scholarly journals Comparative analysis of ChIP-exo peak-callers: impact of data quality, read duplication and binding subtypes

2020 ◽  
Author(s):  
Vasudha Sharma ◽  
Sharmistha MAJUMDAR
Keyword(s):  
Chromatin Immunoprecipitation ◽  
Binding Mode ◽  
Dna Interaction ◽  
Binding Mode Prediction ◽  
Direct Binding ◽  
Single Base Pair ◽  
Self Learning ◽  
Peak Caller ◽  
Better Than

Abstract Background: ChIP (Chromatin immunoprecipitation)-exo has emerged as an important and versatile improvement over conventional ChIP-seq as it reduces the level of noise, maps the transcription factor (TF) binding location in a very precise manner, upto single base-pair resolution, and enables binding mode prediction. Availability of numerous peak-callers for analyzing ChIP-exo reads has motivated the need to assess their performance and report which tool executes reasonably well for the task. Results: This study has focussed on comparing peak-callers that report direct binding events with those that report indirect binding events. The effect of strandedness of reads and duplication of data on the performance of peak-callers has been investigated. The number of peaks reported by each peak-caller is compared followed by a comparison of the annotated motifs present in the reported peaks. The significance of peaks is assessed based on the presence of a motif in top peaks. Indirect binding tools have been compared on the basis of their ability to identify annotated motifs and predict mode of protein-DNA interaction. Conclusion: By studying the output of the peak-callers investigated in this study, it is concluded that the tools that use self-learning algorithms, i.e. the tools that estimate all the essential parameters from the aligned reads, perform better than the algorithms which require formation of peak-pairs. The latest tools that account for indirect binding of TFs appear to be an upgrade over the available tools, as they are able to reveal valuable information about the mode of binding in addition to direct binding. Furthermore, the quality of ChIP-exo reads have important consequences on the output of data analysis.

scholarly journals Comparative analysis of ChIP-exo peak-callers: impact of data quality, read duplication and binding subtypes

2019 ◽  
Author(s):  
Vasudha Sharma ◽  
Sharmistha MAJUMDAR
Keyword(s):  
Chromatin Immunoprecipitation ◽  
Binding Mode ◽  
Dna Interaction ◽  
Binding Mode Prediction ◽  
Direct Binding ◽  
Single Base Pair ◽  
Self Learning ◽  
Peak Caller ◽  
Better Than

Abstract Background: ChIP (Chromatin immunoprecipitation)-exo has emerged as an important and versatile improvement over conventional ChIP-seq as it reduces the level of noise, maps the transcription factor (TF) binding location in a very precise manner, upto single base-pair resolution, and enables binding mode prediction. Availability of numerous peak-callers for analyzing ChIP-exo reads has motivated the need to assess their performance and report which tool executes reasonably well for the task. Results: This study has focussed on comparing peak-callers that report direct binding events with those that report indirect binding events. The effect of strandedness of reads and duplication of data on the performance of peak-callers has been investigated. The number of peaks reported by each peak-caller is compared followed by a comparison of the annotated motifs present in the reported peaks. The significance of peaks is assessed based on the presence of a motif in top peaks. Indirect binding tools have been compared on the basis of their ability to identify annotated motifs and predict mode of protein-DNA interaction. Conclusion: By studying the output of the peak-callers investigated in this study, it is concluded that the tools that use self-learning algorithms, i.e. the tools that estimate all the essential parameters from the aligned reads, perform better than the algorithms which require formation of peak-pairs. The latest tools that account for indirect binding of TFs appear to be an upgrade over the available tools, as they are able to reveal valuable information about the mode of binding in addition to direct binding. Furthermore, the quality of ChIP-exo reads have important consequences on the output of data analysis.

scholarly journals Comparative analysis of ChIP-exo peak-callers: impact of data quality, read duplication and binding subtypes

2019 ◽  
Author(s):  
Vasudha Sharma ◽  
Sharmistha Majumdar
Keyword(s):  
Chromatin Immunoprecipitation ◽  
Binding Mode ◽  
Dna Interaction ◽  
Binding Mode Prediction ◽  
Direct Binding ◽  
Single Base Pair ◽  
Self Learning ◽  
Peak Caller ◽  
Better Than

