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MVF Designer: Design and Visualization of Morse Vector Fields [article]

Youjia Zhou, Janis Lazovskis, Michael J. Catanzaro, Matthew Zabka, Bei Wang
2019 arXiv   pre-print
Vector field design on surfaces was originally motivated by applications in graphics such as texture synthesis and rendering. In this paper, we consider the idea of vector field design with a new motivation from computational topology. We are interested in designing and visualizing vector fields to aid the study of Morse functions, Morse vector fields, and Morse-Smale complexes. To achieve such a goal, we present MVF Designer, a new interactive design system that provides fine-grained control
more » ... er vector field geometry, enables the editing of vector field topology, and supports a design process in a simple and efficient way using elementary moves, which are actions that initiate or advance our design process. Our system allows mathematicians to explore the complex configuration spaces of Morse functions, their gradients, and their associated Morse-Smale complexes. Understanding these spaces will help us expand further their applicability in topological data analysis and visualization.
arXiv:1912.09580v1 fatcat:v6sru5u3dzawvmww436cdhd6z4

Stitch Fix for Mapper and Topological Gains [article]

Youjia Zhou, Nathaniel Saul, Ilkin Safarli, Bala Krishnamoorthy, Bei Wang
2021 arXiv   pre-print
[31] and Zhou et al. [50] to identify subgroups in breast cancer patients. It contains 272 rows, with each row corresponding to the information of a patient.  ... 
arXiv:2105.01961v2 fatcat:ybsv4hrmyfhz3bcpu2ibgbcafy

Hypergraph Co-Optimal Transport: Metric and Categorical Properties [article]

Samir Chowdhury, Tom Needham, Ethan Semrad, Bei Wang, Youjia Zhou
2022 arXiv   pre-print
Zhou et al.  ...  Measure-Preserving Hypergraph Simplification In this section, we give examples that capture changes in hypernetwork distances as we apply multi-scale hypergraph simplification based on the framework of Zhou  ... 
arXiv:2112.03904v2 fatcat:3vntsro5srf5rkox6acq2jwu7m

Visual Demo of Discrete Stratified Morse Theory

Youjia Zhou, Kevin Knudson, Bei Wang, Danny Z. Chen, Sergio Cabello
2020 International Symposium on Computational Geometry  
Discrete stratified Morse theory, first introduced by Knudson and Wang, works toward a discrete analogue of Goresky and MacPherson's stratified Morse theory. It is inspired by the works of Forman on discrete Morse theory by generalizing stratified Morse theory to finite simplicial complexes. The class of discrete stratified Morse functions is much larger than that of discrete Morse functions. Any arbitrary real-valued function defined on a finite simplicial complex can be made into a discrete
more » ... ratified Morse function with the proper stratification of the underlying complex. An algorithm is given by Knudson and Wang that constructs a discrete stratified Morse function on any finite simplicial complex equipped with an arbitrary real-valued function. Our media contribution is an open-sourced visualization tool that implements such an algorithm for 2-complexes embedded in the plane, and provides an interactive demo for users to explore the algorithmic process and to perform homotopy-preserving simplification of the resulting stratified complex.
doi:10.4230/lipics.socg.2020.82 dblp:conf/compgeom/ZhouKW20 fatcat:woajvgjykvfg3hgdqxdsq6c5uq

Arthroscopic debridement of anterior ankle impingement in patients with chronic lateral ankle instability

Qining Yang, Yongwei Zhou, Youjia Xu
2018 BMC Musculoskeletal Disorders  
The aim of this study was to determine the functional and radiological outcomes of arthroscopic treatment of anterior ankle impingement (
doi:10.1186/s12891-018-2168-6 pmid:30025527 pmcid:PMC6053762 fatcat:it36qhclonhdbfwppdjvnuyoxa

Associations between ERAP1 polymorphisms and susceptibility to ankylosing spondylitis

Yuqing Jiang, Yi Ren, Dong Zhou, Youjia Xu
2018 Medicine  
Data curation: Yi Ren, Dong Zhou, Youjia Xu. Formal analysis: Yuqing Jiang, Yi Ren, Dong Zhou. Figure 1 . 1 Search strategy flow diagram.  ... 
doi:10.1097/md.0000000000013263 pmid:30461632 pmcid:PMC6393156 fatcat:x3qc3yafsffqfkzoamotqjk5m4

