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Pearson CR, Kurth AE, Cassels S, Martin DP, Simoni JM, Hoff P, Matediana E, Gloyd S. Modeling HIV transmission risk among Mozambicans prior to their initiating highly active antiretroviral therapy. AIDS Care 2007; 19:594-604. [PMID: 17505919 PMCID: PMC4226799 DOI: 10.1080/09540120701203337] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
Abstract
Understanding sexual behavior and assessing transmission risk among people living with HIV-1 is crucial for effective HIV-1 prevention. We describe sexual behavior among HIV-positive persons initiating highly active antiretroviral therapy (HAART) in Beira, Mozambique. We present a Bernoulli process model (tool available online) to estimate the number of sexual partners who would acquire HIV-1 as a consequence of sexual contact with study participants within the prior three months. Baseline data were collected on 350 HAART-naive individuals 18-70 years of age from October 2004 to February 2005. In the three months prior to initiating HAART, 45% (n = 157) of participants had sexual relationships with 191 partners. Unprotected sex occurred in 70% of partnerships, with evidence suggesting unprotected sex was less likely with partners believed to be HIV-negative. Only 26% of the participants disclosed their serostatus to partners with a negative or unknown serostatus. Women were less likely to report concurrent relationships than were men (21 versus 66%; OR 0.13; 95%CI: 0.06, 0.26). Given baseline behaviors, the model estimated 23.2 infections/1,000 HIV-positive persons per year. The model demonstrated HAART along with syphilis and herpes simplex virus type 2 (HSV-2) treatment combined could reduce HIV-1 transmission by 87%; increasing condom use could reduce HIV-1 transmission by 67%.
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Pearson CR, Micek M, Simoni JM, Matediana E, Martin DP, Gloyd S. Modified directly observed therapy to facilitate highly active antiretroviral therapy adherence in Beira, Mozambique. Development and implementation. J Acquir Immune Defic Syndr 2007; 43 Suppl 1:S134-41. [PMID: 17133197 PMCID: PMC5096448 DOI: 10.1097/01.qai.0000248339.82567.17] [Citation(s) in RCA: 33] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
As resource-limited countries expand access to highly active antiretroviral therapy (HAART) treatment, innovative programs are needed to support adherence in the context of significant health system barriers. Modified directly observed therapy (mDOT) is one such strategy, but little is known about the process of designing and implementing mDOT programs for HAART in resource-limited settings. In this descriptive study, we used a mixed-methods approach to describe the process of implementing mDOT for an ongoing randomized control trial (RCT) in Beira, Mozambique. Interviews with clinic staff, mDOT peers, and participants provided information on design elements, problems with implementation, satisfaction, and benefits. Acceptability and feasibility measures were obtained from the RCT. Most (81%, N = 350) eligible persons agreed to participate, and of those randomized to mDOT (n = 174), 95% reported that their time with peers was beneficial. On average, participants kept 93% of the 30 required daily mDOT visits. Key components of the intervention's success included using peers who were well accepted by clinic staff, adequate training and retention of peers, adapting daily visit requirements to participants' work schedules and physical conditions, and reimbursing costs of transportation. This study identified aspects of mDOT that are effective and can be adopted by other clinics treating HIV patients.
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Halley-Stott RP, Tanzer F, Martin DP, Rybicki EP. The complete nucleotide sequence of a mild strain of Bean yellow dwarf virus. Arch Virol 2007; 152:1237-40. [PMID: 17347772 DOI: 10.1007/s00705-006-0933-6] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2006] [Accepted: 12/21/2006] [Indexed: 10/23/2022]
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Pearson CR, Simoni JM, Hoff P, Kurth AE, Martin DP. Assessing antiretroviral adherence via electronic drug monitoring and self-report: an examination of key methodological issues. AIDS Behav 2007; 11:161-73. [PMID: 16804749 PMCID: PMC5096443 DOI: 10.1007/s10461-006-9133-3] [Citation(s) in RCA: 111] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
We explored methodological issues related to antiretroviral adherence assessment, using 6 months of data collected in a completed intervention trial involving 136 low-income HIV-positive outpatients in the Bronx, NY. Findings suggest that operationalizing adherence as a continuous (versus dichotomous) variable and averaging adherence estimates over multiple assessment points (versus using only one) explains greater variance in HIV-1 RNA viral load (VL). Self-reported estimates provided during a phone interview accounted for similar variance in VL as EDM estimates (R (2) = .17 phone versus .18 EDM). Self-reported adherence was not associated with a standard social desirability measure, and no difference in the accuracy of self-report adherence was observed for assessment periods of 1-3 days. Self-reported poor adherence was more closely associated with EDM adherence estimates than self-reported moderate and high adherence. On average across assessment points, fewer than 4% of participants who reported taking a dose of an incorrect amount of medication.
