Lipopolysaccharide-Induced Sickness Behaviour Evaluated in Different Models of Anxiety and Innate Fear in Rats

The fact that there is a complex and bidirectional communication between the immune and nervous systems has been well demonstrated. Lipopolysaccharide (LPS), a component of gram-negative bacteria, is widely used to systematically stimulate the immune system and generate profound physiological and behavioural changes, also known as sickness behaviour (e.g. anhedonia, lethargy, loss of appetite, anxiety, sleepiness). Different ethological tools have been used to analyse the behavioural modifications induced by LPS; however, many researchers analysed only individual tests, a single LPS dose or a unique ethological parameter, thus leading to disagreements regarding the data. In the present study, we investigated the effects of different doses of LPS (10, 50, 200 and 500 mu g/kg, i.p.) in young male Wistar rats (weighing 180200 g; 89 weeks old) on the ethological and spatiotemporal parameters of the elevated plus maze, light-dark box, elevated T maze, open-field tests and emission of ultrasound vocalizations. There was a dose-dependent increase in anxiety-like behaviours caused by LPS, forming an inverted U curve peaked at LPS 200 mu g/kg dose. However, these anxiety-like behaviours were detected only by complementary ethological analysis (stretching, grooming, immobility responses and alarm calls), and these reactions seem to be a very sensitive tool in assessing the first signs of sickness behaviour. In summary, the present work clearly showed that there are resting and alertness reactions induced by opposite neuroimmune mechanisms (neuroimmune bias) that could lead to anxiety behaviours, suggesting that misunderstanding data could occur when only few ethological variables or single doses of LPS are analysed. Finally, it is hypothesized that this bias is an evolutionary tool that increases animals security while the body recovers from a systemic infection.

Paleoenvironment and Paleoecology of a Late Paleocene High-Latitude Terrestrial Succession, Arkose Ridge Formation at Box Canyon, Southern Talkeetna Mountains, Alaska

Paleogene sedimentary rocks of the Arkose Ridge Formation (Talkeetna Mountains, Alaska) preserve a record of a fluvial-lacustrine depositional environment and its forested ecosystem in an active basin among the convergent margin tectonic processes that shaped southern Alaska. An -800 m measured succession at Box Canyon indicates braid-plain deposition with predominantly gravelly deposits low in the exposure to sandy and muddy facies associations below an overlying lava flow sequence. U-Pb geochronology on zircons from a tuff and a sandstone within the measured section, as well as an Ar/Ar date from the overlying lava constrain the age of the sedimentary succession to between similar to 59 Ma and 48 Ma Fossil plant remains occur throughout the Arkose Ridge Formation as poorly-preserved coalified woody debris and fragmentary leaf impressions. At Box Canyon, however, a thin la-custrine depositional lens of rhythmically laminated mudrocks yielded fish fossils and a well-preserved floral assemblage including foliage and reproductive organs representing conifers, sphenopsids, monocots, and dicots. Leaf physiognomic methods to estimate paleoclimate were applied to the dicot leaf collection and indicate warm temperate paleotemperatures (-11-15 +/- -4 degrees C MAT) and elevated paleoprecipitation (-120 cm/yr MAP) estimates as compared to modem conditions; results that are parallel with previously published estimates from the partly coeval Chickaloon Formation deposited in more distal depositional environments in the same basin. The low abundance of leaf herbivory in the Box Canyon dicot assemblage (-9% of leaves damaged) is also similar to the results from assemblages in the meander-plain depositional systems of the Chickaloon. This new suite of data informs models of the tectonostratigraphic evolution of southern Alaska and the developing understanding of terrestrial paleoecology and paleoclimate at high latitudes during the Late Paleocene-Early Eocene greenhouse climate phase. (c) 2014 Elsevier B.V. All rights reserved.

