gebhart/patrepeval huggingface dataset:
The ORF3 Protein of Porcine Circovirus Type 2 Is Involved in Viral Pathogenesis In Vivo (2006)

Porcine circovirus type 2 (PCV2) is the primary causative agent of an emerging swine disease, postweaning multisystemic wasting syndrome. We previously showed that a novel identified protein, ORF3, was not essential for PCV2 replication in cultured PK15 cells and played a major role in virus-induced apoptosis. To evaluate the role of the ORF3 protein in viral pathogenesis in vivo, we inoculated 8-week-old BALB/c mice that have been developed for PCV2 replication with ORF3-deficient mutant PCV2 (mPCV2). By 42 days postinoculation, all of the mice inoculated with the mPCV2, as well as with wild-type PCV2 (wPCV2), had seroconverted to PCV2 capsid antibody, and the mutant induced levels of PCV2 antibodies that were higher than those of the wPCV2. The PCV2 genomic copy numbers in serum were significantly higher (P<0.05) in the wPCV2-inoculated mice than in mice inoculated with the mPCV2. Also, the wPCV2 caused microscopic lesions characterized by lymphocyte depletion with histiocytic infiltration of lymphoid organs, but the mutant virus failed to induce any obvious pathological lesions. In situ hybridization and immunohistochemical analyses also showed that larger amounts of viral DNA and antigens were detected in the lymph nodes of the wPCV2-inoculated than mPCV2-inoculated mice. Furthermore, animals of the wPCV2-inoculated group showed significant downshifts of CD8(+) T-cell subsets of peripheral blood lymphocytes compared to the control mice (P<0.05) at various time points postinoculation. Also, the proportions of the CD4(+) and CD4(+) CD8(+) cells were significantly reduced in wPCV2-inoculated mice at some time points postinoculation. In contrast, there are some reductions in the proportions of these subsets in the mutant virus-inoculated mice, but the proportions do not decrease significantly. Taken together, these results demonstrate that the ORF3 protein is also dispensable for viral replication in vivo and that it plays an important role in viral pathogenesis.
Reliable deposition of ultra-thin parylene (2016)

This paper reports a novel and reliable process to prepare ultra-thin parylene film based on a principle combining both molecular effusion and diffusion. For the first time, a technique for the deposition of parylene film thinner than 20 nm in a highly controllable and repeatable way is developed. Parylene films with various thicknesses could also be prepared in a single deposition run by using this method. This technique holds promising potentials in extensive applications, such as protection/dielectric layer for needle electrodes and flexible electronics, semi-permeable membrane, and other polymer engineering.
Constant-Weight Gray Codes for Local Rank Modulation (2011)

We consider the local rank-modulation (LRM) scheme in which a sliding window going over a sequence of real-valued variables induces a sequence of permutations. LRM is a generalization of the rank-modulation scheme, which has been recently suggested as a way of storing information in flash memory. We study constant-weight Gray codes for the LRM scheme in order to simulate conventional multilevel flash cells while retaining the benefits of rank modulation. We present a practical construction of codes with asymptotically-optimal rate and weight asymptotically half the length, thus having an asymptotically-optimal charge difference between adjacent cells. Next, we turn to examine the existence of optimal codes by specifically studying codes of weight 2 and 3. In the former case, we upper bound the code efficiency, proving that there are no such asymptotically-optimal cyclic codes. In contrast, for the latter case we construct codes which are asymptotically-optimal. We conclude by providing necessary conditions for the existence of cyclic and cyclic optimal Gray codes.
Complex Patterns of Human Antisera Reactivity to Novel 2009 H1N1 and Historical H1N1 Influenza Strains (2012)

Therefore, there may be a complex set of immune responses that are retained in people infected with seasonal H1N1 that can contribute to the reduced rates of H1N1 influenza infection in older populations.
Idaho Explosives Detection System (2004)

