CRF07_BC Strain Dominates the HIV-1 Epidemic in Injection Drug Users in Liangshan Prefecture of Sichuan, China

The Liangshan prefecture in Sichuan province is an area in China severely affected by the HIV epidemic, with intravenous drug use (IDU) as the main risk factor. No reports on HIV subtypes prevalent in IDUs in Liangshan prefecture could be found. In this study, we have characterized the genotypes of HIV-1 in the IDU population in Liangshan prefecture and further determined the phylogenetic relationship of the CRF07_BC strains to HIV-1 sequences from the other regions of China, including Xinjiang and Yunnan provinces, to explore the pattern and possible diffusion pathway of HIV-1 in these regions. HIV-1-seropositive drug-naive IDUs identified in Liangshan prefecture, Sichuan province were enrolled in 2009. Full-length gag and pol genes were amplified by reverse transcription and nested PCR and then sequenced. All of the sequences were subtyped. Phylogenetic trees were constructed using the neighbor-joining and maximum likelihood methods. Divergence times were estimated using a Bayesian molecular clock approach. CRF07_BC was found to be the predominant strain in IDUs in Liangshan prefecture (95.5%). The CRF07_BC strains from Liangshan prefecture were found to be intermixed with those from Yunnan province in phylogenetic trees. The CRF07_BC sequences from Xinjiang province can be grouped into several clusters, suggesting that the expansion of the CRF07_BC epidemic in Xinjiang province was the result of a local epidemic driven by multiple independent introductions in the late 1990s. Only low-level drug-resistant viruses were found in the IDU population. CRF07_BC strains from Liangshan prefecture were more similar to those from Yunnan province than those from Xinjiang province. This finding will contribute to our understanding of the distribution, the evolution, and the potential source of CRF07_BC founder strains, and will also provide useful information for the development of strategies to prevent transmission

NNCD-IQA: A new neural networks based compressed database for image quality assessment

International audienceObjective and subjective quality assessment is still a challenging problem in various image processing tasks. For instance, in the context of image compression, most of the conducted studies have focused on image datasets encoded using standard algorithms such as JPEG and JPEG2000. In this paper, we propose to further investigate the quality assessment issue in the presence of neural networks-based compressed images. More precisely, a new database of compressed images has been firstly built using JPEG2000 standard as well as four recent neural networks based coding schemes. Then, subjective experiments are performed to obtain the mean opinion scores of the generated distorted images. Finally, an extensive evaluation and analysis of objective image quality assessment metrics is achieved. For instance, in addition to conventional and machine learning metrics, we have considered different deep learning based models, which have been trained on our database. The new subjective database with its associated mean opinion scores as well as the learned models are publicly available at https://github.com/zakopz/NNCD-IQA-Database. The obtained results show the interest of deep learning based metrics in the context of neural networks-based compressed images. Keywords Image compression • Neural networks • Quality assessment • Subjective scores • Learning based metrics Zohaib Amjad Khan and Tassnim Dardouri contributed equally

A Novel Double Ensemble Algorithm for the Classification of Multi-Class Imbalanced Hyperspectral Data

International audienceThe class imbalance problem has been reported to exist in remote sensing and hinders the classification performance of many machine learning algorithms. Several technologies, such as data sampling methods, feature selection-based methods, and ensemble-based methods, have been proposed to solve the class imbalance problem. However, these methods suffer from the loss of useful information or from artificial noise, or result in overfitting. A novel double ensemble algorithm is proposed to deal with the multi-class imbalance problem of the hyperspectral image in this paper. This method first computes the feature importance values of the hyperspectral data via an ensemble model, then produces several balanced data sets based on oversampling and builds a number of classifiers. Finally, the classification results of these diversity classifiers are combined according to a specific ensemble rule. In the experiment, different data-handling methods and classification methods including random undersampling (RUS), random oversampling (ROS), Adaboost, Bagging, and random forest are compared with the proposed double random forest method. The experimental results on three imbalanced hyperspectral data sets demonstrate the effectiveness of the proposed algorithm