Age models and stable isotope analysis on sediment core Site 199-1218 from the equatorial Pacific

A 13-million-year continuous record of Oligocene climate from the equatorial Pacific reveals a pronounced "heartbeat" in the global carbon cycle and periodicity of glaciations. This heartbeat consists of 405,000-, 127,000-, and 96,000-year eccentricity cycles and 1.2-million-year obliquity cycles in periodically recurring glacial and carbon cycle events. That climate system response to intricate orbital variations suggests a fundamental interaction of the carbon cycle, solar forcing, and glacial events. Box modeling shows that the interaction of the carbon cycle and solar forcing modulates deep ocean acidity as well as the production and burial of global biomass. The pronounced 405,000-year eccentricity cycle is amplified by the long residence time of carbon in the oceans.

Age models and sea-surface paleotemperature reconstruction of sediment cores from the eastern equatorial Atlantic

Based on the faunal record of planktonic foraminifers in three long gravity sediment cores from the eastern equatorial Atlantic, the sea-surface temperature history ove the last 750,000 years was studied at a resolution of 3,000 to 10,000 years. Detailed oxygen-isotope and paleomagnetic stratigraphy helped to identify the following major faunal events: Globorotaloides hexagonus and Globorotalia tumida flexuosa became extinct in the eastern tropical Atlantic at the isotope stage 4/5 boundary, now dated at 68,000 years B.P. The persistent occurrence of the pink variety of Globigerinoides ruber started during the late stage 12 at 410,000 years B.P. CARTUNE-age. This datum may provide an easily detectible faunal stratigraphic marker for the mid-Brunhes Chron. The updated scheme of the Ericson zones helped the recognition of a hiatus at the northwestern slope of the Sierra Leone Basin covering oxygen-isotope stages 10 to 12. Classifying the planktonic foraminifer counts into six faunal assemblages, according to the factor analysis derived model of Pflaumann (1985), the tropical and the tropical-upwelling communities account for 57 % at Site 16415, and 86 % at Site 13519, respectively of the variance of the faunal record. A largely continuous paleotemperature record for both winter and summer seasons was obtained from the top of the Sierra Leone Rise with the winter temperatures ranging between 20 and 25 °C, and the summer ones between 24 and 30 °C. The record of cores from greater water depths is frequently interrupted by samples with no-analogue faunal communities and/or poor preservation. Based on the seasonality signal, during cold periods the termal equator shifted to a geographically mnore asymmetrical northern position. Dissolution altering the faunal communities becomes stronger with greater water depth, the estimated mean minimum loss of specimens increases from 70 % to 80 % between 2,860 and 3,850 water depth although some species will be more susceptible than others. Enhanced dissolution occured during stage 4 but also during cold phases in the warm stage 7 and 9. Correlations between the Foraminiferal Dissolution Index and the estimated sea-surface temperatures are significant. Foraminiferal flux rates, negatively correlated to the flux rates of organic carbon and of diatoms, may be a result of enhanced dissolution during cold stages, destroying still more of the faunal signal than indicated by the calculated minimum loss. The fluctuations of the oxygen-isotope curves and the hibernal sea-surfave temperatures are fairly coherent. During warm oxygen-isotope stages the temperature maxima lag often by 5 to 15 ka behind the respective sotope minima. During cold stages, sea-surface temperature changes are partly out of phase and contain additional fluctuations.

Reduced order adaptive models for systems of PDEs using POD

In this work we propose a method to accelerate time dependent numerical solvers of systems of PDEs that require a high cost in computational time and memory. The method is based on the combined use of such numerical solver with a proper orthogonal decomposition, from which we identify modes, a Galerkin projection (that provides a reduced system of equations) and the integration of the reduced system, studying the evolution of the modal amplitudes. We integrate the reduced model until our a priori error estimator indicates that our approximation in not accurate. At this point we use again our original numerical code in a short time interval to adapt the POD manifold and continue then with the integration of the reduced model. Application will be made to two model problems: the Ginzburg-Landau equation in transient chaos conditions and the two-dimensional pulsating cavity problem, which describes the motion of liquid in a box whose upper wall is moving back and forth in a quasi-periodic fashion. Finally, we will discuss a way of improving the performance of the method using experimental data or information from numerical simulations

