Retrieval by Shape Population: An Index Tree Approach

Based on our previous work in deformable shape model-based object detection, a new method is proposed that uses index trees for organizing shape features to support content-based retrieval applications. In the proposed strategy, different shape feature sets can be used in index trees constructed for object detection and shape similarity comparison respectively. There is a direct correspondence between the two shape feature sets. As a result, application-specific features can be obtained efficiently for shape-based retrieval after object detection. A novel approach is proposed that allows retrieval of images based on the population distribution of deformed shapes in each image. Experiments testing these new approaches have been conducted using an image database that contains blood cell micrographs. The precision vs. recall performance measure shows that our method is superior to previous methods.

Index Trees for Efficient Deformable Shape-based Retrieval

An improved method for deformable shape-based image indexing and retrieval is described. A pre-computed index tree is used to improve the speed of our previously reported on-line model fitting method; simple shape features are used as keys in a pre-generated index tree of model instances. In addition, a coarse to fine indexing scheme is used at different levels of the tree to further improve speed while maintaining matching accuracy. Experimental results show that the speedup is significant, while accuracy of shape-based indexing is maintained. A method for shape population-based retrieval is also described. The method allows query formulation based on the population distributions of shapes in each image. Results of population-based image queries for a database of blood cell micrographs are shown.

Monitoring the vegetation start of season (SOS) across the island of Ireland using the MERIS global vegetation index

The aim of this study was to develop a methodology, based on satellite remote sensing, to estimate the vegetation Start of Season (SOS) across the whole island of Ireland on an annual basis. This growing body of research is known as Land Surface Phenology (LSP) monitoring. The SOS was estimated for each year from a 7-year time series of 10-day composited, 1.2 km reduced resolution MERIS Global Vegetation Index (MGVI) data from 2003 to 2009, using the time series analysis software, TIMESAT. The selection of a 10-day composite period was guided by in-situ observations of leaf unfolding and cloud cover at representative point locations on the island. The MGVI time series was smoothed and the SOS metric extracted at a point corresponding to 20% of the seasonal MGVI amplitude. The SOS metric was extracted on a per pixel basis and gridded for national scale coverage. There were consistent spatial patterns in the SOS grids which were replicated on an annual basis and were qualitatively linked to variation in landcover. Analysis revealed that three statistically separable groups of CORINE Land Cover (CLC) classes could be derived from differences in the SOS, namely agricultural and forest land cover types, peat bogs, and natural and semi-natural vegetation types. These groups demonstrated that managed vegetation, e.g. pastures has a significantly earlier SOS than in unmanaged vegetation e.g. natural grasslands. There was also interannual spatio-temporal variability in the SOS. Such variability was highlighted in a series of anomaly grids showing variation from the 7-year mean SOS. An initial climate analysis indicated that an anomalously cold winter and spring in 2005/2006, linked to a negative North Atlantic Oscillation index value, delayed the 2006 SOS countrywide, while in other years the SOS anomalies showed more complex variation. A correlation study using air temperature as a climate variable revealed the spatial complexity of the air temperature-SOS relationship across the Republic of Ireland as the timing of maximum correlation varied from November to April depending on location. The SOS was found to occur earlier due to warmer winters in the Southeast while it was later with warmer winters in the Northwest. The inverse pattern emerged in the spatial patterns of the spring correlates. This contrasting pattern would appear to be linked to vegetation management as arable cropping is typically practiced in the southeast while there is mixed agriculture and mostly pastures to the west. Therefore, land use as well as air temperature appears to be an important determinant of national scale patterns in the SOS. The TIMESAT tool formed a crucial component of the estimation of SOS across the country in all seven years as it minimised the negative impact of noise and data dropouts in the MGVI time series by applying a smoothing algorithm. The extracted SOS metric was sensitive to temporal and spatial variation in land surface vegetation seasonality while the spatial patterns in the gridded SOS estimates aligned with those in landcover type. The methodology can be extended for a longer time series of FAPAR as MERIS will be replaced by the ESA Sentinel mission in 2013, while the availability of full resolution (300m) MERIS FAPAR and equivalent sensor products holds the possibility of monitoring finer scale seasonality variation. This study has shown the utility of the SOS metric as an indicator of spatiotemporal variability in vegetation phenology, as well as a correlate of other environmental variables such as air temperature. However, the satellite-based method is not seen as a replacement of ground-based observations, but rather as a complementary approach to studying vegetation phenology at the national scale. In future, the method can be extended to extract other metrics of the seasonal cycle in order to gain a more comprehensive view of seasonal vegetation development.

Separating the scattering and absorption coefficients using the real and imaginary parts of the refractive index with low-coherence interferometry.

