Predicting changes in abundance and juvenile proportions of earthworms in the field using glmmADMB in R

The study aimed at investigating effects of three differently acting biocides; the insecticide esfenvalerate, the fungicide picoxystrobin and the bactericide triclosan, applied individually and as a mixture, on an earthworm community in the field. A concentration-response design was chosen and results were analyzed using univariate and multivariate approaches. Effects on juvenile proportions were less pronounced and more variable than effects on abundance, but effects in general were species- and chemical-specific, and temporal variations distinct. Esfenvalerate and picoxystrobin appeared to elicit stronger effects than triclosan at laboratory-based ECx values, which is in accordance with our previous laboratory study on Eisenia fetida. The mixture affected abundance and juvenile proportions, but the latter only at high mixture concentrations. Esfenvalerate and picoxystrobin appeared to be the main drivers for the mixture's toxicity. Species-specific toxicity patterns question the reliability of mixture toxicity predictions derived on E. fetida for field earthworms. Biocide concentrations equaling EC50s (reproduction) for E. fetida provoked effects on the field earthworms mainly exceeding 50%, indicating effect intensification from the laboratory to field as well as the influence of indirect effects produced by species interactions. The differing results of the present field study and the previous laboratory study imply that lower- and higher-tier studies may not be mutually exclusive, but to be used in complementary.

Metallic Fluence Monitors and J-value standards

Utilizing the neutron-irradiation parameter J is one of the major uncertainties in 40Ar/39Ar dating. The associated error of the individual J-value for a sample of unknown age depends on the accuracy of the age of the geological standards, the fast-neutron fluence distribution in the reactor and the distances between standards and samples during irradiation. While it is generally assumed that rotating irradiation evens out radial neutron fluence gradients, we observed axial and radial variations of the J-values in sample irradiations in the rotating channels of two reactors. To quantify them, we included three-dimensionally distributed metallic fast- (Ni) and thermal- (Co) neutron fluence monitors in three irradiations and geological age standards in three more. Two irradiations were carried out under Cd-shielding in the FRG1 reactor in Geesthacht, Germany, and four without Cd-shielding in the LVR-15 reactor in Rez, Czech Republic. The 58Ni(nf,p)58Co activation reaction and ?-spectrometry of the 811 keV peak associated with the subsequent decay of 58Co to 58Fe allow to calculate the fast-neutron fluence. The fast-neutron fluences at known positions in the irradiation container correlate with the J-values determined by mass-spectrometric 40Ar/39Ar measurements of the geological age standards. Ra-dial neutron fluence gradients are up to 1.8 %/cm in FRG1 and up to 2.2 %/cm in LVR-15; the corre-sponding axial gradients are up to 5.9 and 2.1 %/cm. We conclude that sample rotation might not al-ways suffice to meet the needs of high-precision dating and gradient monitoring can be crucial.

Seawater carbonate chemistry and pteropod Limacina helicina antarctica shell dissolution during experiments, 2012

Anthropogenic ocean acidification is likely to have negative effects on marine calcifying organisms, such as shelled pteropods, by promoting dissolution of aragonite shells. Study of shell dissolution requires an accurate and sensitive method for assessing shell damage. Shell dissolution was induced through incubations in CO2 enriched seawater for between 4 and 14 days. We describe a procedure that allows the level of dissolution to be assessed and classified into three main types: Type I with partial dissolution of the prismatic layer; Type II with exposure of underlying crossed-lamellar layer, and Type III, where crossed-lamellar layer shows signs of dissolution. Levels of dissolution showed a good correspondence to the incubation conditions, with the most severe damage found in specimens held for 14 d in undersaturated condition (Ohm ~ 0.8). This methodology enables the response of small pelagic calcifiers to acidified conditions to be detected at an early stage, thus making pteropods a valuable bioindicator of future ocean acidification.

