LoAd: a locally adaptive cortical segmentation algorithm

Thickness measurements of the cerebral cortex can aid diagnosis and provide valuable information about the temporal evolution of diseases such as Alzheimer's, Huntington's, and schizophrenia. Methods that measure the thickness of the cerebral cortex from in-vivo magnetic resonance (MR) images rely on an accurate segmentation of the MR data. However, segmenting the cortex in a robust and accurate way still poses a challenge due to the presence of noise, intensity non-uniformity, partial volume effects, the limited resolution of MRI and the highly convoluted shape of the cortical folds. Beginning with a well-established probabilistic segmentation model with anatomical tissue priors, we propose three post-processing refinements: a novel modification of the prior information to reduce segmentation bias; introduction of explicit partial volume classes; and a locally varying MRF-based model for enhancement of sulci and gyri. Experiments performed on a new digital phantom, on BrainWeb data and on data from the Alzheimer's Disease Neuroimaging Initiative (ADNI) show statistically significant improvements in Dice scores and PV estimation (p<10(-3)) and also increased thickness estimation accuracy when compared to three well established techniques.

A framework for using diffusion weighted imaging to improve cortical parcellation

Cortical parcellation refers to anatomical labelling of every point in the cortex. An accurate parcellation is useful in many analysis techniques including the study of regional changes in cortical thickness or volume in ageing and neurodegeneration. Parcellation is also key to anatomic apportioning of functional imaging changes. We present preliminary work on a novel algorithm that takes an entire cortical parcellation and iteratively updates it to better match connectivity information derived from diffusion weighted imaging. We demonstrate the algorithm on a cohort of 17 healthy controls. Initial results show the algorithm recovering artificially induced mis-registrations of the parcellation and also converging to a group-wise average. This work introduces a framework to investigate the relationship between structure and function, with no a-priori knowledge of specific regions of interest.

Automated cross-sectional and longitudinal hippocampal volume measurement in mild cognitive impairment and Alzheimer's disease

Volume and change in volume of the hippocampus are both important markers of Alzheimer's disease (AD). Delineation of the structure on MRI is time-consuming and therefore reliable automated methods are required. We describe an improvement (multiple-atlas propagation and segmentation (MAPS)) to our template library-based segmentation technique. The improved technique uses non-linear registration of the best-matched templates from our manually segmented library to generate multiple segmentations and combines them using the simultaneous truth and performance level estimation (STAPLE) algorithm. Change in volume over 12months (MAPS-HBSI) was measured by applying the boundary shift integral using MAPS regions. Methods were developed and validated against manual measures using subsets from Alzheimer's Disease Neuroimaging Initiative (ADNI). The best method was applied to 682 ADNI subjects, at baseline and 12-month follow-up, enabling assessment of volumes and atrophy rates in control, mild cognitive impairment (MCI) and AD groups, and within MCI subgroups classified by subsequent clinical outcome. We compared our measures with those generated by Surgical Navigation Technologies (SNT) available from ADNI. The accuracy of our volumes was one of the highest reported (mean(SD) Jaccard Index 0.80(0.04) (N=30)). Both MAPS baseline volume and MAPS-HBSI atrophy rate distinguished between control, MCI and AD groups. Comparing MCI subgroups (reverters, stable and converters): volumes were lower and rates higher in converters compared with stable and reverter groups (p< or =0.03). MAPS-HBSI required the lowest sample sizes (78 subjects) for a hypothetical trial. In conclusion, the MAPS and MAPS-HBSI methods give accurate and reliable volumes and atrophy rates across the clinical spectrum from healthy aging to AD.

Patterns of cortical thickness according to APOE genotype in Alzheimer's disease

BACKGROUND

Possession of one or more apolipoprotein E (APOE) epsilon4 alleles may influence the distribution of atrophy and clinical phenotype. We aimed to assess the influence of APOE genotype on cortical thickness and regional brain volumes in AD (Alzheimer's disease).

