Saturday, December 31, 2011

To Uplift Science, Nepal Needs him who Published An Obituary in Nature (Journal)

Recently, Prof. Dr. Uttam Lal RajBhandary has published an obituary [1] of Har Gobind Khorana in Nature, one of the most reputed and famous science journals. Har Gobind Khorana (HGK), Nobel Laureate, chemical biologist, was born in Raipur, Punjab, Pakistan (then India) passed away on 9th November 2011. He, along with Marshall Nirenberg, Heinrich J. Matthaei, and Robert W. Holley, had discovered sequences of RNA (UUU, UGA, AUG…… codons) that code for amino acid synthesis and they received the Nobel Prize in 1968.  Prof. UL RajBhandary, Department of Biology, MIT, USA, has been in close association with him since 1962. Quoting HGK’s statement Prof. UL RajBhandary writes, “If you want to get far, you have to travel alone.” To understand science and research, it needs very much enduring patient and deep study, and sometimes makes isolated from normal social life.  In past post of this blog, I had mentioned the name Lujendra Ojha and Deepak Koirala, Nepali bright young scientists who had published their research article in reputed journal this year.

Achievements of Prof. Dr. Uttam Lal RajBhandary / RajBhandary UL,
Scholar Google: - Citations: 9759; Cited Publications: 232; H-Index: 56
Iisiknowledge: - Times Cited: 7153; Results found: 169; H-Index: 46
Pubmed: - Articles: 187

These articles, where Prof. Dr. Uttam Lal RajBhandary is the author and all of them having impact factor above 5.0 including Nature (Impact factor is 36.1), Nature Biotechnology (Impact factor is 31.1), Cell (Impact factor is 32.4). This is a huge achievement and impressive figure, and probably it may be the highest for any Nepali and gives us happiness with the proud. Almost all scientists will to publish their findings to any one of such prestigious journals.

While I was in class 8-10, our science teacher always used to tell about Har Gobind Khorana, and his contribution to science. At the same time, in various newspapers and magazines particularly in Nava-Yuva, I could see the name of Prof. Uttam L. RajBhandary, Prof. Dayananda Bajracharya, and another few names as the successful Nepali scientist. Nava Yuva, and Yuvamanch were my favorite magazines and hardly had left any issue unread. Because, it always had included at least one article related to science and technology. USA, Russia, UK, Germany and France were frequently cited countries in those magazines. Nowadays, I rarely see the name of Russia in the journals, despite it still has been contributing to science.

Historic buildings, arts, sculptures, statutes, Ayurveda and traditional medicine, etc. are still giving proof that Nepal was leader of ancient science and architecture. For the past two centuries, Nepal has been always in a Dark Era for modern science and technology and becoming in a terrible condition. The condition is worsening day by day. In fact, it is situated almost in the bottom line in several indexes. Such a high profile scientist like Prof. Dr. Uttam Lal RajBhandary can contribute to the development of science and technology in Nepal with international collaboration. The equipment and funding are the biggest challenge for Nepal, are more important in addition to knowledge and hardworking, which we are doing (fruitlessly). Other panic part, we know our government neither knows the importance of science nor allow budget and even, I am doubtful, whether provided or not,  moral support to scientists from the government. Ministry of "science and technology" was established to make happy to some political leaders to include them in cabinet rather than to ease science and technology practitioner, what a shame for us.
However, Happy New Year 2012, Adieu 2011.

1 RajBhandary, U. (2011). Har Gobind Khorana (1922–2011) Nature, 480 (7377), 322-322 DOI: 10.1038/480322aResearchBlogging.org

Wednesday, December 07, 2011

Install OpenBabel in Fedora 16 to convert chemical file formats

OpenBabel is a software that has been widely used by computational chemist. Usually the structure of any compound are drawn using mainly ChemDraw and ACD ChemSketch  softwares and default file format are .cdx and .sk2, respectively. But for the computational study the required file format are; .mol2 or .pdb etc. OpenBabel can convert as pr required.

People who are lazy in typing may become tired in typing "babel [-i (input-type)] (name) [-o (output-type)] (name)" many times to convert the individual files. They may seek to install the graphical version of OpenBabel by the command "cmake ./openbabel-2.x.x -DBUILD_GUI=ON" but thay may face a lot of difficulties in many Linux Distros such as to install wxWidget.

As I have been mentioning Fedora, a kind of Linux operating, is the leader NOT a follower, many latest Linux software repository can be acquired easily in Fedora through yum. Similarly it is very easy to install OpenBabel in Fedora 15 and 16.

  1. Become root by typing su and then your root password.
  2. Type yum install openbabel-gui
  3. wait and then press y.
It will be installed within 10-15 minutes and enjoy.

Monday, November 14, 2011

PhD opportunity for Nepalese

We are lacking of equipment, funds, opportunity, and the policy makers who had never try to understand the value of science so that we have no reputation despite our honesty and laborious work. But we have strong theoretical background in TU and other Universities of Nepal due to tough syllabi/syllabuses  and competition. Erasmus Mundus Europe Asia (EMEA) scholarship has given high priority for Nepalese, and offering full-funded MS, PhD and post-doc positions in different universities of Europe. Nepali passport bearer who completed MSc or 4-year BSc are eligible to apply. Probably, stipend will be 1000-1600 Euro/month. Dead line is December 1, 2011. Click here for more information, also visit about TWAS scholarships.

Wednesday, November 09, 2011

Update Mendeley, Reference Managing Software

Due to different styles of references for thesis or articles to be submitted in different journals or departments, reference managing software is exigent nowadays. Mendeley is a freely available reference managing software, which is the most suitable for Linux user, however, Windows user can also use it. Endnote is another good option for Windows user but we have to pay for license.
        Full version of Mendeley 1.1.3 was released few months ago, download from here.

  1. Extract to your suitable folder e.g., to /media/sda5/softwares
  2. Run by clicking icon "mendeleydesktop" on the location of /media/sda5/softwares/mendeleydesktop-1.1.3-linux-i486/bin
  3. Go to "tools" and "Install OpenOffice Plugin" or "Install LibreOffice Plugin" (if you see the message "it won't find "unopkg" in its default location...................... or something like this" then, locate towards /opt/libreoffice/program and click "unopkg" )
  4. Click on "Add Documents" and locate any one PDF and add
  5. Open "LibreOffice Writer" or "OpenOfficeOrg writer" (equivalent of MS Word) and write something
  6. Click "Insert Citation" then go to Mendeley Desktop and click the PDF in the document section just you have added (BibTex or other format can be added)
  7. Click "send citation to word processor"
  8. Then go to word file and click "insert bibliography"
Enjoy
you can choose different citation styles according to your requirements.

Friday, October 21, 2011

Arthritis (बातज्वर), Molecular Mechanism of Pathogenesis

Please wait for few seconds in case of slow internet.
View my previous abstract post on Pathogenesis of Arthritis

Tuesday, October 11, 2011

Cannot Nobel prize be awarded for Windows OS, Google or Facebook ?

Announcement of Nobel prize soothed pounding of many people. Although no Nepali has been awarded, Nobel prize is the subject in the gossip of literate Nepali. Nobel prize has been becoming the dream and destination not only for scientists but also for politicians, economists, writers and so on. Nobel prize is intended for new discovery, or significant contributor who made life easier and well organized society.

The first step in the discovery of theory or science is the designing of research through literature search. Some search engines certainly have signified and accelerated in this process. There are many search engines, and Google is the widely used and popular. Google search engine script was discovered by Larry Page and Sergey Brin as PhD candidates at Stanford University. 

Analysis and data interpretation of research and experiments needs software for promptness and accuracy. The software needs good platform to be installed. Bill Gates and his colleagues had discovered and developed the popular operating system (OS), DOS, Windows. Mac OS, Unix, Linux, FreeBSD, etc. are the other OS, but still they  are not as popular, and easier as Windows OS. In addition, Microsoft has developed the office packages (Word, Excel, PowerPoint, etc.), which are also essential in research. Nobel prize in Physics has been awarded for research of hard disk miniaturization (2007), and development of integrated circuits (2000), which are essential part of computer hardware. I think, Software developer also has the similar type of contribution and deserves for the Nobel prize. 

Facebook and twitter, however, are not essential in the scientific study, but they are popular among the community and  are good medium to increase the relationship and information. And Facebook is the top web page based on the number of users everyday.

