Background signals and potential measurement errors in miRNA microarray analysis of IVF culture media

Objective: This study aims to identify differentially expressed salivary miRNAs and validate the diagnostic potential for idiopathic Parkinson's disease (PD). Also, the disease specificity of candidate miRNAs was evaluated between PD, multiple system atrophy (MSA), and essential tremor (ET).Methods: We collected salivary samples from 50 PD, 20 ET, and 20 MSA patients, as well as 30 healthy controls (HCs). In the discovery phase, salivary miRNA microarray analysis was performed. In-silico analysis was used to investigate the target genes of differentially expressed miRNAs and clustered pathways. In validation phase, RT-qPCR was performed with samples from 30 PD patients and 30 HCs. Subsequently, we investigated candidate miRNAs in all recruited subjects. Receiver operating characteristic curve and Spearman correlation analysis was performed to determine diagnostic usefulness.Results: We identified 43 miRNAs that were differentially expressed between 5 PD patients and 5 HCs by miRNA microarray analysis. Computational analysis revealed the target genes were clustered in the pathways associated with ubiquitin protein ligase activity. The result of RT-qPCR showed that the miR-29a-3p and miR-29c-3p were found to be significantly downregulated (p = 0.004, p = 0.027), whereas the miR-6756-5p was significantly upregulated in 30 PD patients compared with 30 HCs (p = 0.032). The miR-29a-3p expression level in PD patients was significantly lower than ET patients (p = 0.035), but higher than MSA patients (p < 0.0001). The diagnostic efficacy reached a little higher when the combination of miR-29a-3p and miR-29c-3p.Conclusion: The miRNA combination of salivary miR-29a-3p and miR-29c-3p has potential to be a diagnostic biomarker for idiopathic PD.

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Analysis of heavy ion beam probe potential measurement errors in the Madison Symmetric Torus

Review of Scientific Instruments ◽

10.1063/1.1787953 ◽

2004 ◽

Vol 75 (10) ◽

pp. 3502-3504 ◽

Cited By ~ 1

Author(s):

X. Zhang ◽

J. Lei ◽

K. A. Connor ◽

D. R. Demers ◽

P. M. Schoch ◽

...

Keyword(s):

Measurement Errors ◽

Ion Beam ◽

Heavy Ion ◽

Potential Measurement ◽

Madison Symmetric Torus ◽

Heavy Ion Beam ◽

Heavy Ion Beam Probe ◽

Probe Potential

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Abstract 4008: cDNA and miRNA microarray analysis comparing gastric and metastatic liver gastrointestinal stromal tumors

10.1158/1538-7445.am2014-4008 ◽

2014 ◽

Author(s):

Hirotoshi Kikuchi ◽

Ichirota Iino ◽

Shinichiro Miyazaki ◽

Yusuke Ozaki ◽

Yoshihiro Hiramatsu ◽

...

Keyword(s):

Microarray Analysis ◽

Gastrointestinal Stromal Tumors ◽

Mirna Microarray ◽

Stromal Tumors ◽

Metastatic Liver

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Experimentally friendly approach towards nonlocal correlations in multisetting N-partite Bell scenarios

Quantum ◽

10.22331/q-2021-04-14-430 ◽

2021 ◽

Vol 5 ◽

pp. 430

Author(s):

Artur Barasiński ◽

Antonín Černoch ◽

Wiesław Laskowski ◽

Karel Lemr ◽

Tamás Vértesi ◽

...

Keyword(s):

