gebhart/patrepeval huggingface dataset:
Improving trace cache effectiveness with branch promotion and trace packing (1998)

The increasing widths of superscalar processors are placing greater demands upon the fetch mechanism. The trace cache meets these demands by placing logically contiguous instructions in physically contiguous storage. As a result, the trace cache delivers instructions at a high rate by supplying multiple fetch blocks each cycle.In this paper, we examine two techniques to improve the number of instructions delivered each cycle by the trace cache. The first technique, branch promotion, dynamically converts strongly biased branches into branches with static predictions. Because these promoted branches require no dynamic prediction, the branch predictor suffers less from the negative effects of interference.Branch promotion unlocks the potential of the second technique: trace packing. With trace packing, trace segments are packed with as many instructions as will fit, without regard to naturally occurring fetch block boundaries. With both techniques, the effective fetch rate of the trace cache jumps up 17% over a trace cache which implements neither.On a machine where the execution engine has a very aggressive memory disambiguator, the performance of a machine using branch promotion and trace packing is on average 11% higher than a machine using neither technique.
Amplification of plant U3 and U6 snRNA gene sequences using primers specific for an upstream promoter element and conserved intragenic regions (1990)

U-snRNA genes in higher plants contain two essential promoter elements, the USE with sequence RTCCCACATCG and the TATA-like box, positioned in the -70 and -30 regions, respectively. Using an oligodeoxynucleotide containing the USE motif and oligodeoxynucleotides specific for the intragenic regions conserved in U-snRNAs, several sequences encoding U6 and U3 snRNAs were determined by polymerase chain reaction (PCR) amplification of Arabidopsis thaliana and tobacco genomic DNAs. This method provides a simple and rapid procedure for characterisation of plant U-snRNA genes and their promoters. It could also be used for the characterisation of other genes containing conserved upstream promoter elements. PCR-derived fragments were used as probes for the isolation of the U3 snRNA genes from a genomic library of Arabidopsis. Two isolated U3 genes were shown to be active when transfected into protoplasts of Nicotiana plumbaginifolia. Both U3 genes contain the USE and TATA-like upstream elements located in similar positions to the U6 genes of Arabidopsis. The encoded Arabidopsis U3 snRNAs can be folded into a secondary structure which is more similar to that of U3 RNAs from lower eukaryotes rather than from metazoa.
On extensions and refinements of Hermite-Hadamard inequalities for convex functions (2003)

In this paper, we obtain two theorems: Theorem 1 is extensions and infinite refinements of Hermite-Hadamard inequalities; Theorem 2 is extensions from Theorem 1.
The AUUCU Repeats Responsible for Spinocerebellar Ataxia Type 10 Form Unusual RNA Hairpins (2005)

Spinocerebellar ataxia type 10 is an autosomal dominant disorder caused by expansion of a pentameric repeat tract (ATTCT.AGAAT)(n) in intron 9 of the gene that encodes ataxin-10. We have analyzed duplex DNA containing the repeat, the individual DNA strands, and the RNA that would be generated by transcription of the repeat. Circular dichroism and UV absorbance measurements suggest that the previously reported tendency of the repeat to unpair when supercoiled is probably related simply to GC content rather than reflecting any unusual property of the duplex. DNA containing d(ATTCT)9 forms a folded structure at relatively low temperatures, whereas the antisense strand, d(AGAAT)9, does not form a structure even at 0 degrees C. In contrast r(AUUCU)9 forms a folded structure under physiologically reasonable conditions. S1 nuclease analysis reveals a single region of hypersensitivity in the middle of the repeat tract, whereas V1 digestion is consistent with a hydrogen bonded or well stacked structure. CD spectroscopy shows that the structure is unimolecular and hydrogen bonded and has a significant amount of A-form helix. NMR spectroscopy demonstrates that these hydrogen bonds comprise an equal number of A.U and U.U base pairs. Our data thus suggest that the repeat forms an unusual RNA hairpin. Thus the ability to form an RNA hairpin seems to be a common property of those Repeat Expansion Diseases that are not recessively inherited and are caused by repeats that are transcribed but not translated.
Corporate Soulcraft in the Age of Brutal Markets (1997)

