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Biomedical subjects

E Baker

Publications and source records attributed to E Baker.

At least 19 recordsLinked to original sources
PubMed2005

GeneKeyDB: a lightweight, gene-centric, relational database to support data mining environments.

BACKGROUND: The analysis of biological data is greatly enhanced by existing or emerging databases. Most existing databases, with few exceptions are not designed to easily support large scale computational analysis, but rather offer exclusively a web interface to the resource. We have recognized the growing need for a database which can be used successfully as a backend to computational analysis tools and pipelines. Such database should be sufficiently versatile to allow easy system integration. RESULTS: GeneKeyDB is a gene-centered relational database developed to enhance data mining in biological data sets. The system provides an underlying data layer for computational analysis tools and visualization tools. GeneKeyDB relies primarily on existing database identifiers derived from community databases (NCBI, GO, Ensembl, et al.) as well as the known relationships among those identifiers. It is a lightweight, portable, and extensible platform for integration with computational tools and analysis environments. CONCLUSION: GeneKeyDB can enable analysis tools and users to manipulate the intersections, unions, and differences among different data sets.

Algorithms↗
PubMed2005

Cassini Imaging Science: initial results on Saturn's atmosphere.

The Cassini Imaging Science Subsystem (ISS) began observing Saturn in early February 2004. From analysis of cloud motions through early October 2004, we report vertical wind shear in Saturn's equatorial jet and a maximum wind speed of approximately 375 meters per second, a value that differs from both Hubble Space Telescope and Voyager values. We also report a particularly active narrow southern mid-latitude region in which dark ovals are observed both to merge with each other and to arise from the eruptions of large, bright storms. Bright storm eruptions are correlated with Saturn's electrostatic discharges, which are thought to originate from lightning.

Atmosphere↗
PubMed2005

Cassini Imaging Science: initial results on Phoebe and Iapetus.

The Cassini Imaging Science Subsystem acquired high-resolution imaging data on the outer Saturnian moon, Phoebe, during Cassini's close flyby on 11 June 2004 and on Iapetus during a flyby on 31 December 2004. Phoebe has a heavily cratered and ancient surface, shows evidence of ice near the surface, has distinct layering of different materials, and has a mean density that is indicative of an ice-rock mixture. Iapetus's dark leading side (Cassini Regio) is ancient, heavily cratered terrain bisected by an equatorial ridge system that reaches 20 kilometers relief. Local albedo variations within and bordering Cassini Regio suggest mass wasting of ballistically deposited material, the origin of which remains unknown.

Extraterrestrial Environment↗
PubMed2005

Cassini Imaging Science: initial results on Saturn's rings and small satellites.

Images acquired of Saturn's rings and small moons by the Cassini Imaging Science Subsystem (ISS) during the first 9 months of Cassini operations at Saturn have produced many new findings. These include new saturnian moons; refined orbits of new and previously known moons; narrow diffuse rings in the F-ring region and embedded in gaps within the main rings; exceptionally fine-scale ring structure in moderate- to high-optical depth regions; new estimates for the masses of ring-region moons, as well as ring particle properties in the Cassini division, derived from the analysis of linear density waves; ring particle albedos in select ring regions; and never-before-seen phenomena within the rings.

Journal Article↗
PubMed2005

The Hunter-McAlpine syndrome results from duplication 5q35-qter.

In 1977 Hunter et al. J Med Genet 1977: 14 (6): 430-437, reported a family with six affected members, connected over three generations through unaffected individuals. Subsequently, several other patients purported to have the condition were reported. The condition became known as the Hunter-McAlpine syndrome, and there was debate as to whether or not it was identical to the Ruvalcaba syndrome or a type of tricho-rhino-phalangeal syndrome. In this article we confirm that the original family and a patient reported by Ades et al. Clin Dysmorphol 1993: 2 (2): 123-130 have cryptic translocations resulting in duplication of 5q35-qter. Similarities are noted between our patients and others in the literature with duplication of this chromosome segment.

Abnormalities, Multiple↗
PubMed2005

Frequency of truly cryptic subtelomere abnormalities--a study of 534 patients and literature review.

Frequency of truly cryptic subtelomere abnormalities - a study of 534 patients and literature review. Unbalanced subtelomere chromosome rearrangements are a significant cause of mental retardation with approximately 5% of over 3000 affected individuals tested worldwide having a chromosome rearrangement of this type. Many of these abnormalities are detectable using routine karyotyping at the 550 band level and therefore are not considered to be cryptic. The frequency of truly cryptic subtelomere abnormality should be less than 5% but has not been established. In this study, we defined 'cryptic abnormality' as one not detectable at the 550 band level on routine karyotyping. Using this as one of the selection criteria, we have studied 534 individuals with mental retardation/ developmental delay (MR/DD) and referred for subtelomere study by clinical geneticists. We have identified seven cases with cryptic subtelomere abnormalities. The clinical features of the seven abnormal cases are summarized. Literature review identified five publications on the identification of subtelomere abnormalities which used similar recruitment criteria: (a) normal karyotype at the 550 band level and (b) subjects were selected for subtelomere studies. Combining the data from these studies with those of the current study, 1154 patients were tested and 30 subtelomere abnormalities were identified. We estimate the frequency of truly cryptic subtelomere abnormality to be approximately 2.6% (30/1154) in children with MR/DD who are referred for subtelomere study.

