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Metagenomic binning is an essential technique for genome-resolved characterization of uncultured microorganisms in various ecosystems but hampered by the low efficiency of binning tools in adequately recovering metagenome-assembled genomes (MAGs). Here, we introduce BASALT (Binning Across a Series of Assemblies Toolkit) for binning and refinement of short- and long-read sequencing data. BASALT employs multiple binners with multiple thresholds to produce initial bins, then utilizes neural networks to identify core sequences to remove redundant bins and refine non-redundant bins. Using the same assemblies generated from Critical Assessment of Metagenome Interpretation (CAMI) datasets, BASALT produces up to twice as many MAGs as VAMB, DASTool, or metaWRAP. Processing assemblies from a lake sediment dataset, BASALT produces ~30% more MAGs than metaWRAP, including 21 unique class-level prokaryotic lineages. Functional annotations reveal that BASALT can retrieve 47.6% more non-redundant opening-reading frames than metaWRAP. These results highlight the robust handling of metagenomic sequencing data of BASALT.

Liyu Zhang,1,2 Meng Wang,3 Zeen Zhu,4 Chenxi Ding,1 Shengquan Chen,1 Haibin Wu,2 Ying Yang,2 Fengyu Che,2 Qiao Li,5 Hui Li1,6 1Department of Neonatology, The First Affiliated Hospital of Xi’an Jiaotong University, Xi’an, Shaanxi, People’s Republic of China; 2Shaanxi Institute of Pediatric Diseases, Affiliated Children’s Hospital of Xi’an Jiaotong University, Xi’an, People’s Republic of China; 3Department of Emergency Surgery, Shaanxi Provincial People’s Hospital, Xi’an, Shaanxi, People’s Republic of China; 4Department of Hepatobiliary Surgery, The First Affiliated Hospital of Xi’an Jiaotong University, Xi’an, Shaanxi 710061, People’s Republic of China; 5Department of Clinical Laboratory, Affiliated Children’s Hospital of Xi’an Jiaotong University, Xi’an, People’s Republic of China; 6Department of Neonatology, Affiliated Children’s Hospital of Xi’an Jiaotong University, Xi’an, People’s Republic of ChinaCorrespondence: Hui LiDepartment of Neonatology, The First Affiliated Hospital of Xi’an Jiaotong University, Xi’an, Shaanxi, People’s Republic of ChinaEmail huili@xjtu.edu.cnBackground: GD2 is a mainstream biomarker for neuroblastoma (NB)-targeted therapy. Current anti-GD2 therapeutics exhibit several side effects since GD2 is also expressed at low levels on normal cells. Thus, current anti-GD2 therapeutics can be compromised by the coexistence of the target receptor on both cancer cells and normal cells.Propose: Aptamers are promising and invaluable molecular tools. Because of the pH difference between tumor and normal cells, in this study, we constructed a pH-sensitive aptamer-mediated drug delivery system (IGD-Targeted).Methods: In vivo Systematic Evolution of Ligands by Exponential Enrichment (SELEX) was used to generate a novel

