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PubMed2004

NMRShiftDB -- compound identification and structure elucidation support through a free community-built web database.

Compound identification and support for computer-assisted structure elucidation via a free community-built web database for organic structures and their NMR data is described. The new database NMRShiftDB is available on . As the first NMR database, NMRShiftDB allows not only open access to the database but also open and peer reviewed submission of datasets, enabling the natural products community to build its first free repository of assigned 1H and 13C NMR spectra. In addition to the open access, the underlying database software is built solely from free software and is available under an open source license. This allows collaborating laboratories to fully replicate the database and to create a highly available network of NMRShiftDB mirrors. The database contains about 10,000 structures and assigned spectra, with new datasets constantly added. Its functionality includes (sub-) spectra and (sub-) structure searches as well as shift prediction of 13C spectra based on the current database material.

Databases, Factual↗

PubMed2005

SAGE and the quantitative analysis of gene expression in parasites.

The nature of an organism is defined by the genes that it expresses. Genome- and expressed-sequence-tag (EST) sequencing projects are underway for many of the major parasites of humans and animals. These provide essential datasets that delineate the genes present in an organism and, in the case of ESTs, some quantitative information on gene expression. The temporal and quantitative analysis of gene expression is essential to fully exploit these datasets and define the biology of the parasite at the molecular level. Here, we discuss the application of serial analysis of gene expression (SAGE) for this purpose. SAGE is a technique that allows the rapid, quantitative analysis of thousands of transcripts. It complements microarray analysis with the advantage that it is affordable for standard laboratories. It provides a platform to define complete metabolic pathways and has been applied to study responses to drug treatment and the molecular events that are associated with arrested larval development.

Animals↗

PubMed2005

An intergenerational and lifecourse study of health and mortality risk in parents of the 1958 birth cohort: (I) methods and tracing.

OBJECTIVES: This paper describes the methods used to obtain information on mortality and cancer registrations for the parents of the British 1958 birth cohort, in order to create a dataset that can be used to examine intergenerational relationships on health and growth. STUDY DESIGN: Intergenerational cohort study. METHODS: The 1958 cohort includes all births occurring during 1 week in March 1958 in England, Scotland and Wales. For more than four decades of follow-up, information has been collected on cohort members, their parents and children. Information on the National Health Service (NHS) numbers of the parents was not available, but other details were collated for the Office for National Statistics to trace and flag the biological parents of the cohort members. RESULTS: Tracing was successful in 90.2% of fathers (n = 14,334) and 94.9% of mothers (n = 15,076). The greatest success was achieved for parents in families where there was no indication for additional mother or father figures until the child was 16 years old (96.6% of the mothers traced, n = 14,274; 94.3% of the fathers traced, n = 13,256). Tracing rates were lower than average in unmarried mothers (59%) and for the small group who were separated, widowed or divorced in 1958 (81%); the rates were particularly poor for the corresponding fathers (24.4 and 54.7%, respectively). There were only small variations in tracing rates between different regions of Britain. CONCLUSIONS: The tracing rates achieved were generally very high despite the lack of NHS number, especially where there was family stability throughout the childhood of cohort members. Parental status will need to be considered in future studies. With the high tracing rates achieved, the dataset provides an important resource with which to evaluate multigenerational associations with health and development in parents, their offspring and grandchildren.

Adolescent↗

PubMedDate not supplied

Computational systems analysis of developmental toxicity: design, development and implementation of a Birth Defects Systems Manager (BDSM).

