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Biomedical subjects

P Nadkarni

Publications and source records attributed to P Nadkarni.

At least 19 recordsLinked to original sources
PubMed2001

Web-based UMLS concept retrieval by automatic text scanning: a comparison of two methods.

The Web is increasingly the medium of choice for multi-user application program delivery. Yet selection of an appropriate programming environment for rapid prototyping, code portability, and maintainability remain issues. We summarize our experience on the conversion of a LISP Web application, Search/SR to a new, functionally identical application, Search/SR-ASP using a relational database and active server pages (ASP) technology. Our results indicate that provision of easy access to database engines and external objects is almost essential for a development environment to be considered viable for rapid and robust application delivery. While LISP itself is a robust language, its use in Web applications may be hard to justify given that current vendor implementations do not provide such functionality. Alternative, currently available scripting environments for Web development appear to have most of LISP's advantages and few of its disadvantages.

Artificial Intelligence↗
PubMed2001

Generation of pedigree diagrams for web display using scalable vector graphics from a clinical trials database.

The standard method of studying inherited disease is to observe its pattern of distribution in families, that is, its pattern in a pedigree. For clinical studies focused on inherited disease, a pedigree diagram is a valuable visual tool for the display of inheritance patterns. We describe the creation of a web-based pedigree display module for Trial/DB, a Web accessible database developed at the Yale Center for Medical Informatics (YCMI) to support clinical research studies. The pedigree diagram is generated dynamically from the database. The icons representing each subject in the pedigree are selectable hyperlinks that will display detailed clinical data collected on the subject. Microsoft Active Server Page and Scalable Vector Graphics (SVG) are used to create the interactive pedigree diagrams.

Clinical Trials as Topic↗
PubMed2000

Reengineering a database for clinical trials management: lessons for system architects.

This paper describes the process of enhancing Trial/DB, a database system for clinical studies management. The system's enhancements have been driven by the need to maximize the effectiveness of developer personnel in supporting numerous and diverse users, of study designers in setting up new studies, and of administrators in managing ongoing studies. Trial/DB was originally designed to work over a local area network within a single institution, and basic architectural changes were necessary to make it work over the Internet efficiently as well as securely. Further, as its use spread to diverse communities of users, changes were made to let the processes of study design and project management adapt to the working styles of the principal investigators and administrators for each study. The lessons learned in the process should prove instructive for system architects as well as managers of electronic patient record systems.

Clinical Trials as Topic↗
PubMed2000

Profile of a menopause clinic in an urban population in Malaysia.

The object of this study is to determine the status of an urban Malaysian woman in her menopause age group with reference to her menopausal symptoms, lipid profile, breast, pelvis and bone. One hundred and sixty four women attending the Menopause Clinic of University Hospital, Kuala Lumpur who had not previously been on hormone replacement therapy were studied. Forty nine women were perimenopausal, 74 women were in early menopause (within 5 years of menopause) and 41 women were in late menopause (after 5 years of menopause). The most common symptoms were hot flushes (56%) and generalised tiredness (49%). Eighty four percent (84%) of women had high cholesterol levels. Serum triglycerides were highest in the late menopause group. There were 2 cases of intraductal carcinoma diagnosed on routine mammography, with 8 cases of fibrocystic breast disease and 7 cases of suspicious breast lumps. Routine ultrasound (pelvic and abdominal) revealed two women with ovarian cysts, 6 women with an endometrial thickness of more than 5 mm and 8 women with uterine fibroids. Eighty five women (51.8%) had mild osteoporosis while four women had moderate osteoporosis on dual photon measurements for bone mineral density. Menopause clinics should aim at investigating a woman in her menopause as a whole. Vasomotor symptoms were common in the urban Malaysian menopausal woman. There was a high incidence of lipid abnormalities. Routine mammography, pelvic ultrasound examinations and bone mineral density tests detected significant pathology and abnormalities.