Towards Zero Re-training for Long-term Hand Gesture Recognition via Ultrasound Sensing

Xingchen Yang, Dalin Zhou, Yu Zhou, Youjia Huang, Honghai Liu
2018 IEEE journal of biomedical and health informatics  
While myoelectric pattern recognition is a prevailing way for gesture recognition, the inherent nonstationarity of electromyography (sEMG) signals hinders its long-term application. This study aims to prove a hypothesis that morphological information of muscle contraction detected by ultrasound image is potentially suitable for long-term use. A set of ultrasoundbased algorithms are proposed to realize robust hand gesture recognition over multiple days, with user training only at the first day.
more » ... markerless calibration algorithm is first presented to position the ultrasound probe during donning and doffing; an algorithm combining speeded-up robust features (SURF) and bag-of-features (BoF) model being immune to ultrasound probe shift and rotation is then introduced; a self-enhancing classification method is next adopted to update classification model automatically by incorporating useful knowledge from testing data; finally the performance of long-term hand gesture recognition with zero re-training is validated by a six-day experiment of six healthy subjects, whose outcomes strongly support the hypothesis with about 94% of gesture recognition accuracy for each testing day. This study confirms the feasibility of adoption of ultrasound sensing for long-term musculature related applications.
doi:10.1109/jbhi.2018.2867539 pmid:30176612 fatcat:o46tmlhs5fb5xde6pgbvc6m73i

Bafilomycin A1 inhibits autophagy and induces apoptosis in MG63 osteosarcoma cells

ZONGGANG XIE, YE XIE, YOUJIA XU, HAIBIN ZHOU, WEI XU, QIRONG DONG
2014 Molecular Medicine Reports  
The purpose of the present study was to investigate the effects of bafilomycin A1 (BafA1) on proliferation, apoptosis and autophagy in MG63 osteosarcoma cells. The growth rate of MG63 cells was determined using a Cell Counting Kit-8 assay. The mitochondrial membrane potential (Δψ) was measured using a fluorescent probe, JC-1, and the inhibition of autophagy and apoptosis was monitored by transmission electron microscopy. In addition, the inhibition of autophagy was monitored by western blot
more » ... ysis of microtubule-associated protein 1 light chain 3 (LC3), and the ratio of LC3-II/LC3-I protein levels was calculated as an indicator of the extent of autophagy. Furthermore, the expression levels of specific proteins associated with autophagy, including p53, Beclin1 and p62, were detected in cultured MG63 cells by western blotting. It was shown that the viability of MG63 cells was inhibited following the use of BafA1, and an induction in the expression levels of the apoptosis-related protein p53 and the autophagic protein Beclin1 was detected. Furthermore, a collapse in Δψ was observed, together with an induction of apoptotic cell death, following treatment with BafA1. Therefore, following BafA1-mediated inhibition of autophagy, the inhibition of MG63 cell proliferation and induction of apoptosis were observed.
doi:10.3892/mmr.2014.2281 pmid:24890793 fatcat:z2qx7imuofamfd3n4jvckr67ya

Structure of Human Cytosolic X-prolyl Aminopeptidase

Xin Li, Zhiyong Lou, Xuemei Li, Weihong Zhou, Ming Ma, Youjia Cao, Yunqi Geng, Mark Bartlam, Xuejun C. Zhang, Zihe Rao
2008 Journal of Biological Chemistry  
X-prolyl aminopeptidases catalyze the removal of a penultimate prolyl residue from the N termini of peptides. Mammalian X-prolyl aminopeptidases are shown to be responsible for the degradation of bradykinin, a blood pressure regulator peptide, and have been linked to myocardial infarction. The x-ray crystal structure of human cytosolic X-prolyl aminopeptidase (XPN-PEP1) was solved at a resolution of 1.6 Å . The structure reveals a dimer with a unique three-domain organization in each subunit,
more » ... ther than the two domains common to all other known structures of X-prolyl aminopeptidase and prolidases. The C-terminal catalytic domain of XPNPEP1 coordinates two metal ions and shares a similar fold with other prolyl aminopeptidases. Metal content analysis and activity assays confirm that the enzyme is double Mn(II) dependent for its activity, which contrasts with the previous notion that each XPNPEP1 subunit contains only one Mn(II) ion. Activity assays on an E41A mutant demonstrate that the acidic residue, which was considered as a stabilizing factor in the protonation of catalytic residue His 498 , plays only a marginal role in catalysis. Further mutagenesis reveals the significance of the N-terminal domain and dimerization for the activity of XPNPEP1, and we provide putative structural explanations for their functional roles. Structural comparisons further suggest mechanisms for substrate selectivity in different X-prolyl peptidases. X-prolyl aminopeptidases (aminopeptidase P or AP-P; E.C. 3.4.11.9) are found in a variety of organisms including mammals, yeasts, and bacteria. There are two forms of mammalian AP-P in terms of their cellular locations: a cytosolic form (XPN-PEP1) and a membrane-bound form (XPNPEP2). Both forms can degrade bradykinin, a blood pressure-regulating peptide, and are inhibited by the specific peptide inhibitor apstatin (1-3). The cytosolic form of AP-P has been identified in human
doi:10.1074/jbc.m710274200 pmid:18515364 fatcat:2dkgphp7jne55hikwo257vnekm

