578 Influenza Patients in SL: Or is it the MERS-CoV (Update)

The Nation reports that  4 people have died and 578 have been diagnosed with Influenza. The symptoms are fever, dry cough, muscle and joint pain, tiredness and extreme exhaustion, prolonged headache or sore throat.

Meanwhile there is a MERS-CoV (Middle East Respiratory Syndrome)  initially named Novel Corona Virus (nCoV) that has been affecting Gulf Countries and has also spread to UK and France.

Update:  June 03-2013
Has spread to Italy, 3 cases detected

The Center For Disease Control (CDC) reports

From April 2012 to May 2013, a total of 33 people from Saudi Arabia, Qatar, Jordan, the United Kingdom, the United Arab Emirates, and France were confirmed to have an infection caused by the novel coronavirus.

• Saudi Arabia: 24 people; 13 of them died
• Qatar: 2 people; both survived
• Jordan: 2 people; both died
• UK: 3 people; 2 died, 1 recovered
• UAE: 1 person; died
• France: 1 person, receiving treatment 

Symptoms of novel coronavirus infection?
Most people who got infected with the novel coronavirus developed severe acute respiratory illness with symptoms of fever, cough, and shortness of breath. Only two people experienced a mild respiratory illness

Update June 1st

Of the 50 people who contacted the disease 30 died.
The authors of the study estimated the incubation period at 9-12 days, a long time in which infected people could spread the disease without realizing that they are ill. It still isn’t certain at what stage people carrying the virus are most contagious, the Los Angeles Times reports.
Another concern is that the virus is difficult to identify. Yet doctors could not confirm the presence of the MERS virus in the youngest of the patients, and were not able to confirm it in the two who died until after they passed away.

For more information, see the World Health Organization (WHO).

via http://www.zerohedge.com/news/2013-05-12/two-people-dead-sars-virus-saudi-arabia-two-more-infected-france

Vinegar a Test for Cervical Cancer

In Sri Lanka about 1,250 cases of cervical cancer are detected each year.  Nearly 50 percent of the patients die each year and is the second most dangerous cancer amongst women after breast cancer (LBO). Testing for cervical cancer in its initial stages is done by a Pap smear which requires laboratory work.

Now there is a simple visual test for cervical cancer using vinegar.

Excerpts

A simple vinegar test slashed cervical cancer death rates by one-third in a remarkable study of 150,000 women in the slums of India, where the disease is the top cancer killer of women.

This study tried a test that costs very little and can be done by local people with just two weeks of training and no fancy lab equipment. They swab the cervix with diluted vinegar, which can make abnormal cells briefly change color.

"It's just not possible to provide Pap smear screening in developing countries. We don't have that kind of money" or the staff or equipment, so a simpler method had to be found, Shastri said.

More progress against cervical cancer may come from last month's announcement that two companies will drastically lower prices on HPV vaccines for poor countries. Pilot projects will begin in Asia and Africa; the campaign aims to vaccinate more than 30 million girls in more than 40 countries by 2020.

via http://www.nakedcapitalism.com/2013/06/links-6313.html
http://news.yahoo.com/vinegar-cancer-test-saves-lives-india-study-finds-113800022.html

Vijaya Kuveni: Paradigm for M mtDNA in South Asia

PCA (left) and Admixture Bar (right)  plot

All Sri Lankans know the story of Vijaya and Kuveni from the Mahavamsa and Rajavali.  The basic crux of the story is that invaders, predominantly male married local women.  The gist of what DNA research is saying is that in India (and for Sri Lanka*) our mothers ancestry (mtDNA) is the same, but our paternal lines (Y-DNA) can be different.  One paper found that 70%  of India including 26 tribal populations carried the M mtDNA haplogroup.   In the Harappa DNA project 50% of the few Sri Lankan participants (8) had M mtDNA.  Two of the four self identified Tamils and two of the four self identified Sinhalese.
(* my extrapolation)

Before I get to excerpts of the research articles a few words on the PCA (Principal Component Analysis) plot on this page.  Its one of the few plots that I have seen where PCA captures the geographic distribution without a geo position data in the PCA analysis.  What I am trying to say is the V shape of India's genetic Cline is evident in the in the PCA Plot.

