Another part of my diary.

Hello all,

This part of my diary is particular, as I am writing it after I knew that I am going to do my residency and my research work in one of the hospitals in New York city. Here it is:

"Sunday, 21st of June, 2009.
A strange feeling. It has been a long journey towards the moment that I am in right now. Around 13 years passed since I was introduced to molecular biology, 9 years since I started my first step of USMLE, 7 years since I identified the field that I like as bioinformatics and computational biology, 5 years since I started my residency in neuropsychiatry at Ain Shams University, one and half year since my first travel to the States and few months since that I knew where I will be doing my residency. Also, this place provides for me the suitable atmosphere to pursue the rest of my dreams. Oh yes, a long journey.

A journey during which at several times I said “Yes, this is my career, this is what I want to die doing."

As I am now on the plane, I can feel a strange feeling, different from my previous 2 journeys to the State. The feeling is that this time I know where I am going, and I know what I will be going after. A feeling that I am traveling to get things that can empower me and help me empower others to “be the change we want to see in the world”.

Monday, 22rd of June, 2009.
What an exciting moment. Setting here on the 22nd of June, 2009, the first day of orientation for the residency training, a dream finally coming true(actually only the beginning).

It's now 12:30 pm, the lunch break. We sat in the Alumini Auditorum for around 3 hours for welcoming speeches, guidelines, and notes regarding administrative points.

I am now sitting in the garden just beside Lenox road. As I was walking around, the feeling is overwhelming. Here I am, finally in the States, actually taking the orientation course for the residency. I know that it is a long long journey of hard work, and stress, but it is also a journey full of discovering the wonders of the creation, discovering myself, and working towards helping others from different generations towards a better hope.

Tuesday, 23rd of June, 2009.
The historical overview that we were given today about SUNY Downstate was inspiring. I did feel as a part of this family.

The orientation helped me to identify different resources in the hospital that I can use, so as to make the years as enjoyable and as beneficial as possible."

Some days from my diary in USA!

From my diary:

"This is the first of -hopefully- many pages describing my experience towards my journey to the States. Today is the 3rd of April, 2008, my first day. Me, mum, dad and my brother headed toward Cairo International Airport, terminal 2 at 7 am. During the preparation of the whole journey, several things took place that turned the whole journey to an ideal one.

The airplane took 11 hrs and half. I prayed Al Maghreb and Al Eishaa, although the sun was in the middle of the sky!!!

After we landed, checking in was smooth, and I was able to get my luggages. I rode the air train to the terminal of my second flight, and checked them in, and now I am waiting for my flight. It will be at 10:30 pm to Syracuse and a friend will be waiting for me at the airport. We booked the flight that late because we were afraid of any difficulties that might face me, and would delay me.

All through the journey, I did not feel any strangeness. The main difference that I noticed is the language, and thanks be to God this was not a problem for me. People are nice, and sometimes even helpful. The weather is warm inside the airport, although outside it is really cold (3 degrees centigrade).

Tuesday 8th April, 2008. 10:15 pm

I was just watching a documentary called “Winged Migration”. It is about the migration of birds across continents. It is amazing and the music is fascinating. The way the birds' feathers are beautifully decorated and how they coordinate together is too complex. I was thinking about how things would be really beyond imagination if we thought how did all of this arise, I mean the molecular basis of all of that. It is breathtaking.

The way the documentary was photographed to provide as possible a realistic representation as possible, is outstanding. It took them 4 years to shot such a movie that is no longer than 2 hrs. And it took them a lot of work, effort and planning so that it is made that way. It shows the capability of human beings. We can make a lot of things. Actually, we can do whatever we want, only if we truly wanted it. I hope that I want my dream about molecular psychiatry and bioinformatics to be true strong enough so that I would tell anyone who might come in my way “Mr., I am going to do that whether you liked it or not”.

