scholarly journals GENOMA: a multilevel platform for marine biology

2018 ◽  
Author(s):  
Chiara Colantuono ◽  
Marco Miralto ◽  
Mara Sangiovanni ◽  
Luca Ambrosino ◽  
Maria Luisa Chiusano
Keyword(s):  
Gasterosteus Aculeatus ◽  
Marine Biology ◽  
Marine Species ◽  
Gene Annotations ◽  
Ptychodera Flava ◽  
On Line ◽  
Set Up ◽  
Genome Assemblies ◽  
Next Generation Sequencing Ngs ◽  
Patiria Miniata

Next-generation sequencing (NGS) technologies are greatly facilitating the sequencing of whole genomes leading to the production of different gene annotations, released often from both reference resources (such as NCBI or Ensembl) and specific consortia. All these annotations are in general very heterogeneous and not cross-linked, providing ambiguous knowledge to the users. In order to give a quick view of what is available, and trying to centralize all the genomic information of reference marine species, we set up GENOMA (GENOmes for MArine biology). GENOMA is a multilevel platform that includes all the available genome assemblies and gene annotations about 12 species (Acanthaster planci, Branchiostoma floridae, Ciona robusta, Ciona savignyi, Gasterosteus aculeatus, Octopus bimaculoides, Patiria miniata, Phaeodactylum tricornutum, Ptychodera flava and Saccoglossus kowalevskii). Each species has a dedicated JBroswe and web page, where is summarized the comparison between the different genome versions and gene annotations available, together with the possibility to directly download all the information. Moreover, an interactive table including the union of different gene annotations is also consultable on-line. Finally, a query page system that allows to search specific features in one or more annotations simultaneously, is embedded in the platform. GENOMA is publicly available at http://bioinfo.szn.it/genoma/.

scholarly journals GENOMA: a multilevel platform for marine biology

2018 ◽  
Author(s):  
Chiara Colantuono ◽  
Marco Miralto ◽  
Mara Sangiovanni ◽  
Luca Ambrosino ◽  
Maria Luisa Chiusano
Keyword(s):  
Gasterosteus Aculeatus ◽  
Marine Biology ◽  
Marine Species ◽  
Gene Annotations ◽  
Ptychodera Flava ◽  
On Line ◽  
Set Up ◽  
Genome Assemblies ◽  
Next Generation Sequencing Ngs ◽  
Patiria Miniata

Next-generation sequencing (NGS) technologies are greatly facilitating the sequencing of whole genomes leading to the production of different gene annotations, released often from both reference resources (such as NCBI or Ensembl) and specific consortia. All these annotations are in general very heterogeneous and not cross-linked, providing ambiguous knowledge to the users. In order to give a quick view of what is available, and trying to centralize all the genomic information of reference marine species, we set up GENOMA (GENOmes for MArine biology). GENOMA is a multilevel platform that includes all the available genome assemblies and gene annotations about 12 species (Acanthaster planci, Branchiostoma floridae, Ciona robusta, Ciona savignyi, Gasterosteus aculeatus, Octopus bimaculoides, Patiria miniata, Phaeodactylum tricornutum, Ptychodera flava and Saccoglossus kowalevskii). Each species has a dedicated JBroswe and web page, where is summarized the comparison between the different genome versions and gene annotations available, together with the possibility to directly download all the information. Moreover, an interactive table including the union of different gene annotations is also consultable on-line. Finally, a query page system that allows to search specific features in one or more annotations simultaneously, is embedded in the platform. GENOMA is publicly available at http://bioinfo.szn.it/genoma/.

Respirometry for determination of the influents SS-concentration

1996 ◽  
Vol 33 (1) ◽  
pp. 311-323 ◽  
Author(s):  
A. Witteborg ◽  
A. van der Last ◽  
R. Hamming ◽  
I. Hemmers
Keyword(s):  
Experimental Design ◽  
Activated Sludge ◽  
Substrate Concentration ◽  
Full Scale ◽  
Activated Sludge Process ◽  
Respiration Rates ◽  
On Line ◽  
Large Measurement ◽  
Set Up

