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PubMed2006

Gene selection algorithms for microarray data based on least squares support vector machine.

BACKGROUND: In discriminant analysis of microarray data, usually a small number of samples are expressed by a large number of genes. It is not only difficult but also unnecessary to conduct the discriminant analysis with all the genes. Hence, gene selection is usually performed to select important genes. RESULTS: A gene selection method searches for an optimal or near optimal subset of genes with respect to a given evaluation criterion. In this paper, we propose a new evaluation criterion, named the leave-one-out calculation (LOOC, A list of abbreviations appears just above the list of references) measure. A gene selection method, named leave-one-out calculation sequential forward selection (LOOCSFS) algorithm, is then presented by combining the LOOC measure with the sequential forward selection scheme. Further, a novel gene selection algorithm, the gradient-based leave-one-out gene selection (GLGS) algorithm, is also proposed. Both of the gene selection algorithms originate from an efficient and exact calculation of the leave-one-out cross-validation error of the least squares support vector machine (LS-SVM). The proposed approaches are applied to two microarray datasets and compared to other well-known gene selection methods using codes available from the second author. CONCLUSION: The proposed gene selection approaches can provide gene subsets leading to more accurate classification results, while their computational complexity is comparable to the existing methods. The GLGS algorithm can also better scale to datasets with a very large number of genes.

Algorithms↗

PubMed2004

Economic evaluation of etoricoxib versus non-selective NSAIDs in the treatment of osteoarthritis and rheumatoid arthritis patients in the UK.

INTRODUCTION: The objective of this study was to evaluate the potential economic implications of using etoricoxib versus non-selective NSAID alternatives in the treatment of patients with osteoarthritis (OA) or rheumatoid arthritis (RA) in the UK. STUDY DESIGN: Decision-analytical modelling was used to calculate the expected costs and consequences of the use of etoricoxib compared with non-selective NSAIDs alone, NSAIDs plus proton pump inhibitors (PPIs), NSAIDs plus histamine H2 receptor antagonists and NSAIDs plus misoprostol over a continuous treatment period of 1 year. METHODS: The model considered direct medical costs from the perspective of the UK National Health Service (NHS) and used data from phase IIb and III clinical trials of etoricoxib to determine probabilities of gastrointestinal (GI) events. Model outcomes were defined as resource-consuming GI-related events, including clinically evident gastroduodenal perforations, symptomatic gastroduodenal ulcers, or upper GI bleeding (collectively, PUBs ['perforation, ulcers and/or bleeding']). Resource utilisation and costs (2002 values) for the treatment of OA and RA as well as GI events were based on published literature and information available from UK-specific sources. MAIN OUTCOME MEASURES AND RESULTS: The model suggests that etoricoxib is cost saving compared with non-selective NSAIDs plus PPIs or non-selective NSAIDs plus misoprostol. The model also suggests that etoricoxib is cost effective in terms of the incremental cost per QALY gained for non-selective NSAIDs alone (pound 19,766) and for non-selective NSAIDs plus H2 antagonists (pound 9350). The incremental cost of etoricoxib per PUB avoided was pound 12,446 versus non-selective NSAIDs alone and pound 6438 versus NSAIDs co-prescribed with H2 antagonists. For patients without the presence of specific GI risk factors (history of GI event, corticosteroid use or disability), etoricoxib may be cost effective for patients over age 56 years, assuming a cost-effectiveness threshold of pound 30,000 per QALY gained. Etoricoxib may also be cost effective in patients of all ages who had at least one specific GI risk factor. CONCLUSIONS: The model suggests, with its underlying assumptions and data, that etoricoxib is a cost-effective alternative to therapeutic regimens involving non-selective NSAIDs for OA or RA, from the UK NHS perspective. Etoricoxib may be cost saving and dominant over non-selective NSAIDs used together with a PPI or misoprostol. When compared with non-selective NSAIDs alone or non-selective NSAIDs co-prescribed with H2 antagonists, the incremental cost per QALY gained with use of etoricoxib was within the generally accepted threshold for cost effectiveness (less than pound 30,000 per QALY gained).

