Using IR-n for information retrieval of Genomics Track

Nowadays there is a big amount of biomedical literature which uses complex nouns and acronyms of biological entities thus complicating the task of retrieval specific information. The Genomics Track works for this goal and this paper describes the approach we used to take part of this track of TREC 2007. As this is the first time we participate in this track, we configurated a new system consisting of the following diferenciated parts: preprocessing, passage generation, document retrieval and passage (with the answer) extraction. We want to call special attention to the textual retrieval system used, which was developed by the University of Alicante. Adapting the resources for the propouse, our system has obtained precision results over the mean and median average of the 66 official runs for the Document, Aspect and Passage2 MAP; and in the case of Passage MAP we get nearly the median and mean value. We want to emphasize we have obtained these results without incorporating specific information about the domain of the track. For the future, we would like to further develop our system in this direction.

Calibration of the length of a chain of single gold atoms

Using a scanning tunnelling microscope or mechanically controllable break junction it has been shown that it is possible to control the formation of a wire made of single gold atoms. In these experiments an interatomic distance between atoms in the chain of ∼3.6 Å was reported which is not consistent with recent theoretical calculations. Here, using precise calibration procedures for both techniques, we measure the length of the atomic chains. Based on the distance between the peaks observed in the chain length histogram we find the mean value of the interatomic distance before chain rupture to be 2.5±0.2 Å. This value agrees with the theoretical calculations for the bond length. The discrepancy with the previous experimental measurements was due to the presence of He gas, that was used to promote the thermal contact, and which affects the value of the work function that is commonly used to calibrate distances in scanning tunnelling microscopy and mechanically controllable break junctions at low temperatures.

Impacts on particles and ozone by transport processes recorded at urban and high-altitude monitoring stations

In order to evaluate the influence of particle transport episodes on particle number concentration temporal trends at both urban and high-altitude (Aitana peak-1558 m a.s.l.) stations, a simultaneous sampling campaign from October 2011 to September 2012 was performed. The monitoring stations are located in southeastern Spain, close to the Mediterranean coast. The annual average value of particle concentration obtained in the larger accumulation mode (size range 0.25–1 μm) at the mountain site, 55.0 ± 3.0 cm− 3, was practically half that of the value obtained at the urban station (112.0 ± 4.0 cm− 3). The largest difference between both stations was recorded during December 2011 and January 2012, when particles at the mountain station registered the lowest values. It was observed that during urban stagnant episodes, particle transport from urban sites to the mountain station could take place under specific atmospheric conditions. During these transports, the major particle transfer is produced in the 0.5–2 μm size range. The minimum difference between stations was recorded in summer, particularly in July 2012, which is most likely due to several particle transport events that affected only the mountain station. The particle concentration in the coarse mode was very similar at both monitoring sites, with the biggest difference being recorded during the summer months, 0.4 ± 0.1 cm− 3 at the urban site and 0.9 ± 0.1 cm− 3 at the Aitana peak in August 2012. Saharan dust outbreaks were the main factor responsible for these values during summer time. The regional station was affected more by these outbreaks, recording values of > 4.0 cm− 3, than the urban site. This long-range particle transport from the Sahara desert also had an effect upon O3 levels measured at the mountain station. During periods affected by Saharan dust outbreaks, ozone levels underwent a significant decrease (3–17%) with respect to its mean value.

