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The origin of multiple B mating specificities in Coprinus cinereus.

Mushrooms, such as Coprinus cinereus, possess large families of pheromones and G-protein-coupled receptors that are sequestered at the B mating-type locus and whose function is to confer vast numbers of different mating types. This ability results from complex patterns of cognate and noncognate pheromone/receptor pairings, which potentially offer a unique insight into the molecular interaction between receptor and ligand. In this study we have identified many more members of these families by molecular analysis of strains collected worldwide. There are three groups of genes at each B locus. We have identified two alleles of group 1, five alleles of group 2, and seven alleles of group 3, encoding in total 14 different receptors and 29 different pheromones. The specificity of many newly identified alleles was determined by transformation analysis. One striking finding was that receptors fall into groups based on sequence homology but these do not correspond to the groups defined by position, indicating that complex evolutionary processes gave rise to the B loci. While additional allelic versions may occur in nature, the number of B specificities possible by combination of the alleles that we describe is 70, close to previous estimates based on population analysis.

Alleles↗

Optimal conditional error functions for the control of conditional power.

Ethical considerations and the competitive environment of clinical trials usually require that any given trial have sufficient power to detect a treatment advance. If at an interim analysis the available data are used to decide whether the trial is promising enough to be continued, investigators and sponsors often wish to have a high conditional power, which is the probability to reject the null hypothesis given the interim data and the alternative of interest. Under this requirement a design with interim sample size recalculation, which keeps the overall and conditional power at a prespecified value and preserves the overall type I error rate, is a reasonable alternative to a classical group sequential design, in which the conditional power is often too small. In this article two-stage designs with control of overall and conditional power are constructed that minimize the expected sample size, either for a simple point alternative or for a random mixture of alternatives given by a prior density for the efficacy parameter. The presented optimality result applies to trials with and without an interim hypothesis test; in addition, one can account for constraints such as a minimal sample size for the second stage. The optimal designs will be illustrated with an example, and will be compared to the frequently considered method of using the conditional type I error level of a group sequential design.

Biometry↗

Mycophenolate mofetil reduces the risk of acute rejection less in African-American than in Caucasian kidney recipients.

BACKGROUND: Multicenter clinical trials have shown that mycophenolate mofetil (MMF) reduces the risk of acute rejection, but it is unknown whether African-Americans constitute a subgroup of recipients less likely to benefit from MMF. METHODS: This study compared the acute rejection rates within 6 months of kidney transplantation in MMF-treated transplant patients with those on azathioprine (AZA) at a single center. The study population consisted of 353 consecutive recipients of cadaver or living donor kidney transplants. African-Americans constituted 43% of the patients on AZA and 49% of the patients on MMF. Variables used in a Cox regression analysis included MMF immunosuppression, recipient race, type of transplant, delayed graft function, postoperative immune induction, average cyclosporine trough level, and HLA mismatch. RESULTS: Significantly fewer patients on MMF experienced a biopsy-proven rejection episode than those treated with AZA (24% vs. 42%, respectively; relative risk [RR]=0.57, P=0.001). This decrease in risk was greater in Caucasian transplant recipients (MMF vs. AZA: 16% vs. 46%, RR=0.35, P < 0.001) than in African-American patients (32% vs. 36%, RR=0.88, P=0.6). Within each race stratum, the mean cyclosporine trough levels averaged over 2-week intervals were nearly identical for AZA- compared with MMF-treated patients. In the regression model, the effect of MMF on the incidence of rejection was again less in African-American than in Caucasian patients. CONCLUSIONS: Kidney recipients treated with MMF have a significantly lower risk of acute rejection within 6 months of transplantation than those given AZA. This reduction in risk is significantly less in African-American recipients than Caucasians.

Adult↗

Retrospective risk analysis for early heart-related death after cardiomyoplasty. The Worldwide Cardiomyoplasty Group.

