Learning Deep Latent Spaces for Multi-Label Classification

Multi-label classification is a practical yet challenging task in machine learning related fields, since it requires the prediction of more than one label category for each input instance. We propose a novel deep neural networks (DNN) based model, Canonical Correlated AutoEncoder (C2AE), for solving this task. Aiming at better relating feature and label domain data for improved classification, we uniquely perform joint feature and label embedding by deriving a deep latent space, followed by the introduction of label-correlation sensitive loss function for recovering the predicted label outputs. Our C2AE is achieved by integrating the DNN architectures of canonical correlation analysis and autoencoder, which allows end-to-end learning and prediction with the ability to exploit label dependency. Moreover, our C2AE can be easily extended to address the learning problem with missing labels. Our experiments on multiple datasets with different scales confirm the effectiveness and robustness of our proposed method, which is shown to perform favorably against state-of-the-art methods for multi-label classification.Comment: published in AAAI-201

Distribution and associated factors of optic disc diameter and cup-to-disc ratio in an elderly Chinese population

AbstractBackgroundGlaucoma is the second leading cause of blindness worldwide and East Asian people account for almost half of those affected. Vertical elongation of the optic cup is a characteristic feature of glaucoma. However, there is a significant overlap in the vertical cup-to-disc ratio (VCDR) between normal eyes and eyes affected by glaucoma. The purpose of this study was to determine the distribution of VCDR and vertical disc diameter (VDD) and their predictive factors in a population of elderly Chinese residents in Taiwan.MethodsFour hundred and sixty elderly Chinese residents aged 72 years and older in the Shihpai district, Taipei, Taiwan participated in this study. Slit lamp biomicroscopic measurement of the VCDR and VDD after pupil dilation with a 78 diopter lens was performed by one glaucoma specialist. Multiple linear regression analyses were used to fit the best model for independent variables.ResultsThe VCDR was recorded for 438 right eyes and 430 left eyes. After excluding participants with glaucoma, the mean ± SD VCDR was 0.44 ± 0.17 for both eyes, and the 97.5th percentile was 0.8. A greater VCDR was associated with a longer axial length [VCDR = −0.47 + 0.04(axial length)] under multiple regression analysis. The VDD was obtained for 420 right eyes and 406 left eyes. The mean ± SD VDD for all participants was 1.77 ± 0.22 mm for the right eye and 1.79 ± 0.22 mm for the left eye. A higher body mass index (BMI) and a longer axial length were significantly associated with a larger VDD under multiple regression analysis. [VDD = −0.05 + 0.07 (axial length) + 0.06 (obesity); if BMI <24, then obesity = 0; if BMI ≥24, then obesity = 1]. A larger VDD was associated with a larger VCDR (p < 0.001) and the VCDR could be predicted by the equation VCDR = −0.07 + 0.3VDD.ConclusionA greater VCDR was related to a longer axial length. A greater VDD was related to a higher BMI and a longer axial length

Ser-634 and Ser-636 of Kaposi’s Sarcoma-Associated Herpesvirus RTA are Involved in Transactivation and are Potential Cdk9 Phosphorylation Sites

The replication and transcription activator (RTA) of Kaposi’s sarcoma-associated herpesvirus (KSHV), K-RTA, is a lytic switch protein that moderates the reactivation process of KSHV latency. By mass spectrometric analysis of affinity purified K-RTA, we showed that Thr-513 or Thr-514 was the primary in vivo phosphorylation site. Thr-513 and Thr-514 are proximal to the nuclear localization signal (527KKRK530) and were previously hypothesized to be target sites of Ser/Thr kinase hKFC. However, substitutions of Thr with Ala at 513 and 514 had no effect on K-RTA subcellular localization or transactivation activity. By contrast, replacement of Ser with Ala at Ser-634 and Ser-636 located in a Ser/Pro-rich region of K-RTA, designated as S634A/S636A, produced a polypeptide with ∼10 kDa shorter in molecular weight and reduced transactivation in a luciferase reporter assay relative to the wild type. In contrast to prediction, the decrease in molecular weight was not due to lack of phosphorylation because the overall Ser and Thr phosphorylation state in K-RTA and S634A/S636A were similar, excluding that Ser-634 or Ser-636 motif served as docking sites for consecutive phosphorylation. Interestingly, S634A/S636A lost ∼30% immuno-reactivity to MPM2, an antibody specific to pSer/pThr-Pro motif, indicating that 634SPSP637 motif was in vivo phosphorylated. By in vitro kinase assay, we showed that K-RTA is a substrate of CDK9, a Pro-directed Ser/Thr kinase central to transcriptional regulation. Importantly, the capability of K-RTA in associating with endogenous CDK9 was reduced in S634A/S636A, which suggested that Ser-634 and Ser-636 may be involved in CDK9 recruitment. In agreement, S634A/S636A mutant exhibited ∼25% reduction in KSHV lytic cycle reactivation relative to that by the wild type K-RTA. Taken together, our data propose that Ser-634 and Ser-636 of K-RTA are phosphorylated by host transcriptional kinase CDK9 and such a process contributes to a full transcriptional potency of K-RTA

ATIVS: analytical tool for influenza virus surveillance

The WHO Global Influenza Surveillance Network has routinely performed genetic and antigenic analyses of human influenza viruses to monitor influenza activity. Although these analyses provide supporting data for the selection of vaccine strains, it seems desirable to have user-friendly tools to visualize the antigenic evolution of influenza viruses for the purpose of surveillance. To meet this need, we have developed a web server, ATIVS (Analytical Tool for Influenza Virus Surveillance), for analyzing serological data of all influenza viruses and hemagglutinin sequence data of human influenza A/H3N2 viruses so as to generate antigenic maps for influenza surveillance and vaccine strain selection. Functionalities are described and examples are provided to illustrate its usefulness and performance. The ATIVS web server is available at http://influenza.nhri.org.tw/ATIVS/

