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ItemInteraural asymmetry using dichotic filtered words in children with suspected auditory processing disorder: preliminary findings(2012-05-11) Huston, Lisa; Gibson, Keiko; Kwan, Jason; Martin, Jeffrey S.; School of Behavioral and Brain Sciences• The direction and magnitude of interaural asymmetry (IA) on dichotic listening tests is often evaluated during diagnostic assessment for APD, with excessive IA (e.g., left-ear deficit) often taken as a sign of the disorder. • It is worthwhile to consider that clinical decisions about IA might be improved when the dichotic test itself generates meaningful amounts of asymmetry in the non-clinical population, but without introducing extra-auditory factors on test performance. • In this regard, a recent study evaluated performances to dichotic low-pass filtered speech (dichotic filtered words, DFWs) presented under DIV and DIR test modes in healthy young adults with normal hearing. Previous studies have suggested that the combined utility of DIV and DIR modes may help discern the relatively contributions of perceptual (bottom-up) versus cognitive (top-down) processing biases underlying IA.3,4 Results showed that larger values of IA (e.g., REA) were produced using DFW as compared to traditional non-filtered stimuli. The magnitude of IA for DFWs was similar between test modes. • The purpose of this study was to further evaluate the DFW paradigm in a sample of school-aged children with and without symptoms of APD. ItemInfluence of headphones versus loudspeaker presentation of dichotic speech on ear advantage(2012-08-10) Peshwani, Heena Rakjumar; Martin, Jeffrey S.A right-ear advantage (REA) is a robust phenomenon on dichotic speech tests. Biases in speech perception and cognitive control are believed to produce ear advantage.1 Headphones are often used to deliver dichotic stimuli in order to isolate the two ears, however, similar outcomes have been found in behavioral and electrophysiological studies incorporating loudspeakers. The size of the REA is also known to be influenced by the level of perceptual difficulty (e.g., CV stimuli) and/or linguistic demands placed on the listener (e.g., sentences). ItemOLego: Fast and Sensitive Mapping of Spliced mRNA-Seq Reads Using Small Seeds(Oxford University Press, 2013-04) Wu, Jie; Anczuk©w, Olga; Krainer, Adrian R.; Zhang, Michael Q.; Zhang, Chaolin; 0000 0001 1707 1372 (Zhang, MQ); 99086074 (Zhang, MQ); Zhang, Michael Q.A crucial step in analyzing mRNA-Seq data is to accurately and efficiently map hundreds of millions of reads to the reference genome and exon junctions. Here we present OLego, an algorithm specifically designed for de novo mapping of spliced mRNA-Seq reads. OLego adopts a multiple-seed-and-extend scheme, and does not rely on a separate external aligner. It achieves high sensitivity of junction detection by strategic searches with small seeds (âˆ¼14 nt for mammalian genomes). To improve accuracy and resolve ambiguous mapping at junctions, OLego uses a built-in statistical model to score exon junctions by splice-site strength and intron size. Burrows-Wheeler transform is used in multiple steps of the algorithm to efficiently map seeds, locate junctions and identify small exons. OLego is implemented in C++ with fully multithreaded execution, and allows fast processing of large-scale data. We systematically evaluated the performance of OLego in comparison with published tools using both simulated and real data. OLego demonstrated better sensitivity, higher or comparable accuracy and substantially improved speed. OLego also identified hundreds of novel micro-exons (<30 nt) in the mouse transcriptome, many of which are phylogenetically conserved and can be validated experimentally in vivo. OLego is freely available at http://zhanglab.c2b2.columbia.edu/index.php/OLego.; ItemModeling a Sensor to Improve its Efficacy(Hindawi Publishing Corporation, 2013-05-20) Malakar, Nabin K.; Gladkov, Daniil; Knuth, Kevin H.Robots rely on sensors to provide them with information about their surroundings. However, high-quality sensors can be extremely expensive and cost-prohibitive. Thus many robotic systems must make due with lower-quality sensors. Here we demonstrate via a case study how modeling a sensor can improve its efficacy when employed within a Bayesian inferential framework. As a test bed we employ a robotic arm that is designed to autonomously take its own measurements using an inexpensive LEGO light sensor to estimate the position and radius of a white circle on a black field. The light sensor integrates the light arriving from a spatially distributed region within its field of view weighted by its spatial sensitivity function (SSF). We demonstrate that by incorporating an accurate model of the light sensor SSF into the likelihood function of a Bayesian inference engine, an autonomous system can make improved inferences about its surroundings. The method presented here is data based, fairly general, and made with plug-and-play in mind so that it could be implemented in similar problems. ItemAge-Related