Data visualisation with missing data: A non-linear approach

Exploratory analysis of data in all sciences seeks to find common patterns to gain insights into the structure and distribution of the data. Typically visualisation methods like principal components analysis are used but these methods are not easily able to deal with missing data nor can they capture non-linear structure in the data. One approach to discovering complex, non-linear structure in the data is through the use of linked plots, or brushing, while ignoring the missing data. In this technical report we discuss a complementary approach based on a non-linear probabilistic model. The generative topographic mapping enables the visualisation of the effects of very many variables on a single plot, which is able to incorporate far more structure than a two dimensional principal components plot could, and deal at the same time with missing data. We show that using the generative topographic mapping provides us with an optimal method to explore the data while being able to replace missing values in a dataset, particularly where a large proportion of the data is missing.

Wear and corrosion of mechanical seals

Mechanical seals are used extensively to seal machinery such as pumps, mixers and agitators in the oil, petrochemical and chemical industries. The performance of such machinery is critically dependent on these devices. Seal failures may result in the escape of dangerous chemicals, possibly causing injury or loss of life. Seal performance is limited by the choice of face materials available. These range from cast iron and stellited stainless steel to cemented and silicon carbides. The main factors that affect seal performance are the wear and corrosion of seal faces. This research investigated the feasibility of applying surface coating/treatments to seal materials, in order to provide improved seal performance. Various surface coating/treatment methods were considered; these included electroless nickel plating, ion plating, plasma nitriding, thermal spraying and high temperature diffusion processes. The best wear resistance, as evaluated by the Pin-on-Disc wear test method, was conferred by the sprayed tungsten carbide/nickel/tungsten-chromium carbide deposit, produced by the high energy plasma spraying (Jet-Kote) process. In general, no correlation was found between hardness and wear resistance or surface finish and friction. This is due primarily to the complexity of the wear and frictional oxidation, plastic deformation, ploughing, fracture and delamination. Corrosion resistance was evaluated by Tafel extrapolation, linear polarisation and anodic potentiodynamic polarisation techniques. The best corrosion performance was exhibited by an electroless nickel/titanium nitride duplex coating due to the passivity of the titanium nitride layer in the acidified salt solution. The surface coating/treatments were ranked using a systematic method, which also considered other properties such as adhesion, internal stress and resistance to thermal cracking. The sealing behaviour of surface coated/treated seals was investigated on an industrial seal testing rig. The best sealing performances were exhibited by the Jet-Kote and electroless nickel silicon carbide composite coated seals. The failure of the electroless nickel and electroless nickel/titanium nitride duplex coated seals was due to inadequate adhesion of the deposits to the substrate. Abrasion of the seal faces was the principal wear mechanism. For operation in an environment similar to the experimental system employed (acidified salt solution) the Jet-Kote deposit appears to be the best compromise.

The performance of stabilized and unstabilized minestone in an aqueous environment with emphasis on its erosion resistance

