Publications by authors named "Lingyun Yu"

31 Publications

Vasa expression is associated with sex differentiation in the Asian yellow pond turtle, Mauremys mutica.

J Exp Zool B Mol Dev Evol 2021 Jul 8;336(5):431-442. Epub 2021 Jun 8.

Key Laboratory of Tropical & Subtropical Fishery Resource Application & Cultivation of Ministry of Agriculture and Rural Affairs, Pearl River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou, China.

Vasa, one of the best-studied germ cell markers plays a critical role in germ cell development and differentiation in animals. Vasa deficiency would lead to male-specific sterility in most vertebrates, but female sterility in the fly. However, the role of the vasa gene involved in germ cell differentiation is largely elusive. Here, we first characterized the expression profile of vasa products in the Asian yellow pond turtle by quantitative reverse-transcription polymerase chain reaction and fluorescence immunostaining. The results showed that vasa messenger RNA (mRNA) is initially detected in embryos at stage 16, and then dramatically increased in embryos at stage 19. In particular, like the sex-related genes, vasa mRNA exhibited differential expression in embryos between the male-producing temperature (MPT, 25°C) and the female-producing temperature (FPT, 33°C), whereas there was no difference in methylation levels of vasa promoter detected between FPT and MPT. In contrast, in the adult Asian yellow pond, the level of vasa mRNA was much higher in the testis than ovary. Moreover, the immunostaining on testicular sections and cells showed that Vasa protein was exclusively expressed in germ cells: Weak but detectable in spermatogonia, highest in spermatocytes, moderate and concentrated in chromatid bodies in spermatids and spermatozoa, and bare in somatic cells. The expression profile of Vasa protein is similar in turtle species studied so far but distinct from those in fish species in this study. The findings of this study would provide new insights into our understanding of the conservation and divergence of the vasa gene, even other germ cell genes across phyla.
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http://dx.doi.org/10.1002/jez.b.23064DOI Listing
July 2021

Complete mitochondrial genome and the phylogenetic position of the Burmese narrow-headed softshell turtle (Testudines: Trionychidae).

Mitochondrial DNA B Resour 2021 Mar 26;6(3):1216-1218. Epub 2021 Mar 26.

Key Laboratory of Tropical and Subtropical Fishery Resources Application and Cultivation, Ministry of Agriculture and Rural Affairs, Pearl River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou, China.

Narrow-headed softshell turtles constitute a group of critically endangered freshwater turtles that belong to the family Trionychidae. Here, we determine the complete mitogenome of the Burmese narrow-headed softshell turtle . The length of the mitochondrial genome was 16,614 bp, composed of 13 protein-coding genes, 22 tRNA genes, two rRNA genes, and twelve noncoding regions. The phylogenetic analysis strongly indicated that is closely related to . The mitochondrial genome will contribute to the genetic research and conservation of in the future.
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http://dx.doi.org/10.1080/23802359.2021.1903350DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8008941PMC
March 2021

High-Frame Rate Vector Flow Imaging Technique: Initial Application in Evaluating the Hemodynamic Changes of Carotid Stenosis Caused by Atherosclerosis.

Front Cardiovasc Med 2021 8;8:617391. Epub 2021 Mar 8.

Department of Ultrasound, Zhongshan Hospital, Fudan University, Shanghai, China.

To investigate the value of high-frame rate vector flow imaging technique (V flow) in evaluating the hemodynamic changes of carotid stenosis caused by atherosclerotic plaques. In this prospective study, patients with stenosis rate (diameter) ≥30% caused by carotid atherosclerotic plaques were included. Degrees of carotid stenosis were graded according to North American Symptomatic Carotid Endarterectomy Trial criteria: moderate (30-69%) or severe (70-99%). Mindray Resona 7s ultrasound machine with a linear array transducer (3-11 MHz) was used for ultrasound examinations. The mean WSS value of carotid arteries was measured at the proximal, narrowest region and distal of carotid stenosis. The mean WSS values were correlated with peak systolic velocity (PSV) measured by color Doppler flow imaging and stenosis degree detected by digital subtraction angiography (DSA). The vector arrows and flow streamline detected by V flow dynamic imaging were analyzed. Imaging findings of DSA in carotid arteries were used as the gold standard. Finally, 51 patients were included. V flow measurements were performed successfully in 17 patients (100%) with moderate-grade stenosis and in 30 patients (88.2%) with severe-grade stenosis. Dynamic V flow imaging showed yellow or red vectors at the stenotic segment, indicating fast speed blood flow (up to 260.92 cm/s). Changes of streamlines were detected in the stenotic segment. The mean WSS value measured at the narrowest region of the carotid artery had a moderately positive correlation with stenosis degree ( = 0.58, < 0.05) and PSV value ( = 0.54, < 0.05), respectively. Significant difference was detected in mean WSS value at the narrowest region of the carotid artery between severe carotid stenosis (1.47 ± 0.97 Pa) and moderate carotid stenosis (0.96 ± 0.44 Pa) ( < 0.05). The hemodynamic changes detected by V flow of the carotid stenosis might be a potential non-invasive imaging tool for assessing the degree of carotid stenosis.
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http://dx.doi.org/10.3389/fcvm.2021.617391DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7982422PMC
March 2021

Adsorption of Volatile Organic Compounds (VOCs) on Oxygen-rich Porous Carbon Materials Obtained from Glucose/Potassium Oxalate.

Chem Asian J 2021 May 30;16(9):1118-1129. Epub 2021 Mar 30.

School of Energy Science and Engineering, Central South University, Changsha Hunan, 410083, P. R. China.

To investigate the effects of oxygen-containing functional groups on the adsorption of volatile organic compounds (VOCs) with different polarity, oxygen-rich porous carbon materials (OPCs) were synthesized by heat treatment of glucose/potassium oxalate material. The carbon material had a large specific surface area (1697 m  g ) and a high oxygen content (18.95 at.%). OPC exhibited high adsorption capacity of toluene (309 mg g ) and methanol (447 mg g ). The specific surface area and total pore volume determined the adsorption capacity of toluene and methanol at the high-pressure range, while the oxygen-containing groups became the main factor affecting the methanol adsorption at the low-pressure range due to the hydrogen bond interaction through the density functional theory (DFT) calculations. This study provides an important hint for developing a novel O-doped adsorbent for the VOCs adsorption applications and analyzing the role of oxygen-containing groups in the VOCs adsorption under the low-pressure range.
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http://dx.doi.org/10.1002/asia.202100098DOI Listing
May 2021

Reproductive performance is associated with seasonal plasma reproductive hormone levels, steroidogenic enzymes and sex hormone receptor expression levels in cultured Asian yellow pond turtles (Mauremys mutica).

