gebhart/patrepeval huggingface dataset:
Xrep, a plasmid-stimulating X chromosomal sequence bearing similarities to the BK virus replication origin and viral enhancers (1986)

The human X chromosome-linked fragment, "Xrep," was sequenced because it exerts a positive effect on plasmid growth in both E. coli and Saccharomyces cerevisiae. The sequence revealed three features similar to the human BK virus replication origin: Xrep has a true palindrome, CCTCC(T)3CCTCC, which is similar to "true" palindrome-like sequences found at the replication origins of polyoma [CCTC(T/C)10CTCC], BK [CCTC(A/G)8CCTCC] and SV40 [CCTCC(A)6GCCTCC] viruses. Twenty nucleotides away from the true palindrome, Xrep has the sequence GAATCCTATTCACTTTT while BK virus, the human analogue of SV40, has GAAATCCCTATTCTTTT in exactly the same position relative to the true palindrome. These two 17-mers differ only in the positions of two nucleotides comparing Xrep and BK virus. Also similar to the replication origins of DNA viruses, Xrep appears to have a cluster of enhancers adjacent to the origin-like sequences. Potent enhancer-like activity was detected in pSV1 X CAT/Xrep constructs. Xrep may originate from an endogenous virus, or from an X chromosomal replication origin.
Improved performance in ring diode lasers by controlled reflection feedback (1992)

We show that back reflection from the cleaved output waveguide termination in single-output Y-junction ring lasers has a deleterious effect on the light output by promoting lasing in the non-output-coupled direction. This effect is minimized by tilting the output waveguide about the ring axis by an angle θ. Devices (150-µm radius × 4-µm waveguide) with tilt angles θ = 0°, 5°, and 10° were fabricated. Tilting the laser by 10° increases the cw output power tenfold. Control of the reflection feedback to promote unidirectional lasing is also shown for dual-output ring lasers having separately contacted waveguide extensions that can be biased to control the reflection feedback or to act as photodetectors. Increasing the reflection feedback at one ring output alters the direction of ring lasing and affects the other ring output. Such controlled feedback will allow the development of unidirectional ring lasers.
Indirect model-based speech enhancement (2012)

Model-based speech enhancement methods, such as vector-Taylor series-based methods (VTS) [1, 2], share a common methodology: they estimate speech using the expected value of the clean speech given the noisy speech under a statistical model. We show that it may be better to use the expected value of the noise under the model and subtract it from the noisy observation to form an indirect estimate of the speech. Interestingly, for VTS, this methodology turns out to be related to the application of an SNR-dependent gain to the direct VTS speech estimate. In results obtained on an automotive noise task, this methodology produces an average improvement of 1.6 dB signal-to-noise ratio (SNR), relative to conventional methods.
FUTURE SUPERCONTINUUM MICROSCOPE FOR MEDICAL AND BIOLOGICAL APPLICATIONS (2017)

A supercontinuum (SC) light microscope is proposed for linear and nonlinear optical resonance and non-resonance processes in medical and biological applications. The SC can span from 300nm to 2500nm and may be used for a variety of applications for diagnosis of cancer, wound healing, fusing tissues, stimulation of nerves for therapeutic and treatment of disease. These will be discussed.
Absence of human T‐lymphotropic virus type I <i>tax</i> sequences in a population of normal blood donors in the Baltimore, MD/Washington, DC, area: results from a multicenter study (1999)

HTLV-I tax sequences appear not to be present in this population of 100 blood donors negative for anti-HTLV-I.
Global analysis of G‐protein‐coupled receptor signaling in human tissues (2003)

The G-protein-coupled receptor (GPCR) family mediates a host of cell-cell communications upon activation by diverse ligands. Numerous GPCRs have been shown to display anatomically selective patterns of gene expression, however, our understanding of the complexity of GPCR signaling within human tissues remains unclear. In an effort to characterize global patterns of GPCR signaling in the human body, microarray analysis was performed on a large panel of tissues to monitor the gene expression levels of the receptors as well as related signaling and regulatory molecules. Analysis of the data revealed complex signaling networks in many tissue types, with tissue-specific patterns of gene expression observed for the majority of the receptors and a number of components and regulators of GPCR signaling.
Delay-insensitive pipelined communication on parallel buses (1995)

