Biomedical subjects

D P Martin

Publications and source records attributed to D P Martin.

At least 19 recordsLinked to original sources

PubMed2006

Coat protein gene diversity among Chrysanthemum virus B isolates from India.

The complete coat protein (CP) sequences from 29 Indian isolates of Chrysanthemum virus B (CVB) were determined and analysed in relation to other previously characterized carlaviruses. The CP genes of the Indian CVB isolates were highly heterogeneous, sharing nucleotide sequence identities of 74-98%. Based on phylogenetic analyses, the isolates formed three groups potentially representing either two or three major CVB strain groupings. Recombination analysis revealed at least one definite recombination event involving the exchange of sequences between members of different groups. To our knowledge this is the first reported evidence of homologous recombination in carlaviruses.

Amino Acid Sequence↗

PubMed2006

Ascertainment of intimate partner violence using two abuse measurement frameworks.

OBJECTIVE: To estimate prevalence of intimate partner violence (IPV) according to two abuse ascertainment tools, and agreement between the tools. METHODS: 2504 women randomly selected from a health maintenance organization were asked about IPV exposure in their most recent intimate relationship using five questions on physical and sexual abuse, and fear due to partner's threats and controlling behavior from the Behavioral Risk Factor Surveillance Survey (BRFSS) and 10 questions from the Women's Experience with Battering (WEB) scale. IPV prevalence was estimated according to the BRFSS and WEB, and the proportion of women who were WEB+/BRFSS+, WEB-/BRFSS-, WEB-/BRFSS+, and WEB+/BRFSS-. RESULTS: In their most recent relationship, 14.7% of women reported abuse of any type on the BRFSS versus 7.0% on the WEB scale. In direct comparisons of the WEB and BRFSS questions, a higher percentage of abused women reported any IPV on the five BRFSS questions (88.4%) compared to the 10 WEB questions (42.0%). However, both the BRFSS and WEB identified some women as abused that would have been missed by the other instrument. CONCLUSIONS: Intimate partner violence prevalence depends on how women are asked about abuse. Resources permitting, more than one abuse ascertainment strategy (for example, both the BRFSS and WEB questions) should be tried in order to broadly identify as many women as possible who interpret themselves as abused.

Adolescent↗

PubMed2005

Widespread recombination in published animal mtDNA sequences.

Mitochondrial DNA (mtDNA) recombination has been observed in several animal species, but there are doubts as to whether it is common or only occurs under special circumstances. Animal mtDNA sequences retrieved from public databases were unambiguously aligned and rigorously tested for evidence of recombination. At least 30 recombination events were detected among 186 alignments examined. Recombinant sequences were found in invertebrates and vertebrates, including primates. It appears that mtDNA recombination may occur regularly in the animal cell but rarely produces new haplotypes because of homoplasmy. Common animal mtDNA recombination would necessitate a reexamination of phylogenetic and biohistorical inference based on the assumption of clonal mtDNA transmission. Recombination may also have an important role in producing and purging mtDNA mutations and thus in mtDNA-based diseases and senescence.

Animals↗

PubMed2005

A modified bootscan algorithm for automated identification of recombinant sequences and recombination breakpoints.

We have developed a modified BOOTSCAN algorithm that may be used to screen nucleotide sequence alignments for evidence of recombination without prior identification of nonrecombinant reference sequences. The algorithm is fast and includes a Bonferroni corrected statistical test of recombination to circumvent the multiple testing problems encountered when using the BOOTSCAN method to explore alignments for evidence of recombination. Using both simulated and real datasets we demonstrate that the modified algorithm is more powerful than other phylogenetic recombination detection methods and performs almost as well as one of the best substitution distribution recombination detection methods.

Algorithms↗

PubMed2004

Characterisation of Potato virus Y nnp strain inducing veinal necrosis in pepper: a naturally occurring recombinant strain of PVY.

The full-length genome of Potato virus Y (PVY) nnp strain, recovered from pepper showing veinal necrosis of leaves, was cloned and sequenced, finding an organisation typical for PVY species. It consists of 9699 nucleotides (nt) excluding the 3' terminal poly(A) tail and contains an open reading frame of 9186 nt, encoding the putative polyprotein of 3061 amino acids. In ELISA, the isolate reacted with a monoclonal antibody specific for PVY(C) but not with antibodies against PVY(N) or PVY(O). Sequence analysis strongly suggests that PVY-nnp originated from a recombination event involving a virus of the PVY(O) type and another parental virus, maybe resembling the PVY(NP) isolates, given the reasonably high similarity shared by PVY-nnp and Lye84.2 and Son41 isolates. The recombination event involved a breakpoint near the middle of the P1 gene, around position 603 of the viral genome. Proof for the existence of such a recombination comes from several lines of evidence, including similarity analysis, recombination analysis using six different methods and the different locations of nnp within phylogenetic trees constructed from genomic regions on either side of the identified recombination breakpoint.