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Bonomi AE, Thompson RS, Anderson M, Rivara FP, Holt VL, Carrell D, Martin DP. Ascertainment of intimate partner violence using two abuse measurement frameworks. Inj Prev 2006; 12:121-4. [PMID: 16595428 PMCID: PMC2564437 DOI: 10.1136/ip.2005.009563] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022]
Abstract
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.
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Singh L, Hallan V, Jabeen N, Singh AK, Ram R, Martin DP, Zaidi AA. Coat protein gene diversity among Chrysanthemum virus B isolates from India. Arch Virol 2006; 152:405-13. [PMID: 17006596 DOI: 10.1007/s00705-006-0854-4] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2006] [Accepted: 08/14/2006] [Indexed: 11/29/2022]
Abstract
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.
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Bonomi AE, Holt VL, Martin DP, Thompson RS. Severity of intimate partner violence and occurrence and frequency of police calls. JOURNAL OF INTERPERSONAL VIOLENCE 2006; 21:1354-64. [PMID: 16940400 DOI: 10.1177/0886260506291656] [Citation(s) in RCA: 46] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/11/2023]
Abstract
This article evaluates whether female victims of severe physical, psychological, or sexual intimate partner violence (IPV) call police more often than other abused women. Abused women (431) reported frequency of contacting police (dependent variable), nature and severity of IPV experienced, and characteristics of themselves and their perpetrator (explanatory variables). A two-part regression model estimated likelihood of police contact among all participants and rate of contact among callers. Women with severe physical or psychological IPV or injury were more likely to call police than were other abused women. Among callers, women made 96% more calls if a weapon was involved, 58% more if they were severely sexually abused, and 40% more if they were severely physically abused. Women with children at home made 32% more calls. These results delineate the level and types of IPV and other characteristics of homes that make single and repeat calls to police.
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Bowman SM, Zimmerman FJ, Christakis DA, Sharar SR, Martin DP. Hospital characteristics associated with the management of pediatric splenic injuries. JAMA 2005; 294:2611-7. [PMID: 16304075 DOI: 10.1001/jama.294.20.2611] [Citation(s) in RCA: 75] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]
Abstract
CONTEXT Despite evidence that more than 90% of children with traumatic injuries to the spleen can be successfully managed nonoperatively, there is significant variation in the use of splenectomy. As asplenic children are at increased risk of overwhelming postsplenectomy infection, nonoperative management may be considered a quality of care indicator. OBJECTIVE To test the hypothesis that children are more likely to undergo splenectomy in general hospitals than in children's hospitals. DESIGN Retrospective cohort study using data from the Kid's Inpatient Database (KID) for the year 2000. Multivariable regression was used to control for patient and hospital characteristics. SETTING AND PARTICIPANTS All children aged 0 to 16 years who were hospitalized with a traumatic (noniatrogenic) spleen injury in nonfederal short-stay hospitals in any of the 27 states participating in KID (N = 2851). MAIN OUTCOME MEASURE Splenectomy performed within 1 day of arrival. RESULTS A total of 11 children (3%) with splenic injuries receiving care at children's hospitals underwent splenectomy compared with 383 children (15.4%) cared for at general hospitals (P<.001). After adjusting for patient characteristics, injury severity, and hospital characteristics, splenectomy was more likely among children treated at general hospitals (odds ratio, 5.01; 95% confidence interval, 2.21-11.36) than among children treated at children's hospitals. CONCLUSIONS There is considerable variation in the management of pediatric splenic injuries, with significantly lower rates of splenectomy at designated children's hospitals. Quality improvement interventions, including increased education and training for physicians in general hospitals, may be needed to increase the use of spleen-conserving management practices.
