Parameter Estimation and Uncertainty Quantication for an Epidemic Model

We examine estimation of the parameters of Susceptible-Infective-Recovered (SIR) models in the context of least squares. We review the use of asymptotic statistical theory and sensitivity analysis to obtain measures of uncertainty for estimates of the model parameters and the basic reproductive number (R0 )—an epidemiologically significant parameter grouping. We find that estimates of different parameters, such as the transmission parameter and recovery rate, are correlated, with the magnitude and sign of this correlation depending on the value of R0. Situations are highlighted in which this correlation allows R0 to be estimated with greater ease than its constituent parameters. Implications of correlation for parameter identifiability are discussed. Uncertainty estimates and sensitivity analysis are used to investigate how the frequency at which data is sampled affects the estimation process and how the accuracy and uncertainty of estimates improves as data is collected over the course of an outbreak. We assess the informativeness of individual data points in a given time series to determine when more frequent sampling (if possible) would prove to be most beneficial to the estimation process. This technique can be used to design data sampling schemes in more general contexts

Laboratory Testing of Railroad Flatcars for Use as Highway Bridges on Low-Volume Roads to Determine Ultimate Strength and Redundancy

Railroad flatcars (RRFCs) are a convenient option to replace existing deteriorating bridge structures on low-volume roads. They are typically used as the bridge superstructure by placing two or more flatcars side-by-side to achieve the desired bridge width. Utilizing RRFCs as a bridge allows for rapid construction and greater cost savings compared to traditional practices. These benefits make them an attractive solution for rural communities in Indiana, as well as other states. Uncertainty remains about the response under higher loads than could be easily achieved in the field and the level of redundancy of railroad flatcar bridges. Using RRFCs as bridges becomes less economical for counties if they do not display adequate load-path redundancy and are labeled “fracture critical.” If labeled as such, life-cycle costs would rise due to the requirement of an arms-length inspection for each 24 month inspection period. Laboratory testing of a RRFC bridge with two flatcars placed side-by-side allowed for experimental testing under higher loads, as well as increased amounts of instrumentation to better understand the behavior of the RRFCs. As a result of the experimental data, load rating guidelines were developed for RRFC bridges constructed with a fully composite concrete deck. The research also focused on the level of system redundancy in a RRFC bridge after failure of one of the two main box girders. Procedures were developed to estimate whether the remaining longitudinal members provide sufficient available capacity to carry traffic loads

Reproduction and Dispersal of Biological Soil Crust Organisms

Biological soil crusts (BSCs) consist of a diverse and highly integrated community of organisms that effectively colonize and collectively stabilize soil surfaces. BSCs vary in terms of soil chemistry and texture as well as the environmental parameters that combine to support unique combinations of organisms—including cyanobacteria dominated, lichen-dominated, and bryophyte-dominated crusts. The list of organismal groups that make up BSC communities in various and unique combinations include—free living, lichenized, and mycorrhizal fungi, chemoheterotrophic bacteria, cyanobacteria, diazotrophic bacteria and archaea, eukaryotic algae, and bryophytes. The various BSC organismal groups demonstrate several common characteristics including—desiccation and extreme temperature tolerance, production of various soil binding chemistries, a near exclusive dependency on asexual reproduction, a pattern of aerial dispersal over impressive distances, and a universal vulnerability to a wide range of human-related perturbations. With this publication, we provide literature-based insights as to how each organismal group contributes to the formation and maintenance of the structural and functional attributes of BSCs, how they reproduce, and how they are dispersed. We also emphasize the importance of effective application of molecular and microenvironment sampling and assessment tools in order to provide cogent and essential answers that will allow scientists and land managers to better understand and manage the biodiversity and functional relationships of soil crust communities

Loss of Spin Entanglement For Accelerated Electrons in Electric and Magnetic Fields

Using an open quantum system we calculate the time dependence of the concurrence between two maximally entangled electron spins with one accelerated uniformly in the presence of a constant magnetic field and the other at rest and isolated from fields. We find at high Rindler temperature the proper time for the entanglement to be extinguished is proportional to the inverse of the acceleration cubed.Comment: 10 pages, 4 figures, appendix and other discussion added, fixed some typographical errors and some references were correcte

Band Gap Engineering with Ultralarge Biaxial Strains in Suspended Monolayer MoS2

We demonstrate the continuous and reversible tuning of the optical band gap of suspended monolayer MoS2 membranes by as much as 500 meV by applying very large biaxial strains. By using chemical vapor deposition (CVD) to grow crystals that are highly impermeable to gas, we are able to apply a pressure difference across suspended membranes to induce biaxial strains. We observe the effect of strain on the energy and intensity of the peaks in the photoluminescence (PL) spectrum, and find a linear tuning rate of the optical band gap of 99 meV/%. This method is then used to study the PL spectra of bilayer and trilayer devices under strain, and to find the shift rates and Gr\"uneisen parameters of two Raman modes in monolayer MoS2. Finally, we use this result to show that we can apply biaxial strains as large as 5.6% across micron sized areas, and report evidence for the strain tuning of higher level optical transitions.Comment: Nano Lett., Article ASA