Base Sequence↗

PubMed2004

RDP2: recombination detection and analysis from sequence alignments.

UNLABELLED: RDP2 is a Windows 95/XP program that examines nucleotide sequence alignments and attempts to identify recombinant sequences and recombination breakpoints using 10 published recombination detection methods, including GENECONV, BOOTSCAN, MAXIMUM chi(2), CHIMAERA and SISTER SCANNING. The program enables fast automated analysis of large alignments (up to 300 sequences containing 13 000 sites), and interactive exploration, management and verification of results with different recombination detection and tree drawing methods. AVAILABILITY: RDP2 is available free from the RDP2 website (http://darwin.uvigo.es/rdp/rdp.html) CONTACT: darren@science.uct.ac.za SUPPLEMENTARY INFORMATION: Detailed descriptions of RDP2 and the methods it implements are included in the program manual, which can be downloaded from the RDP2 website.

Algorithms↗

PubMed2004

Tissue engineering of ovine aortic blood vessel substitutes using applied shear stress and enzymatically derived vascular smooth muscle cells.

Compared to native blood vessels, all clinically available blood vessel substitutes perform suboptimally. Numerous approaches to tissue engineer (TE) blood vessels have been pursued using different scaffold materials, cell types, and culture conditions. Several limitations however remain to be overcome prior to the potential application in the arterial system. This study aimed at tissue engineering viable ovine blood vessels suitable for implantation into the systemic circulation of sheep. In recent studies vascular smooth muscle cells (vSMC) were derived by an explant technique. However, in this study we show that homogenous populations of differentiated vSMC were only obtained by enzymatic dispersion as characterized by immunostaining for specific vSMC marker proteins. In contrast the explant method yielded predominantly less differentiated myofibroblast-like cells. Enzymatically derived vSMC were seeded onto P-4-HB scaffolds and incubated either in a pulsatile flow bioreactor or under static conditions. Dynamically cultured TE blood vessel substitutes showed confluent layered tissue formation and were completely water resistant. They displayed significantly increased ECM synthesis, DNA, and protein content as well as vSMC marker expression. Mechanical properties of bioreactor cultured TE blood vessels approached those of native aorta. In conclusion ovine, aortic blood vessel substitutes were successfully created using enzymatically derived vSMC, bioabsorbable scaffolds, and applied shear stress.

Animals↗

PubMed2004

A prospective study of household smoking bans and subsequent cessation related behaviour: the role of stage of change.

OBJECTIVE: To assess the degree to which smokers living with a full household ban on smoking change their cessation related behaviour. DESIGN, SETTING, AND PARTICIPANTS: Prospective cohort study; follow up of a population based cohort of 1133 smokers, identified from a 1997 telephone survey of adult Oregonians. After a median of 21 months, 565 were located and reinterviewed. MAIN OUTCOME MEASURES: Quit attempts, time until relapse, and smoking cessation, defined as seven day and 90 day sustained abstinence at follow up. RESULTS: A full ban at baseline was associated with a doubling of the odds of a subsequent quit attempt (odds ratio (OR) = 2.0, 95% confidence interval (CI), 1.0 to 3.9). Among respondents in the preparation stage at baseline (intention to quit in the next month with a quit attempt in the previous year), a full ban was associated with a lower relapse rate (hazard ratio = 0.5 (95% CI, 0.2 to 0.9)), while for those in precontemplation/contemplation (no intention to quit or intention to quit within the next six months, respectively), there was no significant association between full ban and relapse rate. For respondents in preparation, those with a full ban had over four times the odds of being in cessation for seven or more days before the follow up call (OR = 4.4 (1.1 to 18.7)), but for those in precontemplation/contemplation, full bans were unrelated to cessation. CONCLUSIONS: Full household bans may facilitate cessation among smokers who are preparing to quit by increasing quit attempts. They may also prolong time to relapse among those smokers.

Adolescent↗

PubMed2002

Investigation of Maize streak virus pathogenicity determinants using chimaeric genomes.

