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Freezermas continues with track 3 of our rockin’ anatomy concept album! The number of the beast today is 5 (five days to go in Freezermas!), and I will deviate from the rock/metal theme to embrace the other side of the tracks: hip hop and rap. The Beastie Boys and I go way back: their “Licensed to Ill” album was the second cassette tape I bought (I remember proudly showing it off in Geometry class, circa 1986/7), and still ranks as one of my favourite albums ever. Everyone should own a copy of that, and of this next album…

The Five Felids, featuring KC

If only MCA were still alive to do this follow-up album…

The Beastie Boys’ superb, old school rap NYC-style (and themed) “To The Five Boroughs” (2004) satisfies my search for a #5-themed concept album/song. No track has that title, so I’m going with this one, “Triple Trouble” (song 3; day 3 of Freezermas… c’mon this is all just an excuse for me to talk about music I like and celebrate the concept album/freezers anyway!), as an introduction to a collaborative cat (felid) project we’ve started; and to continue the felid theme from Sunday (also be sure to check out the Snow Leopard dissection I posted on earlier!):

If You If You 
Wanna Know Wanna Know 
The real deal about the cats
Well let me tell you 
We’re felid funded ya’ll 
We’re gonna bring you some mad facts

(yes, that’s painful, I know… be relieved, I tried working some rap jargon into this post’s text but it just looked wack)

Dodgy-looking bagged-up skinned jaguar (bag-uar?) after delivery from Scotland.

Dodgy-looking bagged-up skinned jaguar (bag-uar?) after delivery from Scotland.

Anjali Goswami at University College London, myself, and Stephanie Pierce have teamed up to join the former’s skills in mammalian evolution, morphometrics, evo-devo and more together with our RVC team’s talents in biomechanics, evolution and modelling, and to apply them to resolving some key questions in felid evolution. We’ve hired a great postdoc from Bristol’s PhD programme, soon-to-be-Dr. Andrew Cuff, to do a lot of the experimental/modelling work, and then we have the marvellous Marcela Randau as a PhD student to tackle more of the morphometrics/evo-devo questions, which we’ll then tie together, as our Leverhulme Trust grant’s abstract explains:

“In studying the evolution of vertebrate locomotion, the focus for centuries has been on limb evolution. Despite significant evolutionary and developmental correlations among the limbs, vertebrae, and girdles, no biomechanical studies have examined the entire postcranial skeleton or explicitly considered the genetic and developmental processes that underly morphological variation, which are captured in phenotypic correlations. We propose to conduct experimental and geometric morphometric analyses of living and fossil cats, including the only large, crouching mammals, to study the evolution of locomotion, the mechanical consequences of size-related morphological evolution, and the evolution of correlations (modularity) in the postcranial musculoskeletal system.”

Above: snow leopard (headless) reconstructed and taken for a spin

Our study will integrate some prior studies from Anjali’s group, on modularity for example, and from my group, on the apparent lack of postural change with increasing size in felids (most other birds and mammals get more straight-legged as size increases, to aid in support, cats don’t– paper forthcoming). How does the neglected vertebral column fit into these limb-focused ideas? We’ll find out!

And it’s all very freezer-based research, using a growing stock of specimens that we’ve collected from zoo/park mortalities, many of which are kindly being supplied by Dr. Andrew Kitchener from the National Museums Scotland. We’ll be scanning, dissecting, measuring and modelling them and then returning the skeletons to be curated as museum specimens. This page features five sets of felid specimens involved in the research. We’ll be presenting plenty more about this research on this blog and elsewhere as it continues!

Above: ocelot from Freezermas day 1, now in 3D!

The Bag-o-Cats: whole specimens of a black-footed cat (Felis nigripes), juvenile cheetah, and juvenile snow leopard. I think. Sometimes you get a bag-o-cats and are not sure.

The Bag-o-Cats: x-ray CT slice showing whole specimens of a black-footed cat (Felis nigripes), juvenile cheetah, and juvenile snow leopard. I think. Sometimes you get a bag-o-cats and are not sure.

Panthera atrox (large American lion) from the NHM in LA. Oh yes we'll be applying our insights to strange extinct cats, too!

