Segment-based multiple sequence alignment

Motivation: Many multiple sequence alignment tools have been developed in the past, progressing either in speed or alignment accuracy. Given the importance and wide-spread use of alignment tools, progress in both categories is a contribution to the community and has driven research in the field so far. Results: We introduce a graph-based extension to the consistency-based, progressive alignment strategy. We apply the consistency notion to segments instead of single characters. The main problem we solve in this context is to define segments of the sequences in such a way that a graph-based alignment is possible. We implemented the algorithm using the SeqAn library and report results on amino acid and DNA sequences. The benefit of our approach is threefold: (1) sequences with conserved blocks can be rapidly aligned, (2) the implementation is conceptually easy, generic and fast and (3) the consistency idea can be extended to align multiple genomic sequences. Availability: The segment-based multiple sequence alignment tool can be downloaded from http://www.seqan.de/projects/msa.html. A novel version of T-Coffee interfaced with the tool is available from http://www.tcoffee.org. The usage of the tool is described in both documentations. Contact: [email protected]

Ground-based imaging remote sensing of ice clouds : uncertainties caused by sensor, method and atmosphere

In this study a method is introduced for the retrieval of optical thickness and effective particle size of ice clouds over a wide range of optical thickness from ground-based transmitted radiance measurements. Low optical thickness of cirrus clouds and their complex microphysics present a challenge for cloud remote sensing. In transmittance, the relationship between optical depth and radiance is ambiguous. To resolve this ambiguity the retrieval utilizes the spectral slope of radiance between 485 and 560 nm in addition to the commonly employed combination of a visible and a short-wave infrared wavelength. An extensive test of retrieval sensitivity was conducted using synthetic test spectra in which all parameters introducing uncertainty into the retrieval were varied systematically: ice crystal habit and aerosol properties, instrument noise, calibration uncertainty and the interpolation in the lookup table required by the retrieval process. The most important source of errors identified are uncertainties due to habit assumption: Averaged over all test spectra, systematic biases in the effective radius retrieval of several micrometre can arise. The statistical uncertainties of any individual retrieval can easily exceed 10 µm. Optical thickness biases are mostly below 1, while statistical uncertainties are in the range of 1 to 2.5. For demonstration and comparison to satellite data the retrieval is applied to observations by the Munich hyperspectral imager specMACS (spectrometer of the Munich Aerosol and Cloud Scanner) at the Schneefernerhaus observatory (2650 m a.s.l.) during the ACRIDICON-Zugspitze campaign in September and October 2012. Results are compared to MODIS and SEVIRI satellite-based cirrus retrievals (ACRIDICON – Aerosol, Cloud, Precipitation, and Radiation Interactions and Dynamics of Convective Cloud Systems; MODIS – Moderate Resolution Imaging Spectroradiometer; SEVIRI – Spinning Enhanced Visible and Infrared Imager). Considering the identified uncertainties for our ground-based approach and for the satellite retrievals, the comparison shows good agreement within the range of natural variability of the cloud situation in the direct surrounding

A model sensitivity study of the impact of clouds on satellite detection and retrieval of volcanic ash

Volcanic ash is commonly observed by infrared detectors on board Earth-orbiting satellites. In the presence of ice and/or liquid-water clouds, the detected volcanic ash signature may be altered. In this paper the sensitivity of detection and retrieval of volcanic ash to the presence of ice and liquid-water clouds was quantified by simulating synthetic equivalents to satellite infrared images with a 3-D radiative transfer model. The sensitivity study was made for the two recent eruptions of Eyjafjallajokull (2010) and Grimsvotn (2011) using realistic water and ice clouds and volcanic ash clouds. The water and ice clouds were taken from European Centre for Medium-RangeWeather Forecast (ECMWF) analysis data and the volcanic ash cloud fields from simulations by the Lagrangian particle dispersion model FLEXPART. The radiative transfer simulations were made both with and without ice and liquid-water clouds for the geometry and channels of the Spinning Enhanced Visible and Infrared Imager (SEVIRI). The synthetic SEVIRI images were used as input to standard reverse absorption ash detection and retrieval methods. Ice and liquid-water clouds were on average found to reduce the number of detected ash-affected pixels by 6-12 %. However, the effect was highly variable and for individual scenes up to 40% of pixels with mass loading > 0 : 2 gm 2 could not be detected due to the presence of water and ice clouds. For coincident pixels, i. e. pixels where ash was both present in the FLEXPART (hereafter referred to as "Flexpart") simulation and detected by the algorithm, the presence of clouds overall increased the retrieved mean mass loading for the Eyjafjallajokull (2010) eruption by about 13 %,while for the Grimsvotn (2011) eruption ash-mass loadings the effect was a 4% decrease of the retrieved ash-mass loading. However, larger differences were seen between scenes (standard deviations of +/- 30 and +/- 20% for Eyjafjallajokull and Grimsvotn, respectively) and even larger ones within scenes. The impact of ice and liquid-water clouds on the detection and retrieval of volcanic ash, implies that to fully appreciate the location and amount of ash, hyperspectral and spectral band measurements by satellite instruments should be combined with ash dispersion modelling

Active Electric Imaging: Body-Object Interplay and Object's “Electric Texture”

This article deals with the role of fish's body and object's geometry on determining the image spatial shape in pulse Gymnotiforms. This problem was explored by measuring local electric fields along a line on the skin in the presence and absence of objects. We depicted object's electric images at different regions of the electrosensory mosaic, paying particular attention to the perioral region where a fovea has been described. When sensory surface curvature increases relative to the object's curvature, the image details depending on object's shape are blurred and finally disappear. The remaining effect of the object on the stimulus profile depends on the strength of its global polarization. This depends on the length of the object's axis aligned with the field, in turn depending on fish body geometry. Thus, fish's body and self-generated electric field geometries are embodied in this “global effect” of the object. The presence of edges or local changes in impedance at the nearest surface of closely located objects adds peaks to the image profiles (“local effect” or “object's electric texture”). It is concluded that two cues for object recognition may be used by active electroreceptive animals: global effects (informing on object's dimension along the field lines, conductance, and position) and local effects (informing on object's surface). Since the field has fish's centered coordinates, and electrosensory fovea is used for exploration of surfaces, fish fine movements are essential to perform electric perception. We conclude that fish may explore adjacent objects combining active movements and electrogenesis to represent them using electrosensory information

Psychoanalysis as the Patient: High in Feeling, Low in Energy

This paper examines the increasingly important role that affect is assuming in psychoanalytic research and practice. This rise in the centrality of affect has been at the expense of an independent role for motivation and a dismissal of any energy concept. Difficulties with this affect-first approach are identified and an alternative offered that accords motivation an independent role and accommodates a useful energy concept. Research on esophageal atresia, addiction, and infant suckling are cited in support of this position.Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/66624/2/10.1177_00030651970450031101.pd