scholarly journals The Phase Shift Correlation function uncovers periodic Ulcerative Colitis microbiome relationships without temporal sampling

2020 ◽  
Author(s):  
Robert E. Brown ◽  
Alena Arlova ◽  
Patrick M. Gillevet
Keyword(s):  
Ulcerative Colitis ◽  
Correlation Function ◽  
Phase Shift ◽  
Pearson Correlation ◽  
The Other ◽  
Biological Processes ◽  
Spearman Correlation ◽  
Temporal Sampling ◽  
Phase Variance ◽  
Microbiome Data

AbstractCorrelation analysis is a fundamental technique to determine potential relationships within biological processes. However, many biological processes have been shown to function in a periodic manner. When modeling correlations, the fluctuations that are associated with periodicity cause significant issues. We have implemented a Phase Shift Correlation (PSC) algorithm, with a corresponding value PSCrho, to address the periodicity and phase variance associated with features that vary with the same frequency -- but are phase shifted. The phase shift could well indicate causality with one feature’s quantitative change leading to the change in the other feature.We applied the PSC algorithm to Ulcerative Colitis (UC) microbiome data and compared the resulting feature relationships with the equivalent Spearman correlation function results. PSC located many instances of higher phase shifted correlations, where the corresponding Pearson correlation was low.

scholarly journals Plasma Ephrin-A1 level in a cohort of diabetic retinopathy patients

2020 ◽  
Author(s):  
Danna Mao ◽  
Ying Hu ◽  
Qi Bao ◽  
Kewei Wu ◽  
Yaoding Zheng ◽  
...  
Keyword(s):  
Diabetic Retinopathy ◽  
Human Plasma ◽  
Statistical Difference ◽  
Pearson Correlation ◽  
Fasting Blood Glucose ◽  
The Other ◽  
Spearman Correlation ◽  
Patients With Diabetes ◽  
Pearson Correlation Analysis ◽  
One Way Anova

Abstract Background: To determine plasma ephrin-A1 and VEGF165 levels in a cohort of diabetic retinopathy patients.Methods: Plasma ephrin-A1 and VEGF165 levels in fifty-five subjects including 19 individuals without diabetes (non-DM), 16 patients with diabetes (DM) but without diabetic retinopathy, and 20 patients with diabetic retinopathy (DR), were determined by ELISA. Serum creatinine, total cholesterol, fasting blood glucose and HbA1c were also measured. One-way ANOVA , Kruskal-Wallis Test, Mann-Whitney U Test corrected by Bonferroni, Pearson Correlation Analysis and Spearman Correlation Coefficient Analysis were used for data analysis.Results: Ephrin-A1 expression could be detected in human plasma with an average of 1.52 ± 0.43 (mean ± SEM) ng/ml. In DR subjects, the plasma ephrin-A1concentration was 3.63 ± 4.63 ng/ml, which was significantly higher than that of the other two groups (non-DM: 0.27 ± 0.13 ng/ml, DM: 0.35 ± 0.34 ng/ml). The expression of VEGF165 in human plasma was 34.00 ± 42.55 pg/ml, with no statistical difference among the three groups. There was no correlation between ephrin-A1 and VEGF165 in human plasma, but there was a correlation between plasma ephrin-A1 and duration of diabetes.Conclusions: Plasma ephrin-A1 was highly expressed in patients with diabetic retinopathy, and there was no difference of plasma VEGF165 expression in patients with diabetic retinopathy compared to the other two groups, suggesting that changes of plasma ephrin-A1 may be a more sensitive biomarker than plasma VEGF165 in detecting diabetic retinopathy.

Pengaruh Kotbah, Musik Gereja Dan Fasilitas Gereja Terhadap Tingkat Kehadiran Jemaat

2016 ◽  
Vol 1 (1) ◽  
pp. 1-15
Author(s):  
Frederich Oscar Lontoh
Keyword(s):  
Regression Analysis ◽  
Multiple Regression Analysis ◽  
Church Music ◽  
Pearson Correlation ◽  
Descriptive Analysis ◽  
Target Population ◽  
The Other ◽  
Pearson Correlation Coefficient ◽  
Christian Church ◽  
The City

