Comparison of the Equine Reference Sequence with Its Sanger Source Data and New Illumina Reads

The reference assembly for the domestic horse, EquCab2, published in 2009, was built using approximately 30 million Sanger reads from a Thoroughbred mare named Twilight. Contiguity in the assembly was facilitated using nearly 315 thousand BAC end sequences from Twilight\u27s half brother Bravo. Since then, it has served as the foundation for many genome-wide analyses that include not only the modern horse, but ancient horses and other equid species as well. As data mapped to this reference has accumulated, consistent variation between mapped datasets and the reference, in terms of regions with no read coverage, single nucleotide variants, and small insertions/deletions have become apparent. In many cases, it is not clear whether these differences are the result of true sequence variation between the research subjects\u27 and Twilight\u27s genome or due to errors in the reference. EquCab2 is regarded as The Twilight Assembly. The objective of this study was to identify inconsistencies between the EquCab2 assembly and the source Twilight Sanger data used to build it. To that end, the original Sanger and BAC end reads have been mapped back to this equine reference and assessed with the addition of approximately 40X coverage of new Illumina Paired-End sequence data. The resulting mapped datasets identify those regions with low Sanger read coverage, as well as variation in genomic content that is not consistent with either the original Twilight Sanger data or the new genomic sequence data generated from Twilight on the Illumina platform. As the haploid EquCab2 reference assembly was created using Sanger reads derived largely from a single individual, the vast majority of variation detected in a mapped dataset comprised of those same Sanger reads should be heterozygous. In contrast, homozygous variations would represent either errors in the reference or contributions from Bravo\u27s BAC end sequences. Our analysis identifies 720,843 homozygous discrepancies between new, high throughput genomic sequence data generated for Twilight and the EquCab2 reference assembly. Most of these represent errors in the assembly, while approximately 10,000 are demonstrated to be contributions from another horse. Other results are presented that include the binary alignment map file of the mapped Sanger reads, a list of variants identified as discrepancies between the source data and resulting reference, and a BED annotation file that lists the regions of the genome whose consensus was likely derived from low coverage alignments

Behavioral Variant Frontotemporal Lobar Degeneration with Amyotrophic Lateral Sclerosis with a Chromosome 9p21 Hexanucleotide Repeat

To determine the genetic basis of familial frontotemporal lobar degeneration (FTLD) with amyotrophic lateral sclerosis (ALS) we performed a clinical and genetic analysis of an affected family. A 51-year-old man with behavioral variant FTLD with ALS had a family history of the disease suggestive of autosomal dominant inheritance with incomplete penetrance. Genetic studies in this patient demonstrated the presence of an amplified hexanucleotide repeat (>30) polymorphism in the chromosome 9 open reading frame 72 (C9ORF72) gene which was previously identified as a cause of FTLD. Five others unaffected from the family were negative (all had less than 11 repeats). Because of the clinical and pathological overlap between FTLD and AD we performed a larger genome-wide association study and did not find association of single nucleotide polymorphisms (SNPs) in the C9ORF72 gene with Alzheimer’s disease (AD) risk. Bioinformatic analysis of C9ORF72 using the Gene Expression Omnibus database showed expression differences in patients with muscular dystrophy, neural tube defects, and schizophrenia. We also report analysis of gene expression in brain regions using the Allen Human Brain Atlas. Defects in this recently reported gene are now believed to be the most common cause of inherited ALS and an important cause of inherited FTLD. Our work suggests that the gene may also be important in other neurological and psychiatric conditions

Comparison of the equine reference sequence with its Sanger source data and new Illumina reads

The reference assembly for the domestic horse, EquCab2, published in 2009, was built using approximately 30 million Sanger reads from a Thoroughbred mare named Twilight. Contiguity in the assembly was facilitated using nearly 315 thousand BAC end sequences from Twilight's half brother Bravo. Since then, it has served as the foundation for many genome-wide analyses that include not only the modern horse, but ancient horses and other equid species as well. As data mapped to this reference has accumulated, consistent variation between mapped datasets and the reference, in terms of regions with no read coverage, single nucleotide variants, and small insertions/deletions have become apparent. In many cases, it is not clear whether these differences are the result of true sequence variation between the research subjects' and Twilight's genome or due to errors in the reference. EquCab2 is regarded as "The Twilight Assembly." The objective of this study was to identify inconsistencies between the EquCab2 assembly and the source Twilight Sanger data used to build it. To that end, the original Sanger and BAC end reads have been mapped back to this equine reference and assessed with the addition of approximately 40X coverage of new Illumina Paired-End sequence data. The resulting mapped datasets identify those regions with low Sanger read coverage, as well as variation in genomic content that is not consistent with either the original Twilight Sanger data or the new genomic sequence data generated from Twilight on the Illumina platform. As the haploid EquCab2 reference assembly was created using Sanger reads derived largely from a single individual, the vast majority of variation detected in a mapped dataset comprised of those same Sanger reads should be heterozygous. In contrast, homozygous variations would represent either errors in the reference or contributions from Bravo's BAC end sequences. Our analysis identifies 720,843 homozygous discrepancies between new, high throughput genomic sequence data generated for Twilight and the EquCab2 reference assembly. Most of these represent errors in the assembly, while approximately 10,000 are demonstrated to be contributions from another horse. Other results are presented that include the binary alignment map file of the mapped Sanger reads, a list of variants identified as discrepancies between the source data and resulting reference, and a BED annotation file that lists the regions of the genome whose consensus was likely derived from low coverage alignments

