113 Works

Data from: Blind to morphology: genetics identifies several widespread ecologically common species and few endemics among Indo-Pacific cauliflower corals (Pocillopora, Scleractinia)

Jorge H. Pinzón, Eugenia Sampayo, Evelyn Cox, Leonard J. Chauka, Chaolun Allen Chen, Christian R. Voolstra & Todd C. LaJeunesse
AIM: Using high-resolution genetic markers on samples gathered from across their wide distributional range, we endeavoured to delimit species diversity in reef-building Pocillopora corals. They are common, ecologically important, and widespread throughout the Indo-Pacific, but their phenotypic plasticity in response to environmental conditions and their nearly featureless microskeletal structures confound taxonomic assignments and limit an understanding of their ecology and evolution. LOCATION: Indo-Pacific, Red Sea, Arabian/Persian Gulf. METHODS: Sequence analysis of nuclear ribosomal (internal transcribed...

Additional file 10 of Copy number variant analysis for syndromic congenital heart disease in the Chinese population

Ping Li, Weicheng Chen, Mengru Li, Zhengshan Zhao, Zhiyu Feng, Han Gao, Meijiao Suo, Ziqing Xu, Guixiang Tian, Feizhen Wu, Sheng Wei & Guoying Huang
Additional file 10. Table S7. Recurrent CNVs in previously published syndromic CHD cohorts and our study.

Additional file 2 of Copy number variant analysis for syndromic congenital heart disease in the Chinese population

Ping Li, Weicheng Chen, Mengru Li, Zhengshan Zhao, Zhiyu Feng, Han Gao, Meijiao Suo, Ziqing Xu, Guixiang Tian, Feizhen Wu, Sheng Wei & Guoying Huang
Additional file 2. Table S2. Training gene set generated from RDDC, Phenopedia, and DisGeNET.

Additional file 3 of Copy number variant analysis for syndromic congenital heart disease in the Chinese population

Ping Li, Weicheng Chen, Mengru Li, Zhengshan Zhao, Zhiyu Feng, Han Gao, Meijiao Suo, Ziqing Xu, Guixiang Tian, Feizhen Wu, Sheng Wei & Guoying Huang
Additional file 3. Additional methods. Pathway analysis of the prioritized genes, the databases, and the dataset.

Additional file 3 of Copy number variant analysis for syndromic congenital heart disease in the Chinese population

Ping Li, Weicheng Chen, Mengru Li, Zhengshan Zhao, Zhiyu Feng, Han Gao, Meijiao Suo, Ziqing Xu, Guixiang Tian, Feizhen Wu, Sheng Wei & Guoying Huang
Additional file 3. Additional methods. Pathway analysis of the prioritized genes, the databases, and the dataset.

Additional file 5 of Copy number variant analysis for syndromic congenital heart disease in the Chinese population

Ping Li, Weicheng Chen, Mengru Li, Zhengshan Zhao, Zhiyu Feng, Han Gao, Meijiao Suo, Ziqing Xu, Guixiang Tian, Feizhen Wu, Sheng Wei & Guoying Huang
Additional file 5. Fig. S1. Gene ontology analysis of the 1249 candidate genes (1129 matched).

Additional file 6 of Copy number variant analysis for syndromic congenital heart disease in the Chinese population

Ping Li, Weicheng Chen, Mengru Li, Zhengshan Zhao, Zhiyu Feng, Han Gao, Meijiao Suo, Ziqing Xu, Guixiang Tian, Feizhen Wu, Sheng Wei & Guoying Huang
Additional file 6. Table S4. CNVs in studies of syndromic CHD from different countries or ethnicities.

Additional file 9 of Copy number variant analysis for syndromic congenital heart disease in the Chinese population

Ping Li, Weicheng Chen, Mengru Li, Zhengshan Zhao, Zhiyu Feng, Han Gao, Meijiao Suo, Ziqing Xu, Guixiang Tian, Feizhen Wu, Sheng Wei & Guoying Huang
Additional file 9. Fig. S2. Interaction analyses of prioritized genes by different tools.

Additional file 1 of Early-life antibiotic exposure increases the risk of childhood overweight and obesity in relation to dysbiosis of gut microbiota: a birth cohort study

Ping Li, Xuelian Chang, Xiaoyu Chen, Chuan Wang, Yu Shang, Dongyi Zheng & Kemin Qi
Supplementary Material 1

Endoplasmic reticulum-quality control pathway and endoplasmic reticulum-associated degradation mechanism regulate the N-glycoproteins and N-glycan structures in the diatom Phaeodactylum tricornutum

Jichen Chen, Hong Du, Zidong Liu, Tangcheng Li, Hua Du, Wanna Wang, Muhammad Aslam, Weizhou Chen, Ping Li, Haodong Luo, Hao Fang & Xiaojuan Liu
Abstract Tunicamycin inhibits the first step of protein N-glycosylation modification. However, the physiological, transcriptomic, and N-glycomic effects of tunicamycin on important marine diatom Phaeodactylum tricornutum are still unknown. In this study, comprehensive approaches were used to study the effects of tunicamycin stress. The results showed that cell growth and photosynthesis were significantly inhibited in P. tricornutum under the tunicamycin stress. The soluble protein content was significantly decreased, while the soluble sugar and neutral lipid were...

