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Pakistan-United States Science and Technology Cooperative Program
(ESP-A-00-05-00001-00)

Summary of National Academies Activities, November 1, 2006 – October 31, 2007


This reporting period was the second year in which the program was managed by the
National Academies. Ten of the eleven grants initiated under the 2005 program cycle continued
for a second year in 2007, and sixteen new grants were awarded in the 2006 cycle (thirteen under
the regular Science and Technology Cooperative Program and three under the special
Cooperative Program in Earthquake-Related Research). Despite the challenges of operating at a
time when the security situation in Pakistan was at times more difficult than usual, the 26
projects active in the program as of October 31, 2007, continued to build strong Pakistan-US
linkages in a wide range of fields with a potential impact on Pakistan’s development. With
approximately a dozen more projects to be initiated in early 2008 under the 2007 program cycle,
the coming year will see nearly 40 active projects under way, and it is hoped that future
application cycles will be supported in order to build on existing accomplishments and further
expand the program’s impact.
Following is a summary of administrative activities carried out on the program in the past
year, along with overviews of all projects active during this reporting period.

Pakistan-US Science and Technology Cooperative Program

In December 2006, National Academies staff member Kelly Robbins and US review
panelists Christopher Howson (public health/epidemiology), Rumana Riffat (water resources),
and Russ Zajtchuk (medical) traveled to Pakistan to participate in annual meetings on the
Pakistan-US Science and Technology Cooperative Program with USAID staff and counterparts
from the Higher Education Commission (HEC) and Ministry of Science and Technology
(MoST). On December 11, HEC hosted a meeting at which the eleven Pakistani principal
investigators from the projects funded in the 2005 program cycle made presentations on their
progress over the past year. December 12 was devoted to site visits by the US panelists and
staff: Rumana Riffat traveled to Lahore to visit two projects at the University of Engineering and
Technology, Christopher Howson visited the National University of Sciences and
Technology/National Institute of Transportation in Risalpur (accompanied by the US partners on
the project, who happened to be visiting from Michigan State University at that time), and Russ
Zajtchuk and Kelly Robbins traveled to Faisalabad, where they visited projects at the University
of Agriculture and the National Institute for Biotechnology and Genetic Engineering. On
December 13-14, the US panelists and staff reconvened in Islamabad for joint meetings with
counterparts from HEC and MoST to review new proposals for both the S&T and earthquake
grants programs, select the new awardees, discuss progress made by 2005 grantees, and
authorize continued funding for multi-year projects in that cycle. On December 15, most of the
US panelists departed for home, but Christopher Howson and Kelly Robbins remained for
additional site visits to the Ghulam Ishaq Khan Institute of Engineering Science and Technology
(Topi) and the National University of Sciences and Technology (Rawalpindi), respectively.
They then traveled to Lahore to observe a forensics training workshop presented at the Center for
Applied Molecular Biology on December 16 by one of the 2005 grantees.

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At the joint panel meeting, thirteen new S&T projects were selected for funding
beginning in 2007 (see Appendix A for list; project descriptions follow in the narrative below).
Following the meeting, Academies staff notified the new grantees of their awards and worked
with their institutions to set up the necessary grant paperwork. In addition, applicants whose
proposals were not successful were also notified and upon their request provided with review
comments and guidance on reapplication.
After the awards were made, Academies staff remained in contact with the US grantees
to review and approve their travel plans, pass their itineraries along to the mission as requested,
and gather updated information on their progress for posting on our websites for each project,
which are linked from
http://www7.nationalacademies.org/dsc/PAKUS_Grantees_2005.html
and
http://www7.nationalacademies.org/dsc/PAKUS_Grantees_2006.html
. In addition, cases of
Pakistani program participants who indicated that they were having visa-related problems were
submitted to the International Visitors Office at the National Academies. The staff of this office,
the costs of whose services are not charged to the cooperative agreement, maintains regular
contacts with the State Department to try to help with visa delays.
In the spring of 2007, Academies staff worked with USAID and HEC staff to modify the
program application materials to add to the evaluation criteria a point focusing on the extent to
which applicants have demonstrated a commitment to including women in their projects. After
the materials were revised, the program was publicized by circulating e-mails to interested
individuals and relevant US and Pakistani organizations (see Appendix B for 2007
announcement). A total of 116 proposals arrived for the deadline of June 30, 2007, but shortly
thereafter one US applicant requested that her proposal be withdrawn from consideration (see
Appendix C for a complete list of proposals received). Four new US review panelists were
recruited, three to replace members who were unavailable this year and the other to cover the
field of nanotechnology and materials science, an area in which an increased number of
proposals was received this year (see Appendix D for information on the 2007 panel). The panel
met at the National Academies on October 11-12, 2007, and selected 25 proposals as being of
top priority for funding (see Appendix E). Due to time constraints and the larger number of
active projects up for continuation (eight from the 2005 cycle continuing into their third years,
plus thirteen from the 2006 cycle entering their second years), panel members reviewed the
progress reports of ongoing projects and submitted their comments by e-mail after the meeting.
The US panel’s list of priority projects was circulated to our counterparts at HEC and
MoST and shared with USAID staff. Potential questions regarding the allowability of certain
types of research were also highlighted for resolution in consultation with USAID.

Pakistan-US Cooperative Program in Earthquake-Related Research

At a special session during the December 2006 joint panel meetings in Islamabad,
USAID, HEC, and National Academies staff met to consider evaluations of the twelve full
proposals received for the deadline of October 9, 2006. Evaluations and rankings produced by a
three-member US expert panel were compared with reviews made on the Pakistani side, and
three projects were ultimately selected for funding. A total of $500,000 was awarded on the US
side, while HEC increased its contribution from the originally promised level of $500,000 up to
$590,000. A list of the full proposals reviewed and biographical information on the US panelists
are included at Appendix F, and progress reports on the three projects funded are presented later
in this narrative. In addition, updates on the projects, including links to the full reports submitted

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by the grantees, may be accessed through links on the main program page at
http://www7.nationalacademies.org/dsc/PAKUS_Earthquake_Grants.html
.

Plans in Near Future

The annual joint review panel meeting for 2007 had been scheduled to convene in
Islamabad November 6-9, with US panelists Christopher Howson (public health/epidemiology),
Atif Memon (computer science/information technology), and Henry Vaux (water resources) set
to travel along with Academies staff member Kelly Robbins. All but Dr. Vaux were also
scheduled to make several site visits to currently active projects at the Aga Khan University and
NED University in Karachi on November 5. However, the imposition of the state of emergency
in Pakistan early in the morning of Sunday, November 4, led to the last-minute cancellation of
the trip upon the recommendation of USAID mission staff. Efforts were made to minimize
losses, and fortunately one panelist had not yet departed the United States, so the cost of his
ticket could be recovered, but the very late change of plans unfortunately led to unavoidable
costs for air tickets used and cancellation fees for hotel rooms and meeting arrangements. We
are now trying to find dates in January 2008 that will work for all parties involved, although
budget constraints may require a smaller traveling delegation unless supplemental funds might
be provided.

Summary of Activities to Date on S&T Projects Funded in 2005 Cycle

Following are summaries of the ten projects funded under the Pakistan-US Science and
Technology Cooperative Program in 2005 that continued through 2007 (one other one-year grant
under this cycle was completed on schedule at the end of 2006). Grantees were required to
submit first-year progress reports by September 30, 2007, and copies of those reports are
presented in a separately bound annex to this report.

Development of a Strategic Model for Improvement of Construction Project Management
Education, Research, and Practice in Pakistan (2006-2008)
Syed Mahmood Ahmed, Florida International University, Miami
Sarosh Hashmat Lodi, NED University of Engineering and Technology, Karachi
Pakistani Funding: $275,000
US Funding: $130,000

According to these researchers, the absence of an integrated system of construction
management education, research, and practice in Pakistan has resulted in low output by the
country’s construction industry, which is the second largest sector in the Pakistani economy after
agriculture. To address this problem, Drs. Ahmed and Lodi aim to

• Investigate the current state of the construction industry in Pakistan
• Develop a strategic model for improving construction management education, research,
and practice in Pakistan
• Devise a framework to standardize construction industry practices for achieving
improved performance on cost, time, quality, risk response, aesthetics, reliability, and
safety

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• Build the construction management capacity of academia, industry, and government

After first developing the necessary survey instruments for their study and fine tuning
them based on feedback from pilot surveys, in late 2006 the researchers proceeded to the next
phase of the project—conducting detailed, structured surveys with contractors, consultants,
suppliers, owners, government agencies, educational institutions, and other industry
stakeholders. They collected data on a wide range of issues including general construction
project management practices, causes of delays, delay mitigation practices, risk and safety
management, and the business environment and regulatory framework.
In 2007, Mr. Rizwan Ul Haque Farooqui, an assistant professor at NED University,
continued his PhD studies in construction engineering and management at Florida International
University, having arrived there in the fall semester of 2006. Another NED assistant professor,
Mr. Farhan Saleem, began his Master’s studies at FIU in January 2007, and NED lecturer Mr.
Muhammad Saqib began an on-line Master’s program the same month through FIU’s distance
learning program. Meanwhile, Drs. Ahmed and Lodi and their colleagues continued to compile
and analyze their survey data and develop a strategic model for improving the construction
industry in Pakistan. To this end, Dr. Lodi made a two-week visit to Florida in April 2007 and
Dr. Ahmed spent most of the summer in Karachi. In addition, a total of three workshops and
five training sessions have been organized in Pakistan for more than 360 industry professionals
and academics so far this year. Originally planned for the fall of 2007, an international
conference to further work on developing and implementing the strategic model has been
postponed to the summer of 2008 in view of the current security situation. However, additional
workshops and training sessions will also be presented during the coming year, and Muhammad
Saqib is expected to begin his in-person graduate studies at FIU in the spring of 2008. Dr.
Ahmed also plans to visit Karachi from mid-December 2007 through mid-January 2008.

Development of Guidelines for Asphalt Pavement Recycling in Pakistan (2006-2008)
Gilbert Y. Baladi, Michigan State University, East Lansing
Tayyeb Akram, National University of Sciences and Technology, National Institute of
Transportation, Risalpur
Pakistani Funding: $500,000
US Funding: $350,000

Tremendous increases in vehicle traffic over the past two decades have led to high rates
of pavement deterioration on the Pakistani road system. This project proposes to address this
problem by introducing asphalt recycling technologies to Pakistan and developing guidelines for
their use. Recycling involves the reuse of existing roadway materials in the cost-effective
reconstruction or rehabilitation of pavements. The price of asphalt, a product of petroleum
refining, has increased many times over in recent years, so finding a way to reuse it makes
economic sense. There are environmental benefits as well, as recycling pavement reduces the
amount of waste that must be sent to landfills. This project, which involves several collaborating
researchers at each partner institution as well as linkages with industry and government, includes
both technical studies of asphalt materials and policy studies that will analyze the potential
savings to be realized from recycling and propose implementation plans for Pakistan.
Following up on a two-week training visit by Dr. Tayyeb Akram and three graduate
students in August 2006, Dr. Baladi and MSU co-investigator Dr. Syed Waqar Haider spent two

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weeks in Pakistan in December 2006 working with their colleagues at NIT as well as meeting
with officials from the National Highway Administration and the local asphalt manufacturing
industry. The research team also made site visits to an asphalt mixing plant and both hot and
cold in-place recycling sites. The centerpiece of the visit was a three-day highway engineering
workshop held December 16-18, which covered pavement design and analysis, pavement
preservation and rehabilitation, road safety issues, and pavement recycling techniques. Drs.
Baladi and Hyder summarized their findings and recommendations resulting from their visit and
circulated them to the workshop attendees (this document is also posted at
http://www7.nationalacademies.org/dsc/December_2006_Recommendations.pdf
).
In addition to the training aspects, as of October 2007, the Pakistani counterparts at NIT
had received and installed more than $660,000 worth of research equipment, half funded by HEC
funds awarded under this grant and half supported by NIT’s parent organization NUST as a
demonstration of the institution’s strong support for the project. Thanks to this equipment, the
investigators have worked intensively over the past months on surface distress data collection
and in-situ testing of selected pavement sections.
In December 2007, the US team will again visit Pakistan to conduct a two-day short
course on construction and rehabilitation of asphalt and concrete pavements, consult with their
colleagues on on-going testing and analyses, and meet with officials from the National Highway
Authorities regarding the development and introduction of asphalt recycling guidelines. It is also
expected that by the summer of 2008, four Pakistani graduate students will have submitted
master’s degree theses on research conducted as part of this project. The US team plans a final
visit to Pakistan in March 2008.

