Fast pseudo-enhancement correction in CT colonography using linear shift-invariant filters

This paper presents a novel method to approximate shift-variant Gaussian filtering of an image using a set of shift-invariant Gaussian filters. This approximation affords filtering of the image using fast convolution techniques that rely on the FFT, while achieving a result that closely matches the shift-variant result. We demonstrate the method in a CT colonography application that reduces the pseudo-enhancement effect, which is a local brightening artifact in CT imaging that can result from the use of oral contrast agents. Experimental results demonstrate the effectiveness of the method and emphasize its computational efficiency

Feature Selection for Computer-Aided Polyp Detection using MRMR

In building robust classifiers for computer-aided detection (CAD) of lesions, selection of relevant features is of fundamental importance. Typically one is interested in determining which, of a large number of potentially redundant or noisy features, are most discriminative for classification. Searching all possible subsets of features is impractical computationally. This paper proposes a feature selection scheme combining AdaBoost with the Minimum Redundancy Maximum Relevance (MRMR) to focus on the most discriminative features. A fitness function is designed to determine the optimal number of features in a forward wrapper search. Bagging is applied to reduce the variance of the classifier and make a reliable selection. Experiments demonstrate that by selecting just 11 percent of the total features, the classifier can achieve better prediction on independent test data compared to the 70 percent of the total features selected by AdaBoost

Image segmentation using joint spatial-intensity-shape features: Application to CT lung nodule segmentation

Automatic segmentation of medical images is a challenging problem due to the complexity and variability of human anatomy, poor contrast of the object being segmented, and noise resulting from the image acquisition process. This paper presents a novel non-parametric feature analysis method for the segmentation of 3D medical lesions. The proposed algorithm combines 1) a volumetric shape feature (shape index) based on high-order partial derivatives; 2) mean shift clustering in a joint spatial-intensity-shape (JSIS) feature space; and 3) a modified expectation-maximization (MEM) algorithm on the mean shift mode map to merge the neighboring regions (modes). In such a scenario, the volumetric shape feature is integrated into the process of the segmentation algorithm. The joint spatial–intensity-shape features provide rich information for the segmentation of the anatomic structures or lesions (tumors). The proposed method has been evaluated on a clinical dataset of thoracic CT scans that contains 68 nodules. A volume overlap ratio between each segmented nodule and the ground truth annotation is calculated. Using the proposed method, the mean overlap ratio over all the nodules is 0.80. On visual inspection and using a quantitative evaluation, the experimental results demonstrate the potential of the proposed method. It can properly segment a variety of nodules including juxta-vascular and juxta-pleural nodules, which are challenging for conventional methods due to the high similarity of intensities between the nodules and their adjacent tissues. This approach could also be applied to lesion segmentation in other anatomies, such as polyps in the colon

Enhanced detection in CT colonography using adaptive diffusion filtering

Computer-aided detection (CAD) is a computerized procedure in medical science that supports the medical team’s interpretations and decisions. CAD uses information from a medical imaging modality such as Computed Tomography to detect suspicious lesions. Algorithms to detect these lesions are based on geometrical models which can describe the local structures and thus provide potential region candidates. Geometrical descriptive models are very dependent on the data quality which may affect the false positive rates in CAD. In this paper we propose an efficient adaptive diffusion technique that adaptively controls the diffusion flux of the local structures in the data using robust statistics. The proposed method acts isotropically in the homogeneous regions and anisotropically in the vicinity of jump discontinuities. This method structurally enhances the data and makes the geometrical descriptive models robust. For the iterative solver, we use an efficient gradient descent flows solver based on a PDE formulation of the problem. The whole proposed strategy, which makes use of adaptive diffusion filter coupled with gradient descent flows has been developed and evaluated on clinical data in the application to colonic polyp detection in Computed Tomography Colonoscopy

Redox-neutral organocatalytic Mitsunobu reactions

Nucleophilic substitution reactions of alcohols are amongst the most fundamental and strategically important transformations in organic chemistry. For over half a century these reactions have been achieved using stoichiometric, and often hazardous, reagents to activate the otherwise unreactive alcohols. Here we demonstrate that a specially designed phosphine oxide promotes nucleophilic substitution reactions of primary and secondary alcohols within a redoxneutral catalysis manifold that produces water as the sole by-product. The scope of the catalytic coupling process encompasses a range of acidic pronucleophiles that allow stereospecific construction of carbon-oxygen and carbon-nitrogen bonds

CD94-NKG2A recognition of human leukocyte antigen (HLA)-E bound to an HLA class I leader sequence

The recognition of human leukocyte antigen (HLA)-E by the heterodimeric CD94-NKG2 natural killer (NK) receptor family is a central innate mechanism by which NK cells monitor the expression of other HLA molecules, yet the structural basis of this highly specific interaction is unclear. Here, we describe the crystal structure of CD94-NKG2A in complex with HLA-E bound to a peptide derived from the leader sequence of HLA-G. The CD94 subunit dominated the interaction with HLA-E, whereas the NKG2A subunit was more peripheral to the interface. Moreover, the invariant CD94 subunit dominated the peptide-mediated contacts, albeit with poor surface and chemical complementarity. This unusual binding mode was consistent with mutagenesis data at the CD94-NKG2A–HLA-E interface. There were few conformational changes in either CD94-NKG2A or HLA-E upon ligation, and such a “lock and key” interaction is typical of innate receptor–ligand interactions. Nevertheless, the structure also provided insight into how this interaction can be modulated by subtle changes in the peptide ligand or by the pairing of CD94 with other members of the NKG2 family. Differences in the docking strategies used by the NKG2D and CD94-NKG2A receptors provided a basis for understanding the promiscuous nature of ligand recognition by NKG2D compared with the fidelity of the CD94-NKG2 receptors

