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Article ; Online: Bioinformatic Analysis of the Effect of the Sirtuin Family on Differentiated Thyroid Carcinoma

Lijun Yao / Yinhua Wang

BioMed Research International, Vol

2022 Volume 2022

Abstract: A growing body of experimental evidence suggests that sirtuins (SIRTs) are associated with tumorigenesis in differentiated thyroid cancer (DTC). Nevertheless, the involvement of SIRTs in the pathogenesis of DTC and their clinical value remain ill-defined ...

Abstract	A growing body of experimental evidence suggests that sirtuins (SIRTs) are associated with tumorigenesis in differentiated thyroid cancer (DTC). Nevertheless, the involvement of SIRTs in the pathogenesis of DTC and their clinical value remain ill-defined and should be thoroughly examined. We explored the transcription of SIRTs and survival data of patients with DTC by the systematic utilization of bioinformatics to analyze data of publicly accessible databases including Oncomine, cBioPortal, Kaplan-Meier Plotter, Gene Expression Profiling Interactive Analysis (GEPIA), Protein Atlas, LinkedOmics, and GSCALite. The examination of gene expression profiles showed that SIRT2, SIRT3, SIRT4, SIRT5, and SIRT6 were downregulated in DTC tissues compared with the normal thyroid tissues. The decreased expression levels of SIRT2, SIRT4, and SIRT5 were correlated with advanced tumor stages. The survival results showed that the increased SIRT4 mRNA expression level was associated with improved overall survival (OS) in the DTC patients. In addition, patients with DTC with high SIRT2, SIRT3, SIRT4, and SIRT5 mRNA levels had higher disease-free survival (DFS). These results showed that SIRT2, SIRT3, SIRT4, SIRT5, and SIRT6 are potential targets for precise treatment of DTC patients and that SIRT2, SIRT3, SIRT4, and SIRT5 are novel potential biomarkers for the prognosis of DTC.
Keywords	Medicine ; R
Subject code	616
Language	English
Publishing date	2022-01-01T00:00:00Z
Publisher	Hindawi Limited
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: Therapists and psychotherapy side effects in China

Lijun Yao / Zhiwei Xu / Xudong Zhao / Yang Chen / Liang Liu / Xiaoming Fu / Fazhan Chen

Heliyon, Vol 8, Iss 11, Pp e11821- (2022)

A machine learning-based study

2022

Abstract: Objective: Side effects in the psychotherapy are sometimes unavoidable. Therapists play a significant role in the side effects of psychotherapy, but there have been few quantitative studies on the mechanisms by which therapists contribute to them. ... ...

Abstract	Objective: Side effects in the psychotherapy are sometimes unavoidable. Therapists play a significant role in the side effects of psychotherapy, but there have been few quantitative studies on the mechanisms by which therapists contribute to them. Methods: We designed the psychotherapy Side Effects Questionnaire-Therapist Version (PSEQ-T) and released it online through an official WeChat account, where 530 therapists participated in the cross-sectional analysis. The therapists were classified into groups with and without perceptions of clients’ side effects. A number of features were selected to distinguish the therapists by category. Six machine learning-based algorithms were selected and trained by our dataset to build classification models. We leveraged the Shapley Additive exPlanations (SHAP) method to quantify the importance of each feature to the therapist categories. Results: Our study demonstrated the following: (1) Of the therapists, 316 perceived clients’ side effects in psychotherapy, with a 59.6% incidence of side effects; the most common type was “make the clients or patients feel bad” (49.8%). (2) A Random Forest-based machine-learning classifier offered the best predictive performance to distinguish the therapists with and without perceptions of clients' side effects, with an F1 score of 0.722 and an AUC value of 0.717. (3) “Therapists’ psychological activity” was the most relevant feature for distinguishing the therapist category. Conclusions: Our study revealed that the therapist's mastery of the limitations of psychotherapy technology and theory, especially the awareness and construction of their psychological states, was the most critical factor in predicting the therapist's perception of the side effects of psychotherapy.
Keywords	Side effects ; Psychotherapy ; Therapist ; Machine learning ; Artificial intelligence ; Science (General) ; Q1-390 ; Social sciences (General) ; H1-99
Subject code	150
Language	English
Publishing date	2022-11-01T00:00:00Z
Publisher	Elsevier
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: Intersectin-Mediated Clearance of SNARE Complexes Is Required for Fast Neurotransmission

Maria Jäpel / Fabian Gerth / Takeshi Sakaba / Jelena Bacetic / Lijun Yao / Seong-Joo Koo / Tanja Maritzen / Christian Freund / Volker Haucke

Cell Reports, Vol 30, Iss 2, Pp 409-420.e

2020 Volume 6

Abstract: Summary: The rapid replenishment of release-ready synaptic vesicles (SVs) at a limiting number of presynaptic release sites is required to sustain high-frequency neurotransmission in CNS neurons. Failure to clear release sites from previously exocytosed ... ...

