Segmentation of epidermal tissue with histopathological damage in images of haematoxylin and eosin stained human skin.

Background: Digital image analysis has the potential to address issues surrounding traditional histological techniques including a lack of objectivity and high variability, through the application of quantitative analysis. A key initial step in image analysis is the identification of regions of interest. A widely applied methodology is that of segmentation. This paper proposes the application of image analysis techniques to segment skin tissue with varying degrees of histopathological damage. The segmentation of human tissue is challenging as a consequence of the complexity of the tissue structures and inconsistencies in tissue preparation, hence there is a need for a new robust method with the capability to handle the additional challenges materialising from histopathological damage.Methods: A new algorithm has been developed which combines enhanced colour information, created following a transformation to the L*a*b* colourspace, with general image intensity information. A colour normalisation step is included to enhance the algorithm's robustness to variations in the lighting and staining of the input images. The resulting optimised image is subjected to thresholding and the segmentation is fine-tuned using a combination of morphological processing and object classification rules. The segmentation algorithm was tested on 40 digital images of haematoxylin & eosin (H&E) stained skin biopsies. Accuracy, sensitivity and specificity of the algorithmic procedure were assessed through the comparison of the proposed methodology against manual methods.Results: Experimental results show the proposed fully automated methodology segments the epidermis with a mean specificity of 97.7%, a mean sensitivity of 89.4% and a mean accuracy of 96.5%. When a simple user interaction step is included, the specificity increases to 98.0%, the sensitivity to 91.0% and the accuracy to 96.8%. The algorithm segments effectively for different severities of tissue damage.Conclusions: Epidermal segmentation is a crucial first step in a range of applications including melanoma detection and the assessment of histopathological damage in skin. The proposed methodology is able to segment the epidermis with different levels of histological damage. The basic method framework could be applied to segmentation of other epithelial tissues

An Intermittent Live Cell Imaging Screen for siRNA Enhancers and Suppressors of a Kinesin-5 Inhibitor

Kinesin-5 (also known as Eg5, KSP and Kif11) is required for assembly of a bipolar mitotic spindle. Small molecule inhibitors of Kinesin-5, developed as potential anti-cancer drugs, arrest cell in mitosis and promote apoptosis of cancer cells. We performed a genome-wide siRNA screen for enhancers and suppressors of a Kinesin-5 inhibitor in human cells to elucidate cellular responses, and thus identify factors that might predict drug sensitivity in cancers. Because the drug's actions play out over several days, we developed an intermittent imaging screen. Live HeLa cells expressing GFP-tagged histone H2B were imaged at 0, 24 and 48 hours after drug addition, and images were analyzed using open-source software that incorporates machine learning. This screen effectively identified siRNAs that caused increased mitotic arrest at low drug concentrations (enhancers), and vice versa (suppressors), and we report siRNAs that caused both effects. We then classified the effect of siRNAs for 15 genes where 3 or 4 out of 4 siRNA oligos tested were suppressors as assessed by time lapse imaging, and by testing for suppression of mitotic arrest in taxol and nocodazole. This identified 4 phenotypic classes of drug suppressors, which included known and novel genes. Our methodology should be applicable to other screens, and the suppressor and enhancer genes we identified may open new lines of research into mitosis and checkpoint biology

Ruminant Brucellosis in the Kafr El Sheikh Governorate of the Nile Delta, Egypt: Prevalence of a Neglected Zoonosis

Brucellosis is a zoonosis of mammals caused by bacteria of the genus Brucella. It is responsible for a vast global burden imposed on human health through disability and on animal productivity. In humans brucellosis causes a range of flu-like symptoms and chronic debilitating illness. In livestock brucellosis causes economic losses as a result of abortion, infertility and decreased milk production. The main routes for human infection are consumption of contaminated dairy products and contact with infected ruminants. The control of brucellosis in humans depends on its control in ruminants, for which accurate estimates of the frequency of infection are very useful, especially in areas with no previous frequency estimates. We studied the seroprevalence of brucellosis and its geographic distribution among domestic ruminants in one governorate of the Nile Delta region, Egypt. In the study area, the seroprevalence of ruminant brucellosis is very high and has probably increased considerably since the early 1990s. The disease is widespread but more concentrated around major animal markets. These findings question the efficacy of the control strategy in place and highlight the high infection risk for the animal and human populations of the area and the urgent need for an improved control strategy

Finishing the euchromatic sequence of the human genome

The sequence of the human genome encodes the genetic instructions for human physiology, as well as rich information about human evolution. In 2001, the International Human Genome Sequencing Consortium reported a draft sequence of the euchromatic portion of the human genome. Since then, the international collaboration has worked to convert this draft into a genome sequence with high accuracy and nearly complete coverage. Here, we report the result of this finishing process. The current genome sequence (Build 35) contains 2.85 billion nucleotides interrupted by only 341 gaps. It covers ∼99% of the euchromatic genome and is accurate to an error rate of ∼1 event per 100,000 bases. Many of the remaining euchromatic gaps are associated with segmental duplications and will require focused work with new methods. The near-complete sequence, the first for a vertebrate, greatly improves the precision of biological analyses of the human genome including studies of gene number, birth and death. Notably, the human enome seems to encode only 20,000-25,000 protein-coding genes. The genome sequence reported here should serve as a firm foundation for biomedical research in the decades ahead

The Faber Book of Modern Verse

xx,432hal.;19c

Can internal elastic properties of cartilage be measured using MR elastography?

