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CM-test: An Innovative Divergence Measurement and Its Application in Diabetes Gene Expression Data Analysis FM-test: A Fuzzy Set Theory Based Approach for Discovering Diabetes Genes

 

   
Research Projects/Programs


The University of the District of Columbia is committed to assisting area residents in producing sustainable, healthy environs and communities that will enhance the quality of life for the culturally diverse population of our nation’s capital.

AES undertakes problems and issues identified by the Mayor as the priorities for the District of Columbia.  Priorities for the city government of the District of Columbia include 1) Strengthening Children, Youth, Families and Individuals; 2) Building and Sustaining Healthy Neighborhoods; 3) Promoting Economic Development; 4) Making Government Work; and 5) Enhancing the Unity of Purpose and Democracy.



Sustainable Agriculture Research and Education
Project Leader:  James R. Allen, Ph.D.
Agricultural Experiment Station
(202) 274-7140

(SARE) Program The Sustainable Agriculture Research and Education (SARE) Program works to increase knowledge about -- and help farmers and ranchers adopt -- practices that are economically viable, environmentally sound, and socially responsible.  In the District of Columbia, urban gardeners enjoy raising crops in their home gardens, containers, and community gardens.  The SARE Program at the University of the District of Columbia provides assistance to urban gardeners in propagation, planting techniques, and pesticide management to yield healthy crops for the warm and cool months of the year. Training addresses the needs of gardeners and addresses problems that affect yields.
For example, in the Washington Metropolitan area, successfully growing cool season vegetables such as broccoli, cabbage, cauliflower, and lettuce can be a very difficult task. The major problem in growing these crops is that if they are not transported in the field by mid April, they will fail to produce marketable heads. Seedlings planted later than mid-April tend to grow well through May.  In years when the temperature starts to rise into the high 70’s and above, seedlings will “bolt” before producing marketable heads.  To get the best marketable yield from cool season crops such as broccoli, cabbage, cauliflower, and lettuce, seedlings should be transplanted into garden beds by the first week in April or as soon as climatic conditions are favorable enough to allow for adequate seed bed preparation. 

The SARE Program includes training of urban gardeners, extension agents, master gardeners, school teachers, and lawn and garden professionals in the proper usage of sustainable agricultural techniques in growing horticultural crops. This professional development program introduces sustainable agriculture, trains individuals to successfully grow plants for both indoor and outdoor purposes, and assists teachers with extra curricula activities in their instructional program.  Trained individuals will be used to help community gardeners establish and maintain vegetable gardens throughout the District of Columbia.  Training is accomplished by offering regular classes for extension agents, master gardeners and individual gardeners at UDC.  Additionally, field days and farm tours are arranged so that gardeners can receive hands-on instruction on establishing and maintaining gardens.  The training and education program is a collaborative effort between AES and CES.  Training has also been expanded to include public school teachers who are involved in the USDA supported program, Agriculture in the Classroom.  Training sessions in gardening techniques and distribution of literature with helpful information are some of the ways that the SARE Program works to assure that city residents will be able to raise healthy crops while protecting the environment.

  • James R. Allen, Edit, 1998.  A Survey of Urban Gardening in the District of Columbia.  A UDC Publication.  6pp.
  • James R. Allen, March 2000, Urban Vegetable Gardening in the District of Columbia.  Info-Doc, Agricultural Experiment Station. UDC.
  • Allen, James, 2001:  Using Composted Waste as the Soil Amendment for Vegetable Fall Gardening in the District of Columbia.  Agricultural

      Experiment Station.  Publication Series.  Vol. 2, Issue 4.

  • Allen, James, 2001:  Vegetable Fall Gardening in the District of Columbia. Agricultural Experiment Station.  Publication Series.  Vol. 2, Issue 5.

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The IR-4 Program
Project Leader:  James R. Allen, Ph.D.
Agricultural Experiment Station
(202) 274-7140

IR-4 Program The I-R4 Program is an interregional project that deals with testing, recommending, and monitoring the use of pesticides for minor use crops (vegetables and ornamentals).  The State Liaison Representative (SLR) for the District of Columbia is Dr. James R. Allen.  The I-R4 project has been closely allied with the Sustainable Agriculture Project in the area of Integrated Pest Management.  Dr. Allen works closely with the University of Maryland in monitoring pesticide application in the District of Columbia.  Such monitoring includes evaluating field plots to determine the degree of disease and insects found and methods that are being used to control them.  Consultations in this area are done through the UDC Cooperative Extension Service, the University of Maryland, and the USDA Agricultural Research Service pest control unit in Beltsville, Maryland.

