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PubMed2026

MetaFX: feature extraction from whole-genome metagenomic sequencing data.

MOTIVATION: Microbial communities consist of thousands of microorganisms and viruses and have a tight connection with an environment, such as gut microbiota modulation of host body metabolism. However, the direct relationship between the presence of certain microorganism and the host state often remains unknown. Toolkits using reference-based approaches are limited to microbes present in databases. Reference-free methods often require enormous resources for metagenomic assembly or results in many poorly interpretable features based on k-mers. RESULTS: Here we present MetaFX-an open-source library for feature extraction from whole-genome metagenomic sequencing data and classification of groups of samples. Using a large volume of metagenomic samples deposited in databases, MetaFX compares samples grouped by metadata criteria (e.g. disease, treatment, etc.) and constructs genomic features distinct for certain types of communities. Features constructed based on statistical k-mer analysis and de Bruijn graphs partition. Those features are used in machine learning models for classification of novel samples. Extracted features can be visualized on de Bruijn graphs and annotated for providing biological insights. We demonstrate the utility of MetaFX by building classification models for 590 human gut samples with inflammatory bowel disease. Our results outperform the previous research disease prediction accuracy up to 17%, and improves classification results compared to taxonomic analysis by 9±10% on average. AVAILABILITY AND IMPLEMENTATION: MetaFX is a feature extraction toolkit applicable for metagenomic datasets analysis and samples classification. The source code, test data, and relevant information for MetaFX are freely accessible at https://github.com/ctlab/metafx under the MIT License. Alternatively, MetaFX can be obtained via http://doi.org/10.5281/zenodo.16949369.

Metagenomics↗
PubMed2002

Caring and competency.

The long-term crisis in nursing, particularly in acute care hospitals, is demonstrated in studies on negligence by the Institute of Medicine in To Err is Human: Building a Safer Health System1 and Crossing the Quality Chasm: A New Health System for the 21st Century.2 A review of the nursing literature reflects unclear definitions of competency and its component caring, and no single theory of competency has been adopted from the literature and used in the education of nurses. The American Nurses 2001 Code of Ethics does not resolve this confusion, because it does not correct the individual acts of nursing incompetencies in acute care hospitals. The author defines caring and competency by providing examples of what they are not in examining 200 actual cases of hospital nursing acts of incompetence by nursing discipline. None of these examples of imputed negligence was reported to the National Practitioner Data Bank because the "corporate shield" protected the nurses by not being named in the complaint nor named as part of the settlement against the hospital.A new model of the hospitalist, the nurse hospitalist, is presented to act as a daily teacher and facilitator for hospital nurses based on a curriculum of day-to-day examples of substandard patient care. This nurse specialist is an inpatient generalist advanced practice nurse who is employed by the hospital and reports to the chief nurse executive. The author proposes that this new model of the nurse hospitalist be devoted entirely to collaborating with nurse leaders, educators, charge nurses, and floor nurses throughout disciplines in advancing the competency of nursing. This daily proactive and prospective model of improving nursing performance in a facultative manner offers strategies to mitigate the limitations of the retrospective model of quality control. Total quality improvement practiced retroactively is ineffective. The author recommends no structural change in the institution but an educational agenda by the nurse hospitalist, with hospital administration to assist nurses in a new learning environment.

Clinical Competence↗
PubMed1999

Cloning of a calcium channel alpha1 subunit from the reef-building coral, Stylophora pistillata.

While the mechanisms of cellular Ca2+ entry associated with cell activation are well characterized, the pathway of continuous uptake of the large amount of Ca2+ needed in the biomineralization process remains largely unknown. Scleractinian corals are one of the major calcifying groups of organisms. Recent studies have suggested that a voltage-dependent Ca2+ channel is involved in the transepithelial transport of Ca2+ used for coral calcification. We report here the cloning and sequencing of a cDNA coding a coral alpha1 subunit Ca2+ channel. This channel is closely related to the L-type family found in vertebrates and invertebrates. Immunohistochemical analysis shows that this channel is present within the calicoblastic ectoderm, the site involved in calcium carbonate precipitation. These data and previous results provide molecular evidence that voltage-dependent Ca2+ channels are involved in calcification. Cnidarians are the most primitive organisms in which a Ca2+ channel has been cloned up to now; evolutionary perspectives on Ca2+ channel diversity are discussed.

Amino Acid Sequence↗
PubMed2005

Linear scaling computation of the Fock matrix. VII. Periodic density functional theory at the Gamma point.

