An automated framework for localization, segmentation and super-resolution reconstruction of fetal brain MRI.

High-resolution volume reconstruction from multiple motion-corrupted stacks of 2D slices plays an increasing role for fetal brain Magnetic Resonance Imaging (MRI) studies. Currently existing reconstruction methods are time-consuming and often require user interactions to localize and extract the brain from several stacks of 2D slices. We propose a fully automatic framework for fetal brain reconstruction that consists of four stages: 1) fetal brain localization based on a coarse segmentation by a Convolutional Neural Network (CNN), 2) fine segmentation by another CNN trained with a multi-scale loss function, 3) novel, single-parameter outlier-robust super-resolution reconstruction, and 4) fast and automatic high-resolution visualization in standard anatomical space suitable for pathological brains.

DeepIGeoS: A Deep Interactive Geodesic Framework for Medical Image Segmentation.

Accurate medical image segmentation is essential for diagnosis, surgical planning and many other applications. Convolutional Neural Networks (CNNs) have become the state-of-the-art automatic segmentation methods. However, fully automatic results may still need to be refined to become accurate and robust enough for clinical use.

Interactive Medical Image Segmentation Using Deep Learning With Image-Specific Fine Tuning.

Convolutional neural networks (CNNs) have achieved state-of-the-art performance for automatic medical image segmentation. However, they have not demonstrated sufficiently accurate and robust results for clinical use. In addition, they are limited by the lack of image-specific adaptation and the lack of generalizability to previously unseen object classes (a.

Novel CT-Based Objective Imaging Biomarkers of Long-Term Radiation-Induced Lung Damage.

Purpose: Recent improvements in lung cancer survival have spurred an interest in understanding and minimizing long-term radiation-induced lung damage (RILD). However, there are still no objective criteria to quantify RILD, leading to variable reporting across centers and trials. We propose a set of objective imaging biomarkers for quantifying common radiologic findings observed 12 months after lung cancer radiation therapy.

NiftyNet: a deep-learning platform for medical imaging.

Background And Objectives: Medical image analysis and computer-assisted intervention problems are increasingly being addressed with deep-learning-based solutions. Established deep-learning platforms are flexible but do not provide specific functionality for medical image analysis and adapting them for this domain of application requires substantial implementation effort. Consequently, there has been substantial duplication of effort and incompatible infrastructure developed across many research groups.

GIFT-Cloud: A data sharing and collaboration platform for medical imaging research.

Objectives: Clinical imaging data are essential for developing research software for computer-aided diagnosis, treatment planning and image-guided surgery, yet existing systems are poorly suited for data sharing between healthcare and academia: research systems rarely provide an integrated approach for data exchange with clinicians; hospital systems are focused towards clinical patient care with limited access for external researchers; and safe haven environments are not well suited to algorithm development. We have established GIFT-Cloud, a data and medical image sharing platform, to meet the needs of GIFT-Surg, an international research collaboration that is developing novel imaging methods for fetal surgery. GIFT-Cloud also has general applicability to other areas of imaging research.

Chronic Obstructive Pulmonary Disease: Lobar Analysis with Hyperpolarized Xe MR Imaging.

Purpose To compare lobar ventilation and apparent diffusion coefficient (ADC) values obtained with hyperpolarized xenon 129 (Xe) magnetic resonance (MR) imaging to quantitative computed tomography (CT) metrics on a lobar basis and pulmonary function test (PFT) results on a whole-lung basis in patients with chronic obstructive pulmonary disease (COPD). Materials and Methods The study was approved by the National Research Ethics Service Committee; written informed consent was obtained from all patients. Twenty-two patients with COPD (Global Initiative for Chronic Obstructive Lung Disease stage II-IV) underwent hyperpolarized Xe MR imaging at 1.

Slic-Seg: A minimally interactive segmentation of the placenta from sparse and motion-corrupted fetal MRI in multiple views.

Segmentation of the placenta from fetal MRI is challenging due to sparse acquisition, inter-slice motion, and the widely varying position and shape of the placenta between pregnant women. We propose a minimally interactive framework that combines multiple volumes acquired in different views to obtain accurate segmentation of the placenta. In the first phase, a minimally interactive slice-by-slice propagation method called Slic-Seg is used to obtain an initial segmentation from a single motion-corrupted sparse volume image.

Computational modeling of the obstructive lung diseases asthma and COPD.

