bluuebunny/crossref_metadata_2025 huggingface dataset:
Evolutionary Modeling of Genotype-Phenotype Associations, and Application to primate coding and Non-coding mtDNA Rate Variation
Authors: O'Connor Timothy D. , Mundy Nicholas I.
Published: July 2013

Variation in substitution rates across a phylogeny can be indicative of shifts in the evolutionary dynamics of a protein or nonprotein coding regions. One way to understand these signals is to seek the phenotypic correlates of rate variation. Here, we extended a previously published likelihood method designed to detect evolutionary associations between genotypic evolutionary rate and phenotype over a phylogeny. In simulation with two discrete categories of phenotype, the method has a low false-positive rate and detects greater than 80% of true-positives with a tree length of three or greater and a three-fold or greater change in substitution rate given the phenotype. In addition, we successfully extend the test from two to four phenotype categories and evaluated its performance. We then applied the method to two major hypotheses for rate variation in the mitochondrial genome of primates–-longevity and generation time as well as body mass which is correlated with many aspects of life history–-using three categories of phenotype through discretization of continuous values. Similar to previous results for mammals, we find that the majority of mitochondrial protein-coding genes show associations consistent with the longevity and body mass predictions and that the predominant signal of association comes from the third codon position. We also found a significant association between maximum lifespan and the evolutionary rate of the control region of the mtDNA. In contrast, 24 protein-coding genes from the nuclear genome do not show a consistent pattern of association, which is inconsistent with the generation time hypothesis. These results show the extended method can robustly identify genotype-phenotype associations up to at least four phenotypic categories, and demonstrate the successful application of the method to study factors affecting neutral evolutionary rate in protein-coding and non-coding loci.
Identification of Differentially Evolved Genes: An Alternative Approach to Detection of Accelerated Molecular Evolution from Genome-Wide Comparative Data
Authors: Kim Kyu-Won , Burt David W. , Kim Heebal , Cho Seoae
Published: July 2013

One of the most important measures for detecting molecular adaptations between species/lineages at the gene level is the comparison of relative fixation rates of synonymous (dS) and non-synonymous (dN) mutations. This study shows that the branch model is sensitive to tree topology and proposes an alternative approach, devogs, which does not require phylogenetic topology for analysis. We compared devogs with a branch model method using virtual data and a varying ω ratio, in which parameters were obtained from real data. The positive predictive value, sensitivity, and specificity of the branch model were affected by the phylogenic tree topology. Devogs showed greater positive predictive value, whereas the branch model method had greater sensitivity. In a working example using devogs, a group of human RNA polymerase II-related genes, which are important in mediating alternative splicing, were significantly accelerated compared to four other mammals.
DNA Demethylation Pathways: Recent Insights
Authors: Li Cong-jun
Published: July 2013

DNA methylation is a major epigenetic regulatory mechanism for gene expression and cell differentiation. Until recently, it was still unclear how unmethylated regions in mammalian genomes are protected from de novo methylation and whether or not active demethylating activity is involved. Even the role of molecules and the mechanisms underlying the processes of active demethylation itself is blurred. Emerging sequencing technologies have led to recent insights into the dynamic distribution of DNA methylation during development and the role of this epigenetic mark within a distinct genome context, such as the promoters, exons, or imprinted control regions. This review summarizes recent insights on the dynamic nature of DNA methylation and demethylation, as well as the mechanisms regulating active DNA demethylation in mammalian cells, which have been fundamental research interests in the field of epigenomics.
Dysfunctional Mitochondrial Dynamics in the Pathophysiology of Neurodegenerative Diseases
Authors: Haun Florian , Nakamura Tomohiro , Lipton Stuart A.
Published: July 2013

Mitochondrial dysfunction occurs in neurodegenerative diseases, however molecular mechanisms underlying this process remain elusive. Emerging evidence suggests that nitrosative stress, mediated by reactive nitrogen species (RNS), may play a role in mitochondrial pathology. Here, we review findings that highlight the abnormal mitochondrial morphology observed in many neurodegenerative disorders including Alzheimer's, Parkinson's, and Huntington's diseases. One mechanism whereby RNS can affect mitochondrial function and thus neuronal survival occurs via protein S-nitrosylation, representing chemical reaction of a nitric oxide (NO) group with a critical cysteine thiol. In this review, we focus on the signaling pathway whereby S-nitrosylation of the mitochondrial fission protein Drp1 (dynamin-related protein 1; forming S-nitrosothiol (SNO)-Drp1) precipitates excessive mitochondrial fission or fragmentation and consequent bioenergetic compromise. Subsequently, the formation of SNO-Drp1 leads to synaptic damage and neuronal death. Thus, intervention in the SNO-Drp1 pathway may provide therapeutic benefit in neurodegenerative diseases.
Article Commentary: Grief and Palliative Care: Mutuality
Authors: Moon Paul J.
Published: August 2013