In my opinion, the famous novel, Harry Porter, Miscrosoft OS, Google, Facebook, Twitter, or their designer deserve Nobel prize in literature. Probably, there would be a policy, not to award Nobel prize who had gained popularity and money.

If Nobel prize is awarded for these computer applications, which category would be appropriate for them? Physics, due to the scripts design and engineering? Economics, as these are among top revenue generating companies? Peace,  because Facebook and Twitter had played an important role to dethrone the tyrant of Egypt and other countries. some people may think reverse of it, people agitated and involved in violence due to Facebook and Twitter.

Friday, September 30, 2011

Medicinal Plants in Nepal, Acorus calamus (बोझो)

Since antiquity, man kind has been using plants to treat many diseases and some of these traditional medicines are still included as part of the habitual treatment of various maladies. Nepal also has been relying on locally available medicinal plants and in some remote area of Nepal, still there is few option for modern allopathic treatment. I am posting in serial, some of these important medicinal plants that are frequently used.

Acorus calamus L. (English: Sweet flag; Nepali: बोझो)
It belongs to the family Araceae. It is an erect herb with aromatic rootstock, leaves broad, ensiform, with distinct midrib. Spathe cylindrical and slightly curved. Flowers: bisexual, each with a perianth of six orbicular concave segments, stamens 6, ovary conical, fruits: oblong berries.
Constituents: Monoterpene hydrocarbons, sequestrine ketones, asarone (2, 4, 5-trimethoxy-1-propenylbenzene), and β-asarone contained in the essential oil distillates from root .
Uses: It is used as an analgesic for the relief of toothache or headache, to cure /prevent a hangover, to treat a cough, as a carminative for colic, to treat diabetes, to reduce bowel pains, to lessen swelling and for constipation, to cure fevers, for asthma and bronchitis, and as sedative. It exhibited a good anti-fungal activity as well.
References:

  1. Joshi KK and SD Joshi. Genetic Heritage of Medicinal and Aromatic Plants of Nepal Himalayas. Buddha Academic Publishers and Distributors Pvt. Ltd., Kathmandu, Nepal. P-239 (2001).
  2. Bajracharya MB. Ayurvedic Medicinal Plants and General Treatment. Piyusavarsi Ausadhalaya Mahaboudha, Kathmandu, Nepal. P-230 (1979).
  3. Devkota KP, R Acharya, MP Baral and RP Adhikari.  Antimicrobial activities of some herbal plants used in traditional medicine in Nepal. In: Proceding of 3rd national conference on science and technology. Vol 2: 1311-1317. (1999).
contd....

Friday, September 23, 2011

महिलाहरुमा autoimmune रोगको सम्भावना ज्यादा हुने कारण

चालिस बर्ष उमेरपछिको स्थिती हेर्ने हो भने, पुरुषलाई भन्दा महिलालाई auto-immune रोग लाग्ने सम्भावना तीन गुणा धेरै हुन्छ । अहिले सम्म पाइएको तथ्याङ्क अनुसार, महिला : पुरुष = ३:१ छ । मेरो लेख, Auto-immune रोग के हो त ? हालसालै गरिएको अध्य्यन अनुसार महिलाहरुमा auto-immune रोगको सम्भावना ज्यादा हुने निम्न कारणहरु पत्ता लागेका छन् ।

  1. Estrogens (oestrogens) हार्मोन महिलाहरुमा उत्पादन हुन्छ भने पुरुषहरुमा testosterone हार्मोन । estrogens हार्मोनले immune system ज्यादा सकृय हुन उत्प्रेरणा दिन्छ ।
  2. मानव शरीरमा २३ जोडा अनुबशिंक तत्वहरु (chromosomes) हुन्छन् । प्रत्येक जोडामा एक-बाबु तथा एक-आमाबाट आएका हुन्छन् । पुरुष र महिलामा २२ जोडा chromosome एकै किसिमका हुने भएता पनि २३ औं जोडा भने फरक हुन्छ । २३ औं जोडामा XX (महिला), XY (पुरुष)हुन्छ । यहीँ X chromosme मा immune प्रणालीलाई ज्यादा सकृय बनाउने केही रसायनहरु उत्पादन गर्ने अनुबशिंक तत्वका ईकाइहरु (genes) रहेका हुन्छन् । महिलाहरुमा X-chrosome दुइवटा हुनाले पुरुषको तुलनामा यस्ता रसायन हरु पनि दुईगुणा बढी उत्पादन हुन्छन् । हुन त gene दुईगुणा भयो भन्दैमा त्यसको उत्पादन पनि अनावश्यक रुपमा दुईगुणा नै हुन्छ भन्ने त होइन । नचाहिएको एउटा gene लाई छोपेर राख्ने र यस्को उत्पदन हुन नदिने अर्कै प्रणाली हुन्छ, यदी यो प्रणाली बेकार भएमा मात्र महिलाहरुमा autoimmune रोगको सम्भावना ज्यादा हुन्छ।
  3. Microchimerism:- गर्भावस्थामा रहेको भ्रुण/बच्चा महिलाको रक्तसंचार प्रणाली सँग प्रत्यक्ष सम्पर्कमा रहेको हुँदैन, साल-नाल को माध्यमबाट अप्रत्यक्ष रुपमा संपर्कमा रहेको हुन्छ । तर, कारणबस महिलाको रक्तसंचार प्रणालीमा बच्चाको कोष, तन्तु इत्यादी आउन पुग्यो भने महिलाको Immune system सकृय भाईहाल्छ । यो सकृयता Helper CD4 T-cell ले स्मरण गरिराखेको हुन्छ जसले महिलालाई बच्चाको जन्म पश्चात पनि हानी पुर्याउँछ । सामान्यत: बच्चाको जन्म पश्चात यस्ता Helper CD4 T-cell आँफैँ नस्ट हुन्छन् ।

Tuesday, September 20, 2011

रोग प्रतिरोधात्मक प्रणाली ज्यादा सकृय भएर हुने रोगहरु (Autoimmune Diseases)

हाम्रो शरीरमा बाह्य हानिकारक बस्तुहरु जस्तै: जीवाणु (bacterium), बिषाणु (virus), परजिवी (parasite) इत्यादी प्रवेश हुने बित्तिकै हाम्रो शरीरको रोग प्रतिरोधात्मक प्रणाली (Immune System) सकृय हुन्छ र रोग लाग्न दिदैन । यदि यो प्रणाली कमजोर भयो भने हाम्रो शरीर भित्र प्रवेश गर्ने जीवाणु/ बिषाणु/ परजिवीहरुले तुरुन्त आक्रमण गरिहाल्छन् र हामीलाई रोगहरु जस्तै: झाडा-पखाला, रुघा-खोकी, क्षयरोग, इत्यादी. लाग्छ ।

AIDS वास्तवमा आफैंमा कुनै रोग होइन तर यसले चाँही हाम्रो immune system लाई यती कमजोर बनाइदिन्छ कि निको नै नहुने गरी, अनी सबै किसिमको (सरुवा) रोगहरु लाग्छ र मृत्‍यु हुन्छ ।

तर immune system ज्यादा सकृय अथवा cross reaction भयो भने पनि यसले हाम्रो शरीरका आफ्नै कोष, तन्तु तथा अङ्गहरुलाई आक्रमण गर्न सुरु गर्छ अनी आँफैमा एक रोगको रुप लिन्छ, जसलाई Autoimmune Disease भनिन्छ । यसअन्तर्गत बात (Rheumatoid Arthritis), बिसमज्वर (Rheumatic fever), दम (Allergic Asthma), खास प्रकारको मुटुको रोग (Rheumatic heart disease), Graves' disease, Lupus, Optic neuritis, Pernicious anemia, Sjögren's syndrome, Primary biliary cirrhosism, Myasthenia gravis, Diabetes mellitus type 1, इत्यादी. (यस्ता सय भन्दा बढी किसिमका रोगहरु पत्ता लागेका छन्) ।
क्रमश:

Monday, September 12, 2011

Install LibreOffice in Older Version of Fedora

As I have been writing (can be found under labels: Linux, Fedora, Computer), Linux OS has been improving in graphical user interface and other packages/applications. OpenOffice, which is one of the powerful application/package, was the Linux equivalent of MS Office (Word, Excel, Power-point, Access, etc.). Recently, OpenOffice has been replaced by LibreOffice in Linux OS probably due to license conflict. In the latest version, Fedora 15, it can installed as;

  1. Open terminal, and become root user (type "su" and then type password ".......")
  2. Type "yum install libreoffice" OR type "yum groupinstall "Office/Productivity""
In older version of Fedora (bur not older than Fedora 8), we have to
  1. Download all the required files here (Other options are available to select there, e.g., to install in Windows, ".exe" file can be selected).
  2. Extract the zipped file (mouse-right click and click on "extract here". Careful ! where does this file situated, normally it remains under home/Downloads).
  3. Open terminal, and become root user
  4. Type "yum localinstall /home/bishnu/Downloads/LibO_3.3.4rc1_Linux_x86_install-rpm_en-US/RPMS/* --nogpg" (after few seconds it will ask for permission, then type "y")
  5. Then again type, "rpm -Uvh  /home/bishnu/Downloads/LibO_3.3.4rc1_Linux_x86_install-rpm_en-US/RPMS/desktop-integration/libreoffice3.3-redhat-menus-3.3-401.noarch.rpm --force"
Note: Bishnu can be replaced by your username, or entire /home/bishnu/Downloads can be replaced by actual location of these file. But it will be easier, if we paste this folder (software) under /Downloads, if it was brought from friend's computer/purchased). The file names LibO_3.3.4rc1..... / libreoffice3.3-redhat-menus-3.3-401 are variable with the time.

