Predictive Modeling of Cholera Outbreaks in Bangladesh

Despite seasonal cholera outbreaks in Bangladesh, little is known about the relationship between environmental conditions and cholera cases. We seek to develop a predictive model for cholera outbreaks in Bangladesh based on environmental predictors. To do this, we estimate the contribution of environmental variables, such as water depth and water temperature, to cholera outbreaks in the context of a disease transmission model. We implement a method which simultaneously accounts for disease dynamics and environmental variables in a Susceptible-Infected-Recovered-Susceptible (SIRS) model. The entire system is treated as a continuous-time hidden Markov model, where the hidden Markov states are the numbers of people who are susceptible, infected, or recovered at each time point, and the observed states are the numbers of cholera cases reported. We use a Bayesian framework to fit this hidden SIRS model, implementing particle Markov chain Monte Carlo methods to sample from the posterior distribution of the environmental and transmission parameters given the observed data. We test this method using both simulation and data from Mathbaria, Bangladesh. Parameter estimates are used to make short-term predictions that capture the formation and decline of epidemic peaks. We demonstrate that our model can successfully predict an increase in the number of infected individuals in the population weeks before the observed number of cholera cases increases, which could allow for early notification of an epidemic and timely allocation of resources.Comment: 43 pages, including appendices, 5 figures, 1 table in the main tex

Seismicity induced during the development of the Rittershoffen geothermal field, France

The development of the Rittershoffen deep geothermal field (Alsace, Upper Rhine Graben) between 2012 and 2014 induced unfelt seismicity with a local magnitude of less than 1.6. This seismicity occurred during two types of operations: (1) mud losses in the Muschelkalk formation during the drilling of both wells of the doublet and (2) thermal and hydraulic stimulations of the GRT-1 well. Seismicity was also observed 4 days after the main hydraulic stimulation, although no specific operation was performed. During chemical stimulation, however, no induced seismicity was detected. In the context of all field development operations and their injection parameters (flow rates, overpressures, volumes), we detail the occurrence or lack of seismicity, its magnitude distribution and its spatial distribution. The observations suggest the presence of the rock stress memory effect (Kaiser effect) of the geothermal reservoir as well as uncritically stressed zones connected to the GRT-1 well and/or rock cohesion. A reduction of the seismic rate concurrent with an increase of injectivity was noticed as well as the reactivation of a couple of faults, including the Rittershoffen fault, which was targeted by the wells. These results are derived from the homogeneous and consistent catalogue of more than 1300 local earthquakes that is provided. This reference catalogue is based on a standard detection method, whose output was manually verified and improved. The given absolute locations have been computed in a calibrated, geologically realistic 3D velocity model. Our work builds on previous analyses addressing the seismicity induced by the GRT-1 hydraulic stimulation and places the results into a historical context, thus considering the full dynamics of the observed phenomena. This paper also complements existing descriptions of the hydrothermal characteristics of the deep reservoir by providing insights separate from the wells

Modelling the direct effect of aerosols in the solar near-infrared on a planetary scale

International audienceWe used a spectral radiative transfer model to compute the direct radiative effect (DRE) of natural plus anthropogenic aerosols in the solar near-infrared (IR), between 0.85?10 ?m, namely, their effect on the outgoing near-IR radiation at the top of atmosphere (TOA, ?FTOA), on the atmospheric absorption of near-IR radiation (?Fatmab) and on the surface downward and absorbed near-IR radiation (?Fsurf, and ?Fsurfnet, respectively). The computations were performed on a global scale (over land and ocean) under all-sky conditions, using detailed spectral aerosol optical properties taken from the Global Aerosol Data Set (GADS) supplemented by realistic data for the rest of surface and atmospheric parameters. The computed aerosol DRE, averaged over the 12-year period 1984?1995 for January and July, shows that on a global mean basis aerosols produce a planetary cooling by increasing the scattered near-IR radiation back to space by 0.48 W m?2, they warm the atmosphere by 0.37 W m?2 and cool the surface by decreasing the downward and absorbed near-IR radiation at surface by 1.03 and 0.85 W m?2, respectively. The magnitude of the near-IR aerosol DRE is smaller than that of the combined ultraviolet (UV) and visible DRE, but it is still energetically important, since it contributes to the total shortwave (SW) DRE by 22?31%. The aerosol-produced near-IR surface cooling combined with the atmospheric warming, may affect the thermal dynamics of the Earth-atmosphere system, by increasing the atmospheric stability, decreasing thus cloud formation, and precipitation, especially over desertification threatened regions such as the Mediterranean basin. This, together with the fact that the sign of near-IR aerosol DRE is sometimes opposite to that of UV-visible DRE, demonstrates the importance of performing detailed spectral computations to provide estimates of the climatic role of aerosols for the Earth-atmosphere system. This was demonstrated by sensitivity tests revealing very large differences (up to 300%) between aerosol DREs computed using detailed spectral and spectrally-averaged aerosol optical properties. Our model results indicate thus that the aerosol direct radiative effect on the near-IR radiation is very sensitive to the treatment of the spectral dependence of aerosol optical properties and solar radiation

