Extracting chemical structure from printed diagrams

Thesis (M. Eng.)--Massachusetts Institute of Technology, Dept. of Electrical Engineering and Computer Science, 2009.Cataloged from PDF version of thesis.Includes bibliographical references (p. 117-118).Over the years, a vast amount of literature in the field of chemistry has accumulated, and searching for documents about specific molecules is a formidable task. To the extent that the literature is textual, services like Google enable relatively easy search. While search indexes like Google are very good at finding such things, its difficult to describe molecules completely using text because text can't easily indicate molecular structure, and molecular structure defines chemical properties. ChemWARD is a system that extracts the molecular structure from the printed diagrams that are ubiquitous in chemistry literature and converts them to a machine readable format in order to allow chemists to search the literature by drawing a molecular structure instead of typing a chemical formula. We describe the architecture of the system and report on its performance, demonstrating its ability to achieve an overall accuracy rate of 85.5% on printed diagrams extracted from published chemical literature.by Angelique Moscicki.M.Eng

Spatiotemporal predictions of soil properties and states in variably saturated landscapes

Understanding greenhouse gas (GHG) fluxes from landscapes with variably saturated soil conditions is challenging given the highly dynamic nature of GHG fluxes in both space and time, dubbed hot spots, and hot moments. On one hand, our ability to directly monitor these processes is limited by sparse in situ and surface chamber observational networks. On the other hand, remote sensing approaches provide spatial data sets but are limited by infrequent imaging over time. We use a robust statistical framework to merge sparse sensor network observations with reconnaissance style hydrogeophysical mapping at a well‐characterized site in Ohio. We find that combining time‐lapse electromagnetic induction surveys with empirical orthogonal functions provides additional environmental covariates related to soil properties and states at high spatial resolutions (~5 m). A cross‐validation experiment using eight different spatial interpolation methods versus 120 in situ soil cores indicated an ~30% reduction in root‐mean‐square error for soil properties (clay weight percent and total soil carbon weight percent) using hydrogeophysical derived environmental covariates with regression kriging. In addition, the hydrogeophysical derived environmental covariates were found to be good predictors of soil states (soil temperature, soil water content, and soil oxygen). The presented framework allows for temporal gap filling of individual sensor data sets as well as provides flexible geometric interpolation to complex areas/volumes. We anticipate that the framework, with its flexible temporal and spatial monitoring options, will be useful in designing future monitoring networks as well as support the next generation of hyper‐resolution hydrologic and biogeochemical models

Multicharged Carbon Ion Generation from Laser Plasma

Carbon ions generated by ablation of a carbon target using an Nd:YAG laser pulse (wavelength λ = 1064 nm, pulse width τ = 7 ns, and laser fluence of 10-110 J cm-2) are characterized. Time-of-flight analyzer, a three-mesh retarding field analyzer, and an electrostatic ion energy analyzer are used to study the charge and energy of carbon ions generated by laser ablation. The dependencies of the ion signal on the laser fluence, laser focal point position relative to target surface, and the acceleration voltage are described. Up to C4+ ions are observed. When no acceleration voltage is applied between the carbon target and a grounded mesh in front of the target, ion energies up to ∼400 eV/charge are observed. The time-of-flight signal is analyzed for different retarding field voltages in order to obtain the ion kinetic energy distribution. The ablation and Coulomb energies developed in the laser plasma are obtained from deconvolution of the ion time-of-flight signal. Deconvolution of the time-of-flight ion signal to resolve the contribution of each ion charge is accomplished using data from a retarding field analysis combined with the time-of-flight signal. The ion energy and charge state increase with the laser fluence. The position of the laser focal spot affects the ion generation, with focusing ∼1.9 mm in front of the target surface yielding maximum ions. When an external electric field is applied in an ion drift region between the target and a grounded mesh parallel to the target, fast ions are extracted and separated, in time, due to increased acceleration with charge state. Published by AIP Publishing. [http://dx.doi.org/10.1063/1.4966987

Prevalence of human papillomavirus antibodies in young female subjects in England

Sera from 1483 female subjects in England aged 10–29 years were tested. The age-standardised seroprevalence was 10.7% (95% confidence intervals 9.0–12.3) for human papillomavirus (HPV) 6, 2.7% (1.8–3.6) for HPV 11, 11.9% (10.2–13.6) for HPV 16, 4.7% (3.5–5.8) for HPV 18, and 20.7% (18.6–22.7) for any of the four types

Low grade squamous intra-epithelial lesions and human papillomavirus infection in Colombian women

Low grade squamous intra-epithelial lesions could be considered as a manifestation of human papillomavirus exposition, however the discrepancy between rates of infection with human papillomavirus and development of low grade squamous intra-epithelial lesions is notable. Here we report a cross-sectional three-armed case–control study in the Colombian population, to compare the risk factors of women with low grade squamous intra-epithelial lesions with that of human papillomavirus DNA-negative and positive women with normal cytology

First observation of Bs -> D_{s2}^{*+} X mu nu decays

Using data collected with the LHCb detector in proton-proton collisions at a centre-of-mass energy of 7 TeV, the semileptonic decays Bs -> Ds+ X mu nu and Bs -> D0 K+ X mu nu are detected. Two structures are observed in the D0 K+ mass spectrum at masses consistent with the known D^+_{s1}(2536) and $D^{*+}_{s2}(2573) mesons. The measured branching fractions relative to the total Bs semileptonic rate are B(Bs -> D_{s2}^{*+} X mu nu)/B(Bs -> X mu nu)= (3.3\pm 1.0\pm 0.4)%, and B(Bs -> D_{s1}^+ X munu)/B(Bs -> X mu nu)= (5.4\pm 1.2\pm 0.5)%, where the first uncertainty is statistical and the second is systematic. This is the first observation of the D_{s2}^{*+} state in Bs decays; we also measure its mass and width.Comment: 8 pages 2 figures. Published in Physics Letters

Population-based prevalence of cervical infection with human papillomavirus genotypes 16 and 18 and other high risk types in Tlaxcala, Mexico

This study was supported by the National Institute of Public Health of Mexico, the Coordinación de Investigación en Salud del Instituto Mexicano del Seguro Social, the Secretaría de Salud Tlaxcala, the Instituto Nacional de las Mujeres, and the Consejo Nacional de Ciencia y Tecnología [FOSISS 2013 202468]. Additional support has been provided by Roche Diagnostics, BD Diagnostics, DICIPA and Arbor Vita Corporation. The study sponsors did not played a role in designing the study, collecting, analyzing or interpreting the data, writing the report, or submitting this paper for publication. UC Berkeley Center for Global Public Health, Schoeneman Grant, Joint Medical Program Thesis Grant, and Cancer Research UK (C569/A10404)