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MIT Open Access Articles

Mostrando recursos 1 - 20 de 14,579

1. Genetic Evidence for Recent Population Mixture in India - Moorjani, Priya; Thangaraj, Kumarasamy; Patterson, Nick; Lipson, Mark; Loh, Po-Ru; Govindaraj, Periyasamy; Berger, Bonnie; Reich, David; Singh, Lalji
Most Indian groups descend from a mixture of two genetically divergent populations: Ancestral North Indians (ANI) related to Central Asians, Middle Easterners, Caucasians, and Europeans; and Ancestral South Indians (ASI) not closely related to groups outside the subcontinent. The date of mixture is unknown but has implications for understanding Indian history. We report genome-wide data from 73 groups from the Indian subcontinent and analyze linkage disequilibrium to estimate ANI-ASI mixture dates ranging from about 1,900 to 4,200 years ago. In a subset of groups, 100% of the mixture is consistent with having occurred during this period. These results show that...

2. Computational solutions for omics data - Berger, Bonnie; Peng, Jian; Singh, Mona
High-throughput experimental technologies are generating increasingly massive and complex genomic data sets. The sheer enormity and heterogeneity of these data threaten to make the arising problems computationally infeasible. Fortunately, powerful algorithmic techniques lead to software that can answer important biomedical questions in practice. In this Review, we sample the algorithmic landscape, focusing on state-of-the-art techniques, the understanding of which will aid the bench biologist in analysing omics data. We spotlight specific examples that have facilitated and enriched analyses of sequence, transcriptomic and network data sets.

3. n-relative categories: a model for the homotopy theory of n-fold homotopy theories - Kan, D. M.; Barwick, Clark Edward
We introduce, for every integer n ≥ 1, the notion of an n-relative category and show that the category of the small n-relative categories is a model for the homotopy theory of n-fold homotopy theories, i.e., homotopy theories of… homotopy theories.

4. Focus 3D: Compressive Accommodation Display - Maimone, Andrew; Wetzstein, Gordon; Hirsch, Matthew; Lanman, Douglas; Raskar, Ramesh; Fuchs, Henry
We present a glasses-free 3D display design with the potential to provide viewers with nearly correct accommodative depth cues, as well as motion parallax and binocular cues. Building on multilayer attenuator and directional backlight architectures, the proposed design achieves the high angular resolution needed for accommodation by placing spatial light modulators about a large lens: one conjugate to the viewer's eye, and one or more near the plane of the lens. Nonnegative tensor factorization is used to compress a high angular resolution light field into a set of masks that can be displayed on a pair of commodity LCD panels....

5. Replay: a self-documenting construction kit - Tseng, Tiffany; Hemsley, Robert; Resnick, Mitchel
Replay is a self-documenting construction kit for children to both share their designs with others and reflect on their own design process. Replay consists of a set of angular pieces that can sense their connection and orientation. A virtual model is rendered in real time as a design is constructed, and an on-screen playback interface allows users to view models from multiple perspectives and watch how a design was assembled. This paper describes the early development of Replay and describes potential directions for the documentation of physical designs.

6. Adaptive image synthesis for compressive displays - Heide, Felix; Wetzstein, Gordon; Raskar, Ramesh; Heidrich, Wolfgang
Recent years have seen proposals for exciting new computational display technologies that are compressive in the sense that they generate high resolution images or light fields with relatively few display parameters. Image synthesis for these types of displays involves two major tasks: sampling and rendering high-dimensional target imagery, such as light fields or time-varying light fields, as well as optimizing the display parameters to provide a good approximation of the target content. In this paper, we introduce an adaptive optimization framework for compressive displays that generates high quality images and light fields using only a fraction of the total plenoptic samples....

7. Topological Nature of Optical Bound States in the Continuum - Zhen, Bo; Hsu, Chia Wei; Lu, Ling; Stone, A. Douglas; Soljacic, Marin
Optical bound states in the continuum (BICs) have recently been realized in photonic crystal slabs, where the disappearance of out-of-plane radiation turns leaky resonances into guided modes with infinite lifetimes. We show that such BICs are vortex centers in the polarization directions of far-field radiation. They carry conserved and quantized topological charges, defined by the winding number of the polarization vectors, which ensure their robust existence and govern their generation, evolution, and annihilation. Our findings connect robust BICs in photonics to a wide range of topological physical phenomena.

8. 8D: Interacting with a Relightable Glasses-Free 3D Display - Hirsch, Matthew; Izadi, Shahram; Raskar, Ramesh; Holtzman, Henry N.
We present an 8-dimensional (8D) display that allows glasses-free viewing of 3D imagery, whist capturing and reacting to incident environmental and user controlled light sources. We demonstrate two interactive possibilities enabled by our lens-array-based hardware prototype, and realtime GPU-accelerated software pipeline. Additionally, we describe a path to deploying such displays in the future, using current Sensor-in-Pixel (SIP) LCD panels, which physically collocate sensing and display elements.