Can serious games help to mitigate climate change? Exploring their influence on Spanish and American teenagers’ attitudes

Es urgente y necesario reducir las emisiones de gases de efecto invernadero y mitigar el cambio climático, y esta lucha requiere un cambio en las actitudes de los adolescentes. En la búsqueda de nuevos enfoques dirigidos a los jóvenes, los serious games en formato online parecen una prometedora herramienta de comunicación y educación. Basándonos en el juego 2020 Energy como estudio de caso, el principal objetivo de este artículo es examinar la influencia de dicho juego sobre las actitudes de adolescentes españoles y estadounidenses (N = 108), empleando un diseño pretest-posttest con una condición experimental (jugar al juego) y una condición de control (no jugar al juego). Los resultados muestran que no había diferencias estadísticamente significativas después de jugar al juego, aunque una observación más detallada de cada factor ofrece algunas consecuencias positivas.There is an urgent need to curb emissions and mitigate climate change, and this fight requires a change in teenagers’ attitudes. In search of new approaches targeting youth, online games are seen as a promising tool for communication and education. Using the serious game 2020 Energy as a case study, the main objective of this paper is to examine the influence of the game on Spanish and American teenagers’ attitudes (N = 108), employing a pretest-posttest design with an experimental condition (playing the game) and a control condition (not playing the game). Results show that there have not been statistically significant differences after playing the game, although when looking closer at each factor, some positive consequences can be found.HUM466 Acceso y evaluación de la información científic

Validation of Electroencephalographic Recordings Obtained with a Consumer-Grade, Single Dry Electrode, Low-Cost Device: A Comparative Study

The functional validity of the signal obtained with low-cost electroencephalography (EEG) devices is still under debate. Here, we have conducted an in-depth comparison of the EEG-recordings obtained with a medical-grade golden-cup electrodes ambulatory device, the SOMNOwatch + EEG-6, vs those obtained with a consumer-grade, single dry electrode low-cost device, the NeuroSky MindWave, one of the most a ordable devices currently available. We recorded EEG signals at Fp1 using the two di erent devices simultaneously on 21 participants who underwent two experimental phases: a 12-minute resting state task (alternating two cycles of closed/open eyes periods), followed by 60-minute virtual-driving task. We evaluated the EEG recording quality by comparing the similarity between the temporal data series, their spectra, their signal-to-noise ratio, the reliability of EEG measurements (comparing the closed eyes periods), as well as their blink detection rate. We found substantial agreement between signals: whereas, qualitatively, the NeuroSky MindWave presented higher levels of noise and a biphasic shape of blinks, the similarity metric indicated that signals from both recording devices were significantly correlated. While the NeuroSky MindWave was less reliable, both devices had a similar blink detection rate. Overall, the NeuroSky MindWave is noise-limited, but provides stable recordings even through long periods of time. Furthermore, its data would be of adequate quality compared to that of conventional wet electrode EEG devices, except for a potential calibration error and spectral differences at low frequencies.Spanish Department of Transportation, Madrid, Spain (Grant No. SPIP2014-1426 to L.L.D.S.)A.C. is funded by a Spanish Ministry of Economy and Competitiveness grant (PSI2016-80558-R to A.C.)S.R. is funded by an Andalusian Government Excellence Research grant (P11-TIC-7983)L.J.F. is funded by a Spanish Ministry of Economy and Competitiveness grant (PSI2014-53427-P) and a Fundación Séneca grant (19267/PI/14)L.L.D.S. is currently supported by the Ramón y Cajal fellowship program (RYC-2015-17483)C.D.-P. is currently supported by the CEIMAR program (CEIMAR2018-2)C.D.-P. and L.L.D.S. are supported by a Santander Bank—CEMIX UGR-MADOC grant (Project PINS 2018-15

Multimodal augmented reality tangible gaming

This paper presents tangible augmented reality gaming environment that can be used to enhance entertainment using a multimodal tracking interface. Players can interact using different combinations between a pinch glove, a Wiimote, a six-degrees-of-freedom tracker, through tangible ways as well as through I/O controls. Two tabletop augmented reality games have been designed and implemented including a racing game and a pile game. The goal of the augmented reality racing game is to start the car and move around the track without colliding with either the wall or the objects that exist in the gaming arena. Initial evaluation results showed that multimodal-based interaction games can be beneficial in gaming. Based on these results, an augmented reality pile game was implemented with goal of completing a circuit of pipes (from a starting point to an end point on a grid). Initial evaluation showed that tangible interaction is preferred to keyboard interaction and that tangible games are much more enjoyable

Psychophysiology in games

Psychophysiology is the study of the relationship between psychology and its physiological manifestations. That relationship is of particular importance for both game design and ultimately gameplaying. Players’ psychophysiology offers a gateway towards a better understanding of playing behavior and experience. That knowledge can, in turn, be beneficial for the player as it allows designers to make better games for them; either explicitly by altering the game during play or implicitly during the game design process. This chapter argues for the importance of physiology for the investigation of player affect in games, reviews the current state of the art in sensor technology and outlines the key phases for the application of psychophysiology in games.The work is supported, in part, by the EU-funded FP7 ICT iLearnRWproject (project no: 318803).peer-reviewe

DOI for the annotation data produced in this work.

<p>DOI for the annotation data produced in this work.</p