Comp Biochem Physiol B Biochem Mol Biol 2021 Jun-Jul;254:110566. Epub 2021 Jan 27.

Key Laboratory of Tropical & Subtropical Fishery Resource Application & Cultivation, Ministry of Agriculture and Rural Affairs, Pearl River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou, Guangdong 510380, PR China. Electronic address:

In order to understand the endocrine mechanism associated with fecundity of seasonally breeding animals, we investigated the plasma reproductive hormones levels and detected the differences in steroidogenic enzymes and sex hormone receptor mRNA levels in female Mauremys mutica. These turtles were divided into higher fecundity (HF) group than those in lower fecundity (LF) group based on paternity identification in our previous research. The plasma estrogen (E2), testosterone (T) and progesterone (P4) levels were significantly higher in pre-breeding season (PBS) than those in non-breeding season (NBS) and were markedly higher in the HF group than those in LF group. In the hypothalamus, there was significantly higher mRNA abundance of P450-cholesterol side-chain cleavage enzyme (P450Scc) encoded by Cyp11α1, aromatase (Cyp19α1) and 5-reductase (5α-R), but significantly lower mRNA levels of follicular stimulating hormone receptor (FSHR) and progesterone receptor (PR) detected in PBS than those in NBS. The pituitary steroidogenic acute regulatory protein (StAR), cytochrome P450-17alpha-hydroxylase (Cyp17α1), 3-hydroxy-steroid dehydrogenase (3βHSD), 17-hydroxy-steroid dehydrogenase 3 (17βHSD3), Cyp19α1, 5α-R, FSHR, estrogen receptor 1 (ESR1), androgen receptor (AR) and PR transcriptional levels in HF group were up-regulated significantly compared with the LF group. In the ovary, Cyp17α1 and 17βHSD3 transcriptional levels were markedly higher in PBS than those in NBS. We detected significantly increased expression levels of all steroidogenic enzymes, but notably lower mRNA levels of FSHR and PR in uterus during the PBS, and the HF group has significantly higher expression levels of StAR, Cyp17α1, 5α-R and AR than LF group. Our work reveals seasonal variations in hormone regulation as well as gene regulation in turtles, providing reliable information to understand the mechanisms underlying the different reproductive capacity of reptiles.
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http://dx.doi.org/10.1016/j.cbpb.2021.110566DOI Listing
July 2021

Bioaccessibility-corrected health risk of heavy metal exposure via shellfish consumption in coastal region of China.

Environ Pollut 2021 Jan 18;273:116529. Epub 2021 Jan 18.

School of Environment and Energy, Peking University Shenzhen Graduate School, Shenzhen, 518055, China.

A systematic investigation into bioaccessible heavy metals in shellfish Crassostrea ariakensis, Chlamys farreri, and Sinonovacula constricta from coastal cities Shenzhen, Zhoushan, Qingdao, and Dandong was carried out to assess the potential health risk to residents in coastal regions in China. The bioaccessible fractions of heavy metals were (μg‧g): Zn (0.63-15.01), Cu (0.10-12.91), Cd (0.01-0.64), As (0.11-0.33), Cr (0.07-0.12), Pb (0.01-0.03). The bioaccessibilities of heavy metals were Cr 61.86%, inorganic As (iAs) 60.44%, Pb 55.74%, Cu 46.83%, Zn 28.16%, and Cd 24.99%. As for child and adult, the bioaccessibility-corrected estimated daily intakes were acceptable and the non-carcinogenic risks posed by heavy metals were not obvious. The carcinogenic risks posed by bioaccessible heavy metals at the fifth percentile were 10-fold higher than the acceptable level (10), with iAs and Cd to be the major contributors, regardless of child or adult. The probabilistic estimation showed the low risk of shellfish consumption, which was verified by higher values of maximum allowable consumption rate and monthly meals at the 95 percentile; while some control of consumption rate and monthly meals was necessary for reducing heavy metal exposure of most shellfish samples, except for the safe consumption of S. constricta for both child and adult in Qingdao and Shenzhen, China.
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http://dx.doi.org/10.1016/j.envpol.2021.116529DOI Listing
January 2021

Potential application of dynamic contrast enhanced ultrasound in predicting microvascular invasion of hepatocellular carcinoma.

Clin Hemorheol Microcirc 2021 ;77(4):461-469

Department of Radiology, University Medical Center Regensburg, Regensburg, Germany.

Objective: To investigate the clinical value of dynamic contrast enhanced ultrasound (D-CEUS) in predicting the microvascular invasion (MVI) of hepatocellular carcinoma (HCC).

Patients And Methods: In this retrospective study, 16 patients with surgery and histopathologically proved HCC lesions were included. Patients were classified according to the presence of MVI: MVI positive group (n = 6) and MVI negative group (n = 10). Contrast enhanced ultrasound (CEUS) examinations were performed within a week before surgery. Dynamic analysis was performed by VueBox® software (Bracco, Italy). Three regions of interests (ROIs) were set in the center of HCC lesions, at the margin of HCC lesions and in the surrounding liver parenchyma accordingly. Time intensity curves (TICs) were generated and quantitative perfusion parameters including WiR (wash-in rate), WoR (wash-out rate), WiAUC (wash-in area under the curve), WoAUC (wash-out area under the curve) and WiPi (wash-in perfusion index) were obtained and analyzed.

Results: All of HCC lesions showed arterial hyperenhancement (100 %) and at the late phase as hypoenhancement (75%) in CEUS. Among all CEUS quantitative parameters, the WiAUC and WoAUC were higher in MVI positive group than in MVI negative group in the center HCC lesions (P < 0.05), WiAUC, WoAUC and WiPI were higher in MVI positive group than in MVI negative group at the margin of HCC lesions. WiR and WoR were significant higher in MVI positive group.

