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1. A natural-language-based approach to intelligent data retrieval and representation for cloud BIM

Author

Lin, Jia-Rui, Hu, Zhen-Zhong, Zhang, Jian-Ping, and Yu, Fang-Qiang

Subjects
Computer Science - Human-Computer Interaction
Abstract

As the information from diverse disciplines continues to integrate during the whole life cycle of an Architecture, Engineering, and Construction (AEC) project, the BIM (Building Information Model/Modeling) becomes increasingly large. This condition will cause users difficulty in acquiring the information they truly desire on a mobile device with limited space for interaction. To improve the value of the big data of BIM, an approach to intelligent data retrieval and representation for cloud BIM applications based on natural language processing was proposed. First, strategies for data storage and query acceleration based on the popular cloud-based database were explored to handle the large amount of BIM data. Then, the concepts keyword and constraint were proposed to capture the key objects and their specifications in a natural-language-based sentence that expresses the requirements of the user. Keywords and constraints can be mapped to IFC entities or properties through the International Framework for Dictionaries (IFD). The relationship between the user's requirement and the IFC-based data model was established by path finding in a graph generated from the IFC schema, enabling data retrieval and analysis. Finally, the analyzed and summarized results of BIM data were represented based on the structure of the retrieved data. A prototype application was developed to validate the proposed approach on the data collected during the construction of the terminal of Kunming Airport, the largest single building in China. With this approach, users can significantly benefit from requesting for information and the value of BIM will be enhanced.

Published
2024
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9. A Dynamic Subspace Based BFGS Method for Large Scale Optimization Problem

Author

Li, Zheng, Shu, Shi, and Zhang, Jian-Ping

Subjects
Mathematics - Optimization and Control
Abstract

Large-scale unconstrained optimization is a fundamental and important class of, yet not well-solved problems in numerical optimization. The main challenge in designing an algorithm is to require a few storage locations or very inexpensive computations while preserving global convergence. In this work, we propose a novel approach solving large-scale unconstrained optimization problem by combining the dynamic subspace technique and the BFGS update algorithm. It is clearly demonstrated that our approach has the same rate of convergence in the dynamic subspace as the BFGS and less memory than L-BFGS. Further, we give the convergence analysis by constructing the mapping of low-dimensional Euclidean space to the adaptive subspace. We compare our hybrid algorithm with the BFGS and L-BFGS approaches. Experimental results show that our hybrid algorithm offers several significant advantages such as parallel computing, convergence efficiency, and robustness., Comment: For associated code and experiments, see https: //github.com/LizhengMathAi/F-BFGS

Published
2020

11. PD-1H/VISTA mediates immune evasion in acute myeloid leukemia

Author

Kim, Tae Kon, Han, Xue, Hu, Qianni, Vandsemb, Esten N., Fielder, Carly M., Hong, Junshik, Kim, Kwang Woon, Mason, Emily F., Plowman, R. Skipper, Wang, Jun, Wang, Qi, Zhang, Jian-Ping, Badri, Ti, Sanmamed, Miguel F., Zheng, Linghua, Zhang, Tianxiang, Alawa, Jude, Lee, Sang Won, Zeidan, Amer M., Halene, Stephanie, Pillai, Manoj M., Chandhok, Namrata S., Lu, Jun, Xu, Mina L., Gore, Steven D., and Chen, Lieping

Subjects
United States. Food and Drug Administration -- Analysis, T cells -- Analysis, Immune response -- Analysis, Cancer -- Care and treatment, Apoptosis -- Analysis, Health care industry, Yale University. School of Medicine, Vanderbilt University. Medical Center
Abstract

Acute myeloid leukemia (AML) presents a pressing medical need in that it is largely resistant to standard chemotherapy as well as modern therapeutics, such as targeted therapy and immunotherapy, including anti-programmed cell death protein (anti-PD) therapy. We demonstrate that programmed death-1 homolog (PD-1H), an immune coinhibitory molecule, is highly expressed in blasts from the bone marrow of AML patients, while normal myeloid cell subsets and T cells express PD-1H. In studies employing syngeneic and humanized AML mouse models, overexpression of PD-1H promoted the growth of AML cells, mainly by evading T cell-mediated immune responses. Importantly, ablation of AML cell-surface PD-1H by antibody blockade or genetic knockout significantly inhibited AML progression by promoting T cell activity. In addition, the genetic deletion of PD-1H from host normal myeloid cells inhibited AML progression, and the combination of PD- 1H blockade with anti-PD therapy conferred a synergistic antileukemia effect. Our findings provide the basis for PD- 1H as a potential therapeutic target for treating human AML., Introduction Acute myeloid leukemia (AML) is a heterogenous clonal disorder that is characterized by uncontrolled clonal expansion of myeloid progenitor cells (blasts) that leads to BM failure (1). AML is [...]