Validation of microsatellite markers for cytotype discrimination in the model grass Brachypodium distachyon

Brachypodium distachyon (2n = 2x = 10) is a small annual grass species where the existence of three different cytotypes (10, 20 and 30 chromosomes) has long been regarded as a case of autopolyploid series, with x = 5. However, it has been demonstrated that the cytotypes assumed to be polyploids represent two separate Brachypodium species recently named as B. stacei (2n = 2x = 20) and B. hybridum (2n = 4x = 30). The aim of this study was to find a PCR-based alternative approach that could replace standard cytotyping methods (i. e., chromosome counting and flow cytometry) to characterize each of the three Brachypodium species. We have analyzed with four microsatellite (SSR) markers eighty-three Brachypodium distachyon-type lines from varied locations in Spain, including the Balearic and Canary Islands. Within this set of lines, 64, 4 and 15 had 10, 20 and 30 chromosomes, respectively. The surveyed markers produced cytotype-specific SSR profiles. So, a single amplification product was generated in the diploid samples, with non-overlapping allelic ranges between the 2n = 10 and 2n = 20 cytotypes, whereas two bands, one in the size range of each of the diploid cytotypes, were amplified in the 2n = 30 lines. Furthermore, the remarkable size difference obtained with the SSR ALB165 allowed the identification of the Brachypodium species by simple agarose gel electrophoresis.

Supervisión multidistribuida para el control de procesos de conservación de productos agroalimentarios: optimización de calidad del producto