Linear scaling quantum chemical methods for density functional theory are extended to the condensed phase at the Gamma point. For the two-electron Coulomb matrix, this is achieved with a tree-code algorithm for fast Coulomb summation [M. Challacombe and E. Schwegler, J. Chem. Phys. 106, 5526 (1997)], together with multipole representation of the crystal field [M. Challacombe, C. White, and M. Head-Gordon, J. Chem. Phys. 107, 10131 (1997)]. A periodic version of the hierarchical cubature algorithm [M. Challacombe, J. Chem. Phys. 113, 10037 (2000)], which builds a telescoping adaptive grid for numerical integration of the exchange-correlation matrix, is shown to be efficient when the problem is posed as integration over the unit cell. Commonalities between the Coulomb and exchange-correlation algorithms are discussed, with an emphasis on achieving linear scaling through the use of modern data structures. With these developments, convergence of the Gamma-point supercell approximation to the k-space integration limit is demonstrated for MgO and NaCl. Linear scaling construction of the Fockian and control of error is demonstrated for RBLYP6-21G* diamond up to 512 atoms.

Journal Article↗
PubMed2003

Combination of overlapping bacterial artificial chromosomes by a two-step recombinogenic engineering method.

Recombinogenic engineering or recombineering is a powerful new method to engineer DNA without the need for restriction enzymes or ligases. We report here a general method for using recombineering to combine overlapping bacterial artificial chromosomes (BACs) to build larger, unified BACs. In order to test the feasibility of using recombineering to combine two large DNA fragments (>20 kb), we constructed a unified BAC containing the full-length tyrosinase-related protein-1 (Tyrp-1) gene from two library-derived BACs, one containing the 5' regulatory elements and the other containing the 3' coding exons. This was achieved using a two-step homologous recombination method enabled by the bacteriophage lambda Red proteins. In the first step, retrieval, a large DNA fragment (approximately 22 kb) was retrieved from one of the original BACs. In the second step, recombination, the retrieved DNA fragment was inserted into the second original BAC to form the unified BAC containing all the desired Tyrp-1 sequence. To further demonstrate the general applicability of our approach, an additional DNA fragment (approximately 20 kb) was inserted into the unified BAC downstream of the coding region. This method should prove very useful for enabling BAC manipulation in a variety of scenarios.

Chromosomes, Artificial, Bacterial↗
PubMed1999

3D imaging of the 58 kDa cell binding subunit of the Helicobacter pylori cytotoxin.

Pathogenic strains of Helicobacter pylori produce a potent exotoxin, VacA, which intoxicates gastric epithelial cells and leads to peptic ulcer. The toxin is released from the bacteria as a high molecular mass homo-oligomer of a 95 kDa polypeptide which undergoes specific proteolytic cleavage to 37 kDa and 58 kDa subunits. We have engineered a strain of H. pylori to delete the gene sequence coding for the 37 kDa subunit. The remaining 58 kDa subunit is expressed efficiently and exported as a soluble dimer that is non-toxic but binds target cells in a manner similar to the holotoxin. A 3D reconstruction of the molecule from electron micrographs of quick-freeze, deep-etched preparations reveals the contribution of each building block to the structure and permits the reconstruction of the oligomeric holotoxin starting from individual subunits. In this model P58 subunits are assembled in a ring structure with P37 subunits laying on the top. The data indicate that the 58 kDa subunit is capable of folding autonomously into a discrete structure recognizable within the holotoxin and containing the cell binding domain.

Bacterial Proteins↗
PubMed2026

A framework to infer de novo exonic variants when parental genotypes are missing enhances association studies of autism.

MOTIVATION: Gene-damaging mutations are highly informative for studies seeking to discover genes underlying developmental disorders. Traditionally, these de novo variants are recognized by evaluating high-quality DNA sequence from affected offspring and parents. However, when parental sequence is unavailable, methods are required to infer de novo status and use this inference for association studies. RESULTS: We use data from autism spectrum disorder to illustrate and evaluate methods. Separating de novo from rare inherited variants is challenging because the latter are far more common. Using a classifier for unbalanced data and variants of known inheritance class, we build an inheritance model and then a de novo score for variants when parental data are missing. Next, we propose a new Random Draw (RD) model to use this score for gene discovery. Built into an existing inferential framework, RD produces a more powerful gene-based association test and controls the false discovery rate. AVAILABILITY AND IMPLEMENTATION: Codes are available at Github (https://github.com/HaeunM/TADA-RD) and Zenodo (DOI: https://doi.org/10.5281/zenodo.18531769).

