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Drummond AJ, Rambaut A, Shapiro B, Pybus OG. Bayesian Coalescent Inference of Past Population Dynamics from Molecular Sequences. Mol Biol Evol 2005; 22:1185-92. [PMID: 15703244 DOI: 10.1093/molbev/msi103] [Citation(s) in RCA: 2123] [Impact Index Per Article: 106.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
We introduce the Bayesian skyline plot, a new method for estimating past population dynamics through time from a sample of molecular sequences without dependence on a prespecified parametric model of demographic history. We describe a Markov chain Monte Carlo sampling procedure that efficiently samples a variant of the generalized skyline plot, given sequence data, and combines these plots to generate a posterior distribution of effective population size through time. We apply the Bayesian skyline plot to simulated data sets and show that it correctly reconstructs demographic history under canonical scenarios. Finally, we compare the Bayesian skyline plot model to previous coalescent approaches by analyzing two real data sets (hepatitis C virus in Egypt and mitochondrial DNA of Beringian bison) that have been previously investigated using alternative coalescent methods. In the bison analysis, we detect a severe but previously unrecognized bottleneck, estimated to have occurred 10,000 radiocarbon years ago, which coincides with both the earliest undisputed record of large numbers of humans in Alaska and the megafaunal extinctions in North America at the beginning of the Holocene.
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20 |
2123 |
2
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Gray RD, Drummond AJ, Greenhill SJ. Language phylogenies reveal expansion pulses and pauses in Pacific settlement. Science 2009; 323:479-83. [PMID: 19164742 DOI: 10.1126/science.1166858] [Citation(s) in RCA: 292] [Impact Index Per Article: 18.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
Abstract
Debates about human prehistory often center on the role that population expansions play in shaping biological and cultural diversity. Hypotheses on the origin of the Austronesian settlers of the Pacific are divided between a recent "pulse-pause" expansion from Taiwan and an older "slow-boat" diffusion from Wallacea. We used lexical data and Bayesian phylogenetic methods to construct a phylogeny of 400 languages. In agreement with the pulse-pause scenario, the language trees place the Austronesian origin in Taiwan approximately 5230 years ago and reveal a series of settlement pauses and expansion pulses linked to technological and social innovations. These results are robust to assumptions about the rooting and calibration of the trees and demonstrate the combined power of linguistic scholarship, database technologies, and computational phylogenetic methods for resolving questions about human prehistory.
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Historical Article |
16 |
292 |
3
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Pybus OG, Drummond AJ, Nakano T, Robertson BH, Rambaut A. The epidemiology and iatrogenic transmission of hepatitis C virus in Egypt: a Bayesian coalescent approach. Mol Biol Evol 2003; 20:381-7. [PMID: 12644558 DOI: 10.1093/molbev/msg043] [Citation(s) in RCA: 197] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Hepatitis C virus (HCV) is a leading cause of liver cancer and cirrhosis, and Egypt has possibly the highest HCV prevalence worldwide. In this article we use a newly developed Bayesian inference framework to estimate the transmission dynamics of HCV in Egypt from sampled viral gene sequences, and to predict the public health impact of the virus. Our results indicate that the effective number of HCV infections in Egypt underwent rapid exponential growth between 1930 and 1955. The timing and speed of this spread provides quantitative genetic evidence that the Egyptian HCV epidemic was initiated and propagated by extensive antischistosomiasis injection campaigns. Although our results show that HCV transmission has since decreased, we conclude that HCV is likely to remain prevalent in Egypt for several decades. Our combined population genetic and epidemiological analysis provides detailed estimates of historical changes in Egyptian HCV prevalence. Because our results are consistent with a demographic scenario specified a priori, they also provide an objective test of inference methods based on the coalescent process.
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22 |
197 |
4
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Lambert DM, Ritchie PA, Millar CD, Holland B, Drummond AJ, Baroni C. Rates of evolution in ancient DNA from Adélie penguins. Science 2002; 295:2270-3. [PMID: 11910113 DOI: 10.1126/science.1068105] [Citation(s) in RCA: 177] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
Abstract
Well-preserved subfossil bones of Adélie penguins, Pygoscelis adeliae, underlie existing and abandoned nesting colonies in Antarctica. These bones, dating back to more than 7000 years before the present, harbor some of the best-preserved ancient DNA yet discovered. From 96 radiocarbon-aged bones, we report large numbers of mitochondrial haplotypes, some of which appear to be extinct, given the 380 living birds sampled. We demonstrate DNA sequence evolution through time and estimate the rate of evolution of the hypervariable region I using a Markov chain Monte Carlo integration and a least-squares regression analysis. Our calculated rates of evolution are approximately two to seven times higher than previous indirect phylogenetic estimates.
