gebhart/patrepeval huggingface dataset:
Steady supersonically rotating plasmas in the Maryland Centrifugal Experiment (2005)

The Maryland Centrifugal Experiment MCX [R. F. Ellis, A. B. Hassam, and S. Messer, Phys. Plasmas 8, 2057 (2000)] studies supersonic rotation and enhanced confinement produced by the application of an electric field perpendicular to an axial confining mirror magnetic field; radial shear in the rotation is predicted to stabilize magnetohydrodynamic (MHD) interchange modes. The MCX mirror field is 2.6 m in length, maximum mirror field 1.9 T, maximum midplane field 0.33 T; an inner coaxial core is driven by a 10 KV capacitor bank, producing the radial electric field which drives azimuthal rotation. MCX produces high density (n&amp;gt;1020m−3) fully ionized plasmas and has two operating modes. In the O (ordinary) mode the plasma rotates supersonically with azimuthal velocities in the range of 100 km/s for discharge times exceeding 8 ms. Ion temperatures are ∼30eV and momentum confinement times 100–200 μs. Sonic Mach numbers (uφ∕vti) in the range 1–2 and Alfvén Mach numbers (uφ∕vA)∼0.3 have been achieved for O mode discharges which remain steady for many milliseconds, much longer than MHD instability time scales; plasma lifetime is limited by the capacitance of the capacitor bank. MCX also has an enhanced mode of operation [higher rotation (HR) mode] with higher rotation velocities (&amp;gt;200km∕s), sonic Mach numbers greater than 3, Alfvén Mach numbers &amp;gt;∼0.5, and momentum confinement times of several hundred microseconds. HR mode occurs at higher B fields and lower discharge currents but is transient, transitioning to O mode after a few milliseconds. Both O and HR mode show spectroscopic evidence of radial velocity shear sufficient to satisfy the simplest criterion for MHD stability, but both modes also show significant fluctuations on magnetic probes.
Spamscatter: characterizing internet scam hosting infrastructure (2007)

Few Internet security issues have attained the universal public\nrecognition or contempt of unsolicited bulk email -- SPAM. The engine that\ndrives this enormous activity is not spam itself -- which is simply a means to\nan end -- but the various money-making ``scams'' (legal or illegal) that\nextract value from Internet users. In this paper, we focus on the Internet\ninfrastructure used to host and support such scams. Unlike mail-relays or\nbots, scam infrastructure is directly implicated in the spam profit cycle and\nthus considerably rarer and more valuable. Our goal is to measure and analyze\nthis scam infrastructure to better understand the dynamics and business\npressures exerted on spammers. To identify scam infrastructure, we employ an\nopportunistic technique called spamscatter. The underlying principal is that\neach scam is, by necessity, identified in the link structure of associated\nspams. To this end, we have built a system that mines email, identifies URLs\nin real time and follows such links to their eventual destination server. We\nfurther identify individual scams by clustering scam servers whose rendered Web\npages are graphically similar using a technique called image shingling. Using\nthe spamscatter technique on a large real-time spam feed (roughly 150,000 per\nday) we identify and analyze over 2,000 distinct scams hosted across more than\n7,000 distinct servers.Pre-2018 CSE ID: CS2007-0887
An Example of a Multi-Object Auction Game (1979)

Concurrent auctions of several objects are traditionally analyzed as if they were independent single-object auctions. Such an approximation may be very crude if bidders have budgetary restrictions, capacity constraints, or, in general, have non-linear utility functions. This paper presents a very simple multi-object auction for which explicit equilibrium strategies can be calculated; these equilibrium strategies have several qualitative characteristics arising from the multi-object nature of the example and therefore not present in typical single-object auctions. In particular, these results suggest that the observed variance in bids for offshore oil leases is not solely due to bidder uncertainty, but also to the method of auction currently employed.
Dissecting Aneurysm of the Infrarenal Abdominal Aorta — A Case Report (1989)

One case of primary dissecting aneurysm of the infrarenal abdominal aorta, diagnosed by ultrasound scanning, computed tomography, and angiography, is presented. Etiology, incidence, and diagnosis of abdominal aortic dissection are discussed, and a survey of the literature is included.
A representation of representation applied to a discussion of variable binding (1994)

