FlexTaxD: flexible modification of taxonomy databases for improved sequence classification

Author(s):  
David Sundell ◽  
Caroline Öhrman ◽  
Daniel Svensson ◽  
Edvin Karlsson ◽  
Björn Brindefalk ◽  
...  

Abstract Summary The Flexible Taxonomy Database (FlexTaxD) framework provides a method for modification and merging official and custom taxonomic databases to create improved databases. Using such databases will increase accuracy and precision of existing methods to classify sequence reads. Availability and implementation Source code is freely available at https://github.com/FOI-Bioinformatics/flextaxd and installable through Bioconda.

1979 ◽  
Vol 41 (03) ◽  
pp. 576-582
Author(s):  
A R Pomeroy

SummaryThe limitations of currently used in vitro assays of heparin have demonstrated the need for an in vivo method suitable for routine use.The in vivo method which is described in this paper uses, for each heparin preparation, four groups of five mice which are injected intravenously with heparin according to a “2 and 2 dose assay” procedure. The method is relatively rapid, requiring 3 to 4 hours to test five heparin preparations against a standard preparation of heparin. Levels of accuracy and precision acceptable for the requirements of the British Pharmacopoeia are obtained by combining the results of 3 to 4 assays of a heparin preparation.The similarity of results obtained the in vivo method and the in vitro method of the British Pharmacopoeia for heparin preparations of lung and mucosal origin validates this in vivo method and, conversely, demonstrates that the in vitro method of the British Pharmacopoeia gives a reliable estimation of the in vivo activity of heparin.


2019 ◽  
Vol 2 (1) ◽  
pp. 1-16
Author(s):  
Nana Suarna
Keyword(s):  

Seiring waktu, jumlah surat dalam sebuah perusahaan semakin hari makin banyak, sehingga muncul permasalahan dalam mengelolanya administrasi suarat, baik ketika dalam pencatatan surat maupun proses disposisi, serta pada saat pencarian arsip surat. Hampir sebagai besar surat yang ada di kantor-kantor masih disimpan dalam bentuk file-file yang masih bersifat manual, sehingga memungkinkan surat tersebut menunpuk, dan memerlukan waktu yang lama dalam pencarian dan pemrosesannya. Dengan dibangunnya  sistem manajemen pengarsipan bertujuan untuk mengatasi permasalahan-permasalahan tersebut di atas. Pemrograman  saat ini, baik desktop maupun web based, semakin marak  pengerjaannya menggunakan framework code igniter berbasis PHP. Framework CI memang dikembangkan untuk memudahkan dalam developing aplikasi dengan struktur  file source code-nya menggunakan pendekatan Models-Views-Controller (MVC) dan pemrograman berorientasi objek, oleh sebab itu penulis menggunakan CI dalam developing aplikasi ini. Aplikasi sistem manajemen surat dan pengarsipan ini dapat diakses dalam internal perusahaan web, yang bertujuan untuk memudahkan karyawan  dalam pengelolaan dan  mengaksesnya surat menyurat, selain itu aplikasi ini juga memberikan kemudahan dalam proses pencatatan surat,  disposisi, dan proses pencarian sehingga aplikasisi ini memiliki performa yang handal, mudah untuk di-maintenance dan dikembangkan lebih lanjut seiring perkembangan kebutuhan penggunanya.


Author(s):  
Himanshi Vashisht ◽  
Sanjay Bharadwaj ◽  
Sushma Sharma

Code refactoring is a “Process of restructuring an existing source code.”. It also helps in improving the internal structure of the code without really affecting its external behaviour”. It changes a source code in such a way that it does not alter the external behaviour yet still it improves its internal structure. It is a way to clean up code that minimizes the chances of introducing bugs. Refactoring is a change made to the internal structure of a software component to make it easier to understand and cheaper to modify, without changing the observable behaviour of that software component. Bad smells indicate that there is something wrong in the code that have to refactor. There are different tools that are available to identify and emove these bad smells. A software has two types of quality attributes- Internal and external. In this paper we will study the effect of clone refactoring on software quality attributes.


