Maximum Entropy Linear Manifold for Learning Discriminative Low-dimensional Representation

Representation learning is currently a very hot topic in modern machine learning, mostly due to the great success of the deep learning methods. In particular low-dimensional representation which discriminates classes can not only enhance the classification procedure, but also make it faster, while contrary to the high-dimensional embeddings can be efficiently used for visual based exploratory data analysis. In this paper we propose Maximum Entropy Linear Manifold (MELM), a multidimensional generalization of Multithreshold Entropy Linear Classifier model which is able to find a low-dimensional linear data projection maximizing discriminativeness of projected classes. As a result we obtain a linear embedding which can be used for classification, class aware dimensionality reduction and data visualization. MELM provides highly discriminative 2D projections of the data which can be used as a method for constructing robust classifiers. We provide both empirical evaluation as well as some interesting theoretical properties of our objective function such us scale and affine transformation invariance, connections with PCA and bounding of the expected balanced accuracy error.Comment: submitted to ECMLPKDD 201

Connectionist Temporal Modeling for Weakly Supervised Action Labeling

We propose a weakly-supervised framework for action labeling in video, where only the order of occurring actions is required during training time. The key challenge is that the per-frame alignments between the input (video) and label (action) sequences are unknown during training. We address this by introducing the Extended Connectionist Temporal Classification (ECTC) framework to efficiently evaluate all possible alignments via dynamic programming and explicitly enforce their consistency with frame-to-frame visual similarities. This protects the model from distractions of visually inconsistent or degenerated alignments without the need of temporal supervision. We further extend our framework to the semi-supervised case when a few frames are sparsely annotated in a video. With less than 1% of labeled frames per video, our method is able to outperform existing semi-supervised approaches and achieve comparable performance to that of fully supervised approaches.Comment: To appear in ECCV 201

Investigating Dechlorane Plus (DP) distribution and isomer specific adsorption behavior in size fractionated marine sediments

In this study, Dechlorane Plus (DP) concentrations were analyzed in marine sediments (depth: similar to 10 cm) from two Korean industrial bays. Two sediments were fractionated into 5 sizes by using gravitational split-flow thin fractionation technique and DP distribution was investigated in different particle size fractions. Elevated DP levels in surface sediments were observed at the site closest to land and industrial area. The highest concentrations of DP were detected in the finest grain-size (< 10 mu m, 451.2 and 149.9 pg/g dry weight for the two bays). The fraction of anti-DP to the total DP (f(anti)) in the two fractionated samples increased with reduced grain-size and significantly correlated with organic carbon content (OC), which can be caused by preferential adsorption of anti-DP or higher biodegradation rates of syn-DP in the fine particles. To provide insight into such mechanism, simulated experiments were conducted using activated charcarbon (ACC) to adsorb DP dissolved in methanol and molecular descriptors of both isomers were estimated using Gaussian 03. The adsorption results revealed that syn-DP was preferentially adsorbed by ACC, suggesting syn-DP is more hydrophobic than anti-DP. The preferential adsorption of syn-DP by ACC also supported the hypothesis that the enrichment of anti-DP was more likely due to preferential biodegradation of syn-DP in the sediment. Molecular characterization of anti-DP and syn-DP showed that syn-DP had a higher dipole moment, slightly larger Van der Waals volume, but smaller maximal diameter, which might explain its higher uptake rate in biota. (C) 2014 The Authors. Published by Elsevier B.V. This is an open access article under the CC BY-NC-ND licensX111411Ysciescopu

Synthesis and bioluminescence of electronically modified and rotationally restricted colour-shifting infraluciferin analogues

Synthetic nIR emitting luciferins can enable clearer bioluminescent imaging in blood and tissue. A limiting factor for all synthetic luciferins is their reduced light output with respect to D-luciferin. In this work we explore a design feature of whether rigidification of an exceptionally red synthetic luciferin, infraluciferin, can increase light output through a reduction in the degrees of freedom of the molecule. A rigid analogue pyridobenzimidazole infraluciferin was prepared and its bioluminescence properties compared with its non-rigid counterpart benzimidazole infraluciferin, luciferin, infraluciferin and benzimidazole luciferin. The results support the concept that synthetic rigidification of π-extended luciferins can increase bioluminescence activity while maintaining nIR bioluminescence

Investigation of the [1,5]-hydride shift as a route to nitro-Mannich cyclisations

Conditions were found for the [1,5]-hydride shift nitro-Mannich reaction that led to the synthesis of 2,3-disubstituted tetrahydroquinolines. Two simple cyclic amine substrates gave diastereomerically pure rearranged products in 65 and 90% yields by refluxing in HFIP. A more general procedure used Gd(OTf)3 as a catalyst and successfully rearranged other cyclic and acyclic amines in 42–84% yield with diastereomeric ratios of 75:25 to >95:5 in favour of the anti-diastereoisomer (9 examples). Two examples of sulphur containing heterocycles gave lower yields of 9 and 25%. Electron withdrawing substituents were shown to have a deleterious effect on the success of the reaction. The results indicated the limitation of the [1,5]-hydride shift nitro-Mannich reaction with respect to the stability of the intermediate iminium ion

Defunct brain stem cardiovascular regulation underlies cardiovascular collapse associated with methamphetamine intoxication

