Impact of complex NOTCH1 mutations on survival in paediatric T-cell leukaemia

Background: Molecular alterations occur frequently in T-ALL and the potential impact of those abnormalities on outcome is still controversial. The current study aimed to test whether NOTCH1 mutations and additional molecular abnormalities would impact T-ALL outcome in a series of 138 T-ALL paediatric cases. Methods: T-ALL subtypes, status of SIL-TAL1 fusion, ectopic expression of TLX3, and mutations in FBXW7, KRAS, PTEN and NOTCH1 were assessed as overall survival (OS) and event-free survival (EFS) prognostic factors. OS and EFS were determined using the Kaplan-Meier method and compared using the log-rank test. Results: The frequencies of mutations were 43.5% for NOTCH1, while FBXW7, KRAS and PTEN exhibited frequencies of 19.1%, 9.5% and 9.4%, respectively. In 78.3% of cases, the coexistence of NOTCH1 mutations and other molecular alterations was observed. In multivariate analysis no statistical association was revealed between NOTCH1 mutations and any other variable analyzed. The mean length of the follow-up was 68.4 months and the OS was 50.7%. SIL-TAL1 was identified as an adverse prognostic factor. NOTCH1 mutation status was not associated with outcome, while the presence of NOTCH1 complex mutations (indels) were associated with a longer overall survival (p = 0.031) than point mutations. Conclusion: NOTCH1 mutations alone or in combination with FBXW7 did not impact T-ALL prognosis. Nevertheless, complex NOTCH1 mutations appear to have a positive impact on OS and the SIL-TAL1 fusion was validated as a negative prognostic marker in our series of T-ALL.

Influence of milk type and addition of passion fruit peel powder on fermentation kinetics, texture profile and bacterial viability in probiotic yoghurts

The effect of the addition of passion fruit peel powder (PFPP) on the fermentation kinetics and texture parameters, post-acidification and bacteria counts of probiotic yoghurts made with two milk types were evaluated during 28 days of storage at 4 degrees C. Milks were fermented by Streptococcus thermophilus and Lactobacillus delbrueckii subsp. bulgaricus (CY340), and one strain of probiotic bacteria: Lactobacillus acidophilus (L10 and NCFM), Bifidobacterium animalis subsp. lactis (8104 and HN019). The addition of PFPP reduced significantly fermentation time of skim milk co-fermented by the strains L10, NCFM and HN019. At the end of 28-day shelf-life, counts of B. lactis Bl04 were about 1 Log CFU mL(-1) higher in whole yoghurt fermented with PFPP regarding its control but, in general, the addition of PFPP had less influence on counts than the milk type itself. The titratable acidity in yoghurts with PFPP was significantly higher than in their respective controls, and in skim yoghurts higher than in the whole ones. The PFPP increased firmness, consistency (except for the NCFM strain of L acidophilus) and cohesiveness of all skim yoghurts. The results point out the suitability of using passion fruit by-product in the formulation of both skim and whole probiotic yoghurts. (C) 2012 Elsevier Ltd. All rights reserved.

Author stance in doctoral dissertations of native and non-native speakers of English: a corpus-based study on epistemic adverbs

[EN]Our study concentrates on the epistemic adverbs used in conveying author stance in academic English. The Contrastive Interlanguage Analysis (Granger, 1996) was run to three sets of corpora comprising doctoral dissertations written by native and non-native academic authors of English. Epistemic adverbs occurring in the dissertations were identified through a computer programme and their frequencies were separately computed for each corpus. Lastly, a log-likelihood test was administered to see whether there is a statistically significant difference across the groups in concern concerning the use of these adverbs.

