133 Works

Data from: Emergence and evolution of novel reassortant influenza A viruses in canines in southern China

Ying Chen, Nídia S. Trovão, Guojun Wang, Weifeng Zhao, Ping He, Huabo Zhou, Yanning Mo, Zuzhang Wei, Kang Ouyang, Weijiang Huang, Adolfo García-Sastre, Martha I. Nelson & Weijian Huang
The capacity of influenza A viruses (IAVs) to host jump from animal reservoir species to humans presents an ongoing pandemic threat. Birds and swine are considered major reservoirs of viral genetic diversity, whereas equines and canines have historically been restricted to one or two stable IAV lineages with no transmission to humans. Here, by sequencing the complete genomes of 16 IAVs obtained from canines in southern China (Guangxi Zhuang Autonomous Region [Guangxi]) in 2013 to...

Data from: Niches in the Anthropocene: passerine assemblages show niche expansion from natural to urban habitats

Emilio Pagani-Núñez, Dan Liang, Chao He, Xuemeng Zhou, Xu Luo, Yang Liu & Eben Goodale
Human‐mediated habitat transformation is increasingly evident around the world. Yet, how this transformation influences species’ niche width and overlap remains unclear. On the one hand, human‐mediated habitat transformation promotes increased species similarity through trait‐based filtering, and an increased prevalence of generalist species with broad niches, resulting in functional homogenization. On the other hand, species that colonize transformed habitats could use empty niches, resulting in decreased species similarity and an expansion of assemblage‐level niche space. Here...

Data from: The physiological cold tolerance of warm-climate plants is correlated with their latitudinal range limit

Yin Wen, De-Wen Qin, Bing Leng, Yun-Fei Zhu & Kun-Fang Cao
Plants are moving poleward and upward in response to climate warming. However, such movements lag behind the expanding warming front for many reasons, including the impediment of plant movement caused by unusual cold events. In this study, we measured the maximum photochemical efficiency of PSII (Fv/Fm) in 101 warm-climate angiosperm species to assess their cold tolerance at the end of a severe chilling period of 49 days in a southern subtropical region (Nanning) in China....

Data from: Integration of homogeneous structural region identification and rock mass quality classification

Qingfa Chen & Tingchang Yin
In rock engineering projects, professionals assess the overall rock mass qualities using a sole value. However, the true qualities of partial rock masses are incompatible with such a value. To address this problem, the idea of regionally classifying rock mass qualities is proposed and the associated procedure presented. To achieve this goal, the probabilistic and deterministic joints within the study area were determined, and a three-dimensional joint network model was created. Then, the three-dimensional joint...

Structural defence is coupled with the leaf economic spectrum across saplings of spiny species

Mohammed Armani, Uromi M. Goodale, Tristan Charles-Dominique, Kasey E. Barton, Xin Yao & Kyle W. Tomlinson
Given that the rate of resource capture constrains plant growth and defence, understanding the linkage between the leaf economic spectrum (LES) and defence and how it contributes to growth is central to predicting species performance. In spite of the prevalence of spiny plants in many plant communities, little is known about how the LES relates to defence and growth rate across these species. We grew 42 spiny species, from diverse environments, under common garden conditions...

The dataset of the BCZT ceramic characterizations

Lingyu Wan, Yaohui Chen, Daihua Chen, Liufang Meng, Huilu Yao, Junyi Zhai, Changlai Yuan, Devki N Talwar & Zhe Chuan Feng
All original data used in figures and tables of the manuscript are available in the dataset, which includes the XRD, variable temperature dielectric, room temperature frequency spectrum and ferroelectric performance measurements.A sol-gel method is employed for preparing high quality lead-free glass-ceramic samples (1-x) BCZT-x BBS – incorporating Ba0.85Ca0.15Zr0.1Ti0.9O3 (BCZT) powder and Bi2O3-B2O3-SiO2 (BBS) glass doped additives with different values of x (x = 0, 0.05, 0.1, 0.15). With the increase of BBS content, the polarization...

Land-use and elevation interact to shape bird functional and phylogenetic diversity and structure: Implications for designing optimal agriculture landscapes

Rachakonda Sreekar, Xingfeng Si, Katerina Sam, Jiajia Liu, Salindra Dayananda, Uromi Goodale, Sarath Kotagama & Eben Goodale
Conversion of rainforests into agriculture resulted in massive changes in species diversity and community structure. Although the conservation of the remaining rainforests is of utmost importance, identifying and creating biodiversity-friendly agriculture landscape is vital for preserving biodiversity and their functions. Biodiversity studies in agriculture have often been conducted at low elevations. In this study, we compared the functional diversity (FD), phylogenetic diversity (PD), and community structure of birds along an interacting gradient of land-use (protected...