Asthma and chronic obstructive pulmonary disease (COPD) are characterized by airway obstruction and airflow imitation and pose a huge burden to society. These obstructive lung diseases impact the lung physiology across multiple biological scales. Environmental stimuli are introduced via inhalation at the organ scale, and consequently impact upon the tissue, cellular and sub-cellular scale by triggering signaling pathways.

Review of automatic pulmonary lobe segmentation methods from CT.

The computational detection of pulmonary lobes from CT images is a challenging segmentation problem with important respiratory health care applications, including surgical planning and regional image analysis. Several authors have proposed automated algorithms and we present a methodological review. These algorithms share a number of common stages and we consider each stage in turn, comparing the methods applied by each author and discussing their relative strengths.

An alternate delivery system improves vaccine performance against foot-and-mouth disease virus (FMDV).

Foot-and-mouth disease virus (FMDV) causes vesicular disease of cloven-hoofed animals with severe agricultural and economic implications. One of the most highly infectious and contagious livestock pathogens known, the disease spreads rapidly in naïve populations making it critical to have rapidly acting vaccines. Needle inoculation of killed virus vaccine is an efficient method of swiftly vaccinating large numbers of animals, either in eradication efforts or in outbreak situations in disease free countries, although, to be efficient, this requires utilizing the same needle with multiple animals.

Innate immune defenses induced by CpG do not promote vaccine-induced protection against foot-and-mouth disease virus in pigs.

Emergency vaccination as part of the control strategies against foot-and-mouth disease virus (FMDV) has the potential to limit virus spread and reduce large-scale culling. To reduce the time between vaccination and the onset of immunity, immunostimulatory CpG was tested for its capacity to promote early protection against FMDV challenge in pigs. To this end, CpG 2142, an efficient inducer of alpha interferon, was injected intramuscularly.

Vaccination against foot-and-mouth disease virus confers complete clinical protection in 7 days and partial protection in 4 days: Use in emergency outbreak response.

Recent outbreaks of foot-and-mouth disease virus (FMDV) demonstrate that this highly contagious viral infection of cloven hoofed animals continues to be a significant economic problem worldwide. Debate about the most effective way to respond to outbreaks of FMDV in disease free countries continues to center on the use of vaccines. In this report, we present data showing that a commercially available, standard dose vaccine formulation can fully protect cattle against direct challenge with the virus in as little as 7 days with no carrier transmission to naïve animals.

Natural and vaccine induced immunity to FMD.

A brief overview of the foot-and-mouth disease (FMD) literature over the last 100 years will give the impression that a great deal is known about the immune response of livestock to infection and vaccination. At the practical level, this is indeed the case and our knowledge is more than adequate in relation to the production and supply of potent vaccines for the control of the disease. The deficiencies in our understanding of the immune response are at the fundamental level and, arguably, stand in the way of its rational manipulation to achieve goals such as life-long immunity conferred by vaccination.

Optimisation of the immune response to foot-and-mouth disease vaccines.

Considering the many variables influencing the immune response of the host to vaccination against foot-and-mouth disease (FMD), the properties and characteristics of the vaccine and recommendations concerning its mode of application offer the best opportunity for the manufacturer to provide safe, effective protection of livestock. There are a number of critical elements in the production of FMD vaccines, such as the selection of appropriate strain(s), which have a direct bearing on the quality of the immune response. Equally, development of effective immunity depends on proper and timely application of good quality vaccine.

Heterotypic recognition of recombinant FMDV proteins by bovine T-cells: the polymerase (P3Dpol) as an immunodominant T-cell immunogen.

In this study we have examined the recognition of VP0, VP1, VP2, VP3 and P3Dpol by PBMC and CD4+ T-cells from infected, vaccinated-challenged, and multiply-vaccinated (O1, A24, C1 or ASIA1) cattle using recombinant proteins of an O1 serotype virus. The structural protein VP1 was recognised in an homotypic context whereas VP2, VP3, VP4 and P3Dpol were also recognised by T-cells from animals exposed to heterotypic viruses. Only the non-structural protein P3Dpol was consistently recognised by T-cells from the majority of animals examined and heterotypic recognition correlated with the presence of serologically detectable P3Dpol in purified virus.

Natural and vaccine-induced immunity to foot and mouth disease: the prospects for improved vaccines.

