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At least 415 records · Page 23Linked to original sources
PubMed1996

Anthropomorphic phantom measurements for the validation of a treatment planning system.

A series of eight irradiations of an anthropomorphic phantom has been performed as part of a programme of treatment planning system (TPS) validation. The "treatment' configurations used represent a realistic cross section of those carried out routinely in a radiotherapy centre. The dose distributions within the phantom were determined using 75 LiF TLD chips per irradiation and the measured dose distributions were compared with calculations performed on a TPS for three ranges of dose gradient. The accuracy of the technique per measurement point is estimated to be 3% in dose (low dose gradient) and 3 mm in position (high dose gradient). The measurement and data analysis techniques used permit evaluation of a TPS against recently recommended criteria of acceptability although it is noted that is is not possible to isolate TPS performance from factors depending on, for example, open beam data fitting and treatment set up accuracy.

Anthropometry↗
PubMed2003

Effectiveness, safety, and tolerability of risperidone in adolescents with schizophrenia: an open-label study.

Data on risperidone's efficacy and tolerability in adolescents with schizophrenia are scarce. We found only one prospective, open-label study in this population. The aim of this open-label, prospective study was to estimate the effectiveness, safety, and tolerability of risperidone treatment in adolescents with first-episode schizophrenia. Subjects were adolescent inpatients diagnosed with Diagnostic and Statistical Manual of Mental Disorders (fourth edition) first-episode schizophrenia by the Kiddie Schedule for Affective Disorders and Schizophrenia for School-Age Children-Present Episode version. Most of the patients (10/11) were drug naïve. Improvement was assessed during the first 6 weeks of treatment using the Positive and Negative Syndrome Scale (PANSS), the Brief Psychiatric Rating Scale (BPRS), and the Clinical Global Impression (CGI) scale. Side effects were monitored using the Abnormal Involuntary Movement Scale, the Simpson-Angus Scale, the Barnes Akathisia Rating Scale, and the Udvalg for Kliniske Undersogelser Side Effect Rating Scale. Eleven adolescents between 15.5 and 20 years of age (mean = 17.27, SD = 1.27 years) were included in this study. Risperidone in an average dose of 3.14 mg/day (SD = 1.60 mg/day) produced a significant improvement on the total PANSS score (28%, p < 0.01), BPRS score (30.11%, p < 0.01), and CGI-Severity score (31.36%, p < 0.01). Risperidone was ineffective in the treatment of negative signs as assessed by the PANSS. The major side effects were extrapyramidal side effects, somnolence, depression, and weight gain. In conclusion risperidone appears to be a safe, acceptably tolerated, and effective antipsychotic medication for the treatment of adolescent-onset schizophrenia.

Adolescent↗
PubMed1992

Analysis of the UL36 open reading frame encoding the large tegument protein (ICP1/2) of herpes simplex virus type 1.

Using peptide antisera specific for regions within the N terminus and C terminus of the predicted UL36 gene product, immunoblotting experiments were performed to demonstrate definitively that ICP1/2 is encoded by the UL36 gene. These data also suggest that both the cell- and the virion-associated forms of ICP1/2 are colinear with the complete predicted amino acid sequence of the UL36 gene. Computer-assisted analyses of the predicted amino acid sequence of the UL36 gene revealed the presence of two putative leucine zipper-type motifs and a potential ATP-binding domain. The possible functions of these consensus domains will also be discussed.

Amino Acid Sequence↗
PubMed1999

Ganaxolone: a novel positive allosteric modulator of the GABA(A) receptor complex for the treatment of epilepsy.

Ganaxolone is a member of a novel class of neuroactive steroids which modulates the GABA(A) receptor complex (GRC) via an unique recognition site, distinct from those of benzodiazepines and barbiturates. Preclinical data from an array of chemically- and electrically-induced seizure models demonstrate that ganaxolone possesses broad spectrum anticonvulsant activity with potential clinical utility in both generalised and partial seizures, as well as cocaine-induced seizures. Clinical data to date support a favourable safety profile with somnolence, an extension of GABAergic activity, being the most frequently reported adverse event at higher doses. Target indications include infantile spasms and complex partial seizures. Open-label data in paediatric patients with intractable epilepsy suggest that ganaxolone may be effective in treating infantile spasms. A controlled trial utilising an in-patient, monotherapy design demonstrated that ganaxolone effectively decreases complex partial seizure activity compared to placebo. An important area of further evaluation is ganaxolone's potential role in the treatment of women with catamenial epilepsy.

Journal Article↗
PubMed1991

Genome organization and nucleotide sequence of human papillomavirus type 39.

