scholarly journals pcr: an R package for quality assessment, analysis and testing of qPCR data

2017 ◽  
Author(s):  
Mahmoud Ahmed ◽  
Deok Ryong Kim
Keyword(s):  
Quality Assessment ◽  
Target Genes ◽  
Statistical Significance ◽  
R Package ◽  
Statistical Testing ◽  
Control Group ◽  
Amplification Efficiency ◽  
Relative Expression ◽  
Qpcr Data

Background. Real-time quantitative PCR (qPCR) is a broadly used technique in the biomedical research. Currently, few different analysis models are used to determine the quality of data and to quantify the mRNA level across the experimental conditions. Methods. We developed an R package to implement methods for quality assessment, analysis and testing qPCR data for statistical significance. Double Delta CT and standard curve models were implemented to quantify the relative expression of target genes from CT in standard qPCR control-group experiments. In addition, calculation of amplification efficiency and curves from serial dilution qPCR experiments are used to assess the quality of the data. Finally, two-group testing and linear models were used to test for significance of the difference in expression control groups and conditions of interest.Results. Using two datasets from qPCR experiments, we applied different quality assessment, analysis and statistical testing in the pcr package and compared the results to the original published articles. The final relative expression values from the different models, as well as the intermediary outputs, were checked against the expected results in the original papers and were found to be accurate and reliable.Conclusion. The pcr package provides an intuitive and unified interface for its main functions to allow biologist to perform all necessary steps of qPCR analysis and produce graphs in a uniform way.

scholarly journals pcr: an R package for quality assessment, analysis and testing of qPCR data

2017 ◽  
Author(s):  
Mahmoud Ahmed ◽  
Deok Ryong Kim
Keyword(s):  
Quality Assessment ◽  
Target Genes ◽  
Statistical Significance ◽  
R Package ◽  
Statistical Testing ◽  
Control Group ◽  
Amplification Efficiency ◽  
Relative Expression ◽  
Qpcr Data

Background. Real-time quantitative PCR (qPCR) is a broadly used technique in the biomedical research. Currently, few different analysis models are used to determine the quality of data and to quantify the mRNA level across the experimental conditions. Methods. We developed an R package to implement methods for quality assessment, analysis and testing qPCR data for statistical significance. Double Delta CT and standard curve models were implemented to quantify the relative expression of target genes from CT in standard qPCR control-group experiments. In addition, calculation of amplification efficiency and curves from serial dilution qPCR experiments are used to assess the quality of the data. Finally, two-group testing and linear models were used to test for significance of the difference in expression control groups and conditions of interest.Results. Using two datasets from qPCR experiments, we applied different quality assessment, analysis and statistical testing in the pcr package and compared the results to the original published articles. The final relative expression values from the different models, as well as the intermediary outputs, were checked against the expected results in the original papers and were found to be accurate and reliable.Conclusion. The pcr package provides an intuitive and unified interface for its main functions to allow biologist to perform all necessary steps of qPCR analysis and produce graphs in a uniform way.

scholarly journals pcr: an R package for quality assessment, analysis and testing of qPCR data

PeerJ ◽  
2018 ◽  
Vol 6 ◽  
pp. e4473 ◽  
Author(s):  
Mahmoud Ahmed ◽  
Deok Ryong Kim
Keyword(s):  
Quality Assessment ◽  
Target Genes ◽  
Statistical Significance ◽  
R Package ◽  
Statistical Testing ◽  
Control Group ◽  
Amplification Efficiency ◽  
Relative Expression ◽  
Qpcr Data

Background Real-time quantitative PCR (qPCR) is a broadly used technique in the biomedical research. Currently, few different analysis models are used to determine the quality of data and to quantify the mRNA level across the experimental conditions. Methods We developed an R package to implement methods for quality assessment, analysis and testing qPCR data for statistical significance. Double Delta CT and standard curve models were implemented to quantify the relative expression of target genes from CT in standard qPCR control-group experiments. In addition, calculation of amplification efficiency and curves from serial dilution qPCR experiments are used to assess the quality of the data. Finally, two-group testing and linear models were used to test for significance of the difference in expression control groups and conditions of interest. Results Using two datasets from qPCR experiments, we applied different quality assessment, analysis and statistical testing in the pcr package and compared the results to the original published articles. The final relative expression values from the different models, as well as the intermediary outputs, were checked against the expected results in the original papers and were found to be accurate and reliable. Conclusion The pcr package provides an intuitive and unified interface for its main functions to allow biologist to perform all necessary steps of qPCR analysis and produce graphs in a uniform way.