BACKGROUND: Dynamic cardiomyoplasty is an evolving treatment for heart failure that uses an electrically stimulated latissimus dorsi muscle wrapped around the heart to improve cardiac function. Preoperative patient characteristics and deaths after cardiomyoplasty have been recorded during the past 5 years in a cumulative database representing worldwide experience of 42 medical centers. METHODS: Statistical models of hazards (monthly death rates) were used to identify risk factors for transiently increased risk of cardiovascular mortality within 2 months after cardiomyoplasty. RESULTS: Actuarial survival (n = 261) was 88%, 80%, and 76% at 1, 3, and 6 months after cardiomyoplasty, respectively. The peak hazard of 6% dying per month occurred during the first month after the surgical procedure. Lower ejection fraction, increased number of major coronary arteries with > or = 70% stenotic lesions, and lower chronotropic responses during exercise were independent risk factors for the transient increase in early cardiovascular mortality. Early risk of cardiovascular mortality was significantly reduced as centers gained experience with more than 3 patients. CONCLUSION: Early survival after cardiomyoplasty has improved with experience and might be reduced further by preoperative assessments that identify patients at highest risk.

Actuarial Analysis↗

Time-domain quantitation of 1H short echo-time signals: background accommodation.

Quantitation of 1H short echo-time signals is often hampered by a background signal originating mainly from macromolecules and lipids. While the model function of the metabolite signal is known, that of the macromolecules is only partially known. We present time-domain semi-parametric estimation approaches based on the QUEST quantitation algorithm (QUantitation based on QUantum ESTimation) and encompassing Cramér-Rao bounds that handle the influence of 'nuisance' parameters related to the background. Three novel methods for background accommodation are presented. They are based on the fast decay of the background signal in the time domain. After automatic estimation, the background signal can be automatically (1) subtracted from the raw data, (2) included in the basis set as multiple components, or (3) included in the basis set as a single entity. The performances of these methods combined with QUEST are evaluated through extensive Monte Carlo studies. They are compared in terms of bias-variance trade-off. Because error bars on the amplitudes are of paramount importance for diagnostic reliability, Cramér-Rao bounds accounting for the uncertainty caused by the background are proposed. Quantitation with QUEST of in vivo short echo-time (1)H human brain with estimation of the background is demonstrated.

Brain↗

The influence of pulmonary function testing on the management of asthma in children.

OBJECTIVE: To assess how often in a single encounter that pulmonary function tests (PFTs) influenced management decisions in children with asthma, beyond what was obtained from history and physical examination alone. STUDY DESIGN: Children with asthma (n = 367, age 4 to 18 years) performed spirometry before clinical evaluation. Physicians and nurse practitioners in the outpatient pulmonary office evaluated the children and made initial treatment recommendations before reviewing the spirometry results. Any changes based on the test results were documented. RESULTS: Spirometry was abnormal in 45% of the visits, related to underlying asthma severity but not to clinical findings. PFT results changed management decisions in 15% of visits. This frequency was not affected by the patient's age, disease severity, symptom control, or exam findings. When spirometry did not change treatment decisions, the provider was more likely to maintain therapy (58%) than to increase (17%) or decrease (24%) therapy. In contrast, when spirometry did change treatment decisions, the provider was more likely to increase therapy (75%) than to maintain (20%) or decrease (5%) therapy. CONCLUSION: Without PFTs, providers often overestimated the degree of asthma control. This incorrect assessment could have resulted in suboptimal therapy.

Adolescent↗

Evaluation of shunt malfunction using shunt site reservoir.

OBJECTIVE: To determine the usefulness of a separate reservoir placed at the site of the shunt in evaluation of shunt malfunction. METHODS AND MATERIALS: A ventricular catheter was placed alongside the proximal catheter of the shunt and connected to a subgaleal reservoir in 17 patients, in 9 a double-lumen catheter with integrated reservoir and in 13 patients a dual catheter with a double-port reservoir was used. At presentation of suspected shunt malfunction, a standard shunt function evaluation using shunt tap, CT scan or shunt injection was performed, and subsequently, the pressure from the tap of the reservoir was obtained. RESULTS: Thirty-three patients presented with symptoms of malfunction at an interval of 2.3 +/- 3 months (range 2-429 days). The pretest probability of shunt malfunction in this population was 73%. Posttest probability of shunt malfunction was 82.5% with standard evaluation and improved to 100% by the separate reservoir tap pressure measurement. In 4 patients in whom the shunt tap was dry, shunt infection was diagnosed prior to revision using CSF obtained at the reservoir tap. In 5 patients with proximal malfunction and bradycardia, the reservoir tap allowed early ventricular decompression. CONCLUSION: This study shows that a reservoir placed at the site of the shunt remains patient even when the shunt malfunctions, suggesting that flow rather than catheter position is important in proximal malfunction. It is superior to shunt tap for detection of shunt malfunction and infection, and it allows early ventricular decompression in a sick patient awaiting surgery for shunt revision.

