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  1. Article ; Online: Counterfactual mobility network embedding reveals prevalent accessibility gaps in U.S. cities

    Yunke Zhang / Fengli Xu / Lin Chen / Yuan Yuan / James Evans / Luis Bettencourt / Yong Li

    Humanities & Social Sciences Communications, Vol 11, Iss 1, Pp 1-

    2024  Volume 12

    Abstract: Abstract Living in cities affords expanded access to various resources, infrastructures, and services at reduced travel costs, which improves social life and promotes systemic gains. However, recent research shows that urban dwellers also experience ... ...

    Abstract Abstract Living in cities affords expanded access to various resources, infrastructures, and services at reduced travel costs, which improves social life and promotes systemic gains. However, recent research shows that urban dwellers also experience inequality in accessing urban facilities, which manifests in distinct travel and visitation patterns for residents with different demographic backgrounds. Here, we go beyond simple flawed correlation analysis and reveal prevalent accessibility gaps by quantifying the causal effects of resident demographics on mobility patterns extracted from U.S. residents’ detailed interactions with millions of urban venues. Moreover, to efficiently reveal micro neighborhood-level accessibility gaps, we design a novel Counterfactual RANdom-walks-based Embedding (CRANE) method to learn continuous embedding vectors on urban mobility networks with confounding effects disentangled. Our analysis reveals significant income and racial gaps in mobility frequency and visitation rates to sports and education venues. Besides, bachelor’s degree holders experience greater mobility reduction during the COVID-19 crisis. With extensive experiments on neighborhood-level accessibility prediction and visualizing accessibility gaps with embeddings vectors, we demonstrate that the counterfactual mobility network embeddings can improve the explanatory capacity and robustness of revealed accessibility gaps by extending them from aggregate statistics to individual neighborhoods and allowing for cross-city knowledge transfer. As such, urban mobility networks can reveal consistent accessibility gaps in the U.S., calling for urgent urban design policies to fill in the gaps.
    Keywords History of scholarship and learning. The humanities ; AZ20-999 ; Social Sciences ; H
    Subject code 380
    Language English
    Publishing date 2024-01-01T00:00:00Z
    Publisher Springer Nature
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  2. Article: The mechanism of oxytocin and its receptors in regulating cells in bone metabolism.

    Feixiang, Liu / Yanchen, Feng / Xiang, Li / Yunke, Zhang / Jinxin, Miao / Jianru, Wang / Zixuan, Lin

    Frontiers in pharmacology

    2023  Volume 14, Page(s) 1171732

    Abstract: Oxytocin (OT) is a neuropeptide known to affect social behavior and cognition. The epigenetic modification of the oxytocin receptor (OTR) via DNA methylation stimulates parturition and breast milk secretion and inhibits craniopharyngioma, breast cancer, ... ...

    Abstract Oxytocin (OT) is a neuropeptide known to affect social behavior and cognition. The epigenetic modification of the oxytocin receptor (OTR) via DNA methylation stimulates parturition and breast milk secretion and inhibits craniopharyngioma, breast cancer, and ovarian cancer growth significantly as well as directly regulates bone metabolism in their peripheral form rather than the central form. OT and OTR can be expressed on bone marrow mesenchymal stem cells (BMSCs), osteoblasts (OB), osteoclasts (OC), osteocytes, chondrocytes, and adipocytes. OB can synthesize OT under the stimulation of estrogen as a paracrine-autocrine regulator for bone formation. OT/OTR, estrogen, and OB form a feed-forward loop through estrogen mediation. The osteoclastogenesis inhibitory factor (OPG)/receptor activator of the nuclear factor kappa-B ligand (RANKL) signaling pathway is crucially required for OT and OTR to exert anti-osteoporosis effect. Downregulating the expression of bone resorption markers and upregulating the expression of the bone morphogenetic protein, OT could increase BMSC activity and promote OB differentiation instead of adipocytes. It could also stimulate the mineralization of OB by motivating OTR translocation into the OB nucleus. Moreover, by inducing intracytoplasmic Ca
    Language English
    Publishing date 2023-05-09
    Publishing country Switzerland
    Document type Journal Article ; Review
    ZDB-ID 2587355-6
    ISSN 1663-9812
    ISSN 1663-9812
    DOI 10.3389/fphar.2023.1171732
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  3. Article ; Online: Erroneous pixel prediction for semantic image segmentation

    Lixue Gong / Yiqun Zhang / Yunke Zhang / Yin Yang / Weiwei Xu

    Computational Visual Media, Vol 8, Iss 1, Pp 165-

    2021  Volume 175

    Abstract: Abstract We consider semantic image segmentation. Our method is inspired by Bayesian deep learning which improves image segmentation accuracy by modeling the uncertainty of the network output. In contrast to uncertainty, our method directly learns to ... ...

