Leveraging coherent distributed space-time codes for noncoherent communication in relay networks via training

For point to point multiple input multiple output systems, Dayal-Brehler-Varanasi have proved that training codes achieve the same diversity order as that of the underlying coherent space time block code (STBC) if a simple minimum mean squared error estimate of the channel formed using the training part is employed for coherent detection of the underlying STBC. In this letter, a similar strategy involving a combination of training, channel estimation and detection in conjunction with existing coherent distributed STBCs is proposed for noncoherent communication in Amplify-and-Forward (AF) relay networks. Simulation results show that the proposed simple strategy outperforms distributed differential space-time coding for AF relay networks. Finally, the proposed strategy is extended to asynchronous relay networks using orthogonal frequency division multiplexing.

A high-density consensus map of barley linking DArT markers to SSR, RFLP and STS loci and agricultural traits

Background: Molecular marker technologies are undergoing a transition from largely serial assays measuring DNA fragment sizes to hybridization-based technologies with high multiplexing levels. Diversity Arrays Technology (DArT) is a hybridization-based technology that is increasingly being adopted by barley researchers. There is a need to integrate the information generated by DArT with previous data produced with gel-based marker technologies. The goal of this study was to build a high-density consensus linkage map from the combined datasets of ten populations, most of which were simultaneously typed with DArT and Simple Sequence Repeat (SSR), Restriction Enzyme Fragment Polymorphism (RFLP) and/or Sequence Tagged Site (STS) markers. Results: The consensus map, built using a combination of JoinMap 3.0 software and several purpose-built perl scripts, comprised 2,935 loci (2,085 DArT, 850 other loci) and spanned 1,161 cM. It contained a total of 1,629 'bins' (unique loci), with an average inter-bin distance of 0.7 ± 1.0 cM (median = 0.3 cM). More than 98% of the map could be covered with a single DArT assay. The arrangement of loci was very similar to, and almost as optimal as, the arrangement of loci in component maps built for individual populations. The locus order of a synthetic map derived from merging the component maps without considering the segregation data was only slightly inferior. The distribution of loci along chromosomes indicated centromeric suppression of recombination in all chromosomes except 5H. DArT markers appeared to have a moderate tendency toward hypomethylated, gene-rich regions in distal chromosome areas. On the average, 14 ± 9 DArT loci were identified within 5 cM on either side of SSR, RFLP or STS loci previously identified as linked to agricultural traits. Conclusion: Our barley consensus map provides a framework for transferring genetic information between different marker systems and for deploying DArT markers in molecular breeding schemes. The study also highlights the need for improved software for building consensus maps from high-density segregation data of multiple populations.

DArT markers: Diversity analyses and mapping in Sorghum bicolor

The sequential nature of gel-based marker systems entails low throughput and high costs per assay. Commonly used marker systems such as SSR and SNP are also dependent on sequence information. These limitations result in high cost per data point and significantly limit the capacity of breeding programs to obtain sufficient return on investment to justify the routine use of marker-assisted breeding for many traits and particularly quantitative traits. Diversity Arrays Technology (DArT™) is a cost effective hybridisation-based marker technology that offers a high multiplexing level while being independent of sequence information. This technology offers sorghum breeding programs an alternative approach to whole-genome profiling. We report on the development, application, mapping and utility of DArT™ markers for sorghum germplasm. Results: A genotyping array was developed representing approximately 12,000 genomic clones using PstI+BanII complexity with a subset of clones obtained through the suppression subtractive hybridisation (SSH) method. The genotyping array was used to analyse a diverse set of sorghum genotypes and screening a Recombinant Inbred Lines (RIL) mapping population. Over 500 markers detected variation among 90 accessions used in a diversity analysis. Cluster analysis discriminated well between all 90 genotypes. To confirm that the sorghum DArT markers behave in a Mendelian manner, we constructed a genetic linkage map for a cross between R931945-2-2 and IS 8525 integrating DArT and other marker types. In total, 596 markers could be placed on the integrated linkage map, which spanned 1431.6 cM. The genetic linkage map had an average marker density of 1/2.39 cM, with an average DArT marker density of 1/3.9 cM. Conclusion: We have successfully developed DArT markers for Sorghum bicolor and have demonstrated that DArT provides high quality markers that can be used for diversity analyses and to construct medium-density genetic linkage maps. The high number of DArT markers generated in a single assay not only provides a precise estimate of genetic relationships among genotypes, but also their even distribution over the genome offers real advantages for a range of molecular breeding and genomics applications.

