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1. MdEval: Massively Multilingual Code Debugging

Author

Liu, Shukai, Chai, Linzheng, Yang, Jian, Shi, Jiajun, Zhu, He, Wang, Liran, Jin, Ke, Zhang, Wei, Zhu, Hualei, Guo, Shuyue, Sun, Tao, Liu, Jiaheng, Duan, Yunlong, Hao, Yu, Yang, Liqun, Niu, Guanglin, Zhang, Ge, and Li, Zhoujun

Subjects
Computer Science - Computation and Language
Abstract

Code large language models (LLMs) have made significant progress in code debugging by directly generating the correct code based on the buggy code snippet. Programming benchmarks, typically consisting of buggy code snippet and their associated test cases, are used to assess the debugging capabilities of LLMs. However, many existing benchmarks primarily focus on Python and are often limited in terms of language diversity (e.g., DebugBench and DebugEval). To advance the field of multilingual debugging with LLMs, we propose the first massively multilingual debugging benchmark, which includes 3.6K test samples of 18 programming languages and covers the automated program repair (APR) task, the code review (CR) task, and the bug identification (BI) task. Further, we introduce the debugging instruction corpora MDEVAL-INSTRUCT by injecting bugs into the correct multilingual queries and solutions (xDebugGen). Further, a multilingual debugger xDebugCoder trained on MDEVAL-INSTRUCT as a strong baseline specifically to handle the bugs of a wide range of programming languages (e.g. "Missing Mut" in language Rust and "Misused Macro Definition" in language C). Our extensive experiments on MDEVAL reveal a notable performance gap between open-source models and closed-source LLMs (e.g., GPT and Claude series), highlighting huge room for improvement in multilingual code debugging scenarios., Comment: 15 pages

Published
2024

7. An Image-Based Turbine Blade Parameter Inspection Method

Author

CUI Zeyang, KONG Xiangling, FU Jinglun, and SHI Jiajun

Subjects
gas turbine, blade parameter inspection, image processing, skeleton extraction, Applications of electric power, TK4001-4102, Production of electric energy or power. Powerplants. Central stations, TK1001-1841, Science
Abstract

Accurate inspection of the feature parameters of the blade is a pivotal step to conduct the performance diagnosis and reverse modeling. To improve the inspection efficiency, an image-based parameter inspection method was proposed. First, the skeleton extraction algorithm was used to locate the middle arc of the blade. Then, the middle arc function and the blade thickness distribution function were obtained by the 3-order polynomial curve fitting algorithms. Finally, an optimization algorithm was derived to improve the inspection accuracy. Experimental results show that the proposed image-based feature parameter inspection method has high accuracy, and the relative measurement error is less than 1.5%. It provides a new solution for the rapid and accurate measurement of blade geometric parameters.

Published
2024
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9. The length spectrum of holomorphic quadratic differential metrics

Author

Shi, Jiajun

Subjects
Mathematics - Differential Geometry, Mathematics - Geometric Topology
Abstract

In this paper we prove that on a closed oriented surface, flat metrics determined by holomorphic quadratic differentials can be distinguished from other flat cone metrics by the length spectrum., Comment: Revised version

Published
2021

18. The miR7125‐MdARF1 module enhances the resistance of apple to Colletotrichum gloeosporioides by promoting lignin synthesis in response to salicylic acid signalling.

Author

Liu, Xinmei, Dai, Hongyan, Zhang, Feng, Wang, Jun, Shi, Jiajun, Chen, Junqin, He, Ping, Wang, Feng, and Ma, Yue

Subjects
TRANSCRIPTION factors, DISEASE resistance of plants, SALICYLIC acid, COLLETOTRICHUM gloeosporioides, NATURAL immunity
Abstract

Summary: Apple is an important cash crop in China, and it is susceptible to fungal infections that have deleterious effects on its yield. Apple bitter rot caused by Colletorichum gloeosporioides is one of the most severe fungal diseases of apple. Salicylic acid (SA) is a key signalling molecule in the plant disease resistance signalling pathways. Lignin synthesis also plays a key role in conferring disease resistance. However, few studies have clarified the relationship between the SA disease resistance signalling pathway and the lignin disease resistance pathway in apple. MdMYB46 has previously been shown to promote lignin accumulation in apple and enhance salt and osmotic stress tolerance. Here, we investigated the relationship between MdMYB46 and biological stress; we found that MdMYB46 overexpression enhances the resistance of apple to C. gloeosporioides. We also identified MdARF1, a transcription factor upstream of MdMYB46, via yeast library screening and determined that MdARF1 was regulated by miR7125 through psRNATarget prediction. This regulatory relationship was confirmed through LUC and qRT‐PCR experiments, demonstrating that miR7125 negatively regulates MdARF1. Analysis of the miR7125 promoter revealed that miR7125 responds to SA signals. The accumulation of SA level will result in the decrease of miR7125 expression level. In sum, the results of our study provide novel insights into the molecular mechanisms underlying the resistance of apple to C. gloeosporioides and reveal a new pathway that enhances lignin accumulation in apple in response to SA signals. These findings provide valuable information for future studies aimed at breeding apple for disease resistance. [ABSTRACT FROM AUTHOR]

