Sunday, December 8, 2013

is knowledge really power?

The American College of Medical Genetics and Genomics recommended a collection 57 actionable genes to be that should be evaluated whenever a doctor orders a genome or exome sequence for a patient, EVEN when patients do not want to know the results. The list includes conditions that are highly hereditary, such as hereditary breast and ovarian cancer; Lynch Syndrome; Marfan Syndrome; hypertrophic and dilated cardiomyopathy; familial hypercholesterolemia; retinoblastoma; tuberous sclerosis complex.

But these are merely recommendations. There are no regulations, no rules in place. So, there has to be enough community support in the clinic for a set of guidelines for this to push through. Either that, or a blanket policy that bulldozes its way ahead. Otherwise, such recommendations are not going to take flight.

Part of the inertia can be attributed to the aggressive enforcement that such evaluation is done even when the patient does not want to know the results. I think there should be a middle ground. The decision to live or die is ultimately the choice of the patient. Perhaps, there should be a form for the patient before each genomic test is done, much like what has been practised in the clinic with organ transplant and life support systems in patients with dire conditions. This should explain what the genomic test entails, what it finds, and why the 57 genes, and why they should be concerned.

There are still false negatives and false positives in every test. Patients should have the rights to choose if they want to know. That decision can be a confluence of various factors beyond just having the disease or not - quality of life after knowing, emotional anxiety etc. And for a single test that gives you information more than what is being asked for, it shouldn't be a blanket enforcement. Perhaps a little flexibility might sit well with people.

But then I suspect, the inertia might be bigger than just this issue.

A slight complication: what if the test is not done at the request of a clinician?

All being said, only a small percentage of people should be affected by this at this point - these inherited conditions typically rare in the human population in general. But it is a good opportunity to start thinking about models of delivering/integrating genomic information into the clinic.

FDA harries 23andMe

image from
Dec 5 2013
"After discussion with officials from the Food and Drug Administration today, 23andMe will comply with the FDA’s directive and stop offering new consumers access to health-related genetic tests while the company moves forward with the agency’s regulatory review processes."

"23andMe has been giving consumers access to health information for six years and is committed to finding the right regulatory path for our customers."

"Our lab partner adheres to strict quality standards that are part of the 
Clinical Laboratory Improvement Amendments of 1988."

"As we work with the FDA to get clearance, there will be some significant changes to the site.  Customers who purchased kits on or after the FDA’s warning letter of November 22nd will not have access to health-related results. Those customers will have access to ancestry-related genetic information and their raw data without 23andMe’s interpretation of that data. They may receive health-related results in the future, depending on FDA marketing authorization.

Customers who purchased kits before November 22, 2013 will continue to have access to all the reports they’ve always had."
"This is clearly a much different service than in the past, so we are offering customers who purchased kits on or after November 22, 2013 a full refund if they wish."
"Research is and will continue to be a significant priority for the company.  The 500,000+ customers we have today have given us more than 250 million survey data points."

Dec 3 2013
Other repercussions
"While Illumina supplies chips to the other three leading consumer genomics testing providers –, Family Tree DNA, and National Geographic's Genographic Project – Ro wrote that 23andMe is the "largest customer in this segment," and estimated that sales to 23andMe account for half of the firm's consumer genomics-derived revenues, or about $25 million."

Nov 26 2013
"We stand behind the data that we return to customers — but we recognize that the FDA needs to be convinced of the quality of our data as well."

"This is new territory for both 23andMe and the FDA. This makes the regulatory process with the FDA important because the work we are doing with the agency will help lay the groundwork for what other companies in this new industry do in the future. It will also provide important reassurance to the public that the process and science behind the service meet the rigorous standards required by those entrusted with the public’s safety."

Nov 22 2013
"In a Nov. 22 warning letter, signed by Alberto Gutierrez, director of FDA's Office of In Vitro Diagnostics and Radiological Health, the agency asked 23andMe to "immediately discontinue marketing" its Personal Genome Service "until such time as it receives FDA marketing authorization for the device."

"FDA's action against the Google-backed, Mountain View, Calif.-based firm has ignited a public outcry, with customers petitioning the government to allow 23andMe to maintain its business and one California woman filing a class action lawsuit against the company and asking for her money back."

"Two groups have submitted petitions to We the People and to seeking to collect 100,000 and 10,000 signatures, respectively."

"With other prominent health-oriented DTC genetic testing companies like Navigenics and Decode Genetics being swallowed up by other firms and no longer offering DTC services, 23andMe has for some time been the only option for people who wished to know about their genetic predisposition for diseases and their likelihood for responding to various drugs without having to visit their doctors for a prescription."
--> Navigenics acquired by Life Technologies
--> DeCode acquired by Amgen

"It's clear from the FDA's warning letter that the agency and 23andMe have had extensive interactions – 14 meetings, hundreds of emails, and dozens of written exchanges – about its Personal Genome Service since 2009. "Even after these many interactions with 23andMe, we still do not have any assurance that the firm has analytically or clinically validated the PGS for its intended uses, which have expanded from the uses that the firm identified in its submissions," the FDA states in its letter."

" the agency [FDA] informed the companies that it considered these types of tests medical devices, which require regulatory clearance or approval."

"Unlike its competitors, who in the face of regulatory pressure quickly shifted their marketing strategy to physicians, 23andMe fought to keep its direct-to-consumer philosophy during public hearings and before Congress."

"Based on the latest warning letter, however, FDA's issue with 23andMe seems not so much that the company performs genetic testing in a lab without its blessing, but that consumers can go online and order tests for serious health-related conditions without a doctor's prescription."

Opinions from The American Clinical Laboratory Association (ACLA), a group representing the interests of the lab industry that has been staunchly against FDA regulation of LDTs. "This is not really an issue of whether the spit kit is a component, and therefore any tests that have components that are regulated are medical devices. The issue is DTC. The whole issue there is how they're ordered and also how they're marketed."

Non-comprehensive testing by 23andMe
""We've actually had some of their customers come to us for BRCA testing and say that they thought that 23andMe was offering a more comprehensive test than they actually were," said Rogers. "That firm only tests for 0.02 percent of relevant bases that are important for gauging hereditary breast and ovarian cancer risk."