The 7833-bp nucleotide sequence of human papillomavirus type 39 (HPV39), which is associated with genital intraepithelial neoplasias and invasive carcinomas, has been determined. The genome organization deduced from the sequence shares characteristic features with other genital papillomaviruses. According to sequence comparisons, HPV39 most closely resembles HPV18 and may be a member of a subgroup of genital papillomaviruses distinct from the HPV16/31/33 group. As a novel feature, we report a 1.3-kb open reading frame on the DNA strand which lacks major open reading frames in the other sequenced HPV genomes.

Base Sequence↗
PubMed1992

DNA sequence and analysis of a cryptic 4.2-kb plasmid from the filamentous cyanobacterium, Plectonema sp. strain PCC 6402.

The 4194-bp plasmid, pRF1, from Plectonema sp. Strain PCC 6402 was completely sequenced and analyzed. Seven potential open reading frames were identified. The predicted amino acid sequence of open reading frame C (ORF C) had identities of 34, 29, and 25% with Rep B from the Staphylococcus aureus plasmid, pUB110; Rep from the Bacillus amyloliquefaciens plasmid, pFTB14; and protein A from the S. aureus plasmid, pC194, respectively. A 75-amino-acid region conserved in these proteins (Rep B, Rep, and protein A) also was highly conserved in ORF C with identities of 45, 37, and 40%, respectively. Significantly, 16 of the 21 amino acids conserved in Rep B, Rep, and protein A were found at the same positions in ORF C. This ORF may encode a replication protein that includes a region conserved in some eubacteria. Additional structural features include a 425-bp region that contains palindromes, tandem repeats, and short direct repeats which may correspond to the origin of replication. An 18-bp inverted repeat was located between two open reading frames, A and G.

Amino Acid Sequence↗
PubMed1994

Cloning and expression of genes from the genomic region between genes cd and 30 of bacteriophage T4.

Ten open reading frames (ORFs) from the cd-30 region of bacteriophage T4, as well as genes 31 and rIII, have been cloned, and all were found to be expressed in a T7 RNA polymerase system. Expression data confirm the existence of genes 31.2, 31.1, 31, rIII, 30.9, 30.8, 30.7, 30.6, 30.5, 30.4, 30.3 and 30.2, which predict peptides of 78, 102, 111, 82, 58, 110, 121, 95, 65, 68, 152 and 278 amino acids (aa), respectively. The major product of gene 30.9 is a basic peptide initiated at the second AUG codon that is found 42 nucleotides downstream and in frame from the first AUG. A plasmid carrying gene 30.3 expresses two different peptides, one of which is of the size predicted for gp30.3. By site-directed mutagenesis we have shown that the smaller peptide is encoded by gene 30.3' which is completely embedded within gene 30.3, but in a different reading frame. Gene 30.3' encodes a 75-aa basic peptide with its C terminus rich in charged aa.

Amino Acid Sequence↗
PubMed1996

Cloning and sequencing of the dnaK operon of Bacillus stearothermophilus.

Here, we report the cloning of a 5.8-kb PstI fragment of chromosomal DNA from Bacillus stearothermophilus (Bt) carrying the three genes, grpE, dnaK and dnaJ. This fragment contains, in addition, the 3'-end of an open reading frame which has been shown to be part of the dnaK operon in three bacterial species. The dnaJ gene could complement an Escherichia coli dnaJts mutant for growth at high temperature. Sequencing and hybridization data strongly suggest that the Bt chromosome contains an analog of dnaJ.

Amino Acid Sequence↗
PubMed2000

DNA sequence analysis of the photosynthesis region of Rhodobacter sphaeroides 2.4.1.

This paper describes the DNA sequence of the photosynthesis region of Rhodobacter sphaeroides 2.4.1 (T). The photosynthesis gene cluster is located within a approximately 73 kb Ase I genomic DNA fragment containing the puf, puhA, cycA and puc operons. A total of 65 open reading frames (ORFs) have been identified, of which 61 showed significant similarity to genes/proteins of other organisms while only four did not reveal any significant sequence similarity to any gene/protein sequences in the database. The data were compared with the corresponding genes/ORFs from a different strain of R.sphaeroides and Rhodobacter capsulatus, a close relative of R. sphaeroides. A detailed analysis of the gene organization in the photosynthesis region revealed a similar gene order in both species with some notable differences located to the pucBAC = cycA region. In addition, photosynthesis gene regulatory protein (PpsR, FNR, IHF) binding motifs in upstream sequences of a number of photosynthesis genes have been identified and shown to differ between these two species. The difference in gene organization relative to pucBAC and cycA suggests that this region originated independently of the photosynthesis gene cluster of R.sphaeroides.