Grief and palliative care are interrelated and perhaps mutually inclusive. Conceptually and practically, grief intimately relates to palliative care, as both domains regard the phenomena of loss, suffering, and a desire for abatement of pain burden. Moreover, the notions of palliative care and grief may be construed as being mutually inclusive in terms of one cueing the other. As such, the discussions in this article will center on the conceptualizations of the mutuality between grief and palliative care related to end-of-life circumstances. Specifically, the complementarity of grief and palliative care, as well as a controvertible view thereof, will be considered.
Meperidine: A Continuing Problem
Authors: Clubb Bryce , Loveday William , Ballantyne Susan
Published: July 2013

Letter to the Editor regarding meperidine prescriptions in Queensland, Australia, 1999 to 2010.
Restricting sulfur amino acid intake in growing pigs challenged with lipopolysaccharides decreases plasma protein and albumin synthesis
Authors: Litvak N. , Htoo J. K. , de Lange C. F. M.
Published: August 2013

Litvak, N., Htoo, J. K. and de Lange, C. F. M. 2013. Restricting sulfur amino acid intake in growing pigs challenged with lipopolysaccharides decreases plasma protein and albumin synthesis. Can. J. Anim. Sci. 93: 505–515. Chronic subclinical levels of disease occur frequently in swine production and compromise nutrient utilization efficiency. Methionine and cysteine (M+C) are involved in the pig's response to immune system stimulation (ISS), acting as substrates for the synthesis of compounds involved in the immune response, such as acute phase proteins (APP). This study was conducted to determine the impact of ISS with lipopolysaccharide (LPS) and M+C intake (high vs. low; 4.0 vs. 2.2 g d−1) on the fractional synthesis rate (FSR) of plasma albumin and fibrinogen, as well as protein in plasma and various tissues of starter pigs. Fifteen pigs (9.8±1.4 kg body weight) were allotted to one of three treatments: (1) Control (LPS− and high M+C), (2) LPS+ and high M+C, or (3) LPS+ and low M+C. Pigs were given intramuscular injections of increasing doses of LPS 1 and 3 d before determining FSR using an intravenous infusion of a flooding dose of L-[ring−1H5]-phenylalanine. Plasma levels of APP were not affected by the LPS challenge (P>0.10); only plasma albumin levels decreased with reduced M+C intake (P=0.02). Total plasma protein FSR was increased during the LPS challenge (50.3 vs. 56.9% d−1, SEM = 1.6; P=0.01). Albumin FSR was not affected by an LPS challenge (P>0.10), but decreased with reduced M+C intake during the LPS challenge (49.5 vs. 41.9% d−1, SEM = 1.6; P=0.005). Spleen protein FSR tended to increase during the LPS challenge (P=0.08). There were no treatment effects on protein FSR in liver, small intestine, loin or plasma fibrinogen (P>0.10). Restricting M+C intake during a LPS challenge decreases albumin synthesis and tends to reduce plasma protein synthesis, implicating M+C as important nutrients involved in the immune response.
Short Communication: Energy values and apparent total tract digestibility coefficients of copra meal and palm kernel meal fed to growing pigs
Authors: Jang Y. D. , Kim Y. Y.
Published: August 2013

Jang, Y. D. and Kim, Y. Y. 2013. Short Communication: Energy values and apparent total tract digestibility coefficients of copra meal and palm kernel meal fed to growing pigs. Can. J. Anim. Sci. 93: 517–521. To determine energy values and coefficients of apparent total tract digestibility (CATTD) of copra meal (CM) and palm kernel meal (PKM), 24 growing pigs were fed a corn–soybean meal basal diet and the basal diet replaced by 300 g kg−1 of either CM or PKM. Copra meal had higher CATTD of gross energy (12%), dry matter (DM; 13%), neutral detergent fiber (16%), acid detergent fiber (23%), and crude fiber (79%; P<0.05) than PKM. Copra meal had a slightly higher digestible energy (DE) value than PKM (14.08 vs. 13.01 MJ kg−1 DM; P=0.067), but metabolizable energy (ME; 13.33 vs. 12.83 MJ kg−1 DM), net energy (7.97 vs. 7.36 MJ kg−1 DM), and ME:DE ratio did not differ between CM and PKM. Therefore, compared with PKM, CM can be a better source of dietary energy in swine diets as evidenced by higher CATTD of energy and fiber components.
A Five-Year-Old Child with Renal Hydatidosis
Authors: Moscatelli Guillermo , Moroni Samanta , Freilij Héctor , Salgueiro Fabián , García Bournissen Facundo , Altcheh Jaime
Published: July 2013

Hydatidosis is a zoonosis of worldwide distribution caused by the parasite Echinococcus granulosus. Clinical manifestations include cyst formation, most commonly in the liver (67–89%) and lungs (10–15%). Renal localizations are rare. We report a case of renal hydatidosis in a five-year-old child treated in a tertiary pediatric hospital in Argentina. After the diagnosis was made, elective surgery was performed, which led to a rapid recovery.
Generalisation of Levine's prediction for the distribution of freezing temperatures of droplets: a general singular model for ice nucleation
Authors: Sear R. P.
Published: July 2013