Genes and intergenic regions were reciprocally exchanged between a highly pathogenic Maize streak virus (MSV) isolate (MSV-MatA) and three less pathogenic isolates (MSV-Kom, MSV-R2, and MSV-VW) to determine the contribution of individual genome constituents to MSV pathogenicity in maize. Comparison of disease symptoms produced by the 54 resulting chimaeras and parental viruses enabled identification of genome constituents that are primarily responsible for the heightened pathogenicity of MSV-MatA in maize. Whereas pathogenicity determinants were detected in all of the MSV genomic regions examined, generally only chimaeras containing the MSV-MatA long intergenic region, coat protein gene, and/or movement protein gene were more pathogenic than the milder MSV isolates from which most of their genomes were derived. The pathogenicity of chimeras was strongly influenced by the relatedness of their parental viruses and evidence was found of nucleotide sequence-dependent interactions between both coding and intergenic regions.

Chimera↗

PubMed2001

Sequence diversity and virulence in Zea mays of Maize streak virus isolates.

Full genomic sequences were determined for 12 Maize streak virus (MSV) isolates obtained from Zea mays and wild grass species. These and 10 other publicly available full-length sequences were used to classify a total of 66 additional MSV isolates that had been characterized by PCR-restriction fragment length polymorphism and/or partial nucleotide sequence analysis. A description is given of the host and geographical distribution of the MSV strain and subtype groupings identified. The relationship between the genotypes of 21 fully sequenced virus isolates and their virulence in differentially MSV-resistant Z. mays genotypes was examined. Within the only MSV strain grouping that produced severe symptoms in maize, highly virulent and widely distributed genotypes were identified that are likely to pose the most serious threat to maize production in Africa. Evidence is presented that certain of the isolates investigated may be the products of either intra- or interspecific recombination.

Geminiviridae↗

PubMed2001

Risk of uterine rupture during labor among women with a prior cesarean delivery.

BACKGROUND: Each year in the United States, approximately 60 percent of women with a prior cesarean delivery who become pregnant again attempt labor. Concern persists that a trial of labor may increase the risk of uterine rupture, an uncommon but serious obstetrical complication. METHODS: We conducted a population-based, retrospective cohort analysis using data from all primiparous women who gave birth to live singleton infants by cesarean section in civilian hospitals in Washington State from 1987 through 1996 and who delivered a second singleton child during the same period (a total of 20,095 women). We assessed the risk of uterine rupture for deliveries with spontaneous onset of labor, those with labor induced by prostaglandins, and those in which labor was induced by other means; these three groups of deliveries were compared with repeated cesarean delivery without labor. RESULTS: Uterine rupture occurred at a rate of 1.6 per 1000 among women with repeated cesarean delivery without labor (11 women), 5.2 per 1000 among women with spontaneous onset of labor (56 women), 7.7 per 1000 among women whose labor was induced without prostaglandins (15 women), and 24.5 per 1000 among women with prostaglandin-induced labor (9 women). As compared with the risk in women with repeated cesarean delivery without labor, uterine rupture was more likely among women with spontaneous onset of labor (relative risk, 3.3; 95 percent confidence interval, 1.8 to 6.0), induction of labor without prostaglandins (relative risk, 4.9; 95 percent confidence interval, 2.4 to 9.7), and induction with prostaglandins (relative risk, 15.6; 95 percent confidence interval, 8.1 to 30.0). CONCLUSIONS: For women with one prior cesarean delivery, the risk of uterine rupture is higher among those whose labor is induced than among those with repeated cesarean delivery without labor. Labor induced with a prostaglandin confers the highest risk.

Adolescent↗

PubMed2001

Stereotactic radiosurgery and hypofractionated stereotactic radiotherapy for residual or recurrent cranial base and cervical chordomas.

OBJECT: In patients with chordomas the lesions often recur. Furthermore, the location of some chordomas within the base of the skull and the cervical spine can prevent complete resection from being achieved. Previous series have shown that stereotactic radiosurgery can be used as a treatment for residual chordomas with good overall results. The authors review their experience in using linear accelerator (LINAC) stereotactic radiosurgery to treat patients with recurrent and/or residual cranial base and cervical chordomas. METHODS: Ten patients with chordomas (eight with cranial base and two with cervical lesions [below C-2]) underwent LINAC stereotactic radiosurgery. The mean patient age was 49 years (range 30-73 years). There were seven men and three women. Three patients had undergone one prior surgery, five had undergone two previous surgeries, and two had undergone three prior operations. The mean radiation dose was 19.4 Gy (range 18-24 Gy), and the maximum intratumoral dose averaged 27 Gy (range 24.1-33.1 Gy). The mean secondary collimator size was 14.4 mm (range 7.5-20 mm). The volume of the tumor treated ranged from 1.1 to 21.5 ml. In five patients a standard frame-based LINAC radiosurgery system was used, whereas in the other five the CyberKnife, a frameless image-guided LINAC radiosurgical system, was used. All patients were available for follow-up review, which averaged 4 years (range 1-9 years). Over the course of follow up, one chordoma (10%) was smaller in size, seven were stable, and two chordomas progressed (one in a patient who underwent reoperation and a second course of stereotactic radiosurgery, and the second in a patient who underwent reoperation alone). There were no new neurological deficits noted following radiosurgery in the eight of 10 patients in whom there was no tumor progression, and no patient developed radiation-induced necrosis. CONCLUSIONS: Stereotactic radiosurgery can be used to treat patients with recurrent or residual chordomas with excellent tumor control rates. Longer follow-up review in larger series is warranted to confirm these findings.

