gebhart/patrepeval huggingface dataset:
A Living Fossil in the Genome of a Living Fossil: Harbinger Transposons in the Coelacanth Genome (2011)

Emerging data from the coelacanth genome are beginning to shed light on the origin and evolution of tetrapod genes and noncoding elements. Of particular relevance is the realization that coelacanth retains active copies of transposable elements that once served as raw material for the evolution of new functional sequences in the vertebrate lineage. Recognizing the evolutionary significance of coelacanth genome in this regard, we employed an ab initio search strategy to further classify its repetitive complement. This analysis uncovered a class of interspersed elements (Latimeria Harbinger 1-LatiHarb1) that is a major contributor to coelacanth genome structure and gene content (∼1% to 4% or the genome). Sequence analyses indicate that 1) each ∼8.7 kb LatiHarb1 element contains two coding regions, a transposase gene and a gene whose function is as yet unknown (MYB-like) and 2) copies of LatiHarb1 retain biological activity in the coelacanth genome. Functional analyses verify transcriptional and enhancer activities of LatiHarb1 in vivo and reveal transcriptional decoupling that could permit MYB-like genes to play functional roles not directly linked to transposition. Thus, LatiHarb1 represents the first known instance of a harbinger-superfamily transposon with contemporary activity in a vertebrate genome. Analyses of LatiHarb1 further corroborate the notion that exaptation of anciently active harbinger elements gave rise to at least two vertebrate genes (harbi1 and naif1) and indicate that the vertebrate gene tsnare1 also traces its ancestry to this transposon superfamily. Based on our analyses of LatiHarb1, we speculate that several functional features of harbinger elements may predispose the transposon superfamily toward recurrent exaptive evolution of cellular coding genes. In addition, these analyses further reinforce the broad utility of the coelacanth genome and other "outgroup" genomes in understanding the ancestry and evolution of vertebrate genes and genomes.
Subambient Temperature CO<sub>2</sub> and Light Gas Permeation Through Segmented Block Copolymers with Tailored Soft Phase (2010)

The permeation properties of a series of block copolymers based on poly(ethylene oxide)-ran-poly(propylene oxide) (PEO-ran-PPO) soft segments and monodisperse tetra-amide (T6T6T) hard segments have been studied. The polyether soft segment used in the current study differs from the commonly used pure poly(ethylene oxide) (PEO) soft segment by the fact that it contains 25 wt % randomly distributed poly(propylene oxide) (PPO). The presence of the methyl group of PPO suppresses crystallization of the soft segment and strongly improves the permeability of these materials, especially at subambient temperatures. In addition, the unique monodisperse character of the hard segment ensures a very well phase-separated morphology, resulting in a very pure soft phase. The soft segment length of these block copolymers was varied between 1000 and 10000 g/mol (62-89 wt %). High soft segment concentrations and flexibility were obtained resulting in high CO(2) permeabilities (up to 570 Barrer at 50 degrees C). Due to the random distribution of PPO in the predominantly PEO based soft segment crystallization of PEO was not observed at temperatures as low as -10 degrees C. CO(2) permeabilities exceeding 200 Barrer could be obtained at this low temperature. The CO(2)/light gas selectivity in these materials is governed by the solubility selectivity and consequently only slightly lowered because of the introduction of PPO in the soft segment. Comparison with literature revealed that this block copolymer system has exceptionally high CO(2) permeabilities combined with reasonable CO(2)/light gas selectivities. It is very interesting in CO(2) separation processes where subambient conditions are present (e.g., separation of CO(2) from natural gas), as at these low temperatures, one can take maximum advantage of the increased separation ability of the polymer materials while maintaining excellent transport characteristics.
Wireless Strain Gauge System in a Multipath Environment (2008)

A wireless strain sensing system utilizing passive, wireless, physically small and light weight sensors is desirable for measuring strain in harsh environments such as jet engine compressor and turbine blades.A cluttered and time varying environment results in high loss, blockage, multipath and modulation of the electromagnetic wave.Also, temperature changes affect the sensitivity of the strain measurement.Isolating the information signal from the reverberations in the environment requires time delays in the order of 100s of ns for jet engine environment.Therefore, a wireless strain gauge system that utilizes surface acoustic wave (SAW) strain sensors was studied and tested.
Automotive conformal antenna research at the Ohio State University (2002)

