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  • kubke 15:14 on September 25, 2013 Permalink | Reply  

    Congratulations Cherry 

    Today’s was Cherry’s graduation ceremony – wow – Congratulations.
    And in case you wonder whether us supervisors care, here is some proof of how happy it makes us to see students graduate!DSC02283

  • kubke 15:12 on September 22, 2013 Permalink | Reply
    Tags: , , lifelong learning,   

    Spent a large proportion of the weekend setting up the github repos. I feel like an absolute idiot at times but if I use it enough I am sure that even *I* can get a hang of it. Since I signed up for two coursera classes to learn R, I figured github would be a good place to keep the notes. One step at a time

    • kubke 21:56 on September 25, 2013 Permalink | Reply

      well – turns out that the code of conduct from coursera says I cannot share test questions and answers – so github is no a choice. Dang.

  • kubke 21:27 on September 21, 2013 Permalink | Reply
    Tags: , open research, , thoughts   

    A long chat with Mat Todd 

    After going to my first kiwi foo camp, i began noticing that Rob Inskeep was posting links on twitter to a social network called FriendFeed. Rob had organised getting a list of twitter handles prior to kiwi foo camp, which prompted me to sign up to twitter (yes, that is how it all started). So I joined FriendFeed and one evening I decided to search for “Open Access”. I suddenly found that there were heaps of people there discussing Open Access, Open Science and a whole lot of other things alike.

    It would be fair to say that if my original meeting with Nat Torkington back in 2008 changed my path, finding this community on FriendFeed was what would pave it. Hidden in the public view of FriendFeed was a community that was not just talking about changing the way we do and communicate science but were doing something about it. There were lots of disagreements, lots of trying to find common ground, lots of support, lots of ideas. This community was working together in ways I had never seen before. But for me, most importantly there was lots of learning.

    When FriendFeed got bought by Facebook and support for the platform slowly started to dwindle, the conversation moved to other platforms. But for me, none of them captured the spirit of the community I had found in 2009.

    I got the chance to meet a few of them in person as the years went by, and we have been able to keep up with what each of us were doing. Since then, a lot has changed. Things that were dreams became realities, other battles we lost and others we still keep fighting. I had a long chat with Mat Todd the other night. I discovered him on FriendFeed I don’t know when but probably at the beginning. I remember reading his insights with awe, admiring him from afar (or as afar as you can bee on an online social network).. I told him I always felt like I was stalking him, and what it had meant for me to meet him in person earlier this year. He chuckled and paraphrased a Charles Dickens quote, about moving on to sea and remembering the narrow river from where we came. I looked for that quote for days, and today I found it. The quote is priceless, but the paragraph it is embedded captures how I feel about everything that happened since that fateful day where I agreed to have a coffee with someone who identified himself as one Nat Torkington:

    “My dear Mrs Winter I have been much moved by your letter; and the pleasure it has given me has some little sorrowful ingredient in it. In the strife and struggle of this great world where most of us lose each other so strangely, it is impossible to be spoken to out of the old times without a softened emotion. You so belong to the days when the qualities that have done me most good since, were growing up in my boyish heart that I cannot end my answer to you lightly. […] We are all sailing away to the sea, and have a pleasure in thinking of the river we are upon, when it was very narrow and little.”

    (From Dickens, C. (2012). The Selected Letters of Charles Dickens. Oxford University Press.)

  • kubke 23:17 on September 18, 2013 Permalink | Reply
    Tags: nottebohm,   

    Fernando Nottebohm Plenary, February 1, 2011 (Australian Neuroscience Conference, Auckland)

    • kubke 21:50 on September 21, 2013 Permalink | Reply

      “that which we hold true is most probably the next generation of unrefuted errors”

    • kubke 21:50 on September 21, 2013 Permalink | Reply

      ‘I wanted to make sure that neurogenesis was happening in nature because I am always afraid of laboratory artifacts’

    • kubke 21:50 on September 21, 2013 Permalink | Reply

      ‘these results were a reminder of how soon we become attached to our favourite interpretation’

    • kubke 21:51 on September 21, 2013 Permalink | Reply

      ‘just when we managed to develop a transgenic zebra finch we ran out of funding’

    • kubke 21:51 on September 21, 2013 Permalink | Reply

      ‘we invest millions to Study rats living in little plastic boxes pretending they are not only models for humans but also of humans living normal lives’

    • kubke 21:52 on September 21, 2013 Permalink | Reply

      ‘but try to study a natural phenomenon and it is not considered fundable . when will the coin drop and we will see what an idiotic decision this is’

  • kubke 10:30 on September 18, 2013 Permalink | Reply
    Tags: Einstein,   

    Every day I remind myself that my inner and outer life are based on the labors of other men, living and dead, and that I must exert myself in order to give in the same measure as I have received and am still receiving.