Britain's sea and flood defences are becoming increasingly aged and as a consequence, more fragile and vulnerable. As the government's philosophy on resources shifts against the use of prime quarried and dredged geo-materials, the need to find alternative bulk materials to bolster Britain's prone defences becomes more pressing. One conceivable source for such a material is colliery waste or minestone. Although a plethora of erosion-abrasion studies have been carried out on soils and soil-cements, very little research has been undertaken to determine the resistance of minestone and its cement stabilized form to the effects of water erosion. The thesis reviews the current extent to which soil-cements, minestone and cement stabilized minestone (CSM) have been employed for hydraulic construction projects. A synopsis is also given on the effects of immersion on shales, mudstones and minestone, especially with regard to the phenomena of slaking. A laboratory study was undertaken featuring a selection of minestones from several British coalfields. The stability of minestone and CSM in sea water and distilled water was assessed using slaking tests and immersion monitoring and the bearing on the use of these materials for hydraulic construction is discussed. Following a review of current erosion apparatus, the erosion/abrasion test and rotating cylinder device were chosen and employed to assess the erosion resistance of minestone and CSM. Comparison was made with a sand mix designed to represent a dredged sand, the more traditional, bulk hydraulic construction material. The results of the erosion study suggest that both minestone and CSM were more resistant to erosion and abrasion than equivalently treated sand mixes. The greater resistance of minestone to the agents of erosion and abrasion is attributed to several factors including the size of the particles, a greater degree of cement bonding and the ability of the minestone aggregate to absorb, rather than transmit shock waves produced by impacting abrasive particles. Although minestone is shown to be highly unstable when subjected to cyclic changes in its moisture content, the study suggests that even in an intertidal regime where cyclic immersion does takes place, minestone will retain sufficient moisture within its fabric to prevent slaking from taking place. The slaking study reveals a close relationship between slaking susceptibility and total pore surface area as revealed by porosimetry. The immersion study shows that although the fabric of CSM is rapidly attacked in sea water, a high degree of the disruption is associated with the edges and corners of samples (ie. free surface) while the integrity of the internal fabric remains relatively intact. CSM samples were shown to be resilient when subjected to immersion in distilled water. An overall assessment of minestone and CSM would suggest that with the implementation of judicious selection and appropriate quality control they could be used as alternative materials for flood and sea defences. It is believed, that even in the harsh regime of a marine environment, CSM could be employed for temporary and sacrificial schemes.

Exploratory data analysis with non-linear and missing data in geochemistry

Exploratory analysis of data seeks to find common patterns to gain insights into the structure and distribution of the data. In geochemistry it is a valuable means to gain insights into the complicated processes making up a petroleum system. Typically linear visualisation methods like principal components analysis, linked plots, or brushing are used. These methods can not directly be employed when dealing with missing data and they struggle to capture global non-linear structures in the data, however they can do so locally. This thesis discusses a complementary approach based on a non-linear probabilistic model. The generative topographic mapping (GTM) enables the visualisation of the effects of very many variables on a single plot, which is able to incorporate more structure than a two dimensional principal components plot. The model can deal with uncertainty, missing data and allows for the exploration of the non-linear structure in the data. In this thesis a novel approach to initialise the GTM with arbitrary projections is developed. This makes it possible to combine GTM with algorithms like Isomap and fit complex non-linear structure like the Swiss-roll. Another novel extension is the incorporation of prior knowledge about the structure of the covariance matrix. This extension greatly enhances the modelling capabilities of the algorithm resulting in better fit to the data and better imputation capabilities for missing data. Additionally an extensive benchmark study of the missing data imputation capabilities of GTM is performed. Further a novel approach, based on missing data, will be introduced to benchmark the fit of probabilistic visualisation algorithms on unlabelled data. Finally the work is complemented by evaluating the algorithms on real-life datasets from geochemical projects.

Addressing missing data in geochemistry: a non-linear approach

Exploratory analysis of petroleum geochemical data seeks to find common patterns to help distinguish between different source rocks, oils and gases, and to explain their source, maturity and any intra-reservoir alteration. However, at the outset, one is typically faced with (a) a large matrix of samples, each with a range of molecular and isotopic properties, (b) a spatially and temporally unrepresentative sampling pattern, (c) noisy data and (d) often, a large number of missing values. This inhibits analysis using conventional statistical methods. Typically, visualisation methods like principal components analysis are used, but these methods are not easily able to deal with missing data nor can they capture non-linear structure in the data. One approach to discovering complex, non-linear structure in the data is through the use of linked plots, or brushing, while ignoring the missing data. In this paper we introduce a complementary approach based on a non-linear probabilistic model. Generative topographic mapping enables the visualisation of the effects of very many variables on a single plot, while also dealing with missing data. We show how using generative topographic mapping also provides an optimal method with which to replace missing values in two geochemical datasets, particularly where a large proportion of the data is missing.

