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TMBstable: a variant caller controls performance variation across heterogeneous sequencing samples

BRIEFINGS IN BIOINFORMATICS 2024年第3期25卷 bbae159-bbae159页

作者： Wang, Shenjie Zhu, Xiaoyan Wang, xuwen liu, Yuqian Zhao, Minchao Chang, Zhili Wang, Xiaonan Shao, Yang Wang, Jiayin Xi An Jiao Tong Univ Sch Comp Sci & Technol Xian Peoples R China Nanjing Geneseeq Technol Inc Nanjing Jiangsu Peoples R China

In cancer genomics, variant calling has advanced, but traditional mean accuracy evaluations are inadequate for biomarkers like tumor mutation burden, which vary significantly across samples, affecting immunotherapy patient selection and threshold settings. In this study, we introduce TMBstable, an innovative method that dynamically selects optimal variant calling strategies for specific genomic regions using a meta-learning framework, distinguishing it from traditional callers with uniform sample-wide strategies. The process begins with segmenting the sample into windows and extracting meta-features for clustering, followed by using a pre-trained meta-model to select suitable algorithms for each cluster, thereby addressing strategy-sample mismatches, reducing performance fluctuations and ensuring consistent performance across various samples. We evaluated TMBstable using both simulated and real non-small cell lung cancer and nasopharyngeal carcinoma samples, comparing it with advanced callers. The assessment, focusing on stability measures, such as the variance and coefficient of variation in false positive rate, false negative rate, precision and recall, involved 300 simulated and 106 real tumor samples. Benchmark results showed TMBstable's superior stability with the lowest variance and coefficient of variation across performance metrics, highlighting its effectiveness in analyzing the counting-based biomarker. The TMBstable algorithm can be accessed at https://***/hello-json/TMBstable for academic usage only.

关键词： sequencing data analysis variant calling counting-based biomarker tumor mutation burden immunotherapy meta-learning approach

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SLC24A5 plays fundamental roles in regulating melanophore development in Cyprinidae fish

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Reproduction and Breeding 2021年第3期1卷 167-173页

作者： Yu, Luwei Chen, Honglin Hu, xuwen Chen, Xiaowen liu, Zhiwei Wang, Jun Wang, Chenghui Key Laboratory of Freshwater Aquatic Genetic Resources Ministry of Agriculture Shanghai 201306 China National Demonstration Center for Experimental Fishiers Science Education Shanghai 201306 China Shanghai Engineering Research Center of Aquaculture Shanghai Ocean University Shanghai 201306 China

The mechanism of color pattern formation in animals is complicated. Oujiang color common carp (Cyprinus carpio var. color) is an excellent fish model for studying the molecular mechanism of pigmentation. Solute carrier family 24 member 5 (SLC24A5) was identified as a key gene in regulating melanophore development and melanin distribution in organisms. In this study, functional experiments were conducted on the SLC24A5 gene in Oujiang color common carp. The full-length of SLC24A5 mRNA was cloned and obtained. In Oujiang color common carp, qRT-PCR and whole-mount in situ hybridization indicated that SLC24A5 was highly expressed in tissues in the presence of melanin and initiated its expression along with the presence of melanin during embryo development. The SLC24A5 knocked-out via CRISPR/cas9 caused an obvious loss of melanophore in larva and adult zebrafish. In addition, the homozygous SLC24A5^−/− zebrafish mutant phenotype was rescued by the over expression of the SLC24A5 from Oujiang color common carp. Results suggested that SLC24A5 is essential for regulating melanophore development and that the functional and structures of SLC24A5 are conserved in Cyprinidae fish. © 2021 The Authors

关键词： Cyprinidae fish Melanophore Pigmentation SLC24A5 Zebrafish

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Parental category B vaccine hesitancy and associated factors in China: an online cross-sectional survey

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EXPERT REVIEW OF VACCINES 2022年第1期21卷 145-153页