Repeatability and reproducibility of corneal thickness using SOCT Copernicus HR

Purpose: The aim of this study is to determine the reliability of corneal thickness measurements derived from SOCT Copernicus HR (Fourier domain OCT). Methods: Thirty healthy eyes of 30 subjects were evaluated. One eye of each patient was chosen randomly. Images were obtained of the central (up to 2.0 mm from the corneal apex) and paracentral (2.0 to 4.0 mm) cornea. We assessed corneal thickness (central and paracentral) and epithelium thickness. The intra-observer repeatability data were analysed using the intra-class correlation coefficient (ICC) for a range of 95 per cent within-subject standard deviation (SW) and the within-subject coefficient of variation (CW). The level of agreement by Bland–Altman analysis was also represented for the study of the reproducibility between observers and agreement between methods of measurement (automatic versus manual). Results: The mean value of the central corneal thickness (CCT) was 542.4 ± 30.1 μm (SD). There was a high intra-observer agreement, finding the best result in the central sector with an intra-class correlation coefficient of 0.99, 95 per cent CI (0.989 to 0.997) and the worst, in the minimum corneal thickness, with an intra-class correlation coefficient of 0.672, 95 per cent CI (0.417 to 0.829). Reproducibility between observers was very high. The best result was found in the central sector thickness obtained both manually and automatically with an intra-class correlation coefficient of 0.990 in both cases and the worst result in the maximum corneal thickness with an intra-class correlation coefficient of 0.827. The agreement between measurement methods was also very high with intra-class correlation coefficient greater than 0.91. On the other hand the repeatability and reproducibility for epithelial measurements was poor. Conclusion: Pachymetric mapping with SOCT Copernicus HR was found to be highly repeatable and reproducible. We found that the device lacks an appropriate ergonomic design as proper focusing of the laser beam onto the cornea for anterior segment scanning required that patients were positioned slightly farther away from the machine head-rest than in the setup for retinal imaging.

An XMM-Newton view of FeKα in high-mass X-ray binaries

We present a comprehensive analysis of the whole sample of available XMM-Newton observations of high-mass X-ray binaries (HMXBs) until August 2013, focusing on the FeKα emission line. This line is key to better understanding the physical properties of the material surrounding the X-ray source within a few stellar radii (the circumstellar medium). We collected observations from 46 HMXBs and detected FeKα in 21 of them. We used the standard classification of HMXBs to divide the sample into different groups. We find that (1) different classes of HMXBs display different qualitative behaviours in the FeKα spectral region. This is visible especially in SGXBs (showing ubiquitous Fe fluorescence but not recombination Fe lines) and in γ Cass analogues (showing both fluorescent and recombination Fe lines). (2) FeKα is centred at a mean value of 6.42 keV. Considering the instrumental and fits uncertainties, this value is compatible with ionization states that are lower than Fe xviii. (3) The flux of the continuum is well correlated with the flux of the line, as expected. Eclipse observations show that the Fe fluorescence emission comes from an extended region surrounding the X-ray source. (4) We observe an inverse correlation between the X-ray luminosity and the equivalent width of FeKα (EW). This phenomenon is known as the X-ray Baldwin effect. (5) FeKα is narrow (σline< 0.15 keV), reflecting that the reprocessing material does not move at high speeds. We attempt to explain the broadness of the line in terms of three possible broadening phenomena: line blending, Compton scattering, and Doppler shifts (with velocities of the reprocessing material V ~ 1000 km s-1). (6) The equivalent hydrogen column (NH) directly correlates to the EW of FeKα, displaying clear similarities to numerical simulations. It highlights the strong link between the absorbing and the fluorescent matter. (7) The observed NH in supergiant X-ray binaries (SGXBs) is in general higher than in supergiant fast X-ray transients (SFXTs). We suggest two possible explanations: different orbital configurations or a different interaction compact object – wind. (8) Finally, we analysed the sources IGR J16320-4751 and 4U 1700-37 in more detail, covering several orbital phases. The observed variation in NH between phases is compatible with the absorption produced by the wind of their optical companions. The results clearly point to a very important contribution of the donor’s wind in the FeKα emission and the absorption when the donor is a supergiant massive star.

