Epistemology and the Structure of Language

We are concerned here with how structural properties of language may come to reflect features of the world in which it evolves. As a concrete example, we will consider how a simple term language might evolve to support the principle of indifference over state descriptions in that language. The point is not that one is justified in applying the principle of indifference to state descriptions in natural language. Instead, it is that one should expect a language that has evolved in the context of facilitating successful action to reflect probabilistic features of the world in which it evolved

Epistemology and the Structure of Language

We are concerned here with how structural properties of language may come to reflect features of the world in which it evolves. As a concrete example, we will consider how a simple term language might evolve to support the principle of indifference over state descriptions in that language. The point is not that one is justified in applying the principle of indifference to state descriptions in natural language. Instead, it is that one should expect a language that has evolved in the context of facilitating successful action to reflect probabilistic features of the world in which it evolved

Epistemology and the Structure of Language

We are concerned here with how structural properties of language may come to reflect features of the world in which it evolves. As a concrete example, we will consider how a simple term language might evolve to support the principle of indifference over state descriptions in that language. The point is not that one is justified in applying the principle of indifference to state descriptions in natural language. Instead, it is that one should expect a language that has evolved in the context of facilitating successful action to reflect probabilistic features of the world in which it evolved

A bulk-mass-modeling-based method for retrieving particulate matter pollution using CALIOP observations

In this proof-of-concept paper, we apply a bulk-mass-modeling method using observations from the NASA Cloud-Aerosol Lidar with Orthogonal Polarization (CALIOP) instrument for retrieving particulate matter (PM) concentration over the contiguous United States (CONUS) over a 2-year period (2008–2009). Different from previous approaches that rely on empirical relationships between aerosol optical depth (AOD) and PM2.5 (PM with particle diameters less than 2.5 µm), for the first time, we derive PM2.5 concentrations, during both daytime and nighttime, from near-surface CALIOP aerosol extinction retrievals using bulk mass extinction coefficients and model-based hygroscopicity. Preliminary results from this 2-year study conducted over the CONUS show a good agreement (r2∼0.48; mean bias of −3.3 µg m−3) between the averaged nighttime CALIOP-derived PM2.5 and ground-based PM2.5 (with a lower r2 of ∼0.21 for daytime; mean bias of −0.4 µg m−3), suggesting that PM concentrations can be obtained from active-based spaceborne observations with reasonable accuracy. Results from sensitivity studies suggest that accurate aerosol typing is needed for applying CALIOP measurements for PM2.5 studies. Lastly, the e-folding correlation length for surface PM2.5 is found to be around 600 km for the entire CONUS (∼300 km for western CONUS and ∼700 km for eastern CONUS), indicating that CALIOP observations, although sparse in spatial coverage, may still be applicable for PM2.5 studies

RNA extraction, probe preparation, and competitive hybridization for transcriptional profiling using Neurospora crassa long-oligomer DNA microarrays

We developed protocols optimized for the performance of experiments assaying genomic gene expression using Neurospora crassa long-oligomer microarrays. We present methods for sample growth and harvesting, total RNA extraction, poly(A)+ mRNA selection, preparation of NH3-Allyl Cy3/Cy5 labeled probes, and microarray hybridization. The quality of the data obtained with these protocols is demonstrated by the comparative transcriptional profiling of basal and apical zones of vegetative growth of N. crassa

Low-Dissipation Advection Schemes Designed for Large Eddy Simulations of Hypersonic Propulsion Systems

The 2nd-order upwind inviscid flux scheme implemented in the multi-block, structured grid, cell centered, finite volume, high-speed reacting flow code VULCAN has been modified to reduce numerical dissipation. This modification was motivated by the desire to improve the codes ability to perform large eddy simulations. The reduction in dissipation was accomplished through a hybridization of non-dissipative and dissipative discontinuity-capturing advection schemes that reduces numerical dissipation while maintaining the ability to capture shocks. A methodology for constructing hybrid-advection schemes that blends nondissipative fluxes consisting of linear combinations of divergence and product rule forms discretized using 4th-order symmetric operators, with dissipative, 3rd or 4th-order reconstruction based upwind flux schemes was developed and implemented. A series of benchmark problems with increasing spatial and fluid dynamical complexity were utilized to examine the ability of the candidate schemes to resolve and propagate structures typical of turbulent flow, their discontinuity capturing capability and their robustness. A realistic geometry typical of a high-speed propulsion system flowpath was computed using the most promising of the examined schemes and was compared with available experimental data to demonstrate simulation fidelity

Isoform-specific subcellular localization and function of protein kinase A identified by mosaic imaging of mouse brain.

Protein kinase A (PKA) plays critical roles in neuronal function that are mediated by different regulatory (R) subunits. Deficiency in either the RIβ or the RIIβ subunit results in distinct neuronal phenotypes. Although RIβ contributes to synaptic plasticity, it is the least studied isoform. Using isoform-specific antibodies, we generated high-resolution large-scale immunohistochemical mosaic images of mouse brain that provided global views of several brain regions, including the hippocampus and cerebellum. The isoforms concentrate in discrete brain regions, and we were able to zoom-in to show distinct patterns of subcellular localization. RIβ is enriched in dendrites and co-localizes with MAP2, whereas RIIβ is concentrated in axons. Using correlated light and electron microscopy, we confirmed the mitochondrial and nuclear localization of RIβ in cultured neurons. To show the functional significance of nuclear localization, we demonstrated that downregulation of RIβ, but not of RIIβ, decreased CREB phosphorylation. Our study reveals how PKA isoform specificity is defined by precise localization

