Posts | Alex Hildebrandt

Web of things, knowledge graphs, decentralised AI and responsible AI

Thu, 04 Jun 2020 00:00:00 +0000

This post will inform about topics on artificial intelligence relevant for the INDUSTRY 4.0. Four topics are discussed:

Web of things
Knowledge graphs
Decentralized artificial intelligence
Responsible artificial intelligence

IoT & WoT

IoT is the abbreviation for Internet of Things (IoT). In general, the term IoT is used to connect everyday objects of machines in a private or an industrial environment via the internet. Devices get unique IDs in the network. They have electric intelligence and can communicate through the internet and finish tasks full automatically. They are called Smart Devices.

In addition to the possibility of the devices communicating with each other (machine-to-machine communication, M2M), many of the networked objects provide an interface via the Internet, via which the devices can be operated and controlled by a user from any location.

The IoT distinguishes between private and industrial use. In private, everyday objects are linked together (smart home or smart metering such as controlling audio boxes, thermostats, security systems, etc.). In the industrial environment, the term IoT is also used to refer to Industry 4.0. This means, among other things, the self-organization of industrial processes through the direct communication of machines, systems, goods and people. Not only individual processes, but entire value chains can be automated and made more efficient. Industrial application examples would be e.g. the monitoring of transport routes (just-in-time delivery) or the monitoring of medical processes.

WoT is a sub-area of the IoT. The prerequisite for both is that the smart devices have embedded computers and can communicate with the Internet / Web. Communication with the web can be wired or wireless. Wireless communication technologies would be e.g. WLAN, Bluetooth or cellular standards like UMTS and LTE. The WoT technology is based on software standards and frameworks such as representational state transfer (REST) and HTTP. Applications in which smart devices interact with one another can be implemented via the Internet address. In the industrial environment, RFID technology (radio-frequency-identification) plays an important role in identifying goods and tracking them in logistical processes.

Networking on the Internet also creates opportunities for attack by dialing in or disrupting processes and unauthorized use of data or data-tapping. Therefore, the participating components must be protected against attacks such as denial-of-service attacks or malware. The following security aspects have to be considered with the IoT.

Wirksames und zuverlässiges Identitäts- und Zugriffsmanagement,
Verschlüsselung sämtlicher über das öffentliche Internet übertragener Daten,
Schutz der einzelnen Systeme durch Firewalls oder Firewall-ähnliche Funktionen,
effektive Härtung der Systeme zu Minimierung der Angriffsmöglichkeiten sowie
Software- und Patchmanagement über den kompletten Betriebszeitraum der Systeme zur Behebung von erkannten Fehlern und Sicherheitsmängeln.

Knowledge graphs

Knowledge graphs can be created by accumulating every day digital information into one structure.

Fig. 2: Knowledge graph of google

Internet giants and companies from other industries such as BBC,AstraZeneca and Capital One are using knowledge graphs to harness the knowledge of all data available.

What is a

Decentralized artificial intelligence

Resposnsible artificial intelligence

Exosomes: biogenesis, function and clinical potential

Thu, 28 May 2020 00:00:00 +0000

Exosomes: biogenesis, function and clinical potential

About Exosomes:

Exosomes are small (30-100 nm) biovesicles which are released by all kind of cells into body fluids like blood and urine. In the beginning they thought to be waste resulting from cell damage or by-products of cell homeostasis but recent studies show that they have an important role in intercellular communication through their cargo which may play a role in processes such as signal transduction, antigen presentation and immune response. The cargo of exosomes consists of lipids, proteins and nucleic acids and is enclosed or exposed on the surface. Thereby a large variety have been identified from different cell types with about 4400 proteins, 194 lipids, 1639 mRNAs and 764 miRNAs beside other RNA-species. But the content is strongly dependend on the source of origin. In human plasma derived exosomal RNA species microRNAs (miRNAs)are found to be most abundant. Making up of 42.32% of all raw reads and 76.20% of all mappable reads. Other RNA species including ribosomal RNA (9% of all mappable counts), long non-coding RNAs (3.36%), small nuclear RNA (0.18%) and small nucleor RNA (0.01%). The miRNA profile can provide information about whether changed processes are taking place and provide information about the development of diseases. miR-214, miR-29a, miR-126 and miR-320, which participate in angiogenesis, hematopoiesis, exocytosis and tumorgenesis for example are already mentioned in exosome-based intercellular communication. Since exosomes can be found in all body fluids, they are easily accessible in everyday clinical practice (for example blood derived plasma Exosomes) and could serve as markers for the physiological state through validated studies.

