scholarly journals LCN2 as a Potential Diagnostic Biomarker for Ulcerative Colitis-Associated Carcinogenesis Related to Disease Duration

2022 ◽  
Vol 11 ◽  
Author(s):  
Fushun Kou ◽  
Yuan Cheng ◽  
Lei Shi ◽  
Jiajing Liu ◽  
Yuyue Liu ◽  
...  
Keyword(s):  
Ulcerative Colitis ◽  
Short Duration ◽  
Disease Duration ◽  
Early Stage ◽  
Gene Expression Omnibus ◽  
Cancer Surveillance ◽  
Lipocalin 2 ◽  
Protein Protein Interaction ◽  
Colorectal Mucosa ◽  
Long Duration

BackgroundPatients with long-duration ulcerative colitis (UC) had a higher risk of developing ulcerative colitis-associated carcinogenesis (UCAC) when compared to those with short-duration UC. This study aimed to discover the biomarker for cancer surveillance related to disease duration.MethodsThe microarrays were divided into short-duration (<10 years) UC, long-duration (≥10 years) UC, UCAC, and normal groups in the Gene Expression Omnibus (GEO) datasets. Differentially expressed genes (DEGs) of GEO and the hub genes of the selected weighted gene co-expression network analysis (WGCNA) were intersected to obtain the overlapping genes. Among these genes, the key gene was identified by using the protein–protein interaction (PPI) network, Gene Ontology (GO), Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis, the cytoHubba of Cytoscape, and the expression levels. Also, immunofluorescence of human colonic mucosa and animal experiment were used to validate the expression trend of the key gene in the progress of UC developing into UCAC.ResultsLipocalin-2 (LCN2) was more relevant with disease duration of UC and significantly negatively correlated with the risk of UCAC. The expression level of LCN2 in short-duration UC was higher than that of long-duration UC (P < 0.01), long-duration UC was higher than that of UCAC (P = 0.001), and UC and UCAC were all higher than that of the normal (P < 0.001). We then discovered that the expression trend of LCN2 in blood and stool samples was consistent with that in colorectal mucosa.ConclusionThe research indicates that LCN2 could be a novel biomarker to evaluate cancer surveillance related to disease duration of developing UC into UCAC. Compared with that of blood samples, stool detection of LCN2 may have more advantages for diagnosis value of early stage of UCAC as a complement to colonoscopy surveillance.

scholarly journals Identification of Genes in Patients for Predicting Ulcerative Colitis-Associated Colorectal Cancer

2020 ◽  
Author(s):  
hongyun wei ◽  
qian zhang ◽  
xiaosa chi ◽  
xiaohui yang ◽  
zibin tian ◽  
...  
Keyword(s):  
Gene Expression ◽  
Colorectal Cancer ◽  
Ulcerative Colitis ◽  
Gene Expression Omnibus ◽  
The Cancer Genome Atlas ◽  
Rank Test ◽  
Hub Genes ◽  
Protein Protein Interaction ◽  
Limma Package ◽  
Public Datasets

Abstract BackgroundUlcerative colitis (UC) has been considered as a risk factor for colorectal cancer (CRC). However, effective biomarkers for predicting UC-associated CRC are lacking. Therefore, it is necessary to screen biomarkers associated with UC-related CRC, which could be used to evaluate UC-associated CRC early, and provide possible mechanisms involved in UC-associated CRC. Efficient bioinformatics analysis could help us to explore potential biomarkers.MethodsTwo public datasets, including 44 UC without CRC samples and 17 UC-associated CRC samples were chosen from Gene Expression Omnibus (GEO) database. Sva package was used to remove batch effects, and then we screened out differentially expressed genes (DEGs) with limma package. STRING and Cytoscape were used to achieve protein-protein interaction (PPI) network analysis. The survival curves between high and low gene expression were performed by log rank test based on the cancer genome atlas (TCGA) program. The expression of three identified hub genes was validated based on Oncomine. To validate the expression of three hub genes, we compared the expression of three hub genes between normal and colorectal cancer based on Oncomine.Results405 DEGs were identified, including 256 down-regulated genes and 149 up-regulated genes in UC-associated CRC tissues. 16 hub genes were identified. And among them, RPL6, RPL7, and RPL35 were related to poor prognosis of patients in survival analysis. Higher expression of RPL6, RPL7, and RPL35 was validated in CRC tissues based on Oncomine.ConclusionsOur study showed that overexpressed RPL6, RPL7, and RPL 35 may be potential tumor oncogenes and could act as a prognostic factor in clinical diagnosis and treatment.