Similarities and Differences in Brain Activity Underlying Reversal Learning(2013-05-29) Nashiro, Kaoru; Sakaki, Michiko; Nga, Lin; Mather, MaraThe ability to update associative memory is an important aspect of episodic memory and a critical skill for social adaptation. Previous research with younger adults suggests that emotional arousal alters brain mechanisms underlying memory updating; however, it is unclear whether this applies to older adults. Given that the ability to update associative information declines with age, it is important to understand how emotion modulates the brain processes underlying memory updating in older adults. The current study investigated this question using reversal learning tasks, where younger and older participants (age ranges 19-35 and 61-78, respectively) learn a stimulus-outcome association and then update their response when contingencies change. We found that younger and older adults showed similar patterns of activation in the frontopolar OFC and the amygdala during emotional reversal learning. In contrast, when reversal learning did not involve emotion, older adults showed greater parietal cortex activity than did younger adults. Thus, younger and older adults show more similarities in brain activity during memory updating involving emotional stimuli than during memory updating not involving emotional stimuli.; ItemSynthetic Mammalian Transgene Negative Autoregulation(2013-06-04) Shimoga, Vinay; White, Jacob T.; Li, Yi; Sontag, Eduardo; Bleris, Leonidas; 0000 0001 2535 9739 (Bleris, L); 2012076942 (Bleris, L)Biological networks contain overrepresented small-scale topologies, typically called motifs. A frequently appearing motif is the transcriptional negative-feedback loop, where a gene product represses its own transcription. Here, using synthetic circuits stably integrated in human kidney cells, we study the effect of negative-feedback regulation on cell-wide (extrinsic) and gene-specific (intrinsic) sources of uncertainty. We develop a theoretical approach to extract the two noise components from experiments and show that negative feedback results in significant total noise reduction by reducing extrinsic noise while marginally increasing intrinsic noise. We compare the results to simple negative regulation, where a constitutively transcribed transcription factor represses a reporter protein. We observe that the control architecture also reduces the extrinsic noise but results in substantially higher intrinsic fluctuations. We conclude that negative feedback is the most efficient way to mitigate the effects of extrinsic fluctuations by a sole regulatory wiring.; ItemA New Catalyst-Embedded Hierarchical Air Electrode For High-Performance Li-O₂ Batteries(2013-06-05) Lim, H. -D; Song, H.; Gwon, H.; Park, K. -Y; Kim, J.; Bae, Y.; Kim, H.; Jung, S. -K; Kim, T.; Kim, Y. H.; Lepr©, Xavier; Ovalle-Robles, Raquel; Baughman, Ray H.; Kang, K.; 0000 0003 5232 4253 (Baughman, RH); Lepr©, Xavier; Ovalle-Robles, Raquel; Baughman, Ray H.The Li-O₂ battery holds great promise as an ultra-high-energy- density device. However, its limited rechargeability and low energy efficiency remain key barriers to its practical application. Herein, we demonstrate that the ideal electrode morphology design combined with effective catalyst decoration can enhance the rechargeability of the Li-O₂ battery over 100 cycles with full discharge and charge. An aligned carbon structure with a hierarchical micro-nano-mesh ensures facile accessibility of reaction products and provides the optimal catalytic conditions for the Pt catalyst. The new electrode is highly reversible even at the extremely high current rate of 2 A g⁻¹. Moreover, we observed clearly distinct morphologies of discharge products when the catalyst is used. The effect of catalysts on the cycle stability is discussed. ItemComplete Genome Analysis of Three Acinetobacter Baumannii Clinical Isolates in China for Insight into the Diversification of Drug Resistance Elements(2013-06-24) Zhu, Lingxiang; Yan, Zhongqiang; Zhang, Zhaojun; Zhou, Qiming; Zhou, Jinchun; Wakeland, Edward K.; Fang, Xiangdong; Xuan, Zhenyu; Shen, Dingxia; Li, Quan-Zhen; Xuan, ZhenyuBackground: The emergence and rapid spreading of multidrug-resistant Acinetobacter baumannii strains has become a major health threat worldwide. To better understand the genetic recombination related with the acquisition of drug-resistant elements during bacterial infection, we performed complete genome analysis on three newly isolated multidrug-resistant A. baumannii strains from Beijing using next-generation sequencing technology. Methodologies/Principal Findings: Whole genome comparison revealed that all 3 strains share some common drug resistant elements including carbapenem-resistant blaOXA₂₃ and tetracycline (tet) resistance islands, but the genome structures are diversified among strains. Various genomic islands intersperse on the genome with transposons and insertions, reflecting the recombination flexibility during the acquisition of the resistant elements. The blood-isolated BJAB07104 and ascites-isolated BJAB0868 