scholarly journals Small-scale sequencing enables quality assessment of Ribo-Seq data: an example from Arabidopsis cell culture

Plant Methods ◽  
2021 ◽  
Vol 17 (1) ◽  
Author(s):  
Amir Mahboubi ◽  
Nicolas Delhomme ◽  
Sara Häggström ◽  
Johannes Hanson
Keyword(s):  
Data Analysis ◽  
Quality Assessment ◽  
Deep Sequencing ◽  
Translational Regulation ◽  
Length Distribution ◽  
Great Depth ◽  
Read Length ◽  
Small Scale ◽  
Library Construction ◽  
Site Distribution

Abstract Background Translation is a tightly regulated process, controlling the rate of protein synthesis in cells. Ribosome sequencing (Ribo-Seq) is a recently developed tool for studying actively translated mRNA and can thus directly address translational regulation. Ribo-Seq libraries need to be sequenced to a great depth due to high contamination by rRNA and other contaminating nucleic acid fragments. Deep sequencing is expensive, and it generates large volumes of data, making data analysis complicated and time consuming. Methods and results Here we developed a platform for Ribo-Seq library construction and data analysis to enable rapid quality assessment of Ribo-Seq libraries with the help of a small-scale sequencer. Our data show that several qualitative features of a Ribo-Seq library, such as read length distribution, P-site distribution, reading frame and triplet periodicity, can be effectively evaluated using only the data generated by a benchtop sequencer with a very limited number of reads. Conclusion Our pipeline enables rapid evaluation of Ribo-Seq libraries, opening up possibilities for optimization of Ribo-Seq library construction from difficult samples, and leading to better decision making prior to more costly deep sequencing.

Justifying the data analytical choice in single case research in relation to the expected data pattern

2019 ◽  
Author(s):  
Rumen Manolov
Keyword(s):  
Data Analysis ◽  
Visual Analysis ◽  
Multilevel Models ◽  
Single Case ◽  
Analytical Techniques ◽  
Real Data ◽  
Small Scale ◽  
Data User ◽  
Single Case Research ◽  
User Friendly

The lack of consensus regarding the most appropriate analytical techniques for single-case experimental designs data requires justifying the choice of any specific analytical option. The current text mentions some of the arguments, provided by methodologists and statisticians, in favor of several analytical techniques. Additionally, a small-scale literature review is performed in order to explore if and how applied researchers justify the analytical choices that they make. The review suggests that certain practices are not sufficiently explained. In order to improve the reporting regarding the data analytical decisions, it is proposed to choose and justify the data analytical approach prior to gathering the data. As a possible justification for data analysis plan, we propose using as a basis the expected the data pattern (specifically, the expectation about an improving baseline trend and about the immediate or progressive nature of the intervention effect). Although there are multiple alternatives for single-case data analysis, the current text focuses on visual analysis and multilevel models and illustrates an application of these analytical options with real data. User-friendly software is also developed.

scholarly journals Challenges of Big Data analysis

2014 ◽  
Vol 1 (2) ◽  
pp. 293-314 ◽  
Author(s):  
Jianqing Fan ◽  
Fang Han ◽  
Han Liu
Keyword(s):  
Big Data ◽  
Data Analysis ◽  
Measurement Errors ◽  
Modern Society ◽  
Big Data Analysis ◽  
Small Scale ◽  
Paradigm Change ◽  
Statistical Inferences ◽  
The One ◽  
And Storage

Abstract Big Data bring new opportunities to modern society and challenges to data scientists. On the one hand, Big Data hold great promises for discovering subtle population patterns and heterogeneities that are not possible with small-scale data. On the other hand, the massive sample size and high dimensionality of Big Data introduce unique computational and statistical challenges, including scalability and storage bottleneck, noise accumulation, spurious correlation, incidental endogeneity and measurement errors. These challenges are distinguished and require new computational and statistical paradigm. This paper gives overviews on the salient features of Big Data and how these features impact on paradigm change on statistical and computational methods as well as computing architectures. We also provide various new perspectives on the Big Data analysis and computation. In particular, we emphasize on the viability of the sparsest solution in high-confidence set and point out that exogenous assumptions in most statistical methods for Big Data cannot be validated due to incidental endogeneity. They can lead to wrong statistical inferences and consequently wrong scientific conclusions.

scholarly journals Massive Open Online Course Evaluation Methods: Systematic Review (Preprint)

