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  1. Article ; Online: Population characteristic exploitation-based multi-orientation multi-objective gene selection for microarray data classification.

    Li, Min / Cao, Rutun / Zhao, Yangfan / Li, Yulong / Deng, Shaobo

    Computers in biology and medicine

    2024  Volume 170, Page(s) 108089

    Abstract: Gene selection is a process of selecting discriminative genes from microarray data that helps to diagnose and classify cancer samples effectively. Swarm intelligence evolution-based gene selection algorithms can never circumvent the problem that the ... ...

    Abstract Gene selection is a process of selecting discriminative genes from microarray data that helps to diagnose and classify cancer samples effectively. Swarm intelligence evolution-based gene selection algorithms can never circumvent the problem that the population is prone to local optima in the process of gene selection. To tackle this challenge, previous research has focused primarily on two aspects: mitigating premature convergence to local optima and escaping from local optima. In contrast to these strategies, this paper introduces a novel perspective by adopting reverse thinking, where the issue of local optima is seen as an opportunity rather than an obstacle. Building on this foundation, we propose MOMOGS-PCE, a novel gene selection approach that effectively exploits the advantageous characteristics of populations trapped in local optima to uncover global optimal solutions. Specifically, MOMOGS-PCE employs a novel population initialization strategy, which involves the initialization of multiple populations that explore diverse orientations to foster distinct population characteristics. The subsequent step involved the utilization of an enhanced NSGA-II algorithm to amplify the advantageous characteristics exhibited by the population. Finally, a novel exchange strategy is proposed to facilitate the transfer of characteristics between populations that have reached near maturity in evolution, thereby promoting further population evolution and enhancing the search for more optimal gene subsets. The experimental results demonstrated that MOMOGS-PCE exhibited significant advantages in comprehensive indicators compared with six competitive multi-objective gene selection algorithms. It is confirmed that the "reverse-thinking" approach not only avoids local optima but also leverages it to uncover superior gene subsets for cancer diagnosis.
    MeSH term(s) Humans ; Algorithms ; Neoplasms/diagnosis ; Neoplasms/genetics ; Oligonucleotide Array Sequence Analysis/methods
    Language English
    Publishing date 2024-02-02
    Publishing country United States
    Document type Journal Article
    ZDB-ID 127557-4
    ISSN 1879-0534 ; 0010-4825
    ISSN (online) 1879-0534
    ISSN 0010-4825
    DOI 10.1016/j.compbiomed.2024.108089
    Database MEDical Literature Analysis and Retrieval System OnLINE

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    In stock of ZB MED Cologne/Königswinter

    Zs.A 653: Show issues Location:
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  2. Article: Lipid-lowering drug targets and Parkinson's disease: A sex-specific Mendelian randomization study.

    Zhao, Yangfan / Gagliano Taliun, Sarah A

    Frontiers in neurology

    2022  Volume 13, Page(s) 940118

    Abstract: Parkinson's disease (PD) affects millions of individuals worldwide, and it is the second most common late-onset neurodegenerative disorder. There is no cure and current treatments only alleviate symptoms. Modifiable risk factors have been explored as ... ...

    Abstract Parkinson's disease (PD) affects millions of individuals worldwide, and it is the second most common late-onset neurodegenerative disorder. There is no cure and current treatments only alleviate symptoms. Modifiable risk factors have been explored as possible options for decreasing risk or developing drug targets to treat PD, including low-density lipoprotein cholesterol (LDL-C). There is evidence of sex differences for cholesterol levels as well as for PD risk. Genetic datasets of increasing size are permitting association analyses with increased power, including sex-stratified analyses. These association results empower Mendelian randomization (MR) studies, which, given certain assumptions, test whether there is a causal relationship between the risk factor and the outcome using genetic instruments. Sex-specific causal inference approaches could highlight sex-specific effects that may otherwise be masked by sex-agnostic approaches. We conducted a sex-specific two-sample cis-MR analysis based on genetic variants in LDL-C target encoding genes to assess the impact of lipid-lowering drug targets on PD risk. To complement the cis-MR analysis, we also conducted a sex-specific standard MR analysis (using genome-wide independent variants). We did not find evidence of a causal relationship between LDL-C levels and PD risk in females [OR (95% CI) = 1.01 (0.60, 1.69), IVW random-effects] or males [OR (95% CI) = 0.93 (0.55, 1.56)]. The sex-specific standard MR analysis also supported this conclusion. We encourage future work assessing sex-specific effects using causal inference techniques to better understand factors that may contribute to complex disease risk differently between the sexes.
    Language English
    Publishing date 2022-09-01
    Publishing country Switzerland
    Document type Journal Article
    ZDB-ID 2564214-5
    ISSN 1664-2295
    ISSN 1664-2295
    DOI 10.3389/fneur.2022.940118
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  3. Article: Prevalence and Impact of BK Polyomavirus in the Ureters of Kidney Donors: Research Letter.