Humans↗
PubMed2003

A genetic segmentation of ECG signals.

This paper is concerned with a development of a segmentation technique for electrocardiogram (ECG) signals. Such segmentation is aimed at a lossy signal compression in which each segment can be captured by a simple geometric construct such as, e.g., a linear or quadratic function. The crux of the proposed construct lies in the determination of the optimal segments of data over which they exhibit the highest possible monotonicity (or lowest variability) of the ECG signal. In this sense, the proposed approach generalizes a fundamental and commonly encountered problem of function (data) linearization. The segments are genetically developed using a standard technique of genetic algorithms (GAs). The two fundamental GA constructs, namely a topology of a chromosome and a fitness function governing the optimization process are discussed in detail. The chromosome being coded as a series of floating point numbers contains the endpoints of the segments (segmentation points). The fitness function to be maximized quantifies a level of monotonicity of the ECG data encountered within the segments and takes into consideration differences between the extreme values (minimum and maximum) of its derivatives. As a result of the genetic optimization, we build segments of ECG signals encompassing monotonic (increasing or decreasing) regions of the signal exhibiting a minimal level of variability. A series of experiments dealing with several classes of ECG signals (namely, normal, left bundle branch block beat, and right bundle branch block beat) visualize the effectiveness of the approach and shows the specificity of the linear segments of data. Furthermore, we elaborate on the relationship between the values of the fitness function and the approximation capabilities (quantified by a sum of squared errors between the local model and the data) of the segments of the signal and show that these two descriptors are highly related.

Algorithms↗
PubMed2025

Prioritization of causal genes from genome-wide association studies by Bayesian data integration across loci.

MOTIVATION: Genome-wide association studies (GWAS) have identified genetic variants, usually single-nucleotide polymorphisms (SNPs), associated with human traits, including disease and disease risk. These variants (or causal variants in linkage disequilibrium with them) usually affect the regulation or function of a nearby gene. A GWAS locus can span many genes, however, and prioritizing which gene or genes in a locus are most likely to be causal remains a challenge. Better prioritization and prediction of causal genes could reveal disease mechanisms and suggest interventions. RESULTS: We describe a new Bayesian method, termed SigNet for significance networks, that combines information both within and across loci to identify the most likely causal gene at each locus. The SigNet method builds on existing methods that focus on individual loci with evidence from gene distance and expression quantitative trait loci (eQTL) by sharing information across loci using protein-protein and gene regulatory interaction network data. In an application to cardiac electrophysiology with 226 GWAS loci, only 46 (20%) have within-locus evidence from Mendelian genes, protein-coding changes, or colocalization with eQTL signals. At the remaining 180 loci lacking functional information, SigNet selects 56 genes other than the minimum distance gene, equal to 31% of the information-poor loci and 25% of the GWAS loci overall. Assessment by pathway enrichment demonstrates improved performance by SigNet. Review of individual loci shows literature evidence for genes selected by SigNet, including PMP22 as a novel causal gene candidate.

Genome-Wide Association Study↗
PubMed2001

Bacterial molecular phylogeny using supertree approach.

It has been claimed that complete genome sequences would clarify phylogenetic relationships between organisms but, up to now, no satisfying approach has been proposed to use efficiently these data. For instance, if the coding of presence or absence of genes in complete genomes gives interesting results, it does not take into account the phylogenetic information contained in sequences and ignores hidden paralogy by using a similarity-based definition of orthology. Also, concatenation of sequences of different genes takes hardly in consideration the specific evolutionary rate of each gene. At last, building a consensus tree is strongly limited by the low number of genes shared among all organisms. Here, we use a new method based on supertree construction, which permits to cumulate in one supertree the information and statistical support of hundreds of trees from orthologous gene families and to build the phylogeny of 33 prokaryotes and four eukaryotes with completely sequenced genomes. This approach gives a robust supertree, which demonstrates that a phylogeny of prokaryotic species is conceivable and challenges the hypothesis of a thermophilic origin of bacteria and present-day life. The results are compatible with the hypothesis of a core of genes for which lateral transfers are rare but they raise doubts on the widely admitted "complexity hypothesis" which predicts that this core is mainly implicated in informational processes.

Bacteria↗
PubMed2006

Non-destructive testing techniques for the forensic engineering investigation of reinforced concrete buildings.

