The dynamic decode-and-forward channel: SNR allocation.

In the half-duplex relay channel applying the decode-and-forward protocol the relay introduces energy over random time intervals into the channel as observed at the destination. Consequently, during simulation the average signal power seen at the destination becomes known at run-time only. Therefore, in order to obtain specific performance measures at the signal-to-noise ratio (SNR) of interest, strategies are required to adjust the noise variance during simulation run-time. It is necessary that these strategies result in the same performance as measured under real-world conditions. This paper introduces three noise power allocation strategies and demonstrates their applicability using numerical and simulation results.

Real-Time PCR Assays for the Detection of Puccinia psidii

Puccinia psidii (Myrtle rust) is an emerging pathogen that has a wide host range in the Myrtaceae family; it continues to show an increase in geographic range and is considered to be a significant threat to Myrtaceae plants worldwide. In this study, we describe the development and validation of three novel real-time polymerase reaction (qPCR) assays using ribosomal DNA and β-tubulin gene sequences to detect P. psidii. All qPCR assays were able to detect P. psidii DNA extracted from urediniospores and from infected plants, including asymptomatic leaf tissues. Depending on the gene target, qPCR was able to detect down to 0.011 pg of P. psidii DNA. The most optimum qPCR assay was shown to be highly specific, repeatable, and reproducible following testing using different qPCR reagents and real-time PCR platforms in different laboratories. In addition, a duplex qPCR assay was developed to allow coamplification of the cytochrome oxidase gene from host plants for use as an internal PCR control. The most optimum qPCR assay proved to be faster and more sensitive than the previously published nested PCR assay and will be particularly useful for high-throughput testing and to detect P. psidii at the early stages of infection, before the development of sporulating rust pustules.

Telesia Archaeological Project: Indagini nella basilica e nel foro (2014-2015)

The Telesia Archaeological Project is an initiative that will make a significant contribution to thi historical and archaeological knowledge of the urban area of the Roman city of Telesia, located near Benevento (S. Salvatore Telesino). The first and second season of the Telesia Archaeological Project (2014-2015), conducted under the supervision of the Archaeological Superintendence, and thanks to the indispensable collaboration of a private landowner, provided results of great scientific interest. There was the possibility to investigate part of a significant building of imperial age, richly decorated, identified with the basilica of the city. It was possible to establish, in addition, that this large building (36 by 21 m ca) was opened, through a great brick colonnade, to the forum, localized in summer 2015 with certainty for the first time. The extraordinary large double colonnade (porticus duplex), 9 meters wide, covering the entire façade of that public building, was erased in the fifth century AD, probably after two earthquakes that seriously damaged the city in 346 and 375 AD.

Efeitos da simpaticotomia endoscópica sobre as artérias carótidas e vertebrais na terapêutica cirúrgica da hiperidrose primária

Analisar, em pacientes submetidos a simpaticotomia videotoracoscópica para tratamento da Hiperidrose Primária (HP), as conseqüências hemodinâmicas da desnervação vascular das artérias carótidas e vertebrais após a trans-secção cirúrgica da cadeia simpática torácica (simpaticotomia), através da mensuração de parâmetros ultra-sonográficos. Método: Vinte e quatro pacientes portadores de HP submetidos a quarenta e oito simpaticotomias torácicas endoscópicas foram avaliados através da mensuração da velocidade de pico sistólico (VPS), velocidade de pico diastólico (VPD), índice de pulsatibilidade (IP) e índice de resistência (IR) nas artérias carótidas comuns, internas e externas, além da artéria vertebral bilateralmente usando o eco-doppler duplex scan. As avaliações foram realizadas antes da intervenção cirúrgica e trinta dias após o procedimento. O teste de Wilcoxon foi usado na análise das diferenças entre as variáveis antes e depois da simpaticotomia. Resultados: A simpaticotomia no nível de T3 foi a trans-secção mais realizada (95,83%), seja isoladamente (25%) ou associada a T4 (62,50%) ou a T2 (8,33%). Houve aumento significativo no IR e no IP da artéria carótida comum bilateralmente (p<0,05). A VPD da artéria carótida interna diminuiu em ambos os lados (p<0,05). A VPS e a VPD da artéria vertebral direita também aumentaram (p<0,05). Achados assimétricos foram observados, de modo que artérias do lado direito foram as mais freqüentemente afetadas. Conclusões: Alterações hemodinâmicas foram observadas nas artérias vertebral e carótida após simpaticotomia para tratamento de HP. VPS foi o parâmetro mais freqüentemente alterado, principalmente nas artérias do lado direito, representando alterações assimétricas significantes nas artérias carótida e vertebral. Entretanto, são necessárias pesquisas subseqüentes para verificar se essas alterações são definitivas ou temporárias, uma vez que as inferências clínicas somente terão validação se as alterações forem permanentes

Nonlinear breathing modes at a defect

Recent molecular dynamics (MD) simulations of Cubero et al (1999) of a DNA duplex containing the 'rogue' base difluorotoluene (F) in place of a thymine (T) base show that breathing events can occur on the nanosecond timescale, whereas breathing events in a normal DNA duplex take place on the microsecond timescale. The main aim of this paper is to analyse a nonlinear Klein-Gordon lattice model of the DNA duplex including both nonlinear interactions between opposing bases and a defect in the interaction at one lattice site; each of which can cause localisation of energy. Solutions for a breather mode either side of the defect are derived using multiple-scales asymptotics and are pieced together across the defect to form a solution which includes the effects of the nonlinearity and the defect. We consider defects in the inter-chain interactions and in the along chain interactions. In most cases we find in-phase breather modes and/or out-of-phase breather modes, with one case displaying a shifted mode.