    Albert Einstein

  • kubke 16:21 on September 9, 2013 Permalink | Reply
    Tags: , ,   

    Almost 2 hours meeting with studentC. I can see the shift in the discussion from the “intellectual” to the “executive”. There is still a lot of domain language I need to learn. #morereadingtodo

  • kubke 14:21 on September 4, 2013 Permalink | Reply
    Tags: humour,   

  • kubke 12:44 on September 4, 2013 Permalink | Reply
    Tags: , , manuscripts

    • kubke 12:48 on September 4, 2013 Permalink | Reply

      Perineuronal satellite neuroglia in the telencephalon of New Caledonian crows and other Passeriformes: evidence of satellite glial cells in the central nervous system of healthy birds?

      Felipe S. Medina, Gavin R. Hunt1, Russell D. Gray, J. Martin Wild, M. Fabiana Kubke

      Glia have been implicated in a variety of functions in the central nervous system, including the control of the neuronal extracellular space, synaptic plasticity and transmission, development and adult neurogenesis. Perineuronal glia forming groups around neurons are associated with both normal and pathological nervous tissue. Recent studies have linked reduction in the number of perineuronal oligodendrocytes in the prefrontal cortex with human schizophrenia and other psychiatric disorders. Therefore, perineuronal glia may play a decisive role in homeostasis and normal activity of the human nervous system.

      Here we report on the discovery of novel cell clusters in the telencephala of five healthy Passeriforme, one Psittaciform and one Charadriiforme bird species, which we refer to as Perineuronal Glial Clusters (PGCs). The aim of this study is to describe the structure and distribution of the PGCs in a number of avian species.

      PGCs were identified with the use of standard histological procedures. Heterochromatin masses visible inside the nuclei of these satellite glia suggest that they may correspond to oligodendrocytes. PGCs were found in the brains of nine New Caledonian crows, two Japanese jungle crows, two Australian magpies, two Indian mynah, three zebra finches (all Passeriformes), one Southern lapwing (Charadriiformes) and one monk parakeet (Psittaciformes). Microscopic survey of the brain tissue suggests that the largest PGCs are located in the hyperpallium densocellulare and mesopallium. No clusters were found in brain sections from one Gruiform (purple swamphen), one Strigiform (barn owl), one Trochiliform (green-backed firecrown), one Falconiform (chimango caracara), one Columbiform (pigeon) and one Galliform (chick).

      Our observations suggest that PGCs in Aves are brain region- and taxon-specific and that the presence of perineuronal glia in healthy human brains and the similar PGCs in avian gray matter is the result of convergent evolution. The discovery of PGCs in the zebra finch is of great importance because this species has the potential to become a robust animal model in which to study the function of neuron-glia interactions in healthy and diseased adult brains.

  • kubke 22:44 on June 2, 2013 Permalink | Reply
    Tags: , , publication   

    what a week! Sent 3 manuscripts out, sent out the review for on PLOS ONE paper, did the Women in Leadership workshop, organised the content for 2 courses in 2014, submitted the paper on recommendations for Open Access publishing for the Faculty, submitted the animal ethics protocol, registered for eResearch Symposium and, oh, yes, renegotiated the terms of my mortgage. All and all a very productive week! And monday is a holiday – Yay!

  • kubke 20:21 on May 18, 2013 Permalink | Reply
    Tags: Cereijido, ,   

    There is no need to promote science (it promotes itself)-but rather promoting a culture that is compatibel with science. Not knowing soemething about a process in nature does not mean we shoudl call it a miracle

    Marcelino Cereijido
  • kubke 09:05 on May 5, 2013 Permalink | Reply

    Ok, so moved my very small collection of Posterous files here – a bit of a change of focus, but so be it.

  • kubke 17:51 on April 18, 2013 Permalink | Reply
    Tags: ,   

    Dechorionated zebrafish embryos for about 2 hours today. There is a first time for almost everything. Thouse embryos are really cute!

  • kubke 14:04 on April 16, 2013 Permalink | Reply
    Tags: , Spemann   

    We stand in the presence of riddles, but not without the hope of solving them. And riddles with the hope of solution – what more can a scientist desire?

    Hans Spemann (1927) [in Gilberts Developmental Biology]
  • kubke 13:39 on April 16, 2013 Permalink | Reply
    Tags: ,   

    So I took the plunge and am now on my way to get some zebrafish embryos. Have been in love with them since I came across them as a model for neuromuscular development as I was looking for a lab to do a PhD. Well, that is step 1. Let’s see what happens on Step 2.

