147 Works

Mechanical artifacts in optical projection tomography: classification and automatic calibration

Yan Liu, Jonathan Dong, Thanh-An Pham, Francois Marelli & Michael Unser
Optical projection tomography (OPT) is a powerful tool for biomedical studies. It achieves 3D visualization of mesoscopic biological samples with high spatial resolution using conventional tomographic-reconstruction algorithms. However, various artifacts degrade the quality of the reconstructed images due to experimental imperfections in the OPT instruments. While many efforts have been made to characterize and correct for these artifacts, they focus on one specific type of artifacts, whereas a comprehensive catalog of all sorts of mechanical...

Supracapsular scleral sutured intraocular lens implantation in anterior segment dysgenesis patients with ectopia lentis

Tian-Hui Chen, Ling-hao Song, Lei Jiang, Ye zhao, Yan Liu, Dong-jin Qian, Ze-xu Chen & Yong-Xiang Jiang
ObjectiveTo describe a new strategy to manage ectopia lentis in ASD patients assessing the visual outcomes and safety of supracapsular scleral sutured intraocular lens implantation and analyzing the accuracy of different intraocular lens (IOL) power calculation formulae.MethodsEight patients with ASD (13 eyes) were underwent supracapsular scleral suture fixation of posterior chamber (PC) IOL without capsular extirpation. The preoperative and postoperative clinical features were compared. The prediction error values from four formulae (SRK/T, Holladay 1, Hoffer...

Identification and Analysis of Flax Resistance Genes to Septoria linicola (Speg.) Garassini

Si Chen, Hongmei Yuan, Xue Yang, Le Chen, Jing Chen, Yan Liu, Linlin Wu, Yingying Hu, Wengong Huang, Yubo Yao, Jianzhong Wu, Qinghua Kang, Xixia Song, Weidong Jiang, Wanmin Sheng & Guangwen Wu
In this study, the flax (Linum usitatissimum L.) genes associated with resistance to the disease pasmo (Septoria linicola (Speg.) Garassini) were mapped using genome resequencing and bulked segregant analysis (BSA) of genomic DNA of the pasmo-resistant parent y62–9, pasmo-susceptible parent y64–5, and F2 generation segregants. Pasmo resistance genes were identified using Gene Ontology (GO) functional prediction and gene annotation methods. A Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis revealed the biological information and molecular...

Supplemental materials of: Ignored biodiversity in acid soil islands in karst areas, South China: Impatiens longlinensis (Balsaminaceae), a new critically endangered species

Tian-Tian Xue, Chang-Ying Xia, Magnus Lidén, Wei-Bin Xu, Zhao-Cen Lu, Hai-Ling Chen, Shu-Wan Li & Sheng-Xiang Yu
The karst area in South China is notable for its fragile vegetation and unique flora with many narrow endemics, and is one of the most threatened biodiversity hotspots in the world. However, the biodiversity of acid soil areas scattered in the karst area have previously been underestimated. With a recent increase of new discoveries of plants and animals, the conservation of biodiversity in these acid soil areas has become urgent. This study deals with a...

Long non-coding RNA DUXAP8 promotes the cell proliferation, migration, and invasion of papillary thyroid carcinoma via miR-223-3p mediated regulation of CXCR4

Yan Liu, Hejia Zhang, Hui Wang, Jiarui Du, Peng Dong, Meihan Liu & Yuanqiang Lin
Papillary thyroid carcinoma (PTC) is a differentiated type of thyroid malignancy with a high incidence. Long non-coding RNA (lncRNA) DUXAP8 has been reported to participate in the proliferation, migration, and invasion of several cancer types. However, its association with PTC has not yet been reported. The current study aimed to investigate the role of DUXAP8 in PTC and revealed the underlying mechanisms. The expression of DUXAP8 was knocked down in two PTC cell lines and...

Aromatic glycosides from the aerial part of Bupleurum chinense

Yan Liu, Dong-Xv Lu, Jin Huang, Juan Pan, Wei Guan, Bing-You Yang & Hai-Xue Kuang
A new aromatic glycoside (1) and twelve (2–13) known aromatic glycosides were isolated from the n-butyl alcohol of the 70% EtOH extract of the aerial part of Bupleurum chinense. Among them, compounds 4–7, 9, 11–13 were isolated from Umbelliferae plants for the first time. Their structures were elucidated by NMR and MS spectroscopy, and the absolute configuration of compound 1 was elucidated by single-crystal X-ray diffraction. Compounds 6 and 10 showed moderate cytotoxic activities on...

Phylogenomic and macroevolutionary evidence for an explosive radiation of a plant genus in the Miocene

Hanghui Kong, Fabien L. Condamine, Lihua Yang, AJ Harris, Chao Feng, Fang Wen & Ming Kang
Mountain systems harbor a substantial fraction of global biodiversity and, thus, provide excellent opportunities to study rapid diversification and to understand the historical processes underlying the assembly of biodiversity hotspots. The rich biodiversity in mountains is widely regarded as having arisen under the influence of geological and climatic processes as well as the complex interactions among them. However, the relative contribution of geology and climate in driving species radiation is seldom explored. Here, we studied...

