scholarly journals MetaSanity: an integrated microbial genome evaluation and annotation pipeline

2020 ◽  
Vol 36 (15) ◽  
pp. 4341-4344 ◽  
Author(s):  
Christopher J Neely ◽  
Elaina D Graham ◽  
Benjamin J Tully
Keyword(s):  
Data Analysis ◽  
Microbial Genome ◽  
Quality Analysis ◽  
Supplementary Information ◽  
Microbial Genomes ◽  
Gene Annotations ◽  
Sql Database ◽  
Microbiome Research ◽  
Data Analysis Pipeline

Abstract Summary As the importance of microbiome research continues to become more prevalent and essential to understanding a wide variety of ecosystems (e.g. marine, built, host associated, etc.), there is a need for researchers to be able to perform highly reproducible and quality analysis of microbial genomes. MetaSanity incorporates analyses from 11 existing and widely used genome evaluation and annotation suites into a single, distributable workflow, thereby decreasing the workload of microbiologists by allowing for a flexible, expansive data analysis pipeline. MetaSanity has been designed to provide separate, reproducible workflows that (i) can determine the overall quality of a microbial genome, while providing a putative phylogenetic assignment, and (ii) can assign structural and functional gene annotations with varying degrees of specificity to suit the needs of the researcher. The software suite combines the results from several tools to provide broad insights into overall metabolic function. Importantly, this software provides built-in optimization for ‘big data’ analysis by storing all relevant outputs in an SQL database, allowing users to query all the results for the elements that will most impact their research. Availability and implementation MetaSanity is provided under the GNU General Public License v.3.0 and is available for download at https://github.com/cjneely10/MetaSanity. This application is distributed as a Docker image. MetaSanity is implemented in Python3/Cython and C++. Instructions for its installation and use are available within the GitHub wiki page at https://github.com/cjneely10/MetaSanity/wiki, and additional instructions are available at https://cjneely10.github.io/year-archive/. MetaSanity is optimized for users with limited programing experience. Supplementary information Supplementary data are available at Bioinformatics online.

scholarly journals MetaSanity: An integrated, customizable microbial genome evaluation and annotation pipeline

2019 ◽  
Author(s):  
Christopher J Neely ◽  
Elaina D Graham ◽  
Benjamin J Tully
Keyword(s):  
Data Analysis ◽  
Microbial Genome ◽  
Quality Analysis ◽  
Supplementary Information ◽  
Microbial Genomes ◽  
Gene Annotations ◽  
Sql Database ◽  
Microbiome Research ◽  
Data Analysis Pipeline

AbstractSummaryAs the importance of microbiome research continues to become more prevalent and essential to understanding a wide variety of ecosystems (e.g., marine, built, host-associated, etc.), there is a need for researchers to be able to perform highly reproducible and quality analysis of microbial genomes. MetaSanity incorporates analyses from eleven existing and widely used genome evaluation and annotation suites into a single, distributable workflow, thereby decreasing the workload of microbiologists by allowing for a flexible, expansive data analysis pipeline. MetaSanity has been designed to provide separate, reproducible workflows, that (1) can determine the overall quality of a microbial genome, while providing a putative phylogenetic assignment, and (2) can assign structural and functional gene annotations with varying degrees of specificity to suit the needs of the researcher. The software suite combines the results from several tools to provide broad insights into overall metabolic function and putative extracellular localization of peptidases and carbohydrate-active enzymes. Importantly, this software provides built-in optimization for “big data” analysis by storing all relevant outputs in an SQL database, allowing users to query all the results for the elements that will most impact their research.Availability and implementationMetaSanity is provided under the GNU General Public License v.3.0 and is available for download at https://github.com/cjneely10/MetaSanity. This application is distributed as a Docker image. MetaSanity is implemented in Python3/Cython and C++.Supplementary informationSupplementary data are available below.