Anti-Inflammatory Agents, Non-Steroidal↗

PubMed1990

Efficiency of selection strategies for halothane-negative gene.

Use of a method to estimate the frequency of the halothane-negative allele in boars is illustrated for different sampling schemes for boar testing programs and for testing within closed breeding populations. This method uses information not only on the individual, but also on all mates and relatives including parents, siblings and offspring. Accuracy of the estimates of the allelic frequency in boars was measured through use of Monte Carlo simulation. The selection differential in real frequency of the halothane-negative allele when boars were selected on estimated allelic frequency was used as the criterion for accuracy. In the progeny testing situation, phenotypes of base boars and one generation of offspring were available. The average selection differentials with 90% selection (i.e., culling 10% of boars on estimated allelic frequency) when 2 and 10 litters of two boars each were tested were .017 and .044 in base boars and .013 and .025 in the offspring. The value of the boar's own phenotype was small. Higher selection differentials were found in the closed herd situation, where data on two generations were available. The selection differential in base boars when 10 litters were tested increased from .046 to .066 when the proportion of boars selected decreased from 90% to 50%. No improvement in selection differential with proportion selected was found in the progeny testing situation. Intense selection is most effective when the number of litters per boar is large and data over several generations are used. The estimation procedure for allelic frequencies in boars should improve current screening and selection programs to reduce halothane sensitivity in pigs.

Alleles↗

PubMed1992

Comparison of selection methods at the same level of inbreeding.

Animal geneticists predict higher genetic responses to selection by increasing the accuracy of selection using BLUP with information on relatives. Comparison of different selection methods is usually made with the same total number tested and with the same number of parents and mating structure so as to give some acceptable (low) level of inbreeding. Use of family information by BLUP results in the individuals selected being more closely related, and the levels of inbreeding are increased, thereby breaking the original restriction on inbreeding. An alternative is to compare methods at the same level of inbreeding. This would allow more intense selection (fewer males selected) with the less accurate methods. Stochastic simulation shows that, at the same level of inbreeding, differences between the methods are much smaller than if inbreeding is unrestricted. If low to moderate inbreeding levels are targeted, as in a closed line of limited size, then selection on phenotype can yield higher genetic responses than selection on BLUP. Extra responses by BLUP are at the expense of extra inbreeding. The results derived here show that selection on BLUP of breeding values may not be optimal in all cases. Thus, current theory and teaching on selection methods are queried. Revision of the methodology and a reappraisal of the optimization results of selection theory are required.

Animals↗

PubMed1998

Mate selection by groups.

The two key components in a breeding program can be described as the development of an objective function and the implementation of an algorithm for mate selection to target the objective function. However, mate selection is unacceptably slow for objective functions that involve longer term aims, such as engineering a good connection between herds. This paper proposes animal clustering to facilitate group mate selection, plus a step to refine mate selection for individual animals. Cluster analysis is used to form groups of animals within each sex based on nominated factors such as breed, herd, age, and EBV. Mate selection is then performed on groups, reducing the size of the problem considerably. The example used involved a three-breed crossbred population with a simple objective function to maximize predicted progeny merit. Twenty sires and 500 dams were to be selected from 816 and 1784 candidates. Group mate selection achieved 96.9% efficiency (random selection, 0%; full mate selection, 100%) and took 0.28 s to compute (394.2 s for full mate selection). Permitting more candidates to reach the individual mate selection stage increased efficiency to, for example, 98.9% at the cost of an extra 1.15 s. Efficiency was also improved by permitting more clusters.

Algorithms↗

PubMed1991

Early and late selection in partial report: evidence from degraded displays.