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Bovier PA, Martin DP, Perneger TV. Cost-consciousness among Swiss doctors: a cross-sectional survey. BMC Health Serv Res 2005; 5:72. [PMID: 16281977 PMCID: PMC1308814 DOI: 10.1186/1472-6963-5-72] [Citation(s) in RCA: 32] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2005] [Accepted: 11/10/2005] [Indexed: 12/02/2022] Open
Abstract
Background Knowing what influences physicians attitudes toward health care costs is an important matter, because most health care expenditures are the results of doctors' decisions. Many decisions regarding medical tests and treatments are influenced by factors other than the expected benefit to the patient, including the doctor's demographic characteristics and concerns about cost and income. Methods Doctors (n = 1184) in Geneva, Switzerland, answered questions about their cost-consciousness, practice patterns (medical specialty, public.vs. private sector, number of patients per week, time spent with a new patient), work satisfaction, and stress from uncertainty. General linear models were used to identify independent risk factors of higher cost-consciousness. Results Most doctors agreed that trying to contain costs was their responsibility ("agree" or "totally agree": 90%) and that they should take a more prominent role in limiting the use of unnecessary tests (92%); most disagreed that doctors are too busy to worry about costs (69%) and that the cost of health care is only important if the patient has to pay for it out-of-pocket (88%). In multivariate analyses, cost-consciousness was higher among doctors in the public sector, those who saw fewer patients per week, who were most tolerant of uncertainty, and who were most satisfied with their work. Conclusion Thus even in a setting with very high health care expenditures, doctors' stated cost-consciousness appeared to be generally high, even though it was not uniformly distributed among them.
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Rubenfeld GD, Caldwell E, Peabody E, Weaver J, Martin DP, Neff M, Stern EJ, Hudson LD. Incidence and outcomes of acute lung injury. N Engl J Med 2005; 353:1685-93. [PMID: 16236739 DOI: 10.1056/nejmoa050333] [Citation(s) in RCA: 2695] [Impact Index Per Article: 141.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
BACKGROUND Acute lung injury is a critical illness syndrome consisting of acute hypoxemic respiratory failure with bilateral pulmonary infiltrates that are not attributed to left atrial hypertension. Despite recent advances in our understanding of the mechanism and treatment of acute lung injury, its incidence and outcomes in the United States have been unclear. METHODS We conducted a prospective, population-based, cohort study in 21 hospitals in and around King County, Washington, from April 1999 through July 2000, using a validated screening protocol to identify patients who met the consensus criteria for acute lung injury. RESULTS A total of 1113 King County residents undergoing mechanical ventilation met the criteria for acute lung injury and were 15 years of age or older. On the basis of this figure, the crude incidence of acute lung injury was 78.9 per 100,000 person-years and the age-adjusted incidence was 86.2 per 100,000 person-years. The in-hospital mortality rate was 38.5 percent. The incidence of acute lung injury increased with age from 16 per 100,000 person-years for those 15 through 19 years of age to 306 per 100,000 person-years for those 75 through 84 years of age. Mortality increased with age from 24 percent for patients 15 through 19 years of age to 60 percent for patients 85 years of age or older (P<0.001). We estimate that each year in the United States there are 190,600 cases of acute lung injury, which are associated with 74,500 deaths and 3.6 million hospital days. CONCLUSIONS Acute lung injury has a substantial impact on public health, with an incidence in the United States that is considerably higher than previous reports have suggested.