An overview of eye-related photophobias

This chapter provides an overview of the various eye-related causes of photophobia and the likely mechanisms responsible. Photophobia is the experience of discomfort affecting the eyes as a result of exposure to light. It has a variety of causes, including the result of eye or brain disease, or it can be a side effect of various drugs or laser surgery. Photophobia can also be a symptom of a more serious disorder such as meningitis and therefore, requires appropriate investigation, diagnosis, and treatment. Trauma or disease affecting several structures of the eye are a common cause of photophobia and can be associated with: (1) the ocular adnexia, such as blepharitis and blepharospasm, (2) the cornea, including abrasion, ulcerative keratitis, and corneal dystrophy, (3) problems in eye development, such as aniridia, buphthalmos, coloboma, and aphakia, (4) various eye inflammations, including uveitis, and (5) retinal disorders, such as achromatopsia, retinal detachment, and retinal dystrophy. There may be two main explanations for photophobia associated with these conditions: (1) direct stimulation of the trigeminal nerve due to damage, disease, or excessive light entering the eye and (2) overstimulation of the retina including a specific population of light-sensitive ganglion cells.

Eye-related photophobia

This article provides an overview of the various eye-related causes of photophobia and the likely mechanisms responsible. Photophobia is an experience of discomfort affecting the eyes due to exposure to light. It has a variety of causes including the result of eye or brain disease, or it can be a side effect of various drugs or laser surgery. Photophobia can also be a symptom of a more serious disorder such as meningitis and therefore, requires appropriate investigation, diagnosis, and treatment. Trauma or disease affecting several structures of the eye are a common cause of photophobia and can be associated with: (1) the ocular adnexia, such as blepharitis and blepharospasm, (2) the cornea, including abrasion, ulcerative keratitis, and corneal dystrophy, (3) problems in eye development, such as aniridia, buphthalmos, coloboma, and aphakia, (4) various eye inflammations, including uveitis, and (5) retinal disorders, such as achromatopsia, retinal detachment, and retinal dystrophy. There may be two main explanations for eye-related photophobia: (1) direct stimulation of the trigeminal nerve due to damage, disease, or excessive light entering the eye and (2) overstimulation of the retina including a specific population of light-sensitive ganglion cells.

Source/receptor reconciliation of ambient organic fine particulate matter in Palm Beach County

Airborne particulate matter (PM) is of environmental concern not only in urban but also rural areas that are easily inhalable and have been considered responsible, together with gaseous pollutants, for possible health effects. The objectives of this research study is to generate an extensive data set for ambient PM collected at Belle Glade and Delray Beach that ultimately was used together with published source profiles to predict the contributions of major sources to the overall airborne particle burden in Belle Glade and Delray Beach. ^ The size segregated particle sampling was conducted for one entire year. The samples collected during the months of January and May were further subjected to chemical analysis for organic compounds by Gas Chromatography-Mass Spectrometry. Additional, PM10 sampling was conducted simultaneously with size segregated particle sampling during January and May to analyze for trace elements using Instrumental Neutron Activation Analysis technique. Elements and organic marker compounds were used in Chemical Mass Balance modeling to determine the major source contribution to the ambient fine particle matter burden. ^ Size segregated particle distribution results show bimodal in both sampling sites. Sugarcane pre-harvest burning in the rural site elevated PM10 concentration by about 30% during the sugarcane harvest season compared to sugarcane growing season. Sea salt particles and Saharan dust particles accounted for the external sources. ^ The results of trace element analysis show that Al, Ca, Cs, Eu, Lu, Nd, Sc, Sm, Th, and Yb are more abundant at the rural sampling site. The trace elements Ba, Br, Ce, Cl, Cr, Fe, Gd, Hf, Na, Sb, Ta, V, and W show high abundance at the urban site due to anthropogenic activities except for Na and Cl, which are from sea salt spray. On the other hand, size segregated trace organic compounds measurements show that organic compounds mainly from combustion process were accumulated in PM0.95. ^ In conclusion, major particle sources were determined by the CMB8.2 software as follows: road dust, sugarcane leaf burning, diesel-powered and gasoline powered vehicle exhaust, leaf surface abrasion particles, and a very small fraction of meat cooking. ^

Arc crust-magma interaction in the Andean Southern Volcanic Zone from thermobarometry, mineral composition, radiogenic isotope and rare earth element systematics of the Azufre-Planchon-Peteroa volcanic complex, Chile