scholarly journals Predicting disease course in ulcerative colitis using stool proteins identified through an aptamer-based screen

2021 ◽  
Vol 12 (1) ◽  
Author(s):  
Sanam Soomro ◽  
Suresh Venkateswaran ◽  
Kamala Vanarsa ◽  
Marwa Kharboutli ◽  
Malavika Nidhi ◽  
...  
Keyword(s):  
Ulcerative Colitis ◽  
Inflammatory Bowel Disease ◽  
Bowel Disease ◽  
Fecal Calprotectin ◽  
Disease Monitoring ◽  
Disease Course ◽  
Lipocalin 2 ◽  
Time Points ◽  
Inflammatory Bowel ◽  
Stool Samples

AbstractIn the search for improved stool biomarkers for inflammatory bowel disease (IBD), an aptamer-based screen of 1129 stool proteins was conducted using stool samples from an IBD cohort. Here we report that of the 20 proteins subsequently validated by ELISA, stool Ferritin, Fibrinogen, Haptoglobin, Hemoglobin, Lipocalin-2, MMP-12, MMP-9, Myeloperoxidase, PGRP-S, Properdin, Resistin, Serpin A4, and TIMP-1 are significantly elevated in both ulcerative colitis (UC) and Crohn’s disease (CD) compared to controls. When tested in a longitudinal cohort of 50 UC patients at 4 time-points, fecal Fibrinogen, MMP-8, PGRP-S, and TIMP-2 show the strongest positive correlation with concurrent PUCAI and PGA scores and are superior to fecal calprotectin. Unlike fecal calprotectin, baseline stool Fibrinogen, MMP-12, PGRP-S, TIMP-1, and TIMP-2 can predict clinical remission at Week-4. Here we show that stool proteins identified using the comprehensive aptamer-based screen are superior to fecal calprotectin alone in disease monitoring and prediction in IBD.

Optimal Energy Storage Portfolio for High and Ultrahigh Carbon-Free and Renewable Power Systems

2021 ◽  
Author(s):  
Omar J Guerra ◽  
Joshua Eichman ◽  
Paul Denholm
Keyword(s):  
Energy Storage ◽  
Power Systems ◽  
Short Duration ◽  
Current Literature ◽  
Optimal Energy ◽  
Renewable Power ◽  
Long Duration ◽  
Storage Technologies

Achieving 100% carbon-free or renewable power systems can be facilitated by the deployment of energy storage technologies at all timescales, including short-duration, long-duration, and seasonal scales; however, most current literature...

scholarly journals Gout of feet and ankles in different disease durations: diagnostic value of single-source DECT and evaluation of urate deposition with a novel semi-quantitative DECT scoring system

2021 ◽  
Vol 61 (1) ◽  
Author(s):  
Jin Shang ◽  
Xiao-Hu Li ◽  
Shu-Qin Lu ◽  
Yi Shang ◽  
Lu-Lu Li ◽  
...  
Keyword(s):  
Scoring System ◽  
Diagnostic Performance ◽  
Disease Duration ◽  
Bone Erosion ◽  
Early Stage ◽  
Gouty Arthritis ◽  
Single Source ◽  
Crystal Deposition ◽  
Urate Crystal ◽  
Sensitivity Specificity

Abstract Objectives To investigate the diagnostic performance of single-source dual-energy computed tomography (DECT) based on gemstone spectral imaging technology (including Discovery CT750HD and Revolution CT) in patients with suspected feet/ankles gouty arthritis, and evaluate the urate deposition with a novel semi-quantitative DECT scoring system. Methods A total of 196 patients were consecutively included. Feet and ankles were evaluated in all patients by single-source DECT scan. The 2015 EULAR/ACR criteria were used as the reference for the diagnosis of gout. The sensitivity, specificity, and area under the receiver operating characteristic curve (AUC) of DECT for the diagnosis of gout in the early (≤1 year), middle (1–3 years), and late (> 3 years) disease durations were calculated. Besides, a novel semi-quantitative DECT scoring system was assessed for the measurement of urate deposition, and the correlation between the scores and the clinical and serological data were also evaluated. Moreover, the influences of artifacts on the diagnostic performance of DECT were also determined. Results The sensitivity, specificity, and AUC of DECT in 196 patients were 38.10, 96.43%, and 0.673 in the early-stage group; 62.96, 100.00%, and 0.815 in the middle-stage group; and 77.55, 87.50%, and 0.825 in the late-stage group, respectively. The overall diagnostic accuracies in the AUC of DECT (Discovery CT750HD and Revolution CT) in the middle and late stages of gout were higher than that in the early stage of gout. Besides, the monosodium urate crystals were deposited on the first metatarsophalangeal joints and ankles/midfeet. Age, the presence of tophus, bone erosion, and disease duration considerably affected the total urate score. No statistical difference in the positive detection of nail artifact, skin artifact, vascular calcification, and noise artifact was found between the case and control groups. Conclusion DECT (Discovery CT750HD and Revolution CT) showed promising diagnostic accuracy for the detection of urate crystal deposition in gout but had limited diagnostic sensitivity for short-stage gout. Longer disease duration, the presence of tophus, and bone erosion were associated with the urate crystal score system. The artifacts do not remarkably affect the diagnostic performance of DECT in gout.

