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Article ; Online: A truncated nuclear norm and graph-Laplacian regularized low-rank representation method for tumor clustering and gene selection

Qi Liu

BMC Bioinformatics, Vol 22, Iss S12, Pp 1-

2022 Volume 17

Abstract: Abstract Background Clustering and feature selection act major roles in many communities. As a matrix factorization, Low-Rank Representation (LRR) has attracted lots of attentions in clustering and feature selection, but sometimes its performance is ... ...

Abstract	Abstract Background Clustering and feature selection act major roles in many communities. As a matrix factorization, Low-Rank Representation (LRR) has attracted lots of attentions in clustering and feature selection, but sometimes its performance is frustrated when the data samples are insufficient or contain a lot of noise. Results To address this drawback, a novel LRR model named TGLRR is proposed by integrating the truncated nuclear norm with graph-Laplacian. Different from the nuclear norm minimizing all singular values, the truncated nuclear norm only minimizes some smallest singular values, which can dispel the harm of shrinkage of the leading singular values. Finally, an efficient algorithm based on Linearized Alternating Direction with Adaptive Penalty is applied to resolving the optimization problem. Conclusions The results show that the TGLRR method exceeds the existing state-of-the-art methods in aspect of tumor clustering and gene selection on integrated gene expression data.
Keywords	Low-rank representation ; Graph-Laplacian ; Truncated nuclear norm ; Clustering ; Gene selection ; Computer applications to medicine. Medical informatics ; R858-859.7 ; Biology (General) ; QH301-705.5
Subject code	519
Language	English
Publishing date	2022-01-01T00:00:00Z
Publisher	BMC
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: Study on Structure Design and Motion Characteristics of Pneumatic Flexible Wrist with Braking Function

Hongbo Liu / Qi Liu

Applied Bionics and Biomechanics, Vol

2023 Volume 2023

Abstract: A flexible pneumatic wrist with spatial position maintenance function is developed in this paper to settle the matter of insufficient flexibility of the robot wrist and self-braking technology. The wrist is made up of four artificial muscles and a ... ...

Abstract	A flexible pneumatic wrist with spatial position maintenance function is developed in this paper to settle the matter of insufficient flexibility of the robot wrist and self-braking technology. The wrist is made up of four artificial muscles and a pneumatic spherical brake in parallel, with 2 degrees of freedom. The wrist can realize multidirectional bending and adjust the wrist damping and braking in real time as required to achieve position maintenance. The theoretical model of the wrist bending angle is built based on torque balance. The variation of wrist bending angle and motion trajectory with air pressure is acquired through experiments. Simultaneously, the validity of the bending angle theoretical model is verified experimentally. A normally open pneumatic spherical brake is developed, and the mathematical model of braking torque is built and experimentally validated. Using a 3D dynamic capture system to compare the dynamic characteristics of the wrist under different excitation signals and different damping conditions. The experimental results reveal that the wrist has good flexibility and can achieve the functions of human hand pitch and yaw. The bending angle is 20.72° at 0.34 MPa. The pneumatic spherical brake has the function of spatial multidirection braking, and the braking force is adjustable. The maximum braking torque can reach 1.4 N m at 0.35 MPa.
Keywords	Biotechnology ; TP248.13-248.65 ; Biology (General) ; QH301-705.5
Subject code	629
Language	English
Publishing date	2023-01-01T00:00:00Z
Publisher	Hindawi Limited
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: Measures to sustain endangered languages

Ya Gao / WenQi Liu

PLoS ONE, Vol 18, Iss 6, p e

A bilingual competition model with sliding mode control.

2023 Volume 0287850

Abstract: There are thousands of languages in the world, many of which are in danger of extinction due to language competition and evolution. Language is an aspect of culture, the rise, and fall of a language directly affects its corresponding culture. To preserve ...

