gebhart/patrepeval huggingface dataset:
Attenuation of Porcine Reproductive and Respiratory Syndrome Virus by Molecular Breeding of Virus Envelope Genes from Genetically Divergent Strains (2012)

Molecular breeding via DNA shuffling can direct the evolution of viruses with desired traits. By using a positive-strand RNA virus, porcine reproductive and respiratory syndrome virus (PRRSV), as a model, rapid attenuation of the virus was achieved in this study by DNA shuffling of the viral envelope genes from multiple strains. The GP5 envelope genes of 7 genetically divergent PRRSV strains and the GP5-M genes of 6 different PRRSV strains were molecularly bred by DNA shuffling and iteration of the process, and the shuffled genes were cloned into the backbone of a DNA-launched PRRSV infectious clone. Two representative chimeric viruses, DS722 with shuffled GP5 genes and DS5M3 with shuffled GP5-M genes, were rescued and shown to replicate at a lower level and to form smaller plaques in vitro than their parental virus. An in vivo pathogenicity study revealed that pigs infected with the two chimeric viruses had significant reductions in viral-RNA loads in sera and lungs and in gross and microscopic lung lesions, indicating attenuation of the chimeric viruses. Furthermore, pigs vaccinated with the chimeric virus DS722, but not pigs vaccinated with DS5M3, still acquired protection against PRRSV challenge at a level similar to that of the parental virus. Therefore, this study reveals a unique approach through DNA shuffling of viral envelope genes to attenuate a positive-strand RNA virus. The results have important implications for future vaccine development and will generate broad general interest in the scientific community in rapidly attenuating other important human and veterinary viruses.
Additional Conjugation Methods and Immunogenicity of <i>Bacillus anthracis</i> Poly-γ- <scp>d</scp> -Glutamic Acid-Protein Conjugates (2006)

The capsule of Bacillus anthracis, composed of poly-gamma-d-glutamic acid (gammaDPGA), is an essential virulence factor of B. anthracis. The capsule inhibits innate host defense through its antiphagocytic action. gammaDPGA is a poor immunogen, but when covalently bound to a carrier protein, it elicits serum antibodies. To identify the optimal construct for clinical use, synthetic gammaDPGAs of different lengths were bound to carrier proteins at different densities. The advantages of the synthetic over the natural polypeptide are the homogeneous chain length and end groups, allowing conjugates to be accurately characterized and standardized and their chemical compositions to be related to their immunogenicities. In the present study, we evaluated, in addition to methods reported by us, hydrazone, oxime, and thioether linkages between gammaDPGA and several proteins, including bovine serum albumin, recombinant Pseudomonas aeruginosa exotoxin A, recombinant B. anthracis protective antigen (rPA), and tetanus toxoid (TT). The effects of the dosage and formulation on the immunogenicities of the conjugates were evaluated in mice. All conjugates were immunogenic. The optimal gammaDPGA chain length of 10 to 15 amino acids and the density, an average of 15 mol gammaDPGA per mol of protein, were confirmed. The thioether bond was the optimal linkage type, and TT and rPA were the best carriers. The optimal dosage was 1.2 to 2.5 microg of gammaDPGA per mouse, and adsorption of the conjugates onto aluminum hydroxide significantly increased the antibody response to the protein with a lesser effect on anti-gammaDPGA levels.
Head tilt response: A complementary test to the Subjective Visual Vertical (2010)

This paper studies the phenomenon of the perceived vertical by means of a novel dynamic experiment. This task is inspired in the Subjective Visual Vertical test and can be regarded as complementary in terms of how the information involved varies (visual, otolithic and neck proprioception). The experiment consists in presenting a white stripe in a pair of virtual reality goggles and adjusting the roll angle of the head until the stripe is aligned with the gravitational vertical. The roll angle of the head is measured and recorded along each trial where the white stripe changes position four times, after a specific amount of time. The task was run on a group of 28 normal subjects and a small sample of 5 patients with vestibular hypofunction. Six parameters derived from Control Theory were extracted from the data to characterize the subject transient response. All parameters for normal subjects were found to be normally distributed. Experimental results show that discrimination is possible between normal subjects and patients using just one or two of the parameters studied.
Dynamic spectrum refarming of GSM spectrum for LTE small cells (2013)