    Abstract Abstract We consider semantic image segmentation. Our method is inspired by Bayesian deep learning which improves image segmentation accuracy by modeling the uncertainty of the network output. In contrast to uncertainty, our method directly learns to predict the erroneous pixels of a segmentation network, which is modeled as a binary classification problem. It can speed up training comparing to the Monte Carlo integration often used in Bayesian deep learning. It also allows us to train a branch to correct the labels of erroneous pixels. Our method consists of three stages: (i) predict pixel-wise error probability of the initial result, (ii) redetermine new labels for pixels with high error probability, and (iii) fuse the initial result and the redetermined result with respect to the error probability. We formulate the error-pixel prediction problem as a classification task and employ an error-prediction branch in the network to predict pixel-wise error probabilities. We also introduce a detail branch to focus the training process on the erroneous pixels. We have experimentally validated our method on the Cityscapes and ADE20K datasets. Our model can be easily added to various advanced segmentation networks to improve their performance. Taking DeepLabv3+ as an example, our network can achieve 82.88% of mIoU on Cityscapes testing dataset and 45.73% on ADE20K validation dataset, improving corresponding DeepLabv3+ results by 0.74% and 0.13% respectively.
    Keywords erroneous pixel prediction ; image segmentation ; deep learning ; Electronic computers. Computer science ; QA75.5-76.95
    Subject code 006
    Language English
    Publishing date 2021-10-01T00:00:00Z
    Publisher SpringerOpen
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  4. Article ; Online: A Satellite Imagery Dataset for Long-Term Sustainable Development in United States Cities

    Yanxin Xi / Yu Liu / Tong Li / Jintao Ding / Yunke Zhang / Sasu Tarkoma / Yong Li / Pan Hui

    Scientific Data, Vol 10, Iss 1, Pp 1-

    2023  Volume 15

    Abstract: Abstract Cities play an important role in achieving sustainable development goals (SDGs) to promote economic growth and meet social needs. Especially satellite imagery is a potential data source for studying sustainable urban development. However, a ... ...

    Abstract Abstract Cities play an important role in achieving sustainable development goals (SDGs) to promote economic growth and meet social needs. Especially satellite imagery is a potential data source for studying sustainable urban development. However, a comprehensive dataset in the United States (U.S.) covering multiple cities, multiple years, multiple scales, and multiple indicators for SDG monitoring is lacking. To support the research on SDGs in U.S. cities, we develop a satellite imagery dataset using deep learning models for five SDGs containing 25 sustainable development indicators. The proposed dataset covers the 100 most populated U.S. cities and corresponding Census Block Groups from 2014 to 2023. Specifically, we collect satellite imagery and identify objects with state-of-the-art object detection and semantic segmentation models to observe cities’ bird’s-eye view. We further gather population, nighttime light, survey, and built environment data to depict SDGs regarding poverty, health, education, inequality, and living environment. We anticipate the dataset to help urban policymakers and researchers to advance SDGs-related studies, especially applying satellite imagery to monitor long-term and multi-scale SDGs in cities.
    Keywords Science ; Q
    Language English
    Publishing date 2023-12-01T00:00:00Z
    Publisher Nature Portfolio
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  5. Article ; Online: MBOVPG45_0375 Encodes an IgG-Binding Protein and MBOVPG45_0376 Encodes an IgG-Cleaving Protein in Mycoplasma bovis

    Haoran Zhao / Yunke Zhang / Zhanhui Wang / Mengyao Liu / Pengpeng Wang / Wenxue Wu / Chen Peng

    Frontiers in Veterinary Science, Vol

    2021  Volume 8

    Abstract: Mycoplasma bovis is a significant bacterial pathogen which is able to persist in cattle and cause chronic diseases. This phenomenon may relate to M. bovis evading the immune system of the host. Immunoglobulin-binding proteins are widely distributed in a ... ...

