OFDM-based schemes for next generation wireless systems

The purpose of this study is to investigate two candidate waveforms for next generation wireless systems, filtered Orthogonal Frequency Division Multiplexing (f-OFDM) and Unified Filtered Multi-Carrier (UFMC). The evaluation is done based on the power spectral density analysis of the signal and performance measurements in synchronous and asynchronous transmission. In f-OFDM we implement a soft truncated filter with length 1/3 of OFDM symbol. In UFMC we use the Dolph-Chebyshev filter, limited to the length of zero padding (ZP). The simulation results demonstrates that both waveforms have a better spectral behaviour compared with conventional OFDM. However, the induced inter-symbol interference (ISI) caused by the filter in f-OFDM, and the inter-carrier interference (ICI) induced in UFMC due to cyclic prefix (CP) reduction , should be kept under control. In addition, in a synchronous transmission case with ideal parameters, f-OFDM and UFMC appear to have similar performance with OFDM. When carrier frequency offset (CFO) is imposed in the transmission, UFMC outperforms OFDM and f-OFDM.

Next-generation technologies to develop new therapeutics in oncology and cardiology

This is an abstract of a presented talk at the European Biotechnology Conference held in Latvia during 05–07 May 2016

Domestication and the storage starch biosynthesis pathway: Signatures of selection from a whole sorghum genome sequencing strategy

Next-generation sequencing of complete genomes has given researchers unprecedented levels of information to study the multifaceted evolutionary changes that have shaped elite plant germplasm. In conjunction with population genetic analytical techniques and detailed online databases, we can more accurately capture the effects of domestication on entire biological pathways of agronomic importance. In this study, we explore the genetic diversity and signatures of selection in all predicted gene models of the storage starch synthesis pathway of Sorghum bicolor, utilizing a diversity panel containing lines categorized as either ‘Landraces’ or ‘Wild and Weedy’ genotypes. Amongst a total of 114 genes involved in starch synthesis, 71 had at least a single signal of purifying selection and 62 a signal of balancing selection and others a mix of both. This included key genes such as STARCH PHOSPHORYLASE 2 (SbPHO2, under balancing selection), PULLULANASE (SbPUL, under balancing selection) and ADP-glucose pyrophosphorylases (SHRUNKEN2, SbSH2 under purifying selection). Effectively, many genes within the primary starch synthesis pathway had a clear reduction in nucleotide diversity between the Landraces and wild and weedy lines indicating that the ancestral effects of domestication are still clearly identifiable. There was evidence of the positional rate variation within the well-characterized primary starch synthesis pathway of sorghum, particularly in the Landraces, whereby low evolutionary rates upstream and high rates downstream in the metabolic pathway were expected. This observation did not extend to the wild and weedy lines or the minor starch synthesis pathways.

Domestication and the storage starch biosynthesis pathway: signatures of selection from a whole sorghum genome sequencing strategy

Next-generation sequencing of complete genomes has given researchers unprecedented levels of information to study the multifaceted evolutionary changes that have shaped elite plant germplasm. In conjunction with population genetic analytical techniques and detailed online databases, we can more accurately capture the effects of domestication on entire biological pathways of agronomic importance. In this study, we explore the genetic diversity and signatures of selection in all predicted gene models of the storage starch synthesis pathway of Sorghum bicolor, utilizing a diversity panel containing lines categorized as either ‘Landraces’ or ‘Wild and Weedy’ genotypes. Amongst a total of 114 genes involved in starch synthesis, 71 had at least a single signal of purifying selection and 62 a signal of balancing selection and others a mix of both. This included key genes such as STARCH PHOSPHORYLASE 2 (SbPHO2, under balancing selection), PULLULANASE (SbPUL, under balancing selection) and ADP-glucose pyrophosphorylases (SHRUNKEN2, SbSH2 under purifying selection). Effectively, many genes within the primary starch synthesis pathway had a clear reduction in nucleotide diversity between the Landraces and wild and weedy lines indicating that the ancestral effects of domestication are still clearly identifiable. There was evidence of the positional rate variation within the well-characterized primary starch synthesis pathway of sorghum, particularly in the Landraces, whereby low evolutionary rates upstream and high rates downstream in the metabolic pathway were expected. This observation did not extend to the wild and weedy lines or the minor starch synthesis pathways.