<p>Abstract</p> <p>Background</p> <p>Intoxication from the psychostimulant methamphetamine (METH) because of cardiovascular collapse is a common cause of death within the abuse population. For obvious reasons, the heart has been taken as the primary target for this METH-induced toxicity. The demonstration that failure of brain stem cardiovascular regulation, rather than the heart, holds the key to cardiovascular collapse induced by the pesticide mevinphos implicates another potential underlying mechanism. The present study evaluated the hypothesis that METH effects acute cardiovascular depression by dampening the functional integrity of baroreflex via an action on brain stem nuclei that are associated with this homeostatic mechanism.</p> <p>Methods</p> <p>The distribution of METH in brain and heart on intravenous administration in male Sprague-Dawley rats, and the resultant changes in arterial pressure (AP), heart rate (HR) and indices for baroreflex-mediated sympathetic vasomotor tone and cardiac responses were evaluated, alongside survival rate and time.</p> <p>Results</p> <p>Intravenous administration of METH (12 or 24 mg/kg) resulted in a time-dependent and dose-dependent distribution of the psychostimulant in brain and heart. <b/>The distribution of METH to neural substrates associated with brain stem cardiovascular regulation was significantly larger than brain targets for its neurological and psychological effects; the concentration of METH in cardiac tissues was the lowest among all tissues studied. In animals that succumbed to METH, the baroreflex-mediated sympathetic vasomotor tone and cardiac response were defunct, concomitant with cessation of AP and HR. On the other hand, although depressed, those two indices in animals that survived were maintained, alongside sustainable AP and HR. Linear regression analysis further revealed that the degree of dampening of brain stem cardiovascular regulation was positively and significantly correlated with the concentration of METH in key neural substrate involved in this homeostatic mechanism.</p> <p>Conclusions</p> <p>We conclude that on intravenous administration, METH exhibits a preferential distribution to brain stem nuclei that are associated with cardiovascular regulation. We further found that the concentration of METH in those brain stem sites dictates the extent that baroreflex-mediated sympathetic vasomotor tone and cardiac responses are compromised, which in turn determines survival or fatality because of cardiovascular collapse.</p

Expression of CD80 and CD86 costimulatory molecules are potential markers for better survival in nasopharyngeal carcinoma

<p>Abstract</p> <p>Background</p> <p>B7 Costimulatory signal is essential to trigger T-cell activation upon the recognition of tumor antigens. This study examined the expression of B7-1 (CD80) and B7-2 (CD86) costimulatory molecules along with HLA-DR and the presence of infiltrating lymphocytes and dendritic cells to assess their significance in patients with nasopharyngeal carcinoma (NPC).</p> <p>Methods</p> <p>Expression of CD80, CD86, HLA-DR, S-100 protein and the presence of infiltrating lymphocytes and follicular dendritic reticulum cells were immunohistochemically examined on the paraffin-embedded tissue blocks from newly diagnosed NPC patients (n = 50). The results were correlated with clinical outcome of patients.</p> <p>Results</p> <p>CD80 and CD86 were each expressed in 10 of 50 cases in which they co-expressed in 9 cases. Univariate analysis revealed that patients with CD80/CD86 expression had significantly better overall survival than those without it (P = 0.017), but after adjustment for stage, nodal status, and treatment, the expression of CD80/CD86 did not significantly correlate with overall survival. Expression of HLA-DR and the presence of infiltrating lymphocytes and dendritic cells did not appear to have impact on the survival of patients.</p> <p>Conclusion</p> <p>Expression of CD80 and CD86 costimulatory molecules appears to be a marker of better survival in patient with NPC.</p

Integrative analysis identifies candidate tumor microenvironment and intracellular signaling pathways that define tumor heterogeneity in NF1

Neurofibromatosis type 1 (NF1) is a monogenic syndrome that gives rise to numerous symptoms including cognitive impairment, skeletal abnormalities, and growth of benign nerve sheath tumors. Nearly all NF1 patients develop cutaneous neurofibromas (cNFs), which occur on the skin surface, whereas 40-60% of patients develop plexiform neurofibromas (pNFs), which are deeply embedded in the peripheral nerves. Patients with pNFs have a ~10% lifetime chance of these tumors becoming malignant peripheral nerve sheath tumors (MPNSTs). These tumors have a severe prognosis and few treatment options other than surgery. Given the lack of therapeutic options available to patients with these tumors, identification of druggable pathways or other key molecular features could aid ongoing therapeutic discovery studies. In this work, we used statistical and machine learning methods to analyze 77 NF1 tumors with genomic data to characterize key signaling pathways that distinguish these tumors and identify candidates for drug development. We identified subsets of latent gene expression variables that may be important in the identification and etiology of cNFs, pNFs, other neurofibromas, and MPNSTs. Furthermore, we characterized the association between these latent variables and genetic variants, immune deconvolution predictions, and protein activity predictions

Preserved neural dynamics across animals performing similar behaviour

Animals of the same species exhibit similar behaviours that are advantageously adapted to their body and environment. These behaviours are shaped at the species level by selection pressures over evolutionary timescales. Yet, it remains unclear how these common behavioural adaptations emerge from the idiosyncratic neural circuitry of each individual. The overall organization of neural circuits is preserved across individuals1 because of their common evolutionarily specified developmental programme2-4. Such organization at the circuit level may constrain neural activity5-8, leading to low-dimensional latent dynamics across the neural population9-11. Accordingly, here we suggested that the shared circuit-level constraints within a species would lead to suitably preserved latent dynamics across individuals. We analysed recordings of neural populations from monkey and mouse motor cortex to demonstrate that neural dynamics in individuals from the same species are surprisingly preserved when they perform similar behaviour. Neural population dynamics were also preserved when animals consciously planned future movements without overt behaviour12 and enabled the decoding of planned and ongoing movement across different individuals. Furthermore, we found that preserved neural dynamics extend beyond cortical regions to the dorsal striatum, an evolutionarily older structure13,14. Finally, we used neural network models to demonstrate that behavioural similarity is necessary but not sufficient for this preservation. We posit that these emergent dynamics result from evolutionary constraints on brain development and thus reflect fundamental properties of the neural basis of behaviour