In this paper we propose a novel solution called dynamic spectrum refarming (DSR) for deploying LTE small cells using the same spectrum as existing GSM networks. The basic idea of DSR is that LTE small cells are deployed in the GSM spectrum but suppress transmission of all signals including the reference signals in some specific physical resource blocks corresponding to a portion of the GSM carriers to ensure full GSM coverage. Our study shows that the proposed solution can provide LTE mobile terminals with high speed data services when they are in the coverage of the LTE small cells while minimally affecting the service provided to GSM terminals located within the LTE small cell coverage area. Thus, the proposal allows the normal operation of the existing GSM networks even with LTE small cells deployed in that spectrum. Though the focus of this paper is about GSM spectrum refarming, an analogous approach can be applied to reuse code division multiple access (CDMA) spectrum for LTE small cells.
<title>Mass-producible microholographic tags</title> (1996)

Microtags are microscopic computer-generated holograms with 130-nm features and are mass- producible with EUVL. This fabrication method renders microtags difficult to counterfeit. Applications include tagging and tracking of microprocessors, memory chips, currency, and credit cards.
<title>Audio indexing using speaker identification</title> (1994)

In this paper, a technique for audio indexing based on speaker identification is proposed. When speakers are known a priori, a speaker index can be created in real time using the Viterbi algorithm to segment the audio into intervals from a single talker. Segmentation is performed using a hidden Markov model network consisting of interconnected speaker sub- networks. Speaker training data is used to initiate sub-networks for each speaker. Sub- networks can also be used to model silence, or non-speech sounds such as musical theme. When no prior knowledge of the speakers is available, unsupervised segmentation is performed using a non-real time iterative algorithm. The speaker sub-networks are first initialized, and segmentation is performed by iteratively generating a segmentation using the Viterbi algorithm, and retraining the sub-networks based on the results of the segmentation. Since the accuracy of the speaker segmentation depends on how well the speaker sub-networks are initiated, agglomerative clustering is used to approximately segment the audio according to speaker for initialization of the speaker sub-networks. The distance measure for the agglomerative clustering is a likelihood ratio in which speed segments are characterized by Gaussian distributions. The distance between merged segments is recomputed at each stage of the clustering, and a duration model is used to bias the likelihood ratio. Segmentation accuracy using agglomerative clustering initialization matches accuracy using initialization with speaker labeled data.
PA28, an activator of the 20 S proteasome, is inactivated by proteolytic modification at its carboxyl terminus. (1993)

PA28, a protein activator of the 20 S proteasome, was previously identified in soluble extracts of bovine red blood cells (Ma, C.-P., Slaughter, C. A., and DeMartino, G. N. (1992) J. Biol. Chem. 267, 10515-10523). To determine whether this regulatory protein is as widely distributed as the proteasome, PA28 content and activity were examined in various eukaryotic tissues by immunoblot analysis and by functional assays of tissue extracts. PA28 protein was present in all sources examined. PA28 activity, however, was not detected in many of these sources, including those with the highest level of PA28 protein. To determine the biochemical basis of this result, PA28 was purified from extracts of rat liver, which had high levels of PA28 protein but no PA28 activity. The resulting purified PA28 had no detectable activity but had native and subunit molecular weights indistinguishable from the active PA28 of bovine red blood cells. Using the inactivation of purified PA28 as an assay, a protein that inactivated PA28 without altering its apparent molecular weight on SDS-polyacrylamide gel electrophoresis was identified, purified, and characterized from bovine liver. It had biochemical and catalytic characteristics similar to those of lysosomal carboxypeptidase B. When leupeptin, an inhibitor of lysosomal carboxypeptidase B, was included in the buffers used for the preparation of PA28, PA28 activity was detected in tissues which otherwise failed to demonstrate this activity. A similar result was obtained when extracts were prepared in a manner that minimized disruption of lysosomes. Other carboxypeptidases such as carboxypeptidase Y and pancreatic carboxypeptidase B also inactivated PA28 without altering its apparent molecular weight. Active PA28 binds to the proteasome to form a protease-activator complex that can be isolated after velocity sedimentation centrifugation through glycerol density gradients. Carboxypeptidase-inactivated PA28 failed to form such a complex, suggesting that the carboxyl terminus of PA28 is required for binding to the proteasome. These results indicate the importance of the carboxyl terminus of PA28 for proteasome activation.
Creating navigable multi-level video summaries (2003)