This research is titled " The influence of sermon, church music and church facilities on the level of attendance”. The purpose of research is to identify and analyze whether sermon, church music and church facilities have influence on the the level of attendance. The target population in this study is a Christian church members who live in the city of Surabaya.. Sample required is equal to 47 respondents. Through sampling stratified Random techniques.These influence was measured using Pearson correlation coefficient and multiple regression analysis, t-test and analysis of variance. Descriptive  analysis  were taken to analyze the level of attendance according to demographic groups.The hypothesis in this study are the sermon, church music and church facilities have positive and significant on the level of attendance. The results showed that collectively, there are positive and significant correlation among the sermon, church music and church facilities on the level of attendance  96,2%. It means that 96,2 % of level of attendance influenced by sermon, church music and church facilities and the other 28,9% by others. All of the variable partially have significant correlation to level of attendance.

scholarly journals Dental pulp stem cells overexpressing hepatocyte growth factor facilitate the repair of DSS-induced ulcerative colitis

2021 ◽  
Vol 12 (1) ◽  
Author(s):  
Ning Li ◽  
Yichi Zhang ◽  
Narayan Nepal ◽  
Guoqing Li ◽  
Ningning Yang ◽  
...  
Keyword(s):  
Oxidative Stress ◽  
Ulcerative Colitis ◽  
Body Weight ◽  
Stem Cell ◽  
Dental Pulp ◽  
The Other ◽  
Therapeutic Effects ◽  
Colon Injury ◽  
Treatment Groups ◽  
Hepatocyte Growth

Abstract Background Ulcerative colitis (UC) is a chronic and recurrent disease without satisfactory treatment strategies. Dental pulp stem cell (DPSC) transplantation has been proposed as a potential therapy for UC. This study aimed to investigate the therapeutic effects of the rat hepatocyte growth factor (HGF) gene transduced into DPSCs for UC. Methods The therapeutic effects of HGF-DPSCs transplanted intravenously into a rat model of UC induced by 5% dextran sulphate sodium (DSS) were compared with the other treatment groups (LV-HGF group, DPSCs group and GFP-DPSCs group). Immunofluorescence and immunohistochemistry were used to observe the localization and proliferation of HGF-DPSCs at the site of colon injury. The expression levels of inflammatory factors were detected by real-time quantitative PCR (RT-PCR) and western blotting. The oxidative stress markers were detected by ELISA. DAI scores and body weight changes were used to macroscopically evaluate the treatment of rats in each group. Results Immunofluorescence and immunohistochemistry assays showed that HGF-DPSCs homed to colon injury sites and colocalized with intestinal stem cell (ISC) markers (Bmi1, Musashi1 and Sox9) and significantly promoted protein expression (Bmi1, Musashi1, Sox9 and PCNA). Anti-inflammatory cytokine (TGF-β and IL-10) expression was the highest in the HGF-DPSCs group compared with the other treatment groups, while the expression of pro-inflammatory cytokines (TNF-α and INF-γ) was the lowest. Additionally, the oxidative stress response results showed that malondialdehyde (MDA) and myeloperoxidase (MPO) expression decreased while superoxide dismutase (SOD) expression increased, especially in the HGF-DPSCs group. The DAI scores showed a downward trend with time in the five treatment groups, whereas body weight increased, and the changes were most prominent in the HGF-DPSCs group. Conclusions The study indicated that HGF-DPSCs can alleviate injuries to the intestinal mucosa by transdifferentiating into ISC-like cells, promoting ISC-like cell proliferation, suppressing inflammatory responses and reducing oxidative stress damage, which provides new ideas for the clinical treatment of UC.

Are membrane properties essential for the circadian rhythm of Gonyaulax?

1984 ◽  
Vol 247 (2) ◽  
pp. R250-R256
Author(s):  
H. G. Scholubbers ◽  
W. Taylor ◽  
L. Rensing
Keyword(s):  
Circadian Rhythm ◽  
Phase Shift ◽  
Fluorescence Polarization ◽  
The Other ◽  
Membrane Properties ◽  
Response Curves ◽  
Whole Cells ◽  
Different Temperatures ◽  
Free Running ◽  
Free Running Period