The Bacillus subtilis primosomal protein DnaD untwists supercoiled DNA

The essential Bacillus subtilis DnaD and DnaB proteins have been implicated in the initiation of DNA replication. Recently, DNA remodeling activities associated with both proteins were discovered that could provide a link between global or local nucleoid remodeling and initiation of replication. DnaD forms scaffolds and opens up supercoiled plasmids without nicking to form open circular complexes, while DnaB acts as a lateral compaction protein. Here we show that DnaD-mediated opening of supercoiled plasmids is accompanied by significant untwisting of DNA. The net result is the conversion of writhe (Wr) into negative twist (Tw), thus maintaining the linking number (Lk) constant. These changes in supercoiling will reduce the considerable energy required to open up closed circular plectonemic DNA and may be significant in the priming of DNA replication. By comparison, DnaB does not affect significantly the supercoiling of plasmids. Binding of the DnaD C-terminal domain (Cd) to DNA is not sufficient to convert Wr into negative Tw, implying that the formation of scaffolds is essential for duplex untwisting. Overall, our data suggest that the topological effects of the two proteins on supercoiled DNA are different; DnaD opens up, untwists and converts plectonemic DNA to a more paranemic form, whereas DnaB does not affect supercoiling significantly and condenses DNA only via its lateral compaction activity. The significance of these findings in the initiation of DNA replication is discussed.

OriDB: a DNA replication origin database

Replication of eukaryotic chromosomes initiates at multiple sites called replication origins. Replication origins are best understood in the budding yeast Saccharomyces cerevisiae, where several complementary studies have mapped their locations genome-wide. We have collated these datasets, taking account of the resolution of each study, to generate a single list of distinct origin sites. OriDB provides a web-based catalogue of these confirmed and predicted S.cerevisiae DNA replication origin sites. Each proposed or confirmed origin site appears as a record in OriDB, with each record comprising seven pages. These pages provide, in text and graphical formats, the following information: genomic location and chromosome context of the origin site; time of origin replication; DNA sequence of proposed or experimentally confirmed origin elements; free energy required to open the DNA duplex (stress-induced DNA duplex destabilization or SIDD); and phylogenetic conservation of sequence elements. In addition, OriDB encourages community submission of additional information for each origin site through a User Notes facility. Origin sites are linked to several external resources, including the Saccharomyces Genome Database (SGD) and relevant publications at PubMed. Finally, a Chromosome Viewer utility allows users to interactively generate graphical representations of DNA replication data genome-wide. OriDB is available at www.oridb.org.

Current trends in machinability research

The manufacturing index of a country relies on the quality of manufacturing research outputs. Theemergence of new materials such as composites and multi component alloy has replaced traditionalmaterials in certain design application. Materials with properties like high strength to weight ratio,fatigue strength, wear resistance, thermal stability and damping capacity are a popular choice for adesign engineer. Contrary, the manufacturing engineer is novice to the science of machining thesematerials. This paper is an attempt to focus on the current trends in machinability research and anaddition to the existing information on machining. The paper consist of information on machiningAustempered Ductile Iron (ADI), Duplex Stainless Steel and Nano-Structured Bainitic Steel. Thevarious techniques used to judge the machinability of these materials is described in this paper.Studying the chip formation process in duplex steel using a quick stop device, metallographic analysisusing heat tinting of ADI and cutting force analysis of Nano-structured bainitic steel is discussed.

Initiation and early crack growth in VHCF of stainless steels : Experimental and theoretical analysis

Mechanical fatigue is a failure phenomenon that occurs due to repeated application of mechanical loads. Very High Cycle Fatigue (VHCF) is considered as the domain of fatigue life greater than 10 million load cycles. Increasing numbers of structural components have service life in the VHCF regime, for instance in automotive and high speed train transportation, gas turbine disks, and components of paper production machinery. Safe and reliable operation of these components depends on the knowledge of their VHCF properties. In this thesis both experimental tools and theoretical modelling were utilized to develop better understanding of the VHCF phenomena. In the experimental part, ultrasonic fatigue testing at 20 kHz of cold rolled and hot rolled stainless steel grades was conducted and fatigue strengths in the VHCF regime were obtained. The mechanisms for fatigue crack initiation and short crack growth were investigated using electron microscopes. For the cold rolled stainless steels crack initiation and early growth occurred through the formation of the Fine Granular Area (FGA) observed on the fracture surface and in TEM observations of cross-sections. The crack growth in the FGA seems to control more than 90% of the total fatigue life. For the hot rolled duplex stainless steels fatigue crack initiation occurred due to accumulation of plastic fatigue damage at the external surface, and early crack growth proceeded through a crystallographic growth mechanism. Theoretical modelling of complex cracks involving kinks and branches in an elastic half-plane under static loading was carried out by using the Distributed Dislocation Dipole Technique (DDDT). The technique was implemented for 2D crack problems. Both fully open and partially closed crack cases were analyzed. The main aim of the development of the DDDT was to compute the stress intensity factors. Accuracy of 2% in the computations was attainable compared to the solutions obtained by the Finite Element Method.