We created an alternative approach to existing video summaries that gives viewers control over the summaries by selecting hyper-links to other video with additional information. We structure such summaries as "detail-on-demand" video, a subset of general hypervideo in which at most one link to another video sequence is available at any given time. Our editor for such video, Hyper-Hitchcock, provides a workspace in which an author can select and arrange video clips, generate composites from clips and from other composites, and place links between composites. To simplify dealing with a large number of clips, Hyper-Hitchcock generates iconic representations for composites that can be used to manipulate the composite as a whole. In addition to providing an authoring environment, Hyper-Hitchcock can automatically generate multi-level hypervideo summaries for immediate use or as the starting point for author modification.
Reactivation of latent HIV-1 provirus via targeting protein phosphatase-1 (2015)

We identified a novel class of PP1-targeting compounds that reactivate latent HIV-1 provirus by targeting PP1, increasing CDK9 phosphorylation and enhancing HIV transcription. This compound represents a novel candidate for anti-HIV-1 therapeutics aiming at eradication of latent HIV-1 reservoirs.
<title>Quantitative free-hand 3D ultrasound imaging based on a modified 1D transducer array</title> (2001)

An approach for acquiring dimensionally accurate 3D ultrasound data, based on a modified 1D transducer array, is presented. Th method avoids many of the drawbacks of conventional approaches to 3D ultrasound data acquisition. Scanning is simple and easy to perform in a clinical setting. A modified 1D transducer array is employed comprising a central conventional 1D imaging array and two perpendicular tracking arrays - each integrally mounted at each end of the imaging array. As the transducer is scanned in the elevation direction of the central array, the images acquired by the tracking array remain coplanar and hence it is possible to accurately track image motion using any one of several image tracking techniques. Methods for improving the performance and ergonomics of the transducer array are presented. In particular, a crossed electrode transducer structure is proposed for minimizing the total transducer footprint (contact surface area). The versatility of the approach in terms of its suitability for scanning breast, carotid and prostate is discussed. We have acquired both phantom and in-vivo 3D ultrasound data with the prototype imaging approach. Initial studies suggest that the linear dimensional accuracy in the elevation direction (i.e., the reconstructed direction) is approximately 5%.
Isoferritins in HIV infection (1989)

Placental isoferritins (PLF), known to be immunosuppressive in Hodgkin's disease and other states, were found to be increased in sera of subjects infected with HIV. We assayed for PLF using a 'sandwich' antigen capture enzyme-linked immunosorbent assay (ELISA) employing two monoclonal antibodies. Individuals with lymphadenopathy, with or without symptoms suggestive of AIDS-related complex, had the highest serum levels, which declined with progressive immunodeficiency. Total (normal) ferritins, in contrast, increased progressively with stage of disease. PLF was found on a subset of CD8 lymphocytes and appeared to block detection of the CD8 antigen by specific monoclonal antibodies. Elution of PLF by incubation with levamisole, but not by culture medium alone, led to the unblocking of the CD8 determinant on these cells. Profiles of isoferritins in HIV infection may provide clues to prognosis. PLF, a physiologic down-regulator of hematopoiesis and cellular immunity, could play a role in the progressive immune deficiency, marrow suppression and HIV expression that lead to AIDS.
Biologically active noncalcemic analogs of 1α,25-dihydroxyvitamin D with an abbreviated side chain containing no hydroxyl (2004)

