27 Jul

Electronic Lab Notebooks (ELNs)

In today’s technology-driven world, replacing the old trusty paper lab notebook with an electronic version is quite appealing. I’ve often thought it odd that I would take my digital data and print it out to tape into the composition book that served as my lab notebook. I then bought a Galaxy Note 8.0 to take notes during my classes. That is when I decided to switch to an electronic lab notebook or ELN.

An article by Jim Giles in Nature highlighted some of the benefits of going paperless in the lab – more detailed records, more accessible data sharing, improved efficiency, and even the potential to extract results from data due to improved methods of searching and analyzing. It’s also great if, like me, you often find yourself struggling to read what you wrote last week, you’re constantly flipping through pages looking for that one experiment you did that one time, or if you find that your lab notebook is starting to shed papers like your dog sheds hair.

There are several options for ELNs. Lab Archives and eCAT are two options that are designed specifically for laboratories. They both offer free versions, but you need to upgrade to access all of their functions. Many people are also adapting note taking software such as Microsoft OneNote and Evernote to their needs. Again, there are free versions of both of these available.

After checking them all out, I chose Evernote.

Evernote is an extremely versatile note-taking software that seamlessly syncs between devices. It allows for the transition from the old paper and tape to the new digital rather seamlessly. Rather than using scissors and tape to cut and paste images or tables to a notebook, you use control/command-c and -v. You paste the attachments right into the note or attach a file that can be quickly viewed or opened for further analysis.

The program also allows for efficient searching – the search function will even find text within images – and multiple levels of organization. I’m currently in the process of trying to optimize my layout within the program. I am thinking of organizing by experiment with all procedures, results, and analysis on a single page. Each experiment will be labeled with all samples involved in that experiment so I can quickly view the history of a particular sample.

Some other handy features are the “insert date/time” shortcuts (alt-shift-D in Windows or command-shift-D on a Mac) and the “copy note links” function that allows for a quickly made table of contents and page linking. There is also the added advantage of directly importing snapshots taken with Evernote. You can use Evernote’s WebClipper to capture entire web pages, a particular article on the web you found or save it as a PDF to attach to a note. You can also forward emails directly to Evernote if you upgrade to the Plus/Premium package.

I have noticed that the editing features within a note are limited. As such, I am linking to files rather than pasting images directly in the note. In addition, picture resizing isn’t possible, nor is it possible to use symbols or superscripts/subscripts within the text.

Another advantage is that you can group notebooks together into stacks. I have several “stacks”: my main research project which contains notebooks dedicated to each of the aims of my dissertation project, a school stack where I keep class notes and related files, and a personal stack.

One thing I have discovered is that you want your notebooks to be as discrete as possible. You never want to wonder which notebook a particular note belongs to. If you end up with two notebooks with similar function, you can merge them together.

Here are some additional Evernote resources:

Evernote is free up to a monthly usage of 60 MB/month. If you have large files that you’d regularly like to upload, as well as access to a few premium features such as searching within uploaded files, there is the possibility of upgrading to a premium account for $49.99/year.

Have you tried experimenting with an electronic lab notebook? If so, what tools do you use? How do you integrate them into your workflow and method of organization?

20 Jul

Fake it till you make it!!

Mental health issues are not something to take lightly. According to the ADAA, anxiety disorders affect over 40 million American adults. In addition, it is common for someone with an anxiety disorder to suffer from depression or vice versa.

Anxiety is a normal biological response that helps us get out of danger and prepare for important events. It is Mother Nature’s way of telling us we need to take action. However, problems arise when we experience anxiety that is persistent, seemingly uncontrollable, and overwhelming. If it’s an excessive, irrational dread of everyday situations, it can be disabling. When anxiety interferes with daily activities, you may have an anxiety disorder.

Most people feel depressed at times. Losing a loved one, getting fired from a job, and other difficult situations can lead to a person feeling sad and lonely. These feelings are a normal reaction to life’s stressors. Some people experience these feeling daily, or nearly daily, for no apparent reason, making it difficult to carry on with normal, everyday functioning. Depression is a condition in which a person feels discouraged, sad, hopeless, unmotivated, or disinterested in life in general. When these feelings start interfering with daily activities such as taking care of family, spending time with friends, or going to work or school, it is likely a major depressive episode.

Both of these conditions are treatable illnesses that only roughly one-third of those suffering seek help. If you have mild cases of anxiety or depression, the following tips may help. The Anxiety and Depression Association of American has some great resources for finding help if you need it.

If you are having thoughts of harming yourself or others, please seek professional help immediately. 

Here are some tips to stay positive and move forward.

Don’t be ashamed or embarrassed by your feelings. Depression and anxiety are NOT weaknesses. Very often they are treatable medical conditions. Talk about what you are going through with supportive people.

Foster supportive relationships. At the very least, spend time with one or two other people. Have lunch with a friend, email your sister, Skype with your parents. Make time to have dinner with your significant other each night.

Challenge negative thinking and your own limiting beliefs. Performing experiments can be very self-depreciating. How many times has your experiment failed before it finally worked? In STEM fields, our work is constantly be scrutinized by other scientists, our manuscripts are rejected from journals, and there always seems that answers to our questions just bring more questions. Remember to not be too hard on yourself. Do not measure your value based on the results you do (or don’t) achieve in the lab or the number of papers you publish.