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A Model of Macrophage Particulate Matter Air Pollution Interactions
Project Leader:  Rosie Sneed, Ph.D.
Department:  Biological and Environmental Sciences
Telephone:  (202) 274-6022

Effects of Bradyrhizobial Genotypes

 

 

The rate of asthma amongst children and adults in the District of Columbia has been strongly linked to the air pollution of the city’s urban environment.  One form of air pollution, particulate matter, is associated with increased morbidity and mortality in patients with respiratory and cardiovascular disease, including asthma.  Alveolar macrophages, the resident macrophages of the respiratory tract, are major cellular participants in the asthmatic response.  These cells secrete pro-inflammatory mediators such as nitric oxide and prostaglandins that are important in asthma, and alveolar macrophages may also have important cell-to-cell interactions with other cells of the respiratory tract.  The purpose of this study is to investigate the relationship between particulate air pollution and asthma.

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Current Perceptions on Cancer Prevention and Control and Cancer Intervention for African American Seniors in the District of Columbia
Project Leader:  Carolyn E. Cousin, Ph.D.
Department:  Biological and Environmental Sciences
Telephone:  (202) 274-5874

Soils treated with Biosolids

Limited research has been conducted on courses designed to provide cancer information to older adults.  Seniors require accurate and credible cancer information given that increased age is a major risk factor for most adult-onset cancers.  It is very important that cancer prevention programs continue to prevent some of the anxiety and psychological distress often experienced with cancer diagnosis and during the period of management.  Information provided in the correct format to seniors could solicit dietary and physical activity changes that may likely reduce cancer incidences in the District of Columbia.  The purpose of this study is to highlight common information gaps and psychosocial concerns, as well as, describe the different perspectives offered by participants’ usual sources of information about cancer.

 

 

Finding Diabetes Associated Genes with Fuzzy-Inferenced Decision making
L. Liang, Ph.D.
Department of Computer Science and Information Technology
(202)  274-5086

Diabetes Associated Genes Diabetes is a group of diseases characterized by high levels of blood glucose resulting from defects in insulin production, insulin action, or both.  There are 18.2 million people in the United States, or 6.3% of the population, who have diabetes.  While an estimated 13 million have been diagnosed, unfortunately, 5.2 million people are unaware that they have the disease.  While 8.7% of all people in the age group of 20 years or older have diabetes, the percentage reaches 18.3% for the age group of 60 years or older. 
Non Hispanic blacks are more likely to have diabetes than non Hispanic whites of similar age.  For non Hispanic blacks aged 20 years or older, 11.4% have diabetes (American Diabetes Association).  Diabetes is also one of the leading causes of death in the U.S.  In 2000, it contributed to 213,062 deaths, while still being under reported.  The serious complications diabetes can be associated with include heart disease and stroke, high blood pressure, blindness, kidney disease, and nervous system disease. 

Genetics is important to diabetes prevention and control.  The gene expression profile of a cell determines its phenotype and responses to the environment.  These responses include its responses towards environmental factors, drugs, and therapies.  Gene expression patterns can be determined by measuring the quantity of the end product, protein, or the mRNA template used to synthesize the protein.  Comparison of gene expression profiling in diabetes patients versus the normal counterpart people also furthers our understanding of the disease and identifies leads for therapeutic intervention. 

Interdisciplinary research is being conducted at the University of the District of Columbia to develop an innovative and advanced method for finding diabetes associated with genes using gene expression data.  The diabetes associated genes may be used to predict the disease and also to develop new therapeutic treatments. Since gene expression data is often uncertain (containing noise) and incomplete, the existing prediction methods which require certain and complete patient data can only offer incomplete or inaccurate analysis.  To fill in this gap, we propose the development of a new method, Fuzzy-Inferenced Decision making (FIND), based on the PI’s recent research.  FIND integrates techniques of pattern recognition, data mining, fuzzy inferencing and case-based reasoning to find the associations among gene expressions as well as the associations between gene expression profiles and diabetes.  Thus FIND is able to find the diabetes associated genes on incomplete and noisy data with a high accuracy.  In this project, a software tool for FIND will be developed and applied to the available gene expression data form patients.  Crucial components of FIND will be investigated and developed to achieve the best prediction accuracy.  Successful development of this method will greatly help to develop strategies to prevent and control diabetes will significantly reduce the burden of diabetes on healthcare systems.  Moreover, FIND can be applied for the prognosis of many other diseases. Successful development of this method will greatly help develop strategies to prevent and control diabetes and will significantly reduce the burden of diabetes on healthcare systems. 