  • kubke 09:01 on April 16, 2013 Permalink | Reply
    Tags: , , teaching   

    It sometimes seem that even after teaching is over, it never really is – oh well…..

  • kubke 09:43 on April 8, 2013 Permalink | Reply

    Argh! I am back!

  • kubke 09:38 on January 22, 2013 Permalink | Reply
    Tags: , ,   

    I’ll be happy to see the end of fixing those little buggers

  • kubke 23:24 on December 6, 2012 Permalink | Reply
    Tags: , APR, metrics   

    Academic Performance Review 

    Every year, in December, we are expected to hand in our Academic Performance Reviews. It was due today, and I managed to get it finished 1 hour before midnight.
    One thing I like about the APR is the section where I am asked to set out my goals and objectives for the new year, and examine my year’s achievements against last years goals and objectives. It provides an opportunity to reflect on my career, how I spend my time, those things at which I failed and those at which I succeeded. In February I will be meeting with my Head of Department to discuss it.
    December is probably not a good time for this thoughtful process. I find myself trying to catch up with everything that needs to be done before year end, and sometimes getting things accomplished is a sluggish process because everyone is getting ready for the end of year and Christmas lunches, parties, drinks and dinners, and the closeness to the nearing summer break means that things dont work with the usual level of efficiency, And of course, everyone is trying to tie up the loose knots — so it can all become an uphill battle.
    I do my best thinking over the Christmas break. The University is closed and I can sit at home with my laptop enjoying the sun coming in through my window with no phone calls and few work-related email interruptions. I can think. I can turn the music on, and the change of pace is good.
    So I submitted the APR now, but I am sure I will be looking at it with a slightly different light over the break. I hope I will be allowed to provide a better version before the meeting.
    So what were my favoruite APR items this year?

    1. Engagement outside the University
    2. What we accomplished in New Zealand in the Open space throughout the year
    3. Tha the Open Research Conference is really happening.

    There were a few other things that made me smile as I was typing them: Being invited to join the blogging network at PLOS. Moving along with mentoring seccondary school science students. The manuscript submitted to PeerJ. The work done for PLOS ONE. Getting more work done in the lab. Not having given up on funding. The great student feedback on my teaching. The discussions about making what I teach better. The manuscripts that are almost there ready to submit. The success of my former PhD student. The friendships that developed with unexpected people. (Well, I didnt really type that last one!)

    And APRs are a good opportunity to discuss what I value with respects to “metrics” of my success. Unlike other evaluation processes, I can justify in the discussion why I choose not to offer the impact factor of the journals in which I publish, or why I think that one specific item is more important with respect to impact than another.

    Mainly, it is great to go through one of these APRs to find out that, for the most part the huge effort ends up paying off, and while the failures are there too, they are neither paralizing nor defining.

    Time for a pat on the back, and a good night sleep methinks.

  • kubke 10:52 on December 3, 2012 Permalink | Reply
    Tags: ,   

    Wow – only monday morning and my head is already ready to explode!

  • kubke 21:08 on November 28, 2012 Permalink | Reply

    2012.11.28: Busy (but productive) days 

    It’s been a few busy days – dealing with having to finish fixing the embryos on Monday, which took hours! And the smell of egg yolk just sticks in my nose for almost an entire day. Made much progress though. We managed to get a second order of eggs in, so that should give me enough stuff to do for a while. We also had a meeting about the Open Research Conference in February, that is moving along nicely, and had another chat about the SciFund project. Managed to get all the compliance corrections for the HRC grants in to the research office too, so good luck with that. I accepted two manuscripts to edit, one from PLOS ONE and one for PEERJ, and then a lot of other bits and pieces that just keep popping up. I also managed to do some cool stuff I want to add to my continuation application, and of course Tuesday night was Manaiakalani night.

    We also had a lab meeting Tuesday, it has been ages since we had one, and planned the work for the summer. So here is the plan:

    Need to get the intracellular physiology rig up and running again. We need to get the amplifier that one of our colleagues borrowed, and then it will be trying to sort out the programming in LabView to get it to do what I want. That will take a bit of time.
    We need to get the comparative histology stuff up and running too, so that we can build the 3D models of the brain – lots of bits and pieces to put together, a bit tedious, but looking forward to it.
    I need to get the nerve labels in the embryos I need so I can finally publish that paper
    I need to finish writing the other 3 papers I am writing

    So it will be a busy summer.
    Oh and yay! Got accepted to the Women in Leadership programme!

    All and all a good week so far.

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