Since the discovery of the active metabolite of vitamin D, i.e., 1alpha,25-dihydroxyvitamin D3, there has been a continuous effort to synthesize analogs able to carry out many of the functions of the native hormone without raising serum calcium concentration. The present report provides a series of previously undescribed analogs wherein this goal is realized. We have prepared 2-methylene-19-nor-1alpha-hydroxyvitamin D analogs of 1,25-(OH)2D3 that possess only two to four carbons of the side chain without a hydroxyl thereon. Compared to 1,25-(OH)2D3, these analogs are slightly less active in binding to the vitamin D receptor, in causing HL-60 differentiation, and are slightly less active in in vitro transcription assays using the 24-hydroxylase promoter attached to a luciferase reporter gene. Of considerable importance is that these analogs, given to rats at daily doses of up to 70 microg/kg of body weight per day, are either unable or only slightly able to raise serum calcium concentration but are nevertheless able to suppress parathyroid hormone levels in plasma up to 100% and induce 24-hydroxylase mRNA in skin. Because of their ability to act in vivo without raising serum calcium levels, they may be of considerable interest for the systemic treatment of diseases such as psoriasis, cancer, and secondary hyperparathyroidism of renal failure, where a rise in serum calcium is undesirable.
Using Bayesian Decision Theory to Design a Computerized Mastery Test (1990)

A theoretical framework for mastery testing based on item response theory and Bayesian deci sion theory is described. The idea of sequential testing is developed, with the goal of providing shorter tests for individuals who have clearly mastered (or clearly not mastered) a given subject and longer tests for those individuals for whom the mastery decision is not as clear-cut. In a simulat ed application of the approach to a professional certification examination, it is shown that average test lengths can be reduced by half without sacrifi cing classification accuracy. Index terms:
Rapid Analysis of Normal and Abnormal Cell Types in Human Semen and Testis Biopsies by Flow Cytometry (1983)

A simple, rapid procedure is described that quantitates RNA content and DNA content/chromatin condensation for each of many possible cell types and differentiation levels of the cells present in human semen. A fresh semen sample (1-6 hr postemission) or frozen sample (allowing samples to be accumulated and sent to a laboratory) is treated with a detergent solution, stained with acridine orange (AO), and measured by flow cytometry (FCM); approximately 10 minutes are required to measure 5,000 cells per sample and analyze the data with computer assistance. The following can be learned from a single measurement: a) the percentage of each cell type in semen including, i) mature sperm, ii) immature sperm precursor cells, representing all stages of development from spermatogonia to mature sperm, iii) somatic cells, e.g., leukocytes; b) normality/abnormality of sperm nuclear chromatin condensation. These measurements can be correlated with cell types in testis biopsies identified by two-parameter FCM measurements (RNA versus DNA) using AO as the fluorescent probe.
Controlling Cardiac Chaos (1992)

The extreme sensitivity to initial conditions that chaotic systems display makes them unstable and unpredictable. Yet that same sensitivity also makes them highly susceptible to control, provided that the developing chaos can be analyzed in real time and that analysis is then used to make small control interventions. This strategy has been used here to stabilize cardiac arrhythmias induced by the drug ouabain in rabbit ventricle. By administering electrical stimuli to the heart at irregular times determined by chaos theory, the arrhythmia was converted to periodic beating.
Development of a Time-of-Flight Mass Spectrometer Utilizing a Spiral Ion Trajectory (2009)

A novel time-of-flight mass spectrometer that utilizes a spiral ion trajectory was developed. In this mass spectrometer, the ions sequentially pass through four toroidal electrostatic sectors and revolve along a figure-eight-shaped orbit on a particular projection plane. Each toroidal electrostatic sector has eight stories, and during multiple revolutions, the ion trajectory shifted perpendicular to the projection plane in every cycle, thereby generating a spiral trajectory. Two prototypes, orthogonal acceleration time-of-flight mass spectrometer (OA-TOFMS) and matrix-assisted laser desorption/ionization time-of-flight mass spectrometer (MALDI-TOFMS) were made and tested. The total flight path lengths were 20 and 17 m for OA-TOFMS and MALDI-TOFMS, respectively. By adopting an ion optical system that has a flight path length more than five times longer than that of the commonly used reflectron ion optical system, the m/z-dependent mass resolving power was reduced while improving the mass accuracy of the mass measurements.
Non-scanning x-ray backscattering inspection systems based on x-ray focusing (2007)