There has been a global trend toward more communications, navigation, and sensing applications in the automotive industry in the last few years. Modern automobiles have systems for AM radio, FM radio (with diversity), TV (with diversity), cellular (high and low bands), GPS, keyless entry, and roadside telecommunications. Coupled with this trend is the trend toward conformal or invisible antennas. The automobile manufacturers (and the buyers) want the systems to as be as unobtrusive as possible. New antenna designs are increasingly becoming conformal and imbedded. This means that new antenna designs are much more interdependent on the automobile body shape and material. These new conformal designs couple tightly to the body shape and each new body style requires that the antennas must be redesigned. All this is in an environment of decreasing time to market for new body styles. This paper discusses the conformal antenna research being done at the Ohio State University ElectroScience Laboratory. It discusses on-glass concepts and other hidden antenna concepts. The emphasis is on design techniques and measurement techniques. The use of new material for building the antenna, such as transparent conductive film is also shown.
Fetal tendon wound size modulates wound gene expression and subsequent wound phenotype (2010)

The fetal response to small tendon injury results in regenerative or scarless healing and is characterized by a markedly diminished cellular inflammatory response, lack of fibroplasia, and restoration of normal tissue architecture. We hypothesized that an increasing fetal tendon wound size would lead to increased wound inflammation and a change from regenerative to reparative healing and scar formation. We created small or large tendon wounds in early gestation fetal sheep and used histology to assess tissue architecture, immunohistochemistry to assess the cellular inflammatory response, ovine-specific gene microarrays, and real-time reverse transcription-polymerase chain reaction to measure the gene expression in response to injury. Small tendon wounds showed a regenerative healing phenotype with orderly deposition of collagen fibers while large tendon wounds showed disorderly collagen deposition consistent with scar formation. Small tendon wounds had few inflammatory cells at 7 and 28 days after injury, whereas the large wounds showed a significant inflammatory cell infiltrate at 7 days that resolved by 28 days. At 3 days, the differential expression of genes involved in the response to injury and inflammation were seen between large and small tendon wounds. By real-time polymerase chain reaction at 7 days, large tendon wounds also had significantly increased expression of interleukin-6, interleukin-8, transforming growth factor-β1, and transforming growth factor-β3, compared with the small wounds. Increasing the fetal tendon wound size results in increased proinflammatory gene expression, inflammatory cell infiltration, and a change from regenerative to reparative healing. This model allows the process of regenerative healing to be examined without the confounding variable of gestational age.
Biochemical and Functional Characterization of Inositol 1,3,4,5,6-Pentakisphosphate 2-Kinases (2000)

Synthesis of inositol 1,2,3,4,5,6-hexakisphosphate (IP(6)), also known as phytate, is integral to cellular function in all eukaryotes. Production of IP(6) predominately occurs through phosphorylation of inositol 1,3,4,5,6-pentakisphosphate (IP(5)) by a 2-kinase. Recent cloning of the gene encoding this kinase from Saccharomyces cerevisiae, designated scIpk1, has identified a cellular role for IP(6) production in the regulation of mRNA export from the nucleus. In this report, we characterize the biochemical and functional parameters of recombinant scIpk1. Purified recombinant scIpk1 kinase activity is highly selective for IP(5) substrate and exhibits apparent K(m) values of 644 nm and 62.8 microm for IP(5) and ATP, respectively. The observed apparent catalytic efficiency (k(cat)/K(m)) of scIpk1 is 31,610 s(-)(1) m(-)(1). A sequence similarity search was used to identify an IP(5) 2-kinase from the fission yeast Schizosaccharomyces pombe. Recombinant spIpk1 has similar substrate selectivity and catalytic efficiency to its budding yeast counterpart, despite sharing only 24% sequence identity. Cells lacking sc-IPK1 are deficient in IP(6) production and exhibit lethality in combination with a gle1 mutant allele. Both of these phenotypes are complemented by expression of the spIPK1 gene in the sc-ipk1 cells. Analysis of several inactive mutants and multiple sequence alignment of scIpk1, spIpk1, and a putative Candida albicans Ipk1 have identified residues involved in catalysis. This includes two conserved motifs: E(i/l/m)KPKWL(t/y) and LXMTLRDV(t/g)(l/c)(f/y)I. Our data suggest that the mechanism for IP(6) production is conserved across species.
Development of fabrication technology for low activation vanadium alloys as fusion blanket structural materials (2006)

