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The establishment and maintenance of biobanks is only as worthwhile as the security and logging of the biobank contents. We have designed a monitoring system that continuously measures temperature and gas content, records the movement of samples in and out of the biobank, and also records the opening and closing of the freezers-storing the results and images in a database. We have also incorporated an early warning feature that sends out alerts, via SMS and email, to responsible persons if any measurement is recorded outside the acceptable limits, guaranteeing the integrity of biobanked samples, as well as reagents used in sample analysis. A surveillance system like this increases the value for any biobank as the initial investment is small and the value of having trustworthy samples for future research is high.

The extremely high permittivity of ferroelectric varactors (typically ϵr > 100) imposes specific design and fabrication constraints for microwave and millimeter-wave applications. In this paper, small-size parallel-plate ferroelectric varactors insensitive to fabrication misalignment tolerances are studied experimentally. It is shown that the total resistance of the varactors strongly depends on the shape factor of the plates. Moreover, due to the small sizes of the varactors, the interconnecting strips become narrow and their contribution to the total resistance dominates. A simple procedure for optimization of the shape factor to minimize the varactor resistance is proposed.

Oscillators based on AlN thin-film bulk acoustic resonators are designed, fabricated and measured. The circuits are realised as silicon-on-silicon multichip modules where SiGe transistors are flip-chip mounted on a novel carrier substrate which includes monolithically integrated resonators and passive components. The paper describes the development and processing of the carrier substrate and resonators, as well as the development of the oscillator circuits.

Metagenomics, the sequence characterization of all genomes within a sample, is widely used as a virus discovery tool as well as a tool to study viral diversity of animals. Metagenomics can be considered to have three main steps; sample collection and preparation, sequencing and finally bioinformatics. Bioinformatic analysis of metagenomic datasets is in itself a complex process, involving few standardized methodologies, thereby hampering comparison of metagenomics studies between research groups. In this publication the new bioinformatics framework MetLab is presented, aimed at providing scientists with an integrated tool for experimental design and analysis of viral metagenomes. MetLab provides support in designing the metagenomics experiment by estimating the sequencing depth needed for the complete coverage of a species. This is achieved by applying a methodology to calculate the probability of coverage using an adaptation of Stevens’ theorem. It also provides scientists with several pipelines aimed at simplifying the analysis of viral metagenomes, including; quality control, assembly and taxonomic binning. We also implement a tool for simulating metagenomics datasets from several sequencing platforms. The overall aim is to provide virologists with an easy to use tool for designing, simulating and analyzing viral metagenomes. The results presented here include a benchmark towards other existing software, with emphasis on detection of viruses as well as speed of applications. This is packaged, as comprehensive software, readily available for Linux and OSX users at https://github.com/norling/metlab.

This paper reports a K-band voltage-controlled oscillator based on room-temperature ferroelectric varactors. The circuit is realized as a hybrid module where flip-chip transistors are mounted on a silicon substrate with integrated ferroelectric varactors and passive circuitry. The size of the module is 4.7times2.2 mm2. The measured center frequency is 16.5 GHz with a linear tunability of 6.7% and an output power of 3 dBmplusmn1 dB over the tuning range. The measured phase noise at center frequency is -95 dBc/Hz at 100-kHz offset. Another version of the oscillator is measured operating at 19.6 GHz with a tunability of 3.3% and a phase noise of -102 dBc/Hz at 100-kHz offset

Background There are no commercially available vaccines against human protozoan parasitic diseases, despite the success of vaccination-induced long-term protection against infectious diseases. East Coast fever, caused by the protist Theileria parva, kills one million cattle each year in sub-Saharan Africa, and contributes significantly to hunger and poverty in the region. A highly effective, live, multi-isolate vaccine against T. parva exists, but its component isolates have not been characterized. Here we sequence and compare the three component T. parva stocks within this vaccine, the Muguga Cocktail, namely Muguga, Kiambu5 and Serengeti-transformed, aiming to identify genomic features that contribute to vaccine efficacy. Results We find that Serengeti-transformed, originally isolated from the wildlife carrier, the African Cape buffalo, is remarkably and unexpectedly similar to the Muguga isolate. The 420 detectable non-synonymous SNPs were distributed among only 53 genes, primarily subtelomeric antigens and antigenic families. The Kiambu5 isolate is considerably more divergent, with close to 40,000 SNPs relative to Muguga, including >8,500 non-synonymous mutations distributed among >1,700 (42.5 %) of the predicted genes. These genetic markers of the component stocks can be used to characterize the composition of new batches of the Muguga Cocktail. Conclusions Differences among these three isolates, while extensive, represent only a small proportion of the genetic variation in the entire species. Given the efficacy of the Muguga Cocktail in inducing long-lasting protection against infections in the field, our results suggest that whole-organism vaccines against parasitic diseases can be highly efficacious despite considerable genome-wide differences relative to the isolates against which they protect., BMC Genomics, 16, ISSN:1471-2164