Abstract. Models without an explicit time dependence, called singular models, are widely used for fitting the distribution of temperatures at which water droplets freeze. In 1950 Levine developed the original singular model. His key assumption was that each droplet contained many nucleation sites, and that freezing occurred due to the nucleation site with the highest freezing temperature. The fact that freezing occurs due to the maximum value out of a large number of nucleation temperatures, means that we can apply the results of what is called extreme-value statistics. This is the statistics of the extreme, i.e. maximum or minimum, value of a large number of random variables. Here we use the results of extreme-value statistics to show that we can generalise Levine's model to produce the most general singular model possible. We show that when a singular model is a good approximation, the distribution of freezing temperatures should always be given by what is called the generalised extreme-value distribution. In addition, we also show that the distribution of freezing temperatures for droplets of one size, can be used to make predictions for the scaling of the median nucleation temperature with droplet size, and vice versa.
Diagnosing the transition layer at extratropical latitudes using MLS O3 and MOPITT CO analyses
Authors: Barré J. , El Amraoui L. , Ricaud P. , Lahoz W. A. , Attié J.-L. , Peuch V.-H. , Josse B. , Marécal V.
Published: July 2013

Abstract. The behavior of the extratropical transition layer (ExTL) is investigated using a chemistry transport model (CTM) and analyses derived from assimilation of MLS (Microwave Limb Sounder) O3 and MOPITT (Measurements Of Pollution In The Troposphere) CO data. We firstly focus on a stratosphere–troposphere exchange (STE) case study that occurred on 15 August 2007 over the British Isles (50° N, 10° W). We evaluate the effect of data assimilation on the O3–CO correlations. It is shown that data assimilation disrupts the relationship in the transition region. When MLS O3 is assimilated, CO and O3 values are not consistent between each other, leading to unphysical correlations at the STE location. When MLS O3 and MOPITT CO assimilated fields are taken into account in the diagnostics the relationship happens to be more physical. We then use O3–CO correlations to quantify the effect of data assimilation on the height and depth of the ExTL. When the free-model run O3 and CO fields are used in the diagnostics, the ExTL distribution is found 1.1 km above the thermal tropopause and is 2.6 km wide (2σ). MOPITT CO analyses only slightly sharpen (by −0.02 km) and lower (by −0.2 km) the ExTL distribution. MLS O3 analyses provide an expansion (by +0.9 km) of the ExTL distribution, suggesting a more intense O3 mixing. However, the MLS O3 analyses ExTL distribution shows a maximum close to the thermal tropopause and a mean location closer to the thermal tropopause (+0.45 km). When MLS O3 and MOPITT CO analyses are used together, the ExTL shows a mean location that is the closest to the thermal tropopause (+0.16 km). We also extend the study at the global scale on 15 August 2007 and for the month of August 2007. MOPITT CO analyses still show a narrower chemical transition between stratosphere and troposphere than the free-model run. MLS O3 analyses move the ExTL toward the troposphere and broaden it. When MLS O3 analyses and MOPITT CO analyses are used together, the ExTL matches the thermal tropopause poleward of 50°.
Ultrafine sea spray aerosol over the southeastern Pacific: open-ocean contributions to marine boundary layer CCN
Authors: Blot R. , Clarke A. D. , Freitag S. , Kapustin V. , Howell S. G. , Jensen J. B. , Shank L. M. , McNaughton C. S. , Brekhovskikh V.
Published: July 2013

Abstract. Accurate measurements of natural aerosol emissions over the ocean are needed to estimate the anthropogenic impact on the environment. In this study, we measured sea spray aerosol (SSA) concentrations with diameters larger than 0.040 μm produced by open-ocean breaking waves over the SEP (southeastern Pacific). Robust statistics were established through repeated airborne flights over 1000 km along 20° S from the coastline of Chile to 85° W during VOCALS-REx (VAMOS Ocean-Cloud-Atmosphere-Land-Study Regional Experiment). Non-volatile SSA number concentrations were inferred using a thermally resolved technique constrained for clean conditions with an Ångström exponent below 0.5, black carbon mass concentration at values lower than 15 ng m−3 and organic aerosol concentration less than 0.02 μg m−3. We found that number concentrations of SSAs active as cloud condensation nuclei (CCN) for a supersaturation of 0.25% varied between 17 and 36 cm−3, but these did not increase with the increasing mean wind speed typically observed further offshore along 20° S. Concurrent increases in mean offshore precipitation rate in excess of about 1 mm d−1 indicate that scavenging of SSAs by precipitation exceeds increases in production at wind speeds above about 8 m s−1. This demonstrates the critical role of precipitation as a major sink of SSA over the remote ocean. Finally, we found that under clean conditions and for estimated stratus supersaturations between 0.20 and 0.43%, SSA represented about 20% of the total potential CCN along 20° S.
Cross-field flow and electric potential in a plasma slab
Authors: De Keyser J. , Echim M. , Roth M.
Published: August 2013