Saturday, September 03, 2011

Nepalese in Reputable Science Journals

Probably, there might be some articles published by Nepalese in the famous and reputed science journals, such as science, nature, cell, etc.

Recently, Lujendra Ojha, Mhaipi, Kathmandu has discovered the possibilities of water in the Mars. This made him a famous scientist, and he has been covered in all types of media worldwide. He is an undergraduate research intern at lunar and planetary laboratory, University of Arizona, Tucson, USA. He published his finding as second author in one of the most famous journal (Science, 5 Aug 2011, 333 (6043); 740-743, impact factor of this journal is 31.4).

Another two Nepalese (Deepak Koirala and Soma Dhakal) have published their research article as first and second author in one of the most reputed journal (Nature Chemistry, 28 Aug 2011, impact factor of this journal is 17.9). Deepak Koirala, Rupandehi district, was the batch topper in MSc from Central Department of Chemistry (CDC), TU, Nepal.  Soma Dhakal, Palpa district, also did his MSc from CDC, TU, Nepal and recipient of university fellowship award for his outstanding performance in research from Kent State University, USA. Currently, both are pursuing their PhD from Department of Chemistry and Biochemistry and School of Biomedical Sciences, Kent State University, Kent, Ohio 44242, USA.

Their success not only inspires Nepalese but also shows Nepalese are capable, if got the opportunity. Almost all Nepali who had completed their MSc from Tribhuvan University, Nepal had been doing well in foreign. However, there is no reputation of Nepal in science. International journals usually reject if the corresponding author's affiliation is Nepal (personal experience). This is mainly due to unavailability of good equipments, no budget allocation for research and higher study. Receiving chemicals and reagents used in the laboratories are the expensive and slow process. Ministry of “science and technology” is the least preferred for any political parties and politicians. 

And those Nepali scientists who got the international reputation, should be a leader to develop  / install science and technology and research in Nepal, whatever might be our corrupted government thinks. So that all bright young and brilliant Nepali will get chance to show talent, and do something for science.

Thursday, September 01, 2011

Influencing Google+ Made me Switching off Facebook


Although I am beginner of google+, nowadays I am spending more time in it as compared to Facebook. Obviously, some exciting features of Facebook had been luring not only teenagers but also geriatrics. But some limitations such as  option to add as friend only, though all connected people are not friends. Few years ago, I had requested one of my teacher to add as a friend. He knew me. I am confident he knew me, however, he asked to introduce myself. Even though I introduced myself, he doubt as we were friends. Can't we be connected each other in Facebook because we are student and teacher? That's why I have not requested any of my teachers to connect in Facebook yet.

I was asked to introduce before connecting in Facebook but still not connected

Another limitation of Facebook was some status. It might not be appropriate for my relatives connected, but useful for my class fellow. These status couldn't be hidden from each other.I have to restrict selecting one by one. Jokes that I wanted to post, might be laughable for some of my friend of college, which is not necessarily understandable by my friends of school level.

I hope Facebook overcome these limitation within few weeks (or probably, have updated). Otherwise I prefer google+ to Facebook.

Monday, August 29, 2011

नायक राजेश हमाल र सुक्ष्मजीवहरु

कलाकार / नायक राजेश हमाललाई महानायक बनाएर लेखेका टिपोट को थुप्रो लागिसकेछ । निसन्देह, यो हाँस्य प्रायोजनको लागि मात्र लेखिएको हो । तर, भर्खर-भर्खर Microbiology पढ्न सुरु गर्नेहरुको लागि Bacteria/Virus को characterहरु सम्झिन सजिलो हुन सक्छ ।

  1. राजेश दाइलाई त माईक्रोस्कोप नै नचाहिने रहेछ ब्याक्टेरिया हेर्न को लागि ....
  2. राजेश दाइ सानो हुँदां Staphylococcus र Streptococcus को गुच्चा खेल्नुहुन्थ्यो रे ।
  3. राजेश दाइ सानो हुँदां Escherichia coli र  Vibrio cholera को डण्डीबियो  खेल्नुहुन्थ्यो रे ।  एकदिन, E. coli डण्डीले V. cholera गुलीलाई अलि जोडले हिर्काउनुभएछ, त्यसैले आजसम्म पनि V. cholera बाङ्गोको बाङ्गै छ । 
  4. HIV त राजेश दाइसँग डराएर पो रहेछ, CD4 T-cell भित्र लुकि-लुकी बस्ने । 
  5. राजेश दाइको लामो कपाल देखेर पो Salmonella typhi पनि peritrichous (झुसे) भएको रहेछ ।
  6. २०५१ सालमा नेपालमा ठुलो खडेरी परेको थियो, किन भनेर बुझ्दै जांदा त राजेश दाइले Agaricus biospora (mushroom) को छाता बनाएर ओढ्नु भएको रहेछ ।
  7. राजेश दाइले एउटा भुस्याहा कुकुरलाई गोली हान्नु भएछ, गोली लाग्यो, घाऊ-रगत देखिएन, तर पानी देखी डराउने मात्र भएछ, १४ दिनपछी बल्ल कुकुर मरेछ । यसपल्ट त राजेश दाइपनि अचम्म पर्नुभएछ । (Bullet shaped Rhabdovirus).
  8. राजेश दाइको 'देउता' चलचित्र हेरेपछि Proteus त एकै ठाउँमा बस्न नसक्ने चकचके भएछ । (Swarming motility of Proteus spp.)
बांकी यता     http://www.facebook.com/hamalrajesh
                http://xnepali.net/np/240
बिष्णु प्र. मरासिनी

Tuesday, August 23, 2011

Lumbini, Nepal, The Birth Place of Buddha (Siddhartha Gautam)

2,500 ago, the powerful and influencing Nepal had given birth to Lord Buddha (623 BC) who lead the pathway of peace and civilization for humankind. Currently, this place is located in the Rupandehi district. But in modern days, Nepal ???........  Again, Nepal should be a leading country to the destination for peace and tranquillity.

Use light to show pathway for peace

Origin of peace

Art and peaceful life

Elysium in the mortal world

After following Budhha, Asoka became more happier and greater than as a Emperor

Please, stop violence, share love and knowledge, save the Earth
 Reference: World Heritage List


Tuesday, August 09, 2011

Pathogenesis of Arthritis

Arthritis is the painful disorder of joints, a leading cause for the disability in geriatrics. Osteoarthritis (OA), rheumatoid arthritis (RA), gout, lupus etc. are the common types of arthritis. OA is a disease aquired by 'wear and tear', and injury leading to cartilage degradation. RA is chronic inflammatory disorder attacking mainly the joints. Gout develops due to monosodium urate (MSU) crystal deposition in synovial fluid.

Pathogenesis of arthritis is mainly due to the following reasons. The activation of immune cells because of cross reactivity with bacteria, virus, pollen grains etc., which share common epitope with synovium or defects in genes like HLA-DRB1*0401, single nucleotide polymorphism (PTPN22, STAT4, CDK6, etc.). Complement complex, C5b678(9)n are deposited on synovial lining and opsonize it. These immune cells release pro-inflammatory cytokines, which intitaites  proliferation of fibroblast and osteoclast, and ultimately demineralize and destroy the bone matrix. Agonist of RANK, TLR2, etc. trigger the activation of NF-kB, which ultimately produces matrix metalloproteinase, nitric oxide and other bone degenarating enzymes. Due to obesity, axial  force as well as varus malalignment increases, hence cartilage begin to erode. Uric acid (purine) is overproduced due to some hyperactive enzymes or overturn of nucleic acid rich dietary source, and renal failure (not removing of urate).