A method is presented for determining influent readily biodegradable substrate concentration (SS). The method is based on three different respiration rates, which can be measured with a continuous respiration meter which is operated in a cyclic way. Within the respiration meter nitrification is inhibited through the addition of ATU. Simulations were used to develop the respirometry set-up and decide upon the experimental design. The method was tested as part of a large measurement programme executed at a full-scale plant. The proposed respirometry set-up has been shown to be suitable for a semi-on-line determination of an influent SS which is fully based on the IAWQ #1 vision of the activated sludge process. The YH and the KS play a major role in the principle, and should be measured directly from the process.

scholarly journals Optimization of a WGA-Free Molecular Tagging-Based NGS Protocol for CTCs Mutational Profiling

2020 ◽  
Vol 21 (12) ◽  
pp. 4364
Author(s):  
Giuseppa De Luca ◽  
Barbara Cardinali ◽  
Lucia Del Mastro ◽  
Sonia Lastraioli ◽  
Franca Carli ◽  
...  
Keyword(s):  
Substantial Reduction ◽  
Breast Cancer Patients ◽  
Dna Templates ◽  
Molecular Tagging ◽  
Mutational Profiling ◽  
Optimized Protocol ◽  
Set Up ◽  
Detection Of Mutations ◽  
Almost All ◽  
Next Generation Sequencing Ngs

Molecular characterization of Circulating Tumor Cells (CTCs) is still challenging, despite attempts to minimize the drawbacks of Whole Genome Amplification (WGA). In this paper, we propose a Next-Generation Sequencing (NGS) optimized protocol based on molecular tagging technology, in order to detect CTCs mutations while skipping the WGA step. MDA-MB-231 and MCF-7 cell lines, as well as leukocytes, were sorted into pools (2–5 cells) using a DEPArray™ system and were employed to set up the overall NGS procedure. A substantial reduction of reagent volume for the preparation of libraries was performed, in order to fit the limited DNA templates directly derived from cell lysates. Known variants in TP53, KRAS, and PIK3CA genes were detected in almost all the cell line pools (35/37 pools, 94.6%). No additional alterations, other than those which were expected, were found in all tested pools and no mutations were detected in leukocytes. The translational value of the optimized NGS workflow is confirmed by sequencing CTCs pools isolated from eight breast cancer patients and through the successful detection of variants. In conclusion, this study shows that the proposed NGS molecular tagging approach is technically feasible and, compared to traditional NGS approaches, has the advantage of filtering out the artifacts generated during library amplification, allowing for the reliable detection of mutations and, thus, making it highly promising for clinical use.

WWW.TELD.NET: Online Courseware Engine for Teaching by Examples and Learning by Doing

2001 ◽  
Vol 29 (3) ◽  
pp. 219-235 ◽  
Author(s):  
G. Q. Huang ◽  
B. Shen ◽  
K. L. Mak
Keyword(s):  
Teaching And Learning ◽  
Virtual Classroom ◽  
Learning By Doing ◽  
General Purpose ◽  
Project Based Learning ◽  
Course Materials ◽  
Summative Assessments ◽  
On Line ◽  
Set Up ◽  
Electronic Delivery

TELD stands for “Teaching by Examples and Learning by Doing.” It is an on-line courseware engine over the World Wide Web. There are four folds of meanings in TELD. First, TELD represents a teaching and learning method that unifies a number of contemporary methods such as Problem-Based Learning (PBL) in medical education, Project-Based Learning (PBL) in engineering education, and Case Method (CM) in business education. Second, TELD serves as a Web server for hosting teaching and learning materials especially based on the TELD method. A variety of on-line facilities are provided for editing and uploading course materials such as syllabus, schedule, curriculum, examples of case study, exercises of mini-project, formative and summative assessments, etc. Third, TELD is a courseware search engine where educators are able to register their course materials and search for materials suitable for a particular course. In contrast with general-purpose search engines, TELD is set up for the special purpose of education. Therefore, the time and efforts spent on surfing are expected to be reduced dramatically. Finally, TELD is an on-line virtual classroom for electronic delivery of electronic curriculum materials. In addition to providing the lecture notes, TELD not only provides discussion questions for conducting in-class discussions and homework as formative assessment but also provides facilities for students to plan and submit their group work. This article presents an overview of the TELD courseware engine together with its background and underlying philosophy.

scholarly journals Optimum three-point linkage set up for improving the quality of soil spectra and the accuracy of soil phosphorus measured using an on-line visible and near infrared sensor

