New HIV vaccine target

About a month ago, I posted about an article that had been published from some research I worked on Bangladesh. Just last week, an article was published in Science about some exciting results from one of the vaccine studies we were doing in Rwanda. The study was sponsored by the International AIDS Vaccine Initiative (IAVI) and took place at sites around the world including the U.S., the U.K., Australia, and west, east and southern Africa. At our site, we identified and collected samples from individuals who had been infected with HIV for at least three years but who were clinically well and had never been on antiretroviral therapy (ART). Samples from all sites were sent to international laboratories, where two powerful new broadly neutralizing antibodies against HIV were identified. Results also revealed a new vulnerable spot on the HIV virus that no previously-known antibodies have targeted, which is huge news for vaccine development!

After so many disappointments and so much negativity in the world of HIV vaccine research over the past couple years, it's really exciting to see some new developments. Read more here.

Detained and deported

As much as Egypt parades itself as a free democracy, sometimes reality hits. Last night a good friend was returning to the country after a three-month vacation in England and the U.S. When he arrived at the airport, he was detained, questioned and eventually deported. Although no reason was ever stated, it is most likely that this treatment resulted from his participation several months ago in a peaceful march in protest of Egypt's treatment of Gaza. Read more about his story here.

A day on the beach in Ada

We arrived in Ghana late Saturday night and, even though sleeping in the next day would have been nice, we made plans to get up early to celebrate the birthday of one of our American colleagues who’s based in Accra. She and her husband picked us up early that morning and we headed east to an area called Ada, which is about an hour away from Accra.

Our colleague is married to a Ghanaian who has a cousin who owns a little beach camp right where the Volta River meets the Atlantic Ocean, so we had planned to spend the day there. I knew having a day to relax outside Cairo would be nice, but I had no idea how beautiful and relaxing the area would be.
When we arrived in Ada, we hopped on a little boat on the shore of the Volta River and headed toward the Atlantic. When we were just a short way from the ocean, we pulled over to a little sandy strip of land (barely 100 metres wide) between the river and the ocean. This was our friend’s beach camp and it was perfect – bare bones cabins, empty hammocks and relative silence. We strolled over to the Atlantic and walked on the beach for a while. It was a beautiful day and the waves were powerful and majestic, but, as much as I wanted to, it was impossible to ignore the incredible amount of garbage on the beach. The beach was literally covered in garbage, not from tourists dropping their water bottles and candy wrappers, but from cities all along the West coast of Africa. Ghana, like so many other countries in the world, including the United States, uses the oceans of the world as a giant landfill, and Ada is one of the places where the local population is too poor to clean the beaches, so instead they are covered in garbage.
After walking along the beach, we decided to settle in and relax at the camp for a bit. A couple hours later, our colleague’s husband’s cousin took us out for a tour of the area by boat. I really had no idea how huge the Volta River actually is! Every time I thought we had reached the other side, our captain would turn the boat just so that I could realize that we were instead on the shore of another island.
After riding around for a while, admiring homes of foreign business men and sighing at the contrasting houses of the local population, we stopped on one of the islands. We had been discussing hopping off to walk through a village, so I assumed we had reached our destination, but I was very wrong.
Instead, we had reached one of the distilleries where local Ghanaians make their very own rum, with the claim that Jamaican rum is nothing compared to Ghanaian. (I might argue that “moonshine” would be a better term to describe what we saw and tasted, but “rum” is the local term.) Apparently the process goes something like this:

Step 1: Grind sugar cane through this antique contraption.
Step 2: Transfer the sugar cane juice to these giant pots to ferment.
Step 3: Pour fermented sugar cane juice into this barrel and light a fire underneath (after removing the baby goat, of course).
Step 3: Let the liquid boil and transfer through the coil from one barrel to the other.
Step 4: Let the liquid cool and drain into this glass container, being sure to release and discard the methanol first.
Then somehow the “rum” makes it from the glass container into recycled water bottles that sit for sale in this little store.
After “ooo-ing and “ahhh-ing” and asking questions at every stop during our tour, I thought we would return to the boat and continue our relaxing afternoon of cruising on the river. I was wrong. Apparently there’s no way to get off a rum maker’s island without first tasting his product.