scholarly journals Analisis Kualitas Pelayanan Perpajakan dalam Rangka Meningkatkan Kepatuhan Wajib Pajak (Studi Kasus Kpp Pratama Jakarta Senen 2018)

2020 ◽  
Vol 2 (1) ◽  
pp. 37-44
Author(s):  
Maudy Zuraeva ◽  
Novianita Rulandari
Keyword(s):  
Data Analysis ◽  
Data Collection ◽  
Human Resources ◽  
Qualitative Method ◽  
Study Data ◽  
Quality Analysis ◽  
Descriptive Qualitative

This study aimed to determine the quality analysis of tax services at KPP Pratama Jakarta Senin in order to improve taxpayer compliance. The method used in this research was descriptive qualitative method. Data collection was carried out through interviews, observation and documentation. A total of eight informants were involved in this study.  Data analysis was performed using the Credibility and Transferability Test. The results of this study indicate that service indicators such as reliability, responsiveness, competence, access, courtesy, communication, credibility, security, understanding, and tangibles owned by tax employees of KPP Pratama Jakarta Senin are very good so that taxpayers are satisfied with the services they provide. However, there are still weaknesses in the courtesy indicator, in which some employees are not friendly, and in the tangibles indicator, in which the quality of human resources and the number of computer units is still lacking and the awareness and compliance of taxpayers is still low. These weaknesses have resulted in the failure to achieve the tax achievement target.

scholarly journals Analysis of Learning Quality With Internet-Based Distance Learning During the COVID-19 Pandemic

2021 ◽  
Vol 2 (1) ◽  
pp. 96-110
Author(s):  
Yuli Sutoto Nugroho ◽  
Lilik Anifah ◽  
Edy Sulistiyo ◽  
Sari Cahyaningtias ◽  
Rifqi Firmansyah
Keyword(s):  
Online Learning ◽  
Data Analysis ◽  
Distance Learning ◽  
Teaching And Learning ◽  
Point Of View ◽  
Quality Analysis ◽  
Work From Home ◽  
Quality Of Learning ◽  
Descriptive Qualitative

Analysis of the quality of learning is crucial in the teaching and learning process, to ensure the quality of learning is well maintained. Learning quality assurance instruments are one of the tools to improve quality in education through evaluations produced by studies of students. This research was conducted to test the quality of online learning during the COVID-19 pandemic. This research aims to evaluate Internet-Based Distance Learning which was carried out during the Work From Home (WFH) period. The learning analysis step is carried out through 1) Formulation of the need for quality analysis of learning, 2) Compiling quality analysis instruments, 3) Distribution of questionnaires, 4) Data processing, 5) Data analysis and 6) Compilation of results. The data analysis technique used descriptive qualitative analysis. The data that has been processed will then be analyzed using descriptive qualitative methods to find conclusions about the quality of learning in the Department of Electrical Engineering (JTE) during the 2020 pandemic. From the analysis, results obtained information that the Quality of Learning with Internet-Based Distance Learning during the COVID-19 Pandemic at JTE it can be said that it is good from a student's point of view, while from a lecturer's point of view, It can be concluded that online learning is very good. The implementation of this research is a consideration for JTE to improve the quality of Internet-Based Distance Learning

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

Pengaruh Pemberian Moringa oleifera Terhadap Kuantitas dan Kualitas Semen Sapi Peranakan Ongole

2020 ◽  
Vol 7 (2) ◽  
pp. 119
Author(s):  
Lukman Affandhy ◽  
Muchamad Luthfi ◽  
Dian Ratnawati ◽  
Frediansyah Firdaus
Keyword(s):  
Data Analysis ◽  
Analysis Of Variance ◽  
Research Method ◽  
Moringa Oleifera ◽  
The Third ◽  
Randomized Design ◽  
Leaf Powder ◽  
Completely Randomized Design ◽  
Second Period

