SEARCH · Search PubMed

Results for “Robustness”

Search indexed PubMed citations on genomics, clinical trials, systematic reviews and public health. Explore titles, authors and supplied subject terms, then open the PubMed record.

SourceResearch connectionFrom yearThrough year

Quote a phrase for an exact phrase match. Source license links do not imply unrestricted reuse.

At least 1,009 records · Page 56Linked to original sources

PubMed2002

Reverse engineering gene networks using singular value decomposition and robust regression.

We propose a scheme to reverse-engineer gene networks on a genome-wide scale using a relatively small amount of gene expression data from microarray experiments. Our method is based on the empirical observation that such networks are typically large and sparse. It uses singular value decomposition to construct a family of candidate solutions and then uses robust regression to identify the solution with the smallest number of connections as the most likely solution. Our algorithm has O(log N) sampling complexity and O(N(4)) computational complexity. We test and validate our approach in a series of in numero experiments on model gene networks.

Algorithms↗

PubMed2026

Origin flexibility governs robust ssDNA engagement by the DnaA initiator.

In model bacteria, initiation of chromosome replication requires engagement of single-stranded DNA by oligomers of the DnaA-family initiator assembled within the origin DNA. Although arrays of double-strand motifs recognized by DnaA are a general feature of the origins, the DnaA-binding single-strand elements are elucidated in only a limited number of species, and the mechanical principles governing their recognition remain elusive. Using the Alphaproteobacterium Caulobacter crescentus, we identify a previously uncharacterized GA-rich single-stranded element in the origin that directly engages DnaA oligomers and is essential for robust initiation. This element is positioned at a subkilobase distance from the DnaA oligomerization region and is brought into proximity through dynamic structural rearrangements. Moreover, DnaA oligomers exhibit an unexpectedly broad yet constrained capacity to accommodate single-stranded sequence variation. These findings provide the molecular basis for origin plasticity, highlighting how origins can diverge while preserving initiation logic.

DNA, Single-Stranded↗

PubMed2002

A robust and scalable microfluidic metering method that allows protein crystal growth by free interface diffusion.

Producing robust and scalable fluid metering in a microfluidic device is a challenging problem. We developed a scheme for metering fluids on the picoliter scale that is scalable to highly integrated parallel architectures and is independent of the properties of the working fluid. We demonstrated the power of this method by fabricating and testing a microfluidic chip for rapid screening of protein crystallization conditions, a major hurdle in structural biology efforts. The chip has 480 active valves and performs 144 parallel reactions, each of which uses only 10 nl of protein sample. The properties of microfluidic mixing allow an efficient kinetic trajectory for crystallization, and the microfluidic device outperforms conventional techniques by detecting more crystallization conditions while using 2 orders of magnitude less protein sample. We demonstrate that diffraction-quality crystals may be grown and harvested from such nanoliter-volume reactions.

Crystallization↗

PubMed1977

Robust nonlinear data smoothers: Definitions and recommendations.

Nonlinear data smoothers provide a practical method of finding smooth traces for data confounded with possibly long-tailed or occasionally "spikey" noise. While they are natural tools for analyzing time-series data, they can be applied to any data set for which a sequencing order can be established. Their resistance to the effects of unsupported extreme observations and their ability to respond rapidly to well-supported patterns make them valuable as tools for finding patterns not constrained to specific parametric form and as versatile data-cleaning algorithms. This paper defines some robust nonlinear smoothers that have performed well in Monte-Carlo trials and makes brief recommendations based upon that study.

Journal Article↗

PubMed1999

Neutral evolution of mutational robustness.

We introduce and analyze a general model of a population evolving over a network of selectively neutral genotypes. We show that the population's limit distribution on the neutral network is solely determined by the network topology and given by the principal eigenvector of the network's adjacency matrix. Moreover, the average number of neutral mutant neighbors per individual is given by the matrix spectral radius. These results quantify the extent to which populations evolve mutational robustness-the insensitivity of the phenotype to mutations-and thus reduce genetic load. Because the average neutrality is independent of evolutionary parameters-such as mutation rate, population size, and selective advantage-one can infer global statistics of neutral network topology by using simple population data available from in vitro or in vivo evolution. Populations evolving on neutral networks of RNA secondary structures show excellent agreement with our theoretical predictions.

Evolution, Molecular↗

PubMed2000

Circadian rhythms in Neurospora crassa: lipid deficiencies restore robust rhythmicity to null frequency and white-collar mutants.

