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PubMed2005

Databases, models, and algorithms for functional genomics: a bioinformatics perspective.

A variety of patterns have been observed on the DNA and protein sequences that serve as control points for gene expression and cellular functions. Owing to the vital role of such patterns discovered on biological sequences, they are generally cataloged and maintained within internationally shared databases. Furthermore,the variability in a family of observed patterns is often represented using computational models in order to facilitate their search within an uncharacterized biological sequence. As the biological data is comprised of a mosaic of sequence-levels motifs, it is significant to unravel the synergies of macromolecular coordination utilized in cell-specific differential synthesis of proteins. This article provides an overview of the various pattern representation methodologies and the surveys the pattern databases available for use to the molecular biologists. Our aim is to describe the principles behind the computational modeling and analysis techniques utilized in bioinformatics research, with the objective of providing insight necessary to better understand and effectively utilize the available databases and analysis tools. We also provide a detailed review of DNA sequence level patterns responsible for structural conformations within the Scaffold or Matrix Attachment Regions (S/MARs).

Animals↗
PubMed2001

A simple and rapid analysis of triplet repeat diseases by expand long PCR.

It is now known that 15 monogenic, mostly neurological, disorders are caused by the same type of mutations that occur in trinucleotide repeat sequences in certain genes. Since they share a nonspecific and variable phenotype, the accurate diagnosis could be made only by DNA analysis. We developed an Expand Long PCR assay that provides more reliable molecular diagnosis of such disorders. Its main characteristics are robust amplification of expanded alleles, simplicity, low cost and speed. We suggest the use of Expand Long PCR for routine molecular diagnosis of triplet repeat diseases, and present such analysis of the fragile X syndrome, myotonic dystrophy and Huntington's disease.

Base Sequence↗
PubMed2002

Can temperament identify affectively ill patients who engage in lethal or near-lethal suicidal behavior? A 14-year prospective study.

Among affectively ill patients followed naturalistically for up to 14 years, 36 committed suicide, 120 attempted suicide, and 373 had no recorded suicide attempt. Comparing these three groups on clinical and intake personality revealed that suicide completed within 12 months was predicted by clinical but not personality variables, and suicide beyond 12 months was predicted by newly derived temperament factors, not clinical variables. Attempters and completers shared core characteristics: previous attempts, impulsivity, substance abuse, and psychic turmoil within a cycling/mixed bipolar disorder. Such temperament attributes as impulsivity and assertiveness were the best prospective predictors of completed suicides beyond 12 months with a sensitivity level of 74% and specificity level of 82%.

Adolescent↗
PubMed1995

Indoor air pollution and asthma in hospitalized children in a tropical environment.

We performed a hospital-based study to examine a hypothesis that indoor air pollution was associated with acute asthma in young children living in Kuala Lumpur City. A total of 158 children aged 1 month to 5 years hospitalized for the first time for asthma were recruited as cases. Controls were 201 children of the same age group who were hospitalized for causes other than a respiratory illness. Information was obtained from mothers using a standardized questionnaire. Univariate analysis identified two indoor pollution variables as significant factors. Sharing a bedroom with an adult smoker and exposure to mosquito coil smoke at least three nights in a week were both associated with increased risk for asthma. Logistic regression analysis confirmed that sharing a bedroom with an adult smoker (OR = 1.91, 95% CI 1.13, 3.21) and exposure to mosquito coil smoke (OR = 1.73, 95% CI 1.02, 2.93) were independent risk factors. Other factors independently associated with acute asthma were previous history of allergy, history of asthma in first-degree relatives, low birth weight, and the presence of a coughing sibling. There was no association between asthma and exposure to kerosene stove, wood stove, aerosol mosquito repellent, type of housing, or crowding. We conclude that indoor air pollution is an avoidable factor in the increasing morbidity due to asthma in children in a tropical environment.

Air Pollution, Indoor↗
PubMed2005

Radiologic case study. Seronegative spondyloarthropathy associated with Crohn's disease.

Seronegative arthropathies are a heterogeneous group of arthropathic disorders with negative rheumatoid factors and varying association with the HLA-B27 phenotype. The distribution of involvement and pattern of presentation within this group is variable. However, these disorders share common features of aggressive erosions, bone density preservation, and proliferative bony response to inflammation. These features along with asymmetric involvement of the appendicular skeleton, sacroiliitis, and spine abnormalities usually allow differentiation from rheumatoid arthritis and other inflammatory arthritides based on imaging studies.

