A meta-learning approach to automatic kernel selection for support vector machines

Appropriate choice of a kernel is the most important ingredient of the kernel-based learning methods such as support vector machine (SVM). Automatic kernel selection is a key issue given the number of kernels available, and the current trial-and-error nature of selecting the best kernel for a given problem. This paper introduces a new method for automatic kernel selection, with empirical results based on classification. The empirical study has been conducted among five kernels with 112 different classification problems, using the popular kernel based statistical learning algorithm SVM. We evaluate the kernels’ performance in terms of accuracy measures. We then focus on answering the question: which kernel is best suited to which type of classification problem? Our meta-learning methodology involves measuring the problem characteristics using classical, distance and distribution-based statistical information. We then combine these measures with the empirical results to present a rule-based method to select the most appropriate kernel for a classification problem. The rules are generated by the decision tree algorithm C5.0 and are evaluated with 10 fold cross validation. All generated rules offer high accuracy ratings.

Identification of an attractin-like pheromone in the mucus-secreting hypobranchial gland of the abalone Haliotis asinina linnaeus.

Pheromones are chemicals used to communicate between animals of the same species, and are thought to be used by most marine animals. With limited vision, abalone primarily sense their world chemically, and pheromones may play an important role in settlement, attraction, recognition, alarm, and reproduction. Despite this, there has been no detailed investigation into pheromone substances, both in their precise biochemical nature or pheromonal function. In this study, we investigated the presence of pheromonelike substances from the hypobranchial gland of the abalone Haliotis asinina using bioassays, immunohistochemistry, Western blotting, and reverse-phase high-performance liquid chromatography (RP-HPLC). The hypobranchial gland of many prosobranchial marine molluscs has been classified as a sex auxiliary gland releasing unknown substances during spawning. In our study, cephalic tentacle assays demonstrated that the cell extracts of the hypobranchial gland contain chemical cues that are sensed by conspecifics. An antibody against the sea slug “attractin” pheromone was used as a probe to localize a similar protein in the mucin-secreting cells of the epithelial lining the hypobranchial gland of both male and female abalone. The approximate molecular weight of this abalone attractin-like protein is 30 kDa in both males and females. Fractionation of hypobranchial gland extracts by C5 RP-HPLC could not selectively purify this protein, and no sex-specific differences were observed. We predict that the attractin-like protein could be one of a number of important proteins involved in maturation, aggregation, and/or spawning behavior of abalone. In future research, additional hypobranchial gland components will be tested further for these types of behavior.

Electrooxidation of [(η5-C5H5)Fe(CO)2]2 as a probe of the nucleophilic properties of ionic liquid anions

The oxidative electrochemistry of [CpFe(CO)2]2, 1 (Cp = [η5-C5H5]–), was examined in detail in ionic liquids (ILs) composed of ions of widely varying Lewis acid−base properties. Cyclic voltammetric responses were strongly dependent on the nucleophilic properties of the IL anion, but all observations are consistent with the initial formation of 1+ followed by attack from the IL anion. In [NTf2]–-based ILs ([NTf2]– = bis(trifluoromethylsulfonyl)amide), the process shows nearly ideal chemical reversibility as the reaction between 1+ and [NTf2]– is very slow. This is highly significant, as 1+ is known to be highly susceptible to nucleophilic attack and its stability indicates a remarkable lack of coordinating ability of these ILs. In 1-methyl-3-butylimidazolium hexafluorophosphate, [bmim][PF6], the oxidation of 1 is still largely reversible, but there is more pronounced evidence of [PF6]– coordination. In contrast, 1 exhibits an irreversible two-electron oxidation process in a dicyanamide-based IL. This overall oxidation process is thought to proceed via an ECE mechanism, details of which are presented. Rate constants were estimated by fitting the experimental data to digital simulations of the proposed mechanism. The use of [NTf2]–-based ILs as a supporting electrolyte in CH2Cl2 was examined by using this solvent/electrolyte as a medium in which to perform bulk electrolyses of 1 and 1*, the permethylated analogue [Cp*Fe(CO)2]2 (Cp* = [η5-C5(CH3)5]–). These cleanly yielded the corresponding binuclear radical-cation species, 1+ and 1*+, which were subsequently characterized by electron paramagnetic resonance (EPR) spectroscopy. In addition to the above oxidation studies, the reduction of 1 was studied in each of the ILs; differences in cathodic peak potentials are attributed, in part, to ion-pairing effects. This study illustrates the wide range of electrochemical environments available with ILs and demonstrates their utility for the investigation of the redox properties of metal carbonyls and other organometallic compounds.