Additional file 1 of Construction of a ferroptosis-related five-lncRNA signature for predicting prognosis and immune response in thyroid carcinoma

Yuan Qin, Dai Zhang, Huan Zhang, Lan Hou, Zhe Wang, Liu Yang, Mingkun Zhang, Ge Zhao, Qing Yao, Rui Ling & Juliang Zhang
Additional file 1: Table S1. Ferroptosis-related genes.

Observation on the effectiveness and safety of sodium bicarbonate Ringer’s solution in the early resuscitation of traumatic hemorrhagic shock: a clinical single-center prospective randomized controlled trial

Jizhe Zhang, Dong Han, Kun Zhang, Weiqiang Guan, Li Li & Zhengtao Gu
Abstract Background Traumatic hemorrhagic shock (THS) is the main cause of death in trauma patients with high mortality. Rapid control of the source of bleeding and early resuscitation are crucial to clinical treatment. Guidelines recommend isotonic crystal resuscitation when blood products are not immediately available. However, the selection of isotonic crystals has been controversial. Sodium bicarbonate Ringer solutions (BRS), containing sodium bicarbonate, electrolyte levels, and osmotic pressures closer to plasma, are ideal. Therefore, in this...

Identification of Immune Infiltration and Effective Immune Biomarkers in Acute Lung Injury by Bioinformatics Analysis

Dandan Ling, Xiang Zhang, Jiamin Wu, Qianyun Xu, Zhiyong He & Jun Zhang
Acute lung injury (ALI) is a serious complication in clinical settings. This study aimed to elucidate the immune molecular mechanisms underlying ALI by bioinformatics analysis. Human ALI and six ALI mouse model datasets were collected. Immune cell infiltration between the ALI samples and non-ALI controls was estimated using the ssGSEA algorithm. Least absolute shrinkage and selection operator (LASSO) regression analysis and Wilcoxon test were performed to obtain the significantly different immune cell infiltration types. Immune...

Identification of Immune Infiltration and Effective Immune Biomarkers in Acute Lung Injury by Bioinformatics Analysis

Dandan Ling, Xiang Zhang, Jiamin Wu, Qianyun Xu, Zhiyong He & Jun Zhang
Acute lung injury (ALI) is a serious complication in clinical settings. This study aimed to elucidate the immune molecular mechanisms underlying ALI by bioinformatics analysis. Human ALI and six ALI mouse model datasets were collected. Immune cell infiltration between the ALI samples and non-ALI controls was estimated using the ssGSEA algorithm. Least absolute shrinkage and selection operator (LASSO) regression analysis and Wilcoxon test were performed to obtain the significantly different immune cell infiltration types. Immune...

Additional file 6 of Circulating tumor DNA integrating tissue clonality detects minimal residual disease in resectable non-small-cell lung cancer

Siwei Wang, Ming Li, Jingyuan Zhang, Peng Xing, Min Wu, Fancheng Meng, Feng Jiang, Jie Wang, Hua Bao, Jianfeng Huang, Binhui Ren, Mingfeng Yu, Ninglei Qiu, Houhuai Li, Fangliang Yuan, Zhi Zhang, Hui Jia, Xinxin Lu, Shuai Zhang, Xiaojun Wang, Youtao Xu, Wenjia Xia, Tongyan Liu, Weizhang Xu, Xinyu Xu … & Rong Yin
Additional file 6. Figure S3: Prognostic values of postsurgical ctDNA detection at 3 months and 6 months. A-B) The recurrence-free survival analysis (top panel) and multi-variant Cox regression (bottom panel) of postsurgical ctDNA detection at 3 months (A) and 6 months (B). For the analysis at 6 months after surgeries, only patients with plasma samples available at this scheduled point and followed-up for more than 6 months were included. Abbreviations: RFS – recurrence-free survival, LNM...

Additional file 2 of Circulating tumor DNA integrating tissue clonality detects minimal residual disease in resectable non-small-cell lung cancer

Siwei Wang, Ming Li, Jingyuan Zhang, Peng Xing, Min Wu, Fancheng Meng, Feng Jiang, Jie Wang, Hua Bao, Jianfeng Huang, Binhui Ren, Mingfeng Yu, Ninglei Qiu, Houhuai Li, Fangliang Yuan, Zhi Zhang, Hui Jia, Xinxin Lu, Shuai Zhang, Xiaojun Wang, Youtao Xu, Wenjia Xia, Tongyan Liu, Weizhang Xu, Xinyu Xu … & Rong Yin
Additional file 2. Table S2: Adjuvant treatment information.