"What we learned [through discussion with the agency] is that the FDA doesn't want companies saying anything about a likely medical condition, unless the company is a doctor," Bennett Greenspan, Gene by Gene managing partner and CEO of subsidiary FamilyTreeDNA"

23andMe response
"23andMe declined to comment for this article. In a letter to customers, CEO Anne Wojcicki acknowledged that the firm had fallen behind schedule in responding to the agency's requests."

Disclaimer in 23andMe products:
"However, not every 23andMe customer will receive reports that are directly useful for their health like Durrett did. And 23andMe isn't promising that, at least not in the fine print. The company's terms of service, to which customers have to agree to before buying its tests, states in plain language that the results it reports are for research and informational use only and not meant as medical advice. "While we measure many hundreds of thousands of data points from your DNA, only a small percentage of them are known to be related to human traits or health conditions," the company says in the terms of service.
Furthermore, the company notifies customers that they might learn things about their health that they don't anticipate and they shouldn't change any behaviors based solely on 23andMe's reports. "You should not assume that any information we may be able to provide to you, whether now or as genetic research advances, will be welcome or positive," 23andMe says."

Online response
23andMe advocate: "The FDA seems to think that Americans can't be trusted with more information about their potential health risks because some people might make rash decisions with it. But banning personal genomics isn’t the answer," TechFreedom, a non-profit that promotes technological progress and individual choice"

Berin Szoka, president of TechFreedom and a 23andMe customer, wrote the petition based on his own experience discussing genetic testing with his doctor. The organization believes that instead of restricting 23andMe from offering genetic testing directly to its customers, the agency should educate doctors about the risk and benefits of such testing. "Those of us who have already used the site know the real problem is that doctors themselves are behind the curve," TechFreedom says in the petition. "The only profession slower to change how they do things than doctors is bureaucrats."

"Our point is that 23andMe is providing a much-needed catalyst for change in the medical profession: Getting patients to make the first move," Szoka told PGx Reporter over e-mail."

FDA Advocate : "Having spent some time at the FDA, Ramamurthy is rather amused by the argument that regulation of DTC genetics firms is paternalistic. "If I were to follow that logic, I would say drawing yellow lines on highways is paternalistic. I would think having speed limits is paternalistic," he quipped. "I find the argument about paternalism really disingenuous, unless we live in a free-for-all."

Education to the public
"Although Casey believes there are thousands of 23andMe customers who share her view and want their $99 back, it's hard to know at this point how strong her case is. "Who are the customers?" Conley posited in his blog post. Beyond the dedicated genetic hobbyists, "how many people can there be who (1) know enough to seek out a genetic testing product, but (2) know so little that they’d rely on a cheap and vastly underpredictive consumer product to make heath or reproductive decisions?"

Saturday, November 2, 2013

I remember there used to be a day when you loved me like crazy.

I remember there used to be a day when you loved me like crazy. We could stay awake for days just to be in each others arms. We lived for the next moment we could be together again and were so full of passion… But those days are just a memory now… I want to work on us… but let’s not try to be perfect, let’s just be honest… share with me what’s in your heart, share what triggers your pain, share what excites you and let’s find a way to bring that passion back again… ~Karen Kostyla

Saturday, October 26, 2013

You are not moving

I went to the food carts a few days ago and P and O told me they are moving out of NH - this is going to be their last week here! I wasn't expecting this; I guess I have always thought they would always be here.

Indeed then, the world is moving on. Without me.

Happy places are for happy people

Happy places are for happy people.

I am happily living in a dark place right now. Dark and twisted. Morphing into something closer to vindictive. A shade darker everyday. My precious... A glimpse of the psyche of those who turned from love to hate, vacillate from pole to pole. How simple thoughts can creep, encroach and contort. It only takes a very nuanced notion to find the right niche... with time, it festers and grows.

Everyday, I yell a hundred things inside my head. Every night, I wallow. Sometimes, I look up and see nothing yet see things. It's so surreal. It scares me, yet it's reinvigorating. Maybe I am going schizo.

Happy thoughts are for happy people. 

Wednesday, October 9, 2013

Closer to a Nobel Laureate

One of my bosses' ex-boss is now a Nobel Prize Laureate! Oddly, it does feel a bit surreal to have a "closer relation" to a Nobel celebrity... It's like you have just got a ticket to nepotism or something lolx.

Anyway, he's a super nice guy! Congrats!

Monday, October 7, 2013

One more Nobel Prize Laureate!

It's quite amazing (and inspiring) to see Nobel Prize winners everyday in school: T. Steitz, being one that frequent my floor very much and I sat in his lectures, and sometimes I see S. Altman, walking extremely cautiously... Or you get to see them sprout in school, like today - J. Rothman.

At the same time, it is also heart-wrenching to see professors who are nearly there but didn't get the prize year in year out.

Well, the Nobel Prize in Medicine and Physiology 2013 goes jointly to J. Rothman, Randy Schekman and Thomas Südhof. Definitely something to be proud of - a sterling recognition of an academic's hard work in basic research =) And it's from one of the professors from my school! Congratulations!

Friday, October 4, 2013



Collecting emotions

While nursing a broken heart, I ironically feel more... complete.

This is one emotion I have never experienced before. Rather it's more like several emotions - I taste anger, pity, regret, hurt, grievance... then melancholy - all rolled into one. You can't quite place a finger around it but yet it's more palpable than anything you have felt before. 

Maybe the fact that it's so elusive yet so unmistakably there, makes it so heart-wrenching. Like a wisp dancing in the shadows. It never truly goes away - something, somewhere, somehow - lingering. Then it gets triggered - by a flighty animal, a simple lyric, a mirthful chuckle, a remnant memory. And in the most unexpected way, you feel that familiar deep twist to the heart. Yes, as much figurative as it is literal.

Things weren't turned out to be actually [edit] dramatic. But they still hurt anyway. So very much.

Perhaps this is what they mean by living a life - a collection of experience and emotions. How many have you collected?

--Lewis Carroll
“To love at all is to be vulnerable. Love anything, and your heart will certainly be wrung and possibly be broken. If you want to make sure of keeping it intact, you must give your heart to no one, not even to an animal. Wrap it carefully round with hobbies and little luxuries; avoid all entanglements; lock it up safe in the casket or coffin of your selfishness. But in that casket — safe, dark, motionless, airless — it will change. It will not be broken; it will become unbreakable, impenetrable, irredeemable. The alternative to tragedy, or at least to the risk of tragedy, is damnation. The only place outside of Heaven where you can be perfectly safe from all the dangers and perturbations of love is Hell.”