Experimental investigation on box-wing configuration for UAS

The range for airframe configurations available for UAS is as diverse as those used for manned aircraft and more since the commercial risk in trying unorthodox solutions is less for the UAS manufacturer. This is principally because the UAS airframes are usually much smaller than the manned aircraft and operators are less likely to have a bias against unconventional configurations. One of these unconventional configurations is the box-wing, which is an unconventional solution for the design of the new UAS generation. The existence of two wings separated in different planes that are, however, significantly close together, means that the aerodynamic analysis by theoretical or computational methods is a difficult task, due to the considerable interference existing. Considering the fact that the flight of most UAS takes place at low Reynolds numbers, it is necessary to study the aerodynamics of the box wing configuration by testing different models in a wind tunnel to be able to obtain reasonable results. In the present work, the study is enhanced by varying not only the sweepback angles of the two wings, but also their position along the models’ fuselage. Certain models have shown being more efficient than others, pointing out that certain relative positions of wing exists that can improve the aerodynamics efficiency of the box wing configuration.

Bayesian model selection of structural explanatory models.

In this study we are proposing a Bayesian model selection methodology, where the best model from the list of candidate structural explanatory models is selected. The model structure is based on the Zellner's (1971)explanatory model with autoregressive errors. For the selection technique we are using a parsimonious model, where the model variables are transformed using Box and Cox (1964) class of transformations.

Integration of different models in the design of chemical processes: Application to the design of a power plant

With advances in the synthesis and design of chemical processes there is an increasing need for more complex mathematical models with which to screen the alternatives that constitute accurate and reliable process models. Despite the wide availability of sophisticated tools for simulation, optimization and synthesis of chemical processes, the user is frequently interested in using the ‘best available model’. However, in practice, these models are usually little more than a black box with a rigid input–output structure. In this paper we propose to tackle all these models using generalized disjunctive programming to capture the numerical characteristics of each model (in equation form, modular, noisy, etc.) and to deal with each of them according to their individual characteristics. The result is a hybrid modular–equation based approach that allows synthesizing complex processes using different models in a robust and reliable way. The capabilities of the proposed approach are discussed with a case study: the design of a utility system power plant that has been decomposed into its constitutive elements, each treated differently numerically. And finally, numerical results and conclusions are presented.

Use of an Inverse Method for Time Series to Estimate the Dynamics of and Management Strategies for the Box Jellyfish Carybdea marsupialis

Frequently, population ecology of marine organisms uses a descriptive approach in which their sizes and densities are plotted over time. This approach has limited usefulness for design strategies in management or modelling different scenarios. Population projection matrix models are among the most widely used tools in ecology. Unfortunately, for the majority of pelagic marine organisms, it is difficult to mark individuals and follow them over time to determine their vital rates and built a population projection matrix model. Nevertheless, it is possible to get time-series data to calculate size structure and densities of each size, in order to determine the matrix parameters. This approach is known as a “demographic inverse problem” and it is based on quadratic programming methods, but it has rarely been used on aquatic organisms. We used unpublished field data of a population of cubomedusae Carybdea marsupialis to construct a population projection matrix model and compare two different management strategies to lower population to values before year 2008 when there was no significant interaction with bathers. Those strategies were by direct removal of medusae and by reducing prey. Our results showed that removal of jellyfish from all size classes was more effective than removing only juveniles or adults. When reducing prey, the highest efficiency to lower the C. marsupialis population occurred when prey depletion affected prey of all medusae sizes. Our model fit well with the field data and may serve to design an efficient management strategy or build hypothetical scenarios such as removal of individuals or reducing prey. TThis This sdfsdshis method is applicable to other marine or terrestrial species, for which density and population structure over time are available.

Analytical and numerical analysis of 40 Gbit/s regenerated transmissions using simple black box optical regenerator

A simplified (without phase modulator) scheme of a black box optical regenerator is proposed, where an appropriate nonlinear propagation is used to enhance regeneration. Applying semi-theoretical models the authors optimise and demonstrate feasibility of error-free long distance transmission at 40 Gbit/s.