Liyu Zhang,1,2 Meng Wang,3 Zeen Zhu,4 Chenxi Ding,1 Shengquan Chen,1 Haibin Wu,2 Ying Yang,2 Fengyu Che,2 Qiao Li,5 Hui Li1,6 1Department of Neonatology, The First Affiliated Hospital of Xi’an Jiaotong University, Xi’an, Shaanxi, People’s Republic of China; 2Shaanxi Institute of Pediatric Diseases, Affiliated Children’s Hospital of Xi’an Jiaotong University, Xi’an, People’s Republic of China; 3Department of Emergency Surgery, Shaanxi Provincial People’s Hospital, Xi’an, Shaanxi, People’s Republic of China; 4Department of Hepatobiliary Surgery, The First Affiliated Hospital of Xi’an Jiaotong University, Xi’an, Shaanxi 710061, People’s Republic of China; 5Department of Clinical Laboratory, Affiliated Children’s Hospital of Xi’an Jiaotong University, Xi’an, People’s Republic of China; 6Department of Neonatology, Affiliated Children’s Hospital of Xi’an Jiaotong University, Xi’an, People’s Republic of ChinaCorrespondence: Hui LiDepartment of Neonatology, The First Affiliated Hospital of Xi’an Jiaotong University, Xi’an, Shaanxi, People’s Republic of ChinaEmail huili@xjtu.edu.cnBackground: GD2 is a mainstream biomarker for neuroblastoma (NB)-targeted therapy. Current anti-GD2 therapeutics exhibit several side effects since GD2 is also expressed at low levels on normal cells. Thus, current anti-GD2 therapeutics can be compromised by the coexistence of the target receptor on both cancer cells and normal cells.Propose: Aptamers are promising and invaluable molecular tools. Because of the pH difference between tumor and normal cells, in this study, we constructed a pH-sensitive aptamer-mediated drug delivery system (IGD-Targeted).Methods: In vivo Systematic Evolution of Ligands by Exponential Enrichment (SELEX) was used to generate a novel

Wang M, Wu H, Li Q, et al. Int J Nanomedicine. 2019;14:8707–8724. The authors have advised due to an error at the time of figure assembly, Figure 3A and B on page 8714 is incorrect. The correct Figure 3 is shown below. The authors apologize for this error and advise it does not affect the results of the paper. Read the original article

Wang M, Wu H, Li Q, et al. Int J Nanomedicine. 2019;14:8707–8724. The authors have advised due to an error at the time of figure assembly, Figure 3A and B on page 8714 is incorrect. The correct Figure 3 is shown below. The authors apologize for this error and advise it does not affect the results of the paper. Read the original article

Meng Wang, 1 Haibin Wu, 2, 3 Qiao Li, 4 Ying Yang, 2 Fengyu Che, 2 Guoxia Wang, 2 Liyu Zhang 2, 3 1Department of Orthopaedics, The NO. 946 Hospital of PLA, YiNing, XinJiang 86-835000, People’s Republic of China; 2Shaanxi Institute of Pediatric Diseases, Xi’an Children’s Hospital, Xi’an, Shaanxi 86-710003, People’s Republic of China; 3Key Laboratory of Environment and Genes Related to Diseases, Ministry of Education, Xi’an Jiaotong University Health Science Center, Xi’an, Shaanxi 86-710061, People’s Republic of China; 4Clinical Laboratory, Xi’an Children’s Hospital, Xi’an, Shaanxi 86-710003, People’s Republic of ChinaCorrespondence: Liyu ZhangShaanxi Institute of Pediatric Diseases, Xi’an Children’s Hospital, 69 West JuYuan Alley, LianHu, Xi’an, Shaanxi 86-710003, People’s Republic of ChinaTel +86 18066858662Fax +86 02987692009Email liyu_17@sina.comBackground: The restoration and repair method in the clinic of delayed fracture healing and non-union after comminuted fractures are urgently needed to improve the prognosis of patients. The recruitment of endogenous stem cells has been considered a promising approach in bone defect repair.Propose: The aim of this study was to generate a de novel MSCs aptamer and developed the first, feasible, economical, bio-compatible, and functional MSCs aptamer-directed nanoparticles without complex manufacture to recruit mesenchymal stem cells (MSCs) for bone defect regeneration.Methods: Whole-cell SELEX was used to generate a de novel MSCs aptamer. Flow cytometry was applied to assess the binding specificities, affinities and sorting abilities of the aptamers. Nano-Aptamer Ball (NAB) was constructed by NHS/EDC reaction. The diameter and zeta of NAB were assessed by dynamic light scattering. CCK8 assay was utilized to evaluate whether NAB could cause non-specific cytotoxicity a

