PEg TRAnsfer Workflow recognition challenge report: Do multimodal data improve recognition?

BACKGROUND AND OBJECTIVE

In order to be context-aware, computer-assisted surgical systems require accurate, real-time automatic surgical workflow recognition. In the past several years, surgical video has been the most commonly-used modality for surgical workflow recognition. But with the democratization of robot-assisted surgery, new modalities, such as kinematics, are now accessible. Some previous methods use these new modalities as input for their models, but their added value has rarely been studied. This paper presents the design and results of the "PEg TRAnsfer Workflow recognition" (PETRAW) challenge with the objective of developing surgical workflow recognition methods based on one or more modalities and studying their added value.

METHODS

The PETRAW challenge included a data set of 150 peg transfer sequences performed on a virtual simulator. This data set included videos, kinematic data, semantic segmentation data, and annotations, which described the workflow at three levels of granularity: phase, step, and activity. Five tasks were proposed to the participants: three were related to the recognition at all granularities simultaneously using a single modality, and two addressed the recognition using multiple modalities. The mean application-dependent balanced accuracy (AD-Accuracy) was used as an evaluation metric to take into account class balance and is more clinically relevant than a frame-by-frame score.

RESULTS

Seven teams participated in at least one task with four participating in every task. The best results were obtained by combining video and kinematic data (AD-Accuracy of between 93% and 90% for the four teams that participated in all tasks).

CONCLUSION

The improvement of surgical workflow recognition methods using multiple modalities compared with unimodal methods was significant for all teams. However, the longer execution time required for video/kinematic-based methods(compared to only kinematic-based methods) must be considered. Indeed, one must ask if it is wise to increase computing time by 2000 to 20,000% only to increase accuracy by 3%. The PETRAW data set is publicly available at www.synapse.org/PETRAW to encourage further research in surgical workflow recognition.

Load-Balancing of Kubernetes-Based Edge Computing Infrastructure Using Resource Adaptive Proxy

Kubernetes (K8s) is expected to be a key container orchestration tool for edge computing infrastructures owing to its various features for supporting container deployment and dynamic resource management. For example, its horizontal pod autoscaling feature provides service availability and scalability by increasing the number of replicas. kube-proxy provides traffic load-balancing between replicas by distributing client requests equally to all pods (replicas) of an application in a K8s cluster. However, this approach can result in long delays when requests are forwarded to remote workers, especially in edge computing environments where worker nodes are geographically dispersed. Moreover, if the receiving worker is overloaded, the request-processing delay can increase significantly. To overcome these limitations, this paper proposes an enhanced load balancer called resource adaptive proxy (RAP). RAP periodically monitors the resource status of each pod and the network status among worker nodes to aid in load-balancing decisions. Furthermore, it preferentially handles requests locally to the maximum extent possible. If the local worker node is overloaded, RAP forwards its requests to the best node in the cluster while considering resource availability. Our experimental results demonstrated that RAP could significantly improve throughput and reduce request latency compared with the default load-balancing mechanism of K8s.

Semantic Querying of News Articles With Natural Language Questions

The heterogeneity and the increasing amount of the news published on the web create challenges in accessing them. In the authors' previous studies, they introduced a semantic web-based sports news aggregation system called BKSport, which manages to generate metadata for every news item. Providing an intuitive and expressive way to retrieve information and exploiting the advantages of semantic search technique is within their consideration. In this paper, they propose a method to transform natural language questions into SPARQL queries, which could be applied to existing semantic data. This method is mainly based on the following tasks: the construction of a semantic model representing a question, detection of ontology vocabularies and knowledge base elements in question, and their mapping to generate a query. Experiments are performed on a set of questions belonging to various categories, and the results show that the proposed method provides high precision.

Recent Advances in Effector-Triggered Immunity in Plants: New Pieces in the Puzzle Create a Different Paradigm

Plants rely on multiple immune systems to protect themselves from pathogens. When pattern-triggered immunity (PTI)-the first layer of the immune response-is no longer effective as a result of pathogenic effectors, effector-triggered immunity (ETI) often provides resistance. In ETI, host plants directly or indirectly perceive pathogen effectors via resistance proteins and launch a more robust and rapid defense response. Resistance proteins are typically found in the form of nucleotide-binding and leucine-rich-repeat-containing receptors (NLRs). Upon effector recognition, an NLR undergoes structural change and associates with other NLRs. The dimerization or oligomerization of NLRs signals to downstream components, activates "helper" NLRs, and culminates in the ETI response. Originally, PTI was thought to contribute little to ETI. However, most recent studies revealed crosstalk and cooperation between ETI and PTI. Here, we summarize recent advancements in our understanding of the ETI response and its components, as well as how these components cooperate in the innate immune signaling pathways. Based on up-to-date accumulated knowledge, this review provides our current perspective of potential engineering strategies for crop protection.

Nuclear Localization of HopA1Pss61 Is Required for Effector-Triggered Immunity

Plant resistance proteins recognize cognate pathogen avirulence proteins (also named effectors) to implement the innate immune responses called effector-triggered immunity. Previously, we reported that hopA1 from Pseudomonas syringae pv. syringae strain 61 was identified as an avr gene for Arabidopsis thaliana. Using a forward genetic screen approach, we cloned a hopA1-specific TIR-NBS-LRR class disease resistance gene, RESISTANCE TO PSEUDOMONAS SYRINGAE6 (RPS6). Many resistance proteins indirectly recognize effectors, and RPS6 is thought to interact with HopA1_Pss61 indirectly by surveillance of an effector target. However, the involved target protein is currently unknown. Here, we show RPS6 is the only R protein that recognizes HopA1_Pss61 in Arabidopsis wild-type Col-0 accession. Both RPS6 and HopA1_Pss61 are co-localized to the nucleus and cytoplasm. HopA1_Pss61 is also distributed in plasma membrane and plasmodesmata. Interestingly, nuclear localization of HopA1_Pss61 is required to induce cell death as NES-HopA1_Pss61 suppresses the level of cell death in Nicotiana benthamiana. In addition, in planta expression of hopA1_Pss61 led to defense responses, such as a dwarf morphology, a cell death response, inhibition of bacterial growth, and increased accumulation of defense marker proteins in transgenic Arabidopsis. Functional characterization of HopA1_Pss61 and RPS6 will provide an important piece of the ETI puzzle.

