Tools for participatory and activist cartography

Thesis (S.M.)--Massachusetts Institute of Technology, School of Architecture and Planning, Program in Media Arts and Sciences, 2010.Cataloged from PDF version of thesis.Includes bibliographical references (p. 109-113).Geospatial tools and information play an important role in urban planning and policymaking, and maps have diverse uses in legal, environmental, political, land rights, and social arenas. Widespread participation in mapmaking and access to its benefits is limited by obscure and expensive tools and techniques. This has resulted in poor or nonexistent maps for much of the world's population, especially in areas of urban poverty. In particular, public access to recent and high-resolution satellite imagery is largely controlled by government and large industry. This thesis proposes balloon and kite aerial photography as a low-cost and easy to learn means to collect aerial imagery for mapping, and introduces a novel open-source online tool for orthorectifying and compositing images into maps. A series of case studies where such tools and techniques were used by communities and activists in Lima, Peru and during the 2010 BP oil spill highlight the empowering role broader participation in cartography can play in advocacy, and the potential for increased cartographic literacy to level the playing field in territorial self-determination for small communities. Compared to other efforts to democratize mapmaking, which focus primarily on the presentation and interpretation of existing map data, this project emphasizes participation in the creation of new data at its source - direct imaging of the earth's surface. Accompanying educational materials and workshops with adults and youth, as well as an active online community of participants, have ensured wide adoption of Grassroots Mapping practices.by Jeffrey Yoo Warren.S.M

The Large Scale Bias of Dark Matter Halos: Numerical Calibration and Model Tests

We measure the clustering of dark matter halos in a large set of collisionless cosmological simulations of the flat LCDM cosmology. Halos are identified using the spherical overdensity algorithm, which finds the mass around isolated peaks in the density field such that the mean density is Delta times the background. We calibrate fitting functions for the large scale bias that are adaptable to any value of Delta we examine. We find a ~6% scatter about our best fit bias relation. Our fitting functions couple to the halo mass functions of Tinker et. al. (2008) such that bias of all dark matter is normalized to unity. We demonstrate that the bias of massive, rare halos is higher than that predicted in the modified ellipsoidal collapse model of Sheth, Mo, & Tormen (2001), and approaches the predictions of the spherical collapse model for the rarest halos. Halo bias results based on friends-of-friends halos identified with linking length 0.2 are systematically lower than for halos with the canonical Delta=200 overdensity by ~10%. In contrast to our previous results on the mass function, we find that the universal bias function evolves very weakly with redshift, if at all. We use our numerical results, both for the mass function and the bias relation, to test the peak-background split model for halo bias. We find that the peak-background split achieves a reasonable agreement with the numerical results, but ~20% residuals remain, both at high and low masses.Comment: 11 pages, submitted to ApJ, revised to include referee's coment

Sex differences in infant vocalization and the origin of language

Seeking to discern the earliest sex differences in language-related activities, our focus is vocal activity in the first two years of life, following up on recent research that unexpectedly showed boys produced significantly more speech-like vocalizations (protophones) than girls during the first year of life.We now bring a much larger body of data to bear on the comparison of early sex differences in vocalization, data based on automated analysis of all-day recordings of infants in their homes. The new evidence, like that of the prior study, also suggests boys produce more protophones than girls in the first year and offers additional basis for informed speculation about biological reasons for these differences. More broadly, the work offers a basis for informed speculations about foundations of language that we propose to have evolved in our distant hominin ancestors, foundations also required in early vocal development of modern human infants

