Reducing Spurious Correlations for Aspect-Based Sentiment Analysis with Variational Information Bottleneck and Contrastive Learning

Deep learning techniques have dominated the literature on aspect-based sentiment analysis (ABSA), yielding state-of-the-art results. However, these deep models generally suffer from spurious correlation problems between input features and output labels, which creates significant barriers to robustness and generalization capability. In this paper, we propose a novel Contrastive Variational Information Bottleneck framework (called CVIB) to reduce spurious correlations for ABSA. The proposed CVIB framework is composed of an original network and a self-pruned network, and these two networks are optimized simultaneously via contrastive learning. Concretely, we employ the Variational Information Bottleneck (VIB) principle to learn an informative and compressed network (self-pruned network) from the original network, which discards the superfluous patterns or spurious correlations between input features and prediction labels. Then, self-pruning contrastive learning is devised to pull together semantically similar positive pairs and push away dissimilar pairs, where the representations of the anchor learned by the original and self-pruned networks respectively are regarded as a positive pair while the representations of two different sentences within a mini-batch are treated as a negative pair. To verify the effectiveness of our CVIB method, we conduct extensive experiments on five benchmark ABSA datasets and the experimental results show that our approach achieves better performance than the strong competitors in terms of overall prediction performance, robustness, and generalization

JNK1 activation predicts the prognostic outcome of the human hepatocellular carcinoma

BACKGROUND: Hepatocellular carcinoma (HCC) is one of the most common cancers worldwide with an extremely poor prognosis. The classification of HCC based on the molecular signature is not well-established. RESULTS: In the present study, we reported HCC signature genes based on the JNK1 activation status in 31 HCC specimens relative to the matched distal noncancerous liver tissue from 31 patients. The HCCs with high JNK1 (H-JNK1) and low JNK1 (L-JNK1) were sub-grouped. Two different signature gene sets for both H-JNK1 and L-JNK1 HCC were identified through gene expression profiling. A striking overlap of signature genes was observed between the H-JNK1 HCC and the hepatoblastoma or hepatoblastoma-type HCC. Many established biomarkers for hepatic progenitor cells were over-expressed in H-JNK1 HCC, including AFP, TACSTD1, KRT19, KRT7, THY1, and PROM1. In addition, the majority of the most up-regulated genes were those associated with metastasis and earlier recurrence, whereas the genes for normal liver function were substantially down-regulated in H-JNK1 HCC tissue. A Kaplan-Meier plot demonstrated that the survival of the patients with H-JNK1 HCC was severely impaired. CONCLUSION: Accordingly, we believe that the H-JNK1 HCC may originate from hepatic progenitor cells and is associated with poorer prognosis. The status of JNK1 activation in HCC tissue, thus, might be a new biomarker for HCC prognosis and therapeutic targeting

Rumen microbiota of Tibetan sheep (Ovis aries) adaptation to extremely cold season on the Qighai-Tibetan Platea

Publication history: Accepted - 3 May 2021; Published online - 25 may 2021.The Qinghai-Tibet Plateau is characterized by low temperatures and hypoxia, and this feature is more obvious in the winter. However, it is not clear how Tibetan sheep adapt to extreme cold climates. To address this, we used physiological methods combined with next-generation sequencing technology to explore the differences in growth performance, forage nutrient digestion, serum biochemical indexes, and rumen microbial communities of Tibetan sheep (Ovis aries) between the summer and winter. In the summer, owing to the high nutritional quality of the forage, the Tibetan sheep showed enhanced forage degradation and fermentation though increased counts of important bacteria in the rumen, such as Bacteroidetes, Prevotella_1, Prevotellaceae_UCG-003, Ruminococcus_1, Saccharofermentans, and Ruminococcaceae_UCG-014, to improve the growth performance and increase serum immunity and antioxidant status. In the winter, owing to the low nutritional quality of the forage, the Tibetan sheep presented low values of forage degradation and fermentation indicators. The relative abundance of Firmicutes, the Firmicutes/Bacteroidetes ratio, microbial diversity, interactive activity between microorganisms, and metabolism were significantly increased, implying that the rumen microbiota could promote the decomposition of forage biomass and the maintenance of energy when forage nutritional value was insufficient in the winter. Our study helps in elucidating the mechanism by which Tibetan sheep adapt to the high-altitude harsh environments, from the perspective of the rumen microbiota.This work was supported by the Program for Strategic Priority Research Program of the Chinese Academy of Sciences (Grant No. XDA20100102), the Second Tibetan Plateau Scientific Expedition and Research: Grassland Ecosystem and Ecological Animal Husbandry (Grant No. 2019QZKK0302), and Innovative Research Team of the Ministry of Education (Grant No. IRT_17R50)