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23 |
177 |
5
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Hebert PC, Drummond AJ, Singer J, Bernard GR, Russell JA. A simple multiple system organ failure scoring system predicts mortality of patients who have sepsis syndrome. Chest 1993; 104:230-5. [PMID: 8325076 DOI: 10.1378/chest.104.1.230] [Citation(s) in RCA: 132] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023] Open
Abstract
A simple multiple system organ failure (MSOF) score may predict mortality of patients who have sepsis syndrome. Using an MSOF scoring system, we prospectively determined the presence or absence of respiratory, cardiovascular, renal, hepatic, gastrointestinal, hematologic, and neurologic organ failure on day 1 of sepsis syndrome in 154 consecutive patients who had sepsis syndrome in the ICU of a tertiary care, teaching hospital. We used 30-day hospital mortality as the primary outcome variable. Overall 30-day mortality was 34 percent. There was a strong linear association between number of organ system failures and 30-day mortality (p < 0.0001). Mortality was 20 percent in patients who had less than 3 organ system failures (n = 111) and 70 percent in patients who had 3 or more organ system failures (n = 43). Survival was assessed using the Cox proportional hazards model and was found to be significantly different (p < 0.01) between the two groups defined by the aforementioned dichotomy after adjustment for age and sex using time to death as the primary outcome. The increase in relative risk of death associated with 3 or more organ system failures was 2.77 (95 percent confidence interval, 2.74 to 2.83). Using logistic regression, the adjusted odds ratios (OR) for covariates most predictive of mortality were hematologic (OR = 6.2), neurologic (OR = 4.4), hepatic (OR = 3.4), cardiovascular (OR = 2.6), and age (1.05 per year). The logistic model using the seven organ system failures and age as covariates accurately predicted outcome 75 percent of the time with a sensitivity of 51 percent and specificity of 87 percent. In conclusion, a simple scoring system tabulating the number of organ system failures present on day 1 of sepsis syndrome predicts the mortality of patients who have sepsis syndrome with reasonable accuracy.
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32 |
132 |
6
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Drummond A, Strimmer K. PAL: an object-oriented programming library for molecular evolution and phylogenetics. Bioinformatics 2001; 17:662-3. [PMID: 11448888 DOI: 10.1093/bioinformatics/17.7.662] [Citation(s) in RCA: 107] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Phylogenetic Analysis Library (PAL) is a collection of Java classes for use in molecular evolution and phylogenetics. PAL provides a modular environment for the rapid construction of both special-purpose and general analysis programs. PAL version 1.1 consists of 145 public classes or interfaces in 13 packages, including classes for models of character evolution, maximum-likelihood estimation, and the coalescent, with a total of more than 27000 lines of code. The PAL project is set up as a collaborative project to facilitate contributions from other researchers. AVAILIABILTY: The program is free and is available at http://www.pal-project.org. It requires Java 1.1 or later. PAL is licensed under the GNU General Public License.
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24 |
107 |
7
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Maguire TA, McElnay JC, Drummond A. A randomized controlled trial of a smoking cessation intervention based in community pharmacies. Addiction 2001; 96:325-31. [PMID: 11182878 DOI: 10.1046/j.1360-0443.2001.96232516.x] [Citation(s) in RCA: 95] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
AIMS To evaluate whether a structured community pharmacy-based smoking cessation programme (the PAS model) would give rise to a higher smoking cessation rate compared with ad hoc advice from pharmacists. DESIGN A randomized controlled trial comparing a structured intervention with usual care. SETTING One hundred pharmacists working in community pharmacies in N. Ireland and 24 in London took part in the study and were each asked to enroll 12 smokers; 44% of pharmacists who were trained managed to recruit one or more smokers during the recruitment period of approximately 1 year. PARTICIPANTS A total of 484 smokers were enrolled by the pharmacists and individually randomized into the PAS intervention group (N = 265) or the control group (N = 219). INTERVENTION The PAS intervention involved a structured counselling programme, an information leaflet and a follow-up weekly for the first 4 weeks then monthly as needed. MEASUREMENTS The primary outcome measure of this study was self-reported smoking cessation for 12 months with cotinine validation at the 12-month follow-up. FINDINGS Of smokers in the PAS group, 14.3% (38) were abstinent up to 12 months compared with 2.7% (6) in the control group (p < 0.001 for the difference). CONCLUSION The community pharmacy-based PAS smoking cessation service can be an effective method of helping people stop smoking when delivered by pharmacists willing to adopt this approach.