Extending Recovery of the Primordial Matter Power Spectrum

The shape of the primordial matter power spectrum Plin(k) encodes critical information on cosmological parameters. At large scales, the observable galaxy power spectrum Pobs(k) is expected to follow the shape of Plin(k), but on smaller scales the effects of nonlinearity and galaxy bias make the ratio Pobs(k)/Plin(k) scale-dependent. We develop a method that can extend the dynamic range of the Plin(k) recovery by incorporating constraints on the galaxy halo occupation distribution (HOD) from the projected galaxy correlation function wp. We devise an analytic model to calculate Pobs(k) in real-space and redshift-space. Once HOD parameters are determined by matching wp for a given cosmological model, galaxy bias is completely specified, and our analytic model predicts both the shape and normalization of Pobs(k). Applying our method to SDSS main galaxy samples, we find that the real-space Pobs(k) follows the shape of the nonlinear matter power spectrum at the 1-2% level up to k=0.2 h/Mpc. When we apply our method to SDSS LRG samples, the linear bias approximation is accurate to 5% at k<0.08 h/Mpc, but the scale-dependence of LRG bias prevents the use of linear theory at k>0.08 h/Mpc. Our HOD model prediction is in good agreement with the recent SDSS LRG Pobs(k) measurements at all measured scales (k<0.2 h/Mpc), naturally explaining the shape of Pobs(k). The "Q-model" prescription is a poor description of galaxy bias for the LRG samples, and it can lead to biased cosmological parameter estimates when measurements at k>0.1 h/Mpc are included in the analysis. We quantify the potential bias and constraints on cosmological parameters that arise from applying linear theory and Q-model fitting, and we demonstrate the utility of HOD modeling of future high precision measurements of Pobs(k) on quasi-linear scales.Comment: 19 pages, 15 figures, submitted to The Astrophysical Journa

Finite element modeling and in vivo analysis of electrode configurations for selective stimulation of pudendal afferent fibers

<p>Abstract</p> <p>Background</p> <p>Intraurethral electrical stimulation (IES) of pudendal afferent nerve fibers can evoke both excitatory and inhibitory bladder reflexes in cats. These pudendovesical reflexes are a potential substrate for restoring bladder function in persons with spinal cord injury or other neurological disorders. However, the complex distribution of pudendal afferent fibers along the lower urinary tract presents a challenge when trying to determine the optimal geometry and position of IES electrodes for evoking these reflexes. This study aimed to determine the optimal intraurethral electrode configuration(s) and locations for selectively activating targeted pudendal afferents to aid future preclinical and clinical investigations.</p> <p>Methods</p> <p>A finite element model (FEM) of the male cat urethra and surrounding structures was generated to simulate IES with a variety of electrode configurations and locations. The activating functions (AFs) along pudendal afferent branches innervating the cat urethra were determined. Additionally, the thresholds for activation of pudendal afferent branches were measured in α-chloralose anesthetized cats.</p> <p>Results</p> <p>Maximum AFs evoked by intraurethral stimulation in the FEM and in vivo threshold intensities were dependent on stimulation location and electrode configuration.</p> <p>Conclusions</p> <p>A ring electrode configuration is ideal for IES. Stimulation near the urethral meatus or prostate can activate the pudendal afferent fibers at the lowest intensities, and allowed selective activation of the dorsal penile nerve or cranial sensory nerve, respectively. Electrode location was a more important factor than electrode configuration for determining stimulation threshold intensity and nerve selectivity.</p

Cosmological Constraints from Galaxy Clustering and the Mass-to-Number Ratio of Galaxy Clusters

We place constraints on the average density (Omega_m) and clustering amplitude (sigma_8) of matter using a combination of two measurements from the Sloan Digital Sky Survey: the galaxy two-point correlation function, w_p, and the mass-to-galaxy-number ratio within galaxy clusters, M/N, analogous to cluster M/L ratios. Our w_p measurements are obtained from DR7 while the sample of clusters is the maxBCG sample, with cluster masses derived from weak gravitational lensing. We construct non-linear galaxy bias models using the Halo Occupation Distribution (HOD) to fit both w_p and M/N for different cosmological parameters. HOD models that match the same two-point clustering predict different numbers of galaxies in massive halos when Omega_m or sigma_8 is varied, thereby breaking the degeneracy between cosmology and bias. We demonstrate that this technique yields constraints that are consistent and competitive with current results from cluster abundance studies, even though this technique does not use abundance information. Using w_p and M/N alone, we find Omega_m^0.5*sigma_8=0.465+/-0.026, with individual constraints of Omega_m=0.29+/-0.03 and sigma_8=0.85+/-0.06. Combined with current CMB data, these constraints are Omega_m=0.290+/-0.016 and sigma_8=0.826+/-0.020. All errors are 1-sigma. The systematic uncertainties that the M/N technique are most sensitive to are the amplitude of the bias function of dark matter halos and the possibility of redshift evolution between the SDSS Main sample and the maxBCG sample. Our derived constraints are insensitive to the current level of uncertainties in the halo mass function and in the mass-richness relation of clusters and its scatter, making the M/N technique complementary to cluster abundances as a method for constraining cosmology with future galaxy surveys.Comment: 23 pages, submitted to Ap

