MyoPS A Benchmark of Myocardial Pathology Segmentation Combining Three-Sequence Cardiac Magnetic Resonance Images

Assessment of myocardial viability is essential in diagnosis and treatment management of patients suffering from myocardial infarction, and classification of pathology on myocardium is the key to this assessment. This work defines a new task of medical image analysis, i.e., to perform myocardial pathology segmentation (MyoPS) combining three-sequence cardiac magnetic resonance (CMR) images, which was first proposed in the MyoPS challenge, in conjunction with MICCAI 2020. The challenge provided 45 paired and pre-aligned CMR images, allowing algorithms to combine the complementary information from the three CMR sequences for pathology segmentation. In this article, we provide details of the challenge, survey the works from fifteen participants and interpret their methods according to five aspects, i.e., preprocessing, data augmentation, learning strategy, model architecture and post-processing. In addition, we analyze the results with respect to different factors, in order to examine the key obstacles and explore potential of solutions, as well as to provide a benchmark for future research. We conclude that while promising results have been reported, the research is still in the early stage, and more in-depth exploration is needed before a successful application to the clinics. Note that MyoPS data and evaluation tool continue to be publicly available upon registration via its homepage (www.sdspeople.fudan.edu.cn/zhuangxiahai/0/myops20/)

TNFα Cooperates with IFN-γ to Repress Bcl-xL Expression to Sensitize Metastatic Colon Carcinoma Cells to TRAIL-mediated Apoptosis

BACKGROUND: TNF-related apoptosis-inducing ligand (TRAIL) is an immune effector molecule that functions as a selective anti-tumor agent. However, tumor cells, especially metastatic tumor cells often exhibit a TRAIL-resistant phenotype, which is currently a major impediment in TRAIL therapy. The aim of this study is to investigate the synergistic effect of TNFα and IFN-γ in sensitizing metastatic colon carcinoma cells to TRAIL-mediated apoptosis. METHODOLOGY/PRINCIPAL FINDINGS: The efficacy and underlying molecular mechanism of cooperation between TNFα and IFN-γ in sensitizing metastatic colon carcinoma cells to TRAIL-mediated apoptosis were examined. The functional significance of TNFα- and IFN-γ-producing T lymphocyte immunotherapy in combination with TRAIL therapy in suppression of colon carcinoma metastasis was determined in an experimental metastasis mouse model. We observed that TNFα or IFN-γ alone exhibits minimal sensitization effects, but effectively sensitized metastatic colon carcinoma cells to TRAIL-induced apoptosis when used in combination. TNFα and IFN-γ cooperate to repress Bcl-xL expression, whereas TNFα represses Survivin expression in the metastatic colon carcinoma cells. Silencing Bcl-xL expression significantly increased the metastatic colon carcinoma cell sensitivity to TRAIL-induced apoptosis. Conversely, overexpression of Bcl-xL significantly decreased the tumor cell sensitivity to TRAIL-induced apoptosis. Furthermore, TNFα and IFN-γ also synergistically enhanced TRAIL-induced caspase-8 activation. TNFα and IFN-γ was up-regulated in activated primary and tumor-specific T cells. TRAIL was expressed in tumor-infiltrating immune cells in vivo, and in tumor-specific cytotoxic T lymphocytes (CTL) ex vivo. Consequently, TRAIL therapy in combination with TNFα/IFN-γ-producing CTL adoptive transfer immunotherapy effectively suppressed colon carcinoma metastasis in vivo. CONCLUSIONS/SIGNIFICANCE: TNFα and IFN-γ cooperate to overcome TRAIL resistance at least partially through enhancing caspase 8 activation and repressing Bcl-xL expression. Combined CTL immunotherapy and TRAIL therapy hold great promise for further development for the treatment of metastatic colorectal cancer

Dynamic cascading failure analysis in congested urban road networks with self-organization