  • “CM-test: An Innovative Divergence Measurement and Its Application in Diabetes Gene Expression Data Analysis” by Lily R. Liang, Shiyong Lu, Yi Lu, Puneet Dhawan, and Deepak Kumar submitted to 2006 IEEE International Conference on Granular Computing
  • “FM-test: A Fuzzy Set Theory Based Approach for the Identification of Diabetes Genes” by Yi Lu, Shiyong Lu, Lily R. Liang, and Deepak Kumar submitting to Symposium of Computations in Bioinformatics and Bioscience (SCBB06)

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Juvenile Violent Crime Patterns
Project Leader:  Terri Adams-Fuller, Ph.D.
Location:  Howard University, Department of Sociology and Anthropology
Phone:  (202) 806-6853

Community Development Violence that erupted amongst participants in the drug market economy spilled over to non-participants, as many young people who live within the neighborhoods capitulated to carrying guns themselves (Blumstein 1995, Blumstein and Cork 1996).  Faced with the realization that they could be at risk of becoming a victim of violent crime, non participants began to increasingly carry weapons for their own protection.  The increase in the number of people carrying weapons lead to a proliferation of violence among non-participants in the drug economy as these weapons are often
used to settle interpersonal conflict, thus spreading gun related violence among the populations (Cohen and Tita 1999, Blumstein 1995, and Blumstein and Rosenfield 1998).  This study seeks to examine juvenile violent crime patterns in the District of Columbia for the years 1995 – 2004 using qualitative and quantitative research methods, including exploratory spatial data analysis (ESDA) techniques.  The geographic distributions of juvenile violent crime will be examined to discern changes in patterns over time.  These changes will be examined in relation to changes in the social, economic, and environmental conditions.  In addition, this research will include a review of social service and law enforcement initiatives aimed at “at risk” youth to discern their impact on juvenile violent crime patterns.  Findings from this research have theoretical and practical significance for program and policy developments of youth crime prevention efforts.

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Multi-State Research Projects

 

Improvement of Plant Food Availability and Intake in Older Adults

Program Administrator:  Gloria S. Wyche-Moore, Ph.D.
Associate Dean/Director
Agricultural Experiment Station
(202) 274-7124
   
Project Leader:

Charles L. Jiles, Ph.D.
Department of Biological and Environmental Sciences
(202) 274-5890

 

William Rice, III, MA
Department of Mathematics
(202) 274-5508

Maggie Sone, BS
Agricultural Experiment Station
(202) 274-5949

Senior In addition to conducting research and investigations in the District of Columbia, it is also the duty of the Agricultural Experiment Station to contribute to resolving national problems in agriculture.  Thus, AES is a participant in multi-state research for the improvement of plant food availability and intake in older adults.  Despite the importance of fruit, vegetable and whole grain intake in maintaining health and functional status, older adults are not meeting minimum dietary recommendations.  The Continuing Survey of Food Intakes by Individuals (CSFII) found that only about one-third of adults over the age of 60 consumed the recommended number of servings of fruit per day, half consumed the
minimum daily number of vegetable servings, and about 40% consumed the minimum recommended servings of grains, including whole grains.  Furthermore, only a fraction of the seniors surveyed selected vegetables and grain-based foods considered to be good sources of protective food constituents such as fiber and antioxidants.  In addition and perhaps as a consequence, obesity is extremely high in the older adult population. With the goal of fostering independent living and a high quality of life as a national priority within federal health policy (HP2010) (9), considerable integrated research needs to be conducted in order to improve fruit, vegetable and whole grain intake to reduce diet-related disability, obesity and chronic disease rates among rapidly growing numbers of older Americans.  Thus, there is a need to develop effective assessment techniques and intervention strategies to improve intake of fruit, vegetables and whole grains by the older adult population.

The objectives of this multistate project are to (1) improve methods of measuring intake of fruit, vegetables and whole grains to include biomarkers, dietary assessment and associations with obesity, other biomarkers and functional endpoints in older adults; and (2) develop effective assessment techniques and intervention strategies to improve intake of fruit, vegetables and whole grains by older adults.