The Andean Southern Volcanic Zone (SVZ) is a vast and complex continental arc that has been studied extensively to provide an understanding of arc-magma genesis, the origin and chemical evolution of the continental crust, and geochemical compositions of volcanic products. The present study focuses on distinguishing the magma/sub-arc crustal interaction of eruptive products from the Azufre-Planchon-Peteroa (APP 35°15'S) volcanic center and other major centers in the Central SVZ (CSVZ 37°S–42°S), Transitional SVZ (TSVZ 34.3–37.0°S), and Northern SVZ (NSVZ 33°S–34°30'S). New Hf and Nd isotopic and trace element data for SVZ centers are consistent with former studies that these magmas experienced variable depths of crystal fractionation, and that crustal assimilation is restricted to the lower crustal depths with an apparent role of garnet. Thermobarometric calculations applied to magma compositions constrain the depth of magma separation from mantle sources in all segments of the SVZ to(70-90 km). Magmatic separation at the APP complex occurs at an average depth of ~50 km which is confined to the mantle lithosphere and the base of the crust suggesting localized thermal abrasion both reservoirs. Thermobarometric calculations indicate that CSVZ primary magmas arise from a similar average depth of (~54 km) which confines magma separation to the asthenospheric mantle. The northwards along-arc Sr-Nd-Hf isotopic data and LREE enrichment accompanied with HREE depletion of SVZ mafic magmas correlates well with northward increasing crustal thickness and decreasing primary melt separation from mantle source regions indicating an increased involvement of lower crustal components in SVZ magma petrogenesis. ^ The study concludes that the development of mature subduction zones over millions of years of continuous magmatism requires that mafic arc derived melts stagnate at lower crustal levels due to density similarities and emplace at lower crustal depths. Basaltic underplating creates localized hot zone environments below major magmatic centers. These regions of high temperature/partial melting, and equilibration with underplated mafic rocks provides the mechanism that controls trace element and isotopic variability of primary magmas of the TSVZ and NSVZ from their baseline CSVZ-like precursors.^

Normalização de eletromiografia de superfície dos músculos respiratórios em sujeitos saudáveis: contração voluntária máxima máxima isométrica versus pressões respiratórias máximas

Aim : To evaluate and to standardize surface electromyography (sEMG) normalization procedures for respiratory muscles by comparing muscle activation during Maximal Voluntary Isometric Contraction (MVIC) and Maximal Respiratory Pressures (MIP, MEP and sniff test). Methods: Healthy subjects were evalua ted regarding demographics, spirometry and sEMG during the five maneuvers: sniff test, MIP , MEP and Maximal Voluntary Isometric C ontraction (MVIC) of RA, SCM and SC A . For electrode placement, skin was prepared with abrasion, followed by shaving in the foll owing regions for acquisition of el ectromyographic signals: (1) SC M: lower third of the distance between the mastoid process and t he sternoclavicular joint; (2) SC A : 5 cm to the right from the sternoclavicular joint and at this point, up to 2 cm; and (3 ) RA: the level of umbilicus, 4 cm to the right. In electromyographic variables analysis , the data normality was assessed by Shapiro - Wilk test. Comparisons among studied maneuvers were performed by Friedman Test and Dunn’s post - hoc for multiple comparisons a mong inspiratory maneuvers, and Mann Whitney test for expiratory maneuvers. Subgroups differences between genders were performed by Student's t test or Mann - Whitney test according to data normality. Results: 35 subjects participated in the study, b ut 5 we re excluded (BMI> 25 kg/ m²). Sample consisted of 30 subjects (1 5 women), mean age 27.3±7.43 years, BMI 22.2 ± 1.69 kg/m² and spirometric indices within normal limits. Specific MVIC for SCM, SCA and RA showed the highest RMS. When we grouped sample into gender we found no difference among RMS values for the studied SCM maneuvers, while for SCA, MVIC SCM / SCA was the one with the highest RMS and for RA, MVIC RA in men. Once considering women, MVIC SCM/SCA showed the highest RMS for SCM, SCA and MVIC RA showed t he highest value for RA. Conclusion: MVIC for SCM, SCA and RA muscles showed the highest RMS values. When comparing RMS between the studied groups, there was no significant difference between men and women.