Multi-targeted priming for genome-wide gene expression assays

<p>Abstract</p> <p>Background</p> <p>Complementary approaches to assaying global gene expression are needed to assess gene expression in regions that are poorly assayed by current methodologies. A key component of nearly all gene expression assays is the reverse transcription of transcribed sequences that has traditionally been performed by priming the poly-A tails on many of the transcribed genes in eukaryotes with oligo-dT, or by priming RNA indiscriminately with random hexamers. We designed an algorithm to find common sequence motifs that were present within most protein-coding genes of <it>Saccharomyces cerevisiae </it>and of <it>Neurospora crassa</it>, but that were not present within their ribosomal RNA or transfer RNA genes. We then experimentally tested whether degenerately priming these motifs with multi-targeted primers improved the accuracy and completeness of transcriptomic assays.</p> <p>Results</p> <p>We discovered two multi-targeted primers that would prime a preponderance of genes in the genomes of <it>Saccharomyces cerevisiae </it>and <it>Neurospora crassa </it>while avoiding priming ribosomal RNA or transfer RNA. Examining the response of <it>Saccharomyces cerevisiae </it>to nitrogen deficiency and profiling <it>Neurospora crassa </it>early sexual development, we demonstrated that using multi-targeted primers in reverse transcription led to superior performance of microarray profiling and next-generation RNA tag sequencing. Priming with multi-targeted primers in addition to oligo-dT resulted in higher sensitivity, a larger number of well-measured genes and greater power to detect differences in gene expression.</p> <p>Conclusions</p> <p>Our results provide the most complete and detailed expression profiles of the yeast nitrogen starvation response and <it>N. crassa </it>early sexual development to date. Furthermore, our multi-targeting priming methodology for genome-wide gene expression assays provides selective targeting of multiple sequences and counter-selection against undesirable sequences, facilitating a more complete and precise assay of the transcribed sequences within the genome.</p

Minimum Aerosol Layer Detection Sensitivities and Their Subsequent Impacts on Aerosol Optical Thickness Retrievals in CALIPSO Level 2 Data Products

Due to instrument sensitivities and algorithm detection limits, level 2 (L2) Cloud-Aerosol Lidar with Orthogonal Polarization (CALIOP) 532 nm aerosol extinction profile retrievals are often populated with retrieval fill values (RFVs), which indicate the absence of detectable levels of aerosol within the profile. In this study, using 4 years (20072008 and 20102011) of CALIOP version 3 L2 aerosol data, the occurrence frequency of daytime CALIOP profiles containing all RFVs (all-RFV profiles) is studied. In the CALIOP data products, the aerosol optical thickness (AOT) of any all-RFV profile is reported as being zero, which may introduce a bias in CALIOP-based AOT climatologies. For this study, we derive revised estimates of AOT for all-RFV profiles using collocated Moderate Resolution Imaging Spectroradiometer (MODIS) Dark Target (DT) and, where available, AErosol RObotic NEtwork (AERONET) data. Globally, all-RFV profiles comprise roughly 71 % of all daytime CALIOP L2 aerosol profiles (i.e., including completely attenuated profiles), accounting for nearly half (45 %) of all daytime cloud-free L2 aerosol profiles. The mean collocated MODIS DT (AERONET) 550 nm AOT is found to be near 0.06 (0.08) for CALIOP all-RFV profiles. We further estimate a global mean aerosol extinction profile, a so-called noise floor, for CALIOP all-RFV profiles. The global mean CALIOP AOT is then recomputed by replacing RFV values with the derived noise-floor values for both all-RFV and non-all-RFV profiles. This process yields an improvement in the agreement of CALIOP and MODIS over-ocean AOT

Minimum Aerosol Layer Detection Sensitivities and Their Subsequent Impacts on Aerosol Optical Thickness Retrievals in CALIPSO Level 2 Data Products

Due to instrument sensitivities and algorithm detection limits, level 2 (L2) Cloud-Aerosol Lidar with Orthogonal Polarization (CALIOP) 532 nm aerosol extinction profile retrievals are often populated with retrieval fill values (RFVs), which indicate the absence of detectable levels of aerosol within the profile. In this study, using 4 years (2007– 2008 and 2010–2011) of CALIOP version 3 L2 aerosol data, the occurrence frequency of daytime CALIOP profiles containing all RFVs (all-RFV profiles) is studied. In the CALIOP data products, the aerosol optical thickness (AOT) of any all-RFV profile is reported as being zero, which may introduce a bias in CALIOP-based AOT climatologies. For this study, we derive revised estimates of AOT for all-RFV profiles using collocated Moderate Resolution Imaging Spectroradiometer (MODIS) Dark Target (DT) and, where available, AErosol RObotic NEtwork (AERONET) data. Globally, all-RFV profiles comprise roughly 71 % of all daytime CALIOP L2 aerosol profiles (i.e., including completely attenuated profiles), accounting for nearly half (45 %) of all daytime cloud-free L2 aerosol profiles. The mean collocated MODIS DT (AERONET) 550 nm AOT is found to be near 0.06 (0.08) for CALIOP all-RFV profiles. We further estimate a global mean aerosol extinction profile, a so-called “noise floor”, for CALIOP all-RFV profiles. The global mean CALIOP AOT is then recomputed by replacing RFV values with the derived noise-floor values for both all-RFV and nonall-RFV profiles. This process yields an improvement in the agreement of CALIOP and MODIS over-ocean AOT