Birth defects and developmental disabilities remain an important public health issue worldwide. With the availability of genomic sequences from a growing number of human and model organisms and the rapid expansion of the public repositories holding large-scale gene expression datasets, a computational systems analysis of developmental toxicology can incorporate this vast digital information toward the realization of predictive models for complex disease. Here we describe the initial design, development and implementation of a Birth Defects Systems Manager (BDSM). The project was motivated by the need for a computational-bioinformatics infrastructure to manage vast digital information from functional genomics and for a new knowledge environment specifically engineered for the analysis of developmental processes and toxicities. Proof-of-concept tested BDSM using meta-analysis of gene expression data collected from different laboratories, technology platforms, and study models. The composite dataset incorporated 232 microarray comparisons of RNA samples by single or dual microarray platforms, cDNA or oligonucleotide based probes, and human or mouse sequence information. Preliminary results identified system-level features in the embryonic transcriptome as it reacted to various developmental-teratological stimuli. BDSM is open access through the worldwide web (http://systemsanalysis.louisville.edu/) and can be integrated with other bioinformatics tools and resources to advance the pace of discovery in birth defects research.

Animals↗

PubMed2004

Physico-chemical controls on phosphorus cycling in two lowland streams. Part 1 -- the water column.

This paper investigates phosphorus (P) transport and transformation dynamics in two contrasting sub-catchments of the River Kennet, England. Samples were collected daily under baseflow and hourly under stormflow conditions using autosamplers for 2 years and analysed for a range of determinands (full P fractionation, suspended sediment (SS), cations, pH, alkalinity, temperature and oxygen). Concentrations of SRP, SUP, PP and SS were higher in the flashy River Enborne (means of 0.186, 0.071, 0.101 and 34 mg l(-1), respectively) than the groundwater-fed River Lambourn (0.079, 0.057, 0.028 and 9 mg l(-1), respectively). A seasonal trend in the daily P dataset was evident, with lower concentrations during intermediate flows and the spring (caused by a dilution effect and macrophyte uptake) than during baseflow conditions. However, in the hourly P dataset, highest concentrations were observed during storm events in the autumn and winter (reflecting higher scour with increased capacity to entrain particles). Storm events were more significant in contributing to the total P load in the River Enborne than the River Lambourn, especially during August to October, when dry antecedent conditions were observed in the catchment. Re-suspension of P-rich sediment that accumulated within the channel during summer low flows might account for these observations. It is suggested that a P-calcite co-precipitation mechanism was operating during summer in the River Lambourn, while adsorption by metal oxyhydroxide groups was an important mechanism controlling P fractionation in the River Enborne. The influence of flow conditions and channel storage/release mechanisms on P dynamics in these two lowland rivers is assessed.

Journal Article↗

PubMed2006

90Sr in fish: a review of data and possible model approach.

Data on the relationship between the equilibrium concentration factor of (90)Sr in fish and concentration of Ca in water have been collected and analyzed. The dataset contains 115 values of the concentration factors at different environmental concentrations of Ca. The data included in the dataset are based primarily on publications in Russian and relate to the whole-body concentration factors. An empirical formula was derived to estimate the equilibrium concentration factor of (90)Sr in fish as a inverse relationship of Ca: CF((90)Sr, Bq/kg w.w.)=3940/[Ca, mg/l](water). The derived relationship adequately accounts for the equilibrium concentration factor of (90)Sr in freshwater and marine fish species. A dynamic model was proposed to calculate the (90)Sr bioaccumulation of fish for non-equilibrium situations, for instance, immediately after accidental contamination of water bodies. The model was applied to reconstruct the dynamics of (90)Sr in fish from highly contaminated lake in the Southern Ural (Lake Uruskul). A comparison with data of observations showed that the model is well suited for estimating the dynamic characteristics of (90)Sr bioaccumulation by fish.

Animals↗

PubMed2026

Sleep disturbances in children and adolescents with iron deficiency: Questionnaire-based and actigraphic findings.