ABSTRAK  Penelitian bertujuan untuk mengetahui pengaruh pemberian bubuk daun Moringa oleifera (MO) terhadap kuantitas dan kualitas semen sapi peranakan ongole (PO). Metode penelitian menggunakan percobaan lapang dengan rancangan acak lengkap dengan tiga perlakuan pemberian MO sebesar 0 kg/ekor/hari (P1); 0,05 kg/ekor/hari (P2) dan 0,1 kg/ekor/hari (P3). Analsis data menggunakan one way analysis of variance. Masing-masing perlakuan terdiri atas empat ekor dengan tiga periode pengamatan sebagai ulangan, yaitu periode pertama dan ketiga tanpa MO, dan periode kedua diberikan MO pada P2 dan P3. Hasil penelitian menunjukan bahwa volume dan pH semen perlakuan P1, P2 dan P3 tidak berbeda semua periode pengamatan. Motilitas massa spermatozoa P2 dan P3 periode kedua dan ketiga menunjukan nilai +++ berbeda nyata (P<0,05) dibandingkan dengan P1 (++); motilitas individu  perlakuan P1 menunjukkan nilai terendah 60,56±2,94 % (P<0,05) dibandingkan P2 dan P3 pada periode kedua dan ketiga (75,50±2,29 dan 72,50±2,34%). Konsentrasi spermatozoa P2 dan P3 periode kedua dan ketiga menunjukkan rata-rata  >1.350 juta/ml berbeda nyata (P<0,05) daripada P1 (876±152juta/ml), sedangkan total spermatozoa motil menunjukkan nilai tertinggi 5.647±829 juta/ml pada P3 periode kedua.Viabilitas spermatozoa P2 dan P3 menunjukkan nilai >88-89 % beda nyata (P<0,05) daripada P1 (<84 %) pada periode kedua dan ketiga, sedangkan nilai abnormalitas spermatozoa yang terbaik adalah P2 sebesar 4,30% pada periode kedua dan P3 sebesar 5,33% pada periode ketiga. Disimpulkan pemberian bubuk daun MO dengan dosis 0,1 kg/ekor/hari dapat memperbaiki kuantitas dan kualitas semen (viabilitas dan total spermatozoa motil) sapi pejantan PO.Kata kunci:  kuantitas dan kualitas semen, Moringa oleifera, sapi pejantan ABSTRACTThe research aimed to determine the effect of Moringa oleifera (MO) leaf powder on the quantity and quality of semen of ongole crossbreed. The research method used was a field experiment with a completely randomized design with three treatments giving MO of 0 kg/head/day (P1); 0.05 kg/head/day (P2) and 0.1 kg/head/day (P3). Each treatment consisted of four heads with three periods of observation as replications, namely the first and third periods without MO, and the second period was given MO on P2 and P3. Data analysis used a one-way analysis of variance. The results showed that the volume and pH of semen treated P1, P2, and P3 didn’t different in all observation periods. The second and third period spermatozoa mass motility of P2 and P3 showed that the value of +++ was significantly different (P<0.05) compared to P1 (++); Individual motility of P1 treatment showed the lowest value 60,56±2,94 % (P<0.05) compared to P2 and P3 in the second and third periods (75,50±2,29 and 72,50±2,34%). The second and third periods of P2 and P3 spermatozoa concentrations showed an average of >1,350 million/cc significantly different (P<0.05) than P1 (876±152 million/cc), while the total motile spermatozoa showed the highest value of 5,647±829 million/cc in the second period P3. The spermatozoa viability of P2 and P3 showed values >88-89% significantly different (P<0.05) than P1 (<84%) in the second and third periods, while the best spermatozoa abnormalities were P2 at 4.30% in the second period and P3 at 5.33% in the third period. It was concluded that the giving of MO leaf powder at a dose of 0,1 kg/head/day could improve the quantity and quality of semen (viability and total motile spermatozoa) of Ongole Crossbreed bulls. Keywords: bulls, Moringa oleifera, quantity and quality of semen

