Brain structural and functional recovery following initiation of combination antiretroviral therapy

NeuroAIDS persists in the era of combination antiretroviral therapies. We describe here the recovery of brain structure and function following 6 months of therapy in a treatment-naive patient presenting with HIV-associated dementia. The patient’s neuropsychological test performance improved and his total brain volume increased by more than 5 %. Neuronal functional connectivity measured by magnetoencephalography changed from a pattern identical to that observed in other HIV-infected individuals to one that was indistinguishable from that of uninfected control subjects. These data suggest that at least some of the effects of HIV on the brain can be fully reversed with treatment.

Prediction of wake effects on wind farm power production using a RANS approach. Part II. Offshore: Case studies from the UPWIND project

The estimation of power losses due to wind turbine wakes is crucial to understanding overall wind farm economics. This is especially true for large offshore wind farms, as it represents the primary source of losses in available power, given the regular arrangement of rotors, their generally largerdiameter and the lower ambient turbulence level, all of which conspire to dramatically affect wake expansion and, consequently, the power deficit. Simulation of wake effects in offshore wind farms (in reasonable computational time) is currently feasible using CFD tools. An elliptic CFD model basedon the actuator disk method and various RANS turbulence closure schemes is tested and validated using power ratios extracted from Horns Rev and Nysted wind farms, collected as part of the EU-funded UPWIND project. The primary focus of the present work is on turbulence modeling, as turbulent mixing is the main mechanism for flow recovery inside wind farms. A higher-order approach, based on the anisotropic RSM model, is tested to better take into account the imbalance in the length scales inside and outside of the wake, not well reproduced by current two-equation closure schemes.