This is a preprint of a paper intended for publication in a journal or proceedings. Since changes may be made before publication, this preprint should not be cited or reproduced without permission of the author. This document was prepared as an account of work sponsored by an agency of the United States Government. Neither the United States Government nor any agency thereof, or any of their employees, makes any warranty, expressed or implied, or assumes any legal liability or responsibility for any third party&apos;s use, or the results of such use, of any information, apparatus, product or process disclosed in this report, or represents that its use by such third party would not infringe privately owned rights. The views expressed in this paper are not necessarily those of the U.S. Government or the sponsoring agency.
Stability Issues in Ambient-Temperature Passive Magnetic Bearing Systems (2000)

The ambient-temperature passive magnetic bearing system developed at the Lawrence Livermore National Laboratory achieves rotor-dynamic stability by employing special combinations of levitating and stabilizing elements. These elements, energized by permanent magnet material, create the magnetic and electrodynamic forces that are required for the stable levitation of rotating systems, such as energy-storage flywheels. Stability criteria, derived from theory, describe the bearing element parameters, i.e., stiffnesses and damping coefficients, that are required both to assure stable levitation (''Earnshaw-stability''), and stability against whirl-type rotor-dynamic instabilities. The work described in this report concerns experimental measurements and computer simulations that address some critical aspects of this overall stability problem. Experimentally, a test device was built to measure the damping coefficient of dampers that employ eddy currents induced in a metallic disc. Another test device was constructed for the purpose of measuring the displacement-dependent drag coefficient of annular permanent magnet bearing elements. In the theoretical developments a computer code was written for the purpose of simulating the rotor-dynamics of our passive bearing systems. This code is capable of investigating rotor-dynamic stability effects for both small-amplitude transient displacements (i.e., those within the linear regime), and for large-amplitude displacements, where non-linear effects can become dominant. Under the latter conditions a bearing system that is stable for small-amplitude displacements may undergo a rapidly growing rotor-dynamic instability once a critical displacement is exceeded. A new result of the study was to demonstrate that stiffness anisotropy of the bearing elements (which can be designed into our bearing system) is strongly stabilizing, not only in the linear regime, but also in the non-linear regime.
12-core fiber with one ring structure for extremely large capacity transmission (2012)

The feature of a multicore fiber with one-ring structure is theoretically analyzed and experimentally demonstrated. The one-ring structure overcomes the issues of the hexagonal close-pack structure. The possibility of 10-core fiber with Aeff of 110 μm(2) and 12-core fiber with Aeff of 80 μm(2) is theoretically presented. The fabricated 12-core fibers based on the simulation results realized Aeff of 80 μm(2) and crosstalk less than -40 dB at 1550 nm after 100-km propagation. The MCF with the number of core larger than seven and the small crosstalk was demonstrated for the first time.
Feasibility of a fast inverse dose optimization algorithm for IMRT via matrix inversion without negative beamlet intensities (2005)

A fast optimization algorithm is very important for inverse planning of intensity modulated radiation therapy (IMRT), and for adaptive radiotherapy of the future. Conventional numerical search algorithms such as the conjugate gradient search, with positive beam weight constraints, generally require numerous iterations and may produce suboptimal dose results due to trapping in local minima. A direct solution of the inverse problem using conventional quadratic objective functions without positive beam constraints is more efficient but will result in unrealistic negative beam weights. We present here a direct solution of the inverse problem that does not yield unphysical negative beam weights. The objective function for the optimization of a large number of beamlets is reformulated such that the optimization problem is reduced to a linear set of equations. The optimal set of intensities is found through a matrix inversion, and negative beamlet intensities are avoided without the need for externally imposed ad-hoc constraints. The method has been demonstrated with a test phantom and a few clinical radiotherapy cases, using primary dose calculations. We achieve highly conformal primary dose distributions with very rapid optimization times. Typical optimization times for a single anatomical slice (two dimensional) (head and neck) using a LAPACK matrix inversion routine in a single processor desktop computer, are: 0.03 s for 500 beamlets; 0.28 s for 1000 beamlets; 3.1 s for 2000 beamlets; and 12 s for 3000 beamlets. Clinical implementation will require the additional time of a one-time precomputation of scattered radiation for all beamlets, but will not impact the optimization speed. In conclusion, the new method provides a fast and robust technique to find a global minimum that yields excellent results for the inverse planning of IMRT.
Determining If Two Solid Ellipsoids Intersect (2003)