Impacts of Tides and Typhoon Fanapi (2010) on Seas Around Taiwan

We used satellite data, typhoon-resolving atmospheric forcing and a data assimilating ocean model, the East Asian Seas Nowcast/Forecast System (EASNFS), to investigate circulation and three upwelling regions perturbed by tides and Typhoon Fanapi (2010) in the seas around Taiwan. The three upwelling areas located off northeast Taiwan, off southeast China and over the Penghu Channel off southwest Taiwan are normally limited in expanse before Fanapi. The tidal currents enhance all three. To cope with typhoon strength atmospheric forcing, we applied typhoon-resolving Weather Research and Forecasting (WRF) model wind fields that significantly enhanced Fanapi-induced upwelling. Approaching Taiwan, Fanapi induces a cold wake spreading preferably on the right side of the essentially westward running track in the western Pacific. The three upwelling areas in the East China Sea and Taiwan Strait subsequently become expansive as Fanapi approaches and enters the Taiwan Strait. The mechanisms leading to normal or Fanapi-perturbed upwelling and circulation in seas around Taiwan, especially the latter two mentioned above, are suggested. In essence, Fanapi disrupts circulation in the Taiwan Strait, and also the Taiwan Strait outflow entering the East China Sea, leading to expanded upwelling areas. We also suggest that high-resolution wind and tides application is essential for the upwelling modeling study and also the general circulation in the region with and without typhoons

Genotoxic Klebsiella pneumoniae in Taiwan

Colibactin is a nonribosomal peptide-polyketide synthesized by multi-enzyme complexes encoded by the pks gene cluster. Colibactin-producing Escherichia coli have been demonstrated to induce host DNA damage and promote colorectal cancer (CRC) development. In Taiwan, the occurrence of pyogenic liver abscess (PLA) has been suggested to correlate with an increasing risk of CRC, and Klebsiella pneumoniae is the predominant PLA pathogen in Taiwan

Neuromagnetic amygdala response to pain-related fear as a brain signature of fibromyalgia

Fibromyalgia (FM) is a chronic pain condition characterized by impaired emotional regulation. This study explored the brain response to pain-related fear as a potential brain signature of FM

Arrhythmogenic Calmodulin Mutations Impede Activation of Small-conductance Calcium-Activated Potassium Current

Background Apamin sensitive small-conductance Ca2+-activated K+ (SK) channels are gated by intracellular Ca2+ through a constitutive interaction with calmodulin. Objective We hypothesize that arrhythmogenic human calmodulin mutations impede activation of SK channels. Methods We studied 5 previously published calmodulin mutations (N54I, N98S, D96V, D130G and F90L). Plasmids encoding either wild type (WT) or mutant calmodulin were transiently transfected into human embryonic kidney (HEK) 293 cells that stably express SK2 channels (SK2 Cells). Whole-cell voltage-clamp recording was used to determine apamin-sensitive current (IKAS) densities. We also performed optical mapping studies in normal murine hearts to determine the effects of apamin in hearts with (N=7) or without (N=3) pretreatment with sea anemone toxin (ATX II). Results SK2 cells transfected with WT calmodulin exhibited IKAS density (in pA/pF) of 33.6 [31.4;36.5] (median and confidence interval 25%-75%), significantly higher than that observed for cells transfected with N54I (17.0 [14.0;27.7], p=0.016), F90L (22.6 [20.3;24.3], p=0.011), D96V (13.0 [10.9;15.8], p=0.003), N98S (13.7 [8.8;20.4], p=0.005) and D130G (17.6 [13.8;24.6], p=0.003). The reduction of SK2 current was not associated with a decrease in membrane protein expression or intracellular distribution of the channel protein. Apamin increased the ventricular APD80 (from 79.6 ms [63.4-93.3] to 121.8 ms [97.9-127.2], p=0.010) in hearts pre-treated with ATX-II but not in control hearts. Conclusion Human arrhythmogenic calmodulin mutations impede the activation of SK2 channels in HEK 293 cells

Measuring galaxy cluster mass profiles into the low acceleration regime with galaxy kinematics

We probe the dynamical mass profiles of 10 galaxy clusters from the HIghest X-ray FLUx Galaxy Cluster Sample (HIFLUGCS) using galaxy kinematics. We numerically solve the spherical Jeans equation, and parameterize the dynamical mass profile and the galaxy velocity anisotropy profile using two general functions to ensure that our results are not biased towards any specific model. The mass-velocity anisotropy degeneracy is ameliorated by using two "virial shape parameters" that depend on the fourth moment of velocity distribution. The resulting velocity anisotropy estimates consistently show a nearly isotropic distribution in the inner regions, with an increasing radial anisotropy towards large radii. We compare our derived dynamical masses with those calculated from X-ray gas data assuming hydrostatic equilibrium, finding that massive and rich relaxed clusters generally present consistent mass measurements, while unrelaxed or low-richness clusters have systematically larger total mass than hydrostatic mass by an average of 50\%. This might help alleviate current tensions in the measurement of $\sigma_8$, but it also leads to cluster baryon fractions below the cosmic value. Finally, our approach probes accelerations as low as $10^{-11}$ m s$^{-2}$, comparable to the outskirts of individual late-type galaxies. We confirm that galaxy clusters deviate from the radial acceleration relation defined by galaxies.Comment: 16 pages, 8 figures, 1 table. A&A accepted versio