作者： Han, Ying Wang, Qiang Zhao, Shuangyu Wang, Jianli Dong, Shuheng Cui, Tingting liu, Minqi Shi, Naiyang Yang, liuqing Han, Yue Xiu, Shixin Wang, xuwen Jin, Hui Southeast Univ Sch Publ Hlth Dept Epidemiol & Hlth Stat Nanjing Peoples R China Southeast Univ Sch Publ Hlth Key Lab Environm Med Engn Minist Educ Nanjing Peoples R China Wuxi Ctr Dis Control & Prevent Wuxi Jiangsu Peoples R China

Background Vaccine hesitancy is one of the top ten health threats. We aimed to (1) assess parental Category B vaccines hesitancy and associated sociodemographic factors in China, and (2) explore the association between attitude toward vaccines and self-reported hesitant behavior. Methods A cross-sectional study was performed through a web-based anonymous online questionnaire survey between 9 February and 7 April 2021. Chinese parents aged >= 18 years with one child aged < 6 years were included to assess vaccine hesitancy using the vaccine-hesitancy scale (VHS). Structural equation model was used to determine relationships between variables. Results Of 2952 Chinese parents included in the analysis, 17.5% were highly hesitant in Category B vaccines. Parents who were younger, less educated, engaged in health-related occupations, and had been vaccinated against influenza in the past year were more hesitant when vaccinating their children (P < 0.001). VHS score accuracy to identify vaccine-hesitant behavior was acceptable, and the optimal cutoff was 37.50 (with 61.96% parental vaccine hesitancy). Parents who lack confidence or believe vaccines were risk were more likely to show vaccine hesitant behavior (P < 0.001). Conclusions In China, effective interventions need to be implemented to eliminate parental Category B vaccines hesitancy.

关键词： Vaccine hesitancy Parents Structural equation model Online survey China

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Tribological properties of thin films made by atomic layer deposition sliding against silicon

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JOURNAL OF VACUUM SCIENCE & TECHNOLOGY A 2018年第1期36卷

作者： Kilpi, Lauri Ylivaara, Oili M. E. Vaajoki, Antti liu, xuwen Rontu, Ville Sintonen, Sakari Haimi, Eero Malm, Jari Bosund, Markus Tuominen, Marko Sajavaara, Timo Lipsanen, Harri Hannula, Simo-Pekka Puurunen, Riikka L. Ronkainen, Helena VTT Tech Res Ctr Finland Ltd POB 1000 FI-02044 Espoo Finland Aalto Univ Sch Chem Engn Dept Chem & Mat Sci POB 16100 FI-00076 Aalto Finland Aalto Univ Sch Elect Engn Dept Elect & Nanoengn POB 13500 FI-00076 Aalto Finland Univ Jyvaskyla Dept Phys POB 35 FI-40014 Jyvaskyla Finland Beneq Ltd Ensimmainen Savu FI-01510 Vantaa Finland ASM Microchem Ltd Pietari Kalmin Katu 1 F 2 FI-00560 Helsinki Finland Aalto Univ Sch Chem Engn Dept Chem & Met Engn POB 16100 FI-00076 Aalto Finland

Interfacial phenomena, such as adhesion, friction, and wear, can dominate the performance and reliability of microelectromechanical (MEMS) devices. Here, thin films made by atomic layer deposition (ALD) were tested for their tribological properties. Tribological tests were carried out with silicon counterpart sliding against ALD thin films in order to simulate the contacts occurring in the MEMS devices. The counterpart was sliding in a linear reciprocating motion against the ALD films with the total sliding distances of 5 and 20 m. Al2O3 and TiO2 coatings with different deposition temperatures were investigated in addition to Al2O3-TiO2-nanolaminate, TiN, NbN, TiAlCN, a-C:H [diamondlike carbon (DLC)] coatings, and uncoated Si. The formation of the tribolayer in the contact area was the dominating phenomenon for friction and wear performance. Hardness, elastic modulus, and crystallinity of the materials were also investigated. The nitride coatings had the most favorable friction and wear performance of the ALD coatings, yet lower friction coefficient was measured with DLC a-C: H coating. These results help us to take steps toward improved coating solutions in, e.g., MEMS applications. Published by the AVS.