Measurement Errors ◽

Reference Frames ◽

Simple Procedure ◽

Bell Inequalities ◽

Point Of View ◽

Local Realism ◽

Theoretical Point ◽

Potential Measurement ◽

Complete Knowledge ◽

Feasible Alternative

In this work, we study a recently proposed operational measure of nonlocality by Fonseca and Parisio [Phys. Rev. A 92, 030101(R) (2015)] which describes the probability of violation of local realism under randomly sampled observables, and the strength of such violation as described by resistance to white noise admixture. While our knowledge concerning these quantities is well established from a theoretical point of view, the experimental counterpart is a considerably harder task and very little has been done in this field. It is caused by the lack of complete knowledge about the facets of the local polytope required for the analysis. In this paper, we propose a simple procedure towards experimentally determining both quantities for N-qubit pure states, based on the incomplete set of tight Bell inequalities. We show that the imprecision arising from this approach is of similar magnitude as the potential measurement errors. We also show that even with both a randomly chosen N-qubit pure state and randomly chosen measurement bases, a violation of local realism can be detected experimentally almost 100% of the time. Among other applications, our work provides a feasible alternative for the witnessing of genuine multipartite entanglement without aligned reference frames.

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Measurement errors in vision based displacement monitoring of masonry bridges

IABSE Symposium, Guimarães 2019: Towards a Resilient Built Environment Risk and Asset Management ◽

10.2749/guimaraes.2019.1026 ◽

2019 ◽

Author(s):

Sinan Acikgoz ◽

Matthew J. DeJong ◽

Kenichi Soga

Keyword(s):

Measurement Errors ◽

Measurement Accuracy ◽

Calibration Method ◽

Textured Surfaces ◽

Displacement Monitoring ◽

Camera Model ◽

Vanishing Points ◽

Potential Measurement ◽

Out Of Plane ◽

The Impact

<p>Vision based displacement monitoring techniques are increasingly used to monitor dynamic displacements in operational bridges. These techniques are particularly well-suited to remotely monitor masonry bridges, which possess textured surfaces that enable effective tracking of sub-mm displacements simultaneously at many locations of the bridge. However, end users need to be aware of potential measurement errors which can impact their measurements. This paper discusses two sources of errors which are particularly relevant for monitoring displacements in masonry bridges with the 2D DIC technique: scaling errors and out of plane movement induced errors. The former category of errors occur due to incorrect scaling of tracking results in pixel units to displacements in metric units. In this paper, a new calibration method is proposed to minimise these errors. The method uses the naturally existing parallel lines in the masonry texture to identify two vanishing points in the image. These vanishing points and the known world coordinates of an identified feature in the image are then used to determine the relative rotation of the image and object planes and the correct scaling factors for different displacement points. The second source of error relates to the limitation of 2D DIC to measure only planar displacements. When out of plane movements occur in the object plane, these are registered incorrectly as in-plane movements. Using a pinhole camera model, the impact of out of plane movements on measurement accuracy are quantified. The results provide insight into how out of plane errors may be minimised or removed in order to achieve a higher measurement accuracy. The findings are explained with the application of the aforementioned techniques to the monitoring of a masonry viaduct.</p>

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CDKN2A,NF2, andJUNare dysregulated among other genes by miRNAs in malignant mesothelioma-A miRNA microarray analysis

Genes Chromosomes and Cancer ◽

10.1002/gcc.20669 ◽

2009 ◽

Vol 48 (7) ◽

pp. 615-623 ◽

Cited By ~ 192

Author(s):

Mohamed Guled ◽

Leo Lahti ◽

Pamela M. Lindholm ◽

Kaisa Salmenkivi ◽

Izhar Bagwan ◽

...

Keyword(s):

Microarray Analysis ◽

Malignant Mesothelioma ◽

Mirna Microarray

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Microarray Analysis of Differentially Expressed microRNAs in Allergic Rhinitis

American Journal of Rhinology and Allergy ◽

10.2500/ajra.2011.25.3682 ◽

2011 ◽

Vol 25 (6) ◽

pp. e242-e246 ◽

Cited By ~ 44

Author(s):

Yu Shaoqing ◽

Zhang Ruxin ◽

Liu Guojun ◽

Yan Zhiqiang ◽

Hu Hua ◽

...

