Multi-modal glioblastoma segmentation: man versus machine

BACKGROUND AND PURPOSE Reproducible segmentation of brain tumors on magnetic resonance images is an important clinical need. This study was designed to evaluate the reliability of a novel fully automated segmentation tool for brain tumor image analysis in comparison to manually defined tumor segmentations. METHODS We prospectively evaluated preoperative MR Images from 25 glioblastoma patients. Two independent expert raters performed manual segmentations. Automatic segmentations were performed using the Brain Tumor Image Analysis software (BraTumIA). In order to study the different tumor compartments, the complete tumor volume TV (enhancing part plus non-enhancing part plus necrotic core of the tumor), the TV+ (TV plus edema) and the contrast enhancing tumor volume CETV were identified. We quantified the overlap between manual and automated segmentation by calculation of diameter measurements as well as the Dice coefficients, the positive predictive values, sensitivity, relative volume error and absolute volume error. RESULTS Comparison of automated versus manual extraction of 2-dimensional diameter measurements showed no significant difference (p = 0.29). Comparison of automated versus manual segmentation of volumetric segmentations showed significant differences for TV+ and TV (p<0.05) but no significant differences for CETV (p>0.05) with regard to the Dice overlap coefficients. Spearman's rank correlation coefficients (ρ) of TV+, TV and CETV showed highly significant correlations between automatic and manual segmentations. Tumor localization did not influence the accuracy of segmentation. CONCLUSIONS In summary, we demonstrated that BraTumIA supports radiologists and clinicians by providing accurate measures of cross-sectional diameter-based tumor extensions. The automated volume measurements were comparable to manual tumor delineation for CETV tumor volumes, and outperformed inter-rater variability for overlap and sensitivity.

The Multimodal Brain TumorImage Segmentation Benchmark (BRATS)

In this paper we report the set-up and results of the Multimodal Brain Tumor Image Segmentation Benchmark (BRATS) organized in conjunction with the MICCAI 2012 and 2013 conferences. Twenty state-of-the-art tumor segmentation algorithms were applied to a set of 65 multi-contrast MR scans of low- and high-grade glioma patients - manually annotated by up to four raters - and to 65 comparable scans generated using tumor image simulation software. Quantitative evaluations revealed considerable disagreement between the human raters in segmenting various tumor sub-regions (Dice scores in the range 74-85%), illustrating the difficulty of this task. We found that different algorithms worked best for different sub-regions (reaching performance comparable to human inter-rater variability), but that no single algorithm ranked in the top for all subregions simultaneously. Fusing several good algorithms using a hierarchical majority vote yielded segmentations that consistently ranked above all individual algorithms, indicating remaining opportunities for further methodological improvements. The BRATS image data and manual annotations continue to be publicly available through an online evaluation system as an ongoing benchmarking resource.

Clinical and pharmacokinetic evaluation of S-ketamine for intravenous general anaesthesia in horses undergoing field castration.

BACKGROUND Intravenous anaesthetic drugs are the primary means for producing general anaesthesia in equine practice. The ideal drug for intravenous anaesthesia has high reliability and pharmacokinetic properties indicating short elimination and lack of accumulation when administered for prolonged periods. Induction of general anaesthesia with racemic ketamine preceded by profound sedation has already an established place in the equine field anaesthesia. Due to potential advantages over racemic ketamine, S-ketamine has been employed in horses to induce general anaesthesia, but its optimal dose remains under investigation. The objective of this study was to evaluate whether 2.5 mg/kg S-ketamine could be used as a single intravenous bolus to provide short-term surgical anaesthesia in colts undergoing surgical castration, and to report its pharmacokinetic profile. RESULTS After premedication with romifidine and L-methadone, the combination of S-ketamine and diazepam allowed reaching surgical anaesthesia in the 28 colts. Induction of anaesthesia as well as recovery were good to excellent in the majority (n = 22 and 24, respectively) of the colts. Seven horses required additional administration of S-ketamine to prolong the duration of surgical anaesthesia. Redosing did not compromise recovery quality. Plasma concentration of S-ketamine decreased rapidly after administration, following a two-compartmental model, leading to the hypothesis of a consistent unchanged elimination of the parent compound into the urine beside its conversion to S-norketamine. The observed plasma concentrations of S-ketamine at the time of first movement were various and did not support the definition of a clear cut-off value to predict the termination of the drug effect. CONCLUSIONS The administration of 2.5 mg/kg IV S-ketamine after adequate premedication provided good quality of induction and recovery and a duration of action similar to what has been reported for racemic ketamine at the dose of 2.2 mg/kg. Until further investigations will be provided, close monitoring to adapt drug delivery is mandatory, particularly once the first 10 minutes after injection are elapsed. Taking into account rapid elimination of S-ketamine, significant inter-individual variability and rapid loss of effect over a narrow range of concentrations a sudden return of consciousness has to be foreseen.