METHODS

We included 38 patients (9 epsilon4 non-carriers, 23 epsilon4 heterozygotes, 6 epsilon4 homozygotes) and 23 controls. Each subject had 2 magnetic resonance imaging (MRI) scans and a neuropsychological battery. Cortical thickness and isthmus cingulate volume were measured using FreeSurfer; the volumes of the hippocampus, whole brain, and lateral ventricles were calculated using manual and semi-automated volumetry.

RESULTS

Compared with controls, cortical thickness was significantly lower: in the bilateral temporal, posterior parietal and occipital regions in non-carriers, in the medial temporal and left parietal regions in heterozygotes, and in the medial temporal lobe in homozygotes. Comparisons between AD subgroups did not show significant differences. A trend for larger brain and isthmus cingulate volumes and smaller hippocampal and ventricular volumes with increasing epsilon4 dose were seen. These differences were supported by neuropsychological profiles.

CONCLUSION

These results suggest that APOE genotype may influence the topography of regional atrophy and cortical thinning in AD.

Progressive logopenic/phonological aphasia: erosion of the language network

The primary progressive aphasias (PPA) are paradigmatic disorders of language network breakdown associated with focal degeneration of the left cerebral hemisphere. Here we addressed brain correlates of PPA in a detailed neuroanatomical analysis of the third canonical syndrome of PPA, logopenic/phonological aphasia (LPA), in relation to the more widely studied clinico-anatomical syndromes of semantic dementia (SD) and progressive nonfluent aphasia (PNFA). 32 PPA patients (9 SD, 14 PNFA, 9 LPA) and 18 cognitively normal controls had volumetric brain MRI with regional volumetry, cortical thickness, grey and white matter voxel-based morphometry analyses. Five of nine patients with LPA had cerebrospinal fluid biomarkers consistent with Alzheimer (AD) pathology (AD-PPA) and 2/9 patients had progranulin (GRN) mutations (GRN-PPA). The LPA group had tissue loss in a widespread left hemisphere network. Compared with PNFA and SD, the LPA group had more extensive involvement of grey matter in posterior temporal and parietal cortices and long association white matter tracts. Overlapping but distinct networks were involved in the AD-PPA and GRN-PPA subgroups, with more anterior temporal lobe involvement in GRN-PPA. The importance of these findings is threefold: firstly, the clinico-anatomical entity of LPA has a profile of brain damage that is complementary to the network-based disorders of SD and PNFA; secondly, the core phonological processing deficit in LPA is likely to arise from temporo-parietal junction damage but disease spread occurs through the dorsal language network (and in GRN-PPA, also the ventral language network); and finally, GRN mutations provide a specific molecular substrate for language network dysfunction.

Reduced cortical thickness in the posterior cingulate gyrus is characteristic of both typical and atypical Alzheimer's disease

Alzheimer's disease (AD) and frontotemporal lobar degeneration (FTLD) can be difficult to differentiate clinically due to overlapping symptoms. Subject classification in research studies is often based on clinical rather than pathological criteria which may mean some subjects are misdiagnosed and misclassified. Recently, methods measuring cortical thickness using magnetic resonance imaging have been suggested to be effective in differentiating between clinically-defined AD and frontotemporal dementia (FTD) in addition to showing disease-related patterns of atrophy. In this study we used FreeSurfer, a freely-available and automated software tool, to measure cortical thickness in 28 pathologically-confirmed AD patients, of which 11 had a typical amnestic presentation and 17 an atypical presentation during life, 23 pathologically-confirmed FTLD subjects, and 25 healthy controls. Patients with AD pathology, irrespective of clinical diagnosis, showed reduced cortical thickness bilaterally in the medial temporal lobe, posterior cingulate gyrus, precuneus, posterior parietal lobe, and frontal pole compared with controls. We further showed that lower cortical thickness in the posterior cingulate gyrus, parietal lobe, and frontal pole is suggestive of AD pathology in patients with behavioral or language deficits. In contrast, lower cortical thickness in the anterior temporal lobe and frontal lobe is indicative of the presence of FTLD pathology in patients with a clinical presentation of FTD. Reduced cortical thickness in the posterior cingulate gyrus is characteristic of AD pathology in patients with typical and atypical clinical presentations of AD, and may assist a clinical distinction of AD pathology from FTLD pathology.