Keyword(s):

Allergic Rhinitis ◽

Microarray Analysis ◽

Nasal Mucosa ◽

Molecular Mechanisms ◽

Protein Translation ◽

Differentially Expressed ◽

Common Disease ◽

Rt Pcr ◽

Mirna Microarray ◽

Differentially Expressed Mirnas

Background Allergic rhinitis (AR) is a common disease characterized by chronic inflammation of the nasal mucosa, but we have not fully understood the mechanism responsible for the development of AR. MicroRNAs (miRNAs) are short endogenous noncoding RNAs regulating protein translation through a mechanism known as RNA interference. To understand the molecular mechanisms of miRNA involved in the pathogenesis of AR, expressed miRNAs in AR were investigated through genomewide microarray analysis. Methods Mammalian miRNA microarrays containing whole human mature and precursor miRNA sequences were used for analyzing eight samples of nasal mucosa of AR and eight samples of nonallergic patients. Quantitative reverse transcriptase–polymerase chain reaction (RT-PCR) of some different expressed miRNAs was used to confirm the array results. Results The miRNA microarray chip analysis identified 421 miRNAs differentially expressed in the nasal mucosa of AR, and a total of 9 miRNAs were identified in the AR group with twofold change compared with control samples (p < 0.05). These included up-regulated miRNAs, hsa-hsa-miR-7, and hsa-miRPlus-E1194, and down-regulated miRNAs, hsa-miR-498, hsa-miR-187, hsa-miR-874, hsa-miR-143, hsa-miR-886–3p, hsa-miR-224, and hsa-miR-767–5p. RT-PCR results also confirmed that part of differentially expressed miRNAs as hsa-miR-224, hsa-miR-187, and hsa-miR-143 were down-regulated in AR. Conclusion The report indicated that many miRNA expressions were altered in AR and differentially expressed miRNAs appear to be involved in the development of AR. The study of miRNAs may lead to a better understanding about the roles of identified miRNAs in the pathogenesis of AR; this would be considered in future therapeutic strategies.

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A Thermal Skin Model for Comparing Contact Skin Temperature Sensors and Assessing Measurement Errors

Sensors ◽

10.3390/s21144906 ◽

2021 ◽

Vol 21 (14) ◽

pp. 4906

Author(s):

Braid A. MacRae ◽

Christina M. Spengler ◽

Agnes Psikuta ◽

René M. Rossi ◽

Simon Annaheim

Keyword(s):

Skin Temperature ◽

Measurement Errors ◽

Local Temperature ◽

Experimental Session ◽

Adult Males ◽

Skin Model ◽

Potential Measurement ◽

Temperature Disturbance ◽

Custom Made ◽

Environment Temperature

To improve the measurement and subsequent use of human skin temperature (Tsk) data, there is a need for practical methods to compare Tsk sensors and to quantify and better understand measurement error. We sought to develop, evaluate, and utilize a skin model with skin-like thermal properties as a tool for benchtop Tsk sensor comparisons and assessments of local temperature disturbance and sensor bias over a range of surface temperatures. Inter-sensor comparisons performed on the model were compared to measurements performed in vivo, where 14 adult males completed an experimental session involving rest and cycling exercise. Three types of Tsk sensors (two of them commercially available and one custom made) were investigated. Skin-model-derived inter-sensor differences were similar (within ±0.4 °C) to the human trial when comparing the two commercial Tsk sensors, but not for the custom Tsk sensor. Using the skin model, all surface Tsk sensors caused a local temperature disturbance with the magnitude and direction dependent upon the sensor and attachment and linearly related to the surface-to-environment temperature gradient. Likewise, surface Tsk sensors also showed bias from both the underlying disturbed surface temperature and that same surface in its otherwise undisturbed state. This work supports the development and use of increasingly realistic benchtop skin models for practical Tsk sensor comparisons and for identifying potential measurement errors, both of which are important for future Tsk sensor design, characterization, correction, and end use.

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PO-112 The exploration of constitutively expressed myokines utilizing tissue-engineered skeletal muscle

Exercise Biochemistry Review ◽

10.14428/ebr.v1i4.9773 ◽

2018 ◽

Vol 1 (4) ◽

Author(s):

Tomohiro Nakamura ◽

Tatsuki Shibahara ◽

Aya Takamori ◽

Aki Nunomiya ◽

Makoto Miyata ◽

...