The direct effect of aerosols on solar radiation based on satellite observations, reanalysis datasets, and spectral aerosol optical properties from Global Aerosol Data Set (GADS)

International audienceA global estimate of the seasonal direct radiative effect (DRE) of natural plus anthropogenic aerosols on solar radiation under all-sky conditions is obtained by combining satellite measurements and reanalysis data with a spectral radiative transfer model and spectral aerosol optical properties taken from the Global Aerosol Data Set (GADS). The estimates are obtained with detailed spectral model computations separating the ultraviolet (UV), visible and near-infrared wavelengths. The global distribution of spectral aerosol optical properties was taken from GADS whereas data for clouds, water vapour, ozone, carbon dioxide, methane and surface albedo were taken from various satellite and reanalysis datasets. Using these aerosol properties and other related variables, we generate climatological (for the 12-year period 1984?1995) monthly mean aerosol DREs. The global annual mean DRE on the outgoing SW radiation at the top of atmosphere (TOA, ?FTOA) is ?1.62 W m?2 (with a range of ?15 to 10 W m?2, negative values corresponding to planetary cooling), the effect on the atmospheric absorption of SW radiation (?Fatmab) is 1.6 W m?2 (values up to 35 W m?2, corresponding to atmospheric warming), and the effect on the surface downward and absorbed SW radiation (?Fsurf, and ?Fsurfnet, respectively) is ?3.93 and ?3.22 W m?2 (values up to ?45 and ?35 W m?2, respectively, corresponding to surface cooling). According to our results, aerosols decrease/increase the planetary albedo by ?3 to 13% at the local scale, whereas on planetary scale the result is an increase of 1.5%. Aerosols can warm locally the atmosphere by up to 0.98 K day?1, whereas they can cool the Earth's surface by up to ?2.9 K day?1. Both these effects, which can significantly modify atmospheric dynamics and the hydrological cycle, can produce significant planetary cooling on a regional scale, although planetary warming can arise over highly reflecting surfaces. The aerosol DRE at the Earth's surface compared to TOA can be up to 15 times larger at the local scale. The largest aerosol DRE takes place in the northern hemisphere both at the surface and the atmosphere, arising mainly at ultraviolet and visible wavelengths

Modelling the direct effect of aerosols in the solar near-infrared on a planetary scale

International audienceWe used a spectral radiative transfer model to compute the direct radiative effect (DRE) of natural plus anthropogenic aerosols in the solar near-infrared (IR), between 0.85?10 µm, namely, their effect on the outgoing near-IR radiation at the top of atmosphere (TOA, ?FTOA), on the atmospheric absorption of near-IR radiation (?Fatmab) and on the surface downward and absorbed near-IR radiation (?Fsurf, and ?Fsurfnet, respectively). The computations were performed on a global scale (over land and ocean) under all-sky conditions, using spectral aerosol optical properties taken from the Global Aerosol Data Set (GADS) supplemented by realistic data for the rest of surface and atmospheric parameters. The computed aerosol DRE, averaged over the 12-year period 1984?1995 for January and July, shows that aerosols produce a planetary cooling by increasing the scattered near-IR radiation back to space (by up to 6 Wm?2), they warm the atmosphere (by up to 7 Wm?2) and cool the surface (by up to 12 Wm?2). However, they can also slightly warm the Earth-atmosphere system or cool the atmosphere (by less than 1 Wm?2) over limited areas. The magnitude of the near-IR aerosol DRE is smaller than that of the combined ultraviolet (UV) and visible DRE, but it is still energetically important, since it contributes to the total shortwave (SW) DRE by 22?31%. On a global mean basis, the DREs ?FTOA, ?Fatmab, ?Fsurf, and ?Fsurfnet are equal to about 0.48, 0.37, ?1.03 and ?0.85 Wm?2, i.e. their magnitude is similar to that of climate forcing associated with increasing concentrations of greenhouse gases. The aerosol induced near-IR surface cooling combined with the atmospheric warming, affects the thermal dynamics of the Earth-atmosphere system, by increasing the atmospheric stability, decreasing thus cloud formation, and precipitation, especially over desertification threatened regions such as the Mediterranean basin. This, together with the fact that the sign of near-IR aerosol DRE is sometimes opposite to that of UV-visible DRE, demonstrates the importance of performing detailed spectral computations to provide estimates of the climatic role of aerosols for the Earth-atmosphere system

Utilizing multimodal microscopy to reconstruct Si/SiGe interfacial atomic disorder and infer its impacts on qubit variability