Effectiveness of postural and instrumental reduction in the treatment of thoracolumbar vertebra fracture

Youjia Xu, Xiaozhong Zhou, Chun Yu, Maohua Cheng, Qirong Dong, Zhongming Qian
2007 International Orthopaedics  
We compared the effectiveness of postural reduction and instrumental reduction in the treatment of thoracolumbar and lumbar vertebra fracture in 40 patients. Under general anaesthesia, postural reduction in a stretching prone position was first performed. Instrumental reduction and fixation were then conducted. Radiographs were made after each reduction. Comparisons between the two films and the fracture films were made based on the changes in prevertebral height of both the fractured vertebra
more » ... nd the adjacent superior and inferior intervertebral spaces. It was found that the recovery of the prevertebral height in postural and instrumental reductions was basically identical. The recovery of the prevertebral height in the intervertebral spaces was more significant in instrumental reduction. Both reductions were ineffective in patients whose compression of the diseased vertebra was more than two-thirds of the normal. In cases of lower lumbar vertebra fractures, the effect of both reductions was unsatisfactory. Our findings indicated that the effectiveness of the reduction of vertebra fracture depends on the quantitative change of the spongy bone of the injured vertebra. Instrumental reduction only exerts an indirect tension. Postural reduction is effective in reducing thoracolumbar vertebral fracture, while instrumental reduction exerts only a relatively weak effect but it is particularly useful to maintain the result of postural reduction. Résumé Nous avons comparé le bénéfice de la réduction orthopédique et d'une instrumentation dans le traitement des fractures dorso-lombaires et lombaires chez 40 patients. Sous anesthésie générale une réduction posturale a été réalisée puis une instrumentation a été mise en place avec réduction et fixation. Des radiographies ont été réalisées après chaque temps de réduction. Des comparaisons avec mesure ont été réalisées sur chaque cliché vertébral. Cette étude nous a permis de montrer que l'amélioration de la hauteur vertébrale après réduction orthopédique ou réduction chirurgicale était identique par contre l'espace inter vertébral a été amélioré de façon significative après réduction chirurgicale. Ces deux réductions sont efficaces chez les patients présentant une telle pathologie par contre, lorsque la fracture est lombaire, les réductions se sont révélées inefficaces. Nous pouvons conclure que la réduction orthopédique est efficace et que la réduction chirurgicale a pour rôle de maintenir celle-ci.
doi:10.1007/s00264-007-0338-5 pmid:17333182 pmcid:PMC2323410 fatcat:6jnkggksb5gofamyet7giapxqq