Abstract	Summary: The rapid replenishment of release-ready synaptic vesicles (SVs) at a limiting number of presynaptic release sites is required to sustain high-frequency neurotransmission in CNS neurons. Failure to clear release sites from previously exocytosed material has been shown to impair vesicle replenishment and, therefore, fast neurotransmission. The identity of this material and the machinery that removes it from release sites have remained enigmatic. Here we show that the endocytic scaffold protein intersectin 1 clears release sites by direct SH3 domain-mediated association with a non-canonical proline-rich segment of synaptobrevin assembled into the SNARE complex for neuroexocytosis. Acute structure-based or sustained genetic interference with SNARE complex recognition by intersectin 1 causes a rapid stimulation frequency-dependent depression of neurotransmission due to impaired replenishment of release-ready SVs. These findings identify a key molecular mechanism that underlies exo-endocytic coupling during fast neurotransmitter release at central synapses. : Fast neurotransmission (e.g., during hearing) requires the clearance of exocytosed material from presynaptic release sites. The identity of this material and the machinery involved have remained enigmatic. Jäpel et al. show that the endocytic protein intersectin 1 clears release sites by removal of post-fusion SNARE complexes to enable fast neurotransmission. Keywords: neurotransmission, calyx of Held, hippocampus, synaptic vesicle, exocytosis, endocytosis, release site, active zone, intersectin, SNARE
Keywords	Biology (General) ; QH301-705.5
Subject code	500
Language	English
Publishing date	2020-01-01T00:00:00Z
Publisher	Elsevier
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: Near-Infrared Spectroscopic Analysis of Hemoglobin with Stability Based on Human Hemolysates Samples

Lijun Yao / Zhenyao Liu / Wenjie Huang / Tao Pan

American Journal of Analytical Chemistry , Vol 03, Iss 01, Pp 19-

2012 Volume 23

Abstract: Near-infrared (NIR) spectroscopy combined with the partial least-squares (PLS) regression was successfully applied for the rapid quantitative analysis of hemoglobin (HGB) based on human hemolysates samples. Based on the varied divisions for the ... ...

Abstract	Near-infrared (NIR) spectroscopy combined with the partial least-squares (PLS) regression was successfully applied for the rapid quantitative analysis of hemoglobin (HGB) based on human hemolysates samples. Based on the varied divisions for the calibration and prediction sets, an effective modeling approach using stable model parameters was proposed. Among 255 samples, 80 were randomly selected as the validation set. The remaining 175 samples were divided into the calibration set (110 samples) and the prediction set (65 samples) for a total of 30 times with certain similarities based on partial least squares cross-validation predictive basis (PLSPB). The optimal PLS factor was 8, the modeling effects M-SEPAve, M-RP,Ave, M-SEPStd and M-RP,Std were 3.84g/L, 0.967, 0.16g/L and 0.006, respectively, the validation effects V-SEP, V-RP and V-RSEP were 3.59g/L, 0.980 and 2.7%, respectively. It indicated that the method has high prediction precision and well stability. The results show that NIR spectroscopy of hemolysates is accurate to HGB’s determination, and it is hopeful to be applied to clinic.
Keywords	Hemolysates ; HGB ; NIR Spectroscopy ; PLS ; Stability ; Analytical chemistry ; QD71-142 ; Chemistry ; QD1-999 ; Science ; Q ; DOAJ:Analytical Chemistry ; DOAJ:Chemistry
Subject code	540
Language	English
Publishing date	2012-01-01T00:00:00Z
Publisher	Scientific Research Publishing
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: Correlation Analysis between Mean Corpuscular Hemoglobin and Mean Corpuscular Volume for Thalassemia Screening in Large Population

Xiaoli Long / Junyu Fang / Lijun Yao / Qingqing Xiao / Tao Pan

American Journal of Analytical Chemistry , Vol 05, Iss 14, Pp 901-

2014 Volume 907

Abstract: Correlation analysis between the hematological parameters mean corpuscular hemoglobin (MCH) and mean corpuscular volume (MCV) for thalassemia screening in large population was discussed. A total of 4920 peripheral blood samples of reproductive age ... ...