Membrane properties of whole cells of Gonyaulax polyedra were measured by fluorescence polarization. Circadian changes of fluorescence polarization exist in exponentially growing cultures. They show an amplitude larger than that of stationary cultures, indicating that a part of the change is due to or amplified by an ongoing cell cycle. Measurements of parameters of the circadian glow rhythm were analyzed for possible correlation with the membrane data. Considerable differences (Q10 = 2.5-3.0) in fluorescence polarization were found in cultures kept at different temperatures ranging from 15 to 27.5 degrees C. The free-running period length at different temperatures, on the other hand, differed only slightly (Q10 = 0.9-1.1). Stationary cultures showed higher fluorescence polarization compared with growing cultures, whereas the free-running period lengths did not differ in cultures of various densities and growth rates. Temperature steps of different sign changed the fluorescence polarization slightly in different directions. The phase shift of 4-h pulses (-5, -9, +7 degrees C) resulted in maximal phase advances of 4, 6, and 2 h, respectively. The phasing of the phase-response curves was identical in all these experiments, a finding not to be expected if the pulses act via the measured membrane properties. Pulses of drugs that change the fluorescence polarization (e.g., chlorpromazine and lidocaine) did not or only slightly phase-shift the circadian rhythm.

The Relationship of Undifferentiated Mesenchymal Cells to TMJ Articular Tissue Thickness

1992 ◽  
Vol 71 (11) ◽  
pp. 1816-1821 ◽  
Author(s):  
C.A. Bibb ◽  
A.G. Pullinger ◽  
F. Baldioceda
Keyword(s):  
Soft Tissue ◽  
Inverse Relationship ◽  
Biological Processes ◽  
Spearman Correlation ◽  
Articular Eminence ◽  
Tissue Thickness ◽  
Cartilage Layer ◽  
Soft Tissue Thickness ◽  
Relationship Of ◽  
The Relationship

Undifferentiated mesenchymal (UM) cells, the progenitor cells of the cartilage layer, have been assigned a significant role in TMJ articular tissue maintenance. This was based on reports of UM cell reduction with increased soft-tissue thickness for the condyle and temporal component. However, the strength of this inverse relationship was not presented and remained unclear. The purpose of the present study was to assess the strength of the correlation between UM cell presence and soft-tissue thickness in young adult TMJs at autopsy. Sagittal histological sections from the central thirds of 50 joints were evaluated with respect to articular soft-tissue thickness, histological character, and UM cell presence in the condyle and temporal component. The superior sector ofthe condyle and the articular eminence showed the greatest variability in soft-tissue thickness and were the only areas to show localized UM cell absence. The eminence was the only location to show an inverse relationship between soft-tissue thickness and UM cell presence, and this was consistent in both an ANOVA (p = 0.0016) and a Spearman correlation analysis. However, the strength of this correlation was only moderate (rho = -0.52), and no such relationship was observed in any other location. This study suggests that the relationship between UM cell presence and soft-tissue thickness is more complex than previously hypothesized and that the contribution of UM cells to articular tissue maintenance has been overstated, while other biological processes were overlooked.

scholarly journals Interaction between photoperiod and variation in circadian rhythms in tomato

2022 ◽  
Author(s):  
Yanli Xiang ◽  
Thomas Sapir ◽  
Pauline Rouillard ◽  
Marina Ferrand ◽  
Jose M Jimenez-Gomez
Keyword(s):  
Seasonal Variation ◽  
Circadian Rhythms ◽  
Phase Shift ◽  
Circadian Clock ◽  
Environmental Changes ◽  
Circadian Clocks ◽  
Biological Processes ◽  
Near Isogenic Lines ◽  
Transcriptomic Profiling ◽  
Isogenic Lines

Many biological processes follow circadian rhythmicity and are controlled by the circadian clock. Predictable environmental changes such as seasonal variation in photoperiod can modulate circadian rhythms, allowing organisms to adjust to the time of the year. Modification of circadian clocks is especially relevant in crops to enhance their cultivability in specific regions by changing their sensibility to photoperiod. In tomato, the appearance of mutations in EMPFINDLICHER IM DUNKELROTEN LICHT 1 (EID1, Solyc09g075080) and NIGHT LIGHT-INDUCIBLE AND CLOCK-REGULATED GENE 2 (LNK2, Solyc01g068560) during domestication delayed its circadian rhythms, and allowed its expansion outside its equatorial origin. Here we study how variation in circadian rhythms in tomato affects its perception of photoperiod. To do this, we create near isogenic lines carrying combinations of wild alleles of EID1 and LNK2 and perform transcriptomic profiling under two different photoperiods. We observe that EID1, but not LNK2, has a large effect on the tomato transcriptome and its response to photoperiod. This large effect of EID1 is likely a consequence of the global phase shift elicited by this gene in tomato's circadian rhythms.