MiR-199-3p Suppressed Inflammatory Response by Targeting MECP2 to Alleviate RTX-Induced PHN in Mice

Varicella zoster virus–induced postherpetic neuralgia (PHN) can be alleviated by limited medications with serious side effects. This study aims to investigate the underlying molecular mechanism of miR-199-3p in mediating PHN in mice. 293T cells were transfected with miR-199-3p vectors (mimic/inhibitor). The target relationship between miR-199-3p and MECP2 was confirmed using luciferase reporter assay. PHN mouse model was established by TRX injection. Animal behaviors were evaluated using Hargreaves test and Von Frey test. Western blot was used for protein analysis, and quantitative reverse transcription polymerase chain reaction was performed for messenger RNA quantification. Serum levels of inflammatory mediators were determined using ELISA. Increased thermal withdrawal latency (TWL) and decreased mechanical withdrawal threshold (MWT) were observed in resiniferatoxin-induced PHN mice. Downregulated miR-199-3p and upregulated MECP2 were found in PHN mice. Upregulated miR-199-3p increased PWL and MWT, but inhibited MECP2 in PHN mice. Besides, increased miR-199-3p suppressed proinflammatory indicators and activated anti-inflammatory mediators. It also found that MECP2 was the target of miR-199-3p. Further study showed miR-199-3p enhanced PWL and MWT, and supported inflammatory response via targeting MECP2. miR-199-3p regulated inflammation by targeting MECP2 to alleviate TRX-induced PHN in mice

CRF07_BC Strain Dominates the HIV-1 Epidemic in Injection Drug Users in Liangshan Prefecture of Sichuan, China

The Liangshan prefecture in Sichuan province is an area in China severely affected by the HIV epidemic, with intravenous drug use (IDU) as the main risk factor. No reports on HIV subtypes prevalent in IDUs in Liangshan prefecture could be found. In this study, we have characterized the genotypes of HIV-1 in the IDU population in Liangshan prefecture and further determined the phylogenetic relationship of the CRF07_BC strains to HIV-1 sequences from the other regions of China, including Xinjiang and Yunnan provinces, to explore the pattern and possible diffusion pathway of HIV-1 in these regions. HIV-1-seropositive drug-naive IDUs identified in Liangshan prefecture, Sichuan province were enrolled in 2009. Full-length gag and pol genes were amplified by reverse transcription and nested PCR and then sequenced. All of the sequences were subtyped. Phylogenetic trees were constructed using the neighbor-joining and maximum likelihood methods. Divergence times were estimated using a Bayesian molecular clock approach. CRF07_BC was found to be the predominant strain in IDUs in Liangshan prefecture (95.5%). The CRF07_BC strains from Liangshan prefecture were found to be intermixed with those from Yunnan province in phylogenetic trees. The CRF07_BC sequences from Xinjiang province can be grouped into several clusters, suggesting that the expansion of the CRF07_BC epidemic in Xinjiang province was the result of a local epidemic driven by multiple independent introductions in the late 1990s. Only low-level drug-resistant viruses were found in the IDU population. CRF07_BC strains from Liangshan prefecture were more similar to those from Yunnan province than those from Xinjiang province. This finding will contribute to our understanding of the distribution, the evolution, and the potential source of CRF07_BC founder strains, and will also provide useful information for the development of strategies to prevent transmission

Construction of Whole Genome Radiation Hybrid Panels and Map of Chromosome 5A of Wheat Using Asymmetric Somatic Hybridization

