Vertex-Ball Spring Smoothing: An efficient method for unstructured dynamic hybrid meshes

postprin

AFLP analysis on genetic diversity and population structure of small yellow croaker Larimichthys polyactis

The population genetic structure and diversity of small yellow croaker Larimichthys polyactis in the Bohai Bay, Yellow Sea and East China Sea were analyzed using amplified fragment length polymorphism(AFLP). Ninety-one individuals were collected from six locations representing three stocks of small yellow croaker. A total of 218 putative loci were detected by 3 primer combinations, 148 of which were polymorphic (67.89%). The proportion of polymorphic loci and Nei’s genetic diversity for six populations ranged from 55.34 - 60.09%, and from 0.1244 - 0.1378. AMOVA analysis and pairwise FST revealedsignificant genetic differentiation among the three groups based on the breeding migration routes and over-wintering grounds, supporting separate stocks in this species. The result shows the migratorybehavior might be an important factor which influences the genetic structure of this species. The UPGMA tree also revealed the significant geographic structure in this species. Pattern of isolation bydistance was observed in this species, indicating that significant genetic differentiation among localities of small yellow croaker might be due to the geographic distance

Many-shot from Low-shot: Learning to Annotate using Mixed Supervision for Object Detection

Object detection has witnessed significant progress by relying on large, manually annotated datasets. Annotating such datasets is highly time consuming and expensive, which motivates the development of weakly supervised and few-shot object detection methods. However, these methods largely underperform with respect to their strongly supervised counterpart, as weak training signals \emph{often} result in partial or oversized detections. Towards solving this problem we introduce, for the first time, an online annotation module (OAM) that learns to generate a many-shot set of \emph{reliable} annotations from a larger volume of weakly labelled images. Our OAM can be jointly trained with any fully supervised two-stage object detection method, providing additional training annotations on the fly. This results in a fully end-to-end strategy that only requires a low-shot set of fully annotated images. The integration of the OAM with Fast(er) R-CNN improves their performance by $17\%$ mAP, $9\%$ AP50 on PASCAL VOC 2007 and MS-COCO benchmarks, and significantly outperforms competing methods using mixed supervision.Comment: Accepted at ECCV 2020. Camera-ready version and Appendice

Analysis of Kif5b Expression during Mouse Kidney Development

published_or_final_versio

Human papillomavirus status in southern Chinese women

1. The overall and type-specific human papillomavirus (HPV) prevalence differed between Hong Kong and Guangzhou healthy women. The prevalence of HPV was significantly higher in Guangzhou than Hong Kong women. Younger women had significantly higher risk of HPV infection. 2. HPV16 remained the most common type detected in both regions; the frequency increased with increasing disease severity. The prevalence of HPV58 and HPV52 was relatively high in women with normal cervix and precancerous lesions.published_or_final_versio

Protein 3D Graph Structure Learning for Robust Structure-based Protein Property Prediction

Protein structure-based property prediction has emerged as a promising approach for various biological tasks, such as protein function prediction and sub-cellular location estimation. The existing methods highly rely on experimental protein structure data and fail in scenarios where these data are unavailable. Predicted protein structures from AI tools (e.g., AlphaFold2) were utilized as alternatives. However, we observed that current practices, which simply employ accurately predicted structures during inference, suffer from notable degradation in prediction accuracy. While similar phenomena have been extensively studied in general fields (e.g., Computer Vision) as model robustness, their impact on protein property prediction remains unexplored. In this paper, we first investigate the reason behind the performance decrease when utilizing predicted structures, attributing it to the structure embedding bias from the perspective of structure representation learning. To study this problem, we identify a Protein 3D Graph Structure Learning Problem for Robust Protein Property Prediction (PGSL-RP3), collect benchmark datasets, and present a protein Structure embedding Alignment Optimization framework (SAO) to mitigate the problem of structure embedding bias between the predicted and experimental protein structures. Extensive experiments have shown that our framework is model-agnostic and effective in improving the property prediction of both predicted structures and experimental structures. The benchmark datasets and codes will be released to benefit the community

Celecoxib exerts protective effects in the vascular endothelium via COX-2-independent activation of AMPK-CREB-Nrf2 signalling

Although concern remains about the athero-thrombotic risk posed by cyclo-oxygenase (COX)-2-selective inhibitors, recent data implicates rofecoxib, while celecoxib appears equivalent to NSAIDs naproxen and ibuprofen. We investigated the hypothesis that celecoxib activates AMP kinase (AMPK) signalling to enhance vascular endothelial protection. In human arterial and venous endothelial cells (EC), and in contrast to ibuprofen and naproxen, celecoxib induced the protective protein heme oxygenase-1 (HO-1). Celecoxib derivative 2,5-dimethyl-celecoxib (DMC) which lacks COX-2 inhibition also upregulated HO-1, implicating a COX-2-independent mechanism. Celecoxib activated AMPKα(Thr172) and CREB-1(Ser133) phosphorylation leading to Nrf2 nuclear translocation. Importantly, these responses were not reproduced by ibuprofen or naproxen, while AMPKα silencing abrogated celecoxib-mediated CREB and Nrf2 activation. Moreover, celecoxib induced H-ferritin via the same pathway, and increased HO-1 and H-ferritin in the aortic endothelium of mice fed celecoxib (1000 ppm) or control chow. Functionally, celecoxib inhibited TNF-α-induced NF-κB p65(Ser536) phosphorylation by activating AMPK. This attenuated VCAM-1 upregulation via induction of HO-1, a response reproduced by DMC but not ibuprofen or naproxen. Similarly, celecoxib prevented IL-1β-mediated induction of IL-6. Celecoxib enhances vascular protection via AMPK-CREB-Nrf2 signalling, a mechanism which may mitigate cardiovascular risk in patients prescribed celecoxib. Understanding NSAID heterogeneity and COX-2-independent signalling will ultimately lead to safer anti-inflammatory drugs

The inflammatory microenvironment in colorectal neoplasia

Peer reviewedPublisher PD

An essential function for the ATR-Activation-Domain (AAD) of TopBP1 in mouse development and cellular senescence

ATR activation is dependent on temporal and spatial interactions with partner proteins. In the budding yeast model, three proteins – Dpb11TopBP1, Ddc1Rad9 and Dna2 - all interact with and activate Mec1ATR. Each contains an ATR activation domain (ADD) that interacts directly with the Mec1ATR:Ddc2ATRIP complex. Any of the Dpb11TopBP1, Ddc1Rad9 or Dna2 ADDs is sufficient to activate Mec1ATR in vitro. All three can also independently activate Mec1ATR in vivo: the checkpoint is lost only when all three AADs are absent. In metazoans, only TopBP1 has been identified as a direct ATR activator. Depletion-replacement approaches suggest the TopBP1-AAD is both sufficient and necessary for ATR activation. The physiological function of the TopBP1 AAD is, however, unknown. We created a knock-in point mutation (W1147R) that ablates mouse TopBP1-AAD function. TopBP1-W1147R is early embryonic lethal. To analyse TopBP1-W1147R cellular function in vivo, we silenced the wild type TopBP1 allele in heterozygous MEFs. AAD inactivation impaired cell proliferation, promoted premature senescence and compromised Chk1 signalling following UV irradiation. We also show enforced TopBP1 dimerization promotes ATR-dependent Chk1 phosphorylation. Our data suggest that, unlike the yeast models, the TopBP1-AAD is the major activator of ATR, sustaining cell proliferation and embryonic development