Improving safety and establishing episomal maintenance of Adeno-associated viral vectors

Adeno-associated viral (AAV) vectors are among the most widely used gene transfer systems in basic and pre-clinical research and have been employed in more than 160 clinical trials. AAV vectors are commonly produced in producer cell lines like HEK293 by co-transfection with a so-called vector plasmid and one (in this work) or two so-called helper plasmids. The vector plasmid contains the transgene cassette of interest (TEC) flanked by AAV’s inverted terminal repeats (ITRs) which serve as packaging signals, whereas the helper plasmid provides the required AAV and helper virus functions in trans. A pivotal aspect of AAV vectorology is the manufacturing of AAV vectors free from impurities arising during the production process. These impurities include AAV vector preparations that contain capsids containing prokaryotic sequences, e.g. antibiotic resistance genes originating from the producer plasmids. In the first part of the thesis we aimed at improving the safety of AAV vectors. As we found that encapsidated prokaryotic sequences (using the ampicillin resistance gene as indicator) cannot be re-moved by standard purification methods we investigated whether the producer plasmids could be replaced by Minicircles (MCs). MCs are circular DNA constructs which contain no functional or coding prokaryotic sequences; they only consist of the TEC and a short sequence required for production and purification. MC counterparts of a vector plasmid encoding for enhanced green fluorescent (eGFP) protein and a helper plasmid encoding for AAV serotype 2 (AAV2) and helper Adenovirus (Ad) genes were designed and produced by PlasmidFactory (Bielefeld, Germany). Using all four possible combinations of plasmid and MCs, single-stranded AAV2 vectors (ssAAV) and self-complementary AAV vectors (scAAV) were produced and characterized for vector quantity, quality and functionality. The analyses showed that plasmids can be replaced by MCs without decreasing the efficiency of vector production and vector quality. MC-derived scAAV vector preparations even exceeded plasmid-derived preparations, as they displayed up to 30-fold improved transduction efficiencies. Using MCs as tools, we found that the vector plasmid is the main source of encapsidated prokaryotic sequences. Remarkably, we found that plasmid-derived scAAV vector preparations contained a much higher relative amount of prokaryotic sequences (up to 26.1 %, relative to TEC) compared to ssAAV vector preparations (up to 2.9 %). By replacing both plasmids by MCs the amount of functional prokaryotic sequences could be decreased to below the limit of quantification. Additional analyses for DNA impurities other than prokaryotic sequences showed that scAAV vectors generally contained a higher amount of non-vector DNA (e.g. adenoviral sequences) than ssAAV vectors. For both, ssAAV and scAAV vector preparations, MC-derived vectors tended to contain lower amounts of foreign DNA. None of the vectors tested could be shown to induce immunogenicity. In summary we could demonstrate that the quality of AAV vector preparations could be significantly improved by replacing producer plasmids by MCs. Upon transduction of a target tissue, AAV vector genomes predominantly remain in an episomal state, as duplex DNA circles or concatemers. These episomal forms mediate long-term transgene expression in terminally differentiated cells, but are lost in proliferating cells due to cell division. Therefore, in the second part of the thesis, in cooperation with Claudia Hagedorn and Hans J. Lipps (University Witten/Herdecke) an AAV vector genome was equipped with an autonomous replication element (Scaffold/matrix attachment region (S/MAR)). AAV-S/MAR encoding for eGFP and a blasticidin resistance gene and a control vector with the same TEC but lacking the S/MAR element (AAV-ΔS/MAR) were produced and transduced into highly proliferative HeLa cells. Antibiotic pressure was employed to select for cells stably maintaining the vector genome. AAV-S/MAR transduced cells yielded a higher number of colonies than AAV-ΔS/MAR-transduced cells. Colonies derived from each vector transduction were picked and cultured further. They remained eGFP-positive (up to 70 days, maximum cultivation period) even in the absence of antibiotic selection pressure. Interestingly, the mitotic stability of both AAV-S/MAR and control vector AAV-ΔS/MAR was found to be a result of episomal maintenance of the vector genome. This finding indicates that, under specific conditions such as the mild selection pressure we employed, “common” AAV vectors persist episomally. Thus, the S/MAR element increases the establishment frequency of stable episomes, but is not a prerequisite.