SiGe heteroepitaxial growth yields pristine host material for quantum dot qubits, but residual interface disorder can lead to qubit-to-qubit variability that might pose an obstacle to reliable SiGe-based quantum computing. We demonstrate a technique to reconstruct 3D interfacial atomic structure spanning multiqubit areas by combining data from two verifiably atomic-resolution microscopy techniques. Utilizing scanning tunneling microscopy (STM) to track molecular beam epitaxy (MBE) growth, we image surface atomic structure following deposition of each heterostructure layer revealing nanosized SiGe undulations, disordered strained-Si atomic steps, and nonconformal uncorrelated roughness between interfaces. Since phenomena such as atomic intermixing during subsequent overgrowth inevitably modify interfaces, we measure post-growth structure via cross-sectional high-angle annular dark field scanning transmission electron microscopy (HAADF-STEM). Features such as nanosized roughness remain intact, but atomic step structure is indiscernible in $1.0\pm 0.4$~nm-wide intermixing at interfaces. Convolving STM and HAADF-STEM data yields 3D structures capturing interface roughness and intermixing. We utilize the structures in an atomistic multivalley effective mass theory to quantify qubit spectral variability. The results indicate (1) appreciable valley splitting (VS) variability of roughly $\pm$ $50\%$ owing to alloy disorder, and (2) roughness-induced double-dot detuning bias energy variability of order $1-10$ meV depending on well thickness. For measured intermixing, atomic steps have negligible influence on VS, and uncorrelated roughness causes spatially fluctuating energy biases in double-dot detunings potentially incorrectly attributed to charge disorder.Comment: 12 pages, 6 figure

Ensemble learning frameworks for the discovery of multi-component quantitative models in biomedical applications

Abstrac

Proteasomes generate spliced epitopes by two different mechanisms and as efficiently as non-spliced epitopes

Proteasome-catalyzed peptide splicing represents an additional catalytic activity of proteasomes contributing to the pool of MHC-class I-presented epitopes. We here biochemically and functionally characterized a new melanoma gp100 derived spliced epitope. We demonstrate that the gp100mel47–52/40–42 antigenic peptide is generated in vitro and in cellulo by a not yet described proteasomal condensation reaction. gp100mel47–52/40–42 generation is enhanced in the presence of the β5i/LMP7 proteasome-subunit and elicits a peptide- specific CD8+ T cell response. Importantly, we demonstrate that different gp100mel-derived spliced epitopes are generated and presented to CD8+ T cells with efficacies comparable to non-spliced canonical tumor epitopes and that gp100mel-derived spliced epitopes trigger activation of CD8+ T cells found in peripheral blood of half of the melanoma patients tested. Our data suggest that both transpeptidation and condensation reactions contribute to the frequent generation of spliced epitopes also in vivo and that their immune relevance may be comparable to non-spliced epitopes

Excitons in a Photosynthetic Light-Harvesting System: A Combined Molecular Dynamics/Quantum Chemistry and Polaron Model Study

The dynamics of pigment-pigment and pigment-protein interactions in light-harvesting complexes is studied with a novel approach which combines molecular dynamics (MD) simulations with quantum chemistry (QC) calculations. The MD simulations of an LH-II complex, solvated and embedded in a lipid bilayer at physiological conditions (with total system size of 87,055 atoms) revealed a pathway of a water molecule into the B800 binding site, as well as increased dimerization within the B850 BChl ring, as compared to the dimerization found for the crystal structure. The fluctuations of pigment (B850 BChl) excitation energies, as a function of time, were determined via ab initio QC calculations based on the geometries that emerged from the MD simulations. From the results of these calculations we constructed a time-dependent Hamiltonian of the B850 exciton system from which we determined the linear absorption spectrum. Finally, a polaron model is introduced to describe quantum mechanically both the excitonic and vibrational (phonon) degrees of freedom. The exciton-phonon coupling that enters into the polaron model, and the corresponding phonon spectral function are derived from the MD/QC simulations. It is demonstrated that, in the framework of the polaron model, the absorption spectrum of the B850 excitons can be calculated from the autocorrelation function of the excitation energies of individual BChls, which is readily available from the combined MD/QC simulations. The obtained result is in good agreement with the experimentally measured absorption spectrum.Comment: REVTeX3.1, 23 pages, 13 (EPS) figures included. A high quality PDF file of the paper is available at http://www.ks.uiuc.edu/Publications/Papers/PDF/DAMJ2001/DAMJ2001.pd

Radiative decay of a massive particle and the non-thermal process in primordial nucleosynthesis

We consider the effects on big bang nucleosynthesis (BBN) of the radiative decay of a long-lived massive particle. If high-energy photons are emitted after the BBN epoch ($t \sim 1 - 10^3$ sec), they may change the abundances of the light elements through photodissociation processes, which may result in a significant discrepancy between standard BBN and observation. Taking into account recent observational and theoretical developments in this field, we revise our previous study constraining the abundance of the radiatively-decaying particles. In particular, on the theoretical side, it was recently claimed that the non-thermal production of $^6$Li, which is caused by the photodissociation of \hefour, most severely constrains the abundance of the radiatively-decaying particle. We will see, however, it is premature to emphasize the importance of the non-thermal production of $^6$Li because (i) the theoretical computation of the $^6$Li abundance has large uncertainty due to the lack of the precise understanding of the $^6$Li production cross section, and (ii) the observational data of $^6$Li abundance has large errors.Comment: 15 pages, using REVTeX and 3 postscript figure