关键词： CONTACT AREA MEMS devices TRIBOLOGICAL PROPERTIES friction atomic layer deposition AVS thin films Adrenoleukodystrophy

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Controlling n-Type Molecular Doping via Regiochemistry and Polarity of Pendant Groups on Low Band Gap Donor-Acceptor Copolymers

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MACROMOLECULES 2021年第8期54卷 3886-3896页

作者： Ye, Gang liu, Jian Qiu, Xinkai Stater, Sebastian Qiu, Li liu, Yuru Yang, xuwen Hildner, Richard Koster, L. Jan Anton Chiechi, Ryan C. Shenzhen Univ Ctr Biomed Opt & Photon Cs CBOP Shenzhen 518060 Peoples R China Shenzhen Univ Coll Phys & Optoelect Engn Key Lab Optoelect Devices & Syst Shenzhen 518060 Peoples R China Stratingh Inst Chem NL-9747 AG Groningen Netherlands Zernike Inst Adv Mat NL-9747 AG Groningen Netherlands Yunnan Univ Natl Ctr Int Res Photoelect & Energy Mat Sch Mat & Energy Yunnan Key Lab Micro Nano Mat & Technol Kunming 650091 Yunnan Peoples R China

We demonstrate the impact of the type and position of pendant groups on the n-doping of low-band gap donor-acceptor (D-A) copolymers. Polar glycol ether groups simultaneously increase the electron affinities of D-A copolymers and improve the host/dopant miscibility compared to nonpolar alkyl groups, improving the doping efficiency by a factor of over 40. The bulk mobility of the doped films increases with the fraction of polar groups, leading to a best conductivity of 0.08 S cm(-1) and power factor (PF) of 0.24 mu W m(-1) K-2 in the doped copolymer with the polar pendant groups on both the D and A moieties. We used spatially resolved absorption spectroscopy to relate commensurate morphological changes to the dispersion of dopants and to the relative local doping efficiency, demonstrating a direct relationship between the morphology of the polymer phase, the solvation of the molecular dopant, and the electrical properties of doped films. Our work offers fundamental new insights into the influence of the physical properties of pendant chains on the molecular doping process, which should be generalizable to any molecularly doped polymer films.

关键词： Impurities Ethers Alcohols Doping Copolymers

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BMP亚家族成员中影响绵羊繁殖性能的基因研究进展

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家畜生态学报 2024年第7期45卷 1-8页

作者：刘梦兰邵旭文单雪松姜怀志吉林农业大学动物科学技术学院长春130118 农业农村部畜禽资源(羊)评价利用重点实验室长春130118

排卵数和产羔数是反映绵羊繁殖性状的关键性指标,也是绵羊重要的经济性状,二者属于中低遗传力性状,受基因型、环境和营养状况等多重因素共同影响。由BMP、GDF和AMH等组成的BMP亚家族是TGF-β超家族的重要组成部分,BMPR1B、BMP15和GDF9... 详细信息

排卵数和产羔数是反映绵羊繁殖性状的关键性指标,也是绵羊重要的经济性状,二者属于中低遗传力性状,受基因型、环境和营养状况等多重因素共同影响。由BMP、GDF和AMH等组成的BMP亚家族是TGF-β超家族的重要组成部分,BMPR1B、BMP15和GDF9是目前与绵羊繁殖性能相关性研究最为深入的基因。该文对BMP亚家族成员中提升绵羊排卵数及产羔数的基因的SNP位点进行归纳,总结了这些基因影响繁殖性能的SNP位点的发现,品种、定位、表型,以及对排卵数和产羔率的影响机制,旨在为绵羊多胎品种的选育和高效繁殖提供理论参考。

关键词：突变位点繁殖性状 BMPs 主效基因绵羊

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Effects of Micellization Behavior on the Interfacial Adsorption in Binary Anionic/Nonionic Surfactant Systems: A Molecular Simulation Study

