156 Works

The hornwort genome and early land plant evolution

Jian Zhang, Xin-Xing Fu, Rui-Qi Li, Xiang Zhao, Yang Liu, Ming-He Li, Arthur Zwaenepoel, Hong Ma, Bernard Goffinet, Yan-Long Guan, Jia-Yu Xue, Yi-Ying Liao, Qing-Feng Wang, Qing-Hua Wang, Jie-Yu Wang, Guo-Qiang Zhang, Zhi-Wen Wang, Yu Jia, Mei-Zhi Wang, Shan-Shan Dong, Jian-Fen Yang, Yuan-Nian Jiao, Ya-Long Guo, Hong-Zhi Kong, An-Ming Lu … & Zhi-Duan Chen
Hornworts, liverworts, and mosses are three early diverging clades of land plants, together composing the bryophytes. Here we report the draft genome sequence of the hornwort Anthoceros angustus. Phylogenomic inferences confirm the monophyly of bryophytes, with hornworts sister to liverworts and mosses. The simple morphology of hornworts correlates with low genetic redundancy in plant body plan while the basic transcriptional regulation toolkit for plant development has already been established in this early land plant lineage....

Phylogeny and biogeography of Fagus (Fagaceae) based on 28 nuclear single/low‐copy loci

Zhi-Yong Zhang, Lu Jiang, Qin Bao, Wei He, Deng‐Mei Fan, Shan‐Mei Cheng, Jordi López-Pujol, Myong Gi Chung, Shota Sakaguchi, Arturo Sánchez-González, Aysun Gedik, De‐Zhu Li & Yi‐Xuan Kou
Fagus L. is a key component in temperate deciduous broadleaf forests of the Northern Hemisphere. However, its biogeographic history has not been examined under the framework of a fully resolved and reasonably time-calibrated phylogeny. In this study, we sequenced 28 nuclear single/low-copy loci (18,555 bp in total) of 11 Fagus species/segregates and seven outgroups. Phylogenetic trees were reconstructed using both concatenation-based (ML, MP, BI) and coalescent-based methods (StarBEAST2, ASTRAL). The monophyly of two subgenera (Fagus...

Amblyanthus chenii, a new species and generic record from Xizang, China

Zhuo Zhou, Yong-Jie Guo, Ji-Pei Yue, Hong-Liang Chen, Yun-Hong Tan & Hang Sun
Amblyanthus chenii (Primulaceae; Myrsinoideae), a new species discovered growing in the understory of primeval forests in Medog County, southeast Xizang, China, is described based on morphological evidence. This is also the first generic record of Amblyanthus in China. The new species is most similar morphologically to A. multiflorus based on its axillary inflorescence and connate filament, but it differs in its 2-4 cm long condensed panicle and up to half adnation of its sepals and...

Data from: Does reproductive isolation reflect the segregation of color forms in Spiranthes sinensis (Pers.) Ames complex (Orchidaceae) in the Chinese Himalayas?

Zhi-Bin Tao, Zong-Xin Ren, Peter Bernhardt, Huan Liang, Hai-Dong Li, Yan-Hui Zhao, Hong Wang & De-Zhu Li
Isolation between species, or taxa sharing a common lineage, depends primarily on the relative strengths of various reproductive barriers. Previous studies on reproductive isolation between orchids emphasized mechanical and ethological barriers in flowers of species showing food and/or sexual mimicry. In this study, we investigated and quantified a series of pre- and post-pollination barriers between pink and white forms of Spiranthes sinensis sl, a nectar-secreting complex. We generated ML trees based on trnS-G and matK...

Testing the causes of richness patterns in the paleotropics: time and diversification in cycads (Cycadaceae)

Jian Liu, Anders Lindstrom, Nathalie Nagalingum, John Wiens & Xun Gong
The paleotropics harbor many biodiversity hotspots and show many different species richness patterns. However, it remains unclear which factors are the most important in directly shaping richness patterns among regions in the paleotropics (i.e. diversification rates, colonization times, dispersal frequency). Here we used Cycadaceae as a model system to test the causes of regional richness patterns in the paleotropics. Specifically we tested the roles of dispersal frequency, colonization time, diversification rates, and their combined role...