AbstractBackgroundChIP (Chromatin immunoprecipitation)-exo has emerged as an important and versatile improvement over conventional ChIP-seq as it reduces the level of noise, maps the transcription factor (TF) binding location in a very precise manner, upto single base-pair resolution, and enables binding mode prediction. Availability of numerous peak-callers for analyzing ChIP-exo reads has motivated the need to assess their performance and report which tool executes reasonably well for the task.ResultsThis study has focussed on comparing peak-callers that report direct binding events with those that report indirect binding events. The effect of strandedness of reads and duplication of data on the performance of peak-callers has been investigated. The number of peaks reported by each peak-caller is compared followed by a comparison of the annotated motifs present in the reported peaks. The significance of peaks is assessed based on the presence of a motif in top peaks. Indirect binding tools have been compared on the basis of their ability to identify annotated motifs and predict mode of protein-DNA interaction.ConclusionBy studying the output of the peak-callers investigated in this study, it is concluded that the tools that use self-learning algorithms, i.e. the tools that estimate all the essential parameters from the aligned reads, perform better than the algorithms which require formation of peak-pairs. The latest tools that account for indirect binding of TFs appear to be an upgrade over the available tools, as they are able to reveal valuable information about the mode of binding in addition to direct binding. Furthermore, the quality of ChIP-exo reads have important consequences on the output of data analysis.

scholarly journals Comparative analysis of ChIP-exo peak-callers: impact of data quality, read duplication and binding subtypes

2020 ◽  
Author(s):  
Vasudha Sharma ◽  
Sharmistha Majumdar
Keyword(s):  
Chromatin Immunoprecipitation ◽  
Binding Mode ◽  
Dna Interaction ◽  
Binding Mode Prediction ◽  
Direct Binding ◽  
Single Base Pair ◽  
Self Learning ◽  
Peak Caller ◽  
Better Than

Abstract Background: ChIP (Chromatin immunoprecipitation)-exo has emerged as an important and versatile improvement over conventional ChIP-seq as it reduces the level of noise, maps the transcription factor (TF) binding location in a very precise manner, upto single base-pair resolution, and enables binding mode prediction. Availability of numerous peak-callers for analyzing ChIP-exo reads has motivated the need to assess their performance and report which tool executes reasonably well for the task. Results: This study has focussed on comparing peak-callers that report direct binding events with those that report indirect binding events. The effect of strandedness of reads and duplication of data on the performance of peak-callers has been investigated. The number of peaks reported by each peak-caller is compared followed by a comparison of the annotated motifs present in the reported peaks. The significance of peaks is assessed based on the presence of a motif in top peaks. Indirect binding tools have been compared on the basis of their ability to identify annotated motifs and predict mode of protein-DNA interaction. Conclusion: By studying the output of the peak-callers investigated in this study, it is concluded that the tools that use self-learning algorithms, i.e. the tools that estimate all the essential parameters from the aligned reads, perform better than the algorithms which require formation of peak-pairs. The latest tools that account for indirect binding of TFs appear to be an upgrade over the available tools, as they are able to reveal valuable information about the mode of binding in addition to direct binding. Furthermore, the quality of ChIP-exo reads have important consequences on the output of data analysis.

Kepuasan Masyarakat Terhadap Pelayanan Kelurahan Setelah Pemekaran Di Tangerang Selatan

Liquidity ◽  
2018 ◽  
Vol 2 (2) ◽  
pp. 151-159
Author(s):  
Pitri Yandri
Keyword(s):  
Public Perception ◽  
Service Personnel ◽  
Urban Services ◽  
Hospitality Workers ◽  
Care Workers ◽  
Before And After ◽  
Cartesian Diagram ◽  
Better Than

The purpose of this study is (1) to analyze public perception on urban services before and after the expansion of the region, (2) analyze the level of people's satisfaction with urban services, and (3) analyze the determinants of the variables that determine what level of people's satisfaction urban services. This study concluded that first, after the expansion, the quality of urban services in South Tangerang City is better than before. Secondly, however, public satisfaction with the services only reached 48.53% (poor scale). Third, by using a Cartesian Diagram, the second priority that must be addressed are: (1) clarity of service personnel, (2) the discipline of service personnel, (3) responsibility for care workers; (4) the speed of service, (5) the ability of officers services, (6) obtain justice services, and (7) the courtesy and hospitality workers.