Adult↗
PubMed1999

Adenosine rinse in human orthotopic liver transplantation: results of a randomized, double-blind trial.

OBJECTIVE: The study was aimed at determining whether the vasodilator, adenosine, shown to produce dramatic improvement in liver graft and animal acute and long-term survival, would be beneficial in human liver transplantation. METHODS: A prospective, randomized, double-blind trial of an adenosine rinse preservation solution in human orthotopic liver transplantation (OLTX) was conducted in 43 consecutive transplants. Intraoperative and postoperative care was performed by a single transplant team utilizing a quadruple drug immunosuppressive protocol, with complete 5-year patient follow-up. At implantation all allografts were flushed with a 4 degrees C (pH 7.4) Normosol solution, with 0.12 mM adenosine or without adenosine. RESULTS: Recipient characteristics were similar in the treated and control groups including age, pre-OLTX diagnosis, and United Network for Organ Sharing (UNOS) status. Donor variables were equivalent in the two groups including age, weight, prothrombin time, and serum chemistries. Operative variables showed no differences except a significant (p = 0.006) reduction of veno-venous bypass time in the adenosine treated group. Liver allograft function improved in the adenosine rinse groups as measured by both postoperative bile production (218 +/- 156cc/24h adenosine vs. 116 +/- 78 cc/24 h without adenosine, p = 0.03) and Factor 7 production at day 3 (64 +/- 26% adenosine vs. 51 +/- 20% without adenosine, p = 0.08). The adenosine treated group had an insignificant 10% patient and graft improvement in survival at 6 months to 60 months compared to the control group. CONCLUSIONS: These results suggest that adenosine added to the intraoperative flush solution during human liver transplantation is safe, does not reduce cardiac stability at reperfusion, improves early liver allograft function, but has an insignificant short- and long-term affect on allograft survival.

Adenosine↗
PubMed2005

Using return on equity and total profit margin to evaluate hospital performance in the U.S.: a piecewise regression analysis.

We investigated hospital profitability by comparing Total Profit Margin (TPM) and Return on Equity (ROE) as measures of profitability, while controlling for inflation and other salient factors. We controlled for variables such as, Disproportionate Share Hospital status, location, type of ownership control, teaching status, conversion to or from nonprofit status, Critical Access Hospital status, sole Medicare provider status, case mix adjusted patient length of stay, bed size, number of employees, and occupancy rate. We allowed for nonlinearities in our model, and used 1996 and 1998 data in our analysis to bridge potential effects of the Balanced Budget Act of 1997. Most of the hospitals we examined were nonprofit organizations that did not convert their type of ownership control. As a consequence, we found TPM to be a better measure of profitability than ROE, and profitability was mainly influenced by location, size, occupancy rate, volume of Medicare and Medicaid patients, and teaching status. Our results clarify the primary factors associated with profitability for our sample hospitals, and will assist creditors, managers and regulators in their assessments of comparative hospital financial performance.

Data Collection↗
PubMed2006

[Cloning and analysis of phage Fab antibodies of mouse male specific antigen].

To clone mouse phage antibodies against H-Y antigen from a phage antibody library, three cycles of affinity enrichment of the mouse phage antibody library with male spleen cells and two cycles of nonspecific absorption with female spleen cells were performed. The presence of mouse Fab on the phage surface was determined by ELISA and sequence analysis. 9 of 15 strains can bind to male spleen cells with the specific activity. Recombination rate of the phage antibody library clones is 60%. Sequence analysis of the PCR products of plasmid DNA of E5 clones show VH and Vkappa had common characteristics shared by other known variable region of antibodies. The mouse phage Fab antibody could be used for identifying H-Y antigen, and for the development of sex determination of early embryos in mammals.

Animals↗
PubMed1980

The relationship between biographic profile and job role preceptions of the allied health chair: a national study.

