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John Hamilton

Publications and source records attributed to John Hamilton.

15 recordsLinked to original sources
PubMed2006

The TIGR Rice Genome Annotation Resource: improvements and new features.

In The Institute for Genomic Research Rice Genome Annotation project (http://rice.tigr.org), we have continued to update the rice genome sequence with new data and improve the quality of the annotation. In our current release of annotation (Release 4.0; January 12, 2006), we have identified 42,653 non-transposable element-related genes encoding 49,472 gene models as a result of the detection of alternative splicing. We have refined our identification methods for transposable element-related genes resulting in 13,237 genes that are related to transposable elements. Through incorporation of multiple transcript and proteomic expression data sets, we have been able to annotate 24 799 genes (31,739 gene models), representing approximately 50% of the total gene models, as expressed in the rice genome. All structural and functional annotation is viewable through our Rice Genome Browser which currently supports 59 tracks. Enhanced data access is available through web interfaces, FTP downloads and a Data Extractor tool developed in order to support discrete dataset downloads.

DNA Transposable Elements↗
PubMed2006

Expressed sequence tags from loblolly pine embryos reveal similarities with angiosperm embryogenesis.

The process of embryogenesis in gymnosperms differs in significant ways from the more widely studied process in angiosperms. To further our understanding of embryogenesis in gymnosperms, we have generated Expressed Sequence Tags (ESTs) from four cDNA libraries constructed from un-normalized, normalized, and subtracted RNA populations of zygotic and somatic embryos of loblolly pine (Pinus taeda L.). A total of 68,721 ESTs were generated from 68,131 cDNA clones. Following clustering and assembly, these sequences collapsed into 5,274 contigs and 6,880 singleton sequences for a total of 12,154 non-redundant sequences. Searches of a non-identical amino acid database revealed a putative homolog for 9,189 sequences, leaving 2,965 sequences with no known function. More extensive searches of additional plant sequence data sets revealed a putative homolog for all but 1,388 (11.4%) of the sequences. Using gene ontologies, a known function could be assigned for 5,495 of the 12,154 total non-redundant sequences with 13,633 associations in total assigned. When compared to approximately 72,000 sequences in a collated P. taeda transcript assembly derived from >245,000 ESTs derived from root, xylem, stem, needles, pollen cone, and shoot ESTs, 3,458 (28.5%) of the non-redundant embryo sequences were unique and thereby provide a valuable addition to development of a complete loblolly pine transcriptome. To assess similarities between angiosperm and gymnosperm embryo development, we examined our EST collection for putative homologs of angiosperm genes implicated in embryogenesis. Out of 108 angiosperm embryogenesis-related genes, homologs were present for 83 of these genes suggesting that pine contains similar genes for embryogenesis and that our RNA sampling methods were successful. We also identified sequences from the pine embryo transcriptome that have no known function and may contribute to the programming of gene expression and embryo development.

Amino Acid Sequence↗
PubMed2006

Preventing depression among early adolescents in the primary care setting: a randomized controlled study of the Penn Resiliency Program.

This study evaluated the Penn Resiliency Program's effectiveness in preventing depression when delivered by therapists in a primary care setting. Two-hundred and seventy-one 11- and 12-year-olds, with elevated depressive symptoms, were randomized to PRP or usual care. Over the 2-year follow-up, PRP improved explanatory style for positive events. PRP's effects on depressive symptoms and explanatory style for negative events were moderated by sex, with girls benefiting more than boys. Stronger effects were seen in high-fidelity groups than low-fidelity groups. PRP did not significantly prevent depressive disorders but significantly prevented depression, anxiety, and adjustment disorders (when combined) among high-symptom participants. Findings are discussed in relation to previous PRP studies and research on the dissemination of psychological interventions.

Analysis of Variance↗
PubMed2006

Sonotubometry.

Explore the source record for details and available documents.

Acoustic Impedance Tests↗
PubMed2005

Effect of prize-based incentives on outcomes in stimulant abusers in outpatient psychosocial treatment programs: a national drug abuse treatment clinical trials network study.