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LANGMUIR 2021年第40期37卷 11835-11843页

作者： Lian, Peng Jia, Han Yan, Hui Yuan, Jie Tang, Hongtao Li, Zhe Fan, Fangning Qin, xuwen Lv, Kaihe liu, Dexin China Univ Petr East China Sch Petr Engn Qingdao 266580 Peoples R China China Univ Petr East China Sch Petr Engn Shandong Key Lab Oilfield Chem Qingdao 266580 Peoples R China Liaocheng Univ Sch Pharmaceut Sci Liaocheng 252059 Shandong Peoples R China SINOPEC Shengli Oilfield Co Shengli Oil Prod Plant Dongying 257000 Peoples R China

A surfactant interfacial adsorption process is highly associated with its micellization behaviors in the water phase, which is of great fundamental and practical significance in enhanced oil recovery. In this paper, the typical anionic surfactant 1-dodecanesulfonic acid sodium (DAS) and nonionic surfactants octylphenol polyoxyethylene ether-n (OP-n, n = 1, 5, and 10) are introduced to investigate their micellization behavior and interfacial adsorption process via molecular dynamics simulation. Number density profiles reveal that the additional OP5 molecules in the water phase generate the mixed micelle with DAS molecules and greatly promote its interfacial adsorption. Interaction energy calculation is employed to confirm the interaction of anionic/nonionic surfactants in the mixed micelle. Then, the radial distribution function, solvent-accessible surface area, and solvation free energy are calculated to further explore and verify the adsorption mechanism of the mixed micelle. It is found that the nonionic surfactant obviously decreases the hydrophilicity of the mixed micelle in the water phase, which should be responsible for its intensive tendency of the interfacial adsorption.

关键词： Adsorption Molecules Micelles Surfactants Water

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Coacervate-Based Instant and Repeatable Underwater Adhesive with Anticancer and Antibacterial Properties

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ACS APPLIED MATERIALS & INTERFACES 2021年第40期13卷 48239-48251页

作者： Peng, Qiongyao Wu, Qiuqiu Chen, Jingsi Wang, Tao Wu, Meng Yang, Diling Peng, xuwen liu, Jifang Zhang, Hao Zeng, Hongbo Univ Alberta Dept Chem & Mat Engn Edmonton AB T6G 1H9 Canada Guangzhou Med Univ Affiliated Hosp 6 Qingyuan Peoples Hosp Qingyuan 511500 Guangdong Peoples R China

Underwater adhesion is a great challenge for the development of adhesives as the attractive interfacial intermolecular interactions are usually weakened by the surface hydration layer. The coacervation process of sessile organisms like marine mussels and sandcastle worms has inspired substantial research interest in the fabrication of long-lasting underwater adhesives, but they generally suffer from time-consuming curing triggered by surrounding environmental changes and cannot reserve the adhesiveness once damaged. Herein, an instant and repeatable underwater adhesive was developed based on the coacervation of tannic acid (TA) and poly(ethylene glycol)(77)-b-poly(propylene glycol)(29)-b-poly(ethylene glycol)(77) (PEG-PPG-PEG, F68), which was driven by hydrogen-bonding interaction, and the hydrophobic cores of F68 micelles offered an additional cross-linking to enhance the mechanical properties. The TA-F68 coacervates could be facilely painted on different substrates, exhibiting robust and instant underwater adhesion (with adhesion strength up to 1.1 MPa on porcine skin) and excellent repeatability (at least 1000 cycles), superior to the previously reported coacervates. Due to the biological activities of TA, the underwater adhesive displayed innate anticancer and antibacterial properties against different types of cancer cells and bacteria, showing great potential for diverse biomedical applications, such as injectable drug carriers, tissue glues, and wound dressings.