Panthera atrox (large American lion; “Naegele’s giant jaguar”) from the NHM in LA. Oh yes we’ll be applying our insights to strange extinct cats, too!

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MYSTERY ANATOMY RULES: 5 pts for correct, spot-on and FIRST right answer, 4 pts for very close or second, 3 pts for partly right or third in line with right answer, 2 pts for a good try, 1 pt consolation prize for just trying, or for a good joke!

Poetry rounds have special rules as described there, but the general rule is that cleverness gets more points.

If you post as “anonymous” name then it all goes into the same tomb of the unknown anatomist.

If you change your answer, you may lose ~1 pt if I feel frigidly cruel.

Answers posted via Twitter, Facebook, email or whatever do not count! No appeals. I am a frigid dictator.


FINAL 2014 SCORES- In order from top, ice-cool score to lukewarm ones; congratulations to our winner!

14 = Lorna Steel— coasts into a win without needing to comment in the final round; well done Lorna!

12= Jaime Headden– so close!!

11 = Casey Holliday

10 = filippo

9 = AnJaCo

7 = darkgabi,  Reno Hates Me

6 = Brian Speer, Robin Birrrdegg, Heinrich Mallison, Mark Robinson

5 = Olle Håstad, Crispin (@brainketchup), Brand van Sittert

4 = thebadlizard, Cat, Alejandro Otero

3= Stu Pond, Nick

2 = Henry,  pakasuchus, hypnotosov, Ida Wakely, Richard Forrest, hypnotosov, Andy Farke, Dennis E, Brooke, Lisa Buckley, Jan Prochel, Chris Thomas, Mieke Roth, Michael Doube (All in good company here!)

1 = Stella, William Pérez, zoe

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Freezermas continues! Today we have a treat for you. Lots of detailed anatomy! This post comes from my team’s dissections of an ostrich last week (~3-7 February 2014), which I’ve been tweeting about as part of a larger project called the Open Ostrich.

However, before I go further, it’s as important as ever to note this:

Stomach-Churning Rating: 9/10: bloody pictures of a dissection of a large ostrich follow. Head to toes, it gets messy. Just be glad it wasn’t rotten; I was glad. Not Safe For Lunch!

If the introductory picture below gets the butterflies a-fluttering in your tummy, turn back now! It gets messier. There are tamer pics in my earlier Naked Ostriches post (still, a rating of 6/10 or so for stomach-churning-ness there).

All photo credits  (used with permission) on this post go to palaeoartist Bob Nicholls (please check out his website!), who got to attend and get hands-on experience in extant dinosaur anatomy with my team and Writtle College lecturer Nieky VanVeggel (more from Nieky soon)!

Research Fellow Jeff Rankin, myself and technician/MRes student Kyle Chadwick get to work.

Research Fellow Jeff Rankin, myself and technician/MRes student Kyle Chadwick get to work, removing a wing.

This is a male ostrich, 71.3 kg in body mass, that had gone lame in one foot last summer and, for welfare reasons, we had to put down for a local farmer, then we got the body to study. We took advantage of a bad situation; the animal was better off being humanely put down.

The number for today is 6; six posts left in Freezermas. But I had no idea I’d have a hard time finding a song involving 6, from a concept album. Yet 6 three times over is Slayer’s numerus operandi, and so… The concept album for today is Slayer’s  1986 thematic opus “Reign in Blood” (a pivotal album for speed/death metal). The most appropriate track here is the plodding, pounding, brooding, then savagely furious “Postmortem“, which leads (literally and figuratively, in thunderous fashion) to the madness of the title track, after Tom Araya barks the final verse:

“The waves of blood are rushing near, pounding at the walls of lies

Turning off my sanity, reaching back into my mind

Non-rising body from the grave showing new reality

What I am, what I want, I’m only after death”

I’m not going to try to reword those morbid lyrics into something humorous and fitting the ostrich theme of this post. I’ll stick with a serious tone for now. I like to take these opportunities to provoke thought about the duality of a situation like this. It’s grim stuff; dark and bloody and saturated with our own inner fears of mortality and our disgust at what normally is politely concealed behind the integumentary system’s viscoelastic walls of keratin and collagen.