Sunday, September 29, 2013


Again, I am so amazed by how specific a certain category I took for granted can get (e.g. bulbs, pastries, bread) and am so appalled by my own ignorance haha. I think my brain is wired quite naively - how do people remember all these + many many more!! Ok, I think I sound foolish now lolx.

This infographic about wine glasses and their uses might be even better:

Saturday, September 28, 2013


是時候 該轉身就走
從此放棄 我們渴望的永久 


一切很灑脫 好好看著你走
堅強該是我 給你的自由







Wednesday, September 25, 2013

50 Shades of Grey trilogy
I stumbled upon the first book at a tag sale in Spore and brought it all the way to New Haven before I could read it (I was reading Game of Thrones Book 4 back). Of course, being the bookworm that I am, I had to finish up the other 2 to complete the trilogy, thanks to New Haven Public Library for the e-books.

I was pretty intrigued, because I have never explored erotic literature before. As it turns out, the trilogy is quite a read.

Protagonists: Anastasia Steele and Christan Grey
Synopsis: Recent college graduate Ana Steele and business tycoon Christian Grey met in an unlikely interview and found mutual attraction. Anastasia has never been in a relationship and Christian has a dark brooding past that haunts his present, resulting in his domineering nature. But expectedly, their mindsets of the world and themselves changed when their romance sparked off, along with their erotic adventures, mainly BDSM (Bondage Domination Submission Masochism). They started to embark on a journey of mutual and self-exploration, both physically and emotionally.

E.L. James started this as a fanfiction to the Twilight trilogy, got it published and now it's moving on to the big screen! As it turns out, having also read the Twilight trilogy, I felt there is a lingering sense of similarity. Just a very slight shadow. Like how Christian and Edward are both self-loathing and ashamed/frightful of their past and how they are drawn to Ana and Belle, intrigued by a certain trait that perhaps will only be privy to the male protagonists themselves (C's BDSM tendencies and E's telepathy). And of course, how A and B are portrayed initially as inexperienced or powerless but are in fact very strong women that ultimately saved the day. Their lives as the rich. Similarities between Mia and Alice, Elliot and Emmett.

Well, for romantic suckers, this trilogy will be a great read. I also think this has been pretty educational and enlightening, for my first foray into unexplored literature. The scenes can get really raunchy and graphic and they pique you in the right places. I wonder how the movie is going to be shot.... Beneath all these "kinky fuckery" (sic), I feel there are a number of pertinent messages conveyed about relationships: among them, openness and communication.

So, if you are looking to try a different genre, or an open mind looking for new literary adventure, this might be the one you are looking for. I mean it's got everything: romance, life, action and sex. Just a little more explicit sex. Shrugs.

Saturday, September 21, 2013


Before this, my mind was all about planning the future. Scrimping, saving, a single-minded drive to finish my PhD ASAP, where to plan for my postdoc/industry to set up family, marriage...

Right now, while much of those start to shrivel and wilt (except to finish my PhD ASAP), I need to take stock of where I should be heading. Time off to let things sediment after the storm.

Maybe I should plan a vacation somewhere. That might be a welcoming distraction at the very least.

Friday, September 20, 2013


I got the finality that nailed the coffin.

From here on, I need to pick up my pieces. The very soul that has been shattered to smithereens.

Somehow, there is this lingering sense of betrayal, even though there were no third parties involved. I had no time to ponder, no time to think and no time to react. I had no inkling. Whenever I asked, there was nothing from her and it seems like my fault. Or maybe I had always made it seem like my fault. But all the while for months, she was distancing herself. Unknowingly even to herself, she was preparing her emotional armor. And I was led on, clueless, thinking I was being the unreasonable one and I should be making amends. And she did make me make amends, when all I did was communicate. On hindsight, I was stupid. I couldn't even see the signs. How different she was from before... But I guess, the distance really took its toll...

I need to wake up from all my delusions.

Picking up the pieces will cut me. I need to pull out the thorns, one by one. They will leave scars. But they will also dry and leave scabs. Gosh, this hurts so much. Like a lance, right through the heart.

For now, let me grieve. Let me mourn. Let me cry. Just. Let me be...

Monday, September 9, 2013

I am hurting ... so bad ...

Sorry I haven't been updating on the front. I realize my entries are all in my drafts...

I remember there used to be a day when you loved me like crazy. We could stay awake for days just to be in each others arms. We lived for the next moment we could be together again and were so full of passion… But those days are just a memory now… I want to work on us… but let’s not try to be perfect, let’s just be honest… share with me what’s in your heart, share what triggers your pain, share what excites you and let’s find a way to bring that passion back again… ~Karen Kostyla

Monday, September 2, 2013

Arthroscopy Final

My surgery was 10th June 2013. Now it has been almost 3 months.

There is no pain at all when walking, jogging and post-jogging. The only time I felt a little discomfort is when I bend my knee for too long, due either to sitting down or crossing my legs.

For you guys out there, this is just a feel of the timeline (abridged):

1 week : walk with crutches
2 weeks: walk with limping
4 weeks: walk normally
8 weeks: jogging with post-jogging pain and discomfort; able to travel
12 weeks: normal walking, jogging and post-jogging. discomfort when bendings.

Throughout the whole process, my motto is not to rush things. I tend to add a few days more in addition to the doctor's and physical therapy's instructions, unless they specifically insisted.

I have only tried squash once so far. I will start easing into it slowly.

Hope this helps to give an idea of the timeframe.

And I just received my bill of a $100. It's apparently not free then. But at least it's not $10,000 =)

Thursday, July 25, 2013



在場的同事有一大部分來自中國,但其實我和他們很少用中文溝通。有些同學與同事甚至至今還認爲我對中文是一知半解的。這也難怪,畢竟我開口閉口都是英文。。。好笑的是儅他們第一次聼我說中文的驚訝。。說實在的,中文其實是我的一個語文 - 牙牙學語當初的第一串文字就是中文 =)但是,一般中國或臺灣朋友都不認爲我會說中文。







Wednesday, July 17, 2013

The Hardest Decision

Sometimes I think the most difficult conundrum is whether you should try harder or finally give up and walk away.