grantor: University of TorontoCartilage has internal variations in molecular structure, composition and possibly mechanical properties depending on position within and location of the tissue within the joint. I have examined the possibility of using MR Elastography as a way to measure the internal variations in elastic properties of cartilage. An apparatus was built to compress cartilage and coils were made to obtain the necessary SNR and resolution. Strain data was obtained in homogeneous gel samples. Changes in strain on the order that would be expected for samples differing in Young's modulus by a factor of 2 were measured. Strain was then measured in Young bovine cartilage samples and found to vary both within the sample and between samples. Cartilage proteoglycans were degraded with trypsin, softening the tissue, and the corresponding increase in strain was measured. Strain images and plots representing variations in elastic properties of cartilage were obtained using MR Elastography.M.Sc

Studies on Brucella ovis infection in deer : a thesis presented in fulfilment of the requirements for the degree of Doctor of Philosophy in Veterinary Clinical Science at Massey University, Palmerston North, New Zealand

Brucella ovis was first identified in the New Zealand farmed deer population in 1996 but little was known about the disease in deer. These experiments were undertaken to investigate the epidemiology, pathophysiology and diagnosis of B. ovis infection in deer. In addition, B. ovis isolates from commercial rams and stags were strain typed by pulsed-field gel electrophoresis. Transmission of infection was demonstrated from infected rams to stags grazing in the same paddock, suggesting that the initial source of infection for deer in New Zealand was likely to have been from rams. Transmission between stags did not occur after shifting non-infected stags into paddocks immediately vacated by infected stags, or after grazing non-infected stags in a paddock adjacent to infected stags over a five and a half month period. This suggests that the risk of transmission of B. ovis by the environment or indirect deer to deer contact is low. Stags became infected with B. ovis after experimental inoculation of the conjunctival, nasal and rectal mucous membranes. Behavioural observations identified that stags in all-male groups interact by mounting, sniffing the prepuce and perineum and spraying fluid from an extruded penis, which are considered high risk for the transmission of B. ovis. It was established that while stags are initially as susceptible to B. ovis infection as rams the majority of stags stop shedding B. ovis in semen within 11 months of infection, suggesting resolution of infection. In contrast, all rams remained infected with B. ovis and shed the organism in semen for at least 21 months. During the B. ovis shedding phase of infection, the majority of stags produced semen that had poor sperm motility and morphology and contained large numbers of leukocytes and cellular debris. However, following cessation of shedding stags produced semen that had good sperm motility and morphology, although leukocytes were still present. The sensitivity of the commercially available serological tests at detecting infection in deer was 100% during the early stages of the disease but after 60 to 100 days of infection, their sensitivity decreased to 30 to 70%. In contrast, the sensitivity in rams over a 630-day period was 100%. Detection of lesions of epididymitis by scrotal palpation of stags was an insensitive method of diagnosing infection. Stags infected with B. ovis developed lesions in the epididymes, seminal vesicles and ampullae similar to those reported in rams. In the early stages of the infection, lesions in stags were severe but in more chronic infections the lesions were mild. Vaginal inoculation of hinds immediately prior to mating resulted in no measurable adverse effects on reproduction, suggesting the disease is of little significance in hinds. Stags that mated vaginally-infected hinds became infected, demonstrating venereal transmission of the organism. Pulsed-field gel electrophoresis of B. ovis isolates revealed the presence of two strain types of B. ovis in the New Zealand farmed sheep and deer populations. Cervine isolates from two naturally-occurring cases of B. ovis in stags were different strain types. This confirmed that the two cases were unrelated, again highlighting the importance of rams in the epidemiology of this disease in dee

Poems and some letters. Edited, with a biographical and critical introduction and textual notes by Anne Ridler.

OPLADEN-RUG0

Economic Cost of Ovine Johne’s Disease in Clinically Affected New Zealand Flocks and Benefit-Cost of Vaccination

The aims of this study were to estimate the on-fam economic cost of ovine Johne’s disease (OJD) based on collected incidence and mortality data, and the benefit-cost of OJD vaccination in typical OJD affected flocks in New Zealand after having vaccinated for a number of years. Owners of 20 sheep breeding and finishing farms known to be clinically affected by ovine Johne’s disease in New Zealand participated in the study and were monitored for up to two years. Farms were categorized as fine-wool (Merino, Half-Bred, Corriedale, n = 15), and other breeds (Romney, composite breeds, n = 5). Ovine JD was confirmed by gross- and histo-pathology in 358 ewes culled due to chronic progressive wasting. An additional 228 ewes with low body condition score (BCS), but not targeted for culling, were tested with ELISA to estimate the proportion of OJD in ewes in the lower 5% BCS of the flock. Calculations were done separately for fine-wool and other breeds. Based on the data, mortality due to OJD, its associated cost and the benefit-cost of vaccination were evaluated for a hypothetical farm with 2000 ewes by stochastic simulation. Total ewe mortality was similar in fine-wool and other breeds, but the estimated mortality due to OJD was 2.7 times as high in fine-wool (median 1.8%, interquartile range IQR 1.2–2.7%) than other breeds (median 0.69%, IQR 0.3–1.2%), but with large variation between farms. ELISA results demonstrated fine-wool sheep had a higher seroprevalence than other breeds (39%, 95% CI 18–61% vs. 9%, 95% CI 0–22%). Stochastic modelling indicated that the average annual cost of mortality due to OJD in a flock of 2000 ewes was NZD 13,100 (IQR 8900–18,600) in fine-wool and NZD 4300 (IQR 2200–7600) in other breeds. Vaccinating replacement lambs against OJD may be cost-effective in most flocks when the pre-vaccination annual ewe mortality due to OJD is >1%. To make the best-informed decision about vaccination it is therefore essential for farmers to accurately diagnose OJD to establish incidence