OBJECTIVE: Iron deficiency (ID), without or with anemia (IDA), has been linked to restless sleep and sleep-related movement disorders in childhood, but objective correlates are incompletely defined. We aimed to describe caregiver-reported sleep disturbances, restless legs syndrome (RLS) - related symptoms, and actigraphic sleep patterns in children and adolescents with ID/IDA, and to compare these findings with available sleep-asymptomatic control datasets. We finally explored short-term changes after iron supplementation. METHODS: In this single-center pilot observational study, 31 children with ID/IDA underwent baseline clinical/laboratory assessment and caregiver-reported sleep evaluation with the Sleep Disturbance Scale for Children (SDSC) plus RLS-oriented items. Sixteen also completed home actigraphy, and 8 had follow-up after iron treatment prescribed in routine care. Baseline findings were compared with historical healthy control datasets without reported sleep disturbances; iron-status data were not available for the questionnaire control group; within-subject changes were explored in the follow-up subgroup. RESULTS: Compared with healthy controls, the ID/IDA cohort had higher SDSC total scores (43.97 ± 9.63 vs 34.61 ± 7.50; p < 0.001), with significant differences in the subscales difficulty in initiating and maintaining sleep (DIMS), sleep-wake transition disorders (SWTD), and sleep hyperhidrosis (SHY). Ten of 31 screened children (32.25%) had clinically plausible RLS-related symptoms and higher SWTD scores. Actigraphy showed shorter sleep duration, lower sleep efficiency, longer wake after sleep onset, and greater fragmentation. After iron treatment, parent reported restlessness improved, whereas actigraphic parameters showed only partial normalization. CONCLUSIONS: Pediatric ID/IDA was associated with caregiver-reported and actigraphic sleep disruption, characterized by restless and fragmented sleep. These findings support systematic sleep assessment in children with low iron stores and consideration of iron status in the work-up of restless or nonrestorative sleep.

Humans↗

PubMed2004

Geographical inequalities of mortality by income in two developed island countries: a cross-national comparison of Britain and Japan.

In this paper we examine the ecological relations between household income distribution and age-grouped mortality in Britain and Japan. Comparable datasets were prepared in terms of age intervals of mortality, household income intervals and geographical units for years around 1990. Then we conducted a series of regression analyses to associate absolute and relative income indices with age and sex-specific standardized mortality ratios (SMRs). The results are as follows: (1) In Britain mortality is lower where inequalities in income are lower, while in Japan there is no obvious relationship. It is, however, apparent that-just as in the case of the USA and Canada-Britain and Japan appear to merge and appear part of a greater pattern when considered as a series of city regions. Thus an overall global relationship between income inequality and mortality may exist. To assess such global relationship, further studies using cross-national regional datasets covering a wide rage of rich nations are desirable. (2) Income-mortality relations are consistent among different age-sex groups in Britain, but there are substantial differences in the relationships as revealed between different demographic groups in Japan. In particular, while absolute income levels are correlated negatively with mortality of working-age men in both countries, mortality of elderly people in Japan is higher where absolute income is higher. This indicates the different historical contexts to the health divides these two different geographical contexts, but further consideration of a more historically nuanced understanding of income-mortality relations is required.

Adult↗

PubMed2006

Social relations or social capital? Individual and community health effects of bonding social capital.

Social capital has become one of the most popular topics in public health research in recent years. However, even after a decade of conceptual and empirical work on this subject, there is still considerable disagreement about whether bonding social capital is a collective resource that benefits communities or societies, or whether its health benefits are associated with people, their personal networks and support. Using data from the 2000 and 2002 Health Survey for England this study found that, in line with earlier research, personal levels of social support contribute to a better self-reported health status. The study also suggests that social capital is additionally important for people's health. In both datasets the aggregate social trust variable was significantly related to self-rated health before and after controlling for differences in socio-demographics and/or individual levels of social support. The results were corroborated in the second dataset with an alternative indicator of social capital. These results show that bonding social capital collectively contributes to people's self-rated health over and above the beneficial effects of personal social networks and support.

Adolescent↗

PubMed2026

Up-to-date, and taxonomy-curated mcrA reference databases for methanogen community profiling.