In studies of iconic memory using the bar-probe task, subjects see a brief display of target letters and are probed by an arrow to report one of them. According to the classic early-selection account, subjects use the probe to select material for perceptual analysis from a precategorical (iconic) memory, but according to late-selection theories, subjects first identify the letters and then use the probe to select one letter for report from the set of categorized items. Pashler (1984) based his test for the locus of selection on a manipulation of display quality in previewed displays. He presented a target for 200 msec and then added a probe, together with the target, for an additional 150 msec. Reducing the target's stimulus quality increased response latency. If the subjects identified the characters before the probe appeared and then selected an item for report, the clarity of the original array should not have affected response latency. Hence, Pashler concluded that his subjects used the probe to select from a precategorical store (early selection). Pashler's experiment did not force subjects to rely on memory of the target; hence, although his experiment documented a situation in which subjects used early selection, it did not rule out late selection in studies of information persistence. We replicated Pashler's findings and, using his logic, showed that when subjects are forced to rely on memory of the target, they select from a categorized store.

Adult↗

PubMed2001

Lipoprotein lipase mediates an increase in selective uptake of HDL-associated cholesteryl esters by cells in culture independent of scavenger receptor BI.

Scavenger receptor class B type I (SR-BI) mediates the selective uptake of HDL cholesteryl esters (CEs) by the liver. LPL promotes this selective lipid uptake independent of lipolysis. In this study, the role of SR-BI in the mechanism of this LPL-mediated increase in selective CE uptake was explored. Baby hamster kidney (BHK) cells were transfected with the SR-BI cDNA, and significant SR-BI expression could be detected in immunoblots, whereas no SR-BI was visualized in control cells. Y1-BS1 murine adrenocortical cells were cultured without or with adrenocorticotropic hormone, and cells with no detectable or with SR-BI were obtained. These cells incubated without or with LPL in medium containing 125I/[3H]cholesteryl oleyl ether- labeled HDL3; tetrahydrolipstatin inhibited the catalytic activity of LPL. In BHK and in Y1-BS1 cells without or with SR-BI expression, apparent HDL3 selective CE uptake ([3H]CEt - 125I) was detectable. Cellular SR-BI expression promoted HDL3 selective CE uptake by approximately 250-1,900%. In BHK or Y1-BS1 cells, LPL mediated an increase in apparent selective CE uptake. Quantitatively, this stimulating LPL effect was very similar in control cells and in cells with SR-BI expression. The uptake of radiolabeled HDL3 was also investigated in human embryonal kidney 293 (HEK 293) cells that are an established SR-BI-deficient cell model. LPL stimulated [3H]cholesteryl oleyl ether uptake from labeled HDL3 by HEK 293 cells substantially, showing that LPL can induce selective CE uptake from HDL3 independent of SR-BI. To explore the role of cell surface proteoglycans on lipoprotein uptake, we induced proteoglycan deficiency by heparinase treatment. Proteoglycan deficiency decreased the LPL-mediated promotion of HDL3 selective CE uptake. In summary, evidence is presented that the stimulating effect of LPL on HDL3 selective CE uptake is independent of SR-BI and lipolysis. However, cell surface proteoglycans are required for the LPL action on selective CE uptake. It is suggested that pathways distinct from SR-BI mediate selective CE uptake from HDL.

Adrenal Cortex↗

PubMed2003

Development of a selective medium for the determination of the spore concentrations of Botrytis cinerea in the air.

Gray mold, caused by Botrytis cinerea, is an important disease that causes world-wide extensive damage to a wide range of economically important crops. When it is necessary to determine the spore concentration of Botrytis cinerea in a certain area, it is important to develop a method that can capture the spores of Botrytis cinerea and that can identify them. For the identification and enumeration of the plant pathogen Botrytis cinerea in the environment the easiest method available for the moment is the use of a selective medium. Several selective media for the isolation of Botrytis spp. have been developed by other research groups. All these media contain fungicides that are usually non-toxic towards Botrytis species and tannic acid, which is oxidized to produce a brown pigment that visualises the growth of Botrytis cinerea on the selective media. It seemed that different isolates of Botrytis cinerea that are found in nature have different sensitivities towards the different fungicide concentrations that are used in the selective media. Making the "optimal" selective media for Botrytis cinerea, we have to take in consideration that so many as possible Botrytis cinerea isolates must be able to germinate and grow on this selective medium and that the contamination of other micro-organisms on the selective medium must be minimized. Before the final composition of our selective medium for Botrytis cinerea, different combinations of fungicide concentrations were tried out of the following three fungicides: Rubigan, maneb and PCNB (pentachloronitrobenzene). All these selective media with different fungicides concentrations were tested out for spore germination and mycelium growth of Botrytis cinerea. Because it was obvious that the percentage Botrytis cinerea that germinated on PDA (Potato Dextrose Agar) was higher than on the selective medium a few experiments were executed in which the percentage of spore germination on PDA was compared with the percentage of spore germination on selective media. From the results of these experiments a correction factor was calculated that will be used when spore concentrations have to be determined for air detections that are carried out in glasshouses.