Ensemble wind forecasting based on the HARMONIE model and adaptive finite elements in complex orography

[EN]Ensemble forecasting is a methodology to deal with uncertainties in the numerical wind prediction. In this work we propose to apply ensemble methods to the adaptive wind forecasting model presented in. The wind field forecasting is based on a mass-consistent model and a log-linear wind profile using as input data the resulting forecast wind from Harmonie, a Non-Hydrostatic Dynamic model used experimentally at AEMET with promising results. The mass-consistent model parameters are estimated by using genetic algorithms. The mesh is generated using the meccano method and adapted to the geometry…

Effect of multiple sources of disturbance on rocky benthic assemblages in some localities of Salento, Apulia

The first part of my work consisted in samplings conduced in nine different localities of the salento peninsula and Apulia (Italy): Costa Merlata (BR), Punta Penne (BR), Santa Cesarea terme (LE), Santa Caterina (LE), Torre Inserraglio (LE), Torre Guaceto (BR), Porto Cesareo (LE), Otranto (LE), Isole Tremiti (FG). I collected data of species percentage covering from the infralittoral rocky zone, using squares of 50x50 cm. We considered 3 sites for location and 10 replicates for each site, which has been taken randomly. Then I took other data about the same places, collected in some years, and I combined them together, to do a spatial analysis. So I started from a data set of 1896 samples but I decided not to consider time as a factor because I have reason to think that in this period of time anthropogenic stressors and their effects (if present), didn’t change considerably. The response variable I’ve analysed is the covering percentage of an amount of 243 species (subsequently merged into 32 functional groups), including seaweeds, invertebrates, sediment and rock. 2 After the sampling, I have been spent a period of two months at the Hopkins Marine Station of Stanford University, in Monterey (California,USA), at Fiorenza Micheli's laboratory. I've been carried out statistical analysis on my data set, using the software PRIMER 6. My explorative analysis starts with a nMDS in PRIMER 6, considering the original data matrix without, for the moment, the effect of stressors. What comes out is a good separation between localities and it confirms the result of ANOSIM analysis conduced on the original data matrix. What is possible to ensure is that there is not a separation led by a geographic pattern, but there should be something else that leads the differences. Is clear the presence of at least three groups: one composed by Porto cesareo, Torre Guaceto and Isole tremiti (the only marine protected areas considered in this work); another one by Otranto, and the last one by the rest of little, impacted localities. Inside the localities that include MPA(Marine Protected Areas), is also possible to observe a sort of grouping between protected and controlled areas. What comes out from SIMPER analysis is that the most of the species involved in leading differences between populations are not rare species, like: Cystoseira spp., Mytilus sp. and ECR. Moreover I assigned discrete values (0,1,2) of each stressor to all the sites I considered, in relation to the intensity with which the anthropogenic factor affect the localities. 3 Then I tried to estabilish if there were some significant interactions between stressors: by using Spearman rank correlation and Spearman tables of significance, and taking into account 17 grades of freedom, the outcome shows some significant stressors interactions. Then I built a nMDS considering the stressors as response variable. The result was positive: localities are well separeted by stressors. Consequently I related the matrix with 'localities and species' with the 'localities and stressors' one. Stressors combination explains with a good significance level the variability inside my populations. I tried with all the possible data transformations (none, square root, fourth root, log (X+1), P/A), but the fourth root seemed to be the best one, with the highest level of significativity, meaning that also rare species can influence the result. The challenge will be to characterize better which kind of stressors (including also natural ones), act on the ecosystem; and give them a quantitative and more accurate values, trying to understand how they interact (in an additive or non-additive way).

Sorption and direct speciation of neptunium(V) on aluminium oxide and montmorillonite