Conclusions: D-CEUS with quantitative perfusion analysis has potential clinical value in predicting the existence of MVI in HCC lesions.
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http://dx.doi.org/10.3233/CH-201085DOI Listing
May 2021

Evaluation of Sampling Methods for Scatterplots.

IEEE Trans Vis Comput Graph 2021 Feb 28;27(2):1720-1730. Epub 2021 Jan 28.

Given a scatterplot with tens of thousands of points or even more, a natural question is which sampling method should be used to create a small but "good" scatterplot for a better abstraction. We present the results of a user study that investigates the influence of different sampling strategies on multi-class scatterplots. The main goal of this study is to understand the capability of sampling methods in preserving the density, outliers, and overall shape of a scatterplot. To this end, we comprehensively review the literature and select seven typical sampling strategies as well as eight representative datasets. We then design four experiments to understand the performance of different strategies in maintaining: 1) region density; 2) class density; 3) outliers; and 4) overall shape in the sampling results. The results show that: 1) random sampling is preferred for preserving region density; 2) blue noise sampling and random sampling have comparable performance with the three multi-class sampling strategies in preserving class density; 3) outlier biased density based sampling, recursive subdivision based sampling, and blue noise sampling perform the best in keeping outliers; and 4) blue noise sampling outperforms the others in maintaining the overall shape of a scatterplot.
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http://dx.doi.org/10.1109/TVCG.2020.3030432DOI Listing
February 2021

PlotThread: Creating Expressive Storyline Visualizations using Reinforcement Learning.

IEEE Trans Vis Comput Graph 2021 Feb 28;27(2):294-303. Epub 2021 Jan 28.

Storyline visualizations are an effective means to present the evolution of plots and reveal the scenic interactions among characters. However, the design of storyline visualizations is a difficult task as users need to balance between aesthetic goals and narrative constraints. Despite that the optimization-based methods have been improved significantly in terms of producing aesthetic and legible layouts, the existing (semi-) automatic methods are still limited regarding 1) efficient exploration of the storyline design space and 2) flexible customization of storyline layouts. In this work, we propose a reinforcement learning framework to train an AI agent that assists users in exploring the design space efficiently and generating well-optimized storylines. Based on the framework, we introduce PlotThread, an authoring tool that integrates a set of flexible interactions to support easy customization of storyline visualizations. To seamlessly integrate the AI agent into the authoring process, we employ a mixed-initiative approach where both the agent and designers work on the same canvas to boost the collaborative design of storylines. We evaluate the reinforcement learning model through qualitative and quantitative experiments and demonstrate the usage of PlotThread using a collection of use cases.
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http://dx.doi.org/10.1109/TVCG.2020.3030467DOI Listing
February 2021

Preliminary Clinical Experience with Shear Wave Dispersion Imaging for Liver Viscosity in Preoperative Diagnosis of Focal Liver Lesions.

Z Gastroenterol 2020 Sep 18;58(9):847-854. Epub 2020 Sep 18.

Caritas-Krankenhaus Bad Mergentheim gGmbH, Bad Mergentheim, Germany.

Background:  The aim of our study is to analyze viscosity characteristics of focal liver lesions (FLLs) and the diagnostic performance of shear wave dispersion (SWD) in differentiating benign and malignant FLLs.

Methods:  Between January 2018 and April 2018, 58 consecutive patients (median age 57, age range 21-74 years, 37 males) with 58 FLLs located on the right lobe of liver were prospectively studied. The Aplio i900 series diagnostic ultrasound system (Canon Medical systems) equipped with a curvilinear PV1-475BX transducer (1-8 MHz) was used. SWD slope and viscosity measurements were expressed as mean ± standard deviation for both liver tumors and background liver parenchyma. Histopathological results after surgery were regarded as the gold standard for diagnosis.

Results:  Final diagnosis included 40 cases of malignant and 18 cases of benign FLLs. The mean viscosity value were 14.78 ± 1.86 m/s/kHz for hepatocellular carcinoma (n = 30), 14.81 ± 2.35 m/s/kHz for liver metastasis lesions (n = 10), 13.23 ± 1.31 m/s/kHz for hemangioma (n = 13), and 13.67 ± 2.72 m/s/kHz for focal nodular hyperplasia (n = 5). Malignant FLLs showed higher mean viscosity values (14.79 ± 3.15 m/s/KHz) than benign FLLs (13.36 ± 2.76 m/s/KHz) (p < 0.05). The best performing cut-off value of lesion viscosity was 13.15 m/s/kHz (sensitivity 83.3 %; specificity 56.5 %; area under the curve (AUC) 0.71) for malignancy) (p < 0.05).

Conclusions:  The analysis of SWD slope and liver viscosity parameters provide additional viscoelastic information about FLLs before operation.
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http://dx.doi.org/10.1055/a-1217-7465DOI Listing
September 2020

Proteomic and metabolomic basis for improved textural quality in crisp grass carp (Ctenopharyngodon idellus C.et V) fed with a natural dietary pro-oxidant.

Food Chem 2020 Apr 24;325:126906. Epub 2020 Apr 24.

School of Arts & Sciences, University of Houston-Victoria, Victoria, TX 77901, USA. Electronic address:

Reactive oxygen species (ROS) regulate metabolism and chemical composition of various tissues. To understand how ROS affect the textural quality of fish muscle, we performed a multi-omics analysis on an established crisp grass carp model fed with a natural pro-oxidant faba bean. ROS levels were systemically and significantly increased up to three-fold in crisp grass carp, improving the muscle texture. Lipid metabolism was significantly enhanced up to five-fold in muscle and liver possibly to compensate the impaired carbohydrate metabolism of these tissues, but this caused further local ROS production. Mitochondrial damage associated with autophagy was evident in crisp grass carp. Proteomics revealed that elevated ROS likely disturbed the actin-myosin interaction and collagen turnover inducing fragmentation of myofibrillar proteins, all of which could have positively impacted the textural quality. The systemic metabolic changes that lead to the partial collapse of redox regulation likely underlie the ROS-induced improvement of textural quality.
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http://dx.doi.org/10.1016/j.foodchem.2020.126906DOI Listing
April 2020

The distribution and risk of mercury in Shenzhen mangroves, representative urban mangroves affected by human activities in China.