scholarly journals Identification of key genes and biological processes contributing to colitis associated dysplasia in ulcerative colitis

PeerJ ◽  
2021 ◽  
Vol 9 ◽  
pp. e11321
Author(s):  
Di Zhang ◽  
Pengguang Yan ◽  
Taotao Han ◽  
Xiaoyun Cheng ◽  
Jingnan Li
Keyword(s):  
Ulcerative Colitis ◽  
Mitochondrial Dysfunction ◽  
Single Gene ◽  
Enrichment Analysis ◽  
Functional Enrichment Analysis ◽  
Functional Enrichment ◽  
Cell Junction ◽  
Biological Processes ◽  
Hub Genes ◽  
Key Genes

Background Ulcerative colitis-associated colorectal cancer (UC-CRC) is a life-threatening complication of ulcerative colitis (UC). The mechanisms underlying UC-CRC remain to be elucidated. The purpose of this study was to explore the key genes and biological processes contributing to colitis-associated dysplasia (CAD) or carcinogenesis in UC via database mining, thus offering opportunities for early prediction and intervention of UC-CRC. Methods Microarray datasets (GSE47908 and GSE87466) were downloaded from Gene Expression Omnibus (GEO). Differentially expressed genes (DEGs) between groups of GSE47908 were identified using the “limma” R package. Weighted gene co-expression network analysis (WGCNA) based on DEGs between the CAD and control groups was conducted subsequently. Functional enrichment analysis was performed, and hub genes of selected modules were identified using the “clusterProfiler” R package. Single-gene gene set enrichment analysis (GSEA) was conducted to predict significant biological processes and pathways associated with the specified gene. Results Six functional modules were identified based on 4929 DEGs. Green and blue modules were selected because of their consistent correlation with UC and CAD, and the highest correlation coefficient with the progress of UC-associated carcinogenesis. Functional enrichment analysis revealed that genes of these two modules were significantly enriched in biological processes, including mitochondrial dysfunction, cell-cell junction, and immune responses. However, GSEA based on differential expression analysis between sporadic colorectal cancer (CRC) and normal controls from The Cancer Genome Atlas (TCGA) indicated that mitochondrial dysfunction may not be the major carcinogenic mechanism underlying sporadic CRC. Thirteen hub genes (SLC25A3, ACO2, AIFM1, ATP5A1, DLD, TFE3, UQCRC1, ADIPOR2, SLC35D1, TOR1AIP1, PRR5L, ATOX1, and DTX3) were identified. Their expression trends were validated in UC patients of GSE87466, and their potential carcinogenic effects in UC were supported by their known functions and other relevant studies reported in the literature. Single-gene GSEA indicated that biological processes and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways related to angiogenesis and immune response were positively correlated with the upregulation of TFE3, whereas those related to mitochondrial function and energy metabolism were negatively correlated with the upregulation of TFE3. Conclusions Using WGCNA, this study found two gene modules that were significantly correlated with CAD, of which 13 hub genes were identified as the potential key genes. The critical biological processes in which the genes of these two modules were significantly enriched include mitochondrial dysfunction, cell-cell junction, and immune responses. TFE3, a transcription factor related to mitochondrial function and cancers, may play a central role in UC-associated carcinogenesis.

Simulations in orthopedics and rehabilitation – Part I: Simulators

2016 ◽  
Vol 12 (4) ◽  
Author(s):  
Jacek Dygut ◽  
Piotr Piwowar ◽  
Maria Gołda ◽  
Krzysztof Popławski ◽  
Robert Jakubas ◽  
...  
Keyword(s):  
Computer Simulation ◽  
The Other ◽  
Fine Tuning ◽  
Patient Treatment ◽  
Biological Processes ◽  
Clinical Environment ◽  
Knowledge And Skills ◽  
Simulation Techniques ◽  
Resident Physicians ◽  
Different Types