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Clinical Trial |
24 |
95 |
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McGrath JJ, Hearle J, Jenner L, Plant K, Drummond A, Barkla JM. The fertility and fecundity of patients with psychoses. Acta Psychiatr Scand 1999; 99:441-6. [PMID: 10408266 DOI: 10.1111/j.1600-0447.1999.tb00990.x] [Citation(s) in RCA: 93] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
OBJECTIVE Previous research has suggested that patients with schizophrenia have fewer offspring compared to the general population. Reduced fertility in a disorder with a strong genetic component and an apparently stable incidence has implications for models of genetic transmission. There is also a need to obtain contemporary estimates of the prevalence of parenthood among subjects with psychotic disorders in order to inform service planning. The aim of this study was to determine the fertility and fecundity of a representative sample of individuals with psychoses who were in contact with mental health services, and to explore the interactions between age at first diagnosis and fertility. METHOD All clients of two community mental health clinics and an extended-care psychiatric hospital were surveyed. Data on diagnosis, age at first diagnosis, and the number and age of offspring were collected. Based on interviews with the proband and chart review, a genogram of the probands' family was drawn that identified sex, age, affected status and the number of offspring for each patient and their siblings. RESULTS In total, 36% of all patients were parents. Most women with psychoses (59%) were mothers. Patients with psychoses had fewer offspring compared to their unaffected same-sex siblings. This was especially the case for men with non-affective psychoses. Higher levels of fertility were associated with a later age at first diagnosis. CONCLUSION The consistent finding of reduced 'reproductive fitness' in those with non-affective psychoses needs to be incorporated in the genetic epidemiology of these disorders. Despite this reduction in fertility and fecundity, many patients with psychoses are parents. Services need to remain mindful of the special needs of these patients.
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Comparative Study |
26 |
93 |
9
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69 |
88 |
10
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Innes G, Murphy M, Nijssen-Jordan C, Ducharme J, Drummond A. Procedural sedation and analgesia in the emergency department. Canadian Consensus Guidelines. J Emerg Med 1999; 17:145-56. [PMID: 9950405 DOI: 10.1016/s0736-4679(98)00135-8] [Citation(s) in RCA: 87] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
Procedural sedation and analgesia are core skills in emergency medicine. Various specialty societies have developed guidelines for procedural sedation, each reflecting the perspective of the specialty group. Emergency practitioners are most likely to embrace guidelines developed by people who understand emergency department (ED) skills, procedures, conditions, and case mix. Recognizing this, the Canadian Association of Emergency Physicians (CAEP) determined the need to establish guidelines for procedural sedation in the ED. In March, 1996, a national emergency medicine (EM) working committee, representing adult and pediatric emergency physicians, was established. This committee teleconferenced with representatives of the Canadian Anesthetic Society (CAS) to identify problems, perspectives, and controversial issues, and to define a process for guideline development. The EM committee subsequently reviewed existing literature, determined levels of evidence, and developed the document, which evolved based on feedback from the CAS and CAEP Standards Committees. The final version was approved by the CAEP Standards Committee and the CAEP Board of Directors, then submitted for peer review. These guidelines discuss the goals, definitions, and principles of ED sedation, and make recommendations for pre-sedation preparation, patient fasting, physician skills, equipment and monitoring requirements, and post-sedation care. The guidelines are aimed at non-anesthesiologists practicing part-time or full-time emergency medicine. They are applicable to ED patients receiving parenteral analgesia or sedation for painful or anxiety-provoking procedures. They are intended to increase the safety of procedural sedation in the ED.