Additional file 1 of Decoding the colorectal cancer ecosystem emphasizes the cooperative role of cancer cells, TAMs and CAFsin tumor progression

Rongfang Shen, Ping Li, Botao Zhang, Lin Feng & Shujun Cheng
Additional file 1: Table S1. Basic clinical information and QC metric of SMC and KUL3 cohort.

Additional file 7 of Decoding the colorectal cancer ecosystem emphasizes the cooperative role of cancer cells, TAMs and CAFsin tumor progression

Rongfang Shen, Ping Li, Botao Zhang, Lin Feng & Shujun Cheng
Additional file 7: Table S7. Key resource table.

Additional file 4 of Decoding the colorectal cancer ecosystem emphasizes the cooperative role of cancer cells, TAMs and CAFsin tumor progression

Rongfang Shen, Ping Li, Botao Zhang, Lin Feng & Shujun Cheng
Additional file 4: Table S4. Signature matrix for CIBERSORTx and infered cellular fractions of TCGA-COADREAD. Related to Figure 2.

Additional file 11 of Decoding the colorectal cancer ecosystem emphasizes the cooperative role of cancer cells, TAMs and CAFsin tumor progression

Rongfang Shen, Ping Li, Botao Zhang, Lin Feng & Shujun Cheng
Additional file 11: Figure S4. Dynamic interactions between the EC and MC. A. Relative proportions of epithelial cell clusters and TME cell clusters in the KUL3 cohort. Samples were clustered according to the distribution pattern of epithelial cells with the corresponding TME cell cluster distribution shown in the right panel. B–E. Bar plot showing the number of incoming events and outgoing events for epithelial cells communicating with TME cells in normal tissues of the SMC...

Anatomical distance affects functional connectivity at rest in medicine-free obsessive–compulsive disorder

Dan Lv, Yangpan Ou, Yunhui Chen, Zhenning Ding, Jidong Ma, Chuang Zhan, Ru Yang, Tinghuizi Shang, Guangfeng Zhang, Xiaoyu Bai, Zhenghai Sun, Jian Xiao, Xiaoping Wang, Wenbin Guo & Ping Li
Abstract Background Brain functional abnormalities at rest have been observed in obsessive–compulsive disorder (OCD). However, whether and how anatomical distance influences functional connectivity (FC) at rest is ambiguous in OCD. Methods Using resting-state functional magnetic resonance imaging data, we calculated the FC of each voxel in the whole-brain and divided FC into short- and long-range FCs in 40 medicine-free patients with OCD and 40 healthy controls (HCs). A support vector machine (SVM) was used to...

Additional file 3 of Implementing tuberculosis patient cost surveys in resource-constrained settings: lessons from Tanzania

Andrew Martin Kilale, Charles Makasi, Melkisedeck Majaha, Chacha Dionis Manga, Sylvia Haule, Pudensiana Hilary, Omari Kimbute, Stephen Kitua, Bhavin Jani, Nyagosya Range, Bernard Ngowi, Emmanuel Nkiligi, Emmanuel Matechi, Wilbard Muhandiki, Vishnu Mahamba, Beatrice Mutayoba & Julia Ershova
Additional file 3. TB patient cost survey report

Additional file 4 of Implementing tuberculosis patient cost surveys in resource-constrained settings: lessons from Tanzania

Andrew Martin Kilale, Charles Makasi, Melkisedeck Majaha, Chacha Dionis Manga, Sylvia Haule, Pudensiana Hilary, Omari Kimbute, Stephen Kitua, Bhavin Jani, Nyagosya Range, Bernard Ngowi, Emmanuel Nkiligi, Emmanuel Matechi, Wilbard Muhandiki, Vishnu Mahamba, Beatrice Mutayoba & Julia Ershova
Additional file 4. TBPCS field report.