This study comprised batch experiments, direct speciation studies via EXAFS, and modelling with the 2SPNE SC/CE model to elucidate the mechanisms of Np(V) sorption on montmorillonite and, for reference, on γ-Al2O3. The sorption of pM 239Np(V) and µM 237Np(V) on montmorillonite (STx-1, 4 g/L) and γ-Al2O3 (0.5 g/L) was studied at room temperature in the presence and absence of ambient CO2 covering a pH-range from 2.5 (STx-1) or 5 (γ-Al2O3) to 10.5 with 0.01 or 0.1M NaClO4 as background electrolyte. The Np(V) uptake was determined by γ spectroscopy of the supernatants and calculated as percentage as well as distribution coefficient Kd. Sorption starts from pH ~6 and, under exclusion of CO2, increases continuously, while, in the presence of ambient air, it reaches a maximum at pH ~8.5 (γ-Al2O3: log Kd max ≈ 4 mL/g; STx-1: log Kd max ≈ 2.7 mL/g). Beyond that it decreases again due to the formation of queous neptunium carbonate complexes. Furthermore, neptunium sorption on montmorillonite is influenced by ionic strength at pH <6 through ion exchange processes pointing towards the formation of outer-sphere surface complexes there. Isotherms measured at the sorption maximum showed the precipitation of resumably neptunium carbonate complexes above 3∙10^-5 M under ambient air conditions. Additionally, they indicated progressive saturation of the sorption sites of γ-Al2O3. At selected pH (STx-1: 5.0, 7.0, 8.0, 8.5, 9.0, 9.5; γ-Al2O3: 8.5, 9.5) EXAFS samples were prepared as wet pastes with µM 237Np and measured at room temperature in fluorescence mode at ANKA and ESRF. Several spectra were averaged and analysed with EXAFSPAK and FEFF 8.20 employing models of NaNpO2(CO3) or soddyite, (UO2)2SiO4∙2(H2O). The shorter atomic distances of the neptunyl ion at pH 5 compared to the others hinted at the retention of the hydration shell and, thus, at outer-sphere sorption. On average the bond lengths for Np(V) sorbed on STx-1 at high pH were Oax ≈ 1.84 Å and Oeq ≈ 2.53 Å. At high pH, ternary neptunyl carbonate surface complexes could be identified for montmorillonite (C ≈ 3.00 Å), but not for γ-Al2O3, where an interaction of neptunium with the aluminium surface atoms according to the soddyite model gave better agreement with the experimental data. However, neither structure as suggested by the two models could be excluded for both systems rendering a combination most likely. Modelling of the sorption data provided further evidence for the existence of ternary neptunium carbonate surface complexes in both cases. The results of this study can aid environmental risk assessment for clay-based nuclear waste repositories by providing valuable input data for simulations of radionuclide migration from a final disposal site.

A Bayesian changepoint analysis on spatio-temporal point processes

Changepoint analysis is a well established area of statistical research, but in the context of spatio-temporal point processes it is as yet relatively unexplored. Some substantial differences with regard to standard changepoint analysis have to be taken into account: firstly, at every time point the datum is an irregular pattern of points; secondly, in real situations issues of spatial dependence between points and temporal dependence within time segments raise. Our motivating example consists of data concerning the monitoring and recovery of radioactive particles from Sandside beach, North of Scotland; there have been two major changes in the equipment used to detect the particles, representing known potential changepoints in the number of retrieved particles. In addition, offshore particle retrieval campaigns are believed may reduce the particle intensity onshore with an unknown temporal lag; in this latter case, the problem concerns multiple unknown changepoints. We therefore propose a Bayesian approach for detecting multiple changepoints in the intensity function of a spatio-temporal point process, allowing for spatial and temporal dependence within segments. We use Log-Gaussian Cox Processes, a very flexible class of models suitable for environmental applications that can be implemented using integrated nested Laplace approximation (INLA), a computationally efficient alternative to Monte Carlo Markov Chain methods for approximating the posterior distribution of the parameters. Once the posterior curve is obtained, we propose a few methods for detecting significant change points. We present a simulation study, which consists in generating spatio-temporal point pattern series under several scenarios; the performance of the methods is assessed in terms of type I and II errors, detected changepoint locations and accuracy of the segment intensity estimates. We finally apply the above methods to the motivating dataset and find good and sensible results about the presence and quality of changes in the process.

Formation of caries-like lesions in vitro on the root surfaces of human teeth in solutions simulating plaque fluid

Lesion formation on root surfaces of human posterior teeth was studied in acetate/lactate buffers with a background electrolyte composition based on plaque fluid analyses. Lesion depth after 28 days at 37 degrees C was measured in relation to: the presence or absence of cementum; the concentration of undissociated buffer; the presence or absence of magnesium ions at plaque fluid concentration. Each factor was evaluated at several values of -log(ion activity product for hydroxyapatite): pI(HA). Solutions were formulated to minimize variation in pH, which varied by < or =0.03 for a given comparison (individual pI(HA)) and by 0.42-0.82 over the range of pI(HA) within experiments. Lesions on surfaces from which cementum had been ground were significantly deeper than on intact surfaces, but this is considered to be due to subsurface mechanical damage and not to a solubility difference. Neither the concentration of undissociated buffer nor the presence of magnesium ions significantly affected lesion depth. Lesion depth was strongly influenced by the correlated variations in pI(HA) and pH. At pI(HA) 54 and 55, only extremely shallow lesions formed. From pI(HA) 56, lesion depth increased with increasing pI(HA). The results confirm that the solubility of the mineral of root tissues is higher than that of hydroxyapatite, but indicate that it is probably lower than suggested by Hoppenbrouwers et al. [Arch Oral Biol 1987;32:319-322]. For calcium concentrations of 3-12 mM, the critical pH for root tissue mineral was calculated as 5.22-5.66 assuming solubility equivalent to pI(HA) 54 and 5.08-5.51 assuming pI(HA) 55.

