The effects of training on errors of perceived direction in perspective displays

An experiment was conducted to determine the effects of training on the characteristic direction errors that are observed when subjects estimate exocentric directions on perspective displays. Changes in five subjects' perceptual errors were measured during a training procedure designed to eliminate the error. The training was provided by displaying to each subject both the sign and the direction of his judgment error. The feedback provided by the error display was found to decrease but not eliminate the error. A lookup table model of the source of the error was developed in which the judgement errors were attributed to overestimates of both the pitch and the yaw of the viewing direction used to produce the perspective projection. The model predicts the quantitative characteristics of the data somewhat better than previous models did. A mechanism is proposed for the observed learning, and further tests of the model are suggested

A New Rhesus Macaque Assembly and Annotation for Next-Generation Sequencing Analyses

BACKGROUND: The rhesus macaque (Macaca mulatta) is a key species for advancing biomedical research. Like all draft mammalian genomes, the draft rhesus assembly (rheMac2) has gaps, sequencing errors and misassemblies that have prevented automated annotation pipelines from functioning correctly. Another rhesus macaque assembly, CR_1.0, is also available but is substantially more fragmented than rheMac2 with smaller contigs and scaffolds. Annotations for these two assemblies are limited in completeness and accuracy. High quality assembly and annotation files are required for a wide range of studies including expression, genetic and evolutionary analyses. RESULTS: We report a new de novo assembly of the rhesus macaque genome (MacaM) that incorporates both the original Sanger sequences used to assemble rheMac2 and new Illumina sequences from the same animal. MacaM has a weighted average (N50) contig size of 64 kilobases, more than twice the size of the rheMac2 assembly and almost five times the size of the CR_1.0 assembly. The MacaM chromosome assembly incorporates information from previously unutilized mapping data and preliminary annotation of scaffolds. Independent assessment of the assemblies using Ion Torrent read alignments indicates that MacaM is more complete and accurate than rheMac2 and CR_1.0. We assembled messenger RNA sequences from several rhesus tissues into transcripts which allowed us to identify a total of 11,712 complete proteins representing 9,524 distinct genes. Using a combination of our assembled rhesus macaque transcripts and human transcripts, we annotated 18,757 transcripts and 16,050 genes with complete coding sequences in the MacaM assembly. Further, we demonstrate that the new annotations provide greatly improved accuracy as compared to the current annotations of rheMac2. Finally, we show that the MacaM genome provides an accurate resource for alignment of reads produced by RNA sequence expression studies. CONCLUSIONS: The MacaM assembly and annotation files provide a substantially more complete and accurate representation of the rhesus macaque genome than rheMac2 or CR_1.0 and will serve as an important resource for investigators conducting next-generation sequencing studies with nonhuman primates. REVIEWERS: This article was reviewed by Dr. Lutz Walter, Dr. Soojin Yi and Dr. Kateryna Makova

Sooty Mangabey Genome Sequence Provides Insight into AIDS Resistance in a Natural SIV Host

In contrast to infections with human immunodeficiency virus (HIV) in humans and simian immunodeficiency virus (SIV) in macaques, SIV infection of a natural host, sooty mangabeys (Cercocebus atys), is non-pathogenic despite high viraemia. Here we sequenced and assembled the genome of a captive sooty mangabey. We conducted genome-wide comparative analyses of transcript assemblies from C. atys and AIDS-susceptible species, such as humans and macaques, to identify candidates for host genetic factors that influence susceptibility. We identified several immune-related genes in the genome of C. atys that show substantial sequence divergence from macaques or humans. One of these sequence divergences, a C-terminal frameshift in the toll-like receptor-4 (TLR4) gene of C. atys, is associated with a blunted in vitro response to TLR-4 ligands. In addition, we found a major structural change in exons 3-4 of the immune-regulatory protein intercellular adhesion molecule 2 (ICAM-2); expression of this variant leads to reduced cell surface expression of ICAM-2. These data provide a resource for comparative genomic studies of HIV and/or SIV pathogenesis and may help to elucidate the mechanisms by which SIV-infected sooty mangabeys avoid AIDS

Robust and persistent reactivation of SIV and HIV by N-803 and depletion of CD8+ cells

Human immunodeficiency virus (HIV) persists indefinitely in individuals with HIV who receive antiretroviral therapy (ART) owing to a reservoir of latently infected cells that contain replication-competent virus1–4. Here, to better understand the mechanisms responsible for latency persistence and reversal, we used the interleukin-15 superagonist N-803 in conjunction with the depletion of CD8+ lymphocytes in ART-treated macaques infected with simian immunodeficiency virus (SIV). Although N-803 alone did not reactivate virus production, its administration after the depletion of CD8+ lymphocytes in conjunction with ART treatment induced robust and persistent reactivation of the virus in vivo. We found viraemia of more than 60 copies per ml in all macaques (n = 14; 100%) and in 41 out of a total of 56 samples (73.2%) that were collected each week after N-803 administration. Notably, concordant results were obtained in ART-treated HIV-infected humanized mice. In addition, we observed that co-culture with CD8+ T cells blocked the in vitro latency-reversing effect of N-803 on primary human CD4+ T cells that were latently infected with HIV. These results advance our understanding of the mechanisms responsible for latency reversal and lentivirus reactivation during ART-suppressed infection

The Web Interface for Telescience (WITS)

The Web Interface for Telescience (WITS) has been developed to enable scientists to participate in planetary rover missions from their home institutions, rather than having to travel to JPL as has been required in the past. A scientist accesses WITS via a commercial web browser. WITS provides various views of the scene including a descent image view which allows the user to see where the rover has been and currently is in a global perspective, a panoramic view which is an overhead view of the area immediately around the rover, and a wedge view which is an image from a rover-mounted camera. Scientists can select science targets in a wedge image and science subtasks to perform at those targets. A mission planner can select rover waypoints to traverse between science targets, and waypoint subtasks to perform at those locations. A public version allows the general public to view the same information and plan their own simulated missions. 1. Introduction Scientists currently have to trave..

L Abstract The Web Interface for Telescience

The Web Interface for Telescience (WITS) is an Internet-based tool that enables members of geographically distributed science teams to participate in daily planetary lander and rover mission planning. WITS enables the viewing of downlinked images and results in various ways, terrain feature measurement and annotation, and planning of daily mission activities. WITS is written in the Java language and is accessible by mission scientists and the general public via a web browser. The public can use WITS to plan and simulate their own rover missions. WITS was used during the 1997 Mars Pathfinder mission primarily for public outreach and was evaluated as a science operations tool at JPL. WITS will be used as an operations tool in the 1998 lander and 2001 and 2003 lander-rover missions to Mars.