It's a really tough choice, especially when you have put in your 110%, achieved some, but not sufficient to complete. You have sacrificed too much to simply walk away, but you are getting nowhere staying in the quagmire.

Is it worth holding on? Somehow, you still harbor the hope that your incessant struggle somehow will push you through the mud and inch you forward towards the light at the end of the tunnel. Nurturing that small flicker of a hope...

Hope. It's such an illogical entity. There is no basis for you to believe, yet you hold on. You want to believe that all you have worked for has not come naught. But it's such a weak notion. Deep inside you, you scoff and you jibe. At yourself. Your puny, craven self.

But you didn't realize that hope has been sustaining you. The small fire that has been stoking your passion, and your dreams. Slowly, surely, steadily.

The small candlelight that has cast long shadows down dark alleys and tunnels, so that you may move forward. Slowly, surely, steadily.

As you lift yourself out of the quagmire, you feel that warmth and strength to carry on.

Staying or leaving. Time pushes the quandary to work itself out. You are ready. You move forward. Finally.

Saturday, July 13, 2013

Fitting in

Just when you think you have adapted, the world moves one step ahead.

Travelling 9000 miles around the globe, brought me to this place where I could seemingly be myself. A free country, they say. You see a great spectrum of people - faces, personalities, tenets, mindsets, colors. A diversity running from one end of the world to the other. Surely, I thought, I must fit in this continuum somewhere.

A stranger in a foreign land this time, is not going to make me a tourist. The unfortunate fact is that I am still being judged constantly. So, I did fit in - like a kink in the seams. Or a chip off a side of a piece in the jigsaw puzzle. In this world filled with stereotypes, extroverts and normal people, I am a controversy that stands to challenge them all.

I was taught from young, if you don't fit, you conform. But that's why I wanted this opportunity to come here. In the land where individuality counts.

But sometimes, fitting in is just so exhausting... It's like constantly fighting to wade upstream of a river. *argh*

Wednesday, July 10, 2013

Cersei Lannister
Reading is one thing. But watching all the characters come to life, another. It makes all my favorite characters more enchanting.

And then there are those I would love to slap right across the face. Even in the books.

Second episode, and already I feel like punching her. Gosh.... How in the world do these creatures come into existence.

Alas, they do walk the earth, like all of us.

Friday, July 5, 2013

Accessing the clusters using Private/Public Key pair in Ultraedit instead of password

1) Set up 'FTP Account Settings' and 'General' info as per normal: Account name, SFTP, Port, Username...
2) Go to tab 'SSH/SSL'
   - choose 'Public Key/SSL Certificate Only'
   - include the PRIVATE KEY path

3) Note that the Private and Public Keypair is generated exclusively. So for each public key present in the VM/server you provided for the administrator, you have to provide the unique private key.

4) Be sure the Private Key follows the PEM format.


Tuesday, June 25, 2013

Arthoscopy 15 days later

Last week
There is a vast improvement, so hopefully this trend continues. The PT sessions work wonders really... So I must keep conscientious on my PT exercises. 

The only trouble I have this week is still walking up and down the stairs.

Monday, June 24, 2013

Health Insurance

This is my first time using services from US medical insurance. I have no idea that you have to call to authorize a referral before it can be approved.

*Cross my fingers... I hope I don't get charged more than I am supposed to ... Aaaargh.

Reading this, just exacerbated my worries.... I don't have that amount of money...

Sunday, June 23, 2013

Haze Hype!

Singapore PSI breached the 400 mark!

Gosh... It's as if the climate is not warm enough. Now there are tons of particles up in the air containing even more of that heat and humidity. Plus, there is the respiratory problems that the particulates and irritants can cause.

I do my friends and family are drinking lots of water and taking measures to take care of themselves as best as they can.

I read that the respirators can be kept for about 3 years, so I intend to buy some to bring back for my folks and my gf+her folks for the next 3 years at least. In case, things get depleted next year again, they still have some.

Anyway, found this site showing some of the uses of the different kinds of respirators:

It seems that they are ordered by their increasing capabilities.

Hopefully, people in Singapore are seeing clear skies and breathing better soon. Hang in there people!

Setting up the Apache server on Linux

A malfunction of the website of a tool that we developed inspired me to write this post to whomever may need to do this. This entry is not meant to be exhaustive but it's more of a practical guide to setting up the Apache when I was making the webpage.

1) set up the VM with the system admin. If you have VirtualBox before, this works somewhat like it.
-- be sure to ask for root access.

2) all website content is presented in /var/www/html/
-- put soft links into this folder to direct to other folders if required

3) to make content public on the WWW, we need the switch on the Apache HTTP server. Imagine the Apache as a middle man between your console and the WWW, it 'advertises' your content on the WWW.

Use the following command:
$sudo \/sbin\/service httpd start

Replace 'start' with 'restart' to reboot and 'stop' to switch off.
We should see something like that to know that it is working (or not):
Starting httpd: httpd: Could not reliably determine the server's fully qualified domain name, using for ServerName
                                     [  OK  ]

[sudo] password for user123: 
Reloading httpd:                     [  OK  ]

4) Check on the WWW to see if the website is up. If it's not, debug using the Apache log file.
$less /var/log/httpd/error_log

This log file will tell you what is wrong and the IP of the client that was trying to access the site.

5) When you add files from your home directory, sometimes it doesn't appear on the website and the log file says that it couldn't access it. 

First, make sure you have cleared your cache to see for sure you are looking at a refreshed page.
Second, go to your VM and check the permission of the file that you are looking at:

$ ls -alZ
-- this will help you check the permission and ownership of the files. (1) Apache should be able to read all of them; (2) configuration/permission should be: unconfined_u:object_r:httpd_sys_content_t:s0 not unconfined_u:object_r:user_home_t:s0

$ sudo chown apache:apache file.txt
-- solves (1)
$ sudo restorecon -r file.txt
-- solves (2)

6) Add this line to ensure that the HTTP server reboots together if the VM restarts
$ chkconfig httpd on

Things should be in order now.

Arthroscopy Days after

After Day 10, I can walk on 2 finally. After a mere session of physical therapy, I could feel a huge difference - I think the muscles and bones needed a little more than nudging perhaps to get them back to normal.