    Sarah-Jane, Chagnon / Zhao, Yangfan / Bruno, Lamontagne / Virginie, Royal / Caroline, Lamarche

    Canadian journal of kidney health and disease

    2023  Volume 10, Page(s) 20543581231166478

    Abstract: Background: More than 75% of the population is seropositive for BK polyomavirus (BKV), which remains quiescent in the urothelium in immunocompetent hosts. However, it can reactivate in kidney transplant recipients (KTRs), and up to 30% of them will ... ...

    Abstract Background: More than 75% of the population is seropositive for BK polyomavirus (BKV), which remains quiescent in the urothelium in immunocompetent hosts. However, it can reactivate in kidney transplant recipients (KTRs), and up to 30% of them will develop BKV viremia in the 2 years following transplant, with a risk of developing BKV-associated nephropathy (BKVAN). Viral reactivation is associated with the level of immunosuppression, but there is currently no way to predict which patients are at high risk for reactivation.
    Objective: As BKV originates from kidney donors, our primary objective was to determine the prevalence of detectable BKV in donor ureters. Our secondary objective was to see if there is a correlation between the presence of BKV in donor urothelium and the development of BKV viremia and BKVAN in KTR.
    Design: Prospective cohort study.
    Setting: Single-center academic kidney transplant program.
    Patients: Prospective sequential KTRs that received a kidney transplant between March 2016 and March 2017.
    Measurements: The presence of BKV in donor ureters was determined by TaqMan-based quantitative polymerase chain reaction (PCR; qPCR).
    Methods: We performed a prospective study which was done on 35 out of the 100 donors initially foreseen to take part in the study. During surgery, the distal part of donor ureter was kept and analyzed by qPCR (to establish the presence of BKV in the urothelium). The primary outcome was the development of BKV viremia in KTR over a period of 2 years after transplant. Secondary outcome was the development of BKVAN.
    Results: Out of 35 ureters analyzed, only one had a positive qPCR for BKV (2.86%, 95% confidence interval [CI]: [0.07-14.92]). Considering the primary objective would not be met, the study was interrupted after 35 specimens. After surgery, 9 recipients had a slow graft function and 4 had delayed graft function, one of which never recovered graft function. Over the 2-year follow-up, 13 patients developed BKV viremia, while 5 patients developed BKVAN. The patient who received a graft from a positive qPCR donor eventually developed BKV viremia and nephropathy.
    Limitations: The specimen analyzed was a distal rather than a proximal portion of the ureter. However, BKV replication is known to concentrate in the corticomedullary junction.
    Conclusion: BK polyomavirus prevalence in the distal part of donor ureters is lower than previously reported. It cannot be used as a predictor for the development of BKV reactivation and/or nephropathy.
    Language English
    Publishing date 2023-04-10
    Publishing country England
    Document type Journal Article
    ZDB-ID 2765462-X
    ISSN 2054-3581
    ISSN 2054-3581
    DOI 10.1177/20543581231166478
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  4. Article: Multi-object tracking using Deep SORT and modified CenterNet in cotton seedling counting

    Yang, Hao / Chang, Fangle / Huang, Yuhang / Xu, Ming / Zhao, Yangfan / Ma, Longhua / Su, Hongye

    Computers and electronics in agriculture. 2022 Nov., v. 202

    2022  

    Abstract: Accurate plant density information is important for crop yield and quality. In general, human has to estimate plant density either in field or with accessory equipment, which is time-consuming and inaccurate. In this work, multi-object tracking method ... ...

    Abstract Accurate plant density information is important for crop yield and quality. In general, human has to estimate plant density either in field or with accessory equipment, which is time-consuming and inaccurate. In this work, multi-object tracking method based on tracking-by-detection strategy was developed to automatically count cotton seedlings. Videos were collected 0.5 m above cotton seedlings, and analyzed to train object detection model and evaluate counting accuracy with a separate dataset (TAMU2015-ID). An advanced anchor-free object detection model was developed using CenterNet to detect cotton seedling and extract its identity embedding. The localization and identity information were fused based on Deep SORT for data association. The object detection model outperformed Faster R-CNN model with an F₁ score of 0.982 (IOU0.5) and 0.937 (IOU0.8), and an average precision of 0.9901 (IOU0.5) and 0.8998 (IOU0.8). The counting results were fitted to ground truth with a R² of 0.967 and RMSE of 0.394. We evaluated the method on TAMU2015-ID to get a R² of 0.99 and RMSE of 0.8.
    Keywords agriculture ; cotton ; crop yield ; data collection ; electronics ; equipment ; humans ; models ; plant density ; seedlings
    Language English
    Dates of publication 2022-11
    Publishing place Elsevier B.V.
    Document type Article
    ZDB-ID 395514-x
    ISSN 0168-1699
    ISSN 0168-1699
    DOI 10.1016/j.compag.2022.107339
    Database NAL-Catalogue (AGRICOLA)

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    In stock of ZB MED Bonn / Germany

    Z 4541: Show issues

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  5. Article ; Online: Retaining event files in working memory requires extra object-based attention than the constituent elements.