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Swiontkowski MF, Engelberg R, Martin DP, Agel J. Short musculoskeletal function assessment questionnaire: validity, reliability, and responsiveness. ACTA ACUST UNITED AC 2005. [DOI: 10.1055/s-2005-870091] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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Kurth AE, Martin DP, Golden MR, Weiss NS, Heagerty PJ, Spielberg F, Handsfield HH, Holmes KK. A comparison between audio computer-assisted self-interviews and clinician interviews for obtaining the sexual history. Sex Transm Dis 2005; 31:719-26. [PMID: 15608586 DOI: 10.1097/01.olq.0000145855.36181.13] [Citation(s) in RCA: 136] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
Abstract
OBJECTIVE The objective of this study was to compare reporting between audio computer-assisted self-interview (ACASI) and clinician-administered sexual histories. GOAL The goal of this study was to explore the usefulness of ACASI in sexually transmitted disease (STD) clinics. STUDY The authors conducted a cross-sectional study of ACASI followed by a clinician history (CH) among 609 patients (52% male, 59% white) in an urban, public STD clinic. We assessed completeness of data, item prevalence, and report concordance for sexual history and patient characteristic variables classified as socially neutral (n=5), sensitive (n=11), or rewarded (n=4). RESULTS Women more often reported by ACASI than during CH same-sex behavior (19.6% vs. 11.5%), oral sex (67.3% vs. 50.0%), transactional sex (20.7% vs. 9.8%), and amphetamine use (4.9% vs. 0.7%) but were less likely to report STD symptoms (55.4% vs. 63.7%; all McNemar chi-squared P values <0.003). Men's reporting was similar between interviews, except for ever having had sex with another man (36.9% ACASI vs. 28.7% CH, P <0.001). Reporting agreement as measured by kappas and intraclass correlation coefficients was only moderate for socially sensitive and rewarded variables but was substantial or almost perfect for socially neutral variables. ACASI data tended to be more complete. ACASI was acceptable to 89% of participants. CONCLUSIONS ACASI sexual histories may help to identify persons at risk for STDs.
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Opitz F, Melle C, Schenke-Layland K, Degenkolbe I, Martin DP, Von Eggeling F, Wahlers T, Stock UA. ProteinChip system technology: a powerful tool to analyze expression differences in tissue-engineered blood vessels. ACTA ACUST UNITED AC 2005; 10:611-20. [PMID: 15165477 DOI: 10.1089/107632704323061960] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
At the time of implantation, tissue-engineered constructs should resemble native tissues as closely as possible. At present, histology and biochemical methods are commonly used to compare tissue-engineered constructs with native tissue. A ProteinChip system based on surface-enhanced laser desorption/ionization time of flight mass spectrometry (SELDI) has been developed that allows visualization of complex protein profiles from biological samples. The aim of this study was to determine whether the ProteinChip system is a suitable tool with which to compare the protein expression profiles of tissue-engineered aortic blood vessels with native tissues. Tissue-engineered blood vessel substitutes were fabricated with poly-4-hydroxybutyrate scaffolds, ovine vascular cell seeding, and dynamic tissue culture conditions. Engineered, ovine aortic, and carotid tissues were homogenized and total protein was extracted. Samples were analyzed on ProteinChip arrays. Analysis yielded reproducible protein profiles from all samples. About 150 distinct protein peaks were detected. Comparative analysis with ProteinChip software revealed that the protein profiles from native aorta and native carotid arteries were similar whereas early tissue-engineered samples displayed more distinct deviations. In conclusion, ProteinChip system technology is rapid, reproducible, and highly sensitive in highlighting differentially expressed proteins in tissue-engineered blood vessel substitutes.
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Tsaousis AD, Martin DP, Ladoukakis ED, Posada D, Zouros E. Widespread Recombination in Published Animal mtDNA Sequences1. Mol Biol Evol 2005; 22:925-33. [PMID: 15647518 DOI: 10.1093/molbev/msi084] [Citation(s) in RCA: 132] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
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.
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Martin DP, Posada D, Crandall KA, Williamson C. A modified bootscan algorithm for automated identification of recombinant sequences and recombination breakpoints. AIDS Res Hum Retroviruses 2005; 21:98-102. [PMID: 15665649 DOI: 10.1089/aid.2005.21.98] [Citation(s) in RCA: 620] [Impact Index Per Article: 32.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
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.