Consider a communication channel that consists of several subchannels transmitting simultaneously and asynchronously. As an example of this scheme, we can consider a board with several chips. The subchannels represent wires connecting between the chips where differences in the lengths of the wires might result in asynchronous reception. In current technology, the receiver acknowledges reception of the message before the transmitter sends the following message. Namely, pipelined utilization of the channel is not possible. Our main contribution is a scheme that enables transmission without an acknowledgment of the message, therefore enabling pipelined communication and providing a higher bandwidth. However, our scheme allows for a certain number of transitions from a second message to arrive before reception of the current message has been completed, a condition that we call skew. We have derived necessary and sufficient conditions for codes that can tolerate a certain amount of skew among adjacent messages (therefore, allowing for continuous operation) and detect a larger amount of skew when the original skew is exceeded. These results generalize previously known results. We have constructed codes that satisfy the necessary and sufficient conditions, studied their optimality, and devised efficient decoding algorithms. To the best of our knowledge, this is the first known scheme that permits efficient asynchronous communications without acknowledgment. Potential applications are in on-chip, on-board, and board to board communications, enabling much higher communication bandwidth.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">></ETX>
Toward a Professional Platform for Chinese Character Conversion (2013)

Increasing communication among Chinese-speaking regions using respectively traditional and simplified Chinese character systems has highlighted the subtle-yet-extensive differences between the two systems, which can lead to unexpected hindrance in converting characters from one to the other. This article proposes a new priority-based multi-data resources management model, with a new algorithm called Fused Conversion algorithm from Multi-Data resources (FCMD), to ensure more context-sensitive, human controllable, and thus more reliable conversions, by drawing on reverse maximum matching, n -gram-based statistical model and pattern-based learning and matching. After parameter training on the Tagged Chinese Gigaword corpus, its conversion precision reaches 91.5% in context-sensitive cases, the most difficult part in the conversion, with an overall precision rate at 99.8%, a significant improvement over the state-of-the-art models. The conversion platform based on the model has extra features such as data resource selection and n -grams self-learning ability, providing a more sophisticated tool good especially for high-end professional uses.
microRNAs and the Ebola Virus (2015)

We recently reported an interesting finding that the Ebola virus (EBOV) encodes functional microRNAs (miRNAs) that can be produced through the cellular miRNA processing machinery. In addition, the prediction of EBOV miRNA target genes provided some clues about the regulatory roles of EBOV miRNAs. In summary, our findings provide a basis for further assessing the roles of the EBOV miRNAs in viral infection and virus-host interactions.
Exploring the community structure of newsgroups (2004)

We propose to use the community structure of Usenet for organizing and retrieving the information stored in newsgroups. In particular, we study the network formed by cross-posts, messages that are posted to two or more newsgroups simultaneously. We present what is, to our knowledge, by far the most detailed data that has been collected on Usenet cross-postings. We analyze this network to show that it is a small-world network with significant clustering. We also present a spectral algorithm which clusters newsgroups based on the cross-post matrix. The result of our clustering provides a topical classification of newsgroups. Our clustering gives many examples of significant relationships that would be missed by semantic clustering methods.
Age‐dependent expression of osteochondrosis‐related genes in equine leukocytes (2015)

The study demonstrates that OC-related genes are differentially expressed in horses of different ages compared with their age-matched controls. Some of the genes may be implicated in cell signalling and differentiation as well as carbohydrate and lipid metabolism and inflammation. However, the causal relationship between the differentially expressed genes and the development and progression of the OC lesions needs to be determined.
Two novel techniques for enhancing powering and control of multiple inductively-powered biomedical implants (2002)

Two techniques are presented that are expected to greatly enhance wireless data collection from high-bandwidth biosensors. By steering the aggregate magnetic field from a (near-) orthogonal set of AC-energized coils, selected sensor implants can be powered and communicated with. Communication with individual implants can also be enhanced through half-cycle amplitude modulation. This technique allows bit rates of up to twice the energizing frequency. Initial results and future investigations are discussed.
Analysis and interpretation of infrared microscopic maps: Visualization and classification of skin components by digital staining and multivariate analysis (1999)

Four analytical methods have been applied to infrared microscopic maps of human skin which contained basal cell carcinoma tumors—namely, point spectroscopy, grayscale functional group mapping, digital staining, and fuzzy C-means (FCM) cluster analysis. Spectroscopic interpretation using point spectroscopy allowed discrimination between normal and tumor-bearing skin components. Functional group mapping provided information on the distribution of lipids, proteins, nucleic acids, and collagen within skin sections. While functional group mapping only allowed examination of one material (or a ratio of two materials) at a time, a new approach termed digital staining allowed visualization of the distribution of up to three materials at one time. Digital staining thus gave a more detailed understanding of the tissue section. Finally, application of FCM cluster analysis, a nonsubjective, unsupervised classification methodology, allowed us to group spectra into five distinct clusters, which correlated to distinct tissue components in skin. Tumor-bearing skin was clearly separated from normal skin. When different analytical methods are used in conjunction, a unique understanding of tissues can be obtained. Our results demonstrate that infrared microscopy has potential for the pathological diagnosis of skin tumors. © 1999 John Wiley & Sons, Inc. Biospectroscopy 5: 265–275, 1999
Quality and safety of human hepatitis B vaccine. (1983)