But it’s also profoundly beautiful stuff– anatomy, even in a gory state like this, has a mesmerizing impact: how intricately the varied parts fit together with each other and with their roles in their environment, or even the richness of hues and multifarous patterns that pervade the dissected form, or the surprising variations within an individual that tell you stories about its life, health or growth. Every dissection is a new journey for an anatomist.

OK I’ve given you enough time to gird yourself; into the Open Ostrich we go! The remainder is a photo-blog exploration of ostrich gross anatomy, from our detailed postmortem.

(more…)

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Seven dead old limbs
Seven science wins
Seven icy forms beheld
And our trip begins

Seven anat’my jokes
Seven bloody posts
Seven are our sci-comm fires
Seven frozen choirs…

(props to Iron Maiden’s “Moonchild” opening lyrics, from the iconic “Seventh Son of a Seventh Son” concept album, of lofty, epic, frozen, anatomy-bearing motifs)

7th Son

So we come full circle to another Freezermas, another foolhardy attempt to honour Charles Darwin (his birthday is Weds 12th Feb) with seven blog posts in seven days!

There will be mysterious morphology! Expositions of new projects and a new paper! Detailed dissections showing amazing anatomy! Silly songs and other nonsense! So much more that I have no idea about at this writing but will surely come to me! (there is an amorphous plan)

Last year I invoked the 7 days of Freezermas song, but this year the songcraft has changed. Christmas is so 2013! Time for a 1970smodern approach! We’re doing hard rock/heavy metal concept album songs and motifs each day. I started off with one above. Future posts will try to stick to a theme of songs/albums featuring numbers, counting down from seven. Because we all know that Darwin loved to rock. But let’s get on with the real rockin’: the freezer-based anatomical science!

Today we’ll ease you in to Freezermas: The Concept Album, like the acoustic intro of Moonchild did, with some simple Mystery CT Anatomy…

(insert guitar solo here while you mentally prepare yourself)

Stomach-Churning Rating: 2/10; simple CT scan of a body.

Mystery Anatomy 2014: same rules as before; remember that the scoreboard has been reset.

Identify the animal in the CT scout/pilot image below, as specifically as you can. 

Today’s special rule: Your answer must be in the form of a lyric (at least 2 lines) from a song by Queen (Google some if you’re unfamiliar– but how?).

Why Queen? One should never question Queen; not a little or a lot.

Difficulty: Is this the real life? Is this just fantasy?

You will probably want to click to emgiganticate the image below.

Mystery CT 11

Don’t let this one drive you Stone Cold Crazy! I know you’re feeling Under Pressure; just Tie Your Mother Down and play The Game.

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I am sure someone, in the vast literature on science communication out there, has written about this much better than I can, but I want to share my perspective on an issue I think about a lot: the tension between being a human, full of biases and faults and emotions, and doing science, which at its core seems inimical to these human attributes.

Stomach-Churning Rating: 1/10; nothing but banal meme pics ahead…

This is not a rant; it is an introspective discourse, and I hope that you join in at the end in the Comments with your own reflections. But it fits into my blog’s category of rant-like perambulations, which tend to share an ancestral trait of being about something broader than freezer-based anatomical research. As such, it is far from a well-thought-out product. It is very much a thought-in-progress; ideal for a blog post.

(Dr./Mr.)Spock of the Star Trek series is often conveyed as an enviably ideal scientific mind, especially for his Vulcan trait of being mostly logical– except for occasional outbreaks of humanity that serve as nice plot devices and character quirks. Yet I have to wonder, what kind of scientist would he really be, in modern terms? It wasn’t Spock-fanboying that got me to write this post (I am no Trekkie), but he does serve as a useful straw man benchmark for some of my main points.

“Emotions are alien to me – I am a scientist.” (Spock – Paradise syndrome)

The first ingredient of the tension I refer to above is a core theme in science communication: revealing that scientists are human beings (gasp!) with all the same attributes as other people, and that these human traits may make the story more personable or (perhaps in the best stories) reveal something wonderful, or troubling, about how science works.

The second ingredient is simply the scientific process and its components, such as logic, objectivity, parsimony, repeatability, openness and working for the greater good of science and/or humankind.

There is a maxim in critical thinking that quite a few scientists hold: One’s beliefs (small “B”– i.e. that which we provisionally accept as reality) should be no stronger than the evidence that supports them. A corollary is that one should be swift, or at least able, to change one’s beliefs if the evidence shifts in favour of a better (e.g. more parsimonious/comprehensive) one.

