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Nonrandom extinction and the loss of evolutionary history.

The hierarchical nature of phylogenies means that random extinction of species affects a smaller fraction of higher taxa, and so the total amount of evolutionary history lost may be comparatively slight. However, current extinction risk is not phylogenetically random. We show the potentially severe implications of the clumped nature of threat for the loss of biodiversity. An additional 120 avian and mammalian genera are at risk compared with the number predicted under random extinction. We estimate that the prospective extra loss of mammalian evolutionary history alone would be equivalent to losing a monotypic phylum.

Animals↗

Host cis-mediated extinction of a retrovirus permissive for expression in embryonal stem cells during differentiation.

The use of retroviral vectors for gene transfer into animals has been severely hampered by the lack of provirus transcription in the early embryo and embryonic stem (ES) cells. This primary block in provirus expression is maintained in differentiated cells by a cis-acting mechanism that is not well characterized. Retroviral vectors based on the murine embryonal stem cell virus (MESV), which overcome the transcriptional block in ES cells, were constructed to investigate this secondary mechanism. These vectors transferred G418 resistance to ES cells with the same efficiency as to fibroblasts, but overall transcript levels were greatly reduced. A mosaic but stable expression pattern was observed when single cells from G418-resistant clones were replated in G418 or assayed for expression of LacZ or interleukin-3. The expression levels in independent clones were variable and correlated inversely with methylation. However, a second, more pronounced, block to transcription was found upon differentiation induction. Differentiation of the infected ES cells to cells permissive for retroviral expression resulted in repression and complete extinction of provirus expression. Extinction was not accompanied by increased levels of methylation. Provirus expression is thus regulated by two independent cis-acting mechanisms: (i) partial repression in the undifferentiated state, accompanied by increased methylation but compatible with long-term, low expression of retroviral genes, and (ii) total repression and extinction during early stages of differentiation, apparently independent of changes in methylation. These results indicate a time window early during the transition from an undifferentiated to a differentiated stage in which provirus expression is silenced. The mechanisms are presently unknown, but elucidation of these events will have an important impact on vector development for targeting stem cells and for gene therapy.

Animals↗

Extinction of LINE-1 activity coincident with a major mammalian radiation in rodents.

LINE-1 transposable elements (L1s) are ubiquitous in mammals and are thought to have remained active since before the mammalian radiation. Only one L1 extinction event, in South American rodents in the genus Oryzomys, has been convincingly demonstrated. Here we examine the phylogenetic limits and evolutionary tempo of that extinction event by characterizing L1s in related rodents. Fourteen genera from five tribes within the Sigmodontinae subfamily were examined. Only the Sigmodontini, the most basal tribe in this group, demonstrate recent L1 activity. The Oryzomyini, Akodontini, Phyllotini, and Thomasomyini contain only L1s that appear to have inserted long ago; their L1s lack open reading frames, have mutations at conserved amino acid residues, and show numerous private mutations. They also lack restriction site-defined L1 subfamilies specific to any species, genus or tribe examined, and fail to form monophyletic species, genus or tribal L1 clusters. We determine here that this L1 extinction event occurred roughly 8.8 million years ago, near the divergence of Sigmodon from the remaining Sigmodontinae species. These species appear to be ideal model organisms for studying the impact of L1 inactivity on mammalian genomes.

Animals↗

Contrast dependence of perceptual grouping in brain-damaged patients with visual extinction.