Thermal, stress, and traps effects in AlGaN/GaN HEMTs

GaN y AlN son materiales semiconductores piezoeléctricos del grupo III-V. La heterounión AlGaN/GaN presenta una elevada carga de polarización tanto piezoeléctrica como espontánea en la intercara, lo que genera en su cercanía un 2DEG de grandes concentración y movilidad. Este 2DEG produce una muy alta potencia de salida, que a su vez genera una elevada temperatura de red. Las tensiones de puerta y drenador provocan un stress piezoeléctrico inverso, que puede afectar a la carga de polarización piezoeléctrica y así influir la densidad 2DEG y las características de salida. Por tanto, la física del dispositivo es relevante para todos sus aspectos eléctricos, térmicos y mecánicos. En esta tesis se utiliza el software comercial COMSOL, basado en el método de elementos finitos (FEM), para simular el comportamiento integral electro-térmico, electro-mecánico y electro-térmico-mecánico de los HEMTs de GaN. Las partes de acoplamiento incluyen el modelo de deriva y difusión para el transporte electrónico, la conducción térmica y el efecto piezoeléctrico. Mediante simulaciones y algunas caracterizaciones experimentales de los dispositivos, hemos analizado los efectos térmicos, de deformación y de trampas. Se ha estudiado el impacto de la geometría del dispositivo en su auto-calentamiento mediante simulaciones electro-térmicas y algunas caracterizaciones eléctricas. Entre los resultados más sobresalientes, encontramos que para la misma potencia de salida la distancia entre los contactos de puerta y drenador influye en generación de calor en el canal, y así en su temperatura. El diamante posee une elevada conductividad térmica. Integrando el diamante en el dispositivo se puede dispersar el calor producido y así reducir el auto-calentamiento, al respecto de lo cual se han realizado diversas simulaciones electro-térmicas. Si la integración del diamante es en la parte superior del transistor, los factores determinantes para la capacidad disipadora son el espesor de la capa de diamante, su conductividad térmica y su distancia a la fuente de calor. Este procedimiento de disipación superior también puede reducir el impacto de la barrera térmica de intercara entre la capa adaptadora (buffer) y el substrato. La muy reducida conductividad eléctrica del diamante permite que pueda contactar directamente el metal de puerta (muy cercano a la fuente de calor), lo que resulta muy conveniente para reducir el auto-calentamiento del dispositivo con polarización pulsada. Por otra parte se simuló el dispositivo con diamante depositado en surcos atacados sobre el sustrato como caminos de disipación de calor (disipador posterior). Aquí aparece una competencia de factores que influyen en la capacidad de disipación, a saber, el surco atacado contribuye a aumentar la temperatura del dispositivo debido al pequeño tamaño del disipador, mientras que el diamante disminuiría esa temperatura gracias a su elevada conductividad térmica. Por tanto, se precisan capas de diamante relativamente gruesas para reducer ele efecto de auto-calentamiento. Se comparó la simulación de la deformación local en el borde de la puerta del lado cercano al drenador con estructuras de puerta estándar y con field plate, que podrían ser muy relevantes respecto a fallos mecánicos del dispositivo. Otras simulaciones se enfocaron al efecto de la deformación intrínseca de la capa de diamante en el comportamiento eléctrico del dispositivo. Se han comparado los resultados de las simulaciones de la deformación y las características eléctricas de salida con datos experimentales obtenidos por espectroscopía micro-Raman y medidas eléctricas, respectivamente. Los resultados muestran el stress intrínseco en la capa producido por la distribución no uniforme del 2DEG en el canal y la región de acceso. Además de aumentar la potencia de salida del dispositivo, la deformación intrínseca en la capa de diamante podría mejorar la fiabilidad del dispositivo modulando la deformación local en el borde de la puerta del lado del drenador. Finalmente, también se han simulado en este trabajo los efectos de trampas localizados en la superficie, el buffer y la barrera. Las medidas pulsadas muestran que tanto las puertas largas como las grandes separaciones entre los contactos de puerta y drenador aumentan el cociente entre la corriente pulsada frente a la corriente continua (lag ratio), es decir, disminuir el colapse de corriente (current collapse). Este efecto ha sido explicado mediante las simulaciones de los efectos de trampa de superficie. Por su parte, las referidas a trampas en el buffer se enfocaron en los efectos de atrapamiento dinámico, y su impacto en el auto-calentamiento del dispositivo. Se presenta también un modelo que describe el atrapamiento y liberación de trampas en la barrera: mientras que el atrapamiento se debe a un túnel directo del electrón desde el metal de puerta, el desatrapamiento consiste en la emisión del electrón en la banda de conducción mediante túnel asistido por fonones. El modelo también simula la corriente de puerta, debida a la emisión electrónica dependiente de la temperatura y el campo eléctrico. Además, también se ilustra la corriente de drenador dependiente de la temperatura y el campo eléctrico. ABSTRACT GaN and AlN are group III-V piezoelectric semiconductor materials. The AlGaN/GaN heterojunction presents large piezoelectric and spontaneous polarization charge at the interface, leading to high 2DEG density close to the interface. A high power output would be obtained due to the high 2DEG density and mobility, which leads to elevated lattice temperature. The gate and drain biases induce converse piezoelectric stress that can influence the piezoelectric polarization charge and further influence the 2DEG density and output characteristics. Therefore, the device physics is relevant to all the electrical, thermal, and mechanical aspects. In this dissertation, by using the commercial finite-element-method (FEM) software COMSOL, we achieved the GaN HEMTs simulation with electro-thermal, electro-mechanical, and electro-thermo-mechanical full coupling. The coupling parts include the drift-diffusion model for the electron transport, the thermal conduction, and the piezoelectric effect. By simulations and some experimental characterizations, we have studied the device thermal, stress, and traps effects described in the following. The device geometry impact on the self-heating was studied by electro-thermal simulations and electrical characterizations. Among the obtained interesting results, we found that, for same power output, the distance between the gate and drain contact can influence distribution of the heat generation in the channel and thus influence the channel temperature. Diamond possesses high thermal conductivity. Integrated diamond with the device can spread the generated heat and thus potentially reduce the device self-heating effect. Electro-thermal simulations on this topic were performed. For the diamond integration on top of the device (top-side heat spreading), the determinant factors for the heat spreading ability are the diamond thickness, its thermal conductivity, and its distance to the heat source. The top-side heat spreading can also reduce the impact of thermal boundary resistance between the buffer and the substrate on the device thermal behavior. The very low electrical conductivity of diamond allows that it can directly contact the gate metal (which is very close to the heat source), being quite convenient to reduce the self-heating for the device under pulsed bias. Also, the diamond coated in vias etched in the substrate as heat spreading path (back-side heat spreading) was simulated. A competing mechanism influences the heat spreading ability, i.e., the etched vias would increase the device temperature due to the reduced heat sink while the coated diamond would decrease the device temperature due to its higher thermal conductivity. Therefore, relative thick coated diamond is needed in order to reduce the self-heating effect. The simulated local stress at the gate edge of the drain side for the device with standard and field plate gate structure were compared, which would be relevant to the device mechanical failure. Other stress simulations focused on the intrinsic stress in the diamond capping layer impact on the device electrical behaviors. The simulated stress and electrical output characteristics were compared to experimental data obtained by micro-Raman spectroscopy and electrical characterization, respectively. Results showed that the intrinsic stress in the capping layer caused the non-uniform distribution of 2DEG in the channel and the access region. Besides the enhancement of the device power output, intrinsic stress in the capping layer can potentially improve the device reliability by modulating the local stress at the gate edge of the drain side. Finally, the surface, buffer, and barrier traps effects were simulated in this work. Pulsed measurements showed that long gates and distances between gate and drain contact can increase the gate lag ratio (decrease the current collapse). This was explained by simulations on the surface traps effect. The simulations on buffer traps effects focused on illustrating the dynamic trapping/detrapping in the buffer and the self-heating impact on the device transient drain current. A model was presented to describe the trapping and detrapping in the barrier. The trapping was the electron direct tunneling from the gate metal while the detrapping was the electron emission into the conduction band described by phonon-assisted tunneling. The reverse gate current was simulated based on this model, whose mechanism can be attributed to the temperature and electric field dependent electron emission in the barrier. Furthermore, the mechanism of the device bias via the self-heating and electric field impact on the electron emission and the transient drain current were also illustrated.