Abstract	There are thousands of languages in the world, many of which are in danger of extinction due to language competition and evolution. Language is an aspect of culture, the rise, and fall of a language directly affects its corresponding culture. To preserve languages and prevent their mass extinction, it is crucial to develop a mathematical model of language coexistence. In this paper, we use a qualitative theory of ordinary differential equations to analyze the bilingual competition model, and obtain the trivial and non-trivial solutions of the bilingual competition model without sliding mode control, then analyze the stability of solutions and prove that solutions of the model have positive invariance. In addition, to maintain linguistic diversity and prevent mass extinction of languages, we propose a novel bilingual competition model with sliding control. The bilingual competition model is analyzed by proposing a sliding control policy to obtain a pseudo-equilibrium point. Meanwhile, numerical simulations clearly illustrate the effectiveness of the sliding mode control strategy. The results show that the likelihood of successful language coexistence can be increased by changing the status of languages and the value of monolingual-bilingual interaction, provides theoretical analysis for the development of policies to prevent language extinction.
Keywords	Medicine ; R ; Science ; Q
Subject code	410
Language	English
Publishing date	2023-01-01T00:00:00Z
Publisher	Public Library of Science (PLoS)
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: Chromosomal-scale genome assembly and annotation of the land slug (Meghimatium bilineatum)

Shaolei Sun / Xiaolu Han / Zhiqiang Han / Qi Liu

Scientific Data, Vol 11, Iss 1, Pp 1-

2024 Volume 10

Abstract: Abstract Meghimatium bilineatum is a notorious pest land slug used as a medicinal resource to treat ailments in China. Although this no-model species is unique in terms of their ecological security and medicinal value, the genome resource of this slug is ...

Abstract	Abstract Meghimatium bilineatum is a notorious pest land slug used as a medicinal resource to treat ailments in China. Although this no-model species is unique in terms of their ecological security and medicinal value, the genome resource of this slug is lacking to date. Here, we used the Illumina, PacBio, and Hi-C sequencing techniques to construct a chromosomal-level genome of M. bilineatum. With the Hi-C correction, the sequencing data from PacBio system generated a 1.61 Gb assembly with a scaffold N50 of 68.08 Mb, and anchored to 25 chromosomes. The estimated assembly completeness at 91.70% was obtained using BUSCO methods. The repeat sequence content in the assembled genome was 72.51%, which mainly comprises 34.08% long interspersed elements. We further identified 18631 protein-coding genes in the assembled genome. A total of 15569 protein-coding genes were successfully annotated. This genome assembly becomes an important resource for studying the ecological adaptation and potential medicinal molecular basis of M. bilineatum.
Keywords	Science ; Q
Subject code	572
Language	English
Publishing date	2024-01-01T00:00:00Z
Publisher	Nature Portfolio
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: A Gas Pressure Prediction Model of the Excavation Face Based on Gas Emission

Liang Chen / Qi Liu

International Journal of Environmental Research and Public Health, Vol 19, Iss 4891, p

2022 Volume 4891

Abstract: Gas pressure is one of the important factors related to the occurrence of coal and gas outburst disasters. The accurate gas pressure forecasting is of significance for the prevention and control of a gas disaster. In this work, a gas pressure prediction ... ...

Abstract	Gas pressure is one of the important factors related to the occurrence of coal and gas outburst disasters. The accurate gas pressure forecasting is of significance for the prevention and control of a gas disaster. In this work, a gas pressure prediction model based on the sources of gas emissions was established. The verified results show that the predicted gas pressure was roughly consistent with the actual situation. This model could meet the needs of engineering projects. Coal and gas outburst dynamic phenomenon are successfully predicted in an engineering application using the model. Overall, the prediction of coal and gas outburst using the gas pressure model achieves a continuous and dynamic effect. The model can overcome both the static and sampling shortcomings of traditional methods and solve the difficulty of coal and gas outburst prediction at the excavation face. With its broad applicability and potential prospects, the model is of great importance for guiding gas drainage, and the prevention of coal and gas outburst disasters.
Keywords	gas pressure ; mining ; coal and gas outburst ; warning ; Medicine ; R
Subject code	660
Language	English
Publishing date	2022-04-01T00:00:00Z
Publisher	MDPI AG
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: Effects of Phosphate and Silicate Combined Application on Cadmium Form Changes in Heavy Metal Contaminated Soil

Xiuli Wang / Hongtao Zou / Qi Liu

Sustainability, Vol 15, Iss 4503, p

2023 Volume 4503

Abstract: Pollution by heavy metal cadmium (Cd) in soil is still serious and control measures are constantly updated. In this paper, one indoor culture method was applied to investigate the effect of phosphate and thermo-activated nano silicate combined ... ...

