Stanford automatic photogrammetry research

A feasibility study on the problem of computer automated aerial/orbital photogrammetry is documented. The techniques investigated were based on correlation matching of small areas in digitized pairs of stereo images taken from high altitude or planetary orbit, with the objective of deriving a 3-dimensional model for the surface of a planet

Transcription factor target prediction using multiple short expression time series from Arabidopsis thaliana

BACKGROUND: The central role of transcription factors (TFs) in higher eukaryotes has led to much interest in deciphering transcriptional regulatory interactions. Even in the best case, experimental identification of TF target genes is error prone, and has been shown to be improved by considering additional forms of evidence such as expression data. Previous expression based methods have not explicitly tried to associate TFs with their targets and therefore largely ignored the treatment specific and time dependent nature of transcription regulation. RESULTS: In this study we introduce CERMT, Covariance based Extraction of Regulatory targets using Multiple Time series. Using simulated and real data we show that using multiple expression time series, selecting treatments in which the TF responds, allowing time shifts between TFs and their targets and using covariance to identify highly responding genes appear to be a good strategy. We applied our method to published TF - target gene relationships determined using expression profiling on TF mutants and show that in most cases we obtain significant target gene enrichment and in half of the cases this is sufficient to deliver a usable list of high-confidence target genes. CONCLUSION: CERMT could be immediately useful in refining possible target genes of candidate TFs using publicly available data, particularly for organisms lacking comprehensive TF binding data. In the future, we believe its incorporation with other forms of evidence may improve integrative genome-wide predictions of transcriptional networks

Entropy, Ergodicity and Stem Cell Multipotency

Populations of mammalian stem cells commonly exhibit considerable cell-cell variability. However, the functional role of this diversity is unclear. Here, we analyze expression fluctuations of the stem cell surface marker Sca1 in mouse hematopoietic progenitor cells using a simple stochastic model and find that the observed dynamics naturally lie close to a critical state, thereby producing a diverse population that is able to respond rapidly to environmental changes. We propose an information-theoretic interpretation of these results that views cellular multipotency as an instance of maximum entropy statistical inference.Comment: 6 pages, 3 figure

Quantum estimation of a damping constant

We discuss an interferometric approach to the estimation of quantum mechanical damping. We study specific classes of entangled and separable probe states consisting of superpositions of coherent states. Based on the assumption of limited quantum resources we show that entanglement improves the estimation of an unknown damping constant.Comment: 7 pages, 5 figure

Zirconium stable isotope analysis of zircon by MC-ICP-MS: Methods and application to evaluating intra-crystalline zonation in a zircon megacryst

Zirconium (Zr) plays a key role in the development of phases like zircon (ZrSiO₄) and baddeleyite (ZrO₂) in magmatic systems. These minerals are crucial for the study of geologic time and crustal evolution, and their high resistivity to weathering and erosion results in their preservation on timescales of billions of years. Although zircon and baddeleyite may also preserve a robust record of Zr isotope behavior in high-temperature terrestrial environments, little is known about the factors that control Zr isotope partitioning in magmatic systems, the petrogenetic significance of fractionated compositions, or how these variations are recorded in Zr-rich accessory phases. Here, we describe a new analytical protocol for accurately determining the Zr stable isotope composition of zircon by multicollector-inductively coupled plasma-mass spectrometry (MC-ICP-MS), using the double-spike method to correct for procedural and instrumental mass bias. We apply this technique to test whether zircon crystallization in carbonatite magmatic systems is a driver of Zr isotope fractionation by interrogating the internal zonation of a zircon megacryst from the Mud Tank carbonatite (MTUR1). We find the MTUR1 megacryst to lack internal zoning within analytical uncertainties with a mean μ⁹⁴/⁹⁰Zr_(NIST) = −55 ± 28 ppm (2 SD, n = 151), which suggests that zircon crystallization is not a driver of Zr isotope fractionation in carbonatite magmas. This observation is in stark contrast with those made in silicate magmatic systems, raising the possibility that the bonding environment of Zr⁴⁺ ions may be fundamentally different in carbonatite vs. silicate melts. Because of its remarkable homogeneity, the MTUR1 megacryst is an ideal natural reference material for Zr isotopic analysis of zircon using both solution and spatially resolved methods. The reproducibility of a pure Zr solution and our chemically purified zircon fractions indicate that the external reproducibility of our method is on the order of ±28 ppm for μ⁹⁴/⁹⁰Zr, or ±7 ppm per amu, at 95% confidence