Space-Time Codes Achieving the DMD Tradeoff of the MIMO-ARQ Channel

For the quasi-static, Rayleigh-fading multiple-input multiple-output (MIMO) channel with n(t) transmit and n(r) receive antennas, Zheng and Tse showed that there exists a fundamental tradeoff between diversity and spatial-multiplexing gains, referred to as the diversity-multiplexing gain (D-MG) tradeoff. Subsequently, El Gamal, Caire, and Damen considered signaling across the same channel using an L-round automatic retransmission request (ARQ) protocol that assumes the presence of a noiseless feedback channel capable of conveying one bit of information per use of the feedback channel. They showed that given a fixed number L of ARQ rounds and no power control, there is a tradeoff between diversity and multiplexing gains, termed the diversity-multiplexing-delay (DMD) tradeoff. This tradeoff indicates that the diversity gain under the ARQ scheme for a particular information rate is considerably larger than that obtainable in the absence of feedback. In this paper, a set of sufficient conditions under which a space-time (ST) code will achieve the DMD tradeoff is presented. This is followed by two classes of explicit constructions of ST codes which meet these conditions. Constructions belonging to the first class achieve minimum delay and apply to a broad class of fading channels whenever n(r) >= n(t) and either L/n(t) or n(t)kslashL. The second class of constructions do not achieve minimum delay, but do achieve the DMD tradeoff of the fading channel for all statistical descriptions of the channel and for all values of the parameters n(r,) n(t,) L.

D-MG Tradeoff and Optimal Codes for a Class of AF and DF Cooperative Communication Protocols

Cooperative relay communication in a fading channel environment under the orthogonal amplify-and-forward (OAF), nonorthogonal and orthogonal selection decode-and-forward (NSDF and OSDF) protocols is considered here. The diversity-multiplexing gain tradeoff (DMT) of the three protocols is determined and DMT-optimal distributed space-time (ST) code constructions are provided. The codes constructed are sphere decodable and in some instances incur minimum possible delay. Included in our results is the perhaps surprising finding that the orthogonal and the nonorthogonal amplify-and-forward (NAF) protocols have identical DMT when the time durations of the broadcast and cooperative phases are optimally chosen to suit the respective protocol. Moreover our code construction for the OAF protocol incurs less delay. Two variants of the NSDF protocol are considered: fixed-NSDF and variable-NSDF protocol. In the variable-NSDF protocol, the fraction of time occupied by the broadcast phase is allowed to vary with multiplexing gain. The variable-NSDF protocol is shown to improve on the DMT of the best previously known static protocol when the number of relays is greater than two. Also included is a DMT optimal code construction for the NAF protocol.