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Guideline |
26 |
87 |
11
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Bennett SN, Drummond AJ, Kapan DD, Suchard MA, Muñoz-Jordán JL, Pybus OG, Holmes EC, Gubler DJ. Epidemic dynamics revealed in dengue evolution. Mol Biol Evol 2009; 27:811-8. [PMID: 19965886 DOI: 10.1093/molbev/msp285] [Citation(s) in RCA: 85] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
Dengue is an emerging tropical disease infecting tens of millions of people annually. A febrile illness with potentially severe hemorrhagic manifestations, dengue is caused by mosquito-borne viruses (DENV-1 to -4) that are maintained in endemic transmission in large urban centers of the tropics with periodic epidemic cycles at 3- to 5-year intervals. Puerto Rico (PR), a major population center in the Caribbean, has experienced increasingly severe epidemics since multiple dengue serotypes were introduced beginning in the late 1970s. We document the phylodynamics of DENV-4 between 1981 and 1998, a period of dramatic ecological expansion during which evolutionary change also occurs. The timescale of viral evolution is sufficiently short that viral transmission dynamics can be elucidated from genetic diversity data. Specifically, by combining virus sequence data with confirmed case counts in PR over these two decades, we show that the pattern of cyclic epidemics is strongly correlated with coalescent estimates of effective population size that have been estimated from sampled virus sequences using Bayesian Markov Chain Monte Carlo methods. Thus, we show that the observed epidemiologic dynamics are correlated with similar fluctuations in diversity, including severe interepidemic reductions in genetic diversity compatible with population bottlenecks that may greatly impact DENV evolutionary dynamics. Mean effective population sizes based on genetic data appear to increase prior to isolation counts, suggesting a potential bias in the latter and justifying more active surveillance of DENV activity. Our analysis explicitly integrates epidemiologic and sequence data in a joint model that could be used to further explore transmission models of infectious disease.
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Research Support, U.S. Gov't, Non-P.H.S. |
16 |
85 |
12
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Walker MF, Leonardi-Bee J, Bath P, Langhorne P, Dewey M, Corr S, Drummond A, Gilbertson L, Gladman JRF, Jongbloed L, Logan P, Parker C. Individual Patient Data Meta-Analysis of Randomized Controlled Trials of Community Occupational Therapy for Stroke Patients. Stroke 2004; 35:2226-32. [PMID: 15272129 DOI: 10.1161/01.str.0000137766.17092.fb] [Citation(s) in RCA: 83] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
BACKGROUND AND PURPOSE Trials of occupational therapy for stroke patients living in the community have varied in their findings. It is unclear why these discrepancies have occurred. METHODS Trials were identified from searches of the Cochrane Library and other sources. The primary outcome measure was the Nottingham Extended Activities of Daily Living (NEADL) score at the end of intervention. Secondary outcome measures included the Barthel Index or the Rivermead ADL (Personal ADL), General Health Questionnaire (GHQ), Nottingham Leisure Questionnaire (NLQ), and death. Data were analyzed using linear or logistic regression with a random effect for trial and adjustment for age, gender, baseline dependency, and method of follow-up. Subgroup analyses compared any occupational therapy intervention with control. RESULTS We included 8 single-blind randomized controlled trials incorporating 1143 patients. Occupational therapy was associated with higher NEADL scores at the end of intervention (weighted mean difference [WMD], 1.30 points, 95% confidence intervals [CI], 0.47 to 2.13) and higher leisure scores at the end of intervention (WMD, 1.51 points; 95% CI, 0.24 to 2.79). Occupational therapy emphasizing activities of daily living (ADL) was associated with improved end of intervention NEADL (WMD, 1.61 points; 95% CI, 0.72 to 2.49) and personal activities of daily living (odds ratio [OR], 0.65; 95% CI, 0.46 to 0.91), but not NLQ. Leisure-based occupational therapy improved end of intervention NLQ (WMD, 1.96 points; 95% CI, 0.27 to 3.66) but not NEADL or PADL. CONCLUSIONS Community occupational therapy significantly improved personal and extended activities of daily living and leisure activity in patients with stroke. Better outcomes were found with targeted interventions.