Published
2024
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21. Routability in 3D IC Design: Monolithic 3D vs. Skybridge 3D CMOS

Author

Shi, Jiajun, Li, Mingyu, Khasanvis, Santosh, Rahman, Mostafizur, and Moritz, Csaba Andras

Subjects
Computer Science - Emerging Technologies
Abstract

Conventional 2D CMOS technology is reaching fundamental scaling limits, and interconnect bottleneck is dominating integrated circuit (IC) power and performance. While 3D IC technologies using Through Silicon Via or Monolithic Inter-layer Via alleviate some of these challenges, they follow a similar layout and routing mindset as 2D CMOS. This is insufficient to address routing requirements in high-density 3D ICs and even causes severe routing congestion at large-scale designs, limiting their benefits and scalability. Skybridge is a recently proposed fine-grained 3D IC fabric relying on vertical nanowires that presents a paradigm shift for scaling, while addressing associated 3D connectivity and manufacturability challenges. Skybridge's core fabric components enable a new 3D IC design approach with vertically-composed logic gates, and provide a greater degree of routing flexibility compared to conventional 2D and 3D ICs leading to much larger benefits and future scalability. In this paper, we present a methodology using relevant metrics to evaluate and quantify the benefits of Skybridge vs. state-of-the-art transistor-level monolithic 3D IC (T-MI) and 2D in terms of routability and its impact on large-scale circuits. This is enabled by a new device-to-system design flow with commercial CAD tools that we developed for large-scale Skybridge IC designs in 16nm node. Evaluation for standard benchmark circuits shows that Skybridge yields up to 1.6x lower routing demand against T-MI with no routing congestion (routing demand to resource ratio < 1) at all metal layers. This 3D routability in conjunction with compact vertical gate design in Skybridge translate into benefits of up to 3x lower power and 11x higher density over 2D CMOS, while TLM-3DIC approach only has up to 22% power saving and 2x density improvement over 2D CMOS.

Published
2016

22. Skybridge-3D-CMOS: A Vertically-Composed Fine-Grained 3D CMOS Integrated Circuit Technology

Author

Li, Mingyu, Shi, Jiajun, Rahman, Mostafizur, Khasanvis, Santosh, Bhat, Sachin, and Moritz, Csaba Andras

Subjects
Computer Science - Emerging Technologies
Abstract

Parallel and monolithic 3D integration directions offer pathways to realize 3D integrated circuits (ICs) but still lead to layer-by-layer implementations, each functional layer being composed in 2D first. This mindset causes challenging connectivity, routing and layer alignment between layers when connected in 3D, with a routing access that can be even worse than 2D CMOS, which fundamentally limits their potential. To fully exploit the opportunities in the third dimension, we propose Skybridge-3D-CMOS (S3DC), a fine-grained 3D integration approach that is directly composed in 3D, utilizing the vertical dimension vs. using a layer-by-layer assembly mindset. S3DC uses a novel wafer fabric creation with direct 3D design and connectivity in the vertical dimension. It builds on a uniform vertical nanowire template that is processed as a single wafer; it incorporates specifically architected structures for realizing devices, circuits, and heat management directly in 3D. Novel 3D interconnect concepts, including within the silicon layers, enable significantly improved routing flexibility in all three dimensions and a high-density 3D design paradigm overall. Intrinsic components for fabric-level 3D heat management are introduced. Extensive bottom-up simulations and experiments have been presented to validate the key fabric-enabling concepts. Evaluation results indicate up to 40x density and 10x performance-per-watt benefits against conventional 16-nm CMOS for the circuits studied; benefits are also at least an order of magnitude beyond what was shown to be possible with other 3D directions.

Published
2016

25. Manufacturing Pathway and Experimental Demonstration for Nanoscale Fine-Grained 3-D Integrated Circuit Fabric

Author

Rahman, Mostafizur, Shi, Jiajun, Li, Mingyu, Khasanvis, Santosh, and Moritz, Csaba Andras

Subjects
Computer Science - Other Computer Science
Abstract

At sub-20nm technologies CMOS scaling faces severe challenges primarily due to fundamental device scaling limitations, interconnection overhead and complex manufacturing. Migration to 3D has been long sought as a possible pathway to continue scaling, however, intrinsic requirements of CMOS are not compatible for fine-grained 3D integration. We proposed a truly fine-grained 3D integrated circuit fabric called Skybridge that solves nanoscale challenges and achieves orders of magnitude benefits over CMOS. In Skybridge, device, circuit, connectivity, thermal management and manufacturing issues are addressed in an integrated 3D compatible manner. At the core of Skybridge assembly are uniform vertical nanowires, which are functionalized with architected features for fabric integration. All active components are created primarily using sequential material deposition steps on these nanowires. Lithography and doping are performed prior to any functionalization and their precision requirements are significantly reduced. This paper introduces Skybridge manufacturing pathway that is developed based on extensive process, device simulations and experimental metrology, and uses established processes. Experimental demonstrations of key process steps are also shown.

