Pilot study of changes in the level of piRNA in plasma and serum in women at different stages of physiological pregnancy

Aim. To study changes in the level of piRNA in plasma and serum of pregnant women at different stages of gestation.Material and Methods. A total of 42 samples of plasma and blood serum were obtained from seven women with physiological singleton pregnancy without obstetric and gynecological pathology. The study was carried out at three time points corresponding to 8–13, 18–25, and 30–35 weeks of pregnancy, respectively. To assess the spectrum and levels of piRNA by the NGS method, whole genome sequencing of small RNAs was carried out. Sequencing data analysis was performed using the GeneGlobe Data Analysis Center web application. Differential expression was assessed using the DESeq2 R package.Results and Discussion. The piRNA contents among all small RNAs were 2.29%, 2.61%, and 4.16% in plasma and 7.29%, 7.02%, and 10.82% in serum during the first, second, and third trimesters, respectively. The contents of the following piRNAs increased in blood plasma from the first to the third trimester: piR 000765, piR 020326, piR 019825, piR 020497, piR 015026, piR 001312, and piR 017716. The study showed that the levels of piR 000765, piR 020326, piR 019825, piR 015026, piR 020497, piR 001312, piR 017716, and piR 004153 were significantly higher in serum compared with the corresponding values in plasma whereas the content of only one molecule, piR 018849, was higher in plasma.Conclusion. This pilot work created a basis for understanding the processes of piRNA expression in plasma and serum of pregnant women and can become the foundation for the search for biomarkers of various complications in pregnancy.

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Oasis2.0: improved online analysis of small RNA-seq data

10.1101/170738 ◽

2017 ◽

Author(s):

Raza-Ur Rahman ◽

Abhivyakti Gautam ◽

Jörn Bethune ◽

Abdul Sattar ◽

Maksims Fiosins ◽

...

Keyword(s):

Deep Sequencing ◽

Small Rna ◽

Small Rnas ◽

Web Application ◽

The Novel ◽

Sequencing Data ◽

Essential Information ◽

Deep Sequencing Data ◽

Small Rna Deep Sequencing ◽

User Friendly

AbstractOasis 2 is a new main release of the Oasis web application for the detection, differential expression, and classification of small RNAs in deep sequencing data. Compared to its predecessor Oasis, Oasis 2 features a novel and speed-optimized sRNA detection module that supports the identification of small RNAs in any organism with higher accuracy. Next to the improved detection of small RNAs in a target organism, the software now also recognizes potential cross-species miRNAs and viral and bacterial sRNAs in infected samples. In addition, novel miRNAs can now be queried and visualized interactively, providing essential information for over 700 high-quality miRNA predictions across 14 organisms. Robust biomarker signatures can now be obtained using the novel enhanced classification module. Oasis 2 enables biologists and medical researchers to rapidly analyze and query small RNA deep sequencing data with improved precision, recall, and speed, in an interactive and user-friendly environment.Availability and Implementation: Oasis 2 is implemented in Java, J2EE, mysql, Python, R, PHP and JavaScript. It is freely available at http://oasis.dzne.de

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Random forest based similarity learning for single cell RNA sequencing data

10.1101/258699 ◽

2018 ◽

Author(s):

Maziyar Baran Pouyan ◽

Dennis Kostka

Keyword(s):

Data Analysis ◽

Random Forest ◽

Single Cells ◽

R Package ◽

Similarity Learning ◽

Sequencing Data ◽

Genome Wide ◽

Step Procedure ◽

Exploratory Data ◽

Cell Cell

AbstractMotivationGenome-wide transcriptome sequencing applied to single cells (scRNA-seq) is rapidly becoming an assay of choice across many fields of biological and biomedical research. Scientific objectives often revolve around discovery or characterization of types or sub-types of cells, and therefore obtaining accurate cell–cell similarities from scRNA-seq data is critical step in many studies. While rapid advances are being made in the development of tools for scRNA-seq data analysis, few approaches exist that explicitly address this task. Furthermore, abundance and type of noise present in scRNA-seq datasets suggest that application of generic methods, or of methods developed for bulk RNA-seq data, is likely suboptimal.ResultsHere we present RAFSIL, a random forest based approach to learn cell–cell similarities from scRNA-seq data. RAFSIL implements a two-step procedure, where feature construction geared towards scRNA-seq data is followed by similarity learning. It is designed to be adaptable and expandable, and RAFSIL similarities can be used for typical exploratory data analysis tasks like dimension reduction, visualization, and clustering. We show that our approach compares favorably with current methods across a diverse collection of datasets, and that it can be used to detect and highlight unwanted technical variation in scRNA-seq datasets in situations where other methods fail. Overall, RAFSIL implements a flexible approach yielding a useful tool that improves the analysis of scRNA-seq data.Availability and ImplementationThe RAFSIL R package is available online at www.kostkalab.net/software.html

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Pengaruh Teknik Akupressure Terhadap Nyeri Punggung Pada Ibu Hamil Di Wilayah Puskesmas Jogonalan I Klaten