Wednesday 9th April, 2008. 11:00 pm

Today my observership seems to be delayed for a while because the lady who is responsible for processing the papers is on vacation and will return by coming Monday. I decided not to wait and I continued my readings in bioinformatics, molecular neuroscience and developmental neuroscience. These fields are really AMAZING.

Thursday, 10th of April, 2008. 11:10 pm.

I was worried about my parents. But they are accepting the idea of my traveling (or at least, they were not showing me that they are sad),

Tuesday, 15^th of April, 2008. 11:30 am.

I have just returned from Upstate Medical University hospital. I went there to finish any needed paperwork before I start my observership tomorrow. It was a very nice experience. My appointment with Ms. K the secretary of Dr. M.K. and others was 9:30 am. I was at the hospital by 9:15 am. I passed through the front desk, where she had left my name the day before, and they produced me a sticker of a visitor that I put on my jacket. I then passed to room 1702, which is the room for the liaison psychiatry service. I met Ms. K and she was very nice. She gave me a form to fill so that I can issue my Identification form. After I finished and while waiting for Dr. M.K. to arrive, she introduced me to another Prof, an attending doctor and a resident. Dr. M.K. then arrived. He was really nice and he filled the rest of the form. I told them that I finished my residency in Egypt and that I am interested in a residency with a research track. The lady Prof asked me about do I like a lot of writing. I told her that I don't mind. She said that then I will be able to help her with her paperwork (Just let her ask :) ). She then offered to give me the paper that they will speak about in the journal club tomorrow, I said sure. It was a paper about Delerium.

I then went to the Payroll office, to issue my ID. The lady there was extremely nice, and after we finished everything, she told me that she studied Arabic around 10 years ago, and that she likes it so much and that she is fascinated by the history and how they were able to conquer most of the civilized world. She was fascinated and she wanted to know a number of words like WELCOME and THANK YOU SO MUCH. I wrote it for her and she was extremely happy. She told me that she called her hawk SAQR. She was extremely nice and we agreed that I might pass her by every now and then to exchange a number of arabic phrases.

My impressions are overwhelming. I cannot but remember Dr. AbdelWahab AlMessery' s autobiography book where he described his journey to the States. Tomorrow I will start my observership. Hope that things will go extremely fine, AMEN.

Wednesday, 16^th of April, 2008. 10:00 pm.

I feel now very tired. I am in my bed ready to sleep. Yet, this day cannot pass uncommented upon. Today, I started my observership at Upstate Medical University. It is in the consultation/liaison psychiatry service.

We started by a journal club where they were discussing a paper about delerium. Then we discussed the patients that they saw during the past 2 weeks. After that, each attending psychiatrist went to check some of the consultations, and I went with them.

My level of knowledge was good and I was able to deal with the attending psychiatrists. I was really impressed by my level. It was not bad at all. Plus, my meeting with the attending psychiatrists including the senior ones made by decision regarding the research work more supported. I do enjoy research work."

Hope that these few pages from my diary would help to fuel your enthusiasm more towards pursuing the USMLE goal. I will try to put some more in the near future.

TMT, TLT!

This stands for "Too Many Things, Too Little Time", which mean that I have a lot of things that I want to talk about, but little time. So, I will just mention them shortly:

--- A couple of days ago, there was a meeting to which I was invited by a close friend. The event was held in one of the cafe's in Al Korba, Cairo, Egypt. A group of people were gathering to discuss their plans for the USMLE (United States Medical Licensing Examination). They were really motivated, and I was happy to be able to see such a group of bright, brilliant and enthusiastic minds. I knew that the new generations represent the main hope to our country, and that group was one of the proofs.

--- I went to open an bank account for me (something that will be needed for those traveling to the States). It was in a branch of an international bank. The service was really good, and the staff members were accurate. This helped to answer one of my concerns. If we were going to start a neuroinformatics lab here in Egypt, will the people have the capacity to stick to a system, and respect different rules and regulations? The answer is what I saw today, and what I had seen before several times as I was dealing with some places that are considered international with Egyptian workers.

