Efficient RkNN Retrieval with Arbitrary Non-Metric Similarity Measures

A RkNN query returns all objects whose nearest k neighbors
contain the query object. In this paper, we consider RkNN
query processing in the case where the distances between
attribute values are not necessarily metric. Dissimilarities
between objects could then be a monotonic aggregate of dissimilarities
between their values, such aggregation functions
being specified at query time. We outline real world cases
that motivate RkNN processing in such scenarios. We consider
the AL-Tree index and its applicability in RkNN query
processing. We develop an approach that exploits the group
level reasoning enabled by the AL-Tree in RkNN processing.
We evaluate our approach against a Naive approach
that performs sequential scans on contiguous data and an
improved block-based approach that we provide. We use
real-world datasets and synthetic data with varying characteristics
for our experiments. This extensive empirical
evaluation shows that our approach is better than existing
methods in terms of computational and disk access costs,
leading to significantly better response times.

alpha-Synuclein aggregation in neurodegenerative diseases and its inhibition as a potential therapeutic strategy

There is strong evidence for the involvement of alpha-synuclein in the pathologies of several neurodegenerative disorders, including PD (Parkinson's disease). Development of disease appears to be linked to processes that increase the rate at which alpha-synuclein forms aggregates. These processes include increased protein concentration (via either increased rate of synthesis or decreased rate of degradation), and altered forms of alpha-synuclein (such as truncations, missense mutations, or chemical modifications by oxidative reactions). Aggregated forms of the protein are toxic to cells and one therapeutic strategy would be to reduce the rate at which aggregation occurs. To this end we have designed several peptides that reduce alpha-synuclein aggregation. A cell-permeable version of one such peptide was able to inhibit the DNA damage induced by Fe(II) in neuronal cells transfected with alpha-synuclein (A53T), a familial PD-associated mutation.

Cognitive inhibition and interference in dissociative indentity disorder: the effects of anxiety on specific executive functions:The effects of anxiety on specific executive functions

Using an experimentally based, computer-presented task, this study assessed cognitive inhibition and interference in individuals from the dissociative identity disorder (DID; n=12), generalized anxiety disorder (GAD; n=12) and non-clinical (n=12) populations. Participants were assessed in a neutral and emotionally negative (anxiety provoking) context, manipulated by experimental instructions and word stimuli. The DID sample displayed effective cognitive inhibition in the neutral but not the anxious context. The GAD sample displayed the opposite findings. However, the interaction between group and context failed to reach significance. There was no indication of an attentional bias to non-schema specific negative words in any sample. Results are discussed in terms of the potential benefit of weakened cognitive inhibition during anxious arousal in dissociative individuals.

A strategy for designing inhibitors of alpha-synuclein aggregation and toxicity as a novel treatment for Parkinson's disease and related disorders.

Convergent biochemical and genetic evidence suggests that the formation of alpha-synuclein (alpha-syn) protein deposits is an important and, probably, seminal step in the development of Parkinson's disease (PD), dementia with Lewy bodies (DLB) and multiple system atrophy (MSA). It has been reported that transgenic animals overexpressing human alpha-syn develop lesions similar to those found in the brain in PD, together with a progressive loss of dopaminergic cells and associated abnormalities of motor function. Inhibiting and/or reversing alpha-syn self-aggregation could, therefore, provide a novel approach to treating the underlying cause of these diseases. We synthesized a library of overlapping 7-mer peptides spanning the entire alpha-syn sequence, and identified amino acid residues 64-100 of alpha-syn as the binding region responsible for its self-association. Modified short peptides containing alpha-syn amino acid sequences from part of this binding region (residues 69-72), named alpha-syn inhibitors (ASI), were found to interact with full-length alpha-syn and block its assembly into both early oligomers and mature amyloid-like fibrils. We also developed a cell-permeable inhibitor of alpha-syn aggregation (ASID), using the polyarginine peptide delivery system. This ASID peptide was able to inhibit the DNA damage induced by Fe(II) in neuronal cells transfected with alpha-syn(A53T), a familial PD-associated mutation. ASI peptides without this delivery system did not reverse levels of Fe(II)-induced DNA damage. Furthermore, the ASID peptide increased (P

Cochlin in the eye: Functional implications

Aqueous humor is actively produced in the ciliary epithelium of the anterior chamber and has important functions for the eye. Under normal physiological conditions, the inflow and outflow of the aqueous humor are tightly regulated, but in the pathologic state this balance is lost. Aqueous outflow involves structures of the anterior chamber and experiences most resistance at the level of the trabecular meshwork (TM) that acts as a filter. The modulation of the TM structure regulates the filter and its mechanism remains poorly understood. Proteomic analyses have identified cochlin, a protein of poorly understood function, in the glaucomatous TM but not in healthy control TM from human cadaver eyes. The presence of cochlin has subsequently been confirmed by Western and immunohistochemical analyses. Functionally, cochlin undergoes multimerization induced by shear stress and other changes in the microenvironment. Cochlin along with mucopolysaccharide deposits have been found in the TM of glaucoma patients and in the inner ear of subjects affected by the hearing disorder DNFA9, a late onset, progressive disease that also involves alterations in fluid shear regimes. In vitro, cochlin induces aggregation of primary TM cells suggesting a role in cell adhesion, possibly in mechanosensation, and in modulation of the TM filter.