Description and repeatability of a newly developed spinal cord injury scale for dogs.

The objectives of this study were to describe a new spinal cord injury scale for dogs, evaluate repeatability through determining inter-rater variability of scores, compare these scores to another established system (a modified Frankel scale), and determine if the modified Frankel scale and the newly developed scale were useful as prognostic indicators for return to ambulation. A group of client-owned dogs with spinal cord injury were examined by 2 independent observers who applied the new Texas Spinal Cord Injury Score (TSCIS) and a modified Frankel scale that has been used previously. The newly developed scale was designed to describe gait, postural reactions and nociception in each limb. Weighted kappa statistics were utilized to determine inter-rater variability for the modified Frankel scale and individual components of the TSCIS. Comparisons were made between raters for the overall TSCIS score and between scales using Spearman's rho. An additional group of dogs with surgically treated thoracolumbar disk herniation was enrolled to look at correlation of both scores with spinal cord signal characteristics on magnetic resonance imaging (MRI) and ambulatory outcome at discharge. The actual agreement between raters for the modified Frankel scale was 88%, with a weighted kappa value of 0.93. The TSCIS had weighted kappa scores for gait, proprioceptive positioning and nociception components that ranged from 0.72 to 0.94. Correlation between raters for the overall TSCIS score was Spearman's rho=0.99 (P<0.001). Comparison of the overall TSCIS score to the modified Frankel score resulted in a Spearman's rho value of 0.90 (P<0.001). The modified Frankel score was weakly correlated with the length of hyperintensity of the spinal cord: L2 vertebral body length ratio on mid-sagittal T2-weighted MRI (Spearman's rho=-0.45, P=0.042) as was the overall TSCIS score (Spearman's rho=-0.47, P=0.037). There was also a significant difference in admitting modified Frankel scores (P=0.029) and admitting overall TSCIS scores (P=0.02) between dogs that were ambulatory at discharge and those that were not. Results from this study suggest that the TSCIS is an easy to administer scale for evaluating canine spinal cord injury based on the standard neurological exam and correlates well with a previously described modified Frankel scale.

The use of an electronic von Frey device for evaluation of sensory threshold in neurologically normal dogs and those with acute spinal cord injury

The utility and inter-session repeatability of sensory threshold measurements using an electronic von Frey anesthesiometer (VFA) were assessed in a group of six neurologically normal dogs. Sensory threshold values obtained in neurologically normal dogs were compared to those of dogs with acute spinal cord injury (SCI) caused by intervertebral disc extrusion (n=6) and to a group of neurologically normal dogs with cranial cruciate ligament rupture (CCLR; n=6). Sensory threshold values in neurologically normal dogs were 155.8 ± 37.7 g and 154.7 ± 67.2 g for the left and right pelvic limbs, respectively. The difference in mean sensory threshold values obtained for the group when two distinct testing sessions were compared was not statistically significant (P>0.05). Mean sensory threshold values for the group with SCI were significantly higher than those for neurologically normal dogs at 351.1 ± 116.5 g and 420.3 ± 157.7 g for the left and right pelvic limbs, respectively (P=0.01). A comparison of sensory threshold values for the group with CCLR and neurologically normal dogs was not statistically significant (P>0.05). The modified dorsal technique for VFA described here represents a reliable method to assess sensory threshold in neurologically normal dogs and in those with SCI.