The Conserved Arginine Required for AvrRps4 Processing Is Also Required for Recognition of Its N-Terminal Fragment in Lettuce

Pathogens utilize a repertoire of effectors to facilitate pathogenesis, but when the host recognizes one of them, it causes effector-triggered immunity. The Pseudomonas type III effector AvrRps4 is a bipartite effector that is processed in planta into a functional 133-amino acid N-terminus (AvrRps4-N) and 88-amino acid C-terminus (AvrRps4-C). Previous studies found AvrRps4-C to be sufficient to trigger the hypersensitive response (HR) in turnip. In contrast, our recent work found that AvrRps4-N but not AvrRps4-C triggered HR in lettuce, whereas both were required for resistance induction in Arabidopsis. Here, we initially compared AvrRps4 recognition by turnip and lettuce using transient expression. By serial truncation, we identified the central conserved region consisting of 37 amino acids as essential for AvrRps4-N recognition, whereas the putative type III secretion signal peptide or the C-terminal 13 amino acids were dispensable. Surprisingly, the conserved arginine at position 112 (R112) that is required for full-length AvrRps4 processing is also required for the recognition of AvrRps4-N by lettuce. Mutating R112 to hydrophobic leucine or negatively charged glutamate abolished the HR-inducing capacity of AvrRps4-N, while a positively charged lysine at this position resulted in a slow and weak HR. Together, our results suggest an AvrRps4-N recognition-specific role of R112 in lettuce.[Formula: see text] Copyright © 2021 The Author(s). This is an open access article distributed under the CC BY-NC-ND 4.0 International license.

Screening of pigmented Bacillus aquimaris SH6 from the intestinal tracts of shrimp to develop a novel feed supplement for shrimp

AIMS

To develop a novel feed supplement for shrimp using pigmented spore-forming bacterial strains isolated from their gastrointestinal tracts.

METHODS AND RESULTS

Eight pigmented Bacillus strains were selected from the isolates based on high production of heat-stable spores, typical UV-Vis spectra of produced carotenoids (400-550 nm), and free radical scavenging activity of their extracts. Of the eight strains, the red-orange pigmented Bacillus aquimaris SH6 was selected because it showed the highest abundance in shrimp guts (70% population). Whiteleg shrimp (n = 30 per group) fed with SH6 spores, at >3 × 10⁶  CFU g^-1  pellet for 4 weeks had redder colour (score of 21-23 vs 20-22), 2·7-fold higher astaxanthin level (0·69 vs 0·25 μg g^-1 shrimp), 34% higher weight gain (7·18 vs 5·32 g shrimp^-1 ), and 85% higher phenoloxidase activity (OD490  = 0·265 vs 0·143) than shrimp in the control group.

CONCLUSIONS

The result supports the potential use of B. aquimaris SH6 as a feed supplement for promoting the colourization and weight gain, and for enhancing innate immunity of whiteleg shrimp.

SIGNIFICANCE AND IMPACT OF THE STUDY

This study demonstrates that carotenoids produced by B. aquimaris SH6 can be successfully absorbed and converted to astaxanthin in whiteleg shrimp.

Incidence of childhood cancer in Ho Chi Minh City, Vietnam, 1995-97

Incidence rates of childhood cancer for the city of Ho Chi Minh are presented for the first time. For the 3-year period 1995-97, a total of 302 cancer cases were registered in children under 15 years of age, with a male to female ratio of 1.1. The overall crude rate was 78.8 and the age-standardised incidence rate was 88.4 per million person-years, which was low in comparison with other countries in eastern Asia and with the predominantly white population of Australia. Leukaemia (principally acute lymphocytic), brain tumours and lymphomas were the most common childhood neoplasms, which is consistent with the pattern observed in other registries of the region. The rate of retinoblastoma was higher than in the other regional registries. On the other hand, no cases of hepatocellular carcinoma were registered.

Cancer incidence in Ho Chi Minh City, Viet Nam, 1995-1996

The results from the population-based cancer registry for the city of Ho Chi Minh in 1995-1996 represent the first information on the incidence of cancer in southern Viet Nam. A total of 4,080 cancer cases in males and 4,338 in females were registered, corresponding to age-standardized incidence rates (ASRs) of 130.9 per 100,000 in men and 100.7 per 100,000 in women. As elsewhere in South East Asia, the principal cancer of men was liver cancer (ASR 25.3), with moderately high rates of lung cancer (ASR 24.6) and stomach cancer (ASR 16.5); cancer of the penis, reportedly very common in early case series from Viet Nam, is now rarely seen. In women, cervical cancer was the dominant malignancy (ASR 26.0) followed by breast cancer (ASR 12.2) and stomach cancer (ASR 7.5). Although there may be some under-registration in these early years of operation, the recorded rates of cervical cancer and liver cancer are already high and suggest that southern Viet Nam would benefit from an effective cervical cancer screening programme, as well as efforts to interrupt the transmission of hepatitis B virus to reduce liver cancer incidence and effective anti-smoking programs.