Alcohol consumption and body composition in a population-based sample of elderly Australian men

Background: Alcohol is calorie dense, and impacts activity, appetite and lipid processing. The aim of this study was to therefore investigate the association between alcohol consumption and components of body composition including bone, fat and lean tissue.

Methods: Participants were recruited from a randomly selected, population-based sample of 534 men aged 65 years and older enrolled in the Geelong Osteoporosis Study. Alcohol intake was ascertained using a food frequency questionnaire and the sample categorised as nondrinkers or alcohol users who consumed B2, 3–4 or C5 standard drinks on a usual drinking day. Bone mineral density (BMD), lean body mass and body fat mass were measured using dual energy X-ray absorptiometry; overall adiposity (%body fat), central adiposity (%truncal fat) and body mass index (BMI) were calculated. Bone quality was determined by quantitative heel ultrasound (QUS).

Results: There were 90 current non-drinkers (16.9 %), 266 (49.8 %) consumed 1–2 drinks/day, 104 (19.5 %) 3–4 drinks/day and 74 (13.8 %) C5 drinks/day. Those consuming C5 drinks/day had greater BMI (?4.8 %), fat mass index (?20.1 %), waist circumference (?5.0 %), %body fat (?15.2 %) and proportion of trunk fat (?5.3 %) and lower lean mass (-5.0 %) than non-drinkers after adjustment for demographic and lifestyle factors. Furthermore, they were more likely to be obese than non-drinkers according to criteria based on BMI (OR = 2.83, 95 %CI 1.10–7.29) or waist circumference (OR = 3.36, 95 %CI 1.32–8.54). There was an inverse relationship between alcohol consumption and QUS parameters and BMD at the mid forearm site; no differences were detected for BMD at other skeletal sites.

Conclusion: Higher alcohol intake was associated with greater total and central adiposity and reduced bone quality.

Long-term changes in the diel vertical migration behaviour of zooplankton

Samples historically collected and analysed by the Continuous Plankton Recorder survey were used to examine long-term (1958 to 1994) patterns in the normal diel vertical migration (NDVM) behaviour of 7 copepod taxa in the North Sea: Calanus finmarchicus C5-C6; Calanus spp. C1-C4; Centropages typicus; Centropages hamatus; Temora longicornis; Acartia clausii and Para-Pseudocalanus (this last group included all Paracalanus and Pseudocalanus species). The ratio of night:day abundance near the surface was used as a measure of the extent of NDVM. For all 7 taxa, the extent of NDVM between 1958 and 1994 co-varied with the abundance of herring Clupea harengus in the North Sea. Fisheries data show that during this period the herring stock was a good indicator of the overall abundance of planktivorous fish in the North Sea. These results suggest that changes in the abundance of planktivorous fish in the North Sea over recent decades have resulted in modifications in the NDVM behaviour of many zooplankton taxa.