Abstract. We consider cross-field plasma flow inside a field-aligned plasma slab embedded in a uniform background in a 1-dimensional geometry. This situation may arise, for instance, when long-lasting reconnection pulses inject plasma into the inner magnetosphere. The present paper presents a detailed analysis of the structure of the interfaces that separate the slab from the background plasma on either side; a fully kinetic model is used to do so. Since the velocity shear across both interfaces has opposite signs, and given the typical gyroradius differences between injected and background ions and electrons, the structure of both interfaces can be very different. The behaviour of the slab and its interfaces depends critically on the flow of the plasma transverse to the magnetic field; in particular, it is shown that there are bounds to the flow speed that can be supported by the magnetised plasma. Further complicating the picture is the effect of the potential difference between the slab and its environment.
Revisiting factors controlling methane emissions from high-Arctic tundra
Authors: Mastepanov M. , Sigsgaard C. , Tagesson T. , Ström L. , Tamstorf M. P. , Lund M. , Christensen T. R.
Published: July 2013

Abstract. The northern latitudes are experiencing disproportionate warming relative to the mid-latitudes, and there is growing concern about feedbacks between this warming and methane production and release from high-latitude soils. Studies of methane emissions carried out in the Arctic, particularly those with measurements made outside the growing season, are underrepresented in the literature. Here we present results of 5 yr (2006–2010) of automatic chamber measurements at a high-Arctic location in Zackenberg, NE Greenland, covering both the growing seasons and two months of the following freeze-in periods. The measurements show clear seasonal dynamics in methane emission. The start of the growing season and the increase in CH4 fluxes were strongly related to the date of snowmelt. Within each particular growing season, CH4 fluxes were highly correlated with the soil temperature (R2 > 0.75), which is probably explained by high seasonality of both variables, and weakly correlated with the water table. The greatest variability in fluxes between the study years was observed during the first part of the growing season. Somewhat surprisingly, this variability could not be explained by commonly known factors controlling methane emission, i.e. temperature and water table position. Late in the growing season CH4 emissions were found to be very similar between the study years (except the extremely dry 2010) despite large differences in climatic factors (temperature and water table). Late-season bursts of CH4 coinciding with soil freezing in the autumn were observed during at least three years. The cumulative emission during the freeze-in CH4 bursts was comparable in size with the growing season emission for the year 2007, and about one third of the growing season emissions for the years 2009 and 2010. In all three cases the CH4 burst was accompanied by a corresponding episodic increase in CO2 emission, which can compose a significant contribution to the annual CO2 flux budget. The most probable mechanism of the late-season CH4 and CO2 bursts is physical release of gases accumulated in the soil during the growing season. In this study we discuss possible links between growing season and autumn fluxes. Multiannual dynamics of the subsurface CH4 storage pool are hypothesized to be such a link and an important driver of intearannual variations in the fluxes, capable of overruling the conventionally known short-term control factors (temperature and water table). Our findings suggest the importance of multiyear studies with a continued focus on shoulder seasons in Arctic ecosystems.
A regional climate palaeosimulation for Europe in the period 1500–1990 – Part 1: Model validation
Authors: Gómez-Navarro J. J. , Montávez J. P. , Wagner S. , Zorita E.
Published: July 2013

Abstract. We present and analyse a high-resolution regional climate palaeosimulation encompassing the European region for the period 1500–1990. We use the regional model MM5 driven at the boundaries by the global model ECHO-G. Both models are forced by reconstructions of three external factors: greenhouse gas concentrations, total solar irradiance and volcanic activity. The simulation skill is assessed in a recent period by comparing the model results with the Climate Research Unit (CRU) database. The results show that although the regional model is tightly driven by the boundary conditions, it is able to improve the reliability of the simulations, narrowing the differences to the observations, especially in areas of complex topography. Additionally, the evolution of the spatial distributions of temperature and precipitation through the last five centuries is analysed, showing that the mean values of temperature reflects the influence of the external forcings. However, contrary to the results obtained under climate change scenario conditions, higher-order momenta of seasonal temperature and precipitation are hardly affected by changes in the external forcings.
Reconstruction of Atlantic Water variability during the Holocene in the western Barents Sea
Authors: Groot D. E. , Aagaard-Sørensen S. , Husum K.
Published: July 2013