Genotyping for genetic association studies: Methods and applications

In this thesis, two separate single nucleotide polymorphism (SNP) genotyping techniques were set up at the Finnish Genome Center, pooled genotyping was evaluated as a screening method for large-scale association studies, and finally, the former approaches were used to identify genetic factors predisposing to two distinct complex diseases by utilizing large epidemiological cohorts and also taking environmental factors into account. The first genotyping platform was based on traditional but improved restriction-fragment-length-polymorphism (RFLP) utilizing 384-microtiter well plates, multiplexing, small reaction volumes (5 µl), and automated genotype calling. We participated in the development of the second genotyping method, based on single nucleotide primer extension (SNuPeTM by Amersham Biosciences), by carrying out the alpha- and beta tests for the chemistry and the allele-calling software. Both techniques proved to be accurate, reliable, and suitable for projects with thousands of samples and tens of markers. Pooled genotyping (genotyping of pooled instead of individual DNA samples) was evaluated with Sequenom s MassArray MALDI-TOF, in addition to SNuPeTM and PCR-RFLP techniques. We used MassArray mainly as a point of comparison, because it is known to be well suited for pooled genotyping. All three methods were shown to be accurate, the standard deviations between measurements being 0.017 for the MassArray, 0.022 for the PCR-RFLP, and 0.026 for the SNuPeTM. The largest source of error in the process of pooled genotyping was shown to be the volumetric error, i.e., the preparation of pools. We also demonstrated that it would have been possible to narrow down the genetic locus underlying congenital chloride diarrhea (CLD), an autosomal recessive disorder, by using the pooling technique instead of genotyping individual samples. Although the approach seems to be well suited for traditional case-control studies, it is difficult to apply if any kind of stratification based on environmental factors is needed. Therefore we chose to continue with individual genotyping in the following association studies. Samples in the two separate large epidemiological cohorts were genotyped with the PCR-RFLP and SNuPeTM techniques. The first of these association studies concerned various pregnancy complications among 100,000 consecutive pregnancies in Finland, of which we genotyped 2292 patients and controls, in addition to a population sample of 644 blood donors, with 7 polymorphisms in the potentially thrombotic genes. In this thesis, the analysis of a sub-study of pregnancy-related venous thromboses was included. We showed that the impact of factor V Leiden polymorphism on pregnancy-related venous thrombosis, but not the other tested polymorphisms, was fairly large (odds ratio 11.6; 95% CI 3.6-33.6), and increased multiplicatively when combined with other risk factors such as obesity or advanced age. Owing to our study design, we were also able to estimate the risks at the population level. The second epidemiological cohort was the Helsinki Birth Cohort of men and women who were born during 1924-1933 in Helsinki. The aim was to identify genetic factors that might modify the well known link between small birth size and adult metabolic diseases, such as type 2 diabetes and impaired glucose tolerance. Among ~500 individuals with detailed birth measurements and current metabolic profile, we found that an insertion/deletion polymorphism of the angiotensin converting enzyme (ACE) gene was associated with the duration of gestation, and weight and length at birth. Interestingly, the ACE insertion allele was also associated with higher indices of insulin secretion (p=0.0004) in adult life, but only among individuals who were born small (those among the lowest third of birth weight). Likewise, low birth weight was associated with higher indices of insulin secretion (p=0.003), but only among carriers of the ACE insertion allele. The association with birth measurements was also found with a common haplotype of the glucocorticoid receptor (GR) gene. Furthermore, the association between short length at birth and adult impaired glucose tolerance was confined to carriers of this haplotype (p=0.007). These associations exemplify the interaction between environmental factors and genotype, which, possibly due to altered gene expression, predisposes to complex metabolic diseases. Indeed, we showed that the common GR gene haplotype associated with reduced mRNA expression in thymus of three individuals (p=0.0002).

Ternary function and circuit design using ternary multiplexers

The recent trend towards minimizing the interconnections in large scale integration (LSI) circuits has led to intensive investigation in the development of ternary circuits and the improvement of their design. The ternary multiplexer is a convenient and useful logic module which can be used as a basic building block in the design of a ternary system. This paper discusses a systematic procedure for the simplification and realization of ternary functions using ternary multiplexers as building blocks. Both single level and multilevel multiplexing techniques are considered. The importance of the design procedure is highlighted by considering two specific applications, namely, the development of ternary adder/subtractor and TCD to ternary converter.

A Novel Opto Electro Mechanical Interrogation System for Measuring Wavelength Shifts in Fiber Bragg Grating (FBG) Sensors

Here, we describe a novel FBG interrogation system in which FBGs are used as both sensing and reference elements. The reference FBGs is bonded to a mechanical flexure system having a linear amplification of 1:3.5, which is actuated using a piezo-actuator by applying a 0-150V ramp. The lengths of the reference gratings decide the maximum strain that can be applied to the reference grating, which in turn decides that strain range which can be interrogated. The main advantages of the present system are the on-line measurement of the wavelength shifts, small size, good sensitivity, multiplexing capability and low cost.

