Simplified amino acid alphabets based on deviation of conditional probability from random background

The primitive data for deducing the Miyazawa-Jernigan contact energy or BLOSUM score matrix consists of pair frequency counts. Each amino acid corresponds to a conditional probability distribution. Based on the deviation of such conditional probability from random background, a scheme for reduction of amino acid alphabet is proposed. It is observed that evident discrepancy exists between reduced alphabets obtained from raw data of the Miyazawa-Jernigan's and BLOSUM's residue pair counts. Taking homologous sequence database SCOP40 as a test set, we detect homology with the obtained coarse-grained substitution matrices. It is verified that the reduced alphabets obtained well preserve information contained in the original 20-letter alphabet.Comment: 9 pages,3figure

Structural response of Caribbean dry forests to hurricane winds: a case study from Guanica Forest, Puerto Rico

Tropical dry forests in the Caribbean have an uniquely short, shrubby structure with a high proportion of multiple-stemmed trees compared to dry forests elsewhere in the Neotropics. Previous studies have shown that this structure can arise without the loss of main stems from cutting, grazing, or other human intervention. The Caribbean has a high frequency of hurricanes, so wind may also influence forest stature. Furthermore, these forests also tend to grow on soils with low amounts of available phosphorus, which may also influence structure. The objective of this study was to assess the role of high winds in structuring dry forest, and to determine whether soil nutrient pools influence forest response following hurricane disturbance. Methods: Over 2000 stems in five plots were sampled for hurricane effects within 1 week after Hurricane Georges impacted field sites in 1998. Sprout initiation, growth, and mortality were analysed for 1407 stems for 2 years after the hurricane. Soil nutrient pools were measured at the base of 456 stems to assess association between nutrients and sprout dynamics. Results: Direct effects of the hurricane were minimal, with stem mortality at \u3c 2% and structural damage to stems at 13%, although damage was biased toward stems of larger diameter. Sprouting response was high . over 10 times as many trees had sprouts after the hurricane as before. The number of sprouts on a stem also increased significantly. Sprouting was common on stems that only suffered defoliation or had no visible effects from the hurricane. Sprout survival after 2 years was also high (\u3e 86%). Soil nutrient pools had little effect on forest response as a whole, but phosphorus supply did influence sprout dynamics on four of the more common tree species. Main Conclusions: Hurricanes are able to influence Caribbean tropical dry forest structure by reducing average stem diameter and basal area and generating significant sprouting responses. New sprouts, with ongoing survival, will maintain the high frequency of multi-stemmed trees found in this region. Sprouting is not limited to damaged stems, indicating that trees are responding to other aspects of high winds, such as short-term gravitational displacement or sway. Soil nutrients play a secondary role in sprouting dynamics of a subset of species. The short, shrubby forest structure common to the Caribbean can arise naturally as a response to hurricane winds

Functional and structural brain network correlates of visual hallucinations in Lewy body dementia

Visual hallucinations are a common feature of Lewy body dementia. Previous studies have shown that visual hallucinations are highly specific in differentiating Lewy body dementia from Alzheimer’s disease dementia and Alzheimer-Lewy body mixed pathology cases. Computational models propose that impairment of visual and attentional networks is aetiologically key to the manifestation of visual hallucinations symptomatology. However, there is still a lack of experimental evidence on functional and structural brain network abnormalities associated with visual hallucinations in Lewy body dementia. We used EEG source localisation and Network Based Statistics to assess differential topographical patterns in Lewy body dementia between 25 participants with visual hallucinations and 17 participants without hallucinations. Diffusion tensor imaging was used to assess structural connectivity between thalamus, basal forebrain and cortical regions belonging to the functionally affected network component in the hallucinating group, as assessed with Network Based Statistics. Number of white matter streamlines within the cortex and between subcortical and cortical regions was compared between hallucinating and not hallucinating groups and correlated with average EEG source connectivity of the affected subnetwork. Moreover, modular organisation of the EEG source network was obtained, compared between groups, and tested for correlation with structural connectivity. Network analysis showed that compared to non-hallucinating patients, those with hallucinations feature consistent weakened connectivity within the visual ventral network, and between this network and default mode and ventral attentional networks, but not between or within attentional networks. The occipital lobe was the most functionally disconnected region. Structural analysis yielded significantly affected white matter streamlines connecting the cortical regions to the nucleus basalis of Meynert and the thalamus in hallucinating compared to not hallucinating patients. The number of streamlines in the tract between the basal forebrain and the cortex correlated with cortical functional connectivity in non-hallucinating patients, whilst a correlation emerged for the white matter streamlines connecting the functionally affected cortical regions in the hallucinating group. This study proposes, for the first time, differential functional networks between hallucinating and not hallucinating Lewy body dementia patients, and provides an empirical evidence for existing models of visual hallucinations. Specifically, the outcome of the present study shows that the hallucinating condition is associated with functional network segregation in Lewy body dementia and supports the involvement of the cholinergic system as proposed in the current literature

Practicing Imperfect Forgiveness

Forgiveness is typically regarded as a good thing - even a virtue - but acts of forgiveness can vary widely in value, depending on their context and motivation. Faced with this variation, philosophers have tended to reinforce everyday concepts of forgiveness with strict sets of conditions, creating ideals or paradigms of forgiveness. These are meant to distinguish good or praiseworthy instances of forgiveness from problematic instances and, in particular, to protect the self-respect of would-be forgivers. But paradigmatic forgiveness is problematic for a number of reasons, including its inattention to forgiveness as a gendered trait. We can account for the values and the risks associated with forgiving far better if we treat it as a moral practice and not an ideal

Improved Linear Cryptanalysis of Reduced-Round MIBS

MIBS is a 32-round lightweight block cipher with 64-bit block size and two different key sizes, namely 64-bit and 80-bit keys. Bay et al. provided the first impossible differential, differential and linear cryptanalyses of MIBS. Their best attack was a linear attack on the 18-round MIBS-80. In this paper, we significantly improve their attack by discovering more approximations and mounting Hermelin et al.'s multidimensional linear cryptanalysis. We also use Nguyen et al.'s technique to have less time complexity. We attack on 19 rounds of MIBS-80 with a time complexity of 2^{74.23} 19-round MIBS-80 encryptions by using 2^{57.87} plaintext-ciphertext pairs. To the best of our knowledge, the result proposed in this paper is the best cryptanalytic result for MIBS, so far

Application of compact laser-driven accelerator X-ray sources for industrial imaging

X-rays generated by betatron oscillations of electrons in a laser-driven plasma accelerator were characterised and applied to imaging industrial samples. With a 125TW laser, a low divergence beam with 5.2±1.7 × 107photonsmrad−2 per pulse was produced with a synchrotron spectrum with a critical energy of 14.6±1.3keV. Radiographs were obtained of a metrology test sample, battery electrodes, and a damage site in a composite material. These results demonstrate the suitability of the source for non-destructive evaluation applications. The potential for industrial implementation of plasma accelerators is discussed

Cichlid biogeography: comment and review

Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/72313/1/j.1467-2979.2004.00148.x.pd