gebhart/patrepeval huggingface dataset:
Detecting higher-level similarity patterns in programs (2005)

Cloning in software systems is known to create problems during software maintenance. Several techniques have been proposed to detect the same or similar code fragments in software, so-called simple clones . While the knowledge of simple clones is useful, detecting design-level similarities in software could ease maintenance even further, and also help us identify reuse opportunities. We observed that recurring patterns of simple clones - so-called structural clones - often indicate the presence of interesting design-level similarities. An example would be patterns of collaborating classes or components. Finding structural clones that signify potentially useful design information requires efficient techniques to analyze the bulk of simple clone data and making non-trivial inferences based on the abstracted information. In this paper, we describe a practical solution to the problem of detecting some basic, but useful, types of design-level similarities such as groups of highly similar classes or files. First, we detect simple clones by applying conventional token-based techniques. Then we find the patterns of co-occurring clones in different files using the Frequent Itemset Mining (FIM) technique. Finally, we perform file clustering to detect those clusters of highly similar files that are likely to contribute to a design-level similarity pattern. The novelty of our approach is application of data mining techniques to detect design level similarities. Experiments confirmed that our method finds many useful structural clones and scales up to big programs. The paper describes our method for structural clone detection, a prototype tool called Clone Miner that implements the method and experimental results.
A genetic algorithm for maximum-likelihood phylogeny inference using nucleotide sequence data (1998)

Phylogeny reconstruction is a difficult computational problem, because the number of possible solutions increases with the number of included taxa. For example, for only 14 taxa, there are more than seven trillion possible unrooted phylogenetic trees. For this reason, phylogenetic inference methods commonly use clustering algorithms (e.g., the neighbor-joining method) or heuristic search strategies to minimize the amount of time spent evaluating nonoptimal trees. Even heuristic searches can be painfully slow, especially when computationally intensive optimality criteria such as maximum likelihood are used. I describe here a different approach to heuristic searching (using a genetic algorithm) that can tremendously reduce the time required for maximum-likelihood phylogenetic inference, especially for data sets involving large numbers of taxa. Genetic algorithms are simulations of natural selection in which individuals are encoded solutions to the problem of interest. Here, labeled phylogenetic trees are the individuals, and differential reproduction is effected by allowing the number of offspring produced by each individual to be proportional to that individual's rank likelihood score. Natural selection increases the average likelihood in the evolving population of phylogenetic trees, and the genetic algorithm is allowed to proceed until the likelihood of the best individual ceases to improve over time. An example is presented involving rbcL sequence data for 55 taxa of green plants. The genetic algorithm described here required only 6% of the computational effort required by a conventional heuristic search using tree bisection/reconnection (TBR) branch swapping to obtain the same maximum-likelihood topology.
Amplified spontaneous emission at 523  μm in two-photon excited rubidium vapor (2017)

Population inversion on the 5D5/2−6P3/2 transition in rubidium atoms produced by cw laser excitation at different wavelengths has been analyzed by comparing the generated mid-infrared radiation at 5.23 μm originating from amplified spontaneous emission (ASE) and isotropic blue fluorescence at 420 nm. Using a novel method for detection of two-photon excitation via ASE, we have observed directional co- and counter-propagating emission at 5.23 μm. Evidence of a threshold-like characteristic is found in the ASE dependences on laser detuning and Rb number density. The power dependences of the backward- and forward-directed emission can be very similar; however, their spectral dependences are not identical. A new type of temporally and spatially coherent radiation is suggested.
Induction of c-fos Proto-oncogene in Mesangial Cells by Cadmium (1998)

Cadmium is mitogenic under some circumstances and has been shown to cause accumulation of transcripts for several proto-oncogenes in a variety of cells, but the mechanism(s) remain to be delineated. Here we show that CdCl 2 causes an increase in c-fos mRNA within 30 min of exposure of mesangial cells. At 10 M Cd 2 , this increase persists for at least 8 h in both rat and human cells. The half-life of c-fos mRNA is the same whether it accumulates following 4 h of treatment with Cd 2 or is induced transiently by phorbol ester. Cycloheximide, which stabilizes the transcript, causes a synergistic increase when administered with CdCl 2 . Nuclear run-on analysis confirms that Cd 2 causes transcriptional activation of the c-fos gene. Calmodulin and Ca 2 /calmodulin-dependent kinase, and classical protein kinase C (PKC) isoforms represent two Ca 2 -dependent signaling pathways that can lead to induction of c-fos, and Cd 2 has been shown to activate both calmodulin and PKC in vitro, possibly by virtue of the similar ionic radii of Cd 2 and Ca 2 . Therefore, we investigated the effect of Cd 2 on these pathways in vivo. 10 M CdCl 2 did not increase total PKC activity or Ca 2 /calmodulin-dependent kinase II activity and inhibited the latter at higher concentrations, ruling out either pathway in the Cd 2 -dependent induction of c-fos. However, Cd 2 did lead to a sustained activation of the Erk family mitogenactivated protein kinases (MAPK) that correlated with induction of c-fos. A specific inhibitor of the MAPK kinases, PD98059, partially inhibited the induction of c-fos by Cd 2 . We conclude that Cd 2 induces c-fos at least in part by causing a sustained activation of MAPK independent of its ability to activate PKC and calmodulin in vitro.
The Whip Signature (1999)