2019 ◽  
Author(s):  
Abrar Alturkistani ◽  
Ching Lam ◽  
Kimberley Foley ◽  
Terese Stenfors ◽  
Elizabeth R Blum ◽  
...  
Keyword(s):  
Data Analysis ◽  
Data Collection ◽  
Quality Assessment ◽  
Study Design ◽  
Evaluation Methods ◽  
Course Evaluation ◽  
Data Sources ◽  
Massive Open Online ◽  
Analysis Methods ◽  
Data Analysis Methods

BACKGROUND Massive open online courses (MOOCs) have the potential to make a broader educational impact because many learners undertake these courses. Despite their reach, there is a lack of knowledge about which methods are used for evaluating these courses. OBJECTIVE The aim of this review was to identify current MOOC evaluation methods to inform future study designs. METHODS We systematically searched the following databases for studies published from January 2008 to October 2018: (1) Scopus, (2) Education Resources Information Center, (3) IEEE (Institute of Electrical and Electronic Engineers) Xplore, (4) PubMed, (5) Web of Science, (6) British Education Index, and (7) Google Scholar search engine. Two reviewers independently screened the abstracts and titles of the studies. Published studies in the English language that evaluated MOOCs were included. The study design of the evaluations, the underlying motivation for the evaluation studies, data collection, and data analysis methods were quantitatively and qualitatively analyzed. The quality of the included studies was appraised using the Cochrane Collaboration Risk of Bias Tool for randomized controlled trials (RCTs) and the National Institutes of Health—National Heart, Lung, and Blood Institute quality assessment tool for cohort observational studies and for before-after (pre-post) studies with no control group. RESULTS The initial search resulted in 3275 studies, and 33 eligible studies were included in this review. In total, 16 studies used a quantitative study design, 11 used a qualitative design, and 6 used a mixed methods study design. In all, 16 studies evaluated learner characteristics and behavior, and 20 studies evaluated learning outcomes and experiences. A total of 12 studies used 1 data source, 11 used 2 data sources, 7 used 3 data sources, 4 used 2 data sources, and 1 used 5 data sources. Overall, 3 studies used more than 3 data sources in their evaluation. In terms of the data analysis methods, quantitative methods were most prominent with descriptive and inferential statistics, which were the top 2 preferred methods. In all, 26 studies with a cross-sectional design had a low-quality assessment, whereas RCTs and quasi-experimental studies received a high-quality assessment. CONCLUSIONS The MOOC evaluation data collection and data analysis methods should be determined carefully on the basis of the aim of the evaluation. The MOOC evaluations are subject to bias, which could be reduced using pre-MOOC measures for comparison or by controlling for confounding variables. Future MOOC evaluations should consider using more diverse data sources and data analysis methods. INTERNATIONAL REGISTERED REPORT RR2-10.2196/12087

scholarly journals DISTRIBUSI UKURAN DAN PARAMETER POPULASI LOBSTER PASIR (Panulirus homarus) DI PERAIRAN ACEH BARAT

2015 ◽  
Vol 7 (3) ◽  
pp. 121
Author(s):  
Duranta D Kembaren ◽  
Erfind Nurdin
Keyword(s):  
Spiny Lobster ◽  
Length Distribution ◽  
Total Mortality ◽  
Landing Site ◽  
Point Of View ◽  
Population Parameters ◽  
Site Distribution ◽  
Exploitation Rate ◽  
Curve Method ◽  
Lobster Fishery