Comparative and functional genome analysis of fungi for development of the protein production host Trichoderma reesei

Filamentous fungi of the subphylum Pezizomycotina are well known as protein and secondary metabolite producers. Various industries take advantage of these capabilities. However, the molecular biology of yeasts, i.e. Saccharomycotina and especially that of Saccharomyces cerevisiae, the baker's yeast, is much better known. In an effort to explain fungal phenotypes through their genotypes we have compared protein coding gene contents of Pezizomycotina and Saccharomycotina. Only biomass degradation and secondary metabolism related protein families seem to have expanded recently in Pezizomycotina. Of the protein families clearly diverged between Pezizomycotina and Saccharomycotina, those related to mitochondrial functions emerge as the most prominent. However, the primary metabolism as described in S. cerevisiae is largely conserved in all fungi. Apart from the known secondary metabolism, Pezizomycotina have pathways that could link secondary metabolism to primary metabolism and a wealth of undescribed enzymes. Previous studies of individual Pezizomycotina genomes have shown that regardless of the difference in production efficiency and diversity of secreted proteins, the content of the known secretion machinery genes in Pezizomycotina and Saccharomycotina appears very similar. Genome wide analysis of gene products is therefore needed to better understand the efficient secretion of Pezizomycotina. We have developed methods applicable to transcriptome analysis of non-sequenced organisms. TRAC (Transcriptional profiling with the aid of affinity capture) has been previously developed at VTT for fast, focused transcription analysis. We introduce a version of TRAC that allows more powerful signal amplification and multiplexing. We also present computational optimisations of transcriptome analysis of non-sequenced organism and TRAC analysis in general. Trichoderma reesei is one of the most commonly used Pezizomycotina in the protein production industry. In order to understand its secretion system better and find clues for improvement of its industrial performance, we have analysed its transcriptomic response to protein secretion stress conditions. In comparison to S. cerevisiae, the response of T. reesei appears different, but still impacts on the same cellular functions. We also discovered in T. reesei interesting similarities to mammalian protein secretion stress response. Together these findings highlight targets for more detailed studies.

Low ML-Decoding Complexity, Large Coding Gain, Full-Rate, Full-Diversity STBCs for 2 x 2 and 4 x 2 MIMO Systems

This paper deals with low maximum-likelihood (ML)-decoding complexity, full-rate and full-diversity space-time block codes (STBCs), which also offer large coding gain, for the 2 transmit antenna, 2 receive antenna (2 x 2) and the 4 transmit antenna, 2 receive antenna (4 x 2) MIMO systems. Presently, the best known STBC for the 2 2 system is the Golden code and that for the 4 x 2 system is the DjABBA code. Following the approach by Biglieri, Hong, and Viterbo, a new STBC is presented in this paper for the 2 x 2 system. This code matches the Golden code in performance and ML-decoding complexity for square QAM constellations while it has lower ML-decoding complexity with the same performance for non-rectangular QAM constellations. This code is also shown to be information-lossless and diversity-multiplexing gain (DMG) tradeoff optimal. This design procedure is then extended to the 4 x 2 system and a code, which outperforms the DjABBA code for QAM constellations with lower ML-decoding complexity, is presented. So far, the Golden code has been reported to have an ML-decoding complexity of the order of for square QAM of size. In this paper, a scheme that reduces its ML-decoding complexity to M-2 root M is presented.

Diversity and degrees of freedom of cooperative wireless networks

Two key parameters in the outage characterization of a wireless fading network are the diversity and the degrees of freedom (DOF). These two quantities represent the two endpoints of the diversity multiplexing gain tradeoff, In this paper, we present max-flow min-cut type theorems for computing both the diversity and the DOF of arbitrary single-source single-sink networks with nodes possessing multiple antennas. We also show that an amplify-and-forward protocol is sufficient to achieve the same. The DOF characterization is obtained using a conversion to a deterministic wireless network for which the capacity was recently found. This conversion is operational in the sense that a capacity-achieving scheme for the deterministic network can be converted into a DOF-achieving scheme for the fading network. We also show that the diversity result easily extends to multisource multi-sink networks whereas the DOF result extends to a single-source multi-cast network. Along the way, we prove that the zero error capacity of the deterministic network is the same as its c-error capacity.