Gene Pyramiding through Genetic Engineering for Increased Salt Tolerance in Wheat
(2006-2008)
Eduardo Blumwald, University of California, Davis
Anjuman Arif, National Institute for Biotechnology and Genetic Engineering, Faisalabad
Pakistani Funding: $ 47,880
US Funding: $350,000

This project is aimed at developing salt-tolerant wheat varieties that will grow and
produce high yields in areas where the soils have high salt content or are irrigated with brackish
ground water, conditions common in many parts of Pakistan. The researchers involved in this
project hope to achieve their goals by pyramiding two well-characterized salt tolerance genes
(the Arabidopsis thaliana vacuolar sodium proton antiporter AtNHX1 and a heat shock family-
related transcription factor isolated from Candida tropicalis CtHSR1) that will be introduced in
wheat by Agrobacterium-mediated co- or stepwise transformation.
The project was somewhat delayed at its outset because of difficulties the Pakistani
partners encountered in obtaining visas to visit Dr. Blumwald’s lab, but Dr. Muhamad Arif and
Dr. Anjuman Arif of the National Institute for Biotechnology and Genetic Engineering (NIBGE)
successfully completed one-year working visits at UC Davis at the end of August 2007. In 2007,
the transgenic rice plants created in 2006 were grown and tested in the greenhouse under various
salinity and heat stress conditions. After overcoming some initial problems with the wheat
constructs during the first year of their project, they now have T1 and T2 lines expressing NHX1,
and T1 lines expressing HSR1 were in progress as of late September 2007. Field tests of the
transgenic rice plants are already under way, and similar testing of the wheat plants will begin in

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2008. Although the Arifs have now returned to NIBGE, Dr. Blumwald expects to welcome Dr.
Memoona Rauf and another NIBGE researcher in November 2007 for an extended visit to
continue work on the project. With additional support provided by a grant from the National
Science Foundation, Blumwald also organized a US-Pakistan Symposium on Abiotic Stress in
Crop Plants at UC Davis November 4-6, 2007.
Several additional linkages have been initiated as a result of this project, including with
USDA-ARS in Albany, California, the International Rice Research Institute, the International
Maize and Wheat Improvement Center (CIMMYT), and Arcadia Biosciences, Inc. Dr.
Blumwald reports that these collaborations will be useful not only in bringing additional
expertise to bear but also in carrying out the necessary field trials for the plants being developed.

Antimicrobial Resistance in Pakistan: a Program to Develop and Strengthen Capacity for
Surveillance, Containment, and Diagnosis through Public-Private Sector Partnership
(2006-2008)
Mary Brandt, Centers for Disease Control and Prevention, Atlanta
Rumina Hasan, The Aga Khan Medical University (AKU), Karachi
Pakistani Funding: $500,000
US Funding: $ 75,000

The rising infectious disease burden in Pakistan is a major source of concern, and efforts
to control such diseases are hampered by the incessant increase in antimicrobial resistance
(AMR) in the country. This project aims to initiate a data collection and compilation system to
assess the prevalence of AMR and conduct molecular typing on selected bacterial strains.
Information on AMR is being disseminated to healthcare providers and professional
organizations to help promote data-driven programs for the containment of AMR. Infection
control measures are also being promoted as important intervention strategies. The principal
investigators have assembled a diverse multidisciplinary team with strengths in clinical
microbiology, infectious diseases, epidemiology, and infection control with linkages to key
national and international institutions, including major Pakistani hospitals, research centers, and
government agencies.
Continuing their project after a very active year in which nearly 500 participants were
trained in 2006, the Pakistani partners on this effort launched the Pakistan Antimicrobial
Resistance Network (PARN) in 2007. To extend surveillance for antimicrobial resistance
beyond Karachi and increase awareness about antimicrobial usage and surveillance for
resistance, a national-level meeting was also held in Karachi in March 2007. Participants
included clinical microbiologists and infectious diseases experts from Lahore, Islamabad, and
various Armed Forces hospitals in addition to representatives from the National Institutes of
Health and Pakistan Medical Research Council. A follow-up meeting was held in Islamabad on
June 26, 2007, to discuss extending awareness about antimicrobial stewardship and surveillance
to a larger number of public sector health facilities in the country. The aim of the meeting was to
establish a network of hospitals in which systems could be developed for monitoring
antimicrobial resistance and where resistance information could be utilized to institute
appropriate antimicrobial policies. Issues of antibiotic misuse, surveillance for antimicrobial
resistance, as well as educational programs to encourage good antibiotic prescribing practices
and to develop strategies for appropriate antimicrobial usage were discussed.

6
Five training sessions on infection control practices were also held during 2007,
providing training to approximately 250 medical personnel and hospital auxiliary staff, and a
five-day workshop was held in May 2007 focusing on smear microscopy for tuberculosis
diagnostics, following up on a similar workshop in 2006. Additional mycology, parasitology,
infection control, and biosafety workshops are planned in December 2007 to provide Pakistani
hospital and laboratory personnel with instruction and hands-on experience.
On the US side, CDC hosted two AKU staff members, Ms. Shahida Qureshi and Ms.
Maqboola Dojki, for a BSL-3 laboratory safety training course at Emory University in November
2006, and Ms. Quereshi stayed on for an additional two weeks gaining practical experience in
the clinical microbiology laboratories at Emory. In 2007, Noureen Saeed of AKU, who had
visited in the summer of 2006, returned to CDC for three more months of mycology training and
analytical work on fungal samples (June-September 2007), and three other AKU researchers
received training at CDC and elsewhere. To disseminate and share the information learned
during these visits, mycology, parasitology, infection control and biosafety workshops are
planned in December 2007 in which Pakistani participants will be provided hands-on experience.
US principal investigator Dr. Mary Brandt and a colleague, Dr. Beth Skaggs, chief of the
Antifungal Drugs Unit at the CDC Mycotic Diseases Branch, have been unable to secure the
agency clearance they require to travel to Karachi to conduct a planned workshop on antifungal
susceptibility testing at AKU. Given the current security situation and the unfavorable prospects
for receiving such clearance in the near future, they are currently consulting with their AKU
partners on other options for use of the funds that had been budgeted for their travel.

Capacity Building for Research, Education, and Training in Water Resources Management
in Pakistan (2006-2008)
M. Hanif Chaudhry, University of South Carolina
Muhammad Latif, University of Engineering and Technology (UET), Lahore
Pakistani Funding: $500,000
US Funding: $100,000

This project is aimed at building the capacity of the Center for Excellence in Water
Resources Engineering (CEWRE) at UET Lahore by providing education and training to
Pakistani graduate students through in-person and Internet-based courses, faculty exchanges, and
basic and applied research activities. Beyond the educational aspects, the research goals of the
project focus on providing engineering tools to Pakistani engineers and scientists so that they can
better assess, implement, and monitor their water resources systems. Physical laboratory studies
are being carried out and numerical models developed to plan and evaluate the performance of
hydraulic structures and control channel erosion and sediment transport. Models are also being
developed to study water resources management for irrigation and drainage, and modeling tools
are being applied to evaluate flooding and draining system capacities at selected sites in
Pakistan.
Due to visa problems experienced by Dr. Latif during 2006, the partners communicated
during the first year of their project by telephone and e-mail to work out the details for
undertaking various project tasks. Meanwhile, two concept papers prepared by CEWRE
researchers for conducting cooperative research were reviewed by USC counterparts, two joint
research papers have been accepted for publication in Irrigation and Drainage Journal, and two
more papers are under review by other journals. A list of equipment required for distance

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learning was prepared by CEWRE and reviewed by USC, and as of the fall of 2007 the
equipment has been installed and is being tested.
After waiting more than one year, Dr. Latif finally received his US visa in June 2007. He
and a colleague, Dr. S.M. Saeed Shah, visited USC in August and September 2007, during which
they met with all USC faculty and staff members involved in the project and also visited the
university’s audio-video facility for consultations on establishing the distance learning center at
UET. Dr. Latif also had the opportunity to visit a farmer in eastern South Carolina to learn more
about cotton irrigation using center pivot sprinklers. Dr. Latif also presented a seminar that was
attended by the faculty and graduate students of Civil Engineering Department. Meanwhile, Dr.
Shah worked with Dr. Michael Meadows from USC to plan activities in storm water
management. A visit by another UET researcher, Mr. Waqqas-ur-Rehman, is expected in the
spring of 2008. Two CEWRE faculty members (Mr. Kaleem Sarwar and Mr. Masood) have also
been nominated to pursue their PhDs at USC. One has been accepted and pending resolution of
visa difficulties is expected to begin his studies in the spring of 2008, while the other was
expected to take the required entrance examinations in the fall of 2007.
US co-investigator Dr. Jasim Imran of USC visited Pakistan in January 2007 to take part
in a Workshop on Hydraulics and Sediment Transport in Streams. During his visit, Dr. Imran
also presented seminars and assisted with the development of pilot Internet-based courses,
physical laboratory-based modeling, and mathematical sediment transport modeling. Dr.
Chaudhry is expected to visit Lahore in January 2008, and Dr. Meadows and Dr. Jon Goodall
will visit in the spring of 2008. During their visits, plans call for the USC researchers and their
UET counterparts to participate in workshops and training courses on such topics as hydraulic
modeling of transient flow, storm water management, and GIS and remote sensing applications
in water resources.