Joint damage and pain due to arthritis can be reduced using ice, joint replacement, physiotherapy, hyaluronic acid administration, avoiding purine rich diet, administration of drugs such as methotrexate, etanercept, infliximab, rituximab, tocilizumab, Ibuprofen, corticosteroids, colchicine, diclofenac,  allopurinol, etc.
(To be Continue.....) (Update: View part II)
References
  1. Porth, C.M, and Matfin, G. Pathophysiology, concept of altered health states, 8th edition, Lippincott Willian and Wilkins Publisher (2009)
  2. Firestein, G.S. Evolving concepts of rheumatoid arthritis. Nature 423, 356-361(2003)
  3. El-Gabalawy H. S. et al.,  Non-HLA genes modulate the risk of rheumatoid arthritis associated with HLA-DRB1 in a susceptible North American Native population, Genes and Immunity, Doi :10.1038/gene.2011.30(2011)
  4. Loughlin, J. Osteoarthritis: All types of trouble-defining OA in the genomic era. Nature Reviews Rheumatology 7, 200-201(2011)

Thursday, June 23, 2011

Epidemics of Diarrhea due to Escherichia coli (Shiga toxin producing enterohemorrhagic) in Europe

Recently, enterohemorrhagic Escherichia coli (EHEC) strain has infected over 3,500 and kills over 40 people in the Europe and most of them are German [1]. Initially, it was blamed to salad and vegetables and the farmers for the cause of transmission, as concluded by case-control study. But the causative bacterial strain, EHEC O104:H4 has not been found in any of these salad and vegetables samples. Then authorities realize farmers were not culpable. Then they withdraw the blame with apology and announce the compensation for farmers. Now suspecting on bean, sprout, and agricultural practice [2].

EHEC O104:H4 is a type of E. coli classified on the basis of somatic O-antigen (over 170 different type: 1-170), and flagellar H-antigen (over 50 different types: 1-50). In E. coli, there are different chemical structure and functional group comprising lipopolysaccharide of plasma membrane (O-antigen), polysaccharide of  capsule (K-antigen) and flagella (H-antigen). Combining of these different antigens there could be thousands of different types of E. coli. The infective EHEC O104:H4 is new to Europe but this strain was reported from Korea in 2006 [3]. Does this means this strain is shipped from Korea? Certainly not, or needs exigent research.

Every organism has the tendency to adapt the environment with necessary genotype reshuffle or addition, and phenotypic variation, suitable to survive, as Darwinism. Bacterial strains also, always tend to increase virulence and pathogenicity by adapted gene transfer and mutation. In latent type of infection, plasmid and/or gene transferred from virulent strain to non-virulent may get proliferated for several months without symptom and unknown to health professional. This may be the one of the possible reason for outbreak in Europe, which is still under research to find the source of infection. So, the organism whose reservoir is the environment, they proliferated when the environmental condition becomes optimum, as said by Rita Colwell [6].

Vibrio, Escherichia has the environmental reservoir unlike smallpox and polio virus. So they are always prone to infect mammal once environmental condition become favourable. E. coli is even more dangerous as it is opportunistic pathogen and can acquire antibiotic resistance as well as virulence.

In my study (in NAST), some strains of E. coli were found to be resistant against all commonly used antibiotics (courtesy: Nabaraj Dahal, Pankaj Baral, and Sanjiv Neupane). This shows it is the dreadful strain having most flexibility in genetic variation among bacterial kingdom. However, the innovation and more research on antibiotics may enervates its massive proliferation.
Multi-drug resistant E. coli reconfirmed on M-endo agar.
Antibiotics sensitive E. coli (ATCC 25922) reconfirmed on M-endo agar.
Even in the Europe, the bacterial strain can invade people where living standard is high as well as good sanitation, well managed health system. Also, Nepal had faced problem of diarrhoeal epidemics and hundreds of people died in remote area, two years ago. But it was different scenario, poor people were lack of medicine and ORS.
Few months ago, an unprecedented outbreak of cholera in Haiti was the reason to blame Nepalese peacekeeping soldier. But neither stool nor rectal swab nor antibody test of these soldiers showed positive result of V. cholera (or was not investigated). Even no one could be verified as carrier. And probably, the sample of drinking water, seawater and sewage from different source was not analysed properly to make a conclusion. Only the co-incidence was the bacterial strain found there resembled with the South Asian strain, which is not only confined in Nepal but also other South Asian countries like Bangladesh, India, Pakistan etc.

References:
  1. European Centre for Disease Prevention and Control,  Stockholm, Sweden, 22 June 2011, 11:00
  2. Editorials, 16 June, 2011, Nature, Vol. 474, 251
  3. Woo Kyun Bae, et al., Jun 2006, Yonsei Medical Journal, Vol. 47(3), 437-439
  4. Marian Turner,  9 June, 2011, Nature, Vol. 474, 137
  5. Kai Kupferschmidt, 10 June 2011, Science, Vol. 332, 1249-1250
  6. Martin Enserink, 5 November 2010, Science, Vol. 330, 738-739

Wednesday, June 15, 2011

भानुभक्त आचार्यको पादुका दान अब नयाँँ संस्करणमा

(नेपाली, साहित्य, दशक अगाडिको पानाबाट)

तहाँ सीतारामका चरणतलमा शिर पनि धरी
अयोध्यै लैजान्छु भनिकन ठूलो मनसुब गरी

.............................

तहाँ साथी भाइका चरणतलमा घरि-घरि परी
भरत बिन्ती गर्छ एउटी ठिटी मिलाइदेउ भनी

चुरोटको धुवाँमा होस् या क्यान्टिनको चनामा
उसलाई नै सोच्छ यो भरत आफ्नो मनमा

बियरको बोतल होस् या ल्याबको फ्लास्क
फुटायो कती हो कती अनी छोड्यो क्लास

भ्यागुतो होस् या गड्यौला चिर्दा या लोखर्के
खाली उस्तिर नै आँखा लगाउछँ कर्के-कर्के

क्लासको होस् या प्र्याक्टिकलको कापी सार्दा
उसलाईनै सम्झन्छ ब्याड्मिन्टन पनि हार्दा

मिररको होस् या लेन्सको प्र्याक्टिकलमा
तेर्स्याउँछ ति खाली उसकै अनुहारमा

झिम्क्याउन सिक्ने भनी माइक्रोस्कोप हेर्छ
छोडिदे त्यस्लाई भन्दा हामीलाई कहाँँ टेर्छ

ब्रश नगरेका गन्हाउने ति पहेँला दाँत पनि
भन्ने गर्छ ति सुनका दाँत किन हो कुन्नी

हामीलाई धम्क्याउछ उसलाई नपाए पनि
बिकरको एसिड पनि पिईदिन्छु भनी

साथीभाइ सम्झाउँछन नरो अरु पनि पाईन्छ भनी
उ रुन्छ सिनेमाको पैसा फिर्ता अहिल्यै चाहिन्छ भनी

(दशक पछी थपिंदा....)
एक किलो पाउडर अनी लाली दल्ने त्यो काली
कसरी पर्न गइछे त्यो मोरी त मेरो आफ्नै साली

Tuesday, June 07, 2011

Vying for Identity in Science

Update: Voting period extended upto 11th Jun, 2011

One of my article of this blog (Cholera in Haiti and Association to South Asia....) has been selected for "3QD (3QuarksDaily)" prize for non-professional science writing, which can be found here, and second round of selection depends upon voting and voting ends on June 8, 2011. However, it may not have good quality for worldwide competition. Also, this blog (Science Disdained Nepal) is listed on the blog of famous science journal; Nature, and can be found here (ScienceNepal).

Although suffering due to my poor English, internet access, and availability full text of the journals, this small achievement has encouraged me to continue on science writing and blogging.

Sunday, May 29, 2011

No reputation of Nepal in science sector, poster presentation is option

Poster presentation is the way to show research finding. Poster has great value during conferences and usually prior to publication. It is one the shortest form to explain the results of researches and their benefit to the public (scientists). Hardly, science and research done in Nepal, can be published in the journal of international reputation because of less exposure and prestige of Nepal in science sector. So, poster presentation is the good option.  I have inserted here a template (MS Power point 2007) for poster.