So right now, the routine is basically ice and physical therapy exercises at home and to attend the sessions at the clinic. 

I could feel the swelling subsiding and my knee bones showing, albeit still very slowly. It's almost 2 weeks from the surgery but I still cannot walk normally yet. There is still fluids pressing around my patella. The doc had said that lateral meniscus tear is more difficult to recover than medial meniscus, so I would have to be patient. 

The key is really to keep cool and distract myself and not try to hasten the recovery by doing something stupid. I would probably have to faithfully keep doing my PT and let nature takes its due course... 

Saturday, June 22, 2013

Arthroscopy Days 4 - 8

Ice, ice, ice, ice. Keep icing. As long as there is swelling never stop icing.

Cover knee with polystyrene bag when showering.

Walk with crutches.

I removed my bandage on Day 7. See the 2 incision points and my swollen knee:
See the knee cap on the right side against the swollen knee on the left.
2 incision points
On Day 8, I went for my first post-op. The doctor said that I am healing well and had me walk without crutches and straighten my knee. When I straightened, some blood oozed out of one of the incision points. But doc says it's fine. He recommended that I try to lay off crutches to walk around the house more often - as often as my pain level allows. At this stage, without crutches, I realized I could walk, albeit slowly and limping. He also wanted me to get onto physical therapy ASAP. So I called up the physical therapy at the Health plan for an appointment the day after tomorrow.

Tuesday, June 18, 2013

Arthroscopy Day 2 and 3 - Some survivor tips for living alone

Living alone can be a real bitch when you are on crutches.

Days 1, 2 and 3 are arguably the most crucial to the recovery of the knee. The ICE - ice, compress, and elevate - 30min/30min will reduce swelling and the flexing of the foot will improve blood circulation. You don't want to be moving around too much but the occasional call to nature and for meals, will help against blood clots.

But these are all nice if you have somebody to tend to you. Staying alone prevents you from such a luxury, and you want to be really cautious about the knee.

**WARNING: you are going to need your good knee very much during these 2 days. I would recommend training up a bit LOLX

I would recommend staying off showers for Days 2 and 3, since you are staying at home and it really doesn't stink up very much, especially if you have done so on Day 1 and your house is properly ventilated. I chose this easiest option.

Alternatively, you have several options:
1) Cleanse with wet cloth + shampoo hair using sink -- cover bad knee with plastic/polystyrene bag taped with masking tape
2) Dry bath, what we do when we are out in the jungle in military, where we powder ourselves with talcum powder/'snake' powder

Get a chair in your toilet before the op. I am assuming your toilet is not wheelchair-friendly, so it wouldn't have those bars for you to hold. The chair acts as one of those for additional support to get up and down the toilet bowl. Remember, your crutches always on your bad side to support your bad side.

Before this week, I would have stocked up on groceries for 2 weeks at least. Have some prepared food available in the freezer too.

The main difficulty comes with cooking the food and washing up. In both cases, you need to be carrying things around. But this time, you can only do it ONE AT A TIME. So it requires A LOT of back and forth (especially if you forget something).... But the important thing is to maintain your composure and tell yourself to relax and that this is only temporary.

You would need to have a steady arm the side of your bad knee. As 'luck' as it, I am a left-hander (my left knee is injured). A very simple trick I do as you are moving around on crutches with ONLY A SINGLE DISH in your hand a time please -
1) hold your crutch of the good side as per normal, but the one on the bad bad side, squeeze your crutch under your armpit while you hold the dish.
2) Then to bring the crutch forward, lean on your good side a little, simultaneously rotate your shoulder and swing it forward a small distance, not very wide at all. Try with short distances to gauge how much you need to swing.
3) Next, lean on that swung crutch. Coordinate to bring your bad foot with your right crutch forward together at the same time.

This takes some practice, but it worked quite well for me and got really easy with more practice.

If you have prepared food, make sure to use a plate to hold your microwaved food for easy handling. My other small trick is to get a rice cooker. Get one of those you can steam extra food on top. Put in enough rice for 2 meals, lunch and dinner. Dump in the meat and vegetables on top to steam with the rice. After 1 hour, you would get entire meals very easily.

**You will still have to be extremely slow and extremely cautious. Look out for obstacles and try to clear them before your op, in your kitchen. I took an hour or more for each meal. 'Slow and steady' is the mantra.

I want to take this opportunity to thank the Thai cart couple, P and A, for driving all the way to deliver the food I ordered!!! They are such a wonderfully sweet couple!! Always willing to lend a hand =)



You will get frustrated on how slow you have become and vexed with having to do things so many times. When that happens, I always stop and then reflect that this is only temporary and that I should consider if you have more haste, you would go with less speed. Frustration leads to more mistakes and accidents, e.g. breaking plates, which only serve to make matters worse.

So always maintain a calm composure as you move about your meals especially. Whistle if you must or sing a bit. This is only temporary, but if you hurt your injured knee under such vulnerable circumstances, it will be permanent. So 'more speed, less haste'.

I never realized how much depend on 2 knees until you lose one. I relied so much on my right knee, I could swear it grew much more muscular after this whole ordeal. But it is also with such thoughts that you will be more mindful to not take things for granted.

Arthroscopy Day 1 - SURVIVOR tips for staying alone

June 10th 2013

I picked up my painkillers, Percocet, days before. I live essentially by myself. So I have to reorganize my bedroom a little to make sure I have most of the necessary things at my bedside: a water flask full of water, my pain meds, my books, my readings, pencil case, a small trash bin and my laptop with power cable and iphone charger.

I took a shower in the morning before heading out. Since I reckon I won't be able to shower for the next 2 days at least, I took pains in scrubbing and cleaning things out twice and hard.

No breakfast. No water still.

LA came to pick me up at 9 in the morning. I planned to reach there way ahead of time. The surgical center is in Branford. I was expecting rush hour, but there wasn't! So we reached there way before.