Keyword(s):

Mass Spectrometry ◽

Skeletal Muscle ◽

Molecular Weight ◽

Microarray Analysis ◽

Culture Media ◽

C2c12 Cells ◽

Low Molecular Weight ◽

Rt Pcr ◽

Culture Cells ◽

Muscle Culture

Objective Recent evidence has identified skeletal muscle as a secretory organ. Many myokines, which are bioactive substances secreted from skeletal muscle, have been identified in plane muscle culture cells. Compared to the plane muscle culture cells, the tissue-engineered muscle is an excellent model as culture system mimicked native skeletal muscle. However, constitutively expressed genes and secreted compounds from tissue-engineered muscle have not been analyzed sufficiently. The purposes of this study were 1) to clarify kinetics of constitutively secreted compounds, and 2) to explore constitutively expressed genes in the tissue-engineered muscle. Methods C2C12 cells embedded within collagen gel solution were placed between two tendons made up of elastase-treated acelluar porcine blood vessel. The constructs were cultured in growth media for 2 days and cultured in differentiation media for 6 days. To compare with plane culture cells, C2C12 cells were cultured in plane under the same condition as the construct. The culture media were obtained, and analyzed by MALDI-TOF Mass Spectrometry. Furthermore, constitutively up-regulated genes in tissue-engineered skeletal muscle were explored based on microarray analysis and confirmed by RT-PCR. Results MALDI-TOF Mass Spectrometry revealed that the number of detected peaks in tissue-engineered muscle was abundant compared to that of plane muscle culture cells, especially at range of low molecular weight. Furthermore, the detected peaks were substantially different among these culture media and specific peaks were identified in tissue-engineered muscle. Based on microarray analysis, the transcription of cholecystokinin identified, and confirmed the up-regulation in tissue-engineered skeletal muscle by RT-PCR. Conclusions These results suggested that the tissue-engineered muscle constitutively secreted many compounds compared to plane culture cells, especially at range of low molecular weight. Furthermore, the transcription of cholecystokinin was up-regulated in tissue-engineered skeletal muscle. Besides of the plane muscle culture cells, it is possible to expect to obtain novel myokines utilizing tissue-engineered muscle.

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Numerical study of the evaporation process and parameter estimation analysis of an evaporation experiment

Hydrology and Earth System Sciences Discussions ◽

10.5194/hessd-6-7385-2009 ◽

2009 ◽

Vol 6 (6) ◽

pp. 7385-7427

Author(s):

K. Schneider-Zapp ◽

O. Ippisch ◽

K. Roth

Keyword(s):

Parameter Estimation ◽

Measurement Errors ◽

Hydraulic Properties ◽

Numerical Study ◽

Response Surfaces ◽

Parameter Estimates ◽

Physical Analysis ◽

Potential Measurement ◽

Soil Atmosphere ◽

Experimental Findings

Abstract. Evaporation is an important process in soil-atmosphere interaction. The determination of hydraulic properties is one of the crucial parts in the simulation of water transport in porous media. Schneider et al. (2006) developed a new evaporation method to improve the estimation of hydraulic properties in the dry range. In this study we used numerical simulations of the experiment to study the physical dynamics in more detail, to optimise the boundary conditions and to choose the optimal combination of measurements. The physical analysis exposed, in accordance to experimental findings in the literature, two different evaporation regimes, a soil-atmosphere boundary layer dominated regime (regime I) in the saturated region and a hydraulically dominated regime (regime II). During this second regime a drying front forms which penetrates deeper into the soil as time passes. The sensitivity analysis showed that the result is especially sensitive at the transition between the two regimes. By using boundary condition changes it is possible to force the system to switch between the two regimes, e.g. from II back to I. Based on this findings a multistep experiment was developed. The response surfaces for all parameter combinations are flat and have a unique, localised minimum. Best parameter estimates are obtained if the evaporation flux and a potential measurement in 2 cm depth are used as target variables. Parameter estimation from simulated experiments with realistic measurement errors with a two-stage Monte-Carlo Levenberg-Marquardt procedure and manual rejection of obvious misfits lead to acceptable results for three different soil textures.

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