(Table 3) Grain size composition of Holocene deposits from the Kara Sea

A new generalized schematic map of distribution of recent sediments within Eurasian Arctic shelves is considered. The sediments have accumulated as a result of interaction of various factors and processes specific to high latitudes. They include input of terrigenous material by modern glaciers, ice transport, thermal abrasion, sedimentation controlled by many years of ice cover, and others. Characteristic regularity is marked over Arctic shelves: in seas with heavier ice cover, the most fine-grained deposits are distributed, they contain minimum amount of coarse-grained ice rafted debris; in seas with lighter ice cover mosaic distribution of various types of sediments is observed. Composition of surface sediments from the Arctic shelves corresponds to a relatively cool stage of the modern interglacial period. In the 21-st century a new warming is expected.

Tooth wear in Irish teenagers: a laboratory and epidemiological study

Aim: To investigate the characteristics, development and determinants of toothwear among Irish schoolchildren. Methods: A cross-sectional (examination at 16-years-old) and longitudinal (examinations at 5-,12-,14-years) study were conducted. Two indices were used to measure toothwear, children/parents completed a demographic profile and questionnaire on oral hygiene and dietary practices, health, and lifestyle in both studies. Saliva was collected from consenting 16-year-olds. The explanatory variables for the cross-sectional and longitudinal study were derived from children/parents responses. Differences in salivary profiles were determined for subsets; the protein concentration was determined with Bradford protein assay and protein carbonyl concentration (a protein oxidation marker) was determined spectrophotometrically. Gel-electrophoresis and mass spectrometry determined proteins and ion chromatography inorganic ions. Statistical significance was accepted at p<0.05. Results: At 16-years-old the prevalence of toothwear with dentine visible was 44%. No difference in salivary flow rates existed. In unstimulated saliva a higher mean, protein carbonyl (p<0.0001) and total calcium concentration (p<0.002) existed for the group with moderate toothwear. In stimulated saliva the moderate toothwear group had a lower mean protein concentration(p<0.0001). The 2-DE protein spots prepared for a sub-group differed between those with toothwear and without. Mass spectrometry, identified one of the different proteins as IgA. For 16-year-olds, the self-reported factors indicated that brushing after breakfast was associated with lower toothwear scores(p<0.03). Nail-biting, being asthmatic or reporting a dry mouth were associated with higher toothwear scores(all p<0.05). Eating an apple daily or less was associated with less toothwear(p<0.002). In the longitudinal study toothwear into dentine at age five or 12-years was associated with more toothwear at age 14(all p<0.05). Discussion: The results illustrate the multifactorial aetiology of toothwear. The biochemical and physical correlates of saliva with toothwear requires further research. Conclusion: The impact of previous toothwear, salivary, dietary and personal factors on toothwear in the early permanent dentition is demonstrated.

Stable carbon isotopic analyses of n-alkanes and the calculated C4 plant-derived fractions in the dust samples

Atmospheric dust samples collected along a transect off the West African coast have been investigated for their lipid content and compound-specific stable carbon isotope compositions. The saturated hydrocarbon fractions of the organic solvent extracts consist mainly of long-chain n-alkanes derived from epicuticular wax coatings of terrestrial plants. Backward trajectories for each sampling day and location were calculated using a global atmospheric circulation model. The main atmospheric transport took place in the low-level trade-wind layer, except in the southern region, where long-range transport in the mid-troposphere occurred. Changes in the chain length distributions of the n-alkane homologous series are probably related to aridity, rather than temperature or vegetation type. The carbon preference of the leaf-wax n-alkanes shows significant variation, attributed to a variable contribution of fossil fuel- or marine-derived lipids. The effect of this nonwax contribution on the d13C values of the two dominant n-alkanes in the aerosols, n-C29 and n-C31 alkane, is, however, insignificant. Their d13C values were translated into a percentage of C4 vs. C3 plant type contribution, using a two-component mixing equation with isotopic end-member values from the literature. The data indicate that only regions with a predominant C4 type vegetation, i.e. the Sahara, the Sahel, and Gabon, supply C4 plant-derived lipids to dust organic matter. The stable carbon isotopic compositions of leaf-wax lipids in aerosols mainly reflect the modern vegetation type along their transport pathway. Wind abrasion of wax particles from leaf surfaces, enhanced by a sandblasting effect, is most probably the dominant process of terrigenous lipid contribution to aerosols.