Age models, accumulation rates, and grain size distributions of sediment cores from the northern subtropical Atlantic

The terrigenous sediment proportion of the deep sea sediments from off Northwest Africa has been studied in order to distinguish between the aeolian and the fluvial sediment supply. The present and fossil Saharan dust trajectories were recognized from the distribution patterns of the aeolian sediment. The following timeslices have been investigated: Present, 6,000, 12,000 and 18,000 y. B. P. Furthermore, the quantity of dust deposited off the Saharan coast has been estimated. For this purpose, 80 surface sediment samples and 34 sediment cores have been analysed. The stratigraphy of the cores has been achieved from oxygen isotopic curves, 14C-dating, foraminiferal transfer temperatures, and carbonate contents. Silt sized biogenic opal generally accounts for less than 2 % of the total insoluble sediment proportion. Only under productive upwelling waters and off river mouths, the opal proportion exceeds 2 % significantly. The modern terrigenous sediment from off the Saharan coast is generally characterized by intensely stained quartz grains. They indicate an origin from southern Saharan and Sahelian laterites, and a zonal aeolian transport in midtropospheric levels, between 1.5 an 5.5 km, by 'Harmattan' Winds. The dust particles follow large outbreaks of Saharan air across the African coast between 15° and 21° N. Their trajectories are centered at about 18° N and continue further into a clockwise gyre situated south of the Canary Islands. This course is indicated by a sickle-shaped tongue of coarser grain sizes in the deep-sea sediment. Such loess-sized terrigenous particles only settle within a zone extending to 700 km offshore. Fine silt and clay sized particles, with grain sizes smaller than 10- 15 µm, drift still further west and can be traced up to more than 4,000 km distance from their source areas. Additional terrigenous silt which is poor in stained quartz occurs within a narrow zone off the western Sahara between 20° and 27° N only. It depicts the present dust supply by the trade winds close to the surface. The dust load originates from the northwestern Sahara, the Atlas Mountains and coastal areas, which contain a particularly low amount of stained quartz. The distribution pattern of these pale quartz sediments reveals a SSW-dispersal of dust being consistent with the present trade wind direction from the NNE. In comparison to the sediments from off the Sahara and the deeper subtropical Atlantic, the sediments off river mouths, in particular off the Senegal river, are characterized by an additional input of fine grained terrigenous particles (< 6 µm). This is due to fluvial suspension load. The fluvial discharge leads to a relative excess of fine grained particles and is observed in a correlation diagram of the modal grain sizes of terrigenous silt with the proportion of fine fraction (< 6 µm). The aeolian sediment contribution by the Harmattan Winds strongly decreased during the Climatic Optimum at 6,000 y. B. P. The dust discharge of the trade winds is hardly detectable in the deep-sea sediments. This probably indicates a weakened atmospheric circulation. In contrast, the fluvial sediment supply reached a maximum, and can be traced to beyond Cape Blanc. Thus, the Saharan climate was more humid at 6,000 y B. P. A latitudinal shift of the Harmattan driven dust outbreaks cannot be observed. Also during the Glacial, 18,000 y. B. P., Harmattan dust transport crossed the African coast at latitudes of 15°-20° N. Its sediment load increased intensively, and markedly coarser grains spread further into the Atlantic Ocean. An expanded zone of pale-quart sediments indicates an enhanced dust supply by the trade winds blowing from the NE. No synglacial fluvial sediment contribution can be recognized between 12° and 30° N. This indicates a dry glacial climate and a strengthened stmospheric circulation over the Sahelian and Saharan region. The climatic transition pahes, at 12, 000 y. B. P., between the last Glacial and the Intergalcial, which is compareable to the Alerod in Europe, is characterized by an intermediate supply of terrigenous particles. The Harmattan dust transport wa weaker than during the Glacial. The northeasterly trade winds were still intensive. River supply reached a first postglacial maximum seaward of the Senegal river mouth. This indicates increasing humidity over the southern Sahara and a weaker atmospheric circulation as compared to the glacial. The accumulation rates of the terrigenous silt proportion (> 6 µm) decrcase exponentially with increasing distance from the Saharan coast. Those of the terrigenous fine fraction (< 6 µm) follow the same trend and show almost similar gradients. Accordingly, also the terrigenous fine fraction is believed to result predominantly from aeolian transport. In the Atlantic deep-sea sediments, the annual terrigenous sediment accumulation has fluctuated, from about 60 million tons p. a. during the Late Glacial (13,500-18,000 y. B. P, aeolian supply only) to about 33 million tons p. a. during the Holocene Climatic Optimum (6,000-9,000 y. B. P, mainly fluvial supply), when the river supply has reached a maximum, and to about 45 million tons p. a. during the last 4,000 years B. P. (fluvial supply only south of 18° N).