Published
2015

29. Fine‐scale mapping of 8q24 locus identifies multiple independent risk variants for breast cancer

Author

Shi, Jiajun, Zhang, Yanfeng, Zheng, Wei, Michailidou, Kyriaki, Ghoussaini, Maya, Bolla, Manjeet K, Wang, Qin, Dennis, Joe, Lush, Michael, Milne, Roger L, Shu, Xiao‐Ou, Beesley, Jonathan, Kar, Siddhartha, Andrulis, Irene L, Anton‐Culver, Hoda, Arndt, Volker, Beckmann, Matthias W, Zhao, Zhiguo, Guo, Xingyi, Benitez, Javier, Beeghly‐Fadiel, Alicia, Blot, William, Bogdanova, Natalia V, Bojesen, Stig E, Brauch, Hiltrud, Brenner, Hermann, Brinton, Louise, Broeks, Annegien, Brüning, Thomas, Burwinkel, Barbara, Cai, Hui, Canisius, Sander, Chang‐Claude, Jenny, Choi, Ji‐Yeob, Couch, Fergus J, Cox, Angela, Cross, Simon S, Czene, Kamila, Darabi, Hatef, Devilee, Peter, Droit, Arnaud, Dork, Thilo, Fasching, Peter A, Fletcher, Olivia, Flyger, Henrik, Fostira, Florentia, Gaborieau, Valerie, García‐Closas, Montserrat, Giles, Graham G, Grip, Mervi, Guenel, Pascal, Haiman, Christopher A, Hamann, Ute, Hartman, Mikael, Miao, Hui, Hollestelle, Antoinette, Hopper, John L, Hsiung, Chia‐Ni, Investigators, kConFab, Ito, Hidemi, Jakubowska, Anna, Johnson, Nichola, Torres, Diana, Kabisch, Maria, Kang, Daehee, Khan, Sofia, Knight, Julia A, Kosma, Veli‐Matti, Lambrechts, Diether, Li, Jingmei, Lindblom, Annika, Lophatananon, Artitaya, Lubinski, Jan, Mannermaa, Arto, Manoukian, Siranoush, Le Marchand, Loic, Margolin, Sara, Marme, Frederik, Matsuo, Keitaro, McLean, Catriona, Meindl, Alfons, Muir, Kenneth, Neuhausen, Susan L, Nevanlinna, Heli, Nord, Silje, Børresen‐Dale, Anne‐Lise, Olson, Janet E, Orr, Nick, van den Ouweland, Ans MW, Peterlongo, Paolo, Putti, Thomas Choudary, Rudolph, Anja, Sangrajrang, Suleeporn, Sawyer, Elinor J, Schmidt, Marjanka K, Schmutzler, Rita K, Shen, Chen‐Yang, Hou, Ming‐Feng, Shrubsole, Matha J, and Southey, Melissa C

Subjects
Genetics, Cancer, Breast Cancer, Human Genome, Aetiology, 2.1 Biological and endogenous factors, Alleles, Breast Neoplasms, Case-Control Studies, Chromosome Mapping, Chromosomes, Human, Pair 8, Female, Genetic Variation, Genome-Wide Association Study, Genotype, Haplotypes, Humans, Linkage Disequilibrium, Odds Ratio, Polymorphism, Single Nucleotide, Quantitative Trait Loci, Risk, White People, breast cancer, genetic susceptibility, 8q24, fine-mapping, single nucleotide polymorphism, Mervi Grip, kConFab Investigators, Oncology and Carcinogenesis, Oncology & Carcinogenesis
Abstract

Previous genome-wide association studies among women of European ancestry identified two independent breast cancer susceptibility loci represented by single nucleotide polymorphisms (SNPs) rs13281615 and rs11780156 at 8q24. A fine-mapping study across 2.06 Mb (chr8:127,561,724-129,624,067, hg19) in 55,540 breast cancer cases and 51,168 controls within the Breast Cancer Association Consortium was conducted. Three additional independent association signals in women of European ancestry, represented by rs35961416 (OR = 0.95, 95% CI = 0.93-0.97, conditional p = 5.8 × 10(-6) ), rs7815245 (OR = 0.94, 95% CI = 0.91-0.96, conditional p = 1.1 × 10(-6) ) and rs2033101 (OR = 1.05, 95% CI = 1.02-1.07, conditional p = 1.1 × 10(-4) ) were found. Integrative analysis using functional genomic data from the Roadmap Epigenomics, the Encyclopedia of DNA Elements project, the Cancer Genome Atlas and other public resources implied that SNPs rs7815245 in Signal 3, and rs1121948 in Signal 5 (in linkage disequilibrium with rs11780156, r(2)  = 0.77), were putatively functional variants for two of the five independent association signals. The results highlighted multiple 8q24 variants associated with breast cancer susceptibility in women of European ancestry.