Mar Pollut Bull 2020 Feb 29;151:110866. Epub 2020 Jan 29.

Key Laboratory for Heavy Metal Pollution Control and Reutilization, School of Environment and Energy, Peking University Shenzhen Graduate School, Shenzhen 518055, Guangdong, PR China. Electronic address:

Sediments were collected from urban mangroves in Shenzhen, China, including Shajing (SJ) and Xixiang (XX) featured with industrial district; Futian (FT) and Baguang (BG) featured with central business district and ecological preserve, respectively. Distributions, pollution levels and human health risks of Hg were explored. In both surface and vertical sediments, mean Hg concentration was highest in SJ mangrove, which may be due to its proximity to point-source discharge of Maozhou River in Pearl River Estuary, China. Sediment properties (pH, salinity, TOC and particle size) had limited impact on Hg accumulation due to their non-significant correlations. Geo-accumulation index, pollution load index, potential ecological risk index, and the ecological risk assessment code showed the highest ecological risk in SJ mangrove, followed by XX, FT, and BG mangroves. The assessment of human health risks showed that public experience little adverse health risk due to exposure to Hg polluted sediment in urban mangroves.
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http://dx.doi.org/10.1016/j.marpolbul.2019.110866DOI Listing
February 2020

Clinical application of dynamic contrast enhanced ultrasound in monitoring the treatment response of chemoradiotherapy of pancreatic ductal adenocarcinoma.

Clin Hemorheol Microcirc 2020 ;75(3):325-334

Department of Ultrasound, Zhongshan Hospital, Fudan University, Shanghai, China.

Objectives: To investigate the value of dynamic contrast enhanced ultrasound (D-CEUS) in monitoring the chemoradiotherapy (CRT) therapeutic response of local advanced pancreatic ductal adenocarcinoma (LAPC).

Patients And Methods: From October 2017 to December 2018, 11 patients diagnosed as LAPC were included (7 men, 4 women; mean age: 61.1±8.6 years). The algorithm of CRT was as following: the radiotherapy dose was 50.4 Gy/28Fx with S-1 40 mg bid orally taken in radiotherapy day. Conventional ultrasound scan and CEUS were performed before and 4 weeks after CRT. All ultrasound examinations were performed by an ACUSON Oxana 2 ultrasound equipment (Siemens Medical Solutions, Germany) with a C 6-1 convex array transducer (1-6 MHz). Time intensity curves (TICs) were generated in the region of interests (ROIs) both in LAPC lesions and in its surrounding pancreas parenchyma by SonoLiver software (TOMTEC Imaging Systems). Quantitative perfusion parameters including maximum intensity (MI), rise time (RT), mean transit time (mTT) and time to peak (TTP) were analyzed and compared before and after CRT.

Results: No significant difference could be found by conventional B mode ultrasound scan after CRT. TICs of CEUS showed lower ascending and descending slopes rate after CRT. Among all perfusion quantitative parameters, MI decreased significantly after CRT (42.1±18.8% vs 27.8±17.2%, P < 0.05).

Conclusions: Depending on its unique advantages as non-radiation, effective and convenient, D-CEUS analysis and quantitative parameters, particularly MI, has potential application value in following up of the CRT treatment response in LAPC patients.
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http://dx.doi.org/10.3233/CH-190786DOI Listing
October 2020

SSBP1 Upregulation In Colorectal Cancer Regulates Mitochondrial Mass.

Cancer Manag Res 2019 2;11:10093-10106. Epub 2019 Dec 2.

First Bethune Hospital, Jilin University, Changchun, Jilin, People's Republic of China.

Background: Colorectal cancers (CRC) are one of the most common forms of cancer seen worldwide, and also remain difficult to treat despite recent advances in chemotherapy. Although significant progress has been made in recent years towards precision medicine and mutation-guided therapy, common mechanisms that underlie tumor growth and progression remain incompletely understood.

Methods: Tumor tissue and nearby unaffected tissue were collected from >15 patients at each stage of CRC, from which we generated representative proteomics profiles of three stages. Bioinformatics analysis was performed to discover common differences that may be shared between the representative profiles and across larger cohorts. Flow cytometry was then used to identify functional consequences of SSBP1 depletion in cell lines, since its expression level was consistently increased in tumor cells across all of the datasets analyzed.

Results: Direct comparison of CRC tumor and unaffected tissue at each stage demonstrated that a number of proteins involved in mitochondrial function displayed significantly altered expression patterns. Depletion of SSBP1 in colon cancer cell lines was able to trigger loss of mitochondrial mass and an increase in tumor cell death, and this effect that was further accentuated in the presence of the common chemotherapy drug cisplatin.

Conclusion: Mitochondrial biogenesis and maintenance may play an important part in tumor cell survival during CRC progression, and may be a useful target for directed inhibition or adjuvant targeting in the cases of cisplatin resistance.
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http://dx.doi.org/10.2147/CMAR.S211292DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6896925PMC
December 2019

The distribution, characteristics and ecological risks of microplastics in the mangroves of Southern China.

Sci Total Environ 2020 Mar 5;708:135025. Epub 2019 Nov 5.

Graduate School at Shenzhen, Tsinghua University, Shenzhen 518055, China.