Aged↗
PubMed1999

Ethnicity affects the postprandial regulation of glycogenolysis.

We investigated the effect of nutrient intake on glucose metabolism in normal Mexican-Americans (n = 6) and European-Americans (n = 6). Subjects were studied after an 18-h fast and after 5-6 h of ingestion of hourly meals that supplied 6.35 or 12.75 micromol glucose. kg(-1). min(-1). Endogenous glucose production (EGP), gluconeogenesis (GNG), and glycogenolysis (GLY) were estimated by mass isotopomer analysis with [U-(13)C]glucose infusions. Fasting EGP, GNG, and GLY did not differ between the groups. Food ingestion lowered the molar rate of GNG by only 31%. However, while consuming the lower quantity of nutrients, Mexican-Americans had higher plasma glucose (P < 0.05), a 39% higher rate of EGP (P < 0.05), and a 68% (P < 0.025) higher rate of GLY than the European-Americans. At the higher intake, EGP and GLY were suppressed completely in both groups. There was a linear relationship between insulin concentrations, EGP, and GLY in both groups, but the slope of the line was significantly (P < 0.05) greater in the European-Americans. We conclude that the sensitivity of GLY to nutrient intake differs between ethnic groups and that this may play a role in the increased predisposition of Mexican-Americans to type II diabetes.

Adult↗
PubMed1999

Neuronal database integration: the Senselab EAV data model.

We discuss an approach towards integrating heterogeneous nervous system data using an augmented Entity-Attribute-Value (EAV) schema design. This approach, widely used in implementing electronic patient record systems (EPRSs), allows the physical schema of the database to be relatively immune to changes in domain knowledge. This is because new kinds of facts are added as data (or as metadata) rather than hard-coded as the names of newly created tables or columns. Because the domain knowledge is stored as metadata, a framework developed in one scientific domain can be ported to another with only modest revision. We describe our progress in creating a code framework that handles browsing and hyperlinking of the different kinds of data.

Databases, Factual↗
PubMed1998

Mapmerge: merge genomic maps.

MOTIVATION: When two or more genomic maps of a chromosomal region are available, it is useful to be able to synthesize them to create a merged map. RESULTS: We show that map merging is an exploratory process because there are multiple ways to combine data based upon what the user wishes to focus on, and upon which particular data subset emphasis is desired. We describe Mapmerge, a program for merging two genomic maps, discuss its limitations, and illustrate an example of its use. AVAILABILITY: Freely available (ANSI C source code, a Make file, test data files, documentation) on request from the author. CONTACT: Prakash.Nadkarni@yale.edu

Algorithms↗
PubMed1998

Automatic query mapping among genomic databases: a pilot exploration.

As databases in the human genome project proliferate, it is important for users of one genomic database to identify similar or inconsistent data in other autonomously developed genomic databases. To do so, the user needs to issue the same query across multiple databases. We describe an approach that allows a query issued against one database to be automatically mapped to an equivalent query against another structurally different database. Our approach features two components: 1) a database designed to capture knowledge (metadata) that describes the correspondences among individual database components and 2) a module that utilizes the metadata to perform query mappings. As a demonstration, we apply our query mapping approach to two chromosome map databases (DB/12 and GDB).

Algorithms↗
PubMed1996

PhenoDB: an integrated client/server database for linkage and population genetics.

In this paper we describe PhenoDB, an Internet-accessible client/server database application for population and linkage genetics. PhenoDB stores genetic marker data on pedigrees and populations. A database for population and linkage genetics requires two core functions: data management tasks, such as interactive validation during data entry and editing, and data analysis tasks, such as generating summary population statistics and performing linkage analyses. In PhenoDB we attempt to make these tasks as easy as possible. The client/server architecture allows efficient management and manipulation of large datasets via an easy-to-use graphical interface. PhenoDB data (73 populations, 34 pedigrees, approximately 4200 individuals, and close to 80,000 typings) are stored in a generic format that can be readily exported to (or imported from) the file formats required by various existing analysis programs such as LIPED and Lathrop and Lalouel's Multipoint Linkage. PhenoDB allows performance of complex ad-hoc queries and can generate reports for use in project management. Finally, PhenoDB can produce statistical summaries such as allele frequencies, phenotype frequencies, and Chi-square tests of Hardy-Weinberg ratios of population/pedigree data.

