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  • kubke 19:25 on September 27, 2013 Permalink | Reply
    Tags: academic life, , data analysis,   

    Great week comes to an end on a high note 

    Ending the week with a chat with @nytowler aka Andy – it was way overdue. Hadn’t spoken to him in a while and it is great to be reminded what a great friend he is. Andy is one of the profs where I did my PhD. We had heaps of fun – and stayed in touch after I graduated. He connected me to the “net” (before there was an internet) and taught me electronics and programming. He has been a rock steady friend throughout all these years.
    But the high point (other than catching up and having a few laughs) was discussing liberating some data that we had intended to analyse a long while back. So we discussed how we would do that. He is happy to put the analysis out on github, and I would try to do some programming in R for the analysis.
    The motivation for this is that I signed up for a MOOC to learn R programming (two actually) and playing with this data would be a great opportunity for me to apply what I learn, and do it with someone that can help me solve any coding problems. And of course, the opportunity of working with Andy is just the cherry on the top, and to be honest the cupcake too.
    We both had a laugh, because as we were chatting (online of course) I pointed him to a few online tools, and servers that he hadn’t heard of. What a great opportunity to tease him about how the tables had turned.

    So, there will be more on that later. Right now my job is to create the repo on github, organise the data files, and start slowly trying to get things moving.
    Oh and I got him to open a twitter account. So hopefully this will just be the beginning. Wish us luck!

  • kubke 19:19 on September 25, 2013 Permalink | Reply
    Tags: academic life, engagement, policy   

    So, there are subprofessorial memberships open for several university committees. Thinking that the Research, Library or Staffing would be ones where I could put in a good word or two for open science.
    #pondering. Do I really have the time?

  • kubke 15:15 on September 25, 2013 Permalink | Reply
    Tags: academic life,   

    Software being installed in the microscope – lets hope we can get that beast running again!

  • kubke 15:12 on September 22, 2013 Permalink | Reply
    Tags: academic life, , 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 16:21 on September 9, 2013 Permalink | Reply
    Tags: academic life, ,   

    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 12:44 on September 4, 2013 Permalink | Reply
    Tags: academic life, , 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: academic life, , 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 09:01 on April 16, 2013 Permalink | Reply
    Tags: academic life, , teaching   

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

  • kubke 23:24 on December 6, 2012 Permalink | Reply
    Tags: academic life, 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: academic life,   

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

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