Adult↗

PubMed2001

Pro- and anti-inflammatory cytokine gene expression in rat sciatic nerve chronic constriction injury model of neuropathic pain.

Cytokines may be pathophysiologically involved in hyperalgesia. Uncertainty exists about the types of cytokines and their site of action. To study the role of key pro- and anti-inflammatory cytokines in a chronic constriction model of neuropathic pain, mRNA expression of TNF, IL-1beta, IL-6, and IL-10 was quantified using competitive RT-PCR. Each cytokine mRNA in rat sciatic nerve was examined at days 3, 7, 14, and 45 after chronic constriction injury (CCI). We also undertook behavioral testing of these rats. Thermal warming and touch thresholds were significantly reduced at days 3, 7, and 14 in the CCI group, compared with the sham-operated group. Cytokine gene expression in sciatic nerve was significantly increased at day 7 for IL-1beta and IL-6 and at day 14 for TNF. Expression of IL-10 underwent a gradual and progressive increase, reaching statistical significance at day 45.

Animals↗

PubMed2001

The relative infectivities and genomic characterisation of three distinct mastreviruses from South Africa.

The genomic nucleotide sequences of the cloned agroinfectious genomes of three South African mastreviruses obtained from Zea mays, a Setaria sp., and Panicum maximum (designated MSV-Kom, MSV-Set, and PanSV-Kar respectively), were determined. Additionally, their relative infectivities and virulence were analysed in a range of differentially susceptible wheat, maize, and barley genotypes. MSV-Kom produced moderate to severe streak symptoms in all maize genotypes tested, but only moderate to very mild symptoms in the wheat and barley genotypes. MSV-Set infected only the susceptible to tolerant maize genotypes, but was generally more severe in the barley and wheat genotypes than MSV-Kom. PanSV-Kar was incapable of infecting any of the wheat and barley genotypes and only produced very mild symptoms on the three most sensitive maize genotypes. Genomic characteristics in common with related mastreviruses were identified. Phylogenetic analysis indicated that while MSV-Kom was closely related to previously sequenced MSV isolates, MSV-Set and PanSV-Kar represented distinctly novel strains of MSV and PanSV respectively. In the case of MSV-Set, this is the most distantly related MSV strain yet characterised.

Animals↗

PubMed2001

Cesarean delivery and postpartum mortality among primiparas in Washington State, 1987-1996(1).

OBJECTIVE: To examine the association between delivery method and mortality within 6 months of delivery among primiparas. METHODS: We conducted a population-based, retrospective cohort analysis using statewide, maternally linked birth certificate, hospital discharge, and death certificate data. The present cohort was all primiparas who gave birth to live-born infants in civilian hospitals in Washington State from January 1, 1987 through December 31, 1996 (n = 265,471). Odd ratios (OR) and 95% confidence intervals (CI) were calculated for overall mortality, pregnancy-related mortality, and pregnancy-unrelated mortality associated with delivery method. RESULTS: Thirty-two women (12.1 per 100,000 singleton live births) died within 6 months of delivery of their first child. Eleven of 32 deaths were pregnancy related (4.1 per 100,000 singleton live births, 95% CI 1.6, 6.5), and 21 of the 32 deaths were not pregnancy related (7.9 per 100,000 singleton live births, 95% CI 4.5, 11.3). The pregnancy-related mortality rate was higher among women delivered by cesarean (10.3/100,000) than among women delivered vaginally (2.4/100,000). In logistic regression analyses, women who had cesarean delivery were not at significantly higher risk of death overall after adjustment for maternal age (OR 1.7, 95% CI 0.3, 3.6), pregnancy-related death after adjustment for maternal age and severe preeclampsia (OR 2.2, 95% CI 0.6, 7.9), or pregnancy-unrelated death after adjustment for maternal age and marital status (OR 0.9, 95% CI 0.3, 2.7), relative to women who had vaginal delivery. CONCLUSION: Cesarean delivery might be a marker for serious preexisting morbidities associated with increased mortality risk rather than a risk factor for death in and of itself. Data from additional sources such as medical records and autopsy reports are necessary to disentangle preexisting mortality risk from risk associated solely with delivery method.