Air Microbiology↗

PubMed1989

Phosphonium salts exhibiting selective anti-carcinoma activity in vitro.

Tetraphenylphosphonium cation (TPP) and other phosphonium cations selectively inhibited the growth in vitro of human pancreatic carcinoma-derived cells (PaCa-2) and Ehrlich Lettre Ascites cells (ELA) when compared with untransformed monkey kidney epithelial cells (CV-1). In contrast, neither cisplatin nor cytosine arabinoside showed significant selectivity using these lines. Evidence is presented to support the conclusion that the carcinoma-selective antiproliferative activity of phosphonium salts is due to selective accumulation caused by the abnormally high membrane potentials in carcinoma cells. Inhibition of TPP uptake into PaCa-2 and ELA cells by potassium and (for PaCa-2) valinomycin demonstrates that higher membrane potentials account for the carcinoma-selective uptake and cytostatic selectivity of the cation. For TPP chloride and 16 other phosphonium chlorides with a variety of structures, selective inhibition of PaCa-2 growth relative to CV-1 was optimal for the eight falling in a narrow range of octanol/water partition coefficients (between 0.013 and 0.24). A similar optimal selectivity range was observed for ELA cells relative to CV-1. The relationship between partition coefficients and cytostatic selectivity suggests that the rates of diffusion across cytoplasmic and mitochondrial membranes are key factors in the structure/anticarcinoma selectivity relationship for delocalized phosphonium salts in vitro. The relationship could prove useful for the design of other carcinoma-selective delocalized cations.

Animals↗

PubMed1979

[Use of the control group selected by a method of matched samples in the evaluation of the health status of children from complicated pregnancies].

A method of matched samples consisting in selection of "a partner" for each examined individual according to the established criteria of similarities is one of the methods used owing to its apparent organizational ease in selecting of the control group. The control group selected in this way was used in the evaluation of the effect of bleeding during the first 16 weeks of pregnancy on the health status and physical development of children. The paper points out the advantages of using the control group selected by the method of matched samples. It also presents the difficulties encountered in practice. Typical of this study technical methods and statistical tests used in evaluation of the results were juxtaposed and discussed, then compared to those used when a group was randomly selected. Special attention was paid to 3 basic problems: Time stability is selection of criteria for matched samples. Adjustment of age differences within pairs. Two methods were used for comparison of the anthropometric measurements. The first one consisted in levelling of the differences by the method of regression, the second in the use of various available growth curves. The results obtained by both methods were compared by means of statistical tests. The third problem concerned adequacy of the tests used when the control group was selected by the method of matched samples. Results obtained by application of t-Student test for paired samples were compared to those obtained by t-Student test for independent variables. The merits of the method of matched samples were presented using some examples (table I, II, III). Eleven conclusions were drawn from evaluation of suitability of selecting the control group according to the method of paired samples. These can be put into three main groups: Showing in what kind of studies the control group selected by the method of matched samples is payable . Showing various inconveniences caused by selection of the control group by the method of matched samples, Conclusions concerning methodological or other benefits drawn from this method. It is clearly indicated in this paper that the control group selected by the method of matched samples is recommended only in certain investigations. Before the final decision is taken all pros and cons should be considered.

Anthropometry↗

PubMed1987

Regulation of the selective uptake of high density lipoprotein-associated cholesteryl esters.

