Category Archives: Software

Not so big data

Lesenswert https://www.dasmagazin.ch/2016/12/03/ich-habe-nur-gezeigt-dass-es-die-bombe-gibt/

Zwei Psychologen war in den 1980ern der Nachweis gelungen, dass jeder Charakterzug eines Menschen sich anhand von fünf Persönlichkeitsdimensionen messen lässt, den Big Five: Offenheit (Wie aufgeschlossen sind Sie gegenüber Neuem?), Gewissenhaftigkeit (Wie perfektionistisch sind Sie?), Extraversion (Wie gesellig sind Sie?), Verträglichkeit (Wie rücksichtsvoll und kooperativ sind Sie?) und Neurotizismus (Sind Sie leicht verletzlich?).
… Bald kann sein Modell anhand von zehn Facebooks-Likes eine Person besser einschätzen als ein durchschnittlicher Arbeitskollege. 70 Likes reichen, um die Menschenkenntnis eines Freundes zu überbieten, 150 um die der Eltern, mit 300 Likes kann die Maschine das Verhalten einer Person eindeutiger vorhersagen als deren Partner.

Backlink to http://www.michalkosinski.com and his seminal 2013 PNAS paper. Plus the online prediction.


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Shorten your URL

Based on a tutorialzine.com article, I wrote an own URL shortener. Put everything in directory /s

.htaccess

RewriteEngine On
RewriteCond %{REQUEST_FILENAME} !-f
RewriteCond %{REQUEST_FILENAME} !-d
RewriteRule ^(.*)$ /s/index.php?$1 [last]

index.php

$links = parse_ini_file('links.ini');
$l=filter_var( $_SERVER['REQUEST_URI'], FILTER_SANITIZE_STRING);
$l=preg_replace ('/\/s\//','',$l);
if($l!='' && array_key_exists($l, $links)){
  header('Location: ' . $links[$l]);
}
elseif (substr($l,0,4)=="http") {
  $sl = sprintf( '%04x%04X', mt_rand( 0, 0xffff ), mt_rand( 0,, 0xffff) );
  echo $_SERVER[HTTP_HOST]  . '/s/' . $sl;
  $out = $sl.' = '.$l;
  file_put_contents('links.ini', $out."\n", FILE_APPEND);
}

links.ini

Gel = "https://www.google.com/"

Bookmarklet ShortenURL

javascript: document.location = 'https://www.www.wjst.de/s/' + document.location.href

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Probiotics and allergy

Here is a quick summary on probiotics and allergy as reported by two meta-analysis. The first one is Cuello-Garcia 2015 in JACI

Probiotics used by pregnant women or breast-feeding mothers and/or given to infants reduced the risk of eczema in infants; however, the certainty in the evidence is low.

the second by Zuccoti 2015 in Allergy Continue reading Probiotics and allergy


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Rat race

While working on a review about vitamin D and the microbiome, I came across an interesting article Immune-Microbiota Interactions: Dysbiosis as a Global Health Issue

Recent research, however, demonstrated that a number of specific interventions can lead to (partial) primary prevention of allergy, especially of atopic dermatitis (AD) and food allergy (FA). Three types of primary prevention strategies have been successfully studied: early administration of bacterial products (most studies are on probiotics), early moisturizing in infants at risk for AD and early exposure to allergenic foods (peanut and egg).

I am not so much convinced of any successful probiotics research that prevents all kind of allergy (ref, ref, just to name two). The interesting point, however, is the new recommendation to early exposure of allergenic foods. Does earlier exposure mean less exposure under vitamin D suppression that shouldn’t start before week 6?


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Ciguatera

I will have a paper in the next issue of the  MMW describing a case report of Ciguatera in Cienfuegos / Cuba. Seems to be a common phenomenon there but unfortunately there is nothing in the Cuba guide books so far.
The pathology is extremely interesting  – sodium channel activation by P-CTX. I only wonder why there are no therapeutic attempts with long-lasting class Ia aNa channel blockers  Chinidin, Procainamid, Ajmalin, Disopyramid, Propafenon, Prajmalin. Or valproate for CNS activity.


