gebhart/patrepeval huggingface dataset:
Database Queries that Explain their Work (2014)

Provenance for database queries or scientific workflows is often motivated as providing explanation, increasing understanding of the underlying data sources and processes used to compute the query, and reproducibility, the capability to recompute the results on different inputs, possibly specialized to a part of the output. Many provenance systems claim to provide such capabilities; however, most lack formal definitions or guarantees of these properties, while others provide formal guarantees only for relatively limited classes of changes. Building on recent work on provenance traces and slicing for functional programming languages, we introduce a detailed tracing model of provenance for multiset-valued Nested Relational Calculus, define trace slicing algorithms that extract subtraces needed to explain or recompute specific parts of the output, and define query slicing and differencing techniques that support explanation. We state and prove correctness properties for these techniques and present a proof-of-concept implementation in Haskell.
Bionanoelectronics: Bionanoelectronics (Adv. Mater. 7/2011) (2011)

Abstract Every cell in a living organisms performs a complex array of functions using a vast arsenal of proteins, ion channels, pumps, motors, signaling molecules, and cargo carriers. With all the progress that humankind has made to date in the development of sophisticated machinery and computing capabilities, understanding and communicating with living systems on that level of complexity lags behind. A breakthrough in these capabilities could only come if a way is found to integrate biological components into artificial devices. The central obstacle for this vision of bionanoelectronics is the absence of a versatile interface that facilitates two‐way communication between biological and electronic structures. 1D nanomaterials, such as nanotubes and nanowires, open up the possibility of constructing tight interfaces that could enable such bidirectional flow of information. This report discusses the overall progress in building such interfaces on the level of individual proteins and whole cells and focuses on the latest efforts to create device platforms that integrate membrane proteins, channels, and pumps with nanowire bioelectronics.
Persistence of intracellular HIV-1 mRNA correlates with HIV-1-specific immune responses in infected subjects on stable HAART (2001)

These results suggest that HIV-1-specific immune responses correlate with evidence of ongoing HIV-1 replication.
Using the Particle Swarm Optimization Algorithm for Robotic Search Applications (2007)

This paper describes the experimental results of using the particle swarm optimization (PSO) algorithm to control a suite of robots. In our approach, each bot is one particle in the PSO; each particle/bot makes measurements, updates its own position and velocity, updates its own personal best measurement (pbest) and personal best location (if necessary), and broadcasts to the other bots if it has found a global best measurement/position. We built three bots and tested the algorithm by letting the bots find the brightest spot of light in the room. The tests show that using the PSO to control a swarm can successfully find the target, even in the presence of obstacles
Salient Pitch Cues in the Perception of Contrastive Focus (1996)

The distinction between contrastive and noncontrastive focus in English can be conveyed by the difference between a L+H* vs H* pitch accent [Pierrehumbert and Hirschberg, in Intentions in Communication, edited by Cohen et al. (MIT, Cambridge, MA, 1990)]. It is unclear, however, which acoustic properties of an F0 contour convey to a listener the occurrence of the contrastive L+H* rather than the noncontrastive H*. In these experiments, rise onset F0, peak F0, and slope were varied to see how they alone and together contribute to the contrast between a L+H* vs H* on the focused constituent. Listeners classified the stimuli as either contrastive or noncontrastive, with discourse context distinguishing the two interpretations. Peak height and slope traded in determining the category boundary between interpretations. Implications for the choice of primitives in intonational models and for compositional approaches to tune meaning are discussed. [Work supported by NIH.]
Gene Therapy in Thalassemia and Hemoglobinopathies (2009)