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21 |
83 |
13
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Tang X, Boxer M, Drummond A, Ogston P, Hodgins M, Burden AD. A germline mutation in KIT in familial diffuse cutaneous mastocytosis. J Med Genet 2004; 41:e88. [PMID: 15173254 PMCID: PMC1735799 DOI: 10.1136/jmg.2003.015156] [Citation(s) in RCA: 72] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022]
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Research Support, Non-U.S. Gov't |
21 |
72 |
14
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Drummond A, Rodrigo AG. Reconstructing genealogies of serial samples under the assumption of a molecular clock using serial-sample UPGMA. Mol Biol Evol 2000; 17:1807-15. [PMID: 11110896 DOI: 10.1093/oxfordjournals.molbev.a026281] [Citation(s) in RCA: 69] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Reconstruction of evolutionary relationships from noncontemporaneous molecular samples provides a new challenge for phylogenetic reconstruction methods. With recent biotechnological advances there has been an increase in molecular sequencing throughput, and the potential to obtain serial samples of sequences from populations, including rapidly evolving pathogens, is fast being realized. A new method called the serial-sample unweighted pair grouping method with arithmetic means (sUPGMA) is presented that reconstructs a genealogy or phylogeny of sequences sampled serially in time using a matrix of pairwise distances. The resulting tree depicts the terminal lineages of each sample ending at a different level consistent with the sample's temporal order. Since sUPGMA is a variant of UPGMA, it will perform best when sequences have evolved at a constant rate (i.e., according to a molecular clock). On simulated data, this new method performs better than standard cluster analysis under a variety of longitudinal sampling strategies. Serial-sample UPGMA is particularly useful for analysis of longitudinal samples of viruses and bacteria, as well as ancient DNA samples, with the minimal requirement that samples of sequences be ordered in time.
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Evaluation Study |
25 |
69 |
15
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Alogna VK, Attaya MK, Aucoin P, Bahník Š, Birch S, Birt AR, Bornstein BH, Bouwmeester S, Brandimonte MA, Brown C, Buswell K, Carlson C, Carlson M, Chu S, Cislak A, Colarusso M, Colloff MF, Dellapaolera KS, Delvenne JF, Di Domenico A, Drummond A, Echterhoff G, Edlund JE, Eggleston CM, Fairfield B, Franco G, Gabbert F, Gamblin BW, Garry M, Gentry R, Gilbert EA, Greenberg DL, Halberstadt J, Hall L, Hancock PJB, Hirsch D, Holt G, Jackson JC, Jong J, Kehn A, Koch C, Kopietz R, Körner U, Kunar MA, Lai CK, Langton SRH, Leite FP, Mammarella N, Marsh JE, McConnaughy KA, McCoy S, McIntyre AH, Meissner CA, Michael RB, Mitchell AA, Mugayar-Baldocchi M, Musselman R, Ng C, Nichols AL, Nunez NL, Palmer MA, Pappagianopoulos JE, Petro MS, Poirier CR, Portch E, Rainsford M, Rancourt A, Romig C, Rubínová E, Sanson M, Satchell L, Sauer JD, Schweitzer K, Shaheed J, Skelton F, Sullivan GA, Susa KJ, Swanner JK, Thompson WB, Todaro R, Ulatowska J, Valentine T, Verkoeijen PPJL, Vranka M, Wade KA, Was CA, Weatherford D, Wiseman K, Zaksaite T, Zuj DV, Zwaan RA. Registered Replication Report: Schooler and Engstler-Schooler (1990). PERSPECTIVES ON PSYCHOLOGICAL SCIENCE 2014; 9:556-78. [PMID: 26186758 DOI: 10.1177/1745691614545653] [Citation(s) in RCA: 67] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Trying to remember something now typically improves your ability to remember it later. However, after watching a video of a simulated bank robbery, participants who verbally described the robber were 25% worse at identifying the robber in a lineup than were participants who instead listed U.S. states and capitals-this has been termed the "verbal overshadowing" effect (Schooler & Engstler-Schooler, 1990). More recent studies suggested that this effect might be substantially smaller than first reported. Given uncertainty about the effect size, the influence of this finding in the memory literature, and its practical importance for police procedures, we conducted two collections of preregistered direct replications (RRR1 and RRR2) that differed only in the order of the description task and a filler task. In RRR1, when the description task immediately followed the robbery, participants who provided a description were 4% less likely to select the robber than were those in the control condition. In RRR2, when the description was delayed by 20 min, they were 16% less likely to select the robber. These findings reveal a robust verbal overshadowing effect that is strongly influenced by the relative timing of the tasks. The discussion considers further implications of these replications for our understanding of verbal overshadowing.