This study describes in detail the results of a laboratory investigation where the compressive strength of 150mm side-length cubes was evaluated. Non-destructive testing (NDT) was carried out using ultrasonic pulse velocity (UPV) and impact rebound hammer (IRH) techniques to establish a correlation with the compressive strengths of compression tests. To adapt the Schmidt hammer apparatus and the ultrasonic pulse velocity tester to the type of concrete used in Algeria, concrete mix proportions that are recommended by the Algerian code were chosen. The resulting correlation curve for each test is obtained by changing the level of compaction, water/cement ratio and concrete age of specimens. Unlike other works, the research highlights the significant effect of formwork material on surface hardness of concrete where two different mould materials for specimens were used (plastic and wood). A combined method for the above two tests, reveals an improvement in the strength estimation of concrete. The latter shows more improvement by including the concrete density. The resulting calibration curves for strength estimation were compared with others from previous published literature.

Journal Article↗
PubMed1999

Ill-defined and multiple causes on death certificates--a study of misclassification in mortality statistics.

Biases can distort, limit or inhibit the value of mortality data as an epidemiological re source. From 9500 deaths occurring in Naples (Italy during 1994, a random sample of 372 death certificates reporting ill-defined causes and multiple causes of death was extracted. The code for the underlying cause on the death certificate (assigned code) was compared with the cause reattributed with the aid of interview of the certifying physician or clinical records (modified code). The aim was to investigate the extent of misclassification of 'underlying cause' in deaths attributed to ill-defined and/or multiple causes and the shortcomings in the ICD-IX. Ill-defined underlying causes of death (7.0% of death certificates) were cardiovascular diseases, tumours with no specified site or nature, symptoms, signs, ill-defined conditions and senility. There was disagreement between the initially assigned code and the modified code in 53.8% of ill-defined underlying causes; discordance was high for the certificates filled in by the family physician. Multiple causes of death were observed in 23.6% of certificates; of these 59.2% concerned subjects aged 75 years and over at death. Diabetes was always listed in association with other pathologies but neoplasms and traumas were generally listed alone. Disagreement between codes occurred in 48 (54.5%) certificates indicating multiple causes. In 10 of them, death was established as due to a concurrence of causes. As regards ill-defined causes of death, the authors concluded that specific training on certifying procedures would be insufficient on their own; the physician should be made aware that certification is a fundamental requirement for building up epidemiological data. Evidence-based educational interventions are needed. As regards multiple causes of death, multicausal analysis may be indicated for deaths due to a concurrence of causes.

Age Factors↗
PubMed2002

Model of Vibrio cholerae toxin coregulated pilin capable of filament formation.

A complete three-dimensional model (RCSB001169; PDB code 1qqz ) for the Vibrio cholerae toxin coregulated pilus protein (TcpA), including residues 1-197, is presented. We have used the crystal structure of the Neisseria gonorrhoeae pilin (PilE), available biochemical data about TcpA, variations in the primary sequences of TcpA among various Vibrio cholerae strains and secondary structure prediction, hydrophilicity, surface probability and antigenicity plots for TcpA to build our model. In our TcpA model, the first 137 residues possess a structure similar to the PilE, but the remainder is different. Though the ladle shape is still preserved, TcpA possesses a larger ladle head or globular domain compared to PilE. Using this model, it has been possible to identify two kinds of conserved residues: (i) those forming the core of the TcpA monomer and (ii) those involved in the monomer-monomer interactions leading to fibre formation. Residues on the fibre exterior, important in the mediation of bacterium (pilus)-bacterium (pilus) and bacterium (pilus)-host interactions, show more variability in comparison to those of (i) and (ii).

Amino Acid Sequence↗
PubMed2005

Building messaging substrates for Web and Grid applications.

Grid application frameworks have increasingly aligned themselves with the developments in Web services. Web services are currently the most popular infrastructure based on service-oriented architecture (SOA) paradigm. There are three core areas within the SOA framework: (i) a set of capabilities that are remotely accessible, (ii) communications using messages and (iii) metadata pertaining to the aforementioned capabilities. In this paper, we focus on issues related to the messaging substrate hosting these services; we base these discussions on the NARADABROKERING system. We outline strategies to leverage capabilities available within the substrate without the need to make any changes to the service implementations themselves. We also identify the set of services needed to build Grids of Grids. Finally, we discuss another technology, HPSEARCH, which facilitates the administration of the substrate and the deployment of applications via a scripting interface. These issues have direct relevance to scientific Grid applications, which need to go beyond remote procedure calls in client-server interactions to support integrated distributed applications that couple databases, high performance computing codes and visualization codes.

