Clonal Complexes in Biomedical Ontologies

An accurate classification of bacteria is essential for the proper identification of patient infections and subsequent treatment decisions. Multi-Locus Se-quence Typing (MLST) is a genetic technique for bacterial classification. MLST classifications are used to cluster bacteria into clonal complexes. Importantly, clonal complexes can serve as a biological species concept for bacteria, facilitating an otherwise difficult taxonomic classification. In this paper, we argue for the inclusion of terms relating to clonal complexes in biomedical ontologies

Constructing a lattice of Infectious Disease Ontologies from a Staphylococcus aureus isolate repository

A repository of clinically associated Staphylococcus aureus (Sa) isolates is used to semi‐automatically generate a set of application ontologies for specific subfamilies of Sa‐related disease. Each such application ontology is compatible with the Infectious Disease Ontology (IDO) and uses resources from the Open Biomedical Ontology (OBO) Foundry. The set of application ontologies forms a lattice structure beneath the IDO‐Core and IDO‐extension reference ontologies. We show how this lattice can be used to define a strategy for the construction of a new taxonomy of infectious disease incorporating genetic, molecular, and clinical data. We also outline how faceted browsing and query of annotated data is supported using a lattice application ontology

Towards an Ontological Representation of Resistance: The Case of MRSa

This paper addresses a family of issues surrounding the biological phenomenon of resistance and its representation in realist ontologies. Resistance terms from various existing ontologies are examined and found to be either overly narrow, inconsistent, or
otherwise problematic. We propose a more coherent ontological representation using the antibiotic resistance in Methicillin-Resistant _Staphylococcus aureus_ (MRSa) as a case study

Ontological representation of CDC Active Bacterial Core Surveillance Case Reports

The Center for Disease Control and Prevention’s Active Bacterial Core Surveillance (CDC ABCs) Program is a collaborative effort betweeen the CDC, state health departments, laboratories, and universities to track invasive bacterial pathogens of particular importance to public health [1]. The year-end surveillance reports produced by this program help to shape public policy and coordinate responses to emerging infectious diseases over time. The ABCs case report form (CRF) data represents an excellent opportunity for data reuse beyond the original surveillance purposes

Ontology based annotation of contextualized vital signs

Representing the kinetic state of a patient (posture, motion, and activity) during vital sign measurement is an important part of continuous monitoring applications, especially remote monitoring applications. In contextualized vital sign representation, the measurement result is presented in conjunction with salient measurement context metadata. We present an automated annotation system for vital sign measurements that uses ontologies from the Open Biomedical Ontology Foundry (OBO Foundry) to represent the patient’s kinetic state at the time of measurement. The annotation system is applied to data generated by a wearable personal status monitoring (PSM) device. We demonstrate how annotated PSM data can be queried for contextualized vital signs as well as sensor algorithm configuration parameters

Nurse-friendly nutritional screening for patient benefit

Screening for undernutrition is highly important and may reduce morbidity and mortality. The Minimal Eating Observation and Nutrition Form – Version II (MEONF-II) is a nutritional screening tool specifically developed for use by nurses. Here, we describe the translation, performance and appropriateness of the MEONF-II for the UK. Following translation from Swedish to British English, the user-friendliness and appropriateness of the British MEONF-II was tested by 29 registered nurses and final year student nurses on 266 hospital inpatients. The new British MEONF-II was perceived as highly user-friendly and appropriate. They found the MEONF-II to compare favourably to other similar tools in terms of preference, usefulness and helpfulness in providing good nutritional care. Dependency in activities and poorer subjective health were associated with a higher undernutrition risk. These findings support the appropriateness of the British MEONF-II version and suggest it may act as a user-friendly facilitator towards good nutritional nursing care

Material and Structural Aspects of Bone in Osteogenesis Imperfecta

Bone fragility is a fundamental problem in individuals with osteogenesis imperfecta (OI). The mechanisms behind this fragility, however, are not yet well understood. Multiple factors appear to contribute to the increased fracture risk in OI. At the structural level, bone mass deficiency can result in increased stress levels within bones. The underlying mineral and collagen abnormalities that define OI are also believed to result in compromised material-level properties. The variability of collagen biochemical irregularities causing OI and the corresponding heterogeneity of disease severity result in abnormalities that are not easily generalized within the OI population. The aims of this chapter are to introduce basic mechanical notions pertaining to the strength of structures and materials, and to present a synthesis of existing literature regarding the mechanical properties of bones in OI

Zinc abundances of planetary nebulae

Zinc is a useful surrogate element for measuring Fe/H as, unlike iron, it is not depleted in the gas phase media. Zn/H and O/Zn ratios have been derived using the [Zn IV] emission line at 3.625um for a sample of nine Galactic planetary nebulae, seven of which are based upon new observations using the VLT. Based on photoionization models, O/O++ is the most reliable ionisation correction factor for zinc that can readily be determined from optical emission lines, with an estimated accuracy of 10% or better for all targets in our sample. The majority of the sample is found to be sub-solar in [Zn/H]. [O/Zn] in half of the sample is found to be consistent with Solar within uncertainties, whereas the remaining half are enhanced in [O/Zn]. [Zn/H] and [O/Zn] as functions of Galactocentric distance have been investigated and there is little evidence to support a trend in either case.Comment: Accepted MNRAS, 11 pages, 8 figure

Macroscopic Anisotropic Bone Material Properties in Children with Severe \u3cem\u3eOsteogenesis imperfecta\u3c/em\u3e

Children with severe osteogenesis imperfecta(OI) typically experience numerous fractures and progressive skeletal deformities over their lifetime. Recent studies proposed finite element models to assess fracture risk and guide clinicians in determining appropriate intervention in children with OI, but lack of appropriate material property inputs remains a challenge. This study aimed to characterize macroscopic anisotropic cortical bone material properties and investigate relationships with bone density measures in children with severe OI. Specimens were obtained from tibial or femoral shafts of nine children with severe OI and five controls. The specimens were cut into beams, characterized in bending, and imaged by synchrotron radiation X-ray micro-computed tomography. Longitudinal modulus of elasticity, yield strength, and bending strength were 32–65% lower in the OI group (p \u3c 0.001). Yield strain did not differ between groups (p ≥ 0.197). In both groups, modulus and strength were lower in the transverse direction (p ≤ 0.009), but anisotropy was less pronounced in the OI group. Intracortical vascular porosity was almost six times higher in the OI group (p \u3c 0.001), but no differences were observed in osteocyte lacunar porosity between the groups (p = 0.086). Volumetric bone mineral density was lower in the OI group (p \u3c 0.001), but volumetric tissue mineral density was not (p = 0.770). Longitudinal OI bone modulus and strength were correlated with volumetric bone mineral density (p ≤ 0.024) but not volumetric tissue mineral density (p ≥ 0.099). Results indicate that cortical bone in children with severe OI yields at the same strain as normal bone, and that their decreased bone material strength is associated with reduced volumetric bone mineral density. These results will enable the advancement of fracture risk assessment capability in children with severe OI