It is a pretty damn good maxim, overall. But in viewing, or imagining (as “what-if?” scenarios), you may find that some scientists’ reactions to their beliefs/opinions/ideas — especially regarding conclusions that their research has reached — can occasionally violate this principle. That violation would almost always be caused by some concoction of their human traits opposing the functionality of this maxim and its corollary.

Spock quote

For example (and this is how I got thinking about this issue this week; I started writing the post on 5 December, then paused while awaiting further inspiration/getting normal work done/fucking around), what if Richard Dawkins was confronted with strong evidence that The Selfish Gene’s main precepts were wrong? This is a mere heuristic example, although I was thinking about it because David Dobbs wrote a piece that seemed to be claiming that the balance of scientific evidence was shifting against selfish genes (and he later shifted/clarified his views as part of a very interesting and often confusing discussion, especially with Jerry Coyne– here). It doesn’t matter if it’s Dawkins (or Dobbs) or some other famous scientist and their best or most famous idea. But would they quickly follow the aforementioned maxim and shift their beliefs, discarding all their prior hard work and acclaim? (a later, palaeontological, event in December caused me to reflect on a possibly better example, but it’s so controversial, messy and drenched in human-ness that I won’t discuss it here… sorry. If you really want a palaeo-example, insert Alan Feduccia and “birds aren’t dinosaurs” here as an old one.)

I’d say they’d be reluctant to quickly discard their prior work, and so might I, and to a degree that’s a good, proper thing. A second maxim comes into play here, but it is a tricky one: “Extraordinary claims require extraordinary evidence.” For a big scientific idea to be discarded, one would want extraordinary scientific evidence to the contrary. And additionally, one might not want to quickly shift their views to accomodate that new evidence, perhaps, as a hasty rush to a new paradigm/hypothesis could be very risky if the “extraordinary” evidence later turned out itself to be bunk, or just misinterpreted. Here, basic scientific practice might hold up well.

kirk

But, but… that “extraordinary evidence” could be very hard to interpret– this is the tricky bit. What is “extraordinary?” Often in science, evidence isn’t as stark and crisp as p<0.05 (a statistical threshold of significance). Much evidence requires a judgement call– a human judgement call — at some step in its scrutiny, often as a provisional crutch pending more evidence. Therein lies a predicament for any scientist changing any views they cherish. How good are the methods used to accumulate contrary evidence? Does that evidence and its favoured conclusion pass the “straight-face test” of plausibility?

All this weighing of diverse evidence can lead to subjectivity… but that’s not such a bad thing perhaps. It’s a very human thing. And it weighs heavily in how we perceive the strength of scientific methods and evidence. Much as we strive as scientists to minimize subjectivity, it is there in many areas of scientific inquiry, because we are there doing the science, and because subjectivity can be a practical tool. Sometimes subjectivity is needed to move on past a quagmire of complex science. For example, in my own work, reconstructing the soft tissue anatomy of extinct dinosaurs and other critters is needed, despite some varying degrees of subjectivity, to test hypotheses about their behaviour or physiology. I’ve written at length about that subjectivity in my own research and it’s something I think about constantly. It bugs me, but it is there to stay for some time.

One might look at this kind of situation and say “Aha! The problem is humans! We’re too subjective and illogical and other things that spit in the face of science! What we need is a Dr. Spock. Or better yet, turn the science over to computers or robots. Let amoral, strictly logical machines do our science for us.” And to a degree, that is true; computers help enormously and it is often good to use them as research tools. Evolutionary biology has profited enormously from turning over the critical task of making phylogenetic trees largely to computers (after the very human and often subjective task of character analysis to codify the data put into a computer– but I’d best not go off on this precipitous tangent now, much as I find it interesting!). This has shrugged off (some of) the chains of the too-subjective, too-authority-driven Linnaean/evolutionary taxonomy.