Computer Simulation↗
PubMed2000

Identifying patients with ischaemic heart disease in general practice: cross sectional study of paper and computerised medical records.

OBJECTIVES: To identify patients with ischaemic heart disease by using a practice computer and to estimate the work required to do so. DESIGN: Cross sectional study. Data from the notes and from the computer records of 1680 patients were used to build a database. This was used to compare different methods of identifying patients with ischaemic heart disease. SETTING: 11 general practices in the Battersea primary care group in south London. SUBJECTS: 1 in 40 random sample of patients aged 45 or older. MAIN OUTCOME MEASURES: Numbers of patients identified with ischaemic heart disease. RESULTS: The combination of the Read code for ischaemic heart disease (G3) and a prescription for a nitrate had a 73% sensitivity and a yield (100/positive predictive value) of one case of ischaemic heart disease for every 1.2 sets of notes reviewed. By searching the records of patients also receiving aspirin, atenolol, digoxin, or a statin, the sensitivity was increased to 96% but the yield fell to one in three. CONCLUSION: Although commonly used to identify cases, a computer search for G3 code or nitrate missed almost 30% of patients with ischaemic heart disease. A substantially higher percentage of patients can be identified by adding other drugs to the search strategy.

Aged↗
PubMed1991

Object-oriented design and programming in medical decision support.

The concept of object-oriented design and programming has recently received a great deal of attention from the software engineering community. This paper highlights the realisable benefits of using the object-oriented approach in the design and development of clinical decision support systems. These systems seek to build a computational model of some problem domain and therefore tend to be exploratory in nature. Conventional procedural design techniques do not support either the process of model building or rapid prototyping. The central concepts of the object-oriented paradigm are introduced, namely encapsulation, inheritance and polymorphism, and their use illustrated in a case study, taken from the domain of breast histopathology. In particular, the dual roles of inheritance in object-oriented programming are examined, i.e., inheritance as a conceptual modelling tool and inheritance as a code reuse mechanism. It is argued that the use of the former is not entirely intuitive and may be difficult to incorporate into the design process. However, inheritance as a means of optimising code reuse offers substantial technical benefits.

Adult↗
PubMed2005

Quantitative risk analysis of oil storage facilities in seismic areas.

Quantitative risk analysis (QRA) of industrial facilities has to take into account multiple hazards threatening critical equipment. Nevertheless, engineering procedures able to evaluate quantitatively the effect of seismic action are not well established. Indeed, relevant industrial accidents may be triggered by loss of containment following ground shaking or other relevant natural hazards, either directly or through cascade effects ('domino effects'). The issue of integrating structural seismic risk into quantitative probabilistic seismic risk analysis (QpsRA) is addressed in this paper by a representative study case regarding an oil storage plant with a number of atmospheric steel tanks containing flammable substances. Empirical seismic fragility curves and probit functions, properly defined both for building-like and non building-like industrial components, have been crossed with outcomes of probabilistic seismic hazard analysis (PSHA) for a test site located in south Italy. Once the seismic failure probabilities have been quantified, consequence analysis has been performed for those events which may be triggered by the loss of containment following seismic action. Results are combined by means of a specific developed code in terms of local risk contour plots, i.e. the contour line for the probability of fatal injures at any point (x, y) in the analysed area. Finally, a comparison with QRA obtained by considering only process-related top events is reported for reference.

Disasters↗
PubMed1997

Clinical features and epidemiology of malignant pleural mesothelioma in west Glasgow 1987-1992.

Malignant pleural mesothelioma is almost exclusively caused by exposure to asbestos dust. Recent epidemiological studies have suggested that the national incidence of disease may continue to rise until 2020 and that asbestos exposure in the building trade may be replacing shipyard related exposure as the main source of disease. The objective of the study was to determine if the incidence of malignant pleural mesothelioma was rising in the west of Glasgow from 1987-1992 and whether there had been a change in clinical features compared to previous studies from the same population. Case notes identified from coded returns and the local cancer registry were retrospectively examined: 144 cases were identified. This is an increase in incidence of over 50% compared to the previous study but the yearly incidence did not rise over the period studied. The clinical features and survival times have not changed since previous studies: median survival remains 30 weeks. Only three patients were given definitive treatment reflecting the lack of effective therapy. We suggest that the incidence of mesothelioma in the population studied may already have peaked resulting from the decline in the local shipyard industry over 20 years ago. Non-shipyard sources of asbestos exposure may be less important in this area.

Adult↗