Published
2024
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16. Highly efficient genome editing via CRISPR–Cas9 in human pluripotent stem cells is achieved by transient BCL-XL overexpression

Author

Li, Xiao-Lan, Li, Guo-Hua, Fu, Juan, Fu, Ya-Wen, Zhang, Lu, Chen, Wanqiu, Arakaki, Cameron, Zhang, Jian-Ping, Wen, Wei, Zhao, Mei, Chen, Weisheng V, Botimer, Gary D, Baylink, David, Aranda, Leslie, Choi, Hannah, Bechar, Rachel, Talbot, Prue, Sun, Chang-Kai, Cheng, Tao, and Zhang, Xiao-Bing

Subjects
Biochemistry and Cell Biology, Biological Sciences, Genetics, Stem Cell Research - Induced Pluripotent Stem Cell, Regenerative Medicine, Stem Cell Research, Human Genome, Biotechnology, Stem Cell Research - Induced Pluripotent Stem Cell - Human, 1.1 Normal biological development and functioning, Underpinning research, Generic health relevance, Animals, CRISPR-Cas Systems, Cells, Cultured, Gene Editing, Genome, Human, HEK293 Cells, Humans, Induced Pluripotent Stem Cells, Jurkat Cells, K562 Cells, Mice, Transfection, Up-Regulation, bcl-X Protein, Environmental Sciences, Information and Computing Sciences, Developmental Biology, Biological sciences, Chemical sciences, Environmental sciences
Abstract

Genome editing of human induced pluripotent stem cells (iPSCs) is instrumental for functional genomics, disease modeling, and regenerative medicine. However, low editing efficiency has hampered the applications of CRISPR-Cas9 technology in creating knockin (KI) or knockout (KO) iPSC lines, which is largely due to massive cell death after electroporation with editing plasmids. Here, we report that the transient delivery of BCL-XL increases iPSC survival by ∼10-fold after plasmid transfection, leading to a 20- to 100-fold increase in homology-directed repair (HDR) KI efficiency and a 5-fold increase in non-homologous end joining (NHEJ) KO efficiency. Treatment with a BCL inhibitor ABT-263 further improves HDR efficiency by 70% and KO efficiency by 40%. The increased genome editing efficiency is attributed to higher expressions of Cas9 and sgRNA in surviving cells after electroporation. HDR or NHEJ efficiency reaches 95% with dual editing followed by selection of cells with HDR insertion of a selective gene. Moreover, KO efficiency of 100% can be achieved in a bulk population of cells with biallelic HDR KO followed by double selection, abrogating the necessity for single cell cloning. Taken together, these simple yet highly efficient editing strategies provide useful tools for applications ranging from manipulating human iPSC genomes to creating gene-modified animal models.

Published
2018

23. A simulations approach for meta-analysis of genetic association studies based on additive genetic model

Author

John, Majnu, Lencz, Todd, Malhotra, Anil K, Correll, Christoph U, and Zhang, Jian-Ping

Subjects
Statistics - Applications
Abstract

Genetic association studies are becoming an important component of medical research. To cite one instance, pharmacogenomics which is gaining prominence as a useful tool for personalized medicine is heavily reliant on results from genetic association studies. Meta-analysis of genetic association studies is being increasingly used to assess phenotypic differences between genotype groups. When the underlying genetic model is assumed to be dominant or recessive, assessing the phenotype differences based on summary statistics, reported for individual studies in a meta-analysis, is a valid strategy. However, when the genetic model is additive, a similar strategy based on summary statistics will lead to biased results. This fact about the additive model is one of the things that we establish in this paper, using simulations. The main goal of this paper is to present an alternate strategy for the additive model based on simulating data for the individual studies. We show that the alternate strategy is far superior to the strategy based on summary statistics.

Published
2016
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34. The outcome and predictive model of allogeneic hematopoietic stem cell transplantation among elderly patients with severe aplastic anemia from the Chinese Blood and Marrow Transplant Registry Group

Author

Xu, Zheng-Li, primary, Xu, Lan-Ping, additional, Zhang, Yi-Cheng, additional, Zhou, Yu-Hong, additional, Jiang, Er-Lie, additional, Zhang, Jian-Ping, additional, Fu, Bin, additional, Ouyang, Gui-Fang, additional, Song, Xian-Min, additional, Zhang, Xue-Jun, additional, Dong, Yu-Jun, additional, Li, Nai-Nong, additional, Wang, Ling, additional, Zhang, Xi, additional, He, Peng-Cheng, additional, Kong, Fan-Sheng, additional, Liu, Hui-Xia, additional, Liu, Li, additional, Liu, Lin, additional, Xiao, Tai-Wu, additional, Xu, Wen-Wei, additional, Xu, Xiao-Jun, additional, Yuan, Guo-Lin, additional, Yi, Hai, additional, Yu, Dan, additional, Yu, Li, additional, and Huang, Xiao-Jun, additional

Published
2024
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35. Pharmacogenetic Associations of Antipsychotic Drug-Related Weight Gain: A Systematic Review and Meta-analysis.