Take care of yourself. As a grad student, work often requires long hours in the lab, sleep deprivation and little to no time for eating and exercise. Remember to do one thing for yourself each day. Whether its that yoga class in the afternoon at the student recreational center, going for a run in the morning, cooking dinner, or joining a sports team, taking a little time for yourself each day will go a long ways.

Celebrate successes, no matter how small. Keep a gratitude journal and write down at least one thing you are thankful for each day. Corny, but it works. Keeping the journal makes you more creative and helps you sleep better. Here are some iOS and Android apps to start and keep a gratitude journal on your tablet or phone. Also, keep finding small wins to show off to yourself and other people. Hang that western blot you finally succeeded in performing by your desk. Go out for dinner and drinks with your lab mates when you had a breakthrough.

Try new things, take the unbeaten path. Just because everyone else is going to do a postdoc doesn’t mean you have to as well. Create your own path. Don’t worry about what other people may think about your decisions.

Seek Professional Help. Most universities have student counseling services available for their students. The counselor you will see can help you decided if you need long-term guidance or just short-term help to get through a rough patch. They can provide you with coping mechanisms as well as a place for you to talk about your concerns without being judged.

Two final things to remember:

Follow Dory’s advice:

And Muhammad Ali’s:

ali

 

Have you dealt with anxiety and/or depression while in grad school (or other stressful situation)? What advice would you give someone going through the same thing? Please leave your comments below!

17 Jul

This Week in Science 07-17-2015

Mosquitos are not only are a nuisance, they also can carry numerous diseases. But good luck outsmarting them. The carbon dioxide you exhale, the look of high-contrast objects, and the warmth of bitable bodies all attract mosquitos, but in interacting ways that make it difficult for us to beat them. A recent study concludes that the independent and repetitive nature of the sensory-motor reflexes renders mosquitoes’ host-seeking strategy annoyingly robust.

A mosquito (far left) mixes strategies and clues as it homes in on its next blood meal.

 

For those with chronic pain, a new hope of a potential long-lasting treatment may be in the future. As reported in the Journal of Clinical Investigation, scientists injected mice with a spinal cord injury with cells extracted from mouse bone marrow. These cells flocked to the injured cells and produced a pain-relieving protein, called transforming growth factor beta 1 (TGFB1). The specialized cells found their ultimate destination by following chemical signals released by the injured cells. The cells were able to relieve pain in less than one day and the effects lasted for over a month.

lump-sugar-548647_1280

It turns out that sugar is the culprit of making us want a nap after those large meals. A recent study in the Journal of Neuroscience shows that an increase in glucose (a simple sugar found in most everything) leads to “amping up” of specialized neurons that act as sleep-inducing cells in the brain. These neurons can directly sense the glucose in their neighborhood, other experiments revealed. And the more glucose the neurons detected, the more they fired their sleep-inducing signals. There might even be a good reason to feel drowsy after a large meal. By sleeping, an animal, or human, will stay close to a good food source.

Imagine when someone gets out of hand in a bar. A very burly guy (usually) will appear from seemingly thin air and ask the no-good-doer to leave. This guy is called a bouncer and it is his job it is to keep the party from getting out of control. Scientists have shown that the gene Apc acts as the cellular bouncer. By switching Apc on, researchers turned mouse cancer cells back into normal intestinal tissue. This provides optimism for a genetic approach to beat cancer.

Other randomness:

A 50-million-year-old fossil sperm was discovered in Antarctica.

A handful of studies are linking shift work with not only disruption of our circadian clocks but also affects our metabolic function leading to higher body mass index and increased risks of metabolic syndrome, cancer, and sleep disorders.

And in case you were under a rock the last few days, NASA’s New Horizons flew by Pluto and was able to capture some amazing images (see below). You can see more here and here.

tn-p_lorri_fullframe_color
Pluto is dominated by the feature that is informally named the “Heart”. The Heart is approximately 1,000 miles (1,600 kilometers) across.
pluto-and-charon-01
Full-frame images of Pluto and its moon Charon. This image is a composite image to show the relative reflectivity, size, separation, and orientations of Pluto and Charon.
14 Jul

The Science of Tattoos

With some fresh ink on my arm, I thought I’d take a moment and explain the science behind a tattoo’s permanence.

As this fascinating video from TED explains, tattoos are actually a complicated inflammatory process—a delicate balancing act between your body and the dye that’s invading it.

It turns out my fierce samurai is kind of like an infection—and the reason it’s permanent is because your body keeps on fighting it forever.

Tattoo needles punch through the epidermis, the outer layer of skin, and drive the ink into the dermis, the deeper layer that’s mottled with nerves and blood vessels. “Every time the needle penetrates, it causes a wound that alerts the body to begin the inflammatory process,” the video explains.

That signal sends immune system cells racing to the site of the wound (or multiple wounds, in the case of the five-inch dragon breathing fire across your chest). Special cells called macrophages come to the rescue, eating up the dye in an attempt to “clean up” the inflammation it’s causing. The rest of the dye gets soaked up by skin cells called fibroblasts. The fibroblasts, along with many of the macrophages, stay suspended in the dermis in perpetuity. The dye in the bellies of the trapped macrophages and fibroblasts shows through the skin, projecting your Chinese word for “love” or constellation of tiny blue stars to the outside world.

Oh, and just in case you have “ragrets” about your choice, the video explains how you can get that fixed.

“You have no regrets? Like, not even a single letter?”