We all sat down in the middle of the operation at a table, surrounded by curious children, baby goats and chickens, and a large bottle of “rum” appeared with a shot glass. (The rum maker thought it was hilarious that his shot glass said “Jamaica” and made several references to the fact that his rum was better than any from Jamaica but that he didn’t have a shot glass that said “Ghana”.) The rum maker began making his way around the table, serving each person a shot of rum. There was no opportunity to say no.

My colleague who had traveled with me from Cairo was up first and took her shot like a champ. I was up next. Now, I feel like I’m usually pretty good in these types of situations that involve eating or drinking something that might not necessarily be pleasant. This day I failed miserably. I swallowed down the shot in one gulp, and then I felt every organ from my tongue to my stomach burning. It was all I could do not to cough and cry. But I will say, had it not burned so badly, the flavor wasn’t bad. I’ll also say that the rum maker is some kind of salesman, because I still somehow walked away with a small water bottle as a souvenir.

After we’d all taken a couple obligatory shots of rum, we piled back into our little boat and took off into the river again. After a few minutes we spotted a fishing boat just coming in from the sea and unloading its cargo on the shore. The guys decided to buy some fish, so we stopped. It was an impressive operation. The fishermen stood on the boat unloading their fish into pans atop the heads of local women, who carried the fish to shore and unloaded them into neat stacks. Meanwhile children played in the water and climbed on the boat, and it didn’t take long to realize that they were stealing fish. Occasionally one would surface from under the water and take off running, with a huge grin across his face and a single fish in his hands.

With our load of fish, we took off on foot through the village, heading back up the Volta River toward the spot where we had left the car. We stopped for dinner and to watch the sunset and then headed back to Ghana. Not a bad day at all.

Ramadan kareem!

Clemson in flu news

Well if this didn't just make my day - to see Clemson's name in a high-profile article related to the field I'm in and a lot of the work I'm doing! A summary of the article can be found here on Clemson's website.

Ramadan 101

With Ramadan quickly approaching, an email was sent around the office today, giving a brief overview of the holy month and its significance in Islam. The following news article was first published in the American Forces Press Service News Articles, Oct 20, 2003.

Ramadan Kareem
by Rabia Jami

More than 1.2 billion Muslims worldwide will celebrate the start of Ramadan, Islam's holy month of fasting, on Saturday, 22 August. The start and end dates for Ramadan may vary because the beginning of Islamic lunar months depends on the actual sighting of the new moon.

Followers of Islam believe that during Ramadan, heaven's gates are wide open and hell's gates are locked shut. In the Quran, the Muslim holy book, it is said "You may eat and drink until the white thread of light becomes distinguishable from the dark thread of night at dawn. Then, you
shall fast until the 'layl' (night)."

During the fasting month, Muslims eat a small meal prior to each morning's dawn. They then abstain from food, drink and other physical pleasures during the daylight hours. Believers end their fast just after sunset. Often this meal is taken at a cheerful gathering of family, friends or other community members.

In the evening, many Muslims attend "taraweeh" prayer at their local mosque. This prayer involves the recitation of one thirtieth of the Quran. By going to these prayers each night, a Muslim will hear the entire book recited by the end of the month.

The primary reason for fasting is to invoke God's pleasure. Other benefits and goals of the fast are developing greater self-restraint, having empathy for those who are less fortunate, breaking self-indulgent habits, cultivating patience and improving family ties. There also are well documented medical benefits gained from fasting. Children, old people, and others who may physically or mentally be incapable of understanding the fast or enduring its rigors are not required to take part.

The last 10 days of the month are considered among the most blessed. Those who can will retreat to their local mosque for the duration and spend their time in prayer and reflection. Among these last 10 days is Laylat al-Qadr, the Night of Power. On this night, Muslims believe, Allah sent the Quran to humanity.

Ramadan's fast fits neatly with two of Islam's other five pillars of faith in providing structure to one's spiritual life. Each day there are five prayers, each year there is one month of fasting, and in each person's lifetime -- for those who are physically and financially able -- there is a pilgrimage to Mecca.