    Abstract Mycoplasma bovis is a significant bacterial pathogen which is able to persist in cattle and cause chronic diseases. This phenomenon may relate to M. bovis evading the immune system of the host. Immunoglobulin-binding proteins are widely distributed in a variety of pathogenic bacteria, including some Mycoplasma species. These proteins are considered to help the bacteria evade the immune response of the host. Here we found M. bovis strain PG45 can bind to IgG from several animals. MBOVPG45_0375 encodes a putative membrane protein, has strong amino acid sequence similarity with Immunoglobulin G-binding protein in Mycoplasma mycoides subsp. capri. Hence, we constructed recombinant MBOVPG45_0375 (r0375) in the Escherichia coli expression system and demonstrated that r0375 can bind to IgG non-immunologically rather than specific binding similar to interaction of antigen and antibody. Moreover, r0375 can bind to the Fab fragment of IgG. Also, the binding of r0375 and IgG inhibits the formation of antigen-antibody union. Furthermore, MBOVPG45_0376 encodes an IgG-cleaving protein of M. bovis strain PG45. Nevertheless, r0375 binding to IgG is required for the cleavage activity of recombinant 0376 (r0376). The activity of r0376 is also affected by incubation time and temperature. In addition, we found both MBOVPG45_0375 and MBOVPG45_0376 are membrane proteins of M. bovis strain PG45. These results about MBOVPG45_0375 as an IgG-binding protein and MBOVPG45_0376 as an IgG-cleaving protein offer a new insight into the interaction between M. bovis and its host.
    Keywords Mycoplasma bovis ; MBOVPG45_0375 ; MBOVPG45_0376 ; IgG-binding protein ; IgG-cleaving protein ; membrane protein ; Veterinary medicine ; SF600-1100
    Subject code 570
    Language English
    Publishing date 2021-04-01T00:00:00Z
    Publisher Frontiers Media S.A.
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  6. Article ; Online: Induction of Robust and Specific Humoral and Cellular Immune Responses by Bovine Viral Diarrhea Virus Virus-Like Particles (BVDV-VLPs) Engineered with Baculovirus Expression Vector System

    Zhanhui Wang / Mengyao Liu / Haoran Zhao / Pengpeng Wang / Wenge Ma / Yunke Zhang / Wenxue Wu / Chen Peng

    Vaccines, Vol 9, Iss 350, p

    2021  Volume 350

    Abstract: Bovine viral diarrhea virus (BVDV) is an important animal pathogen that affects cattle. Infections caused by the virus have resulted in substantial economic losses and outbreaks of BVDV are reported globally. Virus-like particles (VLPs) are promising ... ...

    Abstract Bovine viral diarrhea virus (BVDV) is an important animal pathogen that affects cattle. Infections caused by the virus have resulted in substantial economic losses and outbreaks of BVDV are reported globally. Virus-like particles (VLPs) are promising vaccine technology largely due to their safety and strong ability to elicit robust immune responses. In this study, we developed a strategy to generate BVDV-VLPs using a baculovirus expression vector system (BEVS). We were able to assemble BVDV-VLPs composed of dimerized viral proteins E2 and E rns , and the VLPs were spherical particles with the diameters of about 50 nm. Mice immunized with 15 μg of VLPs adjuvanted with ISA201 elicited higher levels of E2-specific IgG, IgG1, and IgG2a antibodies as well as higher BVDV-neutralizing activity in comparison with controls. Re-stimulation of the splenocytes collected from mice immunized with VLPs led to significantly increased levels of CD3 + CD4 + T cells and CD3 + CD8 + T cells. In addition, the splenocytes showed dramatically enhanced proliferation and the secretion of Th1-associated IFN-γ and Th2-associated IL-4 compared to that of the unstimulated control group. Taken together, our data indicate that BVDV-VLPs efficiently induced BVDV-specific humoral and cellular immune responses in mice, showing a promising potential of developing BVDV-VLP-based vaccines for the prevention of BVDV infections.
    Keywords bovine viral diarrhea virus ; virus-like particles ; baculovirus expression vector system ; E rns ; E2 ; vaccine ; Medicine ; R
    Subject code 333
    Language English
    Publishing date 2021-04-01T00:00:00Z
    Publisher MDPI AG
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  7. Article ; Online: Prognostic and clinicopathological value of GATA binding protein 3 in breast cancer

    Yawen Guo / Pan Yu / Zeming Liu / Yusufu Maimaiti / Chen Chen / Yunke Zhang / Xingjie Yin / Shan Wang / Chunping Liu / Tao Huang

    PLoS ONE, Vol 12, Iss 4, p e

    A systematic review and meta-analysis.