Directed and elliptic flow in heavy ion collisions from Ebeam=90E_{\rm beam}=90 MeV/nucleon to Ec.m.=200E_{\rm c.m.}=200 GeV/nucleon

Recent data from the NA49 experiment on directed and elliptic flow for Pb+Pb reactions at CERN-SPS are compared to calculations with a hadron-string transport model, the Ultra-relativistic Quantum Molecular Dynamics (UrQMD) model. The rapidity and transverse momentum dependence of the directed and elliptic flow, i.e. $v_1$ and $v_2$, are investigated. The flow results are compared to data at three different centrality bins. Generally, a reasonable agreement between the data and the calculations is found. Furthermore, the energy excitation functions of $v_1$ and $v_2$ from $E_{\rm beam}=90A$ MeV to $E_{\rm cm}=200A$ GeV are explored within the UrQMD framework and discussed in the context of the available data. It is found that, in the energy regime below $E_{\rm beam}\leq 10A$ GeV, the inclusion of nuclear potentials is necessary to describe the data. Above $40A$ GeV beam energy, the UrQMD model starts to underestimate the elliptic flow. Around the same energy the slope of the rapidity spectra of the proton directed flow develops negative values. This effect is known as the third flow component ("antiflow") and cannot be reproduced by the transport model. These differences can possibly be explained by assuming a phase transition from hadron gas to quark gluon plasma at about $40A$ GeV.Comment: 19 pages, minor changes and modified title as published in PR

“I Don’t Think That’s Something I’ve Ever Thought About Really Before”: A Thematic Discursive Analysis of Lay People’s Talk about Legal Gender

© The Author(s) 2023. This is an open access article distributed under the Creative Commons Attribution License, to view a copy of the license, see: https://creativecommons.org/licenses/by/4.0/This article examines three divergent constructions about the salience of legal gender in lay people’s everyday lives and readiness to decertify gender. In our interviews (and survey data), generally participants minimised the importance of legal gender. The central argument in this article is that feminist socio-legal scholars applying legal consciousness studies to legal reform topics should find scrutinizing the construction of interview talk useful. We illustrate this argument by adapting and applying Ewick and Silbey’s (1998) ‘The Common Place of Law: Stories from Everyday Life', ‘before’, ‘with’ and ‘against’ typology to interview talk about legal gender, and critique their cognitivist approach by offering a constructionist alternative. In our analysis, we offer a detailed discursive explication of three key legal consciousness themes. These themes offer a balanced representation of a dataset problematically ‘skewed’ towards sex-based rights feminist perspectives, namely that ‘before’ legal gender is an anti-decertification account, decertification would be risky for natal females; a ‘with’ legal gender construction is neither for nor against decertification per se, though the impact of decertification is produced in accounts as limited and unimportant; and ‘against’ legal gender is a pro-decertification classification, as not abolished legal gender is constructed as harmful to already marginalised groups. In concluding, we explore the reasoning for the lack of readiness for decertification currently, and return to the value of examining the construction of lay discourse about legal matters as talk is a form of social action. We suggest that applying discursive analysis to themes in legal consciousness studies enables a refocusing on the how rather than purely the what of divergent legal consciousnesses, and that this approach is a fruitful addition to feminist socio-legal studies.Peer reviewe

Increased Hematopoietic Extracellular RNAs and Vesicles in the Lung during Allergic Airway Responses.

Extracellular RNAs (exRNAs) can be released by numerous cell types in vitro, are often protected within vesicles, and can modify recipient cell function. To determine how the composition and cellular sources of exRNAs and the extracellular vesicles (EVs) that carry them change in vivo during tissue inflammation, we analyzed bronchoalveolar lavage fluid (BALF) from mice before and after lung allergen challenge. In the lung, extracellular microRNAs (ex-miRNAs) had a composition that was highly correlated with airway-lining epithelium. Using cell type-specific membrane tagging and single vesicle flow, we also found that 80% of detected vesicles were of epithelial origin. After the induction of allergic airway inflammation, miRNAs selectively expressed by immune cells, including miR-223 and miR-142a, increased and hematopoietic-cell-derived EVs also increased >2-fold. These data demonstrate that infiltrating immune cells release ex-miRNAs and EVs in inflamed tissues to alter the local extracellular environment