Discontinuity spacing analysis in rock masses using 3D point clouds

The complete characterization of rock masses implies the acquisition of information of both, the materials which compose the rock mass and the discontinuities which divide the outcrop. Recent advances in the use of remote sensing techniques – such as Light Detection and Ranging (LiDAR) – allow the accurate and dense acquisition of 3D information that can be used for the characterization of discontinuities. This work presents a novel methodology which allows the calculation of the normal spacing of persistent and non-persistent discontinuity sets using 3D point cloud datasets considering the three dimensional relationships between clusters. This approach requires that the 3D dataset has been previously classified. This implies that discontinuity sets are previously extracted, every single point is labeled with its corresponding discontinuity set and every exposed planar surface is analytically calculated. Then, for each discontinuity set the method calculates the normal spacing between an exposed plane and its nearest one considering 3D space relationship. This link between planes is obtained calculating for every point its nearest point member of the same discontinuity set, which provides its nearest plane. This allows calculating the normal spacing for every plane. Finally, the normal spacing is calculated as the mean value of all the normal spacings for each discontinuity set. The methodology is validated through three cases of study using synthetic data and 3D laser scanning datasets. The first case illustrates the fundamentals and the performance of the proposed methodology. The second and the third cases of study correspond to two rock slopes for which datasets were acquired using a 3D laser scanner. The second case study has shown that results obtained from the traditional and the proposed approaches are reasonably similar. Nevertheless, a discrepancy between both approaches has been found when the exposed planes members of a discontinuity set were hard to identify and when the planes pairing was difficult to establish during the fieldwork campaign. The third case study also has evidenced that when the number of identified exposed planes is high, the calculated normal spacing using the proposed approach is minor than those using the traditional approach.

Health-related quality of life and determinant factors in celiac disease. A population-based analysis of adult patients in Spain

Background: Celiac disease (CD) has a negative impact on the health-related quality of life (HRQL) of affected patients. Although HRQL and its determinants have been examined in Spanish CD patients specifically recruited in hospital settings, these aspects of CD have not been assessed among the general Spanish population. Methods: An observational, transversal study of a non-randomized, representative sample of adult celiac patients throughout all of Spain's Autonomous Regions. Subjects were recruited through celiac patient associations. A Spanish version of the self-administered Celiac Disease-Quality of Life (CD-QOL) questionnaire was used. Determinant factors of HRQL were assessed with the aid of multivariate analysis to control for confounding factors. Results: We analyzed the responses provided by 1,230 patients, 1,092 (89.2%) of whom were women. The overall mean value for the CD-QOL index was 56.3 ± 18.27 points. The dimension that obtained the most points was dysphoria, with 81.3 ± 19.56 points, followed by limitations with 52.3 ± 23.43 points; health problems, with 51.6 ± 26.08 points, and inadequate treatment, with 36.1 ± 21.18 points. Patient age and sex, along with time to diagnosis, and length of time on a gluten-free diet were all independent determinant factors of certain dimensions of HRQL: women aged 31 to 40 expressed poorer HRQL while time to diagnosis and length of time on a gluten-free diet were determinant factors for better HRQL scores. Conclusions: The HRQL of adult Spanish celiac subjects is moderate, improving with the length of time patients remain on a gluten-free diet.

Galectina-3 : indicador de prognóstico : alvo de intervenção terapêutica?

Trabalho Final do Curso de Mestrado Integrado em Medicina, Faculdade de Medicina, Universidade de Lisboa, 2014

Dactilite na artrite psoriática

Trabalho Final do Curso de Mestrado Integrado em Medicina, Faculdade de Medicina, Universidade de Lisboa, 2014

Use of Extended Characteristics of Locomotion and Feeding Behavior for Automated Identification of Lame Dairy Cows.

This study was carried out to detect differences in locomotion and feeding behavior in lame (group L; n = 41; gait score ≥ 2.5) and non-lame (group C; n = 12; gait score ≤ 2) multiparous Holstein cows in a cross-sectional study design. A model for automatic lameness detection was created, using data from accelerometers attached to the hind limbs and noseband sensors attached to the head. Each cow's gait was videotaped and scored on a 5-point scale before and after a period of 3 consecutive days of behavioral data recording. The mean value of 3 independent experienced observers was taken as a definite gait score and considered to be the gold standard. For statistical analysis, data from the noseband sensor and one of two accelerometers per cow (randomly selected) of 2 out of 3 randomly selected days was used. For comparison between group L and group C, the T-test, the Aspin-Welch Test and the Wilcoxon Test were used. The sensitivity and specificity for lameness detection was determined with logistic regression and ROC-analysis. Group L compared to group C had significantly lower eating and ruminating time, fewer eating chews, ruminating chews and ruminating boluses, longer lying time and lying bout duration, lower standing time, fewer standing and walking bouts, fewer, slower and shorter strides and a lower walking speed. The model considering the number of standing bouts and walking speed was the best predictor of cows being lame with a sensitivity of 90.2% and specificity of 91.7%. Sensitivity and specificity of the lameness detection model were considered to be very high, even without the use of halter data. It was concluded that under the conditions of the study farm, accelerometer data were suitable for accurately distinguishing between lame and non-lame dairy cows, even in cases of slight lameness with a gait score of 2.5.