 From Chandrasekar et al

Macrohaplogroup M is ubiquitous in India and covers more than 70 per cent of the Indian mtDNA lineages The lineages M2, M3, M4, M5, M6, M18 and M25 are exclusive to South Asia, with M2 reported to be the oldest lineage on the Indian sub-continent.

The deep rooted lineages of macrohaplogroup ‘M’ suggest in-situ origin of these haplogroups in India. Most of these deep rooting lineages are represented by multiple ethnic/linguist groups including tribals of India

From Discover Magazine

An interesting point though is that the mtDNA, the female lineage, does not seem to diverge from other South Asians much at all. I find it intriguing that this is the same pattern we see along the major NW-SE axis of variation. It seems that mtDNA lineages unite South Asians, while the Y lineages separate them (by caste and region). The generality has many exceptions, but it points to a peculiar sex mediated admixture process from both the northwest and northeast. Men on the move have reshaped the genetics and culture of South Asia, but the mtDNA lineages still point to an ancient Eurasian group with distant but stronger affinities to the east than the west. The mtDNA are likely the purest distillation of ASI (Ancestral South Indian). 

From  Witas et al in PLOSone

Ancient DNA methodology was applied to analyse freshly unearthed remains (teeth) of 4 individuals. Dated to the period between 2.5 Kyrs BC and 0.5 Kyrs AD the studied individuals carried mtDNA haplotypes corresponding to the M4b1, M49 and/or M61 haplogroups, which are believed to have arisen in the area of the Indian subcontinent during the Upper Paleolithic and are absent in people living today in Syria . 

Studied remains were excavated at two archaeological sites in the middle Euphrates valley and dated between the Early Bronze Age and the Late Roman period. The obtained data enrich the as yet modest database of Mesopotamian ancient DNA and suggest a possible genetic link of the region with the Indian subcontinent in the past leaving no traces in the modern population.

Update
This means the genes of prehistoric people are still prevalent among modern Sri Lankans

We report here the first complete mitochondrial sequences for Mesolithic hunter-gatherers from two cave sites. The mitochondrial haplogroups of pre-historic individuals were M18a and M35a. Pre-historic mitochondrial lineage M18a was found at a low prevalence among Sinhalese, Sri Lankan Tamils, and Sri Lankan Indian Tamil in the Sri Lankan population, whereas M35a lineage was observed across all Sri Lankan populations with a comparatively higher frequency among the Sinhalese.

First AASI mtDNA genomes from Sri Lanka (2500 and 5500 BC)
Please Read comments as well, knowledgeable
https://www.brownpundits.com/2022/11/30/first-aasi-mtdna-genomes-from-sri-lanka-2500-and-5500-bc/

Also see:

Sinhalese and Tamil DNA Admixture Analyis
My DNA 01: Heroin Addiction, Smoking etc
Sri Lankan Population DNA Genetics 01
Basic Primer on Population DNA Genetics
List of reference and excerpts

Sivalingam Sivanathan named a White House Champion of Change

Sivalingam Sivanathan,  Professor of Physics and Director, Microphysics Laboratory at UIC  has been named a White House Champion of Change .  He is a graduate of the University of Peradeniya (1980) and also  Faculty Adviser  of the Sri Lankan Graduate Student Association at University of Illinois at Chicago (SLGSA).

University of Illinois Press Release

Sivalingam Sivananthan, Professor of Physics at the University of Illinois at Chicago, has been named a White House Champion of Change. He was presented with the honor at a ceremony this morning at the White House.

Sivananthan’s work with a semiconductor material, mercury cadmium telluride or MCT, is at the heart of night vision technology and made the raid that took down Osama Bin Laden on a moonless night possible. Developing “technology that protects our protectors” has given him the opportunity to give back to his adopted country, said Sivananthan.