States or state sequences in neural network models are made to represent concepts from applications. This paper motivates, introduces and discusses a formalism for denoting such representations; a representation for representations. The formalism is illustrated by using it to discuss the representation of variable binding and inference abstractly, and then to present four specific representations. One of these is an apparently novel hybrid of phasic and tensor-product representations which retains the desirable properties of each.
Direct Monolithic Integration of Organic Photovoltaic Circuits on Unmodified Paper (2011)

Organic photovoltaic circuits are monolithically fabricated directly on a variety of common paper substrates using oxidative chemical vapor deposition to vapor print conformal conductive polymer electrodes. The paper photovoltaic arrays produce >50 V, power common electronic displays in ambient indoor lighting, and can be tortuously flexed and folded without loss of function. Detailed facts of importance to specialist readers are published as ”Supporting Information”. Such documents are peer-reviewed, but not copy-edited or typeset. They are made available as submitted by the authors. Please note: The publisher is not responsible for the content or functionality of any supporting information supplied by the authors. Any queries (other than missing content) should be directed to the corresponding author for the article.
COMPUTER-BASED DESIGN OF NOVEL PROTEIN STRUCTURES (2005)

Over the past 10 years there has been tremendous success in the area of computational protein design. Protein design software has been used to stabilize proteins, solubilize membrane proteins, design intermolecular interactions, and design new protein structures. A key motivation for these studies is that they test our understanding of protein energetics and structure. De novo design of novel structures is a particularly rigorous test because the protein backbone must be designed in addition to the amino acid side chains. A priori it is not guaranteed that the target backbone is even designable. To address this issue, researchers have developed a variety of methods for generating protein-like scaffolds and for optimizing the protein backbone in conjunction with the amino acid sequence. These protocols have been used to design proteins from scratch and to explore sequence space for naturally occurring protein folds.
The PD-1/PD-L1 Axis and Virus Infections: A Delicate Balance (2019)

Programmed cell death protein (PD-1) and its ligands play a fundamental role in the evasion of tumor cells from antitumor immunity. Less well appreciated is the fact that the PD-1/PD-L1 axis also regulates antiviral immune responses and is therefore modulated by a number of viruses. Upregulation of PD-1 and its ligands PD-L1 and PD-L2 is observed during acute virus infection and after infection with persistent viruses including important human pathogens such as human immunodeficiency virus (HIV), hepatitis C virus (HCV), and hepatitis B virus (HBV). Experimental evidence suggests that insufficient signaling through the PD-1 pathway promotes immunopathology during acute infection by exaggerating primary T cell responses. If chronic infection is established, however, high levels of PD-1 expression can have unfavorable immunological consequences. Exhaustion and suppression of antiviral immune responses can result in viral immune evasion. The role of the PD-1/PD-L1 axis during viral infections is further complicated by evidence that PD-L1 also mediates inflammatory effects in the acute phase of an immune response. In this review, we discuss the intricate interplay between viruses and the PD-1/PD-L1 axis.
Cross-binding of factors to functionally different promoter elements in c-fos and skeletal actin genes. (1989)

A conserved 28-base-pair element in the skeletal actin promoter was sufficient to activate muscle-specific expression when placed upstream of a TATA element. This muscle regulatory element (MRE) is similar in structure to the serum response element (SRE), which is present in the promoters of the c-fos proto-oncogene and the nonmuscle actin genes. The SRE can function as a constitutive promoter element. Though the MRE and SRE differed in their tissue-specific expression properties, both elements bound to the same protein factors in vitro. These proteins are the serum response factor (SRF) and the muscle actin promoter factors 1 and 2 (MAPF1 and MAPF2). The SRF and MAPF proteins were resolved by chromatographic procedures, and they differed in their relative affinities for each element. The factors were further distinguished by their distinct, but overlapping, methylation interference footprint patterns on each element. These data indicate that the differences in tissue-specific expression may be due to a complex interaction of protein factors with these sequences.
Biological and biochemical characterization of a cloned Leu-3- cell surviving infection with the acquired immune deficiency syndrome retrovirus. (1986)