La presente Tesis está orientada al análisis de la supervisión multidistribuida de tres procesos agroalimentarios: el secado solar, el transporte refrigerado y la fermentación de café, a través de la información obtenida de diferentes dispositivos de adquisición de datos, que incorporan sensores, así como el desarrollo de metodologías de análisis de series temporales, modelos y herramientas de control de procesos para la ayuda a la toma de decisiones en las operaciones de estos entornos. En esta tesis se han utilizado: tarjetas RFID (TemTrip®) con sistema de comunicación por radiofrecuencia y sensor de temperatura; el registrador (i-Button®), con sensor integrado de temperatura y humedad relativa y un tercer prototipo empresarial, módulo de comunicación inalámbrico Nlaza, que integra un sensor de temperatura y humedad relativa Sensirion®. Estos dispositivos se han empleado en la conformación de redes multidistribuidas de sensores para la supervisión de: A) Transportes de producto hortofrutícola realizados en condiciones comerciales reales, que son: dos transportes terrestre de producto de IV gama desde Murcia a Madrid; transporte multimodal (barco-barco) de limones desde Montevideo (Uruguay) a Cartagena (España) y transporte multimodal (barco-camión) desde Montevideo (Uruguay) a Verona (Italia). B) dos fermentaciones de café realizadas en Popayán (Colombia) en un beneficiadero. Estas redes han permitido registrar la dinámica espacio-temporal de temperaturas y humedad relativa de los procesos estudiados. En estos procesos de transporte refrigerado y fermentación la aplicación de herramientas de visualización de datos y análisis de conglomerados, han permitido identificar grupos de sensores que presentan patrones análogos de sus series temporales, caracterizando así zonas con dinámicas similares y significativamente diferentes del resto y permitiendo definir redes de sensores de menor densidad cubriendo las diferentes zonas identificadas. Las metodologías de análisis complejo de las series espacio-temporales (modelos psicrométricos, espacio de fases bidimensional e interpolaciones espaciales) permitieron la cuantificación de la variabilidad del proceso supervisado tanto desde el punto de vista dinámico como espacial así como la identificación de eventos. Constituyendo así herramientas adicionales de ayuda a la toma de decisiones en el control de los procesos. Siendo especialmente novedosa la aplicación de la representación bidimensional de los espacios de fases en el estudio de las series espacio-temporales de variables ambientales en aplicaciones agroalimentarias, aproximación que no se había realizado hasta el momento. En esta tesis también se ha querido mostrar el potencial de un sistema de control basado en el conocimiento experto como es el sistema de lógica difusa. Se han desarrollado en primer lugar, los modelos de estimación del contenido en humedad y las reglas semánticas que dirigen el proceso de control, el mejor modelo se ha seleccionado mediante un ensayo de secado realizado sobre bolas de hidrogel como modelo alimentario y finalmente el modelo se ha validado mediante un ensayo en el que se deshidrataban láminas de zanahoria. Los resultados sugirieron que el sistema de control desarrollado, es capaz de hacer frente a dificultades como las variaciones de temperatura día y noche, consiguiendo un producto con buenas características de calidad comparables a las conseguidas sin aplicar ningún control sobre la operación y disminuyendo así el consumo energético en un 98% con respecto al mismo proceso sin control. La instrumentación y las metodologías de análisis de datos implementadas en esta Tesis se han mostrado suficientemente versátiles y transversales para ser aplicadas a diversos procesos agroalimentarios en los que la temperatura y la humedad relativa sean criterios de control en dichos procesos, teniendo una aplicabilidad directa en el sector industrial ABSTRACT This thesis is focused on the analysis of multi-distributed supervision of three agri-food processes: solar drying, refrigerated transport and coffee fermentation, through the information obtained from different data acquisition devices with incorporated sensors, as well as the development of methodologies for analyzing temporary series, models and tools to control processes in order to help in the decision making in the operations within these environments. For this thesis the following has been used: RFID tags (TemTrip®) with a Radiofrequency ID communication system and a temperature sensor; the recorder (i-Button®), with an integrated temperature and relative humidity and a third corporate prototype, a wireless communication module Nlaza, which has an integrated temperature and relative humidity sensor, Sensirion®. These devices have been used in creating three multi-distributed networks of sensors for monitoring: A) Transport of fruits and vegetables made in real commercial conditions, which are: two land trips of IV range products from Murcia to Madrid; multimodal transport (ship - ship) of lemons from Montevideo (Uruguay) to Cartagena (Spain) and multimodal transport (ship - truck) from Montevideo (Uruguay) to Verona (Italy). B) Two coffee fermentations made in Popayan (Colombia) in a coffee processing plant. These networks have allowed recording the time space dynamics of temperatures and relative humidity of the processed under study. Within these refrigerated transport and fermentation processes, the application of data display and cluster analysis tools have allowed identifying sensor groups showing analogical patterns of their temporary series; thus, featuring areas with similar and significantly different dynamics from the others and enabling the definition of lower density sensor networks covering the different identified areas. The complex analysis methodologies of the time space series (psychrometric models, bi-dimensional phase space and spatial interpolation) allowed quantifying the process variability of the supervised process both from the dynamic and spatial points of view; as well as the identification of events. Thus, building additional tools to aid decision-making on process control brought the innovative application of the bi-dimensional representation of phase spaces in the study of time-space series of environmental variables in agri-food applications, an approach that had not been taken before. This thesis also wanted to show the potential of a control system based on specialized knowledge such as the fuzzy logic system. Firstly, moisture content estimation models and semantic rules directing the control process have been developed, the best model has been selected by an drying assay performed on hydrogel beads as food model; and finally the model has been validated through an assay in which carrot sheets were dehydrated. The results suggested that the control system developed is able to cope with difficulties such as changes in temperature daytime and nighttime, getting a product with good quality features comparable to those features achieved without applying any control over the operation and thus decreasing consumption energy by 98% compared to the same uncontrolled process. Instrumentation and data analysis methodologies implemented in this thesis have proved sufficiently versatile and cross-cutting to apply to several agri-food processes in which the temperature and relative humidity are the control criteria in those processes, having a direct effect on the industry sector.