Femur Specific Polyaffine Model to Regularize the Log-Domain Demons Registration

Osteoarticular allograft transplantation is a popular treatment method in wide surgical resections with large defects. For this reason hospitals are building bone data banks. Performing the optimal allograft selection on bone banks is crucial to the surgical outcome and patient recovery. However, current approaches are very time consuming hindering an efficient selection. We present an automatic method based on registration of femur bones to overcome this limitation. We introduce a new regularization term for the log-domain demons algorithm. This term replaces the standard Gaussian smoothing with a femur specific polyaffine model. The polyaffine femur model is constructed with two affine (femoral head and condyles) and one rigid (shaft) transformation. Our main contribution in this paper is to show that the demons algorithm can be improved in specific cases with an appropriate model. We are not trying to find the most optimal polyaffine model of the femur, but the simplest model with a minimal number of parameters. There is no need to optimize for different number of regions, boundaries and choice of weights, since this fine tuning will be done automatically by a final demons relaxation step with Gaussian smoothing. The newly developed synthesis approach provides a clear anatomically motivated modeling contribution through the specific three component transformation model, and clearly shows a performance improvement (in terms of anatomical meaningful correspondences) on 146 CT images of femurs compared to a standard multiresolution demons. In addition, this simple model improves the robustness of the demons while preserving its accuracy. The ground truth are manual measurements performed by medical experts.

Geometry-Aware Multiscale Image Registration via OBBTree-Based Polyaffine Log-Demons

Non-linear image registration is an important tool in many areas of image analysis. For instance, in morphometric studies of a population of brains, free-form deformations between images are analyzed to describe the structural anatomical variability. Such a simple deformation model is justified by the absence of an easy expressible prior about the shape changes. Applying the same algorithms used in brain imaging to orthopedic images might not be optimal due to the difference in the underlying prior on the inter-subject deformations. In particular, using an un-informed deformation prior often leads to local minima far from the expected solution. To improve robustness and promote anatomically meaningful deformations, we propose a locally affine and geometry-aware registration algorithm that automatically adapts to the data. We build upon the log-domain demons algorithm and introduce a new type of OBBTree-based regularization in the registration with a natural multiscale structure. The regularization model is composed of a hierarchy of locally affine transformations via their logarithms. Experiments on mandibles show improved accuracy and robustness when used to initialize the demons, and even similar performance by direct comparison to the demons, with a significantly lower degree of freedom. This closes the gap between polyaffine and non-rigid registration and opens new ways to statistically analyze the registration results.

First report about the mode of action of combined butafosfan and cyanocobalamin on hepatic metabolism in nonketotic early lactating cows

The primary aim was to investigate the effect of combined butafosfan and cyanocobalamin on liver metabolism in early lactating cows through mRNA expression measurements of genes encoding 31 enzymes and transport proteins of major metabolic processes in the liver using 16 multiparous early lactating dairy cows. The treatments included i.v. injection of 10 mL/100 kg of body weight combined butafosfan and cyanocobalamin (TG, n = 8) on 3 d consecutively at 25 +/- 3 d in milk or injection with physiological saline solution similarly applied (CG, n = 8). Results include a higher daily milk production for TG cows (41.1 +/- 0.9 kg, mean +/- SEM) compared with CG cows (39.5 +/- 0.7 kg). In plasma, the concentration of inorganic phosphorus was lower in the TG cows (1.25 +/- 0.08 mmol/L) after the treatment than in the CG cows (1.33 +/- 0.07 mmol/L). The plasma beta-hydroxybutyrate concentration was 0.65 +/- 0.13 mmol/L for all cows before the treatment, and remained unaffected post treatment. The unique result was that in the liver, the mRNA abundance of acyl-coenzyme A synthetase long-chain family member 1, involved in fatty acid oxidation and biosynthesis, was lower across time points after the treatment for TG compared with CG cows (17.5 +/- 0.15 versus 18.1 +/- 0.24 cycle threshold, log(2), respectively). In conclusion, certain effects of combined butafosfan and cyanocobalamin were observed on mRNA abundance of a gene in the liver of nonketotic early lactating cows.