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Imagick library for R

When working for an exhibition in 2017, I found a new R library that allows nearly every image modification you could think of.

install.packages("magick")
library(magick)
magick_config()

gives you

image_read(path, density = NULL, depth = NULL)
image_write(image, path = NULL, format = NULL, quality = NULL, flatten = FALSE)
image_display(image, animate = TRUE)
image_browse(image, browser = getOption("browser"))
image_append(image, stack = FALSE)
image_average(image)
image_coalesce(image)
image_flatten(image, operator = NULL)
image_fft(image)
image_map(image, map, dither = FALSE)
image_montage(image)
image_morph(image, frames)
image_mosaic(image, operator = NULL)
image_join(...)
image_info(image)
image_animate(image, fps = 10, loop = 0, dispose = c("background","previous", "none"))

 


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“Doodle” calendars on mobile devices

It’s always difficult if you can’t see all calendar entries on the road. So I am setting up new dates at wjst.de/dudel, cut + paste the subscription link to the Nextcloud/Owncloud calendar web frontend.

screen

“Doodle” dates will then magically appear on all other devices.


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Low serum vitamin D – reverse causation or true risk factor?

Even with thousands of studies, one of the most basic questions in vitamin D research is being unanswered. Low serum 25(OH)D3 – is it reverse causation or a true risk factor? As plasma 25(OH)D3 can be easily determined, it became the standard measurement for vitamin D supply. Unfortunately numerous other factors – season, genetics, sex, age, race – all influence serum 25(OH)D3 levels.

Then in 2011 David Reid et al. published a paper of 25(OH)Dfollowing up changes during acute inflammatory response after knee surgery. In essence, plasma concentrations of 25(OH)D decreased after an inflammatory insult and are not a reliable measure of 25(OH)D status in subjects with a significant systemic inflammatory response. This observation is being confirmed in the meantime by 2 further studies (Barker 2012 and Waldron 2013). I think this is a clear result now.

I have never been convinced that Mendelian randomization will help here at all – as done in earlier studies. These are clearly situations where Mendelian randomization does not work as shown  by Smith and Ebrahim back in 2004

—failure to establish reliable genotype (seldom)
—intermediate phenotype genotype—disease associations (frequent)
—confounding of genotype—intermediate phenotype—disease associations (unclear)
—horizontal pleiotropy and multi-functional genes (frequent)
—canalization and developmental compensation (unclear, but expected to be frequent)
—Lack of suitable polymorphisms for studying modifiable exposures of interest (no more a problem)

So, 25(OH)D3 is more an acute phase indicator where low levels in inflammatory diseases is effect not a cause but an effect. A recent review concludes therefore

Reversed causality is described as a possible factor interfering with the correct assessment of the Vit D status. It is concluded that further widespread fortification of foods and stimulation of supplement use should be reconsidered.

It is, however, unclear if low 25(OH)D levels is due to an increased demand (as the vitamin D lobby argues), a shift in free/bioavailable metabolite by hemodilution, binding protein capacity (what I am expecting) or just some unknown further factors.

 


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So many new layers

More recently, I have updated http:/cycleplanner.wjst.de with many more custome layers. It’s  a bit cumbersome to find  the best data sets out there while using it in leaflet is usually straightforward.screen Openstreetmap items work great with the overpass api which has a bit complicated syntax. Here is an example of an OR (union) query

var fuel = new L.OverPassLayer({
query: "(node['amenity'='fuel'](BBOX);node['amenity'='fast_food'](BBOX);node['amenity'='kiosk'](BBOX););(._;>;);out;"
});

bildschirmfoto-2016-11-03-um-16-11-50


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Gentest vor Vitamin D Prophylaxe?