Constraining primordial non-Gaussianity with future galaxy surveys

We study the constraining power on primordial non-Gaussianity of future surveys of the large-scale structure of the Universe for both near-term surveys (such as the Dark Energy Survey - DES) as well as longer term projects such as Euclid and WFIRST. Specifically we perform a Fisher matrix analysis forecast for such surveys, using DES-like and Euclid-like configurations as examples, and take account of any expected photometric and spectroscopic data. We focus on two-point statistics and we consider three observables: the 3D galaxy power spectrum in redshift space, the angular galaxy power spectrum, and the projected weak-lensing shear power spectrum. We study the effects of adding a few extra parameters to the basic LCDM set. We include the two standard parameters to model the current value for the dark energy equation of state and its time derivative, w_0, w_a, and we account for the possibility of primordial non-Gaussianity of the local, equilateral and orthogonal types, of parameter fNL and, optionally, of spectral index n_fNL. We present forecasted constraints on these parameters using the different observational probes. We show that accounting for models that include primordial non-Gaussianity does not degrade the constraint on the standard LCDM set nor on the dark-energy equation of state. By combining the weak lensing data and the information on projected galaxy clustering, consistently including all two-point functions and their covariance, we find forecasted marginalised errors sigma (fNL) ~ 3, sigma (n_fNL) ~ 0.12 from a Euclid-like survey for the local shape of primordial non-Gaussianity, while the orthogonal and equilateral constraints are weakened for the galaxy clustering case, due to the weaker scale-dependence of the bias. In the lensing case, the constraints remain instead similar in all configurations.Comment: 20 pages, 10 Figures. Minor modifications; accepted by MNRA

Structure-based Ligand Design of Novel Human Toll-like Receptor 8 Agonists

This is the peer reviewed version of the following article: Kokatla, H. P., Sil, D., Tanji, H., Ohto, U., Malladi, S. S., Fox, L. M., … David, S. A. (2014). Structure-based Ligand Design of Novel Human Toll-like Receptor 8 Agonists. ChemMedChem, 9(4), 719–723. http://doi.org/10.1002/cmdc.201300573, which has been published in final form at doi.org/10.1002/cmdc.201300573. This article may be used for non-commercial purposes in accordance with Wiley Terms and Conditions for Self-Archiving.Toll-like receptor (TLR)-8 agonists activate adaptive immune responses by inducing robust production of T helper 1-polarizing cytokines, suggesting that TLR8-active compounds may be promising candidate adjuvants. We recently reported pure TLR8 agonistic activity in a C2-butyl furo[2,3-c]quinoline. We have obtained the structure of human TLR8 ectodomain co-crystallized with the furoquinoline compound, which indicates ligand-induced reorganization of the binding pocket of TLR8. The loss of a key H-bond between the oxygen atom of the furanyl ring of the agonist and Thr574 in TLR8 suggested that the furan ring was dispensable. We employed a disconnection strategy and examined 3- and 4-substituted aminoquinolines. Focused structure-based ligand design studies led to the identification of 3-pentyl-quinoline-2-amine as a novel, structurally simple, and highly potent human TLR8-specific agonist