Extracellular vesicles and the biogenesis of exosomes:

Extracellular vesicles (EVs) interact with and modify the behavior of target cells. Thereby EVs can be devided into three major groups: plasma membrane-budded microvesicles (MVs), apoptotic bodies and exosomes. Figure 1 illustrates the biogenesis of exosomes and MVs:

Fig. 1. Schematic representation of exosome and microvesicle biogenesis pathways. While microvesicles bud directly from the plasma membrane, exosomes are generated within MVB subpopulations that upon maturation fuse with the plasma membrane. Alternative MVB pathways include fusion with lysosomes or with autophagosomes, although little is known about the mechanisms determining MVB fate. MVB fusion with the plasma membrane is a tightly regulated multistep process that includes MVB trafficking along microtubules, docking at the plasma membrane and SNARE-mediated fusion. (https://doi.org/10.1016/j.pharmthera.2018.02.013) license

Thereby the ESCRT complex composed of four seperate proteins (ESCRTs 0 to III) facilitates MVB (multivesicular body) formation, vesicle budding and protein cargo sorting. Exosomes are part of the MVBs. MVBs can either fuse with the plasma membrane to secrete exosomes or degrade their cargo by fusing with lysosomes. A shifted balance towards exosomal cargo release was observed from transformed cells.

MVBs that are intended for exocytosis are transported along microtubules by the molecular motor kinesin. The release of MVBs might be cell type-specific and can not be described generally. The processes involved have different actors and can differ in their mechanisms. E.g. it has been shown that RAB35 mediates MVB docking in oligodendroglial cells, wheras RAB27 controls this process in several cancer cell lines (in vivo and in vitro). After docking the fusion of the MVBs with the plasma membrane is initiated by the SNARE (soluble N-ethylmaleimide-sensitive component attachment protein receptor) membrane fusion machinery. There, also different acotrs in different cell types were observed.

Finally exosomes are released into the extracellular space. Here they interact with the extracellular matrix and cells in the microenvironment. They can also enter the circulation via lymph of blood. It has to be mentioned that some studies report that in certain cell-types a proportion of exosomes remains attached to the cell surface. Here they might function as signaling platforms for juxtacrine communication.

Function of exosomes:

Exosomes are small mini versions of their original cell. In a way they reflect the status quo of the cell. And they serve to transmit bioactive molecules. Depending on the type molecule, they can trigger very different processes.

The bioactive molecules contained in exosomes have been shown to impact target cells via the following mechanisms: (1) direct stimulation of target cells via surface-bound ligands; (2) transfer of activated receptors to recipient cells; and (3) epigenetic reprogramming of recipient cells via delivery of functional proteins, lipids, and RNAs (Fig. 2).

Fig. 2 The schematic diagram of pathways involved in exosome mediated cell-to-cell communication. (1) Exosomes signal recipient cells via direct surface-bound ligands. (2) Exosomes transfer activated receptors to recipient cells. (3) Exosomes may epigenetically reprogram recipient cells via delivery of functional proteins, lipids, and RNAs (Zhang, Yuan, Liu, Yunfeng, Liu, Haiying, Tang, Wai Ho: 2019: Exosomes: Biogenesis, biologic function and clinical potential) license

Proteins

Exosomes are enriched in proteins, such as tetraspanins (CD9, CD63, CD81, CD82). They are present in processes like cell penetration, invasion and fusion tasks; heat shok proteins HSP70, HSP90): MVB formation proteins that are involved in exosome release (Alix, TSG101): Proteins responsible for membrane transport and fusion(annexins and Rab): proteins enriched in exosomes are used as marker proteins (e.g. TSG101, HSP70, CD81, CD63). Table 1 is a summary of protein components found in exosomes.