(Table 1) Crystal sizes of measured samples

Due to experimental difficulties grain size distributions of gas hydrate crystallites are largely unknown in natural samples. For the first time, we were able to determine grain size distributions of six natural gas hydrates for samples retrieved from the Gulf of Mexico and from Hydrate Ridge offshore Oregon from varying depths. High-energy synchrotron radiation provides high photon fluxes as well as high penetration depth and thus allows for investigation of bulk sediment samples. The gas hydrate crystallites appear to be (log-) normally distributed in the natural samples and to be of roughly globular shape. The mean grain sizes are in the range from 300-600 µm with a tendency for bigger grains to occur in greater depth, possibly indicating a difference in the formation age. Laboratory produced methane hydrate, starting from ice and aged for 3 weeks, shows half a log-normal curve with a mean value of ~40 µm. This one order-of-magnitude smaller grain sizes suggests that care must be taken when transposing grain-size sensitive (petro-)physical data from laboratory-made gas hydrates to natural settings.

Proxy calibration on two sedimentary sequences off Lisbon

High-resolution proxy data analyzed on two high-sedimentation shallow water sedimentary sequences (PO287-26B and PO287-28B) recovered off Lisbon (Portugal) provide the means for comparison to long-term instrumental time series of marine and atmospheric parameters (sea surface temperature (SST), precipitation, total river flow, and upwelling intensity computed from sea level pressure) and the possibility to do the necessary calibration for the quantification of past climate conditions. XRF Fe is used as proxy for river flow, and the upwelling-related diatom genus Chaetoceros is our upwelling proxy. SST is estimated from the coccolithophore-synthesized alkenones and Uk'37 index. Comparison of the Fe record to the instrumental data reveals its similarity to a mean average run of the instrumentally measured winter (JFMA) river flow on both sites. The upwelling diatom record concurs with the upwelling indices at both sites; however, high opal dissolution, below 20-25 cm, prevents its use for quantitative reconstructions. Alkenone-derived SST at site 28B does not show interannual variation; it has a mean value around 16°C and compares quite well with the instrumental winter/spring temperature. At site 26B the mean SST is the same, but a high degree of interannual variability (up to 4°C) appears to be determined by summer upwelling conditions. Stepwise regression analyses of the instrumental and proxy data sets provided regressions that explain from 65 to 94% of the variability contained in the original data, and reflect spring and summer river flow, as well as summer and winter upwelling indices, substantiating the relevance of seasons to the interpretation of the different proxy signals. The lack of analogs and the small data set available do not allow quantitative reconstructions at this time, but this might be a powerful tool for reconstructing past North Atlantic Oscillation conditions, should we be able to find continuous high-resolution records and overcome the analog problem.

Monitoring salivary lamotrigine concentrations

Lamotrigine concentrations were measured simultaneously (as far as was feasible) in stimulated and unstimulated saliva samples, and in plasma, from seven adult volunteers over a 32 h period following a single 50 mg dose of the drug, and in 20 children and adolescents during the course of routine antiepileptic therapy. In individuals there was a close correlation between the measurements at least 2 It after ingestion of the drug. Concentrations in stimulated and unstimulated saliva were similar; the stimulation produced little change in the saliva secretion rate. The saliva-to-plasma concentration ratio increased linearly by 0.78% for each 1 mg/L plasma lamotrigine concentration, with a mean value of 48.8% at a plasma lamotrigine concentration of 10 mg/L. With appropriate precautions as to the timing of saliva collections, and a single plasma lamotrigine concentration measurement to calibrate the salivary values in the individual, salivary lamotrigine concentration measurement appears to be a practicable approach to therapeutic drug monitoring. This has significant implications for the elucidation of the pharmacokinetics of lamotrigine in the paediatric population.