During the production, use and disposal of plastic products, microplastics (MPs) are dispersed into the surrounding environment and have inevitable impacts on mangrove ecosystems in estuaries and offshore areas. In the mangroves of Southern China, the systematic evaluation of the distribution, characteristics and ecological risks of MPs is lacking. In this study, surface sediments (0-5 cm depth) were collected from six representative mangroves in China to explore MP contamination and its associated ecological risk. Based on the results, MP concentrations of MPs in mangrove sediments were as follows: FT (2249 ± 747 items/kg), ZJ (736 ± 269 items/kg), DF (649 ± 443 items/kg), DZG (431 ± 170 items/kg), YX (424 ± 127 items/kg), and FCG (227 ± 173 items/kg). The higher MP concentration in the Futian mangrove was mainly related to inputs from the Pearl River, the third largest river in China. The predominant shape, colour, and size of MPs were fibrous, white-transparent, and 500-5000 μm, respectively. The main MP polymer types were polypropylene, polyethylene, and polystyrene. Degradation artefacts were present on surface of MPs as well as metallic and non-metallic elements. MPs concentration in mangrove sediments increased with increasing social-economic development of surrounding districts, which indicated the clear influence of anthropogenic activity on MP pollution in these mangroves. Furthermore, total organic carbon (TOC) and silt content were positively associated with MPs (P < 0.01), indicating a facilitatory role in deposition of MPs in mangroves. Based on a comprehensive evaluation using the potential ecological risk factor (E), potential ecological risk (RI), polymer risk index (H) and pollution load index (PLI), MPs were found to present ecological risks in these mangroves, with the highest risk occurring in the Futian mangrove.
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http://dx.doi.org/10.1016/j.scitotenv.2019.135025DOI Listing
March 2020

Incidentally detected focal fundal gallbladder wall thickening: Differentiation contrast enhanced ultrasound features with high-resolution linear transducers.

Clin Hemorheol Microcirc 2020 ;74(3):315-325

Department of Ultrasound, Zhongshan Hospital, Fudan University, Shanghai, China.

Aim: To investigate the value of contrast enhanced ultrasound with high resolution linear transducers (HF-CEUS) for differential diagnosis of focal fundal gallbladder (GB) wall thickening.

Methods: A total of 32 patients with incidentally detected focal fundal GB wall thickening were included. After conventional B mode ultrasound (BMUS) examinations, HF-CEUS were performed with a 7.5-12 MHz 9L4 linear transducer (S2000 HELX OXANA unit, Siemens). Two radiologists independently reviewed the HF-CEUS enhancement patterns to determine the differential features between malignancy and benignity with a five-point confidence scale. The diagnostic accuracy of BMUS and HF-CEUS for GB wall thickening was compared. The final gold standard was surgery with histological examination.

Results: Final diagnoses included GB adenocarcinoma (n = 16), adenomyomatosis (n = 12), Xanthogranulomatous (n = 2) and cholecystitis (n = 2). HF-CEUS features associated with GB adenocarcinoma including arterial phase inhomogeneous hyperenhancement, venous phase hypoenhancement and disruption of GB wall layer structure (P < 0.05). Two small (5 mm) liver metastasis were confirmed by HF-CEUS during the late phase liver sweep as hypoenhanced lesions. Nonenhanced Rokitansky-Aschoff sinuses were clearly observed in 83.3% focal adenomyomatosis. Overall sensitivity, specificity and accuracy for differentiation between malignant and benign focal fundal GB wall thickening of HF-CEUS and BMUS were 84.3% vs 53.1%, 90.6% vs 59.3% and 87.5% vs 56.2% (P < 0.005).

Conclusions: CEUS performed with high frequency linear transducers could be a useful alternative in the differential diagnosis of focal fundal GB wall thickening on conventional ultrasound.
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http://dx.doi.org/10.3233/CH-190697DOI Listing
July 2020

LassoNet: Deep Lasso-Selection of 3D Point Clouds.

IEEE Trans Vis Comput Graph 2019 Aug 19. Epub 2019 Aug 19.

Selection is a fundamental task in exploratory analysis and visualization of 3D point clouds. Prior researches on selection methods were developed mainly based on heuristics such as local point density, thus limiting their applicability in general data. Specific challenges root in the great variabilities implied by point clouds (e.g., dense vs. sparse), viewpoint (e.g., occluded vs. non-occluded), and lasso (e.g., small vs. large). In this work, we introduce LassoNet, a new deep neural network for lasso selection of 3D point clouds, attempting to learn a latent mapping from viewpoint and lasso to point cloud regions. To achieve this, we couple user-target points with viewpoint and lasso information through 3D coordinate transform and naive selection, and improve the method scalability via an intention filtering and farthest point sampling. A hierarchical network is trained using a dataset with over 30K lasso-selection records on two different point cloud data. We conduct a formal user study to compare LassoNet with two state-of-the-art lasso-selection methods. The evaluations confirm that our approach improves the selection effectiveness and efficiency across different combinations of 3D point clouds, viewpoints, and lasso selections. Project Website: https://lassonet.github.io.
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http://dx.doi.org/10.1109/TVCG.2019.2934332DOI Listing
August 2019

Differential diagnosis of focal gallbladder lesions: The added value of contrast enhanced ultrasound with liner transducers.

Clin Hemorheol Microcirc 2020 ;74(2):167-178

Department of Ultrasound, Zhongshan Hospital, Fudan University, Shanghai, China.

Background And Aim: To evaluate the benefits of contrast-enhanced ultrasound (CEUS) with high frequency transducers in characterization of focal gallbladder lesions (FGL).

Material And Methods: From January 2017 to April 2019, 59 FGL detected by B mode ultrasound (BMUS) were examined, first with the low frequency convex transducer (1-5 MHz) and afterwards with high frequency transducer (7.5-12 MHz). High frequency dynamic CEUS were applied after bolus injection of 4.8 ml Sulphur hexafluoride microbubbles (SonoVue®, Milan). The BMUS and CEUS imaging features were recorded and compared. All lesions were confirmed by surgical resection and histopathologic results.

Results: The final diagnoses of 59 FGL included gallbladder adenocarcinoma (n = 15), gallbladder polyps (n = 11), gallbladder adenomas (n = 18), focal adenomyomatosis (n = 9), and gallbladder Ascariasis debris (n = 6). The mean diameter of FGL was 24.5±11.4 mm, and mean depth to the abdominal wall was 21.2±7.3 mm. While applying CEUS with high frequency transducer, specific diagnostic features, including arterial phase irregular intralesional vascularity (10/15, 66.7%), late phase hypoenhancement (12/15, 80%), destruction of gallbladder wall (8/15, 53.3%), infiltration to the adjacent liver (6/15, 40.0%) were significantly higher in malignant FGL. The overall sensitivity, specificity and diagnostic accuracy for the correct characterization of malignant FGL were significantly improved by CEUS with high frequency transducer (sensitivity 93.3%, specificity 88.5%, accuracy 100%).