Unlocking the mystery of the hard-to-sequence phage genome: PaP1 methylome and bacterial immunity

BACKGROUND: Whole-genome sequencing is an important method to understand the genetic information, gene function, biological characteristics and survival mechanisms of organisms. Sequencing large genomes is very simple at present. However, we encountered a hard-to-sequence genome of Pseudomonas aeruginosa phage PaP1. Shotgun sequencing method failed to complete the sequence of this genome. RESULTS: After persevering for 10 years and going over three generations of sequencing techniques, we successfully completed the sequence of the PaP1 genome with a length of 91,715 bp. Single-molecule real-time sequencing results revealed that this genome contains 51 N-6-methyladenines and 152 N-4-methylcytosines. Three significant modified sequence motifs were predicted, but not all of the sites found in the genome were methylated in these motifs. Further investigations revealed a novel immune mechanism of bacteria, in which host bacteria can recognise and repel modified bases containing inserts in a large scale. This mechanism could be accounted for the failure of the shotgun method in PaP1 genome sequencing. This problem was resolved using the nfi(-) mutant of Escherichia coli DH5α as a host bacterium to construct a shotgun library. CONCLUSIONS: This work provided insights into the hard-to-sequence phage PaP1 genome and discovered a new mechanism of bacterial immunity. The methylome of phage PaP1 is responsible for the failure of shotgun sequencing and for bacterial immunity mediated by enzyme Endo V activity; this methylome also provides a valuable resource for future studies on PaP1 genome replication and modification, as well as on gene regulation and host interaction. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (doi:10.1186/1471-2164-15-803) contains supplementary material, which is available to authorized users

Actively implementing an evidence-based feeding guideline for critically ill patients (NEED): a multicenter, cluster-randomized, controlled trial

Background: Previous cluster-randomized controlled trials evaluating the impact of implementing evidence-based guidelines for nutrition therapy in critical illness do not consistently demonstrate patient benefits. A large-scale, sufficiently powered study is therefore warranted to ascertain the effects of guideline implementation on patient-centered outcomes. Methods: We conducted a multicenter, cluster-randomized, parallel-controlled trial in intensive care units (ICUs) across China. We developed an evidence-based feeding guideline. ICUs randomly allocated to the guideline group formed a local "intervention team", which actively implemented the guideline using standardized educational materials, a graphical feeding protocol, and live online education outreach meetings conducted by members of the study management committee. ICUs assigned to the control group remained unaware of the guideline content. All ICUs enrolled patients who were expected to stay in the ICU longer than seven days. The primary outcome was all-cause mortality within 28 days of enrollment. Results: Forty-eight ICUs were randomized to the guideline group and 49 to the control group. From March 2018 to July 2019, the guideline ICUs enrolled 1399 patients, and the control ICUs enrolled 1373 patients. Implementation of the guideline resulted in significantly earlier EN initiation (1.20 vs. 1.55 mean days to initiation of EN; difference − 0.40 [95% CI − 0.71 to − 0.09]; P = 0.01) and delayed PN initiation (1.29 vs. 0.80 mean days to start of PN; difference 1.06 [95% CI 0.44 to 1.67]; P = 0.001). There was no significant difference in 28-day mortality (14.2% vs. 15.2%; difference − 1.6% [95% CI − 4.3% to 1.2%]; P = 0.42) between groups. Conclusions: In this large-scale, multicenter trial, active implementation of an evidence-based feeding guideline reduced the time to commencement of EN and overall PN use but did not translate to a reduction in mortality from critical illness. Trial registration: ISRCTN, ISRCTN12233792. Registered November 20th, 2017

Actively implementing an evidence-based feeding guideline for critically ill patients (NEED): a multicenter, cluster-randomized, controlled trial.