The review considers both the immune responses of livestock to foot and mouth disease (FMD) virus after infection or vaccination, and the characteristics and properties of FMD viruses and vaccines which are relevant to protection. Particular attention is given to possible approaches which could be used to improve conventional vaccines or produce novel vaccines against this most important disease.

International bank for foot-and-mouth disease vaccine: assessment of Montanide ISA 25 and ISA 206, two commercially available oil adjuvants.

The International Vaccine Bank at Pirbright has recently installed large-scale vaccine formulation equipment for the preparation of oil-adjuvanted vaccines. Such vaccines are claimed to offer a number of advantages over Al(OH)3, particularly their ability to raise better immunity in pigs. This paper reports on the potency in pigs, cattle and guinea-pigs of foot-and-mouth disease vaccines prepared with two novel oil adjuvants, Montanide ISA 25 and 206 (Seppic, Paris).

A protective anti-peptide antibody against the immunodominant site of the A24 Cruzeiro strain of foot-and-mouth disease virus and its reactivity with other subtype viruses containing the same minimum binding sequence.

A synthetic peptide vaccine of the general sequence Cys-Cys-(200-213)-Pro-Pro-Ser-(l41-158)-Pro-Cys-Gly(peptide A40), where the numbered residues refer to the VP1 sequence of foot-and-mouth disease virus (FMDV) strain A24 Cruzeiro, has previously been shown to elicit neutralizing and protective antibodies in guinea-pigs and cattle. To examine this immunogenic tract in more detail monoclonal antibodies (MAbs) were raised to this peptide. One such MAb C1.

Recognition of foot-and-mouth disease virus and its capsid protein VP1 by bovine peripheral T lymphocytes.

The role of T cells in immunity to foot-and-mouth disease virus is still poorly defined compared to that of the humoral response. In this paper we describe a systematic, longitudinal study on the cellular recognition of FMDV and its subunit protein VP1 by bovine peripheral blood T lymphocytes. Multiple vaccination with a single virus serotype induced a serotype cross-reactive proliferative T cell repertoire that varied in magnitude between individual animals and with the serotype of the vaccine used.

The expression of the proteins of equine herpesvirus 1 which share homology with herpes simplex virus 1 glycoproteins H and L.

Several expression systems were used in studies aimed at characterizing the equine herpesvirus 1 (EHV-1) glycoprotein H and L homologues of HSV-1 (EHV-1 gH and gL) and the products were compared to the authentic proteins synthesized in virus infected cells. Using an in vitro transcription/translation system two gH species were detected (an unprocessed 89 kDa and a processed 116 kDa product). Three low molecular weight proteins were found in the case of gL (21.

Emergency vaccination against foot-and-mouth disease: rate of development of immunity and its implications for the carrier state.

Emergency foot-and-mouth disease (FMD) vaccines prepared from antigens held in the International Vaccine Bank at Pirbright were administered to cattle and pigs and the levels of protection were assessed following challenge by contact with infected pigs. Both Al(OH)3/saponin and oil-based cattle vaccines proved to be extremely effective and protected soon after vaccination (4 days postvaccination), whereas the pigs were seldom protected before 21 and 28 days postvaccination, probably due to lower levels of antibody and overwhelming challenge conditions. Early production of cattle occurred in the absence of significant levels of circulating antibody as measured by enzyme-linked immunosorbent assay, a neutralization assay and a passive protection test.

Detection of foot-and-mouth disease viral sequences in clinical specimens and ethyleneimine-inactivated preparations by the polymerase chain reaction.

The polymerase chain reaction method (PCR) has been applied to the diagnosis of foot-and-mouth disease viral RNA in tissues and, particularly, oesophageal-pharyngeal fluid (probang) samples from cattle. Using primer sets which corresponded to conserved regions of the VP1 sequence of the viral genome, it was possible to amplify sequences regardless of the serotype/strain of the virus. In comparison with infectivity assays, the PCR was generally more sensitive although there were a number of examples where only infectivity was detectable.

Foot-and-mouth disease: the risk for Great Britain after 1992.

Mass annual vaccination against foot-and-mouth disease, previously applied by eight member states in the European Community (EC), was progressively phased out during 1990-91. The other four member states (the United Kingdom, Denmark, the Republic of Ireland and Greece) either never have vaccinated or ceased to do so several years ago. The EC should increase its international competitiveness if it maintains its present foot-and-mouth disease-free, non-vaccinating status.