Charity is also an obligatory pillar of Islam. After one acquires the necessities of life -- food and shelter -- and before spending money on niceties, Muslims first donate 2.5 percent of their money to the needy.

The remaining pillar is a Muslim's verbal declaration of faith: There is nothing worthy of worship but Allah; Muhammad is Allah's prophet. The Arabic word "Allah" translates into English as "The One God." Just as the words "salaam" and "peace" mean the same thing, the word Allah is used in the Arabic speaking world by both Christians and Muslims to imply the same entity.

As for the second part of the declaration, Muslims view Muhammad as the last in a line of prophets that started with Adam and passed through other respected figures such as Abraham, Moses and Jesus.

At the month's conclusion Eid-al-Fitr, the three-day Feast of the Fast-Breaking, begins. This holiday is expected to begin 21-22 September.

In the United States, an estimated 7 million Muslims will be observing Ramadan. Muslims have been fasting in America since at least the colonial era. Many Muslims were brought to the United States as slaves, one of these being Kunte Kinte, who was made famous by Alex Halley's novel "Roots." There is evidence indicating that a Muslim fought on the colonial side at the Battle of Bunker Hill. A Muslim known as Nicolas Said served in the 55th Regiment of Massachusetts Colored Volunteers during the Civil War.

Zinc treatments for diarrhea

TIME published an article this week called "Can one pill tame the illness no one wants to talk about?" which discusses results from some research I had an opportunity to help with while I was in Bangladesh a couple years ago. It's pretty awesome to see that research turning into results and action that may truly make a difference in peoples' lives!

Dead Sea

On our way back to Amman from Petra, we made a detour to drive by the Dead Sea. I already had the opportunity to see the sea from the Israeli side and to float on the surface of its buoyant water last December (see "Dead Sea Spa"), but I had heard that the view from the Jordanian side was quite different. I was curious to see if it really was. When I visited the Dead Sea in Israel, we had to walk from the foot of the mountains down a long, long boardwalk over salty mineral deposits to reach the water. In Jordan, though, the water came right up to the foot of the mountains and there was very little mineral deposit along the shore. It looked completely different from the Israeli side, but was still a beautiful site!

Petra Kitchen

After a long day of walking around the ruins of Petra, three of us decided to take a cooking class at the Petra Kitchen, a restaurant in Wadi Musa (the modern town next to Petra) that offers nightly cooking classes in Middle Eastern cuisine.
Our course was taught by a Jordanian chef and his Egyptian assistant, who were both great and made the evening a ton of fun. We had quite a menu to prepare. For mezza, we fixed green wheat soup (chicken stock, wheat, onion and spices), Arabic salad (tomato, cucumber, mint, parsley), baba ganuj (eggplant dip), galaya bandura (spicy sauteed tomatoes) and foul (a common dish made of fava beans). The main course was sawani dajaj (a pan-roasted chicken dish with potatoes, tomatoes and onions). We had such a blast fixing all the dishes and then sat down to enjoy the delicious meal. At the end of the night, we were even given copies of the recipes to take home with us to try to duplicate on our own. I can't wait to give them a shot!

Petra

Perhaps the most famous site in Jordan is Petra, the "ancient rose-red city of the Nabataeans, Arabs who controlled the frankincense trade routes of the region in pre-Roman times" (according to the Lonely Planet). This weekend I hopped a plane to Amman, the capital of Jordan, met up with a friend who was there for work and rented a car to drive three hours south to see the ancient city.

I had been so busy with work during the week leading up to the trip, that I hadn't done much reading about the site before I arrived. Pretty quickly, though, I decided that wasn't necessarily a bad thing. Rather than knowing just what to expect and just what I was going to see, I wandered through the ancient ruins encountering surprise after surprise. It was a perfect example of one of my favorite Paulo Coelho quotes, "at the same time, since all things are new, you see only the beauty in them and feel happy to be alive."