We have previously shown in rats that the cholesteryl ester component of high density lipoproteins (HDL) is taken up at a greater fractional rate than is the apolipoprotein A-I component (selective uptake) by liver and steroidogenic tissues. Selective uptake was also exhibited by cultured cells from these organs as well as by a wider range of cells in vitro (e.g., rat and human fibroblasts). We report here regulation of this pathway according to the cholesterol status of cells. Uptake of HDL cholesteryl esters by rat fibroblasts was decreased by prior loading of the cells with cholesterol, even while uptake of HDL-associated apoA-I actually increased. At high levels of cholesterol, the two were taken up about in parallel, i.e., selective uptake was suppressed. A similar regulation of selective uptake in primary rat hepatocytes in culture was not observed. To examine regulation of selective uptake in vivo, hypocholesterolemia was induced in rats using either 4-aminopyrazolo[3,4-d]pyrimidine or 17 alpha-ethinyl estradiol. Rat HDL, doubly labeled in both the apoprotein A-I and cholesteryl ester moieties with intracellularly trapped tracers, were injected into untreated and treated rats. The plasma decay kinetics and the tissue sites of uptake were then determined. Hypocholesterolemia increased the plasma fractional catabolic rates of both tracers. Selective uptake was observed in tissues of treated rats that did not exhibit selective uptake in untreated rats (muscle, adipose tissue, and skin). Similarly, hypocholesterolemia increased the contribution of selective uptake to total HDL cholesteryl ester uptake by adrenal and ovary. In contrast, regulation of selective uptake by liver could not be demonstrated under these conditions. Thus, selective uptake of HDL cholesteryl esters can be regulated in extrahepatic tissues of rats in vivo and in vitro, suggesting a role for selective uptake in the maintenance of cholesterol homeostasis in these tissues.

Adenine↗

PubMed1994

Kunitz domain inhibitors of tissue factor-factor VIIa. II. Potent and specific inhibitors by competitive phage selection.

Active-site inhibitors of the human tissue factor-Factor VIIa complex (TF.FVIIa) that are both potent and specific have been selected from Alzheimer's amyloid beta-protein precursor inhibitor (APPI) Kunitz domain libraries using a strategy termed competitive phage selection. Phage display Libraries I-III, previously sorted by direct selection, were sorted by competitive selection against immobilized TF.FVIIa in which increasing amounts of Factor XIa (FXIa) were added to the selection buffer to remove phage with high affinity for FXIa. The most striking difference in the selected Kunitz domain sequences was at the P4' position where Lys was highly preferred instead of Leu which was found here by direct selection (Dennis, M. S., and Lazarus, R. A. (1994) J. Biol. Chem. 269, 22129-22136). In addition, both Lys and Arg were selected in the P1 position as opposed to Arg alone. A new library (Library IV) was constructed which contained all previously observed amino acids at 9 positions in the primary and secondary binding loops of APPI. Comparable results were obtained by sorting Library IV against immobilized TF.FVIIa in the presence of either FXIa alone or FXIa, plasma kallikrein, and plasmin. The Kunitz domains obtained by either competitive selection strategy potently inhibited TF.FVIIa, with Ki* values ranging from about 2 to 20 nM; the Ki* values were generally > 1 microM for FXIa and plasma kallikrein and ranged from 4 to 200 nM for plasmin. Variants selective for TF.FVIIa were assayed for free FVIIa and FXa inhibitory activity and characterized in coagulation assays. A rationale for the selection of Lys at both the P4' and P1 positions based upon comparison of sequences and structures of relevant serine proteases and inhibitors is presented.

Amino Acid Sequence↗

PubMed1996

[Autologous transplantation of hematopoietic precursor cells following CD34 selection].