Alleles↗
PubMed1996

DNA workbench: a database package to manage regional physical mapping.

DNA Workbench (DW) is a client-server database to manage physical mapping data that will form the basis for sequencing and efforts in biologically interesting regions of a chromosome. DW draws maps at different levels of resolution in either of two modes: proportional, when the sizes of objects and the physical distances between them are known accurately or approximately, and nonproportional, when most physical distance information in a region is not available, but order information is. DW interacts with the user primarily through the map graphic. Selection of individual objects on the graphic lets the user inspect and modify the underlying data. DW also manages dependency tracking between map objects and has a rudimentary form of version control. It is currently used to manage information on the DRD2 region on chromosome 11, and on the HOX region of chromosome 17.

Chromosome Mapping↗
PubMed1996

What factors predetermine the risk of having a high-order multiple pregnancy with gamete intra-fallopian transfer?

Limiting the number of oocytes transferred at gamete intra-Fallopian transfer (GIFT) has limited the incidence of high-order pregnancy but at the same time compromised the fertility potential of some patients. A review of 300 patients who have undergone GIFT using a flexible approach as to the number of oocytes transferred identifies the patients at risk of high-order pregnancy as those aged under 30 years in whom more than six oocytes are returned and whose partner's spermatozoa have high progressive motility.

Adult↗
PubMed1994

Percutaneous epididymal sperm aspiration for obstructive azoospermia.

We report the use of percutaneous epididymal sperm aspiration as a simpler and more acceptable alternative to microscopic epididymal sperm aspiration for patients with obstructive azoospermia in whom bypass surgery is not feasible or has not been successful. Some contamination of the aspirate with blood is inevitable, but with careful sperm preparation techniques this can be reduced substantially in the final aliquot used for assisted conception. Spermatozoa with active forward progression may be used for gamete intra-Fallopian transfer treatment, but when this capacity is absent intracytoplasmic sperm injection is recommended. Three pregnancies were obtained in seven couples and a set of twins has been delivered.

Epididymis↗
PubMed1994

Day care management of severe ovarian hyperstimulation syndrome avoids hospitalization and morbidity.

Severe ovarian hyperstimulation syndrome (OHSS) is a dreaded complication of ovulation induction for assisted reproduction treatment. In the past, conservative management has been recommended and this leads to prolonged hospitalization. A total of 18 patients who developed severe OHSS were managed according to two protocols. The first group (n = 8) was managed conservatively with hospitalization, i.v. hydration and supportive therapy. The average duration of hospitalization was 11 days and the patients were uncomfortable throughout. A second group (n = 10) was managed on an out-patient basis with early, ultrasound-guided trans-abdominal paracentesis. While the patient was hydrated intravenously, 1-3 1 of fluid were removed over 2-3 h. The duration of hospitalization was between 6 and 7 h and no in-patient stay was required. Prompt relief of symptoms was reported and none of the patients required re-tapping. Pregnancy was achieved in 68% of all patients. Day care management with easy abdominal paracentesis was found to be simple, safe and effective; patients found it more acceptable as it avoided in-patient hospitalization.

Ambulatory Care↗
PubMed1992

PFGE MAPPER and PFGE READER: two tools to aid in the analysis and data input of pulse field gel electrophoresis maps.

Pulse field gel electrophoresis mapping is an important technique for characterizing large segments of DNA. We have developed two tools to aid in the construction of pulse field electrophoresis gel maps: PFGE READER which stores experimental conditions and calculates fragment sizes and PFGE MAPPER which constructs pulse field gel electrophoresis maps.