After some time in the waiting room, they started prepping me for the op. I changed into surgical gown. The nurse C was extremely cordial, asking if I am cold and if I wanna watch TV. So I have blankets, even though I wasn't very cold and there was TV. Channel surfing isn't my favourite pastime but it's better than stoning. She gave me 2 pills, 1 Reglan and 1 Zantac, for the stomach, since I didn't have any food since 12 yesterday. And then she taught me how to use the crutches, which she got one pair for my height. I was then put on saline IV. C was commenting on the bruises I had from the pre-op blood-taking. Because they took twice (they forgot they had additional tests..) side by side, she said they look like a vampire bite LOLX. Haha, either it's due to the 'True Blood' and 'Twilight' frenzy or otherwise, I feel slightly amused. She could have likened that to a viper bite or dragon bite or simply a fanged bite or said nothing at all, which is probably what many nurses would have done. We and some nurses laughed and the mood lightened a lot.

Throughout the whole thing, I felt really taken care of - which is the general feeling I got out of the whole COS experience. I don't feel neglected and rushed, which I thought was a good change from public hospitals back in Singapore haha, even though I must say the nurses did their best there too. Though I could say less for the doctors...

One of the nurses came to ask me if I am allergic to pain meds and other meds. I was pleasantly surprised they asked me if I know if lesser dosage is required for me since I am an Asian. Some people might find this offensive. However, as a scientist-in-training and having my previous work being on ethnicity influences on drug effects (there is a substantial influence) and their clinical uses, I must say I am absolutely impressed.

Then Dr Diana came to mark me on my left knee with his initials 'RD'. Kind of like branding haha (too much 'Spartacus') but it's comforting to know that they take precautions to make sure they don't open up the wrong limb or the wrong person or both. I think that's what patients need from the clinicians - that sense of reassurance to entrust part of us to him, even if it's fleeting/temporary. Put also confidence and soothing words of encouragement into the mix. Oh, since I am on local anaesthesia, and I opted to watch as he does the menisectomy =) I saw a video online, but nothing really beats watching a video of your own surgery as it unfurls right there =p You can watch a sample right here and more info here.

The surgery is only about 30-minute long. The nurses in the op room were amazing! They kept me relaxed. Even though I am sedated locally, I could feel my senses dulling down a few notches... Throughout the procedure, Dr Diana walked me through what he is doing. He first made 2 incisions on the skin of my knee cap to push the instrument through. I did feel a sharp pain, maybe just before the anaethesia sets in. After I sounded out, all's good thereafter. Then the surgery proper. He pointed to the meniscus and the bones (watch the video above). He pointed to a hole that was my tear. Imagine white thin fabric against the sun, and there's a medium-sized hole in the middle. That's how I saw it. There was some snipping, and some 'vaccuming' of the debris. Then it was done. Faster than I expected, maybe because the watching took my mind off the time elapsed.

I was wheeled into the recovery room. There, I was given an energy bar and water!! I was pleasantly surprised by this gesture haha; my stomach was growling by then. I still felt light-headed. LA came in to help me remember things that the nurse was about to say. She taught crutches again, for normal walking and up and down the stairs (very important since I stay on the second floor); icing and compression devices, which they provided (pleasant surprises everywhere). I am going to list them below later if anybody might find useful.

Keep yourself hydrated all the time!! I will provide more stuff in later updates.

***A very important thing to do is to flex your foot while you are icing to increase circulation.
***Do not stay in bed all the time, walk about for meals and bathroom to increase circulation. Increasing circulation prevents blood clots (which the doc says is something people neglect)!!!

A huge shoutout and thank you so much to LA, for ever being such a great great friend for driving me there and sending me back and making sure I was properly settled in. And also helping me to remember things.



Check that crutches are of good height, just below your armpits.

Normal walking:
Since I can exert partial pressure on my 'bad' knee, and full pressure on my 'good' knee,
1) 3 things go forward together, the foot with bad knee, and the 2 crutches, then your good foot goes forward.
2) crutches are always kept on the bad side.
3) to turn around, walk in an ellipse
4) to sit down, walk to forward to the chair, gauge, turn around using (3), then inch back till your leg touches the chair, move your crutches to the bad side, hold the handle of the chair, lean on your good foot, stretch out your bad foot. Never bend the knee beyond 90 degrees.

-- good detailed video here to demo how to use the crutches.

Going up stairs:
1) crutches level with where you are standing
2) good leg up first
3) then crutches + bad foot

Going down stairs
1) crutches + bad foot down first
2) then good foot

-- good video here



I have to spend the next 48 hours icing and compressing for 30 minutes then leave off for 30 minutes then repeat. This reduces swelling.

***A very important thing to do is to flex your foot while you are icing to increase circulation.
***Do not stay in bed all the time, walk about for meals and bathroom to increase circulation. Increasing circulation prevents blood clots (which the doc says is something people neglect)!!!

I didn't know they were going to provide a compression device (the link I provide from Amazon, with the pump, comes only with one ice gel I think) and 2 ice gels. I got the one I had for my ankle and bought another one from Amazon. So I rotate between these 4, very well keeping the gels cold all the time. My ankle gel needs about 2 hours or more to be really cold (it's got a really a lot of gel in there), so I guess having 4 is good. Check how long it takes to cool them if you are buying them online.

1) I have to apply ice gel.
2) layer the compression OVER the ice gel then pump air to compress.
3) lift the knee above heart level on bed by propping up 2 or more pillows.
For 30 min.

Then fallow for 30 min before repeating.

At night, I don't follow the cycle. I put one ice gel before I sleep then I remove only when I wake up for bathroom. I will also swap out the old warm gel for a new cold gel from the freezer.

Game of thrones

Old stories are like old friends. You have to visit them from time to time.

"Brandon Stark"
G. Martin

Monday, June 17, 2013

Arthroscopy Pre-op

I think it was a novel enough experience that I should blog about it. The last time I had an operation was a surgery on my finger. And it was quite a lousy experience, considering I wanted to punch someone with my other arm. -_-|||  But that's a story for another day...

This time round, I have Dr Richard Diana from Connecticut Orthopaedic Surgery for a surgery on my left knee - a lateral meniscus tear. He is extremely patient, walked me through his diagnosis, the MRI and what he recommends I do and what he was going to do. Answered my queries and concerns about insurance coverage and risks. Wasn't pushy when I said I wanted to give it some thought, since surgery does have its risks, no matter how small the surgery is and also I had to consider other factors like family inaccessibility, staying on the second floor, my schedule etc.