    2017  Volume 0174843

    Abstract: The potential prognostic value of GATA binding protein 3 (GATA3) in breast cancer has recently increased, although the evidence is inconclusive. This meta-analysis of 10 articles involving 5,080 breast cancer patients explored the prognostic and ... ...

    Abstract The potential prognostic value of GATA binding protein 3 (GATA3) in breast cancer has recently increased, although the evidence is inconclusive. This meta-analysis of 10 articles involving 5,080 breast cancer patients explored the prognostic and clinicopathological value of GATA3 in breast cancer. Time to tumor progression (TTP) and overall survival (OS) were primary endpoints. Pooled hazard ratio (HR), pooled risk ratio (RR), and 95% confidence interval (CI) were calculated to evaluate the association between GATA3, prognosis, and clinicopathological parameters. High GATA3 expression predicts breast cancer, with a HR (HR = 0.671; 95% CI = 0.475-0.947; P = 0.023) of TTP, but is not associated with OS (HR = 0.889; 95% CI = 0.789-1.001; P = 0.052). GATA3 overexpression is associated with positive ER (RR = 3.155; 95% CI = 1.680-5.923; P = 0.000), positive PR (RR = 3.949; 95% CI = 1.567-9.954, P = 0.004), lower nuclear grade (RR = 0.435; 95% CI = 0.369-0.514; P = 0.000), and smaller tumor size (RR = 0.816; 95% CI = 0.709-0.940; P = 0.005). High GATA3 expression may predict TTP in breast cancer, and such patients may show better clinicopathological features.
    Keywords Medicine ; R ; Science ; Q
    Subject code 616 ; 610
    Language English
    Publishing date 2017-01-01T00:00:00Z
    Publisher Public Library of Science (PLoS)
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  8. Article ; Online: iTRAQ-Based Proteomics Analysis of Plasma of Myasthenia Gravis Patients Treated with Jia Wei Bu Zhong Yi Qi Decoction

    Yunke Zhang / Junhong Yang / Yingzhe Chen / Jie Lv / Jing Zhang / Yingna Zhang / Xue Zhao / Hua Fang / Chongchong Liu / Qingyong Zhang / Xinzheng Cui / Xiaohan Wang / Feng Gao

    Evidence-Based Complementary and Alternative Medicine, Vol

    2019  Volume 2019

    Abstract: Myasthenia gravis (MG) is an autoimmune disease. A proportion of MG patients did not get satisfactory results after treatment with pyridostigmine and prednisone. Jia Wei Bu Zhong Yi Qi (Jia Wei BZYQ) decoction, a water extract from multiple herbs, has ... ...

    Abstract Myasthenia gravis (MG) is an autoimmune disease. A proportion of MG patients did not get satisfactory results after treatment with pyridostigmine and prednisone. Jia Wei Bu Zhong Yi Qi (Jia Wei BZYQ) decoction, a water extract from multiple herbs, has been demonstrated to be effective in the treatment of multiple “Qi deficiency type” diseases including MG in China. In this text, we investigated protein alterations in the plasma from healthy volunteers (C), MG patients without any treatment (T1), MG patients with routine western medical treatment (T2), and MG patients with combined treatments of Jia Wei BZYQ decoction and routine western medicines (T3) and identified some potential proteins involved in the pathogenesis and treatment of MG. iTRAQ (isobaric tags for relative and absolute quantitation) and 2D-LC-MS/MS (two-dimensional liquid chromatography-tandem mass spectrometry technologies) were employed to screen differentially expressed proteins. The identification, quantification, functional annotation, and interaction of proteins were analyzed by matching software and databases. In our project, 618 proteins were identified, among which 447 proteins had quantitative data. The number of differentially expressed proteins was 110, 117, 143, 115, 86, and 158 in T1 vs. C, T2 vs. C, T2 vs. T1, T3 vs. C, T3 vs. T1, and T3 vs. T2 groups, respectively. Functional annotation results showed that many differentially expressed proteins were closely associated with immune responses. For instance, some key proteins such as C-reactive protein, apolipoprotein C-III, apolipoprotein A-II, alpha-actinin-1, and thrombospondin-1 have been found to be abnormally expressed in T3 group compared to T1 group or T2 group. Interaction network analyses also provided some potential biomarkers or targets for MG management.
    Keywords Other systems of medicine ; RZ201-999
    Subject code 610
    Language English
    Publishing date 2019-01-01T00:00:00Z
    Publisher Hindawi Limited
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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