We present an analytical method that yields the real and imaginary parts of the refractive index (RI) from low-coherence interferometry measurements, leading to the separation of the scattering and absorption coefficients of turbid samples. The imaginary RI is measured using time-frequency analysis, with the real part obtained by analyzing the nonlinear phase induced by a sample. A derivation relating the real part of the RI to the nonlinear phase term of the signal is presented, along with measurements from scattering and nonscattering samples that exhibit absorption due to hemoglobin.

Measurements of nonlinear refractive index in scattering media.

We have recently developed a spectral re-shaping technique to simultaneously measure nonlinear refractive index and nonlinear absorption. In this technique, the information about the nonlinearities is encoded in the frequency domain, rather than in the spatial domain as in the conventional Z-scan method. Here we show that frequency encoding is much more robust with respect to scattering. We compare spectral re-shaping and Z-scan measurements in a highly scattering environment and show that reliable spectral re-shaping measurements can be performed even in a regime that precludes standard Z-scans.

Optical-CT 3D Dosimetry Using Fresnel Lenses with Minimal Refractive-Index Matching Fluid.

Telecentric optical computed tomography (optical-CT) is a state-of-the-art method for visualizing and quantifying 3-dimensional dose distributions in radiochromic dosimeters. In this work a prototype telecentric system (DFOS-Duke Fresnel Optical-CT Scanner) is evaluated which incorporates two substantial design changes: the use of Fresnel lenses (reducing lens costs from $10-30K t0 $1-3K) and the use of a 'solid tank' (which reduces noise, and the volume of refractively matched fluid from 1 ltr to 10 cc). The efficacy of DFOS was evaluated by direct comparison against commissioned scanners in our lab. Measured dose distributions from all systems were compared against the predicted dose distributions from a commissioned treatment planning system (TPS). Three treatment plans were investigated including a simple four-field box treatment, a multiple small field delivery, and a complex IMRT treatment. Dosimeters were imaged within 2 h post irradiation, using consistent scanning techniques (360 projections acquired at 1 degree intervals, reconstruction at 2mm). DFOS efficacy was evaluated through inspection of dose line-profiles, and 2D and 3D dose and gamma maps. DFOS/TPS gamma pass rates with 3%/3mm dose difference/distance-to-agreement criteria ranged from 89.3% to 92.2%, compared to from 95.6% to 99.0% obtained with the commissioned system. The 3D gamma pass rate between the commissioned system and DFOS was 98.2%. The typical noise rates in DFOS reconstructions were up to 3%, compared to under 2% for the commissioned system. In conclusion, while the introduction of a solid tank proved advantageous with regards to cost and convenience, further work is required to improve the image quality and dose reconstruction accuracy of the new DFOS optical-CT system.

Estimation of chlorophyll degradation into phaeophytinin Anaptychia ciliaris as a method to detect air pollution

Se estudia la influencia de los siguientes factores sobre el valor del cociente de feofitinización DO 435 nm/DO 415 nm en el líquen Anaptychia ciliaris (L.) Kórber: edad del líquen, concentración final de pigmentos, trasplante de los líquenes a áreas distintas sobre sustratos diferentes o similares y el valor de pH del sustrato original o el adoptado tras el trasplante. Se discute la utilización de A. ciliaris como un bioindicador de la presencia de factorcs acidificantes en la atmósfera o en el agua de lluvia que provoquen la feofitinización de las clorofilas.

Effect of a COL1A1 Sp1 Binding Site Polymorphism on Arterial Pulse Wave Velocity: An Index of Compliance.

Reduced arterial compliance precedes changes in blood pressure, which may be mediated through alterations in vessel wall matrix composition. We investigated the effect of the collagen type I-1 gene (COL1A1) +2046G>T polymorphism on arterial compliance in healthy individuals. We recruited 489 subjects (251 men and 238 women; mean age, 22.6±1.6 years). COL1A1 genotypes were determined using polymerase chain reaction and digestion by restriction enzyme Bal1. Arterial pulse wave velocities were measured in 3 segments, aortoiliac (PWVA), aortoradial (PWVB), and aorto-dorsalis-pedis (PWVF), as an index of compliance using a noninvasive optical method. Data were available for 455 subjects. The sample was in Hardy-Weinberg equilibrium with genotype distributions and allele frequencies that were not significantly different from those reported previously. The T allele frequency was 0.22 (95% confidence interval, 0.19 to 0.24). Two hundred eighty-three (62.2%) subjects were genotype GG, 148 (35.5%) subjects were genotype GT, and 24 (5.3%) subjects were genotype TT. A comparison of GG homozygotes with GT and TT individuals demonstrated a statistically significant association with arterial compliance: PWVF 4.92±0.03 versus 5.06±0.05 m/s (ANOVA, P=0.009), PWVB 4.20±0.03 versus 4.32±0.04 m/s (ANOVA, P=0.036), and PWVA 3.07±0.03 versus 3.15±0.03 m/s (ANOVA, P=0.045). The effects of genotype were independent of age, gender, smoking, mean arterial pressure, body mass index, family history of hypertension, and activity scores. We report an association between the COL1A1 gene polymorphism and arterial compliance. Alterations in arterial collagen type 1A deposition may play a role in the regulation of arterial compliance