scholarly journals Differential Expression of mRNAs in Peripheral Blood Related to Prodrome and Progression of Alzheimer’s Disease

2020 ◽  
Vol 2020 ◽  
pp. 1-10
Author(s):  
Weishuang Xue ◽  
Jinwei Li ◽  
Kailei Fu ◽  
Weiyu Teng
Keyword(s):  
Alzheimer’S Disease ◽  
Alzheimer's Disease ◽  
Peripheral Blood ◽  
Bioinformatics Analysis ◽  
Gene Expression Omnibus ◽  
Venn Diagram ◽  
Ppi Network ◽  
Hub Genes ◽  
Protein Protein Interaction ◽  
Ppi Networks

Alzheimer’s disease (AD) is a chronic progressive neurodegenerative disease that affects the quality of life of elderly individuals, while the pathogenesis of AD is still unclear. Based on the bioinformatics analysis of differentially expressed genes (DEGs) in peripheral blood samples, we investigated genes related to mild cognitive impairment (MCI), AD, and late-stage AD that might be used for predicting the conversions. Methods. We obtained the DEGs in MCI, AD, and advanced AD patients from the Gene Expression Omnibus (GEO) database. A Venn diagram was used to identify the intersecting genes. Gene Ontology (GO) and Kyoto Gene and Genomic Encyclopedia (KEGG) were used to analyze the functions and pathways of the intersecting genes. Protein-protein interaction (PPI) networks were constructed to visualize the network of the proteins coded by the related genes. Hub genes were selected based on the PPI network. Results. Bioinformatics analysis indicated that there were 61 DEGs in both the MCI and AD groups and 27 the same DEGs among the three groups. Using GO and KEGG analyses, we found that these genes were related to the function of mitochondria and ribosome. Hub genes were determined by bioinformatics software based on the PPI network. Conclusions. Mitochondrial and ribosomal dysfunction in peripheral blood may be early signs in AD patients and related to the disease progression. The identified hub genes may provide the possibility for predicting AD progression or be the possible targets for treatments.

Intracellular analysis of trigeminal motoneuron rhythmical activity during stimulation of pontomedullary reticular formation in anesthetized guinea pig

1989 ◽  
Vol 62 (6) ◽  
pp. 1225-1236 ◽  
Author(s):  
S. M. Gurahian ◽  
S. H. Chandler ◽  
L. J. Goldberg
Keyword(s):  
Reticular Formation ◽  
Short Duration ◽  
Field Potential ◽  
Membrane Potentials ◽  
Repetitive Stimulation ◽  
Jaw Movements ◽  
Postsynaptic Potentials ◽  
Duration Stimulus ◽  
Long Duration ◽  
Stimulation Of