DMT of Multi-hop Cooperative Networks-Part II: Layered and Multi-Antenna Networks

We consider single-source, single-sink (ss-ss) multi-hop relay networks, with slow-fading Rayleigh links. This two part paper aims at giving explicit protocols and codes to achieve the optimal diversity-multiplexing tradeoff (DMT) of two classes of multi-hop networks: K-parallel-path (KPP) networks and Layered networks. While single-antenna KPP networks were the focus of the first part, we consider layered and multi-antenna networks in this second part. We prove that a linear DMT between the maximum diversity d(max). and the maximum multiplexing gain of 1 is achievable for single-antenna fully-connected layered networks under the half-duplex constraint. This is shown to be equal to the optimal DMT if the number of relaying layers is less than 4. For the multiple-antenna case, we provide an achievable DMT, which is significantly better than known lower bounds for half duplex networks. Along the way, we compute the DMT of parallel MIMO channels in terms of the DMT of the component channel. For arbitrary ss-ss single-antenna directed acyclic networks with full-duplex relays, we prove that a linear tradeoff between maximum diversity and maximum multiplexing gain is achievable using an amplify-and-forward (AF) protocol. Explicit short-block-length codes are provided for all the proposed protocols. Two key implications of the results in the two-part paper are that the half-duplex constraint does not necessarily entail rate loss by a factor of two as previously believed and that simple AN protocols are often sufficient to attain the best possible DMT.

DMT of Multi-hop Cooperative Networks-Part I: K-Parallel-Path Networks

We consider single-source, single-sink multi-hop relay networks, with slow-fading Rayleigh fading links and single-antenna relay nodes operating under the half-duplex constraint. While two hop relay networks have been studied in great detail in terms of the diversity-multiplexing tradeoff (DMT), few results are available for more general networks. In this two-part paper, we identify two families of networks that are multi-hop generalizations of the two hop network: K-Parallel-Path (KPP) networks and Layered networks. In the first part, we initially consider KPP networks, which can be viewed as the union of K node-disjoint parallel paths, each of length > 1. The results are then generalized to KPP(I) networks, which permit interference between paths and to KPP(D) networks, which possess a direct link from source to sink. We characterize the optimal DMT of KPP(D) networks with K >= 4, and KPP(I) networks with K >= 3. Along the way, we derive lower bounds for the DMT of triangular channel matrices, which are useful in DMT computation of various protocols. As a special case, the DMT of two-hop relay network without direct link is obtained. Two key implications of the results in the two-part paper are that the half-duplex constraint does not necessarily entail rate loss by a factor of two, as previously believed and that, simple AF protocols are often sufficient to attain the best possible DMT.

MAC design for heterogeneous application support in OFDM based wireless systems

With the increasing adoption of wireless technology, it is reasonable to expect an increase in file demand for supporting both real-time multimedia and high rate reliable data services. Next generation wireless systems employ Orthogonal Frequency Division Multiplexing (OFDM) physical layer owing, to the high data rate transmissions that are possible without increase in bandwidth. Towards improving file performance of these systems, we look at the design of resource allocation algorithms at medium-access layer, and their impact on higher layers. While TCP-based clastic traffic needs reliable transport, UDP-based real-time applications have stringent delay and rate requirements. The MAC algorithms while catering to the heterogeneous service needs of these higher layers, tradeoff between maximizing the system capacity and providing fairness among users. The novelly of this work is the proposal of various channel-aware resource allocation algorithms at the MAC layer. which call result in significant performance gains in an OFDM based wireless system.

OFDM Based Distributed Space Time Coding for Asynchronous Relay Networks

Recently Li and Xia have proposed a transmission scheme for wireless relay networks based on the Alamouti space time code and orthogonal frequency division multiplexing to combat the effect of timing errors at the relay nodes. This transmission scheme is amazingly simple and achieves a diversity order of two for any number of relays. Motivated by its simplicity, this scheme is extended to a more general transmission scheme that can achieve full cooperative diversity for any number of relays. The conditions on the distributed space time block code (DSTBC) structure that admit its application in the proposed transmission scheme are identified and it is pointed out that the recently proposed full diversity four group decodable DST-BCs from precoded co-ordinate interleaved orthogonal designs and extended Clifford algebras satisfy these conditions. It is then shown how differential encoding at the source can be combined with the proposed transmission scheme to arrive at a new transmission scheme that can achieve full cooperative diversity in asynchronous wireless relay networks with no channel information and also no timing error knowledge at the destination node. Finally, four group decodable distributed differential space time block codes applicable in this new transmission scheme for power of two number of relays are also provided.