Sickle cell disease (SCD) and ß-thalassemia represent the most common hemoglobinopathies caused, respectively, by the alteration of structural features or deficient production of the ß-chain of the Hb molecule. Other hemoglobinopathies are characterized by different mutations in the α- or ß-globin genes and are associated with anemia and might require periodic or chronic blood transfusions. Therefore, ß-thalassemia, SCD and other hemoglobinopathies are excellent candidates for genetic approaches since they are monogenic disorders and, potentially, could be cured by introducing or correcting a single gene into the hematopoietic compartment or a single stem cell. Initial attempts at gene transfer of these hemoglobinopathies have proved unsuccessful due to limitations of available gene transfer vectors. With the advent of lentiviral vectors many of the initial limitations have been overcame. New approaches have also focused on targeting the specific mutation in the ß-globin genes, correcting the DNA sequence or manipulating the fate of RNA translation and splicing to restore ß-globin chain synthesis. These techniques have the potential to correct the defect into hematopoietic stem cells or be utilized to modify stem cells generated from patients affected by these disorders. This review discusses gene therapy strategies for the hemoglobinopathies, including the use of lentiviral vectors, generation of induced pluripotent stem cells (iPS) cells, gene targeting, splice-switching and stop codon readthrough.
Modeling of real defect outlines for defect size distribution and yield prediction (2002)

For efficient yield, prediction defects are usually modeled by circular disks or squares. A more accurate model is presented. It considers the real outline of physical defects. To utilize this model, only the maximum and the minimum extension of detected defects must be determined. That can be done easily using a checkerboard test structure including a defect localization procedure. The accuracy of the predicted number of defects can be substantially enhanced by modeling real defect outlines with this elliptical model. If the elliptical model of the defect outlines is applied, the defect size distribution implicitly contains information about the physical defect outlines. Hence, for yield prediction the inspection of defect outlines can be omitted.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">></ETX>
Molecular SCF Calculations on PH3, PO, PO−, and P2 (1967)

Wavefunctions, Hamiltonian matrices, and population analyses are obtained for PH3, PO, PO−, and P2 from accurate self-consistent-field calculations in which multicentered basis sets of Slater orbitals have been employed. The P3d exponent was optimized at 1.40 in PO and 1.10 in PO−, assuming Slater exponents for other orbitals. These 3d orbitals were found to be important in the bonding in each of these molecules. Studies were also made of dipole moments, ionization potentials, and binding energies.
Targeting levels or oligomerization of nucleophosmin 1 induces differentiation and loss of survival of human AML cells with mutant NPM1 (2011)

Nucleophosmin 1 (NPM1) is an oligomeric, nucleolar phosphoprotein that functions as a molecular chaperone for both proteins and nucleic acids. NPM1 is mutated in approximately one-third of patients with AML. The mutant NPM1c+ contains a 4-base insert that results in extra C-terminal residues encoding a nuclear export signal, which causes NPM1c+ to be localized in the cytoplasm. Here, we determined the effects of targeting NPM1 in cultured and primary AML cells. Treatment with siRNA to NPM1 induced p53 and p21, decreased the percentage of cells in S-phase of the cell cycle, as well as induced differentiation of the AML OCI-AML3 cells that express both NPMc+ and unmutated NPM1. Notably, knockdown of NPM1 by shRNA abolished lethal AML phenotype induced by OCI-AML3 cells in NOD/SCID mice. Knockdown of NPM1 also sensitized OCI-AML3 to all-trans retinoic acid (ATRA) and cytarabine. Inhibition of NPM1 oligomerization by NSC348884 induced apoptosis and sensitized OCI-AML3 and primary AML cells expressing NPM1c+ to ATRA. This effect was significantly less in AML cells coexpressing FLT3-ITD, or in AML or normal CD34+ progenitor cells expressing wild-type NPM1. Thus, attenuating levels or oligomerization of NPM1 selectively induces apoptosis and sensitizes NPM1c+ expressing AML cells to treatment with ATRA and cytarabine.
A methodology for exploring biomarker – phenotype associations: application to flow cytometry data and systemic sclerosis clinical manifestations (2015)

IRIS flow cytometry data provides useful information in assessing the ILD status of SSc patients. Our new approach combining Conditional Random Forests and Gene Set Enrichment Analysis was successful in identifying a subset of flow cytometry variables to create a screening tool that proved effective in correctly identifying ILD patients in the training and validation data sets. From a somewhat broader perspective, the identification of subsets of flow cytometry variables that exhibit coordinated movement (i.e., multi-variable up or down regulation) may lead to insights into possible effector pathways and thereby improve the state of knowledge of systemic sclerosis pathogenesis.
Novedades y retos de la Ley de rehabilitación: hablan los técnicos (2013)