Semi-engineered earthquake-resistant structures: one-storey buildings built up with gabion-box walls

This thesis studies the static and seismic behavior of simple structures made with gabion box walls. The analysis was performed considering a one-story building with standard dimensions in plan (6m x 5m) and a lightweight timber roof. The main focus of the present investigation is to find the principals aspects of the seismic behavior of a one story building made with gabion box walls, in order to prevent a failure due to seismic actions and in this way help to reduce the seismic risk of developing countries where this natural disaster have a significant intensity. Regarding the gabion box wall, it has been performed some calculations and analysis in order to understand the static and dynamic behavior. From the static point of view, it has been performed a verification of the normal stress computing the normal stress that arrives at the base of the gabion wall and the corresponding capacity of the ground. Moreover, regarding the seismic analysis, it has been studied the in-plane and out-of-plane behavior. The most critical aspect was discovered to be the out-of-plane behavior, for which have been developed models considering the “rigid- no tension model” for masonry, finding a kinematically admissible multiplier that will create a collapse mechanism for the structure. Furthermore, it has been performed a FEM and DEM models to find the maximum displacement at the center of the wall, maximum tension stresses needed for calculating the steel connectors for joining consecutive gabions and the dimensions (length of the wall and distance between orthogonal walls or buttresses) of a geometrical configuration for the standard modulus of the structure, in order to ensure an adequate safety margin for earthquakes with a PGA around 0.4-0.5g. Using the results obtained before, it has been created some rules of thumb, that have to be satisfy in order to ensure a good behavior of these structure.

Age models and stable isotopes of sediment cores from the northern seas

Oxygen and carbon isotope measurements were carried out on tests of planktic foraminifers N. pachyderma (sin.) from eight sediment cores taken from the eastern Arctic Ocean, the Fram Strait, and the lceland Sea, in order to reconstruct Arctic Ocean and Norwegian-Greenland Sea circulation patterns and ice covers during the last 130,000 years. In addition, the influence of ice, temperature and salinity effects on the isotopic signal was quantified. Isotope measurements on foraminifers from sediment surface samples were used to elucidate the ecology of N. pachyderma (sin.). Changes in the oxygen and carbon isotope composition of N. pachyderma (sin.) from sediment surface samples document the horizontal and vertical changes of water mass boundaries controlled by water temperature and salinity, because N. pachyderma (sin.) shows drastic changes in depth habitats, depending on the water mass properties. It was able to be shown that in the investigated areas a regional and spatial apparent increase of the ice effect occurred. This happened especially during the termination I by direct advection of meltwaters from nearby continents or during the termination and in interglacials by supply of isotopically light water from rivers. A northwardly proceeding overprint of the 'global' ice effect, increasing from the Norwegian-Greenland Sea to the Arctic Ocean, was not able to be demonstrated. By means of a model the influence of temperature and salinity on the global ice volume signal during the last 130,000 years was recorded. In combination with the results of this study, the model was the basis for a reconstruction of the paleoceanographic development of the Arctic Ocean and the Norwegian-Greenland Sea during this time interval. The conception of a relatively thick and permanent sea ice cover in the Nordic Seas during glacial times should be replaced by the model of a seasonally and regionally highly variable ice cover. Only during isotope stage 5e may there have been a local deep water formation in the Fram Strait.

Predicting Transcript Production Rates in Yeast With Sparse Linear Models

To provide biological insights into transcriptional regulation, a couple of groups have recently presented models relating the promoter DNA-bound transcription factors (TFs) to downstream gene’s mean transcript level or transcript production rates over time. However, transcript production is dynamic in response to changes of TF concentrations over time. Also, TFs are not the only factors binding to promoters; other DNA binding factors (DBFs) bind as well, especially nucleosomes, resulting in competition between DBFs for binding at same genomic location. Additionally, not only TFs, but also some other elements regulate transcription. Within core promoter, various regulatory elements influence RNAPII recruitment, PIC formation, RNAPII searching for TSS, and RNAPII initiating transcription. Moreover, it is proposed that downstream from TSS, nucleosomes resist RNAPII elongation.

