Etalon Array Reconstructive Spectrometry.

Compact spectrometers are crucial in areas where size and weight may need to be minimized. These types of spectrometers often contain no moving parts, which makes for an instrument that can be highly durable. With the recent proliferation in low-cost and high-resolution cameras, camera-based spectrometry methods have the potential to make portable spectrometers small, ubiquitous, and cheap. Here, we demonstrate a novel method for compact spectrometry that uses an array of etalons to perform spectral encoding, and uses a reconstruction algorithm to recover the incident spectrum. This spectrometer has the unique capability for both high resolution and a large working bandwidth without sacrificing sensitivity, and we anticipate that its simplicity makes it an excellent candidate whenever a compact, robust, and flexible spectrometry solution is needed

Cooperative Gating and Spatial Organization of Membrane Proteins through Elastic Interactions

Biological membranes are elastic media in which the presence of a transmembrane protein leads to local bilayer deformation. The energetics of deformation allow two membrane proteins in close proximity to influence each other's equilibrium conformation via their local deformations, and spatially organize the proteins based on their geometry. We use the mechanosensitive channel of large conductance (MscL) as a case study to examine the implications of bilayer-mediated elastic interactions on protein conformational statistics and clustering. The deformations around MscL cost energy on the order of 10 kT and extend ~3nm from the protein edge, as such elastic forces induce cooperative gating and we propose experiments to measure these effects. Additionally, since elastic interactions are coupled to protein conformation, we find that conformational changes can severely alter the average separation between two proteins. This has important implications for how conformational changes organize membrane proteins into functional groups within membranes.Comment: 12 pages, 6 figures, 63 references, submitted to PLoS Computational Biolog

Evaluation of Landsat-8 and Sentinel-2A Aerosol Optical Depth Retrievals Across Chinese Cities and Implications for Medium Spatial Resolution Urban Aerosol Monitoring

In urban environments, aerosol distributions may change rapidly due to building and transport infrastructure and human population density variations. The recent availability of medium resolution Landsat-8 and Sentinel-2 satellite data provide the opportunity for aerosol optical depth (AOD) estimation at higher spatial resolution than provided by other satellites. AOD retrieved from 30 m Landsat-8 and 10 m Sentinel-2A data using the Land Surface Reflectance Code (LaSRC) were compared with coincident ground-based Aerosol Robotic Network (AERONET) Version 3 AOD data for 20 Chinese cities in 2016. Stringent selection criteria were used to select contemporaneous data; only satellite and AERONET data acquired within 10 min were considered. The average satellite retrieved AOD over a 1470 m1470 m window centered on each AERONET site was derived to capture fine scale urban AOD variations. AERONET Level 1.5 (cloud-screened) and Level 2.0 (cloud-screened and also quality assured) data were considered. For the 20 urban AERONET sites in 2016 there were 106 (Level 1.5) and 67 (Level 2.0) Landsat-8 AERONET AOD contemporaneous data pairs, and 118 (Level 1.5) and 89 (Level 2.0) Sentinel-2A AOD data pairs. The greatest AOD values (>1.5) occurred in Beijing, suggesting that the Chinese capital was one of the most polluted cities in China in 2016. The LaSRC Landsat-8 and Sentinel-2A AOD retrievals agreed well with the AERONET AOD data (linear regression slopes > 0.96; coefficient of determination r(exp 2) > 0.90; root mean square deviation < 0.175) and demonstrate that the LaSRC is an effective and applicable medium resolution AOD retrieval algorithm over urban environments. The Sentinel-2A AOD retrievals had better accuracy than the Landsat-8 AOD retrievals, which is consistent with previously published research.The implications of the research and the potential for urban aerosol monitoring by combining the freely available Landsat-8 and Sentinel-2 satellite data are discussed

Efficient Correlated Topic Modeling with Topic Embedding

Correlated topic modeling has been limited to small model and problem sizes due to their high computational cost and poor scaling. In this paper, we propose a new model which learns compact topic embeddings and captures topic correlations through the closeness between the topic vectors. Our method enables efficient inference in the low-dimensional embedding space, reducing previous cubic or quadratic time complexity to linear w.r.t the topic size. We further speedup variational inference with a fast sampler to exploit sparsity of topic occurrence. Extensive experiments show that our approach is capable of handling model and data scales which are several orders of magnitude larger than existing correlation results, without sacrificing modeling quality by providing competitive or superior performance in document classification and retrieval.Comment: KDD 2017 oral. The first two authors contributed equall

PseudoFuN: Deriving functional potentials of pseudogenes from integrative relationships with genes and microRNAs across 32 cancers

BACKGROUND: Long thought "relics" of evolution, not until recently have pseudogenes been of medical interest regarding regulation in cancer. Often, these regulatory roles are a direct by-product of their close sequence homology to protein-coding genes. Novel pseudogene-gene (PGG) functional associations can be identified through the integration of biomedical data, such as sequence homology, functional pathways, gene expression, pseudogene expression, and microRNA expression. However, not all of the information has been integrated, and almost all previous pseudogene studies relied on 1:1 pseudogene-parent gene relationships without leveraging other homologous genes/pseudogenes. RESULTS: We produce PGG families that expand beyond the current 1:1 paradigm. First, we construct expansive PGG databases by (i) CUDAlign graphics processing unit (GPU) accelerated local alignment of all pseudogenes to gene families (totaling 1.6 billion individual local alignments and >40,000 GPU hours) and (ii) BLAST-based assignment of pseudogenes to gene families. Second, we create an open-source web application (PseudoFuN [Pseudogene Functional Networks]) to search for integrative functional relationships of sequence homology, microRNA expression, gene expression, pseudogene expression, and gene ontology. We produce four "flavors" of CUDAlign-based databases (>462,000,000 PGG pairwise alignments and 133,770 PGG families) that can be queried and downloaded using PseudoFuN. These databases are consistent with previous 1:1 PGG annotation and also are much more powerful including millions of de novo PGG associations. For example, we find multiple known (e.g., miR-20a-PTEN-PTENP1) and novel (e.g., miR-375-SOX15-PPP4R1L) microRNA-gene-pseudogene associations in prostate cancer. PseudoFuN provides a "one stop shop" for identifying and visualizing thousands of potential regulatory relationships related to pseudogenes in The Cancer Genome Atlas cancers. CONCLUSIONS: Thousands of new PGG associations can be explored in the context of microRNA-gene-pseudogene co-expression and differential expression with a simple-to-use online tool by bioinformaticians and oncologists alike