An analytical method is presented for determining if two ellipsoids share the same volume. The formulation involves adding an extra dimension to the solution space and examining eigenvalues that are associated with degenerate quadric surfaces. The eigenvalue behavior is characterized and then demonstrated with an example. The same method is also used to determine if two ellipsoids appear to share the same projected area based on an observer' s viewing angle. The following approach yields direct results without approximation, iteration, or any form of numerical search. It is computationally efe cient in the sense that no dimensional distortions, coordinate rotations, transformations, or eigenvector computations are needed. S the U.S. Satellite Catalog transitions from general perturba- tions to special perturbations, the positional accuracy of each space object will be readily available in the form of a covariance matrix. These covariances can be used to determine probability of collision, radio-frequency interference, and/or incidental laser illu- mination. Because the probability calculations can be computation- allyburdensome,itis desirable to prescreen candidate objectsbased on user-dee ned thresholds. Specie cally, each object can be repre- sented by a covariance-based ellipsoid and then processed to deter- mine if its uncertainty volume shares some space in common with another' s. Solid ellipsoids (or their projections) that do not intersect can be eliminated from further processing. This paper presents a simple analytical method to perform such screening. To date, all ellipsoidal prescreening methods involve numerical searches. 1 For computational efe ciency such prescreening is often reduced to spheres or keep-out boxes that have much larger vol- umes but allow for quick distance comparisons. The drawback to suchscreeningisthattheselargervolumescausemanyobjectstobe- come candidates for further (albeit unnecessary) processing. These methods result in increased downstream computational processing and/or increased operator workload to further assess potential satel- lite conjunctions. The following method adds an extra dimension to the solution space. The subset of eigenvalues that are associated with inter- secting degenerate quadric surfaces are then examined. The same method is also used to determine if two ellipsoids appear to share the same projected area based on viewing angle. The approach yields direct results without approximation, iteration, or any form of numerical search. It is computationally efe cient in the sense that no dimensional distortions, coordinate rotations, transforma- tions, or eigenvector computations are needed. This method ex- pands the two-dimensional work of Hill 2 in his formulation of degenerate conics (i.e., the characteristic matrix is singular). It also furthers his work by examining the associated eigenvalue behavior.
Operation principles of micro-plasma field effect transistor (2013)

We present design and theory of 3-dimensional micro-plasma field effect transistors (MOPFETs) that operate with atmospheric plasma. Both rf and dc plasmas were generated internally inside the MOPFET or using a separate device that generates the plasma for the MOPFET. The voltage applied to the MOPFET gate modifies the ionization rates of the gases in the channel between the drain and source. When the drain-source distance is larger than a few micrometers, the standard Paschen curve dictates the breakdown voltage while for smaller gaps a modified Paschen behavior based on the ion-enhanced field emission predicts a breakdown field that scales linearly with the gap distance becoming smaller for smaller gaps. MOPFETs terminal characteristics along with its hybrid pi model parameters are described.
Process Design and Economics for the Conversion of Algal Biomass to Biofuels: Algal Biomass Fractionation to Lipid- and Carbohydrate-Derived Fuel Products (2014)

Beginning in 2013, NREL began transitioning from the singular focus on ethanol to a broad slate of products and conversion pathways, ultimately to establish similar benchmarking and targeting efforts. One of these pathways is the conversion of algal biomass to fuels via extraction of lipids (and potentially other components), termed the 'algal lipid upgrading' or ALU pathway. This report describes in detail one potential ALU approach based on a biochemical processing strategy to selectively recover and convert select algal biomass components to fuels, namely carbohydrates to ethanol and lipids to a renewable diesel blendstock (RDB) product. The overarching process design converts algal biomass delivered from upstream cultivation and dewatering (outside the present scope) to ethanol, RDB, and minor coproducts, using dilute-acid pretreatment, fermentation, lipid extraction, and hydrotreating.
Coding for intersymbol interference channels-combined coding and precoding (1996)