Recovery of Disruptions in Rapid Transit Networks

This paper studies the disruption management problem of rapid transit rail networks. Besides optimizing the timetable and the rolling stock schedules, we explicitly deal with the effects of the disruption on the passenger demand. We propose a two-step approach that combines an integrated optimization model (for the timetable and rolling stock) with a model for the passengers’ behavior. We report our computational tests on realistic problem instances of the Spanish rail operator RENFE. The proposed approach is able to find solutions with a very good balance between various managerial goals within a few minutes. Se estudia la gestión de las incidencias en redes de metro y cercanías. Se optimizan los horarios y la asignación del material rodante, teniendo en cuenta el comportamiento de los pasajeros. Se reallizan pruebas en varias líneas de la red de cercanías de Madrid, con resultados satisfactorios.

Cardiac arrest in rodents: Maximal duration compatible with a recovery of neuronal activity

We report here that during a permanent cardiac arrest, rodent brain tissue is “physiologically” preserved in situ in a particular quiescent state. This state is characterized by the absence of electrical activity and by a critical period of 5–6 hr during which brain tissue can be reactivated upon restoration of a simple energy (glucose/oxygen) supply. In rat brain slices prepared 1–6 hr after cardiac arrest and maintained in vitro for several hours, cells with normal morphological features, intrinsic membrane properties, and spontaneous synaptic activity were recorded from various brain regions. In addition to functional membrane channels, these neurons expressed mRNA, as revealed by single-cell reverse transcription–PCR, and could synthesize proteins de novo. Slices prepared after longer delays did not recover. In a guinea pig isolated whole-brain preparation that was cannulated and perfused with oxygenated saline 1–2 hr after cardiac arrest, cell activity and functional long-range synaptic connections could be restored although the electroencephalogram remained isoelectric. Perfusion of the isolated brain with the γ-aminobutyric acid A receptor antagonist picrotoxin, however, could induce self-sustained temporal lobe epilepsy. Thus, in rodents, the duration of cardiac arrest compatible with a short-term recovery of neuronal activity is much longer than previously expected. The analysis of the parameters that regulate this duration may bring new insights into the prevention of postischemic damages.

