Finally, we got Publication in International Journal

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After a long waiting, between frustration and enthusiasm, we read enthusiastic and pleasant news about the acceptance of our article in international journal. And surprisingly, it is included in top five "highly accessed" articles for this month (February, 2012).

We had spent almost two years in this research including literature search and writing time. Kathmandu Model Hospital and Central Department of Microbiology had provided lab facility.  Although we had not got any kind of stipend and financial support and even no internet facility in lab or university (it was not free), we did it.  We used to visit Cyber café @ Rs. 20-40 /hour for literature search and related articles. The co-authors, Pankaj Baral and Sanjiv Neupane had spent their pocket money to purchase chemicals such as DNA ladder, restriction enzymes, etc. I spend pocket money for collection of various medicinal plants and some medicines (in kg) that we are using traditionally. Some of our relatives and colleagues used to laugh at us and say it was craziness. This had created a bit disappointment, but we had the enthusiasm for science and research. These days, scientists from most of the developed countries are demanding from Government not to cut the budget for Science and Technology, where as we are struggling for a fraction of amount the budget for Science and Technology.

We would like to thank and express a heartful gratitude to Prof. Dr. Ronald Bauerele, Virginia University School of Medicine, USA, who trained us about the technique of Molecular Biology during six months stay in Nepal. Also, he provided technical and moral support along with science discussion. Thanks to Prof. Dr. Anjana Singh, Central Department of Microbiology, Dr. Bharat Pradhan, Kathmandu Model Hospital and obviously our mentors for guidance and for the arrangement of laboratory.

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

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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: 10.1038/480322a

Install OpenBabel in Fedora 16 to convert chemical file formats

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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.

PhD opportunity for Nepalese

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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.

Update Mendeley, Reference Managing Software

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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.

Arthritis (बातज्वर), Molecular Mechanism of Pathogenesis

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

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

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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.

Medicinal Plants in Nepal, Acorus calamus (बोझो)

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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....

महिलाहरुमा autoimmune रोगको सम्भावना ज्यादा हुने कारण

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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 ।

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

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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:

Install LibreOffice in Older Version of Fedora

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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.

Nepalese in Reputable Science Journals

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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.