 Sivananthan is the founder of the high-tech, Bell-Labs-styled incubator, Sivananthan Laboratories, Inc. in Bolingbrook, Ill. The Laboratories’ focus is on infared technology, radiation detection, materials research and biosensors.

Because, at its most fundamental, MCT technology is about transforming light into electricity, Sivananthan is also leading an effort to develop next-generation solar power. To that end, he helped found InSPIRE (the non-profit Institute for Solar Photovoltaic Innovation, Research, and Edu-training), whose mission is training Illinois’s workforce and exciting Illinois undergraduate and high school students to create a renewable energy and solar eco-system in Illinois.

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β-Carotene for Ice Cream produced from Algae

May or may not really be made of people

β-Carotene is also used as a substance to colour products such as juice, cakes, desserts, butter, ice cream and margarine. It is approved for use as a food additive.  One of the many steps toward Soylent Green.

The photograph is of a β-Carotene alage farm in Kalbarri, Western Australia

About β-Carotene from wiki
Most of the world's synthetic supply of carotene comes from a manufacturing complex located in Freeport, Texas and owned by DSM. The other major supplier BASF also uses a chemical process to produce β-carotene. Together these suppliers account for about 85% of the β-carotene on the market. In Spain Vitatene produces natural β-carotene from fungus Blakeslea trispora, as does DSM but at much lower amount when compared to its synthetic β-carotene operation. In Australia, organic β-carotene is produced by Aquacarotene Limited from dried marine algae Dunaliella salina grown in harvesting ponds situated in Karratha, Western Australia. Cognis Australia Pty. Ltd., a subsidiary of the Germany-based company Cognis, is also producing β-carotene from micro algae grown in two sites in Australia that are the world’s largest algae farms. In Portugal, the industrial biotechnology company Biotrend is producing natural all-trans-β-carotene from a non genetically modified bacteria of the Sphingomonas genus isolated from soil.

β-Carotene algae farms Kalbarri, Western Australia

Groundwater Depletion, Chronic Kidney Disease (CKDu) and Jaffna River Project

From Hidayathulla and Karunaratna

A recent research article by Thushyanthy Mikunthan and C.S. De Silva highlight the accelerating
depletion of the limestone groundwater aquifer in Jaffna peninsula. There are two serious concerns that need to be addressed because of this.

a) As the authors point out, with thousands of people returning to settle in the former war zone, groundwater extraction is bound to increase, resulting in  shortages of water supply in the Jaffna peninsula for agriculture and domestic use.

b) With pesticides and fertilizer runoff seeping into the groundwater  the main source of drinking water in the Jaffna peninsula, kidney and other health issues are going to become more common.  I think the Chronic Kidney Disease (CKDu) prevalent in Anuradhapura will be be a walk in the park, compared to what is probably in store for the Jaffna dwellers.   CKDu incidence in Jaffna has been low probably because agriculture and use of fertilizer/pesticides were minimal due to lack of access to markets in the South during the civil war.

Background on Chronic Kidney Disease (CKDu).

The majority of CKDu patients are from the Anuradhapura, Polonnaruwa, Kebithigollewa, Girandurukotte, Padaviya, Vilachchiya and Ampara  areas. In the Anuradhapura area CKDu prevalence averages around 12% and affects more women (62%)  than men (32%).  The disease progresses slowly and majority of patients do not have any symptoms until they are in the late stages of the disease

Many causes have being attributed to CKDu excessive cadmium in the natural environment; high levels of fluoride in drinking water; using fluoride-rich water in low quality aluminium pots; “hard water” with higher than normal levels of minerals; and toxins generated by blue-green bacteria in the water and of course Arsenic.  My untested opinion is that dioxins too may be a cause (see Dioxin causes Kidney Disease: Alternative Explanation to Arsenic). If Dioxins are one of the causes of CKDu then not just the individuals exposed, but potentially the great-grandchildren may experience increased adult-onset disease susceptibility.