Leu-3- cells that survive infection with the acquired immune deficiency syndrome (AIDS) retrovirus can be induced with IUdR to express infectious virus. A cellular clone (8E5), isolated by limiting dilution of a mass culture of survivor cells, was found to contain a single, integrated provirus that was constitutively expressed. Although IUdR treatment of 8E5 cells failed to induce infectious virus, cocultivation with Leu-3+ cells generated the characteristic syncytia associated with acute AIDS retrovirus infection. The single integrated copy of proviral DNA directs the synthesis of all major viral structural proteins except p64, as monitored by immunoblotting. The relationship of the 8E5 clone to viral latency and persistence is discussed.
L-Dopa: Effect on Concentrations of Dopamine, Norepinephrine, and Serotonin in Brains of Mice (1970)

Large doses of L-dopa given to mice produced marked increases in brain dopamine, no change in norepinephrine, and a remarkable decrease in brain serotonin. This reduction apparently results from a release or displacement, or both, of serotonin from its storage sites.
A major costimulatory molecule on antigen-presenting cells, CTLA4 ligand A, is distinct from B7. (1993)

CTLA4 ligands are important costimulatory molecules because soluble CTLA4Ig blocks the induction of T cell responses and induces T cell tolerance. As CTLA4 immunoglobulin (CTLA4Ig) binds B7 when the latter is expressed on fibroblasts, it was widely assumed that CTLA4Ig blocks T cell costimulation by blocking the function of B7. Here we show that the major costimulatory ligand bound by CTLA4Ig (which we term CTLA4 ligand A) on antigen-presenting cells are not encoded by the B7 gene. CTLA4 ligand A also differs from B7 in cellular distribution and in the respective levels of expression. Both B7 and CTLA4 ligand A are critically involved in T cell costimulation.
Digital watermarking opportunities enabled by mobile media proliferation (2009)

Consumer usages of mobile devices and electronic media are changing. Mobile devices now include increased computational capabilities, mobile broadband access, better integrated sensors, and higher resolution screens. These enhanced features are driving increased consumption of media such as images, maps, e-books, audio, video, and games. As users become more accustomed to using mobile devices for media, opportunities arise for new digital watermarking usage models. For example, transient media, like images being displayed on screens, could be watermarked to provide a link between mobile devices. Applications based on these emerging usage models utilizing watermarking can provide richer user experiences and drive increased media consumption. We describe the enabling factors and highlight a few of the usage models and new opportunities. We also outline how the new opportunities are driving further innovation in watermarking technologies. We discuss challenges in market adoption of applications based on these usage models.
Severe Toxicity in Nonhuman Primates and Piglets Following High-Dose Intravenous Administration of an Adeno-Associated Virus Vector Expressing Human SMN (2018)

Neurotropic adeno-associated virus (AAV) serotypes such as AAV9 have been demonstrated to transduce spinal alpha motor neurons when administered intravenously (i.v.) at high doses. This observation led to the recent successful application of i.v. AAV9 delivery to treat infants with spinal muscular atrophy, an inherited deficiency of the survival of motor neuron (SMN) protein characterized by selective death of lower motor neurons. To evaluate the efficiency of motor neuron transduction with an AAV9 variant (AAVhu68) using this approach, three juvenile nonhuman primates (NHPs; aged 14 months) and three piglets (aged 7-30 days) were treated with an i.v. injection of an AAVhu68 vector carrying a human SMN transgene at a dose similar to that employed in the spinal muscular atrophy clinical trial. Administration of 2 × 10<sup>14</sup> genome copies per kilogram of body weight resulted in widespread transduction of spinal motor neurons in both species. However, severe toxicity occurred in both NHPs and piglets. All three NHPs exhibited marked transaminase elevations. In two NHPs, the transaminase elevations resolved without clinical sequelae, while one NHP developed acute liver failure and shock and was euthanized 4 days after vector injection. Degeneration of dorsal root ganglia sensory neurons was also observed, although NHPs exhibited no clinically apparent sensory deficits. There was no correlation between clinical findings and T-cell responses to the vector capsid or transgene product in NHPs. Piglets demonstrated no evidence of hepatic toxicity, but within 14 days of vector injection, all three animals exhibited proprioceptive deficits and ataxia, which profoundly impaired ambulation and necessitated euthanasia. These clinical findings correlated with more severe dorsal root ganglia sensory neuron lesions than those observed in NHPs. The liver and sensory neuron findings appear to be a direct consequence of AAV transduction independent of an immune response to the capsid or transgene product. The present results and those of another recent study utilizing a different AAV9 variant and transgene indicate that systemic and sensory neuron toxicity may be general properties of i.v. delivery of AAV vectors at high doses, irrespective of the capsid serotype or transgene. Preclinical and clinical studies involving high systemic doses of AAV vectors should include careful monitoring for similar toxicities.
The Binding Sites for Competitive Antagonistic, Allosteric Antagonistic, and Agonistic Antibodies to the I Domain of Integrin LFA-1 (2004)