Pelvic floor muscle electromyography during different running speeds: an exploratory and reliability study.

PURPOSE Stress urinary incontinence (SUI) affects women of all ages including young athletes, especially those involved in high-impact sports. To date, hardly any studies are available testing pelvic floor muscles (PFM) during sports activities. The aim of this study was the description and reliability test of six PFM electromyography (EMG) variables during three different running speeds. The secondary objective was to evaluate whether there was a speed-dependent difference between the PFM activity variables. METHODS This trial was designed as an exploratory and reliability study including ten young healthy female subjects to characterize PFM pre-activity and reflex activity during running at 7, 9 and 11 km/h. Six variables for each running speed, averaged over ten steps per subject, were presented descriptively, tested regarding their reliability (Friedman, ICC, SEM, MD) and speed difference (Friedman). RESULTS PFM EMG variables varied between 67.6 and 106.1 %EMG, showed no systematic error and were low for SEM and MD using the single value model. Applying the average model over ten steps, ICC (3,k) were >0.75 and SEM and MD about 50 % lower than for the single value model. Activity was found to be highest in 11 km/h. CONCLUSION EMG variables showed excellent ICC and very low SEM and MD. Further studies should investigate inter-session reliability and PFM reactivity patterns of SUI patients using the average over ten steps for each variable as it showed very high ICC and very low SEM and MD. Subsequently, longer running distances and other high-impact sports disciplines could be studied.

Epidemiologic and methodological issues in serial measurements of blood pressure: The blood pressure study in Mexican children

The Blood Pressure Study in Mexican Children (BPSMC) is a short term longitudinal study of serial blood pressure collected in three observation periods by standardized examinations of 233 female children, 10 to 12 years of age, enrolled in public and private primary schools in Tlalpan, Mexico. Study objectives were: (1) to describe from baseline information the distribution and relationship of blood pressure to age and selected anthropometric factors, as well as to compare the BPSMC results with other blood pressure studies, (2) to examine the sources and amount of variation present in serial blood pressure of 123 children, and (3) to evaluate observer performance by means of intra- and inter-observer variability.^ Stepwise regression results from baseline revealed that of all anthropometric factors and age, weight was the best predictor for blood pressure.^ The results of serial blood pressure measurements show that, besides the known sources of blood pressure variability (subject, day, reading), the physiologic event of menarche has an important bearing upon the variability and characterization of blood pressure in young girls. The assessment of the effects of blood pressure variability and reliability upon the design and analysis of epidemiologic studies, became apparent among post-menarcheal girls; where blood pressure measurements taken from them have low reliability. Research is needed to propose alternatives for assessing blood pressure during puberty.^ Finally, observer performance of blood pressure and anthropometry were evaluated. Anthropometric measurements had reliabilities in excess of R = 0.96. Acceptable reliabilities (R = 0.88 to 0.95) were obtained for systolic and diastolic (phase 4 and 5) blood pressures. The BPSMC showed a 50 percent decrease in measurement error from the first to the third observation periods. ^