BackgroundPrevious cluster-randomized controlled trials evaluating the impact of implementing evidence-based guidelines for nutrition therapy in critical illness do not consistently demonstrate patient benefits. A large-scale, sufficiently powered study is therefore warranted to ascertain the effects of guideline implementation on patient-centered outcomes.MethodsWe conducted a multicenter, cluster-randomized, parallel-controlled trial in intensive care units (ICUs) across China. We developed an evidence-based feeding guideline. ICUs randomly allocated to the guideline group formed a local "intervention team", which actively implemented the guideline using standardized educational materials, a graphical feeding protocol, and live online education outreach meetings conducted by members of the study management committee. ICUs assigned to the control group remained unaware of the guideline content. All ICUs enrolled patients who were expected to stay in the ICU longer than seven days. The primary outcome was all-cause mortality within 28 days of enrollment.ResultsForty-eight ICUs were randomized to the guideline group and 49 to the control group. From March 2018 to July 2019, the guideline ICUs enrolled 1399 patients, and the control ICUs enrolled 1373 patients. Implementation of the guideline resulted in significantly earlier EN initiation (1.20 vs. 1.55 mean days to initiation of EN; difference - 0.40 [95% CI - 0.71 to - 0.09]; P = 0.01) and delayed PN initiation (1.29 vs. 0.80 mean days to start of PN; difference 1.06 [95% CI 0.44 to 1.67]; P = 0.001). There was no significant difference in 28-day mortality (14.2% vs. 15.2%; difference - 1.6% [95% CI - 4.3% to 1.2%]; P = 0.42) between groups.ConclusionsIn this large-scale, multicenter trial, active implementation of an evidence-based feeding guideline reduced the time to commencement of EN and overall PN use but did not translate to a reduction in mortality from critical illness.Trial registrationISRCTN, ISRCTN12233792 . Registered November 20th, 2017

Actively implementing an evidence-based feeding guideline for critically ill patients (NEED): a multicenter, cluster-randomized, controlled trial (vol 26, 46, 2022)

BackgroundPrevious cluster-randomized controlled trials evaluating the impact of implementing evidence-based guidelines for nutrition therapy in critical illness do not consistently demonstrate patient benefits. A large-scale, sufficiently powered study is therefore warranted to ascertain the effects of guideline implementation on patient-centered outcomes.MethodsWe conducted a multicenter, cluster-randomized, parallel-controlled trial in intensive care units (ICUs) across China. We developed an evidence-based feeding guideline. ICUs randomly allocated to the guideline group formed a local "intervention team", which actively implemented the guideline using standardized educational materials, a graphical feeding protocol, and live online education outreach meetings conducted by members of the study management committee. ICUs assigned to the control group remained unaware of the guideline content. All ICUs enrolled patients who were expected to stay in the ICU longer than seven days. The primary outcome was all-cause mortality within 28 days of enrollment.ResultsForty-eight ICUs were randomized to the guideline group and 49 to the control group. From March 2018 to July 2019, the guideline ICUs enrolled 1399 patients, and the control ICUs enrolled 1373 patients. Implementation of the guideline resulted in significantly earlier EN initiation (1.20 vs. 1.55 mean days to initiation of EN; difference - 0.40 [95% CI - 0.71 to - 0.09]; P = 0.01) and delayed PN initiation (1.29 vs. 0.80 mean days to start of PN; difference 1.06 [95% CI 0.44 to 1.67]; P = 0.001). There was no significant difference in 28-day mortality (14.2% vs. 15.2%; difference - 1.6% [95% CI - 4.3% to 1.2%]; P = 0.42) between groups.ConclusionsIn this large-scale, multicenter trial, active implementation of an evidence-based feeding guideline reduced the time to commencement of EN and overall PN use but did not translate to a reduction in mortality from critical illness.Trial registrationISRCTN, ISRCTN12233792 . Registered November 20th, 2017

A Low-Cost and High-Precision Underwater Integrated Navigation System

The traditional underwater integrated navigation system is based on an optical fiber gyroscope and Doppler Velocity Log, which is high-precision but also expensive, heavy, bulky and difficult to adapt to the development requirements of AUV swarm, intelligence and miniaturization. This paper proposes a low-cost, light-weight, small-volume and low-computation underwater integrated navigation system based on MEMS IMU/DVL/USBL. First, according to the motion formula of AUV, a five-dimensional state equation of the system was established, whose dimension was far less than that of the traditional. Second, the main source of error was considered. As the velocity observation value of the system, the velocity measured by DVL eliminated the scale error and lever arm error. As the position observation value of the system, the position measured by USBL eliminated the lever arm error. Third, to solve the issue of inconsistent observation frequencies between DVL and USBL, a sequential filter was proposed to update the extended Kalman filter. Finally, through selecting the sensor equipment and conducting two lake experiments with total voyages of 5.02 km and 3.2 km, respectively, the correctness and practicality of the system were confirmed by the results. By comparing the output of the integrated navigation system and the data of RTK GPS, the average position error was 4.12 m, the maximum position error was 8.53 m, the average velocity error was 0.027 m/s and the average yaw error was 1.41°, whose precision is as high as that of an optical fiber gyroscope and Doppler Velocity Log integrated navigation system, but the price is less than half of that. The experimental results show that the proposed underwater integrated navigation system could realize the high-precision and long-term navigation of AUV in the designated area, which had great potential for both military and civilian applications