Adolescent↗

PubMed2001

Analysis of the diversity of African streak mastreviruses using PCR-generated RFLPs and partial sequence data.

Maize streak virus (MSV) is the most economically significant member of a diverse group of African grass-infecting Mastrevirus species in the family Geminiviridae. We designed a single set of degenerate primers which enables the PCR amplification of an approximately 1300 bp DNA fragment spanning both conserved (the RepA gene) and variable (the long intergenic region and MP gene) portions of these viruses' genomes. Using restriction fragment length polymorphism (RFLP) analysis of PCR products obtained from 39 MSV, one SSV, and two PanSV isolates, it was possible to both identify the different virus species, which differ in nucleotide sequence by up to 40%, and to differentiate between MSV isolates sharing up to 99% sequence identity. The reliability of the RFLP data for typing the MSV isolates was verified by the phylogenetic analysis of the partial genomic nucleotide sequences of a representative subset of the MSV isolates. Based on both the RFLP and sequence data, the MSV isolates could be clearly differentiated into the four groups: these were a group of predominantly maize-infecting isolates, and three groups containing grass/wheat-infecting isolates. RFLP analysis also revealed a number of mixed virus infections in which, in certain instances, it was possible to identify individual population members.

Africa↗

PubMed2001

Delivery method and self-reported postpartum general health status among primiparous women.

Despite nearly four million deliveries in the United States each year, minimal information exists on unintended health consequences following childbirth, particularly in relation to delivery method. The purpose of this study was to assess the association between method of delivery and the general health status, sexual, bowel and urinary functioning of primiparous women as measured at 7 weeks postpartum. Data from the Statewide Obstetrical Review of Quality System (StORQS) Survey of Maternity Care in Washington State were analysed. Participants included all primiparous women with a delivery of a singleton infant discharged alive between August and December 1991 from 10 non-federal short-stay hospitals who responded to the StORQS Survey of Maternity Care (n = 971). The main outcome measures included the modified Medical Outcomes Study 36-Item Short-Form Health Survey and self-reported sexual, bowel and urinary functioning. At 7 weeks postpartum, women who had caesarean or assisted vaginal deliveries reported significantly lower postpartum general health status scores than women with unassisted vaginal delivery. Additionally, women with assisted vaginal delivery reported significantly worse sexual, bowel and urinary functioning. Our results suggest that more careful attention to the postpartum general health and sexual functioning of women with caesarean and assisted vaginal delivery may be merited.

Activities of Daily Living↗

PubMed2001

Image-guided hypo-fractionated stereotactic radiosurgery to spinal lesions.

OBJECTIVE: This article demonstrates the technical feasibility of noninvasive treatment of unresectable spinal vascular malformations and primary and metastatic spinal tumors by use of image-guided frameless stereotactic radiosurgery. METHODS: Stereotactic radiosurgery delivers a high dose of radiation to a tumor volume or vascular malformation in a limited number of fractions and minimizes the dose to adjacent normal structures. Frameless image-guided radiosurgery was developed by coupling an orthogonal pair of x-ray cameras to a dynamically manipulated robot-mounted linear accelerator that guides the therapy beam to treatment sites within the spine or spinal cord, in an outpatient setting, and without the use of frame-based fixation. The system relies on skeletal landmarks or implanted fiducial markers to locate treatment targets. Sixteen patients with spinal lesions (hemangioblastomas, vascular malformations, metastatic carcinomas, schwannomas, a meningioma, and a chordoma) were treated with total treatment doses of 1100 to 2500 cGy in one to five fractions by use of image-guided frameless radiosurgery with the CyberKnife system (Accuray, Inc., Sunnyvale, CA). Thirteen radiosurgery plans were analyzed for compliance with conventional radiation therapy. RESULTS: Tests demonstrated alignment of the treatment dose with the target volume within +/-1 mm by use of spine fiducials and the CyberKnife treatment planning system. Tumor patients with at least 6 months of follow-up have demonstrated no progression of disease. Radiographic follow-up is pending for the remaining patients. To date, no patients have experienced complications as a result of the procedure. CONCLUSION: This experience demonstrates the feasibility of image-guided robotic radiosurgery for previously untreatable spinal lesions.

Adolescent↗