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Bonomi AE, Holt VL, Thompson RS, Martin DP. Ascertainment of intimate partner violence in women seeking legal protection. Am J Prev Med 2005; 28:52-8. [PMID: 15626555 DOI: 10.1016/j.amepre.2004.09.011] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
BACKGROUND Brief questions are necessary for identification of women seeking emergency professional services for intimate partner violence (IPV), and for initiating dialogue with women presenting for care who have previously reported abuse. We compare three questions that inquire about physical and psychological abuse to the Conflict Tactics Scale, version 2 (CTS-2) in a cohort of women seeking legal protection for IPV. METHODS A total of 448 urban women reporting IPV to police or the court system completed surveys at 8 weeks (baseline), and 5 and 10 months after the incident to assess IPV. Sensitivity and specificity of brief questions on physical assault/abuse (one question) and psychological abuse (two questions) were assessed at baseline and in the periods between baseline and follow-up, using items from the CTS-2 reflecting minor and severe physical and psychological IPV as reference standards. RESULTS Compared to the CTS-2 severe items, the physical abuse question at baseline detected 93% of abused women, and the two psychological abuse questions 94%. Sensitivity varied at follow-up (74% to 95% for physical, and 89% to 90% psychological), but remained higher when the severe versus minor CTS-2 items were reference standards. Specificity was reasonable for the physical question compared to the severe CTS-2 section (77% to 95%), but was more varied for the psychological questions (29% to 74%). CONCLUSIONS Three brief questions reasonably identified women who experienced severe IPV and sought legal protection. The low specificity of the psychological questions suggests that women's abuse experience may not fit within the CTS-2 framework. The three questions should be considered for further testing in real-world settings as a tool for initiating conversation with women about abuse.
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Fanigliulo A, Comes S, Pacella R, Harrach B, Martin DP, Crescenzi A. Characterisation of Potato virus Y nnp strain inducing veinal necrosis in pepper: a naturally occurring recombinant strain of PVY. Arch Virol 2004; 150:709-20. [PMID: 15592887 DOI: 10.1007/s00705-004-0449-x] [Citation(s) in RCA: 33] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2004] [Accepted: 10/12/2004] [Indexed: 11/25/2022]
Abstract
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.
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Pizacani BA, Martin DP, Stark MJ, Koepsell TD, Thompson B, Diehr P. A prospective study of household smoking bans and subsequent cessation related behaviour: the role of stage of change. Tob Control 2004; 13:23-8. [PMID: 14985591 PMCID: PMC1747832 DOI: 10.1136/tc.2003.003038] [Citation(s) in RCA: 70] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Abstract
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.
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Martin DP, Williamson C, Posada D. RDP2: recombination detection and analysis from sequence alignments. Bioinformatics 2004; 21:260-2. [PMID: 15377507 DOI: 10.1093/bioinformatics/bth490] [Citation(s) in RCA: 759] [Impact Index Per Article: 38.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
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.