Speciation along the elevation gradient: divergence of Roscoea species within the south slope of the Himalayas

Jian-Li Zhao, Babu Ram Paudel, Xiang-Qin Yu, Jie Zhang & Qing-Jun Li
The Himalayas with dramatic elevation gradient is one of the global biodiversity hotspots. Although origin of biodiversity of the Himalayas is of great concern, the speciation process within the Himalayas is poorly known. Roscoea within the Himalayas serve as a good model system to test the speciation process along an elevation gradient. 32375 unlinked SNPs were used to reconstruct phylogenetic relationships and introgression analyses in D-statistics and Fastsimicoal2. Species distribution modeling (SDM) was used to...

Phylogenomics of Fargesia and Yushania reveals a history of reticulate evolution

Ye Xiaying, Peng‐Fei Ma, Cen Guo & De‐Zhu Li
Reticulate evolution is a common and important driving force in angiosperm evolution. In this study, we analyzed the phylogenetic signals of genomic regions with different inheritance patterns to understand the evolutionary process of organisms using species‐rich Himalaya–Hengduan taxa of bamboos (Fargesia Franchet and Yushania Keng). We constructed phylogenetic trees using different sampling strategies and reconstruction methods based on genome skimming and double digest restriction‐site‐associated DNA sequencing data. We assessed the congruence of topologies generated from...

Data from: The topological differences between visitation and pollen transport networks: a comparison in species rich communities of the Himalaya-Hengduan Mountains

Yan-Hui Zhao, Amparo Lazaro, Zong-Xin Ren, Wei Zhou, Hai-Dong Li, Zhi-Bin Tao, Kun Xu, Zhi-Kun Wu, Lorne M. Wolfe, Li De-Zhu & Wang Hong
Pollination networks are usually constructed and assessed by direct field observations which commonly assume that all flower visitors are true pollinators. However, this assumption is often invalid and the use of data based on mere visitors to flowers may lead to a misunderstanding of intrinsic pollination networks. Here, using a large dataset by both sampling floral visitors and analyzing their pollen loads, we constructed 32 networks pairs (visitation vs. pollen transport) across one flowering season...

Data from: Upward elevation and northwest range shifts for alpine Meconopsis species in the Himalaya-Hengduan Mountains region

Xie He, Kevin Burgess, Xuefei Yang, Antje Ahrends, Lian-Ming Gao & De-Zhu Li
Climate change may impact the distribution of species by shifting their ranges to higher elevations or higher latitudes. The impacts on alpine plant species may be particularly profound due to a potential lack of availability of future suitable habitat. To identify how alpine species have responded to climate change during the past century as well as to predict how they may react to possible global climate change scenarios in the future, we investigate the climatic...

Data from: Resolution, conflict and rate shifts: Insights from a densely sampled plastome phylogeny for Rhododendron (Ericaceae)

Zhi-Qiong Mo, Chao-Nan Fu, Ming-Shu Zhu, Richard I. Milne, Jun-Bo Yang, Jie Cai, Han-Tao Qin, Wei Zheng, Peter M. Hollingsworth, De-Zhu Li & Lian-Ming Gao
Background and Aims Rhododendron is a species-rich and taxonomically challenging genus due to recent adaptive radiation and frequent hybridization. A well-resolved phylogenetic tree would help to understand the diverse history of Rhododendron in the Himalaya–Hengduan Mountains where the genus is most diverse. Methods We reconstructed the phylogeny based on plastid genomes with broad taxon sampling, covering 161 species representing all eight subgenera and all 12 sections, including ~45 % of the Rhododendron species native to...

Description of Four Novel Species in Pleosporales associated with Coffee in Yunnan, China

Li Lu, Samantha C. Karunarathna, Dong-Qin Dai, Yin-ru Xiong, Nakarin Suwannarach, Steven L. Stephenson, Abdallah M. Elgorban, Salim Al-Rejaie, Ruvishika S. Jayawardena & Saowaluck Tibpromma
Based on molecular phylogenetic analyses of combined ITS, LSU, SSU, rpb2, and tef1-α sequence data and morphological characteristics, four new species viz. Deniquelata yunnanensis, Paraconiothyrium yunnanensis, Pseudocoleophoma puerensis and Pse. yunnanensis and three new records viz. Austropleospora keteleeriae, Montagnula thailandica and Xenocamarosporium acaciae in Pleosporales are introduced.