Analysis of the behavior of multijunction solar cells under high irradiance Gaussian light profiles showing chromatic aberration with emphasis on tunnel junction performance

In this work, we explain the behavior of multijunction solar cells under non-uniform (spatially and in spectral content) light profiles in general and in particular when Gaussian light profiles cause a photo-generated current density, which exceeds locally the peak current density of the tunnel junction. We have analyzed the implications on the tunnel junction's limitation, that is, in the loss of efficiency due to the appearance of a dip in the I–V curve. For that, we have carried out simulations with our three-dimensional distributed model for multijunction solar cells, which contemplates a full description of the tunnel junction and also takes into account the lateral resistances in the tunnel junction. The main findings are that the current density photo-generated spreads out through the lateral resistances of the device, mainly through the tunnel junction layers and the back contact. Therefore, under non-uniform light profiles these resistances are determinant not only to avoid the tunnel junction's limitation but also for mitigating losses in the fill factor. Therefore, taking into account these lateral resistances could be the key for jointly optimizing the concentrator photovoltaic system (concentrator optics, front grid layout and semiconductor structure)

A model system to study genomic imprinting of human genes

Somatic-cell hybrids have been shown to maintain the correct epigenetic chromatin states to study developmental globin gene expression as well as gene expression on the active and inactive X chromosomes. This suggests the potential use of somatic-cell hybrids containing either a maternal or a paternal human chromosome as a model system to study known imprinted genes and to identify as-yet-unknown imprinted genes. Testing gene expression by using reverse transcription followed by PCR, we show that functional imprints are maintained at four previously characterized 15q11–q13 loci in hybrids containing a single human chromosome 15 and at two chromosome 11p15 loci in hybrids containing a single chromosome 11. In contrast, three γ-aminobutyric acid type A receptor subunit genes in 15q12–q13 are nonimprinted. Furthermore, we have found that differential DNA methylation imprints at the SNRPN promoter and at a CpG island in 11p15 are also maintained in somatic-cell hybrids. Somatic-cell hybrids therefore are a valid and powerful system for studying known imprinted genes as well as for rapidly identifying new imprinted genes.

Establishment of a reedbed within a created surface water fed wetland nature reserve

In the early 1990's, outline designs for two wetland nature reserves were being prepared: the Teeside International Nature Reserve (TINR) and the Cardiff Bay Barrage Environmental Compensation Measures at Redwick, Gwent. The initial design for both proposals identified reedbed as a desirable habitat for establishment. The initial design works identified the importance of reedbed evapotranspiration [ET(Reed)] within the water budget, however, literature searches identified a paucity of information on this parameter. Field experiments for the measurement of ET(Reed) from Phragmites australis are described for three sites distributed across England and Wales. Reference Crop Evapotranspiration (ETo) was calculated using techniques recommended by the Food and Agriculture Organisation. A technique for the calculation of a reedbed crop coefficient [Kc(Reed)[, from ET(Reed) and ETo data is discussed. Kc(Reed) values produced in the project were found to be similar to those developed previously in continental Europe. Mean monthly and crop development stage Kc(Reed) values are presented which are applicable in the UK and possibly worldwide. A conceptual hydrological model of surface water fed reedbed systems is developed, and used to calculate the hydrological sustainability of reedbed creation areas in the UK. Finally, the water budget model is verified using data from a small clay catchment located on the TINR. In addition, a methodology is developed for the hydrological design of surface water fed reedbed systems, and recommendations required for the feasibility, design and establishment stage of reedbed creation sites. Further research needs are also identified.

Remote sensing applied to land use and erosion hazard studies in Jamaica

The northern half of the parish of St. Catherine in Jamaica was selected as a test area to study, by means of remote sensing, the problems of soil erosion in a tropical environment. An initial study was carried out to determine whether eroded land within this environment could be successfully interpreted and mapped from the available 1: 25,000 scale aerial photographs. When satisfied that a sufficiently high percentage of the eroded land could be interpreted on the aerial photographs the main study was initiated. This involved interpreting the air photo cover of the study area for identifying and classifying land use and eroded land, and plotting the results on overlays on topographic base maps. These overlays were then composited with data on the soils and slopes of the study area. The areas of different soil type/slope/land use combinations were then measured, as was the area of eroded land for each of these combinations. This data was then analysed in two ways. The first way involved determining which of the combinations of soil type, slope and land use were most and least eroded and, on the basis of this, to draw up recommendations concerning future land use. The second analysis was aimed at determining which of the three factors, soil type, slope and land use, was most responsible for determining the rate of erosion. Although it was possible to show that slope was not very significant in determining the rate of erosion, it was much more difficult to separate the effects of land use and soil type. The results do, however, suggest that land use is more significant than soil type in determining the rate of erosion within the study area.