Abnormalities, Multiple↗
PubMed2004

Quality of life as conveyed by pediatric patients with cancer.

Quality-of-life instruments have provided important advances in measuring the quality of life of pediatric patients receiving treatment for cancer. However, the bases of these instruments have not included first-hand reports from the patients; thus, these instruments may be conceptually incomplete. We directly solicited from pediatric patients their perspectives regarding their quality of life during treatment for cancer. We conducted two pilot studies: 23 patients (aged 8-15 years) participated in the first, a cross-sectional study; and 13 patients (aged 10-18 years) participated in the second, a 2-year longitudinal study. Data were analyzed by using a semantic-content method, and the following six domains were recognized in data from both of the studies: symptoms, usual activities, social/family interactions, health status, mood, and the meaning of being ill. These domains were compared with those of seven established pediatric oncology quality-of-life instruments, none of which included all six of these domains; the domain most frequently missing was the meaning of being ill domain. Here we present a new definition of the quality of life of pediatric oncology patients that is based on six domains; this definition may ensure the completeness and sensitivity of these important instruments.

Adolescent↗
PubMed2003

Two further cases of Ohdo syndrome delineate the phenotypic variability of the condition.

Ohdo syndrome (MIM 249620) is a multiple malformation syndrome characterized by blepharophimosis, ptosis, dental hypoplasia, hearing impairment and intellectual disability. A wide range of dysmorphic features and congenital abnormalities have been described in cases reported as Ohdo and Ohdo-like syndromes. We report a further two cases of Ohdo syndrome, one with mild features and the other more severely affected, illustrating the phenotypic variability of the condition. A review of the literature highlights the severe phenotype associated with distinctive facial features, as seen in Case 2 in this report All cases with the severe phenotype have been sporadic. Subtelomeric FISH studies of all chromosome arms on the two cases showed no abnormality. We propose clinical criteria for the diagnosis of Ohdo syndrome and delineate features of the severe phenotype.

Blepharophimosis↗
PubMed2003

Forgotten fragile sites and related phenomena.

Fragile sites have been recognised since 1965. Extensive molecular characterisation of them has occurred in the last decade. Yet there are a number of interesting phenomena relating to fragile sites and similar lesions on chromosomes that have not been subject to recent published research. The aim of this short review is to stimulate interest in some of these aspects of fragile sites in the hope that a more complete picture of their nature and properties will emerge.

Antimetabolites, Antineoplastic↗
PubMed2002

A familial cryptic subtelomeric deletion 12p with variable phenotypic effect.

A 15-year-old-boy and his mother, both carrying a cryptic deletion within 12p13.33, are described. The proband has a mild phenotype with moderate mental retardation and severe behavioural problems. The mother had some learning difficulties at school. Conventional GTL-banded high-resolution chromosome analysis showed normal karyotypes. Subsequent analysis by fluorescence in situ hybridization using a set of probes specific for the subtelomeric regions of all chromosomes, plus a series of probes at 12p13.33 extending from the 12p telomere, showed that both mother and son carry a 1.65 Mb terminal deletion in this region. There are 10 predicted genes within the deleted region. The unanticipated familial nature of the deletion emphasizes the value of family studies in all cases with subtelomeric abnormalities. It also demonstrates the difficulty in making a clinical diagnosis of individuals with this deletion. To the best of the present authors' knowledge, the proband and his mother are the first patients described with a submicroscopic deletion at 12p13.33.

Abnormalities, Multiple↗
PubMed2001

Effect of iron chelators on proliferation and iron uptake in hepatoma cells.

BACKGROUND: The siderophore desferrioxamine mesylate (DFO) is used routinely in clinical practice to treat diseases of iron (Fe) overload. Recent studies suggest that DFO and other chelators may have potential in the treatment of cancer. The current study reports the findings obtained when a number of chelators with varying membrane permeability, Fe-binding affinity, and preference for either Fe(3+) or Fe(2+) were assessed for their antineoplastic potential in vitro against hepatocellular carcinoma cells (HCC) because to the authors' knowledge there are few effective treatment methods for this aggressive neoplasm. METHODS: A number of criteria were investigated, including the effects of the chelators on cell proliferation, selectivity, Fe uptake, toxicity, and cell cycle progression. RESULTS: The results obtained showed that Fe binding affinity did appear to influence Fe chelator activity but was not an absolute factor, and that certain ferric and ferrous, membrane-permeable and membrane-impermeable Fe chelators demonstrated antiproliferative activity and selectivity against HCC. All effective chelators inhibited Fe uptake from Tf-(59)Fe in both hepatoma cells and normal hepatocytes. However, these chelators all had much lower effects on the survival of normal proliferating and nonproliferating cells. The effects on cell cycle were more varied between chelators, as were levels of toxicity. CONCLUSIONS: The results of the current study indicate that a number of different Fe chelators have the potential to treat HCC, and that further investigation into their mechanisms of action is warranted.