Conclusion: With its superior contrast resolution, CEUS performed with high frequency transducers is helpful to achieve better visualization of gallbladder fundus and make differential diagnosis of gallbladder lesions, which might greatly improve diagnostic confidence between malignant and benign FGL.
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http://dx.doi.org/10.3233/CH-190639DOI Listing
July 2020

iStoryline: Effective Convergence to Hand-drawn Storylines.

IEEE Trans Vis Comput Graph 2018 Aug 20. Epub 2018 Aug 20.

Storyline visualization techniques have progressed significantly to generate illustrations of complex stories automatically. However, the visual layouts of storylines are not enhanced accordingly despite the improvement in the performance and extension of its application area. Existing methods attempt to achieve several shared optimization goals, such as reducing empty space and minimizing line crossings and wiggles. However, these goals do not always produce optimal results when compared to hand-drawn storylines. We conducted a preliminary study to learn how users translate a narrative into a hand-drawn storyline and check whether the visual elements in hand-drawn illustrations can be mapped back to appropriate narrative contexts. We also compared the hand-drawn storylines with storylines generated by the state-of-the-art methods and found they have significant differences. Our findings led to a design space that summarizes 1) how artists utilize narrative elements and 2) the sequence of actions artists follow to portray expressive and attractive storylines. We developed iStoryline, an authoring tool for integrating high-level user interactions into optimization algorithms and achieving a balance between hand-drawn storylines and automatic layouts. iStoryline allows users to create novel storyline visualizations easily according to their preferences by modifying the automatically generated layouts. The effectiveness and usability of iStoryline are studied with qualitative evaluations.
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http://dx.doi.org/10.1109/TVCG.2018.2864899DOI Listing
August 2018

Gonadal Transcriptome Analysis of Pacific Abalone Haliotis discus discus: Identification of Genes Involved in Germ Cell Development.

Mar Biotechnol (NY) 2018 Aug 3;20(4):467-480. Epub 2018 Apr 3.

Faculty of Fisheries, Kagoshima University, 4-50-20 Shimoarata, Kagoshima, 890-0056, Japan.

Little is known about the molecular mechanisms governing gonadal developmental processes in abalones. Here, we conducted transcriptome analysis of Pacific abalone Haliotis discus discus for gene discovery in the brain, ovary, testis, and unfertilized eggs. Among the annotated unigenes, 48.6% of unigenes were identified by Venn diagram analysis as having universal or tissue-specific expression. Twenty-three genes with gonad-biased gene ontology (GO) terms were first obtained. Secondly, 36 genes were found by screening known gene names related to germ cell development. Finally, 17 genes were obtained by querying the annotated unigene database for zygotically expressed gonadal genes (ovary and testis) and maternally expressed gonadal genes (ovary, testis, and unfertilized eggs) using keywords related to reproduction. To further verify tissue distribution pattern and subcellular localization of these genes, RT-PCR and in situ hybridization were performed using a unigene encoding a germ cell marker, vasa, as control. The results showed that vasa was expressed mainly in the early developmental stages of germ cells in both sexes. One of the candidate genes, vitelline envelope zona pellucida domain protein 12 (ZP12), was expressed in the primordial germ cells of immature gonad and early developmental stages of germ cells of the adult female. The results obtained from the present study suggest that vasa and ZP12 are involved in germ cell development of Pacific abalone and that ZP12 is an especially useful germ cell-specific marker in immature adults. The current gonadal transcriptome profile is an extensive resource for future reproductive molecular biology studies of this species.
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http://dx.doi.org/10.1007/s10126-018-9809-5DOI Listing
August 2018

Complete mitochondrial genome of Ctenopharyngodon idella var. Gold grass carp and its intraspecific comparison.

Mitochondrial DNA A DNA Mapp Seq Anal 2017 05 23;28(3):372-374. Epub 2016 May 23.

a Key Laboratory of Tropical & Subtropical Fishery Resource Application & Cultivation Ministry of Agriculture , Pearl River Fisheries Research Institute of Chinese Academy of Fishery Sciences , Guangzhou , China.

We determined the complete mitochondrial genome (Mitogome) of Ctenopharyngodon idella var. gold grass carp (C. idella var.) (Accession No.:KT894100) and compered it with a previously published mitogenome (Accession No.:NC010288.1) of Chinese common grass carp. The total length of mitogenome is 16 609 bp with 13 protein-coding genes, 2 rRNA genes, 22 tRNA genes and a control region. The nucleotide compositions of the L-strand are 31.87% for A, 26.20% for T, 15.68% for G, 26.26% for C. Most of the protein-coding genes began with an ATG start codon except for COX1 and ND3 gene. The sequence similarity was 99.81% between each other. There were 32 variation loci obtained, including of 23 transitions, 7 transversions and 2 INDELs.
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http://dx.doi.org/10.3109/19401736.2015.1126828DOI Listing
May 2017

The complete mitochondrial genome of Carassius auratus var. high back crucian carp (Cypriniformes: Cyprinidae).

Mitochondrial DNA A DNA Mapp Seq Anal 2017 01 28;28(1):91-92. Epub 2015 Dec 28.

a Pearl River Fisheries Research Institute, Chinese Academy of Fishery Science , Guangzhou , Guangdong , P. R. China and.

In this study, the complete mitochondrial genome sequence of Carassius auratus var. high back crucian carp (C. auratus var.) was determined (GenBank accession number is KT756205). The mitochondrial genome sequence of C. auratus var. was a circular molecule with 16 581 bp in length, and contained 37 typical animal mitochondrial genes, including 2 ribosomal RNA genes, 13 protein-coding genes, 22 transfer RNA genes and a control region (D-loop). Four nucleotide compositions and their relative proportions of the entire mitogenome was 26.19% C, 16.06% G, 31.57% A and 26.18% T, with contents of A + T and G + C being 57.75% and 42.25%, respectively.
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http://dx.doi.org/10.3109/19401736.2015.1110813DOI Listing
January 2017

CAST: Effective and Efficient User Interaction for Context-Aware Selection in 3D Particle Clouds.

IEEE Trans Vis Comput Graph 2016 Jan 12;22(1):886-95. Epub 2015 Aug 12.