1. The effects of repetitive stimulation of the nucleus pontis caudalis and nucleus gigantocellularis (PnC-Gi) of the reticular formation on jaw opener and closer motoneurons were examined. The PnC-Gi was stimulated at 75 Hz at current intensities less than 90 microA. 2. Rhythmically occurring, long-duration, depolarizing membrane potentials in jaw opener motoneurons [excitatory masticatory drive potential (E-MDP)] and long-duration hyperpolarizing membrane potentials [inhibitory masticatory drive potentials (I-MDP)] in jaw closer motoneurons were evoked by 40-Hz repetitive masticatory cortex stimulation. These potentials were completely suppressed by PnC-Gi stimulation. PnC-Gi stimulation also suppressed the short-duration, stimulus-locked depolarizations [excitatory postsynaptic potentials (EPSPs)] in jaw opener motoneurons and short-duration, stimulus-locked hyperpolarizations [inhibitory postsynaptic potentials (IPSPs)] in jaw closer motoneurons, evoked by the same repetitive cortical stimulation. 3. Short pulse train (3 pulses; 500 Hz) stimulation of the masticatory area of the cortex in the absence of rhythmical jaw movements activated the short-latency paucisynaptic corticotrigeminal pathways and evoked short-duration EPSPs and IPSPs in jaw opener and closer motoneurons, respectively. The same PnC-Gi stimulation that completely suppressed rhythmical MDPs, and stimulus-locked PSPs evoked by repetitive stimulation to the masticatory area of the cortex, produced an average reduction in PSP amplitude of 22 and 17% in jaw closer and opener motoneurons, respectively. 4. PnC-Gi stimulation produced minimal effects on the amplitude of the antidromic digastric field potential or on the intracellularly recorded antidromic digastric action potential. Moreover, PnC-Gi stimulation had little effect on jaw opener or jaw closer motoneuron membrane resting potentials in the absence of rhythmical jaw movements (RJMs). PnC-Gi stimulation produced variable effects on conductance pulses elicited in jaw opener and closer motoneurons in the absence of RJMs. 5. These results indicate that the powerful suppression of cortically evoked MDPs in opener and closer motoneurons during PnC-Gi stimulation is most likely not a result of postsynaptic inhibition of trigeminal motoneurons. It is proposed that this suppression is a result of suppression of activity in neurons responsible for masticatory rhythm generation.

scholarly journals Intercropping Short and Long Duration Groundnut (Arachis Hypogaea) Genotypes to Increase Productivity in Environments Prone to End-of-season Droughts

1990 ◽  
Vol 26 (1) ◽  
pp. 63-72 ◽  
Author(s):  
R. C. Nageswara Rao ◽  
K. D. R. Wadia ◽  
J. H. Williams
Keyword(s):  
Arachis Hypogaea ◽  
Short Duration ◽  
Total Biomass ◽  
Season Length ◽  
Water Deficits ◽  
Pod Yield ◽  
Long Duration ◽  
Increase Productivity

SUMMARYThree short duration and one long duration groundnut genotypes, grown either ‘sole’ or as intercrops (in 1:1 ratios of the short duration with the long duration genotypes), were compared in four trials. The intercrop treatments resulted in Land Equivalent Ratios (LERs) of up to 1.25 for pod yield and total biomass despite moderate or severe water deficits at the end of the season. Specific combinations of genotypes were necessary to maximize the LER. The results indicate there is scope for achieving greater productivity in environments with a variable season length by growing late and early genotypes together in an intercrop system.

scholarly journals Identification of Key Genes and miRNAs in Osteosarcoma Patients with Chemoresistance by Bioinformatics Analysis

2018 ◽  
Vol 2018 ◽  
pp. 1-10 ◽  
Author(s):  
Binbin Xie ◽  
Yiran Li ◽  
Rongjie Zhao ◽  
Yuzi Xu ◽  
Yuhui Wu ◽  
...  
Keyword(s):  
Enrichment Analysis ◽  
Gene Expression Omnibus ◽  
Differentially Expressed ◽  
Pathway Enrichment Analysis ◽  
Regulation Of Transcription ◽  
Functional Annotations ◽  
Protein Protein Interaction ◽  
Ppi Networks ◽  
Search Tool ◽  
Poor Outcomes

Chemoresistance is a significant factor associated with poor outcomes of osteosarcoma patients. The present study aims to identify Chemoresistance-regulated gene signatures and microRNAs (miRNAs) in Gene Expression Omnibus (GEO) database. The results of Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) included positive regulation of transcription, DNA-templated, tryptophan metabolism, and the like. Then differentially expressed genes (DEGs) were uploaded to Search Tool for the Retrieval of Interacting Genes (STRING) to construct protein-protein interaction (PPI) networks, and 9 hub genes were screened, such as fucosyltransferase 3 (Lewis blood group) (FUT3) whose expression in chemoresistant samples was high, but with a better prognosis in osteosarcoma patients. Furthermore, the connection between DEGs and differentially expressed miRNAs (DEMs) was explored. GEO2R was utilized to screen out DEGs and DEMs. A total of 668 DEGs and 5 DEMs were extracted from GSE7437 and GSE30934 differentiating samples of poor and good chemotherapy reaction patients. The Database for Annotation, Visualization, and Integrated Discovery (DAVID) was used to perform GO and KEGG pathway enrichment analysis to identify potential pathways and functional annotations linked with osteosarcoma chemoresistance. The present study may provide a deeper understanding about regulatory genes of osteosarcoma chemoresistance and identify potential therapeutic targets for osteosarcoma.