THE IMPACT OF FAMILY HISTORY ON MEDULLARY THYROID CANCER IN MEN2A PATIENTS

The American Thyroid Association recently classified all MEN2A-associated codons into increasing risk levels A-C and stated that some patients may delay prophylactic thyroidectomy if certain criteria are met. One criterion is a less aggressive family history of MTC but whether families with the same mutated codon have variable MTC aggressiveness is not well described. We developed several novel measures of MTC aggressiveness and compared families with the same mutated codon to determine if there is significant inter-familial variability. Pedigrees of families with MEN2A were reviewed for codon mutated and proportion of RET mutation carriers with MTC. Individuals with MTC were classified as having local or distant MTC and whether they had progressive MTC. MTC status and age were assessed at diagnosis and most advanced MTC stage. For those without MTC, age was recorded at prophylactic thyroidectomy or last follow-up if the patient did not have a thyroidectomy. For each pedigree, the mean age of members without MTC, with MTC, and the proportion of RET mutation carriers with local or distant and progressive MTC were calculated. We assessed differences in these variables using ANOVA and the Fisher’s exact test. Sufficient data for analysis were available for families with mutated codons 609 (92 patients from 13 families), 618 (41 patients from 7 families), and 634 (152 patients from 13 families). The only significant differences found were the mean age of patients without MTC between families with codon 609 and 618 mutations even after accounting for prophylactic thyroidectomy (p=0.006 and 0.001, respectively), and in the mean age of MTC diagnosis between families with codon 618 and 634 mutations even after accounting for symptomatic presentation (p=0.023 and 0.014, respectively). However, these differences may be explained by generational differences in ascertainment of RET carriers and the availability of genetic testing when the proband initially presented.

Sediment volume variations inferred from DGPS measurements within Bossons glacier proglacial area (Mont-Blanc massif, France)

This dataset presents Differential Global Positioning System data (DGPS) acquired within the Bossons glacier proglacial area. Bossons glacier is a rapidly retreating glacier and its proglacial area is deglaciated for ~30 years. Bossons stream is one of the outlets of the subglacial drainage system. It starts as a 800 m steep cascade reach, then flows through an area with gentler slope : the Plan des Eaux (PdE). PdE is a 300 m long, 50 m wide proglacial alluvial plain with an increasing channel mobility in the downstream direction but decreasing slope gradient and incision. As it may act a sediment trap, studying periglacial and proglacial erosion processes in the Bossons catchment requires to quantify PdE sediment volume evolution. A several meter-sized block located within Bossons proglacial area was set up as GPS base : its location was measured by one antenna (Topcon Hyper Pro) by performing 600 consecutive measurements throughout one day. A second antenna (Topcon Hyper Pro) was then used to measure XYZ location of points in the proglacial area with a ~2 m grid. Radio communication between the two antennas allowed differential calculations to be automatically carried out on field using the Topcon FC-250 hand controller. This methodology yields 3 cm XY and 1.5 cm Z uncertainties. DGPS data have been acquired through 10 campaigns from 2004 to 2014; campaigns from 2004 to 2008 cover a smaller area than those from 2010 to 2014. Digital Elevation Model (DEM) have been interpolated from DGPS data and difference between two DEMs yields deposited and eroded volume within PdE. Maps of PdE volume variation between two campaigns show that incision mainly occurs in the upper and lower sections where as deposition dominates in the middle section. Deposition, denudation and net rate (deposition rate - denudation rate) are calculated by normalizing volumes by DEM areas. Deposition dominates results with a mean net rate of 29 mm/yr. However, strong inter-annual variability exists and some years are dominated by denudation : -36 mm/yr and -100 mm/yr for 2006 and 2011, respectively. Nonetheless, oldest campaigns (2004 to 2008) were carried out on the lower part part of the alluvial plain and ruling them out to keep only complete DEM (2010 to 2014) yields a mean net rate of ~15 mm/yr. This results is coherent with field observations of both strong deposition (e.g. flood deposits) and strong erosion (e.g. 30 cm incision) evidences. Bossons glacier proglacial area is thus dynamic with year-to-year geormorphological changes but may leans toward increasing its mean elevation through a deposition dominated system.