Meng Wang, 1 Haibin Wu, 2, 3 Qiao Li, 4 Ying Yang, 2 Fengyu Che, 2 Guoxia Wang, 2 Liyu Zhang 2, 3 1Department of Orthopaedics, The NO. 946 Hospital of PLA, YiNing, XinJiang 86-835000, People’s Republic of China; 2Shaanxi Institute of Pediatric Diseases, Xi’an Children’s Hospital, Xi’an, Shaanxi 86-710003, People’s Republic of China; 3Key Laboratory of Environment and Genes Related to Diseases, Ministry of Education, Xi’an Jiaotong University Health Science Center, Xi’an, Shaanxi 86-710061, People’s Republic of China; 4Clinical Laboratory, Xi’an Children’s Hospital, Xi’an, Shaanxi 86-710003, People’s Republic of ChinaCorrespondence: Liyu ZhangShaanxi Institute of Pediatric Diseases, Xi’an Children’s Hospital, 69 West JuYuan Alley, LianHu, Xi’an, Shaanxi 86-710003, People’s Republic of ChinaTel +86 18066858662Fax +86 02987692009Email liyu_17@sina.comBackground: The restoration and repair method in the clinic of delayed fracture healing and non-union after comminuted fractures are urgently needed to improve the prognosis of patients. The recruitment of endogenous stem cells has been considered a promising approach in bone defect repair.Propose: The aim of this study was to generate a de novel MSCs aptamer and developed the first, feasible, economical, bio-compatible, and functional MSCs aptamer-directed nanoparticles without complex manufacture to recruit mesenchymal stem cells (MSCs) for bone defect regeneration.Methods: Whole-cell SELEX was used to generate a de novel MSCs aptamer. Flow cytometry was applied to assess the binding specificities, affinities and sorting abilities of the aptamers. Nano-Aptamer Ball (NAB) was constructed by NHS/EDC reaction. The diameter and zeta of NAB were assessed by dynamic light scattering. CCK8 assay was utilized to evaluate whether NAB could cause non-specific cytotoxicity a

Hongda Ma,1 Yao Yao,2 Changli Wang,1 Liyu Zhang,3 Long Cheng,4 Yiren Wang,5 Tao Wang,6 Erguang Liang,6 Hui Jia,1 Qinong Ye,4 Mingxiao Hou,1 Fan Feng11Department of Pharmacy, General Hospital of Shenyang Military Area Command, Shenyang, 2Department of Pharmacy, Women & Infants Hospital of Zhengzhou, Zhengzhou, 3Shaanxi Institute of Pediatric Disease, Xi’an Children’s Hospital, Xi’an, 4Institute of Biotechnology, Chinese Military Medical Science Academy, Beijing, 5School of Life Science, Shenyang Pharmaceutical University, Shenyang, 6Institute of Toxicology and Pharmacology, Chinese Military Medical Science Academy, Beijing, People’s Republic of ChinaAbstract: Many kinds of endocrine-disrupting chemicals (EDCs), for example, the environmental estrogens bisphenol A and nonylphenol, may regulate the activity of estrogen receptor α (ERα) and therefore induce potential disruption of normal endocrine function. However, the involvement of EDCs in human cancers, especially in endocrine-related cancer neuroblastoma regulation, is not very clear. In this work, results showed that upon bisphenol A or nonylphenol treatment, the transcription factor activity of ERα was significantly increased in neuroblastoma cell line SH-SY5Y. Bisphenol A and nonylphenol could enhance ERα activity via recruiting it to the target gene promoter. Furthermore, treatment of bisphenol A and nonylphenol enhanced the in vitro proliferation, invasion, and migration ability of neuroblastoma cells. By investigating the role of EDC-induced ERα upregulation, our data extend the understanding of the function of EDCs and further suggest that ERα might be a potential therapeutic target in human neuroblastoma treatment.Keywords: neuroblastoma, endocrine-disrupting chemicals, environmental estrogens, bisphenol A and nonylphenol, proliferation and metastasis