Peripheral blood is increasingly used instead of bone marrow as a source of hemopoietic precursor cells for transplantation. The optimal technique still needs to be defined. Selection of CD34+ cells in transplant material may be of benefit in allogeneic and autologous peripheral blood precursor cell transplantation (PBPCT), since it allows elimination of unwanted CD34-negative cells, such as T-cells and contaminating tumor cells. We have evaluated the feasibility of CD34 selection in PB transplants and studied hemopoietic reconstitution after autologous transplantation of CD34 selected precursor cells. Between August 1994 and June 1995 CD34 selection was performed on 12 transplants for 9 patients with malignant disease (non-Hodgkin lymphoma [n = 5]; Ewing sarcoma [n = 1]; chronic lymphocytic leukemia [n = 1]; breast cancer [n = 1]; multiple myeloma [n = 1]). PBPC were collected with a Fenwall CS 3000 harvester after stimulation with G-CSF. For selection of CD34+ cells the Ceprate LC34 system (CellPro) was used. A median CD34 purity of 73% (range 40-94%) was achieved. The median number of CD34 positive cells per transplant was 4.8 x 10(6)/kg body weight (range 0.7-15.8). The median number of colony forming cells per transplant was 31 x 10(4)/kg body weight (range 1.5-131.3). For autologous PBPCT the minimal number of CD34 positive cells required in the transplantate was arbitrarily set at 1.0 x 10(6)/kg body weight. This number was achieved in 10 of the 12 transplants. The median loss of CD34+ cells during selection was 1.5 x 10(6)/kg body weight (range 0.2-6.4). In 2 patients the total number was reduced to below the critical value of 1.0 x 10(6)/kg. 7 of the 9 patients received the CD34 selected transplant after intensive chemotherapy and irradiation. The median follow-up time after PBPCT was 196 days (range 62-278). All 7 patients are now alive and with normal hemopoietic function. A granulocyte count above 0.5 x 10(9)/l and a platelet count above 20 x 10(9)/l was achieved on day 14 (median), and on day 19 after PBPCT. We conclude that CD34 selection is technically feasible and that CD34 selected cells can be used for PBPCT. The procedure is time consuming and expensive; it requires complex organization at laboratory level, and the benefit of CD34 selection with regard to T-cell depletion and tumor purging still needs to be proven. However, CD34+ selection is likely to open new perspectives in transplantation medicine.

Adolescent↗

PubMed1997

Measurement of glomerular charge selectivity in non-diabetic renal disease.

BACKGROUND: Until now, the renal clearance index of IgG to IgG4 (IgG/IgG4) as well as pancreatic to salivary amylase (PA/SA) were separately used as parameters of renal charge selectivity in diabetic and non-diabetic albuminuria. The suitability of the IgG index may be questioned because urinary loss of IgG rather reflects a size selective defect. In contrast, the amylase index seems more appropriate to reflect renal charge selectivity because its molecular size is comparable to albumin. We questioned whether IgG/IgG4 and PA/SA reflect renal charge selectivity in a comparable way in subjects with non-diabetic albuminuria over a wide range. METHODS: Renal fractional clearances of albumin, IgG, IgG4, PA and SA were estimated from ambulatory 24-h urine samples in 12 subjects with normo-albuminuria (UAE 4 [3-17] micrograms/min), six with micro-albuminuria (UAE: 147[36-200] micrograms/min), and 20 with macro-albuminuria (UAE: 2301 [608-13611] micrograms/min). RESULTS: Macro-albuminuria is associated with a reduced IgG/IgG4 and PA/SA, whereas micro-albuminuria is only associated with a reduced IgG/IgG4 compared to normo-albuminuria. A reduction of IgG/IgG4 (r = -0.75, P < 0.001) and PA/SA (r = -0.52, P < 0.001) correlates with an increased albuminuria. In addition, IgG/IgG4 correlates with PA/SA in the total population (r = 0.49, P < 0.01). IgG/IgG4 (r = 0.51, P < 0.05) correlates with the size selective index IgG/albumin in an opposite way to PA/SA (r = -0.52, P < 0.05) in 20 subjects with macro-albuminuria. Multiple regression analysis revealed IgG clearance to be the variable which contributes to the variance of albuminuria clearance for the greater part in our population. CONCLUSION: Both charge selective indices do not appear to correlate in micro-albuminuria. In addition, the presence of a size selective defect has a opposing effect on both charge selective indices. Although the reduction of IgG/IgG4 and PA/SA with increasing albuminuria suggests a progressive charge selective defect, albuminuria in our population is almost entirely explained by urinary loss of IgG. These data seriously question whether either one or both charge selective indices IgG/IgG4 and PA/SA do specifically reflect glomerular charge selectivity.