Zooplankton biovolume time series at station STARESO (Bay of Calvi, Corsica)

A long-term time series of subsurface zooplankton is performed in the oligotrophic Bay of Calvi (Corsica, Ligurian Sea, NW Mediterranean) from 2003 onwards. It is carried out from the marine station STARESO and is based on weekly measurement of zooplankton biovolumes. The main objectives are (i) to determine the seasonal cycle and inter-annual variability of the organisms, (ii) to study the dynamics of the populations, and (iii) to understand zooplankton interactions with other co-sampled hydrographic, meteorological and phytoplankton variables at the site.

(Table 1) Characteristics of South Pole personnel according to forced expiratory flow (FEF25-75) response to altitude

The impact of acute altitude exposure on pulmonary function is variable. A large inter-individual variability in the changes in forced expiratory flows (FEFs) is reported with acute exposure to altitude, which is suggested to represent an interaction between several factors influencing bronchial tone such as changes in gas density, catecholamine stimulation, and mild interstitial edema. This study examined the association between FEF variability, acute mountain sickness (AMS) and various blood markers affecting bronchial tone (endothelin-1, vascular endothelial growth factor (VEGF), catecholamines, angiotensin II) in 102 individuals rapidly transported to the South Pole (2835 m). The mean FEF between 25 and 75% (FEF25-75) and blood markers were recorded at sea level and after the second night at altitude. AMS was assessed using Lake Louise questionnaires. FEF25-75 increased by an average of 12% with changes ranging from -26 to +59% from sea level to altitude. On the second day, AMS incidence was 36% and was higher in individuals with increases in FEF25-75 (41 vs. 22%, P = 0.05). Ascent to altitude induced an increase in endothelin-1 levels, with greater levels observed in individuals with decreased FEF25-75. Epinephrine levels increased with ascent to altitude and the response was six times larger in individuals with decreased FEF25-75. Greater levels of endothelin-1 in individuals with decreased FEF25-75 suggest a response consistent with pulmonary hypertension and/or mild interstitial edema, while epinephrine may be upregulated in these individuals to clear lung fluid through stimulation of beta2-adrenergic receptors.

Ocean acidification impacts on sperm mitochondrial membrane potential bring sperm swimming behaviour near its tipping point

Broadcast spawning marine invertebrates are susceptible to environmental stressors such as climate change, as their reproduction depends on the successful meeting and fertilization of gametes in the water column. Under near-future scenarios of ocean acidification, the swimming behaviour of marine invertebrate sperm is altered. We tested whether this was due to changes in sperm mitochondrial activity by investigating the effects of ocean acidification on sperm metabolism and swimming behaviour in the sea urchin Centrostephanus rodgersii. We used a fluorescent molecular probe (JC-1) and flow cytometry to visualize mitochondrial activity (measured as change in mitochondrial membrane potential, MMP). Sperm MMP was significantly reduced in delta pH -0.3 (35% reduction) and delta pH -0.5 (48% reduction) treatments, whereas sperm swimming behaviour was less sensitive with only slight changes (up to 11% decrease) observed overall. There was significant inter-individual variability in responses of sperm swimming behaviour and MMP to acidified seawater. We suggest it is likely that sperm exposed to these changes in pH are close to their tipping point in terms of physiological tolerance to acidity. Importantly, substantial inter-individual variation in responses of sperm swimming to ocean acidification may increase the scope for selection of resilient phenotypes, which, if heritable, could provide a basis for adaptation to future ocean acidification.

(Table 2) Carbon and nitrogen isotopic ratios in blood sampled from arctic foxes (Vulpes lagopus) on Bylot Island between 2003-2008