Published
2016

30. Genome-wide association studies in East Asians identify new loci for waist-hip ratio and waist circumference.

Author

Wen, Wanqing, Kato, Norihiro, Hwang, Joo-Yeon, Guo, Xingyi, Tabara, Yasuharu, Li, Huaixing, Dorajoo, Rajkumar, Yang, Xiaobo, Tsai, Fuu-Jen, Li, Shengxu, Wu, Ying, Wu, Tangchun, Kim, Soriul, Guo, Xiuqing, Liang, Jun, Shungin, Dmitry, Adair, Linda S, Akiyama, Koichi, Allison, Matthew, Cai, Qiuyin, Chang, Li-Ching, Chen, Chien-Hsiun, Chen, Yuan-Tsong, Cho, Yoon Shin, Choi, Bo Youl, Gao, Yutang, Go, Min Jin, Gu, Dongfeng, Han, Bok-Ghee, He, Meian, Hixson, James E, Hu, Yanling, Huang, Tao, Isono, Masato, Jung, Keum Ji, Kang, Daehee, Kim, Young Jin, Kita, Yoshikuni, Lee, Juyoung, Lee, Nanette R, Lee, Jeannette, Wang, Yiqin, Liu, Jian-Jun, Long, Jirong, Moon, Sanghoon, Nakamura, Yasuyuki, Nakatochi, Masahiro, Ohnaka, Keizo, Rao, Dabeeru, Shi, Jiajun, Sull, Jae Woong, Tan, Aihua, Ueshima, Hirotsugu, Wu, Chen, Xiang, Yong-Bing, Yamamoto, Ken, Yao, Jie, Ye, Xingwang, Yokota, Mitsuhiro, Zhang, Xiaomin, Zheng, Yan, Qi, Lu, Rotter, Jerome I, Jee, Sun Ha, Lin, Dongxin, Mohlke, Karen L, He, Jiang, Mo, Zengnan, Wu, Jer-Yuarn, Tai, E Shyong, Lin, Xu, Miki, Tetsuro, Kim, Bong-Jo, Takeuchi, Fumihiko, Zheng, Wei, and Shu, Xiao-Ou

Subjects
Humans, Obesity, Genetic Predisposition to Disease, Waist-Hip Ratio, Sex Factors, Quantitative Trait, Heritable, Polymorphism, Single Nucleotide, Quantitative Trait Loci, Asian Continental Ancestry Group, Asia, Female, Male, Waist Circumference, Genome-Wide Association Study, Quantitative Trait, Heritable, Polymorphism, Single Nucleotide, Clinical Research, Genetics, 2.1 Biological and endogenous factors, Cardiovascular, Biochemistry and Cell Biology, Other Physical Sciences
Abstract

Sixty genetic loci associated with abdominal obesity, measured by waist circumference (WC) and waist-hip ratio (WHR), have been previously identified, primarily from studies conducted in European-ancestry populations. We conducted a meta-analysis of associations of abdominal obesity with approximately 2.5 million single nucleotide polymorphisms (SNPs) among 53,052 (for WC) and 48,312 (for WHR) individuals of Asian descent, and replicated 33 selected SNPs among 3,762 to 17,110 additional individuals. We identified four novel loci near the EFEMP1, ADAMTSL3 , CNPY2, and GNAS genes that were associated with WC after adjustment for body mass index (BMI); two loci near the NID2 and HLA-DRB5 genes associated with WHR after adjustment for BMI, and three loci near the CEP120, TSC22D2, and SLC22A2 genes associated with WC without adjustment for BMI. Functional enrichment analyses revealed enrichment of corticotropin-releasing hormone signaling, GNRH signaling, and/or CDK5 signaling pathways for those newly-identified loci. Our study provides additional insight on genetic contribution to abdominal obesity.

Published
2016

31. Skybridge: 3-D Integrated Circuit Technology Alternative to CMOS

Author

Rahman, Mostafizur, Khasanvis, Santosh, Shi, Jiajun, Li, Mingyu, and Moritz, Csaba Andras

Subjects
Computer Science - Emerging Technologies, Computer Science - Hardware Architecture
Abstract

Continuous scaling of CMOS has been the major catalyst in miniaturization of integrated circuits (ICs) and crucial for global socio-economic progress. However, scaling to sub-20nm technologies is proving to be challenging as MOSFETs are reaching their fundamental limits and interconnection bottleneck is dominating IC operational power and performance. Migrating to 3-D, as a way to advance scaling, has eluded us due to inherent customization and manufacturing requirements in CMOS that are incompatible with 3-D organization. Partial attempts with die-die and layer-layer stacking have their own limitations. We propose a 3-D IC fabric technology, Skybridge[TM], which offers paradigm shift in technology scaling as well as design. We co-architect Skybridge's core aspects, from device to circuit style, connectivity, thermal management, and manufacturing pathway in a 3-D fabric-centric manner, building on a uniform 3-D template. Our extensive bottom-up simulations, accounting for detailed material system structures, manufacturing process, device, and circuit parasitics, carried through for several designs including a designed microprocessor, reveal a 30-60x density, 3.5x performance per watt benefits, and 10X reduction in interconnect lengths vs. scaled 16-nm CMOS. Fabric-level heat extraction features are shown to successfully manage IC thermal profiles in 3-D. Skybridge can provide continuous scaling of integrated circuits beyond CMOS in the 21st century., Comment: 53 Pages