Robust atrophy rate measurement in Alzheimer's disease using multi-site serial MRI: tissue-specific intensity normalization and parameter selection

We describe an improved method of measuring brain atrophy rates from serial MRI for multi-site imaging studies of Alzheimer's disease (AD). The method (referred to as KN-BSI) improves an existing brain atrophy measurement technique-the boundary shift integral (classic-BSI), by performing tissue-specific intensity normalization and parameter selection. We applied KN-BSI to measure brain atrophy rates of 200 normal and 141 AD subjects using baseline and 1-year MRI scans downloaded from the Alzheimer's Disease Neuroimaging Initiative database. Baseline and repeat images were reviewed as pairs by expert raters and given quality scores. Including all image pairs, regardless of quality score, mean KN-BSI atrophy rates were 0.09% higher (95% CI 0.03% to 0.16%, p=0.007) than classic-BSI rates in controls and 0.07% higher (-0.01% to 0.16%, p=0.07) higher in ADs. The SD of the KN-BSI rates was 22% lower (15% to 29%, p<0.001) in controls and 13% lower (6% to 20%, p=0.001) in ADs, compared to classic-BSI. Using these results, the estimated sample size (needed per treatment arm) for a hypothetical trial of a treatment for AD (80% power, 5% significance to detect a 25% reduction in atrophy rate) would be reduced from 120 to 81 (a 32% reduction, 95% CI=18% to 45%, p<0.001) when using KN-BSI instead of classic-BSI. We concluded that KN-BSI offers more robust brain atrophy measurement than classic-BSI and substantially reduces sample sizes needed in clinical trials.

Comparison of phantom and registration scaling corrections using the ADNI cohort

Rates of brain atrophy derived from serial magnetic resonance (MR) studies may be used to assess therapies for Alzheimer's disease (AD). These measures may be confounded by changes in scanner voxel sizes. For this reason, the Alzheimer's Disease Neuroimaging Initiative (ADNI) included the imaging of a geometric phantom with every scan. This study compares voxel scaling correction using a phantom with correction using a 9 degrees of freedom (9DOF) registration algorithm. We took 129 pairs of baseline and 1-year repeat scans, and calculated the volume scaling correction, previously measured using the phantom. We used the registration algorithm to quantify any residual scaling errors, and found the algorithm to be unbiased, with no significant (p=0.97) difference between control (n=79) and AD subjects (n=50), but with a mean (SD) absolute volume change of 0.20 (0.20) % due to linear scalings. 9DOF registration was shown to be comparable to geometric phantom correction in terms of the effect on atrophy measurement and unbiased with respect to disease status. These results suggest that the additional expense and logistic effort of scanning a phantom with every patient scan can be avoided by registration-based scaling correction. Furthermore, based upon the atrophy rates in the AD subjects in this study, sample size requirements would be approximately 10-12% lower with (either) correction for voxel scaling than if no correction was used.

Crystal structure of a nucleosome core particle containing the variant histone H2A.Z

Activation of transcription within chromatin has been correlated with the incorporation of the essential histone variant H2A.Z into nucleosomes. H2A.Z and other histone variants may establish structurally distinct chromosomal domains; however, the molecular mechanism by which they function is largely unknown. Here we report the 2.6 A crystal structure of a nucleosome core particle containing the histone variant H2A.Z. The overall structure is similar to that of the previously reported 2.8 A nucleosome structure containing major histone proteins. However, distinct localized changes result in the subtle destabilization of the interaction between the (H2A.Z-H2B) dimer and the (H3-H4)(2) tetramer. Moreover, H2A.Z nucleosomes have an altered surface that includes a metal ion. This altered surface may lead to changes in higher order structure, and/or could result in the association of specific nuclear proteins with H2A.Z. Finally, incorporation of H2A.Z and H2A within the same nucleosome is unlikely, due to significant changes in the interface between the two H2A.Z-H2B dimers.