Additional file 2 of Implementing tuberculosis patient cost surveys in resource-constrained settings: lessons from Tanzania

Andrew Martin Kilale, Charles Makasi, Melkisedeck Majaha, Chacha Dionis Manga, Sylvia Haule, Pudensiana Hilary, Omari Kimbute, Stephen Kitua, Bhavin Jani, Nyagosya Range, Bernard Ngowi, Emmanuel Nkiligi, Emmanuel Matechi, Wilbard Muhandiki, Vishnu Mahamba, Beatrice Mutayoba & Julia Ershova
Additional file 2. Report Nothern Zone

Implementing tuberculosis patient cost surveys in resource-constrained settings: lessons from Tanzania

Andrew Martin Kilale, Charles Makasi, Melkisedeck Majaha, Chacha Dionis Manga, Sylvia Haule, Pudensiana Hilary, Omari Kimbute, Stephen Kitua, Bhavin Jani, Nyagosya Range, Bernard Ngowi, Emmanuel Nkiligi, Emmanuel Matechi, Wilbard Muhandiki, Vishnu Mahamba, Beatrice Mutayoba & Julia Ershova
Abstract Tuberculosis (TB) disproportionally affects persons and families who are economically and socially disadvantaged. Therefore, a patient cost survey was conducted in Tanzania to evaluate the costs incurred by patients and their households before and after the diagnosis of TB. It was the first survey in Tanzania to ascertain baseline information and experience for subsequent surveys. This paper aims to share the experience encountered during the survey to ensure a standardized approach and elimination of...

Additional file 1 of Editing of the rice importin gene IMPα1b results in sequestration of TAL effectors from plant cell nuclei

Jinfeng Peng, Jingyuan Nie, Xiaochen Chen, Liyuan Zhang, Xiaohui Yao, Ping Li, Huicong Shi, Congfeng Song & Hansong Dong
Additional file 1. Table S1. Rice importins retrieved from Rice Genome Annotation Project databases. Table S2. Early characterizations of OsIMPα1a-edited (OsIMPα1a-ED) and OsIMPα1b-edited (OsIMPα1b-ED) rice lines. Table S3. Information on genes tested and primers used in this study.

Data from: Performance of five food regimes on Anopheles gambiae senso stricto larval rearing to adult emergence in Insectary

Happiness S. Kivuyo, Paschal H. Mbazi, Denis S. Kisika, Stephen Munga, Susan F. Rumisha, Felister M. Urasa & Eliningaya J. Kweka
Background: Rearing of Anopheles gambiae s.s mosquitoes in insectary with quality cheap food sources is of paramount importance for better and healthy colony. This study evaluated larval survival and the development rate of aquatic stages of An.gambiae s.s under five food regimes; tetramin fish food (a standard insectary larval food), maize pollen, Cerelac, green filamentous algae and dry powdered filamentous algae. Methods: Food materials were obtained from different sources, cerelac was made locally, fresh filamentous...

Additional file 3 of Endoplasmic reticulum-quality control pathway and endoplasmic reticulum-associated degradation mechanism regulate the N-glycoproteins and N-glycan structures in the diatom Phaeodactylum tricornutum

Jichen Chen, Hong Du, Zidong Liu, Tangcheng Li, Hua Du, Wanna Wang, Muhammad Aslam, Weizhou Chen, Ping Li, Haodong Luo, Hao Fang & Xiaojuan Liu
Additional file 3: Table S2. The up- and down-regulated N-glycopeptides.

Additional file 14 of Decoding the colorectal cancer ecosystem emphasizes the cooperative role of cancer cells, TAMs and CAFsin tumor progression

Rongfang Shen, Ping Li, Botao Zhang, Lin Feng & Shujun Cheng
Additional file 14: Figure S7. Characterization of stromal cells in the KUL3 cohort. A. UMAP plot of stromal cells colored by cell cluster and sample origin. B. Heat map of marker genes identified through Seurat. For each cell cluster, cells were down-sampled to 100. C. Differentiation trajectory inferred by Monocle2. Dots represent stromal cells colored by identified cell cluster. D. Heat map plot of the top ranked regulons. E. Dot plot of the correlation between...

Additional file 15 of Decoding the colorectal cancer ecosystem emphasizes the cooperative role of cancer cells, TAMs and CAFsin tumor progression

Rongfang Shen, Ping Li, Botao Zhang, Lin Feng & Shujun Cheng
Additional file 15: Figure S8. Workflow of this study. Single-cell transcriptomes and bulk RNA-seq data were integrated to fully analyze the complicated relationship between colorectal epithelium and surrounding environment. C4 cells were featured with high invasive potential and related with TAMs and CAFs, and further validated in vitro using IHC and mIHC.

Decoding the colorectal cancer ecosystem emphasizes the cooperative role of cancer cells, TAMs and CAFsin tumor progression

Rongfang Shen, Ping Li, Botao Zhang, Lin Feng & Shujun Cheng
Abstract Background Single-cell transcription data provided unprecedented molecular information, enabling us to directly encode the ecosystem of colorectal cancer (CRC). Characterization of the diversity of epithelial cells and how they cooperate with tumor microenvironment cells (TME) to endow CRC with aggressive characteristics at single-cell resolution is critical for the understanding of tumor progression mechanism. Methods In this study, we comprehensively analyzed the single-cell transcription data, bulk-RNA sequencing data and pathological tissue data. In detail, cellular...

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