Published
2014

34. Fine-scale mapping of the 4q24 locus identifies two independent loci associated with breast cancer risk.

Author

Arndt, Volker, Beckmann, Matthias, Beeghly-Fadiel, Alicia, Benitez, Javier, Blot, William, Bogdanova, Natalia, Bojesen, Stig, Brauch, Hiltrud, Brenner, Hermann, Brinton, Louise, Broeks, Annegien, Brüning, Thomas, Burwinkel, Barbara, Cai, Hui, Canisius, Sander, Chang-Claude, Jenny, Choi, Ji-Yeob, Couch, Fergus, Cox, Angela, Cross, Simon, Czene, Kamila, Darabi, Hatef, Devilee, Peter, Droit, Arnaud, Dörk, Thilo, Fasching, Peter, Fletcher, Olivia, Flyger, Henrik, Fostira, Florentia, Gaborieau, Valerie, García-Closas, Montserrat, Giles, Graham, Grip, Mervi, Guénel, Pascal, Haiman, Christopher, Hamann, Ute, Hartman, Mikael, Hollestelle, Antoinette, Hopper, John, Hsiung, Chia-Ni, Ito, Hidemi, Jakubowska, Anna, Johnson, Nichola, Kabisch, Maria, Kang, Daehee, Khan, Sofia, Knight, Julia, Kosma, Veli-Matti, Lambrechts, Diether, Le Marchand, Loic, Li, Jingmei, Lindblom, Annika, Lophatananon, Artitaya, Lubinski, Jan, Mannermaa, Arto, Manoukian, Siranoush, Margolin, Sara, Marme, Frederik, Matsuo, Keitaro, McLean, Catriona, Meindl, Alfons, Muir, Kenneth, Neuhausen, Susan, Nevanlinna, Heli, Nord, Silje, Olson, Janet, Orr, Nick, Peterlongo, Paolo, Putti, Thomas, Rudolph, Anja, Sangrajrang, Suleeporn, Sawyer, Elinor, Schmidt, Marjanka, Schmutzler, Rita, Shen, Chen-Yang, Shi, Jiajun, Shrubsole, Martha, Southey, Melissa, Swerdlow, Anthony, Teo, Soo, Thienpont, Bernard, Toland, Amanda, Tollenaar, Robert, Tomlinson, Ian, Truong, Thérèse, Tseng, Chiu-Chen, van den Ouweland, Ans, Wen, Wanqing, Winqvist, Robert, Wu, Anna, Yip, Cheng, Zamora, M, Zheng, Ying, Hall, Per, Pharoah, Paul, Simard, Jacques, Chenevix-Trench, Georgia, Dunning, Alison, Easton, Douglas, and Zheng, Wei

Subjects
Breast Neoplasms, Case-Control Studies, Chromosome Mapping, Chromosomes, Human, Pair 4, Female, Genetic Loci, Genetic Markers, Genetic Predisposition to Disease, Genome-Wide Association Study, Humans, Logistic Models, Polymorphism, Single Nucleotide, Risk Factors
Abstract

BACKGROUND: A recent association study identified a common variant (rs9790517) at 4q24 to be associated with breast cancer risk. Independent association signals and potential functional variants in this locus have not been explored. METHODS: We conducted a fine-mapping analysis in 55,540 breast cancer cases and 51,168 controls from the Breast Cancer Association Consortium. RESULTS: Conditional analyses identified two independent association signals among women of European ancestry, represented by rs9790517 [conditional P = 2.51 × 10(-4); OR, 1.04; 95% confidence interval (CI), 1.02-1.07] and rs77928427 (P = 1.86 × 10(-4); OR, 1.04; 95% CI, 1.02-1.07). Functional annotation using data from the Encyclopedia of DNA Elements (ENCODE) project revealed two putative functional variants, rs62331150 and rs73838678 in linkage disequilibrium (LD) with rs9790517 (r(2) ≥ 0.90) residing in the active promoter or enhancer, respectively, of the nearest gene, TET2. Both variants are located in DNase I hypersensitivity and transcription factor-binding sites. Using data from both The Cancer Genome Atlas (TCGA) and Molecular Taxonomy of Breast Cancer International Consortium (METABRIC), we showed that rs62331150 was associated with level of expression of TET2 in breast normal and tumor tissue. CONCLUSION: Our study identified two independent association signals at 4q24 in relation to breast cancer risk and suggested that observed association in this locus may be mediated through the regulation of TET2. IMPACT: Fine-mapping study with large sample size warranted for identification of independent loci for breast cancer risk.