An efficient freight transportation system is a core part of the modern urban logistics. The transportation system depends on an efficient urban road network. In urban road networks, the failure of some components leads to others failing in succession, triggering cascading failures. This may cause the collapse of the freight transportation system. A cascading failure model is proposed for analyzing the propagation of failures on urban road networks, which can provide guidance for the planning of freight transportation routes in case of emergency. When analyzing the cascading failure process, failed components are commonly deleted permanently. Travelers will avoid failed components, resulting in no increase in traffic flow on the failed components. At the same time, vehicles on these failed components will evacuate slowly to alleviate congestion. Considering this point, this paper proposes a dynamic cascading failure model. This model is established based on a hybrid routing strategy in which traffic flow is distributed according to global and local information. Specifically, the new input traffic demand is assigned along efficient paths in an urban road network (using global information). Efficient paths are determined according to the weights of all edges in urban road networks. Meanwhile, failed edges transfer some traffic flow to their normally working neighbors by self-organization (using local information). The proportion of transferred traffic flow is determined by the residual capacity of the failed edges' normally working neighbors. The feasibility of the proposed model is verified in a partial road network in Changchun, China.Published versio

Identification of critical links in a large-scale road network considering the traffic flow betweenness index.

The traditional full-scan method is commonly used for identifying critical links in road networks. This method simulates each link to be closed iteratively and measures its impact on the efficiency of the whole network. It can accurately identify critical links. However, in this method, traffic assignments are conducted under all scenarios of link disruption, making this process prohibitively time-consuming for large-scale road networks. This paper proposes an approach considering the traffic flow betweenness index (TFBI) to identify critical links, which can significantly reduce the computational burden compared with the traditional full-scan method. The TFBI consists of two parts: traffic flow betweenness and endpoint origin-destination (OD) demand (rerouted travel demand). There is a weight coefficient between these two parts. Traffic flow betweenness is established by considering the shortest travel-time path betweenness, link traffic flow and total OD demand. The proposed approach consists of the following main steps. First, a sample road network is selected to calibrate the weight coefficient between traffic flow betweenness and endpoint OD demand in the TFBI using the network robustness index. This index calculates changes in the whole-system travel time due to each link's closure under the traditional full-scan method. Then, candidate critical links are pre-selected according to the TFBI value of each link. Finally, a given number of real critical links are identified from the candidate critical links using the traditional full-scan method. The applicability and computational efficiency of the TFBI-based approach are demonstrated for the road network in Changchun, China

Enhancement of biodesulfurization by Pseudomonas delafieldii in a ceramic microsparging aeration system

A 700 ml membrane-aerated, stirred glass reactor equipped with four vertical baffles was constructed. Biodesulfurization of model oil (n-dodecane containing dibenzothiophene-DBT) and hydrodesulfurized diesel was carried out using Pseudomonas delafieldii strain R-8. Microbubble aeration gave an activity of 1.3 mg DBT removed g(-1) h(-1) and 277 mu g sulfur g(-1) h(-1) for model oil and hydrodesulfurized diesel, respectively. These values were 1.9- and 1.6-times higher than using a traditional bubble aeration process. This is a promising method for the biodesulfurization of petroleum feedstocks

Integrated analysis of clinical and genetic factors on the interindividual variation of warfarin anticoagulation efficacy in clinical practice

Abstract Aim The anticoagulation effect of warfarin is usually evaluated by percentage of time in therapeutic range (PTTR), which is negatively correlated with the risk of warfarin adverse reactions. This study aimed to explore the effects of genetic and nongenetic factors on anticoagulation efficacy of warfarin during different therapeutic range. Methods We conducted an observational retrospective study aiming at evaluating the impact of clinical and genetic factors on PTTR from initial to more than six months treatment. This analysis included patients with heart valve replace (HVR) surgery who underwent long-term or life-long time treatment with standard-dose warfarin for anticoagulation control in Second Xiangya Hospital. All patients were followed for at least 6 months. We genotyped single nucleotide polymorphisms in VKORC1 and CYP2C9 associated with altered warfarin dose requirements and tested their associations with PTTR. Results A total of 629 patients with intact clinical data and available genotype data were enrolled in this study, and only 38.63% patients achieved good anticoagulation control (PTTR > 0.6). Clinical factors, including male gender, older age, overweight, AVR surgery and stroke history, were associated with higher PTTR. Patients with VKORC1 -1639AA genotype had significantly higher PTTR level compared with GA/GG genotype carriers only in the first month of treatment. Patients with CYP2C9*3 allele had higher PTTR compared with CYP2C9*1*1 carriers. Moreover, compared with VKORC1 -1639 AG/GG carriers, INR > 4 was more likely to be present in patients with AA genotype. The frequency of CYP2C9*1*3 in patients with INR > 4 was significantly higher than these without INR > 4. Conclusion We confirmed the relevant factors of warfarin anticoagulation control, including genetic factors (VKORC1 -1639G > A and CYP2C9*3 polymorphisms) and clinical factors (male gender, older age, overweight, AVR surgery and stroke history), which could be helpful to individualize warfarin dosage and improve warfarin anticoagulation control during different treatment period

