Ambiguous Locations Research Articles

Updates to the RMAP short-read mapping software

Summary: We report on a major new version of the RMAP software for mapping reads from short-read sequencing technology. General improvements to accuracy and space requirements are included, along with novel functionality. Included in the RMAP software package are tools for mapping paired-end reads, mapping using more sophisticated use of quality scores, collecting ambiguous mapping locations and mapping bisulfite-treated reads.Availability: The applications described in this note are available for download at http://www.cmb.usc.edu/people/andrewds/rmap and are distributed as Open Source software under the GPLv3.0. The software has been tested on Linux and OS X platforms.Contact: andrewds@usc.edu; mzhang@cshl.eduThe RMAP algorithm was introduced by (Smith et al., 2008) as one of the earliest available programs for mapping reads from the Illumina second-generation sequencing technology. One important contribution of RMAP was to incorporate the use of quality scores directly into the mapping process: read positions with too low a quality score were not considered while mapping, and that quality score cutoff could be adjusted by the user. Subsequently, numerous mapping algorithm have appeared (Langmead et al., 2009; Li,H. et al., 2008; Li,R. et al., 2008; Lin et al., 2008; Schatz, 2009; Yanovsky et al., 2008), with improvements in both efficiency and breadth of functionality (e.g. ability to map paired-end reads; integrated SNP calling). Investigators requiring solutions to mapping problems now have many options. As new applications of short-read sequencing emerge, many variations on the analysis task of read mapping emerge. Diversity in performance characteristics of existing mapping tools becomes potentially valuable.We report the first major update to RMAP. The basic algorithmic framework in RMAP is still to preprocess reads and scan the genome, but several modifications have been made and much additional functionality has been included. Importantly, RMAP has a memory footprint that depends on the number of reads being mapped. This feature allows RMAP to be used effectively in cluster environments with commodity nodes, because partitioning the reads allows natural parallelizations with linear reduction in memory requirements per processor core used.Included in this release of the RMAP software package is functionality for mapping paired-end reads, making more sophisticated use of quality scores, collecting mapping locations for ambiguously mapping reads and mapping bisulfite-treated reads.

Anxiety-induced cognitive bias in non-human animals

As in humans, ‘cognitive biases’ in the way in which animals judge ambiguous stimuli may be influenced by emotional state and hence a valuable new indicator of animal emotion. There is increasing evidence that animals experiencing different emotional states following exposure to long-term environmental manipulations show contrasting biases in their judgement of ambiguous stimuli. However, the specific type of induced emotional state is usually unknown. We investigated whether a short-term manipulation of emotional state has a similar effect on cognitive bias, using changes in light intensity; a treatment specifically related to anxiety-induction. Twenty-four male rats were trained to discriminate between two different locations, in either high (‘H’) or low (‘L’) light levels. One location was rewarded with palatable food and the other with aversive food. Once the rats had shown spatial discrimination, by running significantly faster to the rewarded location, they were tested with three ambiguous locations intermediate between the rewarded and aversive locations, and their latency to approach each location recorded. Half the rats were tested in the same light levels as during training, the remainder were switched. Rats switched from high to low light levels (putatively the least negative emotional manipulation) ran significantly faster to all three ambiguous probes than those rats switched from low to high light levels (putatively the most negative manipulation). This suggests that the judgement bias technique might be useful as an indicator of short-term changes in anxiety for non-human animals.

Automation of 3D reconstruction of neural tissue from large volume of conventional serial section transmission electron micrographs

We describe an approach for automation of the process of reconstruction of neural tissue from serial section transmission electron micrographs. Such reconstructions require 3D segmentation of individual neuronal processes (axons and dendrites) performed in densely packed neuropil. We first detect neuronal cell profiles in each image in a stack of serial micrographs with multi-scale ridge detector. Short breaks in detected boundaries are interpolated using anisotropic contour completion formulated in fuzzy-logic framework. Detected profiles from adjacent sections are linked together based on cues such as shape similarity and image texture. Thus obtained 3D segmentation is validated by human operators in computer-guided proofreading process. Our approach makes possible reconstructions of neural tissue at final rate of about 5 μm 3/man h, as determined primarily by the speed of proofreading. To date we have applied this approach to reconstruct few blocks of neural tissue from different regions of rat brain totaling over 1000 μm 3, and used these to evaluate reconstruction speed, quality, error rates, and presence of ambiguous locations in neuropil ssTEM imaging data.