La aprobacion definitiva del la Ley 8/2013 , de rehabilitacion, regeneracion y renovacion urbanas es, a juicio del autor, una muestra mas de la apuesta del Gobierno por recuperar el potencial economico y empleador del sector de la edificacion. Con esta normativa, la rehabilitacion reivindica un protagonismo que la etapa de crecimiento desaforado parecia haberle negado, centrados como estabamos en la obra nueva.
Study on time-frequency extractors for partial discharge pulse current used in sequence grouping and identification (2011)

This paper introduces a general way to make feature extraction for partial discharge (PD) pulse waveshape used in sequence grouping resorting with equivalent time-frequency method. A digital ac PD pulse detection system with bandwidth of 10 kHz 40 MHz and sampling rate of 100 MS/s is introduced, which was developed to study those feature extractors. Simulation and test results with gas insulated switch (GIS) show that they are practical and effective to develop PD detection system with grouping and identification technique. Streszczenie. Dokonano ekstrakcji impulsu wyladowania niezupelnego przy wykorzystaniu odpowiedniej metody czasowo-czestotliwościowej. Wykorzystano system cyfrowy z pasmem 10 kHz – 40 MHz i czestotliwością probkowania 100 MS/s. Badania wylącznika gazowego potwierdzily skutecznośc metody. (Czasowo-czestotliwościowa ekstrakcja i identyfikacja impulsu wyladowania niezupelnego)
Notes on Matrices (1970)

It is very desirable when teaching mathematics not merely to state definitions and prove theorems, but also to show the train of thought that would lead us naturally to these definitions and theorems. Students are thus enabled to see mathematics as an alive, continuously developing subject. They are reminded of the interdependence of the various branches of mathematics; the memory of each branch is kept alive in the students’ minds, because it is continually being revisited, and the student finds it easier to remember results when he understands the thinking that produced them. This approach also encourages a student to try to carry the train of thought further and to make his own discoveries.
Towards a self-managing software patching process using black-box persistent-state manifests (2004)

We describe an approach to self-managing software patching. We identify visibility into patch impact as the key missing component in automating the current patching process, and we present a suite of components that provides this visibility by constructing black-box persistent-state manifests through self-monitoring of dependencies. Additionally, we use the component suite to measure the actual impact of recent patches on several important commercial applications.
Introduction (2002)

Abstract The Introduction outlines the purpose of the book which is to present an intellectual history of the political ideas that inspired republican, separatist rebellion in 18th-century Ireland. The main focus is the expression and evolution of three key political themes: patriotism, radicalism, and republicanism. This work is primarily a history of political thought and language, but one that connects ideas and rhetoric to events and individuals. Its purpose is threefold: first, to describe the political languages and ideas used by patriots, radicals, and republicans in Ireland from the American Revolution until the Rebellion; second, to understand how and why these languages and ideas developed over this period; and third, to show how they informed the mentalités of the individuals who expressed these ideas in order to understand their political actions.
Efficacy of Dihydroartemisinin-Piperaquine for Treatment of Uncomplicated Plasmodium falciparum and Plasmodium vivax in Cambodia, 2008 to 2010 (2012)

