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Month: October 2016

Radiotherapy for the Utilization of Proton Beam and Clinical Indications

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Rita Jánosi
Tuesday, 25 October 2016 / Published in Clinical Trial Support

“Proton beam therapy (PBT) is more expensive process than conventional radiotherapy (XRT), but some studies suggest PBT causes less side effects. PBT is not a new invention, the first patients were treated by PBT in 1954. PBT is becoming more widespread, althought this therapy requires large investments, high operation costs and big infrastructure. As of December 2015, 57 proton therapy centers are in operation worldwide and others are under building or planning.

Clinical benefit (improving survival rate or less toxicity) of proton therapy compared to other treatments has yet to be proved. The biggest handicap of the proton therapy is the lack of randomized trials to demonstrate the benefits of this therapy. The main argument of opponents of therapy is the high cost.
The author mentions some thoughts on treatment of various types of cancer by proton therapy (pediatric tumors, adult tumors: prostate tumor, uveal melanoma, chordoma and chondrosarcoma, breast cancer, lung cancer, brain tumors, head and neck cancers, GI malignancies, Hodgkin’s lymphoma, re-irradiation).

The author’s final conclusion: proton therapy at present is costly and accessible to a few patients only. The missions of the future: oncologist community should agree that the PBT is effective and new technical developments should be done that enable this technology to become cheaper and more accessible.” – Maurizio Amichetti

What is proton therapy?

 „Proton therapy is an advanced way of treating cancer patients who need radiation therapy. Treatment involves using a beam of protons — subatomic particles carrying a positive charge — that is generated by accelerating hydrogen gas in a particle accelerator called a cyclotron. This proton beam is then directed to the cancerous site in the patient’s body. The beam can be shaped precisely to match the specific size and shape of the tumor. As the beam passes through DNA molecules in cancerous cells, the positive charge of the protons pulls negatively charged electrons in the DNA out of place. This ionization process changes the fundamental characteristics of the individual atoms that make up the DNA molecule, which in turn changes how its base pairs interact and replicate. The DNA becomes so damaged that the cell can no longer function and undergoes apoptosis, or programmed cell death, in which the cell sends out signals to break down its own structures.”

How is proton therapy different from radiation therapy?

„Traditional radiation therapy uses X-rays, which expose the patient to potentially harmful electromagnetic radiation as they enter and exit the body. Protons, on the other hand, stop at a pre-determined depth inside the patient and do not deposit any radiation dose beyond that depth.”

source: http://scienceline.org/2016/01/proton-therapy-and-the-future-of-cancer/

Read more: Here

Metabase 0.20 is out — With Permissions, Oracle Support and more

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Nandor Sperl
Wednesday, 19 October 2016 / Published in Data Analysis

It’s been a long wait, but it’s worth it. A new version of Metabase is ready for you (and end users)!

You can download the new version of Metabase at http://www.metabase.com/start/

To upgrade, see the instructions for your platform at http://www.metabase.com/docs/latest/operations-guide/start.html#upgrading-metabase

Let’s see what Metabase says about their new version:

 

Data access permissions

A way to control access to sensitive data has been one of the most requested features since we launched. With 0.20, we’ve taken the first major step in giving you the ability to lock down an instance. We now allow you to create user groups, and control their access to databases, tables and raw SQL queries. This lets you control access to sensitive data while still allowing your end users to answer their own questions within the datasets they’re allowed access to.

Getting started guides
In most places we’ve worked, there’s typically an email that gets forwarded around, or a Google doc that describes how to use the analytics systems available. Some more sophisticated setups use an internal wiki or other website that has an inventory of what’s available. We believe that the best way to keep these current is to have them be built into the application. Now you can create a cheatsheet to help new users know which dashboards, metrics and reports are the most important as well as provide caveats for use, advice on who to contact for help, and more.

Charting improvements – Part 2

Following up on our previous releases’ improvements to charting, we’ve added new chart types (progress, scatter and bubble charts), improved your control over axes, and allowed you to customize the display of dashboard cards made up of multiple questions.

Oracle driver

Lots of you have been clamoring for a way to use Metabase with Oracle databases. Now you can! Due to Oracle’s license for the underlying JDBC driver, you’ll need to do a few extra steps — check out www.metabase.com/docs/latest/administration-guide/databases/oracle.md for details.