Extinction is manifested in conditions of bilateral simultaneous stimulation, as a failure to detect the stimulus contra-lateral to the side of a cerebral lesion, while the same stimulus is correctly detected there when presented in isolation. The phenomenon is usually interpreted in terms of impaired mobilization of attention from an attended to an unattended object. We have recently shown, using pairs of Gabor patches as stimuli, that pair detection is maximally improved in conditions where the two stimuli presented simultaneously to the two halves of the visual field are co-oriented and co-axial and their location is not too eccentric. Here we add new information by showing that contrast isotropy of the stimulus pair is important in producing this orientation-similarity gain. The further advantage of co-oriented co-linear stimuli over co-oriented parallel (vertical) stimuli was shown exclusively with iso-contrast stimulus pairs, and was significantly enhanced when the contrast level of the stimulus pair was low. Stimulus properties producing reduced extinction seem to correlate with the selectivity pattern and contrast dependence of (a) spatial lateral facilitation observed in psychophysical studies with normal observers, and (b) long-range interactions observed in the primary visual cortex. Thus, two remote visual stimuli seem to be processed as a single object when the corresponding neuronal activities are linked via long-range lateral interactions. The present demonstration of contrast dependency in such processing, strengthens our previous conjecture that even in the presence of significant, extinction producing, parietal damage, the primary visual cortex preserves the capacity to encode, using long-range lateral interactions, an image description in which visual objects are already segregated from background.

Aged↗

Transient and persistent right ear extinction in dichotic listening: subcortical lesions.

Nine patients with aphasia had right ear extinction in dichotic listening to words in the first month after an ischemic stroke; they were reassessed after 3 months. Four showed complete recovery from the right ear extinction; in five, the abnormality persisted. In those who recovered, CT revealed a subcortical lesion lateral to the frontal horn of the lateral ventricle without a lesion of Heschl's gyrus or geniculo-temporal pathways; a lesion in those structures was found in patients who did not recover. As reported for subcortical aphasia, a subcortical mechanism may explain contralateral ear extinction in dichotic listening.

Adult↗

Experiments on light scattering and extinction by small, micrometer-sized aggregates of spheres.

We performed experiments to study the extinction, scattering, and polarization of light by ensembles of fractal dust aggregates that consist of spherical monomers large compared with the wavelength. Extinction was measured on a homogeneous dust cloud. Scattering and polarization were measured on a collimated dust beam. We found that polarization and extinction are determined only by a small size scale that is defined by a monomer and its closest neighbors in an aggregate. The scattering function might also depend on the overall size of the aggregate or the total number of monomers in an aggregate.

Journal Article↗

Wavelength-dependent optical extinction of carbonaceous particles in atmospheric aerosols and interstellar dust.

Optical extinction spectra for particles of structurally disordered carbonaceous material (carbon black, soot) are discussed in terms of the effects of size and shape and the difference between coagulated and coalesced particles. For this purpose, the orientation-averaged specific extinction for several compact and open aggregates of spherical particles is calculated and compared with the specific extincton by homogeneous particles, i.e., volume-equivalent sphere and elongated spheroids. The extinction spectra are calculated for wavelengths from 0.2 to 1000 microm by use of the optical constants for the carbonaceous materials of Jäger et al. [Astron. Astrophys. 332, 291 (1998)] and Schnaiter et al. [Astrophys. J. 498, 486 (1998)]. Comparisons with the model case of particles composed of graphite and with measurements of diesel soot aerosols are made.

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Vortex-induced flame extinction in two-phase counterflow diffusion flames with CH planar laser-induced fluorescence and particle-image velocimetry.

Here the interaction between a laminar two-phase, non-pre-mixed counterflow flame and a vortex is examined. Special emphasis is given to the influence of different flame and vortex parameters on the extinction behavior of the flame. Simultaneous planar laser-induced fluorescence of the CH radical layer produced by the flame and particle-image velocimetry measurements of the flowfield are used to characterize the flame-vortex interaction. These simultaneous diagnostics are used for the first time in this configuration. The extinction processes occurring during the flame-vortex interaction can be analyzed by this method, especially the influence of strain at the flame surface. The influence of the droplets on the extinction behavior appears clearly compared with a fully gaseous flame. The spray flame is weaker and extinguishes earlier than does a gaseous flame. In the measurements an additional broadband signal in the vicinity of the CH layer is probably due to the induced fluorescence of polycyclic aromatic hydrocarbons, excited at the same wavelength.