Abstract	Correlation analysis between the hematological parameters mean corpuscular hemoglobin (MCH) and mean corpuscular volume (MCV) for thalassemia screening in large population was discussed. A total of 4920 peripheral blood samples of reproductive age persons were collected from Guangdong province of China. The hematological parameters MCH and MCV values of samples were first measured, and then the DNA analyses for thalassemia were conducted. All samples were composed by 4463 non-thalassemia and 457 thalassemia, and among 457 thalassemia samples, 311 were α -thalassemia, 133 were β -thalassemia, and 13 were α & β -thalassemia. In accordance with non-thalassemia, thalassemia, α -thalassemia, β -thalassemia, α & β -thalassemia and the entire group itself, a total of six sample groups were divided. The corresponding correlation coefficients between the measured MCH and MCV values for the six sample groups were 0.880, 0.968, 0.966, 0.962, 0.980 and 0.965 respectively. For the thalassemia carriers, highly significant correlation between MCH and MCV were observed. The fitting equations between MCH and MCV values were also obtained. The results indicated that the feasibility for thalassemia screening using MCV or MCH independently as parameter, and provided suitable strategy to select parameters and models for thalassemia screening in large population.
Keywords	Thalassemia Screening ; Large Population ; Mean Corpuscular Hemoglobin ; Mean Corpuscular Volume ; Correlation Analysis ; Analytical chemistry ; QD71-142 ; Chemistry ; QD1-999 ; Science ; Q
Subject code	630
Language	English
Publishing date	2014-09-01T00:00:00Z
Publisher	Scientific Research Publishing
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: Evolution and structure of clinically relevant gene fusions in multiple myeloma

Steven M. Foltz / Qingsong Gao / Christopher J. Yoon / Hua Sun / Lijun Yao / Yize Li / Reyka G. Jayasinghe / Song Cao / Justin King / Daniel R. Kohnen / Mark A. Fiala / Li Ding / Ravi Vij

Nature Communications, Vol 11, Iss 1, Pp 1-

2020 Volume 12

Abstract: Multiple myeloma is characterised by frequent gene fusions. Here, the authors use data from the Multiple Myeloma Research Foundation CoMMpass Study to further investigate fusion genes in this disease and their clinical relevance. ...

Abstract	Multiple myeloma is characterised by frequent gene fusions. Here, the authors use data from the Multiple Myeloma Research Foundation CoMMpass Study to further investigate fusion genes in this disease and their clinical relevance.
Keywords	Science ; Q
Language	English
Publishing date	2020-05-01T00:00:00Z
Publisher	Nature Portfolio
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: Evolution and structure of clinically relevant gene fusions in multiple myeloma

Steven M. Foltz / Qingsong Gao / Christopher J. Yoon / Hua Sun / Lijun Yao / Yize Li / Reyka G. Jayasinghe / Song Cao / Justin King / Daniel R. Kohnen / Mark A. Fiala / Li Ding / Ravi Vij

Nature Communications, Vol 11, Iss 1, Pp 1-

2020 Volume 12

Abstract	Multiple myeloma is characterised by frequent gene fusions. Here, the authors use data from the Multiple Myeloma Research Foundation CoMMpass Study to further investigate fusion genes in this disease and their clinical relevance.
Keywords	Science ; Q
Language	English
Publishing date	2020-05-01T00:00:00Z
Publisher	Nature Publishing Group
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: Cross center single-cell RNA sequencing study of the immune microenvironment in rapid progressing multiple myeloma

npj Genomic Medicine, Vol 8, Iss 1, Pp 1-

2023 Volume 18

Abstract: Abstract Despite advancements in understanding the pathophysiology of Multiple Myeloma (MM), the cause of rapid progressing disease in a subset of patients is still unclear. MM’s progression is facilitated by complex interactions with the surrounding ... ...