scholarly journals The influence of the Kinesio Taping on selected ultrasonography measurements, and quality of life in patients with rotator cuff lesions

2020 ◽  
Vol 10 (1) ◽  
Author(s):  
Aneta Bac ◽  
Magdalena Wróbel ◽  
Katarzyna Ogrodzka-Ciechanowicz ◽  
Edyta Michalik ◽  
Anna Ścisłowska-Czarnecka
Keyword(s):  
Quality Of Life ◽  
Rotator Cuff ◽  
Statistical Significance ◽  
Control Group ◽  
Subacromial Space ◽  
Kinesio Taping ◽  
Significant Difference ◽  
Rotator Cuff Lesions ◽  
Significant Change

Abstract The assessment of the six-week influence of Kinesio Taping combined with a rehabilitation on selected ultrasonography measurements, the level of disability, and the quality of life in patients with rotator cuff lesions. 60 participants were randomly assigned into a taping group (KT combined with a six-week rehabilitating protocol) and a control group (only rehabilitation protocol). In all patients the following assessments were performed twice: USG, UEFI and NHP questionnaires. In the examination of the subacromial space and the subacromial bursa in the taping group, no statistical significance was observed. A statistically significant change in the thickness of the muscles was obtained only for the thickness of the infraspinatus in the taping group. A statistically significant change was obtained in the assessment of tendinopathy only for the supraspinatus muscle in both groups. Within both groups a statistically significant difference was observed in the average UEFI and NHP scores; however, the differences in the scores obtained between the groups were not statistically significant. The use of KT with a rehabilitation program did not yield statistically significantly better results in the improvement of selected shoulder region indicators, the function of the upper limb and the quality of life.

scholarly journals Implementation of the Omega (ω) Index to detect large-scale systematic cheating

2019 ◽  
Author(s):  
Alvin Vista
Keyword(s):  
Standardized Testing ◽  
Large Scale ◽  
Type I Error ◽  
R Package ◽  
Statistical Testing ◽  
System Level ◽  
Control Group ◽  
Type I ◽  
Data Contamination ◽  
Cheating Detection

Cheating detection is an important issue in standardized testing, especially in large-scale settings. Statistical approaches are often computationally intensive and require specialised software to conduct. We present a two-stage approach that quickly filters suspected groups using statistical testing on an IRT-based answer-copying index. We also present an approach to mitigate data contamination and improve the performance of the index. The computation of the index was implemented through a modified version of an open source R package, thus enabling wider access to the method. Using data from PIRLS 2011 (N=64,232) we conduct a simulation to demonstrate our approach. Type I error was well-controlled and no control group was falsely flagged for cheating, while 16 (combined n=12,569) of the 18 (combined n=14,149) simulated groups were detected. Implications for system-level cheating detection and further improvements of the approach were discussed.

scholarly journals Evaluation of edna: arts and dance for older people

2016 ◽  
Vol 20 (1) ◽  
pp. 46-56 ◽  
Author(s):  
Ann Skingley ◽  
Stephanie De'Ath ◽  
Luci Napleton
Keyword(s):  
Quality Of Life ◽  
Mixed Methods ◽  
Older People ◽  
Statistical Significance ◽  
Small Scale ◽  
Control Group ◽  
Life Questionnaire ◽  
Content Type ◽  
Art Forms

Purpose – The purpose of this paper is to evaluate the impact on health and well-being of participation in dance and arts activities by older people living in the community. Design/methodology/approach – A small-scale, mixed methods research design comprising pretest-posttest evaluation of a three month dance and arts programme. Two groups of older people underwent physical measures and completed a self-report quality of life questionnaire. Written comments and interview data were also gathered. Findings – Physical tests (n=14) demonstrated improvements in posture, shoulder mobility and balance in both groups following the intervention, with some measures reaching statistical significance. Quality of life evaluations (n=21) also showed improvement, with the mental health subscale reaching statistical significance. Qualitative data showed that participants enjoyed the programme and felt physical, psychological and social benefits. Research limitations/implications – The research involved only a small sample of volunteers and a limited programme length which limits its generalisability. The absence of a control group means that causality cannot be inferred. Future research should extend recruitment to a wider geographical area and a longer intervention which includes a control group. Practical implications – Future arts interventions for older people should include consultation prior to, and throughout the project. Commissioners should consider supporting arts for health projects, building in additional funding for evaluative work. Originality/value – This study has added to the evidence base through combining art forms within a mixed methods framework, illustrating the interplay between the art forms, the outcomes and the potential role of social context.