Jurnal Kebidanan dan Kesehatan Tradisional ◽

10.37341/jkkt.v3i1.61 ◽

2018 ◽

Vol 3 (1) ◽

Author(s):

Niken Tri Sukeksi ◽

Gita Kostania ◽

Emy Suryani

Keyword(s):

Back Pain ◽

Data Analysis ◽

Experimental Design ◽

Pregnant Women ◽

Test Data ◽

Gestational Age ◽

Severe Pain ◽

Third Trimester ◽

Labour Process ◽

In Pregnancy

Abstract: Acupressure, Back Pain, Pregnancy. Acupressure is effective to relieve back pain in Meridian point. Acupressure technique is done to help pregnant women in relieving complaints in pregnancy such as nausea and vomiting. In labour process, this technique can be an induction of labor, and can reduce anxiety. The purpose is to know the influence of acupressure technique to relieve back pain for pregnant women in Puskesmas Jogonalan I area of Klaten. Research is pre experimental design with one group pretest posttest approach. The population is all pregnant women in Puskesmas Jogonalan I area of Klaten. The population target is all third trimester of pregnant women in Puskesmas Jogonalan I area of Klaten. Technique sampling is purposive sampling with 30 peopole, ang using t-test data analysis. The characteristics of respondents showed that most of them are 20-35 years old, their gestational age are 3137 weeks, their occupation are housewives, and most of them have 2-3 children. Degree of back pain in pregnant women before acupressure as many as 21 people (70%) are in severe pain. Degree of back pain in pregnant women after given acupressure as many as 24 people (80%) are in mild pain. There is influence of acupressure technique to relieve back pain for pregnant women in Puskesmas Jogonalan I area of Klaten (t =9,893; p=0,001<0,05).

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Pengaruh Terapi Musik Klasik terhadap Tingkat Kecemasan Pada Ibu Hamil Primigravida Trimester III

Window of Nursing Journal ◽

10.33096/won.v2i1.370 ◽

2021 ◽

Vol 2 (1) ◽

pp. 191-200

Author(s):

Hijrianti Suharnah ◽

Fatma Jama ◽

Suhermi Suhermi

Keyword(s):

Data Analysis ◽

Music Therapy ◽

Pregnant Women ◽

Research Design ◽

Classical Music ◽

Wilcoxon Test ◽

P Value ◽

Third Trimester ◽

Significance Level ◽

Anxiety Levels

Primigravida pregnancy is a condition that causes physical and psychological changes. One of the psychological aspects that affect pregnancy and can cause anxiety. This study aims to determine the effect of classical music therapy on anxiety levels in third trimester primigravida pregnant women at UPTD Puskesmas Turikale Kab. Maros. The research design used was a quasi experiment. The research design used was "One Group Pretest-Postest Design". The sample determination is done by total sampling technique with a sample size of 23 respondents. The intervention was given for 6 times of intervention for 2 weeks. The data analysis used was the Wilcoxon test data analysis with a significance level of α = 0.05. If the p value <0.05 then Ha is accepted, it means that there is an effect of the independent variable on the dependent variable The research results from statistical analysis using the Wilcoxon test obtained the value of ρ = 0.000, where the value of ρ is smaller than the value of α = 0.05, then Ha is accepted. The results of the study prove that there is an effect of classical music therapy on anxiety levels in Primigravida Trimester III pregnant women. The conclusion of this study is the effect of classical music therapy on the anxiety level of primigravida pregnant women. Before being given classical music therapy, the level of anxiety in the third trimester of primigravida pregnant women was mild anxiety, moderate anxiety and severe anxiety. Meanwhile, after being given classical music therapy intervention, there was a decrease in anxiety levels, namely not anxious, mild anxiety and moderate anxiety.

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rANOMALY: AmplicoN wOrkflow for Microbial community AnaLYsis

F1000Research ◽

10.12688/f1000research.27268.1 ◽

2021 ◽

Vol 10 ◽

pp. 7

Author(s):

Sebastien Theil ◽

Etienne Rifa

Keyword(s):

Data Analysis ◽

Microbial Community ◽

Statistical Tests ◽

Marker Gene ◽

R Package ◽

Microbial Community Analysis ◽

Differential Analysis ◽

Sequencing Data ◽

Statistical Validation ◽

Bioinformatic Tools

Bioinformatic tools for marker gene sequencing data analysis are continuously and rapidly evolving, thus integrating most recent techniques and tools is challenging. We present an R package for data analysis of 16S and ITS amplicons based sequencing. This workflow is based on several R functions and performs automatic treatments from fastq sequence files to diversity and differential analysis with statistical validation. The main purpose of this package is to automate bioinformatic analysis, ensure reproducibility between projects, and to be flexible enough to quickly integrate new bioinformatic tools or statistical methods. rANOMALY is an easy to install and customizable R package, that uses amplicon sequence variants (ASV) level for microbial community characterization. It integrates all assets of the latest bioinformatics methods, such as better sequence tracking, decontamination from control samples, use of multiple reference databases for taxonomic annotation, all main ecological analysis for which we propose advanced statistical tests, and a cross-validated differential analysis by four different methods. Our package produces ready to publish figures, and all of its outputs are made to be integrated in Rmarkdown code to produce automated reports.