The conidiation rhythm in the fungus Neurospora crassa is a model system for investigating the genetics of circadian clocks. Null mutants at the frq (frequency) locus (frq(9) and frq(10)) make no functional frq gene products and are arrhythmic under standard conditions. The white-collar strains (wc-1 and wc-2) are insensitive to most effects of light, and are also arrhythmic. All three genes are proposed to be central components of the circadian oscillator. We have been investigating two mutants, cel (chain-elongation) and chol-1 (choline-requirer), which are defective in lipid synthesis and affect the period and temperature compensation of the rhythm. We have constructed the double mutant strains chol-1 frq(9), chol-1 frq(10), chol-1 wc-1, chol-1 wc-2, cel frq(9), cel frq(10), and cel wc-2. We find that these double mutant strains are robustly rhythmic when assayed under lipid-deficient conditions, indicating that free-running rhythmicity does not require the frq, wc-1, or wc-2 gene products. The rhythms in the double mutant strains are similar to the cel and chol-1 parents, except that they are less sensitive to light. This suggests that the frq, wc-1, and wc-2 gene products may be components of a pathway that normally supplies input to a core oscillator to transduce light signals and sustain rhythmicity. This pathway can be bypassed when lipid metabolism is altered.

Cell Division↗

PubMed2000

A highly efficient and robust cell-free protein synthesis system prepared from wheat embryos: plants apparently contain a suicide system directed at ribosomes.

Current cell-free protein synthesis systems can synthesize proteins with high speed and accuracy, but produce only a low yield because of their instability over time. Here we describe the preparation of a highly efficient but also robust cell-free system from wheat embryos. We first investigated the source of the instability of existing systems in light of endogenous ribosome-inactivating proteins and found that ribosome inactivation by tritin occurs already during extract preparation and continues during incubation for protein synthesis. Therefore, we prepared our system from extensively washed embryos that are devoid of contamination by endosperm, the source of tritin and possibly other inhibitors. In a batch system, we observed continuous translation for 4 h, and sucrose density gradient analysis showed formation of large polysomes, indicating high protein synthesis activity. When the reaction was performed in a dialysis bag, enabling the continuous supply of substrates together with the continuous removal of small byproducts, translation proceeded for >60 h, yielding 1-4 mg of enzymatically active proteins, and 0.6 mg of a 126-kDa tobacco mosaic virus protein, per milliliter of reaction volume. Our results demonstrate that plants contain endogenous inhibitors of translation and that after their elimination the translational apparatus is very stable. This contrasts with the common belief that cell-free translation systems are inherently unstable, even fragile. Our method is useful for the preparation of large amounts of active protein as well as for the study of protein synthesis itself.

Cell-Free System↗

PubMed2000

The robustness of faecal steroid determination for pregnancy testing Kaimanawa feral mares under field conditions.

AIMS: To investigate the utility of faecal oestrone sulphate (OS) concentrations for detecting pregnancy in mares during behavioural studies of feral horses, in which the collection and preservation of samples is not immediate. METHODS: Oestrone sulphate concentrations were measured in fresh dung samples collected from 153 free-roaming Kaimanawa mares throughout the year. In addition, multiple samples were taken from the same pile to investigate the reliability of diagnosis from a single sample, as well as the influence of time until preservation on OS concentrations. Samples were also taken before and after a 10mm simulated rainfall event to test for dilution of OS concentrations by rain. Oestrone sulphate concentrations in all samples were measured using an enzyme immunoassay. RESULTS: From approximately 150 to 250 days of gestation, OS concentrations were consistently >80 ng/g in mares which subsequently foaled. Mares which did not foal and had low faecal OS concentrations in multiple samples throughout the year had faecal OS concentrations of 31+/-13 ng/g (mean+/-s.d.) with an upper 95% confidence limit of 57 ng/g. Mares sampled from 1 week before to 1 month after behavioural oestrus, and that did not foal in the previous and subsequent seasons, had OS concentrations of 37+/-32 ng/g (mean+/-s.d.) with an upper 95% confidence limit of 100 ng/g. The standard error of oestrone sulphate concentrations in multiple samples from the same dung pile ranged from 1 to 37% of the mean. This large within-pile variation, however, did not result in incorrect diagnoses from single samples unless mares were within 18 days of parturition. Keeping samples at ambient temperatures for up to 16 hours did not affect OS concentrations. Simulated rainfall caused a 17% mean reduction in OS concentrations, but did not change pregnancy diagnoses. CONCLUSIONS: Faecal OS concentrations >100 ng/g were indicative of pregnancy in Kaimanawa mares. For mares more than 150 days post-mating, OS concentrations <57 ng/g were indicative of non-pregnancy, while concentrations between 57 and 100 ng/g provided an inconclusive diagnosis. A single sample from each dung pile collected within 16 hours of defecation was sufficient to accurately diagnose pregnancy in mares 150-250 days post conception. CLINICAL RELEVANCE: Measurement of OS concentrations in dung samples was a reliable and robust indicator of pregnancy status in feral mares 150-250 days post mating. This corresponds approximately to the period from May to August, given the seasonal breeding pattern in this population. This method of determining pregnancy status is suitable for field use in behavioural and demographic studies of wild horse populations.