Adult↗

PubMed2000

Selective serotonin reuptake inhibitors versus tricyclic and heterocyclic antidepressants: comparison of drug adherence.

BACKGROUND: Selective serotonin reuptake inhibitors are thought to have better discontinuation rates (i.e. less people dropping out) than tricyclic and heterocyclic antidepressant drugs. It is important to quantify the drop-out rates of different antidepressant drugs in order to have a better understanding of the relative tolerability of these drugs. OBJECTIVES: To assess the comparative tolerability of selective serotonin reuptake inhibitors and tricyclic/heterocyclic antidepressant drugs. SEARCH STRATEGY: We searched the Cochrane Collaboration Depression, Anxiety and Neurosis Controlled Trials Registers (1997 to 1999), MEDLINE (1966 to 1999), EMBASE (1974 to 1999) We also searched specialist journals, the reference lists of relevant papers and previous systematic reviews, conference abstracts and government documents. Representatives of the pharmaceutical industry were contacted. SELECTION CRITERIA: Parallel group randomised controlled trials comparing selective serotonin reuptake inhibitors with tricyclic or heterocyclic antidepressants in people with depression. DATA COLLECTION AND ANALYSIS: Two reviewers independently extracted data and a third reviewer checked any cases of disagreement. MAIN RESULTS: We included 136 trials. The selective serotonin reuptake inhibitors showed less participants dropping out compared to the tricyclic/heterocyclic group (odds ratio 1.21, 95% confidence interval 1.12 to 1.30). A statistically significant difference was found in total drop-outs between the selective serotonin reuptake inhibitors and the old tricyclics as well as the newer tricyclics. When the selective serotonin reuptake inhibitors were compared to the heterocyclic antidepressants, there was a non significant difference favouring the selective serotonin reuptake inhibitors. The poor tolerability profile of the old tricyclics was explained by differences in drop-outs for side-effects, but not for inefficacy. REVIEWER'S CONCLUSIONS: Whilst selective serotonin reuptake inhibitors do appear to show an advantage over tricyclic drugs in terms of total drop-outs, this advantage is relatively modest. This has implications for pharmaco-economic models, some of which may have overestimated the difference of drop-out rates between selective serotonin reuptake inhibitors and tricyclic antdepressants. These results are based on short-term randomised controlled trials, and may not generalise into clinical practice.

Antidepressive Agents↗

PubMed1984

Kin groups and trait groups: population structure and epidemic disease selection.

A Monte Carlo simulation based on the population structure of a small-scale human population, the Semai Senoi of Malaysia, has been developed to study the combined effects of group, kin, and individual selection. The population structure resembles D.S. Wilson's structured deme model in that local breeding populations (Semai settlements) are subdivided into trait groups (hamlets) that may be kin-structured and are not themselves demes. Additionally, settlement breeding populations are connected by two-dimensional stepping-stone migration approaching 30% per generation. Group and kin-structured group selection occur among hamlets the survivors of which then disperse to breed within the settlement population. Genetic drift is modeled by the process of hamlet formation; individual selection as a deterministic process, and stepping-stone migration as either random or kin-structured migrant groups. The mechanism for group selection is epidemics of infectious disease that can wipe out small hamlets particularly if most adults become sick and social life collapses. Genetic resistance to a disease is an individual attribute; however, hamlet groups with several resistant adults are less likely to disintegrate and experience high social mortality. A specific human gene, hemoglobin E, which confers resistance to malaria, is studied as an example of the process. The results of the simulations show that high genetic variance among hamlet groups may be generated by moderate degrees of kin-structuring. This strong microdifferentiation provides the potential for group selection. The effect of group selection in this case is rapid increase in gene frequencies among the total set of populations. In fact, group selection in concert with individual selection produced a faster rate of gene frequency increase among a set of 25 populations than the rate within a single unstructured population subject to deterministic individual selection. Such rapid evolution with plausible rates of extinction, individual selection, and migration and a population structure realistic in its general form, has implications for specific human polymorphisms such as hemoglobin variants and for the more general problem of the tempo of evolution as well.