Identification and potential mechanism of different components from the aerial part of Bupleurum chinense DC. for epileptic treatment

Xiaomao Li, Yan Liu, Siyi Wang, Wei Guan, Juan Pan, Haixue Kuang & Bingyou Yang
The present study aimed to assess the effects of epileptic treatment of the aerial part of Bupleurum chinense DC. in kainic acid (KA)-induced epilepsy rats and LPS-induced BV2 cells, as well as to identify the active chemical constituents. The in vivo and vitro results showed that 20% ethanol elution fractions of the aerial part of B. chinense DC. (BCE-20) and 70% ethanol elution fractions of the aerial part of B. chinense DC. (BCE-70) could improve...

Data from: Papilio butterfly vs. hawkmoth pollination explains floral syndrome dichotomy in a clade of Lilium

Chang-Qiu Liu
This dataset contains data described in the paper recently accepted by Botanical Journal of the Linnean Society:“ Liu C-Q, Niu Y, Lu Q-B, Chen Z, Cai B, Fang Y, Gao Y-D. (2021) Papilio butterfly vs. hawkmoth pollination explains floral syndrome dichotomy in a clade of Lilium". The Leucolirion clade of Lilium contains species with either tepal-recurved or trumpet-shaped flowers. We hypothesized that the tepal-recurved flowers might be pollinated by butterflies and/or birds while the trumpet-shaped...

Additional file 1 of Epidemiological and etiological characteristics of mild hand, foot and mouth disease in children under 7 years old, Nanjing, China, 2010–2019

Junjun Wang, Songning Ding, Weijia Xie, Taiwu Wang, Ying Qin, Jiandong Zheng, Xiaokun Yang, Hongting Zhao, Zhibin Peng & Tao Ma
Additional file 1: Supplementary Table 1. Spatial cluster scan of mild hand, foot, and mouth disease cases aged < 7 years in Nanjing, China, 2010-2019. Supplementary Table 2. Enterovirus serotypes distribution for mild hand, foot, and mouth disease cases aged < 7 years in Nanjing, China, 2010-2019.

Epidemiological and etiological characteristics of mild hand, foot and mouth disease in children under 7 years old, Nanjing, China, 2010–2019

Junjun Wang, Songning Ding, Weijia Xie, Taiwu Wang, Ying Qin, Jiandong Zheng, Xiaokun Yang, Hongting Zhao, Zhibin Peng & Tao Ma
Abstract Background Mild hand, foot and mouth disease (HFMD) cases make up a relatively high proportion of HFMD while have often been overlooked. This study aimed to investigate the epidemiological and etiological characteristics of mild HFMD in Nanjing. Methods Data on mild HFMD cases, during 2010–2019 in Nanjing, were collected from the China Information System for Disease Control and Prevention. This study mainly focused on mild cases aged < 7 years. Descriptive analysis was used...

Additional file 2 of Transcriptomic analysis of paternal behaviors in prairie voles

Florian Duclot, Yan Liu, Samantha K. Saland, Zuoxin Wang & Mohamed Kabbaj
Additional file 2. Analysis of variance (ANOVA) results for all behaviors scored during the parental behavior test.

Additional file 4 of Transcriptomic analysis of paternal behaviors in prairie voles

Florian Duclot, Yan Liu, Samantha K. Saland, Zuoxin Wang & Mohamed Kabbaj
Additional file 4. Depiction of individual behavioral bouts across the parental behavior test. The bouts of the autogroom, carry, huddling, licking & grooming, nest building, and sniffing behaviors are depicted across time throughout the entire parental behavior test session. Each row represents a distinct animal.

Additional file 8 of Transcriptomic analysis of paternal behaviors in prairie voles

Florian Duclot, Yan Liu, Samantha K. Saland, Zuoxin Wang & Mohamed Kabbaj
Additional file 8. Comparisons of slopes for linear regressions between behaviors scored during the parental behaviors test. Slopes (a) and their differences between groups (b) are listed for all linear regressions with a significant interaction with Group (see Additional file 7).

Additional file 1 of Transcriptomic analysis of paternal behaviors in prairie voles

Florian Duclot, Yan Liu, Samantha K. Saland, Zuoxin Wang & Mohamed Kabbaj
Additional file 1. Time spent in each behavior during the parental behavior test. The total duration across the entire test session is depicted for each animal for the autogrooming, carry, huddling, licking & grooming, locomotion, nest building, and sniffing behaviors; each data point thus represents a distinct animal. The horizontal line in the shaded violin represents the 50% quantile of the density estimate.

Additional file 20 of Transcriptomic analysis of paternal behaviors in prairie voles

Florian Duclot, Yan Liu, Samantha K. Saland, Zuoxin Wang & Mohamed Kabbaj
Additional file 20. Analysis of variance (ANOVA) results for the estimated proportions of the “Neurons” cell type in the genes differentially expressed in the medial preoptic area (MPOA), nucleus accumbens (NAc), and lateral septum (LS).)