Exploring trust in E-B2B relationships

The Internet’s unbounded opportunity for inter-firm exchanges is limited by concerns about trust, however, little is known about the development and formation of trust in the area of electronic business-to-business relationships. Drawing on existing research the aim of paper is to explore differences arising between trust in the traditional and in the electronic business to business relationship. In addition, an overall research framework is developed which links trust formation to three dimensions: the type of interaction, the stage of the relationship lifecycle and the type of transacting organizations. These dimensions are further examined in different relationship scenarios. Finally, implications for the agri-food industry are examined.

Enhanced skip -list search algorithm in 3-layer mediator framework

The Three-Layer distributed mediation architecture, designed by Secure System Architecture laboratory, employed a layered framework of presence, integration, and homogenization mediators. The architecture does not have any central component that may affect the system reliability. A distributed search technique was adapted in the system to increase its reliability. An Enhanced Chord-like algorithm (E-Chord) was designed and deployed in the integration layer. The E-Chord is a skip-list algorithm based on Distributed Hash Table (DHT) which is a distributed but structured architecture. DHT is distributed in the sense that no central unit is required to maintain indexes, and it is structured in the sense that indexes are distributed over the nodes in a systematic manner. Each node maintains three kind of routing information: a frequency list, a successor/predecessor list, and a finger table. None of the nodes in the system maintains all indexes, and each node knows about some other nodes in the system. These nodes, also called composer mediators, were connected in a P2P fashion. ^ A special composer mediator called a global mediator initiates the keyword-based matching decomposition of the request using the E-Chord. It generates an Integrated Data Structure Graph (IDSG) on the fly, creates association and dependency relations between nodes in the IDSG, and then generates a Global IDSG (GIDSG). The GIDSG graph is a plan which guides the global mediator how to integrate data. It is also used to stream data from the mediators in the homogenization layer which connected to the data sources. The connectors start sending the data to the global mediator just after the global mediator creates the GIDSG and just before the global mediator sends the answer to the presence mediator. Using the E-Chord and GIDSG made the mediation system more scalable than using a central global schema repository since all the composers in the integration layer are capable of handling and routing requests. Also, when a composer fails, it would only minimally affect the entire mediation system. ^

Mechanisms of Bicarbonate Use Influence the Photosynthetic Carbon Dioxide Sensitivity of Tropical Seagrasses

The photosynthetic bicarbonate () use properties of three widely distributed tropical seagrasses were compared using a series of laboratory experiments. Photosynthetic rates of Thalassia testudinum, Halodule wrightii, and Syringodium filiforme were monitored in an enclosed chamber while being subjected to shifts in pH and dissolved inorganic carbon. Specific mechanisms of seagrass use were compared by examining the photosynthetic effects of the carbonic anhydrase inhibitor acetazolamide (AZ). All seagrasses increased photosynthetic rates with reduced pH, suggesting a large effect of dissolved aqueous carbon dioxide (CO2(aq)). However, there was considerable interspecific variation in pH response. T. testudinum was highly sensitive, increasing photosynthetic rates by 100% as the pH was reduced from 8.2 to 7.4, whereas rates in H. wrightii and S. filiforme increased by only 20% over a similar range, and displayed prominent photosynthetic plateaus, indicating an increased capacity for use. Additional incubations that manipulated [] under constant [CO2(aq)] support these findings, as only H. wrightii and S. filiforme increased photosynthetic rates with increasing []. T. testudinum responded to AZ addition, indicating that carbonic anhydrase enzymes facilitate limited use. H. wrightii and S. filiforme showed no response to AZ, suggesting alternate, more efficient mechanisms of use. Estimated kinetic parameters, Ks(CO2) and Vmax, revealed interspecific variation and further support these conclusions. Variation in photosynthetic pH responses and AZ sensitivity indicate distinctions in the carbon use properties of seagrasses exposed to similar environmental conditions. These results suggest that not all seagrasses will similarly respond to future increases in CO2(aq) availability. Attention towards potential shifts in competitive interactions within multispecific seagrass beds is warranted.