The purpose of the study was to construct a professional profile of medical technology and physical therapy baccalaureate chairs to compare male and female respondents in the areas of (1) biographic background, (2) career aspiration, (3) influence in decision making, (4) job-related stress, (5) goals important to role as chair, (6) skills important to role as chair, and (7) perception of ideal power. The response rate to a 1978 national survey was 72%. Statistical analysis on the 25 physical therapy females, 23 physical therapy males, and 20 medical technology female respondents revealed they were comparable in terms of the above variables. The three groups shared a common biographic profile except in the areas of marital status and clinical experience. These chairs exhibited low scholarly productivity and little interest in careers in academic administration or the clinical setting. Rather, they indicated sustained interest in departmental chair status or a return to fulltime faculty status. There was also perceived high participation in decision making, low to moderate job-related stress, and high concern for personal and faculty development. They agreed that selected administrative skills were necessary to their role as chairs. Finally, they reported that a considerable amount of power was necessary to their role as chairs in their institutions. Implications for chair development and recommendations for future research are discussed.

Allied Health Personnel↗
PubMed1998

[Laboratory diagnosis of Lyme borreliosis].

Some direct methods that can be used for the diagnosis of Lyme borreliosis are the culture, direct visualization or the detection of microbial DNA using polymerase chain reactions, in body tissues or fluids. Unfortunately, all these methods have a low sensitivity. There is a wide assortment of tests and antigens for indirect diagnosis, and the most recommended are ELISA tests and Western blot. The main inconvenient of these tests are the existence of shared serologic reactions, the variability of immune response and the difficult interpretation of results. Therefore, we propose the following guidelines for the diagnosis of Lyme borreliosis: For sero-epidemiological studies and to diagnose infection, antibodies should be determined in subjects with a compatible clinical picture, using an ELISA test that must be positive in at least two separate samples. All positive ELISA results should be confirmed with Western blot analysis, that must be interpreted using established criteria. Polymerase chain reactions should be used when they are available.

Borrelia burgdorferi Group↗
PubMedDate not supplied

Characteristics of drug abusers that discriminate needle-sharers.

To identify variables that discriminate needle-sharing among drug abusers, 224 male drug abusers were studied. They had been admitted to a 30-day inpatient drug treatment program over a 19-month period (September 1983 through March 1985). The variables examined were divided into three categories: demographic (age, race, education), personality (Minnesota Multiphasic Personality Inventory [MMPI] scores and MMPI deviant scores), and drug use patterns (drug of choice, use of single or multiple [mixed] drugs, severity of drug use, and place of use). Three variables were identified that discriminated needle-sharers from other drug abusers. Compared with other drug abusers, needle-sharers used more multiple drugs, were more likely to use a "shooting gallery," and had more problems related to drug use. No demographic or personality variables discriminated needle-sharers from nonsharers. The data suggested that needle-sharing is widespread in the drug culture. Needle-sharing was not confined to a particular racial group, educational level, or personality type. These findings can be used to structure education programs about acquired immunodeficiency syndrome (AIDS) for drug abusers. Drug treatment programs appear to provide an important opportunity to educate drug abusers about AIDS and related health issues associated with needle-sharing.

Adult↗
PubMed1980

A program for sampling, assessment of stationarity and variability analysis of neuronal spike trains, run under control of a time-sharing system.

A system has been developed for off-line analysis of discharge characteristics of continuously firing nerve cells. The programs, which are mainly written in FORTRAN IV, determine mean firing rates, variability and other parameters of the impulse activity, and construct interspike interval histograms. They are run under time-sharing on a small laboratory computer. To disclose possible non-stationarities in the data all interspike interval samples are analysed with the non-parametric Kolmogorov-Smirnov test. This test is very powerful in detecting any differences between two samples and is still very easy to implement in programming. Raw data and computed statistics are stored in random access data files.

Computers↗
PubMed1995

Leishmania (Viannia) braziliensis: genetic relationships between strains isolated from different areas of Brazil as revealed by DNA fingerprinting and RAPD.

Leishmania (Viannia) braziliensis isolates from two different geographic areas in Brazil were studied by DNA fingerprinting with the 33.15 multilocal probe and PCR with arbitrary primers (random amplification of polymorphic DNA-RAPD). The genetic distance of strains was measured by band sharing. The results showed that the strains isolated in Minas Gerais, southeastern Brazil, are very different from those isolated in Pará, northern Brazil. Strains from Minas Gerais constituted a relatively homogeneous group, presenting DNA fingerprint patterns with 76% of shared bands and RAPD profiles with 93% of shared bands. In contrast, strains from Pará showed higher genetic variability, with only 17 and 45% of shared bands in DNA fingerprint and RAPD patterns, respectively. This study suggests that genetic differences between L. braziliensis from both areas might have an epidemiological significance.

