Identification of the expressome by machine learning on omics data.

Accurate annotation of plant genomes remains complex due to the presence of many pseudogenes arising from whole-genome duplication-generated redundancy or the capture and movement of gene fragments by transposable elements. Machine learning on genome-wide epigenetic marks, informed by transcriptomic and proteomic training data, could be used to improve annotations through classification of all putative protein-coding genes as either constitutively silent or able to be expressed. Expressed genes were subclassified as able to express both mRNAs and proteins or only RNAs, and CG gene body methylation was associated only with the former subclass. More than 60,000 protein-coding genes have been annotated in the reference genome of maize inbred B73. About two-thirds of these genes are transcribed and are designated the filtered gene set (FGS). Classification of genes by our trained random forest algorithm was accurate and relied only on histone modifications or DNA methylation patterns within the gene body; promoter methylation was unimportant. Other inbred lines are known to transcribe significantly different sets of genes, indicating that the FGS is specific to B73. We accurately classified the sets of transcribed genes in additional inbred lines, arising from inbred-specific DNA methylation patterns. This approach highlights the potential of using chromatin information to improve annotations of functional genes

Additive Manufacturing of High-Refractive-Index, Nanoarchitected Titanium Dioxide for 3D Dielectric Photonic Crystals

Additive manufacturing at small scales enables advances in micro- and nanoelectromechanical systems, micro-optics, and medical devices. Materials that lend themselves to AM at the nanoscale, especially for optical applications, are limited. State-of-the-art AM processes for high-refractive-index materials typically suffer from high porosity and poor repeatability and require complex experimental procedures. We developed an AM process to fabricate complex 3D architectures out of fully dense titanium dioxide (TiO₂) with a refractive index of 2.3 and nanosized critical dimensions. Transmission electron microscopy (TEM) analysis proves this material to be rutile phase of nanocrystalline TiO₂, with an average grain size of 110 nm and <1% porosity. Proof-of-concept woodpile architectures with 300–600 nm beam dimensions exhibit a full photonic band gap centered at 1.8–2.9 μm, as revealed by Fourier-transform infrared spectroscopy (FTIR) and supported by plane wave expansion simulations. The developed AM process enables advances in 3D MEMS, micro-optics, and prototyping of 3D dielectric PhCs

Development of transparent microwell arrays for optical monitoring and dissection of microbial communities

Citation: Halsted, M., Wilmoth, J. L., Briggs, P. A., Hansen, R. R., Briggs, D. P., Timm, A. C., & Retterer, S. T. (2016). Development of transparent microwell arrays for optical monitoring and dissection of microbial communities. Journal of Vacuum Science & Technology B, 34(6), 5. doi:10.1116/1.4962739Microbial communities are incredibly complex systems that dramatically and ubiquitously influence our lives. They help to shape our climate and environment, impact agriculture, drive business, and have a tremendous bearing on healthcare and physical security. Spatial confinement, as well as local variations in physical and chemical properties, affects development and interactions within microbial communities that occupy critical niches in the environment. Recent work has demonstrated the use of silicon based microwell arrays, combined with parylene lift-off techniques, to perform both deterministic and stochastic assembly of microbial communities en masse, enabling the high-throughput screening of microbial communities for their response to growth in confined environments under different conditions. The implementation of a transparent microwell array platform can expand and improve the imaging modalities that can be used to characterize these assembled communities. Here, the fabrication and characterization of a next generation transparent microwell array is described. The transparent arrays, comprised of SU-8 patterned on a glass coverslip, retain the ability to use parylene lift-off by integrating a low temperature atomic layer deposition of silicon dioxide into the fabrication process. This silicon dioxide layer prevents adhesion of the parylene material to the patterned SU-8, facilitating dry lift-off, and maintaining the ability to easily assemble microbial communities within the microwells. These transparent microwell arrays can screen numerous community compositions using continuous, high resolution, imaging. The utility of the design was successfully demonstrated through the stochastic seeding and imaging of green fluorescent protein expressing Escherichia coli using both fluorescence and brightfield microscopies. (C) 2016 American Vacuum Society

High-performance Si microwire photovoltaics

Crystalline Si wires, grown by the vapor–liquid–solid (VLS) process, have emerged as promising candidate materials for lowcost, thin-film photovoltaics. Here, we demonstrate VLS-grown Si microwires that have suitable electrical properties for high-performance photovoltaic applications, including long minority-carrier diffusion lengths (L_n » 30 µm) and low surface recombination velocities (S « 70 cm·s^(-1)). Single-wire radial p–n junction solar cells were fabricated with amorphous silicon and silicon nitride surface coatings, achieving up to 9.0% apparent photovoltaic efficiency, and exhibiting up to ~600 mV open-circuit voltage with over 80% fill factor. Projective single-wire measurements and optoelectronic simulations suggest that large-area Si wire-array solar cells have the potential to exceed 17% energy-conversion efficiency, offering a promising route toward cost-effective crystalline Si photovoltaics

