Wrapping Up Asia Project

Today, I have begun to clean up my office space to sort out what I will keep and what I will throw away. Asia project is wrapping up. I have sent Boss the work, and in return, she wrote a nice performance appraisal for me (for Asia School). In September, my research assistantship will end, and I will return to the UK for full-time schooling again.

Emotionally, I feel weird about the departure. Part of me is very much ready to move on and return to school full-time because taking up this Asia project has significantly slowed down my progress of school. Yet, part of me feels insecure about leaving Asia City, where I have grown quite comfortable with the routine.

Well, who knows? I might return to Asia. UK School has bigger names in my field, but Asia School (and its European connections) has the courses, patients, and expertise in the area that I am interested in.

Anyhow, the next step for me is to finish up the research proposal for my PhD.  Once it is done, I’ll need to apply for fellowships/ scholarships again.  Wish me luck.

Can’t Wait To Be A Grown-Up

When you were a kid, were you the type who couldn’t wait to grow up? Somehow, this is exactly how I feel at this stage on my journey to becoming a scientist. I feel like a teenager who wants so badly to be seen as equal by the grown-ups, so I can’t wait to become big and be independent. Yet, deep down, I know that I am still a teenager (if not a pre-teen), and I hate it.

This month’s theme of Scientiae is:

“A voice in the crowd” - are you heard? How are you heard? Are you one of a team that works as a choir or does discordance rule the roost?

If you’re singing solo in the shower, can you be idolised for your Idol-qualities or not care if you’re called tone-deaf - as long as you’re enjoying your song?

There’s many ways that we can let ourselves be heard but who really has control of the megaphone? And who carries the tune after you’ve stopped?

In many sense, this blog has satisfied my desire to be heard. A year ago as a first year grad student, I established this blog as a platform to post my science-y posts. Thinking no readers? No problem. I was convinced that if only one reader found a post of mine inspiring, insightful, or even educational, I would be more than happy to continue to write. Even as a grad student, I tried not to let discouragements, such as those from my Uncle, to get to me. I have been taking classes, learning how to do good science, or generally having fun on doing what I do, so I am convinced that I will continue to do it until someone kicks me out.

But do I wish that I were more knowledgeable about my specialty? I were better skilled at doing my area of science? You bet! In fact, I wish that I had already graduated and someone have handed me a real job already. I can’t wait.

I suppose that’s why when I received an invitation to write at a science site about issues in my specialty, I could not resist the offer even though I could come up with too many reasons to decline it. I literally felt like I was given a megaphone, and all of a sudden, I am part of the grow-ups science community, and I wanted the opportunity!

Even though I have been giving a megaphone, deep down though, I know that I am still a grad student. To grow, I need to continue to learn, to do more research, to pay more attention, to think harder, to read quicker, …, so that I can publish (more) at good journals and be a skilled scientist, of which really does take time.

Yet, sometimes, I feel like I can wait no longer.

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This post is written for the Scientiae Carnvial. The upcoming edition will be posted at PodBlack Cat Blog, home of superstition investigation, on July 3.

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Btw, my editor at the said science site likes my first submission, saying it is in “high quality”, so she has sent it out for peer-review (and possibly some professional editing).  Yay!

Also, to those in Canada - Happy Canada Day.  To the Americans, Happy 4th!

Self-Grading this Blog

You know in school, we often receive assessments on the work we produce? Lately, I sat down and evaluated this blog too.

Why? I received an invitation from a science site to write commentaries about issues in my specialty. Not that I am good or anything, but my geographical location gives me supposedly unique perspective of my area of speciality (remember I told you that my specialty involves field work?), and so the editors of the site invited me to contribute.

Of course, I am excited about the opportunity as I recognize that grad students do not generally get to write commentaries and reviews, and even when we do, we do not get to do it until we are about to finish the doctorate degree, and I have only started. Yet, it is precisely why I am also very anxious about it. Am I up to it? After all, it is going to be very different from blogging.

For one, I will be writing as me, so whatever I write, they will have my full name and school affliction printed on them. Will I put garage out and ruin my school’s reputation? Hmm. Do I really have something insightful and interesting to say regularly? Hmm.

Staring at my blog, I think it contains all the good reasons for declining the invitation. It has plenty of posts that I do not want my name and school affliction printed on them, and there are rarely posts that are interesting or insightful.

You see. When I established this blog last year, I wanted to write two things: (1) posts related to medical science, and (2) bits and pieces of my journey of finishing med school/ grad school, in this order of proportion.

I have obviously failed in my attempts at producing such blog. What went wrong? Well, for one, I have recognized that my education at present has qualified me to comment on nothing but being a professional student. But just as equally important is that for science-y things that I feel that I can (and want to) comment on, I have found it difficult to talk about them without the fear of being outed. I think I fare better at writing about my grad school experience though. Nevertheless, there were also times when I did not want any of those posts on my blog because to me, they were more like my private journal entries, which were whiney and uninteresting. They were most often than not pieces of writing that not even I am interested in reading again once I am done with writing them.