2009 ◽  
Vol 103 (1) ◽  
pp. 144-152 ◽  
Author(s):  
A.M. Mouazen ◽  
M.R. Maleki ◽  
L. Cockx ◽  
M. Van Meirvenne ◽  
L.H.J. Van Holm ◽  
...  
Keyword(s):  
Near Infrared ◽  
Soil Phosphorus ◽  
Infrared Sensor ◽  
On Line ◽  
Set Up

Portal imaging for evaluation of daily on-line set up errors and off-line organ motion for radiotherapy of carcinoma of prostate

1998 ◽  
Vol 42 (1) ◽  
pp. 293
Author(s):  
H. Alasti ◽  
C. Catton ◽  
N. Middlemiss ◽  
G. Ottewell ◽  
L. Green ◽  
...  
Keyword(s):  
Organ Motion ◽  
Portal Imaging ◽  
On Line ◽  
Set Up ◽  
Line Organ

Developing a Class Session Using Audio and Video Streaming

2000 ◽  
pp. 103-116
Author(s):  
Al Bento
Keyword(s):  
Video Streaming ◽  
Streaming Media ◽  
Media Streaming ◽  
Class Session ◽  
On Line ◽  
The Media ◽  
Media Server ◽  
Set Up ◽  
Streaming Media Server

The objective of this chapter is to describe the process of creating audio and video streaming content for an on-line class session1 . An overall model of audio and video streaming is described, together with the media streaming process, in the introduction. The next parts of the chapter discuss how to create a class session with audio streaming only, audio and graphics, and audio and video. The chapter ends with a discussion on how to set up a streaming media server.

On-Line Industrial 3D Measurement Techniques for Large Volume Objects

2005 ◽  
Vol 295-296 ◽  
pp. 423-430 ◽  
Author(s):  
Ji Gui Zhu ◽  
S.H. Ye ◽  
Xue You Yang ◽  
Xing Hua Qu ◽  
C.J. Liu ◽  
...  
Keyword(s):  
Large Volume ◽  
Measurement Techniques ◽  
Integrated System ◽  
3D Measurement ◽  
Digital Cameras ◽  
Combined Use ◽  
Small Set ◽  
Close Range ◽  
On Line ◽  
Set Up

Rapid progress in modern manufacturing demands for better measurement technique with on-line characteristics. This paper presents a systematic visual solution for on-line industrial 3D measurement. The solution comprises two parts, a multi-sensor visual inspecting station (MSVIS) and a digital close-range visual inspecting station (DCVIS). MSVIS is an integrated system with many sensors. It can meet the requirement of application with sparse measuring points distributed within a large volume. DCVIS only contains two digital cameras with one or more projectors. It has high relative accuracy and a small set up volume and is suitable for applications with dense measuring points. The combined use of MSVIS and DCVIS can provide a general solution for on-line industrial 3D measurement.

Rapid Photon-Excited Energy-Dispersive X-Ray Fluorescence Analysis for Solid and Liquid Mineralogical Samples

1975 ◽  
Vol 19 ◽  
pp. 267-272 ◽  
Author(s):  
W. Ratyński ◽  
J. Parus ◽  
J. Tys ◽  
A. Ciszek
Keyword(s):  
Fluorescence Analysis ◽  
Semiconductor Detectors ◽  
X Rays ◽  
Copper Ore ◽  
X Ray ◽  
Large Numbers ◽  
Important Benefit ◽  
Versatile Tool ◽  
On Line ◽  
Set Up

X-ray fluorescence spectroscopy is new becoming a tool in research and. industry. Semiconductor detectors are proving valuable in measuring fluorescent X rays, and so are providing a versatile tool for rapid multielement analysis of many types of samples. This paper will mainly be concerned with, different types of copper ore. An experimental setup has been designed to determine Cu, Fe and Pb of concentration ranging from 0.1 to 20, to 5, and to 4 percent, respectively, with analytical precision of 20% relative at 0.1% Cu, and 3% relative at 20% Cu. For excitation a 100 mCi Pu-238 source and/or a low power air-cooled X-ray tube were used. Data acquisition and “on-line” evaluation for each sample takes about 100 seconds. Electronics blocks and sub-systems used In the set-up are available commercially. The most important benefit to be obtained from the setup is the ability to provide precise, reproducible determinations of large numbers of samples day after day.

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