View management for lifelong visual maps

The time complexity of making observations and loop closures in a graph-based visual SLAM system is a function of the number of views stored. Clever algorithms, such as approximate nearest neighbor search, can make this function sub-linear. Despite this, over time the number of views can still grow to a point at which the speed and/or accuracy of the system becomes unacceptable, especially in computation- and memory-constrained SLAM systems. However, not all views are created equal. Some views are rarely observed, because they have been created in an unusual lighting condition, or from low quality images, or in a location whose appearance has changed. These views can be removed to improve the overall performance of a SLAM system. In this paper, we propose a method for pruning views in a visual SLAM system to maintain its speed and accuracy for long term use.Comment: IEEE International Conference on Intelligent Robots and Systems (IROS), 201

Si microwire-array solar cells

Si microwire-array solar cells with Air Mass 1.5 Global conversion efficiencies of up to 7.9% have been fabricated using an active volume of Si equivalent to a 4 μm thick Si wafer. These solar cells exhibited open-circuit voltages of 500 mV, short-circuit current densities (J_(sc)) of up to 24 mA cm^(-2), and fill factors >65% and employed Al_2O_3 dielectric particles that scattered light incident in the space between the wires, a Ag back reflector that prevented the escape of incident illumination from the back surface of the solar cell, and an a-SiN_x:H passivation/anti-reflection layer. Wire-array solar cells without some or all of these design features were also fabricated to demonstrate the importance of the light-trapping elements in achieving a high J_(sc). Scanning photocurrent microscopy images of the microwire-array solar cells revealed that the higher J_(sc) of the most advanced cell design resulted from an increased absorption of light incident in the space between the wires. Spectral response measurements further revealed that solar cells with light-trapping elements exhibited improved red and infrared response, as compared to solar cells without light-trapping elements

Crab in Amber Reveals an Early Colonization of Nonmarine Environments During the Cretaceous

Amber fossils provide snapshots of the anatomy, biology, and ecology of extinct organisms that are otherwise inaccessible. The best-known fossils in amber are terrestrial arthropods—principally insects—whereas aquatic organisms are rarely represented. Here, we present the first record of true crabs (Brachyura) in amber—from the Cretaceous of Myanmar [~100 to 99 million years (Ma)]. The new fossil preserves large compound eyes, delicate mouthparts, and even gills. This modern-looking crab is nested within crown Eubrachyura, or “higher” true crabs, which includes the majority of brachyuran species living today. The fossil appears to have been trapped in a brackish or freshwater setting near a coastal to fluvio-estuarine environment, bridging the gap between the predicted molecular divergence of nonmarine crabs (~130 Ma) and their younger fossil record (latest Cretaceous and Paleogene, ~75 to 50 Ma) while providing a reliable calibration point for molecular divergence time estimates for higher crown eubrachyurans

Fear of the unknown: a pre-departure qualitative study of Turkish international students

This paper presents findings from eleven in-depth interviews with Turkish undergraduate students, who were, by the time of data collection, about to spend a semester at a European university under the Erasmus exchange scheme. The students all agreed to be interviewed about their feelings about studying in a foreign culture, and were found to be anxious prior to departure about the quality of accommodation in the new destination, their language ability and the opportunity to form friendships. Fears were expressed about possible misconceptions over Turkey as a Muslim and a developing country. Suggestions are made for HEI interventions to allay student travellers’ concerns

Observations of GRB 990123 by the Compton Gamma-Ray Observatory

GRB 990123 was the first burst from which simultaneous optical, X-ray and gamma-ray emission was detected; its afterglow has been followed by an extensive set of radio, optical and X-ray observations. We have studied the gamma-ray burst itself as observed by the CGRO detectors. We find that gamma-ray fluxes are not correlated with the simultaneous optical observations, and the gamma-ray spectra cannot be extrapolated simply to the optical fluxes. The burst is well fit by the standard four-parameter GRB function, with the exception that excess emission compared to this function is observed below ~15 keV during some time intervals. The burst is characterized by the typical hard-to-soft and hardness-intensity correlation spectral evolution patterns. The energy of the peak of the nu f_nu spectrum, E_p, reaches an unusually high value during the first intensity spike, 1470 +/- 110 keV, and then falls to \~300 keV during the tail of the burst. The high-energy spectrum above ~MeV is consistent with a power law with a photon index of about -3. By fluence, GRB 990123 is brighter than all but 0.4% of the GRBs observed with BATSE, clearly placing it on the -3/2 power-law portion of the intensity distribution. However, the redshift measured for the afterglow is inconsistent with the Euclidean interpretation of the -3/2 power-law. Using the redshift value of >= 1.61 and assuming isotropic emission, the gamma-ray fluence exceeds 10E54 ergs.Comment: Submitted to The Astrophysical Journal. 16 pages including 4 figure