But I opine that Spock would be a miserable scientist, and much as it is inevitable that computers and robots will increasingly come to dominate key procedures in science, it is vital that humans remain in the driver’s seat. Yes, stupid, biased, selfish, egocentric, socially awkward, meatbag humans. Gotta love ’em. But we love science partly because we love our fellow meatbags, and we love the passion that a good scientist shares with a good appreciator of science– this is the lifeblood of science communication itself. Science is one of the loftier things that humans do– it jostles our deeper emotions of awe and wonder, fear and anxiety. Without human scientists doing science, making human mistakes that make fantastic stories about science and humanity, and without those scientists promoting science as a fundamentally human endeavour, much of that joy and wonder would be leached out of science along with the uncomfortable bits.

Bendernator

Spock represents the boring -but necessary- face of science. Sure, Spock as a half-human could still have watered-down, plot-convenient levels of the same emotions that fuel human scientists, and he had to have them to be an enjoyable character (as did his later analogue, Data; to me, emotion chip or not, Data still had some emotions).

But I wouldn’t want to have Spock running my academic department, chairing a funding body, or working in my lab.

Spock might be a good lab technician (or not), but could he lead a research team, inspiring and mentoring them to new heights of achievement? Science is great because we humans get to do it. We get to discover stuff that makes us feel like superheroes, and we get to share the joy of those discoveries with others, to celebrate another achievement of humanity in comprehending the universe.

And science is great because it involves this tension between the recklessly irrational human side of our nature and our capacity to be ruthlessly logical. I hear a lot of scientists complaining about aspects of being a scientist that are more about aspects of being human. Yes, academic job hiring, and departmental politics, and grant funding councils, and the peer review/publishing system, and early career development, and so many other (all?) aspects of being a scientist have fundamental flaws that can make them very aggravating and leave people despondent (or worse). And there are ways that we can improve these flaws and make the system work better. We need to discuss those ways; we need to subject science itself to peer review.

But science, like any human endeavour, might never be fair. As long as humans do science, science will be full of imbalance and error. I am not trying to excuse our naughty species for those faults! We need to remain vigilant for them both in ourselves and in others! However, I embrace them, like I might an embarrassingly inept relative, as part of a greater whole; a sloppy symptom of our meatbaggy excellence. To rid ourselves of the bad elements of human-driven science, to some degree, would require us to hand over science to some other agency. In the process, we’d be robbing ourselves of a big, steamy, stinky. glorious, effervescent, staggeringly beautiful chunk of our humanity.

Spock isn’t coming to take over science anytime soon, and I celebrate that. To err is human, and to do science is to err, from time to time. But science, messy self-correcting process that it is, will untangle that thicket of biases and cockups over time. If we inspect it closely it will always be full of things we don’t like, and weeding those undesirables out is the job of every scientist of any stripe. Self-reflection and doubt are important weed-plucking tools in our arsenal for this task, because every scientist should keep their own garden tidy while they scrutinize others’. This is a task that I, as a scientist, try to take seriously but I admit my own failures (e.g. being an overly harsh, competitive, demanding reviewer in my younger years… I have mellowed).

humanity-and-logic

So here’s to human-driven science. Live long and publish!

Up next: FREEZERMAS!!! A week-long extraganza of all that this blog is really about, centred around Darwin’s birthday. Starts Sunday!

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Hey, a short post here to say go check this new blog out! I love it. The first main post-introductory post is a dissection of a snow leopard, documenting a real vet case attempting to figure out why it died. The “Veterinary Forensics blog” is going cool places, and it is a kindred spirit to this blog. You might, as I do sometimes when walking into a veterinary pathology/postmortem facility, see surprising and rare stuff– like in this photo of urban foxes:

troop of foxes

 

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Today, to help thaw you poor Americans out of that Arctic Vortex, we have a guest post bringing the heat, by my PhD student Sophie Regnault! This relates to some old posts about rhinos, which are a mainstay here at the WIJF blog- I’ve posted a lot about the rhino extinction crisisfeet, skin, big and bigger bones, and more, but this is our first rhinoceros-focused, actual published scientific paper! Take it away, Sophie! (We’re planning a few more “guest” blog posts from my team, so enjoy it, folks!)

Almost a year ago to the day, I submitted my first paper written with John Hutchinson and Renate Weller at the RVC and it has (finally!) just been published. To celebrate, I have been allowed to temporarily hijack ‘What’s in John’s Freezer?’ for my first foray into the world of blogging. I started the paper back as an undergraduate veterinary student. It was my first experience of proper research, and so enjoyable that I’m now doing a PhD, studying sesamoid bones like the patella!