Abstract. The gravity core JM09-KA11-GC from 345 m water depth on the western Barents Sea margin was investigated for distribution patterns of benthic foraminifera, stable isotopes, and sedimentological parameters to reconstruct the flow of Atlantic Water during the Holocene. The core site is located below the Atlantic water masses flowing into the Arctic Ocean and close to the Arctic Front. The results show continuous presence of Atlantic Water at the margin throughout the Holocene. During the Early Holocene, (11 700–9400 cal yr BP), bottom water temperatures rose by 2.5 °C due to the increased influence of Atlantic Water, although sea-ice was still present at this time. The transition to the Mid Holocene is characterized by a local shift in current regime, resulting in a ceased supply of fine-grained material to the core location. Throughout the Mid Holocene the δ18O values indicate a slight cooling, thereby following changes in insolation. In the last 1500 yr, inflow of Atlantic Water increased but was interrupted by periods of increased influence of Arctic Water causing periodically colder and more unstable conditions.
Seasonal velocities of eight major marine-terminating outlet glaciers of the Greenland ice sheet from continuous in situ GPS instruments
Authors: Ahlstrøm A. P. , Andersen S. B. , Andersen M. L. , Machguth H. , Nick F. M. , Joughin I. , Reijmer C. H. , van de Wal R. S. W. , Merryman Boncori J. P. , Box J. E. , Citterio M. , van As D. , Fausto R. S. , Hubbard A.
Published: July 2013

Abstract. We present 17 velocity records derived from in situ stand-alone single-frequency Global Positioning System (GPS) receivers placed on eight marine-terminating ice sheet outlet glaciers in South, West and North Greenland, covering varying parts of the period summer 2009 to summer 2012. Common to all the observed glacier velocity records is a pronounced seasonal variation, with an early melt season maximum generally followed by a rapid mid-melt season deceleration. The GPS-derived velocities are compared to velocities derived from radar satellite imagery over six of the glaciers to illustrate the potential of the GPS data for validation purposes. Three different velocity map products are evaluated, based on ALOS/PALSAR data, TerraSAR-X/Tandem-X data and an aggregate winter TerraSAR-X data set. The velocity maps derived from TerraSAR-X/Tandem-X data have a mean difference of 1.5% compared to the mean GPS velocity over the corresponding period, while velocity maps derived from ALOS/PALSAR data have a mean difference of 9.7%. The velocity maps derived from the aggregate winter TerraSAR-X data set have a mean difference of 9.5% to the corresponding GPS velocities. The data are available from the GEUS repository at doi:10.5280/GEUS000001.
Statistical modelling of the snow depth distribution in open alpine terrain
Authors: Grünewald T. , Stötter J. , Pomeroy J. W. , Dadic R. , Moreno Baños I. , Marturià J. , Spross M. , Hopkinson C. , Burlando P. , Lehning M.
Published: August 2013

Abstract. The spatial distribution of alpine snow covers is characterised by large variability. Taking this variability into account is important for many tasks including hydrology, glaciology, ecology or natural hazards. Statistical modelling is frequently applied to assess the spatial variability of the snow cover. For this study, we assembled seven data sets of high-resolution snow-depth measurements from different mountain regions around the world. All data were obtained from airborne laser scanning near the time of maximum seasonal snow accumulation. Topographic parameters were used to model the snow depth distribution on the catchment-scale by applying multiple linear regressions. We found that by averaging out the substantial spatial heterogeneity at the metre scales, i.e. individual drifts and aggregating snow accumulation at the landscape or hydrological response unit scale (cell size 400 m), that 30 to 91% of the snow depth variability can be explained by models that are calibrated to local conditions at the single study areas. As all sites were sparsely vegetated, only a few topographic variables were included as explanatory variables, including elevation, slope, the deviation of the aspect from north (northing), and a wind sheltering parameter. In most cases, elevation, slope and northing are very good predictors of snow distribution. A comparison of the models showed that importance of parameters and their coefficients differed among the catchments. A "global" model, combining all the data from all areas investigated, could only explain 23% of the variability. It appears that local statistical models cannot be transferred to different regions. However, models developed on one peak snow season are good predictors for other peak snow seasons.
A bivariate return period based on copulas for hydrologic dam design: accounting for reservoir routing in risk estimation
Authors: Requena A. I. , Mediero L. , Garrote L.
Published: August 2013

Abstract. A multivariate analysis on flood variables is needed to design some hydraulic structures like dams, as the complexity of the routing process in a reservoir requires a representation of the full hydrograph. In this work, a bivariate copula model was used to obtain the bivariate joint distribution of flood peak and volume, in order to know the probability of occurrence of a given inflow hydrograph. However, the risk of dam overtopping is given by the maximum water elevation reached during the routing process, which depends on the hydrograph variables, the reservoir volume and the spillway crest length. Consequently, an additional bivariate return period, the so-called routed return period, was defined in terms of risk of dam overtopping based on this maximum water elevation obtained after routing the inflow hydrographs. The theoretical return periods, which give the probability of occurrence of a hydrograph prior to accounting for the reservoir routing, were compared with the routed return period, as in both cases hydrographs with the same probability will draw a curve in the peak-volume space. The procedure was applied to the case study of the Santillana reservoir in Spain. Different reservoir volumes and spillway lengths were considered to investigate the influence of the dam and reservoir characteristics on the results. The methodology improves the estimation of the Design Flood Hydrograph and can be applied to assess the risk of dam overtopping.
Modeling insights from distributed temperature sensing data
Authors: Buck C. R. , Null S. E.
Published: August 2013