High-precision TIMS U-series and AMS C-14 dating of a coral reef lagoon sediment core from southern South China Sea

Accurate dating of lagoon sediments has been a difficult problem, although lagoon profiles, usually with high deposition rates, have a great potential for high-resolution climate reconstruction. We report 26 high-precision TIMS U-series dates (on 25 coral branches) and five AMS C-14 dates (on foraminifera) for a 15.4-m long lagoon core from Yongshu Reef, Nansha area, southern South China Sea. All the dates are in the correct stratigraphical sequence, providing the best chronology so far reported for lagoon deposits. The results reveal a similar to 4000-a continuous depositional history, with sedimentation rates varying from 0.8 to 24.6 mm a(-1), with an average of 3.85 mm a(-1), which corresponds to an average net carbonate accumulation rate of similar to 2700 g CaCO3 m(-2) a(-1), significantly higher than the mean value (800 +/- 400 g CaCO3 m(-2) a(-1)) used for lagoons in general in previous studies of global carbonate budget. Episodes of accelerated depositions within the last 1000 years correlate well with strong storm events identified by U-series dates of storm-transported coral blocks in the area. However, in the longer term, the sedimentation rates during the past 1000 years were much higher than earlier on, probably due to more vigorous wave-reef interaction as a result of relative sea-level fall since 500 AD and expansion of reef flat area, supplying more sediments. The coral TIMS U-series ages and foraminifera AMS 14C dates reveal intriguing apparent radiocarbon reservoir ages (R) from 572 to 1052 years, which are much higher than global mean values of similar to 400 years. (c) 2006 Elsevier Ltd. All rights reserved.

Avaliação das coroas dos primeiros e terceiros molares superiores, nos tratamentos com extrações de segundos molares superiores

A presente pesquisa teve como objetivo avaliar, por meio de modelos de gesso, a posição das coroas dos primeiros e terceiros molares superiores permanentes, após a irrupção espontânea dos terceiros molares, na posição dos segundos molares extraídos com finalidade ortodôntica, comparando-os com as coroas dos primeiros e segundos molares superiores permanentes de uma amostra de oclusão normal natural. A amostra experimental constituiu-se de 25 indivíduos, leucodermas, com idade média no início do tratamento de 15,6 anos, sendo 17 do sexo feminino e 8 do sexo masculino, tratados com extrações de segundos molares superiores. A amostra controle constituiu-se de 60 indivíduos do sexo masculino e sexo feminino, com idade média de 15,6 anos e faixa etária compreendida entre 12 e 21 anos, que apresentavam oclusão normal. Foram avaliadas as angulações, as inclinações e as distâncias mésio-distais das coroas dentárias dos terceiros molares e primeiros molares do grupo tratado e dos segundos molares e primeiros molares do grupo controle ou normal. Foram, também, verificadas as diferenças de alturas entre as coroas dentárias dos dois grupos. Verificou-se que nos casos tratados os valores médios das angulações mésio-distais e das inclinações vestíbulo-linguais das coroas dos terceiros molares superiores e dos primeiros molares superiores foram estatisticamente diferentes dos valores médios das angulações mésio-distais e das inclinações vestíbulo-linguais das coroas dos segundos molares superiores e dos primeiros molares superiores na amostra de oclusão normal natural. Observou-se que somente as distâncias mésio-distais das coroas dos terceiros molares superiores mostraram ser significativamente menores que as coroas dos segundos molares superiores da amostra de oclusão normal natural, tanto para o sexo feminino quanto para o masculino. O valor médio da diferença de altura entre as coroas dos primeiros molares e terceiros molares do grupo experimental e das coroas dos primeiros molares e segundos molares do grupo controle foi de 1,11mm, não havendo diferença entre os grupos. Ocorreu a presença de dimorfismo sexual nos valores da distância mésio-distais das coroas dentárias dos primeiros molares superiores do grupo controle e experimental, na distância mésio-distal das coroas dentárias dos segundos molares superiores do grupo controle e na inclinação vestíbulo-linguais das coroas dos terceiros molares superiores do grupo experimental. Nas demais avaliações não houve dimorfismo sexual.