9. Tensor displays: compressive light field synthesis using multilayer displays with directional backlighting - Wetzstein, Gordon; Lanman, Douglas; Hirsch, Matthew; Raskar, Ramesh
We introduce tensor displays: a family of compressive light field displays comprising all architectures employing a stack of time-multiplexed, light-attenuating layers illuminated by uniform or directional backlighting (i.e., any low-resolution light field emitter). We show that the light field emitted by an N-layer, M-frame tensor display can be represented by an Nth-order, rank-M tensor. Using this representation we introduce a unified optimization framework, based on nonnegative tensor factorization (NTF), encompassing all tensor display architectures. This framework is the first to allow joint multilayer, multiframe light field decompositions, significantly reducing artifacts observed with prior multilayer-only and multiframe-only decompositions; it is also...

10. Mechanical and Transport Properties of Layer-by-Layer Electrospun Composite Proton Exchange Membranes for Fuel Cell Applications - Mannarino, Matthew M.; Liu, David S.; Hammond, Paula T.; Rutledge, Gregory C.
Composite membranes composed of highly conductive and selective layer-by-layer (LbL) films and electrospun fiber mats were fabricated and characterized for mechanical strength and electrochemical selectivity. The LbL component consists of a proton-conducting, methanol-blocking poly(diallyl dimethyl ammonium chloride)/sulfonated poly(2,6-dimethyl-1,4-phenylene oxide) (PDAC/sPPO) thin film. The electrospun fiber component consists of poly(trimethyl hexamethylene terephthalamide) (PA 6(3)T) fibers in a nonwoven mat of 60–90% porosity. The bare mats were annealed to improve their mechanical properties, which improvements are shown to be retained in the composite membranes. Spray LbL assembly was used as a means for the rapid formation of proton-conducting films that fill the...

11. A Review of Electrospun Carbon Fibers as Electrode Materials for Energy Storage - Mao, Xianwen; Hatton, T. Alan; Rutledge, Gregory C.
The applications of electrospun carbon fiber webs to the development of energy storages devices, including both supercapacitors and lithium ion batteries (LIB) , are reviewed. Following a brief discussion of the fabrication process and characterization methods for ultrafine electrospun carbon fibers, recent advances in their performance as supercapacitors and LIBs anode materials are summarized. Optimization of the overall electrochemical properties of these materials through choice of thermal treatment conditions, incorporation of additional active components (such as carbon nanotubes, metal oxides, and catalysts), and generation of novel fibrous structures (such as core-shell, multi-channel or porous fibers) is highlighted. Further challenges related...

12. Molecular Dynamics Simulation of Homogeneous Crystal Nucleation in Polyethylene - Yi, Peng; Locker, C. Rebecca; Rutledge, Gregory C.
Using a realistic united-atom force field, molecular dynamics simulations were performed to study homogeneous nucleation of the crystal phase at about 30% supercooling from the melts of n-pentacontahectane (C150) and a linear polyethylene (C1000), both of which are long enough to exhibit the chain folding that is characteristic of polymer crystallization. The nucleation rate was calculated and the critical nuclei were identified using a mean first-passage time analysis. The nucleation rate was found to be insensitive to the chain length in this range of molecular weight. The critical nucleus contains about 150 carbons on average and is significantly smaller than...

13. Electrospun Polyaniline Fibers as Highly Sensitive Room Temperature Chemiresistive Sensors for Ammonia and Nitrogen Dioxide Gases - Zhang, Yuxi; Kim, Jae Jin; Chen, Di; Tuller, Harry L.; Rutledge, Gregory C.
Electrospun polyaniline (PAni) fibers doped with different levels of (+)-camphor-10-sulfonic acid (HCSA) are fabricated and evaluated as chemiresistive gas sensors. The experimental results, based on both sensitivity and response time, show that doped PAni fibers are excellent ammonia sensors and that undoped PAni fibers are excellent nitrogen dioxide sensors. The fibers exhibit changes in measured resistances up to 60-fold for ammonia sensing, and more than five orders of magnitude for nitrogen dioxide sensing, with characteristic response times on the order of one minute in both cases. A time-dependent reaction-diffusion model is used to extract physical parameters from fitting experimental sensor...

14. Exploring the Mechanism of Biocatalyst Inhibition in Microbial Desulfurization - Abin-Fuentes, Andres; Mohamed, Magdy El-Said; Wang, Daniel I.; Prather, Kristala L. Jones
Microbial desulfurization, or biodesulfurization (BDS), of fuels is a promising technology because it can desulfurize compounds that are recalcitrant to the current standard technology in the oil industry. One of the obstacles to the commercialization of BDS is the reduction in biocatalyst activity concomitant with the accumulation of the end product, 2-hydroxybiphenyl (HBP), during the process. BDS experiments were performed by incubating Rhodococcus erythropolis IGTS8 resting-cell suspensions with hexadecane at 0.50 (vol/vol) containing 10 mM dibenzothiophene. The resin Dowex Optipore SD-2 was added to the BDS experiments at resin concentrations of 0, 10, or 50 g resin/liter total volume. The...