Poster presentation template; explain the science and result in conferences (download pptx)

Tuesday, May 24, 2011

Reasons of Fedora 15 for Chemistry Related Programs

Today, final version of Fedora 15 is going to be released. Fedora is a type (distro) of Linux Operating System. I have been using this OS (Red Hat Linux before 2004) for a decade. See my previous article; Pros and cons of Linux OS.
 
Reasons and features of preferred Fedora 15
As I mentioned Fedora is the leader not follower, so, some of the latest software and Linux repositories are available in Fedora 15. Few of them are;
  • KDE 4.6.x,
  • Xfce 4.8,
  • GCC 4.6, 
  • GNOME 3,
  • LibreOffice 3.3.0,
  • gnome-chemistry-utils-0.12.8,
  • Rupee Sign,
  • improved SPICE support,
  • /var/run mounted as tmpfs,
  • /var/lock mounted as systemd, etc. and
  •  Yum is not necessary to upgrade.
Several Chemistry related programs are available under gnome-chemistry-utils package. Chemistry-utils can appear in Gnome-3 menu that conatins as follows: (These were available inside “education” menu in previous Fedora).
  • 3D molecular structure viewer (GChem3D)
  • Chemical calculator (GChemCalc)
  • 2D structure editor (GChemPaint)
  • periodic table of the elements application (GChemTable)
  • crystalline structure editor (GCrystal)
  • spectra viewer (Gspectrum).
GNOME 3 is somewhat similar to aerospace of Windows vista and 7 that make feel with gnome-shell. This helps window management. It provides a top bar that hosts the 'system status', a clock, and a hot corner that switches to 'overview' mode, which provides easy access to applications and windows. Also, it provides controls for keyboards, monitors, network, sound and power. There is only a close button, not a minimize or maximize button. Double-clicking the title bar of a window maximizes and vice-versa. This type of inclusion may make confusion to some people who were enjoying previous Gnome.  

Sunday, May 22, 2011

Anxiety, Anger Soothed by the Pigeons 2

Contd from part 1. When I opened the balcony door considering to seize these disturbing pigeons, I could see the nest with two eggs.
Best place to make nest; neither eagle nor weather attack, I assure nor human
Each door covered with extra panel of net, to avoid mosquito and other insects. But there is neither spring nor peg in the balcony door so that outsider panel remains a little bit open and there is always a gap between two panels of the door. No problem in the main entrance door, both panels are good. I had been requesting the in-charge of this house to solve the problem. What is the value of this extra net-panel if it always remains open? He always had been saying tomorrow-tomorrow for past four months. It is just a 15 minutes work to install spring or peg. Now, I give up to request.
A small gap created between two panels of the doors
Certainly, take benefit of the gap
I remembered, Kabi Siromani, Lekhnath Poudel’s poem, “Gauthali Bolyo Chiribiri Chyarrya”. Both swallow and the person were saying the house belonged to them, and the poet became confused.

I also became confused whether this room belonged to me or bird, or stay together. I decided to let it. Might the pigeon-pair (parents) be watching me and their nest from a short distance. The pigeon-pair, the nest and eggs soothed my anger and anxiety. I forgot what happened the whole day and returned to bed for asleep.

Sunday, May 08, 2011

Chemistry Journal's Impact Factor in 2010

Please wait for Chemistry Journal's Impact Factor, if net is slow.
This impact factor (2010) is the unofficial collection by Bishnu Marasini but it may change in 2011.
Please e-mail me if you need the document.

Friday, April 29, 2011

Anxiety and Anger Soothed by the Pigeons, Symbol of Peace

I love research work. In childhood, I used to spend several hours on electronics circuit board; forgot hunger-ness, and ultimately scolded by mother. In these days, from  8 AM to 11 PM stay in laboratory (subtracting tea, lunch and dinner time), and sleep immediately after reaching the room. Even in holidays, I have the same routine.

Few days ago, we went in tour. It was a lab missing day for me after several months. All of us had enjoyed the tour. But while returning, my colleague, the newcomer of this institute, noticed the mobile, which was not used for last five hours, was missing from the bag. Oops! The mobile was in bag and the bag was never taken out of the vehicle.  I was among the seniors, who stayed here for a long time, had some responsibility to take care of newcomer, but I, in fact all seniors failed. That created us a pressure and forced to analyze whether the mobile was lost or stolen.

During this 5 hours period we were in three spots. Among 3 spots, the last spot, where vehicle was abandoned for 1 hour while boating to reach middle of the lake, and there were a lot of people in the vicinity of the vehicle. But the driver insisted, “I locked every windows and doors, and there is no sign of opening”. He was the last while leaving the vehicle, and the first while catching up it, after boating. Before and after joining boat, we had spent few minutes on snapping and clicking and were not caring for unlocked vehicle and goods. Probably someone had stolen at that time. The colleague mentioned, "Only mobile is stolen not money and others". This statement made the situation more complex to analyze. We checked the vehicle very carefully, everyone's bag, but no success! Inept! This time, compared to the lab cases that I witnessed, the case is entirely different, no sufficient control group for retrospective study. How can it be interpretable?

Thinking and agitating I couldn't sleep, though I was tired. In the late midnight, I could hear the "coo" of pigeons (probably such sound made in previous days but deep sleep might made unnoticed, I didn't know whether the pigeons were taking shelter in balcony). That 'coo' made irritation to tensioned mind it was like adding ghee in the fire. That increased my anger, I wanted to remove these pigeons from balcony. To appease the anger, I suddenly got up and opened the balcony door, then I found ....Pigeon (Rock Pigeon)......(contd....see part-2)

Sunday, April 17, 2011

Cholera in Haiti and Association to South Asia and Scientific Study to Reduce Recurrence

In the fall of last year, unprecedented outbreak and epidemics of cholera in Haiti agitated locals, news media, health workers. There has been a long debate about this epidemics. The situation has been highlighted by famous science journals, and come to my attention.

Although the cholera outbreak had been diminishing, and the overall fatality rate was down to 2 % from earlier 9%, and 4,550 deaths and 231,070 cases were reported, still there were few cases, as United Nations, Geneva said at the beginning of February. The serotype of the causative agent, Vibrio cholerae, has been identified that resembles with South Asian strain. The mortality rates of untreated cholera is 50-60% (one of the highest mortality rate).

Transmission
Vibrio cholerae is transmitted to humans as fecal oral route via water or food. The reservoir of the organism is suspected as the aquatic environment. In its extreme manifestation, cholera is one of the most rapidly fatal illnesses known.

Clinical Symptoms
Cholera begins with sudden onset of massive diarrhoea, excretion of protein-free fluid and associated electrolytes, bicarbonates and ions within a day or two. This loss of fluid leads to dehydration, anuria, acidosis and shock. The watery diarrhoea is speckled with flakes of mucus and epithelial cells ("rice-water stool") and contains enormous numbers of vibrios. The loss of potassium ions may result in cardiac complications and circulatory failure.

(Technical Terms Starts)  
"Vibrio cholerae, Morphology and Culture
It is a Gram-negative non-sporing, non-capsulated, curved rod, motile, monotrichous (single polar flagellum), oxidase-positive (distinguished from enteric), glucose fermenter, non-lactose fermenter bacterium. Widely used enrichment medium for this bacterium are; alkaline peptone water (APW), Cary-Blair transport medium, etc. And the common selective media for the isolation are; alkaline bile salt agar (BSA) medium (colonies are very similar to those on nutrient agar), Monsur's gelatin tauro cholate trypticase tellurite agar (GTTA) medium (small translucent colonies with a grayish black center), Thiosulpbate citrate bile salt (TCBS) agar medium (yellow nucleated colonies), polymyxin-mannose-tellurite (PMT) agar medium (differentiate between V. cholerae O1 from V. cholerae non-O1 based on mannose-fermentation), etc.

Disease Mechanism
V. cholerae start to produce the toxic proteins (cholera toxin, CTX / CT) only after reaching the intestine. It is an oligomeric complex made up of six subunits: one (A subunit), and five (B subunit). The B subunits binds to GM1 gangliosides on the intestinal epithelium cells. So the protein enter the cell via receptor-mediated endocytosis. Then the A1 subunit becomes free and bind with ADP-ribosylation factor 6 (Arf6), which permanently ribosylate the Gs alpha subunit of the heterotrimeric G protein. This results in constitutive cAMP production and pump out Cl−, HCO3−, etc., into the lumen of the small intestine which prevents sodium ions from entering the cell, and these ions create a salt-water environment, which through osmosis can pull up to 6 L  of water per day through the intestinal cells, creating the massive amounts of diarrhoea, and rapid dehydration. 