Diabetes ◽  
2020 ◽  
Vol 69 (Supplement 1) ◽  
pp. 849-P ◽  
Author(s):  
ALEXANDRA MIGDAL ◽  
ELIAS SPANAKIS ◽  
RODOLFO J. GALINDO ◽  
GEORGIA DAVIS ◽  
LAKSHMI G. SINGH ◽  
...  

2020 ◽  
Vol 2020 (1) ◽  
pp. 91-95
Author(s):  
Philipp Backes ◽  
Jan Fröhlich

Non-regular sampling is a well-known method to avoid aliasing in digital images. However, the vast majority of single sensor cameras use regular organized color filter arrays (CFAs), that require an optical-lowpass filter (OLPF) and sophisticated demosaicing algorithms to suppress sampling errors. In this paper a variety of non-regular sampling patterns are evaluated, and a new universal demosaicing algorithm based on the frequency selective reconstruction is presented. By simulating such sensors it is shown that images acquired with non-regular CFAs and no OLPF can lead to a similar image quality compared to their filtered and regular sampled counterparts. The MATLAB source code and results are available at: http://github. com/PhilippBackes/dFSR


Author(s):  
Klimenko Lina Yu ◽  
Shkarlat Galyna L ◽  
Shovkova Zoia V ◽  
Yaremenko Vitaliy D ◽  
Shpychak Oleg S

Metronidazole is the most popular representative of antiprotozoal medicines from the group of 5-nitroimidazoles. Metronidazole blocks the enzymes of alcohol dehydrogenase and acetaldehyde dehydrogenase, therefore when its joint taking with alcohol it is observed the strong intoxication syndrome and fatal poisonings too. Therefore metronidazole can be a potential object of chemical toxicological investigations. The purpose of our paper is to develop HPLC/UV-procedure of metronidazole quantification with application of the system of HPLC-analyzer MiLiChrome® A-0230 implemented in practice of forensic medical laboratories in Russia and Ukraine and carry out step-by-step validation of the developed procedure. Chromatographic conditions: Eluent A (0.2 M LiClO4 – 0.005 M HClO4) and Eluent B (acetonitrile) wereused as the mobile phase components; HPLC microcolumn Ø2×75 mm and ProntoSIL 120-5-C18 AQ, 5 μm were used as an analytical column; temperature was 40°С; flow rate was 100 μl/min; gradient elution mode was from 5% to 100% Eluent B for 40 min, then 100% Eluent B for 3 min; detection was performed at 277 nm. Retention time for metronidazole is 5.95 min. Since metronidazole is easy soluble and stable enough in the solutions of diluted alkalis 0.001 M sodium hydroxide solution has been proposed for preparation of the solutions in developing HPLC/UV-procedure of metronidazole quantification. Validation of the procedure has been carried out in the variants of the method of calibration curve and method of standard by such parameters as in process stability, linearity/calibration model, accuracy and precision within 3 different analytical runs using different batches of reagents and different glassware; experiments have been performed by three different analysts. New procedure of metronidazole quantitative determination by the method of HPLC/UV has been developed. Its validation has been carried out and acceptability for application has been shown.


Author(s):  
Tran Thanh Luong ◽  
Le My Canh

JavaScript has become more and more popular in recent years because its wealthy features as being dynamic, interpreted and object-oriented with first-class functions. Furthermore, JavaScript is designed with event-driven and I/O non-blocking model that boosts the performance of overall application especially in the case of Node.js. To take advantage of these characteristics, many design patterns that implement asynchronous programming for JavaScript were proposed. However, choosing a right pattern and implementing a good asynchronous source code is a challenge and thus easily lead into less robust application and low quality source code. Extended from our previous works on exception handling code smells in JavaScript and exception handling code smells in JavaScript asynchronous programming with promise, this research aims at studying the impact of three JavaScript asynchronous programming patterns on quality of source code and application.


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