Just inside the gate that marks the entrance to Petra, there are a few caves carved into the rock walls lining the path. Not too far down the path is the Obelisk Tomb and Bab As-Siq Triclinium, which was an impressive first sight to see (though not nearly as impressive as the things to come, I later realized!).
From the Triclinium, we passed a few more caves before arriving at the entrance to As-Siq. The Siq marks the ancient entrance to Petra and is an impressive, narrow gorge between rock walls that rise up as high as 80 meters! The Siq itself is 1200 meters long (appx. 12 football fields!) and was formed by tectonic forces that literally pulled the rock apart to create the passageway.
The journey through the Siq was incredible, with beautiful rock colors and formations, tons of twists and turns in the path and even tiny alters carved into the walls along the way. With so many things to observe within the Siq, its end comes seemingly out of nowhere. And just as you exit the Siq, you find yourself face-to-face with Al-Khazneh, also known as the Treasury. There are not words to describe how impressive the Treasury is, especially when it appears before you after a long walk through the Siq. The building face is carved into the stone wall and was created as a tomb, though it has been misnamed the "Treasury" by a local belief that an Egyptian pharaoh hid his treasure here. (Another random fact, the Treasury was made famous by "Indiana Jones and the Last Crusade.")
Beyond the Treasury, the path that began as the Siq continues, though the path is much wider and the walls less towering here. This area is known as the Street of Facades and is lined with over 40 ancient tombs.
Just past the Street of Facades are the Royal Tombs, carved higher on the rock face with more ornate and impressive details than the tombs of Street of Facades. Unfortunately these tombs have been affected by erosion over the years, so they show a little wear and tear, but they are still stunning. The largest of the Royal Tombs is the Urn Tomb which was carved around 70 AD and used in the fifth century as a Byzantine church. We spent a good bit of time climbing around and through this tomb and marveling at its beauty.

The Urn Tomb (on the left side of the picture)

Main chamber inside the Urn Tomb
The natural colors of the rock on the ceiling inside the Urn Tomb

On the first level of the Urn Tomb, looking up to higher levels

When we were satisfied with our exploration of the Royal Tombs, we continued toward the city centre of ancient Petra. The road leading to the city centre is called the Colonnaded Street and was once lined with temples, public buildings and shops.

Colonnaded Street

Looking up to the Great Temple

Inside the ruins of the Great Temple, facing the main altar

Inside the ruins of the Great Temple, looking back toward the Royal Tombs

After passing through the city centre, we continued our journey toward the furthest site from the entrance to Petra (appx. 6 kilometers, or 4 miles, from where we had started at the entrance gate). Ad-Deier, or the Monastery (named for its use by the Byzantine church), is perhaps the most impressive (in my opinion) of the sites at Petra. The hike from the city centre to the top of the hill where the Monastery is found takes around 45 minutes and includes over 800 stairs, but the trip is most definitely worth it!
Further past the Monastery are a couple view points that look out over Israel and the Palestinian Territories. The views were nice, but I think the most impressive view was looking back toward the Monastery, which really put everything into perspective.

Looking back toward the Monastery

With Israel and the Palestinian Territories in the background

After visiting the Monastery and view points, we were exhausted from the heat and the hiking and hauled ourselves back down the mountain, where we took a quick break and then headed back toward the entrance. It was a long day, but so nice to be outside in fresh air and seeing so many incredible ancient sites!

Hear ye, hear ye

This morning I received word that the Egyptian government had issued a decree (thus the "Hear ye, hear ye" title) related to the control of H5N1, also known as highly-pathogenic avian influenza (HPAI). For just the very briefest of moments – and I do mean the very briefest; the thought couldn’t have lasted more than perhaps half a second – I was excited.

You see, Egypt has been hit by the H5N1 influenza strain harder than any other country in the world outside Asia. When the total number of cases is considered, and even when Asia is included, Egypt still falls third on the list, after Indonesia and Vietnam. However, unlike Indonesia and Vietnam and most other countries where H5N1 has been reported, the number of cases in Egypt is not decreasing. Already this year there have been 30 cases. Compare that with 18 cases in 2006, 25 in 2007 and 8 in 2008, and it’s not hard to see that over a third of all cases of H5N1 in Egypt have occurred this year – and it’s only the beginning of August! Not only that, but there hasn’t been much H5N1 reported elsewhere in the world in 2009; over 80% of all cases of H5N1 reported this year are in Egypt.