Druid performance and timezone fixes

We’ve made some improvements to how Metabase works with Druid that fix a number of timezone bugs and improve charting performance.

Metabase also fixed many reported issues and bugs from their GitHub page.

Integrating One More Data Source: The Semantic Web

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Márk Szepesi
Wednesday, 19 October 2016 / Published in KNIME

The Semantic Web

According to the W3C Linked Data page, the Semantic Web refers to a technology stack to support the “Web of data”. Semantic Web technologies enable people to create data stores on the Web, build vocabularies, and write rules for handling data. Linked data are empowered by technologies such as RDF, SPARQL, OWL, and SKOS.

  • RDF. Resource Description Framework is a standard data model for representing the metadata of resources in the Web; it represents all resources – even those that cannot be directly retrieved. RDF especially helps to process, mix, expose, and share such metadata. In terms of the relational model, an RDF statement specifies a relationship between two resources and it is similar to a triple relation with subject, predicate, and object.
  • OWL. Ontology Web Language is based on the basic elements of RDF, but uses a wider vocabulary to describe properties and classes.
  • SKOS. Simple Knowledge Organization System is also based on RDF and specifically designed to express hierarchical information. If needed, it is also extendable into OWL.
  • SPARQL. Simple Protocol and RDF Query Language is an RDF-based query language used to retrieve and manipulate public and private metadata stored in RDF format.

A commonly used instance of the semantic web is the DBPedia project, which was created to extract structured content from Wikipedia.

Our latest release KNIME Analytics Platform 3.2 includes a great feature: semantic web integration! A full node category is dedicated to querying and manipulating semantic web resources. The new semantic web nodes treat the web of data exactly like a database, with connector nodes, query nodes, and manipulation nodes. Additional nodes are provided to read and write files in various formats.

Read more

KNIME; Semantic Web

3D Printing of Organs for Transplantation: Where Are We and Where Are We Heading?

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Rita Jánosi
Wednesday, 19 October 2016 / Published in 3D Bioprinting

Authors

Armando Salim Munoz-Abraham, Manuel I. Rodriguez-Davalos, Alessandra Bertacco, Brian Wengerter, John P. Geibel, David C. Mulligan

Current Transplantation Reports

March 2016, Volume 3, Issue 1, pp 93-99

 

The 3D bioprinting process can be achieved by three different printer modalities based on the current technologies, know as micro-extrusion bioprinting, inkjet bioprinting, or laser bioprintin. The article describes briefly the 3D-bioprinting process.

The use of 3D bioprinting has already resulted in printing of blood vessels and vascular networks, bones, cartilage, ears, tracheal grafts – the three greatest success: replacement the complete skull with a 3D-printed, tailor-made plastic skull without adverse event, succesful transplantation of engineered bladder in humans without any major complications, creating a 3D-printed bionic ear.

About current developments:

  • vascular structures: tissue-engineered vascular-graft without aneurismal change or graft rupture
  • liver: Organovo demonstrated the feasibility of printing metabolically functional 3D hepatic structures and proving that the tissue was capable of cell-cell interaction, protein production, and enzymatic activity
  • kidney: Organovo presented their in vitro model of a multicellular, three-dimensional tissue model of human kidney proximal tubule

Future horizonts and Conclusion: the ultimate aim is the complete ontogenic repliation, but it requires a better  understanding of intercellular communication and tissue microenvironments futhermore creating of printing protocols.

For more information read the original article in: here

OpenTrials launches beta version

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László Szakács
Monday, 17 October 2016 / Published in Open access

OpenTrials aims to provide a comprehensive picture of the data and documents on all clinical trials conducted on medicines and other treatments. The platform will present data aggregated from a wide variety of existing sources, starting with clinical trial registers and moving on to academic journals, systematic reviews and other data sources.

The intention is to create an open, freely re-usable index of all such information, to increase discoverability, facilitate research, identify inconsistent data, enable audits on the availability and completeness of this information, support advocacy for better data and drive standards around open data in evidence-based medicine.

Explore the public beta version of OpenTrials here.

Clinical trialsOpen access

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