Inter-individual variation in diet within generalist animal populations is thought to be a widespread phenomenon but its potential causes are poorly known. Inter-individual variation can be amplified by the availability and use of allochthonous resources, i.e., resources coming from spatially distinct ecosystems. Using a wild population of arctic fox as a study model, we tested hypotheses that could explain variation in both population and individual isotopic niches, used here as proxy for the trophic niche. The arctic fox is an opportunistic forager, dwelling in terrestrial and marine environments characterized by strong spatial (arctic-nesting birds) and temporal (cyclic lemmings) fluctuations in resource abundance. First, we tested the hypothesis that generalist foraging habits, in association with temporal variation in prey accessibility, should induce temporal changes in isotopic niche width and diet. Second, we investigated whether within-population variation in the isotopic niche could be explained by individual characteristics (sex and breeding status) and environmental factors (spatiotemporal variation in prey availability). We addressed these questions using isotopic analysis and Bayesian mixing models in conjunction with linear mixed-effects models. We found that: i) arctic fox populations can simultaneously undergo short-term (i.e., within a few months) reduction in both isotopic niche width and inter-individual variability in isotopic ratios, ii) individual isotopic ratios were higher and more representative of a marine-based diet for non-breeding than breeding foxes early in spring, and iii) lemming population cycles did not appear to directly influence the diet of individual foxes after taking their breeding status into account. However, lemming abundance was correlated to proportion of breeding foxes, and could thus indirectly affect the diet at the population scale.

Calcium isotope fractionation in cultured, modern and fossil scleractinian coral skeleton

The present study investigates the influence of environmental (temperature, salinity) and biological (growth rate, inter-generic variations) parameters on calcium isotope fractionation (d44/40Ca) in scleractinian coral skeleton to better constrain this record. Previous studies focused on the d44/40Ca record in different marine organisms to reconstruct seawater composition or temperature, but only few studies investigated corals. This study presents measurements performed on modern corals from natural environments (from the Maldives for modern and from Tahiti for fossil corals) as well as from laboratory cultures (Centre Scientifique de Monaco). Measurements on Porites sp., Acropora sp., Montipora verrucosa and Stylophora pistillata allow constraining inter-generic variability. Our results show that the fractionation of d44/40Ca ranges from 0.6 to 0.1 per mil, independent of the genus or the environmental conditions. No significant relationship between the rate of calcification and d44/40Ca was found. The weak temperature dependence reported in earlier studies is most probably not the only parameter that is responsible for the fractionation. Indeed, sub-seasonal temperature variations reconstructed by d18O and Sr/Ca ratio using a multi-proxy approach, are not mirrored in the coral's d44/40Ca variations. The intergeneric variability and intrageneric variability among the studied samples are weak except for S. pistillata, which shows calcium isotopic values increasing with salinity. The variability between samples cultured at a salinity of 40 is higher than those cultured at a salinity of 36 for this species. The present study reveals a strong biological control of the skeletal calcium isotope composition by the polyp and a weak influence of environmental factors, specifically temperature and salinity (except for S. pistillata). Vital effects have to be investigated in situ to better constrain their influence on the calcium isotopic signal. If vital effects could be extracted from the isotopic signal, the calcium isotopic composition of coral skeletons could provide reliable information on the calcium composition and budget in ocean.

Abundance and biomass of in- and epibenthic invertebrate macrofauna in the German Bight from 1969 to 2000

In order to examine the long-term development of offshore macrozoobenthic soft-bottom communities of the German Bight, four representative permanent stations (MZB-SSd, -FSd, -Slt, -WB) have been sampled continuously since 1969. Inter-annual variability and possible long-term trends were analysed based on spring-time samples from 1969 until 2000. This is part of the ecological long-term series of the AWI and is supplemented by periodic large-scale mapping of the benthos. The main factors influencing the development of the benthic communities are biological interactions, climate, food supply (eutrophication) and the disturbance regime. The most frequent disturbances are sediment relocations during strong storms or by bottom trawling, while occasional oxygen deficiencies and extremely cold winters are important disturbance events working on a much larger scale. Benthic communities at the sampling stations show a large inter-annual variability combined with a variation on a roughly decadal scale. In accordance with large-scale system shifts reported for the North Sea, benthic community transitions occurred between roughly the 1970ies, 80ies and 90ies. The transitions between periods are not distinctly marked by strong changes but rather reflected in gradual changes of the species composition and dominance structure.