The specificity of antibody responses in cattle naturally exposed to Fasciola hepatica

Fasciola hepatica causes significant morbidity and mortality in dairy cattle in the Andean region of Cajamarca, Peru, where prevalence of infection of up to 78% has been reported. ELISA and Western blot analyses were used to characterise antibody responses in dairy cattle to adult F. hepatica to excretory-secretory (E/S), somatic (SO) and surface (SU) antigens. Three groups of dairy cattle - calves, heifers and adult cows - naturally exposed to F. hepatica in this region, were monitored every 2 months over a 2-year period. Calves, heifers and adult cows all had antibodies which recognised a 28kDa protein in the SO preparation, whereas only adult cows had antibodies that recognised a 28kDa protein in E/S products. All three groups of cattle responded to a 60-66kDa group of proteins in E/S and SU preparations and a 17kDa antigen in SO products was recognised by antibodies from cows and heifers but not calves. The total antibody response to E/S antigens measured by ELISA, increased over time in calves and remained constantly high over the 2-year period in all three groups of cattle. Slight fluctuations in the antibody response occurred in the group of heifers and cows coinciding with seasonal changes in the level of challenge.

Distinct importin recognition properties of histones and chromatin assembly factors

Synthesis of the protein components of nuclear chromatin occurs in the cytoplasm, necessitating specific import into the nucleus. Here, we report the binding affinities of the nuclear localisation sequence (NLS)-binding importin subunits for a range of histones and chromatin assembly factors. The results suggest that import of histones to the nucleus may be mediated predominantly by importin beta1, whereas the import of the other components probably relies on the conventional alpha/beta1 import pathway. Differences in recognition by importin beta1 were observed between histone H2A and the variant H2AZ, as well as between histone H3/4 with or without acetylation. The results imply that different histone variants may possess distinct nuclear import properties, with acetylation possibly playing an inhibitory role through NLS masking.

Regions of variant histone His2AvD required for Drosophila development

One way in which a distinct chromosomal domain could be established to carry out a specialized function is by the localized incorporation of specific histone variants into nucleosomes. H2AZ, one such variant of the histone protein H2A, is required for the survival of Drosophila melanogaster, Tetrahymena thermophila and mice (R. Faast et al., in preparation). To search for the unique features of Drosophila H2AZ (His2AvD, also referred to as H2AvD) that are required for its essential function, we have performed amino-acid swap experiments in which residues unique to Drosophila His2AvD were replaced with equivalently positioned Drosophila H2A.1 residues. Mutated His2AvD genes encoding modified versions of this histone were transformed into Drosophila and tested for their ability to rescue null-mutant lethality. We show that the unique feature of His2AvD does not reside in its histone fold but in its carboxy-terminal domain. This C-terminal region maps to a short alpha-helix in H2A that is buried deep inside the nucleosome core.

The effect of cyclic temperatures on the growth of Fasciola hepatica and Lymnaea viatrix

The experiment aimed to measure the effect of constant and variable temperatures on the growth of Lymnaea viatrix snails, on the development of a Peruvian isolate of Fasciola hepatica eggs and on the development of F. hepatica in the snails. This was carried out by cultivating infected and uninfected snails and fluke eggs in artificial, temperature controlled chambers. L. viatrix snails were found to develop at a rate dependent on environmental temperature, but developed at least as well under conditions of varying temperature as at the same mean constant temperature. F. hepatica eggs held at constant or varying temperatures, developed at a rate comparable to other reports. However, eggs developing at varying temperatures appeared to have reduced hatchability. Parasite development within the snails was slow, though within the limits calculated from the literature, and varying temperature did not appear to reduce development compared to constant temperatures.

Strategic control of fasciolosis in the inter-Andean valley of Cajamarca, Peru

Fasciolosis is recognised as a major problem in dairy cattle in Cajamarca, Peru. The infection has an annual cycle, with the major period of infection from January to March. A control programme, involving two doses of the fasciolicide triclabendazole aimed at reducing the passage of Fasciola hepatica eggs on to the pasture, together with the use of the molluscicide, niclosamide, was evaluated against traditional treatment programmes. The double treatment regimen did not significantly reduce the overall parasite burden, as measured by faecal egg counts, but did control the parasites to a level similar to that achieved by traditional programmes averaging 3-7 treatments per year. The cows' eosinophil counts and serum liver enzyme activities were significantly lower than in animals treated by the traditional programmes. The use of niclosamide in addition to the triclabendazole treatments gave no clear advantage, although there was a significant reduction in the number of intermediate host snails after the application of the molluscicide.