Hence, overall, I think I am a bad writer.

But I did end up accepting the invitation to write at the said science site anyway for a promise that I will be working with an editor who is also in my specialty. Hopefully, she will be a gatekeeper and a mentor and stop me from making a fool of myself when my articles are not up to standard. [Fingers crossed]

So now, what am I going to do with this blog when I will be writing the kind of posts that I wanted to write at another site? Or do I? Hmm. After some contemplating, I have figured that I still want a platform where I can write science-y posts that are not related to my specialty as well as for the random thoughts relating to being a science grad student.  A platform where I can vent and be irrational once in a while without too much censorship. More importantly though, I like that this blog has allowed me to connect with an online community of women in STEM, which I have found valuable. Through these women’s comments, I have found support on this often isolated journey of academic pursuit. And through their stories, I have learned from their experience as grad students and scientists. They are my much needed reminder that women are capable of having a promising scientific career despite people sometimes tell me otherwise. Their existence makes me feel like I can accomplish something on my own too. For this constant reminder, I am grateful. And for that, I would like to keep this blog and to keep this connection.  Thank you y’ll.

Umm.. Good to Know

You Should Get a PhD in Science (like chemistry, math, or engineering)

You’re both smart and innovative when it comes to ideas.Maybe you’ll find a cure for cancer - or develop the latest underground drug.

What Advanced Degree Should You Get?

 

Um.. Good to know that I am on the right track.  I don’t know what I would do if this silly little quiz tells me that I should’ve switched major. =p

Simple Mathematical Model for Epidemics

In light of the new animal cases of H5N1 found in Hong Kong, where it was first discovered that the virus jumped barriers from birds to humans in 1997, let’s talk about how modelers describe epidemics of infectious disease, shall we?

First of all, there are a couple of reasons why mathematical models may be useful to epidemiologists.

1. For predictions. Being able to predict the future has always been one of the perpetual dreams of mankind. Thus, we have weather forecasts, economical forecasts, palm readings, fortune telling, astrology, etc. In medical science, some epidemiologists specialize in creating mathematical models to predict occurrences of new cases.

2. For understanding. Mathematical models are often a simplified version of the actual scenario. By removing factors that are less important, these models help investigators to understand the actual scenario, which are often rather complex to comprehend.

3. To anwer questions. Many mathematical models are being used to answer questions that cannot be answered in other ways. Often because the scenario that is modeled has not happened (like a disease outbreak), and we do not want to make it happen just so that we can do measurements, so investigators make use of mathematical models and change various factors on them in order to find out the effects of, say certain interventions, environmental factors, etc.

To begin, let’s start with some basic terms, shall we?

Basic reproductive rate, Ro.

What the heck is that?! Well, by definition, Ro is the average number of individuals being directly infected by an infectious case in a totally susceptible population (i.e., everyone in the population is susceptible to be infected).

Say, a chicken (whom we call it a primary case) is infected by chicken flu (the above definition is applicable to humans as well as to poultry). But the poultry workers do not know that it is sick and put it into a big cage with a whole bunch of other chickens, that are well, to get ready for sell. This primary case chicken has no face mask, cannot cover its mouth when it sneezes, and it is just basically being very, very sick. So it cannot help but sneezes at these other chickens that are living in the cage with him.  Sneeezz-chu.  Excuse me, he says.  Despite apologizing, these sneezes nevertheless get other chickens next to him, say, two of them, infected. In this case, then Ro = 2.

Once an outbreak is underway, the reproductive rate is denoted by R, the net reproductive rate, which is the average number of individuals being directly infected by an infectious case in a partially susceptible population.

From this above reasoning, it can be deduced that the necessary condition for an epidemic is that R is greater than 1.

R > 1 => there will be an epidemic
R = 1 => the disease will become an endemic
R < 1 => the disease will eventually disappear

Now, what does Ro (or R) depends upon?  According to literature, the basic formula for Ro is:
Ro = c * p * d, where
c = number of potential infectious contacts (per unit time)
p = transmission probability per contact
d = duration of infectiousness of an infected case

In this scenario, the c would be the number of chickens in the cage.

The p is different for difference diseases, and I do not have the number for chicken flu among chickens. However, take HIV infectious (among humans) as an example, the p is somewhere between 0.001 and 0.1 for sexual intercourse; but the p is virtually 1.0 for blood transfusion (Giesecke, 1995).

The d is a biological constant for any disease. For human flu, antibiotics can often shorten the d.

Implication
To lower Ro, we need to lower the c, p, or d.