The Anxiety of Pregnant Women in Post Abortion by Reading Ayatus Syifa and Lavender Aromatherapy

2020 ◽  
Vol 7 (3) ◽  
pp. 404-409
Author(s):  
Inna Sholicha Fitriani ◽  
Nurhidayati Nurhidayati
Keyword(s):  
Data Analysis ◽  
Pregnant Woman ◽  
Pregnant Women ◽  
Test Group ◽  
Total Sample ◽  
Anxiety Level ◽  
Wilcoxon Test ◽  
Post Test ◽  
Post Abortion

Pregnancy and abortion can be a stressor that can increase anxiety. The Qur'an is just as a doubt antidote and diseases that are in the chest and it is commonly known as the heart. The Lavender one of essential oil which popular and it is widely used in the field of clinical health which especially addressing psychosomatic in gynecology. The purpose of this research was to determine the potential decrease of anxiety on pregnant women in post-abortion by reading verses syifa and lavender aromatherapy. The research used experimental design of Pre and Post Test-Group with a sample of all pregnant women who had abortion. The total sample was 24 people. The research was conducted in Aisyiyah Hospital and Muhammadiyah Hospital of Ponorogo in Juny - August 2018. The data analysis used T and Wilcoxon test. The result of data analysis were 0,003 <0,05 and there was comparison between potential decrease of anxiety in pregnant women post abortion by reading verses syifa and giving aromatherapy  of lavender.  The comparison showed that the potency of decreasing of anxiety in pregnant woman post abortion by reading ayatus syifa and giving aromatherapy of lavender, 38% decreased anxiety level in pregnant woman post abortion because of lavender therapy and 62% was due to other factor. Then 89%decreased in anxiety level in pregnant woman post abortion because of reading ayatus syifa and 11% due to other factor. Research products can be used as media in the treatment of non pharmacological psikomatic in order to support quality of public health.

STUDI PERBANDINGAN KUALITAS AIR BERSIH DALAM KAITANYA DENGAN AKTIVITAS MASYARAKAT DI SEKITAR SUMBER AIR PADA DESA WAINITU, BATUMERAH, AMAHUSU, DAN HALONG

2017 ◽  
Vol 13 (2) ◽  
pp. 111-119
Author(s):  
Lela Uyara ◽  
Pieter Kunu ◽  
Silwanus M Talakua
Keyword(s):  
Water Quality ◽  
Quality Standard ◽  
Total Coliform ◽  
Quality Analysis ◽  
Clean Water ◽  
Water Quality Analysis ◽  
E Coli ◽  
Microbiological Parameters ◽  
Standard Quality

The study aims to determine the quality of clean water in the villages of Wainitu, Batumerah, Amahusu and Halong by comparing the result of water quality analysis with water quality standard. Water quality analysis includes Physiscal, Chemical, and Microbiological parameters. This research uses descriptive method, this method describes systematics, accurate about facts and characteristic of the quality of clean water of each research location. The results showed that the source of clean water in the village of Batumerah did not meet the standard of clean water quality standards indicated by the number of E. coli and the high total coliform.  Keywords: standard quality of clean water, water quality, Wainitu, Batumerah, Amahusu and Halong villages   ABSTRAK Penelitian yang bertujuan untuk menetapkan kualitas air bersih di Desa Wainitu, Batumerah, Amahusu dan Halong, dengan membandingkan hasil analisis kualitas air dengan standar baku mutu air bersih. Analisis kualitas air meliputi parameter fisika, kimia dan mikrobiologi. Penelitian ini menggunakan metode deskriptif; metode ini menggambarkan sicara sistematis, akurat, fakta dan karakteristik mengenai kualitas air bersih di masing-masing lokasi penelitian. Hasil penelitian menunjukkan bahwa sumber air bersih di Desa Batumerah tidak memenuhi standar baku mutu air bersih yang ditunjukkan oleh jumlah E. coli dan total Koliform yang tinggi. Kata Kunci: baku mutu air bersih, Desa Wainitu, Batumerah, Amahusu dan Halong, kualitas air