Effects of Age on the Posttranscriptional Regulation of CCAAT/Enhancer Binding Protein α and CCAAT/Enhancer Binding Protein β Isoform Synthesis in Control and LPS-Treated Livers

The CCAAT/enhancer binding protein α (C/EBPα) and CCAAT/enhancer binding protein β (C/EBPβ) mRNAs are templates for the differential translation of several isoforms. Immunoblotting detects C/EBPαs with molecular masses of 42, 38, 30, and 20 kDa and C/EBPβs of 35, 20, and ∼8.5 kDa. The DNA-binding activities and pool levels of p42C/EBPα and p30C/EBPα in control nuclear extracts decrease significantly whereas the binding activity and protein levels of the 20-kDa isoforms increase dramatically with LPS treatment. Our studies suggest that the LPS response involves alternative translational initiation at specific in-frame AUGs, producing specific C/EBPα and C/EBPβ isoform patterns. We propose that alternative translational initiation occurs by a leaky ribosomal scanning mechanism. We find that nuclear extracts from normal aged mouse livers have decreased p42C/EBPα levels and binding activity, whereas those of p20C/EBPα and p20C/EBPβ are increased. However, translation of 42-kDa C/EBPα is not down-regulated on polysomes, suggesting that aging may affect its nuclear translocation. Furthermore, recovery of the C/EBPα- and C/EBPβ-binding activities and pool levels from an LPS challenge is delayed significantly in aged mouse livers. Thus, aged livers have altered steady-state levels of C/EBPα and C/EBPβ isoforms. This result suggests that normal aging liver exhibits characteristics of chronic stress and a severe inability to recover from an inflammatory challenge.

Transcriptome of a mouse kidney cortical collecting duct cell line: Effects of aldosterone and vasopressin

Aldosterone and vasopressin are responsible for the final adjustment of sodium and water reabsorption in the kidney. In principal cells of the kidney cortical collecting duct (CCD), the integral response to aldosterone and the long-term functional effects of vasopressin depend on transcription. In this study, we analyzed the transcriptome of a highly differentiated mouse clonal CCD principal cell line (mpkCCDcl4) and the changes in the transcriptome induced by aldosterone and vasopressin. Serial analysis of gene expression (SAGE) was performed on untreated cells and on cells treated with either aldosterone or vasopressin for 4 h. The transcriptomes in these three experimental conditions were determined by sequencing 169,721 transcript tags from the corresponding SAGE libraries. Limiting the analysis to tags that occurred twice or more in the data set, 14,654 different transcripts were identified, 3,642 of which do not match known mouse sequences. Statistical comparison (at P < 0.05 level) of the three SAGE libraries revealed 34 AITs (aldosterone-induced transcripts), 29 ARTs (aldosterone-repressed transcripts), 48 VITs (vasopressin-induced transcripts) and 11 VRTs (vasopressin-repressed transcripts). A selection of the differentially-expressed, hormone-specific transcripts (5 VITs, 2 AITs and 1 ART) has been validated in the mpkCCDcl4 cell line either by Northern blot hybridization or reverse transcription–PCR. The hepatocyte nuclear transcription factor HNF-3-α (VIT39), the receptor activity modifying protein RAMP3 (VIT48), and the glucocorticoid-induced leucine zipper protein (GILZ) (AIT28) are candidate proteins playing a role in physiological responses of this cell line to vasopressin and aldosterone.