scholarly journals The training schedule affects the stability, not the magnitude, of the interlimb transfer of learned dynamics

2013 ◽  
Vol 110 (4) ◽  
pp. 984-998 ◽  
Author(s):  
Wilsaan M. Joiner ◽  
Jordan B. Brayanov ◽  
Maurice A. Smith
Keyword(s):  
Short Duration ◽  
Dynamic Environment ◽  
Internal Representation ◽  
Motor Adaptation ◽  
Training Period ◽  
Visually Guided ◽  
Brief Training ◽  
Long Duration ◽  
The Stability ◽  
The Right

The way that a motor adaptation is trained, for example, the manner in which it is introduced or the duration of the training period, can influence its internal representation. However, recent studies examining the gradual versus abrupt introduction of a novel environment have produced conflicting results. Here we examined how these effects determine the effector specificity of motor adaptation during visually guided reaching. After adaptation to velocity-dependent dynamics in the right arm, we estimated the amount of adaptation transferred to the left arm, using error-clamp measurement trials to directly measure changes in learned dynamics. We found that a small but significant amount of generalization to the untrained arm occurs under three different training schedules: a short-duration (15 trials) abrupt presentation, a long-duration (160 trials) abrupt presentation, and a long-duration gradual presentation of the novel dynamic environment. Remarkably, we found essentially no difference between the amount of interlimb generalization when comparing these schedules, with 9–12% transfer of the trained adaptation for all three. However, the duration of training had a pronounced effect on the stability of the interlimb transfer: The transfer elicited from short-duration training decayed rapidly, whereas the transfer from both long-duration training schedules was considerably more persistent (<50% vs. >90% retention over the first 20 trials). These results indicate that the amount of interlimb transfer is similar for gradual versus abrupt training and that interlimb transfer of learned dynamics can occur after even a brief training period but longer training is required for an enduring effect.

scholarly journals A circular RNAs dataset landscape reveals potential signatures for the detection and prognosis of early-stage lung adenocarcinoma

BMC Cancer ◽  
2021 ◽  
Vol 21 (1) ◽  
Author(s):  
Zhiying Chen ◽  
Jiahui Wei ◽  
Min Li ◽  
Yongjuan Zhao
Keyword(s):  
Functional Analysis ◽  
Survival Analysis ◽  
Lung Adenocarcinoma ◽  
Target Genes ◽  
Interaction Analysis ◽  
Early Stage ◽  
Gene Interaction ◽  
Gene Expression Omnibus ◽  
Circular Rnas ◽  
Cerna Network

Abstract Background This study aimed to identify potential circular ribonucleic acid (circRNA) signatures involved in the pathogenesis of early-stage lung adenocarcinoma (LAC). Methods The circRNA sequencing dataset of early-stage LAC was downloaded from the Gene Expression Omnibus database. First, the differentially expressed circRNAs (DEcircRNAs) between tumour and non-tumour tissues were screened. Then, the corresponding miRNAs and their target genes were predicted. In addition, prognosis-related genes were identified using survival analysis and further used to build a network of competitive endogenous RNAs (ceRNAs; DEcircRNA–miRNA–mRNA). Finally, the functional analysis and drug–gene interaction analysis of mRNAs in the ceRNA network was performed. Results A total of 35 DEcircRNAs (30 up-regulated and 5 down-regulated circRNAs) were identified. Moreover, 135 DEcircRNA–miRNA and 674 miRNA–mRNA pairs were predicted. The survival analysis of these target mRNAs revealed that 60 genes were significantly associated with survival outcomes in early-stage LAC. Of these, high levels of PSMA 5 and low levels of NAMPT, CPT 2 and TNFSF11 exhibited favourable prognoses. In addition, the DEcircRNA–miRNA–mRNA network was constructed, containing 5 miRNA–circRNA (hsa_circ_0092283/hsa-miR-762/hsa-miR-4685-5p; hsa_circ_0070610/hsa-let-7a-2-3p/hsa-miR-3622a-3p; hsa_circ_0062682/hsa-miR-4268) and 60 miRNA–mRNA pairs. Functional analysis of the genes in the ceRNA network showed that they were primarily enriched in the Wnt signalling pathway. Moreover, PSMA 5, NAMPT, CPT 2 and TNFSF11 had strong correlations with different drugs. Conclusion Three circRNAs (hsa_circ_0062682, hsa_circ_0092283 and hsa_circ_0070610) might be potential novel targets for the diagnosis of early-stage LAC.

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