Author

Zhang, Jian-Ping, Lencz, Todd, Zhang, Ryan X, Nitta, Masahiro, Maayan, Lawrence, John, Majnu, Robinson, Delbert G, Fleischhacker, W Wolfgang, Kahn, Rene S, Ophoff, Roel A, Kane, John M, Malhotra, Anil K, and Correll, Christoph U

Subjects
Pharmacology and Pharmaceutical Sciences, Biomedical and Clinical Sciences, Serious Mental Illness, Brain Disorders, Schizophrenia, Neurosciences, Obesity, Mental Health, Genetics, Aetiology, 2.1 Biological and endogenous factors, Antipsychotic Agents, Humans, Pharmacogenetics, Psychotic Disorders, Weight Gain, pharmacogenetics, SNP, antipsychotics, weight gain, BMI, meta-analysis, Medical and Health Sciences, Psychology and Cognitive Sciences, Psychiatry, Clinical sciences
Abstract

Although weight gain is a serious but variable adverse effect of antipsychotics that has genetic underpinnings, a comprehensive meta-analysis of pharmacogenetics of antipsychotic-related weight gain is missing. In this review, random effects meta-analyses were conducted for dominant and recessive models on associations of specific single nucleotide polymorphisms (SNP) with prospectively assessed antipsychotic-related weight or body mass index (BMI) changes (primary outcome), or categorical increases in weight or BMI (≥7%; secondary outcome). Published studies, identified via systematic database search (last search: December 31, 2014), plus 3 additional cohorts, including 222 antipsychotic-naïve youth, and 81 and 141 first-episode schizophrenia adults, each with patient-level data at 3 or 4 months treatment, were meta-analyzed. Altogether, 72 articles reporting on 46 non-duplicated samples (n = 6700, mean follow-up = 25.1wk) with 38 SNPs from 20 genes/genomic regions were meta-analyzed (for each meta-analysis, studies = 2-20, n = 81-2082). Eleven SNPs from 8 genes were significantly associated with weight or BMI change, and 4 SNPs from 2 genes were significantly associated with categorical weight or BMI increase. Combined, 13 SNPs from 9 genes (Adrenoceptor Alpha-2A [ADRA2A], Adrenoceptor Beta 3 [ADRB3], Brain-Derived Neurotrophic Factor [BDNF], Dopamine Receptor D2 [DRD2], Guanine Nucleotide Binding Protein [GNB3], 5-Hydroxytryptamine (Serotonin) Receptor 2C [HTR2C], Insulin-induced gene 2 [INSIG2], Melanocortin-4 Receptor [MC4R], and Synaptosomal-associated protein, 25kDa [SNAP25]) were significantly associated with antipsychotic-related weight gain (P-values < .05-.001). SNPs in ADRA2A, DRD2, HTR2C, and MC4R had the largest effect sizes (Hedges' g's = 0.30-0.80, ORs = 1.47-1.96). Less prior antipsychotic exposure (pediatric or first episode patients) and short follow-up (1-2 mo) were associated with larger effect sizes. Individual antipsychotics did not significantly moderate effect sizes. In conclusion, antipsychotic-related weight gain is polygenic and associated with specific genetic variants, especially in genes coding for antipsychotic pharmacodynamic targets.

Published
2016

44. PD-1H/VISTA mediates immune evasion in acute myeloid leukemia

Author

Kim, Tae Kon, primary, Han, Xue, additional, Hu, Qianni, additional, Vandsemb, Esten N., additional, Fielder, Carly M., additional, Hong, Junshik, additional, Kim, Kwang Woon, additional, Mason, Emily F., additional, Plowman, R. Skipper, additional, Wang, Jun, additional, Wang, Qi, additional, Zhang, Jian-Ping, additional, Badri, Ti, additional, Sanmamed, Miguel F., additional, Zheng, Linghua, additional, Zhang, Tianxiang, additional, Alawa, Jude, additional, Lee, Sang Won, additional, Zeidan, Amer M., additional, Halene, Stephanie, additional, Pillai, Manoj M., additional, Chandhok, Namrata S., additional, Lu, Jun, additional, Xu, Mina L., additional, Gore, Steven D., additional, and Chen, Lieping, additional

Published
2023
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46. Readout of a single electron spin in a double quantum dot using a quantum point contact

Author

Zhang, Jian-Ping, Ouyang, Shi-Hua, Lam, Chi-Hang, and You, J. Q.

Subjects
Condensed Matter - Mesoscale and Nanoscale Physics, Quantum Physics
Abstract

We study the dynamics of a single electron spin in a double quantum dot (DQD) and its readout via a quantum point contact (QPC). We model the system microscopically and derive rate equations for the reduced electron density matrix of the DQD. Two cases with one and two electrons in the DQD are studied. In the one-electron case, with different Zeeman splittings in the two dots, the electron spin states are distinctly characterized by a constant and an oscillatory current through the QPC. In the two-electron case, the readout of the spin state of the electron in one of the dots called the qubit dot is essentially similar after considering hyperfine interactions between the electrons and the nuclear spins of the host materials and a uniform magnetic field applied to the DQD. Moreover, to ensure that an electron is properly injected into the qubit dot, we propose to determine the success of the electron injection from the variations of the QPC current after applying an oscillating magnetic field to the qubit dot., Comment: 18 pages, 7 figures

Published
2008
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