AbstractNowadays, medical simulators and computer simulation programs are used to train various skills required in medicine. The development of medicine, including orthopedics and rehabilitation, has meant that resident physicians, within a much shorter period of time, must acquire the knowledge and skills that their older colleagues gained over years, learning as they operated on patients. For this reason, simulation very often helps the doctor and others engaged in health care train some techniques necessary during the work before they start working in a clinical environment. They have a chance of fine-tuning certain skills under nonclinical environment. On the other hand, simulation techniques are used in medical scientific research to know and explain the different biological processes that can be used for better patient treatment in the future. In this paper (Part I), the authors focused on the presentation of different types of simulators for the following purposes: test (conducted under laboratory conditions), training (incorporated into school, universities syllabus), diagnostic and therapeutic (within the hospital, clinics, private medical practice).

scholarly journals Advancing System Performance with Redundancy: From Biological to Artificial Designs

2019 ◽  
Vol 31 (3) ◽  
pp. 555-573 ◽  
Author(s):  
Anh Tuan Nguyen ◽  
Jian Xu ◽  
Diu Khue Luu ◽  
Qi Zhao ◽  
Zhi Yang
Keyword(s):  
Neural Network ◽  
System Performance ◽  
Human Vision ◽  
The Other ◽  
Superior Performance ◽  
Fundamental Characteristic ◽  
Unified Theory ◽  
Biological Processes ◽  
Accuracy And Precision ◽  
Similar Operation

Redundancy is a fundamental characteristic of many biological processes such as those in the genetic, visual, muscular, and nervous systems, yet its driven mechanism has not been fully comprehended. Until recently, the only understanding of redundancy is as a mean to attain fault tolerance, which is reflected in the design of many man-made systems. On the contrary, our previous work on redundant sensing (RS) has demonstrated an example where redundancy can be engineered solely for enhancing accuracy and precision. The design was inspired by the binocular structure of human vision, which we believe may share a similar operation. In this letter, we present a unified theory describing how such utilization of redundancy is feasible through two complementary mechanisms: representational redundancy (RPR) and entangled redundancy (ETR). We also point out two additional examples where our new understanding of redundancy can be applied to justify a system's superior performance. One is the human musculoskeletal system (HMS), a biological instance, and the other is the deep residual neural network (ResNet), an artificial counterpart. We envision that our theory would provide a framework for the future development of bio-inspired redundant artificial systems, as well as assist studies of the fundamental mechanisms governing various biological processes.

scholarly journals Variations of Salminus hilarii diet (Ostariophysi, Characidae): seasonal and ontogenetic effects

2015 ◽  
Vol 75 (3) ◽  
pp. 574-580
Author(s):  
GA Villares Junior ◽  
R Goitein
Keyword(s):  
Prey Size ◽  
Pearson Correlation ◽  
Feeding Activity ◽  
Stomach Contents ◽  
Food Composition ◽  
Spearman Correlation ◽  
Statistical Comparison ◽  
Significant Difference ◽  
Ontogenetic Effects ◽  
Size And Morphology

AbstractThis study described the variations seasonal and ontogenetic of Salminus hilarii diet. Samples were collected in the Sorocaba River, São Paulo, Brazil, one of the few rivers where individuals of the species still occur in a higher frequency. The preys consumed were analyzed by Importance Alimentary Index (AIi). To determine similarities between year seasons, the AIi data were analyzed by the Morisita-Horn index and reduced in cluster analysis, along with a statistical comparison made by one-way ANOSIM test (5%). The feeding activity was analyzed according to the stomach repletion index and compared among the year seasons using non parametric variance analysis Kruskal-Wallis test (5%). Comparison of prey consumed between immature and adult individuals was made by Spearman correlation (5%). A Pearson correlation (5%) was applied between the standard length of the fish and prey consumed, as well as between the mouth and prey heights. The analyzes of stomach contents showed that the diet of this species was exclusively piscivorous, with significant difference of prey consumption during the period, the same happening among adult and immature individuals. It was observed that these fishes use to swallow their prey whole and that significant correlations between size of predator and prey size can be observed. There is also correlation between the mouth height and the maximum prey depth. Salminus hilarii feeds on the available prey, and the species food composition and feeding activity depends on prey`s abundance, their size and morphology, as do the water temperatures.

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