Estrogen Induces Vav1 Expression in Human Breast Cancer Cells

Ming-juan Du, Xiang-dong Chen, Xiao-li Zhou, Ya-juan Wan, Bei Lan, Cui-zhu Zhang, Youjia Cao, Jun Li
2014 PLoS ONE  
Vav1, a guanine nucleotide exchange factor (GEF) for Rho family GTPases, is a hematopoietic protein involved in a variety of cellular events. In recent years, aberrant expression of Vav1 has been reported in non-hematopoietic cancers including human breast cancer. It remains to be answered how Vav1 is expressed and what Vav1 does in its non-resident tissues. In this study, we aimed to explore the mechanism for Vav1 expression in breast cancer cells in correlation with estrogen-ER pathway. We
more » ... only verified the ectopic expression of Vav1 in human breast cancer cell lines, but also observed that Vav1 expression was induced by 17b-estradiol (E 2 ), a typical estrogen receptor (ER) ligand, in ER-positive cell lines. On the other hand, Tamoxifen, a selective estrogen receptor modulator (SERM), and ICI 182,780, an ER antagonist, suppressed the expression of Vav1. The estrogen receptor modulating Vav1 expression was identified to be a form, not b. Furthermore, treatment of E 2 increased the transcription of vav1 gene by enhancing the promoter activity, though there was no recognizable estrogen response element (ERE). Nevertheless, two regions at the vav1 gene promoter were defined to be responsible for E 2 -induced activation of vav1 promoter. Chromatin immunoprecipitation (ChIP) and co-immunoprecipitation (Co-IP) analyses suggested that ERa might access to the vav1 promoter via interacting with transcription factors, c-Myb and ELF-1. Consequently, the enhanced expression of Vav1 led to the elevation of Cyclin D1 and the progression of cell cycle. The present study implies that estrogen-ER modulates the transcription and expression of Vav1, which may contribute to the proliferation of cancerous cells.
doi:10.1371/journal.pone.0099052 pmid:24905577 pmcid:PMC4048212 fatcat:7fsypjcj3ngifnijzi2hvxsrfi

Pheno-Mapper: An Interactive Toolbox for the Visual Exploration of Phenomics Data [article]

Youjia Zhou, Methun Kamruzzaman, Patrick Schnable, Bala Krishnamoorthy, Ananth Kalyanaraman, Bei Wang
2021 arXiv   pre-print
High-throughput technologies to collect field data have made observations possible at scale in several branches of life sciences. The data collected can range from the molecular level (genotypes) to physiological (phenotypic traits) and environmental observations (e.g., weather, soil conditions). These vast swathes of data, collectively referred to as phenomics data, represent a treasure trove of key scientific knowledge on the dynamics of the underlying biological system. However, extracting
more » ... formation and insights from these complex datasets remains a significant challenge owing to their multidimensionality and lack of prior knowledge about their complex structure. In this paper, we present Pheno-Mapper, an interactive toolbox for the exploratory analysis and visualization of large-scale phenomics data. Our approach uses the mapper framework to perform a topological analysis of the data, and subsequently render visual representations with built-in data analysis and machine learning capabilities. We demonstrate the utility of this new tool on real-world plant (e.g., maize) phenomics datasets. In comparison to existing approaches, the main advantage of Pheno-Mapper is that it provides rich, interactive capabilities in the exploratory analysis of phenomics data, and it integrates visual analytics with data analysis and machine learning in an easily extensible way. In particular, Pheno-Mapper allows the interactive selection of subpopulations guided by a topological summary of the data and applies data mining and machine learning to these selected subpopulations for in-depth exploration.
arXiv:2106.13397v2 fatcat:sej4lq4x4jhb7oov3si53frmqq

The effect of complicated febrile convulsion on hippocampal function and its antiepileptic treatment significance

Bin Li, Youjia Wu, Qingjuan He, Hui Zhou, Jin Cai
2021 Translational Pediatrics  
This study aimed to explore the effects of complex febrile seizures on hippocampal function and the significance of antiepileptic therapy. A total of 150 children with complex febrile seizures admitted to our hospital from July 2017 to July 2020 were included in the study. The VPA group was given sodium valproate treatment; the LEV group was given levetiracetam treatment; and the observation group was given basic treatment. The efficacy of the patients was evaluated after medication. A complex
more » ... ebrile seizure young mouse model was constructed, and the hippocampal cell morphology and BCL-2 expression of the mice pups were analyzed. A Morris water maze was used to detect the changes in cognitive function of the young mice with complex febrile seizures. After treatment, the recurrence-free rate of the VPA group was significantly higher than that of the observation group (P=0.0045). After 1 month and 6 months, the improvement rate of EEG in VPA group was significantly higher than that in observation group (P<0.05). After treatment, the levels of BCL-2 in the VPA group and the LEV group decreased and were significantly lower than the observation group during the same period (P<0.05), and the M/C of the two groups was significantly higher than the observation group (P<0.05). The neuronal cells in the hippocampus of the young rats in the VPA group and the LEV group were regular, the matrix was more uniform, and nuclear pyknotic cells were occasionally seen. The pathological changes were less obvious than the model group, followed by the degree of pathological changes (0.92±1.31, 0.94±1.24). The incubation period of pups in the model group was significantly higher than that of the normal group, VPA group, and LEV group (P<0.05), and the number of crossing the station area was significantly less than that of the normal group, VPA group, and LEV group (P<0.05). Antiepileptic drugs are effective in preventing the recurrence of complicated febrile seizures (CFS), and the main mechanism may be related to the targeted regulation of BCL-2 on the apoptosis of the hippocampus in the nervous system.
doi:10.21037/tp-20-458 pmid:33708526 pmcid:PMC7944171 fatcat:qb47cyw2gjekppurjuni5zbwvm

