Denoising Cosine Similarity: A Theory-Driven Approach for Efficient Representation Learning

Representation learning has been increasing its impact on the research and practice of machine learning, since it enables to learn representations that can apply to various downstream tasks efficiently. However, recent works pay little attention to the fact that real-world datasets used during the stage of representation learning are commonly contaminated by noise, which can degrade the quality of learned representations. This paper tackles the problem to learn robust representations against noise in a raw dataset. To this end, inspired by recent works on denoising and the success of the cosine-similarity-based objective functions in representation learning, we propose the denoising Cosine-Similarity (dCS) loss. The dCS loss is a modified cosine-similarity loss and incorporates a denoising property, which is supported by both our theoretical and empirical findings. To make the dCS loss implementable, we also construct the estimators of the dCS loss with statistical guarantees. Finally, we empirically show the efficiency of the dCS loss over the baseline objective functions in vision and speech domains

Biological responses according to the shape and size of carbon nanotubes in BEAS-2B and MESO-1 cells

This study aimed to investigate the influence of the shape and size of multi-walled carbon nanotubes (MWCNTs) and cup-stacked carbon nanotubes (CSCNTs) on biological responses in vitro. Three types of MWCNTs - VGCF (R)-X, VGCF (R)-S, and VGCF (R) (vapor grown carbon fibers; with diameters of 15, 80, and 150 nm, respectively) - and three CSCNTs of different lengths (CS-L, 20-80 mu m; CS-S, 0.5-20 mu m; and CS-M, of intermediate length) were tested. Human bronchial epithelial (BEAS-2B) and malignant pleural mesothelioma cells were exposed to the CNTs (1-50 mu g/mL), and cell viability, permeability, uptake, total reactive oxygen species/superoxide production, and intracellular acidity were measured. CSCNTs were less toxic than MWCNTs in both cell types over a 24-hour exposure period. The cytotoxicity of endocytosed MWCNTs varied according to cell type/size, while that of CSCNTs depended on tube length irrespective of cell type. CNT diameter and length influenced cell aggregation and injury extent. Intracellular acidity increased independently of lysosomal activity along with the number of vacuoles in BEAS-2B cells exposed for 24 hours to either CNT (concentration, 10 mu g/mL). However, total reactive oxygen species/superoxide generation did not contribute to cytotoxicity. The results demonstrate that CSCNTs could be suitable for biological applications and that CNT shape and size can have differential effects depending on cell type, which can be exploited in the development of highly specialized, biocompatible CNTs.ArticleINTERNATIONAL JOURNAL OF NANOMEDICINE. 9:1979-1990 (2014)journal articl

Preliminary evaluation of translated and culturally adapted internet-delivered cognitive therapy for social anxiety disorder: multicenter, single-arm trial in japan

Background: Internet-delivered cognitive therapy for social anxiety disorder (iCT-SAD), which is a therapist-guided modular web-based treatment, has shown strong efficacy and acceptability in English-language randomized controlled trials in the United Kingdom and Hong Kong. However, it is not yet known whether iCT-SAD can retain its efficacy following linguistic translation and cultural adaptation of treatment contents and implementation in other countries such as Japan. Objective: This study aimed to examine the preliminary efficacy and acceptability of the translated and culturally adapted iCT-SAD in Japanese clinical settings. Methods: This multicenter, single-arm trial recruited 15 participants with social anxiety disorder. At the time of recruitment, participants were receiving usual psychiatric care but had not shown improvement in their social anxiety and required additional treatment. iCT-SAD was provided in combination with usual psychiatric care for 14 weeks (treatment phase) and for a subsequent 3-month follow-up phase that included up to 3 booster sessions. The primary outcome measure was the self-report version of the Liebowitz Social Anxiety Scale. The secondary outcome measures examined social anxiety–related psychological processes, taijin kyofusho (the fear of offending others), depression, generalized anxiety, and general functioning. The assessment points for the outcome measures were baseline (week 0), midtreatment (week 8), posttreatment (week 15; primary assessment point), and follow-up (week 26). Acceptability was measured using the dropout rate from the treatment, the level of engagement with the program (the rate of module completion), and participants’ feedback about their experience with the iCT-SAD. Results: Evaluation of the outcome measures data showed that iCT-SAD led to significant improvements in social anxiety symptoms during the treatment phase (P<.001; Cohen d=3.66), and these improvements were maintained during the follow-up phase. Similar results were observed for the secondary outcome measures. At the end of the treatment phase, 80% (12/15) of participants demonstrated reliable improvement, and 60% (9/15) of participants demonstrated remission from social anxiety. Moreover, 7% (1/15) of participants dropped out during treatment, and 7% (1/15) of participants declined to undergo the follow-up phase after completing the treatment. No serious adverse events occurred. On average, participants completed 94% of the modules released to them. Participant feedback was positive and highlighted areas of strength in treatment, and it included further suggestions to improve suitability for Japanese settings. Conclusions: Translated and culturally adapted iCT-SAD demonstrated promising initial efficacy and acceptability for Japanese clients with social anxiety disorder. A randomized controlled trial is required to examine this more robustly