关键词： instant and repeatable underwater adhesive coacervation hydrogen-bonding interaction hydrophobic interaction anticancer antibacterial

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Recent advances in the synthesis of biodegradable polyesters by sustainable polymerization: lipase-catalyzed polymerization

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RSC ADVANCES 2020年第59期10卷 36230-36240页

作者： liu, Ying Song, Lijie Feng, Na Jiang, Wei Jin, Yongri Li, xuwen Jilin Univ Coll Chem 2699 Qianjin Rd Changchun 130012 Jilin Peoples R China Jilin Prov Acad Tradit Chinese Med Clin Hosp 1 Changchun 130021 Peoples R China Zhengzhou Univ Acad Med Sci Dept Mol Pathol Applicat Ctr Precis MedAffiliated Hosp 2 Zhengzhou 450052 Henan Peoples R China

Over the past three decades, enzymatic polymerization has dramatically developed and gradually broadened as a creative methodology in the construction of polymeric materials with tailor-made structures and properties. Compared with transition metal catalyst polymerizations, enzymatic polymerization is more attractive in the biomedicine field due to the metal-free residue, good biocompatibility, and few by-products. Meanwhile, enzymatic polymerization has far more activity towards macrolides. In this review, the synthesis of lipase-catalyzed polymer materials is systematically summarized, focusing on the synthesis of the complex and well-defined polymers. The enzymatic polyester synthesis was then discussed concerning the different reaction types, including ring-opening polymerization, polycondensation, a combination of ring-opening polymerization with polycondensation, and chemoenzymatic polymerization. Besides, exploration of novel biocatalysts and reaction media was also described, with particular emphasis on the enzymes obtainedviaimmobilization or protein engineering strategies, green solvents, and reactors. Finally, recent developments in catalytic kinetics and mechanistic studies through the use of spectroscopy, mathematics, and computer techniques have been introduced. Besides, we addressed the remaining central issues in enzymatic polymerization and discussed current studies aimed at providing answers.

关键词： Ring opening polymerization

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Sporophytic control of anther development and male fertility by glucose-6-phosphate/phosphate translocator 1(OsGPT1) in rice

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Journal of Genetics and Genomics 2021年第8期48卷 695-705页

作者： Aili Qu Yan Xu Xinxing Yu Qi Si xuwen Xu Changhao liu liuyi Yang Yueping Zheng Mengmeng Zhang Shuqun Zhang Juan Xu State Key Laboratory of Plant Physiology and Biochemistry College of Life SciencesZhejiang UniversityHangzhouZhejiang 310058China Department of Plant Pathology College of Plant ProtectionNanjing Agricultural UniversityNanjingJiangsu 210095China Division of Biochemistry University of MissouriColumbiaMO 65211USA

Coordination between the sporophytic tissue and the gametic pollen within anthers is tightly controlled to achieve the optimal pollen fitness. Glucose-6-phosphate/phosphate translocator(GPT) transports glucose-6-phosphate, a key precursor of starch and/or fatty acid biosynthesis, into plastids. Here, we report the functional characterization of Os GPT1 in the rice anther development and pollen fertility. Pollen grains from homozygous osgpt1 mutant plants fail to accumulate starch granules, resulting in pollen sterility. Genetic analyses reveal a sporophytic effect for this mutation. Os GPT1 is highly expressed in the tapetal layer of rice anther. Degeneration of the tapetum, an important process to provide cellular contents to support pollen development, is impeded in osgpt1 plants. In addition, defective intine and exine are observed in the pollen from osgpt1 plants. Expression levels of multiple genes that are important to tapetum degeneration or pollen wall formation are significantly decreased in osgpt1 anthers. Previously, we reported that At GPT1 plays a gametic function in the accumulation of lipid bodies in Arabidopsis pollen. This report highlights a sporophytic role of Os GPT1 in the tapetum degeneration and pollen development. The divergent functions of Os GPT1 and At GPT1 in pollen development might be a result of their independent evolution after monocots and dicots diverged.

关键词： Glucose-6-phosphate/phosphate translocator Male fertility Starch accumulation Sporophytic control Pollen development Tapetum degeneration Intine and exine formation Rice

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