Clinical Laboratory Information Systems↗
PubMed1991

The reproductive outcome following a superhigh response to stimulation in gamete intrafallopian transfer program.

A retrospective analysis was carried out to assess the outcome of gamete intrafallopian transfer (GIFT) in cycles when more than 10 oocytes were retrieved (superhigh responders) from October 1987 through June 1989. There were 276 (13%) cycles with more than 10 oocytes retrieved among all GIFT cycles initiated during the period. Clomiphene citrate and gonadotropin were employed for ovarian stimulation in 105 (38%) cycles, and gonadotropin releasing hormone agonist in the remaining 171 (62%) cycles, employing either the flare (104 cycles) or the pituitary down-regulation (67 cycles) protocol. A maximum number of four oocytes was transferred per GIFT (3.5 +/- 0.4). The mean number of oocytes retrieved was 14.7 +/- 4.4 (range, 11 to 35). A significantly younger age group (less than 30 years) of patients was noticed in the study (31.9), and fewer women aged 40 and over (6.2%), compared to the general population of our patients. The pregnancy rate was 33.3% (n = 92) per cycle, with a delivery rate of 23.6% (n = 64) per cycle; the pregnancy loss rate was 30.8%. The reproductive outcome was lower in women aged 40 and over (pregnancy rate was 23.5%, but delivery rate was only 5.8% per cycle). The delivery rate was lower in the clomiphene citrate- and gonadotropin-stimulated cycles (51.7% per pregnancy) in relation to gonadotropin-releasing analogue and gonadotropin cycles (76.6% per pregnancy) and significantly so compared with the pituitary down-regulation protocol (83.3% per pregnancy). We conclude that a superhigh response develops more in younger women, and in such circumstances, the use of pituitary down-regulation with gonadotropin-releasing hormone will improve the reproductive outcome.

Adult↗
PubMed1991

Parallelizing genetic linkage analysis: a case study for applying parallel computation in molecular biology.

Parallel computers offer a solution to improve the lengthy computation time of many conventional, sequential programs used in molecular biology. On a parallel computer, different pieces of the computation are performed simultaneously on different processors. LINKMAP is a sequential program widely used by scientists to perform genetic linkage analysis. We have converted LINKMAP to run on a parallel computer, using the machine-independent parallel programming language, Linda. Using the parallelization of LINKMAP as a case study, the paper outlines an approach to converting existing highly iterative programs to a parallel form. The paper describes the steps involved in converting the sequential program to a parallel program. It presents performance benchmarks comparing the sequential version of LINKMAP with the parallel version running on different parallel machines. The paper also discusses alternative approaches to the problem of "load balancing," making sure the computational load is shared as evenly as possible among the available processors.

Chromosome Mapping↗
PubMed1988

A prospective, randomized double-blind trial comparing metoclopramide alone with metoclopramide plus dexamethasone in preventing emesis induced by high-dose cisplatin.

We observed 50 patients receiving high-dose cisplatin-based chemotherapy in a prospective, randomized double-blind trial. One group received metoclopramide (MCP) alone (total dose, 6 mg/kg), whereas the other group was given dexamethasone (DMS) (total dose, 60 mg) in addition to MCP. The patient characteristics of the two groups were comparable, confirming satisfactory randomization. Multivariate regression analysis failed to show any statistical significance in the antiemetic response between the two treatment groups. However, female patients receiving Adriamycin (Adria Laboratories, Columbus, OH) concurrently and obese persons exhibited more vomiting. The overall antiemetic response rate was 66%. Because the side effects were minimal, a higher dose of MCP is expected to improve emetic control without increasing toxicity. The use of a 36-hour assessment period in our study gave more meaningful data. An exponential increase in the dose of MCP is probably required, with respect to weight, to obtain the same antiemetic efficacy.

Adult↗