Connecting people and ideas from around the world: global innovation platforms for next-generation ecology and beyond

We present a case for using Global Community Innovation Platforms (GCIPs), an approach to improve innovation and knowledge exchange in international scientific communities through a common and open online infrastructure. We highlight the value of GCIPs by focusing on recent efforts targeting the ecological sciences, where GCIPs are of high relevance given the urgent need for interdisciplinary, geographical, and cross-sector collaboration to cope with growing challenges to the environment as well as the scientific community itself. Amidst the emergence of new international institutions, organizations, and meetings, GCIPs provide a stable international infrastructure for rapid and long-term coordination that can be accessed by any individual. This accessibility can be especially important for researchers early in their careers. Recent examples of early-career GCIPs complement an array of existing options for early-career scientists to improve skill sets, increase academic and social impact, and broaden career opportunities. We provide a number of examples of existing early-career initiatives that incorporate elements from the GCIPs approach, and highlight an in-depth case study from the ecological sciences: the International Network of Next-Generation Ecologists (INNGE), initiated in 2010 with support from the International Association for Ecology and 20 member institutions from six continents.

Evolution of genome sequencing techniques

The quality and the speed for genome sequencing has advanced at the same time that technology boundaries are stretched. This advancement has been divided so far in three generations. The first-generation methods enabled sequencing of clonal DNA populations. The second-generation massively increased throughput by parallelizing many reactions while the third-generation methods allow direct sequencing of single DNA molecules. The first techniques to sequence DNA were not developed until the mid-1970s, when two distinct sequencing methods were developed almost simultaneously, one by Alan Maxam and Walter Gilbert, and the other one by Frederick Sanger. The first one is a chemical method to cleave DNA at specific points and the second one uses ddNTPs, which synthesizes a copy from the DNA chain template. Nevertheless, both methods generate fragments of varying lengths that are further electrophoresed. Moreover, it is important to say that until the 1990s, the sequencing of DNA was relatively expensive and it was seen as a long process. Besides, using radiolabeled nucleotides also compounded the problem through safety concerns and prevented the automation. Some advancements within the first generation include the replacement of radioactive labels by fluorescent labeled ddNTPs and cycle sequencing with thermostable DNA polymerase, which allows automation and signal amplification, making the process cheaper, safer and faster. Another method is Pyrosequencing, which is based on the “sequencing by synthesis” principle. It differs from Sanger sequencing, in that it relies on the detection of pyrophosphate release on nucleotide incorporation. By the end of the last millennia, parallelization of this method started the Next Generation Sequencing (NGS) with 454 as the first of many methods that can process multiple samples, calling it the 2º generation sequencing. Here electrophoresis was completely eliminated. One of the methods that is sometimes used is SOLiD, based on sequencing by ligation of fluorescently dye-labeled di-base probes which competes to ligate to the sequencing primer. Specificity of the di-base probe is achieved by interrogating every 1st and 2nd base in each ligation reaction. The widely used Solexa/Illumina method uses modified dNTPs containing so called “reversible terminators” which blocks further polymerization. The terminator also contains a fluorescent label, which can be detected by a camera. Now, the previous step towards the third generation was in charge of Ion Torrent, who developed a technique that is based in a method of “sequencing-by-synthesis”. Its main feature is the detection of hydrogen ions that are released during base incorporation. Likewise, the third generation takes into account nanotechnology advancements for the processing of unique DNA molecules to a real time synthesis sequencing system like PacBio; and finally, the NANOPORE, projected since 1995, also uses Nano-sensors forming channels obtained from bacteria that conducts the sample to a sensor that allows the detection of each nucleotide residue in the DNA strand. The advancements in terms of technology that we have nowadays have been so quick, that it makes wonder: ¿How do we imagine the next generation?