Additional file 25 of Transcriptomic analysis of paternal behaviors in prairie voles

Florian Duclot, Yan Liu, Samantha K. Saland, Zuoxin Wang & Mohamed Kabbaj
Additional file 25. Functional enrichment of gene ontologies of the cellular components category in gene co-expression modules derived from the weighted gene coexpression network analysis (WGCNA).

Additional file 25 of Transcriptomic analysis of paternal behaviors in prairie voles

Florian Duclot, Yan Liu, Samantha K. Saland, Zuoxin Wang & Mohamed Kabbaj
Additional file 25. Functional enrichment of gene ontologies of the cellular components category in gene co-expression modules derived from the weighted gene coexpression network analysis (WGCNA).

Additional file 27 of Transcriptomic analysis of paternal behaviors in prairie voles

Florian Duclot, Yan Liu, Samantha K. Saland, Zuoxin Wang & Mohamed Kabbaj
Additional file 27. Functional enrichment of pathways from the Kyoto Encyclopedia of Genes and Genomes (KEGG) in gene co-expression modules derived from the weighted gene coexpression network analysis (WGCNA).

Additional file 11 of Transcriptomic analysis of paternal behaviors in prairie voles

Florian Duclot, Yan Liu, Samantha K. Saland, Zuoxin Wang & Mohamed Kabbaj
Additional file 11. Summary statistics for the differential expression analysis. DE: differentially expressed. LS: lateral septum, MPOA: medial preoptic area, NAc: nucleus accumbens.

Additional file 12 of Transcriptomic analysis of paternal behaviors in prairie voles

Florian Duclot, Yan Liu, Samantha K. Saland, Zuoxin Wang & Mohamed Kabbaj
Additional file 12. Volcano plots for the differential expression analysis. These plots depict the log2 fold-change (x-axis) against the -log10 of the uncorrected p-value (y-axis) for each gene in each pairwise comparison in the medial preoptic area (MPOA, A), nucleus accumbens (NAc, B), and lateral septum (LS, C). Differentially expressed genes are depicted in red.

Additional file 13 of Transcriptomic analysis of paternal behaviors in prairie voles

Florian Duclot, Yan Liu, Samantha K. Saland, Zuoxin Wang & Mohamed Kabbaj
Additional file 13. Functional enrichment of genes differentially expressed in the medial preoptic area (MPOA). For each pairwise comparison, the functional enrichments in gene ontologies of the biological processes (A), cellular components (B), and molecular functions (C) categories were tested for the differentially expressed genes up- or down-regulated (UP, and DOWN, respectively). The labels of pairwise comparisons were coded in two letters: the first one represents the phenotype (M: mothers, F: fathers, P: paternal males,...

Predictors of HbA1c reduction and hypoglycemia in type 2 diabetes mellitus individuals switching from premixed to basal insulin: an exploratory analysis of optimization study

Wenying Yang, Juan Du, Minlu Zhang, Jing Hou, Xia Zhang & Nan Cui
To identify population with type 2 diabetes mellitus (T2DM) who are more likely to benefit from switching to basal insulin (BI) treatment from premixed insulin. This secondary analysis included data from a previously published study (Optimization: NCT00693771) which was a single-arm, multicenter, 16 weeks, phase IV study. The analysis included participants with T2DM inadequately controlled with premixed insulin plus oral hypoglycemic drugs (OADs) who switched to BI plus OADs. Among the 297 participants included for...

The complete mitochondrial genome and phylogenetic analysis of the ocellated angelshark: Squatina tergocellatoides Chen, 1963

Chunbin Jia, Binbin Shan, Yan Liu, Changping Yang, Liangming Wang & Dianrong Sun
The ocellated angelshark (Squatina tergocellatoides Chen, 1963) is a threatened shark within the family Squatinidae. In the present study, we reported the mitochondrial genome sequence of the ocellated angelshark. The complete mitochondrial genome is 16,683 bp in length and contains 37 mitochondrial genes and a control region as similar to most fishes. In addition, we constructed a maximum-likelihood phylogenetic tree of S. tergocellatoides and its relative species. This work will provide molecular data for further...

Additional file 1 of Specific triacylglycerol, diacylglycerol, and lyso-phosphatidylcholine species for the prediction of type 2 diabetes: a ~ 16-year prospective study in Chinese

Junda Zhong, Chloe Y. Y. Cheung, Xiuli Su, Chi-Ho Lee, Yi Ru, Carol H. Y. Fong, Yan Liu, Cynthia K. Y. Cheung, Karen S. L. Lam, Zongwei Cai & Aimin Xu
Additional file 1. Methods. Figure S1. WGCNA of the lipid species profile. Figure S2. Boruta analysis result. Figure S3. Violin Plot of the Targeted Lipidomics. Figure S4. Correlation among identified lipid species.

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