Understanding and Control of Plant Viral Disease Complexes in Pakistan (2006-2008)
Claude M. Fauquet, Donald Danforth Plant Science Center
Shahid Mansoor, National Institute for Biotechnology and Genetic Engineering (NIBGE),
Faisalabad
Pakistani Funding: $142,000
US Funding: $175,000

Plant viruses are becoming increasingly widespread and virulent in Pakistan, leading to
reduced yields for food and fiber crops. This project aims to enhance the laboratory
infrastructure at NIBGE and improve the expertise of its researchers in molecular virology
techniques to understand and control plant viruses. Specifically, the researchers will work on
developing new diagnostic tools such as DNA chip technology for the detection of multiple plant
viruses and their recombinants and on increasing their understanding of host-virus interactions
and viral proteins that overcome host defense responses.
The Pakistani principal investigator, Dr. Shahid Mansoor, reports that the grant has
allowed him to attract a large number of PhD students and researchers, several of whom are
currently working on project objectives. A young researcher from NIBGE, Dr. M. Shah Nawaz
Khan, was to have begun work as a post-doc at the Danforth Center earlier in 2006 but was
delayed in completing his PhD, pushing back the anticipated date of his arrival in St. Louis by a
few months. When he arrived in early February 2007, he brought with him a number of plasmid
DNA samples prepared at NIBGE for use in research at the Danforth Center. For this part of the

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work, he had surveyed fields in central Pakistan, an area that has been severely impacted by
geminiviruses over the last two decades. During his survey visits to different fields, he worked
in cooperation with experts from cotton-growing areas, including researchers from the Central
Cotton Research Institute at Multan.
US principal investigator Dr. Claude Fauquet traveled to Faisalabad in November 2006 to
participate in a training course on molecular virology at NIGBE and meet with Dr. Mansoor to
review the project. This training course was funded by other sources, but as it dealt with
complementary topics pertaining to viruses and gene silencing, Fauquet reports that it greatly
benefited the project and the students who participated. In November 2007, he also plans to host
another NIBGE researcher, Imran Amin, for a nine-month stay. Dr. Khan is expected to remain
at the Danforth Center until at least August 2008, and another NIBGE researcher, Ms. Javaria
Qazi, has also been nominated to visit St. Louis on the project.
The first two years of this project have already brought a wealth of information on the
viruses and their satellites that are related to cotton leaf curl virus disease, as well as on the
function of some of the viral genes. The project participants report that they are beginning to
understand where these viruses and satellites are coming from, what forces are driving their
evolution, and what potential exists for the appearance of new diseases affecting cotton. They
are also gaining insights as to the function of some of the genes for which these molecules are
coding, either to survive or to be more virulent against the domesticated hosts. There is still
much more to do to completely understand all these elements, but an important first step has
been made. This project has also provided an opportunity to train young Pakistani scientists and
give them access to new technologies such as rolling circle amplification, which has been
extremely important in accessing and cloning a wealth of new viruses and satellites.

Development of Computational Mechanics Infrastructure and Human Resources for
Advancing Engineering Design Practices in Pakistani Industry (2006-2008)
Arif Masud, University of Illinois at Urbana-Champaign (UIUC) and Ashfaq Khokhar,
University of Illinoi at Chicago
Abdullah Sadiq, Ghulam Ishaq Khan Institute (GIKI) of Engineering Science and
Technology, Topi
Pakistani Funding: $302,000
US Funding: $220,000

Computational mechanics supports simulation-based design leading to virtual prototyping
of engineering devices, serving as a bridge between physical engineering design and theoretical
and conceptual modeling. While other countries have invested in developing indigenous
expertise in the field in order to enhance their industrial competitiveness, Pakistan’s
computational mechanics resources have up to now been limited. This project aims to address
the problem by developing both human resources and the technical infrastructure to promote the
application of advanced engineering design methodologies in contemporary product
development. It is hoped that the program being created at GIKI will grow into a self-sustaining
center that will serve as a liaison with industry on emerging industrial design needs.
This project includes organization of hands-on tutorials and workshops on computational
methods and simulation techniques for faculty, students, and industry practitioners, development
of an interdisciplinary computational mechanics curriculum at GIKI, and creation of a high-
performance computing platform to support large-scale simulation needs. After consultations

9
with the US partners, the components for the Beowulf cluster were purchased and installed in the
fall of 2006. This 64-node Beowulf PC cluster connected via gigabit Ethernet is the centerpiece
of the new High Performance Computing Lab. Available for use by faculty and research staff as
well students, this cluster provides the backbone for large-scale computational projects at GIKI.
In December 2006, Dr. Masud returned to Pakistan for a third visit on the project to
review progress on the new course curriculum, help evaluate the performance of the new PhD
candidates and Master’s students, and work with GIKI colleagues to install additional codes on
the new Beowulf cluster. During the summer of 2007, Drs. Masud and Khokhar presented
another short course at GIKI on nonlinear finite element methods June 4-8, 2007, and Dr. Masud
and another UIUC colleague, Dr. Rizwan Uddin, presented seminars on related topics in
mechanics that were well attended by GIKI staff, students, and representatives of other
academic, industrial, and research institutions. A website on the project has also been
established at
http://www.giki.edu.pk/go/pakus/index.htm
.
So far, this project has already spurred increased awareness among academicians and
industry practitioners on the importance of computational mechanics in engineering design and
analysis. Approximately 200 professionals have been trained through workshops and seminars,
including graduate students and practitioners from different industrial and academic
organizations. Thanks to the high performance computing infrastructure now available at GIKI,
and some off-the-shelf available professional software, high-end solutions to problems of
importance to industry are now possible in Pakistan, solutions that would not have been possible
otherwise. National University (NU-FAST) faculty members trained at GIKI workshops offered
under this project have started teaching parallel computing courses and carrying out small
projects on parallel computing and distributed networking. GIKI has been requested to allow NU
students and faculty to utilize GIKI’s computational infrastructure for research, and other
Pakistani academic institutions are also showing interest in utilizing the high-end computing
infrastructure developed at GIKI.
Plans for the coming year include a December 2007 visit by the US investigators to GIKI,
a short course on nonlinear finite element methods to be presented at GIKI in the summer of
2008, and a condensed course on high performance computing and advanced data structures.
The Pakistani partners on the project are expected to visit UIUC in the summer, and a GIKI PhD
student, Mr. Masroor Hussain, is expected to arrive for a one-year stay in January 2008.
Meanwhile, the original Pakistani principal investigator, Dr. Sadiq, left his position at GIKI as of
September 17, 2007, and has been replaced on this project by Dr. Mohammad Abid, who had
formerly been involved as a co-investigator.

Establishment of Extrusion Center of Institute of Food Science and Technology, University
of Agriculture, Faisalabad (2006-2007)
Mian Nadeem Riaz, Texas Engineering Experiment Station
Faqir Muhammad Anjum, University of Agriculture (UAF) Institute of Food Science and
Technology, Faisalabad
Pakistani Funding: $389,000
US Funding: $320,000

Extrusion is a cooking process that produces an expanded or puffed crispy product
generally based on cereals or legumes. During the process, proteins and other additives made be
incorporated to enhance the quality of the end product. Extrusion processing for both food and

10
animal feed products has become very popular worldwide, but until now Pakistan has not had
access to this technology. This project aims to establish a new extrusion center at the Institute of
Food Science and Technology in Faisalabad in order to train scientists, students, and food and
feed industry personnel in the use of extrusion technology for processing foods, oilseed crops,
and feed ingredients.
After consulting with Dr. Riaz during the first year of the project, UAF began offering a a
new course in Extrusion Technology to undergraduate students in the fall 2007 semester. Dr.
Riaz returned to Faisalabad for visits in February and June 2007 to continue work on the project,
monitor progress on the new center, present papers at conferences, deliver lectures at UAF, and
advise graduate students who have begun working on extrusion-related research projects. Two
food technologists have been hired to develop new food and feed projects based on locally-
grown ingredients and to work with other Institute researchers and representatives of private
industry to promote the use of extrusion technology. Drs. Riaz and Anjum have met with at least
two Pakistani food companies who are interested in becoming involved in the project, and they
are also seeking cooperation with relevant NGOs focused on efforts to combat malnutrition.
Dr. Anjum visited the United States for three weeks in July-August 2007. In addition to
extensive consultations with Dr. Riaz and other faculty members at Texas A&M, he also visited
Kansas State University, Michigan State University, and Indiana State University and attended
the annual meeting of the Institute of Food Technologists along with Dr. Riaz. He also visited
the manufacturer of the extruder purchased by UAF to discuss installation and operation of the
equipment, which arrived at his university in late July 2007. Meanwhile, a Pakistani graduate
student was also accepted to Texas A&M and began his PhD program in food science and
technology under Dr. Riaz’s supervision in January 2007. In October-November 2007, Dr. Riaz
made a final visit to UAF on the project, during which he attended the official inauguration of
the new extrusion center and participated in the International Symposium on Emerging Trends in
Food Science and Technology.

Determination of Heavy Metals and Polycyclic Aromatic Hydrocarbons in Airborne
Particulates in Lahore, Pakistan, and Madison, Wisconsin, USA (2006-2008)
James Jay Schauer, University of Wisconsin-Madison
Tauseef A. Quraishi, University of Engineering and Technology (UET), Lahore
Pakistani Funding: $107,625
US Funding: $ 80,000

Implementation of an air pollution control strategy is still at its early stage in Pakistan,
and while some emissions standards have been set, national and provincial environmental
protection agencies lack the resources and expertise needed for monitoring and enforcement.
The researchers involved in this project are collecting data on ambient air quality in Lahore,
especially with regard to particulates, heavy metals, and polycyclic aromatic hydrocarbons.
Source apportionment techniques developed at the University of Wisconsin are being applied to
the Lahore data to identify the main sources of air pollutants. By identifying and quantifying the
pollution sources, they then aim to devise a cost-effective control strategy to improve air quality
in Pakistan. The project includes improvements in the laboratory infrastructure at UET Lahore
as well as in the capabilities of its faculty to conduct research and train much-needed new PhDs
in this field.

11
In January 2007, Dr. Quraishi and his graduate students began conducting a year-long air
sampling project in Lahore, following up on the pilot study they conducted in the spring of 2006.
They are using a comprehensive PM
2.5
and PM
10
sampler—the same model being used by the
University of Wisconsin for other projects the Middle East and Asia—that was prepared for use
during Dr. Quraishi’s summer 2006 visit to Madison. Dr. Quraishi has also initiated several new
analytical methods in his laboratory both for use in this project and in future efforts. Chemical
analyses of the samples collected in the study have commenced at the University of Wisconsin
and UET Lahore. These measurements and associated source apportionment analyses will
continue through the end of Year 2 of the project and will be completed in Year 3. This work is
expected to lead to several publications detailing the sources of particulate matter pollution in
Lahore and comparing these results with the parallel measurements in the Middle East, Asia, and
the United States being conducted under Dr. Schauer’s direction.
As part of these efforts, Dr. Quraishi returned to Madison as a visiting professor during
the summer of 2007, and additional exchange visits are planned in 2008. Two joint papers on
the unique data set compiled during the project were presented at the 14
th
World Congress of the
International Union of Air Pollution Prevention and Environmental Protection Associations, held
in Brisbane in September 2007. In addition, one manuscript covering the pilot study has already
been submitted for publication, and two additional manuscripts will be submitted before the end
of Year 2 of the project.