Carcinoma, Hepatocellular↗
PubMed2001

Kinetics of efficient recombinant adeno-associated virus transduction in retinal pigment epithelial cells.

The aim of this study was to investigate the premise that retinal pigment epithelial (RPE) cells are more permissive to recombinant adeno-associated virus (rAAV) transduction than other cells. We investigated the kinetics and mechanisms of rAAV transduction in RPE cells and found that the transduction efficiencies of cultured RPE cells HRPE51 and ARPE19 were significantly higher than those of 293 (P < 0.008) and HeLa (P < 0.025) cells. In addition, RPE cells reached maximum transduction efficiency at a much lower m.o.i. (m.o.i. 10) than 293 cells (m.o.i. 25). Competition experiments using 1 microg/ml heparin inhibited the high level of transduction in RPE cells by 30%, but additional heparin failed to reduce rAAV transduction further. Southern hybridization of low-molecular-weight DNA from transduced RPE cells indicated that 42% of single-stranded rAAV DNA was translocated into the nucleus by 2 h postinfection. By 6 h postinfection, double-stranded rAAV DNA was observed, which coincided with the onset of transgene expression. Southern and fluorescence in situ hybridization of total genomic DNA indicated that long-term transgene expression in RPE cells was maintained by the integration of rAAV into the cellular chromosome. Together, these results suggest that the high permissiveness of RPE cells is not related to the presence of heparan sulfate receptors or nuclear trafficking but may be due to an enhanced rate of second-strand synthesis and that integration in RPE cells is responsible for long-term transgene expression.

Anticoagulants↗
PubMed2001

Isolation, tissue distribution, and chromosomal localization of a novel testis-specific human four-transmembrane gene related to CD20 and FcepsilonRI-beta.

CD20 and the beta subunit of the high affinity receptor for IgE (FcepsilonRIbeta) are related four-transmembrane molecules that are expressed on the surface of hematopoietic cells and play crucial roles in signal transduction. Herein, we report the identification and characterization of a human gene, TETM4, that encodes a novel four-transmembrane protein related to CD20 and FcepsilonRIbeta. The predicted TETM4 protein is 200 amino acids and contains four putative transmembrane regions, N- and C-terminal cytoplasmic domains, and three inter-transmembrane loop regions. TETM4 shows 31.0 and 23.2% overall identity with CD20 and FcepsilonRIbeta respectively, with the highest identity in the transmembrane regions, whereas the N- and C-termini and inter-transmembrane loops are more divergent. Northern blot and RT-PCR analysis suggest that TETM4 mRNA has a highly restricted tissue distribution, being expressed selectively in the testis. Using fluorescence in situ hybridization and radiation hybrid analysis, the TETM4 gene has been localized to chromosome 11q12. The genes for CD20 and FcepsilonRIbeta have also been mapped to the same region of chromosome 11 (11q12-13.1), suggesting that these genes have evolved by duplication to form a family of four-transmembrane genes. TETM4 is the first nonhematopoietic member of the CD20/FcepsilonRIbeta family, and like its hematopoietic-specific relatives, it may be involved in signal transduction as a component of a multimeric receptor complex.

Alternative Splicing↗
PubMed2001

Molecular cloning of a human Vent-like homeobox gene.

We have isolated a previously unknown human homeobox-containing cDNA, VENT-like homeobox-2 (VENTX2), using PCR with a bone marrow cDNA library and primers designed from the VENTX1 (alias HPX42) homeobox sequence. Here we describe the molecular cloning, chromosomal localization to 10q26.3, and functional analysis of this gene. The 2.4-kb human VENTX2 cDNA encoded a protein with a predicted molecular weight of 28 kDa containing a homeodomain with 65% identity to the Xenopus laevis ventralizing gene Xvent2B. VENTX2 antisera detected a 28-kDa protein in cells transfected with a VENTX2 expression construct, in a human erythroleukemic cell line and in bone marrow samples obtained from patients in recovery phase after chemotherapy. The similarity of the homeodomains from VENTX2 and the X. laevis Vent gene family places them in the same homeodomain class. Consistent with this structural classification, overexpression of VENTX2 in zebrafish embryos led to anterior truncations and failure to form a notochord, which are characteristics of ventralization.

Amino Acid Sequence↗
PubMed2001

Psycholinguistic models of speech development and their application to clinical practice.

This article presents an introduction to psycholinguistic models of speech development. Two specific types of models are addressed: box-and-arrow models and connectionist or neural network models. We review some historical and some current models and discuss recent applications of such models to the management of speech impairment in children. We suggest that there are two ways in which a psycholinguistic approach can influence clinical practice: by directly supplementing a speech-language pathologist's repertoire of assessment and treatment approaches and by offering a new way to conceptualize speech impairment in children.

Brain↗