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Research Support, Non-U.S. Gov't |
11 |
67 |
16
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Edwards CTT, Holmes EC, Pybus OG, Wilson DJ, Viscidi RP, Abrams EJ, Phillips RE, Drummond AJ. Evolution of the human immunodeficiency virus envelope gene is dominated by purifying selection. Genetics 2006; 174:1441-53. [PMID: 16951087 PMCID: PMC1667091 DOI: 10.1534/genetics.105.052019] [Citation(s) in RCA: 54] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2005] [Accepted: 08/17/2006] [Indexed: 11/18/2022] Open
Abstract
The evolution of the human immunodeficiency virus (HIV-1) during chronic infection involves the rapid, continuous turnover of genetic diversity. However, the role of natural selection, relative to random genetic drift, in governing this process is unclear. We tested a stochastic model of genetic drift using partial envelope sequences sampled longitudinally in 28 infected children. In each case the Bayesian posterior (empirical) distribution of coalescent genealogies was estimated using Markov chain Monte Carlo methods. Posterior predictive simulation was then used to generate a null distribution of genealogies assuming neutrality, with the null and empirical distributions compared using four genealogy-based summary statistics sensitive to nonneutral evolution. Because both null and empirical distributions were generated within a coalescent framework, we were able to explicitly account for the confounding influence of demography. From the distribution of corrected P-values across patients, we conclude that empirical genealogies are more asymmetric than expected if evolution is driven by mutation and genetic drift only, with an excess of low-frequency polymorphisms in the population. This indicates that although drift may still play an important role, natural selection has a strong influence on the evolution of HIV-1 envelope. A negative relationship between effective population size and substitution rate indicates that as the efficacy of selection increases, a smaller proportion of mutations approach fixation in the population. This suggests the presence of deleterious mutations. We therefore conclude that intrahost HIV-1 evolution in envelope is dominated by purifying selection against low-frequency deleterious mutations that do not reach fixation.
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Comparative Study |
19 |
54 |
17
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Potter J, Robinson T, Ford G, James M, Jenkins D, Mistri A, Bulpitt C, Drummond A, Jagger C, Knight J, Markus H, Beevers G, Dewey M, Lees K, Moore A, Paul S. CHHIPS (Controlling Hypertension and Hypotension Immediately Post-Stroke) Pilot Trial: rationale and design. J Hypertens 2005; 23:649-55. [PMID: 15716709 DOI: 10.1097/01.hjh.0000160224.94220.e7] [Citation(s) in RCA: 51] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
RATIONALE High and low blood pressure (BP) levels are common following acute stroke, with up to 60% of patients being hypertensive (SBP > 160 mmHg) and nearly 20% having relative hypotension (SBP < or = 140 mmHg), within the first few hours of ictus, both conditions being associated with an adverse prognosis. At present, the optimum management of blood pressure in the immediate post-stroke period is unclear. OBJECTIVE The primary aim of the Controlling Hypertension and Hypotension Immediately Post-Stroke (CHHIPS) Pilot Trial is to assess whether hypertension and relative hypotension, manipulated therapeutically in the first 24 h following acute stroke, affects short-term outcome measures. DESIGN The CHHIPS Pilot Trial is a UK based multi-centre, randomized, double-blind, placebo-controlled, titrated dose trial. SETTING Acute stroke and medical units in teaching and district general hospitals, in the UK. PATIENTS The CHHIPS Pilot Study aims to recruit 2050 patients, with clinically suspected stroke, confirmed by brain imaging, who have no compelling indication or contraindication for BP manipulation. STUDY OUTCOMES The primary outcome measure will be the effects of acute pressor therapy (initiated < or = 12 h from stroke onset) or depressor therapy (started < or = 24 h post-ictus) on death and dependency at 14 days post-stroke. Secondary outcome measures will include the influence of therapy on early neurological deterioration, the effectiveness of treatment in manipulating BP levels, the influence of time to treatment and stroke type on response and a cost-effectiveness analysis.