We describe here the results of antimalarial therapeutic efficacy studies conducted in Cambodia from 2008 to 2010. A total of 15 studies in four sentinel sites were conducted using dihydroartemisinin-piperaquine (DP) for the treatment of Plasmodium falciparum infection and chloroquine (CQ) and DP for the treatment of P. vivax infection. All studies were performed according to the standard World Health Organization protocol for the assessment of antimalarial treatment efficacy. Among the studies of DP for the treatment of P. falciparum, an increase in treatment failure was observed in the western provinces. In 2010, the PCR-corrected treatment failure rates for DP on day 42 were 25% (95% confidence interval [CI] = 10 to 51%) in Pailin and 10.7% (95% CI = 4 to 23%) in Pursat, while the therapeutic efficacy of DP remained high (100%) in Ratanakiri and Preah Vihear provinces, located in northern and eastern Cambodia. For the studies of P. vivax, the day 28 uncorrected treatment failure rate among patients treated with CQ ranged from 4.4 to 17.4%; DP remained 100% effective in all sites. Further study is required to investigate suspected P. falciparum resistance to piperaquine in western Cambodia; the results of in vitro and molecular studies were not found to support the therapeutic efficacy findings. The emergence of artemisinin resistance in this region has likely put additional pressure on piperaquine. Although DP appears to be an appropriate new first-line treatment for P. vivax in Cambodia, alternative treatments are urgently needed for P. falciparum-infected patients in western Cambodia.
Effect of food on the bioavailability of low‐dose methotrexate in patients with rheumatoid arthritis (1992)

Bioavailability of oral methotrexate shows marked interindividual variation but is not affected by the presence of food.
A true single-phase-clock dynamic CMOS circuit technique (1987)

The authors describe two dynamic circuit techniques, using only a single-phase clock which is never inverted. This class of circuits has the advantages of simple clock distribution, small area for clock lines reduced clock skew problems, and high speed. Several examples are demonstrated.
Static analysis of upper and lower bounds on dependences and parallelism (1994)

Existing compilers often fail to parallelize sequential code, even when a program can be manually transformed into parallel form by a sequence of well-understood transformations (as in the case for many of the Perfect Club Benchmark programs). These failures can occur for several reasons: the code transformations implemented in the compiler may not be sufficient to produce parallel code, the compiler may not find the proper sequence of transformations, or the compiler may not be able to prove that one of the necessary transformations is legal. When a compiler fails to extract sufficient parallelism from a program, the programmer may try to extract additional parallelism. Unfortunately, the programmer is typically left to search for parallelism without significant assistance. The compiler generally does not give feedback about which parts of the program might contain additional parallelism, or about the types of transformations that might be needed to realize this parallelism. Standard program transformations and dependence abstractions cannot be used to provide this feedback. In this paper, we propose a two-step approach to the search for parallelism in sequential programs. In the first step, we construct several sets of constraints that describe, for each statement, which iterations of that statement can be executed concurrently. By constructing constraints that correspond to different assumptions about which dependences might be eliminated through additional analysis, transformations, and user assertions, we can determine whether we can expose parallelism by eliminating dependences. In the second step of our search for parallelism, we examine these constraint sets to identify the kinds of transformations needed to exploit scalable parallelism. Our tests will identify conditional parallelism and parallelism that can be exposed by combinations of transformations that reorder the iteration space (such as loop interchange and loop peeling). This approach lets us distinguish inherently sequential code from code that contains unexploited parallelism. It also produces information about the kinds of transformations needed to parallelize the code, without worrying about the order of application of the transformations. Furthermore, when our dependence test is inexact we can identify which unresolved dependences inhibit parallelism by comparing the effects of assuming dependence or independence. We are currently exploring the use of this information in programmer-assisted parallelization.
IRON‐INDUCED OXYGEN RADICAL METABOLISM IN WATERLOGGED PLANTS (1985)

Roots of the iron-sensitive wetland plant, Epilobium hirsutum L., respond to oxygen-depletion by enhanced uptake of ferrous ions. Evidence is presented for an iron-catalyzed reaction within roots leading to super oxide radical formation and the induction of superoxide dismutase. The immediate product, H<sub>2</sub> O<sub>2</sub> , appears to accumulate in the absence of catalase and low activity of root peroxidases, resulting in hydroxyl radical formation, inhibition of protein synthesis, increased lipid peroxidation and gross cellular damage. Evidence for alternative 'healthy' responses is given. A scheme is presented which outlines a biochemical mechanism for iron-mediated flood or waterlogging tolerance and intolerance in plants.
A novel primary bile acid in the Shoebill stork and herons and its phylogenetic significance (2002)