Table 1: Common protein components of exosomes. license

RNAs

Beside proteins all kinds of RNA species are found in exosomes. miRNAs can transfered through exosomes can change the phenotype of the recipient cells transient or persistent. lncRNAs and circRNAs can be found as well and are reported to have impact of a variety of biological processes. lncRNA TUC339 was highly significant expressed and linked to modulating tumor cell growth and adhesion. Other lncRNAs were linked to different diseases: lncRNA CRNDE-h in colorectal cancer , lncARSR in sunitinib resistance of renal cancer, lncRNA Hotair in rheumatoid arthritis, lincRNA-p21 and ncRNA-CCND1 in bleomycin-induced DNA damage.

Lipids

Generally, exosomes are enriched in phos- phatidylserine (PS), phosphatidic acid, cholesterol, sphingomyelin (SM), arachidonic acid and other fatty acids, prostaglandins, and leukotrienes, which account for their stability and structural rigidity. Table 2 is showing some bioactive lipids in exosomes:

Table 2: Bioactive lipids in exosomes. license

Clinical potential:

Since exosomes can be found in many different biofluids (urine, saliva, breast milk, cerebrospinal fluid, semen, amniotic fluid, ascites) that can be obtained with non-invasive metnods, the diagnostic potential of exosomes is very high. The profile and level of individual bioactive molecules could be used as a basis for decision-making. However, this information is not yet used in everyday clinical practice.

The clinical potential of exosomes opens up not only because of the diagnostic but also because of the therapeutic possibilities. Generally, a variety of therapeutic material, such as short interfering-RNA (siRNA), antagomirs, recombinant proteins, and anti-inflammatory drugs, can be encapsu- lated for exosome-mediated delivery via several delivery approaches, including: (1) Isolation of exosomes from donor cells ex vivo, and incorporated therapeutic agents into exosomes; (2) Encapsulation of donor cells with the therapeutic agent, which can be sorted into exosomes while exosomal formation; (3) Transfection of donor cells with the drug-encoding DNA, which can be expressed and sorted into exosomes.

References:

Zhang, Yuan, Liu, Yunfeng, Liu, Haiying, Tang, Wai Ho: 2019: Exosomes: Biogenesis, biologic function and clinical potential

Django admin backend

Wed, 20 May 2020 00:00:00 +0000

Create an admin user for the backend

When starting a django project an admin backend is created automatically. To hace access to this backend first a superuser has to be created. Before this can be done you have to migrate databases with the following command (virtual environement activated):

pyhton3 manag3.py makemigrations
pyhton3 manag3.py migrate

This ensures that all tables are available in the backend. Next you need to create a superuser with:

python3 manage.py createsuperuser

After typing name and password of the backend admin you can launch it.

Django Database

Wed, 20 May 2020 00:00:00 +0000

Handling databases in Django

When starting a project sqlite is preinstalled. This database is in development sufficient. When going to production it is recommended to use postgresDB.

In django you can create new databases within the models.py of your app. Each app will have its own databases. The code for a models entry could look like this:

from django.db import models
from django.utils impor timezone
from django.contrib.auth.models import User
class Post(models.Model):
title = models.CharField(max_length=100)
content = models.TextField()
date_posted = models.DateTimeField(default=timezone.now)
author = models.ForeignKey(User, on_delete=models.CASCADE)

Here a database wiht the name Post is created. This table has different columns which are defined by the Fields parameter. You need to run python3 manage.py makemigrations to get migration of the model. In the migrations directory now a file is created which holds all the informations. To see what sql is doing behind the scene you can type:

python3 manage.py sqlmigrate blog 0001

blog is the app name and 0001 is the created filename in the migrations folder. The output is what you have to write in sql.