Arthroscopic Posterior Cruciate Ligament Reconstruction Using LARS Artificial Ligament: A Retrospective Study

Guangsi Shen, Youjia Xu, Qirong Dong, Haibin Zhou, Chen Yu
2012 Journal of Surgical Research  
Background. The aims of this study were to analyze the preliminary clinical effects of arthroscopic reconstruction of posterior cruciate ligament (PCL) using Ligament Advanced Reinforcement System (LARS) artificial ligament. It is hypothesized that LARS artificial ligament is a safe and effective choice for PCL reconstruction, providing good knee stability. Materials and Methods. Forty-one patients who underwent PCL reconstruction using LARS artificial ligament were enrolled in this
more » ... e study. Average age at time of surgery was 34 y (range, 23-57 y). Average time from injury to surgery was 15 d (range, 5-45 d). Average follow-up period was 44 mo (range, 36-54 months). Follow-up examinations included the Lysholm Knee Score and the International Knee Documentation Committee (IKDC) score. Results. The average Lysholm knee score was 64.9 ± 8.8 preoperatively (range, 47-75) versus 92.1 ± 3.3 three years after operation (range, 79-100). Thirty-six of 41 patients (88%) showed good or excellent results at final assessment. The final IKDC score at 3 y postoperatively rated as normal in 21 patients (51%), nearly normal in 17 patients (42%), abnormal in three patients (7%). Conclusions. The results shows that LARS artificial ligament appears to be an effective device for PCL reconstruction leading to good ligamentous stability and knee function. Long-term follow-up should be performed to confirm the durable stability of the knee and the tolerance of the knee to the LARS artificial ligament. Ó
doi:10.1016/j.jss.2010.08.015 pmid:20888585 fatcat:y57wajyvtjclbi5g6b3nfjrf2y

Ultrasound-Based Sensing Models for Finger Motion Classification

Youjia Huang, Xingchen Yang, Yuefeng Li, Dalin Zhou, Keshi He, Honghai Liu
2018 IEEE journal of biomedical and health informatics  
Motions of the fingers are complex since hand grasping and manipulation are conducted by spatial and temporal coordination of forearm muscles and tendons. The dominant methods based on surface electromyography (sEMG) could not offer satisfactory solutions for finger motion classification due to its inherent nature of measuring the electrical activity of motor units at the skin's surface. In order to recognize morphological changes of forearm muscles for accurate hand motion prediction,
more » ... d imaging is employed to investigate the feasibility of detecting mechanical deformation of deep muscle compartments in potential clinical applications. In this study, finger motion classification has been represented as subproblems: recognizing the discrete finger motions and predicting the continuous finger angles. Predefined 14 finger motions are presented in both sEMG signals and ultrasound images and captured simultaneously. Linear discriminant analysis classifier shows the ultrasound has better average accuracy (95.88%) than the sEMG (90.14%). On the other hand, the study of predicting the metacarpophalangeal (MCP) joint angle of each finger in non-period movements also confirms that classification method based on ultrasound achieves better results (average correlation 0.89 ± 0.07 and NRMSE 0.15 ± 0.05) than sEMG (0.81 ± 0.09 and 0.19 ± 0.05). The research outcomes evidently demonstrate that the ultrasound can be a feasible solution for muscle-driven machine interface, such as accurate finger motion control of prostheses and wearable robotic devices.
doi:10.1109/jbhi.2017.2766249 pmid:29990031 fatcat:ngspbbz7h5ashatlyup7rwfexa
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