Abstract	Pollution by heavy metal cadmium (Cd) in soil is still serious and control measures are constantly updated. In this paper, one indoor culture method was applied to investigate the effect of phosphate and thermo-activated nano silicate combined application on soil cadmium (Cd) speciation transformation. A total of 7 treatments were designed, which were: simulated cadmium-contaminated soil without phosphate and silicate recorded as the reference (CK) treatment; mixtures of 0.5%, 1.0%, and 2.0% soil heavy dose of potassium dihydrogen phosphate and 700 °C thermo-activated nano serpentine (potassium dihydrogen phosphate: thermo-activated nano serpentine ratio = 1:2) added to simulated cadmium-contaminated soil, denoted as nPS 700 -0.5, nPS 700 -1.0, and nPS 700 -2.0, respectively; and 0.5%, 1.0%, and 2.0% soil heavy dose of potassium dihydrogen phosphate and 700 °C thermo-activated nano zeolite mixture (potassium dihydrogen phosphate: thermo-activated nano zeolite ratio = 1:2) added to simulated cadmium-contaminated soil, denoted as nPF 700 -0.5, nPF 700 -1.0, and nPF 700 -2.0, respectively. The results showed that the combined application of potassium dihydrogen phosphate with thermo-activated nano serpentine or potassium dihydrogen phosphate with thermo-activated nano zeolite reduced the soil exchangeable Cd content to varying degrees and increased levels of carbonate-bound, Fe-Mn oxide-bound, organic-bound, and residual Cd forms to different degrees. In combined application of phosphate and thermo-activated nano silicate, the higher the dosage level, the greater the reduction of exchangeable Cd content and the better the effect on Cd-contaminated soil remediation: nPS 700 -2.0 > nPS 700 -1.0 > nPS 700 -0.5, nPF 700 -2.0 > nPF 700 -1.0 > nPF 700 -0.5 (N, P, S, and F represent nano, KH 2 PO 4 , serpentine, and zeolite, respectively, and 700 represents the activation temperature). At the same dosage level, the combined application of potassium dihydrogen phosphate and thermo-activated nano serpentine was ...
Keywords	potassium dihydrogen phosphate ; serpentine ; zeolite ; nanomaterials ; the Cd forms ; Environmental effects of industries and plants ; TD194-195 ; Renewable energy sources ; TJ807-830 ; Environmental sciences ; GE1-350
Subject code	290
Language	English
Publishing date	2023-03-01T00:00:00Z
Publisher	MDPI AG
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: Robustness of Significant Dichotomous Outcomes in Randomized Controlled Trials in the Treatment of Patients with COVID-19

Qi Liu / Hong Chen / Yonghua Gao / Changju Zhu

Intensive Care Research, Vol 3, Iss 1, Pp 38-

A Systematic Analysis

2023 Volume 49

Abstract: Abstract Purpose Significant results of randomized controlled trials (RCTs) should be properly weighed. This study adopted fragility index (FI) to evaluate the robustness of significant dichotomous outcomes from RCTs on coronavirus disease 2019 (COVID-19) ...