Intensification of Forensic Services and Research at Centre for Applied Molecular Biology
(2006-2007)
Mohammad Ashraf Tahir, Strand Analytical Laboratories, LLC
Sheikh Riazuddin, Centre for Applied Molecular Biology, Lahore
Pakistani Funding: $118,650
US Funding: $160,000

The Centre for Applied Molecular Biology (CAMB) is currently the only dedicated
laboratory in Pakistan engaged in forensic DNA research, and it provides DNA testing services
in criminal cases, mass disasters, and paternity disputes. This multifaceted project is designed to
address the three primary elements of forensic science—evidence collection, analysis, and
presentation—in expanding CAMB’s technical infrastructure and improving the skills of its staff
and others involved in the collection and use of evidence. For example, law enforcement and
medical personnel will be trained in evidence collection techniques, and attorneys will be
instructed on the basics of forensic science so that they can adequately use such evidence for
prosecution or defense purposes. On the infrastructure side, CAMB’s existing DNA testing and
serology facilities will be improved and new capacities will be added for the analysis of
fingerprints, hair, fiber, and chemical trace evidence.
Building on the success of several training programs offered in Year 1 of the project,
several additional workshops were held at CAMB this past year. On December 15-16, 2006, a
two-day workshop on crime scene search and modern forensic techniques attracted 79 attendees
from various civilian and military police agencies and medico-legal physicians. In conjunction
with this event, a one-day workshop for members of the judiciary, “DNA for Justice,” was
conducted on December 16, 2006. In addition to Dr. Tahir, US presenters included Judge Lisa
Borges (formerly a public prosecutor) and Mr. Terry Gilbert, a defense attorney. Supreme Court
Justice Rana Bhagwan Das (who was subsequently removed from office after the declaration of

12
the state of emergency in November 2007) served as keynote speaker for the event, which was
attended by twenty-four judges, prominent lawyers, and members of the CEMB staff. On July
18-19, 2007, another two-day workshop on crime scene evidence collection, preservation, and
chain-of-custody was held at CAMB, and a final workshop was held November 21-22, 2007.
After four young staff members from CAMB successfully completed six months of training at
Strand in 2006, two more arrived for a similar training program in September 2007. Also, Dr.
Tahir left Strand in June 2007 and has now been replaced as principal investigator on the project
by Strand Chief Operating Officer Susan Narveson.

Summary of Activities to Date on S&T Projects Funded in the 2006 Cycle

Association of Particulate Matter with Daily Morbidity in Urban Populations (2007-2009)
David O. Carpenter, University at Albany
Gregory Pappas, Aga Khan University, Karachi
Pakistani Funding: $148,739
US Funding: $126,295

In recent years, interest in the health effects of air pollution in Asia is rapidly growing
due to increasing knowledge of the health effects of air pollution and to the alarmingly high
levels of air pollution in Asia’s major cities. The rapid and continuing increase in the population,
vehicular traffic, and industrial development combined with meteorological conditions,
inadequate transport infrastructure, lax environmental legislation and enforcement, weak
institutions, and lack of sufficient skilled research and policy personnel have resulted in poorly
planed urbanization and severe air pollution problems in Pakistan with serious health impacts.
This study will investigate the effect of short-term exposure of fine particulate matter
(PM
2.5
) in ambient air on hospital admissions and emergency room (ER) visits for respiratory
and cardiovascular diseases among adults and young children in Karachi. The PM
2.5
mass will be
collected for 24 hours at multiple sites in the city, and daily records of hospitalizations and ER
visits for respiratory and cardiovascular diseases at six hospitals serving the areas will be
examined for three years to estimate associations with air pollution on ER visits or
hospitalizations while controlling for long-term trends, seasonality, and weather. This first-of-its-
kind study aims to provide Pakistani scientists and decision makers with scientific evidence on
the magnitude of health effects related to air pollution in urban centers of Pakistan over the next
few years.
During this first year of the project, the investigators report that they have been hindered
by the slow process of obtaining the necessary institutional review board approvals from the
various Pakistani and US entities involved. As of late October 2007, however, the problem
appeared to be resolved, and Dr. Carpenter and his co-investigator Dr. Haider Khwaja visited
AKU at that time to confer with their partners on next steps. Despite the IRB approval delays,
the US partners report that real progress has been made in planning the project even though data
collection has not begun. Thanks to other funding, Pakistani collaborator Dr. Aftab Turabi
visited Albany for nine months and has now returned to Pakistan, where he helped to move the
approval processes along. In addition, numerous conference calls have helped in shaping plans
for program implementation. Now that the institutional approvals are in order, the participants on
both sides hope to move forward quickly on their sampling and analytical work.


13
Secure Pakistan Wheat Production through Controlling Rusts (2007-2009)
Xianming Chen, Washington State University
Muhammad Ashraf, Quaid-e-Azam University, Islamabad
Pakistani Funding: $241,884
US Funding: $100,001

Wheat is an essential food resource and grown all across Pakistan, and with ever-
increasing yield targets to meet national production goals, incorporation of stripe rust resistance
into Pakistan’s leading cultivars is currently a high priority. Monoculture of the Inqilab 91
variety has caused the disease to become widespread, and cultivar susceptibility is posing serious
problems. The need for new genes to counter the threat is crucial, and this project is aimed at
identifying genes offering protection against rust virulences and transferring them into
commercial cultivars using efficient molecular tools. Wheat rusts are a major threat to
production in the United States as well, so successful accomplishment of the objectives of this
project will benefit wheat producers in both countries.
The project will adapt the system, approaches and technologies established in the US
partner’s laboratory in studying epidemiology of wheat stripe and stem and leaf rusts, identifying
wheat germplasm resistance to these diseases, and developing molecular markers for efficient
breeding resistant wheat cultivars to control these diseases and thus securing wheat production in
Pakistan. Another goal of this project is to establish a genotyping lab at Quaid-i-Azam
University along the lines of a laboratory recently established in the USDA-ARS unit at
Washington State University, which will give Pakistani researchers new opportunities to use
modern molecular techniques. Through the proposed project, the partners involved will exchange
wheat germplasm with rust resistance and other valuable traits, an exchange that should also be
beneficial for wheat breeding programs in the United States.
During the first year of the project, researchers on both sides have been busy analyzing
the germplasm samples they have collected and conducting field trials on more than 40 wheat
lines to determine their susceptibility to leaf, stripe, and stem rusts. New crosses are also being
cultivated and studied. On the Pakistani side, a research associate and PhD and MS students
have been engaged to work on the project. A Pakistani postdoc is expected to visit Dr. Chen’s
laboratory for one year, and a PhD student will visit for six months. Additional field trials and
collection trips are also planned for the coming year. In addition to the primary partner
institution, Quaid-i-Azam University, the project will also involve researchers from the National
Wheat Research Stations, including Ayub Agriculture Research Institute in Faisalabad, the
Nuclear Institute for Food and Agriculture in Peshawar, the National Institute of Tandojam, and
the Regional Agriculture Institute at Bahawalpur.

Capacity Building in Research Ethics and for Research on Ethics (2007-2008)
Adnan A. Hyder, The Johns Hopkins University
Aasim Ahmad, Aga Khan University
Pakistani Funding: $232,732
US Funding: $150,000

The goal of this project is (1) to improve the ethical conduct of human subject research in
light of indigenous sociocultural values in Pakistan and (2) to develop skills and capacity to
conduct research on ethics in Pakistan. The development of capacity in Pakistan in research

14
ethics involves the rationale that not only international collaborative research involving
developing counties is increasing exponentially, but there is also a concerted effort to increase
the number of researchers in these countries. To achieve this objective, this proposal envisages
six research ethics certificate courses of three months duration over two years. Thus, at the end
of two years this project will have trained and certified 120 researchers from all over Pakistan in
research ethics. This will be achieved by Johns Hopkins faculty members conducting workshops
and seminars in Pakistan and by Pakistani faculty from AKU attending short courses at Johns
Hopkins. During the first year of the project, participants will also develop three research
projects to be carried out by AKU personnel in the second year, thus providing them with further
capacity development opportunities.
The proposed certificate course will have two components comprising modules in basic
bioethics and research ethics. The former will be a foundational module comprising 80 contact
hours with a focus on three broad areas: bioethics history and issues to date; Western thoughts;
and Islam and its philosophic tradition. The research ethics module, comprising 40 contact hours,
will aim to discuss the essential principles for human subject research. It will examine different
ethical issues raised by clinical trials, epidemiological studies and public health research,
especially in the context of developing countries and international collaborative research. The
long term goal of this project is for the individuals trained to become resource persons in their
respective institutions not only for ethical review of research, but also for eventual establishment
of similar training programs.
Despite several months of funding delays on the Pakistani side, the investigators in this
project report a good deal of progress in getting their activities under way. In May 2007, Dr.
Aasim Ahmad visited JHU for planning meetings with his counterparts, including Dr. Adnan
Hyder (US director), Dr. Hilary Bok (US co-director), and Ms. Lynne Harris (US coordinator).
When the first research ethics workshop was announced in mid-July, it attracted 150 applicants
in only one week, attesting to the great interest in the topic in Pakistan. Thirty students were
selected to participate in the workshop, which was held in Karachi August 4-8, 2007, with Drs.
Hyder and Bok and Ms. Harris serving as key presenters. In October 2007, Dr. Ahmad again
visited the United States and met with the JHU team to plan upcoming activities, including the
selection and placement of two Pakistani research ethics fellows at JHU and the organization of a
longer course in research ethics at AKU scheduled for January 2008. Dr. Ahmad has recently
been informed that he has been awarded a grant from the National Institutes of Health that will
support complementary activities in the area of research ethics education and training, including
the development of a master’s program in this field. These new funds available from NIH will
help to leverage the resources available to his existing joint project with JHU.

The Development, Optimization, and Application of a High-Performing
Engineered Fertilizer (2007-2009)
Syed H. Imam, Gregory Glenn, and Mark Jackson, USDA Agricultural Research Service,
Western Regional Research Center
Farooq-e-Azam, Nuclear Institute of Food and Agriculture, Peshawar
Pakistani Funding: $100,000
US Funding: $116,250

This is a multidisciplinary project that aims to combine fundamental knowledge of plant
growth and development with polymer science and engineering to create a novel, high-impact

15
fertilizer of superior functionality with an inherent sustained delivery mechanism. In view of the
substantial losses of fertilizer nitrogen in the environment, the specific goal of the project is to
engineer a high-performance plant fertilizer (HPF) by encapsulating fertilizer nitrogen for
sustained release. Additionally, in conjunction with fertilizer nitrogen, encapsulation matrices
will also contain essential nutrients, growth stimulants, and biocontrol agents, as well as natural
microbes that fix nitrogen and synthesize humic and growth promoting compounds for optimal
performance. The encapsulation matrix will be constructed from biopolymers such as cellulosic
fiber and starch, as well as nanosized mineral clays as a binder. Sustained release of the active
materials will be achieved via manipulation of biodegradation properties of the matrix polymer.
Upon exposure to soil, microbes, humidity, sunlight, and so forth, the matrix polymers will
degrade at a controlled rate, causing the loosening of the matrix and facilitating the sustained
release of encapsulated agents over a long period. As opposed to multiple applications of a
convention fertilizer, a single application of the HPF will be sufficient until the crop is harvested,
which would not only save time, energy, water, and overall cost, but would also benefit the
environment.
The HPF will initially be tested in a greenhouse using wheat and cotton as test plants for
its impact on the root development, plant growth, and successful colonization of the roots by
useful bacteria. Furthermore, kinetics of the release of nutrients from the matrix will be
determined. Field trials will follow the greenhouse studies to correlate the performance of the
HPF with overall crop yield. The long-term goal of this study is to conduct extensive field trials
to assess the impact of the HPF formulation and evaluate its commercial viability.
As of late September 2007, the project participants reported that they had completed
almost all of their Year 1 objectives, including selection and characterization and matrix
polymers, acquisition and characterization of microbes, evaluation of bacteria for plant growth
promotion, identification of optimal matrices, and preparation and evaluation of humates. Work
on evaluation of plant growth regulator precursors is still under way. The US partners have
presented papers on their work on the project at the International Symposium on Polymers and
the Environment: Emerging Technology and Science, held in Vancouver, British Columbia,
October 17-19, 2007. Although no visits have yet been carried out, Dr. Azam and a colleague
are expected to visit California in 2008 to learn the processing and production of encapsulation
matrices, and Dr. Imam will visit Pakistan to assist with the large-scale production of fertilizer
for greenhouse and field studies. Also during the coming year, the biocontrol agents will be
produced and provided by Dr. Mark Jackson at USDA in Peoria, and cultures will be transferred
to Dr. Azam. Encapsulated biocontrol agents will be tested in greenhouse conditions for their
efficacy against some of the diseases and pests common to major economic crops in Pakistan.
Finally, a matrix with the selected microbial components will be produced in large quantities in
cooperation with the Pakistan Fertilizer Corporation.