We present a family of three interactive Context-Aware Selection Techniques (CAST) for the analysis of large 3D particle datasets. For these datasets, spatial selection is an essential prerequisite to many other analysis tasks. Traditionally, such interactive target selection has been particularly challenging when the data subsets of interest were implicitly defined in the form of complicated structures of thousands of particles. Our new techniques SpaceCast, TraceCast, and PointCast improve usability and speed of spatial selection in point clouds through novel context-aware algorithms. They are able to infer a user's subtle selection intention from gestural input, can deal with complex situations such as partially occluded point clusters or multiple cluster layers, and can all be fine-tuned after the selection interaction has been completed. Together, they provide an effective and efficient tool set for the fast exploratory analysis of large datasets. In addition to presenting Cast, we report on a formal user study that compares our new techniques not only to each other but also to existing state-of-the-art selection methods. Our results show that Cast family members are virtually always faster than existing methods without tradeoffs in accuracy. In addition, qualitative feedback shows that PointCast and TraceCast were strongly favored by our participants for intuitiveness and efficiency.
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http://dx.doi.org/10.1109/TVCG.2015.2467202DOI Listing
January 2016

A strain of Siniperca chuatsi rhabdovirus causes high mortality among cultured Largemouth Bass in South China.

J Aquat Anim Health 2013 Sep;25(3):197-204

a Ministry of Agriculture of the People's Republic of China Key Laboratory of Tropical and Subtropical Fishery Resource Application and Cultivation, Pearl River Fisheries Research Institute , Chinese Academy of Fishery Sciences , Guangzhou , 510380 , China.

In April 2011, 40% mortality of Largemouth Bass Micropterus salmoides juveniles occurred at a farm of Zhongshan City, Guangdong Province, China. Infected fish became lethargic, exhibited corkscrew and irregular swimming, and developed a distended abdomen and crooked body. Fish began to die within 2 d after the appearance of clinical signs. In order to analyze the pathogeny and diagnose the disease earlier, observation of clinical signs, cell infection, titer calculation, electron microscopy, immersion infection assay for fish, and nucleotide sequence analysis were carried out. Fathead minnow (FHM) cell cultures, inoculated with filtrate of liver and spleen homogenates from the diseased fish, developed the obvious cytopathic effect 46 h after inoculation in the primary culture and 24 h at the first passage. Typical rhabdovirus particles, 115-143 nm in length and 62-78 nm in diameter, were observed in infected FHM cells by direct transmission electron microscopy. The isolated virus produced a titer of 10(7.15) TCID50/mL. Immersion-Fish infected with the virus had similar clinical signs and 80% mortality with 10(2.5) LD50/mL. The data indicated that the rhabdovirus was the lethal pathogeny of the current disease. Based on nucleoprotein-gene nucleotide sequence multiple alignment analysis, the newly isolated virus is a strain of Siniperca chuatsi rhabdovirus (SCRV) under family Rhabdoviridae, which was initially isolated from Mandarin Fish Siniperca chuatsi. Up to the present, at least four virus strains have been isolated from diseased Largemouth Bass, which have had different clinical signs. Comparison of the clinical signs can help in an early diagnosis of the disease.
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http://dx.doi.org/10.1080/08997659.2013.799613DOI Listing
September 2013

Efficient Structure-Aware Selection Techniques for 3D Point Cloud Visualizations with 2DOF Input.

IEEE Trans Vis Comput Graph 2012 Dec;18(12):2245-54

University of Groningen, the Netherlands.

Data selection is a fundamental task in visualization because it serves as a pre-requisite to many follow-up interactions. Efficient spatial selection in 3D point cloud datasets consisting of thousands or millions of particles can be particularly challenging. We present two new techniques, TeddySelection and CloudLasso, that support the selection of subsets in large particle 3D datasets in an interactive and visually intuitive manner. Specifically, we describe how to spatially select a subset of a 3D particle cloud by simply encircling the target particles on screen using either the mouse or direct-touch input. Based on the drawn lasso, our techniques automatically determine a bounding selection surface around the encircled particles based on their density. This kind of selection technique can be applied to particle datasets in several application domains. TeddySelection and CloudLasso reduce, and in some cases even eliminate, the need for complex multi-step selection processes involving Boolean operations. This was confirmed in a formal, controlled user study in which we compared the more flexible CloudLasso technique to the standard cylinder-based selection technique. This study showed that the former is consistently more efficient than the latter - in several cases the CloudLasso selection time was half that of the corresponding cylinder-based selection.
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http://dx.doi.org/10.1109/TVCG.2012.217DOI Listing
December 2012

Simultaneous determination of Cr(III) and Cr(VI) in tannery wastewater using low pressure ion chromatography combined with flow injection spectrophotometry.

Spectrochim Acta A Mol Biomol Spectrosc 2012 Mar 15;88:49-55. Epub 2011 Dec 15.

National Engineering Laboratory for Clean Technology of Leather Manufacture, Sichuan University, Chengdu, Sichuan, PR China.

Trivalent and hexavalent chromium have been successfully separated and determined using low pressure ion chromatography combined with flow injection spectrophotometric analysis (LPIC-FIA). A column packed with crosslinking starch microspheres was used for on-line separation of Cr(III) from Cr(VI) in a flow-injection system because of its absorptive effect on Cr(III). To determine the concentration of Cr(III) and Cr(VI) in samples, we used 3.0 mmol/L nitric acid to elute adsorbed Cr(III) from the column and then used ceric sulfate-sulfuric acid as oxidant to convert all Cr(III) into Cr(VI). Then, Cr(VI) directly came from the samples and Cr(VI) came from Cr(III) successively formed a amaranthine complex with diphenycarbazide and the complex shows a maximum absorption at 530 nm. Analytical parameters including the concentration of eluent and oxidant solution, oxidizing temperature, length of oxidizing reaction coil, reaction coil and injection coil, interfering effects, etc., were optimized. The limit of detection was 1.25 μg/L for Cr(VI) and 3.76 μg/L for Cr(III). The linear relationship between absorption with the concentration of Cr(VI) and Cr(III) was 0.001-1.000 mg/L and 0.030-1.000 mg/L with correlation coefficients of 0.9995 and 0.9994, respectively. The relative standard deviation of Cr(VI) and Cr(III) was 1.21% and 1.66%, respectively (n=10). Major cations and anions did not show any interference. We validated this method through certified reference materials and through measuring the recovery in tannery wastewater.
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http://dx.doi.org/10.1016/j.saa.2011.11.053DOI Listing
March 2012

Genotypes, haplotypes and diplotypes of IGF-II SNPs and their association with growth traits in largemouth bass (Micropterus salmoides).