PENGARUH KUALITAS PRODUK, HARGA, MEREK DAN SALURAN DISTRIBUSI TERHADAP VOLUME PENJUALAN PADA PT. GELANG GEMILANG JAYA BELLA SPRING BED SEMARANG

2020 ◽  
Vol 15 (1) ◽  
pp. 217-230
Author(s):  
Untung Widodo
Keyword(s):  
Data Analysis ◽  
Product Quality ◽  
Sampling Technique ◽  
Distribution Channels ◽  
Sales Volume ◽  
Independent Variables ◽  
Variable Distribution ◽  
Data Analysis Methods ◽  
Variable Quality

This research was conducted in order to test how much influence product quality, price and brand to the volume of sales at PT. Gemilang Jaya Bella bracelets Spring Bed Semarang. Independent variables include variable product quality, price and brand while the dependent variable is the volume of sales.In determining the data to be studied sampling technique used is the census. Census is a sampling technique when all members of the population used as a sample .. Respondents were selected is the consumer stores PT. Gemilang Jaya Bella bracelets Spring Bed Semarang. Thus obtained sample was 50 respondents. Data analysis methods used to perform hypothesis testing is multiple linear regression analysis.Based on the results of research that has been conducted on all data obtained, the importance of the research that 1). There is a positive and significant effect of the variable quality of the product (X1) to sales volume (Y). 2). There is a positive and significant impact on price variable (X2) to sales volume (Y). 3). There is a positive and significant impact on brand variables (X3) to sales volume (Y). 4). There is a positive and significant effect of the variable distribution channels (X4) to sales volume (Y)

scholarly journals A quality analysis of the YouTube video content on meniscus repair surgery

2021 ◽  
Vol 9 (2_suppl) ◽  
pp. 2325967121S0001
Author(s):  
François Sigonney ◽  
Camille Steltzlen ◽  
Pierre Alban Bouché ◽  
Nicolas Pujol
Keyword(s):  
Medical Information ◽  
Cruciate Ligament ◽  
Meniscus Repair ◽  
Quality Analysis ◽  
Video Content ◽  
Source Type ◽  
Keywords Meniscus ◽  
Youtube Videos ◽  
Anterior Cruciate

Objectives: The Internet, especially YouTube, is an important and growing source of medical information. The content of this information is poorly evaluated. The objective of this study was to analyze the quality of YouTube video content on meniscus repair. The hypothesis was that this source of information is not relevant for patients. Methods: A YouTube search was carried out using the keywords "meniscus repair". Videos had to have had more than 10,000 views to be included. The videos were analyzed by two evaluators. Various features of the videos were recorded (number of views, date of publication, "likes", "don’t likes", number of comments, source, type of content and the origin of the video). The quality of the video content was analyzed by two validated information system scores: the JAMA benchmark score (0 to 4) and the Modified DISCERN score (0 to 5). A specific meniscus repair score (MRSS scored out of 22) was developed for this study, in the same way that a specific score has been developed for other similar studies (anterior cruciate ligament, spine, etc.). Results: Forty-four (44) videos were included in the study. The average number of views per video was 180,100 (± 222,000) for a total number of views of 7,924,095. The majority of the videos were from North America (90.9%). In most cases, the source (uploader) that published the video was a doctor (59.1%). A manufacturer, an institution and a non-medical source were the other sources. The content actually contained information on meniscus repair in only 50% of the cases. The mean scores for the JAMA benchmark, MD score and MRSS were 1.6/4± 0.75, 1.2/5 ± 1.02 and 4.5/22 (± 4.01) respectively. No correlation was found between the number of views and the quality of the videos. The quality of videos from medical sources was not superior to those from other sources. Conclusion: The content of YouTube videos on meniscus repair is of very low quality. Physicians should inform patients and, more importantly, contribute to the improvement of these contents.

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