The methyl-coenzyme M reductase subunit alpha gene (mcrA) is an important phylogenetic marker for high throughput ecological profiling of methanogenic archaea, central to industrial biological methane production and greenhouse gas emissions. Yet, dedicated reference databases predate current relevant NCBI sequence accumulation and archaeal taxonomic revision. We present three updated mcrA reference databases: (i) one derived from NCBI-catalogued methanogen genomes (1572 sequences); (ii) a database built by expansion of a previously published reference dataset, leveraging the NCBI nucleotide collection (27,942 sequences); (iii) a curated-taxonomy version of the latter. The updated amplicon databases provide a ∼ 3.5-fold sequence richness expansion, extend genus-level richness from 31 to 83 taxa, more than 4-fold species-level richness, and incorporate novel lineages compared with the previous reference dataset (e.g. Thermoplasmatota-encompassed). All databases were formatted to support analysis with relevant contemporary software pipelines and packages. Overall, the generated databases facilitate a highly improved characterization of methanogen diversity and ecology.

Archaea↗

PubMed2004

Prediction of the reproductive status of cattle on the basis of milk progesterone measures: model description.

Reproductive management, in particular timely oestrus detection, is important for profitable dairy production. The aim of this study was to develop a biological model to predict reproductive state on the basis of milk progesterone measures. A number of additional inputs were incorporated to make use of other known effectors of reproductive performance that are not reflected in progesterone levels. These are: days from calving, breed, parity, signs of behavioural oestrus, insemination dates, pregnancy determinations, energy status, body fat status, milk urea content and reproductive disorders associated with calving. A dynamic, deterministic model was developed. It is designed to run each time a new trigger input (progesterone, behavioural oestrus, inseminations, pregnancy determinations) occurs using the current and previous values and can run in the absence of the additional inputs. The milk progesterone values are smoothed using an extended Kalman filter before being processed in the biological component of the model. The model predicts the reproductive status of the cow, which can be one of three mutually exclusive states: postpartum anoestrus, oestrus cycling, and potentially pregnant. The other model outputs are all reproductive status specific with the exception of days to next sample (DNS), which is calculated in each model run regardless of reproductive status. DNS is designed to feedback to the sampling system so that the frequency of milk sampling (i.e. progesterone measurement) can be varied according to the predicted likelihood of a future reproductive event, such as onset of oestrus cycling. The other model outputs are: risk of prolonged postpartum anoestrus, risk and type of ovarian cyst, onset of oestrus, likelihood of a potential insemination succeeding, and likelihood of being pregnant (following oestrus). The model was evaluated using three simulated datasets consisting of a timeseries of progesterone values centred on each of the three reproductive statuses and including relevant additional information. Test runs were carried out on the full datasets and then on reduced data. The data reductions were made by using only those values that would have been available if the model days to next sample function was used to control sampling frequency. The sensitivity of the model to noise in the raw progesterone data was examined by adding 1, 2, or 3 residual standard deviations (1.85 ng/ml) random variation to the original data and evaluating model performance. The model was found to be able to readily identify and distinguish reproductive states. A reduction in sampling frequency to 36% of original sample resulted in an average increase in days to detection of oestrus of 0.36. The addition of 1 S.D. noise did not cause additional oestruses to be detected and all oestruses were correctly identified. However, when 2 or 3 S.D. noise were added, the model found on average 1.4 and 3 extra oestruses. It was concluded that reproductive status can be predicted from milk progesterone values using a biological model and that such a model is robust to reductions in sampling frequency number and to a doubling in the random variation in the raw progesterone values. It therefore has the potential to provide the basis for a useful reproductive management tool.

Anestrus↗

PubMed2005

Pathways to the analysis of microarray data.