Base Sequence↗
PubMed2001

Comparative analysis of the gene-dense ACHE/TFR2 region on human chromosome 7q22 with the orthologous region on mouse chromosome 5.

Chromosome 7q22 has been the focus of many cytogenetic and molecular studies aimed at delineating regions commonly deleted in myeloid leukemias and myelodysplastic syndromes. We have compared a gene-dense, GC-rich sub-region of 7q22 with the orthologous region on mouse chromosome 5. A physical map of 640 kb of genomic DNA from mouse chromosome 5 was derived from a series of overlapping bacterial artificial chromosomes. A 296 kb segment from the physical map, spanning ACHE: to Tfr2, was compared with 267 kb of human sequence. We identified a conserved linkage of 12 genes including an open reading frame flanked by ACHE: and Asr2, a novel cation-chloride cotransporter interacting protein Cip1, Ephb4, Zan and Perq1. While some of these genes have been previously described, in each case we present new data derived from our comparative sequence analysis. Adjacent unfinished sequence data from the mouse contains an orthologous block of 10 additional genes including three novel cDNA sequences that we subsequently mapped to human 7q22. Methods for displaying comparative genomic information, including unfinished sequence data, are becoming increasingly important. We supplement our printed comparative analysis with a new, Web-based program called Laj (local alignments with java). Laj provides interactive access to archived pairwise sequence alignments via the WWW. It displays synchronized views of a dot-plot, a percent identity plot, a nucleotide-level local alignment and a variety of relevant annotations. Our mouse-human comparison can be viewed at http://web.uvic.ca/~bioweb/laj.html. Laj is available at http://bio.cse.psu.edu/, along with online documentation and additional examples of annotated genomic regions.

Acetylcholinesterase↗
PubMed1996

Analysis of a 26 kb region on the left arm of yeast chromosome XV.

In the framework of the EC programme for sequencing yeast chromosome XV, we have determined the nucleotide sequence of a 26 kb region. Subsequent analysis revealed 13 non-overlapping open reading frames, three of which correspond to known yeast genes. A pair of tRNA genes associated with remnant Ty elements were localized in this region. From structural parameters and/or similarity searches with entries in the current data libraries, a preliminary functional assessment of several of the putative novel gene products can be made. The gene density in this region amounts to one gene in 2 kb. Protein coding regions occupy 61% of the total DNA sequence. Within the intergenic regions, potential regulatory elements can be predicted. The data obtained here may serve as a basis for a more detailed biochemical analysis of the novel genes. The complete nucleotide sequence of the 26 kb segment as depicted in Figure 1 has been deposited at the EBI data library under Accession Number X91067.

Amino Acid Sequence↗
PubMed2000

Cloning and expression of secretagogin, a novel neuroendocrine- and pancreatic islet of Langerhans-specific Ca2+-binding protein.

We have cloned a novel pancreatic beta cell and neuroendocrine cell-specific calcium-binding protein termed secretagogin. The cDNA obtained by immunoscreening a human pancreatic cDNA library using the recently described murine monoclonal antibody D24 contains an open reading frame of 828 base pairs. This codes for a cytoplasmic protein with six putative EF finger hand calcium-binding motifs. The gene could be localized to chromosome 6 by alignment with GenBank genomic sequence data. Northern blot analysis demonstrated abundant expression of this protein in the pancreas and to a lesser extent in the thyroid, adrenal medulla, and cortex. In addition it was expressed in scant quantity in the gastrointestinal tract (stomach, small intestine, and colon). Thyroid tissue expression of secretagogin was restricted to C-cells. Using a sandwich capture enzyme-linked immunosorbent assay with a detection limit of 6.5 pg/ml, considerable amounts of constitutively secreted protein could be measured in tissue culture supernatants of stably transfected RIN-5F and dog insulinoma (INS-H1) cell clones; however, in stably transfected Jurkat cells, the protein was only secreted upon CD3 stimulation. Functional analysis of transfected cell lines expressing secretagogin revealed an influence on calcium flux and cell proliferation. In RIN-5F cells, the antiproliferative effect is possibly due to secretagogin-triggered down-regulation of substance P transcription.

Amino Acid Sequence↗
PubMed1993

Nucleotide sequence of tobamovirus Ob which can spread systemically in N gene tobacco.

The genomic RNA sequence of tobamovirus Ob (Ob), which can spread systemically in tobacco carrying the N gene, was determined. It consists of 6507 nucleotides and contains four open reading frames, exactly corresponding to the genomic organization of tobamoviruses known so far, i.e. encoding the 130K, 180K, 30K and coat proteins. There were no nucleotide overlaps between any open reading frames. The Ob nucleic acid sequence, predicted protein sequences and gene organization were compared with those of other tobamoviruses reported previously. This virus was originally reported as a tomato mosaic virus; however, the nucleotide sequence data given here refute this classification. The determinants that allow tobamovirus Ob to overcome the N gene, a feature peculiar to this virus, were not identified apart from sequence data. This virus should be regarded as a new tobamovirus. The determinants interacting with the tentative N gene product have not yet been analysed.