Implementasi Voip Server Berbasis IPV6 Dengan Raspberry PI

2019 ◽  
Vol 9 (01) ◽  
pp. 47-54
Author(s):  
Rabbai San Arif ◽  
Yuli Fitrisia ◽  
Agus Urip Ari Wibowo
Keyword(s):  
Internet Protocol ◽  
Wireless Transmission ◽  
Raspberry Pi ◽  
Test Results ◽  
Average Delay ◽  
Ipv6 Network ◽  
Ip Network ◽  
Selection Of ◽  
Better Than

Voice over Internet Protocol (VoIP) is a telecommunications technology that is able to pass the communication service in Internet Protocol networks so as to allow communicating between users in an IP network. However VoIP technology still has weakness in the Quality of Service (QoS). VOPI weaknesses is affected by the selection of the physical servers used. In this research, VoIP is configured on Linux operating system with Asterisk as VoIP application server and integrated on a Raspberry Pi by using wired and wireless network as the transmission medium. Because of depletion of IPv4 capacity that can be used on the network, it needs to be applied to VoIP system using the IPv6 network protocol with supports devices. The test results by using a wired transmission medium that has obtained are the average delay is 117.851 ms, jitter is 5.796 ms, packet loss is 0.38%, throughput is 962.861 kbps, 8.33% of CPU usage and 59.33% of memory usage. The analysis shows that the wired transmission media is better than the wireless transmission media and wireless-wired.

Motilitas dan Vabilitas Spermatozoa Ayam Kampung pada Suhu 5°C Menggunakan Pengencer dan Lama Simpan yang Berbeda

2018 ◽  
Vol 5 (2) ◽  
pp. 102
Author(s):  
Enike Dwi Kusumawati ◽  
Selvinus Lawu Woli ◽  
Aju Tjatur Nugroho Krisnaningsih ◽  
Waluyo Edi Susanto ◽  
Syam Rahadi
Keyword(s):  
Data Analysis ◽  
Storage Temperature ◽  
Coconut Water ◽  
Laboratory Research ◽  
Ringer Lactate ◽  
Randomized Design ◽  
Native Chicken ◽  
Lactate Solution ◽  
Better Than

ABSTRAKPenelitian ini dilakukan untuk mengetahui motilitas dan viabilitas spermatozoa ayam kampung pada suhu 5oC menggunakan pengencer dan lama simpan yang berbeda. Metode yang digunakan dalam penelitian ini adalah penelitian laboratorium menggunakan Rancangan Acak Lengkap (RAL) Faktorial dengan pengencer ringer lactat solution, air kelapa dan tanpa pengencer serta lama simpan 0, 3, 6, 9, 12, 15, 18, 21, 24, 27, 30, masing-masing diulang 10 kali. Variabel yang diamati yaitu motilitas dan viabilitas spermatozoa. Analisa data yang digunakan adalah analisis varian. Hasil analisis data menunjukkan bahwa motilitas dan viabilitas spermatozoa menggunakan pengencer ringer lactat solution lebih tinggi (P<0,01) serta dapat bertahan sampai lama simpan 24 jam dibandingkan air kelapa dan tanpa pengencer. Adapun nilai motilitas ringer lactat solution, air kelapa dan tanpa pengencer pada lama simpan 24 jam masing-masing sebesar 43,5±17,17%; 8±4,83%; 6,5±2,4%, sedangkan nilai viabilitasnya sebesar 83,2±7,25%; 64,6±3,20%; dan 63,1±2,33%. Kesimpulan dari hasil penelitian ini adalah ringer lactat solution lebih baik dibandingkan air kelapa dan tanpa pengencer dalam mempertahankan kualitas semen ayam kampung pada suhu simpan 5oC sampai lama simpan 24 jam.Kata Kunci : air kelapa, ayam kampung, motilitas, spermatozoa, viabilitas  ABSTRACTThis study was conducted to determine the motility and viability of spermatozoa of Native chickens at 5oC using different diluents and time storage. The method used in this study was laboratory research using Factorial Completely Randomized Design with ringer lactate solution, coconut water and without diluent at 0, 3, 6, 9, 12, 15, 18, 21, 24, 27, 30 hours of time storage each repeated 10 times. The variables observed were motility and viability of sperm. Data analysis used is variance analysis. The results of data analysis showed that the motility and viability of spermatozoa using ringer lactate solution diluents was higher (P <0.05) than coconut water and without diluents. The motility values of ringer lactat solution, coconut water and without diluents were 43,5±17,17%; 8±4,83%; 6,5±2,4% respectively, while the viability values were 83,2±7,25%; 64,6±3,20% and 63,1±2,33%. The conclusion of this study is that ringer lactat solution is better than coconut water an without diluents in maintaining the quality of Native chicken semen at a storage temperature of 5oC until 24 hours.Keywords: coconut water, motility, native chicken, sperm, viability