 - Right knee profile -
medial is inner, lateral is outer of the knee and typically blood vessels are in the outer rim of the meniscus
I had my concerns. I read some forums about how some surgeries were done badly, how people still had pain after surgeries and how it was worse than before!! *gasp*

Ultimately, while it took me more than a month to consider, I decided to go ahead. My main rationale was to get it done early, especially when I am still young, fit and healthy. Many of the people who had very dire complaints were of more advanced age or with more sedentary lifestyles. Recovery might come more of a concern later in life, particularly if the tear worsens. This thing has been plaguing me since 16 or so and I think it just broke through a certain threshold when I came to the US. Hence, I thought might as well reduce the risk of further damage now. Also, the university insurance coverage seems to mean I don't have to pay much at all - that eased my financial concerns. The last push factor is second opinions I got from my other doctor friends (a sports medicine doc one of them, thanks A and YM!!) and my friends who have known people who did the surgeries and said they worked well for them. They did caution that the physical therapy is the life-saver for them. I must keep that in mind.

Pre-op, I had an MRI and an X-ray done. X-ray didn't show up anything, but MRI did. I was told that, the tear was not near blood vessels for healing (inner rim of the meniscus; blood vessels on outer). For healing to occur, the tear would have to be sufficiently close to the blood vessels for nutrients and materials brought by the blood to help in the healing process. Alas, the tear would have to be snipped away (menisectomy) instead of being stitched. Finally, I was given a rough idea of the recovery time for a typical person: within a week I would able to limp without crutches, within 2 weeks walk, and within a month jog lightly. I like that. I like knowing my schedule, so I can plan my stuff around it, and putting extra time to buffer.

- Different kinds of tears -
I was imagining mine to be like (d), but when I saw it on screen, it looks like (b), so maybe a combination of both like (c)??
I have tried explaining this to my mum what I think is happening, as lay as possible. I think it makes sense, so I shall try explaining it here too. The (two) menisci act to distribute the force exerted by both the tibia (calf bone) and the femur (thigh bone). So when you have a tear, you experience some form of discomfort when the bone brushes over a tear instead of a smooth fibrocartilage. Snipping away does reduce the size of the meniscus but it beats leaving the tear there. I liken this to a piece of paper. When there is a small partial tear, it is much more likely and easily that the paper will be torn further via that tear, then if a new tear were to start someplace else away from that tear (try with a piece of rough paper). Snipping that tear away will reduce the probability of further damage to the cartilage via that tear. However, it does reduce the cartilage area, hence your cartilage will not as resilient as your original whole cartilage, but to damage it, the impact would have to make a new tear instead of worsening an old one.

Before the surgery, I had to do the routine pre-op within 30 days of the surgery - draw blood to test for cholesterol levels and the likes. Happy to know I was good to go. 12 midnight on the day of the surgery, I was to stop eating and drinking - basically just sleep with no supper and breakfast.

Friday, April 12, 2013

One more week

One more week to go !!! There's more excitement than worry right now. Perhaps it's the caffeine.

Looking back at my previous entry. I think I sounded juvenile. Oh whatever.

Thursday, April 4, 2013

Sometimes... Perhaps... - a soliloquy

The road to qualifying hasn't been smooth but it's been too rough either; could have been worse. Now that I have only 2 more weeks to go for my quals, I am feeling restless. This is my usual jumpiness, especially whenever there is a preliminary round of something and then a final round - I end up doing badly for the final round... 

Sometimes, the jumpiness involves me raising doubts about my PhD crusade. Like now. I am keenly aware that I am surrounded by brilliant minds, talking brilliant sense, and doing brilliant things. Sometimes, I just feel so tiny against this whole backdrop and I start wondering if I am ever cut out to be here at all... Which is dumb. Because I am here. And I should be focusing on being here and not anywhere else.

It's like I am so different from so many of them. I am not fast in thought and I am not versed in method. So what am I actually? In this cutthroat world of the intellectuals, I try to work as much as I can, but I take so many breaks and shortcuts, they almost always make me feel guilty - to myself and to people around me. I make a fool out of myself during meetings asking seemingly dumb questions. I try to think if the colleague sitting next to me picturing me as a dud, trying to make a living out of smoke bombs. Or my supervisors haven't already found out that I am masquerading as an intellectual. Or perhaps that's where my challenge lies, to blend in. But it's so tiring blending in, treading on fine lines and playing political games, when you know the moment you bare yourself, people might recoil and turn away. Perhaps to be thick-skinned, is the lesson I should learn. An emotional Colossus.

I am also poignantly aware that my work is sometimes very different from the other people around me. It is first very eclectic, which sometimes makes me wonder if this runs counter to the theme of a PhD - to be very knowledgeable in a specific field. In another way, perhaps my PhD is in broadness, but to be very 'deep' in broadness, would probably be either oxymoronic or require me to be very versed in every field - which is itself insurmountable in my opinion. Or, it can be sarcastic too and a mockery at the PhD system, in even allowing me to do a PhD in the first place. Perhaps, I am just wasting time and resources. Perhaps, I am just waiting to be weeded. Perhaps, I am one of those outliers that fall at the other end of the success spectrum...

My different work, foreign drawl and unintelligible gestures garner numerous uninterested, glazed looks whenever I give talks. My own inspiration for my work starts to wane exponentially. Sometimes, it's hard to distinguish if I am here to try to be more versed, or thick-skinned or both... So, an afterthought is the rationalization that I tend to be sensitive to other people's opinions of me. Even though over the years I have been honed to disregard that ultimately, my natural instinct always kicks in first such that the damage has already been done - so in effect, you disregard the wound but not the act of wounding.

Quals is around the corner but I am letting my imagination run wild and not focusing... Perhaps that's why in the first place I do badly for final rounds. Or perhaps...

Saturday, March 30, 2013

i need an outlet

Ok, I need an outlet and this is it.


Ok. Better.

Friday, February 22, 2013

Navigating the PhD: beyond the science

Having finally some headway in my qualifying exam preparation, I decided to take a short breather and take stock of my PhD career so far.

Even having 2 first-author research papers, a couple of perspective/journalistic articles, and a few more co-author papers under my belt, I am still terribly unconvinced that I will be having a smooth qualifying examination, let alone a career that is so fraught with uncertainties. As much as I like the science, I can't lament enough over things beyond just pursuing knowledge - things like politics, people relationships, your own life etc. After a frustrating 1.5-month of scheduling, waiting and rejections, I have finally formed my qualifying committee. I have learnt a few things along the way about people and politics and PhD qualifying exam in general. I have particular thoughts on selecting professors.