CONTEXT: Contingency management interventions that provide tangible incentives based on objective indicators of drug abstinence are efficacious in improving outcomes in substance abusers, but these treatments have rarely been implemented in community-based settings. OBJECTIVE: To evaluate the efficacy of an abstinence-based contingency management intervention as an addition to usual care in community treatment settings. DESIGN: Random assignment to usual care or usual care plus abstinence-based incentives for 12 weeks. SETTING: Eight community-based outpatient psychosocial drug abuse treatment programs. PARTICIPANTS: A total of 415 cocaine or methamphetamine users beginning outpatient substance abuse treatment. INTERVENTION: All participants received standard care, and those assigned to the abstinence-based incentive condition also earned chances to win prizes for submitting substance-free urine samples; the chances of winning prizes increased with continuous time abstinent. MAIN OUTCOME MEASURES: Retention, counseling attendance, total number of substance-free samples provided, percentage of stimulant- and alcohol-free samples submitted, and longest duration of confirmed stimulant abstinence. RESULTS: Participants assigned to the abstinence-based incentive condition remained in treatment for a mean +/- SD of 8.0 +/- 4.2 weeks and attended a mean +/- SD of 19.2 +/- 16.8 counseling sessions compared with 6.9 +/- 4.4 weeks and 15.7 +/- 14.4 sessions for those assigned to the usual care condition (P<.02 for all). Participants in the abstinence-based incentive condition also submitted significantly more stimulant- and alcohol-free samples (P<.001). The abstinence-based incentive group was significantly more likely to achieve 4, 8, and 12 weeks of continuous abstinence than the control group, with odds ratios of 2.5, 2.7, and 4.5, respectively. However, the percentage of positive samples submitted was low overall and did not differ between conditions. CONCLUSION: The abstinence-based incentive procedure, which provided a mean of 203 dollars in prizes per participant, was efficacious in improving retention and associated abstinence outcomes.

Adult↗
PubMed2005

Trends in use of antidepressants, lithium, and anticonvulsants in Kaiser Permanente-insured youths, 1994-2003.

In view of the current controversy regarding the use of antidepressants in children and adolescents, we examined trends from 1994 to 2003 in the use of antidepressants, lithium, and anticonvulsants by enrollees, aged 5-17 years, of Kaiser Permanente in Northern California. We found that the use of antidepressants more than doubled from 9.4 per 1000 enrollees to 21.3 per 1000. Most of this increase is associated with selective serotonin reuptake inhibitors (SSRIs), which increased from 4.6 to 14.5 per 1000. The use of tricyclic antidepressants (TCAs) decreased markedly, while the increase of other newer antidepressants rose from 1.3 to 6.5 per 1000. The use of anticonvulsants nearly doubled, from 3.5 to 6.9 per 1000, while lithium use was relatively stable at a rate of nearly 1 per 1000. Use of SSRIs, newer antidepressants, and anticonvulsants increased in boys as well as girls in each of three age groups: 5-9, 10-14, and 15-17 years. An increasing percentage of the antidepressant users had a diagnosis of depression, and an increasing percentage of anticonvulsant users had a diagnosis of bipolar disorder. Although the safety and efficacy of antidepressants in youths needs to be more firmly established, these findings may reflect progress in the diagnosis and treatment of mental illness.

Adolescent↗
PubMed2005

The institute for genomic research Osa1 rice genome annotation database.

We have developed a rice (Oryza sativa) genome annotation database (Osa1) that provides structural and functional annotation for this emerging model species. Using the sequence of O. sativa subsp. japonica cv Nipponbare from the International Rice Genome Sequencing Project, pseudomolecules, or virtual contigs, of the 12 rice chromosomes were constructed. Our most recent release, version 3, represents our third build of the pseudomolecules and is composed of 98% finished sequence. Genes were identified using a series of computational methods developed for Arabidopsis (Arabidopsis thaliana) that were modified for use with the rice genome. In release 3 of our annotation, we identified 57,915 genes, of which 14,196 are related to transposable elements. Of these 43,719 non-transposable element-related genes, 18,545 (42.4%) were annotated with a putative function, 5,777 (13.2%) were annotated as encoding an expressed protein with no known function, and the remaining 19,397 (44.4%) were annotated as encoding a hypothetical protein. Multiple splice forms (5,873) were detected for 2,538 genes, resulting in a total of 61,250 gene models in the rice genome. We incorporated experimental evidence into 18,252 gene models to improve the quality of the structural annotation. A series of functional data types has been annotated for the rice genome that includes alignment with genetic markers, assignment of gene ontologies, identification of flanking sequence tags, alignment with homologs from related species, and syntenic mapping with other cereal species. All structural and functional annotation data are available through interactive search and display windows as well as through download of flat files. To integrate the data with other genome projects, the annotation data are available through a Distributed Annotation System and a Genome Browser. All data can be obtained through the project Web pages at http://rice.tigr.org.