We wanted to discover more about the types of bony disease rhinos get in their feet, of which there isn’t much known. Rhinos, of course, are big, potentially dangerous animals – difficult enough to examine and doubly difficult to x-ray clearly because of their thick skin. Unlike diseases which are fairly easy to spot (like abscesses or splitting of the nails and footpad), there is hardly anything out there in the scientific literature on bony diseases in rhino feet. It’s no small issue, either. When your feet each need to support over 900kg (typical for a large white rhino), even a relatively minor problem can be a major pain. Progressing unseen under their tough hide, lesions in the bone can eventually become so serious than the only solution is euthanasia, but even mild conditions can have negative consequences. For example, foot problems in other animals are known to have knock-on effects on fertility, which would be a big deal for programs trying to breed these species in captivity.

Hidden treasures abound!

Hidden treasures abound! (Photos can be clicked to embiggen)

Data gathering was a blast. I got to travel to Cambridge, Oxford, and London during one of England’s better summers, and these beautiful old museums were letting me snoop around their skeleton collections. I’d been there often as a visitor, but it was anatomy-nerd-heaven to go behind the scenes at the Natural History Museum, and to be left alone with drawers and drawers of fantastic old bones. Some of the specimens hadn’t been touched for decades – at Cambridge University Museum of Zoology, we opened an old biscuit tin filled with the smallest rhinoceros foot bones, only to realise they were wrapped in perfectly preserved 1940’s wartime Britain newspaper.

rhino-feet (2)

rhino-feet (4)

rhino-feet (3)

Osteomyelitis… (3 clickable pics above) the toe’s probably not meant to come off like that!

In addition to my museum studies, I had another fun opportunity to do hands-on research.  John (of course!) had freezers full of rhino legs (looking disconcertingly like doner kebabs, but maybe that’s just me!), which we CT scanned to see the bones. Although it is a pretty standard imaging technique, at this point I had only just started my clinical studies at the vet hospital, and being able to flick through CT scans felt super badass. Most vet students just get to see some horse feet or dog/cat scans, at best.

Another osteomyelitis fracture, visible in a CT scan.

Another osteomyelitis fracture, visible in a CT scan reconstruction.

We expected to find diseases like osteoarthritis (a degenerative joint disease) and osteomyelitis (bone infection and inflammation). Both had previously been reported in rhinoceroses, although it was interesting that we saw three cases of osteomyelitis in only 27 rhinos, perhaps making it a fairly common complication. It’s an ugly-looking disease, and in two of the cases led to the fat, fluffy bones fracturing apart.

We also had several unexpected findings, like flakes of fractured bone, mild dislocations, tons of enthesiophytes (bone depositions at tendon/ligament attachments) and lots of holes in the bones (usually small, occasionally massive). For me, writing up some of these findings was cool and freaky paranoid in equal measures. They hadn’t been much described before, and we were unsure of their significance. Was it normal, or pathological? Were we interpreting it correctly? Discussions with John and Renate (often involving cake) were reassuring, as was the realisation that in science (unlike vet school at the time, where every question seemed to have a concrete answer) you can never be 100% sure of things. Our study has a few important limitations, but has addressed a gap in the field and found some neat new things. Six months into my PhD, I’m enjoying research more than ever, and hoping that this paper will be the first of many (though I promise I won’t keep nicking John’s blog for my own shameless self-promotion if that happens!  EDIT BY JOHN: Please do!).

Nasty osteoarthritis wearing away the bone at the joint surface. Most cases occurred in the most distal joint.

Nasty osteoarthritis wearing away the bone at the joint surface. Most cases occurred in the most distal joint.

Deep holes in some of the bones: infection, injury?

Deep holes in some of the bones: infection, injury?

The paper:
Sophie Regnault, Robert Hermes, Thomas Hildebrandt, John Hutchinson, and Renate Weller (2013) OSTEOPATHOLOGY IN THE FEET OF RHINOCEROSES: LESION TYPE AND DISTRIBUTION. Journal of Zoo and Wildlife Medicine: December 2013, Vol. 44, No. 4, pp. 918-927.

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