The economic and political arguments for the market principle over alternative forms of economic organization are to my mind irrefutable. It is on the moral level that the perplexing concerns about capitalism center, concerns that have been raised from the beginnings of the industrial era down to the present time. This essay focuses on one major aspect of the ongoing moral test of capitalism: the test of whether our major corporations can both succeed in their profit-making efforts and also serve as one of society’s chief mediating structures that stand, like family, church and community, between the individual and the state. Should the corporation serve not simply as a utilitarian arrangement for the efficient production of high quality goods and services, but also as a moral community that shapes human character and behavior? How can it do so in this age of brutal markets? James Q. Wilson, professor of management at UCLA, has no doubt about the answer. In an article last year, he said: “The problem of imbuing large-scale enterprise with a decent moral life is fundamental.” Corporations “are systems of human action that cannot for long command the loyalty of their members if their standards of collective action are materially lower than those of their individual members.” Capitalists should recognize, he concluded, “that, while free markets will ruthlessly eliminate inefficient firms, the moral sentiments of man will only gradually and uncertainly penalize immoral ones. But, while the quick destruction of inefficient corporations threatens only individual firms, the slow anger at immoral ones threatens capitalism, and thus freedom itself.”
Projecting Global Occurrence ofCryptococcus gattii (2009)

Cryptococcus gattii and C. neoformans cause pulmonary and systemic cryptococcosis. Recently, C. gattii was recognized as a distinct pathogen of humans and animals. We analyzed information from 400 publications (1948-2008) to examine whether the fungus occurs globally. Known distribution of C. gattii is possibly limited because specialized reagents for differentiation from C. neoformans are not readily available and not always used, and environmental surveys are patchy. However, autochthonous reports of C. gattii cryptococcosis have now been recognized from tropical and temperate regions. An ongoing outbreak in western Canada strengthens the case that the range of the pathogen has expanded. A few studies have highlighted differences in cryptococcosis between C. gattii and C. neoformans. More than 50 tree species have yielded C. gattii especially from decayed hollows suggesting a possible ecologic niche. This pathogen merits more attention so its environmental occurrence and role in cryptococcosis can be accurately determined.
Filamentous Polymer Nanocarriers of Tunable Stiffness that Encapsulate the Therapeutic Enzyme Catalase (2009)

Therapeutic proteins are prone to inactivation by aggregation, proteases and natural inhibitors, motivating development of protective delivery systems. Here we focus on protective encapsulation of the potent antioxidant enzyme, catalase, by filamentous polymer nanocarriers (f-PNC), with the specific goal of addressing whether polymer molecular weight (MW) controls formation and structural properties such as size and stiffness. While maintaining the same MW ratio of polyethylene glycol to polylactic acid, a series of PEG-b-PLA diblock copolymers were synthesized, with total MW ranging from about 10 kg/mol to 100 kg/mol. All diblocks formed f-PNC upon processing, which encapsulated active enzyme that proved resistant to protease degradation. Further, f-PNC stiffness, length, and thickness increased with increasing MW. Interestingly, heating above a polymer's glass transition temperature (<30 degrees C) increased f-PNC flexibility. Thus, we report here for the first time f-PNC that encapsulate an active enzyme with polymer MW-tunable flexibility, offering several potential therapeutic applications.
Adaptive management report for the Clark County, Nevada Multiple Species Habitat Conservation Plan (2006)

The Desert Conservation Program administers an incidental take permit for desert tortoise and 77 other species. The permit was issued in 2001 by the United States Fish and Wildlife Service in accordance with the Endangered Species Act. Compliance with the permit requires implementation of the Clark County Multiple Species Habitat Conservation Plan. This plan requires an adaptive management program and a biennial report by an independent science advisor to assess the status of the plan and make recommendations for future funding. The 2008 Adaptive Management Report reviews current data on land use trends, habitat loss, species status, plan implementation, programmatic effectiveness, and makes recommendations for the future.
The Bottom-Up Approach to Molecular-Level Devices and Machines (2002)

The macroscopic concepts of a device and a machine can be extended to the molecular level. Molecular-level devices and machines are constructed by a bottom-up approach. The atom-by-atom bottom-up approach is unrealistic from the chemical viewpoint. The bottom-up approach molecule-by-molecule following the guidelines of supramolecular (multicomponent) chemistry has proved to be successful. The extension of the concepts of a device and a machine to the molecular level is of interest not only for basic research, but also for the growth of nanoscience and the development of nanotechnology.
Patterns of unexpected in-hospital deaths: a root cause analysis (2011)

The traditional threshold breach method of detecting instability on hospital wards was not scientifically derived; explaining the failure of threshold based monitoring and rapid response team activation in randomized trials. Furthermore, the thresholds themselves are arbitrary and capricious. There are three common fundamental pathophysiologic patterns of unexpected hospital death. These patterns are too complex for early detection by any unifying numeric threshold. New methods and technologies which detect and identify the actual patterns of evolving death should be investigated.
An Introduction to Least Commitment Planning (1994)

Recent developments have clarified the process of generating partially ordered, partially specified sequences of actions whose execution will achieve an agent's goal. This article summarizes a progression of least commitment planners, starting with one that handles the simple STRIPS representation and ending with UCPOP, a planner that manages actions with disjunctive precondition, conditional effects, and universal quantification over dynamic universes. Along the way, I explain how Chapman's formulation of the modal truth criterion is misleading and why his NP-completeness result for reasoning about plans with conditional effects does not apply to UCPOP.
Design of Quad-Edge-Triggered Sequential Logic Circuits for Ternary Logic (2019)