PERBANDINGAN KUALITAS PELAYANAN ANTARA PERPUSTAKAAN PROVINSI KEPRI DENGAN KOTA TANJUNG PINANG

2017 ◽  
Vol 2 (3) ◽  
pp. 288
Author(s):  
Dimas Satriadi
Keyword(s):  
Service Quality ◽  
Public Service ◽  
Quantitative Methods ◽  
Quality Service ◽  
Data Collecting ◽  
Service Institution ◽  
Better Than

<p><em>The quality of public service is an important and it must have bye the each public service institution. Includes the library as a public service institution giving service for the all visitors. This research aims to know the comparisation of Kepri Province Libraries quality service  and Tanjungpinang City Libraries quality service. The method used in this research is quantitative methods with questionnaire to 40 responden as samples. This questionnaire as an data collecting instruments. These results indicate the quality of two libraries is good. But, if they compared the service quality of  Province Kepri  Libraries is better than  Tanjungpinang City Libraries. This look from average scored  results is 152,61 points  for Kepri Province Libraries, and 150,66 points for Tanjungpinang City Libraries, in the good categories</em></p><p>Kualitas pelayanan publik merupakan hal yang penting dan harus dimiliki oleh masing-masing lembaga pelayanan publik. Termasuk perpustakaan sebagai lembaga pelayanan publik yang memberikan pelayanan kepada semua pengunjung. Penelitian ini bertujuan untuk mengetahui perbandingan kualitas layanan Perpustakaan Provinsi Kepri dan kualitas pelayanan Perpustakaan Kota Tanjungpinang. Metode yang digunakan dalam penelitian ini adalah metode kuantitatif dengan 40 responden sebagai sampel. Kuesioner ini sebagai alat pengumpul data. Hasil penelitian ini menunjukkan kualitas kedua perpustakaan suda bagus. Tapi jika dibandingkan kualitas pelayanan Perpustakaan Provinsi Kepri lebih baik dari pada Perpustakaan Kota Tanjungpinang. Hasil dari hasil rata-rata ini adalah 152,61 poin untuk Perpustakaan Kepri Province, dan 150,66 poin untuk Perpustakaan Kota Tanjungpinang, dalam kategori baik.</p><p><em><br /></em></p>

scholarly journals Performance Evaluation of IMERG GPM Products during Tropical Storm Imelda

Atmosphere ◽  
2021 ◽  
Vol 12 (6) ◽  
pp. 687
Author(s):  
Salman Sakib ◽  
Dawit Ghebreyesus ◽  
Hatim O. Sharif
Keyword(s):  
Stage Iv ◽  
Tropical Storm ◽  
Average Correlation ◽  
Acceptable Range ◽  
Precipitation Estimates ◽  
Overall Performance ◽  
Early Late ◽  
Statistical Metrics ◽  
Better Than

Tropical Storm Imelda struck the southeast coastal regions of Texas from 17–19 September, 2019, and delivered precipitation above 500 mm over about 6000 km2. The performance of the three IMERG (Early-, Late-, and Final-run) GPM satellite-based precipitation products was evaluated against Stage-IV radar precipitation estimates. Basic and probabilistic statistical metrics, such as CC, RSME, RBIAS, POD, FAR, CSI, and PSS were employed to assess the performance of the IMERG products. The products captured the event adequately, with a fairly high POD value of 0.9. The best product (Early-run) showed an average correlation coefficient of 0.60. The algorithm used to produce the Final-run improved the quality of the data by removing systematic errors that occurred in the near-real-time products. Less than 5 mm RMSE error was experienced in over three-quarters (ranging from 73% to 76%) of the area by all three IMERG products in estimating the Tropical Storm Imelda. The Early-run product showed a much better RBIAS relatively to the Final-run product. The overall performance was poor, as areas with an acceptable range of RBIAS (i.e., between −10% and 10%) in all the three IMERG products were only 16% to 17% of the total area. Overall, the Early-run product was found to be better than Late- and Final-run.