Preparation of hepatitis B vaccine in our laboratories consists of a series of steps that include initial concentration of surface antigen by ammonium sulfate precipitation, followed by isopycnic banding and rate zonal centrifugation in a K-II centrifuge. The partially purified antigen concentrate is digested with pepsin at pH2 and the antigen is unfolded in 8M urea solution followed by renaturation. After gel filtration, the antigen is treated with formalin in 1:4000 dilution, adsorbed onto alum, and preserved with thimerosal. The final product contains essentially pure hepatitis B surface antigen. The process relies both on physical elimination of infectious virus particles and treatment with highly viral-destructive reagents in the pepsin, urea and formalin steps. The process is known to be highly destructive of all known viruses tested and to include procedures that are known to be highly destructive of representatives of all known groups of animal viral agents. The three-step process in inactivation provides a fail-safe system for establishing safety of the product. Tests in more than 20'000 persons, who are under surveillance, have shown no untoward effect and have confirmed the safety of the product.
Atomic Structures of the 30S Subunit and Its Complexes with Ligands and Antibiotics (2001)

The two subunits that make up the ribosome have both distinct and cooperative functions. The 30S ribosomal subunit binds messenger RNA (mRNA) and is involved in the selection of cognate transfer RNA (tRNA) by monitoring codon–anticodon base-pairing during the decoding process. The 50S subunit catalyzes peptide-bond formation. Both subunits work in concert to move tRNAs and mRNAs relative to the ribosome in translocation, and both are the target of a large number of naturally occurring antibiotics. Thus, useful information about the mechanism of translation can be gleaned from structures of both individual subunits and the intact ribosome. In this paper, we describe our work on the determination of the atomic structure of the 30S ribosomal subunit and its complexes with RNA ligands, antibiotics, and initiation factor IF1. The results provide structural insights into how the ribosome recognizes cognate tRNA and discriminates against near-cognate tRNA. They also provide a structural basis for understanding the action of various antibiotics that target the 30S subunit.
Multonic Markov word models for large vocabulary continuous speech recognition (1993)

A new class of hidden Markov models is proposed for the acoustic representation of words in an automatic speech recognition system. The models, built from combinations of acoustically based sub-word units called fenones, are derived automatically from one or more sample utterances of a word. Because they are more flexible than previously reported fenone-based word models, they lead to an improved capability of modeling variations in pronunciation. They are therefore particularly useful in the recognition of continuous speech. In addition, their construction is relatively simple, because it can be done using the well-known forward-backward algorithm for parameter estimation of hidden Markov models. Appropriate reestimation formulas are derived for this purpose. Experimental results obtained on a 5000-word vocabulary natural language continuous speech recognition task are presented to illustrate the enhanced power of discrimination of the new models.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">></ETX>
Using a three-dimensional optical simulation to investigate uncertainty in image-based dimensional measurements (2014)

Many advanced dimensional measurements exist that incorporate two-dimensional images of the object to be measured, such as structured-light measurements and photogrammetry. The measurements are quite complex and often suitable calibration artifacts are not available; consequently, a traceable uncertainty analysis is difficult. Advanced optical simulation packages can be used to assess important aspects of the uncertainty. These packages can simulate a virtual object to be measured, simulate a virtual camera, and trace rays as they leave a light source, scatter from the object, propagate through the camera, and arrive at the camera image plane. The result is a virtual image of the object whose dimensions are known. The virtual image(s) can then be processed as part of a dimensional measurement and the results compared to the known dimensions of the object. This allows different uncertainty aspects to be isolated and explored. It can be used to validate and understand the current methods of estimating measurement uncertainty, explore optimal measurement conditions, and/or test data analysis algorithms. These types of measurements involve a camera calibration process and the technique can also be used to check this step. This paper demonstrates the approach as applied to a photogrammetry measurement of a box.
Generating interconnect models from prototype hardware (2002)

With widespread acceptance of the IEEE 1149.1 standard, structured interconnect testing has become extremely important at the MCM, PWB and system levels. In the conventional paradigm, an interconnect topology model of the system under test is extracted from design information. From this model, interconnect test patterns can be generated by means of well understood algorithms. We demonstrate a new approach whereby the interconnect topology model is extracted by directly probing a hardware prototype of the system under test. This Golden Model can then be used to generate interconnect tests for other systems whose interconnect topology matches that of the prototype. Algorithms for this Golden Model extraction are presented and analyzed, empirical results are given, and the benefits and drawbacks of the approach are discussed.
Properties of EHD pump with combination of rod-to-rod and meshy parallel plates electrode assemblies (2009)