We propose a quad-edge-triggered flip-flop which captures and propagates a ternary data signal at four-edges of a ternary clock signal. The proposed ci <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">r</sup> cuit uses carbon nanotube FETs and consists of four types of logic gate: ternary clock driver, standard ternary inverter, binary inverter, and transmission gate. HSPICE simulation result has confirmed that power consumption of QETFF is lower than conventional single-edge-triggered flip-flop. The average power consumption is reduced by 31% in flip-flop and 75% in clock tree. We designed a ternary serial adder using QETFF and the energy efficiency of the proposed circuit is significantly improved compared to the previous design of ternary serial adder.
Light-Independent Phytochrome Signaling Mediated by Dominant GAF Domain Tyrosine Mutants ofArabidopsisPhytochromes in Transgenic Plants (2007)

The photoreversibility of plant phytochromes enables continuous surveillance of the ambient light environment. Through expression of profluorescent, photoinsensitive Tyr-to-His mutant alleles of Arabidopsis thaliana phytochrome B (PHYB(Y276H)) and Arabidopsis phytochrome A (PHYA(Y242H)) in transgenic Arabidopsis plants, we demonstrate that photoconversion is not a prerequisite for phytochrome signaling. PHYB(Y276H)-expressing plants exhibit chromophore-dependent constitutive photomorphogenesis, light-independent phyB(Y276H) nuclear localization, constitutive activation of genes normally repressed in darkness, and light-insensitive seed germination. Fluence rate analyses of transgenic plants expressing PHYB(Y276H), PHYA(Y242H), and other Y(GAF) mutant alleles of PHYB demonstrate that a range of altered light-signaling activities are associated with mutation of this residue. We conclude that the universally conserved GAF domain Tyr residue, with which the bilin chromophore is intimately associated, performs a critical role in coupling light perception to signal transduction by plant phytochromes.
Phage display: applications, innovations, and issues in phage and host biology (1998)

In the 7 years since the first publications describing phage-displayed peptide libraries, phage display has been successfully employed in a variety of research. Innovations in vector design and methods to identify target clones account for much of this success. At the same time, not all ventures have been entirely successful and it appears that phage and host biology play important roles in this. A key issue concerns the role played by a displayed peptide or protein in its successful expression and incorporation into virions. While few studies have examined these issues specifically in context of phage display, the literature as a whole provides insight. Accordingly, we review phage biology, relevant aspects of host biology, and phage display applications with the goals of illustrating (i) relevant aspects of the interplay between phage-host biology and successful phage display and (ii) the limitations and considerable potential of this important technology.Key words: bacteriophage M13, phage display, pIII, pVIII, expression libraries.
Crystallization and Polymorphism of Conformationally Flexible Molecules:  Problems, Patterns, and Strategies (2000)

Two effects of conformational flexibility on crystallization, namely conformational polymorphism and reduction of crystallization tendency, are discussed using examples from the literature and our own studies. The preferred molecular conformations observed in several polymorphic systems are correlated with the nature of the forces present in the crystals. The reduction of crystallization tendency for conformationally flexible molecules arises from the presence of multiple conformers in the crystallizing media and the need for certain molecules to crystallize in high-energy conformations. Despite their peculiarities, the control of crystallization of conformationally flexible molecules should begin with traditional approaches applicable to most crystallization situations. However, special techniques, including conformational mimicry, solvent-mediated self-assembly, and templated growth, have been devised to introduce molecular-level control to the crystallization process.
Nitroxyl in the Central Nervous System (2011)

Nitroxyl (HNO) is the one-electron-reduced and protonated congener of nitric oxide (NO). Compared to NO, it is far more reactive with thiol groups either in proteins or in small antioxidant molecules either converting those into sulfinamides or inducing disulfide bond formation. HNO might mediate cytoprotective changes of protein function through thiol modifications. However, HNO is a strong oxidant that in vitro reacts with glutathione to form glutathione disulfide and glutathione sulfinamide. The resulting oxidative stress might aggravate tissue damage in inflammatory diseases. In this review, we will summarize the current knowledge of how exogenous HNO affects the central nervous system, especially nerve cells and glia in health and disease. Unlike most other organs, the brain is separated from the circulation by the blood-brain barrier, which limits access of many pharmacological compounds. Given that, we will review what is known about the ability of currently used HNO donors to cross the blood-brain barrier. Moreover, considering that the physiology and composition of the brain has unique properties, for example, expression of brain-specific enzymes like neuronal NO synthase, its high iron content, and increased energy metabolism, we will discuss possible sources of endogenous HNO in the brain.
New quick method for isolating RNA from laser captured cells stained by immunofluorescent immunohistochemistry; RNA suitable for direct use in fluorogenic TaqMan one-step real-time RT-PCR (2005)