Adolescent↗

Health and functional status of adult recipients 1 year after allogeneic haematopoietic stem cell transplantation.

Increasing numbers of patients are surviving after allogeneic haematopoietic stem cell transplantation (SCT). Among these patients, a number of late complications have been described but few data on the risk factors of these long-term effects of SCT are available. We report the analysis on 105 adult patients, surviving free of haematological disease at a median time of 15 months after SCT. At the time of screening, 52% had returned to work, general health status was normal in 67% and 47% were sexually active. Female patient gender odds ratio (OR) 2.9 (P = 0.01) and age > 25 years (OR = 3.2, P = 0.02) were associated with non-return to work. Decreased general status was associated with chronic graft-versus-host disease (GvHD) (OR = 3.2, P = 0.009) and irradiation (OR = 3.6, P = 0.004). Sexual inactivity was associated with younger age (OR = 7.0, P = 0.0002) and chronic GvHD (OR = 3.3, P = 0.006). Risk factors for altered pulmonary function tests included previous smoking habits, irradiation and chronic GvHD. Obstructive lung disease was associated with a previous history of asthma. Sicca syndrome and conjunctivitis were increased in patients with previous acute GvHD and cataracts were less frequent in patients with aplastic anaemia. Persistent impaired hair re-growth was less frequent in patients who received irradiation (OR = 0.18, P = 0.002) but increased in patients with previous acute GvHD (OR = 5.3, P = 0.007). Microalbuminuria was more frequent in irradiated patients (OR = 9.4, P = 0.05). Raised cholesterol was associated with age (OR = 20.8, P < 0.001), previous acute GvHD (OR = 4.7, P = 0.03), steroid use (OR = 6.3, P = 0.001) and familial hypercholesterolaemia (OR = 4.4, P = 0.04). Decreased bone density was associated with chronic GvHD (OR = 3.9, P = 0.001). Thus, using routine tests in adult patients we were able to detect significant numbers of-non-symptomatic complications enabling early treatment.

Acute Disease↗

"Click test": rapid diagnosis of the respiratory distress syndrome.

Appropriate and early treatment with exogenous surfactant has clinical and economic benefits for neonates with pulmonary surfactant deficiency. In order to rapidly and reliably identify such neonates, we have evaluated the shake and click tests, biophysical tests of surfactant function, using 0.2 mL samples of tracheal (TA) and gastric aspirates (GA). Samples from 181 neonates with a gestational age range of 24-40 weeks were shaken with 95% ethanol. If bubbles formed (positive shake test) they were examined in air-free water under a microscope. In a positive shake or click test, the bubbles rhythmically increase and then decrease in size, denoting the presence of active surfactant. The probability of the tests to predict clinical surfactant deficiency was analyzed. The latter was defined as respiratory distress syndrome or transient tachypnea of the newborn diagnosed by chest radiography and clinical criteria. The click test on TA from preterm infants was most accurate, with a 100% positive predictive value and specificity, and a 93% and 94% negative predictive value and sensitivity respectively. These values for GA were 73%, 84%, 97%, and 95%, respectively. The test is quick, simple, inexpensive, reproducible, and unaffected by contamination with blood. The accuracy of this test on TA in diagnosing surfactant deficiency in neonates would permit early and optimal treatment with exogenous surfactant. When performed on GA, the test could aid decisions regarding transfer of neonates to tertiary level care.

Biophysical Phenomena↗

Incorporating HIV test data into forecasts of the AIDS epidemic in Scotland.