Ontogenetic and seasonal variation in the Diel Vertical Migration of the Copepods Metridia lucens and Metridia longa

Plankton samples collected and analyzed by the Continuous Plankton Recorder survey were used to examine the length of time spent near the surface in the North Atlantic and the North Sea by three closely related groups of zooplankton (copepodite stages 1-4 Metridia spp., copepodite stages 5-6 Metridia lucens, and copepodite stages 5-6 Metridia longa). For all three groups, the mean daily length of time spent near the surface in each month of the year covaried seasonally with day length. In addition, the amount of time spent near the surface varied significantly between the three groups, being longest for the copepods of smallest body size (C 1-C4 Metridia spp.) and shortest for the copepods of largest body size (C5-C6 M. longa). These results support the suggestion that diel vertical migration serves to reduce the risk of mortality from visually orienting predators

Allosteric Modulation of the HIV-1 gp120-gp41 Association Site by Adjacent gp120 Variable Region 1 (V1) N-Glycans Linked to Neutralization Sensitivity

The HIV-1 gp120-gp41 complex, which mediates viral fusion and cellular entry, undergoes rapid evolution within its external glycan shield to enable escape from neutralizing antibody (NAb). Understanding how conserved protein determinants retain functionality in the context of such evolution is important for their evaluation and exploitation as potential drug and/ or vaccine targets. In this study, we examined how the conserved gp120-gp41 association site, formed by the N- and Cterminal segments of gp120 and the disulfide-bonded region (DSR) of gp41, adapts to glycan changes that are linked to neutralization sensitivity. To this end, a DSR mutant virus (K601D) with defective gp120-association was sequentially passaged in peripheral blood mononuclear cells to select suppressor mutations. We reasoned that the locations of suppressors point to structural elements that are functionally linked to the gp120-gp41 association site. In culture 1, gp120 association and viral replication was restored by loss of the conserved glycan at Asn136 in V1 (T138N mutation) in
conjunction with the L494I substitution in C5 within the association site. In culture 2, replication was restored with deletion of the N139INN sequence, which ablates the overlapping Asn141-Asn142-Ser-Ser potential N-linked glycosylation sequons in
V1, in conjunction with D601N in the DSR. The 136 and 142 glycan mutations appeared to exert their suppressive effects by altering the dependence of gp120-gp41 interactions on the DSR residues, Leu593, Trp596 and Lys601. The 136 and/or 142
glycan mutations increased the sensitivity of HIV-1 pseudovirions to the glycan-dependent NAbs 2G12 and PG16, and also pooled IgG obtained from HIV-1-infected individuals. Thus adjacent V1 glycans allosterically modulate the distal gp120-
gp41 association site. We propose that this represents a mechanism for functional adaptation of the gp120-gp41 association site to an evolving glycan shield in a setting of NAb selection.

Collagen type III and VI turnover in response to long-term immobilization

BACKGROUND: Muscle mass and function are perturbed by immobilization and remobilization. When muscle mass changes, the quality and quantity of the extracellular matrix protein, particularly the collagens, change with it. In this study, we investigated the temporal profile of three peptide biomarkers derived from turnover of collagen type III and type VI in a long-term immobilization and remobilization study. We also compared individual biomarker levels with Lean body Mass (LBM) and changes therein, hypothesizing that these biomarkers would be biomarkers of the remodeling processes associated with immobilization and/or remobilization. METHODS: In the Berlin bed rest study, 20 young men were recruited and randomly assigned to 8-week's strict bed rest with or without resistive vibration exercise countermeasure. We measured three neo-epitope ELISA kits in the serum samples of this study: Pro-C3, measured the synthesis of collagen type III; Pro-C6, measured the synthesis of collagen type VI; and C6M measured the degradation of collagen type VI induced by MMP-2 and MMP-9 cleavage. RESULTS: Pro-C3 and Pro-C6 biomarkers are up-regulated with both immobilization and remobilization, whereas C6M is hardly affected at all. We found that Pro-C3 and C6M levels are related to LBM at baseline and that high levels of Pro-C6 are associated with smaller changes in muscle mass during both immobilization and remobilization. CONCLUSION: The Pro-C3 and-C6 biomarkers change likely reflect remodeling changes in response to unloading or reloading, whereas C6M does not appear to respond to unloading. Pro-C3 and C6M levels correlate with LBM at baseline, while Pro-C6 is related to the anabolic and catabolic responses to unloading and reloading.