A selective peroxisome proliferator-activated receptor δ agonist promotes reverse cholesterol transport

The peroxisome proliferator-activated receptors (PPARs) are dietary lipid sensors that regulate fatty acid and carbohydrate metabolism. The hypolipidemic effects of the fibrate drugs and the antidiabetic effects of the glitazone drugs in humans are due to activation of the α (NR1C1) and γ (NR1C3) subtypes, respectively. By contrast, the therapeutic potential of the δ (NR1C2) subtype is unknown, due in part to the lack of selective ligands. We have used combinatorial chemistry and structure-based drug design to develop a potent and subtype-selective PPARδ agonist, GW501516. In macrophages, fibroblasts, and intestinal cells, GW501516 increases expression of the reverse cholesterol transporter ATP-binding cassette A1 and induces apolipoprotein A1-specific cholesterol efflux. When dosed to insulin-resistant middle-aged obese rhesus monkeys, GW501516 causes a dramatic dose-dependent rise in serum high density lipoprotein cholesterol while lowering the levels of small-dense low density lipoprotein, fasting triglycerides, and fasting insulin. Our results suggest that PPARδ agonists may be effective drugs to increase reverse cholesterol transport and decrease cardiovascular disease associated with the metabolic syndrome X.

The current biodiversity extinction event: Scenarios for mitigation and recovery

The current massive degradation of habitat and extinction of species is taking place on a catastrophically short timescale, and their effects will fundamentally reset the future evolution of the planet's biota. The fossil record suggests that recovery of global ecosystems has required millions or even tens of millions of years. Thus, intervention by humans, the very agents of the current environmental crisis, is required for any possibility of short-term recovery or maintenance of the biota. Many current recovery efforts have deficiencies, including insufficient information on the diversity and distribution of species, ecological processes, and magnitude and interaction of threats to biodiversity (pollution, overharvesting, climate change, disruption of biogeochemical cycles, introduced or invasive species, habitat loss and fragmentation through land use, disruption of community structure in habitats, and others). A much greater and more urgently applied investment to address these deficiencies is obviously warranted. Conservation and restoration in human-dominated ecosystems must strengthen connections between human activities, such as agricultural or harvesting practices, and relevant research generated in the biological, earth, and atmospheric sciences. Certain threats to biodiversity require intensive international cooperation and input from the scientific community to mitigate their harmful effects, including climate change and alteration of global biogeochemical cycles. In a world already transformed by human activity, the connection between humans and the ecosystems they depend on must frame any strategy for the recovery of the biota.

Neurocytopathic effects of beta-amyloid-stimulated monocytes: a potential mechanism for central nervous system damage in Alzheimer disease.

Growing evidence indicates that cells of the mononuclear phagocyte lineage, which includes peripheral blood monocytes (PBM) and tissue macrophages, participate in a variety of neurodestructive events and may play a pivotal role in neurodegenerative conditions such as Alzheimer disease. The present study sought to determine whether exposure of PBM to beta-amyloid peptide (A beta), the major protein of the amyloid fibrils that accumulate in the brain in Alzheimer disease, could induce cytopathic activity in these cells upon their subsequent incubation with neural tissue. PBM were incubated with A beta for 3 days, centrifuged and washed to remove traces of cell-free A beta, and then applied to organotypic cultures of rat brain for varying periods of time. By using a cell-viability assay to quantitate neurocytopathic effect, an increase in the ratio of dead to live cells was detected in cultures containing A beta-stimulated PBM versus control PBM (stimulated with either bovine serum albumin or reverse A beta peptide) as early as 3 days after coculture. The ratio of dead to live cells increased further by 10 days of coculture. By 30 days of coculture, the dead to live cell ratio remained elevated, and the intensity of neurocytopathic effect was such that large areas of brain mass dissociated from the cultures. These results indicate that stimulation of PBM with A beta significantly heightens their neurocytopathic activity and highlight the possibility that inflammatory reactions in the brain play a role in the neurodegeneration that accompanies Alzheimer disease.

Cardioprotective effects of 70-kDa heat shock protein in transgenic mice.

Heat shock proteins are proposed to limit injury resulting from diverse environmental stresses, but direct metabolic evidence for such a cytoprotective function in vertebrates has been largely limited to studies of cultured cells. We generated lines of transgenic mice to express human 70-kDa heat shock protein constitutively in the myocardium. Hearts isolated from these animals demonstrated enhanced recovery of high energy phosphate stores and correction of metabolic acidosis following brief periods of global ischemia sufficient to induce sustained abnormalities of these variables in hearts from nontransgenic littermates. These data demonstrate a direct cardioprotective effect of 70-kDa heat shock protein to enhance postischemic recovery of the intact heart.

