Minecraft on old Lenovo M58p

Friday, January 29th, 2016 by hinrich

Minecraft

I have purchased an old M58p and tried my luck to upgrade it somewhat. Swapping the hard drive for a SSD was fairly straight forward. However, getting to install Windows 10 and then finding the right drivers was a bit more challenging...

In the unlikely event that you are trying the same - or that you are also struggling to get Minecraft running on such a machine, you will know that there are issues with OpenGL and finding a working graphics driver for the Intel Q45/Q43 express chipset. The following driver works for me - even though the frame rate is not spectacular, it does work decently if you reduce your settings:

b2vdo11us14.exe - Intel Onboard VGA driver for Windows 7 (64-bit - old version from March 2010)
w4aud06us17.exe - ADI Audio codecs AD1988A and AD1882 driver
c3amt02us17.exe - Intel Active Management Technology driver

ThinkCentre M58p
Machine type: 6136

Good luck!

Posted in Computer


PuberPester or how to sensibly provide internet access for kids

Monday, May 25th, 2015 by hinrich

DrayTek Vigor Router

More and more schools rely on parents to provide their children with internet access. Whether we are talking about websites to check the agenda for the next school day, get to know the scores from the latest exams or to find out whether a lesson will be dropped tomorrow due to the absence of one of the teachers, more and more is done via internet.

Sure, this is only logical as the society is moving towards an internet-enabled system for many aspects of life. Still, parents are left to their own devices on how to deal with this necessity at home. What, if you don't favor the two extremes of either no internet for the kids or completely free access? There are middle grounds like a computer at a table where mom or dad can have an eye on things every now and then. But isn't that a form of policing?

What if you want to deal with the whole situation in a way that tries to balance the necessity for access with certain restrictions while leaving as much as possible liberty for the kids? And don't forget to throw in some extra complexity such as smartphones and tablets - not just Windows desktops or laptops!

A daunting task...

I have taken it on with a compromise: provide a system that gives each kid a time quota. They need to log in and then the clock starts ticking across all devices. I have combined this further with some web site restrictions via OpenDNS. The system works for all devices as the accounts are linked to each kids own device and via account log-in for the shared devices. Furthermore, there are restrictions regarding time of day to ensure that internet is off during the night.

But what if your oldest one comes to tell you that his time is up and he still needs to check something for school?

Here my solution is a separate "school" account. It has unlimited access and only works on white-listed sites (those sites absolutely needed for school). And what when they figure out that it is difficult to deal with https sites? To prevent endless YouTube watching via the school account, there is a data quota of 50 MB per day on that account ("op is op" as they say in Dutch).

Is this the best solution? Probably not. But it is my current attempt to strike a balance between providing the needed access to the internet while restricting it in a way that limits policing...

Posted in Computer


Replacing my Nexus 5 battery

Wednesday, February 18th, 2015 by hinrich

LG BL-T9 2300mAh replacement battery

This was the first time I have attempted to replace a smartphone battery. After having used an iPhone 3GS for several years (with two battery replacements done by someone who knew what he was doing...) I had switched to a Nexus 5 end of 2013.

It was peculiar that I had all kinds of strange crashes after having moved to Lollipop. I tried various battery saving apps, but at some point wondered whether replacing the battery would not be more sensible. So I got a LG BL-T9 2300mAh replacement battery and went ahead with a knife and a screwdriver. And I must say, it was not that difficult.

I found the descriptions at IFixIt quite useful. Even though they mention "The battery is held in place with some adhesive.", it took me quite a while to finally apply sufficient force (= not too much - it requires some patience) to get the battery out. To my surprise the battery had "swollen" a bit and felt a bit spongy - certainly when comparing to the new replacement battery. I only recall that the Nexus had gotten somewhat warmer the weeks before I had ordered a new battery, so I wonder whether my battery had become funny...

One last remark: I found descriptions where they start by placing the new battery first and then attach the daughter board connector. If you have no experience, the connector feels unknown and you wonder whether you are placing it properly. I removed the battery again and first attached the connector before placing the battery. That was much easier.

All in all, really something that can be done if you have some patience and don't apply too much force.