Impact of weather and climate on the incidence of acute coronary syndromes

BACKGROUND: First investigations of the interactions between weather and the incidence of acute myocardial infarctions date back to 1938. The early observation of a higher incidence of myocardial infarctions in the cold season could be confirmed in very different geographical regions and cohorts. While the influence of seasonal variations on the incidence of myocardial infarctions has been extensively documented, the impact of individual meteorological parameters on the disease has so far not been investigated systematically. Hence the present study intended to assess the impact of the essential variables of weather and climate on the incidence of myocardial infarctions. METHODS: The daily incidence of myocardial infarctions was calculated from a national hospitalization survey. The hourly weather and climate data were provided by the database of the national weather forecast. The epidemiological and meteorological data were correlated by multivariate analysis based on a generalized linear model assuming a log-link-function and a Poisson distribution. RESULTS: High ambient pressure, high pressure gradients, and heavy wind activity were associated with an increase in the incidence of the totally 6560 hospitalizations for myocardial infarction irrespective of the geographical region. Snow- and rainfall had inconsistent effects. Temperature, Foehn, and lightning showed no statistically significant impact. CONCLUSIONS: Ambient pressure, pressure gradient, and wind activity had a statistical impact on the incidence of myocardial infarctions in Switzerland from 1990 to 1994. To establish a cause-and-effect relationship more data are needed on the interaction between the pathophysiological mechanisms of the acute coronary syndrome and weather and climate variables.

Impact of viral E2-gene status on outcome after radiotherapy for patients with human papillomavirus 16-positive cancer of the uterine cervix

PURPOSE: Integration of high-risk papillomavirus DNA has been considered an important step in oncogenic progression to cervical carcinoma. Disruption of the human papillomavirus (HPV) genome within the E2 gene is frequently a consequence. This study investigated the influence of episomal viral DNA on outcome in patients with advanced cervical cancer treated with primary radiotherapy. METHODS AND MATERIALS: Paraffin-embedded biopsies of 82 women with locally advanced cervical cancer could be analyzed for HPV infection by multiplex polymerase chain reaction (PCR) by use of SPF1/2 primers. E2-gene intactness of HPV-16-positive samples was analyzed in 3 separate amplification reactions by use of the E2A, E2B, E2C primers. Statistical analyses (Kaplan-Meier method; log-rank test) were performed for overall survival (OS), disease-free survival (DFS), local progression-free survival (LPFS), and distant metastases-free survival (DMFS). RESULTS: Sixty-one (75%) of 82 carcinomas were HPV positive, 44 of them for HPV-16 (72%). Seventeen of the 44 HPV-16-positive tumors (39%) had an intact E2 gene. Patients with a HPV-16-positive tumor and an intact E2 gene showed a trend for a better DFS (58% vs. 38%, p = 0.06) compared with those with a disrupted E2 gene. A nonsignificant difference occurred regarding OS (87% vs. 66%, p = 0.16) and DMFS (57% vs. 48%, p = 0.15). CONCLUSION: E2-gene status may be a promising new target, but more studies are required to elucidate the effect of the viral E2 gene on outcome after radiotherapy in HPV-positive tumors.