Another interesting fact about the cases in Egypt thus far this year is that only 4 patients (13%) have died from the virus. Although this may still seem like a high mortality ratio for an influenza virus, it’s very low relative to the average for H5N1, which is around 60% (or 64% if this year’s cases in Egypt are excluded).

Still, perhaps the most interesting aspect of this year’s cases of H5N1 in Egypt is the demographic affected by the disease. The vast majority of cases have occurred not among young men working on poultry farms or young women slaughtering chickens at home. Most cases have been among children and toddlers as young as eighteen months. Although there are a number of theories circulating about this shift in the age distribution of cases, the most believable (in my opinion) is rather simple. In rural areas of Egypt, where many families raise chickens and other poultry in their households for food and sustenance, it is common when it gets cold to bring the poultry inside the house for protection against the cold. Once inside the house, the children, who often already consider the chickens their pets, play with the poultry in very close quarters. Thus they are exposed to H5N1 and contract the virus. Voilà.

So, in summary, there’s a deadly disease circulating in Egypt that’s killed a high percentage of the people it’s infected and now it’s infecting a lot of very young children. And the government issued a decree today that it’s going to do something about it. As I already said, I was excited.

But then I realized that this decree was coming from the same government that ordered the culling of all the swine in the country when H1N1 – a strain of influenza that has never been transmitted from a pig to a human, that has never even been isolated in swine – broke out in the United States. I immediately knew the decree was going to be disappointing, and I was right.

The government of Egypt has now decreed that all official poultry farms will be moved out into the desert (a.k.a. the middle of nowhere) so as to eliminate any proximity to humans and strict biosafety measures will be implemented. At the same time, all unofficial poultry farms will be closed.

Now, if poultry farmers were the ones being affected by H5N1, this might seem like a logical and effective plan. Unfortunately, however, it seems to be just another attempt by the Egyptian government to show that they’re doing something, whether or not that something is appropriate.

Martha Stewart in Cairo

Summertime has been pretty quiet in Cairo. I haven't been traveling for work nearly as much as usual, and it's been way too hot to get excited about doing anything outside, so I've spent a good bit of time inside my flat.

I've taken on a few projects around the place and now have all kinds of ideas for painting walls and redecorating and the like. (You may need to refer to this post to understand why I feel the need to redecorate.) You might say I've been paying more attention than usual to the Martha Stewart-esque side of my personality. My most recent project has been to re-cover most of the furniture. I guess blue and yellow floral stripes just aren't my thing. And neither are black and gold Asian prints.

I started with the dining room chairs since they seemed easiest and posted the progress a while ago. Recently I decided to tackle the living room furniture. I knew this was an entirely new game for me. The dining room chairs project required nothing more than a pair of scissors, a hammer and a staple gun, but I knew the living room would require an actual sewing machine.

I thought I might want to purchase a sewing machine so I began looking. After about three weeks, I concluded that a sewing machine must be an incredibly difficult commodity to track down in Cairo, because I hadn't been able to find a single one. Thankfully, one of my colleagues told me that she had one and offered to loan it to me. I was thrilled at the prospect and took her up on the offer, ignoring her warnings that it's "a little old". I assured her it would be just fine.

I stopped by her flat one day after work to pick up the machine and quickly discovered that it was more than just "a little old". The machine weighs about 46 pounds (ok, that may be a slight exaggeration), comes with a bag of random metal pieces and a can of oil, and I'm pretty sure it hasn't been used in several years. I was terrified I would break it and intimidated, to say the least.
But thankfully, the antique sewing machine came with a small instruction booklet that, while also antique itself, was quite helpful, even if I was scared that the book itself would disintegrate any second!
Anyway, it wasn't nearly as bad as I had expected. I haven't finished quite finished the seat cushions, but I'm pretty proud of my accomplishments so far, so I thought I'd post a couple pictures of my progress.
(I know this is a little off the usual travel/social justice/health subjects about which I usually write, but it's another side of me and has taken up a lot of my time lately, so I had to go ahead and post it. Hope it's not too boring!)

Contruction elevator

There is no way that packing this many people into a tiny elevator over twelve stories in the air on a construction site can possibly be a good idea. It made me nervous even just to catch a glimpse of it out of the corner of my eye while at dinner tonight.