Mol Biol Rep 2012 Apr 6;39(4):4359-65. Epub 2011 Sep 6.

Key Laboratory of Tropical & Subtropical Fishery Resource Application & Cultivation, Ministry of Agriculture of the People's Republic of China, Pearl River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou, 510380, Guangdong, People's Republic of China.

Insulin-like growth factor II (IGF-II) is involved in the regulation of somatic growth and metabolism in many fishes. IGF-II is an important candidate gene for growth traits in fishes and its polymorphisms were associated with the growth traits. The aim of this study is to screen single nucleotide polymorphisms (SNPs) of the largemouth bass (Micropterus salmoides) IGF-II gene and to analyze potential association between IGF-II gene polymorphisms and growth traits in largemouth bass. Four SNPs (C127T, T1012G, C1836T and C1861T) were detected and verified by DNA sequencing in the largemouth bass IGF-II gene. These SNPs were found to organize into seven haplotypes, which formed 13 diplotypes (haplotype pairs). Association analysis showed that four individual SNPs were not significantly associated with growth traits. Significant associations were, however, noted between diplotypes and growth traits (P < 0.05). The fish with H1H3 (CTCC/CGCC) and H1H5 (CTCC/TTTT) had greater body weight than those with H1H1 (CTCC/CTCC), H1H2 (CTCC/TGTT) and H4H4 (TGCT/TGCT/) did. Our data suggest a significant association between genetic variations in the largemouth bass IGF-II gene and growth traits. IGF-II SNPs could be used as potential genetic markers in future breeding programs of largemouth bass.
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http://dx.doi.org/10.1007/s11033-011-1223-2DOI Listing
April 2012

Health behaviors of victims and related factors in Wenchuan earthquake resettlement sites.

Ann Epidemiol 2011 Mar;21(3):221-9

School of Public Health, Sichuan University, Chengdu, China.

Purpose: The purpose of this study was to describe the health behaviors of earthquake victims related to gastrointestinal and respiratory infectious diseases in the centralized transitional earthquake resettlement sites in Wenchuan, China; and to identify key factors related to health behaviors that may inform local infectious diseases prevention and control strategies.

Methods: Data were collected using a questionnaire that included questions about socio-demographic characteristics and health beliefs and behaviors. In total, 1411 participants were included through a two-stage random sampling strategy. A bivariate multilevel model was used to explore the related factors.

Results: Approximately 67% of the participants wash their hands after going to lavatories every time, and 87% felt uncomfortable spitting on the ground. The more the participants perceived their susceptibility to and the severity of infectious diseases, the better their health-related behaviors (P < 0.05). Both health-related behaviors were influenced by communication modes of health education (P = 0.01) and socio-demographic characteristics. There was heterogeneity of health-related behaviors among different resettlement sites (P < 0.01).

Conclusions: Health education intervention, based on the Health Belief Model, is one of the main preventative strategies that should be implemented to inspire self-efficacy and to enhance better health-related behaviors among earthquake victims. Appropriate health education communication modes should be considered among different resettlement sites.
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http://dx.doi.org/10.1016/j.annepidem.2010.11.005DOI Listing
March 2011

FI3D: direct-touch interaction for the exploration of 3D scientific visualization spaces.

IEEE Trans Vis Comput Graph 2010 Nov-Dec;16(6):1613-22

University of Groningen, the Netherlands.

We present the design and evaluation of FI3D, a direct-touch data exploration technique for 3D visualization spaces. The exploration of three-dimensional data is core to many tasks and domains involving scientific visualizations. Thus, effective data navigation techniques are essential to enable comprehension, understanding, and analysis of the information space. While evidence exists that touch can provide higher-bandwidth input, somesthetic information that is valuable when interacting with virtual worlds, and awareness when working in collaboration, scientific data exploration in 3D poses unique challenges to the development of effective data manipulations. We present a technique that provides touch interaction with 3D scientific data spaces in 7 DOF. This interaction does not require the presence of dedicated objects to constrain the mapping, a design decision important for many scientific datasets such as particle simulations in astronomy or physics. We report on an evaluation that compares the technique to conventional mouse-based interaction. Our results show that touch interaction is competitive in interaction speed for translation and integrated interaction, is easy to learn and use, and is preferred for exploration and wayfinding tasks. To further explore the applicability of our basic technique for other types of scientific visualizations we present a second case study, adjusting the interaction to the illustrative visualization of fiber tracts of the brain and the manipulation of cutting planes in this context.
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http://dx.doi.org/10.1109/TVCG.2010.157DOI Listing
December 2010

Validation of reference genes of grass carp Ctenopharyngodon idellus for the normalization of quantitative real-time PCR.

Biotechnol Lett 2010 Aug 2;32(8):1031-8. Epub 2010 Apr 2.

Pearl River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Key Laboratory of Tropical & Subtropical Fish Breeding & Cultivation, CAFS, Guangzhou 510380, People's Republic of China.

Expression of four reference genes of grass carp, including beta-actin (ACTB), glyceraldehyde-3-phosphate dehydrogenase (GAPDH), 18S rRNA (18S) and elongation factor-1 alpha (EF1alpha), was studied in tissues of normal individuals and bacteria-infected individuals. EF1alpha had the most stable expressions followed by 18S rRNA then GAPDH; ACTB had the least stability. After being infected with bacteria, the grass carp showed minimal changes in expression levels of EF1alpha in the liver and head kidney, while ACTB had the most stable expressions in spleen but the least stable in liver. EF1alpha is thus the optimal reference gene in quantitative real-time PCR analysis to quantitate the expression levels of target genes in tissues of grass carp.
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http://dx.doi.org/10.1007/s10529-010-0258-0DOI Listing
August 2010
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