Index of sources of stress in nursing students: a confirmatory factor analysis.

Aim. This paper is a report of a study to test the proposed factor structure of the Index of Sources of Stress in Nursing Students. Background. Research across many countries has identified a number of sources of distress in nursing students but little attempt has been made to understand and measure sources of eustress or those stressors likely to enhance performance and well-being. The Index of Sources of Stress in Nursing Students was developed to do this. Exploratory factor analysis suggested a three-factor structure, the factors being labelled: learning and teaching; placement-related and course organization. It is important, however, to subject the instrument to confirmatory factor analysis as a further test of construct validity. Method. A convenience sample of final year nursing students (n = 176) was surveyed in one university in Northern Ireland in 2007. The Index of Sources of Stress in Nursing Students, which measures sources of stress likely to contribute to distress and eustress, was completed electronically. The LISREL programme was used to carry out the confirmatory factor analysis and test the factor structure suggested in the exploratory analysis. Findings. The proposed factor structure for the items measuring ‘Uplifts’ proved to be a good fit to the data and the proposed factor structure for the items measuring ‘Hassles’ showed adequate fit. Conclusion. In nursing programmes adopting the academic model and combining university-based learning with placement experience, this instrument can be used to help identify the sources of stress or course demands that students rate as distressing and those that help them to achieve. The validity of the ISSN could be further evaluated in other education settings.

A new method of measuring plastic limit of fine materials

Index properties such as the liquid limit and plastic limit are widely used to evaluate certain geotechnical parameters of fine-grained soils. Measurement of the liquid limit is a mechanical process, and the possibility of errors occurring during measurement is not significant. However, this is not the case for plastic limit testing, despite the fact that the current method of measurement is embraced by many standards around the world. The method in question relies on a fairly crude procedure known widely as the ‘thread rolling' test, though it has been the subject of much criticism in recent years. It is essential that a new, more reliable method of measuring the plastic limit is developed using a mechanical process that is both consistent and easily reproducible. The work reported in this paper concerns the development of a new device to measure the plastic limit, based on the existing falling cone apparatus. The force required for the test is equivalent to the application of a 54 N fast-static load acting on the existing cone used in liquid limit measurements. The test is complete when the relevant water content of the soil specimen allows the cone to achieve a penetration of 20 mm. The new technique was used to measure the plastic limit of 16 different clays from around the world. The plastic limit measured using the new method identified reasonably well the water content at which the soil phase changes from the plastic to the semi-solid state. Further evaluation was undertaken by conducting plastic limit tests using the new method on selected samples and comparing the results with values reported by local site investigation laboratories. Again, reasonable agreement was found.

The circle in the relationship between space and body. Photo-essay based on Isidro Blasco and the BAPNE method

This article demonstrates a visual study on the educational space in which the teaching of body percussion is carried out in universities. The methodological framework is chosen by the Visual Arts Based Educational Research, using the work of an artist as a conceptual and methodological model. The research remains notable (1) due to the theoretical reference to the BAPNE method, (2) due to the visual reference to the work of Isidro Blasco – especially with the piece “Shanghai Planet 2009” - ;(3) due to the parallelisms established between the object of study in this investigation -the spatial analysis- and the focuses of interest revealed by the art critics in relation to the work of this artist. By means of a visual speech formed with 7 photo-collages the relationship between body and educational space is visualized in the basic disposition of circular learning. The visual constructions by way of photo-collage and their aesthetic charge brings us closer to the intimacy of the educational space, in the style in which it is distributed to the students in the music classroom, the materialization of interpersonal relationships, the occupied and empty volumes.