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Treggiari MM, Hudson LD, Martin DP, Weiss NS, Caldwell E, Rubenfeld G. Effect of acute lung injury and acute respiratory distress syndrome on outcome in critically ill trauma patients. Crit Care Med 2004; 32:327-31. [PMID: 14758144 DOI: 10.1097/01.ccm.0000108870.09693.42] [Citation(s) in RCA: 126] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
OBJECTIVE Acute lung injury (ALI) and acute respiratory distress syndrome (ARDS) are known to be associated with increased mortality and costs in trauma patients. We estimated the independent impact of these conditions on mortality and cost, beyond the severity of injury with which they are correlated. DESIGN One-year prospective cohort. PATIENTS AND SETTING All trauma patients admitted to the intensive care unit in a level I center were evaluated daily for ALI/ARDS using the American-European Consensus Conference definition. MEASUREMENTS AND MAIN RESULTS The main outcome measures were hospital mortality and costs. Logistic regression was used to model hospital mortality in relation to the presence of ALI and ARDS, adjusting for trauma severity (Injury Severity Score), Acute Physiology Score, and age. Hospital costs were modeled using multivariable linear regression. Of the 1,296 trauma patients surviving beyond the first day, 4% experienced ALI (defined as Pao2/Fio2 of 201-300 mm Hg) and 12% had ARDS (Pao2/Fio2 < or = 200 mm Hg). The crude relative risk of mortality was 2.24 (95% confidence interval, 0.92-5.45) in patients with ALI and 3.84 (95% confidence interval, 2.41-6.13) in patients with ARDS compared with those without ALI/ARDS. However, there was no association of mortality with ALI (relative risk, 0.99; 95% confidence interval, 0.29-3.36) or with ARDS (relative risk, 1.23; 95% confidence interval, 0.63-2.43) after adjustment for age, Injury Severity Score, and Acute Physiology Score. Among patients of comparable age, severity score, and length of stay, median cost was 20% to 30% higher for those with ALI/ARDS. CONCLUSIONS There is no additional mortality associated with ALI/ARDS above and beyond the factors that can be measured at intensive care unit admission. Therefore, mortality in trauma patients is explained by injury severity at admission and is not affected by the subsequent occurrence of ALI/ARDS. Nonetheless, ALI/ARDS was associated with increased intensive care unit stay and hospital cost, independent of trauma severity.
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Opitz F, Schenke-Layland K, Richter W, Martin DP, Degenkolbe I, Wahlers T, Stock UA. Tissue Engineering of Ovine Aortic Blood Vessel Substitutes Using Applied Shear Stress and Enzymatically Derived Vascular Smooth Muscle Cells. Ann Biomed Eng 2004; 32:212-22. [PMID: 15008369 DOI: 10.1023/b:abme.0000012741.85600.f1] [Citation(s) in RCA: 46] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
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.
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Pizacani BA, Martin DP, Stark MJ, Koepsell TD, Thompson B, Diehr P. Household smoking bans: which households have them and do they work? Prev Med 2003; 36:99-107. [PMID: 12473430 DOI: 10.1006/pmed.2002.1123] [Citation(s) in RCA: 80] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
BACKGROUND This study characterized Oregon households according to type and degree of restrictions on smoking and explored whether smoking restrictions are associated with decreased environmental tobacco smoke (ETS) exposure. METHODS A population-based, random-digit-dialed cross-sectional telephone survey of 6,199 adult Oregonians was performed in 1997 to provide baseline data on tobacco use in Oregon. RESULTS Seventy percent of Oregon households were composed of nonsmokers only, and 85% of those had a full ban on smoking inside the home. Of the households containing one or more smokers, 38% had a full household ban on smoking. Among respondents with a full ban in place, 99% of nonsmoker-only households reported that no one smoked in the home in the previous month, compared with 91% of households with at least one smoker. In both nonsmoker-only households and those with at least one smoker, full bans were strongly associated with awareness of the harm of ETS (OR = 12.8, 95% CI 7.3-22.3, and OR = 6.6, 95% CI 3.6-12.3, respectively). The presence of children in the household was also closely associated with full bans in the two types of households (OR = 4.6, 95% CI 2.8-7.6, and OR = 3.0, 95% CI 2.1-4.4, respectively). Nevertheless, 50% of households with children and a smoker present did not have a full ban in place. CONCLUSIONS While the prevalence of household smoking restrictions is high in Oregon, there remains room for improvement, since 50% of households with a smoker and a child present do not have a full ban on indoor smoking. Public health messages that focus on household smoking restrictions may help protect nonsmokers from exposure to ETS.
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Abstract
OBJECTIVES Examine individual and statewide factors associated with hospital as location of death. DESIGN An observational study using large national databases. PARTICIPANTS All 1997 U.S. decedents (all ages, all causes.) RESULTS The West has the lowest percentage of deaths occurring in an acute care hospital, and the highest percentage of deaths at home. Increased hospital bed availability is significantly associated with greater chance of dying in an acute care hospital. Hispanic, nonwhite, and less educated decedents are more likely to die in a hospital (as opposed to home or nursing home). CONCLUSIONS Hospital bed availability profoundly influences the likelihood of dying in a hospital. Individual characteristics such as race and education affect location of death as well. These three factors account for approximately 75% of the trend in the West to a lower in-hospital death rate and more deaths at home. Additional factors may include formal out of hospital orders to limit transfer.