Experimental infection of pregnant ewes with Chlamydia pecorum

Pregnant ewes were infected in midpregnancy with three isolates of Chlamydia pecorum derived from the feces of healthy lambs from three different farms. Oral infection, alone or together with Fasciola hepatica, did not result in tissue invasion, since all placental and fecal samples were negative for chlamydiae. Intravenous infection resulted in placental infection in 16 of 18 ewes in that chlamydiae were cultured from placentas or vaginal swabs. Two ewes bore dead lambs after a shortened gestation time. The chlamydiae isolated were all C. pecorum. There were no significant differences between the weights of the lambs from the infected groups and those from uninfected control ewes. Most ewes showed no serological evidence of infection by the complement fixation test; therefore, it is unlikely that the enteric subtype of C. pecorum is responsible for the cross-reactions sometimes seen in flocks being tested for C. psittaci infection.

Acute phase toxoplasma abortions in sheep

Within 13 days of the experimental infection of 15 oestrus-synchronised ewes with 2000 sporulated oocysts of Toxoplasma gondii at 80 to 90 days of gestation 11 had aborted. The infection induced pyrexia and specific antibody in all the ewes. One ewe resorbed its fetus, 11 ewes aborted and three delivered, at full term, live congenitally infected lambs whose pre-colostral serum was antibody-positive. Tissues from the aborted fetuses and placentae from the live lambs were examined for toxoplasma infection by polymerase chain reaction (PCR) amplification of the B1 gene and by mouse inoculation. The live lambs were all shown to be infected by both methods, but there was no evidence of infection in any of the tissues from the acute phase abortions, suggesting that these fatalities occurred before the placenta or the fetus had been invaded by T gondii. Such toxoplasma-induced, acute-phase abortions are likely to be impossible to diagnose from fetal tissues. These results have implications not only for the diagnosis of naturally occurring ovine abortions but also for the understanding of the pathogenesis of toxoplasma-induced abortion.

Diagnosis of toxoplasma abortion in ewes by polymerase chain reaction

Eighteen oestrus-synchronised ewes were infected experimentally with 1500 sporulated oocysts of Toxoplasma gondii between 80 and 90 days of gestation. The infection induced pyrexia and specific antibody in all the ewes. One ewe resorbed its fetus, five ewes aborted and 12 delivered live, congenitally-infected lambs whose pre-colostral serum was antibody-positive. Tissues from the aborted fetuses and placentae from the live lambs were examined for toxoplasma infection by polymerase chain reaction (PCR) amplification of the B1 gene and by mouse inoculation. Using a simple protocol of tissue preparation without DNA extraction and a nested format, PCR was as sensitive as mouse inoculation. Placental cotyledon gave a higher sensitivity of detection than brain, lung or liver, and 16 of 19 placentae were positive by PCR compared with 13 of 18 by mouse inoculation. In mock-infected tissues, as few as 10 tachyzoites could be detected. The PCR could be applied to tissues unfit for mouse inoculation.

Isolation of faecal chlamydia from sheep in Britain and their characterization by cultural properties

Faeces samples were taken per rectum from sheep on 26 farms in England and Wales and examined for the presence of chlamydia by culture in McCoy cell monolayers. Thirteen of the farms were known to have had abortion outbreaks associated with Chlamydia psittaci (enzootic abortion) and 13 were free of this infection. The chlamydia isolated were characterized by cultural techniques. Chlamydia were isolated from the faeces of lambs on all 26 farms and the prevalence of infection varied form 5-50% on individual farms. There was no significant difference between the proportion of infected lambs on farms where enzootic abortion was present or absent. Lambs first showed infection when they were 3 months old and the prevalence rate of infection increased up to 9 months old. No chlamydia were isolated from the faeces of 316 adult ewes. The chlamydia were identified as enteric rather than abortion type and thus were C. pecorum rather than C. psittaci.