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HTSstation: A Web Application and Open-Access Libraries for High-Throughput Sequencing Data Analysis

PLoS ONE ◽

10.1371/journal.pone.0085879 ◽

2014 ◽

Vol 9 (1) ◽

pp. e85879 ◽

Cited By ~ 67

Author(s):

Fabrice P. A. David ◽

Julien Delafontaine ◽

Solenne Carat ◽

Frederick J. Ross ◽

Gregory Lefebvre ◽

...

Keyword(s):

Data Analysis ◽

Open Access ◽

High Throughput ◽

Web Application ◽

High Throughput Sequencing ◽

Sequencing Data ◽

High Throughput Sequencing Data ◽

Sequencing Data Analysis

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Hubungan Pengetahuan Ibu Hamil Trimester III tentang Antenatal Care Terhadap Pelaksanaan K4

Jurnal Ilmiah PANNMED (Pharmacist, Analyst, Nurse, Nutrition, Midwivery, Environment, Dentist) ◽

10.36911/pannmed.v16i1.1022 ◽

2021 ◽

Vol 16 (1) ◽

pp. 120-124

Author(s):

Omiati Natalia ◽

Nurul Hikmah Annisa

Keyword(s):

High Education ◽

Data Analysis ◽

Antenatal Care ◽

Pregnant Women ◽

Third Trimester ◽

Chi Square ◽

Cross Sectional ◽

The Third ◽

The Relationship ◽

Mental And Physical Health

Antenatal care is a pregnancy check to optimize the mental and physical health of pregnant women, monitor the progress of pregnancy to ensure the health of the mother and the development of the baby. Recognizing early on any abnormalities or complications that may occur during pregnancy. The purpose of this study was to determine the relationship between the knowledge of third trimester pregnant women about antenatal care to the implementation of K4. The design used in this research is descriptive correlation withapproach cross sectional. Sampling was done by purposive sampling. Data analysis with chi square. From the results of the study the majority of respondents had good knowledge as many as 42 respondents (73.7%), and the majority of respondents did K4 as many as 50 respondents (87.7%). It can be concluded that there is a correlation between the knowledge of pregnant women in the third trimester of antenatal care to the implementation of K4 (value p = 0.000). From the results of this study it is known that with high education, the knowledge that is owned will be better and affect someone in applying it to implementation.

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RETA: An R package for whole exome and targeted region sequencing data analysis

10.1101/121384 ◽

2017 ◽

Author(s):

Mengbiao Guo ◽

Jing Yang ◽

Yu lung Lau ◽

Wanling Yang

Keyword(s):

Data Analysis ◽

R Package ◽

Targeted Sequencing ◽

Sequencing Data ◽

Comprehensive Understanding ◽

Mendelian Diseases ◽

Whole Exome ◽

One Stop ◽

Sequencing Data Analysis ◽

Advanced Visualization

AbstractWhole exome and targeted sequencing have been playing a major role in diagnoses of Mendelian diseases, but analysis of these data involves using many complicated tools and comprehensive understanding of the analysis results is difficult.Here, we report RETA, an R package to provide a one-stop analysis of these data and a comprehensive, interactive and easy-to-understand report with many advanced visualization features. It facilitates clinicians and scientists alike to better analyze and interpret this type of sequencing data for disease diagnoses.Availability and implementationhttps://github.com/reta-s/reta/[email protected]

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Fetal transverse cerebellar diameter measurement in intrauterine growth restriction: a more accurate parameter for gestational age assessment at term

International Journal of Reproduction Contraception Obstetrics and Gynecology ◽

10.18203/2320-1770.ijrcog20194862 ◽

2019 ◽

Vol 8 (11) ◽

pp. 4391

Author(s):

Saroj Mourya ◽

Harish Kumar Mourya ◽

Vimla Jain ◽

Manoj Verma

Keyword(s):

Pregnant Women ◽

Gestational Age ◽

Accurate Estimation ◽

Growth Disorders ◽

Third Trimester ◽

Singleton Pregnancy ◽

Age Assessment ◽

Medical College ◽

Significant Difference ◽

Reliable Parameter

Background: Assessment of fetal gestational age (GA) is an essential part of obstetric USG. Accurate knowledge of fetal GA is important to facilitate the best possible prenatal care and successful pregnancy outcome. For the estimation of GA the commonly used parameters in third trimester are:- BPD, HC, AC and FL. As all these parameters are affected by fetal growth disorders and fetal position. TCD can be used as another parameter for the estimation of GA in growth restricted fetuses.Methods: This study was conducted at Mahila Chikitsalaya Sanganeri Gate; SMS Medical College Jaipur from July 2005 to September 2006. A total of 80 pregnant women in third trimester with singleton pregnancy including 40 pregnant women with known cases of IUGR and 40 AGA fetuses were studied for TCD measure.Results: Correlation coefficient between TCD and gestational age was highly significant and no significant difference was found in TCD of AGA and IUGR fetuses.Conclusions: TCD measurement can be used as more reliable parameter for accurate estimation of gestational age in IUGR fetuses in third trimester.

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