Additional file 11 of Evolution and functional analysis of the GRAS family genes in six Rosaceae species

Yibo Bai, Hui Liu, Kaikai Zhu & Zong-Ming Cheng
Additional file 11: Table S1. Total of 333 GRAS genes were identified in six Rosaceae species. Table S2. Ks values of six Rosaceae species. Table S3. Duplication events of six Rosaceae species. Table S4. ka/Ks values of six Rosaceae species. Table S5. Primers used to detect drought stress and salt stress gene expression.

sj-tex-3-pio-10.1177_1748006X221146367 – Supplemental material for A new failure times model for one and two failure modes system: A Bayesian study with Hamiltonian Monte Carlo simulation

Badamasi Abba & Hong Wang
Supplemental material, sj-tex-3-pio-10.1177_1748006X221146367 for A new failure times model for one and two failure modes system: A Bayesian study with Hamiltonian Monte Carlo simulation by Badamasi Abba and Hong Wang in Proceedings of the Institution of Mechanical Engineers, Part O: Journal of Risk and Reliability

Additional file 2 of Chronic constriction injury-induced changes in circular RNA expression profiling of the dorsal root ganglion in a rat model of neuropathic pain

Wanxia Xiong, Min Wei, Li Zhang, Jie Wang, Fan Liu & Zhiyao Wang
Additional file 2: Table S2. List of total circRNAs detected in the DRG of NC and CCI rats. RNA-seq was performed to profile circRNA expression in four paired DRG samples. A total of 13,172 circRNAs were detected in the L4–L5 DRG samples from the CCI and NC groups (4 mice per group).

Additional file 3 of Chronic constriction injury-induced changes in circular RNA expression profiling of the dorsal root ganglion in a rat model of neuropathic pain

Wanxia Xiong, Min Wei, Li Zhang, Jie Wang, Fan Liu & Zhiyao Wang
Additional file 3: Table S3. List of DEcircRNAs were identified between the CCI and NC groups. Following differential expression analysis, 374 DEcircRNAs were identified between the CCI and NC groups (4 mice per group) by using FC filtering (FC ≥ 2 or ≤ 0.5) and FDR (Q < 0.001).

Additional file 4 of Chronic constriction injury-induced changes in circular RNA expression profiling of the dorsal root ganglion in a rat model of neuropathic pain

Wanxia Xiong, Min Wei, Li Zhang, Jie Wang, Fan Liu & Zhiyao Wang
Additional file 4: Table S4. List of circRNAs and miRNA predicted by using miRanda and TargetScan. Potential connections between circRNAs and microRNAs were predicted by using TargetScan and miRanda, and the interaction results were displayed by Cytoscape. All the circRNAs and miRNAs were listed.

Getting the ROC into Sync

Liu Yang, Kajal Lahiri & Adrian Pagan
Judging the conformity of binary events in macroeconomics and finance has often been done with indices that measure synchronization. In recent years, the use of Receiver Operating Characteristic (ROC) curve has become popular for this task. This article shows that the ROC and synchronization approaches are closely related, and each can be derived from a decision-making framework. Furthermore, the resulting global measures of the degree of conformity can be identified and estimated using the standard...

Sinosenecio yangii (Asteraceae), a new species from Guizhou, China

Qiang Zhou, Jing-Yi Peng, Dai-Gui Zhang, Tao Deng, Xian-Han Huang, Jun-Tong Chen, Ying Meng & Yi Wang
A new species Sinosenecio yangii D.G. Zhang & Q. Zhou (Asteraceae, Senecioneae) from Guizhou Province, China, is described and illustrated based on its morphological characteristics and molecular evidence. It closely resembles S. confervifer and S. guangxiensis, the former in the scapigerous habit and smooth and glabrous achene surface, the latter in the calyculate involucre and purple abaxial leaf surface, and both in the shape and indumentum of leaf lamina, but differs markedly from the latter...

Additional file 9 of Genome-wide profiling of retroviral DNA integration and its effect on clinical pre-infusion CAR T-cell products

Lipei Shao, Rongye Shi, Yingdong Zhao, Hui Liu, Alexander Lu, Jinxia Ma, Yihua Cai, Tatyana Fuksenko, Alejandra Pelayo, Nirali N. Shah, James N. Kochenderfer, Scott M. Norberg, Christian Hinrichs, Steven L. Highfill, Robert P Somerville, Sandhya R. Panch, Ping Jin & David F. Stroncek
Additional file 9: Table S4. Differential integration sites at gene locus based on clinical outcomes.