exhibit high similarity on their genome structure with most of the global clone II strains, suggesting these two strains belong to the dominant outbreak strains prevalent worldwide. A large resistance island (RI) of about 121-kb, carrying a cluster of resistance-related genes, was inserted into the ATPase gene on BJAB07104 and BJAB0868 genomes. A 78-kb insertion element carrying tra-locus and blaOXA₂₃ island, can be either inserted into one of the tniB gene in the 121-kb RI on the chromosome, or transformed to conjugative plasmid in the two BJAB strains. The third strains of this study, BJAB0715, which was isolated from spinal fluid, exhibit much more divergence compared with above two strains. It harbors multiple drug-resistance elements including a truncated AbaR-22-like RI on its genome. One of the unique features of this strain is that it carries both blaOXA-23 and blaOXA-58 genes on its genome. Besides, an Acinetobacter lwoffii adeABC efflux element was found inserted into the ATPase position in BJAB0715. Conclusions: Our comparative analysis on currently completed Acinetobacter baumannii genomes revealed extensive and dynamic genome organizations, which may facilitate the bacteria to acquire drug-resistance elements into their genomes. ItemTranscripts for Combined Synthetic MicroRNA and Gene Delivery(2013-06-26) Kashyap, Neha; Pham, Bich; Xie, Zhen; Bleris, Leonidas; 0000 0001 2535 9739 (Bleris, L)MicroRNAs (miRNAs) are a class of short noncoding RNAs which are endogenously expressed in many organisms and regulate gene expression by binding to messenger RNA (mRNA). MicroRNAs are either produced from their independent transcription units in intergenic regions or lie in intragenic regions. Intragenic miRNAs and their host mRNAs are produced from the same transcript by the microprocessor and the spliceosome protein complex respectively. The details and exact timing of the processing events have implications for downstream RNA interference (RNAi) efficiency and mRNA stability. Here we engineer and study in mammalian cells a range of synthetic intragenic miRNAs co-expressed with their host genes. Furthermore, we study transcripts which carry the target of the miRNA, thereby emulating a common regulation mechanism. We perform fluorescence microscopy and flow cytometry to characterize the engineered transcripts and investigate the properties of the underlying biological processes. Our results shed additional light on miRNA and pre-mRNA processing but importantly provide insight into engineering transcripts customized for combined delivery and use in synthetic gene circuits.; ItemFastDMA: An Infinium Humanmethylation450 Beadchip Analyzer(2013-09-05) Wu, D.; Gu, J.; Zhang, Michael Q.; 0000 0001 1707 1372 (Zhang, MQ); 99086074 (Zhang, MQ); Zhang, Michael Q.DNA methylation is vital for many essential biological processes and human diseases. Illumina Infinium HumanMethylation450 Beadchip is a recently developed platform studying genome-wide DNA methylation state on more than 480,000 CpG sites and a few CHG sites with high data quality. To analyze the data of this promising platform, we developed FastDMA which can be used to identify significantly differentially methylated probes. Besides single probe analysis, FastDMA can also do region-based analysis for identifying the differentially methylated region (DMRs). A uniformed statistical model, analysis of covariance (ANCOVA), is used to achieve all the analyses in FastDMA. We apply FastDMA on three large-scale DNA methylation datasets from The Cancer Genome Atlas (TCGA) and find many differentially methylated genomic sites in different types of cancer. On the testing datasets, FastDMA shows much higher computational efficiency than current tools. FastDMA can benefit the data analyses of large-scale DNA methylation studies with an integrative pipeline and a high computational efficiency. The software is freely available via http://bioinfo.au.tsinghua.edu.cn/software/fastdma/. ItemSuperconductivity in an inhomogeneous bundle of metallic and semiconducting nanotubes(2013-09-06) Grigorenko, I.; Zakhidov, Anvar A.; 0000 0003 5287 0481 (Zakhidov, AA); Zakhidov, Anvar A.Using Bogoliubov-de Gennes formalism for inhomogeneous systems, we have studied superconducting properties of a bundle of packed carbon nanotubes, making a triangular lattice in the bundle's transverse cross-section. The bundle consists of a mixture of metallic and doped semiconducting nanotubes, which have different critical transition temperatures. We investigate how a spatially averaged superconducting order parameter and the critical transition temperature depend on the fraction of the doped semiconducting carbon nanotubes in the bundle. Our simulations suggest that the superconductivity in the bundle will be suppressed when the fraction of the doped semiconducting carbon nanotubes will be less than 0.5, which is the percolation threshold for a two-dimensional triangular lattice. ItemConductive Functional Biscrolled Polymer and Carbon Nanotube Yarns(2013-10-10) Kim, S. H.; Sim, H. J.; Shin, M. K.; Choi, A. Y.; Kim, Y. T.; Lima, Marcio