Virulent strains of V. cholerae is due to temperate bacteriophage called CTXf or CTXφ. V. cholerae is well adapted and can, economically, produce different proteins in different environment e.g., in intestine, TcpP/TcpH proteins, which, together with the ToxR/ToxS proteins, activate the expression of the ToxT regulatory protein. ToxT then directly activates expression of cholera toxins, and allowing the bacteria to colonize the intestine." (Technical Terms Finished)

Risk Factors
For cholera, anybody can be at risk, i.e., there is no correlation between vulnerability of infection and age, gender, malnutrition status, etc. It is one of the dangerous infectious disease that can kill healthy people quickly. After the onset of symptoms, victim may die within 4 hours to few days if no treatment is provided. However, people whose stomach is making less amounts of gastric acid than normal or recently had stomach surgery or taking drugs that inhibit the gastric acid production or person of blood type O, are at higher risk. In Peru, virtually all indigenous people have blood type O, and were at higher risk.

In Nepal, May-July is the main season of cholera outbreaks.

Treatment of Cholera
Treatment involves the rapid intravenous replacement of the lost fluid and ions. Following this replacement, administration of isotonic maintenance solution should continue until the diarrhoea ceases. By this simple treatment, the mortality rate of cholera can be reduced by ten-fold. A few antibiotics (e.g. tetracyclines) may shorten the duration of diarrhoea and reduce fluid loss.

Few years ago, I got chance to study on  V. cholerae, 01, El Tor, Ogawa biotype, while I was in NAST (former RONAST), the strain was kindly provided by Mr. Nabaraj Dahal, Patan Hospital. It was not so dangerous in terms of antibiotics resistance as compared to other strains, I investigated, such as Escherichia coli, Pseudomonas aeruginosa, Staphylococcus aureus, etc., which were almost all commonly used antibiotics resistant. Diarrhoea due to enteropathogenic E. coli is more complicated than cholera, in therapy.

The problem with the management of cholera is the consumption of unhygienic food and contaminated water. Contamination problem is mainly during both dry and rainy seasons. This is significantly enhanced due to drinking water pipe, which remains together with sewage pipe, and in some places, drinking water pipe remains inside sewage Hume pipe.

In Haiti, cholera had proliferated due to flood. Certainly, flood not only contaminate drinking water, but also destroy human's habitat and obstacle the disease treatment strategy. There are many places in Nepal where people rely on river, stream for drinking water, so they are always in risk of these kind of diarrhoeal diseases. Two years ago, death of more than 200 people due to the epidemics of diarrhea (one of the simple/neglected disease), in rural area of Nepal indicates inaccessibility of modern medicine, and in fact they still have to rely on medicinal plants and rituals.
water purifier
Make pure water
water purifier in bicycle
Water purifier operated by bicycle
Recently, Singapore water company, Glowtec has discovered a water purifying filter system, which can filter Decaliters of pure water within a minute (800 liter/hr). This can be operated by chain and the paddle of bicycle, and it can be transported anywhere as it is simple and light. It has been found very effective and significantly reduced the incident of waterborne diseases in flood affected area of Pakistan, Myanmar, Yemen, Taiwan, Philippines, and Vietnam. Vaccination is good option to avoid cholera epidemics. Nepal, and probably all developing countries can't afford the cost and also, V. cholerae has the high mutation rate, and new vaccination antigen and strategy needed within short period of time for full coverage. People should keep re-hydration solution like Jeevanjal, standby and should be immediately available in each home.

Acknowledgment: I thank to Dr. Joachim Schindler for reviewing and some suggestions.
Picture : Quantum geoservices

References:
  1. Martin Enserink, Science, 330, 5 November 2010, p. 738-739, Haiti’s Outbreak is Latest in Cholera’s New Global Assault
  2. Martin Enserink, Science, 331, 28 January 2011, p. 388-389, Despite Sensitivities, Scientists Seek to Solve Haiti’s Cholera Riddle
  3. Declan Butler, Nature, 468, p. 483-484 (2010), Cholera tightens grip on Haiti
  4. David Cyranoski, Nature, 469, p. 273-274 (2011), Cholera vaccine plan splits experts
  5. Kalpit P., Asianews, 2009 July 23, Epidemic hits western Nepal, More than 200 dead.
  6. Katherine Harmon, ScientificAmerican, 25 October 2010, Why Is Cholera Spreading in Haiti Now?  
  7. Debora MacKenzie, NewScientist, 15 November 2010, Haiti faces years of cholera
  8. Debora MacKenzie, NewScientist, 07 December 2010, Haiti: Epidemics of denial must end
  9. Debora MacKenzie, NewScientist, 10 December 2010, Haitian cholera strain could dominate the Americas

Thursday, April 14, 2011

Happy New Year 2068 for all Honest, Brave, and Wise Nepalese

सम्पूर्ण नेपालीहरु लाई नयाँ बर्ष २०६८ को हार्दिक मंगलमय शुभकामना ।। सबैको मनमा सुख शान्ती ह्रोस । आपसी द्वेष र ईर्ष्यां हटी सम्पूर्ण नेपाली हरुमा एकता रहोस् । बहादुर र ईमान्दार नेपालीको परिचय नगुमोस बरु तीक्ष्ण बुद्धिका नेपाली पनि भनेर चिनिऊन् । जय नेपाल ।।

Thursday, April 07, 2011

Blogspot, remove unnecessary hyperlinks created by JavaScript Void (0)

If blogspot contains blog archive (history) gadget, this history gadget helps to show topics of the posts according to published date, month-wise (or week-wise), and year-wise. Because of this blog archive, two kinds of hyperlink will be generated for each post. One, which links for posts (page). Another, javascript : void (0) that links homepage without any anchor text. This code, "JavaScript Void (0)", prevents the browser from loading a new page (or refreshing the current page). Although it is not a big issue, unnecessary and repeated "javascript : void (0)", may create an ill SEO. This code and hyperlinks can be removed by the following tricks.
  1. Login to your dashboard-----> Design -----> Edit HTML      OR      Login to blogger, choose "Layout -----> Template ------> Edit HTML
  2. Click "Download Full Templates" link to back up your template, in case if you don't like the changes, reverse by uploading this back up.
  3. Click on "Expand Widget Templates".
  4. Find the following code "Zippy toggle-open".
find unwanted hyperlink creator
find javascript : void (0)
5) Delete the whole words "href = 'javascript :void (0)'".
delete code to remove unwanted hyperlink
delete javascript : void (0)
6) Save your setting. Enjoy

Tuesday, March 29, 2011

Survived from Formaldehyde Fuming

I am preferring the evening/night shift in the crowded cell culture lab to maintain peace. Another lab in day shift. One room is divided in three different compartments each facilitated with laminar hood, inverted microscope, centrifuge, liquid nitrogen tank, and incubators. My cell culture lab is one of them. Last week, as usual, when I entered the lab, pungent like smell and eye irritating environment made me to get out immediately.

I asked a colleague, next to the cell culture lab (thanks at least one was there), whether it was fumigated or not. He replied, “no”, later he said mocking me, “I don't know.” I again returned to the cell culture lab and checked every compartments of the lab and notice board. There should be notice and information for fuming, but nothing could be found as the indicator of fuming except AC was switched off and dustbin was full of waste. “Probably the smell and irritation due to this waste and no air circulation”, I assumed. I had felt such kind of odor on microbiological work, few years ago. Then I decided to work putting mask. Sooner, I felt suffocation and severe headache. It was fuming gas ! ? # Promptly, I rushed to lawn for fresh air breathing.

After 15 minutes, eye irritation reduced but headache persisted then I returned to the room immediately. Thanks I survived. Next day, though appeared in the institute but could not work due to headache. Meanwhile, the same colleague with whom yesterday I asked, bemocked me informing about the fuming. One of the research assistant (or graduate student ?) had fumed with formaldehyde to sterilize one of their compartment at the last time of office hour.

Saturday, March 19, 2011

Scholarships Opportunity for Nepali in PhD, and Advanced Research

TWAS (Third World Academy of Sciences); TWAS, the academy of sciences for the developing world is one of the largest organization to promote science and technology. Nepal is the member of TWAS. Recently, TWAS has announced for various fellowships targeted in developing countries with the emphasis for women. Nepalese can apply who have completed their M.Sc. Or 4 year B.Sc. in science and engineering.