15. Bioengineered Probes for Molecular Magnetic Resonance Imaging in the Nervous System - Hsieh, Vivian; Jasanoff, Alan Pradip
The development of molecular imaging probes has changed the nature of neurobiological research. Some of the most notable successes have involved the use of biological engineering techniques for the creation of fluorescent protein derivatives for optical imaging, but recent work has also led to a number of bioengineered probes for magnetic resonance imaging (MRI), the preeminent technique for noninvasive investigation of brain structure and function. Molecular MRI agents are beginning to be applied for experiments in the nervous system, where they have the potential to bridge from molecular to systems or organismic levels of analysis. Compared with canonical synthetic small...

16. Musashi proteins are post-transcriptional regulators of the epithelial-luminal cell state - Katz, Yarden; Li, Feifei; Lambert, Nicole J; Tam, Wai-Leong; Airoldi, Edoardo M; Lengner, Christopher J; Yu, Zhengquan; Jaenisch, Rudolf; Sokol, Ethan Samuel; Cheng, Albert W.; Gupta, Piyush; Burge, Christopher B.
The conserved Musashi (Msi) family of RNA binding proteins are expressed in stem/progenitor and cancer cells, but generally absent from differentiated cells, consistent with a role in cell state regulation. We found that Msi genes are rarely mutated but frequently overexpressed in human cancers and are associated with an epithelial-luminal cell state. Using ribosome profiling and RNA-seq analysis, we found that Msi proteins regulate translation of genes implicated in epithelial cell biology and epithelial-to-mesenchymal transition (EMT), and promote an epithelial splicing pattern. Overexpression of Msi proteins inhibited the translation of Jagged1, a factor required for EMT, and repressed EMT in...

17. Insight into the molecular mechanism of water evaporation via the finite temperature string method - Musolino, Nicholas; Trout, Bernhardt L.
The process of water's evaporation at its liquid/air interface has proven challenging to study experimentally and, because it constitutes a rare event on molecular time scales, presents a challenge for computer simulations as well. In this work, we simulated water's evaporation using the classical extended simple point charge model water model, and identified a minimum free energy path for this process in terms of 10 descriptive order parameters. The measured free energy change was 7.4 kcal/mol at 298 K, in reasonable agreement with the experimental value of 6.3 kcal/mol, and the mean first-passage time was 1375 ns for a single...

18. Bezier curve string method for the study of rare events in complex chemical systems - Bellucci, Michael A.; Trout, Bernhardt L.
We present a new string method for finding the most probable transition pathway and optimal reaction coordinate in complex chemical systems. Our approach evolves an analytic parametric curve, known as a Bezier curve, to the most probable transition path between metastable regions in configuration space. In addition, we demonstrate that the geometric properties of the Bezier curve can be used to construct the optimal reaction coordinate near the most probable reaction path, and can further be used to devise a ranking vector capable of identifying precisely which collective variables are most important for governing the transition between metastable states. We...

19. Metallocene/carbon hybrids prepared by a solution process for supercapacitor applications - Mao, Xianwen; Simeon, Fritz; Rutledge, Gregory C.; Hatton, T. Alan; Achilleos, Dimitra
Efficient and scalable solution-based processes are not generally available to integrate well-studied pseudocapacitive materials (i.e., metal oxides and conducting polymers) with other components such as porous carbon, mainly because these classes of pseudocapacitive systems have poor solubilities in solvents and exhibit no specific interactions with the other component. Here we report, for the first time, the integration of a metallocene polymer, polyvinylferrocene (PVF), with carbon nanotubes (CNTs) via a simple solution process for supercapacitor applications. The solution processability of the PVF/CNT hybrid is due to the high solubilities of PVF in organic solvents and the unique ability of the metallocene/carbon...

20. Compressibility of electrospun fiber mats - Choong, Looh Tchuin; Mannarino, Matthew M.; Basu, Sandip; Rutledge, Gregory C.
Compressive properties of electrospun fiber mats are reported for the first time. Mats of bisphenol-A polysulfone (PSU) and of poly(trimethyl hexamethylene terephthalamide) [PA 6(3)T] were electrospun and annealed over a range of temperatures spanning the glass transition temperature of each polymer. The data for applied stress versus mat solidity were found to be well-described by a power law of the form σ[subscript zz] = kE(ϕ[superscript n] − ϕ[n over 0]), where σ[subscript zz] is the applied stress and ϕ is solidity, in accord with the analysis of Toll (Polym Eng Sci 38(8):1337, 2004). The values of n range from 3.2...

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