Multiplex Immunoassays for the Detection of Tuberculosis (2007-2008)
Paul A. Luciw and Imran Khan, University of California, Davis
Azra Khanum, University of Arid Agriculture
Pakistani Funding: $173,945
US Funding: $189,500

The high prevalence of tuberculosis (TB) in Pakistan is a significant burden to the
country’s healthcare system and its economy. Methods for accurate and cost-effective diagnosis

16
of infection with pathogenic Mycobacterium tuberculosis (M. tb.) are essential for controlling the
spread of this disease in the population. It is critical to detect both the earliest stage of infection
and latent infection and to monitor the efficacy of therapy, but current methods have various
limitations in terms of sensitivity, accuracy, and time-to-result. Building on recent advances in
knowledge of mycobacterial genomics, proteomics, and immunology and in novel multiplex
diagnostic instrumentation for infectious disease, this project is aimed at building healthcare
capacity in Pakistan by developing new multiplex diagnostic methods for detecting TB.
Harnessing the power of collaboration between scientists in Pakistan and the United States, this
project applies recombinant DNA technology and the multiplex immunoassay technology to
achieve four objectives:

• Development and optimization of the Luminex/BioPlex multiplex system for detecting
antibodies and cell-based immune responses to M. tb. and detecting M. tb. antigens.
• Installation of the Luminex/Bioplex instrument at UAAR and training of technical staff in
multiplex detection of TB.
• Application of these novel multiplex assays for cross-sectional and longitudinal studies of
TB patients at the National Tuberculosis Center in Rawalpindi.
• Preparation of a detailed laboratory manual and other training materials that can be used
in Pakistan for detecting M. tb. infection by multiplex immunoassay.

In the course of this collaborative research, several Pakistani graduate students, post-
docs, and research technicians will receive training in the novel multiplex technology for
infectious disease detection. The multiplex methods will be developed and optimized at UC
Davis, and subsequently this technology will be transferred to Dr. Azra Khanum’s research
laboratory at UAAR. Importantly, for evaluation of the multiplex diagnostic system in the field,
clinical samples from M. tb.-infected individuals will be provided by Drs. S.K. Shah and Sabira
Tahseen at the National Tuberculosis Center in Rawalpindi. At the end of the two-year project,
the data will be used to compare the novel multiplex immunoassay diagnostic method with
conventional methods for TB diagnosis and to determine the cost effectiveness of the new
method. If these comparisons prove favorable, then a full clinical validation study can be done
to attain the long-term goal of significantly improved TB diagnosis through implementation of
the new multiplex diagnostic technology.
As of October 2007, two graduate students in Dr. Khanum’s laboratory, Ms. Irum Nawaz
and Mr. Kumail Rizvi, have been duly trained and are actively involved in the collection of
blood samples at the NTBC. To date, blood samples have been collected from approximately 90
TB patients for analysis. Dr. Khan made a two-week visit to Rawalpindi September 26 to
October 10, 2007, to (1) review procedures of collection, processing, and storage of patient blood
samples, (2) monitor progress on expression of M. tb. proteins in genetically engineered bacterial
vectors by Dr. Khanum’s laboratory personnel, and (3) assist in the purchase of the multiplex
instrument. He plans to return for another two weeks in December 2007 to continue work on the
project. In addition, arrangements have been made for Ms. Nawaz and Mr. Rizvi to spend three
months at UC Davis to be trained on multiplex immunoassay development.


17
Building Molecular Biology Capacity for Preventing Tick-Transmitted (2007-2009)
Diseases in Pakistan
Thomas N. Mather, University of Rhode Island
Abdullah G. Arijo, Sindh Agricultural University
Pakistani Funding: $225,451
US Funding: $290,000

In Pakistan, more than 75 percent of the rural population practices livestock husbandry,
and a majority of these people depend upon livestock for their subsistence. Crimean-Congo
Hemorrhagic Fever virus and other significant tick-transmitted pathogens of humans and animals
are endemic to certain regions of Pakistan and have the potential to cause significant human
morbidity and mortality and impact Pakistan’s agricultural economy and the livelihood of its
rural citizens. This project proposes to establish a molecular entomology laboratory at Sindh
Agricultural University (SAU) to build Pakistani capabilities to study and prevent tick-
transmitted diseases in Pakistan. The project will focus on developing high-throughput
transcriptomic, functional genomic, and proteomic systems and strategies aimed at identifying
tick salivary proteins that can produce strong delayed-type hypersensitivity or DTH-like
responses, antibody responses, or a combination of both, that correlate with protection from tick-
borne disease (TBD). It may be that this novel approach will accelerate anti-tick and TBD
vaccine development by informing the vaccine candidate selection process. Moreover,
functional genomic screens involving inhibitory RNA are expected to identify novel pharmaco-
therapeutic targets for disrupting tick feeding and pathogen transmission.
In addition to continued work on methodology development at the University of Rhode
Island (URI), the project will also use a series of experiential training workshops at SAU to train
Pakistani faculty, researchers, and students in the cutting-edge techniques needed to build and
advance an appropriate molecular biology capacity that can be applied to various programs for
preventing tick-transmitted diseases in Pakistan. Dr. Mather and his colleagues at URI will
continue their studies on vaccine and small molecular targets to disrupt feeding of black-legged
ticks (Ixodes scapularis) and transmission of the agents causing Lyme disease, anaplasmosis, and
babesiosis. Dr. Arijo and his fellow researchers at SAU will (1) develop TBD surveillance and
assessment capabilities to identify and prioritize vector tick species in Sindh Province; (2)
establish a capacity at SAU to conduct TBD diagnostics using rapid polymerase chain reaction
(PCR) and reverse transcription PCR (RT-PCR) assays without requiring specialized
biocontainment facilities; and (3) focus vaccine and pharmaceutical discovery research on
important Pakistani tick species identified by the activities described in aims 1 and 2.
So far in 2007, the Pakistani partners at SAU have begun rehabilitation work on a
molecular entomology lab and animal space following suggested guidelines from URI scientists.
Equipment lists with required specifications were prepared by URI and pro forma quotations
were obtained from Pakistani vendors. Project participants will consult with one another before
making final decisions concerning equipment and molecular kits and reagents purchases. Plans
for conducting training workshops necessarily have been delayed until completion of the SAU
molecular entomology laboratory construction and equipment purchases. Meanwhile, SAU has
hired and begun training a senior scientist, lab technician, computer operator, and four
postgraduate students on the project, and efforts to collect ticks from livestock in various regions
of Pakistan are under way. In addition, URI invited Dr. Arijo to visit the URI molecular
entomology lab and assisted him in obtaining a visa. He arrived in October 2007 and is spending

18
approximately one month working with URI scientists to further develop training curricula and
training workshop plans. Initially, plans called for holding three training workshops at SAU in
late 2007 and 2008, but these plans are currently under review given the current security
situation. Alternatives for possibly conducting the training at another site are being considered.

Establishment of Virtual Trainer Lab for Improving Minimally Invasive Surgery Skills of
Post-Graduate Trainees and Faculty of the Surgery Department of Rawalpindi Medical
College and Allied Hospitals
*and*
Multitasking of Telemedicine/E-health Training Center (2007-2008)
Ronald Merrell, Virginia Commonwealth University
Asif Zafar Malik, Holy Family Hospital
Pakistani Funding: $270,000
US Funding: $213,000

This project includes two separate but related components aimed at building Pakistani
capacity in the healthcare sphere. The first involves laparoscopic or minimally invasive surgery
(MIS), which has become very popular in the last 15 years. Because many operations that were
once performed “open” are now done almost exclusively laparoscopically, skills training in this
area is becoming necessary for many surgical subspecialties. The emerging field of surgical
simulation and training offers an opportunity to teach and practice laparoscopic skills outside of
the operating room environment. There is enormous potential to address patient safety, risk
management concerns and operating room management with more efficient and effective
training methods. The current goal of simulator training is to help trainees acquire the skills
needed to perform complex, minimally invasive surgical procedures prior to practicing them on
living patients. Unfortunately, minimally invasive surgery training facilities are not available in
most of the teaching hospitals of Pakistan. During the proposed project, a virtual training
laboratory will be established at Surgical Unit II, Holy Family Hospital, in collaboration with the
Medical Informatics and Technology Applications Consortium at Virginia Commonwealth
University. The lab, which will include box trainers, virtual reality simulators, and full
procedural simulators, will be used to train surgical residents. The operating rooms and training
lab will be linked together and also to minimal invasive training centers in the United States.
The training will be in three modules, including laparoscopic training lectures and
demonstrations, work on virtual simulators, and finally hands-on training on patients supervised
by consultants through telementoring and tele-presence surgery.
The second project component focuses on expanding an existing joint telemedicine
training program at Holy Family Hospital. Pakistan is one of the most densely populated
countries in the world, but the doctor-to-patient ratio is only 1 to 1,555, and there is just one
specialist available for every 15,000 citizens. Moreover, the majority of the population resides in
rural areas, while medical facilities are concentrated in the urban areas. One solution to bridge
this rural-urban disparity is to build new hospitals in rural areas and send specialists to those
areas, but this is difficult for a variety of reasons. The other feasible solution is using
telemedicine to address the limited availability of specialists at remote sites. The implementation
of telemedicine requires health professionals trained in this field, which was previously unknown
in Pakistan. In 2003, these partners received a grant under the Pakistan-US Science and
Technology Cooperative Program in its previous format to provide telemedicine training to

19
medical personnel in Rawalpindi and Islamabad. During this six-month project, 45 doctors and
nurses from various institutions were trained, and they are now pursuing telemedicine projects in
their own institutions. During the new project, medical staff from all over Pakistan will be
trained at the telemedicine/E-health training center established at Holy Family Hospital. In
addition, this facility will be utilized to provide telemedicine training and tele-rehabilitation
services to paraplegic victims of the October 2005 earthquake.
Although both sides experienced significant delays in setting up their grant accounts and
agreements at their respective institutions, in May 2007 the VCU team met with Dr. Zafar in
Nashville at the American Telemedicine Association annual meeting and agreed upon the final
revision of the training curriculum and budget. At this meeting, Dr. Zafar and his colleague Dr.
Faisal Murad made three presentations on earthquake relief with telemedicine, telemedicine for
follow-up of earthquake patients, and telemedicine for pre- and post-operative follow-up of
elective surgical patients. The partners all agreed on revision of a formal report on the scientific
lessons learned from their first project for publication in the ATA journal Telemedicine and e-
Health, and that paper is expected to be published in early 2008. They also planned a week-long
visit by Dr. Murad to Richmond later that month to examine a variety of telemedicine products
and systems in anticipation of setting the equipment list for the project. In addition to working
with equipment for training and courses of instruction, he visited with vendor representatives and
established the necessary links for purchase orders from Pakistan to the United States. As of
October 2007, the necessary subagreement had finally been sent from VCU to HFH and funds
for the equipment purchase were to be transferred. Between December 2007 and June 2008,
eight Pakistani trainees are expected to come to VCU for two weeks of training.