Here, we provide a machine learning framework to predict transcript production rates from DNA sequences. We applied this framework in the S. cerevisiae yeast for two scenarios: a) to predict the dynamic transcript production rate during the cell cycle for native promoters; b) to predict the mean transcript production rate over time for synthetic promoters. As far as we know, our framework is the first successful attempt to have a model that can predict dynamic transcript production rates from DNA sequences only: with cell cycle data set, we got Pearson correlation coefficient Cp = 0.751 and coefficient of determination r2 = 0.564 on test set for predicting dynamic transcript production rate over time. Also, for DREAM6 Gene Promoter Expression Prediction challenge, our fitted model outperformed all participant teams, best of all teams, and a model combining best team’s k-mer based sequence features and another paper’s biologically mechanistic features, in terms of all scoring metrics.

Moreover, our framework shows its capability of identifying generalizable fea- tures by interpreting the highly predictive models, and thereby provide support for associated hypothesized mechanisms about transcriptional regulation. With the learned sparse linear models, we got results supporting the following biological insights: a) TFs govern the probability of RNAPII recruitment and initiation possibly through interactions with PIC components and transcription cofactors; b) the core promoter amplifies the transcript production probably by influencing PIC formation, RNAPII recruitment, DNA melting, RNAPII searching for and selecting TSS, releasing RNAPII from general transcription factors, and thereby initiation; c) there is strong transcriptional synergy between TFs and core promoter elements; d) the regulatory elements within core promoter region are more than TATA box and nucleosome free region, suggesting the existence of still unidentified TAF-dependent and cofactor-dependent core promoter elements in yeast S. cerevisiae; e) nucleosome occupancy is helpful for representing +1 and -1 nucleosomes’ regulatory roles on transcription.

AN EXAMINATION OF HYDROXYL RADICAL: OUR CURRENT UNDERSTANDING OF THE OXIDATIVE CAPACITY OF THE TROPOSPHERE THROUGH EMPIRICAL, BOX, AND GLOBAL MODELING APPROACHES

Hydroxyl radical (OH) is the primary oxidant in the troposphere, initiating the removal of numerous atmospheric species including greenhouse gases, pollutants that are detrimental to human health, and ozone-depleting substances. Because of the complexity of OH chemistry, models vary widely in their OH chemistry schemes and resulting methane (CH4) lifetimes. The current state of knowledge concerning global OH abundances is often contradictory. This body of work encompasses three projects that investigate tropospheric OH from a modeling perspective, with the goal of improving the tropospheric community’s knowledge of the atmospheric lifetime of CH4. First, measurements taken during the airborne CONvective TRansport of Active Species in the Tropics (CONTRAST) field campaign are used to evaluate OH in global models. A box model constrained to measured variables is utilized to infer concentrations of OH along the flight track. Results are used to evaluate global model performance, suggest against the existence of a proposed “OH Hole” in the tropical Western Pacific, and investigate implications of high O3/low H2O filaments on chemical transport to the stratosphere. While methyl chloroform-based estimates of global mean OH suggest that models are overestimating OH, we report evidence that these models are actually underestimating OH in the tropical Western Pacific. The second project examines OH within global models to diagnose differences in CH4 lifetime. I developed an approach to quantify the roles of OH precursor field differences (O3, H2O, CO, NOx, etc.) using a neural network method. This technique enables us to approximate the change in CH4 lifetime resulting from variations in individual precursor fields. The dominant factors driving CH4 lifetime differences between models are O3, CO, and J(O3-O1D). My third project evaluates the effect of climate change on global fields of OH using an empirical model. Observations of H2O and O3 from satellite instruments are combined with a simulation of tropical expansion to derive changes in global mean OH over the past 25 years. We find that increasing H2O and increasing width of the tropics tend to increase global mean OH, countering the increasing CH4 sink and resulting in well-buffered global tropospheric OH concentrations.