Animals↗
PubMed2004

Alternative splicing of Drosophila Dscam generates axon guidance receptors that exhibit isoform-specific homophilic binding.

Dscam is an immunoglobulin (Ig) superfamily protein required for the formation of neuronal connections in Drosophila. Through alternative splicing, Dscam potentially gives rise to 19,008 different extracellular domains linked to one of two alternative transmembrane segments, resulting in 38,016 isoforms. All isoforms share the same domain structure but contain variable amino acid sequences within three Ig domains in the extracellular region. We demonstrate that different isoforms exhibit different binding specificity. Each isoform binds to itself but does not bind or binds poorly to other isoforms. The amino acid sequences of all three variable Ig domains determine binding specificity. Even closely related isoforms sharing nearly identical amino acid sequences exhibit isoform-specific binding. We propose that this preferential homophilic binding specificity regulates interactions between cells and contributes to the formation of complex patterns of neuronal connections.

Alternative Splicing↗
PubMed1998

Genetic and environmental influences on MMPI factor scales: joint model fitting to twin and adoption data.

In general, the shared family environment appears to play a negligible role in determining individual differences in personality and interests. Nevertheless, scattered reports of significant shared environmental influence on such variables appear in the literature. Using data from the Texas Adoption Project (TAP), the current study attempted to replicate twin study findings of significant shared environmental variance on four of nine Minnesota Multiphasic Personality Inventory (MMPI) factor scales (Rose, 1988). Conventional behavioral genetic analyses of the adoption data agreed in affirming a significant shared environmental influence on individual differences in Religious Orthodoxy only. Subsequent simultaneous modeling of Rose's twin data and TAP adoption data resulted in three scales (Extraversion, Inadequacy, and Religious Orthodoxy) showing significant shared environmental influence. Again, effects were most substantial for Religious Orthodoxy, where the shared environment accounted for nearly 50% of the variance. It is argued that assortative mating cannot explain this finding.

Adolescent↗
PubMed1992

Clonal evolution of a follicular lymphoma: evidence for antigen selection.

The potential role antigens play in growth stimulation or in clonal selection of follicular lymphomas is unknown. To study this issue, we sequenced the immunoglobulin heavy chain variable region genes expressed by a follicular lymphoma from multiple biopsy specimens and also cloned and sequenced the corresponding germ-line variable gene from this patient. Comparison to the germ-line gene revealed numerous nucleotide substitutions in all of the lymphoma variable gene sequences. Some of the substitutions may have occurred in the nonmalignant precursor B cell that gave rise to this lymphoma because they were shared among all of the variable genes, but many of the mutations accumulated as the malignant clone expanded. The mutations were distributed in such a way that strongly suggested the majority of tumor cells had been positively selected through their antigen receptor. This was especially evident for the mutations that developed late in the clonal evolution of this lymphoma. These findings indicate that antigen stimulation may be involved in the growth of follicular lymphoma tumors.

Antigens, Neoplasm↗
PubMed1994

Correlates of needle sharing among injection drug users.

OBJECTIVES: The sharing of contaminated injection equipment is the primary mode of human immunodeficiency virus (HIV) transmission for injection drug users. This study examined demographic factors, life events, and drug use practices that are potential risk factors for sharing injection equipment. METHODS: Between February 1988 and March 1989, 2921 active injection drug users were interviewed and questioned about their backgrounds, life-styles, and patterns of injection drug use. RESULTS: Of 2524 participants who reported injecting drugs within the 6 months prior to study enrollment, 70.4% reported recent needle sharing. A multivariate analysis found needle sharing to be more frequent among those with a history of arrest and lower socioeconomic status, even after accounting for other demographic and drug use variables. In addition, recent needle sharing was higher in male homosexual or bisexual men than in their heterosexual counterparts. CONCLUSIONS: These data suggest that injection drug users have an economic motive to share needles and that the availability of free and legal needles may reduce levels of needle sharing.

Adult↗