This paper describes a new coding scheme for transmission over intersymbol interference (ISI) channels. This scheme, called ISI coding, combines trellis coding with precoding (used to combat ISI). Like the recently introduced precoding scheme of Laroia, Tretter, and Farvardin (LTF), the ISI coder makes it possible to achieve both shaping and coding gains over ISI channels. By combining coding and precoding, however, the ISI coder makes the "precoding loss" independent of the number of coset partitions used to generate the trellis code. At high rates (large signal-to-noise ratio (SNR)), this makes it possible to approach the Shannon capacity of an ISI channel. The V.34 (formerly V.fast) international modem standard for high-speed (up to 28.8 kb/s) communication over voice-band telephone lines uses the version of the ISI coder described in Section IV of this paper.
Insect juvenile hormones and pheromones of isopentenoid biogenesis (1978)

In their diversity, speciation, and sheer numerical superiority, few should question that insects are the dominant life-form on earth. Their utilization of the multifunctional isopentenoids to regulate their life processes is equally diverse. To catalog or even summarize the contribution of isopentenoids in the regulatory chemistry of insect feeding, development, reproduction, diaproduction, diapause, and behavior is beyond the scope of this review. However, a topical treatment of the chemistry of insect juvenile hormones and pheromones provides an insight into the dependence of insects upon isopentenoids.
The biogenic amine transporter activity of vinylogous amphetamine analogs (2016)

Vinylogous amphetamine analog<bold>S</bold>-<bold>6</bold>is a potent dual dopamine/serotonin (DA/5-HT) releaser with no activity at 5-HT<sub>2</sub>receptors.
3D Prostate Boundary Segmentation From Ultrasound Images Using 2D Active Shape Models (2006)

Boundary outlining, or segmentation, of the prostate is an important task in diagnosis and treatment planning for prostate cancer. This paper describes an algorithm for semi-automatic, three-dimensional (3D) segmentation of the prostate boundary from ultrasound images based on two-dimensional (2D) active shape models (ASM) and rotation-based slicing. Evaluation of the algorithm used distance- and volume-based error metrics to compare algorithm generated boundary outlines to gold standard (manually generated) boundary outlines. The mean absolute distance between the algorithm and gold standard boundaries was 1.09+/-0.49 mm, the average percent absolute volume difference was 3.28+/-3.16%, and a 5x speed increase as compared manual planimetry was achieved.
HTLV envelopes and their receptor GLUT1, the ubiquitous glucose transporter: a new vision on HTLV infection? (2004)

We identified the ubiquitous glucose transporter GLUT1 as a receptor for Deltaretroviruses HTLV-1 and HTLV-2 envelopes (Env), mediating viral binding and entry. Here, we review the context and key observations that led us to this finding: functional modules of HTLV SU are similar to those of Gammaretrovirus Env which use multimembrane-spanning nutrient transporters as receptors; the HTLV Env receptor is an early marker of T lymphocyte activation; and HTLV Env inhibits glucose transport. We review several molecular, viral, cellular and physiological aspects of HTLV infection in relation to the in vivo and in vitro properties of GLUT1. Also, we examine the implications of HTLV-1 Env-GLUT1 interactions and altered glucose transport on the two major HTLV-1-induced diseases, adult T cell leukemia (ATL) and neurodegenerative tropical spastic paraparesis/HTLV-associated myelopathy (TSP/HAM). Complementary to the classical models of disease progression, we propose new schemes that emphasize the potential metabolic alterations caused in different cellular compartments. Finally, we review the potential use of HTLV Env-derived constructs as tools for labeling GLUT1 in vivo and inhibiting GLUT1 transport in tumor cells.
The Role for Interleukin‐12 Therapy of Cutaneous T Cell Lymphoma (2001)