The development of microarray technology allows the simultaneous measurement of the expression of many thousands of genes. The information gained offers an unprecedented opportunity to fully characterize biological processes. However, this challenge will only be successful if new tools for the efficient integration and interpretation of large datasets are available. One of these tools, pathway analysis, involves looking for consistent but subtle changes in gene expression by incorporating either pathway or functional annotations. We review several methods of pathway analysis and compare the performance of three, the binomial distribution, z scores, and gene set enrichment analysis, on two microarray datasets. Pathway analysis is a promising tool to identify the mechanisms that underlie diseases, adaptive physiological compensatory responses and new avenues for investigation.

Algorithms↗

PubMed2006

Capturing cellular machines by systematic screens of protein complexes.

Two recent studies have provided the most complete screen for protein complexes in yeast to date, in which partners were identified for approximately half of the proteome. A comparison shows that these two datasets are complementary. In addition, one of the analyses points to a modular organization of the cellular protein network. These data will prove useful in defining principles and trends that arise when combining large-scale datasets of different natures, and in deriving properties of protein machines in cellular systems.

Models, Biological↗

PubMed2005

Risk factors for cross-country horse falls at one-day events and at two-/three-day events.

The cross-country phase of eventing competitions has been associated with injuries and fatalities to horses and riders. A case-control study was carried out to identify variables that were associated with increased or decreased risk of a horse fall on the cross-country phase at event competitions. After initial analysis, the dataset was split according to the categories of one-day events as compared to two- or three-day events to establish whether significant risk factors varied between the different types of eventing competitions. Data were collected for 121 cases (horse falls) at one-day events, 59 cases at two- or three-day events and for their 540 matched controls. The data were analysed using conditional logistic regression. The variables of no previous refusals on the course, fences with a landing in water and the combined variable of the angle and the spread of the fence were significantly associated with the risk of a horse fall in both datasets. Additional risk factors for one-day event falls were: fences requiring a take-off from water, a drop landing, the rider's knowledge of their position before the cross-country phase and if the rider received cross-country tuition. Three-day event risk factors in the multivariable model included: the camber of the fence and participation in non-equestrian sports by the rider. This study identified variables that were significantly associated with an increase or a decrease in the risk of a horse fall during the cross-country phase of different types of eventing competitions. Some of these variables are modifiable and the results of this study have been reported to the governing body of the sport of eventing in the UK so that possible interventions might be considered.

Accidental Falls↗

PubMed2005

Imaging and characterization of fine gamma' precipitates in a commercial nickel-base superalloy.

Empirical datasets of volume fractions and size distributions of small gamma' precipitates from "real" multi-component engineering nickel-based superalloys are vital to calibrate and validate the computer models which predict high sensitivities of mechanical properties to size and volume fraction of these fine gamma precipitates, and in order to accelerate microstructure and alloy development. Consequently, we investigated a number of imaging techniques available in a Tecnai F-20 FEG/TEM and selected the technique which best enabled rapid and extensive acquisition of these datasets using the engineering alloy, René 88'DT. The EFTEM technique was found to be the most appropriate method for imaging fine gamma' precipitates while further investigation showed that the Cr-M-edge, in comparison with other ionization-edges provided the best images based largely on contrast-to-noise ratio. Imaging of the Cr-M-edge elemental maps were further improved by investigating the effects of microscope parameters, imaging filter parameters and analysis of the experimental electron energy loss spectra obtained from this alloy. In addition, a novel technique to determine the volume fraction of the fine gamma' precipitates without the need to determine the absolute thickness of the TEM foil is proposed.

Journal Article↗

PubMed2004

An ultrasonic transducer array for velocity measurement in underwater vehicles.