For AIDS cases in Scotland the date of HIV antibody positive diagnosis (HIV test date) is recorded on the AIDS case reports. Data are also available on the total numbers of individuals with HIV positive test reports in Scottish laboratories in each year since testing became available. These data are incorporated into a model of the HIV epidemic described in terms of testing rates by calendar year. The HIV infection curve is modelled as a step function, and the testing rates are allowed to differ between steps. Results are presented for intravenous drug users (IDUs) and for homosexual/bisexual men. The estimated rates of testing for the IDUs (estimates from 19 per cent to 44 per cent per year) are considerably higher than those for homosexual/bisexual men (estimates of 10 per cent to 17 per cent per year). Data on the year of testing for AIDS diagnoses gave relatively little improvement in estimates of the HIV infection curve. However, when this information is combined with data on the total number of HIV positive diagnoses per year, there is a dramatic improvement in the estimate of the HIV infection curve. This is particularly marked for infections in the most recent period and for the estimates of cumulative infections up to the present. However, these improvements are gained at the cost of assumptions of similar testing rates applying to all sections of the HIV infected populations, which will be difficult to check in practice. This suggests that these methods should not be used in isolation but in combination with other evidence about the spread of HIV infection in a population.

Acquired Immunodeficiency Syndrome↗

An episode of accelerated amino acid change in Drosophila esterase-6 associated with a change in physiological function.

In most lineages of the subgenus Sophophora esterase-6 is a homodimeric haemolymph protein. In the melanogaster subgroup of species it has become a monomer which is mainly expressed in the male sperm ejaculatory duct. Our analyses of esterase-6 sequences from three melanogaster subgroup species and two close relatives reveal a brief period of accelerated amino acid sequence change during the transition between the ancestral and derived states. In this period of 2-6Myr the ratio of replacement to silent site substitutions (0.51) is about three times higher than the values in other lineages of the phylogeny. There are about 50 more replacements in this period than would be predicted from the ratios of replacement to silent site substitutions found elsewhere in the phylogeny. Modelling on the known structure of a related acetylcholinesterase suggests that an unusually high proportion of the replacements in the transitional branch are non-conservative changes on the protein surface. Up to half the accelerated replacement rate can be accounted for by clusters of changes to the face of the molecule containing the opening of the active site gorge. This includes changes in and around regions homologous to peripheral substrate binding sites in acetylcholinesterase. There are also three changes in glycosylation status. One region predicted to lie on the protein surface which becomes markedly more hydrophilic is proposed to be the ancestral dimerisation site that is lost in the transitional branch.

Amino Acid Sequence↗

Use of decision analysis in planning a management strategy for the stage N0 neck.

OBJECTIVE: There are three major strategies in the treatment of patients with a stage N0 neck with squamous cell cancer of the head and neck: elective neck dissection, elective neck irradiation, and observation. Each has appropriate salvage strategies in the event of local recurrence. We used decision analysis to determine the optimal strategy for neck treatment as a function of the probability of occult cervical metastasis. DATA SOURCES: We used the bibliographies of current articles and books to access clinical studies of patients with stage N0 neck cancer. STUDY SELECTION: Studies that included large numbers of patients and contained a minimum 2-year follow-up, with results analyzed in terms of outcome as a function of stage of neck disease, were included. DATA EXTRACTION: Specific data points were extracted from the studies independently by multiple observers, and mean values were used in the decision analysis. DATA SYNTHESIS: A decision tree was constructed with use of a computer model to compare the three management strategies. Probabilities of each of the possible events depicted in the trees were inserted into the tree structure. These probabilities were gleaned from the literature as described above. A sensitivity analysis was performed to determine the optimal threshold for treatment of the neck. CONCLUSION: A patient with primary squamous cell carcinoma of the head and neck and stage N0 neck status should be observed if the probability of occult cervical metastasis is less than 20%. If the probability is greater than 20%, treatment of the neck is warranted. The treatment plan should ideally involve a single modality of therapy; both neck dissection and radiation therapy are quite efficacious in the clinical context, and the decision of which one to employ should be driven by the treatment of the primary lesion. Decision analysis is useful in complex clinical situations.

Carcinoma, Squamous Cell↗

Urochordate betagamma-crystallin and the evolutionary origin of the vertebrate eye lens.

