From cheek swabs to consensus sequences : an A to Z protocol for high-throughput DNA sequencing of complete human mitochondrial genomes

Background: Next-generation DNA sequencing (NGS) technologies have made huge impacts in many fields of biological research, but especially in evolutionary biology. One area where NGS has shown potential is for high-throughput sequencing of complete mtDNA genomes (of humans and other animals). Despite the increasing use of NGS technologies and a better appreciation of their importance in answering biological questions, there remain significant obstacles to the successful implementation of NGS-based projects, especially for new users. Results: Here we present an ‘A to Z’ protocol for obtaining complete human mitochondrial (mtDNA) genomes – from DNA extraction to consensus sequence. Although designed for use on humans, this protocol could also be used to sequence small, organellar genomes from other species, and also nuclear loci. This protocol includes DNA extraction, PCR amplification, fragmentation of PCR products, barcoding of fragments, sequencing using the 454 GS FLX platform, and a complete bioinformatics pipeline (primer removal, reference-based mapping, output of coverage plots and SNP calling). Conclusions: All steps in this protocol are designed to be straightforward to implement, especially for researchers who are undertaking next-generation sequencing for the first time. The molecular steps are scalable to large numbers (hundreds) of individuals and all steps post-DNA extraction can be carried out in 96-well plate format. Also, the protocol has been assembled so that individual ‘modules’ can be swapped out to suit available resources

High throughput spatial convolution filters on FPGAs

Digital signal processing (DSP) on field- programmable gate arrays (FPGAs) has long been appealing because of the inherent parallelism in these computations that can be easily exploited to accelerate such algorithms. FPGAs have evolved significantly to further enhance the mapping of these algorithms, included additional hard blocks, such as the DSP blocks found in modern FPGAs. Although these DSP blocks can offer more efficient mapping of DSP computations, they are primarily designed for 1-D filter structures. We present a study on spatial convolutional filter implementations on FPGAs, optimizing around the structure of the DSP blocks to offer high throughput while maintaining the coefficient flexibility that other published architectures usually sacrifice. We show that it is possible to implement large filters for large 4K resolution image frames at frame rates of 30–60 FPS, while maintaining functional flexibility

Implicit and explicit risk perception, affect, and trust : an investigation of food "traffic lights"

Obesity is a health problem in many developed countries and is a growing problem worldwide. In an effort to improve food choices the "traffic lights" nutritional labelling system has been developed. This system informs consumers of the relative (low, medium, high) levels of fat, saturated fats, sugar, and salt, along with energy information. There is debate over what type of thought processing drives perceptions of affect (or emotion) and risk regarding food products. These are System 1 (quick, intuitive) processing and System 2 (slower, deliberative) processing. In order to capture data on both types of processing, we used explicit and implicit measures (we developed an implicit measure of risk for this study). We also investigated the relationships of risk with affect, and trust. The results showed the presence of food "traffic lights" sometimes influenced both risk and affect perceptions but this was more pronounced for explicit measures. We also found that high risk was associated with negative affect, and low risk with positive affect, with larger effects when the “traffic lights” were present. We concluded that "traffic lights" can influence risk perception at both explicit and implicit levels but the influence was stronger if either the risk information was clear or the person was consciously evaluating the risk. Future research was discussed

CAN PROMOTING CULTURAL DIVERSITY BACKFIRE? A LOOK AT THE IMPLICIT EFFECTS OF PSYCHOLOGICAL REACTANCE

Psychological reactance occurs when an individual's freedom to engage in a particular behavior is compromised, resulting in a greater urge to engage in that behavior (Brehm, 1966). The current study examined the role of reactance in the divergence between implicit and explicit attitudes, and considered the possibility that reactance itself may be experienced either implicitly or explicitly. Participants (N = 162) watched a cultural sensitivity video or control video in a study administered by a White or Black experimenter. It was found that the cultural sensitivity video elicited implicit reactance, but only for participants whose motivation to appear non-prejudiced was internal. Participants whose motivation to appear non-prejudiced was external had the highest levels of implicit racism with the White experimenter and the control video. Finally, participants showed higher scores on the Modern Racism Scale when they had the White experimenter than when they had the Black experimenter. This study suggests that there are circumstances in which cultural sensitivity videos may backfire, and that the distinction between people who are internally versus externally motivated to appear non-prejudiced is an important one, with regard to the effects of such videos

Priming the Pump: The Case for a Sector Based Approach to Impact Investing

The impact investing sector, while still in its infancy, has made remarkable progress in building awareness that business can generate a positive social impact. Although individual firms remain the essential innovators and building blocks of social change, they are means to a broader end of creating innovations that can touch the lives of hundreds of millions. It is time now to evolve the conversation, and our resource commitments in the direction of sparking, nurturing, and scaling these new industry sectors that are the true promise of the impact investing industry. What is readily apparent according to this report is that no one organization, or one type of organization, can do this alone. Success does not depend upon perfect coordination or a grand plan. After all, we are talking about innovation, which requires experimentation, learning, and serendipity. But success does require a determined, thoughtful, and frequently collaborative effort by those who believe that the power of markets and the inspiration of entrepreneurs can be tapped to create opportunity and a brighter future for billions

Similarities and differences of pumping conventional and self-compacting concrete

In Practice, Self-Compacting Concrete (SCC) is Considered as a Simple Extension of Conventional Vibrated Concrete (CVC) When Pumping is Concerned. the Same Equipment, Materials, Pumping Procedures and Guidelines Used for CVC Are Applied When Pumping SCC. on the Other Hand, It Has Been Clearly Shown that the Rheological Properties and the Mix Design of SCC Are Different Than CVC. Can the Same Pumping Principles Employed for CVC Be Applied for SCC? This Paper Compares the Some Published Results of Pumping of CVC with Those for SCC. a First Striking Difference between Pumping of CVC and SCC is the Flow Behaviour in the Pipes. the Flow of CVC is a Plug, Surrounded by a Lubricating Layer, While during the Flow of SCC, Part of the Concrete Volume itself is Sheared Inside the Pipe. as a Result, the Importance of Viscosity Increases in Case of SCC. Due to the Low Yield Stress of SCC, the Behaviour in Bends is Different, But Quite Complex to Study. Due to the Lower Content of Aggregate and Better Stability of SCC, as It is Less Prone to Internal Water Migration, Blocking is Estimated to Occur at Lower Frequency in Case of SCC. © RILEM 2010