Capacity Building and Quality Assurance/Quality Control Procedures for the Network of
Water Quality Laboratories in Pakistan (2007)
Michael T. Meyer and Ingrid M. Verstraeten, U.S. Geological Survey (USGS)
Muhammad Akram Kahlown, Pakistan Council of Research in Water Resources (PCRWR)
Pakistani Funding: $30,000
US Funding: $45,000

The overall purpose of this one-year project (February 2007-January 2008) is for USGS
personnel to work with PCRWR technical and research staff to develop an organic analysis
capacity and to provide a comprehensive laboratory review of all facets of the PCRWR
laboratories. The specific project objectives are as follows:

• Undertake an overview of all aspects of the PCRWR laboratories, prioritize pollutants for
study, and provide expertise and training to implement specific and well-established
methods for the analysis of widely applied herbicides using solid-phase extraction (SPE)
gas chromatography/mass spectrometry (GC/MS)
• Provide a comprehensive laboratory review of the current inorganic analysis program
including quality assurance and quality control procedures, operational procedures,
methods, and protocols
• Initiate advanced comprehensive training on analytical methods, instrumentation, and
technologies used to analyze and evaluate organic contaminants including persistent
organic pesticides (POPs) and their degradates at the USGS Organic Geochemistry
Research Laboratory

20

Work to accomplish these objectives has proceeded in two phases. In June 2007, Dr.
Verstraeten, Dr. Meyer, Dr. Mary Voytek, and Mr. Tedmund Struzeski visited Islamabad for one
week to provide training to PCRWR analytical lab personnel, review procedures at the lab, and
work with lab staff to develop and prioritize a list of contaminants of concern for which the lab
would be capable of analyzing. They prepared a detailed interim report on this visit including
recommendations for actions to be taken by PCRWR (see
http://www7.nationalacademies.org/dsc/USGS_PCRWR_Interim_2007.doc
). In phase two of
the project, two PCRWR staff members, Ms. Saiqa Imran, chemist and technical manager, and
Ms. Hifza Rasheed, microbiologist and deputy director of the PCRWR National Water Quality
Laboratory, visited the USGS offices in Kansas and Colorado October 22 through November 16,
2007, for organic and inorganic chemistry training focused on specific aspects of the analytical
method implemented at PCRWR in phase one. The primary Pakistani counterpart, PCRWR
Chairman Dr. Muhammad Akram Kahlown, was also expected to visit USGS headquarters, the
US Environmental Protection Agency, and the USGS facilities in Kansas and Colorado later in
November along with Dr. Muhammad Aslam Tahir, director general of the PCRWR National
Water Quality Laboratory, and Mr. Abdul Raoof, regional director of the PCRWR Regional
Center in Lahore. However, the imposition of the state of emergency in early November caused
these plans to be put on hold. Dr. Verstraeten has advised Academies staff that a no-cost
extension beyond the current project end date of January 31, 2008, may be required in order to
allow sufficient time for this final visit to be rescheduled.

Development of Biosecure, Sustainable, and Cost-Effective Culture Technologies for Edible
Shrimp (Fenneropenaeus merguiensis) in Pakistan, Establishment of Viral-Pathogen-Free
Populations of Farfantepenaeus duorarum, and Refinements of Super-Intensive Production
Practices for Table-Litopenaeus vannamei in the United States (2007-2009)
Tzachi Samocha, Texas A&M University
Zarrien Ayub, University of Karachi
Pakistani Funding: $271,677
US Funding: $116,003

Shrimp form the backbone of capture marine fisheries in Pakistan, but over the last
decade, overfishing has caused a tremendous stress on wild shrimp stocks, which is evident from
the fact that despite the increase in the number of fishing trawlers, shrimp catches have declined
considerably. This decline might be alleviated by the development of shrimp farming in the
country while using sustainable and biosecure management practices. Pakistan does not have a
previous history of farming shrimp, although it possesses considerable potential and resources
for the development of such an industry, with vast areas with adequate water and climatic
conditions available for aquaculture development along the Balochistan coast. With the help of
American partners, Pakistan can establish management practices for the successful production of
edible shrimp under local environmental conditions, with an emphasis on biosecurity and
sustainability.
This project also has potential benefits for the US shrimp industry. Although demand for
edible shrimp in the United States is high, local commercial fishermen and shrimp farmers
cannot compete successfully with low-cost imports. In order to survive, this industry has to
develop product that satisfy niche markets in which foreign imports cannot compete. One such

21
option is the development of super-intensive closed recirculating systems, which should provide
a year-round supply of live and fresh table-size shrimp for which customers are willing to pay a
premium price. Because sustainability and disease are the major obstacles for developing the
shrimp farming industry, the focus of the proposed research at the Texas Agriculture Experiment
Station of Texas A&M University will be refinements of sustainable and biosecure culture
practices. This project will focus on production of viral-pathogen-free (VPF) broodstock
populations of the Atlantic pink shrimp and on refinements of production practices for table-size
Pacific white shrimp while providing great opportunities for training and technology transfer to
Pakistan.
The US side, which received its grant funds earlier in 2007, began its research on F.
duorarum. Dr. Samocha also provided conceptual designs, equipment lists, and reviews of plans
of the research facilities to be built in Pakistan. Meanwhile, although the Pakistani side did not
receive its funds until August, extensive efforts proceeded through the spring and summer to
acquire land for the proposed research center at Damb, Sonmiani, Balochistan. The Governor of
Balochistan took a personal interest in the issue, and on July 12 he heard a presentation on the
project. It was decided that a four-acre plot would be provided for the purpose at Sonmiani,
where the hatchery of the National Institute of Oceanography (NIO) is located. The Governor
visited the site on September 4, 2007, and the land acquisition was finalized. At the Governor’s
recommendation, an agreement will be signed between NIO and the Center of Excellence in
Marine Biology at the University of Karachi instituting research cooperation between the two
parties for the development of shrimp farming in Pakistan. All conceptual designs of the systems
to be built have been finalized, and as of late September 2007 preparations were in the final
stages to request bids for the construction of the water purification and treatment systems, the
induced maturation, larval rearing, algae production, Artemia hatching, nursery buildings and
tanks, and the grow-out ponds.

Identification and Cloning of Drought-Related Genes in Wheat (T. aestivum) (2007-2009)
Daniel Schachtman, Donald Danforth Plant Science Center
Nasir Saeed, National Institute for Biotechnology & Genetic Engineering
Pakistani Funding: $100,000
US Funding: $109,963

Wheat is the staple food of millions of people around the world, and drought is the major
limiting factor in its production. Pakistan is located in arid and semi arid climate zones and is
facing severe and growing shortages of irrigation water. The average wheat yield is 2.5 metric
tons per hectare, which is quite low compared with other countries like China (4.27), Egypt
(6.07) and Mexico (4.62), and Pakistan has been a net importer of wheat grain in the last decade.
To feed its growing population, there is a great need to focus on developing drought tolerant
crops that can grow with limited water.
This project includes identification and cloning of key genes involved in adaptation of
wheat to drought stress using microarray technology. Candidate genes will be cloned into
expression vectors for transformation and development of drought tolerant wheat. Wheat crop
productivity and yield stability are affected by a number of factors (biotic and abiotic). In the
past, attempts have been made to introduce drought tolerance genes by conventional breeding.
Wheat and other crop genomes are under sequencing, and many different genes have been tested
under a range of conditions to determine whether they may contribute to drought tolerance. In

22
this study, four drought tolerance enhancing genes (HVA1, WXP1, DREB1A and AtNCED3)
and a stress responsive constitutive promoter rd29A have been chosen. Over-expression of these
genes may enhance drought tolerance and agronomic value of wheat. Few studies have addressed
the topic of drought tolerance in wheat using molecular tools; although breeding efforts and
germplasm screens have been undertaken. In addition to using the above approach, microarray
technology offers new ways to find gene expression changes and manipulate them for
developing drought tolerant crops. It is particularly useful to examine where and when specific
genes associated with water deficit stress are expressed. Full length cDNAs of a few candidate
genes that are regulated by drought will be cloned into plant expression vectors for
transformation. The over-expression of these genes will be tested for their ability to increase
wheat production under drought conditions.
The timeline for this project was pushed back by several months due to delays in receipt
of grant funds on the Pakistani side. However, Dr. Schachtman has been assisting Dr. Saeed by
cloning genes for transformation into local wheat varieties. Meanwhile, Dr. Saeed has worked
on transforming wheat and will continue to do so in the next growing season during March-April
2008. One Arabidopsis gene DREB1A under the control of a constitutive promoter (FMV) and a
drought inducible promoter rd29 has been cloned, and the US side has sent vectors to Pakistan
containing AVP1 and AVP1D for transformation into wheat. Three more genes (HVA1, WXP1,
and NCED3) are being cloned, and each cDNA will be cloned into plant transformation vectors
containing a constitutive promoter and a drought inducible promoter. The cloning will be
finished by November 2007 and the remainder of the vectors will be sent to Pakistan. Drought
experiments and gene expression analysis using microarrays have been delayed in order to allow
Dr. Saeed to be present at the Danforth Center to participate in the work. He is currently awaiting
approval of his US visa in order to make the trip.

Assessment and Development of Renewable Ground Water Resources in the
Quetta Valley, Pakistan (2007-2009)
Mohamed Sultan, Western Michigan University, and Shuhab Khan, University of Houston
Abdul Salam Khan, University of Balochistan
Pakistani Funding: $254,590
US Funding: $199,986

Balochistan is the largest province in Pakistan, yet it has the smallest number of people
per unit area, largely due to the scarcity of its water resources. Furthermore, the indiscriminate
and unplanned use of groundwater resources to meet water requirements in Balochistan in
general and in the Quetta Valley in particular has lead in recent years to unsustainable
overexploitation of groundwater. This has resulted in progressive depletion of groundwater
levels in Quetta, which has had serious socioeconomic impacts due to the migration of the
population from rural to urban areas. All of this points to the urgent need for assessing and
developing the groundwater resources of the Quetta Valley. With funding previously provided
by the United Nations Development Program and the Global Environmental Facility, researchers
at one of the US partner institutions on this project, Western Michigan University, have
developed cost-effective methodologies for groundwater assessment and exploration in arid
lands. These experiences and methodologies will be brought to bear in the current project.
The partners involved in this project propose to apply an integrated multidisciplinary
approach for groundwater exploration in the Quetta Valley in which inferences from remote