Penelitian tentang distribusi ukuran dan parameter populasi lobster pasir di perairan Aceh Barat dilakukan pada bulanApril sampai November 2013. Penelitian ini bertujuan untukmengkaji status lobster di perairan Aceh Barat dilihat dari aspek distribusi ukuran dan parameter populasinya. Pengamatan dan pengukuran lobster dilakukan di tempat pengumpul lobster dengan sistem sampling acak. Sebaran frekuensi panjang karapas selanjutnya ditabulasikan dan dianalisa dengan metode kurva logistik. Struktur ukuran lobster yang tertangkap menunjukkan bahwa lobster jantan dominan tertangkap dibawah ukuran nilai tengah 72,5 mm dan sebaliknya diatas ukuran nilai tengah 72,5 mm yang didominasi jenis kelamin betina. Lobster terlebih dahulu tertangkap sebelum mencapai ukuran matang gonad (Lc = 65,8mm< Lm= 76,8 mm). Puncak musim pemijahan terjadi pada bulan Mei dan Agustus. Panjang asimtosis (CL∞ ) sebesar 119,5 mm dengan laju pertumbuhan (K) 0,39/tahun serta laju kematian total (Z) 1,44/tahun, laju kematian alamiah (M) 0,67/tahun dan laju keamatian akibat penangkapan (F) 0,77/tahun. Laju eksploitasi sudah mengarah kepada penangkapan yang berlebih (E=0,54), oleh karena itu perlu dilakukan tindakan pengelolaan perikanan lobster yang berkelanjutan. Salah satu upaya yang dapat di tempuh adalah dengan menerapkan sistem penutupan musim penangkapan lobster pada saat terjadinya puncak musim pemijahan.Research on the length distribution and population parameters of scalloped spiny lobster conducted in the Aceh Barat waters during April to November 2013. The aim of this study was to assess lobster fishery status in this waters from the point of view their length size and population parameters. Sampel collected randomly in the lobster landing site. Distribution of carapace length frequency was tabulated and analysed using logistic curve method. Length composition of male lobster was dominated under 72,5 mm midlenght, while female lobster was dominated above 72,5 mm midlength. This study found that the scalloped spiny lobster was caught before their reach the size of maturity (Lc = 65,8 mm < Lm = 76,8 mm). The peak season of spawning was indicated on May and August. Asimtotic length (CL∞) of scalloped spiny lobster was 119,5 mm with the growth rate (K) 0,39/year, total mortality (Z) 1,44/year, natural mortality (M) 0,67/year, and fishing mortality (F) 0,77/year. Exploitation rate was leading to the overfishing condition (E=0,54). Thus, it is needed to manage the lobster fishery in this area to gain the sustainability. We suggest that closing system season should be applied, especially in the peak spawning season.

scholarly journals PENGARUH LATIHAN SMALL SIDED GAME TERHADAP AKURASI PASSING PADA SISWA EKSTRAKULIKULER FUTSAL SMP NEGERI 1 MUARO JAMBI

2019 ◽  
Vol 1 (2) ◽  
pp. 81-88
Author(s):  
Ahmad Muzaffar ◽  
Adhe Saputra
Keyword(s):  
High School ◽  
Data Analysis ◽  
Statistical Analysis ◽  
Junior High School ◽  
T Test ◽  
Small Scale ◽  
Training Method ◽  
Scale Field ◽  
Post Test ◽  
Soccer Training

Small sided-games training is a small-scale field, an appropriate situation developed for young players, so they can learn and develop. Small sided games training is also one of the methods of soccer training using smaller fields with fewer players. This training method  is a fairly effective exercise in physical improvement, techniques and tactics Passing is to feed the ball or pass the ball to a friend, while passing determination is the ability to set goals / pass the ball according to the goal or target. This research is an experimental research conducted with the aim to find out whether or not there is a result of something done on the sample to be studied. The research began with a pretest and ended with a posttest. The number of samples in this study amounted to 20 people. The training given was done during 16 meetings. This research was tested using a statistical analysis of the hipotsis test (t test). Based on data analysis, it can be concluded that the small sided games exercise gives a significant effect on the accuracy of passing on extracurricular students at SMP Negeri  1 Muaro Jambi, proven in the pre-test and post-test assessments with an average pre-test = 505 and post-test = 7.65, with the increment difference of 7.65. This can be seen by the T test that is Tcount = 3.492787 ˃ Ttable = 1.72913. Based on the results of research and  calculations from the data and discussions that have been carried out, this research proves that there is an influence of small sided games training on the passing accuracy of extracurricular students at Muaro Jambi State Junior High School. Small sided-games training is a small-scale field, an appropriate situation developed for young players, so they can learn and develop. Small sided games training is also one of the methods of soccer training using smaller fields with fewer players. This training method  is a fairly effective exercise in physical improvement, techniques and tactics Passing is to feed the ball or pass the ball to a friend, while passing determination is the ability to set goals / pass the ball according to the goal or target. This research is an experimental research conducted with the aim to find out whether or not there is a result of something done on the sample to be studied. The research began with a pretest and ended with a posttest. The number of samples in this study amounted to 20 people. The training given was done during 16 meetings. This research was tested using a statistical analysis of the hipotsis test (t test). Based on data analysis, it can be concluded that the small sided games exercise gives a significant effect on the accuracy of passing on extracurricular students at SMP Negeri  1 Muaro Jambi, proven in the pre-test and post-test assessments with an average pre-test = 505 and post-test = 7.65, with the increment difference of 7.65. This can be seen by the T test that is Tcount = 3.492787 ˃ Ttable = 1.72913. Based on the results of research and  calculations from the data and discussions that have been carried out, this research proves that there is an influence of small sided games training on the passing accuracy of extracurricular students at Muaro Jambi State Junior High School.

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