Abstract. Distributed Temperature Sensing (DTS) technology can collect abundant high resolution river temperature data over space and time to improve development and performance of modeled river temperatures. These data can also identify and quantify thermal variability of micro-habitat that temperature modeling and standard temperature sampling do not capture. This allows researchers and practitioners to bracket uncertainty of daily maximum and minimum temperature that occurs in pools, side channels, or as a result of cool or warm inflows. This is demonstrated in a reach of the Shasta River in Northern California that receives irrigation runoff and inflow from small groundwater seeps. This approach highlights the influence of air temperature on stream temperatures, and indicates that physically-based numerical models may under-represent this important stream temperature driver. This work suggests DTS datasets improve efforts to simulate stream temperatures and demonstrates the utility of DTS to improve model performance and enhance detailed evaluation of hydrologic processes.
DEVISING A VISUAL INSPECTION SYSTEM FOR CANAL TUNNELS: PRELIMINARY STUDIES
Authors: Albert J.-L. , Charbonnier P. , Chavant P. , Foucher P. , Muzet V. , Prybyla D. , Perrin T. , Grussenmeyer P. , Guillemin S. , Koehl M.
Published: July 2013

Abstract. In France, most tunnel canals were built during the 19th and 20th centuries. Maintaining them is not only a matter of heritage preservation but also a question of security. Inspecting tunnel canals is difficult and time consuming, which motivates the development of an image-based surveying system, as already exists for railway or road tunnels. However, while the imaging configuration is similar, referencing the data acquisition device is more difficult in the case of underground waterways, due to the drifts of the inspection barge. In this paper, we introduce the recording prototype we have designed and report the results of the test that were performed in an underground waterway, Niderviller's tunnel, to assess the feasibility of the system. In particular, we give details on the imaging system design. We also analyze the pros and cons of each location method, in terms of costs, practicability, computational burden and accuracy.
A 3D GIS METHOD APPLIED TO CATALOGING AND RESTORING: THE CASE OF AURELIAN WALLS AT ROME
Authors: Canciani M. , Ceniccola V. , Messi M. , Saccone M. , Zampilli M.
Published: July 2013

Abstract. The project involves architecture, archaeology, restoration, graphic documentation and computer imaging. The objective is development of a method for documentation of an architectural feature, based on a three-dimensional model obtained through laser scanning technologies, linked to a database developed in GIS environment. The case study concerns a short section of Rome's Aurelian walls, including the Porta Latina. The city walls are Rome's largest single architectural monument, subject to continuous deterioration, modification and maintenance since their original construction beginning in 271 AD. The documentation system provides a flexible, precise and easily-applied instrument for recording the full appearance, materials, stratification palimpsest and conservation status, in order to identify restoration criteria and intervention priorities, and to monitor and control the use and conservation of the walls over time. The project began with an analysis and documentation campaign integrating direct, traditional recording methods with indirect, topographic instrument and 3D laser scanning recording. These recording systems permitted development of a geographic information system based on three-dimensional modelling of separate, individual elements, linked to a database and related to the various stratigraphic horizons, the construction techniques, the component materials and their state of degradation. The investigations of the extant wall fabric were further compared to historic documentation, from both graphic and descriptive sources. The resulting model constitutes the core of the GIS system for this specific monument. The methodology is notable for its low cost, precision, practicality and thoroughness, and can be applied to the entire Aurelian wall and to other monuments.
OBLIQUE AERIAL IMAGES AND THEIR USE IN CULTURAL HERITAGE DOCUMENTATION
Authors: Höhle J.
Published: July 2013

Abstract. Oblique images enable three-dimensional (3d) modelling of objects with vertical dimensions. Such imagery is nowadays systematically taken of cities and may easily become available. The documentation of cultural heritage can take advantage of these sources of information. Two new oblique camera systems are presented and characteristics of such images are summarized. A first example uses images of a new multi-camera system for the derivation of orthoimages, façade plots with photo texture, 3d scatter plots, and dynamic 3d models of a historic church. The applied methodology is based on automatically derived point clouds of high density. Each point will be supplemented with colour and other attributes. The problems experienced in these processes and the solutions to these problems are presented. The applied tools are a combination of professional tools, free software, and of own software developments. Special attention is given to the quality of input images. Investigations are carried out on edges in the images. The combination of oblique and nadir images enables new possibilities in the processing. The use of the near-infrared channel besides the red, green, and blue channel of the applied multispectral imagery is also of advantage. Vegetation close to the object of interest can easily be removed. A second example describes the modelling of a monument by means of a non-metric camera and a standard software package. The presented results regard achieved geometric accuracy and image quality. It is concluded that the use of oblique aerial images together with image-based processing methods yield new possibilities of economic and accurate documentation of tall monuments.
AN INTERDISCIPLINARY CONSERVATION MODULE FOR CONDITION SURVEY ON CULTURAL HERITAGES WITH A 3D INFORMATION SYSTEM
Authors: Pedelì C.
Published: July 2013

