A-SFS: Semi-supervised Feature Selection based on Multi-task Self-supervision

Feature selection is an important process in machine learning. It builds an interpretable and robust model by selecting the features that contribute the most to the prediction target. However, most mature feature selection algorithms, including supervised and semi-supervised, fail to fully exploit the complex potential structure between features. We believe that these structures are very important for the feature selection process, especially when labels are lacking and data is noisy. To this end, we innovatively introduce a deep learning-based self-supervised mechanism into feature selection problems, namely batch-Attention-based Self-supervision Feature Selection(A-SFS). Firstly, a multi-task self-supervised autoencoder is designed to uncover the hidden structure among features with the support of two pretext tasks. Guided by the integrated information from the multi-self-supervised learning model, a batch-attention mechanism is designed to generate feature weights according to batch-based feature selection patterns to alleviate the impacts introduced by a handful of noisy data. This method is compared to 14 major strong benchmarks, including LightGBM and XGBoost. Experimental results show that A-SFS achieves the highest accuracy in most datasets. Furthermore, this design significantly reduces the reliance on labels, with only 1/10 labeled data needed to achieve the same performance as those state of art baselines. Results show that A-SFS is also most robust to the noisy and missing data.Comment: 18 pages, 7 figures, accepted by knowledge-based system

Reinforcement of natural rubber with core-shell structure silica-poly(Methyl Methacrylate) nanoparticles

A highly performing natural rubber/silica (NR/SiO2) nanocomposite with a SiO2 loading of 2 wt% was prepared by combining similar dissolve mutually theory with latex compounding techniques. Before polymerization, double bonds were introduced onto the surface of the SiO2 particles with the silane-coupling agent. The core-shell structure silica-poly(methyl methacrylate), SiO2-PMMA, nanoparticles were formed by grafting polymerization of MMA on the surface of the modified SiO2 particles via in situ emulsion, and then NR/SiO2 nanocomposite was prepared by blending SiO2-PMMA and PMMA-modified NR (NR-PMMA). The Fourier transform infrared spectroscopy results show that PMMA has been successfully introduced onto the surface of SiO2, which can be well dispersed in NR matrix and present good interfacial adhesion with NR phase. Compared with those of pure NR, the thermal resistance and tensile properties of NR/SiO2 nanocomposite are significantly improved

Nevirapine Plasma Concentrations Are Associated with Virologic Response and Hepatotoxicity in Chinese Patients with HIV Infection

BACKGROUND: Limited information is available on the relationship between nevirapine plasma concentrations and virologic response or liver toxicity in Chinese patients with HIV infection. The objective of this prospective study was to test this relationship and to determine the minimal therapeutic trough concentration of nevirapine for Chinese patients. METHODS: A total of 227 HIV-infected, treatment naïve patients were enrolled into this study. Blood samples were taken at C(trough) (12 hr postdose) and C(2) (2 hr postdose) for measurement of nevirapine concentrations 6 months after treatment initiation. Therapeutic outcomes, viral load and CD4 cell count, were assessed at 3 and 6 months after starting therapy, while the evaluation of hepatotoxicity was undertaken 12 months after nevirapine treatment. RESULTS: A significant correlation between nevirapine trough concentrations and viral load was noticed after 6 months of treatment, particularly in patients with partial response and viral failure (p<0.01). The therapeutic C(trough) of nevirapine for Chinese patients was determined to be 3.9 µg/ml using the receiver operating characteristic curve. Virologic failure was observed in 21% (6/29) of patients with low nevirapine concentrations (<3.9 µg/ml) versus 5% (4/87) in patients with concentrations higher than 3.9 µg/ml (p = 0.015). Hepatotoxicity was significantly associated with the median nevirapine trough concentrations among male patients (8.20 vs. 5.48 µg/ml, p = 0.015) and hepatitis C virus co-infection (p = 0.039). CONCLUSIONS: Among Chinese patients with HIV infection, the therapeutic C(trough) of nevirapine was 3.9 µg/ml, higher than the recommended 3.0 µg/ml. The correlation between nevirapine concentrations, efficacy and hepatotoxicity suggests the benefit of dosage adjustment based on therapeutic drug monitoring among Chinese HIV-infected patients to optimize nevirapine containing antiretroviral therapy