A high pressure required to drive the liquid can be generated by the compact electrohydrodynamic (EHD) pumps with multiple pairs of the rod-to-rod and meshy parallel plates electrode assemblies arranged in series. In this work, the performance of EHD pumps with electrodes up to nine pairs has been examined as a function of the applied voltage using a semi-insulating liquid. The pressure generated by energized electrodes gives rise to the vigorous liquid flow and the liquid ejects from the pump outlet. The flow direction always is from the cathode toward the anode. The pressure increases with nearly the square of the applied voltage and in proportion to the number of electrode pairs. The maximum pressure head achieved with a series of nine electrode pairs is 25.3 kPa at 18 kV with maximum power consumption of 7.2 W. The generated pressure is maintained stably at constant level of the corresponding value. EHD pumping is attributed to conduction pumping based on an unbalance of heterocharges with single ionic polarity in the vicinity of the anode and cathode.
Stability and piezoresistive properties of indium-tin-oxide ceramic strain gages (2004)

Thin film strain gages were developed to assess the mechanical behavior of components used for power and propulsion systems in harsh environments. Several types of strain sensors were fabricated with indium tin oxide (ITO) active strain elements and were tested at temperatures up to 1560/spl deg/C. These ceramic sensors exhibited excellent thermal stability and piezoresistive response at elevated temperature. A self-compensated ceramic strain gage (8 /spl mu/m thick) with thin film platinum resistors placed in series with the ITO active element exhibited a gage factor of 20.9 and a drift rate of 0.010%/hour at 1443/spl deg/C. To further increase the sensitivity and responsiveness of the ceramic sensors, uncompensated ITO strain gages prepared with an enlarged active area showed an increased piezoresistive response at 1455/spl deg/C with a gage factor of 39.1. Thus, at temperatures beyond 1400/spl deg/C, thickness of the ITO elements played a significant role in the high temperature stability and sensitivity of the gages. Self-compensated ITO sensors prepared with 8 /spl mu/m thick survived 20 hours at 1481/spl deg/C with a gage factor 2.36 and drift rate 0.0092%/hour. However, 10 /spl mu/m thick ITO strain gages were operated at temperatures beyond 1500/spl deg/C for tens of hours. The latter sensors exhibited a drift rate < 0.00001%/hour and a gage factor of 131 at 1530/spl deg/C. SEM micrographs of thick ITO sensors revealed a partially sintered microstructure with a uniform distribution of nanopores. To reproduce this microstructure by alternative means, ceramic sensors were prepared in nitrogen rich environments and tested to verify the large piezoresistive response at temperatures above 1550/spl deg/C. The results of our efforts to improve the stability and piezoresistive response of ITO strain gages at high temperature are presented here and the potential applications of these nanoporous ceramic sensors are discussed.
Efficient Optimal Search under Expensive Edge Cost Computation (2017)

Optimal heuristic search has been successful in many domains, including journey planning, route planning and puzzle solving. Existing work typically assumes that the cost of each action can easily be obtained. However, in many problems, the exact edge cost is expensive to compute. Existing search algorithms face a significant performance bottleneck, due to an excessive overhead associated with dynamically calculating exact edge costs. We present DEA*, an algorithm for problems with expensive edge cost computations. DEA* combines heuristic edge cost evaluations with delayed node expansions, reducing the number of exact edge computations. We formally prove that DEA* is optimal and it is efficient with respect to the number of exact edge cost computations. We empirically evaluate DEA* on multiple-worker routing problems where the exact edge cost is calculated by invoking an external multi-modal journey planning engine. The results demonstrate the effectiveness of our ideas in reducing the computational time and improving the solving ability. In addition, we show the advantages of DEA* in domain-independent planning, where we simulate that accurate edge costs are expensive to compute.
Couplers for multiterminal data-distribution systems (1979)

Fiber-optic versions of multiterminal data distribution systems for ship and aircraft platforms require specialized optical couplers for their realization. NRL has concentrated in the development of planar star1 and fused-tapered fiber-access couplers to be used with multimode single-fiber data-transmissions lines.
Superplastic deformation behavior of high strength aluminum alloy 7475 sheet. (1986)

7475 aluminum alloy sheet with a grain size of about 10 μm showed a large elongation of 780% when deformed at 516°C with the strain rate (ε) of 2×10-4 sec-1. The plastic deformation behavior was greatly affected by grain size (d), deformation temperature and strain rate, and was represented by εαd-n where n=1.8-2.5 at 516°C. Moreover, an activation energy for the deformation was found to be 84 kJ/mol, which is about a half of that of creep deformation. The superplastic deformation can be explained by a diffusion accomodated grain boundary sliding model.