A correlation velocity log (CVL) is an ultrasonic navigation aid for marine applications, in which velocity is estimated using an acoustic transmitter and a receiver array. CVLs offer advantages over Doppler velocity logs (DVLs) in many autonomous underwater vehicle (AUV) applications, since they can achieve high accuracy at low velocities even during hover manoeuvres. DVLs require narrow beam widths, whilst ideal CVL transmitters have wide beam widths. This gives CVLs the potential to use lower frequencies thus permitting operation in deeper water, reducing power requirements for the same depth, or allowing the use of smaller transducers. Moving patterns in the wavefronts across a 2D receiver array are detected by calculating correlation coefficients between bottom reflections from consecutive transmitted pulses, across all combinations of receiver pairings. The position of the peak correlation value, on a surface representing receiver-pairing separations, is proportional to the vessel's displacement between pulses. A CVL aimed primarily for AUVs has been developed. Its acoustical and signal processing design has been optimised through sea trials and computer modelling of the sound field. This computer model is also used to predict how the distribution of the correlation coefficients varies with distance from the peak position. Current work seeks to increase the resolution of the peak estimate using surface fitting methods. Numerical simulations suggest that peak estimation methods significantly improve system precision when compared with simply identifying the position of the maximum correlation coefficient in the dataset. The peak position may be estimated by fitting a quadratic model to the measured data using least squares or maximum likelihood estimation. Alternatively, radial basis functions and Gaussian processes successfully predict the peak position despite variation between individual correlation datasets. This paper summarises the CVL's main acoustical features and signal processing techniques and includes results of sea trials using the device.

Journal Article↗

PubMed2004

Prediction of CTL epitopes using QM, SVM and ANN techniques.

Cytotoxic T lymphocyte (CTL) epitopes are potential candidates for subunit vaccine design for various diseases. Most of the existing T cell epitope prediction methods are indirect methods that predict MHC class I binders instead of CTL epitopes. In this study, a systematic attempt has been made to develop a direct method for predicting CTL epitopes from an antigenic sequence. This method is based on quantitative matrix (QM) and machine learning techniques such as Support Vector Machine (SVM) and Artificial Neural Network (ANN). This method has been trained and tested on non-redundant dataset of T cell epitopes and non-epitopes that includes 1137 experimentally proven MHC class I restricted T cell epitopes. The accuracy of QM-, ANN- and SVM-based methods was 70.0, 72.2 and 75.2%, respectively. The performance of these methods has been evaluated through Leave One Out Cross-Validation (LOOCV) at a cutoff score where sensitivity and specificity was nearly equal. Finally, both machine-learning methods were used for consensus and combined prediction of CTL epitopes. The performances of these methods were evaluated on blind dataset where machine learning-based methods perform better than QM-based method. We also demonstrated through subgroup analysis that our methods can discriminate between T-cell epitopes and MHC binders (non-epitopes). In brief this method allows prediction of CTL epitopes using QM, SVM, ANN approaches. The method also facilitates prediction of MHC restriction in predicted T cell epitopes.

Algorithms↗

PubMedDate not supplied

Application of simple mathematical expressions to relate the half-lives of xenobiotics in rats to values in humans.

INTRODUCTION: Previous publications from GlaxoSmithKline and University of Toledo laboratories convey our independent attempts to predict the half-lives of xenobiotics in humans using data obtained from rats. The present investigation was conducted to compare the performance of our published models against a common dataset obtained by merging the two sets of rat versus human half-life (hHL) data previously used by each laboratory. METHODS: After combining data, mathematical analyses were undertaken by deploying both of our previous models, namely the use of an empirical algorithm based on a best-fit model and the use of rat-to-human liver blood flow ratios as a half-life correction factor. Both qualitative and quantitative analyses were performed, as well as evaluation of the impact of molecular properties on predictability. RESULTS: The merged dataset was remarkably diverse with respect to physiochemical and pharmacokinetic (PK) properties. Application of both models revealed similar predictability, depending upon the measure of stipulated accuracy. Certain molecular features, particularly rotatable bond count and pK(a), appeared to influence the accuracy of prediction. DISCUSSION: This collaborative effort has resulted in an improved understanding and appreciation of the value of rats to serve as a surrogate for the prediction of xenobiotic half-lives in humans when clinical pharmacokinetic studies are not possible or practicable.

Algorithms↗