Additional file 4 of Circulating tumor DNA integrating tissue clonality detects minimal residual disease in resectable non-small-cell lung cancer

Siwei Wang, Ming Li, Jingyuan Zhang, Peng Xing, Min Wu, Fancheng Meng, Feng Jiang, Jie Wang, Hua Bao, Jianfeng Huang, Binhui Ren, Mingfeng Yu, Ninglei Qiu, Houhuai Li, Fangliang Yuan, Zhi Zhang, Hui Jia, Xinxin Lu, Shuai Zhang, Xiaojun Wang, Youtao Xu, Wenjia Xia, Tongyan Liu, Weizhang Xu, Xinyu Xu … & Rong Yin
Additional file 4. Figure S1: Availability of plasma samples. The availability of plasma samples for analysis at each schedule collection time point. Blue and red blocks denote samples collected before and after disease recurrence, respectively. Abbreviations: LUAD – lung adenocarcinoma, LUSC - lung squamous-cell carcinoma, RFS – recurrence-free survival, AT – adjuvant therapy, RT – radiotherapy, LNM – lymph node metastasis.

Additional file 12 of Circulating tumor DNA integrating tissue clonality detects minimal residual disease in resectable non-small-cell lung cancer

Siwei Wang, Ming Li, Jingyuan Zhang, Peng Xing, Min Wu, Fancheng Meng, Feng Jiang, Jie Wang, Hua Bao, Jianfeng Huang, Binhui Ren, Mingfeng Yu, Ninglei Qiu, Houhuai Li, Fangliang Yuan, Zhi Zhang, Hui Jia, Xinxin Lu, Shuai Zhang, Xiaojun Wang, Youtao Xu, Wenjia Xia, Tongyan Liu, Weizhang Xu, Xinyu Xu … & Rong Yin
Additional file 12. Supplementary discussion.

Circulating tumor DNA integrating tissue clonality detects minimal residual disease in resectable non-small-cell lung cancer

Siwei Wang, Ming Li, Jingyuan Zhang, Peng Xing, Min Wu, Fancheng Meng, Feng Jiang, Jie Wang, Hua Bao, Jianfeng Huang, Binhui Ren, Mingfeng Yu, Ninglei Qiu, Houhuai Li, Fangliang Yuan, Zhi Zhang, Hui Jia, Xinxin Lu, Shuai Zhang, Xiaojun Wang, Youtao Xu, Wenjia Xia, Tongyan Liu, Weizhang Xu, Xinyu Xu … & Rong Yin
Abstract Background Circulating tumor DNA (ctDNA) has been proven as a marker for detecting minimal residual diseases following systemic therapies in mid-to-late-stage non-small-cell lung cancers (NSCLCs) by multiple studies. However, fewer studies cast light on ctDNA-based MRD monitoring in early-to-mid-stage NSCLCs that received surgical resection as the standard of care. Methods We prospectively recruited 128 patients with stage I–III NSCLCs who received curative surgical resections in our Lung Cancer Tempo-spatial Heterogeneity prospective cohort. Plasma samples...

Additional file 1 of Comparison of response evaluation criteria in solid tumors and tumor regression grade in evaluating the effect of preoperative systemic therapy of gastric cancer

Ming-Yu Lai, Shi-Yang Kang, Yu-Ting Sun, Ting-Ting Quan, Shi-Xun Lu, Cai-Yun He, Zhi-Wei Zhou, Li-Qiong Yang, Hui-Yan Luo, Feng-Hua Wang, Yu-Hong Li, Rui-Hua Xu, Wen-Long Guan & Miao-Zhen Qiu
Additional file 1.

Additional file 3 of Comparison of response evaluation criteria in solid tumors and tumor regression grade in evaluating the effect of preoperative systemic therapy of gastric cancer

Ming-Yu Lai, Shi-Yang Kang, Yu-Ting Sun, Ting-Ting Quan, Shi-Xun Lu, Cai-Yun He, Zhi-Wei Zhou, Li-Qiong Yang, Hui-Yan Luo, Feng-Hua Wang, Yu-Hong Li, Rui-Hua Xu, Wen-Long Guan & Miao-Zhen Qiu
Additional file 3.