We explore the binding sites for mAbs to the alpha I domain of the integrin alphaLbeta2 that can competitively inhibit, allosterically inhibit, or activate binding to the ligand ICAM-1. Ten mAbs, some of them clinically important, were mapped to species-specific residues. The results are interpreted with independent structures of the alphaL I domain determined in seven different crystal lattices and in solution, and which are present in three conformational states that differ in affinity for ligand. Six mAbs bind to adjacent regions of the beta1-alpha1 and alpha3-alpha4 loops, which show only small (mean, 0.8 angstroms; maximum, 1.8 angstroms) displacements among the eight I domain structures. Proximity to the ligand binding site and to noncontacting portions of the ICAM-1 molecule explains competitive inhibition by these mAbs. Three mAbs bind to a segment of seven residues in the beta5-alpha6 loop and alpha6 helix, in similar proximity to the ligand binding site, but on the side opposite from the beta1-alpha1/alpha3-alpha4 epitopes, and far from noncontacting portions of ICAM-1. These residues show large displacements among the eight structures in response to lattice contacts (mean, 3.6 angstroms; maximum, 9.4 angstroms), and movement of a buried Phe in the beta5-alpha6 loop is partially correlated with affinity change at the ligand binding site. Together with a lack of proximity to noncontacting portions of ICAM-1, these observations explain variation among this group of mAbs, which can either act as competitive or allosteric antagonists. One agonistic mAb binds distant from the ligand binding site of the I domain, to residues that show little movement (mean, 0.5 angstroms; maximum, 1.0 angstroms). Agonism by this mAb is thus likely to result from altering the orientation of the I domain with respect to other domains within an intact integrin alphaLbeta2 heterodimer.
Management of cough in advanced cancer. (2006)

Cough is a common symptom in cancer, with causes that can be benign or malignant. When severe, it affects patients' quality of life and well being. Treatment begins with a detailed history and careful physical examination, followed by chest imaging. Managing cough is directed at correcting the reversible causes. Empiric treatment of cough is valuable in both reversible and irreversible causes. We prefer hydrocodone as first-line empiric treatment, but when the cough is resistant to this, our second-line therapy would be the addition or substitution of benzonatate. Bronchodilators, as well as corticosteroids, are commonly employed in our practice and can be useful in unsuspected bronchospasm.
Modeling and evaluating heterogeneous memory architectures by trace-driven simulation (2008)

With the evolution of memory technologies, more types of memories are increasingly becoming available besides traditional DRAM. This paper focuses on the exploration how to organize heterogeneous memories for better performance. Two different models are introduced: Flat and Hierarchy. To evaluate our designs, the system bus trace is collected for trace-driven simulation. We use applications from SPEC jbb2005 and SPEC CPU2006 suite - typical server and desktop benchmark applications to compare the two models. It is shown that Hierarchical model can save much time in writing access and the average reading access time of it may longer or shorter than that of Flat according to the heterogeneous memory parameters. The Hierarchical model may also help to extend the life time of lower level memory while the Flat model can be used in a QoS enabled environment. Another contribution of our work is the recommended memory parameters in building the Hierarchical model.
A Focused He+ Ion Beam with a High Angular Current Density (1992)