Vanadium alloys, candidate fusion reactor blanket materials, consist of intrinsic low activation elements for 14 MeV fusion neutrons (e.g. vanadium, chromium and titanium). From 500 to 1000 K, the tensile strength of vanadium alloys is independent of temperature, enabling the fusion blanket to be operated at least 100 K higher than a blanket made from ferritic steel. However, most of the data have come from laboratory-scale fabricated vanadium alloy, so a feasibility study on large scale production of vanadium alloy products is required. In the present study, high-purity vanadium alloy products (e.g. plates, wires and tubes) were fabricated from reference high-purity V-4Cr-4Ti ingots designated as NIFS–HEAT, with the use of technologies applicable to industrial scale fabrication. A critical issue for NIFS–HEAT large-scale melting was to reduce the levels of interstitial impurities (e.g. C, N and O) that are known to deteriorate mechanical properties before and after neutron irradiation. Impurity behaviour during working and annealing processes and its effect on mechanical properties were investigated. Mechanical properties of the products were significantly improved by the control of Ti-C, N and O precipitation induced during the processes. Good mechanical properties comparable to laboratory-scale alloys were obtained at above 96% in cold working degree.
An analysis of pilot symbol assisted 16QAM for digital mobile communications (2002)

An analytical investigation of PSAM (pilot symbol assisted modulation) 16 QAM (quadrature amplitude modulation) is presented. Closed-form expressions for the optimized receiver coefficients, and a tight upper bound for the resulting symbol error rate in PSAM 16 QAM are given. The performance is within 2.4 dB of that of a perfect reference system when the Doppler spread is 5% of the symbol rate. At 1% Doppler, the loss is only 1 dB, and it can be further reduced at lower Doppler values.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">></ETX>
Beyond Nuclear Transport (1999)

T ' S not easy being a nuclear transport factor. During the G1, S, and G2 phases of the cell cycle, the nucleocytoplasmic transport machinery must tirelessly zigzag between the nucleus and cytoplasm while directing other proteins to the correct subcellular compartment. When M phase finally arrives, and the nucleus breaks down, do these proteins finally get to take a break? Apparently not. In the case of the Ran-GTPase and its associated nuclear transport factors, there is no rest for the weary. Instead, Ran and its associated proteins shift their focus from nuclear transport to the regulation of microtubule dynamics. Recent findings by several groups have shown that the GTP-bound form of Ran is necessary for the nucleation and organization of microtubule structures during M phase. Moreover, the implication that the active form of Ran is concentrated in the vicinity of chromosomes suggests that these findings may resolve the longstanding question of how chromosomes can influence spindle assembly in the absence of microtubule-nucleating organelles (i.e., as in plant mitosis or mammalian meiosis).
<title>Polyplanar optical display electronics</title> (1997)

The polyplanar optical display (POD) is a unique display screen which can be used with any projection source. The prototype ten inch display is two inches thick and has a matte black face which allows for high contrast images. The prototype being developed is a form, fit and functional replacement display for the B-52 aircraft which uses a monochrome ten-inch display. In order to achieve a long lifetime, the new display uses a 100 milliwatt green solid- state laser at 532 nm as its light source. To produce real- time video, the laser light is being modulated by a digital light processing (DLP) chip manufactured by Texas Instruments. In order to use the solid-state laser as the light source and also fit within the constraints of the B-52 display, the digital micromirror device (DMD) circuit board is removed from the Texas Instruments DLP light engine assembly. Due to the compact architecture of the projection system within the display chassis, the DMD chip is operated remotely from the Texas Instruments circuit board. We discuss the operation of the DMD divorced from the light engine and the interfacing of the DMD board with various video formats including the format specific to the B-52 aircraft. A brief discussion of the electronics required to drive the laser is also presented.
Protective multilayer packaging for long-term implantable medical devices (2014)