Additional file 4 of Comparison of response evaluation criteria in solid tumors and tumor regression grade in evaluating the effect of preoperative systemic therapy of gastric cancer

Ming-Yu Lai, Shi-Yang Kang, Yu-Ting Sun, Ting-Ting Quan, Shi-Xun Lu, Cai-Yun He, Zhi-Wei Zhou, Li-Qiong Yang, Hui-Yan Luo, Feng-Hua Wang, Yu-Hong Li, Rui-Hua Xu, Wen-Long Guan & Miao-Zhen Qiu
Additional file 4.

Additional file 6 of Comparison of response evaluation criteria in solid tumors and tumor regression grade in evaluating the effect of preoperative systemic therapy of gastric cancer

Ming-Yu Lai, Shi-Yang Kang, Yu-Ting Sun, Ting-Ting Quan, Shi-Xun Lu, Cai-Yun He, Zhi-Wei Zhou, Li-Qiong Yang, Hui-Yan Luo, Feng-Hua Wang, Yu-Hong Li, Rui-Hua Xu, Wen-Long Guan & Miao-Zhen Qiu
Additional file 6.

Data from: Leaf trait variations associated with habitat affinity of tropical karst tree species

Nalaka Geekiyanage, Uromi Goodale, Kunfang Cao, Kaoru Kitajima & Uromi Manage Goodale
1. Karst hills, i.e., jagged topography created by dissolution of limestone and other soluble rocks, are distributed extensively in tropical forest regions, including southern parts of China. They are characterized by a sharp mosaic of water and nutrient availability, from exposed hilltops with poor soil development to valleys with occasional flooding, to which trees show species specific distributions. Here we report the relationship of leaf functional traits to habitat preference of tropical karst trees. 2....

Data from: The cover uncovered: bark control over wood decomposition

Gbadamassi G.O. Dossa, Douglas Schaefer, Jiao-Lin Zhang, Jian-Ping Tao, Kun-Fang Cao, Richard T. Corlett, Anthony B. Cunningham, Jian-Chu Xu, Johannes H. C. Cornelissen, Rhett D. Harrison & Gbadamassi G. O. Dossa
1. Woody debris (WD) represents a globally significant carbon stock and its decomposition returns nutrients to the soil while providing habitat to microbes, plants and animals. Understanding what drives WD decomposition is therefore important. 2. WD decomposition rates differ greatly among species. However, the role of bark in the process remains poorly known. 3. We ask how, and how much, interspecific variation in bark functional traits related to growth and protection have afterlife effects on...

Museomics for reconstructing historical floristic exchanges: Divergence of Stone Oaks across Wallacea

Joeri Strijk, Hoang Thi Bin Thi Bin, Ferry Slik, Rahayu Sukri, Yoshihisa Suyama, Shuichiro Tagane, Jan Wieringa, Tetsukazu Yahara & Damien Hinsinger
Natural history collections and tropical tree diversity are treasure troves of biological and evolutionary information, but its accessibility is impeded by several properties. DNA in historical specimens generally occurs in a highly fragmented state, complicating the recovery of high-grade genetic material for scientific studies. Our understanding of hyperdiverse, wide-spread tree assemblages suffers from patchy information on distributions, phenology and paucity of diagnostic characters. This prohibits rapid identification and the strengthening of taxonomic frameworks and in...

Environment filtering and dispersal limitation jointly shaped the taxonomic and phylogenetic beta diversity of natural forests in southern China

Wei Shi, Yong-Qiang Wang, Wu-Sheng Xiang, Xian-Kun Li & Kun-Fang Cao
Aim The mechanisms underlying the maintenance of biodiversity remain to be elucidated. Taxonomic diversity alone remains an unresolved issue, especially in terms of the mechanisms of species co-existence. We hypothesized that phylogenetic information could help to elucidate the mechanism of community assembly and the services and functions of ecosystems. The aim of this study was to explore the mechanisms driving floral diversity in subtropical forests and evaluate the relative effects of these mechanisms on diversity...

Crop heterogeneity is positively associated with beneficial insect diversity in subtropical farmlands

Eben Goodale, Tharaka S. Priyadarshana, Myung-Bok Lee, John S. Ascher & Lu Qiu
Increasing crop configurational heterogeneity – smaller crop fields with more field margins – has been repeatedly found to support farmland biodiversity. But research on compositional crop heterogeneity – the number and evenness of crop types – has usually shown only weak effects. However, much of this research has been conducted in large-scale temperate agroecosystems. We examined smallholder subtropical agroecosystems in southern China to assess the effects of crop heterogeneity on beneficial insect biodiversity. In addition...

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