Researchers from the states of RI, CT, MA, and the District of Columbia (DC) will be working on Objective # 2.  The purpose of this portion of the experiment is to evaluate if nutrition education prevention promoting improvement in intake of nutrient dense food sources will affect overall dietary quality, serum cholesterol, serum glucose, and BMI, and further, to determine if improving the nutrient density of fruit and vegetables alone, whole grains alone, or the two groups in combination is the most effective in improving these parameters overall for the target population.  The nutrient dense food sources being studied include 1) deep-colored fruit and vegetables only; 2) whole grains only; and 3) both deep-colored fruit and vegetables and whole grains.

Nutrition education interventions will consist of face to face interviews and interactive workshops that will include information related to nutrient dense food choices and recipes.  Interview protocols, questions, and coding will be developed, pre-tested, and revised.  Interviews will be audio-recorded and transcribed.  Content analysis of transcripts will be conducted by participating researchers.  Emerging themes and trends will be identified.  Use of confirmatory statistical analysis will be explored.  Results will be used to identify gaps in knowledge, to develop strategies to help consumers identify whole grains at the point of purchase, and to develop appropriate educational interventions aimed at increasing the intake of whole grain foods.  The effectiveness of the intervention to positively change attitudes and behavior will be evaluated.  Researchers will work with the Senior Farmers’ Market Nutrition Program (SFMNP) and senior residents in the District of Columbia to assess the level of participation of seniors, to assess factors influencing participation (cognitive interviewing techniques will be folded into this effort), and to evaluate purchases and impact of these purchases on diet quality and longer term behaviors related to sustained or improved overall intake of fruit/vegetables. Nutrition educational materials related to the purchase, preparation, storage and nutrient/phytochemical content of a variety of foods available through SFMNPs will be identified, or developed and tested.  These materials will be distributed through community based workshops provided through cooperating stations and through existing SFMNP networks.  This work will be coordinated with the Maine station.

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An Integrated Approach to Prevention of Obesity in the High Risk Families

Project Leader:

Lily Liang, Ph.D.
Department: Computer Science and INformation Systems
Phone:  (202) 274-5086

  It has been shown that children with obese parents are more likely to be obese. In addition to genetics and inheritance, parent-child interaction can be a major factor that is responsible for this influence. When parents and children share the same food, diet, and other behavioral habits, it is very likely that these behaviors might result in similar conditions: obesity or normal. The purpose of this study is to determine key behaviors that lead to pediatric obesity as well as those behaviors that lead to resilience to pediatric obesity. This will allow us to develop a Not-to-Do list for the prevention of pediatric obesity and to develop a To-Do list to stay away from pediatric obesity.

 

 

Joint Research with the Water Resources Research Institute

 

Palletized Poultry Effect on Vegetable Production and Vadose Zone Water Quality
Project Leader:

James R. Allen, Ph.D.
Agricultural Experiment Station
(202) 274-7140

William Hare
Water Resources Research Institute
(202) 274-7133  
Roster

Poultry manure produced from Delaware, Maryland, and Virginia (DELMARVA) poultry industries is applied on farmland along with chemical fertilizer for crop production.  However, a significant amount of unused manure is stored for future usage or remains to be disposed of.  State governments have instituted several cost share programs to serve as incentives to promote additional use of poultry manure and reduce nutrient load to the Bay.  The manure transport program pays for movement of manure from farms over-enriched in soil phosphorus to farms with low phosphorus levels. It also pays for transport of manure from farm to mushroom operations and Perdue AgriRecycle manure palletizing plant.

Nutrient management plans, written by certified consultants for each farm operation in Maryland, have become a mandatory state law to prevent over application of nutrients.  Cover crops in statewide cost-share programs help recycle unused nutrients in the dormant portion of the crop production cycle.

Perdue AgriRecycle, Inc. has cleaned, sterilized, and palletized poultry manure for easy handling and movement in crop and vegetable production.  This material has been analyzed for nutrient content; however, not much data is available to demonstrate it’s effectiveness in crop and vegetable production as well as its effect on ground water quality or pfeisteria proliferation.  Residents of Washington, DC grow vegetables in their backyards and could potentially use this material as a soil amendment.  Therefore, this experiment is designed to determine the effectiveness of palletized poultry manure as a soil amendment in vegetable production and its potential effect on DC water resources.  Information generated will be used for extension and outreach to benefit the residents of the District of Columbia.

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