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51 |
18
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Axler O, Tousignant C, Thompson CR, Dalla'va-Santucci J, Drummond A, Phang PT, Russell JA, Walley KR. Small hemodynamic effect of typical rapid volume infusions in critically ill patients. Crit Care Med 1997; 25:965-70. [PMID: 9201048 DOI: 10.1097/00003246-199706000-00012] [Citation(s) in RCA: 41] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
OBJECTIVES To determine what volumes are commonly used for rapid volume infusions in critically ill patients admitted to the intensive care unit (ICU) for > 12 hrs; and to determine the effectiveness of a typical rapid volume infusion in producing hemodynamic change and increasing left ventricular end-diastolic volume. DESIGN A prospective survey of clinical practice (part 1) and a prospective clinical investigation (part 2). SETTING Two hospital ICUs (11 and six beds) of which one is university affiliated. PATIENTS Critically ill patients admitted to the ICU for > 12 hrs. INTERVENTIONS Infusion of 500 mL of normal saline over 5 to 10 mins. MEASUREMENTS AND MAIN RESULTS For 1 month, we recorded the volume and composition of all volume infusions given as a rapid bolus in patients admitted to the ICU for > 12 hrs. We then measured the effected the median rapid volume infusion in a subset of 13 patients by measuring hemodynamics (using arterial and pulmonary artery flotation catheters) and left ventricular end-diastolic area (using transgastric short-axis views from transesophageal echocardiograms). During 470 patient days, 159 rapid volume infusions were administered. The average rapid volume infusion administered was 390 +/- 160 mL (median 500; interquartile range 250 to 500). Crystalloid solutions were used for two thirds of the rapid volume infusions and colloid solutions were used for one third of the rapid volume infusions. The rapid volume infusion of 500 mL of saline did not significantly increase mean arterial pressure (78.0 +/- 11.9 to 79.3 +/- 14.6 mm Hg), cardiac index (4.3 +/- 1.7 to 4.6 +/- 1.8 L/min/m2), right atrial pressure (11.1 +/- 3.8 to 12.4 +/- 3.3 mm Hg), left ventricular end-diastolic area (8.6 +/- 1.7 to 9.1 +/- 1.8 cm2/m2), or left ventricular end-systolic area (3.5 +/- 1.5 to 3.6 +/- 1.5 cm2/m2). Pulmonary artery occlusion pressure increased slightly but significantly from 12.9 +/- 3.4 to 14.7 +/- 3.3 mm Hg (p < .05). CONCLUSIONS After patients are admitted to the ICU for > 12 hrs, rapid volume infusions are common therapeutic interventions but the rapid volume infusions are typically small. The effect of a typical rapid volume infusion on hemodynamics and left ventricular areas in these patients is surprisingly small.
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28 |
41 |
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Abstract
Patients were questioned 40-78 weeks after stroke to ascertain their previous and current levels of leisure participation. The results indicate a decrease with regard to both the number of activities and the frequency of participation when compared to reported pre-stroke leisure activity.
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Burger HG, Fuller PJ, Chu S, Mamers P, Drummond A, Susil B, Neva P, Robertson DM. The inhibins and ovarian cancer. Mol Cell Endocrinol 2001; 180:145-8. [PMID: 11451584 DOI: 10.1016/s0303-7207(01)00519-6] [Citation(s) in RCA: 38] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Interest in inhibin as a marker of ovarian malignancy was stimulated by the description of elevated immunoreactive inhibin levels in the sera of patients with granulosa cell tumours. Several groups have confirmed the value of serum inhibin in the diagnosis and follow-up of patients with this uncommon malignancy. Immunoreactive inhibin levels are also frequently elevated in patients with mucinous cystadenocarcinoma and less frequently in other forms of ovarian tumour. Assay of sera using the specific dimeric inhibin assays has shown that ovarian tumours are able to secrete dimeric inhibin particularly inhibin B. The less specific alpha-subunit directed assays, however, most frequently show elevated concentrations. Used in combination with CA125 as a dual tumour marker, it appears in principle that inhibin can be a useful diagnostic agent. Immunohistochemistry for the inhibin subunits has been reported with increasing frequency as a helpful method to assess suspected ovarian stromal cell tumours. Its diagnostic accuracy for other types of ovarian adenocarcinoma appears less reliable. Expression of the inhibin subunit mRNAs has been demonstrated in a variety of ovarian malignancies. The observation that inhibin levels are elevated in ovarian cancer has stimulated studies of their relevance to the molecular pathogenesis of these malignancies. Findings to date have been largely negative with no evidence for activating mutations of the FSH receptor or of the post-receptor signalling pathway proteins.