Exploring the environmental diversity of kinetoplastid flagellates in the high-throughput DNA sequencing era

The class Kinetoplastea encompasses both free-living and parasitic species from a wide range of hosts. Several representatives of this group are responsible for severe human diseases and for economic losses in agriculture and livestock. While this group encompasses over 30 genera, most of the available information has been derived from the vertebrate pathogenic genera Leishmania and Trypanosoma. Recent studies of the previously neglected groups of Kinetoplastea indicated that the actual diversity is much higher than previously thought. This article discusses the known segment of kinetoplastid diversity and how gene-directed Sanger sequencing and next-generation sequencing methods can help to deepen our knowledge of these interesting protists.

The Sensing Enterprise: Towards the Next Generation Dynamic Virtual Organisations

Part 6: Engineering and Implementation of Collaborative Networks

Next-generation transcriptome assembly of an Amazon palm (Euterpe precatoria).

2016

FABRICATION, CHARACTERIZATION, AND IRRADIATION OF AN AUSTENITIC OXIDE DISPERSION STRENGTHENED STEEL SUITED FOR NEXT GENERATION NUCLEAR APPLICATIONS

As nuclear energy systems become more advanced, the materials encompassing them need to perform at higher temperatures for longer periods of time. In this Master’s thesis we experiment with an oxide dispersion strengthened (ODS) austenitic steel that has been recently developed. ODS materials have a small concentration of nano oxide particles dispersed in their matrix, and typically have higher strength and better extreme temperature creep resistance characteristics than ordinary steels. However, no ODS materials have ever been installed in a commercial power reactor to date. Being a newer research material, there are many unanswered phenomena that need to be addressed regarding the performance under irradiation. Furthermore, due to the ODS material traditionally needing to follow a powder metallurgy fabrication route, there are many processing parameters that need to be optimized before achieving a nuclear grade material specification. In this Master’s thesis we explore the development of a novel ODS processing technology conducted in Beijing, China, to produce solutionized bulk ODS samples with ~97% theoretical density. This is done using relatively low temperatures and ultra high pressure (UHP) equipment, to compact the mechanically alloyed (MA) steel powder into bulk samples without any thermal phase change influence or oxide precipitation. By having solutionized bulk ODS samples, transmission electron microscopy (TEM) observation of nano oxide precipitation within the steel material can be studied by applying post heat treatments. These types of samples will be very useful to the science and engineering community, to answer questions regarding material powder compacting, oxide synthesis, and performance. Subsequent analysis performed at Queen’s University included X-ray diffraction (XRD) and inductively coupled plasma optical emission spectrometry (ICP-OES). Additional TEM in-situ 1MeV Kr2+ irradiation experiments coupled with energy dispersive X-ray (EDX) techniques, were also performed on large (200nm+) non-stoichiometric oxides embedded within the austenite steel grains, in an attempt to quantify the elemental compositional changes during high temperature (520oC) heavy ion irradiation.

Behavioural outcomes of next-generation family members’ commitment to their firm

Are there variations in behaviours and leadership styles of next-generation family members or descendants who join their family business due to different forms of commitment? Evidence from a dual respondent study of 109 Canadian and Swiss family firms suggests that descendants with affective commitment to their family firms are more likely to engage in discretionary activities going beyond the job description, thereby contributing to organizational performance. Next-generation members with normative commitment are more likely to engage in transformational leadership behaviours. Both affectively and normatively motivated next-generation members use contingent reward forms of leadership. A surprising finding of this study is the binding force of normative commitment on positive leadership behaviours of next-generation members. This study empirically tests the generalizability of the three-component model of commitment to family businesses, a context in which different forms of commitment may play a unique role.