Abstract	Abstract Purpose Significant results of randomized controlled trials (RCTs) should be properly weighed. This study adopted fragility index (FI) to evaluate the robustness of significant dichotomous outcomes from RCTs on coronavirus disease 2019 (COVID-19) treatment. Materials and methods ClinicalTrials.gov and PubMed were searched from inception to July 31, 2021. FIs were calculated and their distribution was depicted. FI’s categorical influential factors were analyzed. Spearman correlation coefficient (r s) was reported for the relationship between FI and the continuous characteristics of RCTs. Results Fifty RCTs with 120 outcomes in 7869 patients were included. The FI distribution was abnormal with median 3 (interquartile range 1–7, P = 0.0001). The FIs and robustness were affected by the outcomes of interest, various patient populations, and interventions (T = 18.215,16.667, 23.107; P = 0.02,0.0001, 0.001, respectively). A cubic relationship between the FIs and absolute difference of events between groups with R square of 0.848 (T = 215.828, P = 0.0001, R square = 0.865) was observed. A strong negative logarithmic relationship existed between FI and the P value with R square = – 0.834. Conclusion The robustness of significant dichotomous outcomes of COVID-19 treatments was fragile and affected by the outcomes of interest, patients, interventions, P value, and absolute difference of events between the groups. FI was an useful quantitative metric for the binary significant outcomes on COVID-19 treatments. Registration PROSPERO (CRD42021272455).
Keywords	Fragility index ; Fragility quotient ; Coronavirus disease 2019 (COVID-19) ; Randomized controlled trials ; Robustness ; Medical emergencies. Critical care. Intensive care. First aid ; RC86-88.9 ; Medicine ; R
Subject code	610
Language	English
Publishing date	2023-01-01T00:00:00Z
Publisher	Springer
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: Runoff from upstream changes the structure and energy flow of food web in estuary

Yujun Yi / Fanxuan Zhao / Qi Liu / Jie Song

Frontiers in Marine Science, Vol

2023 Volume 10

Abstract: IntroductionSediment and nutrients flow into estuary with runoff, and then influence the estuary ecosystem. Much work has been done for investigating the response of water quality and species group (eg. phytoplankton or zooplankton) to the runoff from ... ...

Abstract	IntroductionSediment and nutrients flow into estuary with runoff, and then influence the estuary ecosystem. Much work has been done for investigating the response of water quality and species group (eg. phytoplankton or zooplankton) to the runoff from upstream, while few research has been taken to evaluate the response of the whole ecosystem.MethodsFood webs of different seasons and regions were established based on stable isotope analysis and Bayesian mixing model. The influences of upstream runoff and sediment transport on the estuarine food webs were analyzed.ResultsFood web in estuary had highly spatial-temporal variability. The stable isotope values of organisms were higher on the northern shore than that on the southern shore. The area with high-turbidity freshwater inflow nurtured more terrestrial- organic- matter (TOM) relying species. And the contribution of TOM to food web was higher in flood season than that in non-flood season. The trophic levels of major consumers in the non-flood season were generally higher than that in the flood season. Significant differences in the average TP of species between two shores appeared during the non-flood season (P < 0.05). Expect for the C value, all of the topological indexes of food webs on the northern shore were higher than those on the southern shore, and they were higher in the flood period.DiscussionThe input and diffusion of sediment and nutrients carried by runoff led to the changes in the dietary structure of estuarine organisms and the decrease in trophic levels of major consumers. At the same time, flow pulse with high sediment also aggravated the spatial differences of the structure of food webs. The higher contribution of TOM to consumers increased the link density of food web on the southern shore, making it a more robust system. However, the high diversity of food sources and aquatic species made the food web more complex on the northern shore.
Keywords	food web ; stable isotope ; energy flow ; flow regime ; estuarine ecology ; Science ; Q ; General. Including nature conservation ; geographical distribution ; QH1-199.5
Subject code	590
Language	English
Publishing date	2023-03-01T00:00:00Z
Publisher	Frontiers Media S.A.
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: Cost efficient management of complex financial energy trading systems

Qi Liu / Pengbo Wan / Fen Chen / Weiting Li

Journal of Innovation & Knowledge, Vol 8, Iss 1, Pp 100323- (2023)

Knowledge-based blockchain technique

2023

Abstract: Industry 4.0 has led to the growth of smart cities utilizing the Internet of Things (IoT). Wireless sensor network (WSN) has drawn considerable interest as an important element of the IoT. The Energy Internet (EI) is growing in importance as a ... ...