Derivation and validation of a model to predict acute kidney injury following cardiac surgery in patients with normal renal function

Penghua Hu, Zhiming Mo, Yuanhan Chen, Yanhua Wu, Li Song, Li Zhang, Zhilian Li, Lei Fu, Huaban Liang, Yiming Tao, Shuangxin Liu, Zhiming Ye & Xinling Liang
The study aimed to construct a clinical model based on preoperative data for predicting acute kidney injury (AKI) following cardiac surgery in patients with normal renal function. A total of 22,348 consecutive patients with normal renal function undergoing cardiac surgery were enrolled. Among them, 15,701 were randomly selected for the training group and the remaining for the validation group. To develop a model visualized as a nomogram for predicting AKI, logistic regression was performed with...

miR-199a-3p plays an anti-tumorigenic role in lung adenocarcinoma by suppressing anterior gradient 2

Hui Liu, Yanfeng Wang, Yi Wang, Daoyuan Wu & He Zhang
Previous studies have explored the association between protein-coding genes and microRNAs (miRNAs) in lung adenocarcinoma (LUAD). However, the influence of the miR-199a-3p/anterior gradient 2 (AGR2) axis in LUAD has not yet been fully explored. Therefore, this study aimed to examine the underlying roles of AGR2 and miR-199a-3p in the development of LUAD. The expression levels of miR-199a-3p and AGR2 in LUAD tissues and cells were detected via quantitative reverse transcription-polymerase chain reaction (qRT-PCR). A luciferase...

Changes in the spectrum of kidney diseases: a survey of 2803 patients from 2010 to 2018 at a single center in southeastern China

Linfeng Zheng, Luxia Tu, Haowen Huang, Li Zhang, Ying Wang, Jing Zhou, Qinkai Chen & Xin Wei
Primary glomerular disease was the leading cause of chronic kidney disease (CKD) in China; however, changes in the economy and environment introduce variations in the spectrum of kidney diseases. This study aimed to analyze renal biopsy data to inform disease prevention and public health interventions. In this retrospective cohort study, data from 2,803 consecutive renal biopsies conducted at our center between January 2010 and December 2018 were analyzed. The sample was disaggregated by age and...

Protective effects of psoralen polymer lipid nanoparticles on doxorubicin - induced myocardial toxicity

Fansu Meng, Yong Ouyang, Qianqian Ma, Manling Du, Hui Liu, Yong Zhuang, Mujuan Pang, Tiange Cai & Yu Cai
Abstract Doxorubicin (DOX) induced myocardial toxicity may limit its therapeutic use in clinic. Psoralen (PSO), a major active tricyclic furocoumarin extracted from Psoralea corylifolia, is widely used as an antineoplastic agent in treatment of leukemia and other cancers. This study is aim to find the protective effect of psoralen polymer lipid nanoparticles (PSO-PLN) on doxorubicin-induced myocardial toxicity in mice. The model of myocardial toxicity induced by DOX was established. The experiment was divided into 6...

Optimal timing and drug combination of selinexor in multiple myeloma: a systematic review and meta-analysis

Xinyuan Gu, Chunyan Sun, Juan Xu, Zhimei Lin, Li Zhang & Yuhuan Zheng
Multiple myeloma (MM) remains an incurable disease despite advances in treatment options. Recently, selinexor has shown promising efficacy for relapsed/refractory multiple myeloma (RRMM), whereas its optimal timing and drug combination remain unclear. In order to assess the various regimens that incorporate selinexor, a systematic review and meta-analysis was conducted. Clinical trials and real-world studies involving MM patients treated with selinexor were included. Pooled risk ratio (RR) was calculated to compare the rates, along with a...

Data from: Role of selection and gene flow in population differentiation at the edge vs. interior of the species range differing in climatic conditions

Sergei Volis, Danara Ormanbekova & Irina Shulgina
Evaluating the relative importance of neutral and adaptive processes as determinants of population differentiation across environments is a central theme of evolutionary biology. We applied the QST-FST comparison flanked by a direct test for local adaptation to infer the role of climate-driven selection and gene flow in population differentiation of an annual grass Avena sterilis in two distinct parts of the species range, edge and interior, which represent two globally different climates, desert and Mediterranean....

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  • Kunming Institute of Botany
  • Chinese Academy of Sciences
  • Zhejiang University
  • University of Chinese Academy of Sciences
  • Sichuan University
  • Capital Medical University
  • Anhui Medical University
  • Chinese Academy of Medical Sciences & Peking Union Medical College
  • Sun Yat-sen University Cancer Center
  • Huazhong University of Science and Technology