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Ice clouds and Asian dust studied with lidar measurements of particle extinction-to-backscatter ratio, particle depolarization, and water-vapor mixing ratio over Tsukuba.

The tropospheric particle extinction-to-backscatter ratio, the depolarization ratio, and the water-vapor mixing ratio were measured by use of a Raman lidar and a polarization lidar during the Asian dust seasons in 2001 and 2002 in Tsukuba, Japan. The apparent (not corrected for multiple-scattering effects) extinction-to-backscatter ratios (Sp) showed a dependence on the relative humidity with respect to ice (RHice) obtained from the lidar-derived water-vapor mixing ratio and radiosonde-derived temperature; they were mostly higher than 30 sr in dry air (RHice < 50%), whereas they were mostly lower than 30 sr in ice-supersaturated air (RHice > or = 100%), where the apparent extinction coefficients were larger than 0.036 km(-1). Both regions showed mean particle depolarization ratios of 20%-22%. Comparisons with theoretical calculations and the previous experiments suggest that the observed dependence of Sp on RHice is attributed to the difference in the predominant particles: nonspherical aerosols (mainly the Asian dust) in dry air and cloud particles in ice-supersaturated air.

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Use of equivalent spheres to model the relation between radar reflectivity and optical extinction of ice cloud particles.

The effect of ice crystal size and shape on the relation between radar reflectivity and optical extinction is examined. Discrete-dipole approximation calculations of 95-GHz radar reflectivity and ray-tracing calculations are applied to ice crystals of various habits and sizes. Ray tracing was used primarily to calculate optical extinction and to provide approximate information on the lidar backscatter cross section. The results of the combined calculations are compared with Mie calculations applied to collections of different types of equivalent spheres. Various equivalent sphere formulations are considered, including equivalent radar-lidar spheres; equivalent maximum dimension spheres; equivalent area spheres, and equivalent volume and equivalent effective radius spheres. Marked differences are found with respect to the accuracy of different formulations, and certain types of equivalent spheres can be used for useful prediction of both the radar reflectivity at 95 GHz and the optical extinction (but not lidar backscatter cross section) over a wide range of particle sizes. The implications of these results on combined lidar-radar ice cloud remote sensing are discussed.

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Imaginary refractive-index effects on desert-aerosol extinction versus backscatter relationships at 351 nm: numerical computations and comparison with Raman lidar measurements.

A numerical model is used to investigate the dependence at 351 nm of desert-aerosol extinction and backscatter coefficients on particle imaginary refractive index (mi). Three ranges (-0.005 < or = mi < or = -0.001, -0.01 < or = mi < or = -0.001, and -0.02 < or = mi < or = -0.001) are considered, showing that backscatter coefficients are reduced as /mi/ increases, whereas extinction coefficients are weakly dependent on mi. Numerical results are compared with extinction and backscatter coefficients retrieved by elastic Raman lidar measurements performed during Saharan dust storms over the Mediterranean Sea. The comparison indicates that a range of -0.01 to -0.001 can be representative of Saharan dust aerosols and that the nonsphericity of mineral particles must be considered.

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Retrieval of aerosol refractive index from extinction spectra with a damped harmonic-oscillator band model.

A new method for the retrieval of the spectral refractive indices of micrometer-sized particles from infrared aerosol extinction spectra has been developed. With this method we use a classical damped harmonic-oscillator model of molecular absorption in conjunction with Mie scattering to model extinction spectra, which we then fit to the measurements using a numerical optimal estimation algorithm. The main advantage of this method over the more traditional Kramers-Kronig approach is that it allows the full complex refractive-index spectra, along with the parameters of the particle size distribution, to be retrieved from a single extinction spectrum. The retrieval scheme has been extensively characterized and has been found to provide refractive indices with a maximum uncertainty of approximately 10% (with a minimum of approximately 0.1%). Comparison of refractive indices calculated from measurements of a ternary solution of HNO3, H2SO4, and H2O with those published in J. Phys. Chem. A 104, 783 (2000) show similar differences as found by other authors.