Some thoughts on Juan Antonio Ramírez´s iconologic-paranoid method for the study of Dali´s works

In 1990, Juan Antonio Ramírez made known his iconological paranoiac method to the academic world. It is a system devised to study Dalí´s work, born of happy matrimony between the catalonian artist´s critical paranoiac method and the first iconographic school of Warburg and Panofsky. What, at first sight, seemed to be an extravagant methodology with little academic credibility, turned out to be, by going forward in time, an effective research method when analyzing Dali´s initial works. It is no wonder that, at the beginning of XXI century, this hybridization between Dalí´s and Panofsky’s methods, were regarded as a strange and nonsensical idea. Nevertheless, twenty years after, blatant examples have been noted, which endorse the advantages of this new system for “iconographic” study. As usual, this new contribution by Juan Antonio Ramirez to art history methodology is called upon to have a successful future survival, in forthcoming generations. This article, attempts to analyze this method, inquiring into the validity, effectiveness and practical utility.

Whole Slide Image Cytometry: a Novel Method for the Detection and Quantification of Abnormal DNA Contents in Barrett’s Oesophagus

Background: Barrett's oesophagus (BO) is a well recognized precursor of the majority of cases of oesophageal adenocarcinoma (OAC). Endoscopic surveillance of BO patients is frequently undertaken in an attempt to detect early OAC, high grade dysplasia (HGD) or low grade dysplasia (LGD). However histological interpretation and grading of dysplasia is subjective and poorly reproducible. The alternative flow cytometry and cytology-preparation image cytometry techniques require large amounts of tissue and specialist expertise which are not widely available for frontline health care.
Methods: This study has combined whole slide imaging with DNA image cytometry, to provide a novel method for the detection and quantification of abnormal DNA contents. 20 cases were evaluated, including 8 Barrett's specialised intestinal metaplasia (SIM), 6 LGD and 6 HGD. Feulgen stained oesophageal sections (1µm thickness) were digitally scanned in their entirety and evaluated to select regions of interests and abnormalities. Barrett’s mucosa was then interactively chosen for automatic nuclei segmentation where irrelevant cell types are ignored. The combined DNA content histogram for all selected image regions was then obtained. In addition, histogram measurements, including 5c exceeding ratio (xER-5C), 2c deviation index (2cDI) and DNA grade of malignancy (DNA-MG), were computed.
Results: The histogram measurements, xER-5C, 2cDI and DNA-MG, were shown to be effective in differentiating SIM from HGD, SIM from LGD, and LGD from HGD. All three measurements discriminated SIM from HGD cases successfully with statistical significance (pxER-5C=0.0041, p2cDI=0.0151 and pDNA-MG=0.0057). Statistical significance is also achieved differentiating SIM from LGD samples with pxER-5C=0.0019, p2cDI=0.0023 and pDNA-MG=0.0030. Furthermore the differences between LGD and HGD cases are statistical significant (pxER-5C=0.0289, p2cDI=0.0486 and pDNA-MG=0.0384).
Conclusion: Whole slide image cytometry is a novel and effective method for the detection and quantification of abnormal DNA content in BO. Compared to manual histological review, this proposed method is more objective and reproducible. Compared to flow cytometry and cytology-preparation image cytometry, the current method is low cost, simple to use and only requires a single 1µm tissue section. Whole slide image cytometry could assist the routine clinical diagnosis of dysplasia in BO, which is relevant for future progression risk to OAC.

Pepsin in bronchoalveolar lavage fluid:a specific and sensitive method of diagnosing gastro-oesophageal reflux-related pulmonary aspiration

Gastro-oesophageal reflux (GOR)-related aspiration is associated with respiratory disease, but the current "gold standard" investigation, the lipid-laden macrophage index (LLMI), is flawed. A specific marker of GOR-related aspiration should originate in the stomach, but not the lung. An assay to detect gastric pepsin in the bronchoalveolar lavage (BAL) of children was developed and validated.

A scaling method for modelling the crashworthiness of novel roadside barrier designs

In this paper, a novel method for modelling a scaled vehicle–barrier crash test similar to the 20◦ angled barrier test specified in EN 1317 is reported. The intended application is for proof-of-concept evaluation of novel roadside barrier designs, and as a cost-effective precursor to full-scale testing or detailed computational modelling. The method is based on the combination of the conservation of energy law and the equation of motion of a spring mass system representing the impact, and shows, for the first time, the feasibility of applying classical scaling theories to evaluation of roadside barrier design. The scaling method is used to set the initial velocity of the vehicle in the scaled test and to provide scaling factors to convert the measured vehicle accelerations in the scaled test to predicted full-scale accelerations. These values can then be used to calculate the Acceleration Severity Index score of the barrier for a full-scale test. The theoretical validity of the method is demonstrated by comparison to numerical simulations of scaled and full-scale angled barrier impacts using multibody analysis implemented in the crash simulation software MADYMO. Results show a maximum error of 0.3% ascribable to the scaling method.