--- I was considering putting some of my diaries while I was in USA so as that group of USMLE takers would feel how is it to be in the States, from the point of view of someone who first visited it when he was 28 years old.

The city with the most beautiful night.

Imagine this, you are walking after midnight, feeling safe, with people around you returning home, tired, but if you greeted them, they would smile and greet you back. Everyone of them has his/her problems, and an outstanding life that makes a great story if you cared to stop and listen. People here can open for you easily, and would tell you their life's stories, their worries, their concerns, their hopes and everything else that you want to know.

Then as you drive your car, you can see the lights passing by, you looking through your window to the same city that was fully awake just a few hours ago, and you know that in a while it will wake up again.

In spite of all the problems that people are suffering here, the poverty, the economic crisis, the lack of hope and the lack of a future vision, the people are still living, surviving, enjoying music, laughing at jokes and although there is no apparent set of rules governing their life, they have their own code of ethics that they live according to. How mysterious human beings are!

I think that you had known which city I am talking about. I have just returned from Downtown, Cairo. It was 2 am in the morning. The streets were not crowded. I went to Sherif street and Soliman Basha square, then passed by Al-Hussein. I walked for around half an hour then drove home. Then I sat down to post this, and it is your luck (good or bad) to read it.

Inspirations that I met!

Sorry for being away for all that time. Things have been busy around here.

I have thought several times before changing the title of the blog. The previous title described my dream, however, the new one describes the message that I want to give through the blog.

During the past month, as I was surfing the net, I met some things that helped to charge me, and maintain my hope that anyone can see his/her dream coming true.

The first is Brad Pitt's company for helping building the houses that have been destroyed by the hurricane Katrina in New Orleans. I know that this is old news (It was initated in early 2008), yet I did not come to visit the web site of the company. You can find here. It is called Make It Right.

The second is an institute for neuroscience that has been founded in Brazil, in collaboration with the Brazilian neuroscientist Miguel Nicolelis, M.D., Ph.D., working now in Duke University. This is a link to his lab at Duke. The institute is called Edmond and Lilly Safra International Institute of Neuroscience of Natal (ELS-IINN). What is unusual about the institute is that it has a school and a health center joined to it. In that school, the students receive education that is focused more on science (including math, biology, chemistry & physics), and on electronics and robotics. For me, the health center avoids the separation that usually happens between basic science research centres and the problems that people face in their daily life. Yes, reserach centres are essential for the development of any soceity on the long term, but we should not forget the short term sufferings of people.

I hope that after you browse those websites, that you would be charged to continue moving towards the light in the end of the tunnel, like they have charged me.

I will post a new post telling you how do I feel as I prepare to travel to start a new life in a new country, and to start to realize my dream :)

My second visit to the USA! 1

I reached JFK airport the day before yesterday (Saturday the 8th of November, 2008). I stayed with a friend of mine in NYC, then yesterday I head to Burlington, VT, where will be my first interview for psychiatry residency. The Amtrak journey was somehow long (10 hrs), yet I enjoyed reading some of the BABLE book, which is the manual of GENESIS, the neuronal simulation software. I reached Essex junction, then took a taxi cab to Hilton in Burlington, VT at around 10 pm.

Today was my first day to explore the town of Burlington. The Hilton is located near the downtown (walking distance, I have no car). I walked to the water front, as the Hilton is located on the Burlington bay of Lake Champlain. It was outstanding with the view of the mountains in the horizon. I then walked to Church street to explore the downtown of the city, and to find a place to eat. What I really liked about the street is how peaceful the people look. They are all enjoying their time. I know that this is not true, and that this is due to the blindness of ignorance of the tourist (me). But you can tell the difference between people living here, and people living in a crowded city.

