PhyloCSF: a comparative genomics method to distinguish protein-coding and non-coding regions

As high-throughput transcriptome sequencing provides evidence for novel transcripts in many species, there is a renewed need for accurate methods to classify small genomic regions as protein-coding or non-coding. We present PhyloCSF, a novel comparative genomics method that analyzes a multi-species nucleotide sequence alignment to determine whether it is likely to represent a conserved protein-coding region, based on a formal statistical comparison of phylogenetic codon models. We show that PhyloCSF's classification performance in 12-species _Drosophila_ genome alignments exceeds all other methods we compared in a previous study, and we provide a software implementation for use by the community. We anticipate that this method will be widely applicable as the transcriptomes of many additional species, tissues, and subcellular compartments are sequenced, particularly in the context of ENCODE and modENCODE

The Changing Face of Genomics

A report on the 5th annual Advances in Genome Biology and Technology (AGBT) and Automation in DNA Mapping and Sequencing (AMS) meeting, Marco Island, USA, 4-7 February 2004

Mysticism: from the Eleusinian Mysteries to Today

In the Hellenistic world, ‘mystical’ referred to “secret” religious rituals, specifically starting with the Eleusinian Mysteries in Ancient Greece. The mysteries were taken up in the same form in the Roman Empire and then morphed, as the dominant religion in the West shifted from the Olympians to the Way. This paper first focuses on the original meaning of the word, specifically as it refers to the Eleusinian Mysteries, the most significant Pan-Hellenic transcendence initiation ceremony aimed at accepting death and opening the consciousness into the superhuman understanding. The origins of the concept of mysteries, exploring in particular the Eleusinian mysteries, are briefly described, by investigating accounts from classical texts and archeological evidence. In the beginning of the last century the term mysticism reappeared and evolved in definition in religious studies and an account of the understanding is presented in the second part. The definition of the term “experience” is complex in general and even more complex for a term such as “mystical experience”. The last part of this paper explores the idea of what constitutes a mystical experience and how it relates to the accounts from the Eleusinian Mysteries. This paper uses literary and scholarly sources, in Ancient Greek, Greek and English.

An All-Optical Excitonic Switch Templated on a DNA Scaffold Operated in the Liquid and Solid Phases

The natural excitonic circuitry of photosynthetic organisms, including light harvesting antennas, provides a distinctive example of a highly attractive bio-inspired alternative to electronic circuits. Excitonics, which capitalizes on spatially arranged optically active molecules ability to capture and transfer light energy below the diffraction limit of light has garnered recognition as a potential disruptive replacement for electronic circuits. However, assembly of optically active molecules to construct even simple excitonic devices has been impeded by the limited maturity of suitable molecular scale assembly technologies. An example of nanophotonic circuitry, natural light harvesting antennas employ proteins as scaffolds to organize and self-assemble light-active molecules into excitonic networks capable of capturing and converting light to excitonic energy, and transferring that energy at ambient temperature. Protein self-assembly is extremely complex due to the over 20 amino acids building blocks used in the self-assembly process and the difficulty of predicting how proteins actually fold. An alternative method for organization and self-assembly may be found in the field DNA nanotechnology. DNA nanotechnology provides the most viable means to organize optically active molecules as there are only four nucleic acid building blocks and well-established simple design rules. Leveraging DNA nanotechnology will meet the requirements of precise proximity (selectivity) and appropriate number (specificity) needed to create larger arrays of multifunctional optically active molecules. Employing the design rules of DNA self-assembly, we have designed, engineered and operated an all-optical excitonic switch consisting of donor and acceptor chromophores and diarylethene photochromic modulating units assembled with nanometer scale precision. This work demonstrates the first integration of three diarylethene photochromic units into a single DNA oligonucleotide. Photoisomerization of diarylethenes has been shown to be one of the fastest photochemical reactions thereby affording potential switching speeds in the 10’s of picoseconds. Adopting diarylethenes as optically reversible switching units provided the ability to operate the all-optical excitonic switch through nearly 200 cycles without overt cyclic fatigue and excellent ON/OFF stability in both the liquid and solid phases. Assessing the static and dynamic cycling behavior of the all-optical excitonic switch allowed for the development of a model to predict characteristic switching times (τ) of 17.0 and 23.3 seconds for the liquid and solid phases, respectively which align well with the experimental data thereby validating the model. While these times are much faster than that of other non-optically based DNA-templated excitonic switches (τ ~ 10’s of minutes), the times noted here are limited by the steady-state optical instrumentation, (i.e., photon flux, detector integration time, and slit cycling speed), used to characterize the all-optical excitonic switches. Our model predicts switching times in the picosecond range could be achieved with the use of a high peak power ultrafast laser. First-order calculations estimate the all-optical excitonic switch has a footprint 37X smaller, a smaller volume by over 3 orders of magnitude and over an order of magnitude less energy per cycle than a state-of-the-art MOSFET. These findings, combined with no production of waste products and the potential ability to switch at speeds in the 10’s of picoseconds, establishes a prospective pathway toward all-optical excitonic circuits

Doctor of Philosophy

dissertationThis dissertation describes the use of cortical surface potentials, recorded with dense grids of microelectrodes, for brain-computer interfaces (BCIs). The work presented herein is an in-depth treatment of a broad and interdisciplinary topic, covering issues from electronics to electrodes, signals, and applications. Within the scope of this dissertation are several significant contributions. First, this work was the first to demonstrate that speech and arm movements could be decoded from surface local field potentials (LFPs) recorded in human subjects. Using surface LFPs recorded over face-motor cortex and Wernickes area, 150 trials comprising vocalized articulations of ten different words were classified on a trial-by-trial basis with 86% accuracy. Surface LFPs recorded over the hand and arm area of motor cortex were used to decode continuous hand movements, with correlation of 0.54 between the actual and predicted position over 70 seconds of movement. Second, this work is the first to make a detailed comparison of cortical field potentials recorded intracortically with microelectrodes and at the cortical surface with both micro- and macroelectrodes. Whereas coherence in macroelectrocorticography (ECoG) decayed to half its maximum at 5.1 mm separation in high frequencies, spatial constants of micro-ECoG signals were 530-700 ?m-much closer to the 110-160 ?m calculated for intracortical field potentials than to the macro-ECoG. These findings confirm that cortical surface potentials contain millimeter-scale dynamics. Moreover, these fine spatiotemporal features were important for the performance of speech and arm movement decoding. In addition to contributions in the areas of signals and applications, this dissertation includes a full characterization of the microelectrodes as well as collaborative work in which a custom, low-power microcontroller, with features optimized for biomedical implants, was taped out, fabricated in 65 nm CMOS technology, and tested. A new instruction was implemented in this microcontroller which reduced energy consumption when moving large amounts of data into memory by as much as 44%. This dissertation represents a comprehensive investigation of surface LFPs as an interfacing medium between man and machine. The nature of this work, in both the breadth of topics and depth of interdisciplinary effort, demonstrates an important and developing branch of engineering

Alien Registration- Wentworth, Mercina J. (Pittsfield, Somerset County)

https://digitalmaine.com/alien_docs/6472/thumbnail.jp