The Shoebill stork, an enigma phylogenetically, was found to contain as its dominant biliary bile acid 16alpha-hydroxychenodeoxycholic acid, a heretofore undescribed bile acid. The bile acid occurred as its taurine N-acyl amidate; structure was established by nuclear magnetic resonance (NMR) and mass spectrometry (MS). A search for this novel bile acid in other Ciconiiformes showed that it constituted >92% of biliary bile acids in five of nine herons in the Ardidae, but was absent in all other families (Ciconiidae, Threskiornithidae, Scopidae, Phoenicopteridae). The presence of this biochemical trait in the Shoebill stork and certain herons suggests that these birds are closely related.
PRECIPITATION REACTIONS OF MENINGOCOCCUS STRAINS WITH IMMUNE SERUM IN AGAR PLATES IN RELATION TO ANTIGENIC ACTIVITY* (1934)

Journal Article PRECIPITATION REACTIONS OF MENINGOCOCCUS STRAINS WITH IMMUNE SERUM IN AGAR PLATES IN RELATION TO ANTIGENIC ACTIVITY Get access MARY B. KIRKBRIDE, MARY B. KIRKBRIDE Search for other works by this author on: Oxford Academic PubMed Google Scholar SOPHIA M. COHEN SOPHIA M. COHEN Search for other works by this author on: Oxford Academic PubMed Google Scholar American Journal of Epidemiology, Volume 20, Issue 2, September 1934, Pages 444–453, https://doi.org/10.1093/oxfordjournals.aje.a118082 Published: 01 September 1934 Article history Received: 12 April 1934 Published: 01 September 1934
Magnetic alignment of collagen during self-assembly (1984)

Magnetically induced birefringence is used to monitor the thermally induced self-assembly of collagen fibrils from a solution of molecules. The magnetic torque alone can, at best, only orient the fibrils into planes normal to the field direction. Nevertheless, the gels formed have a high degree of uniaxial alignment, probably due to the additional ordering effects of surface interactions. Thus magnetic orientation is potentially useful in the study of fibrillogenesis and in the production of highly oriented collagen gels.
Activation of ventrolateral preoptic neurons by the somnogen prostaglandin D <sub>2</sub> (1998)

Prostaglandin D2 (PGD2) is an extensively studied sleep-promoting substance, but the neuroanatomical basis of PGD2-induced sleep is only partially understood. To determine potential regions involved in this response, we used Fos immunohistochemistry to identify neurons activated by infusion of PGD2 into the subarachnoid space below the rostral basal forebrain. PGD2 increased nonrapid eye movement sleep and induced striking expression of Fos in the ventrolateral preoptic area (VLPO), a cluster of neurons that may promote sleep by inhibiting the tuberomammillary nucleus, the source of the ascending histaminergic arousal system. Fos expression in the VLPO was positively correlated with the preceding amount of sleep and negatively correlated with Fos expression in the tuberomammillary nucleus. PGD2 also increased Fos immunoreactivity in the basal leptomeninges and several regions implicated in autonomic regulation. These observations suggest that PGD2 may induce sleep via leptomeningeal PGD2 receptors with subsequent activation of the VLPO.
Preparation of thin-film neutron converter foils for imaging detectors (2004)

With the pending delivery of the new Spallation Neutron Source at Oak Ridge National Laboratory, a new generation of highly efficient, position sensitive neutron detectors needs to be developed. One promising prospect for detector development has been the neutron imaging detector consisting of a conversion foil, which produce amongst other things /spl alpha/ and /spl gamma/ particles from incident neutrons, and a position sensitive charge particle detector. In order to understand the materials chemistry between layered converters as well as to maximize the production and transmission of the daughter products, we have prepared and characterized a series of thin-films from naturally occurring isotopes of the strong neutron absorbers lithium (Li), boron (B), and gadolinium (Gd). The films have been created using a combination of sputtering and evaporation techniques. The composition of the resulting films have been investigated using EDS and RBS, while the interfacial mixing between the layers has been studied using a combination of RBS and SEM experiments. Experiments studying the aging of the detector films in the detector gas as well as alloying of Li and the film substrate, have also been undertaken and the results are reported here.