Communicable Diseases↗

PubMed2003

The contribution of ancestry, chance, and past and ongoing selection to adaptive evolution.

The relative contributions of ancestry, chance, and past and ongoing selection to variation in one adaptive (larval feeding rate) and one seemingly nonadaptive (pupation height) trait were determined in populations of Drosophila melanogaster adapting to either low or high larval densities in the laboratory. Larval feeding rates increased rapidly in response to high density, and the effects of ancestry, past selection and chance were ameliorated by ongoing selection within 15-20 generations. Similarly, in populations previously kept at high larval density, and then switched to low larval density, the decline of larval feeding rate to ancestral levels was rapid (15-20 generations) and complete, providing support for a previously stated hypothesis regarding the costs of faster feeding in Drosophila larvae. Variation among individuals was the major contributor to variation in pupation height, a trait that would superficially appear to be nonadaptive in the environmental context of the populations used in this study because it did not diverge between sets of populations kept at low versus high larval density for many generations. However, the degree of divergence among populations (F(ST)) for pupation height was significantly less than expected for a selectively neutral trait, and we integrate results from previous studies to suggest that the variation for pupation height among populations is constrained by stabilizing selection, with a flat, plateau-like fitness function that, consequently, allows for substantial phenotypic variation within populations. Our results support the view that the genetic imprints of history (ancestry and past selection) in outbreeding sexual populations are typically likely to be transient in the face of ongoing selection and recombination. The results also illustrate the heuristic point that different forms of selection-for example directional versus stabilizing selection-acting on a trait in different populations may often not be due to differently shaped fitness functions, but rather due to differences in how the fitness function maps onto the actual distribution of phenotypes in a given population. We discuss these results in the light of previous work on reverse evolution, and the role of ancestry, chance, and past and ongoing selection in adaptive evolution.

Adaptation, Physiological↗

PubMed2003

Bayesian analysis suggests that most amino acid replacements in Drosophila are driven by positive selection.

One of the principal goals of population genetics is to understand the processes by which genetic variation within species (polymorphism) becomes converted into genetic differences between species (divergence). In this transformation, selective neutrality, near neutrality, and positive selection may each play a role, differing from one gene to the next. Synonymous nucleotide sites are often used as a uniform standard of comparison across genes on the grounds that synonymous sites are subject to relatively weak selective constraints and so may, to a first approximation, be regarded as neutral. Synonymous sites are also interdigitated with nonsynonymous sites and so are affected equally by genomic context and demographic factors. Hence a comparison of levels of polymorphism and divergence between synonymous sites and amino acid replacement sites in a gene is potentially informative about the magnitude of selective forces associated with amino acid replacements. We have analyzed 56 genes in which polymorphism data from D. simulans are compared with divergence from a reference strain of D. melanogaster. The framework of the analysis is Bayesian and assumes that the distribution of selective effects (Malthusian fitnesses) is Gaussian with a mean that differs for each gene. In such a model, the average scaled selection intensity (gamma = N(e)s) of amino acid replacements eligible to become polymorphic or fixed is -7.31, and the standard deviation of selective effects within each locus is 6.79 (assuming homoscedasticity across loci). For newly arising mutations of this type that occur in autosomal or X-linked genes, the average proportion of beneficial mutations is 19.7%. Among the amino acid polymorphisms in the sample, the expected average proportion of beneficial mutations is 47.7%, and among amino acid replacements that become fixed the average proportion of beneficial mutations is 94.3%. The average scaled selection intensity of fixed mutations is +5.1. The presence of positive selection is pervasive with the single exception of kl-5, a Y-linked fertility gene. We find no evidence that a significant fraction of fixed amino acid replacements is neutral or nearly neutral or that positive selection drives amino acid replacements at only a subset of the loci. These results are model dependent and we discuss possible modifications of the model that might allow more neutral and nearly neutral amino acid replacements to be fixed.

Amino Acid Substitution↗