23
sensing data are integrated with observations extracted from other data sources, such as
geochemistry, field geology, drilling, geophysics, and surface runoff and groundwater flow
modeling to gain a better understanding of the hydrological setting and identify locations of
potential productive wells. A five-fold exercise will be conducted to assess the groundwater
potentials in the Quetta Valley. First, a field campaign will be conducted to collect and analyze
groundwater and surface water samples for geochemical, isotopic, and geochronologic analysis.
Second, a database will be created to incorporate all relevant data sets in a GIS environment for a
better understanding of the spatial relationships between these data sets. Third, a web-based GIS
interface (ArcIMS) will be developed and applied along with geophysical methods to identify
locations for potential productive wells targeting different types of shallow (<200m) reservoirs.
Fourth, calibrated rainfall-runoff models and groundwater flow models will be developed to
simulate runoff and recharge and to compute sustainable extraction. Fifth, throughout the
duration of the project, the Pakistani researchers will receive training both in Pakistan and the
United States on various aspects of the adopted integrated applications and approaches and
specifically in the applications of GIS, remote sensing, geochemistry, surface runoff modeling,
groundwater flow modeling, and geophysics in groundwater exploration.
Dr. Khan visited Pakistan in May 2007 to coordinate efforts with the Pakistani
collaborators, conduct a preliminary field trip in the study area, and address logistical aspects of
the project. During the trip, he and his colleagues identified and collected preliminary geologic
and hydrogeologic data for the project, identified sites for water sampling, met with officials
from several governmental agencies for potential collaboration (including the Geological Survey
of Pakistan, Water and Power Development Authority, Water and Sanitation Agency, Irrigation
Department, and others), and interviewed and selected Pakistani students and technicians who
will work on the project. Dr. Khan also conducted an informal training session at the Center of
Excellence in Mineralogy (CEM) at the University of Balochistan, Quetta. The session, which
covered the basics of water sampling, laboratory analysis and GIS and remote sensing
methodologies, was attended by the Pakistani PIs and other faculty members from CEM and the
Departments of Chemistry and Geology.
The web-based GIS mentioned above has been created and posted for public access at
(
http://www.esrs.wmich.edu/groundwater__resources_in_quetta_pakistan.htm
). Upon
completion, it will include comprehensive coverage in categories such as geophysics, geology,
land use, precipitation, and remote sensing data sets. In addition, Drs. Khan and Sultan have
made two presentations related to their work in the Quetta Valley at the annual meeting of the
Geological Society of America in Denver, October 28-31, 2007. They plan to travel to Pakistan
in December 2007 to continue work on the project.

Development of an ITS-Based Traffic Management Model for Metropolitan Areas of
Pakistan with Karachi as a Pilot Study (2007-2009)
Waheed Uddin, University of Mississippi
Mir Shabbar Ali, NED University of Engineering and Technology
Pakistani Funding: $195,988
US Funding: $94,000

Over the past decade, Pakistan has worked intensively to build and modernize motorways
and national highways as part of the country’s overall economic development efforts. However,
traffic-related fatalities are alarmingly high, and about 41 percent of all crashes involve deaths, a

24
figure that is significantly higher than in most other countries. Frequent congestion and
transportation choke points in most urban and metropolitan areas are adversely affecting travel
time, business inventory costs, freight movement costs, and air quality. Increased air pollution
(particulate matter and ground-level ozone) is affecting public health, especially respiratory
diseases and mortality rates. These problems require modern solutions emphasizing efficiency
and safety as the primary goals of traffic management. The primary objective of this project is to
strengthen the capabilities of the Pakistani partner institution, NED University of Engineering
and Technology in Karachi, for adapting modern geospatial technologies and science models of
traffic flow and air quality. The implementation products will lead to increased transportation
efficiency and safety, which can enhance economic prosperity, reduce public health costs, and
benefit the people of Pakistan.
The proposed research approach involves adapting and implementing an Intelligent
Transportation System (ITS) framework of traffic monitoring and evaluation technologies in
which various traffic flow parameters and real-time traffic data are integrated to formulate an
efficient Traffic Management System (TMS). Using the case study of the most populated
metropolitan urban city of Karachi, a geo-referenced road network database using geographical
information system (GIS) is proposed as the ITS backbone. A comprehensive benefit-cost
analysis methodology will be implemented to assess traffic management strategies considering
savings from reduced user and societal costs. The US partner institution, the University of
Mississippi, is assisting NED in adapting US ITS experience, providing training in
GIS/geospatial analysis and traffic simulation models, and developing self-reliance in these
technologies. The project deliverable will be an efficient GIS-based TMS to be recommended
for implementation to Karachi City Traffic Officials (CDGK-EDO Transport). Regional
workshops will disseminate the methodologies and key results to other major Pakistani cities and
universities. Further benefits include a better trained professional workforce as well as
modernization of curricula at both the undergraduate and graduate levels in Pakistan.
In the first exchange visit on this project, Dr. Waheed Uddin and his colleagues at NED
presented a workshop at NED June 18-21, 2007, on GIS and imagery-based geospatial analysis
for transportation planning. The workshop provided training to 43 participants, including
professionals from CDGK, the National Highway Authority, the Pakistan Space and Upper
Atmosphere Research Commission, the Jinnah Postgraduate Medical Centre’s Traffic Safety
Project, consulting engineers, professors and graduate students. On July 30, a stakeholders
meeting was held in Karachi to involve officials and planners from local transportation agencies.
Highlighting the importance of traffic concerns to the Pakistani public, the meeting received
coverage in two major Pakistani newspapers, Dawn and The News. During his six-week visit,
Dr. Uddin and his colleagues also sampled data for congestion assessment not only in Karachi,
the focus of their study, but also in Lahore and Islamabad. While in the latter city, Dr. Uddin
presented a lecture at the National Highway Authority and visited that agency’s offices for
consultations on remote sensing technologies for airborne terrain mapping to facilitate road
construction in Pakistan’s mountainous northern region. He delivered additional lectures to
engineers at National Engineering Services (NESPAK) headquarters and to engineering students
at NED.


25
Nanomedicine for Cancer Research (2007-2009)
Kenneth Watkin, Brian Cunningham, and Irfan Ahmad, University of Illinois
at Urbana-Champaign
Atiya Abbasi, University of Karachi
Pakistani Funding: $137,219
US Funding: $250,000

More than 70 percent of the developing world’s population still depends on
complementary and alternative systems of medicine (CAM). Evidence-based CAM therapies
have shown remarkable success in healing acute as well as chronic diseases. The Indo-Pakistani
subcontinent is rich in such remedial sources, most of which remain untouched and unstudied.
Pakistan is among the world’s leading exporters of medicinal plants, but there is a need to build
partnerships that help provide the infrastructure and training to apply and use recently develop
new rapid screening techniques for evidence-based evaluation of various plant extracts.
Researchers at UIUC have employed a new label-free optical biosensor system for high-
throughput evaluation of natural products. This new biosensor system is being used for rapid
evaluation of the breast cancer apoptotic potential of plant extracts. Preliminary research has
revealed several potential extracts that kill breast cancer cells. The potential cancer treatment
extract candidates will progress to clinical evaluation. In order to achieve this vision, the
partners involved in this project have devised a systematic plan for excellence by concentrating
on cancer research and education and integrating these aspects with existing capabilities and
infrastructure at the HEJ Research Institute of Chemistry at the University of Karachi. The
application of this type of nanomedicine technology has enormous potential, not only for cancer
treatment but also for the medicinal plant industry in Pakistan. Applications include high-
throughput pharmaceutical compound screening, molecular diagnostics, PCR, electrophoresis,
label-free microarrays, proteomics, environmental detection, and whole cell assays.
As of fall 2007, purchases of microplate readers and reagents for plant extractions and
DNA and proteins are under way at both UIUC and HEJ. In addition, a flow cytometer was
recently purchased at UIUC and will be used by Pakistani faculty and graduate students during
their upcoming visits to UIUC. On the US side, two graduate students and a part-time post-doc
have been hired on the project. The researchers have been using plant extracts to induce cancer
cell apoptosis using the photonic crystal biosensors developed in the UIUC Micro and
Nanotechnology Laboratory in collaboration with SRU Biosystems. These biosensors will be
made available to researchers from Pakistan after training is conducted at UIUC. A course
entitled Current Topics in Nanomedicine is being conducted jointly by the University of Illinois
and Washington University in Saint Louis during the Fall 2007 semester
(http://courses.uiuc.edu/cis/schedule/urbana/2007/Fall/BIOE/598.html). Video lectures for the
course, which is directed to graduate students and seniors interested in life and medical sciences
and nanotechnology, are now being made available via the web to students and faculty at the
University of Karachi.
Dr. Atiya Abbasi and her student(s) are scheduled to visit UIUC in early 2008. In
addition to meeting with their US counterparts to plan future work on their joint project, they
will also familiarize themselves with research under way in the relevant labs and departments at
UIUC. At present, plans call for Drs. Watkin and Ahmad to visit HEJ in the summer of 2008 to
present a summer course on nanomedicine. Meanwhile, the US PIs report that they hope to
leverage this grant as well as their grant from the National Cancer Institute to support a Cancer

26
Nanotechnology Excellence Project (2005-2010) in order to attract additional funding in which
their Pakistani counterparts will be included as co-PIs. Collaborative relationships for
nanomedicine for cancer research topics have also been established with the Siteman Cancer
Center Teaching Hospital at Washington University in Saint Louis, Missouri, and locally in
Urbana-Champaign with the Mills Breast Cancer Institute at Carle Clinic and with the Cancer
Center at Provena Hospital. It is expected that the Pakistani participants in this project will be
exposed to these cancer teaching hospitals and facilities on visits to UIUC. Similar
collaborations will be explored with the Aga Khan Hospital in Karachi and the Shaukat Khanum
Memorial Cancer Hospital in Lahore.

Summary of Activities to Date on Earthquake-Related Research Projects Funded in 2006 Cycle

Education and Learning after the Pakistan Earthquake: Can the Children Recover?
(2007-2009)
Ali Cheema, Lahore University of Management Sciences
Tahir Andrabi, Pomona College
Pakistani Funding: $240,000
US Funding: $83,700

One lasting image of the October 2005 earthquake is that of trapped children under
collapsed schools. Indeed, documentary evidence shows that schoolchildren died
disproportionately in this disaster. While the government and donors have made significant
plans and some progress in reconstructing school buildings, the researchers conducting this
project believe that virtually no attention is being paid to learning—ultimately the end goal of
schooling. Learning has been disrupted because of direct damage to schools, disruption to
households arising from death, injuries, and displacement, and the considerable impact the
events of October 7, 2005, had on children's emotional well being. This project aims to
document the medium-term effects of the earthquake on learning and education through a
representative longitudinal study of 600 primary schools (out of a total of about 3,000) in the
hardest-hit districts of Bagh and Muzaffarabad in Azad Kashmir. The first educational outcome
of interest is enrollment and retention patterns before and after the earthquake. The researchers
will then look directly at changes in learning—the key contribution of this study. Using
specially designed tools, they will test more than 10,000 fourth-graders in English, Urdu, math,
and civics. The testing will be supplemented by detailed surveys of school infrastructure and
resources, a teacher survey, and documentation of the socioeconomic conditions of the children’s
households. Special assessments will also be conducted regarding the emotional well being of
the children. The representative survey will be designed so as to ensure a sample of schools at
varying distances from the fault line and thus with varying intensities of damage. This variation
will be exploited along with the other data collected using sophisticated multivariate statistical
techniques with a rich set of control variables and an instrumental variable strategy to control for
various selection biases.
It is less well known that apart from the growth in the public (government-run) school
sector, the Azad Kashmir region has seen a phenomenal increase in small, family-run, for-profit,
“English-medium” schools. These private schools are built, managed, and financed by “mom-
and-pop” local entrepreneurs and depend on the small but growing pool of locally educated
females to provide the teaching input. Their growth is large enough that more than one-third of

27
all students in the primary age group were attending such schools at the time of the earthquake.
(Note that these schools are not the madrassahs that are the focus of much attention in the
context of the war on terror. Their numbers are very small in Azad Kashmir, according to earlier
research conducted by the participants in this project.) Analysis of private schools will help to
provide a better understanding of the mechanisms underlying the observed resilience of the
population in recovering from the earthquake with very little support from the government or
donors. Results from the planned teacher survey in the private schools will also be used to
examine changes in female labor force participation in the aftermath of the quake—a key
element in potential changes in household behavior after the earthquake.
Dr. Andrabi visited Pakistan in June and August 2007 to being work on the project with
his Pakistani partners. Their initial efforts focused on mapping the spatial distribution of the
earthquake shock to draw a statistically representative sample of the affected communities,
compiling a list of interventions, and partnering with major earthquake reconstruction
organizations to create a list of interventions that need to be documented in order to evaluate the
recovery from the shock. Crucial linkages have been established with NESPAK, a government
firm that is the largest provider of engineering services in the earthquake area, and with the
Earthquake Reconstruction and Rehabilitation Agency, the official Pakistani government body
that coordinates all earthquake-related activity in the region. Questionnaires to be administered
to school administrators, teachers, and children have been developed, and research assistants and
survey teams have been hired and trained. Sampling field visits and questionnaire piloting were
expected to begin in November 2007, but imposition of the state of emergency (during which Dr.
Cheema was arrested and detained for three days before being released on bail) and the
subsequent deterioration of security conditions in the region have caused those plans to be put on
hold, as the researchers felt it was not safe to send the survey teams out into the field. School
visits and a mapping exercise were to follow in December 2007-January 2008, with further
surveys and testing to be conducted in February–April 2008 and the data to be compiled and
analyzed during the summer and fall. However, the security situation may unfortunately cause
these plans as well as Dr. Andrabi’s expected January 2008 visit to be postponed.