Association between vaginal bacterial microbiota and the presence and clinical presentation of vulvovaginal candidiasis

Thesis (Master's)--University of Washington, 2016-08

Near-infraread observation of supernovae with the Nordic Optical Telescope (NOT)

Supernova (SN) is an explosion of a star at the end of its lifetime. SNe are classified to two types, namely type I and II through the optical spectra. They have been categorised based on their explosion mechanism, to core collapse supernovae (CCSNe) and thermonuclear supernovae. The CCSNe group which includes types IIP, IIn, IIL, IIb, Ib, and Ic are produced when a massive star with initial mass more than 8 M⊙ explodes due to a collapse of its iron core. On the other hand, thermonuclear SNe originate from white dwarfs (WDs) made of carbon and oxygen, in a binary system. Infrared astronomy covers observations of astronomical objects in infrared radiation. The infrared sky is not completely dark and it is variable. Observations of SNe in the infrared give different information than optical observations. Data reduction is required to correct raw data from for example unusable pixels and sky background. In this project, the NOTCam package in the IRAF was used for the data reduction. For measuring magnitudes of SNe, the aperture photometry method with the Gaia program was used. In this Master’s thesis, near-infrared (NIR) observations of three supernovae of type IIn (namely LSQ13zm, SN 2009ip and SN2011jb), one type IIb (SN2012ey), in addition to one type Ic (SN2012ej) and type IIP (SN 2013gd) are studied with emphasis on luminosity and colour evolution. All observations were done with the Nordic Optical Telescope (NOT). Here, we used the classification by Mattila & Meikle (2001) [76], where the SNe are differentiated by the infrared light curves into two groups, namely ’ordinary’ and ’slowly declining’. The light curves and colour evolution of these supernovae were obtained in J, H and Ks bands. In this study, our data, combined with other observations, provide evidence to categorize LSQ13zm, SN 2012ej and SN 2012ey as being part of the ordinary type. We found interesting NIR behaviour of SN 2011jb, which lead it to be classified as a slowly declining type.

Molecular cloning of a novel human I-mfa domain-containing protein that differently regulates human T-cell leukemia virus type I and HIV-1 expression.

Regulation of viral genome expression is the result of complex cooperation between viral proteins and host cell factors. We report here the characterization of a novel cellular factor sharing homology with the specific cysteine-rich C-terminal domain of the basic helix-loop-helix repressor protein I-mfa. The synthesis of this new factor, called HIC for Human I-mfa domain-Containing protein, is controlled at the translational level by two different codons, an ATG and an upstream non-ATG translational initiator, allowing the production of two protein isoforms, p32 and p40, respectively. We show that the HIC protein isoforms present different subcellular localizations, p32 being mainly distributed throughout the cytoplasm, whereas p40 is targeted to the nucleolus. Moreover, in trying to understand the function of HIC, we have found that both isoforms stimulate in T-cells the expression of a luciferase reporter gene driven by the human T-cell leukemia virus type I-long terminal repeat in the presence of the viral transactivator Tax. We demonstrate by mutagenesis that the I-mfa-like domain of HIC is involved in this regulation. Finally, we also show that HIC is able to down-regulate the luciferase expression from the human immunodeficiency virus type 1-long terminal repeat induced by the viral transactivator Tat. From these results, we propose that HIC and I-mfa represent two members of a new family of proteins regulating gene expression and characterized by a particular cysteine-rich C-terminal domain.