Focusing characteristics of an ion beam from a He field ion source were investigated. For a W emitter as installed, a beam with an ion current of 0.7 pA was focused into 0.2 µm because the angular current density did not exceed 0.02 µA/sr. Improvement of angular current density was attempted by using the emission from a cleaned W (111) facet treated by field evaporation. From observation of field ion microscope images, it was found that the angular current density in the axial direction is dependent on the size of the (111) facet. For a large facet, a ringlike emission was obtained and the angular current density in the axial direction was not improved by adjustment of the extraction voltage. It is necessary to fabricate a facet of less than a few tens of atoms to achieve high current beam of axial direction. A beam with an angular current density of about 1 µA/sr was applicable to a focused ion beam after appropriate field evaporation.
VCAM-1 upregulation via PKCδ-p38 kinase-linked cascade mediates the TNF-α-induced leukocyte adhesion and emigration in the lung airway epithelium (2004)

Vascular cell adhesion molecule (VCAM)-1 plays a central role in the recruitment of inflammatory cells, and its expression is rapidly induced by proinflammatory cytokines such as TNF-alpha. In the present study, we show that pretreatment with rottlerin, a specific inhibitor of protein kinase C (PKC)-delta, or transient transfection with antisense PKCdelta oligonucleotides significantly inhibits TNF-alpha-induced expression of VCAM-1, but not of intercellular adhesion molecule (ICAM)-1 in human lung epithelium A549 cells. In addition, TNF-alpha was shown to induce the expression of VCAM-1 in a p38 kinase-dependent manner; also, TNF-alpha-induced p38 kinase activation was blocked by inhibition of PKCdelta, suggesting that p38 kinase is apparently situated downstream of PKCdelta in the TNF-alpha-signaling pathway to VCAM-1 expression. Notably, inhibition of the PKCdelta-p38 kinase cascade also attenuated the TNF-alpha-induced adhesion of neutrophils to lung epithelium and the trafficking of leukocytes across the epithelium into the airway lumen in vivo. Together, these findings indicate that signaling via PKCdelta-p38 kinase-linked cascade specifically induces expression of VCAM-1 in lung epithelium in response to TNF-alpha and that this effect is both functionally and clinically significant.
The Value of Acute Phase Protein Measurements in Clinical Practice (1992)

There is clearly a role for the measurement of acute phase proteins and other indices of the acute phase reaction but it is equally clear that no one laboratory test is suitable for use in all clinical situations. The choice of acute phase protein measurement depends on the diagnostic sensitivity and specificity of the measurement in the particular clinical situation. The choice of measurement must also include a decision on time of sampling and whether single or serial sampling would be more appropriate. In most situations where acute phase measurement is useful CRP is the assay of choice with alpha 1-antichymotrypsin also being useful in inflammatory bowel disease and other situations where a wider time window is required. The ESR or plasma viscosity can be useful to screen for disease. Cytokine and enzyme-inhibitor complex measurements may be important assays in the future.
Short- and long-term benefits of cognitive training (2011)

Does cognitive training work? There are numerous commercial training interventions claiming to improve general mental capacity; however, the scientific evidence for such claims is sparse. Nevertheless, there is accumulating evidence that certain cognitive interventions are effective. Here we provide evidence for the effectiveness of cognitive (often called "brain") training. However, we demonstrate that there are important individual differences that determine training and transfer. We trained elementary and middle school children by means of a videogame-like working memory task. We found that only children who considerably improved on the training task showed a performance increase on untrained fluid intelligence tasks. This improvement was larger than the improvement of a control group who trained on a knowledge-based task that did not engage working memory; further, this differential pattern remained intact even after a 3-mo hiatus from training. We conclude that cognitive training can be effective and long-lasting, but that there are limiting factors that must be considered to evaluate the effects of this training, one of which is individual differences in training performance. We propose that future research should not investigate whether cognitive training works, but rather should determine what training regimens and what training conditions result in the best transfer effects, investigate the underlying neural and cognitive mechanisms, and finally, investigate for whom cognitive training is most useful.