The IFixIt article can be found here:
https://www.ifixit.com/Guide/Nexus+5+Battery+Replacement/26009
And here is an image of another Nexus 5 user who had a similarly "swollen" battery:
http://i.imgur.com/CZW0l7u.jpg

Posted in Computer


Bedaquiline for Patients with NTM Lung Disease?

Friday, February 13th, 2015 by hinrich

Structure of TMC207/R207910

The journal Chest has recently published an article describing an off-label use of Bedaquiline (TMC207/R207910). Philley et al. have explored the effects of the drug in patients with nontuberculous mycobacterial (NTM) lung disease. They treated in total 10 patients with the same bedaquiline dosage used in TB trials.

While the authors clearly point at the small sample size of the study, they did not observe abnormal EKG findings - something which is of concern as the drug has a black-box warning for arrhythmias (=> long QT syndrome).

I hope we will be able to quickly gather more information over potential long QT risks so that we get a better view on the risk/benefit balance.

You can find the article here:
http://journal.publications.chestnet.org/article.aspx?articleID=2119207

Posted in Tuberculosis


Toxic tuberculosis drug

Friday, January 02th, 2015 by hinrich

Structure of TMC207/R207910

I admit I am biased. I have contributed to our understanding of the molecular mechanisms of bedaqueline and wish the drug to become a successful aid in curing patients with MDR-TB. Therefore I was concerned and curious to learn more when I saw this heading twice on 31st of December:

"New treatment strategy allows lower doses of toxic tuberculosis drug without compromising potency"

Of course, learning that a person is working in / for the pharmaceutical industry triggers a broad spectrum of associations with different people. Similarly, for me reading characterizations such as "toxic tuberculosis drug" or "higher toxic doses of bedaquiline" bring up associations of bad news as you would not want people to be treated with "toxic drugs".

After reading the articles I came to realize that the choice of words for the heading might have been too strong as also one of the authors (Dr. Gupta) states in an interview: "In a phase 2 trial involving patients with advanced MDR-TB, a significantly higher number of participants receiving bedaquiline died than those receiving placebo although the causes of mortality were not directly attributable to the drug."

Over the next two days I stumbled across two more sites referring to the same research. Here the headings read a little differently: "Hypertension Medication May Enhance Tuberculosis Treatment" and "Study indicates new strategy to treat tuberculosis".

Choosing the right words for a heading sure is difficult - especially when they concern words that elicit an emotional response in some readers. To me "toxic" is one of them.

Here are the articles I am referring to:
http://www.eurekalert.org/pub_releases/2014-12/jhm-nts123014.php
http://medicalxpress.com/news/2014-12-treatment-strategy-doses-toxic-tuberculosis.html
http://medicalresearch.com/infections/hypertension-medication-may-enhance-tuberculosis-treatment/10317/
http://vaccinenewsdaily.com/news/332489-study-indicates-new-strategy-to-treat-tuberculosis/

Posted in Tuberculosis


Annotated data lake

Tuesday, December 23th, 2014 by hinrich

Science

During a discussion with colleagues on the necessity to make our various data sources easily accessible for integrated analyses, we of course considered recent trends in IT ("Big Data", "The Cloud", "High Performance Computing", ...). It still strikes me how difficult it is to see the whole picture. Technological concepts such as "Data Lake" make perfect sense in this context: they conceptually enable you to do analyses that you could not do in the past because the various data types were just not available for a joint analysis. Still, data analysts frequently spend a lot of time in chasing down the correct annotation of their data: Which exact chemical structure has been tested? In which well of a microtiter plate was which sample tested? Where are the controls located? Did this experiment test exactly the same compound or do I only have a generic name and thereby won't know which chemical structure has been profiled?

Spending time to obtain answers to these questions is a necessary evil to ensure that any analysis results are likely to be useful. However, they are typically not considered or even recognized when thinking about data analysis.

So, I coined on the spot a new term to reflect what we really need: an "Annotated Data Lake" (quick Google search did not give any hits, so I am curious whether it will change as a number of my colleagues seemed to like the term...). We need to make a substantial effort here today to enable big data analytics / integrated data analysis tomorrow.

Posted in Science


Coffee grounds on vacation

Friday, November 07th, 2014 by hinrich

Ground Coffee

Coffee degrades over time. Depending on the surface area it will degrade faster. Therefore coffee grounds should be stored in airtight containers. Still, they go stale in days. This process speeds up under conditions of high temperature, light, or high humidity.