Amino Acid Sequence↗
PubMedDate not supplied

Using ethnography to improve intervention design.

PURPOSE: The purpose of this research was to use a three-phase ethnographic approach to examine the range of factors that affect people's decisions about physical activity and diet. DESIGN: We used open-ended data collection strategies, analyzed inductively, to inform, the development of a family intervention. SETTING: The study was conducted in a small low-income town in Colorado. SUBJECTS: Families with young children were selected to include social, economic, and ethnic diversity. Twenty-nine of 31 invited families participated (94%). MEASURES: The measures consisted of 21 open-ended interviews in the first phase; 12 semistructured interviews in the second phase, and six home visits in the third phase. The Atlas.ti program25 was used for data analysis. RESULTS: Significant barriers to regular exercise and good dietary habits were grouped as social/structural (e.g., working parents, costs of exercise) and cultural (e.g., perception that fast food is normal). Behavioral facilitators include disease in the family and community opportunities for exercise. Results revealed family values and dynamics that other methods would have missed. CONCLUSIONS: These data suggest that families are embedded in a multicomponent "web" of factors that influence diet and physical activity. It is feasible and desirable to use ethnographic methods to discern the interactions of these factors that make each household unique. These results argue for dynamic intervention designs that operate from a broad contextual perspective.

Adult↗
PubMed1999

Commissioning, clinical implementation and quality assurance of Siemen's Virtual Wedge.

This report presents the results of commissioning, clinical implementation and quality assurance of Siemens Virtual Wedge. Our measurements show that: (1) wedge factors are within 2% of unity, (2) percentage depth doses are within 1% of open beam data, and (3) wedged beam profiles can be modeled similarly to a physical wedge and follow a well defined equation to facilitate modeling of an arbitrary wedge angle. The gantry angle dependence of wedge profiles is similar to open beam profiles. The output of wedged fields is linear with delivered monitor units within 1%. Quality assurance results indicate the wedge profiles are very stable over time. Day to day variations of two points measured along the wedge gradient direction are within 1.5%.

Algorithms↗
PubMed2003

Positive selection during the diversification of class I vomeronasal receptor-like (V1RL) genes, putative pheromone receptor genes, in human and primate evolution.

Vomeronasal receptors are the major receptors for pheromones in vertebrates, and five putative type 1 vomeronasal receptors (V1RL) have been identified in humans. The evolution of the V1RL1 gene in non-human primates, and patterns of selection on V1RL genes, were investigated. The presumed ortholog of V1RL1 was sequenced from 13 species of nonhuman primate, and in eight of these species V1RL1 was a pseudogene. Phylogenetic reconstructions reveal that V1RL1 pseudogene formation occurred independently in multiple primate lineages. Using maximum likelihood estimates of dN/dS ratios in PAML, we show that V1RL genes have evolved under neutral evolution in lineages in which they became a pseudogene. In contrast, among lineages in which V1RL genes contain an open reading frame, the majority of sites are under purifying selection and a minority are under significant positive selection. These results provide an interesting case where all three categories of selection can be teased apart in the same data set using maximum likelihood methods. The finding of positive selection on V1RL genes during primate evolution provides indirect support for the hypothesis that V1RL genes have a function in species-specific pheromone detection in primates.

Amino Acid Sequence↗
PubMed2004

A short insert in the leader sequence of RNA 3L, a long variant of Alfalfa mosaic virus RNA3, introduces two unidentified reading frames.

N20-RNA 3L, a large form of RNA 3 associated with Alfalfa mosaic virus (AMV) strain N20 comprises 2281 nt and has approximately 97% overall sequence similarity to the longest previously described RNA 3 of AMV strain YSMV (YSMV-RNA 3; 2188 nt). Compared with YSMV-RNA 3, N20-RNA 3L contains an additional 97 nt in the 5' leader upstream of the open reading frames for movement protein (MP) and coat protein (CP). Two overlapping unidentified reading frames (URF1 and URF2) result from this modification, each of which code for putative translation products of 21 amino acids. The URF1 putative peptide has a hydrophilic N-terminus and a hydrophobic C-terminus, indicating a possible association with both host cell membrane and cytosol whereas the putative URF2 product is predominantly hydrophobic. A further structural modification found in N20-RNA 3L is a new tandem repeat of 243 nts which overlaps with the MP open reading frame.

5' Untranslated Regions↗