scholarly journals A Critical Overview of Systematic Reviews and Meta-Analyses on Acupuncture for Poststroke Insomnia

2020 ◽  
Vol 2020 ◽  
pp. 1-7
Author(s):  
Jinke Huang ◽  
Manli Wu ◽  
Simin Liang ◽  
Xiaohui Qin ◽  
Min Shen ◽  
...  
Keyword(s):  
Quality Assessment ◽  
Systematic Reviews ◽  
Methodological Quality ◽  
Acupuncture Treatment ◽  
Descriptive Analysis ◽  
Control Group ◽  
Evidence Quality ◽  
Meta Analyses ◽  
Quality Evidence

Objectives. Acupuncture has increasingly been used for insomnia relief after stroke. We aimed to evaluate the methodological quality and summarize the evidence regarding the effectiveness of acupuncture for poststroke insomnia (PSI) from systematic reviews/meta-analyses (SRs/MAs). Methods. Eight databases were searched from inception through August 23, 2020. SRs/MAs on acupuncture treatment for PSI were included. Methodological quality assessment was performed using Assessing the Methodological Quality of Systematic Reviews 2 (AMSTAR-2), and evidence quality assessment was performed using the Grading of Recommendations, Assessment, Development, and Evaluation (GRADE). Results. Six SRs/MAs on acupuncture treatment for PSI were included. The AMSTAR-2 showed that the methodological quality of all included SRs/MAs was rated as critically low. According to the evaluation results of GRADE, 38.9% (7/18) of outcomes were rated as very low-quality evidence, 22.2% (4/18) were low-quality evidence, and 8.9% (7/18) were moderate-quality evidence. Descriptive analysis results showed that acupuncture was an effective treatment modality for PSI. Conclusions. All included reviews indicated that acupuncture was more effective than the control group for the treatment of PSI, but the credibility of the results is limited owing to the generally low methodological and evidence quality of the included SRs/MAs. More high-quality evidence is needed to determine whether acupuncture is more effective than other treatments.

scholarly journals Effect of generalized ligamentous hyperlaxity related of quality of life in the foot: a case controlled study

2018 ◽  
Vol 64 (9) ◽  
pp. 819-823
Author(s):  
Patricia Palomo-López ◽  
Ricardo Becerro-de-Bengoa-Vallejo ◽  
Marta Elena Losa-Iglesias ◽  
Daniel López-López ◽  
David Rodríguez-Sanz ◽  
...  
Keyword(s):  
Quality Of Life ◽  
Statistical Significance ◽  
Health Centre ◽  
Controlled Study ◽  
Control Group ◽  
Foot Health ◽  
Health Differences ◽  
Related Quality ◽  
Health Related

SUMMARY Generalized ligamentous hyperlaxity (GLH) has been shown to predispose an individual to a number of orthopaedic conditions. Little is known about how GLH affects people’ foot health-related quality of life. This study analyses a sample of people with GLH and people without GLH with normalised reference values of the scores collected with regard to using the Foot Health Status Questionnaire (FSHQ). A total of 100 respondents with mean age of 22.69 ± 3.78 years old, who attended a health centre were classified as GLH (n = 50) or non-GLH (n = 50). The GLH was determined of the patients with and without GLH using assessment with Beighton tool and the scores on the FHSQ were compared. The control group recorded higher scores in the First Section for foot pain, foot function and general foot health, and lower scores in footwear. In the Second Section, they obtained higher scores in social capacity and lower scores in physical activity, vigour and general health. Differences between the two groups were evaluated through a t-test for independent samples, showing statistical significance (P<0.001). This study has detected measurable differences of association between GLH (Beighton score ≥4) with impaired quality of life related to foot health.

scholarly journals Effects of Natural Convalescent Factors Combined with Motor Intelligence Management on Patients’ Blood Pressure

2021 ◽  
Vol 2021 ◽  
pp. 1-7
Author(s):  
Shasha Li ◽  
Zhuoming Hu ◽  
Jianping Zhang
Keyword(s):  
Quality Of Life ◽  
Blood Pressure ◽  
Physical Function ◽  
Statistical Significance ◽  
Blood Pressure Level ◽  
Control Group ◽  
Observation Group ◽  
Research Subjects ◽  
The Difference