<div><p>To explore the feasibility of constructing a whole genome radiation hybrid (WGRH) map in plant species with large genomes, asymmetric somatic hybridization between wheat (<em>Triticum aestivum</em> L.) and <em>Bupleurum scorzonerifolium</em> Willd. was performed. The protoplasts of wheat were irradiated with ultraviolet light (UV) and gamma-ray and rescued by protoplast fusion using <em>B. scorzonerifolium</em> as the recipient. Assessment of SSR markers showed that the radiation hybrids have the average marker retention frequency of 15.5%. Two RH panels (RHPWI and RHPWII) that contained 92 and 184 radiation hybrids, respectively, were developed and used for mapping of 68 SSR markers in chromosome 5A of wheat. A total of 1557 and 2034 breaks were detected in each panel. The RH map of chromosome 5A based on RHPWII was constructed. The distance of the comprehensive map was 2103 cR and the approximate resolution was estimated to be ∼501.6 kb/break. The RH panels evaluated in this study enabled us to order the ESTs in a single deletion bin or in the multiple bins cross the chromosome. These results demonstrated that RH mapping via protoplast fusion is feasible at the whole genome level for mapping purposes in wheat and the potential value of this mapping approach for the plant species with large genomes.</p> </div

Individual marker retention frequency and donor DNA retention frequency of wheat in radiation hybrids.

<p>A: Individual marker retention frequencies in 155 radiation hybrids derived from seven asymmetric hybridization combinations. Forty-two microsatellite loci across the wheat genome are listed to the left of the figure. B–D: Donor DNA retention frequency of wheat in hybrids. B: Average donor DNA retention frequencies of A, B, D genome of wheat in each hybridization combination; C: Average donor DNA retention frequencies of seven chromosome groups of wheat in each of hybridization combinations; D: Average donor DNA retention frequencies of seven asymmetric hybridization combinations and control combination.</p

Identification of hybrid cell clones.

<p>A: RAPD amplification pattern generated using primer <i>OPV-07</i>. W: Wheat; B: <i>B. scorzonerifolium</i>; 1–21: Regenerated cell clones; arrowhead: <i>B. scorzonerifolium</i> characteristic band; arrow: Wheat characteristic band; cell clone No.7 was identified as a hybrid due to the presence of both parental specific bands. B-E: GISH analysis. B: Wheat; C: <i>B. scorzonerifolium</i>; D: Hybrid cell clone No.10 in WB5K showing two chromosomal fragments of wheat inserted into the genome of <i>B. scorzonerifolium</i>; E: Hybrid cell clone No.7 in WB60 showing three recombined chromosomes; arrow: Chromosomal fragments of wheat; <i>Bar</i>: 5 µm. F–I: Differentiation of hybrid cell clones. F: The shoots regenerated from hybrid clone No.64 in WB120; G: The plantlet of intermediate type regenerated from hybrid cell clone No.88 in WB60; H: The plantlet resembled <i>B. scorzonerifolium</i> regenerated from hybrid cell clone No.41 in WB60; I: Diverse morphology of regenerated shoots in combination WB120; <i>Bar</i>: 1cm.</p

Genotyping of nuclear SSR markers and the RH map of wheat chromosome 5A.

<p>A: Genotyping of SSR loci <i>Xgwm186</i>, <i>Xbarc1</i>, <i>Xcfa2250</i> and <i>Xcfa2155</i> in RH panel. W: Wheat; B: <i>B. scorzonerifolium</i>; 47–138: Radiation hybrids; <i>M</i>: 100 bp DNA ladder; arrow: SSR-PCR products of wheat; Solid squares represent retained markers, open squares represent eliminated markers and asterisks represent undetermined data. B: Wheat chromosome 5A RH map (right) as compared with the genetic (left) and the deletion map (middle). The black lines on the deletion map refer to bins assigned to the chromosome 5A. The RH map has an estimated total length of 2103 cR covered by 68 SSR markers.</p

Alignment of RH map to physical map.

<p>Comparison between wheat chromosome 5A RH linkage group (right) with deletion map (left). The solid lines between markers show the consistent order between RH map and deletion map. The broken lines show the inconsistent marker order between two maps.</p