Metatranscriptome of human faecal microbial communities in a cohort of adult men

The gut microbiome is intimately related to human health, but it is not yet known which functional activities are driven by specific microorganisms\u27 ecological configurations or transcription. We report a large-scale investigation of 372 human faecal metatranscriptomes and 929 metagenomes from a subset of 308 men in the Health Professionals Follow-Up Study. We identified a metatranscriptomic \u27core\u27 universally transcribed over time and across participants, often by different microorganisms. In contrast to the housekeeping functions enriched in this core, a \u27variable\u27 metatranscriptome included specialized pathways that were differentially expressed both across participants and among microorganisms. Finally, longitudinal metagenomic profiles allowed ecological interaction network reconstruction, which remained stable over the six-month timespan, as did strain tracking within and between participants. These results provide an initial characterization of human faecal microbial ecology into core, subject-specific, microorganism-specific and temporally variable transcription, and they differentiate metagenomically versus metatranscriptomically informative aspects of the human faecal microbiome

Stability of the human faecal microbiome in a cohort of adult men

Characterizing the stability of the gut microbiome is important to exploit it as a therapeutic target and diagnostic biomarker. We metagenomically and metatranscriptomically sequenced the faecal microbiomes of 308 participants in the Health Professionals Follow-Up Study. Participants provided four stool samples—one pair collected 24–72 h apart and a second pair ~6 months later. Within-person taxonomic and functional variation was consistently lower than between-person variation over time. In contrast, metatranscriptomic profiles were comparably variable within and between subjects due to higher within-subject longitudinal variation. Metagenomic instability accounted for ~74% of corresponding metatranscriptomic instability. The rest was probably attributable to sources such as regulation. Among the pathways that were differentially regulated, most were consistently over- or under-transcribed at each time point. Together, these results suggest that a single measurement of the faecal microbiome can provide long-term information regarding organismal composition and functional potential, but repeated or short-term measures may be necessary for dynamic features identified by metatranscriptomics

Routine activities and proactive police activity: a macro-scale analysis of police searches in London and New York City

This paper explored how city-level changes in routine activities were associated with changes in frequencies of police searches using six years of police records from the London Metropolitan Police Service and the New York City Police Department. Routine activities were operationalised through selecting events that potentially impacted on (a) the street population, (b) the frequency of crime or (c) the level of police activity. OLS regression results indicated that routine activity variables (e.g. day of the week, periods of high demand for police service) can explain a large proportion of the variance in search frequency throughout the year. A complex set of results emerged, revealing cross-national dissimilarities and the differential impact of certain activities (e.g. public holidays). Importantly, temporal frequencies in searches are not reducible to associations between searches and recorded street crime, nor changes in on-street population. Based on the routine activity approach, a theoretical police-action model is proposed

CAHM, a long non-coding RNA gene hypermethylated in colorectal neoplasia

Copyright © 2014 Landes Bioscience This is an open-access article licensed under a Creative Commons Attribution 3.0 Unported License. The article may be redistributed, reproduced, and reused for non-commercial purposes, provided the original source is properly cited. Permission is granted subject to the terms of the License under which the work was published. Please check the License conditions for the work which you wish to reuse. Full and appropriate attribution must be given. This permission does not cover any third party copyrighted material which may appear in the work requested.The CAHM gene (Colorectal Adenocarcinoma HyperMethylated), previously LOC 100526820, is located on chromosome 6, hg19 chr6:163 834 097–163 834 982. It lacks introns, encodes a long non-coding RNA (lncRNA) and is located adjacent to the gene QKI, which encodes an RNA binding protein. Deep bisulphite sequencing of ten colorectal cancer (CRC ) and matched normal tissues demonstrated frequent hypermethylation within the CAHM gene in cancer. A quantitative methylation-specific PCR (qMSP ) was used to characterize additional tissue samples. With a threshold of 5% methylation, the CAHM assay was positive in 2/26 normal colorectal tissues (8%), 17/21 adenomas (81%), and 56/79 CRC samples (71%). A reverse transcriptase-qPCR assay showed that CAHM RNA levels correlated negatively with CAHM % methylation, and therefore CAHM gene expression is typically decreased in CRC . The CAHM qMSP assay was applied to DNA isolated from plasma specimens from 220 colonoscopy-examined patients. Using a threshold of 3 pg methylated genomic DNA per mL plasma, methylated CAHM sequences were detected in the plasma DNA of 40/73 (55%) of CRC patients compared with 3/73 (4%) from subjects with adenomas and 5/74 (7%) from subjects without neoplasia. Both the frequency of detection and the amount of methylated CAHM DNA released into plasma increased with increasing cancer stage. Methylated CAHM DNA shows promise as a plasma biomarker for use in screening for CRC