I went to Leunig's Bistro restaurant. It is located on 115 Church street. It is really nice and homey. I felt like I am in a restaurant in old London, and the people there were really easy, talking and making nice polite jokes. I had Caesar salad and their special for Mondays, which is beef meatloaf, with French fries. I think that I might return there tomorrow after my interview in the Fletcher Allen Health Care.

I will try tomorrow to post some pictures of how nice the city is. Wish me good luck with the interview.

Computational biology & Bioinformatics: solution for scientists in low-income countries? 1

Since that I am a psychiatrist, my focus will be on neuroscience and mental illness. Many times me and my colleagues came across a patient suffering from a clinical picture that arisen among us several questions regarding brain circuits and signaling. Then when we think about how can we design some form of study to try to clarify things, we are faced by the problem of the absence of research funding.

Other times, we read about a new study and we become so excited about it. We try to imagine how fascinating it would be to be looking at something that no one before looked at; to enjoy being the first people to look at it. Yet, come again the problem of no funding, and we are back to earth again.

I can imagine also other colleagues in other scientific disciplines facing the same problem, the problem of minimal funding.

Then come the other problem. In low-income countries, we suffer from inadequacy of team work. So, everyone of us becomes alone, and since that he/she cannot solve the problem all alone, we stop. And in the end, the person pay from his/her own money. And since that research is expensive, usually the story ends with the researcher doing the study according to lower standards than he/she wished.
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Computational biology techniques, or the so called "dry biology", need less money (according to my point of view which I hope is shared by many people). You don't need biochemical kits, DNA sequencing facilities, or places to keep the animals. But you need an adequate understanding of your problem at the molecular level, you need mathematical knowledge to some extent, so that you can understand different algorithms designed for a particular problem, and to design a mathematical model if needed. You also need some basic knowledge of computer sciences (and preferably one or more programming languages).

Yes, this looks hard, and it is hard, but it needs less money. As learning sources are out there, mostly for free, learning becomes possible. As the access to different biological databases and different bioinformatics servers is available, some for free, and some others for a sum of money (that can pay well back), the tools to shape our questions and answer them become within the reach of hand.

Also, the use of computational biology techniques in tackling the mysteries of mental illness would require the collaboration between psychiatrists, neurologists, neuroscientists, in addition to mathematicians, and computer scientists. This can start to create a highly creative scientific atmosphere within our country.

Next comes the point of where to get the research question. In psychiatry, we spend a lot of time with our patients. We listen to them talking about their fears, what make them uncomfortable, what disturbs them, the side effects they are suffering with our medications, the lack of support that they feel, or hopefully, the support that they are finding from their families. Listening to them describing their illness and their childhood helps us to make what we usually call the psychodynamic formulation (or actually, the psychodynamic hypothesis of why this patient is suffering that illness in that particular way).

Using the advancements in molecular neuroscience, neuroimaging, and developing animal models of illness, we can start to generate hypotheses regarding the cause (etiology) and mechanism (pathogenesis) of the illness. Usually this is the path taken to reach to a research question. What I think that we, as psychiatrists with low funds for research can do, is to see how computational biology techniques can help the "wet biology" research taking place in other areas of the globe where there is better funding opportunities. This will make our countries share in the global advancement of the understanding of the mechanism of mental illness.

"Dry biology" techniques are complementary to the wet biology. The hypothesis can be generated from findings resulting from wet biology, and then checked and elaborated using the dry techniques (eg, the effect of a mutation on the binding affinity between two proteins). Things can also go the other way round. Hypothesis can be generated from results obtained from computational biology work, then tested using wet biology techniques (eg, identifying new molecular targets for medications).

An article that I think is worth reading for scientists in low income countries is "Ten Simple Rules for Aspiring Scientists in a Low-Income Country" by Edgardo Moreno and José-María Gutiérrez, in PLoS Computational Biology.

This is a rough scheme for how I see computational biology can help psychiatrists understand more about mental illness.

To be continued..... :)