Journal Article↗

PubMed1983

A technique for promoting robust free recall in chronic organic amnesia.

A learning technique was developed for chronically amnesic subjects which linked word-list items in a novel manner utilizing ridiculously-imaged-stories (RIS). By the 8th week of once-weekly 45 minute training sessions with RIS the five amnesic subjects were able to freely recall an average of 14 items from a 20-item list after a 1-week interval, but showed minimal recall after the same interval of another 20-word list that had been concurrently learned in a cued, modified free-recall condition. The effective RIS technique producing this robust recall combines stimuli embedded in a novel-arousing context with high-imagery, storyline, cuing, and spaced repetition. The net effect of this technique is interpreted as providing artificial "chunks" that can be encoded and transferred relatively normally into long-term memory.

Adult↗

PubMed2001

An efficient, accurate and robust radiometer configuration for microwave temperature measurement for industrial and medical applications.

The theoretical and practical design of a type of microwave radiometer particularly suited to industrial and medical temperature measurement is described. The use of sequential switching of source and reference signals with synchronous demodulation of switched signal components gives an efficient and robust instrument configuration. The radiometer measures the true, matched-impedance effective temperature of the coupled source. Changes in noise-figure, gain or frequency response of the radiometer microwave amplification do not affect the temperature measurement. Practical microwave radiometers using this configuration can be simply calibrated, and have inherently stable calibration and excellent accuracy.

Engineering↗

PubMed1989

The need for a more robust ozone air quality standard.

The present National Ambient Air Quality Standard for ozone has many statistical problems, including use of extreme values which have inherent large fluctuations, a compliance test that can gradually lower the target of the design value below the standard level, and inconsistencies between the number-of-exceedances criterion and the design value. The above problems can be avoided or minimized by using a more robust statistic, such as the 95th percentile, and applying a statistical compliance test, without sacrificing the stringency of the standard. Analysis of EPA's ozone data shows that the annual 95th percentiles and their three-year means have less variability than the annual second highest values and the fourth highest values in three years, respectively. At t test for the mean of the annual 95th percentiles is proposed for compliance testing not only to preserve the averaging concept of the present standard, but also to take account of ozone concentration fluctuations in order to increase the stability of the compliance status of a site or a Metropolitan Statistical Area. A procedure is provided to adjust the level of the 95th-percentile standard so that the stringency of the present standard is preserved.

Air Pollutants, Occupational↗

PubMedDate not supplied

Levels of processing, transfer-appropriate processing, and the concept of robust encoding.

The theoretical status of levels of processing and its relation to the general principle of transfer-appropriate processing is discussed. One possible description of this relationship is that levels of processing has its effect by influencing the likelihood that the processing will prove to be transfer-appropriate. This transfer account of the levels effect is discussed in terms of the concept of robust encoding (Lockhart & Craik, 1990). Available evidence provides little support for any simple form of this concept, but a modified version is suggested as a possibility.

Cognition↗

PubMed2005

A robust and fast method of sampling and analysis of delta13C of dissolved inorganic carbon in ground waters.

The stable carbon isotopic composition of dissolved inorganic carbon (delta13C(DIC)) is traditionally determined using either direct precipitation or gas evolution methods in conjunction with offline gas preparation and measurement in a dual-inlet isotope ratio mass spectrometer. A gas evolution method based on continuous-flow technology is described here, which is easy to use and robust. Water samples (100-1500 microl depending on the carbonate alkalinity) are injected into He-filled autosampler vials in the field and analysed on an automated continuous-flow gas preparation system interfaced to an isotope ratio mass spectrometer. Sample analysis time including online preparation is 10 min and overall precision is 0.1 per thousand. This method is thus fast and can easily be automated for handling large sample batches.

Air Pollutants↗

PubMed2004

Murine gammaherpesvirus-68 elicits robust levels of interleukin-12 p40, but not interleukin-12 p70 production, by murine microglia and astrocytes.