We describe a new approach for reliably isolating one-step real-time quantitative RT-PCR-quality RNA from laser captured cells retrieved from frozen sections previously subjected to immunofluorescent immunohistochemistry (IF-IHC) and subsequently subjected to fluorogenic one-step real-time RT-PCR analysis without the need for costly, time-consuming linear amplification. One cell's worth of RNA can now be interrogated with confidence. This approach represents an amalgam of technologies already offered commercially by Applied Biosystems, Arcturus and Invitrogen. It is the primary focus of this communication to expose the details and execution of an important new LCM RNA isolation technique, but also provide a detailed account of the IF-IHC procedure preceding RNA isolation, and provide information regarding our approach to fluorogenic one-step real-time RT-PCR in general. Experimental results shown here are meant to supplement the primary aim and are not intended to represent a complete scientific study. It is important to mention, that since LCM-RT-PCR is still far less expensive than micro-array analysis, we feel this approach to isolating RNA from LCM samples will be of continuing use to many researchers with limited budgets in the years ahead.
Analysis of TPA Pulsed-Laser-Induced Single-Event Latchup Sensitive-Area (2017)

Two-photon absorption (TPA) pulsed-laser testing is used to analyze the TPA-induced single-event latchup sensitive-area of a specially designed test structure. This method takes into account the existence of an onset region in which the probability of triggering latchup transits between 0 and 1 as the laser pulse energy increases. This variability is attributed to a combination of laser pulse-to-pulse variability and variations in local carrier density and temperature. For each spatial position, the latchup probability associated with a given energy is calculated. Calculation of latchup cross section at lower laser energies, relative to onset, is improved significantly by taking into account the full probability distribution. The transition from low probability of latchup to high probability is more abrupt near the source contacts than for surrounding areas.
Single and Combination Herpes Simplex Virus Type 2 Glycoprotein Vaccines Adjuvanted with CpG Oligodeoxynucleotides or Monophosphoryl Lipid A Exhibit Differential Immunity That Is Not Correlated to Protection in Animal Models (2011)

Despite several attempts to develop an effective prophylactic vaccine for HSV-2, all have failed to show efficacy in the clinic. The most recent of these failures was the GlaxoSmithKline (GSK) subunit vaccine based on the glycoprotein gD with the adjuvant monophosphoryl lipid A (MPL). In a phase 3 clinical trial, this vaccine failed to protect from HSV-2 disease, even though good neutralizing antibody responses were elicited. We aimed to develop a superior, novel HSV-2 vaccine containing either gD or gB alone or in combination, together with the potent adjuvant CpG oligodeoxynucleotides (CPG). The immunogenic properties of these vaccines were compared in mice. We show that gB/CPG/alum elicited a neutralizing antibody response similar to that elicited by gD/CPG/alum vaccine but a significantly greater gamma interferon (IFN-γ) T cell response. Furthermore, the combined gB-gD/CPG/alum vaccine elicited significantly greater neutralizing antibody and T cell responses than gD/MPL/alum. The efficacies of these candidate vaccines were compared in the mouse and guinea pig disease models, including a novel male guinea pig genital disease model. These studies demonstrated that increased immune response did not correlate to improved protection. First, despite a lower IFN-γ T cell response, the gD/CPG/alum vaccine was more effective than gB/CPG/alum in mice. Furthermore, the gB-gD/CPG/alum vaccine was no more effective than gD/MPL/alum in mice or male guinea pigs. We conclude that difficulties in correlating immune responses to efficacy in animal models will act as a deterrent to researchers attempting to develop effective HSV vaccines.
PROBENECID (BENEMID) (1955)

PROBENECID (Benemid) * resulted from a prolonged research effort directed toward the discovery of a safe agent that, administered orally, would physiologically inhibit the renal tubular secretion of penicillin.<sup>1</sup>Introduced into clinical medicine on July 22, 1949,<sup>2</sup>the use for which it was intended has increased steadily, and new indications for the drug have been disclosed. A conservative estimate indicates that 4,000,000 patient days (15,626 patient years) of therapy have been administered. Granting that the record of side-effects following the use of any therapeutic agent is not static, and that continuing use will bring to light an increasing number of side-effects and toxic manifestations, an appraisal from time to time seems appropriate. A preliminary assessment of the toxicity of probenecid was presented in 1951 on the basis of 701 patients,<sup>49</sup>and it is now possible to report on 2,502 patients. The information reported here has been derived from