Epidemiology of lameness in dairy cattle: the influence of cubicles and indoor and outdoor walking surfaces

A survey of cubicles and indoor and outdoor walking surfaces on 37 farms served by four veterinary practices in Somerset, Cheshire, Wirral and west. Wales was carried out in 1989 to 1991. A study of the space requirements of Friesian/Holstein cows at pasture showed that they required approximately 240 cm x 120 cm lying space and a further 60 cm lunging space for rising. By these standards, 87 per cent of the cubicles were too short and 50 per cent were too wide or too narrow. Over 1500 observations on cows lying down, rising and standing indicated that only 12 per cent of the cubicles permitted real freedom of movement; 91 per cent of top partition rails were judged to be too low and 70 per cent of bottom rails too low or too high. In addition, the kerb was very high in 76 per cent of the cubicles. As a result, 10 per cent of cows appeared moderately or severely restricted when lying down, 33 per cent when rising and 55 per cent when standing. Over 2000 cubicle beds were also studied; 75 per cent had a concrete base and of those, 63 per cent were judged to have too little bedding and 11 per cent next to none. Higher incidences and prevalences of lameness were associated with limited borrowing space (P < 0.01) low bottom rails (P < 0.05), high kerbs (P < 0.05) and inadequate bedding (P < 0.01). Of 3190 walking surfaces, only 25 per cent were classified as satisfactory in the first winter and 34 per cent in the second. In general, surfaces in silage bays were too rough and those in other sites were too smooth. The farms with the smoothest indoor walking surfaces had a significantly higher incidence of lameness (P < 0.01). Of 3335 outdoor walking surfaces only 25 per cent were classified as satisfactory, and 70 per cent were too rough. The incidence of lameness was not significantly related to these findings.

Epidemiology of lameness in dairy cattle: description and analysis of foot lesions

Information from 37 dairy farms, in four regions of England and Wales provided data on 8991 lesions and the preventive trimming of 4837 cows' feet. Of the total of 13,828 forms returned, veterinary surgeons treated 32 per cent and farmers or stockmen 46 per cent. Of the 8645 lesions associated with episodes of lameness, lesions in the hindlimbs accounted for 92 per cent, of which 65 per cent were in the outer claw, 20 per cent in the skin and 14 per cent in the inner claw. Sole ulcers (40 per cent) and white line lesions (29 per cent) were the predominant diseases of horn, and digital dermatitis (40 per cent) was the most common disease of the skin. Subjective assessments showed that sandcrack, penetration of the sole by foreign bodies and interdigital necrobacillosis were associated with the most severe cases of lameness. There was a significant seasonal effect in the reporting of lesions.

Incidence and prevalence of lameness in dairy cattle

A survey was made of 37 dairy farms in Wirral, mid-Cheshire, mid-Somerset and Dyfed, Wales, to assess the incidence and prevalence of lameness in the cows between May 1989 and September 1991. The incidence was obtained from records made whenever a cow was examined for lameness or received preventive foot-trimming. The mean annual incidence was 54.6 new cases per 100 cows with a range from 10.7 to 170.1 and the mean values during summer and winter were 22.9 and 31.7, respectively. The prevalence of lameness was measured by regular visits at which locomotion was scored on a scale of 1 to 5, and the prevalence of lameness was calculated for each visit as the proportion of cows with scores of 3 or more. The mean annual prevalence over the whole period was 20.6 per cent with a range from 2.0 to 53.9 per cent for the 37 farms. The mean prevalences during summer and winter were 18.6 and 25.0 per cent, respectively. The prevalence measured at a single visit in midsummer or midwinter was significantly correlated with the mean prevalence over the whole corresponding period and may be useful as an assessment of the extent of lameness in a herd and the efficacy of control measures. There was evidence that training farmers to recognise early cases of lameness and request veterinary treatment resulted in a marked reduction in the duration of cases of lameness.