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Review |
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38 |
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Drummond A, Forsberg R, Rodrigo AG. The inference of stepwise changes in substitution rates using serial sequence samples. Mol Biol Evol 2001; 18:1365-71. [PMID: 11420374 DOI: 10.1093/oxfordjournals.molbev.a003920] [Citation(s) in RCA: 34] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
It is frequently true that molecular sequences do not evolve in a strictly clocklike manner. Instead, substitution rate may vary for a number of reasons, including changes in selection pressure and effective population size, as well as changes in mean generation time. Here we present two new methods for estimating stepwise changes in substitution rates when serially sampled molecular sequences are available. These methods are based on multiple rates with dated tips (MRDT) models and allow different rates to be estimated for different intervals of time. These intervals may correspond to the sampling intervals or to a priori--defined intervals that are not coincident with the times the serial samples are obtained. Two methods for obtaining estimates of multiple rates are described. The first is an extension of the phylogeny-based maximum-likelihood estimation procedure introduced by Rambaut. The second is a new parameterization of the pairwise distance least-squares procedure used by Drummond and Rodrigo. The utility of these methods is demonstrated on a genealogy of HIV sequences obtained at five different sampling times from a single patient over a period of 34 months.
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Drummond A, Micallef-Eynaud P, Douglas WS, Hay I, Holyoake TL, Drummond MW. A spectrum of skin reactions caused by the tyrosine kinase inhibitor imatinib mesylate (STI 571, Glivec). Br J Haematol 2003; 120:911-3. [PMID: 12614232 DOI: 10.1046/j.1365-2141.2003.04151_4.x] [Citation(s) in RCA: 34] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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Letter |
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34 |
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Fanthome Y, Lincoln NB, Drummond A, Walker MF. The treatment of visual neglect using feedback of eye movements: a pilot study. Disabil Rehabil 1995; 17:413-7. [PMID: 8573702 DOI: 10.3109/09638289509166654] [Citation(s) in RCA: 32] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Abstract
Feedback of eye movements was evaluated as a treatment for visual neglect in right hemisphere stroke patients. Patients with visual neglect identified on the Behavioural Inattention Test (BIT) were randomly allocated to two groups. One group (n = 9) was treated for 2 h 40 min a week for 4 weeks, by wearing glasses which provided a reminder bleep if patients failed to move their eyes to the left in a 15 s interval. The control group (n = 9) received no treatment for their visual inattention. Comparison of the groups after 4 weeks treatment and a further 4 weeks follow-up showed no significant difference either in eye movements or on the BIT. However, there was a trend towards a difference between eye movements in the two groups at 8 weeks, suggesting treatment may have influenced eye movements without changing neglect.
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Clinical Trial |
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Drummond A, Kane D, Bilsland D. Legal claims in Scottish National Health Service Dermatology Departments 1989-2001. Br J Dermatol 2003; 149:111-4. [PMID: 12890203 DOI: 10.1046/j.1365-2133.2003.05344.x] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
BACKGROUND An area of current National Health Service (NHS) interest is risk management as it is one of the requirements of clinical governance. If there are aspects of dermatological practice prone to mishap or dispute then a review of legal claims in dermatology may highlight these areas. This would then allow input into these specific areas of practice to try and minimize future risk. OBJECTIVES To review all legal claims relating to NHS Dermatology in Scotland and characterize the main areas of risk. METHODS Staff at the Central Legal Office in Edinburgh reviewed all legal claims in NHS Dermatology between 1989 and 2001. Details provided were general, and claimants, staff, hospitals and regions of Scotland could not be identified. RESULTS Thirty claims were identified relating to five main areas of dermatological practice: (i) phototherapy (eight claims); (ii) therapeutics (eight); (iii) cryosurgery/cryotherapy (six); (iv) surgery (four); and (v) misdiagnosis (three) and one alleged neurological problem after fainting. As well as consultants, nurses featured in phototherapy claims and junior medical staff in cryosurgery claims. Twelve of the 30 (40%) claims have reached settlement; three claims are presently outstanding. CONCLUSIONS Given the numbers of patients seen annually at Scottish NHS Hospital Dermatology units the absolute number of claims is low. Five main areas within dermatology were highlighted as at risk of litigation and this has implications for all U.K. dermatology departments with regard to funding, staff training and patient information and consent.
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