Published
2015

35. Technologies and Applications of Narrowband Internet of Things

Author

Chen, Jia, Shi, Jiajun, Chen, Xiangxu, Wu, Yuan, Qian, Liping, Huang, Liang, Akan, Ozgur, Editorial Board Member, Bellavista, Paolo, Editorial Board Member, Cao, Jiannong, Editorial Board Member, Coulson, Geoffrey, Editorial Board Member, Dressler, Falko, Editorial Board Member, Ferrari, Domenico, Editorial Board Member, Gerla, Mario, Editorial Board Member, Kobayashi, Hisashi, Editorial Board Member, Palazzo, Sergio, Editorial Board Member, Sahni, Sartaj, Editorial Board Member, Shen, Xuemin (Sherman), Editorial Board Member, Stan, Mircea, Editorial Board Member, Jia, Xiaohua, Editorial Board Member, Zomaya, Albert Y., Editorial Board Member, Meng, Limin, editor, and Zhang, Yan, editor

Published
2018
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36. Joint Time and Power Allocations for Uplink Nonorthogonal Multiple Access Networks

Author

Wu, Yuan, Zhang, Cheng, Ni, Kejie, Shi, Jiajun, Qian, Liping, Huang, Liang, Lu, Weidang, Meng, Limin, Akan, Ozgur, Editorial Board Member, Bellavista, Paolo, Editorial Board Member, Cao, Jiannong, Editorial Board Member, Coulson, Geoffrey, Editorial Board Member, Dressler, Falko, Editorial Board Member, Ferrari, Domenico, Editorial Board Member, Gerla, Mario, Editorial Board Member, Kobayashi, Hisashi, Editorial Board Member, Palazzo, Sergio, Editorial Board Member, Sahni, Sartaj, Editorial Board Member, Shen, Xuemin (Sherman), Editorial Board Member, Stan, Mircea, Editorial Board Member, Jia, Xiaohua, Editorial Board Member, Zomaya, Albert Y., Editorial Board Member, Meng, Limin, editor, and Zhang, Yan, editor

Published
2018
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38. Large-Scale Genome-Wide Association Study of East Asians Identifies Loci Associated With Risk for Colorectal Cancer

Author

Lu, Yingchang, Kweon, Sun-Seog, Tanikawa, Chizu, Jia, Wei-Hua, Xiang, Yong-Bing, Cai, Qiuyin, Zeng, Chenjie, Schmit, Stephanie L., Shin, Aesun, Matsuo, Keitaro, Jee, Sun Ha, Kim, Dong-Hyun, Kim, Jeongseon, Wen, Wanqing, Shi, Jiajun, Guo, Xingyi, Li, Bingshan, Wang, Nan, Zhang, Ben, Li, Xinxiang, Shin, Min-Ho, Li, Hong-Lan, Ren, Zefang, Oh, Jae Hwan, Oze, Isao, Ahn, Yoon-Ok, Jung, Keum Ji, Conti, David V., Schumacher, Fredrick R., Rennert, Gad, Jenkins, Mark A., Campbell, Peter T., Hoffmeister, Michael, Casey, Graham, Gruber, Stephen B., Gao, Jing, Gao, Yu-Tang, Pan, Zhi-Zhong, Kamatani, Yoichiro, Zeng, Yi-Xin, Shu, Xiao-Ou, Long, Jirong, Matsuda, Koichi, and Zheng, Wei

Published
2019
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39. Meta-analysis of genome-wide association studies in East Asian-ancestry populations identifies four new loci for body mass index

Author

Wen, Wanqing, Zheng, Wei, Okada, Yukinori, Takeuchi, Fumihiko, Tabara, Yasuharu, Hwang, Joo-Yeon, Dorajoo, Rajkumar, Li, Huaixing, Tsai, Fuu-Jen, Yang, Xiaobo, He, Jiang, Wu, Ying, He, Meian, Zhang, Yi, Liang, Jun, Guo, Xiuqing, Sheu, Wayne Huey-Herng, Delahanty, Ryan, Guo, Xingyi, Kubo, Michiaki, Yamamoto, Ken, Ohkubo, Takayoshi, Go, Min Jin, Liu, Jian Jun, Gan, Wei, Chen, Ching-Chu, Gao, Yong, Li, Shengxu, Lee, Nanette R, Wu, Chen, Zhou, Xueya, Song, Huaidong, Yao, Jie, Lee, I-Te, Long, Jirong, Tsunoda, Tatsuhiko, Akiyama, Koichi, Takashima, Naoyuki, Cho, Yoon Shin, Ong, Rick TH, Lu, Ling, Chen, Chien-Hsiun, Tan, Aihua, Rice, Treva K, Adair, Linda S, Gui, Lixuan, Allison, Matthew, Lee, Wen-Jane, Cai, Qiuyin, Isomura, Minoru, Umemura, Satoshi, Kim, Young Jin, Seielstad, Mark, Hixson, James, Xiang, Yong-Bing, Isono, Masato, Kim, Bong-Jo, Sim, Xueling, Lu, Wei, Nabika, Toru, Lee, Juyoung, Lim, Wei-Yen, Gao, Yu-Tang, Takayanagi, Ryoichi, Kang, Dae-Hee, Wong, Tien Yin, Hsiung, Chao Agnes, Wu, I-Chien, Juang, Jyh-Ming Jimmy, Shi, Jiajun, Choi, Bo Youl, Aung, Tin, Hu, Frank, Kim, Mi Kyung, Lim, Wei Yen, Wang, Tzung-Dao, Shin, Min-Ho, Lee, Jeannette, Ji, Bu-Tian, Lee, Young-Hoon, Young, Terri L, Shin, Dong Hoon, Chun, Byung-Yeol, Cho, Myeong-Chan, Han, Bok-Ghee, Hwu, Chii-Min, Assimes, Themistocles L, Absher, Devin, Yan, Xiaofei, Kim, Eric, Kuo, Jane Z, Kwon, Soonil, Taylor, Kent D, Chen, Yii-Der I, Rotter, Jerome I, Qi, Lu, Zhu, Dingliang, Wu, Tangchun, Mohlke, Karen L, and Gu, Dongfeng