Wireless Network Analytics for Next Generation Spectrum Awareness

The importance of networks, in their broad sense, is rapidly and massively growing in modern-day society thanks to unprecedented communication capabilities offered by technology. In this context, the radio spectrum will be a primary resource to be preserved and not wasted. Therefore, the need for intelligent and automatic systems for in-depth spectrum analysis and monitoring will pave the way for a new set of opportunities and potential challenges. This thesis proposes a novel framework for automatic spectrum patrolling and the extraction of wireless network analytics. It aims to enhance the physical layer security of next generation wireless networks through the extraction and the analysis of dedicated analytical features. The framework consists of a spectrum sensing phase, carried out by a patrol composed of numerous radio-frequency (RF) sensing devices, followed by the extraction of a set of wireless network analytics. The methodology developed is blind, allowing spectrum sensing and analytics extraction of a network whose key features (i.e., number of nodes, physical layer signals, medium access protocol (MAC) and routing protocols) are unknown. Because of the wireless medium, over-the-air signals captured by the sensors are mixed; therefore, blind source separation (BSS) and measurement association are used to estimate the number of sources and separate the traffic patterns. After the separation, we put together a set of methodologies for extracting useful features of the wireless network, i.e., its logical topology, the application-level traffic patterns generated by the nodes, and their position. The whole framework is validated on an ad-hoc wireless network accounting for MAC protocol, packet collisions, nodes mobility, the spatial density of sensors, and channel impairments, such as path-loss, shadowing, and noise. The numerical results obtained by extensive and exhaustive simulations show that the proposed framework is consistent and can achieve the required performance.

Synthetic data generation for the assessment of antimicrobial resistance through machine learning

As a consequence of the diffusion of next generation sequencing techniques, metagenomics databases have become one of the most promising repositories of information about features and behavior of microorganisms. One of the subjects that can be studied from those data are bacteria populations. Next generation sequencing techniques allow to study the bacteria population within an environment by sampling genetic material directly from it, without the needing of culturing a similar population in vitro and observing its behavior. As a drawback, it is quite complex to extract information from those data and usually there is more than one way to do that; AMR is no exception. In this study we will discuss how the quantified AMR, which regards the genotype of the bacteria, can be related to the bacteria phenotype and its actual level of resistance against the specific substance. In order to have a quantitative information about bacteria genotype, we will evaluate the resistome from the read libraries, aligning them against CARD database. With those data, we will test various machine learning algorithms for predicting the bacteria phenotype. The samples that we exploit should resemble those that could be obtained from a natural context, but are actually produced by a read libraries simulation tool. In this way we are able to design the populations with bacteria of known genotype, so that we can relay on a secure ground truth for training and testing our algorithms.

An integrated genomic analysis of human glioblastoma Multiforme

Glioblastoma multiforme ( GBM) is the most common and lethal type of brain cancer. To identify the genetic alterations in GBMs, we sequenced 20,661 protein coding genes, determined the presence of amplifications and deletions using high- density oligonucleotide arrays, and performed gene expression analyses using next- generation sequencing technologies in 22 human tumor samples. This comprehensive analysis led to the discovery of a variety of genes that were not known to be altered in GBMs. Most notably, we found recurrent mutations in the active site of isocitrate dehydrogenase 1 ( IDH1) in 12% of GBM patients. Mutations in IDH1 occurred in a large fraction of young patients and in most patients with secondary GBMs and were associated with an increase in overall survival. These studies demonstrate the value of unbiased genomic analyses in the characterization of human brain cancer and identify a potentially useful genetic alteration for the classification and targeted therapy of GBMs.

Estudo mutacional em tumor de Wilms por sequenciação de nova geração

O Tumor de Wilms (TW) é o tumor renal mais comum da infância, com uma incidência de 1 em ~10000 crianças. Esta patologia é de etiologia genética complexa e diversificada. No entanto, cerca de um terço dos doentes apresenta mutações somáticas associadas aos genes WT1, CTNNB1, TP53 e/ou AMER1. Assim, foi desenvolvido um painel de amplicões destes 4 genes para a identificação de mutações num grupo de doentes portugueses com TW, através de uma metodologia baseada na sequenciação de nova geração. As bibliotecas de DNA foram preparadas a partir de amostras de sangue periférico e tumor de 36 doentes com TW e sequenciadas no MiSeq. Foram identificadas alterações somáticas em 7 dos 36 (19,4%) doentes estudados. Conclui-se que a sequenciação de um painel de genes é um método rápido para a deteção de mutações somáticas quando desenhado com cuidado de forma a serem evitados problemas de perda de cobertura.