Abstract. In order to make the most of the digital outsourced documents, based on new technologies (e.g.: 3D LASER scanners, photogrammetry, etc.), a new approach was followed and a new ad hoc information system was implemented. The obtained product allow to the final user to reuse and manage the digital documents providing graphic tools and an integrated specific database to manage the entire documentation and conservation process, starting from the condition assessment until the conservation / restoration work. The system is organised on two main modules: Archaeology and Conservation. This paper focus on the features and the advantages of the second one. In particular it is emphasized its logical organisation, the possibility to easily mapping by using a very precise 3D metric platform, to benefit of the integrated relational database which allows to well organise, compare, keep and manage different kind of information at different level. Conservation module can manage along the time the conservation process of a site, monuments, object or excavation and conservation work in progress. An alternative approach called OVO by the author of this paper, force the surveyor to observe and describe the entity decomposing it on functional components, materials and construction techniques. Some integrated tools as the "ICOMOS-ISCS Illustrated glossary … " help the user to describe pathologies with a unified approach and terminology. Also the conservation project phase is strongly supported to envision future intervention and cost. A final section is devoted to record the conservation/restoration work already done or in progress. All information areas of the conservation module are interconnected to each other to allows to the system a complete interchange of graphic and alphanumeric data. The conservation module it self is connected to the archaeological one to create an interdisciplinary daily tool.
DIGITAL DOCUMENTATION IN THE CONSERVATION OF CULTURAL HERITAGE: FINDING THE PRACTICAL IN BEST PRACTICE
Authors: Beck L. S.
Published: July 2013

Abstract. Documentation of treatment is one of the central tenets of conservation as a profession, and a necessary aspect of the preservation of cultural heritage. Photographic documentation has been an essential technique for recording the nature of heritage objects and illustrating conservation procedures. The routine use of digital photography in recent years has opened many avenues to conservators, but also poses unique threats to the long-term stability of the conservation record. Digital documentation is subject to decay just as physical or "analogue" records are, with the stark difference that digital data corrupts absolutely, where physical records can remain legible through various stages of deterioration. It is therefore necessary to understand the options that conservators have with regards to preservation of their records for the future. The various guidelines presently available regarding digital documentation may be synthesized into a coherent "best practice" specific to digital conservation documentation. This practice, however, must be reconsidered within the framework of what is necessary to ensure that photographic records are preserved, versus what is feasible. In order to determine if conservators are aware of the limitations of digital technology, thirty practicing conservators were asked to respond to a questionnaire regarding their own documentation practices. The responses identified a lack of best practice, and indicated that there are multiple factors which prevent conservators from developing effective methods for creating, storing, and accessing documentation. To address this, a modified form of best practice, the "best practical" method, is developed as a series of guidelines with the intent of being feasible for practicing conservators. This method aims to reduce the time and economic costs required of best practice, while minimizing the risk to the conservation record. The "best practical" guidelines are being designed to be applicable to a wide range of professional contexts, from large public institutional conservators to independent private contractors. The significance of selection of documentation for long-term survival is also emphasized. The value of these guidelines lies in the identification of small changes to current practice that have the potential to make large differences in the amount of information preserved for future conservators, scholars, and other interested parties.
Polymer composite based microbolometers
Authors: Nocke A.
Published: August 2013

Abstract. This work focuses on the basic suitability assessment of polymeric materials and the corresponding technological methods for the production of infrared (micro-) bolometer arrays. The sensitive layer of the microbolometer arrays in question is composed of an electrically conductive polymer composite. Semi-conducting tellurium and vanadium dioxide, as well as metallic silver, are evaluated concerning their suitability as conductive filling agents. The composites with the semi-conducting filling agents display the higher temperature dependence of electrical resistance, while the silver composites exhibit better noise performance. The particle alignment – homogeneous and chain-shaped alike – within the polymer matrix is characterized regarding the composites' electrical properties. For the production of microbolometer arrays, a technology chain is introduced based on established coat-forming and structuring standard technologies from the field of polymer processing, which are suitable for the manufacture of a number of parallel structures. To realize the necessary thermal isolation of the sensitive area, all pixels are realized as self-supporting structures by means of the sacrificial layer method. Exemplarily, 2 × 2 arrays with the three filling agents were manufactured. The resulting sensor responsivities lie in the range of conventional microbolometers. Currently, the comparatively poor thermal isolation of the pixels and the high noise levels are limiting sensor quality. For the microbolometers produced, the thermal resolution limit referring to the temperature of the object to be detected (NETD) has been measured at 6.7 K in the superior sensitive composite layer filled with silver particles.
Modeling the land-use correlates of vehicle-trip lengths for assessing the transportation impacts of land developments
Authors: Srinivasan Sivaramakrishnan , Provost Russell , Steiner Ruth
Published: August 2013