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Gaudino JA, deHart MP, Cheadle A, Martin DP, Moore DL, Schwartz SJ, Schulman B. Childhood immunization registries: gaps between knowledge and action among family practice physicians and pediatricians in Washington state, 1998. ARCHIVES OF PEDIATRICS & ADOLESCENT MEDICINE 2002; 156:978-85. [PMID: 12361442 DOI: 10.1001/archpedi.156.10.978] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]
Abstract
OBJECTIVES To assess the availability and use of Washington State's CHILD (Children's Health, Immunization, Linkages, and Development) Profile and other computerized immunization tracking systems, to determine physicians' attitudes about these systems, and to identify factors associated with using them. DESIGN Randomized, population-based, cross-sectional survey. PARTICIPANTS Washington family physician and pediatrician specialty organization members providing childhood immunizations in 1998 (N = 2472). MAIN OUTCOME MEASURE Reported CHILD Profile and other computerized systems use. RESULTS The adjusted response rate was 75% (n = 1331). Overall, 37.7% of respondents had heard of CHILD Profile, 6.3% used it, and 24.9% used other systems. Groups significantly more likely not to use computerized systems than referent pediatricians in areas fully implementing CHILD Profile were family physicians (adjusted odds ratio [aOR], 2.4; 95% confidence interval [CI], 1.4-4.0), private physicians (aOR, 8.0; 95% CI, 3.2-20.1), physicians taking fewest opportunities to immunize (aOR, 2.3; 95% CI, 1.4-3.7), and physicians practicing in local health jurisdiction areas with CHILD Profile marketing activity (aOR, 2.1; 95% CI, 1.2-3.9) or in those areas with little or no registry activity (aOR, 2.6; 95% CI, 1.6-4.4). Those with systems agreed that they save time (71.0%), make status checks easier (87.1%), and increase immunization coverage (88.6%). Those without systems agreed that they help practices (90.3%) and increase efficiency (76.5%), but fewer agreed that they reduce costs (30.2%). CONCLUSIONS Although most physicians agreed that computerized systems are useful, few had them or used them. Provider-based systems can improve immunization coverage, but the feasibility and effectiveness of communitywide and statewide systems remain unexplored. Because these systems depend on participation, more understanding is needed to help organizations implement them. Interventions to increase availability and use should address provider and health organization needs.
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Hallstrand TS, Curtis JR, Koepsell TD, Martin DP, Schoene RB, Sullivan SD, Yorioka GN, Aitken ML. Effectiveness of screening examinations to detect unrecognized exercise-induced bronchoconstriction. J Pediatr 2002; 141:343-8. [PMID: 12219053 DOI: 10.1067/mpd.2002.125729] [Citation(s) in RCA: 104] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
OBJECTIVE To determine if a physician-administered physical examination and screening questionnaire accurately detects exercise-induced bronchoconstriction (EIB) in adolescent athletes. STUDY DESIGN Cross-sectional study of 256 adolescents participating in organized sports from 3 suburban high schools. The number of persons screened positive for EIB by physical examination and questionnaire was compared with the number of persons with EIB diagnosed by a "gold standard" test that consisted of a 7-minute exercise challenge followed by serial spirometry. RESULTS We diagnosed EIB in 9.4% of adolescent athletes. The screening history identified persons with symptoms or a previous diagnosis suggestive of EIB in 39.5% of the participants, but only 12.9% of these persons actually had EIB. Among adolescents with a negative review of symptoms of asthma or EIB, 7.8% had EIB. Among adolescents with no previous diagnosis of asthma, allergic rhinitis, or EIB, 7.2% had EIB diagnosed by exercise challenge. Persons who screened negative on all questions about symptoms or history of asthma, EIB, and allergic rhinitis accounted for 45.8% of the adolescents with EIB. CONCLUSIONS EIB occurs frequently in adolescent athletes, and screening by physical examination and medical history does not accurately detect it.
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