Monday, March 14, 2011

Recent Developments in HIV Therapy

Human immunodeficiency virus (HIV), which is responsible for acquired immunodeficiency syndrome (AIDS), one of the public health threatening virus, needs arduous work to eliminate. Various strategies like, Reverse transcriptase (RT) Inhibitors, HIV-1 Protease Inhibitors, HIV Integrase Inhibitors, HIV Maturation Inhibitors, Viral Entry Inhibition, Gene Therapy, Immunotherapy / T-Cell Gene Therapy, etc. methods has been implicated to combat it.
I had written in the World AIDS day 2009. Detail is here in my previous post

Friday, March 11, 2011

Sometime Google, Yahoo and Bing alone or together make fool to user

Probably, all of us have noticed, the result shown by Google was different than those actually typed and intended to search. I realize this many times. I read the whole web page or pdf file recommended/indexed by Google/Yahoo/Bing search but no word even the meaning of that word could be found for a keyword (phrase) that I had searched. Sometime, in worse case, these search engine index with the web site of different language.

Why Google (or Yahoo or Bing) index these non-sense web site in their first page ? Whether any advertisement scheme or payment scheme is available, so that any web page is indexed in first page for any keyword? Or, is there bug or fault in their search engine code? Or, if high ranked webpage links to, or embed feed-proxy of low ranked web page, then the content of low ranked page is indexed to high ranked web page? Or, spider's visit mistakenly understood as owner by these search engine?

This is still mysterious that I have been willing to know the actual fact for several years. I have not mentioned any example here because it is dynamic and once mistakenly indexed site (webpage) might have corrected after a week. Sometime it makes trouble to the internet users from the countries like Nepal where internet-speed and electricity are precious.

Monday, February 28, 2011

Metarhizium anisopliae as Eco-friendly Antimalarial Biopesticide

Malaria is one of the major public health problem for Nepal, indeed all developing countries are facing the problem. Although epidemics of malaria has been reduced, emergence of drug resistant Plasmodium spp (causative agent of malaria), poor sanitation, agricultural dependency etc. still making malaria as frightening.

Living in the Terai region of Nepal was avoided due to malaria. This is the fact of just 60-70 years ago. During Rana rule in Nepal, prisoners were sent to this Terai area as punishment, where malaria was a big threat. After the discovery of anti-malarial drugs, deforestation and people's migration began and the Terai gradually overcrowded and become Nepal's dense populated area. I remember, whole houses were sprayed by DDT to get rid from the diseases transmitted by mosquito. But DDT exhibited serious environmental and public health hazards. And neither, malaria could be eliminated.

The finding (gift of science and research ?) from the University of Maryland may be helpful to combat malaria and mosquito related diseases in Eco-friendly and biological way. A fungus Metarhizium anisopliae, which is a plants symbiont protecting plants from insect, infects mosquito and some other insects and attenuates then kills. This fungus has been genetically modified (GM) and have very narrow host range e.g., only infect harmful insects. Also, this GM fungus express SM1 and scorpion proteins, toxic to Plasmodium sporozoites in mosquito that enhance the rate of killing in short time period. This fungus easily invade and infect the mosquito through the surface like if contacted to cuticle; unlike bacterial and viral infection. So, like DDT, spore of this fungus can be sprayed in bed net, house; so that it would be easily contact with mosquito and to eliminate Plasmodium spp. And, it could infect larvae of mosquito, hence meta-acid and hazardous chemicals can be replaced by the fungal spore in ditches and stagnant water pool.

However, whether this genetic engineered fungus can survive freely in environment or work significantly? Or might it create bad impact in ecology? Or will it be available easily for poor countries to use? What happens if it infect honey bee and other beneficial insects ? We have to wait.

Reference: Fang et al., Science (25 February, 2011), 331; 1074-1077

Sunday, February 20, 2011

Spy thru' Mozilla Firefox or else ?

       Every-time when I open Firefox, after computer start (not after restart of Firefox without restarting the computer), CPU fan run in the fastest speed with busy HDD indicator for initial 15 minutes. This was surprising, it shouldn't be, and in another user account; no such abnormality could be seen.
       Upon checking the “System Monitor”, the CPU was busy and astonishingly there was peak in the graph of sent and received items, even-though, I hadn't opened any web site. I don't remember that I had activated any automatic update in this Fedora 12. 
Peak in this graph is indicating something is downloading
Here CPU is busy and making cooling fan work hard
CPU, memory and network usage graph in Fedora
 I deleted this user profile and recreated with the same name, the problem solved. Again after few months later, the problem reappeared in both user accounts this time, and I deleted and reopened both with the same name, and nowadays working well. However, I am still skeptical what was uploading and downloading or installing or whether, was it normal process ?

Tuesday, February 15, 2011

नेपालीमा ब्लग लेखन र ब्लग भेला, एक अनुभव

       यो टाँसो दैंतरीमा (dautari.org) नेपाली ब्लग भेलामा मैले राखेका कुराहरुलाई क्रमबद्ब गरेको मात्र हो ।
       मेरो ब्लग खोल्नुको उद्धेश्य, मैले रचना गरेका टुक्रा-टुक्री साहित्य पस्कनु र लेखाइमा निखार ल्याउनु थियो । तर, एक त नेपालीमा टाइप गर्नुको झर्को, टाइप गरिहालेपनि कापीमा लेखे जस्तो ह्रस्व-दीर्घ मिलाउन अनी स्क्रिनमा शुद्ध बर्ण उतार्नको कठिनाईले गर्दा आफ्नो लेख आँफैलाई अनौठो लाग्ने भएकोले नेपाली लेखलाई निरन्तरता दिन सकेन । यसकारणले अनियमित नै भएपनि अङ्रेजीमै बिशेष गरी कम्प्युटर, बिज्ञान तथा प्रविधी परिधिका तथा केही अनुभवका लेख लेखेर भए पनि उपस्थिती जनाइरहे । अशुद्ध लेख्नु भन्दा नलेख्नु नै बेश भन्ठानेर बसे पनि कहिले-काँही चाँही लेख्न खसखस लाग्ने रहेछ । अङ्रेजीको आफ्नो लेखमा व्याकरण अशुद्ध भएपनि अङ्रेजी आफुले त्यती नजान्ने भएकोले आँफैले पढ्दा त्यती अनौठो लाग्दैन ।
       नेपालीद्वारा लेखिएका सयौं ब्लग भए पनि आफ्नै मौलिकताले भरीएका र नियमित हुने (महिनामा कम्तिमा १ लेख) त २०-२२ वटा मात्र पाएको छु, जसको म नियमित पाठक हुँ । तर त्यसमध्ये पनि सदैव शुद्ध र व्याकरण मिल्ने लेख हुने त जम्मा ८-१० वटा मात्र भए जस्तो लाग्छ । त्यस्तै झिलिमिली बनाएका ब्लगहरु पनि धेरै छन्, जुन खुल्न धेरै समय लाग्छ किनकी नेपाल मा अझै पनि सुस्त गतिकै ईन्टरनेट छ । साथै नेपाली ब्लगको संख्यात्मक भन्दा पनि मौलिकतामा र रचनात्मक लेखमा ध्यान पुर्‍याउनु पर्ने जस्तो देखिन्छ । blogger.com.np त्यस्तै अरु वेबसाईटमा सम्पूर्ण नेपाली ब्लगरहरुको नामाँकन त छ । तर, कुन बिषय बस्तु मा लेखिएको हो, समुह छैन । त्यसैले, विकीपिडीयामा नेपाली ब्लगको जानकारी, गुगल समूह वा अरु कुनै वेबसाईट बनाएर नेपाली ब्लगरहरुको बिषयसुचीको आधारमा समूह पनि बनाउन पहल गर्ने कि ? जस्तो समाचारमुलक, कथा, साहित्य, बिज्ञान, प्रविधी, अर्थ, राजनैतीक ब्लग इत्यादी.
       अर्को कुरा, प्राय: ब्लगहरुमा समाचारहरुमात्र (अथवा कुनै सामाग्री भए), त्यो पनि अरुको चोरी गरेर लेखिएका छन्, मलाई त्यस्ता ब्लग खोल्नै मन लाग्दैन । अरुको चोरी गर्ने र कपी पेस्ट गर्ने ब्लगहरु त म आजकाल बहिस्कार गरेको छु, ति ब्लग मैले खोल्दै खोल्दैन; त्यसैले सबै जनाले नखोल्दिए-नहेर्दिए ती चोरी गर्नेहरु निरुत्साहित हुन्थे कि ? बिज्ञापन हेरिदिएर सहयोग गरे जस्तै शुद्ध लेख्न पनि सुझाव र प्राविधिक सहयोग गरिदिए, अनी लिंक साटासाट गरिदिए पनि नेपाली ब्लग प्रवर्दनमा सहयोग पुग्ने थियो ।
       सोख नहुने हो भने त ब्लग लेख्न सार्है झन्झटिलो र पट्यारिलो काम हो । नियमित र रचनात्मक नेपाली लेख ब्लग मार्फत ईन्टरनेटमा उपलब्ध गराइदिनुहुने सम्पूर्ण नेपाली ब्लगरहरुप्रति हार्दिक आभार ब्यक्त गर्दछु ।