So, what do you do when you go on vacation and forgot clips or other things at home (like I typically do...)? As you can see on the little picture, I use a fork. It looks funny but does the trick. And I also try to buy half pound packages so that I use the coffee ground more quickly.

Of course, the quality of the resulting coffee is still not getting to close to what a Jura can produce, but it normally suffices for me...

Posted in Misc


Retrieving the serial number of a computer

Monday, September 01th, 2014 by hinrich

ThinkPad X220

Looking for a software way under Windows to figure out the serial number of your laptop while it is docked?

When you go to the support website of the manufacturer, companies frequently describe you ways that rely on you being able to turn your laptop upside down, but there is also a way via the command line:

Open the Windows command line (All Programs => Accessories => Command Prompt) and go to the follwing folder:
C:\Windows\System32\wbem

Then using this command you will be able to retrieve it:
wmic bios get serialnumber

This command is also useful if you want to figure out the part number:
wmic csproduct get name

Posted in Computer


120 week results of Bedaquiline phase 2 study

Friday, August 22th, 2014 by hinrich

Structure of TMC207/R207910

The New England Journal of Medicine has just published the results of the Bedaquiline (TMC207/R207910) phase 2 study by Diacon et al. Having analysed the data after 120 weeks, the researchers demonstrated a statistically higher cure rate in patients infected with multi-drug resistant tuberculosis (MDR-TB) compared to placebo: nearly twice as many MDR-TB patients were cured when given bedaquiline.

In a second article, Edward Cox and Katherine Laessig of the FDA looked at the benefit-risk balance for treating drug-resistant tuberculosis also in the context of the finding that more patients in the bedaquiline group died than in the placebo group.

While the number of people who died in the bedaquiline is still small ("Among the 4 other patients in the bedaquiline group who died, there was no apparent common cause of death".), this is certainly of concern. Even though Cox and Laessig remark that "[...] the length of time between the last receipt of bedaquiline and death makes it difficult to discern a mechanism by which bedaquiline could be directly related to the deaths, even if we take bedaquiline's long half-life into consideration.", I hope we will be able to quickly either identify a link with bedaquiline or obtain information that show that these deaths were not linked to the use of bedaquiline.

Even more so as they remark that "The previously cited historical data show that outcomes are very poor in patients who do not receive adequate treatment."

Here are both articles:
http://www.nejm.org/doi/full/10.1056/NEJMp1314385
http://www.nejm.org/doi/full/10.1056/NEJMoa1313865

Posted in Tuberculosis


Innovative technologies

Thursday, June 05th, 2014 by hinrich

Science

I am continuously confronted with the following balancing act - easy to describe - difficult to judge, decide and act upon...

One side looks for new technologies (also called innovation) that can provide us with new scientific insights into the compounds that we would like to develop into new medicines. Here elements like cutting-edge technologies, competitive advantages, novel types of insights, automation, throughput, etc., weigh a lot.

The other side (you could summarize them simply as the more conservative aspects) look at applicability. What kind of data are produced? What do they mean? Do we fully understand how to translate the novel data / information into knowledge and understanding about our chemical structures?

An example to illustrate this are technologies or approaches that will provide us with information about the polypharmacology of compounds - something that we increasingly get with modern high dimensional biology technologies. What do the measurements mean that, e.g., implicate an effect on a molecular level in a context that we cannot directly link to the desired effect? Will they turn out to harm the further development by creating concerns that may not be justified?

Often times such new approaches are being positioned at early stages of the discovery pipeline and are accordingly utilizing simple model systems (e.g., cell lines). Here we will frequently be left with the question of how such findings will translate into the human situation? And furthermore, even if undesired effects were to be correctly indicated, it is usually impossible to predict at what concentration the desired therapeutic effect will be seen in humans. And maybe the detected undesired effects might not yet be induced to an extent that would cause concern when using a concentration that is sufficient for inducing the desired therapeutic effect.

However, while such thoughts are important to consider, it is also necessary to continue to explore new ways of obtaining important information on compounds early to help in prioritizing the structures that have the highest chances of being successful. Tricky...

Posted in Science


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