State of the art packaging for implantable devices uses metal or glass housings that are reliable but limited from a miniaturisation viewpoint as well as cost-intensive. We suggest a hermetic and biocompatible thin film packaging based on alternating organic/inorganic coatings for further miniaturisation of smart implantable MEMS devices that can be applied for long-term implantation. The combination of high intrinsic molecular density silicon oxide (SiOx) and pinhole-free and stress releasing poly-para-xylylene (parylene-C) thin films creates a new composite material, which is optimal for hermetic and biocompatible packaging. A novel single-chamber thin film deposition process was developed for the fabrication of SiOx/parylene thin film multilayer structures, using a modified chemical vapour deposition (CVD) process. According to permeation and conformity aspects, the inorganic layer is the crucial layer of the coating. Permeation measurements the highly ceramic SiOx material revealed a low helium gas permeation and a non-critical cracking thickness up to 300 nm. The morphology of the multilayer structure was analysed by scanning electron microscopy; an algorithm for defining ideal layer conformity was established and no local thickness deficiencies of deposited SiOx layers could be observed. To evaluate the corrosion protection, an adapted calcium mirror test based on water droplet permeation was developed, and the water permeation of conventional parylene-C layers (4.5 μm) was compared to multilayer stacks composed of 3 SiOx interlayers (4.7 μm). In this paper, it could be shown that by tailoring the thickness ratio between the involved layers, the percolative pathway and thereby, the permeation for direct water exposure could be considerably reduced compared to conventional parylene-C single layers with the same thickness.
Group III nitride and SiC based MEMS and NEMS: materials properties, technology and applications (2007)

With the increasing requirements for microelectromechanical systems (MEMS) regarding stability, miniaturization and integration, novel materials such as wide band gap semiconductors are attracting more attention. Polycrystalline SiC has first been implemented into Si micromachining techniques, mainly as etch stop and protective layers. However, the outstanding properties of wide band gap semiconductors offer many more possibilities for the implementation of new functionalities. Now, a variety of technologies for SiC and group III nitrides exist to fabricate fully wide band gap semiconductor based MEMS. In this paper we first review the basic technology (deposition and etching) for group III nitrides and SiC with a special focus on the fabrication of three-dimensional microstructures relevant for MEMS. The basic operation principle for MEMS with wide band gap semiconductors is described. Finally, the first applications of SiC based MEMS are demonstrated, and innovative MEMS and NEMS devices are reviewed.
VCE: A New Personated Virtual Cluster Engine for Cluster Computing (2008)

Visualization addresses the problem of making more efficient use of available computer resources. Recently, virtual clusters try either to virtualize a single physical cluster into multiple independent virtual clusters to provide a virtual server as a highly scalable and highly available server built on a cluster of real servers, or to share physical clusters to offer economies of scale and more effective use of resources by multiplexing. However, since programs running on a cluster demonstrate different types of requirements as their executions proceeds, such as support for intensive processing, security, and massive data communications, it is therefore quite unrealistic to assume that a statically configured cluster with a predetermined number of nodes with specific features and support can do any good for such programs. This paper presents a different usage for virtualization in the context of distributed computing using virtual clusters, called virtual cluster engine (VCE), that provides a computing environment that can be both statistically and dynamically (re)organized according to the needs and requirements of programs, so that they can achieve the best possible performance as they suit themselves, indeed within the constraints of available resources. Feasibility of the proposed architecture for VCE has been studied on an experimental platform using seven real machines, VMWare ESX, VMotion, and VMWare programming kit, and a number of virtual machines. On average, 20% improvement on response times under VCE was experienced.
Modulation of the motility of the vagina vera of <i>Ascaris suum in vitro</i> by FMRFamide-related peptides (1998)