Development of a Framework for Probabilistic Seismic Hazard Maps for Pakistan
(2007-2009)
Noorul Amin and Akhtar Naeem Khan, NWFP University of Engineering
and Technology, Peshawar
Scott Olson and Youssef Hashash, University of Illinois at Urbana-Champaign
Pakistani Funding: $130,000
US Funding: $174,705

The October 2005 Kashmir earthquake demonstrated the extent of damage that an
earthquake in Pakistan can cause. Given Pakistan’s seismo-tectonic setting, this earthquake is
not a one-time event, but part of a sequence of earthquakes that have happened in the past and
will happen again in the future. More importantly, the earthquake highlighted the severe
limitations of existing seismic hazard characterization in Pakistan. Several efforts by the
Pakistan Meteorological Department and collaborations with the U.S. Geologic Survey as well as
groups in Japan and Norway are under way to better define seismicity in Pakistan through
various mapping, instrumentation, and data collection activities. These groups will use the
collected data to generate region-specific attenuation relationships and ground motion estimates.

28
However, an important gap remains in these efforts at the interface between seismology and
earthquake engineering. That is, a need exists to develop appropriate factors to account for local
soil response and topographic effects. These “site response” factors are a common component in
design codes worldwide to translate ground motions developed by seismic hazard mapping
efforts for use by design engineers. And perhaps more importantly, there is a need to train
current and future Pakistani engineers to use the seismic hazard mapping tools and products that
others are producing. This proposal focuses on building Pakistani capacity in the area of seismic
hazard characterization for engineering applications and for developing loss scenarios and
emergency response plans. The following proposed activities, combined with the efforts of the
other groups mentioned above, should represent a significant step in improving the design and
engineering of structures in Pakistan in order to reduce casualties and economic losses associated
with future earthquakes:

1. Courses: The partners involved in this project plan to develop and deliver course
modules and short courses on the use of seismic hazard characterization for engineering
applications. This would include how to use available seismic hazard characterization
tools and how to develop appropriate ground motion parameters.

2. Input for seismic hazard analysis: Data will be collected from the literature to define
inputs to available seismic hazard analysis software such as OPENSHA and EZ-FRISK.
These data will be updated throughout this project based on other ongoing studies and in
close collaboration with USGS efforts in Pakistan.

3. Field Studies: Two sites will be characterized and instrumented to aid in defining
local site and topographic effects in Pakistan.

4. Local site and topographic effect factors: Due to differences in the soil deposits in
Pakistan and the United States, it is not appropriate to simply adopt the site coefficients
proposed in the National Earthquake Hazards Reduction Program (1996 and 2003) that
are widely utilized in US design codes. Furthermore, US design codes do not account for
topographic amplification effects, and the European code has only limited provisions to
consider topographic effects. Therefore, a series of analyses will be performed to
develop appropriate site and topographic effects using field data and the results of
numerical modeling.

Since the project began in early 2007, the US and Pakistani partners have worked closely
to develop a semester-long course on Seismology and Seismic Hazard Analysis to be offered for
the first time at NWFP UET in the fall 2007 semester. Many of the course lectures will be
delivered remotely by the US partners on the project. In addition to developing the course
curriculum and materials, the US team has also collected and reviewed relevant literature on
seismicity in Pakistan and worked on adapting two seismic hazard analysis software packages
for use with Pakistani data. Meanwhile, the Pakistani partners have collected literature, maps,
and other data and worked to identify potential sites for conducting field investigations and
installing seismic instrumentation. The researchers also devoted time to planning a workshop for
practitioners in seismic hazard analysis, which was to have been presented in Peshawar or
Islamabad in January 2008. Recent events have led to the postponement of this workshop,

29
however, but the partners hope to present it as soon as conditions allow. Site selection and site
characterization work will also be completed in the coming year and field instrumentation will be
installed. Once established, the site will be used as a field laboratory to teach students and
practitioners about the importance of field work for seismic hazard analysis and earthquake
engineering, as well as to obtain preliminary data on topographic effects.

Building Pakistan’s Capacity for Instruction, Research, and Practice in Earthquake
Engineering and Retrofit (2007-2009)
Sahibzada Rafeeqi, NED University of Engineering and Technology, Karachi
Brian E. Tucker, GeoHazards International, Palo Alto
Pakistani Funding: $220,000
US Funding: $241,595

This project aims to improve Pakistan’s capacity for reducing earthquake risk by building
the capacity of its universities to teach and conduct research in earthquake engineering and
transfer the knowledge needed to seismically retrofit essential structures to both new graduates
and practitioners. The approach integrates formal instruction in theory with practice by using
case studies of existing buildings typical of the local building stock. It recognizes that
earthquake engineering exists in a broader societal context that balances safety with competing
demands and values by employing multidisciplinary earthquake risk management decision-
making processes. The project will promote sustainable academic interest in earthquake
engineering research by encouraging cooperative research and professional relationships with
American researchers through academic exchange and a study tour in California, consultation on
research topics that directly impact seismic safety in Pakistan, and creation of a Pakistan
Earthquake Engineering Research Agenda.
The project began when five US participants (Dr. Gregory Deierlein of Stanford
University, Mr. David Mar of Tipping-Mar+Associates, Dr. Khalid Mosalam of the University
of California Berkeley, Dr. Janise Rodgers of GHI, and Mr. L. Thomas Tobin of GHI) traveled
to Pakistan July 21-28, 2007, to meet with their counterparts and visit several sites in Karachi,
Islamabad, and the earthquake-affected areas in Rawalakot, Bagh, Chakothi, and Muzaffarabad.
The purpose of the visit was threefold: beginning to develop the case studies, improving the
existing curriculum, and meeting with project partners throughout the country. The case study
development began with defining characteristic building types and training a selected group of
graduate students and junior faculty to screen buildings rapidly. Curriculum improvement efforts
began with determining how the project can help build on existing capacity in earthquake
engineering in Pakistan’s universities and benefit from the experiences of US universities such as
the University of California Berkeley and Stanford. During the visit, the US research team met
with Pakistani project partners in academia, private practice, and government. On July 21, 2007,
the Pakistan Chapter of the American Concrete Institute organized and sponsored a seminar
given by the US research team members entitled “Performance-Based Earthquake Engineering
and Applications to the Evaluation and Retrofit of Existing Buildings.” The seminar was well-
attended, attracting approximately 100 students, faculty, and practicing engineers.
The research team conducted similar activities when the participants from Pakistan
visited the San Francisco Bay area in late October 2007 to interact with interested faculty and
practicing engineers. A small group of ten key participants visited California for first-hand
observation of seismic retrofit techniques, plus academic exchange with American researchers

30
with the intent of encouraging future research collaboration and student exchange. Throughout
the project, participants will apply the concepts learned through case studies of existing
buildings, which will then, along with theory, form the basis for courses in seismic assessment
and retrofit, comprising both practical training courses for practitioners and academic courses for
students. American faculty members and practicing professionals will work with Pakistani
participants to develop, teach, evaluate, and revise these courses, which will be piloted in
workshops for practicing professionals and as regular courses at NED University and other
participating universities. After assessment and revision, courses for practitioners will be taught
at six workshops with twenty participants each in Islamabad, Muzaffarabad, and the four
provincial headquarters. Several workshops will be held to build the capacity of additional
faculty and students from participating institutions.
At the end of its three-year duration, the project should result in (1) a cadre of university
educators in Pakistan who are versed in earthquake engineering, analysis of existing buildings
and design of seismic retrofits, and have professional relationships with American counterparts;
(2) more than 100 practicing building professionals who understand earthquake performance and
retrofit of existing buildings; (3) evaluations and retrofit designs for case study buildings; (4)
academic exchanges between Pakistani and American researchers and students; (5) courses in
earthquake engineering and seismic retrofit developed and taught to students and practitioners,
and (6) an earthquake engineering research agenda. The project will create a virtual center of
excellence in earthquake engineering, a critical mass of knowledgeable faculty members, and
administrators with professional relationships with American counterparts. Earthquake safety
begins with the construction of earthquake-resistant new buildings. The analysis of existing
buildings and factors that lead to vulnerability helps engineers learn the lessons needed to build
new buildings properly. The most striking outcome of this project will be the understanding
students and practitioners gain and then apply to new construction.

Problems Encountered

On the positive side, somewhat fewer delays and problems in obtaining US visas were
reported this past year than in the previous year by Pakistani visitors under the program.
However, events in Pakistan at times caused some US travelers to postpone their travel,
particularly after the recent imposition of the state of emergency. The security situation is a
particular problem for US government personnel, who require agency and post clearances to
travel, so some US participants in this category are working to restructure their project travel
plans so as to host their Pakistani colleagues instead or to hold meetings in alternate Pakistani
locations where security is greater and clearances may be obtained.
Reports of delays in Pakistani partners receiving their grant funds from HEC and MoST
were a new problem that arose for the first time this year. Pakistani principal investigators on
several projects in both the 2005 cycle (who were receiving their Year 2 payments) and the 2006
cycle (receiving their first payments) complained that they did not receive this year’s funds until
August 2007, which left them unable to hire staff and students, purchase equipment and supplies,
and make travel arrangements. It was not clear whether these late payments were the result of
bureaucratic delays or some underlying budget problems within the Pakistani agencies, but it is
hoped that these problems might be discussed with our counterparts at our next annual meeting.
Several of the investigators have indicated that they will likely need no-cost extensions on their
awards due to the late start by the Pakistani partners in their projects. These extensions will be

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no problem on the US side, but we will work to ensure that our counterparts at HEC and MoST
will also be receptive to authorizing them on the Pakistani side.

Financial Reporting

Quarterly accruals data have been provided by the Academies program office to the
Islamabad mission. Other required financial reports are submitted directly by the Office of
Contracts and Grants.

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