Subjects
Biological Sciences, Genetics, Obesity, Nutrition, Human Genome, Women's Health, 5'-Nucleotidase, Aldehyde Dehydrogenase, Aldehyde Dehydrogenase, Mitochondrial, Asian People, Blood Proteins, Body Mass Index, Cardiac Myosins, Asia, Eastern, Female, Genetic Predisposition to Disease, Genome-Wide Association Study, Glycoproteins, Humans, KCNQ1 Potassium Channel, Male, Myosin Light Chains, Polymorphism, Single Nucleotide, Proteinase Inhibitory Proteins, Secretory, Medical and Health Sciences, Genetics & Heredity
Abstract

Recent genetic association studies have identified 55 genetic loci associated with obesity or body mass index (BMI). The vast majority, 51 loci, however, were identified in European-ancestry populations. We conducted a meta-analysis of associations between BMI and ∼2.5 million genotyped or imputed single nucleotide polymorphisms among 86 757 individuals of Asian ancestry, followed by in silico and de novo replication among 7488-47 352 additional Asian-ancestry individuals. We identified four novel BMI-associated loci near the KCNQ1 (rs2237892, P = 9.29 × 10(-13)), ALDH2/MYL2 (rs671, P = 3.40 × 10(-11); rs12229654, P = 4.56 × 10(-9)), ITIH4 (rs2535633, P = 1.77 × 10(-10)) and NT5C2 (rs11191580, P = 3.83 × 10(-8)) genes. The association of BMI with rs2237892, rs671 and rs12229654 was significantly stronger among men than among women. Of the 51 BMI-associated loci initially identified in European-ancestry populations, we confirmed eight loci at the genome-wide significance level (P < 5.0 × 10(-8)) and an additional 14 at P < 1.0 × 10(-3) with the same direction of effect as reported previously. Findings from this analysis expand our knowledge of the genetic basis of obesity.

Published
2014

41. Association Between Long-Term Regular Exercise and Gut Microbiota Among Middle-Aged and Older Urban Chinese.

Author

Shi, Jiajun, Yu, Danxia, Yang, Yaohua, Cai, Hui, Wu, Jie, Cai, Qiuyin, Long, Jirong, Zheng, Wei, Xu, Wanghong, and Shu, Xiao-Ou

Subjects
*RESEARCH, *ANALYSIS of variance, *GUT microbiome, *MULTIVARIATE analysis, *REGRESSION analysis, *PHYSICAL activity, *SURVEYS, *MATHEMATICAL variables, *EXERCISE, *QUESTIONNAIRES, *LOGISTIC regression analysis, *MIDDLE age, *OLD age
Abstract

Increasing evidence has suggested that physical activity may modulate gut microbiome composition. We investigated associations of long-term regular exercise with gut microbiota among middle-aged and older urban Chinese individuals. Gut microbiota was assessed using 16S ribosomal ribonucleic acid gene sequencing of stool samples from 2,151 participants from the Shanghai Women's Health Study and Shanghai Men's Health Study. Participants were free of cancer, diabetes, and cardiovascular diseases at the time of stool sample collection. Physical activity was assessed in repeat surveys between 1996 and 2015 using validated questionnaires. Regular exercise was defined as any type of leisure-time physical activity with a standard metabolic equivalent score >3.0. Stool samples were collected using the 95% ethanol method between 2015 and 2018 with an average of 3.0 years (SD = 0.9) after the latest exposure assessment. General linear regression and permutational multivariate analysis of variance were carried out to evaluate associations of microbial α- and β-diversity with regular exercise participation. Logistic regression and linear regression models were used to evaluate the prevalence and relative abundance of individual taxa in association with regular exercise. Regular exercise was significantly associated with β-diversity (Bray–Curtis and Jaccard dissimilarities, both false discovery rates = 0.03%, 0.12% and 0.09% variance explained, respectively) but not with α-diversity. Relative abundance of genus Ruminococcus was significantly lower among regular exercisers compared with nonexercisers (median relative abundance: 0.64% vs. 0.81%, false discovery rate <0.10). Further studies are needed to validate the findings from this study and evaluate health benefits of regular exercise on gut microbiota. [ABSTRACT FROM AUTHOR]