Abstract	Abstract Despite advancements in understanding the pathophysiology of Multiple Myeloma (MM), the cause of rapid progressing disease in a subset of patients is still unclear. MM’s progression is facilitated by complex interactions with the surrounding bone marrow (BM) cells, forming a microenvironment that supports tumor growth and drug resistance. Understanding the immune microenvironment is key to identifying factors that promote rapid progression of MM. To accomplish this, we performed a multi-center single-cell RNA sequencing (scRNA-seq) study on 102,207 cells from 48 CD138- BM samples collected at the time of disease diagnosis from 18 patients with either rapid progressing (progression-free survival (PFS) < 18 months) or non-progressing (PFS > 4 years) disease. Comparative analysis of data from three centers demonstrated similar transcriptome profiles and cell type distributions, indicating subtle technical variation in scRNA-seq, opening avenues for an expanded multicenter trial. Rapid progressors depicted significantly higher enrichment of GZMK + and TIGIT + exhausted CD8+ T-cells (P = 0.022) along with decreased expression of cytolytic markers (PRF1, GZMB, GNLY). We also observed a significantly higher enrichment of M2 tolerogenic macrophages in rapid progressors and activation of pro-proliferative signaling pathways, such as BAFF, CCL, and IL16. On the other hand, non-progressive patients depicted higher enrichment for immature B Cells (i.e., Pre/Pro B cells), with elevated expression for markers of B cell development (IGLL1, SOX4, DNTT). This multi-center study identifies the enrichment of various pro-tumorigenic cell populations and pathways in those with rapid progressing disease and further validates the robustness of scRNA-seq data generated at different study centers.
Keywords	Medicine ; R ; Genetics ; QH426-470
Subject code	610
Language	English
Publishing date	2023-01-01T00:00:00Z
Publisher	Nature Portfolio
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: Epigenetic and transcriptomic characterization reveals progression markers and essential pathways in clear cell renal cell carcinoma

Yige Wu / Nadezhda V. Terekhanova / Wagma Caravan / Nataly Naser Al Deen / Preet Lal / Siqi Chen / Chia-Kuei Mo / Song Cao / Yize Li / Alla Karpova / Ruiyang Liu / Yanyan Zhao / Andrew Shinkle / Ilya Strunilin / Cody Weimholt / Kazuhito Sato / Lijun Yao / Mamatha Serasanambati / Xiaolu Yang /

Nature Communications, Vol 14, Iss 1, Pp 1-

2023 Volume 25

Abstract: Tumour heterogeneity in clear cell renal cell carcinoma (ccRCC) remains to be investigated. Here, the integration of spatial omics, transcriptional and chromatin accessibility profiling at the single-nucleus level and bulk proteogenomics data reveal ... ...

Abstract	Tumour heterogeneity in clear cell renal cell carcinoma (ccRCC) remains to be investigated. Here, the integration of spatial omics, transcriptional and chromatin accessibility profiling at the single-nucleus level and bulk proteogenomics data reveal markers and pathways important for ccRCC.
Keywords	Science ; Q
Language	English
Publishing date	2023-03-01T00:00:00Z
Publisher	Nature Portfolio
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: Long-Term Water Temperature Variations in Daya Bay, China Using Satellite and In Situ Observations

Jing Yu / Danling Tang / Lijun Yao / Pimao Chen / Xiaoping Jia / Chunhou Li

Terrestrial, Atmospheric and Oceanic Sciences, Vol 21, Iss 2, p

2010 Volume 375

Abstract: Daya Bay is a shallow, semi-en closed bay in the northern section of the South China Sea. The present study analyzed variations of water temperature in Daya Bay over the past 21 years (1985 - 2005) using Advanced Very High Resolution Radiometer (AVHRR) ... ...

Abstract	Daya Bay is a shallow, semi-en closed bay in the northern section of the South China Sea. The present study analyzed variations of water temperature in Daya Bay over the past 21 years (1985 - 2005) using Advanced Very High Resolution Radiometer (AVHRR) satellite remote sensing data and in situ observations. Results showed that AVHRR readings of sea surface temperature (SST) increased by 0.07°C y-1. Linear regression anal y sis for monthly SST anomalies (SSTA) showed a shift from negative to positive from 1995 - 1996, when the Daya Bay nuclear power station commenced operations in 1994. The slope of linear regression analysis for SSTA nearly doubled from 0.05 (1985 - 1993) to 0.09 (1994 - 2005). Monthly AVHRR images showed a thermal plume from the power station and revealed the in crease of SST over 21 years. In situ observations in water temperature also showed an in creasing trend for the same period (1985 - 2005). Variations in water temperature in Daya Bay were connected with climatic perturbations and in creasing human activity including thermal discharge from nuclear power stations and the rapid economic development around the bay area.
Keywords	Seasurface temperature ; AVHRR ; Remote sensing ; In situ observation ; Daya Bay ; China ; Geography (General) ; G1-922 ; Geology ; QE1-996.5
Language	English
Publishing date	2010-01-01T00:00:00Z
Publisher	Chinese Geoscience Union
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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