A Spectroscopic Analysis of Blue Stragglers, Horizontal Branch Stars, and Turnoff Stars in Four Globular Clusters

We present a spectroscopic analysis of HST STIS and FOS low- and intermediate-resolution spectroscopy of 55 stars in four globular clusters (47 Tucanae, M3, NGC 6752, and NGC 6397). Stars hotter than Teff = 5750 K and with a signal-to-noise ratio larger than 15 were analyzed with non-local thermodynamic equilibrium model atmospheres, and values for their effective temperatures and gravities were obtained. Using photometric fluxes, we also obtained radii, luminosities, and spectroscopic masses. Twenty-four stars in our sample are blue stragglers (BSs). Their photometric colors and magnitudes place these BSs above and redward of the clusters' zero-age main sequence: this is consistent with the gravities we find for these stars, which are lower than zero-age main-sequence gravities. A comparison with stellar evolutionary tracks shows that almost all of our BSs are in the Hertzsprung gap. This is contrary to theory, because of the short timescale expected for stars in this evolutionary phase. The mean BS mass is 1.04 M☉ for 14 nonvariable stars, or 1.07 M☉ counting all 24 BSs in our sample. For the nonvariable stars the mean BS masses for individual clusters are 1.73, 1.01, 0.95, and 0.72 M☉ for NGC 6397, NGC 6752, 47 Tuc, and M3, respectively. Adding the variable stars (which improves the statistics but increases the uncertainty), the mean masses become 1.27, 1.05, 0.99, and 0.99 M☉, respectively. Although there is considerable scatter, the BS spectroscopic masses correlate with both effective temperature and brightness of the stars, as expected. The mean nonvariable turnoff star mass (0.58 M☉) is significantly below the values determined for the BSs and below the main-sequence turnoff mass. The mean nonvariable horizontal-branch (HB) star mass is higher than expected (0.79 M☉). In particular, several HB stars have masses well above the main-sequence turnoff mass. Some of these HB stars are suspected of actually being BSs, since most of them reside at ambiguous locations on the CMD, making them prone to misclassification. Values and limits to the stellar rotation rates (v sin i) are imposed by fitting weak metal lines, the Ca II K line wings, or the helium lines for the hotter stars. Five BSs with reasonably constrained rotations show average and median v sin i values of 109 and 100 km s-1, respectively, suggesting v ~ 160 km s-1. At least some GC BSs are very rapid rotators, but this information cannot yet constrain their origin as stellar collision or binary mergers because of the lack of clear theoretical predictions. Six extreme HB stars have rotation rates v sin i between 50 and 200 km s-1, which are high for these stars and might indicate a binary origin. De Marco et al. found that four BSs and two HB stars in our sample have Balmer jumps that are too large for the effective temperatures implied by the slopes of their Paschen continua. Two additional HB stars are now identified in the current study as having the same feature. For these stars, the presence of a disk of partly ionized material is suspected, although high stellar rotation rates could also partly explain the data.

Inactivation of the dorsal hippocampus does not affect learning during exploration of a novel environment

The conditioned cue preference (CCP) task was used to study the ability of rats to discriminate between spatial locations. Food-deprived rats explored an eight-arm radial maze with no food present (pre-exposure). On subsequent days, they were alternately confined in one arm of the maze with food and in another arm with no food (training), followed by a preference test with no food present, to determine if they had learned to discriminate between the two arm locations. No injections were given during the two latter phases. With adjacent radial maze arms, rats given three 10-min pre-exposure sessions and four food-pairing trials exhibited a preference for their food-paired arms; rats not pre-exposed did not exhibit this preference. Rats pre-exposed 30 min after dorsal hippocampus injections of muscimol exhibited the preference. With widely separated maze arms, rats given two training trials with no pre-exposure exhibited a preference for the food-paired arm; rats that were given one pre-exposure session did not. Rats pre-exposed 30 min after dorsal hippocampus injections of muscimol did not exhibit the preference. The same intrahippocampal muscimol injections that failed to affect the influence of pre-exposure on CCP learning with both arm configurations impaired win-shift performance, a standard test of spatial learning. These findings suggest that a functional dorsal hippocampus is not required for the (incidental or latent) learning that occurs during unreinforced exploration of a novel environment. The information acquired during this activity subsequently produces a latent learning effect if it is used to discriminate between two ambiguous locations (adjacent arms) or a latent inhibition--like effect if it is used to discriminate between two unambiguous locations (separated maze arms).

Algebraic two-satellite TOA/FOA position solution on an ellipsoidal Earth

A direct algebraic solution is given for estimates of the ambiguous locations of an RF emitter on the surface of an ellipsoidal Earth given time-of-arrival (TOA) and frequency-of-arrival (FOA) measurements at two satellites.

Developing mechanisms of temperamental effortful control.

Studies of temperament from early childhood to adulthood have demonstrated inverse relationships between negative affectivity and effortful control. Effortful control is also positively related to the development of conscience and appears as a protective factor in the development of behavior disorders. In this study, the development of attentional mechanisms underlying effortful control was investigated in 2- to 3-year-old children, as indexed by their performance in a) making anticipatory eye movements to ambiguous locations and b) resolving conflict between location and identity in a spatial conflict task. The ability to make anticipatory eye movements to ambiguous locations within a sequence was clearly present at 24 months. By 30 months, children could also successfully perform a spatial conflict task that introduced conflict between identity and location, and at that age, children's success on ambiguous anticipatory eye movements was related to lower interference from conflict in the spatial conflict task. Children's performance on the eye-movement task was correlated with performance and reaction time on spatial tasks, and both were related to aspects of effortful control and negative affect as measured in children's parent-reported temperament.