Now you need to make the database available with:

python3 manage.py migrate

If you want to use this database on a site you need to import it in the views.py file:

from django.shortcuts import render
from .models import Post
def home(request):
context = {
'posts': Post.objects.all()
}
return render(request, 'blog/home.html', context)
def about(request):
return render(request, 'blog/about.html', {'title': 'About'})

If you want to make your models / databases available in the backend, you need to register the models in the admin.py file of your app:

from django.contrib import admin
from .models import Post
admin.site.register(Post)

In the backend you can easy handle the models/databases. Create new entries and change metadata information.

Django templates

Wed, 20 May 2020 00:00:00 +0000

.html templates in Django & how to inherit layout

In Django it is a good practice to inherit layout. Therefor you first need to make a template directory in your app. There you can save a base.html. This site has the base layout of all sites which are extended wwith it. This is how a base.html file can look like:

 {% load static %}
<!DOCTYPE html>
<html lang="en" dir="ltr">
<head>
<meta charset="utf-8">
<!-- Required meta tags -->
<meta charset="utf-8">
<meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no">
<!-- Bootstrap CSS -->
<link rel="stylesheet" href="https://maxcdn.bootstrapcdn.com/bootstrap/4.0.0/css/bootstrap.min.css" integrity="sha384-Gn5384xqQ1aoWXA+058RXPxPg6fy4IWvTNh0E263XmFcJlSAwiGgFAW/dAiS6JXm" crossorigin="anonymous">
<link rel="stylesheet" type="text/css" href="{% static 'blog/main.css' %}">
{% if title %}
<title> Django Blog - {{ title }} </title>
{% else %}
<title> Django Blog </title>
{% endif %}
</head>
<body>
<header class="site-header">
<nav class="navbar navbar-expand-md navbar-dark bg-steel fixed-top">
<div class="container">
<!-- clicking on django blog in the nav bar will go to blog-home of urls.py - blog -->
<a class="navbar-brand mr-4" href="{% url 'blog-home' %}">Django Blog</a>
<button class="navbar-toggler" type="button" data-toggle="collapse" data-target="#navbarToggle" aria-controls="navbarToggle" aria-expanded="false" aria-label="Toggle navigation">
<span class="navbar-toggler-icon"></span>
</button>
<div class="collapse navbar-collapse" id="navbarToggle">
<div class="navbar-nav mr-auto">
<!-- clicking on django blog in the nav bar will go to blog-home of urls.py - blog -->
<a class="nav-item nav-link" href="{% url 'blog-home' %}">Home</a>
<!-- clicking on django blog in the nav bar will go to blog-about of urls.py - blog -->
<a class="nav-item nav-link" href="{% url 'blog-about' %}">About</a>
</div>
<!-- Navbar Right Side -->
<div class="navbar-nav">
<a class="nav-item nav-link" href="#">Login</a>
<a class="nav-item nav-link" href="#">Register</a>
</div>
</div>
</div>
</nav>
</header>
<main role="main" class="container">
<div class="row">
<div class="col-md-8">
{% block content %}{% endblock %}
</div>
<div class="col-md-4">
<div class="content-section">
<h3>Our Sidebar</h3>
<p class='text-muted'>You can put any information here you'd like.
<ul class="list-group">
<li class="list-group-item list-group-item-light">Latest Posts</li>
<li class="list-group-item list-group-item-light">Announcements</li>
<li class="list-group-item list-group-item-light">Calendars</li>
<li class="list-group-item list-group-item-light">etc</li>
</ul>
</p>
</div>
</div>
</div>
</main>
<!-- Optional JavaScript -->
<!-- jQuery first, then Popper.js, then Bootstrap JS -->
<script src="https://code.jquery.com/jquery-3.2.1.slim.min.js" integrity="sha384-KJ3o2DKtIkvYIK3UENzmM7KCkRr/rE9/Qpg6aAZGJwFDMVNA/GpGFF93hXpG5KkN" crossorigin="anonymous"></script>
<script src="https://cdnjs.cloudflare.com/ajax/libs/popper.js/1.12.9/umd/popper.min.js" integrity="sha384-ApNbgh9B+Y1QKtv3Rn7W3mgPxhU9K/ScQsAP7hUibX39j7fakFPskvXusvfa0b4Q" crossorigin="anonymous"></script>
<script src="https://maxcdn.bootstrapcdn.com/bootstrap/4.0.0/js/bootstrap.min.js" integrity="sha384-JZR6Spejh4U02d8jOt6vLEHfe/JQGiRRSQQxSfFWpi1MquVdAyjUar5+76PVCmYl" crossorigin="anonymous"></script>
</body>
</html>