Doppler Wind Lidar From UV to NIR: A Review With Case Study Examples

Doppler wind lidar (DWL) uses the optical Doppler effect to measure atmospheric wind speed with high spatial-temporal resolution and long detection range and has been widely applied in scientific research and engineering applications. With the development of related technology, especially laser and detector technology, the performance of the DWL has significantly improved for the past few decades. DWL utilizes different principles and different tracers to sense the wind speed from the ground to the mesosphere, which leads to the difference in choosing the laser working wavelength. This article will review the working wavelength consideration of DWL, and typical DWLs will present from ultraviolet to near-infrared, after which three typical applications will be shown

Association Between Gut Microbiota and CD4 Recovery in HIV-1 Infected Patients

Composition of the gut microbiota has been linked with human immunedeficiency virus (HIV)-infected patients on antiretroviral therapy (ART). Evidence suggests that ART-treated patients with poor CD4+ T-cell recovery have higher levels of microbial translocation and immune activation. However, the association of the gut microbiota and immune recovery remains unclear. We performed a cross-sectional study on 30 healthy controls (HC) and 61 HIV-infected individuals, including 15 immunological ART responders (IRs), 20 immunological ART non-responders (INRs) and 26 untreated individuals (VU). IR and INR groups were classified by CD4+ T-cell counts of ≥350 cells/mm3 and &lt;350 cells/mm3 after 2 years of ART, respectively. Each subject’s gut microbiota composition was analyzed by metagenomics sequencing. Levels of CD4+ T cells, CD8+HLA-DR+ T cells and CD8+CD38+ T cells were measured by flow cytometry. We identified more Prevotella and fewer Bacteroides in HIV-infected individuals than in HC. Patients in INR group were enriched with Faecalibacterium prausnitzii, unclassified Subdoligranulum sp. and Coprococcus comes when compared with those in IR group. F. prausnitzii and unclassified Subdoligranulum sp. were overrepresented in individuals in VU group with CD4+ T-cell counts &lt;350 cells/mm3. Moreover, we found that the relative abundance of unclassified Subdoligranulum sp. and C. comes were positively correlated with CD8+HLA-DR+ T-cell count and CD8+HLA-DR+/CD8+ percentage. Our study has shown that gut microbiota changes were associated with CD4+ T-cell counts and immune activation in HIV-infected subjects. Interventions to reverse gut dysbiosis and inhibit immune activation could be a new strategy for improving immune reconstitution of HIV-1-infected individuals

Three Generic Nevirapine-Based Antiretroviral Treatments in Chinese HIV/AIDS Patients: Multicentric Observation Cohort