To explore the application of natural convalescent factors combined with exercise intelligence management in blood pressure control of patients with hypertension, 102 patients with hypertension who were admitted from January 2017 to August 2019 were selected as the research subjects. According to the odd-even number method, they were divided into two groups with 51 cases in each group. The control group was treated with natural convalescent factor therapy alone, and the observation group was treated with natural convalescent factor combined with motor intelligence management. The application effects of the two groups were compared. Before sports intelligence management, the levels of systolic blood pressure (SBP) in control group and observation group were (145.45 ± 8.44) mmHg (1 mmHg = 0.133 kPa) and (146.55 ± 8.37) mmHg, respectively; the diastolic blood pressure (DBP) levels of the control group and the observation group were (98.47 ± 3.48) mmHg and (98.94 ± 3.48) mmHg, respectively, with no statistical significance ( P > 0.05 ). After the exercise intelligence management, the SBP levels of the control group and the observation group were (132.76 ± 4.48) mmHg and (130.06 ± 2.48) mmHg, respectively. The DBP levels of the control group and the observation group were (85.48 ± 5.38) mmHg and (83.47 ± 3.35) mmHg, respectively. The difference was statistically significant ( P < 0.05 ). The scores of each index of quality of life in the observation group were higher than those in the control group, and the differences of physical function and psychological/mental scores were significant. The scores of physical function in the two groups before administration were (48.36 ± 1.69) and (48.74 ± 1.62), and the differences were not statistically significant ( P > 0.05 ). After management, the physiological function scores of the two groups were (40.32 ± 1.33) and (32.15 ± 1.54) and the difference was statistically significant ( P < 0.05 ). There were no significant differences in the psychological (30.75 ± 1.26)/mental scores (30.26 ± 1.48) between the two groups before management ( P > 0.05 ), but there were significant differences in the psychological (25.30 ± 1.02)/mental scores (18.76 ± 1.36) between the two groups after management ( P < 0.05 ). The combination of natural convalescent factors and intelligent exercise management can effectively control the blood pressure level and improve the quality of life of patients with hypertension, and the clinical application effect is good.

The Effect of Combination Use of Hemodialysis and Hemoperfusion on Microinflammation in Elderly Patients with Maintenance Hemodialysis

2022 ◽  
pp. 1-8
Author(s):  
Jun Li ◽  
Hui Li ◽  
Wenjiao Deng ◽  
Lixin Meng ◽  
Wenya Gong ◽  
...  
Keyword(s):  
Quality Of Life ◽  
Elderly Patients ◽  
Adverse Reactions ◽  
Statistical Significance ◽  
Continuous Treatment ◽  
Maintenance Hemodialysis ◽  
Control Group ◽  
Observation Group ◽  
Significant Difference

<b><i>Background:</i></b> Patients with maintenance hemodialysis (MHD) generally have a microinflammatory state. The aim of this study was to investigate the effects of hemodialysis (HD) combined with hemoperfusion (HP) on microinflammatory state in elderly patients with MHD. <b><i>Methods:</i></b> One hundred and fifty elderly patients with MHD were randomly divided into the control group and the observation group. The control group received simple HD treatment, and the observation group received combined HD + HP treatment on the basis of the control group. After 6 months of continuous treatment, the patients were evaluated to compare the quality of life, inflammation, adverse reactions, and nutritional indicators in the 2 groups before and after treatment. <b><i>Results:</i></b> There was no significant difference in the quality of life between the 2 groups before treatment. After treatment, the scores of psychological aspects, physiological aspects, social aspects, environmental aspects, and independent ability in the observation group were higher than those in the control group, with statistical significance (<i>p</i> &#x3c; 0.05). There was no statistical significance in the level of inflammation between 2 groups before treatment. After treatment, the levels of hs-CRP, Hcy, IL-6, and TNF-α in the observation group were significantly lower than those in the control group, with statistical significance (<i>p</i> &#x3c; 0.05). The incidence of dry mouth, skin reaction, neuritis, and subcutaneous tissue fibrosis in the observation group was lower than that in the control group, with statistical significance (<i>p</i> &#x3c; 0.05). There was no statistical significance in nutritional level indexes between 2 groups before treatment (<i>p</i><sub>1</sub> &#x3e; 0.05). After treatment, the levels of hemoglobin, total protein, albumin, and transferrin in the observation group were significantly higher than those in the control group, with statistical significance (<i>p</i> &#x3c; 0.05). <b><i>Conclusion:</i></b> The clinical effect of HD combined with HP in elderly MHD patients is significant, which can effectively reduce the incidence of adverse reactions and inflammation in the patients and improve the quality of life and nutritional indicators of the patients.

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