The file refers to online available bootstrap and CSS stylesheets as well as to JacaScript files.

<!-- Bootstrap CSS -->
<link rel="stylesheet" href="https://maxcdn.bootstrapcdn.com/bootstrap/4.0.0/css/bootstrap.min.css" integrity="sha384-Gn5384xqQ1aoWXA+058RXPxPg6fy4IWvTNh0E263XmFcJlSAwiGgFAW/dAiS6JXm" crossorigin="anonymous">
<link rel="stylesheet" type="text/css" href="{% static 'blog/main.css' %}">
<!-- Optional JavaScript -->
<!-- jQuery first, then Popper.js, then Bootstrap JS -->
<script src="https://code.jquery.com/jquery-3.2.1.slim.min.js" integrity="sha384-KJ3o2DKtIkvYIK3UENzmM7KCkRr/rE9/Qpg6aAZGJwFDMVNA/GpGFF93hXpG5KkN" crossorigin="anonymous"></script>
<script src="https://cdnjs.cloudflare.com/ajax/libs/popper.js/1.12.9/umd/popper.min.js" integrity="sha384-ApNbgh9B+Y1QKtv3Rn7W3mgPxhU9K/ScQsAP7hUibX39j7fakFPskvXusvfa0b4Q" crossorigin="anonymous"></script>
<script src="https://maxcdn.bootstrapcdn.com/bootstrap/4.0.0/js/bootstrap.min.js" integrity="sha384-JZR6Spejh4U02d8jOt6vLEHfe/JQGiRRSQQxSfFWpi1MquVdAyjUar5+76PVCmYl" crossorigin="anonymous"></script>

It has a navigation bar in the header of the page:

<header class="site-header">
<nav class="navbar navbar-expand-md navbar-dark bg-steel fixed-top">
<div class="container">
<!-- clicking on django blog in the nav bar will go to blog-home of urls.py - blog -->
<a class="navbar-brand mr-4" href="{% url 'blog-home' %}">Django Blog</a>
<button class="navbar-toggler" type="button" data-toggle="collapse" data-target="#navbarToggle" aria-controls="navbarToggle" aria-expanded="false" aria-label="Toggle navigation">
<span class="navbar-toggler-icon"></span>
</button>
<div class="collapse navbar-collapse" id="navbarToggle">
<div class="navbar-nav mr-auto">
<!-- clicking on django blog in the nav bar will go to blog-home of urls.py - blog -->
<a class="nav-item nav-link" href="{% url 'blog-home' %}">Home</a>
<!-- clicking on django blog in the nav bar will go to blog-about of urls.py - blog -->
<a class="nav-item nav-link" href="{% url 'blog-about' %}">About</a>
</div>
<!-- Navbar Right Side -->
<div class="navbar-nav">
<a class="nav-item nav-link" href="#">Login</a>
<a class="nav-item nav-link" href="#">Register</a>
</div>
</div>
</div>
</nav>
</header>

And the main page consists of a sidebar and the individual content of each site:

<main role="main" class="container">
<div class="row">
<div class="col-md-8">
{% block content %}{% endblock %}
</div>
<div class="col-md-4">
<div class="content-section">
<h3>Our Sidebar</h3>
<p class='text-muted'>You can put any information here you'd like.
<ul class="list-group">
<li class="list-group-item list-group-item-light">Latest Posts</li>
<li class="list-group-item list-group-item-light">Announcements</li>
<li class="list-group-item list-group-item-light">Calendars</li>
<li class="list-group-item list-group-item-light">etc</li>
</ul>
</p>
</div>
</div>
</div>
</main>