Non-invasive real-time detection and identification of high explosives and improvised explosive devices, illicit materials hidden inside suitcases, vehicles, containers or behind metal and non-metal walls become critically important for safety and security worldwide. In this paper we will discuss non-scanning, portable real-time detection X-ray backscattering system based on novel Lobster-Eye X-ray focusing optics, which focuses backscatter photons from fully obscured objects several meters away that are being irradiated by short high-power X-ray pulses. Due to the ability of Lobster-Eye lenses to focus X-rays, such imaging systems collect more photons into a smaller spot, compared to traditional pinhole systems. This results in a higher signal-to-noise ratio and better spatial resolution. The signal-to-noise ratio can be further improved by using pulsed X-ray irradiation and a gated X-ray camera. The images can be further improved by software processing, which allows to reconstruct the object with high accuracy adequate for detection with high probability and low false alarm rate.
CloudDT: efficient tape resource management using deduplication in cloud backup and archival services (2012)

Cloud-based backup and archival services use large tape libraries as a cost-effective cold tier in their online storage hierarchy today. These services leverage deduplication to reduce the disk storage capacity required by their customer data sets, but they usually re-duplicate the data when moving it from disk to tape.Deduplication does not add significant I/O overhead when performed on disk storage pools. However, when deduplicated data is naively placed on tape storage, the high degree of data fragmentation caused by deduplication--combined with the high seek and mount times of today's tape technology--leads to high retrieval times. This negatively impacts the recovery time objectives (RTO) that the service provider has to meet as a part of the service level agreement (SLA).This work proposes CloudDT, an extension to Cloud backup and archival services to efficiently support deduplication on tape pools. This paper (i) details the main challenges to enable efficient deduplication on tape libraries, (ii) introduces a class of solutions based on graph-modeling of similarity between data items that enables efficient placement on tapes, and (iii) presents the design and initial evaluation of algorithms that alleviate tape mount time overhead and reduce on-tape data fragmentation.Using 4.5 TB of real-world workloads, our initial evaluations show that our algorithms retain at least 95% of the deduplication storage efficiency, and offer up-to 40% faster restore performance compared to the case of restoring non-deduplicated data. Therefore, our techniques allow the backup service provider to increase tape resource utilization using deduplication, while also improving the restore time performance for the end-user.
Restoring Bladder Function by Spinal Cord Neuromodulation in SCI (2015)

Abstract : We are submitting our Annual progress report for our grant entitled Restoring Bladder Function by Spinal Cord Neuromodulation in SCI (SC103209).Over the last year, we have initiated and completed the pilot study on five nave subjects and their follow-up and started to delineate the best magnetic stimulating parameter for restoring bladder function in SCI patients. As you will see in the report, we have noticed a significant difference between high frequency and low frequency magnetic stimulations in order to restoring urinary functions in SCI individuals. This also correlates with some electrophsiological findings. In the upcoming year, we are planning on enrolling more subjects to continue testing our hypothesis and complete the pilot phase of the study. As you can appreciate from the progress report, we remain on time to accomplish the tasks set forth in the study. We believe this study will yield important information to restore bladder function in SCI patients that will make a dramatic impact on the lives of those living with SCI.
Expression of FMS-like Tyrosine Kinase 3 Ligand by Oncolytic Herpes Simplex Virus Type I Prolongs Survival in Mice Bearing Established Syngeneic Intracranial Malignant Glioma (2012)

Treatment with G47Δ-Flt3L improves survival of glioma-bearing mice.