Recent phase I and phase II trials using recombinant human interleukin-12 (rhIL-12) for cutaneous T cell lymphoma (CTCL) have been completed. Observations on 32 evaluable patients revealed an overall response rate approaching 50 percent. Biopsy of regressing lesions revealed an increase in numbers of CD8+ and/or TIA-1+ T cells. These results suggest that rhIL-12 may induce lesion regression by augmenting antitumor cytotoxic T cell responses. Future trials will be focused on strategies for further immune enhancement by the concomitant use of additional immune augmenting cytokines with rhIL-12.
Fast 3D Cardiac Cine MR Imaging (1999)

We describe a technique for three-dimensional cine MR imaging. By using short repetition times (TR) and interleaved slice encoding, volumetric cine data can be acquired throughout the cardiac cycle with a temporal resolution of approximately 80 msec. A T1-shortening agent is used to produce contrast between blood and myocardium. A comparison between the acquisition times of this and several other two-dimensional techniques is presented.
An automated reasoning technique for providing moment-by-moment advice concerning the operation of a process (1987)

A system for continuously providing advice about the operation of some other device or process, rather than just problem diagnoses, must not only function in real time, but also cope with dynamic problem courses. The reasoning technique underlying such a system must not assume that faults have single causes, that queries to the user will be answered and advice to the user will be followed, nor that aspects of a problem, once resolved, will not reoccur. This paper presents a reasoning technique that can be used in conjunction with an inference engine to model the state of a problem situation throughout the entire problem-handling process, from discovery to final resolution. The technique has been implemented and installed on-line in a factory control room, as part of a real time expert system for advising the operators of a manufacturing process.
Automated segmentation of breast lesions in ultrasound images (2005)

Breast cancer is one of the leading causes of death in women. As a convenient and safe diagnosis method, ultrasound is most commonly used second to mammography for early detection and diagnosis of breast cancer. Here we proposed an automatic method to segment lesions in ultrasound images. The images are first filtered with anisotropic diffusion algorithm to remove speckle noise. The edge is enhanced to emphasize the lesion regions. Normalized cut is a graph theoretic that admits combination of different features for image segmentation, and has been successfully used in object parsing and grouping. In this paper we combine normalized cut with region merging method for the segmentation. The merging criteria are derived from the empirical rules used by radiologists when they interpret breast images. In the performance evaluation, we compared the computer-detected lesion boundaries with manually delineated borders. The experimental results show that the algorithm has efficient and robust performance for different kinds of lesions.
A Novel Endogenous Corticotropin Release Inhibiting Factor (1998)

ACTH is the major regulator of the body's adaptive response to stress and the physiological stimulus for glucocorticoid secretion. A hypothalamic corticotropin release inhibiting factor (CRIF) that inhibits ACTH synthesis and secretion has long been postulated but was not characterized until recently. We have recently identified a 22 amino acid peptide, prepro-thyrotropin releasing hormone (TRH) 178-199 that inhibits basal and stimulated ACTH synthesis and secretion in vitro and stress-induced ACTH secretion in vivo. Prepro-TRH 178-199 is abundant in several brain regions, including the external zone of the median eminence, where its concentration changes in response to stress. We propose that this peptide is a physiological regulator of ACTH production: an endogenous CRIF. Because prepro-TRH 178-199 is encoded within the same precursor as TRH, its expression is likely to be negatively regulated by thyroid hormones leading to changes in endogenous glucocorticoid levels. Streptococcal cell wall (SCW)-induced inflammation, a model of rheumatoid arthritis (RA), was alleviated after long-term thyroxine treatment. Inversely, a hypothyroid milieu led to decreased basal hypothalamic-pituitary-adrenal activity, but increased expression of IL-1 beta and MIP-1 alpha, specific markers for RA in humans. These results suggest that this putative CRIF may be an important component in the development of RA and that regulation of prepro TRH may be highly relevant to the development of other autoimmune diseases that are also exacerbated by low endogenous glucocorticoid levels.