Soil horizons regulate bacterial community structure and functions in Dabie Mountain of the East China

Abstract Soil bacterial communities regulate nutrient cycling and plant growth in forests. Although these bacterial communities vary with soil nutrients and plant traits, the variation and degree with soil horizons in different forest types remain unclear. Here, bacterial communities of 44 soil samples from organic horizon (O horizon) and mineral horizon (M horizon) of three forest types (Cunninghamia, broad-leaved and Pinus forests) in subtropical forests of Dabie Mountain, China were analyzed based on amplicon sequencing. We assessed the effects of soil horizons and forest types on bacterial communities. The results showed that the bacterial richness and diversity were significantly higher in the O horizon than in the M horizon. Furthermore, the bacterial community composition and functions were also remarkably different between the two soil horizons. Furthermore, forest types could affect bacterial community composition but not for diversity and functions. Moreover, soil organic matter, including the total organic carbon, available phosphorus, total organic nitrogen, available potassium, ammonium nitrogen, and pH were main drivers for bacterial community composition. The results propose robust evidence that soil horizons strongly driven bacterial community composition and diversity, and suggest that microhabitat of soil bacterial communities is important to maintain the stability of forest ecosystem

Robust online learning based on siamese network for ship tracking

Abstract The complex and changeable inland river scenes resulting out of frequent occlusions of ships in the available tracking methods are not accurate enough to estimate the motion state of the target ship leading to object tracking drift or even loss. In view of this, an attempt is made to propose a robust online learning ship tracking algorithm based on the Siamese network and the region proposal network. Firstly, the algorithm combines the off-line Siamese network classification score and the online classifier score for discriminative learning, and establishes an occlusion determination mechanism according to the classification the fusion score. When the target is in the occlusion state, the target template is not updated, and the global search mechanism is activated to relocate the target, thereby avoiding object tracking drift. Secondly, an efficient adaptive online update strategy, UpdateNet, is introduced to improve the template degradation in the tracking process. Finally, on comparing the state-of-the-art tracking algorithms on the inland river ship datasets, the experimental results of the proposed algorithm show strong robustness in occlusion scenarios with an accuracy and success rate of 56.8% and 57.2% respectively. Supportive source codes for this research are publicly available at https://github.com/Libra-jing/SiamOL

Genome-Wide Identification and Characterization of <i>YUCCA</i> Gene Family in <i>Mikania micrantha</i>

Auxin is a general coordinator for growth and development throughout plant lifespan, acting in a concentration-dependent manner. Tryptophan aminotransferases (YUCCA) family catalyze the oxidative decarboxylation of indole-3-pyruvic acid (IPA) to form indole-3-acetic acid (IAA) and plays a critical role in auxin homeostasis. Here, 18 YUCCA family genes divided into four categories were identified from Mikania micrantha (M. micrantha), one of the world’s most invasive plants. Five highly conserved motifs were characterized in these YUCCA genes (MmYUCs). Transcriptome analysis revealed that MmYUCs exhibited distinct expression patterns in different organs and five MmYUCs showed high expression levels throughout all the five tissues, implying that they may play dominant roles in auxin biosynthesis and plant development. In addition, MmYUC6_1 was overexpressed in DR5::GUS Arabidopsis line to explore its function, which resulted in remarkably increased auxin level and typical elevated auxin-related phenotypes including shortened roots and elongated hypocotyls in the transgenic plants, suggesting that MmYUC6_1 promoted IAA biosynthesis in Arabidopsis. Collectively, these findings provided comprehensive insight into the phylogenetic relationships, chromosomal distributions, expression patterns and functions of the MmYUC genes in M. micrantha, which would facilitate the study of molecular mechanisms underlying the fast growth of M. micrantha and preventing its invasion