This study developed models that relate trip lengths to the land-use characteristics at the trip ends (both production and attraction ends). Separate models were developed by trip purpose. The results indicate several statistically significant and intuitively reasonable effects of land-use patterns. High residential densities and a good mix of complementary land uses are associated with shorter trips. Larger establishments attract longer trips, and the lengths of home-based other trips decrease with an increase in the number of convenient commercial land- use parcels in the neighborhood. The connectivity provided by the roadway network and the urban form of the area (measured in terms of number of intersections and cul-de-sacs) affect trip lengths. In addition to the local land-use characteristics, trip lengths also vary significantly by the location of the neighborhood within the region. All these results hold even after controlling for several trip and traveler characteristics. The models have been implemented in a spreadsheet program for use in assessing the transportation impacts of new land developments.
Explaining walking distance to public transport: The dominance of public transport supply
Authors: Daniels Rhonda , Mulley Corinne
Published: August 2013

Potential influences on explaining walking distance from home to access public transport are investigated, including trip and demographic characteristics and public transport supply. In Sydney, Australia, people walk farther to the train than to the bus, the distributions of walking distances are different for each mode, and the trip and demographic characteristics of train and bus users are different. Given the decision to walk to public transport, demographic characteristics such as age, gender, income, and labor force status and trip characteristics such as trip purpose, time of day and week, fare and ticket type, and trip duration are not significant in explaining walking distance to each mode of public transport. The mode of the public transport trip is the most important determinant of walking distance, reflecting the different supply and spacing of each mode. For instance, there are many more bus stops than train stations. The differences between train and bus users suggest that accessibility initiatives for public transport might not be the same for each mode.
Mobility, access, and choice: a new source of evidence
Authors: Metz David
Published: August 2013

The availability of a large national data set of accessibility indicators allows investigation of the relationship between mobility and access to, and choice of, key destinations for the population of England. The destinations considered are primary and secondary schools, further education colleges, family doctors, hospitals, food stores, and places of employment. For the populations of 353 local authorities, the average extent of choice of these destinations is estimated as a function of travel time and mode. It is concluded that high levels of access and choice are available to the large part of the population that has available a car or good public transport. This finding is consistent with the suggestion that the demand for daily travel has saturated.
Patient- and family-centered care in Qatar: A primary care perspective
Authors: Verjee Mohamud A. , Robertson-Malt Suzanne
Published: July 2013

Healthcare policies in Qatar place a high value on the concept of patient and family-centered care (PFCC) in primary care. The Institute of Medicine raised the concern of patient care in 2001 and Davis et al. advocates of PFCC, promoted the concept. The Primary Health Care Corporation (PHCC) and Hamad Medical Corporation (HMC) in Qatar provide all the government health services of the country at this time. They have sought to integrate PFCC into its systems, while preserving the traditional Qatari way of life. Families in times past were excluded from healthcare involvement as medical specialization progressed, but the undervalued importance of families contributing to healthcare was later realized. Twenty-one established health centers in 2013, are to be augmented by thirty more within five years. By 2011, all Qatar's major hospitals and its Ambulance Service had achieved JCI accreditation. Entitlement to government healthcare is free for Qatari nationals, or at a small charge for expatriates who maintain a valid health card. Patients have access to a physician at health centers, but have to be referred for hospital consultant appointments. A range of services is available, including a pharmacy, at every health center. A Charter of Patient, Family, and Children's Rights is in place for HMC supporting family participation in care. The Center for Health Care Improvement (CHCI) was launched in 2008 and focuses on PFCC. Eight core objectives of the CHCI are outlined. Effective patient education with the adoption of sound healthcare policies and fiscal responsibility should help Qatar attain the goals it requires.
Pharmaceutical care in the
Arabic-speaking Middle East: literature review and country informant feedback
Authors: Kheir Nadir , Al Saad Doua , Al Naimi Shaikha
Published: July 2013

Background The philosophy and practice of pharmaceutical care (PC) has challenged Middle Eastern pharmacists to embrace a new paradigm that focuses on outcomes of care rather than products or tasks. Although the application of PC was found to be associated with a reduction in adverse drug reactions, length of hospital stay and cost of care in the developed world, the status and application of the practice remains less clear in the Arabic-speaking Middle East (ME). The aim of this project was to describe the current status of PC services in a number of Arabic-speaking ME countries. Methods We conducted literature search to identify what had been published on the status of PC in the ME. We also invited individuals who have good understanding of the pharmacy environment in the respective country. The individuals identified were asked to respond to a set of standardized questions relating to PC services in their countries. Results The literature search generated 12 publications in total. Ten country informants agreed to provide information on PC practice and pharmacy practice in general in their respective countries and they ultimately provided information related to these areas. Conclusions The PC concept is still often confused with clinical pharmacy, which remains to be a priority in several countries in the region. Pharmacy education is rapidly changing change in many of the ME. These changes are hoped to reflect a wider recognition and application of PC services in the hospital and community settings.