The purpose of this study was to evaluate the efficacy and safety of three nevirapine-based antiretroviral treatments for adult antiretroviral-naïve Chinese patients with HIV-1 infection.This was a prospective, multicenter study. 198 antiretroviral-naïve HIV-1 positive subjects with CD4 lymphocyte counts between 100/ul and 350/ul and plasma HIV-1 RNA levels more than 500 copies/ml were randomized to start three NVP-based antiretroviral treatments: group A, NVP+AZT+ddI; group B, NVP+3TC+d4T; group C, NVP+AZT+3TC. Viral responses, immunologic responses, adverse events and drug resistance were monitored at baseline and the end of week 4, 12, 24, 36, 52. Viralogical response and immunological response were also compared in different strata of baseline CD4 T lymphocyte counts and plasma HIV-1 RNA concentrations. At baseline, the plasma HIV-1 RNA was 4.44+/-0.68, 4.52+/-0.71 and 4.41+/-0.63 lg copies/ml in group A, B and C respectively (p = 0.628). At the end of the study, the plasma viral load reached 2.54+/-1.11, 1.89+/-0.46 and 1.92+/-0.58 lg copies/ml in group A, B and C respectively (p<0.001). At week 52, suppression of plasma HIV-1 RNA to less than 50 copies/ml was achieved in more patients in group B and C than in group A (68.2%, 69% vs. 39.7%; p<0.001). In planned subgroup analyses, the decrease of viral response rate was seen in group A when CD4 cell count >200/ul (subgroup H). But in subgroup L, viral response rate of three groups has no significant statistic difference. There were no statistically significant differences among three groups in immunological response within any of the CD4 or pVL strata. 3 out of 193 patients with available genotype at baseline showed primary drug resistant. Of 26 patients with virologic failure, 17 patients showed secondary drug resistant, 16 subjects in group A and 1 subject in group B. Logistic regression analysis indicated that presence of hepatotoxicity was associated with HCV-Ab positive (OR = 2.096, 95%CI: 1.106-3.973, P = 0.023) and higher CD4 baseline (CD4 count >250/ul) (OR = 2.096, 95%CI: 1.07-4.107, P = 0.031).Our findings strongly support the use of 3TC+d4T and 3TC+AZT as the nucleoside analogue combination in NVP-based antiretroviral therapy. The regimen of AZT+ddI+NVP produced poor virological response especially in the stratum of CD4 count more than 200/ul. More patients showed secondary drug resistant in this arm too. Patients with HCV-Ab+ and CD4 count >250/ul appear to have significantly high risk of hepatoxicity.ClinicalTrials.gov NCT00618176

Spatiotemporal transcriptomic atlas of mouse organogenesis using DNA nanoball-patterned arrays.

Spatially resolved transcriptomic technologies are promising tools to study complex biological processes such as mammalian embryogenesis. However, the imbalance between resolution, gene capture, and field of view of current methodologies precludes their systematic application to analyze relatively large and three-dimensional mid- and late-gestation embryos. Here, we combined DNA nanoball (DNB)-patterned arrays and in situ RNA capture to create spatial enhanced resolution omics-sequencing (Stereo-seq). We applied Stereo-seq to generate the mouse organogenesis spatiotemporal transcriptomic atlas (MOSTA), which maps with single-cell resolution and high sensitivity the kinetics and directionality of transcriptional variation during mouse organogenesis. We used this information to gain insight into the molecular basis of spatial cell heterogeneity and cell fate specification in developing tissues such as the dorsal midbrain. Our panoramic atlas will facilitate in-depth investigation of longstanding questions concerning normal and abnormal mammalian development.This work is part of the ‘‘SpatioTemporal Omics Consortium’’ (STOC) paper package. A list of STOC members is available at: http://sto-consortium.org. We would like to thank the MOTIC China Group, Rongqin Ke (Huaqiao University, Xiamen, China), Jiazuan Ni (Shenzhen University, Shenzhen, China), Wei Huang (Center for Excellence in Brain Science and Intelligence Technology, Chinese Academy of Sciences, Shanghai, China), and Jonathan S. Weissman (Whitehead Institute, Boston, USA) for their help. This work was supported by the grant of Top Ten Foundamental Research Institutes of Shenzhen, the Shenzhen Key Laboratory of Single-Cell Omics (ZDSYS20190902093613831), and the Guangdong Provincial Key Laboratory of Genome Read and Write (2017B030301011); Longqi Liu was supported by the National Natural Science Foundation of China (31900466) and Miguel A. Esteban’s laboratory at the Guangzhou Institutes of Biomedicine and Health by the Strategic Priority Research Program of the Chinese Academy of Sciences (XDA16030502), National Natural Science Foundation of China (92068106), and the Guangdong Basic and Applied Basic Research Foundation (2021B1515120075).S