Real time measurements of elongation by a reverse transcriptase using surface plasmon resonance.

A rapid direct assay for polymerase-induced elongation along a given template is an obligate requirement for understanding the processivity of polymerization and the mode of action of drugs and inhibitors on this process. Surface plasmon resonance can be used to follow the association and the dissociation rates of a given reverse transcriptase on DNA.RNA and DNA.DNA hybrids immobilized on a biotin-streptavidin surface. The addition of nucleotides complementary to the template strand produces an increase in the local mass, as deduced from an increase in the measured signal, due to elongation of the primer strand that allows an estimation of both the extent and rate of the polymerization process. The terminator drug 3'-deoxy-3'-azidothymidine triphosphate completely abolishes the increase in signal as would be expected from an inhibition of elongation. This technique provides a sensitive assay for the affinities of different polymerases for specific templates and for the effects of terminators of the elongation process.

Effects of TH1 and TH2 cytokines on CD8+ cell response against human immunodeficiency virus: implications for long-term survival.

CD8+ cells from long-term survivors [LTS; infected with human immunodeficiency virus (HIV) for 10 or more years and having CD4+ cell counts of > or = 500 cells per microliters] have a 3-fold greater ability to suppress HIV replication than do CD8+ cells from patients who have progressed to disease (progressors) during the same time period. A change in the pattern of cytokines produced in the host from those that typically favor cell-mediated immunity (T helper 1, TH1 or type 1) to those that down-regulate it (T helper 2, TH2 or type 2) was investigated as a cause of this reduced CD8+ cell anti-HIV function. Treatment of CD8+ cells from LTS with the TH1 cytokine interleukin (IL)-2 enhanced their anti-HIV activity, whereas exposure of these cells to TH2 cytokines IL-4 or IL-10 reduced their ability to suppress HIV replication and to produce IL-2. IL-2 could prevent and reverse the inhibitory effects of IL-4 and IL-10. Moreover, prolonged exposure of CD8+ cells from some progressors to IL-2 improved the ability of these cells to suppress HIV replication. These observations support previous findings suggesting that strong CD8+ cell responses play an important role in maintaining an asymptomatic state in HIV infection. The data suggest that the loss of CD8+ cell suppression of HIV replication associated with disease progression results from a shift in cytokine production within the infected host from a TH1 to a TH2 pattern. Modulation of these cytokines could provide benefit to HIV-infected individuals by improving their CD8+ cell anti-HIV activity.

The Effects of Oil and Gas Exploration on Greater Sage Grouse Populations

Energy production throughout the greater Rocky Mountain Region has increased dramatically in the past decade. Pristine habitat areas historically home to the greater sage grouse are being impaired by these energy development actions. Ongoing studies by state and federal biologists have shown a decrease in overall reproductive activity and a decrease in population on historical mating grounds. This project identifies actions to conserve and restore the habitat of sage grouse populations and reverse the decline of the species. Recommended measures presented in this project include using directional drilling of multiple wells from one single drill pad, creating a GIS mapping data base, funding additional scientific studies regarding impacts from energy development and improved cooperation between state, federal and private agencies.

Reverse Vending Machines: A Potential Solution for the Florida Plastic Waste Management Challenge

The waste of plastic beverage bottles creates environmental problems and takes up a large volume of landfill space. The high rate of consumption of plastics in the State of Florida is challenging the disposal capacity of waste authorities. The lack of the reverse vending machines in the State of Florida, including applicable scientific or technical literature represented an opportunity for this research to discuss the applicability of this equipment as a potential solution for the management of the plastic waste in Florida. With this research document, I will propose a recycling system for plastic bottles made with PET based on the implementation of reverse vending machines, stressing the importance of the creation of policies that promote recycling and public participation.