compared with the Paredes-Gershman-Alkhansari and Sezginer-Sari codes, the proposed code has the same decoding complexity for nonrectangular QAM constellations. Simulation results, which compare the codeword error rate (CER) performance, are presented.

Bi-directional Switch Commutation for a Resonant Matrix Converter supplying a Contactless Energy Transmission System

This paper describes a bi-directional switch commutation strategy for a resonant matrix converter loaded with a contactless energy transmission system. Due to the different application compared to classical 3 phase to 3 phase matrix converters supplying induction machines a new investigation of possible commutation principles is necessary. The paper therefore compares the full bridge series-resonant converter with the 3 phase to 2 phase matrix converter. From the commutation of the full bridge series-resonant converter, conditions for the bi-directional switch commutation are derived. One of the main benefits of the derived strategy is the minimization of commutation steps, which is independent from the load current sign.

Full spin and spatial symmetry adapted technique for correlated electronic hamiltonians: Application to an icosahedral cluster

One of the long standing problems in quantum chemistry had been the inability to exploit full spatial and spin symmetry of an electronic Hamiltonian belonging to a non-Abelian point group. Here, we present a general technique which can utilize all the symmetries of an electronic (magnetic) Hamiltonian to obtain its full eigenvalue spectrum. This is a hybrid method based on Valence Bond basis and the basis of constant z-component of the total spin. This technique is applicable to systems with any point group symmetry and is easy to implement on a computer. We illustrate the power of the method by applying it to a model icosahedral half-filled electronic system. This model spans a huge Hilbert space (dimension 1,778,966) and in the largest non-Abelian point group. The C60 molecule has this symmetry and hence our calculation throw light on the higher energy excited states of the bucky ball. This method can also be utilized to study finite temperature properties of strongly correlated systems within an exact diagonalization approach. (C) 2011 Wiley Periodicals, Inc. Int J Quantum Chem, 2012

An Accurate Fractional Period Delay Generation System

An all-digital technique is proposed for generating an accurate delay irrespective of the inaccuracies of a controllable delay line. A subsampling technique-based delay measurement unit (DMU) capable of measuring delays accurately for the full period range is used as the feedback element to build accurate fractional period delays based on input digital control bits. The proposed delay generation system periodically measures and corrects the error and maintains it at the minimum value without requiring any special calibration phase. Up to 40x improvement in accuracy is demonstrated for a commercial programmable delay generator chip. The time-precision trade-off feature of the DMU is utilized to reduce the locking time. Loop dynamics are adjusted to stabilize the delay after the minimum error is achieved, thus avoiding additional jitter. Measurement results from a high-end oscilloscope also validate the effectiveness of the proposed system in improving accuracy.

Decentralized linear quadratic power system stabilizers for multi-machine power systems

Linear quadratic stabilizers are well-known for their superior control capabilities when compared to the conventional lead-lag power system stabilizers. However, they have not seen much of practical importance as the state variables are generally not measurable; especially the generator rotor angle measurement is not available in most of the power plants. Full state feedback controllers require feedback of other machine states in a multi-machine power system and necessitate block diagonal structure constraints for decentralized implementation. This paper investigates the design of Linear Quadratic Power System Stabilizers using a recently proposed modified Heffron-Phillip's model. This model is derived by taking the secondary bus voltage of the step-up transformer as reference instead of the infinite bus. The state variables of this model can be obtained by local measurements. This model allows a coordinated linear quadratic control design in multi machine systems. The performance of the proposed controller has been evaluated on two widely used multi-machine power systems, 4 generator 10 bus and 10 generator 39 bus systems. It has been observed that the performance of the proposed controller is superior to that of the conventional Power System Stabilizers (PSS) over a wide range of operating and system conditions.

Interplay of software bloat, hardware energy proportionality and system bottlenecks

In large flexible software systems, bloat occurs in many forms, causing excess resource utilization and resource bottlenecks. This results in lost throughput and wasted joules. However, mitigating bloat is not easy; efforts are best applied where savings would be substantial. To aid this we develop an analytical model establishing the relation between bottleneck in resources, bloat, performance and power. Analyses with the model places into perspective results from the first experimental study of the power-performance implications of bloat. In the experiments we find that while bloat reduction can provide as much as 40% energy savings, the degree of impact depends on hardware and software characteristics. We confirm predictions from our model with selected results from our experimental study. Our findings show that a software-only view is inadequate when assessing the effects of bloat. The impact of bloat on physical resource usage and power should be understood for a full systems perspective to properly deploy bloat reduction solutions and reap their power-performance benefits.

Full-rate full-diversity achieving MIMO precoding with partial CSIT

In this paper, we consider a slow-fading nt ×nr multiple-input multiple-output (MIMO) channel subjected to block fading. Reliability (in terms of achieved diversity order) and rate (in number of symbols transmitted per channel use) are of interest in such channels. We propose a new precoding scheme which achieves both full diversity (nt ×nrth order diversity) as well as full rate (nt symbols per channel use) using partial channel state information at the transmitter (CSIT). The proposed scheme achieves full diversity and improved coding gain through an optimization over the choice of constellation sets. The optimization maximizes dmin2 for our precoding scheme subject to an energy constraint. The scheme requires feedback of nt - 1 angle parameter values, compared to 2ntnr real coefficients in case of full CSIT. Further, for the case of nt × 1 system, we prove that the capacity achieved by the proposed scheme is same as that achieved with full CSIT. Error rate performance results for nt = 3,4,8 show that the proposed scheme performs better than other precoding schemes in the literature; the better performance is due to the choice of the signal sets and the feedback angles in the proposed scheme.

Hierarchical artificial immune system for crop stage classification

This paper presents a new hierarchical clustering algorithm for crop stage classification using hyperspectral satellite image. Amongst the multiple benefits and uses of remote sensing, one of the important application is to solve the problem of crop stage classification. Modern commercial imaging satellites, owing to their large volume of satellite imagery, offer greater opportunities for automated image analysis. Hence, we propose a unsupervised algorithm namely Hierarchical Artificial Immune System (HAIS) of two steps: splitting the cluster centers and merging them. The high dimensionality of the data has been reduced with the help of Principal Component Analysis (PCA). The classification results have been compared with K-means and Artificial Immune System algorithms. From the results obtained, we conclude that the proposed hierarchical clustering algorithm is accurate.

A nine-level inverter topology for medium-voltage induction motor drive with open-end stator winding

A new scheme for nine-level voltage space-vector generation for medium-voltage induction motor (IM) drives with open-end stator winding is presented in this paper. The proposed nine-level power converter topology consists of two conventional three-phase two-level voltage source inverters powered by isolated dc sources and six floating-capacitor-connected H-bridges. The H-bridge capacitor voltages are effectively maintained at the required asymmetrical levels by employing a space vector modulation (SVPWM) based control strategy. An interesting feature of this topology is its ability to function in five-or three-level mode, in the entire modulation range, at full-power rating, in the event of any failure in the H-bridges. This feature significantly improves the reliability of the proposed drive system. Each leg of the three-phase two-level inverters used in this topology switches only for a half cycle of the reference voltage waveform. Hence, the effective switching frequency is reduced by half, resulting in switching loss reduction in high-voltage devices. The transient as well as the steady-state performance of the proposed nine-level inverter-fed IM drive system is experimentally verified in the entire modulation range including the overmodulation region.