    Lu, Xiqian / Ma, Xiaochi / Zhao, Yangfan / Gao, Zaifeng / Shen, Mowei

    Quarterly journal of experimental psychology (2006)

    2019  Volume 72, Issue 9, Page(s) 2225–2239

    Abstract: Retaining events containing action-related information in working memory (WM) is vital to daily activities such as action planning and social interaction. During processing of such events, action-related information is bound with other visual elements (e. ...

    Abstract Retaining events containing action-related information in working memory (WM) is vital to daily activities such as action planning and social interaction. During processing of such events, action-related information is bound with other visual elements (e.g., colours) as event files. In this study, we explored whether retaining event files in WM consumes more attention than retaining the constituent elements. Considering that object-based attention underlies the rehearsal of static feature bindings in WM, we hypothesised that object-based attention played a key role in retaining event files in WM. As biological motion (BM) is one of the most frequently observed events in daily life, we employed BM-related event files as the tested stimuli. In separate blocks, we required participants to memorise BM, colours (or locations), or the binding between these elements (i.e., event files). Critically, we added an object-feature report task, which consumed object-based attention, during the WM maintenance phase. We predicted that the added secondary task would lead to larger impairment for BM event files than for the constituent elements. In line with this prediction, Experiments 1 and 2 consistently revealed a selective impairment to BM event files, which could not be attributed to an unbalanced number of elements between memory conditions (Experiment 3), or to the visual processing of a secondary task (Experiment 4). Taken together, these results suggest that object-based attention plays a pivotal role in maintaining event files in WM.
    MeSH term(s) Adult ; Attention/physiology ; Executive Function/physiology ; Female ; Humans ; Male ; Memory, Short-Term/physiology ; Motion Perception/physiology ; Visual Perception/physiology ; Young Adult
    Language English
    Publishing date 2019-04-04
    Publishing country England
    Document type Journal Article
    ZDB-ID 219170-2
    ISSN 1747-0226 ; 0033-555X ; 1747-0218
    ISSN (online) 1747-0226
    ISSN 0033-555X ; 1747-0218
    DOI 10.1177/1747021819839993
    Database MEDical Literature Analysis and Retrieval System OnLINE

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    In stock of ZB MED Cologne/Königswinter

    Zs.B 1109: Show issues Location:
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  6. Article ; Online: Binding biological motion and visual features in working memory.

    Ding, Xiaowei / Zhao, Yangfan / Wu, Fan / Lu, Xiqian / Gao, Zaifeng / Shen, Mowei

    Journal of experimental psychology. Human perception and performance

    2015  Volume 41, Issue 3, Page(s) 850–865

    Abstract: Working memory mechanisms for binding have been examined extensively in the last decade, yet few studies have explored bindings relating to human biological motion (BM). Human BM is the most salient and biologically significant kinetic information ... ...

    Abstract Working memory mechanisms for binding have been examined extensively in the last decade, yet few studies have explored bindings relating to human biological motion (BM). Human BM is the most salient and biologically significant kinetic information encountered in everyday life and is stored independently from other visual features (e.g., colors). The current study explored 3 critical issues of BM-related binding in working memory: (a) how many BM binding units can be retained in working memory, (b) whether involuntarily object-based binding occurs during BM binding, and (c) whether the maintenance of BM bindings in working memory requires attention above and beyond that needed to maintain the constituent dimensions. We isolated motion signals of human BM from non-BM sources by using point-light displays as to-be-memorized BM and presented the participants colored BM in a change detection task. We found that working memory capacity for BM-color bindings is rather low; only 1 or 2 BM-color bindings could be retained in working memory regardless of the presentation manners (Experiments 1-3). Furthermore, no object-based encoding took place for colored BM stimuli regardless of the processed dimensions (Experiments 4 and 5). Central executive attention contributes to the maintenance of BM-color bindings, yet maintaining BM bindings in working memory did not require more central attention than did maintaining the constituent dimensions in working memory (Experiment 6). Overall, these results suggest that keeping BM bindings in working memory is a fairly resource-demanding process, yet central executive attention does not play a special role in this cross-module binding.
    MeSH term(s) Adolescent ; Adult ; Attention ; Color Perception ; Female ; Humans ; Male ; Memory, Short-Term ; Models, Psychological ; Motion Perception ; Photic Stimulation ; Reaction Time ; Task Performance and Analysis ; Visual Perception ; Young Adult
    Language English
    Publishing date 2015-06
    Publishing country United States
    Document type Journal Article ; Research Support, Non-U.S. Gov't
    ZDB-ID 189734-2
    ISSN 1939-1277 ; 0096-1523
    ISSN (online) 1939-1277
    ISSN 0096-1523
    DOI 10.1037/xhp0000061
    Database MEDical Literature Analysis and Retrieval System OnLINE

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