Saturday, February 05, 2011

Nepal, Nepali and Blogging; Experience of Nearly a Decade

       What comes between computer hardware and software? I certainly say, Nepal. Ridiculous, isn’t it? Let me explain. China has been dominating in production of computer parts (hardware) including CPU and India is advance in software design and outsourcing, Nepal is between them (but geographically).
       Could it be possible technically or really towards the development of computer hardware or software or both in New Nepal / e-Nepal? Probably Not! during my life. Success may skew towards software but electricity availability condition …….? Somewhat improvement in IT sectors like telecommunication, Nepal could be an example. But no enough to mention in example, I assume. However, a decade ago, there was trend (fashion) to learn and get trained in basic computer and still it is an essential skill to get any kind of job. Also, it was the matter of self dignity. But it has been limited only in training, not extended to any discovery or industrialization.
       My engrossment was in electronics. Trend to learn computer, and my engrossment / enthusiasm in computer hardware (and still! nevertheless could become a professional), I used to spend several hours in computer related articles, experiments, and in cyber café (Rs. 30-50/hr, later Rs.15-25/hr). http://www.geocities.yahoo.com/bishnu.........(extinct) was the first website (or blog?) that I created. I was at learning stage of html code, jumped from hardware. Initially, it was used to view change in html code after change made using yahoo’s website builder. This site was used for html code practice (observe code, after change in template and vice versa), rather than to publish any article or any advertisement. Later, I used to post some jokes, computer tips (windows, and basic code of html).
       Half of my diary was filled with poems and stories (written in Nepali) and hence, I thought, only thought to post them in the website (geocities). Both, laziness and difficulty in typing and posting in Nepali font (Unicode was unknown to me at that time) made these literature unexposed to public. Later on King Gyanendra’s regime, I found blogspot and wordpress were better to post such kind of literature (in Nepali) and creativity. But the weakness in typing, achieving correct orthography in screen unlike in handwritten manuscript, enervated…oops! Although a revolution made due to Unicode system to post in Nepali, typing time, grammar and punctuation are still making obstacle to post article in Nepali language. I feel odd when reading Nepali article typed by me. I rarely posted these Nepali article (or deleted later) because some word I couldn’t type with correct spelling. I am poor in English, so, I rarely feel odd when reading grammatically mistaken my article.
       Therefore, again, both blogspot and wordpress were used to change template and to design in different ways (wordpress having less option) as in geocities in initial days. Posting and writing couldn’t be continued. Later a decision was made to write article in Nepali for wordpress and in English for blogspot, whatever may be the topic. Article proliferated in blogspot which I hadn’t imagined during opening of its account; just thought Nepali article and literacy will be proliferated as it is easy to create and write; but typing skill made it reverse.
       I salute them (I am not mentioning some important names at this moment, sorry) who not only continuing blog in Nepali but also encouraging other Nepali with correct grammar and spelling, and technical guidance.

Wednesday, January 26, 2011

Seagate Hard Disk Failure with Soft tick ... tick... tick....Noise

       I have been using many Seagate Hard Disks for a decade, also recommending it to friends/colleagues as a (amateur) technician. It has been found durable, efficient and cheap. None of them reported as failure although, some other computer parts complained to be repaired or replaced.
       But 3 years ago, my hard disk (Seagate, SATA, 80 GB) was not recognized by BIOS after sudden power cut off during windows installation, at the point of disk format. It was within warranty period, so I took to the vendor. Their BIOS system was also unable to recognize my hard disk. After 3 days, he called me notifying that hard disk was working properly without any repair. Both of us astonished; it worked automatically (without repairing? was he telling the truth?). Recovery software helped to recover most of my files except some photos (recovered but damaged), and office 2007 documents (*.docx, *.xlsx etc. But office 2003 format like *.doc, *.xls were fine). This HDD is still working well with dual operating system of Linux and Windows XP.
       Then another case of HDD failure also happened to me. Ten months ago, I had purchased a 250 GB SATA (16 MB cache), Seagate Barracuda ES (China); Date Code 08133; site code WV; Lot: 10111209. Five partition was made, 3 with Ext-2 and initial 2 with NTFS format. Fedora 12 was installed for the reason that virus might not able to transfer while back up from normal hard disk containing windows XP. Although I kept this hard disk inside the computer, power cable and data cable was connected only once a month. But used as primary (regular hard disk as secondary for a moment) to copy and paste (from regular HDD) using its own operating system i.e. Fedora.
       Up to six months it worked well but suddenly, screen was frozen (hanged) without any external interruption like shock, electricity failure. Upon restart, BIOS did not recognize this HDD. It disappointed me. Then I disconnected  power and data cable for one month and after a month it worked properly but failed in the middle of file copy. It made me doom. I had strong belief on hard disk, I felt power cable was loose, and I purchased a new power cable (regular HDD is PATA). Didn't work !??@!!!. Tried with another computer, no luck. I noticed a soft sound of tick...tick.... tick... while connecting with power cable. This HDD was dumped for a month.
       I was willing to change it, and irritated vendor (shopkeeper) checked upon my request, it worked fine. This time, the HDD betrayed me. It was amazing how it worked, I requested to restart and repeat but he refused. I requested him to copy some important files (a few MB), which was not in regular HDD. He scolded me, and tried to manifest his importance indexing customers.  I had little hope, however, tried again but didn't work, and same soft tick...tick.... tick...!!!
       I am still confused, whether this lot/HDD is faulty one or shopkeeper provided refurbished/ used one (lying as new), or I have to think twice before recommending to use Seagate HDD as the best.

Tuesday, January 18, 2011

Presentation Styles of European/American Scientists and South Asian Scientists

I have been attending some national and international symposiums and getting chance to listen seminars by veterans from many countries. Two weeks ago, I got chance to take part in two inauguration ceremonies in a day. It was really an exciting experience as two inaugurations in a single day. Surprisingly, a distinct way of presentation styles between South Asian scientists and European/American scientists that I have realized, however, may not be interacted with sufficient eminent scientists.
South Asian
  1. The sentence starts as, I/my colleague discovered........
  2. Content : most of the literature survey, and long introduction, and few result.
  3. Slide filled with most of copied and pasted texts, and definitions.
  4. Seminar deliver : just read text that written in slide somewhat similar to reading news and make audience sleep.
  5. Spend time just to define few scientific terms.
  6. Acknowledge : no or very few.
  7. Don't care for allocated time limit.
European/American
  1. The sentence starts as, we/our team discovered........
  2. Content : most of their own result and less literature survey, and short introduction.
  3. Slide filled with most of pictorial and graphical representation of their experimental findings.
  4. Seminar deliver : describe picture or graph try to make audience understand of new discovery.
  5. Spend time using scientific terms to describe the results, science and mechanism.
  6. Acknowledge : whole team(s).
  7. Aware of time limit.
Important, this is not intended to make a conclusion that all South Asian scientists do as mentioned above, and neither all European/American scientists can always do in this manner.

Wednesday, January 05, 2011

View a Glimpse and Visit Ravishing Nepal

       Sometimes, lacking of development, and abhorring science and technology may be beneficial preserving natural beauty and ecosystem, ancient culture and heritage, etc. Nepal has the evidence of it.
       In spite of small territory, diverse flora and fauna, language, ethnic group and culture, religion along with the highest peak in the world (Mt. Everest), seraph of peace (Buddha) has been stowed in Nepal, which is not in other country.
       Nepal is celebrating 2011 as "Nepal Tourism Year 2011".


       Courtesy: http://www.vn2011.blogspot.com