For instance, if we totally isolate this speaking, yet very sick chicken, then c would become zero.  If there is no other flu-infected chickens in the cage, nor are we putting more flu-infected chicken into the cage, then the disease will eventually die out as far as the chicken population within this cage is concerned. However, things will get a little more complicated if we have problem identifying which one is the sick chicken. (Opps!)

Vaccinating chickens essentially lower the proportion of susceptible chickens within the population.

Or else, having the sick chicken wearing face mask should reduce p.

Otherwise, d will be shortened by providing antiviral drugs to this sick chicken (if available).

Fun, huh?  Obviously, I am only scratching the surface of the subject, but that’s one of the applications of mathematics in medical science, and that’s why we have the kind of public health measures that we have.

Reference:
Giesecke, Johan. Modern Infectious Disease Epidemiology. Oxford University Press, New York. 1995.

First in the Family & Blessful Music

I went out for dinner with an Uncle who visits from Canada yesterday, which should have been fun as we had not seen each other since I left North America for med school. But it wasn’t.

You see. Aside from the two professors from the extended family and me, this Uncle from Canada from my parental side has the highest educational level in the family. He has a taught Master’s.

In my generation, however, I am the first and only to go to grad school. I do not know if it is because I am a woman, or if the idea of me wanting a research career is simply too unfathomable, this Uncle had (too) much to say about me quitting my job to head to med school/ grad school a few years back. He did not think I could finish the programme and graduate. In fact, he still does not think I will.  And I have no idea where this idea comes from, although he and his wife were one of those people who told me that “girls shouldn’t go to college” in front of my father when I was applying for college.

Beside questioning my competence, another reason of his open opposition of my career choice is that I do have financial obligation to my parents. Yet, the aspiration of becoming a scientist required years of additional study, which conflicts with my parents’ expectation of me having a job and making twice as much as everyone else after college graduation (or after getting a professional degree) - like my lawyer cousins for instance… (One of them is this Uncle’s daughter by the way).

There is not much I can do about their perception of my lack of competence to finish grad school, but I did make financial arrangments* so that I can support myself and have enough to send home during school thus far. Yet, it does not stop this Uncle from perceiving me as a loser who “avoids having a real job” by staying in school.

Whatever.  I blame it to his ignorant.  But the dinner was nevertheless unplesant and it made me feel awful about myself afterwards.  After all, I so wish that my parents would be proud of what I am trying to accomplish, but instead, he makes them worry about how I am doing.

And many of these things I simply do not talk about with friends unless they are also grad students. Sometimes, this grad school thing makes me feel very lonely.

In all honesty, I wish my Uncle did not go as far as telling me what I can or cannot do with my career like I am a one-year-old when I am fulfilling my financial obligation to my family.

Anyhow, today I went out to see Indy 4 with Friend. The movie threater is at a rather grand, fancy mall, which is not at all unusual in this part of the world to have a movie threatre in a fancy mall. When I was waiting for Friend and for the movie to begin, I walked around the mall and saw a trio (piano, violin, and cello) playing music - some very beautiful music. That did wonder.

The music was so beautiful that it reminded me that I am having a blessed life. I am alive and well, doing what I love for a living, having a pair of loving parents, a nice brother whom I can call friend, and having a few wiser and blissful friends. With all of these, I can handle having a jerk as an uncle.  Besides, I honestly don’t want him to ruin the rest of the summer for me.

I did tell you there are ridiculously harsh and unreasonable people just a few days back, didn’t I? Um-m. There are.

*From personal savings, scholarship, RAship, as well as loans.  To finish up the rest of the programme, I will have to drop the RAship and rely solely on scholarships/ fellowships, which I am not sure if I will be able to get, but that is a topic for another post.

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The music I heard in the mall reminded me of Armstrong’s What a Wonderful World. What a beautiful voice and beautiful lyrics, huh?

 

Writing Research Papers

A few days ago, EcoGeoFemme wrote a post about how to write research papers and asked if readers approach it differently.

Personally, as you can probably tell by reading my blog posts, I like to write freely. No outline. Begin with Methods first, putting all the relevant thoughts on the page then move on to the Results and Discussions sessions, and leaving Introduction and Background to the last. After getting the first draft done, I will start refining the text over and over until I am happy with the product and calling it final.

I do not know if this method is particularly efficient for me ’cause as you can tell by reading my blog, I ramble a lot. Sometimes, when I re-read posts that I posted a few days back, I do not even know what I wanted to say! (Poor you, dear readers. Trust me. I know that). Luckily, UK school has class teaches us how to write. It may not be the most efficient and effective way of writing a paper, but I’d like to share what I have learned anyhow.