Quartz grain microtextures of sediments from ODP Hole 188-1166A (Table 1)

This paper presents the results of the scanning electron microscopic (SEM) analysis of quartz grains from a selection of samples at Site 1166. Ocean Drilling Program Leg 188 drilled Site 1166 on the Prydz Bay continental shelf, Antarctica, to document onset and fluctuations of East-Antarctic glaciation. This site recovered Upper Pliocene-Holocene glacial sediments directly above Cretaceous through Lower Oligocene sediments recording the transition from preglacial to early glacial conditions. SEM analysis of quartz grains at Site 1166 was used to characterize the glacial and preglacial sediments by their diagnostic textures. Angular edges, edge abrasion as well as arcuate to straight steps, are the most frequent features in glacial deposits. The highest frequency of grains with round edges is present in Middle-Late Eocene fluvio-deltaic sands. However, angular outlines, fractured plates with subparallel linear fractures and edge abrasion indicating glacier influence are also present. Preglacial carbonaceous mudstone and laminated gray claystone show distinctive high relief quartz grains and some chemical weathering on grain surfaces. The results of the microtextural analysis of quartz grains are used to verify some critical periods of ice sheet evolution, such as the transition from the East Antarctic preglacial to glacial conditions on the continental shelf from Middle/Late Eocene to Late Eocene/Early Oligocene time.

Occurrence of microtextures recorded from quartz sand grains of ODP Hole 178-1101A (Table 1)

Sediment drifts on the continental rise are located proximal to the western side of the Antarctic Peninsula and recorded changes in glacial volume and thermal regime over the last ca. 15 m.y. At Ocean Drilling Program (ODP) Site 1101 (Leg 178), which recovered sediments back to 3.1 Ma, glacial-interglacial cyclicity was identified based on the biogenic component and sedimentary structures observed in X-radiographs, magnetic susceptibility and lithofacies descriptions. Glacial intervals are dominated by fine-grained laminated mud and interglacial units consist of bioturbated muds enriched in biogenic components. From 2.2 to 0.76 Ma, planktonic foraminifera and calcareous nannofossils dominate in the interglacials suggesting a shift of the Antarctic Polar Front (APF) to the south near the drifts. Prior to 2.2 Ma, cyclicity cannot be identified and diatoms dominate the biogenic component and high percent opal suggests warmer conditions south of the APF and reduced sea ice over the drifts. Analyses of the coarse-grained terrigenous fraction (pebbles and coarse sand) from Sites 1096 and 1101 record glaciers at sea-level releasing iceberg-rafted debris (IRD) throughout the last 3.1 m.y. Analyses of quartz sand grains in IRD with the scanning electron microscope (SEM) show an abrupt change in the frequency of occurrence of microtextures at ~1.35 Ma. During the Late Pliocene to Early Pleistocene, the population of quartz grains included completely weathered grains and a low frequency of crushing and abrasion, suggesting that glaciers were small and did not inundate the topography. Debris shed from mountain peaks was transported supraglacially or englacially allowing weathered grains to pass through the glacier unmodified. During glacial periods from 1.35-0.76 Ma, glaciers expanded in size. The IRD flux was very high and dropstones have diverse lithologies. Conditions resembling those at the Last Glacial Maximum (LGM) have been episodically present on the Antarctic Peninsula since ~0.76 Ma. Quartz sand grains show high relief, fracture and abrasion common under thick ice and the IRD flux is low with a more restricted range of dropstone lithologies.