Computational Biology↗
PubMed2004

Are graduate entry programmes the answer to recruiting and selecting tomorrow's doctors?

OBJECTIVE: In the wake of the introduction of graduate entry programmes, this paper aims to promote discussion and debate on student recruitment and selection, with a view to achieving a better match between the medical student population and the health needs of the population as a whole. SETTING: Government initiatives in the UK and Australia have increased the number of medical school places, with a substantial proportion allocated to graduate entry students. In the UK, a government priority is to widen access to applicants from disadvantaged areas and lower socio-economic groups. In Australia, additional concerns for the government include ensuring medical services for rural and remote areas and improving indigenous health. At the same time, the governments in both countries are shifting costs in the direction of a 'user pays' system. OUTCOME: Graduate entry programmes represent a particular approach to minimising the effects of disadvantage, increasing the representation of students from diverse backgrounds, achieving a better match between the medical student population and the general population, and encouraging more flexible and inclusive selection and admissions policies. They also have certain disadvantages. It is possible to define a set of principles to increase the diversity of the medical school class with respect to both academic and personal qualities, whether in undergraduates or in graduate entrants. CONCLUSIONS: Graduate entry programmes can contribute to increased student diversity, but are unlikely to have much impact without other strategies to reinforce this aim. A nationwide collaboration could provide opportunities for research to establish more efficient and effective ways of selecting tomorrow's doctors.

Australia↗
PubMed2002

Carcinoid tumor and bariatric surgery.

Carcinoid is a rare gastrointestinal tumor. We have noticed a high incidence of carcinoid in our patient population during the gastric reduction-duodenal switch operation. Further studies are needed to identify any potential correlation between morbid obesity and carcinoid tumors.

Carcinoid Tumor↗
PubMed2002

A prospective, multicenter study of laboratory cross-contamination of Mycobacterium tuberculosis cultures.

A prospective study of false-positive cultures of Mycobacterium tuberculosis that resulted from laboratory cross-contamination was conducted at three laboratories in California. Laboratory cross-contamination accounted for 2% of the positive cultures. Cross-contamination should be a concern when an isolate matches the genotype of another sample processed during the same period.

Bacterial Typing Techniques↗
PubMedDate not supplied

Modeling aggregate exposures to glycol ethers from use of commercial floor products.

Computer modeling of aggregate exposure provides the capability to estimate the range of doses that can occur from product use and to understand the relative importance of different routes of exposure. This paper presents an assessment of aggregate occupational exposure to two glycol ethers used as solvents in floor maintenance products for industrial and institutional facilities, using a simulation tool named PROMISE. Three commercial floor-care products were assumed to be applied in sequence--a floor stripper, then a floor cleaner, and lastly a protective coating. The glycol ethers modeled were ethylene glycol butyl ether (EGBE) in the floor stripper and in the floor cleaner, and dipropylene glycol methyl ether (DPGME) in the coating. Modeling uncertainty was assessed through a comparison of the PROMISE inhalation exposure estimates with those from an independent model (MCCEM), and parameter uncertainty was investigated using PROMISE software's Monte Carlo simulation capabilities. Modeling results indicated that inhalation is the dominant exposure route. The predicted average air concentration and inhalation dose from PROMISE agreed with the second model (MCCEM) within 10%. Monte Carlo simulation indicated that the upper end of the aggregate-dose distribution for the scenario was more than 50% higher than the value of the point estimate. The modeled 8-h TWA concentrations for EGBE and DPGME were lower than the corresponding permissible exposure limits American Conference of Governmental Industrial Hygienists (ACGIH) Threshold Limit Values (TLV) by at least a factor of 20, indicating that under the assumed conditions workplace exposures to glycol ethers are below levels of concern.

Adult↗