Published
2022
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43. Evaluation of students' online teaching satisfaction based on the concept of user experience ——A cross-sectional data study from medical schools in northern China

Author

Xie, Yuzhuo, primary, Li, Yuanheng, additional, Wang, Yazhou, additional, Zhang, Yuwei, additional, Ma, Mingxue, additional, Wang, Jingzhi, additional, Guo, Jiaqi, additional, Shi, Jiajun, additional, Zhu, Liling, additional, Jiang, Deyou, additional, and Jiao, Mingli, additional

Published
2023
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45. Identification of novel breast cancer susceptibility loci in meta-analyses conducted among Asian and European descendants

Author

Shu, Xiang, Long, Jirong, Cai, Qiuyin, Kweon, Sun-Seog, Choi, Ji-Yeob, Kubo, Michiaki, Park, Sue K., Bolla, Manjeet K., Dennis, Joe, Wang, Qin, Yang, Yaohua, Shi, Jiajun, Guo, Xingyi, Li, Bingshan, Tao, Ran, Aronson, Kristan J., Chan, Kelvin Y. K., Chan, Tsun L., Gao, Yu-Tang, Hartman, Mikael, Kee Ho, Weang, Ito, Hidemi, Iwasaki, Motoki, Iwata, Hiroji, John, Esther M., Kasuga, Yoshio, Soon Khoo, Ui, Kim, Mi-Kyung, Kong, Sun-Young, Kurian, Allison W., Kwong, Ava, Lee, Eun-Sook, Li, Jingmei, Lophatananon, Artitaya, Low, Siew-Kee, Mariapun, Shivaani, Matsuda, Koichi, Matsuo, Keitaro, Muir, Kenneth, Noh, Dong-Young, Park, Boyoung, Park, Min-Ho, Shen, Chen-Yang, Shin, Min-Ho, Spinelli, John J., Takahashi, Atsushi, Tseng, Chiuchen, Tsugane, Shoichiro, Wu, Anna H., Xiang, Yong-Bing, Yamaji, Taiki, Zheng, Ying, Milne, Roger L., Dunning, Alison M., Pharoah, Paul D. P., García-Closas, Montserrat, Teo, Soo-Hwang, Shu, Xiao-ou, Kang, Daehee, Easton, Douglas F., Simard, Jacques, and Zheng, Wei

Published
2020
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46. Comparison between renal pelvic and ureteral tumors in muscle‐invasive upper tract urothelial carcinoma

Author

Chen Qiwei, Shi Jiajun, Liang Cheng, Huang Shengbo, Kuai Yue, Wang Shujing, Wenlong Liu, Zhu Xinqing, Wang Hongyu, and Yang Deyong

Subjects
Cancer Research, Oncology, General Medicine
Abstract

Although renal pelvic and ureteral urothelial carcinoma share similarities in their origins, disparities on a genetic and clinical level make them divergent entities. Clinical information from the Surveillance, Epidemiology, and End Results (SEER) database was used to validate the characteristics and molecular subtypes using single-center data, which were compared between the two types of muscle-invasive tumors. Simultaneously, to expand the sample size for further verification, we explored a deep learning algorithm to correctly classify molecular subtypes from HE histology slides. We suggested that the renal pelvic group might have a proclivity towards luminal and the ureter towards basal and P53-like. Furthermore, we explore the heterogeneity of matrix and immune tumor microenvironment, and the ureteral group had more immune cell infiltration and higher stiffness. Collectively, these results showed that muscle-invasive upper tract urothelial carcinoma exist in distinct properties of clinical characteristics, molecular subtype, and tumor microenvironment.

Published
2022

50. Data from Pathway Analyses Identify TGFBR2 as Potential Breast Cancer Susceptibility Gene: Results from a Consortium Study among Asians

Author

Ma, Xiangyu, primary, Beeghly-Fadiel, Alicia, primary, Lu, Wei, primary, Shi, Jiajun, primary, Xiang, Yong-Bing, primary, Cai, Qiuyin, primary, Shen, Hongbing, primary, Shen, Chen-Yang, primary, Ren, Zefang, primary, Matsuo, Keitaro, primary, Khoo, Ui Soon, primary, Iwasaki, Motoki, primary, Long, Jirong, primary, Zhang, Ben, primary, Ji, Bu-Tian, primary, Zheng, Ying, primary, Wang, Wenjing, primary, Hu, Zhibin, primary, Liu, Yao, primary, Wu, Pei-Ei, primary, Shieh, Ya-Lan, primary, Wang, Shenming, primary, Xie, Xiaoming, primary, Ito, Hidemi, primary, Kasuga, Yoshio, primary, Chan, Kelvin Y.K., primary, Iwata, Hiroji, primary, Tsugane, Shoichiro, primary, Gao, Yu-Tang, primary, Shu, Xiao Ou, primary, Moses, Harold L., primary, and Zheng, Wei, primary

Published
2023
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