Tag Archives: Summer2016

On the Shelf…

For work…

Experimental Design for Biologists

Experimental Design for Biologists, by David Glass

Location: HHSL Book Stacks, Sackler, 5th Floor, QH 323.5 G549e 2014

This handbook is designed to teach the fundamentals of experimental design.  The author, who is the executive director of the Muscle Diseases and Aging Initiative at the Novartis Institute for Biomedical Research, held a workshop on campus in May.

And leisure…

The Summer Before the War

The Summer Before the War, by Helen Simonson

Location: HHSL Leisure Reading, Sackler, 4th Floor, Fiction S611s 2016

Set in an English village on the cusp of World War I, this novel tells the story of a woman selected to be the first female Latin teacher in the local school.  A little ponderous and predictable, but an easy summer read.

Notes From the Library…Author Identifiers

What are author identifiers?

An author identifier is a unique identifier that distinguishes one researcher from another, eliminating confusion in scholarly publication and grant funding.

Why do we need author identifiers?

If you have ever tried to do an author search a database, then you know how difficult it can be to find all articles by a particular author.  An author may have a common surname, publish under variations of the same name, change their name, or different geographical/cultural conventions for reporting their name.  Affiliation and field of study relieve some of the ambiguity associated with author names, but inclusion of this information in a search does completely eliminate the problem.  Two authors with the same name may work in the same field.  Like author names, there are often multiple ways to list the name of a department, school or university, and affiliations change as an author moves from one institution to another.  Moreover, some databases only provide the affiliation of the first author, or allow an author to list only one affiliation.  PubMed/MEDLINE did not include affiliation for all authors until 2014.  For these reasons, a simple search for articles by one author can easily become complicated.

What options exist for author identifiers? 

Over the past few years, one author identifier system has emerged as the frontrunner: Open Researcher and Contributor ID, or ORCID (http://orcid.org/).  ORCID is an open, non-profit community effort that provides unique persistent digital identifiers for researchers.  ORCID partners and members include universities, commercial research organizations, publishers, professional societies and funders, such as Nature Publishing Group and the National Institutes of Health (NIH).  Several publishers offer the option of including an ORCID ID when submitting an article, and some plan to make an ORCID ID mandatory for corresponding authors (http://blogs.plos.org/plos/2016/01/author-credit-plos-orcid-update/).

A few publishers have their own author identifier system.  For example, when researchers register for Thomson Reuters free online community, ResearcherID, they are assigned a unique alphanumeric identifier that can be used to track their publications and get citation metrics in Web of Science.  Authors of articles indexed in Scopus, an Elsevier database, are automatically assigned a unique identification number.

This sounds like one more account to maintain, do I really need an author identifier?

Yes, an ORCID ID is another account to create and maintain.  However, ORCID has gained traction amongst universities, publishers and funders, and if this pattern continues, then hopefully it will alleviate author ambiguity.

Any researcher can register for a free ORCID ID.  You can use your Tufts username and password to register for, or link to an existing, ORCID ID.  To get started, go to this page: https://orcid.org/signin.  Choose to sign in using your institutional account and search for Tufts.  You will be prompted to enter your Tufts username and password.  Once you do so, select the ‘Register for an ORCID ID’ link.  For more information about creating and managing your ORCID account, see: http://support.orcid.org/knowledgebase/topics/32827-using-the-orcid-registry.

PubMed Tip of the Month: Saving Searches and Creating Alerts

You can save searches to your My NCBI account (see PubMed Tip of the Month for March 2016), and choose to receive daily, weekly or monthly emails when new articles meeting your search criteria become available.  To save a search, simply click the ‘Create alert’ link under the PubMed search box on any results page.  If you are not already signed in to your My NCBI account, then you will be prompted to do so.  Name your search and select whether or not you wish to receive email alerts.  Once you have saved a search, it will appear in the Saved Searches box in My NCBI, where you can see a list of your searches, the last time you ran a search and any new articles that have been added to PubMed since you last ran the search.  Saving searches saves time and frustration, and allows you to remain current on articles in your area of research.

Create alert link on PubMed results page
PubMed Create Alert

Notes from the North – The Science of Lobster

The other week my family and I were driving home from an afternoon on the beach playing in the waves, poking through tide pools, and eating seaweed (only Ronan indulged in this last pursuit) when we IMG_20160713_204129_894[1]made a spur of the moment stop at a local farm to pick up lobster and a couple pounds of steamers1. Standing at the counter in flip-flops and a swimsuit as the lobsterman weighed out our “bug”, I began to ponder this quintessential Maine summertime treat. In preparing and eating whole lobster the consumer becomes acutely aware of the animal’s physiology; an experience most of us are divorced from for most of the produce we eat.

 To start with, you have to decide as you are making your purchase whether you would like a hard-shell or a soft-shell lobster. A soft-shell lobster is one that has recently undergone ecdysis, a shedding of the exoskeleton. The lobster does this by inflating a newly grown exoskeleton with water within the old carapace causing it to pop open and expose the soft new shell. The reason these soft-shell lobsters cost less per-pound than the hard-shell lobsters is that a good proportion of their weight comes from that water rather than meat.

When you get your lobster home and are facing the decision of how to cook him or her2, you might begin to wonder “why on earth do I need to buy it live?” In part this goes back to the molting cycle again: powerful proteases (four members of the calpain family) induce muscle atrophy in the claws in order to reduce the volume of tissue that will need to be withdrawn from the old shell. When the lobster is dead, these proteases cause rapid degradation of the flesh. The other part of the answer lies in the presence of metabolites from micro-organisms. The combination means a much shorter shelf-life for raw lobster meat than you might otherwise imagine.

This inconvenient brevity of freshness forces the chef to consider the question of lobster nociception.  The avoidance behaviors (tail-flipping) exhibited by lobsters upon being placed in boiling water clearly demonstrate that at the very least lobsters have evolved to respond to noxious stimuli. Pain is typically understood to be comprised both of physical sensation and emotional distress, but since it is difficult to observe or define emotion in non-humans using only our experience of human emotion it seems reasonable to minimize the animals’ exposure to noxious stimuli. In Europe this is accomplished by electrocuting crustaceans prior to cooking, but the best compromise I have seen in the US is to make a cut through the lobster’s brain while it is still cold from the fridge before cooking.

There is a huge body of scientific literature out there both utilizing lobster as a model organism and studying it directly (the lobster fishery just in Maine is worth over $1 billion!), but I’ll leave you with just one last lobster physiology anecdote. Ed Kravitz, one of my grandmentors (mentor’s mentor) demonstrated that GABA is a neurotransmitter using lobster (the shell apparently makes a convenient receptacle in which to bath the muscle and nerves), but I was always told that Ed’s favorite part of studying lobster was the taste test!

  1. Scrumptious little soft shell clams that are cooked by steaming. In our family we bring the cooking brine to the table so we can rinse each clam clean of sand before dipping in butter to consume whole.
  2. The most infallible method to determine the gender of your lobster is by looking at the first pair of swimmerets that appear on the ventral surface of the animal where the tail joins the cephalothorax. In females these are soft and flattened while in males they are stiff and curve to form a tube through which spermatophores are deposited in the female during mating.Lobster anotomy