D.; Baughman, Ray H.; Kim, S. J.; 0000 0003 5232 4253 (Baughman, RH); Lima, Marcio D.; Baughman, Ray H.Biscrolling aligned electrospun fiber (AEF) sheets and carbon nanotube (CNT) sheets were fabricated for conductive, functional yarns by a versatile dry composite method. Our biscrolling (twist-based spinning) method is based on spinnable polymer fiber sheets and spinnable CNT sheets unlike the previous biscrolling technique using unspinnable nanopowders and spinnable CNT sheets. The CNT sheet in composite yarns acted as effective electrical wires forming dual Archimedean multilayer rolled-up nanostructures. The weight percent of the electrospun polymer fibers in the composite yarns was over 98%, and the electrical conductivity values of the composite yarns was 3 orders higher than those of other non-conducting polymer/CNT composite fibers which were electrospun from polymer solutions containing similar loading of CNTs. We also demonstrate that biscrolled yarns having various structures can be fabricated from spinnable AEF sheets and spinnable CNT sheets. ItemElectrochemically Gated Organic Photovoltaic with Tunable Carbon Nanotube Cathodes(2013-10-18) Cook, Alexander B.; Yuen, Jonathan D.; Zakhidov, Anvar A.; 0000 0003 5287 0481 (Zakhidov, AA); Zakhidov, Anvar A.We demonstrate an organic photovoltaic (OPV) device with an electrochemically gated carbon nanotube (CNT) charge collector. Bias voltages applied to the gate electrode reconfigure the common CNT electrode from an anode into a cathode which effectively collects photogenerated electrons, dramatically increasing all solar cell parameters to achieve a power conversion efficiency of âˆ¼3%. This device requires very little current to initially charge and the leakage current is negligible compared to the photocurrent. This device can also be viewed as a hybrid tandem OPV-supercapacitor with a common CNT electrode. Other regimes of operation are briefly discussed. ItemIntegrated Omics Study Delineates the Dynamics of Lipid Droplets in Rhodococcus Opacus PD630(Oxford University Press, 2013-10-22) Chen, Yong; Ding, Yunfeng; Yang, Li; Yu, Jinhai; Liu, Guiming; Wang, Xumin; Zhang, Shuyan; Zhang, Michael Q.; Li, Yanda; 0000 0001 1707 1372 (Zhang, MQ); 99086074 (Zhang, MQ); Zhang, Michael Q.Rhodococcus opacus strain PD630 (R. opacus PD630), is an oleaginous bacterium, and also is one of few prokaryotic organisms that contain lipid droplets (LDs). LD is an important organelle for lipid storage but also intercellular communication regarding energy metabolism, and yet is a poorly understood cellular organelle. To understand the dynamics of LD using a simple model organism, we conducted a series of comprehensive omics studies of R. opacus PD630 including complete genome, transcriptome and proteome analysis. The genome of R. opacus PD630 encodes 8947 genes that are significantly enriched in the lipid transport, synthesis and metabolic, indicating a super ability of carbon source biosynthesis and catabolism. The comparative transcriptome analysis from three culture conditions revealed the landscape of gene-altered expressions responsible for lipid accumulation. The LD proteomes further identified the proteins that mediate lipid synthesis, storage and other biological functions. Integrating these three omics uncovered 177 proteins that may be involved in lipid metabolism and LD dynamics. A LD structure-like protein LPD06283 was further verified to affect the LD morphology. Our omics studies provide not only a first integrated omics study of prokaryotic LD organelle, but also a systematic platform for facilitating further prokaryotic LD research and biofuel development. ItemAccess to High School Arts Education: Why Student Participation Matters as much as Course Availability(2013-11-04) Thomas, M. K.; Singh, Priyanka; Klopfenstein, K.; Henry, T.There is renewed interest in the role of arts education in the curriculum of U.S. public schools not only because of the intrinsic value of the arts and its believed impact on achievement, but because cultivating creativity is thought to promote innovation and fuel economic growth. Still, we know little about basic access to arts education. Using individual-level administrative data from The University of Texas at Dallas Education Research Center (UTD-ERC), we develop several distinct indices of access to identify high schools rich in the arts. We find that high schools offering an extensive number of courses in the arts do not necessarily enjoy high rates of student participation. Policymakers who examine access based only on course counts in the arts will identify predominately large, non-rural high schools as having arts-rich environments. Evaluating arts programs along a single dimension, as is common in federal reports and other studies, fails to provide an accurate representation of access to arts education. Any examination of access to arts education should jointly consider course availability and student engagement in the arts. Policymakers can follow our approach and develop similar indices to assess the current state of arts education in their states.