Influence of different spacers on the biological profile of a DOTA-somatostatin analogue

Radiolabeled somatostatin analogues have been successfully used for targeted radiotherapy and for imaging of somatostatin receptor (sst1-5)-positive tumors. Nevertheless, these analogues are subject to improving their tumor-to-nontarget ratio to enhance their diagnostic or therapeutic properties, preventing nephrotoxicity. In order to understand the influence of lipophilicity and charge on the pharmacokinetic profile of [1,4,7,10-tetraazacyclododecane-1,4,7,10-tetraacetic acid (DOTA)]-somatostatin-based radioligands such as [DOTA,1-Nal3]-octreotide (DOTA-NOC), different spacers (X) based on 8-amino-3,6-dioxaoctanoic acid (PEG2), 15-amino-4,7,10,13-tetraoxapentadecanoic acid (PEG4), N-acetyl glucosamine (GlcNAc), triglycine, beta-alanine, aspartic acid, and lysine were introduced between the chelator DOTA and the peptide NOC. All DOTA-X-NOC conjugates were synthesized by Fmoc solid-phase synthesis. The partition coefficient (log D) at pH = 7.4 indicated that higher hydrophilicity than [111In-DOTA]-NOC was achieved with the introduction of the mentioned spacers, except with triglycine and beta-alanine. The high affinity of [InIII-DOTA]-NOC for human sst2 (hsst2) was preserved with the structural modifications, while an overall drop for hsst3 affinity was observed, except in the case of [InIII-DOTA]-beta-Ala-NOC. The new conjugates preserved the good affinity for hsst5, except for [InIII-DOTA]-Asn(GlcNAc)-NOC, which showed decreased affinity. A significant 1.2-fold improvement in the specific internalization rate in AR4-2J rat pancreatic tumor cells (sst2 receptor expression) at 4 h was achieved with the introduction of Asp as a spacer in the parent compound. In sst3-expressing HEK cells, the specific internalization rate at 4 h for [111In-DOTA]-NOC (13.1% +/- 0.3%) was maintained with [111In-DOTA]-beta-Ala-NOC (14.0% +/- 1.8%), but the remaining derivatives showed <2% specific internalization. Biodistribution studies were performed with Lewis rats bearing the AR4-2J rat pancreatic tumor. In comparison to [111In-DOTA]-NOC (2.96% +/- 0.48% IA/g), the specific uptake in the tumor at 4 h p.i. was significantly improved for the 111In-labeled sugar analogue (4.17% +/- 0.46% IA/g), which among all the new derivatives presented the best tumor-to-kidney ratio (1.9).

Application of well log tomography to the Dundee and Rogers City Limestones, Michigan Basin, USA

The Michigan Basin is located in the upper Midwest region of the United States and is centered geographically over the Lower Peninsula of Michigan. It is filled primarily with Paleozoic carbonates and clastics, overlying Precambrian basement rocks and covered by Pleistocene glacial drift. In Michigan, more than 46,000 wells have been drilled in the basin, many producing significant quantities of oil and gas since the 1920s in addition to providing a wealth of data for subsurface visualization. Well log tomography, formerly log-curve amplitude slicing, is a visualization method recently developed at Michigan Technological University to correlate subsurface data by utilizing the high vertical resolution of well log curves. The well log tomography method was first successfully applied to the Middle Devonian Traverse Group within the Michigan Basin using gamma ray log curves. The purpose of this study is to prepare a digital data set for the Middle Devonian Dundee and Rogers City Limestones, apply the well log tomography method to this data and from this application, interpret paleogeographic trends in the natural radioactivity. Both the Dundee and Rogers City intervals directly underlie the Traverse Group and combined are the most prolific reservoir within the Michigan Basin. Differences between this study and the Traverse Group include increased well control and “slicing” of a more uniform lithology. Gamma ray log curves for the Dundee and Rogers City Limestones were obtained from 295 vertical wells distributed over the Lower Peninsula of Michigan, converted to Log ASCII Standard files, and input into the well log tomography program. The “slicing” contour results indicate that during the formation of the Dundee and Rogers City intervals, carbonates and evaporites with low natural radioactive signatures on gamma ray logs were deposited. This contrasts the higher gamma ray amplitudes from siliciclastic deltas that cyclically entered the basin during Traverse Group deposition. Additionally, a subtle north-south, low natural radioactive trend in the center of the basin may correlate with previously published Dundee facies tracts. Prominent trends associated with the distribution of limestone and dolomite are not observed because the regional range of gamma ray values for both carbonates are equivalent in the Michigan Basin and additional log curves are needed to separate these lithologies.