1) Find people you know who share your interest by getting to know them early in your graduate career.
I have a very secluded personality, making this point very hard for me. I also have a very non-straightforward situation of having very few people in the entire institution that share my eclectic research interests and consequently my qualifying proposal. That's when I realize retrospectively while smaller, private graduate programs tend to have a diversity of faculty specializing in various fields, this can both be a pro and a con. The most obvious pro is the choices you have in choosing a lab/labs you like. But the downside is that you have very few potential mentors sharing the interest you have, especially when some of them would end up declining being on your qualifying committee, and you are left with nobody else that is marginally involved in your work. I don't have a direct advice here about how to circumvent this problem. Except to try to identify certain areas you are interested in early and clarify those goals, so that you can hook up with the right professors way before your qualifying exams. If not, look at (2).

2) Otherwise, you have to steel your skin and bulldoze your way.
Which is what I did. I consulted with my advisors (I have two) who gave me alternatives. Alternatives bring with them a whole slew of issues because they are typically very very remotely associated with your fields of interest. Some of them ended up rejecting to be on my committee on various grounds. I wouldn't mind, even if it was a terse 'no'. At least, there was a CONCRETE, relatively QUICK reply. I have the experience of waiting 1.5 months for a reply from a professor that showed keen interest but would never set a specific time until after 1.5 months (nearing 2 now). His timing would then uncannily coincide with the time, I thought he was uninterested and moved on to find another professor, who agreed to be on my committee. Consequently, I would have to form the committee without him and hope that he doesn't take offense... There is always this distaste in how all these things seem to time themselves to happen at almost exactly the same moment. (Ya, like aligning the same time with when your toilet clogs, deadlines of your papers and everything else that's life.)

3) Politics
Look out also for signs of discord between you and the stranger professors and/or between them and your own professors. That's why communicating with your advisors are extremely important because they will only tell you those they can work with. Write emails that ask for discussion to be on the committee, rather than asking them to be on your committee right off the email... Even though, sometimes, this might get glossed over. You might have to emphasize that. Meeting with these professors is a match-making for a mutual fit, that you feel comfortable with him as much as he feels so with you. 

4) Being a worrier.
And if you are a big worrier like me, you would freak out with such a confluence of uncertainties and situations. My friend calls it by a fancy name (defensive pessimist). Over the years, I have adopted an odd take on this, inspired by the autobiography of Ms Aung San Suu Kyi. The idea is that this worrying is periodic. I would then accelerate the process of allowing myself to be worried to the max, and there will be this nadir which I will hit. That's when I will tell myself 'enough is enough' and then resolutely start climbing out of that abyss... I know. it's a weird concept... The assumption, of course, is that you would not fall off the depression cliff. So don't try, if you are not confident.

My friends who have gone past the stage keep telling me that this is a rite of passage that every PhD student goes through. It is not a matter of life and death. I will look back in the future and mock at why I was so worried. Well, until that day comes, I will continue to worry, I guess.

People, politics and PhD. My enigmatic love for alliteration doesn't make me like that combination at all. Not one bit. 

Tuesday, February 19, 2013

Genomics and Microsoft Research

I didn't realize that Microsoft Research branch does genomics research. A recent article in Scientific Reports surprised me. More search came up a list of Computational Biology tools on one of their websites.

Perhaps Mr Gates' eclectic interests in biomedical sciences and philanthropy outside his company have converged somehow at Microsoft after all.

Friday, February 15, 2013

Reducing Skype to the system tray

Ever since Microsoft announced the closure of MSN messenger, I have been dreading the switch because it would mean some reconfiguration and I am not in a very good position now to do too many of those. Alas, they decided to merge MSN contact list with Skype.

So my Skype is not very well-configured, specifically, it doesn't reduce to the system tray or "the notification area at the right hand lower corner of your Windows screen". I like that because then it wouldn't clutter up my task bar. So I will write here a walkthrough which I used before on MSN to do the same thing for Windows 7:

1) First, open Skype, go to Tools > Options > Advanced, and uncheck "Keep Skype in the taskbar while I'm signed in"

2) Close Skype

3) Go to Start Menu, right click on the "Skype" icon. Go to Properties > Compatibility.

4) Check "Run this program in compatibility mode for:" and choose "Windows Vista (Service Pack 2)" on the pulldown.

5) Click "Apply" and "OK"

6) Restart Skype and it should minimize to systray now!!

Apparently you could do that for a number of different software that used to reduce to systray but does not do that anymore in Windows 7.

Sunday, February 10, 2013

3D printer

I recently officially inherited a 3D printer from my lab.

I am quite enthusiastic about new technology, particularly if the things are very practical and directly useful to me. I like the the idea of pseudo-owning a 3D printer, but I have no idea what to do with it.

Then incidentally, my friend TC was assembling a 3D printer himself and he told me to take a look at this Thingiverse website. There are so many things one can do with a 3D printer!! I started looking through lab equipment and fashion accessories...

I will see what I will do after my quals... For now, nothing seems to set my mind on fire - except the notion of passing (or failing).

PS: Oh I found that Pinterest has quite interesting selections. I will try it eventually I guess...

Thursday, February 7, 2013

The inertia of status quo and the tyranny of old ideas
“In short, I’m less worried about the risks of polarisation than I am about the effects of incumbency, the inertia of the status quo, and the tyranny of old ideas.” - Donald Low

I am really liking this quote. Not only because it incisively points out my point of view when I voted in the last elections, but also about work and life in general.

How many of us have encountered situations where traditional people have ensconced upon their thrones and start quashing all novel opinions that try to change the status quo ("because it works" they always say) without even giving the opportunity to try them out?

Monday, January 14, 2013


Kind of interesting

Traditionally the attraction to intelligence, however it can also be extended to the attraction of proper, full sentences and the use of grammar.

Do I read the Toronto Sun? No, I am a total sapiosexual, I like sentences, paragraphs and grammar.

(adj) A form of sexual orientation characterized by a strong attraction tointelligence in others, often regardless of gender and/or conventional attractiveness.

(n) A sapiosexual person. 
"I am sapiosexual. I think geeks and nerds are sexy--I often want to rub my clit against their minds." -Kayar Silkenvoice