First. Suggested Steps of Writing:
1. Write Title, Outline, and Abstract
2. Construct tables in the Results section
3. Write the first draft of the Results text
4. Write the Discussions and Conclusions sections
5. Write Introduction and Methodology

The class recommends writing an outline, so that all key points are noted down under each session. Based on this reasoning, it also recommends writing a preliminary version of an abstract first in order to help organizing what we would like to put down on the actual paper. Besides, it noted, many people will judge your paper on the Abstract alone. Hence, we should write an Abstract that provides a clear, concise summary of all the important features of our paper.

Now, if you are like me who feels odd about writing Methodology last, this process is suggested based on the idea that our results are the focus of the paper (”the story”). Hence, we begin with the Result section, and then proceed logically to Discussions and Conclusions before writing Introduction and Methodology. However, if you are like me, who starts writing a paper before you are done with your experiment, I do not see any problem with beginning to write the Methodology session before beginning Step #1. We can always refine the session after finishing Step #4.

What about the title?  What makes a good title?

According to the lecturer, a good title provides readers with enough information to enable them to judge whether or not the paper is likely to answer questions that they are interested in (when they scan through TOC or e-database), which may include information such as subject matter, experiment/ study design, characteristics of patients involved, etc.  The title should present this essential information in a clear, easily accessible format.  In fact, the class suggests to begin a title with the most important term(s), i.e., the ones that you want to catch your readers’ attention, such as the concerned disease, new aspect of the paper, being a RCT if it is a clinical research paper since it indicates rigorously designed study.

Now, what should be included in a paper? For my particular area of specialty, it means this:

Introduction

• Why the research was started/ gap(s) in current literature addressed by the study question
• The main study question
• Brief statement of the experiment/ research study, observations to be made, characteristics of patients involved
• Background information that is directly relevant to the main study question
• Why the study question is important - how relevant it is to public health, clinical medicine, and/or furthering scientific knowledge

Method

• Methods should be described in enough detail to enable readers to:
  • Judge whether the methods where appropriate for answering the study question
  • Judge any weaknesses in methodology that could influence the interpretation of the results
  • Repeat the study if they wish to do so
• Experiment/ Study design
• Characteristics of patients involved
• Observations
  • Measurements
  • Validity and reliability of the instruments used
• Analysis
  • Software application being used for analysis
  • List of outcomes
  • Statistical tests being used and tests of interferences being used if applicable

Results

• Data that support the answer to the main study question
  • Data that enable reader to judge the validity of your conclusions (e.g., comparing the characteristics of the study groups, data on participant drop out, etc)
  • Data that directly support the answer to the main study question
• Comparison of the study groups
• Known findings (i.e., findings from control group)
• Unknown findings (i.e., findings from experimental group)
• Statistical analyses

Discussion

• Providing a summary of the answer given by the data discussed in the Results section on the 1st paragraph to the main research question
• An evaluation of my methods, including any possible sources of errors
• Presentation and evaluation of evidence from other papers that support or contradict your findings
• An attempt to explain any differences between your findings and previous research

Conclusion

• Clearly state the final answer to your main study question
• The implications of your answer, including an assessment of:
  • Generalizability of your findings
  • Theoretical implications (including suggestions for future research)
  • Practical implications (for public policy or clinical practice)
• If you cannot resolve conflicting evidence from your experiement and experiements by others, you may wish to suggest how the discrepancy could be resolved in a new experiment

Please note that this is only steps to write out the first draft.  The class did talk briefly about what should be noted when we begin editing.  One helpful point it bought up was the importance of identifing drafts, especially when there are different co-authors. The suggestion essentially involves this:

Mark down on each page of a draft the following:

• Number of the draft
• Page number
• Date
• E.g., on header: [Kate Lastname, 2nd draft] [14 Jul 08]

If various sections are worked on by different coauthors, maintain each section as a separate file with its own sequence of page numbers. Then assemble the sections in their right order eventually.

I have not tried out this approach, but I will when I start writing my proprosal.  What do you think of it?

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For more information, and if you are in medical sciences, check out Edward J. Huth’s “Writing and Publishing in Medicine”.  I find it practical and through (although a little outdated with regard to technologies relating to writing aids).  Much of the information I noted above is from this book - on top of my lecturers, of course, whom I wish I could give credits to.

Summer!

Summer is here! ‘Cause I am done with exams! Yay-a!

How did it go? I’d say I did respectably well. There’re some tough questions, and I was challenged, but I’d say I managed, which makes me feel rather proud of myself of how much I have learned in order to hold my own against the challenges. Hopefully, the result would not come out to be anything surprising.  =p  [Fingers crossing]

Now that I am done, it’s time to call up friends for movies! I have not seen Indy 4 yet.

After some movies and catching up with friends, I will need to catch up on the unread 1000+ journal articles and blog posts on my Google reader (Google reader gave up counting the actual number of unread posts for me a while back), and then I will start wrapping up the Asia project and begin writing the research proposal that I was supposed to submit… like… last year.

Yay. Summer!