So what can be done

a) Better testing and monitoring of ground water (and blood).
b) Increased rain water collection and harvesting.
c) Controlled use of Fertilizer, Pesticide

Testing and Monitoring of Ground Water 

Ms. Thushyanthy Mikunthan has publications on water quality.  However, the analysis are for rudimentary components, e.g. chloride, iron and sulphate concentration, total alkalinity, total dissolved solids,  pH and Nitrate.  Let alone dioxins and dioxin-like product, metals or arsenic are not tested.  Most likely this is because the equipment and material needed for sophisticated testing (e.g. HPLC's) are unavailable in Jaffna and/or testing in Colombo is cost prohibitive.

So maybe its time to consider a project to test/monitor groundwater for metals, dioxins and dioxin-like chemicals.  Maybe donation of instruments, or a collaborative research project to link agricultural use, dioxin content in ground water incidence CKDu and effect of alleviation methods such as rain water harvesting.

Increased rain water collection and harvesting

The biggest project for Rainwater collection that has been proposed and partially completed is the Jaffna River project. The basic concept is to create fresh water lakes from the Elephant Pass, Vadamarachchi and Upparu lagoons, by preventing saltwater intrusions.  More details from D. L. O Mendis in the Daily News. 

As  Dr Rajasingham Narendran says
The ‘ River for Jaffna’ project, which is vital for Jaffna is stalled , although considerable work has been recently done. The Elephant Pass lagoon has been isolated from the sea on both sides. I was pleasantly shocked to learn yesterday at a seminar on water resources that this work was completed by the government in 2008, amidst the war. Further, after the war the Thondamanaru and Ariyalai barrages have been reconstructed. However, the construction of the Mulliyan canal to connect Elephant Pass reservoir with the Vadamaracchchi lagoon has not commenced. The bund of the Iranaimadu tank has been raised preventing a natural spill into Kanagarayan Aru and flow into the Elephant Pass reservoir. Mr. Anandasangari is leading the effort against Iranaimadu waters spilling over to fill the Elephant Pass reservoir. It is imperative that the government make the visionary river project for Jaffna of the Late Engr. Arumugam come true. There can be no greater blessing for Jaffna. This project if completed will make Jaffna bloom in every possible way – agriculture, tourism, inland fisheries, industrialisation fresh water availability, good quality ground water availability, greenery etc.,

Resources
http://www.scidev.net/en/south-asia/news/jaffna-aquifer-depleting-from-overuse.html
http://idosi.org/aejaes/jaes7%281%29/15.pdf
http://www.gsslweb.org/home/files/109-113-hidayathulla-final.pdf
http://archive.riversymposium.com/index.php?element=ARUMUGAM

Water Resources Development, Jaffna Peninsula by  K. Shanmugarajah, Fast Books, Australia, 1993

 

Rock The Past: Brian Knower and Christo Dhason

Its another Friday, Vesak in Sri Lanka, Memorial Day weekend in the US.

A few days back saw a post by/about Nirmalan Dhas and thought it was the same Dhas I knew many years ago.  My classmate Shantha Weerakoon set me straight.  It was Christo Dhasan.  It brought back memories of Kokos and the Colombo Rock scene in the late 70's.  The times that Aruna Batuwantudawe (passed away), Richard Simon and I were regulars at Kokos.  Maybe semi regulars,  I had to raise money by giving tuition for entry fees and other ancillary (hmm..) expenses.  I think Richard and Batu had similar issues. A couple of times we met another classmate G. H. T. de Silva who also played with a band and was featured at Kokos.  GHT was the youngest of the GH* de Silva brothers (GHT where the hell are you ?)

Back to Kokos.  Kokos was owned by Darup Peiris a Thomian, Brian Knower and Christo Dhason were also Thomians and  I think classmates of Darup.  So, think Kokos was let out at minimal cost for these occasions. 

Brian Knower's site: http://bryanknower.com/  and music http://www.reverbnation.com/bryanknower
Please Check out 60's Top of the Pops  as well

http://www.sundayobserver.lk/2004/04/18/mag05.html  some where they seem to have forgotten Kumar Navartnam who did the Havelock Park concerts before we were old enough to attend.