A new approach based on graph matching and evolutionary approach for sport scheduling problem

2020 ◽  
pp. 1-16
Author(s):  
Meriem Khelifa ◽  
Dalila Boughaci ◽  
Esma Aïmeur
Keyword(s):  
Graph Matching ◽  
State Of The Art ◽  
Travel Cost ◽  
Round Robin ◽  
New Approach ◽  
Traveling Tournament Problem ◽  
Significant Interest ◽  
National League ◽  
Better Than

The Traveling Tournament Problem (TTP) is concerned with finding a double round-robin tournament schedule that minimizes the total distances traveled by the teams. It has attracted significant interest recently since a favorable TTP schedule can result in significant savings for the league. This paper proposes an original evolutionary algorithm for TTP. We first propose a quick and effective constructive algorithm to construct a Double Round Robin Tournament (DRRT) schedule with low travel cost. We then describe an enhanced genetic algorithm with a new crossover operator to improve the travel cost of the generated schedules. A new heuristic for ordering efficiently the scheduled rounds is also proposed. The latter leads to significant enhancement in the quality of the schedules. The overall method is evaluated on publicly available standard benchmarks and compared with other techniques for TTP and UTTP (Unconstrained Traveling Tournament Problem). The computational experiment shows that the proposed approach could build very good solutions comparable to other state-of-the-art approaches or better than the current best solutions on UTTP. Further, our method provides new valuable solutions to some unsolved UTTP instances and outperforms prior methods for all US National League (NL) instances.

scholarly journals Post audio-visual biofeedback training visual functions and quality of life in paediatric idiopathic infantile nystagmus: A pilot study

2021 ◽  
pp. 112067212199104
Author(s):  
Monica Daibert-Nido ◽  
Yulia Pyatova ◽  
Michelle Markowitz ◽  
Maryam Taheri-Shirazi ◽  
Samuel N Markowitz
Keyword(s):  
Quality Of Life ◽  
Pilot Study ◽  
Contrast Sensitivity ◽  
Reading Speed ◽  
Biofeedback Training ◽  
Visual Functions ◽  
Infantile Nystagmus ◽  
Fixation Stability ◽  
Better Than

Purpose: Biofeedback training (BT) was adapted to idiopathic infantile nystagmus syndrome (IINS) cases to enhance visual functions and quality of life (QoL). Methods: 10 patients (age 9 ± 3.2 years) treated with the audio-visual BT module of the MAIA microperimeter (Centervue, Padova, Italy) were assessed in two baseline visits and 1week post-BT (BT 80 min in total). The outcomes were distance and near binocular best corrected visual acuity (BBCVA), fixation stability, reading speed, contrast sensitivity, stereopsis and Children’s Visual Function Questionnaire. One-way repeated measured ANOVA and paired t-tests were used. Results: Distance BBCVA improved from 0.46 ± 0.21 and 0.43 ± 0.18 pre-BT to 0.33 ± 0.2 logMAR post-BT ( F (2,27) = 13.75, p = 0.0002). Post-BT was better than baseline ( p = 0.0001) and pre-BT ( p = 0.001). Near BBCVA improved from 0.23 ± 0.09 and 0.21 ± 0.14 pre-BT to 0.04 ± 0.08 post-BT (F (2,27) = 22.12, p = 0.000014), post-BT was better than baseline ( p = 0.0001) and pre-BT ( p = 0.0006). Stereopsis improved from 283 ± 338″ to 39 ± 32.2″ ( p = 0.04), contrast sensitivity from 0.26 ± 0.17 to 0.08 ± 0.12 log units ( p = 0.01), and reading speed improved from 74.7 ± 51.2 wpm to 104.7 ± 53.6 wpm ( p = 0.0006). Fixation stability improved from 33.6 ± 28.1 to 14.3 ± 10.1 sq. QoL increased from 23.8 ± 2.2 to 26.3 ± 2.3 units ( p = 0.001). Conclusion: BT benefited all visual functions and QoL in this pilot study, heralding a new possibility for Low Vision Rehabilitation in IINS.

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