Murine gammaherpesvirus-68 (gamma HV-68) is a tractable model to investigate the pathophysiology of human gammaherpesvirus infections, including Epstein-Barr virus (EBV). Herpesvirus infections are thought to play a role in the pathology of damaging, inflammatory diseases states of the central nervous system (CNS), such as multiple sclerosis. The ability of the host to mount a strong cell-mediated immune response is critical in determining the outcome of viral infections. Interleukin (IL)-12 is an important inflammatory cytokine that plays a pivotal role in the development of protective cell-mediated immune responses to viral infections. Given recent reports of associations between gammaherpesvirus infections and inflammatory disorders of the CNS, the authors investigated the ability of gamma HV-68 to induce the production of bioactive IL-12 in resident CNS cell types. In the present study, the authors demonstrate that gamma HV-68 infection is a potent stimulus for IL-12p40 production by murine microglia and astrocytes. However, despite the elevated expression of mRNA encoding IL-12p40 subunit, concomitant with robust secretion of IL-12p40 protein, gamma HV-68 failed to elicit the production of the bioactive IL-12p70 heterodimer. This failure did not result from an absence of T lymphocyte-derived signals or interactions between CNS cell types as determined by coculture studies. Taken together, these data suggest that the resident CNS cell types, astrocytes and microglia, are not significant sources of proinflammatory IL-12p70 in response to gammaherpesvirus infection. Indeed, the production of IL-12p40 may point to an anti-inflammatory role for these cells during herpesvirus infections of the CNS.

Animals↗

PubMed2002

Some objective measures indicative of perceived voice robustness in student teachers.

One of the problems confronted in the teaching profession is the maintenance of a healthy voice. This basic pedagogical tool is subjected to extensive use, and frequently suffers from overload, with some teachers having to give up their profession altogether. In some teacher training schools, it is the current practice to examine the student's voice, and to refer any perceived susceptibility to strain to voice specialists. For this study, a group of vocally healthy students were examined first at the teacher training schools, and then at the ENT clinic at the University Hospital of Nijmegen. The aim was to predict whether the subject's voice might be at risk for occupational dysphonia as a result of the vocal load of the teaching profession. We tried to find objective measures of voice quality in student teachers, used in current clinical practice, which reflect the judgements of the therapists and phoniatricians. We tried to explain such measures physiologically in terms of robustness of, and control over voicing. Objective measures used included video-laryngostroboscopy, phonetography and spectrography. Maximum phonation time, melodic range in conjunction with maximum intensity range, and the production of soft voice are suggested as possible predictive parameters for the risk of occupational voice strain.

Adolescent↗

PubMed2000

Robustness of the quartiles of survival time and survival probability.

A simulation study was undertaken to investigate the robustness of the quartiles of survival times, survival probability (when survival time was equal to the quartile), and regression coefficients in the presence of covariates [by comparing the estimated values under the correct model (Weibull) with those obtained under the assumed models, such as Weibull, exponential, loglogistic, Cox proportional hazards, and product-limit estimator] when the assumptions related to the underlying model were violated. Two simulation experiments were conducted: the first for when the underlying model was Weibull with no covariate, and the second for when the underlying model was Weibull with one continuous covariate. An evaluation of the objectives of this study was done utilizing a real data set from the Lung Cancer Study Group 771. The results for both simulation experiments were quite comparable and consistent. In general, the exponential model performed poorly in estimating the quartiles (except the median) and the survival probabilities. The loglogistic model and product-limit estimator performed reasonably well for lower quartile and median. For the upper quartile when the shape parameter was less than 1.5 the performance was poor. For the regression coefficients, the estimates for beta1 and beta2 were biased under exponential model and the estimate for mu was quite biased under the loglogistic model. The performance of the Cox model was quite reasonable and only when the shape parameter was 0.7, the amount of bias for beta2 was slightly more than 10%. The results for the real data and the simulated data were comparable, which demonstrates the real application of this study.

Bias↗

PubMed2001

Robust estimators of the concordance correlation coefficient.

This paper proposes a generalized version of Lin' s concordance correlation coefficient for the agreement assessment of continuous data. Lin's coefficient evaluates the accuracy and precision between two measures, and is based on the expected value of the squared distance function. We generalize Lin's coefficient, apply alternative distance functions, and produce more robust versions of the concordance correlation coefficient. In this paper, we develop the asymptotic theory for this class of estimators, investigate small-sample properties via computer simulation, and demonstrate their use with two real data examples.

Algorithms↗

PubMed2002

Robust estimation of the median lethal dose.

Alternatives to M-estimation for robust estimation of the median lethal dose in biological assays are developed. A class of link functions based on the Student-t distribution is proposed, where degrees of freedom are estimated from the data by maximum likelihood. Other alternatives include slash and finite mixture distributions. For bioassays from a pharmaceutical company, these methods extend the standard probit and logistic models, as well as the Huber's M-estimator. They are also applied to several standard examples from the literature.

Animals↗