Thereby the content of each site is refered with:

<div class="col-md-8">
{% block content %}{% endblock %}
</div>

The individual sites are also stored in the templates directory of your app and are extended with the base.html file. Sytax look like this:

{% extends "blog/base.html" %}
{% block content %}
<h1>About page!</h1>
{% endblock content %}

The navabar header is referencing his links with:

<div class="navbar-nav mr-auto">
<!-- clicking on django blog in the nav bar will go to blog-home of urls.py - blog -->
<a class="nav-item nav-link" href="{% url 'blog-home' %}">Home</a>
<!-- clicking on django blog in the nav bar will go to blog-about of urls.py - blog -->
<a class="nav-item nav-link" href="{% url 'blog-about' %}">About</a>
</div>

Thereby href=“{% url ‘blog-home’ %} refers to the urls.py file of the app. Syntax of the urls.py file looks like this:

from django.urls import path
from . import views
urlpatterns = [
path('', views.home, name='blog-home'),
path('about/', views.about, name='blog-about'),
]

This file itself refers to the views.py file in the app directory. This file contains this code:

 from django.shortcuts import render
posts = [
{
'author':'Alex',
'title' : 'Blog Post 1',
'content': 'First post content',
'date_posted': 'May 20, 2020'
},
{
'author':'Bettina',
'title' : 'Blog Post 2',
'content': 'second post content',
'date_posted': 'May 21, 2020'
}
]
def home(request):
context = {
'posts': posts
}
return render(request, 'blog/home.html', context)
def about(request):
return render(request, 'blog/about.html', {'title': 'About'})

Each app has its own urls.py file. And the django project refers to this urls in the settings.py file in the project directory with this code:

....
from django.urls import path, include
from django.contrib import admin
urlpatterns = [
path('admin/', admin.site.urls),
path('', include('blog.urls')),
]
....

References: Youtube django series

Academic theme layout & functionality

Thu, 14 May 2020 00:00:00 +0000

Getting started: Docs of Academic Theme

Alert Box

some important content

Deploy Blogdown site with github & netlify

Thu, 14 May 2020 00:00:00 +0000

Reference: storybench

Markdown cheat sheet

Wed, 13 May 2020 00:00:00 +0000

Basic stuff

bold text :

use asterics like this: **its bold**

italic text :

use underscore like this: _its italic_

bold & italic :

use asterics and underscore **_bold&italic_**

header: use hash mark (the more the smaller the header become)

#header
##header
###header
####header

Links : Inline links

[Visit GitHub!](www.github.com)

Links : Reference links

 Here's [a link to something else][another place].
Here's [yet another link][another-link].
And now back to [the first link][another place].
[another place]: www.github.com
[another-link]: www.google.com

Images : Inline image link with the titel Benjamin Bannekat

![Benjamin Bannekat](https://octodex.github.com/images/bannekat.png

Benjamin Bannekat

Blockquotes : Just use the bigger than ‘>’ character

text with blockquote

Lists: use asterics

* Milk
* Eggs
* Salmon
* Butter

Milk
Eggs
Salmon
Butter

Posts | Alex Hildebrandt

Web of things, knowledge graphs, decentralised AI and responsible AI

IoT & WoT

Knowledge graphs

What is a

Decentralized artificial intelligence

Resposnsible artificial intelligence

Exosomes: biogenesis, function and clinical potential

Exosomes: biogenesis, function and clinical potential

About Exosomes:

Extracellular vesicles and the biogenesis of exosomes:

Function of exosomes:

Proteins

RNAs

Lipids

Clinical potential:

References:

Django admin backend

Create an admin user for the backend

Django Database

Handling databases in Django

Django templates

.html templates in Django & how to inherit layout

References: Youtube django series

Academic theme layout & functionality

Deploy Blogdown site with github & netlify

Markdown cheat sheet

Basic stuff

Reference: Markdown tutorial, R Markdown: The definitive guide, PDF cheat sheet