Culture medium type affects endocytosis of multi-walled carbon nanotubes in BEAS-2B cells and subsequent biological response

AbstractWe examined the cytotoxicity of multi-walled carbon nanotubes (MWCNTs) and the resulting cytokine secretion in BEAS-2B cells or normal human bronchial epithelial cells (HBEpCs) in two types of culture media (Ham’s F12 containing 10% FBS [Ham’s F12] and serum-free growth medium [SFGM]). Cellular uptake of MWCNT was observed by fluorescent microscopy and analyzed using flow cytometry. Moreover, we evaluated whether MWCNT uptake was suppressed by 2 types of endocytosis inhibitors. We found that BEAS-2B cells cultured in Ham’s F12 and HBEpCs cultured in SFGM showed similar biological responses, but BEAS-2B cells cultured in SFGM did not internalize MWCNTs, and the 50% inhibitory concentration value, i.e., the cytotoxicity, was increased by more than 10-fold. MWCNT uptake was suppressed by a clathrin-mediated endocytosis inhibitor and a caveolae-mediated endocytosis inhibitor in BEAS-2B cells cultured in Ham’s F12 and HBEpCs cultured in SFGM. In conclusion, we suggest that BEAS-2B cells cultured in a medium containing serum should be used for the safety evaluation of nanomaterials as a model of normal human bronchial epithelial cells. However, the culture medium composition may affect the proteins that are expressed on the cytoplasmic membrane, which may influence the biological response to MWCNTs

The FLUXNET2015 dataset and the ONEFlux processing pipeline for eddy covariance data

The FLUXNET2015 dataset provides ecosystem-scale data on CO2, water, and energy exchange between the biosphere and the atmosphere, and other meteorological and biological measurements, from 212 sites around the globe (over 1500 site-years, up to and including year 2014). These sites, independently managed and operated, voluntarily contributed their data to create global datasets. Data were quality controlled and processed using uniform methods, to improve consistency and intercomparability across sites. The dataset is already being used in a number of applications, including ecophysiology studies, remote sensing studies, and development of ecosystem and Earth system models. FLUXNET2015 includes derived-data products, such as gap-filled time series, ecosystem respiration and photosynthetic uptake estimates, estimation of uncertainties, and metadata about the measurements, presented for the first time in this paper. In addition, 206 of these sites are for the first time distributed under a Creative Commons (CC-BY 4.0) license. This paper details this enhanced dataset and the processing methods, now made available as open-source codes, making the dataset more accessible, transparent, and reproducible.Peer reviewe

Overexpression of lung resistance-related protein and P-glycoprotein and response to induction chemotherapy in acute myelogenous leukemia

Lung resistance-related protein (LRP) and P-glycoprotein (P-gp) are associated with multidrug resistance. P-gp overexpression reduces intracellular anticancer drug concentrations and is correlated with low remission rates. However, whether the presence of LRP influences the response to induction chemotherapy remains controversial. Therefore, we investigated the relationship of LRP and P-gp overexpression with the response to induction chemotherapy. Univariate analysis revealed that there was a significant difference between complete remission rates for acute myelogenous leukemia patients depending on their blast cell expressions, between LRP positive versus negative, P-gp positive versus negative, and LRP/P-gp double positive versus other groups. Crude odds ratios (ORs) for complete remission were 0.390, 0.360, and 0.307 for LRP positive, for P-gp positive, and LRP/P- gp double positive patients, respectively. After controlling the confounding variables by stepwise multivariate logistical regression analysis, the presence of LRP/P-gp double positivity and P-gp positivity were found to be independent prognostic factors; adjusted ORs were 0.233 and 0.393, respectively. Furthermore, the monoclonal antibody against LRP significantly increased daunorubicin acumulation (P=0.004) in the nuclei of leukemic blast cells with LRP positivity in more than 10% of the cells. An LRP reversing agent, PAK-104P, was found to increase the daunorubicin content with marginal significance (P=0.060). The present results suggest that not only the presence of P-gp, but also LRP in leukemic blast cells is a risk factor for resistance to induction chemotherapy. Inhibiting LRP function, similar to the inhibition of P-gp function, will be necessary to improve the effectiveness of induction chemotherapy