Es gibt eine kindliche Erkrankung, die nur bei Vitamin D Prophylaxe auftritt: die idiomatische infantile Hyperkalzämie Lightwood (OMIM 143880). Die Ursache, eine oder mehrere Mutationen im Vitamin besser Hormon D abbauenden Enzym CYP24A1, wurden  erstmals durch Schlingmann 2011 charakterisiert. Diese Kinder leiden an einer Hyperkalzämie, Wachstumsverzögerung, Erbrechen, Dehydration und Nephrokalzinose. Mittlerweile sind noch mehr Mutationen bekannt:

 

Schlingmann, NEJM 2011
Clinvar 2016Funktion
A475fsX490pathogen
E143delNM_000782.4(CYP24A1):c.428_430delAAG (p.Glu143del)
GRCh38: Chr20:54172928-54172930
pathogen
E151XNM_000782.4(CYP24A1):c.451G>T (p.Glu151Ter)
GRCh38:
Chr20:54171669
pathogen
L409SNM_000782.4(CYP24A1):c.1226T>C (p.Leu409Ser)
GRCh38:
Chr20:54158096
schwach pathogen
R396WNM_000782.4(CYP24A1):c.1186C>T (p.Arg396Trp)
GRCh38:
Chr20:54158136
pathogen
R159QNM_000782.4(CYP24A1):c.476G>A (p.Arg159Gln)
GRCh38:
Chr20:54171644
pathogen
E322KNM_000782.4(CYP24A1):c.964G>A (p.Glu322Lys)
GRCh38:
Chr20:54162743
pathogen
c.445_449(+1) delATCCTg-hetpathogen
NM_000782.4(CYP24A1):c.1039C>T (p.Gln347Ter)
GRCh38:
Chr20:54159075
vermutlich pathogen
NM_000782.4(CYP24A1):c.1426_1427delCT (p.Cys477Leufs)
GRCh38:
Chr20:54157395-54157396
pathogen

Offensichtlich gibt es hier auch  benigne Formen. Ob ein Mutationsscreening vor einer Vitamin D Prophylaxe Sinn macht (“Präzisionsmedizin“)? Dazu müsste man erstmal die Prävalenz der CYP24A1 Varianten in der Bevölkerung kennen, Schlingmann schätzt zumindest 100 Fälle / Jahr in England.

 


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Akademische Vor-träge

academics hat einen interessanten Kommentar

So wird von einem Abendvortrag Grundsätzliches und Überspannendes erwartet, wohingegen ein Vortrag am späteren Samstagnachmittag allenfalls zarte Ergänzungen beisteuern sollte. Die performative Herausforderung schließt unmittelbar daran an, indem der Referent darauf geprüft wird, ob er die ihm zugedachte Rolle auszufüllen vermag. Verzichtet der Abendvortragende auf die große Geste des Universalgelehrten, gilt er als Enttäuschung. Übt sich der Nachwuchs hingegen in zu forscher Thesenbildung, wirkt er anmaßend. Die Kunst der Tagungsorganisation besteht darin, die Choreografie der Rollen möglichst passgenau vorzuzeichnen. Nachwuchsleute werden daher meist auf Zeiten gesetzt, in denen sich Hunger mit nachlassender Konzentration und Abfahrtszeiten von Zügen überschneidet. Die akademischen Top-Acts wiederum eröffnen Sektionen, stemmen einen Solopart oder den Impulsvortrag zum Tagungsauftakt. So besitzt jede Rolle ihre eigene Uhrzeit.


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Value free science

There is an interesting course at ETH Zürich

Should science be free from moral, political or ideological influences? According to the so-called value-free ideal it should. Many scientists think of themselves as committed to truth and objectivity and nothing else. In this seminar, we will track the history of the value-free ideal and engage in a debate about the potential role of so-called non-epistemic values in science.
Course Objective
In the past decades, philosophers of science have begun to challenge the value-free ideal in science. With the help of recent literature from the philosophy of science, students will be introduced to the debate on values in science and the reasons for why the value-free ideal has come under attack. They will be familiarized with the distinction between epistemic (truth-conducive) values and so-called non-epistemic values. The course aims at enabling students to critically reflect the potential role of non-epistemic values in science.


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