Ascaris suum contains a large number of FMRFamide-related peptides (FaRPs) of which KNEFIRFamide (AF1), KHEYLRFamide (AF2) and KSAYMRFamide (AF8, also called PF3) have been extensively studied and are known to exert actions on somatic muscle strips of the worm. In the present study, the effects of AF1, AF2 and AF8 on the activity of the vagina vera of female A. suum have been examined in vitro. The vagina vera is a muscular tube connecting the uterus and vagina uteri to the gonopore and is probably involved in regulating egg output. The tissue exhibited spontaneous, rhythmic contractions in vitro, which were modulated by each of the FaRPs tested. The effects of each of the peptides were qualitatively and quantitatively different, and in each case were reversible. AF1 (1 microM) caused a biphasic response in the form of a transient lengthening of the preparation, followed by a shortening; contractions were initially inhibited but resumed 5 min post-addition of the peptide. Lower concentrations (< or = 0.1 microM) induced a less marked effect, with rhythmic contractions returning 5 min post-addition. AF2 and AF8 reduced contraction frequency at concentrations > or = 0.1 microM. Both peptides also caused the tissue to shorten, although the effects of AF8 on baseline tension were inconsistent. The apparent potencies of AF1 and AF8 on contraction frequency of the vagina vera were 10-fold greater than AF2 and, unlike their actions on A. suum somatic body wall muscles, the actions of AF1 and AF2 were qualitatively different. Indeed, the effects of each of these FaRPs on the vagina vera were markedly different from those observed on the somatic muscle.
Pattern smoothing compressed video transmission (2002)

In this paper we introduce a video smoothing algorithm for MPEG compressed live video. This algorithm, called pattern smoothing, transmits compressed video via both constant bit rate (CBR) and variable bit rate (VBR) channels. In order to take advantage of the gains achieved through statistical multiplexing of multiple sources over a single link, this algorithm utilizes a CBR channel to reduce the peak rate and variance of the VBR transmission. In addition to presenting this new algorithm, we compare it against three smoothing techniques presented in the literature. Key attributes used for comparison include receiver buffer size, live video support, startup delay, losslessness versus lossiness, and smoothing scale. Because network utilization is the most important performance metric for any smoothing algorithm, we provide a performance analysis of the pattern smoothing algorithm via simulation and compare these results to the best of the three presented smoothing algorithms.
A fuzzy logic controlled Anti-lock Braking System (ABS) for improved braking performance and directional stability (2008)

A simple and effective fuzzy logic controller is designed for an Anti-Lock Braking System (ABS) to improve the braking performance and directional stability of an automobile during braking, and steering-braking manoeuvres on uniform and nonuniform (µ-split) friction surfaces. The system consists of two controllers working in tandem. The first controller works on the longitudinal slip, and the second controller is responsible for the side-slip motion control of the vehicle. The fuzzy logic controller is implemented on a four-wheel nonlinear vehicle model with nonlinear tyre behaviour. Simulations are carried out and comparisons are made using the vehicle model with and without the fuzzy logic controlled ABS to assess controller performance.
New supramolecular polymers containing both terpyridine metal complexes and quadruple hydrogen bonding unitsElectronic supplementary information (ESI) available: experimental details. See http://www.rsc.org/suppdata/cc/b3/b314459n/ (2004)

Molecules containing quadruple hydrogen-bonding units as well as metal-complexing terpyridine moieties have been designed and assembled to result in a supramolecular polymer where both interactions are present in the main chain.
Clinical significance of DNA aberrant methylation in bladder cancer (2009)

Hie morbidity and mortality of bladder cancer are both the highest among urinary cancers in China. As a critical component of epigenetics, DNA abnormal methylation plays an important role during the occurrence and progression of bladder cancer. Recently, researchers focusing on the DNA methylation in bladder cancer have done much on it The results are of great clinical significance for screening,diagnosis and therapy of bladder cancer.

Key words: 
Bladder neoplasms;  DNA methylation;  Epigenetics