Integration possibilities of Ba x Sr 1-x TiO 3 (BST) based tunable Thin Film Bulk Acoustic Wave Resonators (TFBAR) using all-dielectric SiO 2 /AlN Bragg reflectors deposited on a high resistivity silicon strate are considered. SiO 2 /AlN reflectors withstand the high deposition temperature (≫600C) of the BST films opening up possibilities for heterogeneous integration of complex microwave circuits.

A model and a robust extraction procedure for tunable thin-film bulk acoustic resonators (TFBARs) are proposed. The TFBARs are based on induced piezoelectricity in Ba x Sr 1−x TiO 3 films. Their tunable characteristics as represented by the extracted model parameters are interpreted and discussed.

A 2 GHz oscillator based on a solidly mounted AlN Thin-Film Bulk Acoustic Resonator (TFBAR) is reported. The oscillator is realised as a silicon-on-silicon Multi-Chip Module (MCM) where all passive elements, including the TFBAR, are monolithically integrated on a High-Resistivity Silicon (HRS) carrier. SiGe transistors are flipchip mounted on the MCM carrier. Measurements of the oscillators reveal a best phase-noise of −125 dBc/Hz at 100 kHz offset.

This paper describes low-frequency measurements and comparative analysis of methods used for surface passivation of high-resistivity silicon (HR-Si). A number of substrates are evaluated; n-type and p-type HR-Si, with and without surface passivation by means of polysilicon or Ar-ion implantation. Additionally, a selection of samples is prepared with a layer of ferroelectric material. Substrate characteristics are extracted from measurements of the samples, allowing comparison of passivation methods and evaluation of the influence of the ferroelectric film. The study shows all passivation methods successful in removing any bias-dependence of substrate properties. Further, the high-temperature processing of the ferroelectric film is observed increasing the extracted substrate conductivity by about 70% for the Ar-ion implanted samples, and about 50% for the p-type samples passivated by poly-Si. The effective substrate conductivity of the n-type samples passivated by RTA-crystallised poly-Si appears unaffected.

Coplanar waveguides (CPWs) on surface passivated highly resistive Si (HRS) covered by ferroelectric film are studied. The focus is on passivation techniques reducing losses caused by surface charge accumulation at the Si/SiO2 interface. Different passivation methods are considered, Ar-ion bombardment into the silicon substrate and deposition of poly-Si below the oxide layer. Both methods remove any bias-dependence and decrease the losses associated with surface charge accumulation. It is also concluded that the effect of passivation remains after pulsed laser deposition of a ferroelectric thin film.

The use of metagenomics for detection and characterisation of viruses has several difficult steps, including high throughput sequencing and bioinformatics analysis. We present MetLab, a new program aimed at providing scientists with a simple baseline for experimental design and analysis of viral metagenomics.

This paper reports the circuit model of a SiGe HBT transistor flip chipped onto a high-resistivity silicon carrier (substrate). It includes the parasitic capacitances and inductances associated with bumps, the flipped transistor chip and takes into account the effect of the high-permittivity ferroelectric film deposited on the silicon carrier.

This paper describes the design and measurement of a 2 GHz oscillator based on a Solidly Mounted Thin Film Bulk Acoustic wave Resonator (SM TFBAR). The circuitry is patterned on an alumina substrate on which the transistors and capacitors are soldered. The SM TFBAR chip is integrated by means of wirebonding. The measured oscillator centre frequency is about 2.038 GHz with an output power of 0 dBm.

Metagenomic methods for detection of viruses provide new diagnostic tools to veterinary and public health laboratories, with powerful capacities to detect and to monitor the viromes in clinical samples. The Metagenomics methodology is divided into three main activities or steps: (1) wet-lab methodology; (2) sequencing; and (3) data analysis. The aim of the work is to provide insight into using the metagenomics approach for detection of emerging viruses, monitoring wildlife for known pathogens as well as providing a tool for rapid characterization of viral pathogens in outbreak situations. The main goal of the work is now to define Standard Operating Procedures for metagenomic investigations of clinical material and continuously provide a technology watch for the use of NGS within metagenomics in the Veterinary medicine field.