A refracting lens is a key component of our image-forming camera eye; however, its evolutionary origin is unknown because precursor structures appear absent in nonvertebrates. The vertebrate betagamma-crystallin genes encode abundant structural proteins critical for the function of the lens. We show that the urochordate Ciona intestinalis, which split from the vertebrate lineage before the evolution of the lens, has a single gene coding for a single domain monomeric betagamma-crystallin. The crystal structure of Ciona betagamma-crystallin is very similar to that of a vertebrate betagamma-crystallin domain, except for paired, occupied calcium binding sites. The Ciona betagamma-crystallin is only expressed in the palps and in the otolith, the pigmented sister cell of the light-sensing ocellus. The Ciona betagamma-crystallin promoter region targeted expression to the visual system, including lens, in transgenic Xenopus tadpoles. We conclude that the vertebrate betagamma-crystallins evolved from a single domain protein already expressed in the neuroectoderm of the prevertebrate ancestor. The conservation of the regulatory hierarchy controlling betagamma-crystallin expression between organisms with and without a lens shows that the evolutionary origin of the lens was based on co-option of pre-existing regulatory circuits controlling the expression of a key structural gene in a primitive light-sensing system.

Amino Acid Sequence↗

Pharmacokinetic parameter estimations by minimum relative entropy method.

For estimating pharmacokinetic parameters, we introduce the minimum relative entropy (MRE) method and compare its performance with least squares methods. There are several variants of least squares, such as ordinary least squares (OLS), weighted least squares, and iteratively reweighted least squares. In addition to these traditional methods, even extended least squares (ELS), a relatively new approach to nonlinear regression analysis, can be regarded as a variant of least squares. These methods are different from each other in their manner of handling weights. It has been recognized that least squares methods with an inadequate weighting scheme may cause misleading results (the "choice of weights" problem). Although least squares with uniform weights, i.e., OLS, is rarely used in pharmacokinetic analysis, it offers the principle of least squares. The objective function of OLS can be regarded as a distance between observed and theoretical pharmacokinetic values on the Euclidean space RN, where N is the number of observations. Thus OLS produces its estimates by minimizing the Euclidean distance. On the other hand, MRE works by minimizing the relative entropy which expresses discrepancy between two probability densities. Because pharmacokinetic functions are not density function in general, we use a particular form of the relative entropy whose domain is extended to the space of all positive functions. MRE never assumes any distribution of errors involved in observations. Thus, it can be a possible solution to the choice of weights problem. Moreover, since the mathematical form of the relative entropy, i.e., an expectation of the log-ratio of two probability density functions, is different from that of a usual Euclidean distance, the behavior of MRE may be different from those of least squares methods. To clarify the behavior of MRE, we have compared the performance of MRE with those of ELS and OLS by carrying out an intensive simulation study, where four pharmaco-kinetic models (mono- or biexponential, Bateman, Michaelis-Menten) and several variance models for distribution of observation errors are employed. The relative precision of each method was investigated by examining the absolute deviation of each individual parameter estimate from the known value. OLS is the best method and MRE is not a good one when the actual observation error magnitude conforms to the assumption of OLS, that is, error variance is constant, but OLS always behaves poorly with the other variance models. On the other hand, MRE performs better than ELS and OLS when the variance of observation is proportional to its mean. In contrast, ELS is superior to MRE and OLS when the standard deviation of observation is proportional to its mean. In either case the difference between MRE and ELS is relatively small. Generally, the performance of MRE is comparable to that of ELS. Thus MRE provides as reliable a method as ELS for estimating pharmacokinetic parameters.

Humans↗

Tertiary trisomics in the garden pea as a model of B chromosome evolution in plants.

It is hypothesized that, in plants, genetically empty B chromosomes may originate from the extra chromosome (E) of tertiary trisomics if (i) the region of basic chromosomes homologous to the E (H-region) harbors a sporophytic lethal covered by the wild-type allele in E, and (ii) crossing-over between E and the H-region is suppressed. Under these conditions, most loss-of-function mutations occurring in the H-region are deleterious for haploid gametophytes, whereas those occurring in E are neutral or advantageous for hyperploid (n+1) gametophytes. As a result, natural selection at the gametophyte level can lead to the degeneration of E, leaving the H-region intact. Using Hammarlund translocation T(3-6)a, we synthesized two trisomic lines of the garden pea (Pisum sativum L.), where E was composed of the short arms of chromosomes 3 and 6 and the H-region carried recessive markers. In the trisomic line TRIS, we found few crossovers between E and the H-region. In the trisomic line TRUST, obtained after a change of basic chromosome constitution, recombination in this region was completely suppressed. After induction in the H-region of TRUST of a recessive sporophytic mutation rmv, two 15-chromosome lines of stable trisomics were established. One of them passed 11 generations, having produced more than 6000 individuals, all of them trisomic, and E remained present as a single element with no pairing partners. No tetrasomics were detected in these lines. If such trisomics occurred in nature, their extra chromosomes are likely to become a B chromosome.