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Empirical relationships between extinction coefficient and visibility in fog.

Relationships between visibility and an extinction coefficient that is due to fog in optical windows that are free from molecular absorption are derived. The extinction coefficients in the visible (0.55 microm), the near IR (1.2 microm), and the mid IR (3.7 microm) are comparable to and roughly twice as much as that in the far IR (10.6 microm) when visibility is less than a few hundred meters. The advantage of far-IR radiation compared with shorter wavelengths grows as visibility exceeds 500 m. Correspondingly, the relationship between extinction coefficient and visibility becomes more sensitive to variations in the particle-size distribution of fog.

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Particle extinction measured at ambient conditions with differential optical absorption spectroscopy. 2. Closure study.

Spectral particle extinction coefficients of atmospheric aerosols were measured with, to the best of our knowledge, a newly designed differential optical absorption spectroscopy (DOAS) instrument. A closure study was carried out on the basis of optical and microphysical aerosol properties obtained from nephelometer, particle soot/absorption photometer, hygroscopic tandem differential mobility analyzer, twin differential mobility particle sizer, aerodynamic particle sizer, and Berner impactors. The data were collected at the urban site of Leipzig during a period of 10 days in March 2000. The performance test also includes a comparison of the optical properties measured with DOAS to particle optical properties calculated with a Mie-scattering code. The computations take into account dry and ambient particle conditions. Under dry particle conditions the linear regression and the correlation coefficient for particle extinction are 0.95 and 0.90, respectively. At ambient conditions these parameters are 0.89 and 0.97, respectively. An inversion algorithm was used to retrieve microphysical particle properties from the extinction coefficients measured with DOAS. We found excellent agreement within the retrieval uncertainties.

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Tungsten source integrated cavity output spectroscopy for the determination of ambient atmospheric extinction coefficient.

Broadband integrated cavity output spectroscopy (ICOS) utilizing an incoherent tungsten lamp as a spectroscopic source is described. This novel approach has been termed W-ICOS. The technique has been applied to make quantitative measurements of Rayleigh scattering by carbon dioxide between 570 and 590 nm and to make measurements of aerosol and atmospheric extinction. Minimum detectable extinction coefficients (kext) made in a 94 cm optical cavity ranged between 3.4 and 35 Mm(-1) depending on the level of signal averaging employed. The level of sensitivity achieved should allow measurements on static gas samples and regular, quantitative measurements of the atmospheric extinction coefficient.

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Macroecological analyses support an overkill scenario for late Pleistocene extinctions.

The extinction of megafauna at the end of Pleistocene has been traditionally explained by environmental changes or overexploitation by human hunting (overkill). Despite difficulties in choosing between these alternative (and not mutually exclusive) scenarios, the plausibility of the overkill hypothesis can be established by ecological models of predator-prey interactions. In this paper, I have developed a macroecological model for the overkill hypothesis, in which prey population dynamic parameters, including abundance, geographic extent, and food supply for hunters, were derived from empirical allometric relationships with body mass. The last output correctly predicts the final destiny (survival or extinction) for 73% of the species considered, a value only slightly smaller than those obtained by more complex models based on detailed archaeological and ecological data for each species. This illustrates the high selectivity of Pleistocene extinction in relation to body mass and confers more plausibility on the overkill scenario.

Animals↗

Stimulus control in the goldfish after massed extinction.

Compared with the data of goldfish trained only with stimuli correlated with reinforcement, interspersed reinforcement-stimulus and extinction-stimulus trials resulted in sharper stimulus control and a marked reduction in the percentage of key-presses emitted in the presence of stimuli located near the extinction stimulus on the test dimension. If non-reinforced trials were not interspersed with reinforced trials, there was no sharpening of stimulus control and less reduction in key presses in the presence of stimuli near the extinction stimulus on the test dimension.

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