Abstract	Industry 4.0 has led to the growth of smart cities utilizing the Internet of Things (IoT). Wireless sensor network (WSN) has drawn considerable interest as an important element of the IoT. The Energy Internet (EI) is growing in importance as a significant component of constructing the intelligent city, especially in terms of its reliability and security. EI is moving in a new direction of energy trading advancement where distributed energy transaction models are replacing the conventional centralized layout. Blockchain technology, which is the underlying support, has gained interest as a result of its benefits, namely integrity, and nonrepudiation. Privacy disclosure, despite the benefits, is a concern for many blockchain-enabled trading layouts. The paper presents encryption according to the cryptographic text properties as the main scheme for reconstructing the dealing layout in order to resolve the issue in the electricity market. In particular, the blockchain energy trade plan with privacy (BETPWP) has been developed to manage the distributed transaction. Transaction arbitration in ciphertext form is employed for achieving precise access control. As a result of this method, the transaction layout could be made considerably more secure and reliable, as well as maximizing the security of private data. BETPWP also proposes a credibility-enabled equity proof consensus method that would significantly improve operational performance. A study of security and the test assessment of the suggested method are performed in order to demonstrate its effectiveness.
Keywords	A10 ; C89 ; P48 ; History of scholarship and learning. The humanities ; AZ20-999 ; Social sciences (General) ; H1-99
Subject code	690 ; 650
Language	English
Publishing date	2023-01-01T00:00:00Z
Publisher	Elsevier
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: A Practical Model for Predicting Esophageal Variceal Rebleeding in Patients with Hepatitis B-Associated Cirrhosis

Linxiang Liu / Yuan Nie / Qi Liu / Xuan Zhu

International Journal of Clinical Practice, Vol

2023 Volume 2023

Abstract: Background. Variceal rebleeding is a significant and potentially life-threatening complication of cirrhosis. Unfortunately, currently, there is no reliable method for stratifying high-risk patients. Liver stiffness measurements (LSM) have been shown to ... ...

Abstract	Background. Variceal rebleeding is a significant and potentially life-threatening complication of cirrhosis. Unfortunately, currently, there is no reliable method for stratifying high-risk patients. Liver stiffness measurements (LSM) have been shown to have a predictive value in identifying complications associated with portal hypertension, including first-time bleeding. However, there is a lack of evidence to confirm that LSM is reliable in predicting variceal rebleeding. The objective of our study was to evaluate the ability of generating a extreme gradient boosting (XGBoost) algorithm model to improve the prediction of variceal rebleeding. Methods. This retrospective analysis examined a cohort of 284 patients with hepatitis B-related cirrhosis. XGBoost models were developed using laboratory data, LSM, and imaging data to predict the risk of rebleeding in the patients. In addition, we compared the XGBoost models with traditional logistic regression (LR) models. We evaluated and compared the two models using the area under the receiver operating characteristic curve (AUROC) and other model performance parameters. Lastly, we validated the models using nomograms and decision curve analysis (DCA). Results. During a median follow-up of 66.6 weeks, 72 patients experienced rebleeding, including 21 (7.39%) and 61 (21.48%) patients who rebleed within 6 weeks and 1 year, respectively. In brief, the AUC of the LR models in predicting rebleeding at 6 weeks and 1 year was 0.828 (0.759–0.897) and 0.799 (0.738–0.860), respectively. In contrast, the accuracy of the XGBoost model in predicting rebleeding at 6 weeks and 1 year was 0.985 (0.907–0.731) and 0.931 (0.806–0.935), respectively. LSM and high-density lipoprotein (HDL) levels differed significantly between the rebleeding and nonrebleeding groups, with LSM being a reliable predictor in those models. The XGBoost models outperformed the LR models in predicting rebleeding within 6 weeks and 1 year, as demonstrated by the ROC and DCA curves. Conclusion. The XGBoost algorithm ...
Keywords	Medicine ; R
Subject code	610
Language	English
Publishing date	2023-01-01T00:00:00Z
Publisher	Hindawi-Wiley
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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