Chromosomes, Plant↗

Optimized mixed Markov models for motif identification.

BACKGROUND: Identifying functional elements, such as transcriptional factor binding sites, is a fundamental step in reconstructing gene regulatory networks and remains a challenging issue, largely due to limited availability of training samples. RESULTS: We introduce a novel and flexible model, the Optimized Mixture Markov model (OMiMa), and related methods to allow adjustment of model complexity for different motifs. In comparison with other leading methods, OMiMa can incorporate more than the NNSplice's pairwise dependencies; OMiMa avoids model over-fitting better than the Permuted Variable Length Markov Model (PVLMM); and OMiMa requires smaller training samples than the Maximum Entropy Model (MEM). Testing on both simulated and actual data (regulatory cis-elements and splice sites), we found OMiMa's performance superior to the other leading methods in terms of prediction accuracy, required size of training data or computational time. Our OMiMa system, to our knowledge, is the only motif finding tool that incorporates automatic selection of the best model. OMiMa is freely available at 1. CONCLUSION: Our optimized mixture of Markov models represents an alternative to the existing methods for modeling dependent structures within a biological motif. Our model is conceptually simple and effective, and can improve prediction accuracy and/or computational speed over other leading methods.

Algorithms↗

Positive selection on MMP3 regulation has shaped heart disease risk.

BACKGROUND: The evolutionary forces of mutation, natural selection, and genetic drift shape the pattern of phenotypic variation in nature, but the roles of these forces in defining the distributions of particular traits have been hard to disentangle. To better understand the mechanisms contributing to common variation in humans, we investigated the evolutionary history of a functional polymorphism in the upstream regulatory region of the MMP3 gene. This single base pair insertion/deletion variant, which results in a run of either 5 or 6 thymidines 1608 bp from the transcription start site, alters transcription factor binding and influences levels of MMP3 mRNA and protein. The polymorphism contributes to variation in arterial traits and to the risk of coronary heart disease and its progression. RESULTS: Phylogenetic and population genetic analysis of primate sequences indicate that the binding site region is rapidly evolving and has been a hot spot for mutation for tens of millions of years. We also find evidence for the action of positive selection, beginning approximately 24,000 years ago, increasing the frequency of the high-expression allele in Europe but not elsewhere. Positive selection is evident in statistical tests of differentiation among populations and haplotype diversity within populations. Europeans have greater arterial elasticity and suffer dramatically fewer coronary heart disease events than they would have had this selection not occurred. CONCLUSIONS: Locally elevated mutation rates and strong positive selection on a cis-regulatory variant have shaped contemporary phenotypic variation and public health.

Animals↗

A non-parametric framework for estimating threshold limit values.

BACKGROUND: To estimate a threshold limit value for a compound known to have harmful health effects, an 'elbow' threshold model is usually applied. We are interested on non-parametric flexible alternatives. METHODS: We describe how a step function model fitted by isotonic regression can be used to estimate threshold limit values. This method returns a set of candidate locations, and we discuss two algorithms to select the threshold among them: the reduced isotonic regression and an algorithm considering the closed family of hypotheses. We assess the performance of these two alternative approaches under different scenarios in a simulation study. We illustrate the framework by analysing the data from a study conducted by the German Research Foundation aiming to set a threshold limit value in the exposure to total dust at workplace, as a causal agent for developing chronic bronchitis. RESULTS: In the paper we demonstrate the use and the properties of the proposed methodology along with the results from an application. The method appears to detect the threshold with satisfactory success. However, its performance can be compromised by the low power to reject the constant risk assumption when the true dose-response relationship is weak. CONCLUSION: The estimation of thresholds based on isotonic framework is conceptually simple and sufficiently powerful. Given that in threshold value estimation context there is not a gold standard method, the proposed model provides a useful non-parametric alternative to the standard approaches and can corroborate or challenge their findings.

Air Pollutants, Occupational↗