Speeds of sound, isentropic compressibilities, and excess molar volumes of cycloalkanes, alkanes and aromatic hydrocarbons at 303.15 K. II. Results for cycloalkanes+aromatic hydrocarbons

The speeds of sound u, isentropic compressibilities ?S, molar sound functions R, excess isentropic compressibilities ?SE and excess molar volumes VE for eight binary mixtures of cyclopentane, cyclohexane, cyclooctane and methylcyclohexane with benzene and of cyclohexane with toluene, ethyl benzene, p-xylene and propyl benzene at 303.15 K are reported. The effects of molecular sizes and shapes of the component molecules and of interaction energy in the mixture have been discussed. The Prigogine–Flory–Patterson theory has been applied to analyze the present binary mixtures along with the mixtures of cis- and trans-decalins with benzene and toluene taken from the literature.

Densities, speeds of sound, isentropic compressibilities, refractive indices and viscosities of binary mixtures of tetrahydrofuran with hydrocarbons at 303.15 K

Isentropic compressibilities, Rao's molar sound functions, molar refractions, excess isentropic compressibilities, excess molar volumes, viscosity deviations and excess Gibbs energies of activation of viscous flow for seven binary mixtures of tetrahydrofuran (THF) with cyclohexane, methylcyclohexane, n-hexane, benzene, toluene, p-xylene and propylbenzene over the entire range of composition at 303.15 K have been derived from experimental densities, speeds of sound, refractive indices and viscosities. The excess partial molar volumes of THF in different solvents have been estimated. The experimental results have been analyzed in terms of the Prigogine–Flory–Patterson theory.

New catanionic surfactants based on 1-alkyl-3-methylimidazolium alkylsulfonates, [C(n)H(2n+1)mim][CmH2m+1SO3]: mesomorphism and aggregation

Anionic and cationic alkyl-chain effects on the self-aggregation of both neat and aqueous solutions of 1-alkyl-3-methylimidazolium alkylsulfonate salts ([C(n)H(2n+ 1)mim][CmH2m+1SO3]; n = 8, 10 or 12; m = 1 and n = 4 or 8; m = 4 or 8) have been investigated. Some of these salts constitute a novel family of pure catanionic surfactants in aqueous solution. Examples of this class of materials are rare; they are distinct from both mixed cationic-anionic surfactants (obtained by mixing two salts) and gemini surfactants (with two or more amphiphilic groups bound by a covalent linker). Fluorescence spectroscopy and interfacial tension measurements have been used to determine critical micelle concentrations (CMCs), surface activity, and to compare the effects of the alkyl-substitution patterns in both the cation and anion on the surfactant properties of these salts. With relatively small methylsulfonate anions (n = 8, 10 and 12, m = 1), the salts behave as conventional single chain cationic surfactants, showing a decrease of the CMC upon increase of the alkyl chain length (n) in the cation. When the amphiphilic character is present in both the cation and anion (n = 4 and 8, m = 4 and 8), novel catanionic surfactants with CMC values lower than those of the corresponding cationic analogues, and which exhibited an unanticipated enhanced reduction of surface tension, were obtained. In addition, the thermotropic phase behaviour of [C(8)H(18)mim][C8H18SO3] (n = m = 8) was investigated using variable temperature X-ray scattering, polarising optical microscopy and differential scanning calorimetry; formation of a smectic liquid crystalline phase with a broad temperature range was observed.

Resolving genetic functions within microbial populations: In situ analyses using rRNA and mRNA stable isotope probing coupled with single-cell raman-fluorescence in situ hybridization

Prokaryotes represent one-half of the living biomass on Earth, with the vast majority remaining elusive to culture and study within the laboratory. As a result, we lack a basic understanding of the functions that many species perform in the natural world. To address this issue, we developed complementary population and single-cell stable isotope (C-13)-linked analyses to determine microbial identity and function in situ. We demonstrated that the use of rRNA/mRNA stable isotope probing (SIP) recovered the key phylogenetic and functional RNAs. This was followed by single-cell physiological analyses of these populations to determine and quantify in situ functions within an aerobic naphthalene-degrading groundwater microbial community. Using these culture-independent approaches, we identified three prokaryote species capable of naphthalene biodegradation within the groundwater system: two taxa were isolated in the laboratory (Pseudomonas fluorescens and Pseudomonas putida), whereas the third eluded culture (an Acidovorax sp.). Using parallel population and single-cell stable isotope technologies, we were able to identify an unculturable Acidovorax sp. which played the key role in naphthalene biodegradation in situ, rather than the culturable naphthalene-biodegrading Pseudomonas sp. isolated from the same groundwater. The Pseudomonas isolates actively degraded naphthalene only at naphthalene concentrations higher than 30 mu M. This study demonstrated that unculturable microorganisms could play important roles in biodegradation in the ecosystem. It also showed that the combined RNA SIP-Raman-fluorescence in situ hybridization approach may be a significant tool in resolving ecology, functionality, and niche specialization within the unculturable fraction of organisms residing in the natural environment.