A structural basis for selection and cross-species reactivity of the semi-invariant NKT cell receptor in CD1d/glycolipid recognition

Little is known regarding the basis for selection of the semi-invariant αβ T cell receptor (TCR) expressed by natural killer T (NKT) cells or how this mediates recognition of CD1d–glycolipid complexes. We have determined the structures of two human NKT TCRs that differ in their CDR3β composition and length. Both TCRs contain a conserved, positively charged pocket at the ligand interface that is lined by residues from the invariant TCR α- and semi-invariant β-chains. The cavity is centrally located and ideally suited to interact with the exposed glycosyl head group of glycolipid antigens. Sequences common to mouse and human invariant NKT TCRs reveal a contiguous conserved “hot spot” that provides a basis for the reactivity of NKT cells across species. Structural and functional data suggest that the CDR3β loop provides a plasticity mechanism that accommodates recognition of a variety of glycolipid antigens presented by CD1d. We propose a model of NKT TCR–CD1d–glycolipid interaction in which the invariant CDR3α loop is predicted to play a major role in determining the inherent bias toward CD1d. The findings define a structural basis for the selection of the semi-invariant αβ TCR and the unique antigen specificity of NKT cells

Natural HLA Class I Polymorphism Controls the Pathway of Antigen Presentation and Susceptibility to Viral Evasion

HLA class I polymorphism creates diversity in epitope specificity and T cell repertoire. We show that HLA polymorphism also controls the choice of Ag presentation pathway. A single amino acid polymorphism that distinguishes HLA-B*4402 (Asp116) from B*4405 (Tyr116) permits B*4405 to constitutively acquire peptides without any detectable incorporation into the transporter associated with Ag presentation (TAP)-associated peptide loading complex even under conditions of extreme peptide starvation. This mode of peptide capture is less susceptible to viral interference than the conventional loading pathway used by HLA-B*4402 that involves assembly of class I molecules within the peptide loading complex. Thus, B*4402 and B*4405 are at opposite extremes of a natural spectrum in HLA class I dependence on the PLC for Ag presentation. These findings unveil a new layer of MHC polymorphism that affects the generic pathway of Ag loading, revealing an unsuspected evolutionary trade-off in selection for optimal HLA class I loading versus effective pathogen evasion

Reproductive health for refugees by refugees in Guinea III: maternal health

BACKGROUND: Maternal mortality can be particularly high in conflict and chronic emergency settings, partly due to inaccessible maternal care. This paper examines associations of refugee-led health education, formal education, age, and parity on maternal knowledge, attitudes, and practices among reproductive-age women in refugee camps in Guinea. METHODS: Data comes from a 1999 cross-sectional survey of 444 female refugees in 23 camps. Associations of reported maternal health outcomes with exposure to health education (exposed versus unexposed), formal education (none versus some), age (adolescent versus adult), or parity (nulliparous, parous, grand multiparous), were analysed using logistic regression. RESULTS: No significant differences were found in maternal knowledge or attitudes. Virtually all respondents said pregnant women should attend antenatal care and knew the importance of tetanus vaccination. Most recognised abdominal pain (75%) and headaches (24%) as maternal danger signs and recommended facility attendance for danger signs. Most had last delivered at a facility (67%), mainly for safety reasons (99%). Higher odds of facility delivery were found for those exposed to RHG health education (adjusted odds ratio 2.03, 95%CI 1.23-3.01), formally educated (adjusted OR 1.93, 95%CI 1.05-3.92), or grand multipara (adjusted OR 2.13, 95%CI 1.21-3.75). Main reasons for delivering at home were distance to a facility (94%) and privacy (55%). CONCLUSIONS: Refugee-led maternal health education appeared to increase facility delivery for these refugee women. Improved knowledge of danger signs and the importance of skilled birth attendance, while vital, may be less important in chronic emergency settings than improving facility access where quality of care is acceptable

Missing children: risks, repeats and responses

Investigating reports of missing children is a major source of demand for the police in the UK. Repeat disappearances are common, can indicate underlying vulnerabilities and have been linked with various forms of exploitation and abuse. Inspired by research on repeat victimisation, this paper examines the prevalence and temporal patterns of repeat missing episodes by children, as well as the characteristics of those involved. Using data on all missing children incidents recorded by one UK police service in 2015 (n = 3,352), we find that: (a) 75% of missing incidents involving children were repeats, i.e. attributed to children who had already been reported missing in 2015; (b) a small proportion of repeatedly missing children (n = 59; 4%) accounted for almost a third of all missing children incidents (n = 952, 28%); (c) over half of all first repeat disappearances occurred within four weeks of an initial police recorded missing episode; and (d) children recorded as missing ten times or more over the one year study period were significantly more likely than those recorded missing once to be teenagers, in the care system or to have drug and/or alcohol dependencies. We conclude by discussing the implications of our findings for future research and the prevention of repeat disappearances by children