Metagenomic methods provide the veterinary and public health sciences with the promise of new and improved diagnostic tools with unprecedented ability to detect a plethora of known and unknown viromes in clinical samples. Successful metagenomics is based on three main activities where each one must be consistent and reliable for the method to be useful, these are (1) wet-lab preparation, (2) sequencing, and (3) bioinformatics analysis of the results. The aim of the work is to provide insight into the feasibility of using the metagenomics approach for detection of emerging viruses, monitoring wildlife for known pathogens as well as providing a tool for rapid characterization of viral pathogens in outbreak situations from a veterinary standpoint.

Metagenomic methods for detection of viruses provide new diagnostic tools to the veterinary and public health laboratories, with powerful capacities to detect and to monitor the viromes in clinical samples. Our groups at the OIE Collaborating Centre for the Biotechnology-based Diagnosis of Infectious Diseases in Veterinary Medicine, Uppsala, Sweden and at the SLU Global Bioinformatics Centre, Uppsala, Sweden are working with the development and evaluation of the methodological and technological platforms for viral metagenomics. Together with the National Veterinary Institute (SVA), we develop and test methods for extraction of viromes, feasibility of sequencing platforms to deliver metagenomic data-sets and evaluate bioinformatics tools as well as combine them into software packages for analysis and exploration of metagenomes. The aim of the work is to provide insight into using the metagenomics approach for detection of emerging viruses.

Next Generation Sequencing (NGS) technologies promise a revolution in genetic research. Generating enormous amounts of data, they bring both new opportunities and new challenges to researchers. SEQscoring was designed to facilitate analysis and enable extraction of the most essential information from data produced in NGS resequencing projects. Its main functionality is to help researchers locate the most likely causative mutations for a specific trait or disease, but it can advantageously be used whenever the goal is to compare and explore haplotype patterns and to locate variations positioned in evolutionary conserved genomic elements. SEQscoring uses input data containing information about coverage and variations produced by other programs, like MAQ and SAMtools, and put the emphasis on methods for data visualisation and interpretation. We compare cases and controls in several ways and also utilise the power of comparative genomics, by scoring all variations according to their degree of conservation. The SEQscoring tool is publicly accessible via the Web. It has an intuitive interface and can easily be used by biologists, medical researchers, veterinarians as well as bioinformaticians. We exemplify how SEQscoring was used in a recent study as a subsequent step to a Genome Wide Association Studies (GWAS) to extract a set of candidate mutations. Availability: http://www.seqscoring.org

The P&PR-PC main goal is to enhance EMBnet visibility and to establish cooperation/collaboration with other (even dissimilar) major groups, networks and societies. This is the report of the Committee's activies from November 2009 to June 2010.

Parallel-plate capacitors based on ferroelectric thin films are considered as high density capacitors and varactors. Due to the small thickness of the ferroelectric films, typically less than 1.0 mu m, high electric fields are generated even at relatively low voltages inducing piezoelectric effect associated with electrostriction. This induced piezoelectric effect has negative impact on ferroelectric capacitors since it causes extra loss (electroacoustic transformation of microwave energy). In this work the use of Bragg reflectors between the substrate and ferroelectric film is proposed as a possible way of suppression of the enhanced losses associated with the piezoelectric activity of the ferroelectric film.

Field and temperature dependent parameters of the dc field induced resonances in BaxSr1-xTiO3-based tunable thin film bulk acoustic resonators

Urine proteomics is emerging as a powerful tool for biomarker discovery. The purpose of this study is the development of a well-characterized "real life" sample that can be used as reference standard in urine clinical proteomics studies.We report on the generation of male and female urine samples that are extensively characterized by different platforms and methods (CE-MS, LC-MS, LC-MS/MS, 1-D gel analysis in combination with nano-LC MS/MS (using LTQ-FT ultra), and 2-DE-MS) for their proteome and peptidome. In several cases analysis involved a definition of the actual biochemical entities, i.e. proteins/peptides associated with molecular mass and detected PTMs and the relative abundance of these compounds.The combination of different technologies allowed coverage of a wide mass range revealing the advantages and complementarities of the different technologies. Application of these samples in "inter-laboratory" and "inter-platform" data comparison is also demonstrated.These well-characterized urine samples are freely available upon request to enable data comparison especially in the context of biomarker discovery and validation studies. It is also expected that they will provide the basis for the comprehensive characterization of the urinary proteome.