Over the past fifteen years, in the heat and ferment of lively feminist debate, the work of nineteenth-century American women poets seems to have changed, both in style and content. They used to be figures we might think of as favourite aunts, then they became our literary foremothers, and just recently they have come to seem more like sisters, uncannily bringing to the surface our own shameful lapses of pride and perversity. Obviously, the changes in these literary personalities have come about because of changes in the critical aperture through which we view them. In the early years of feminist literary criticism, Americans tended to use a wide-angle lens, lining up Emily Dickinson, for instance, against disabling and enabling Others: male Romantics, British female novelists, and other American women poets. In this phase pre-modern women seemed like our favourite aunts: sharp-tongued, eccentric, but always seen in the context of their familial relations. As we viewed these slightly off-centre figures from the past, we were especially sympathetic to the misfortunes they had suffered and the disabling conditions they had endured. Fifteen years ago when I wrote The Nightingale’s Burden, about ‘Women Poets and American Culture Before 1900’, the anxieties of authorship were a principal concern of American feminist critics like myself. There were so many circumstances, it seemed to us then, that inhibited the flow of female creativity.
Visual Loss after Spine Surgery (2003)

From the Department of Anesthesiology, Medical College of Wisconsin, Milwaukee, WI. Reprints: Kathryn K. Lauer, MD, Department of Anesthesiology, Medical College of Wisconsin, 9200 West Wisconsin Ave., Milwaukee, WI 53226 (e-mail: [email protected]).
Selective Recovery and Recycling of Germanium for the Design of Sustainable Zeolite Catalysts (2020)

Germanosilicate zeolites with extra-large-/multidimensional pore systems have a high potential for catalytic applications. However, their insufficient hydrothermal stability, high cost, and lack of strong acid sites limit their use. This work presents a synthetic approach involving post-synthesis degermanation/germanium recycling and remetalation steps for the cost-efficient preparation of Brønsted and Lewis acid zeolite catalysts. Optimization of degermanation conditions (i.e., pH and duration of the leaching treatment) allowed to recover up to 78–94% germanium from ITH, IWW, and UTL zeolites. Further metalation of hydrolyzed IWW zeolites resulted in a set of Al-, Ti-, and Sn-substituted catalysts showing enhanced activity in model acid-catalyzed reactions, such as 1-hexanol tetrahydropyranylation, 1-octene epoxidation, and Baeyer–Villiger oxidation of cyclohexanone. Noticeably, the phase selectivity of zeolite formation upon germanium recycling strongly depended on the method for parent zeolite separation from the leaching solution. In contrast to microfiltration, which produces a versatile source of germanium for the preparation of various zeolites, filtration leads to the formation of germanosilicates with the topology of the parent zeolite regardless of recycling conditions. Such a “memory effect” was rationalized based on the characterization of the germanium source and crystallization products using a combination of techniques (e.g., X-ray diffraction, Fourier transform infrared spectroscopy, scanning electron microscopy, and transmission electron microscopy).
A microRNA Link to Glioblastoma Heterogeneity (2012)

Glioblastomas (GBM) are one of the most malignant adult primary brain tumors. Through decades of research using various model systems and GBM patients, we have gained considerable insights into the mechanisms regulating GBM pathogenesis, but have mostly failed to significantly improve clinical outcome. For the most part GBM heterogeneity is responsible for this lack of progress. Here, we have discussed sources of cellular and microenvironmental heterogeneity in GBMs and their potential regulation through microRNA mediated mechanisms. We have focused on the role of individual microRNAs (miRNA) through their specific targets and miRNA mediated RNA-RNA interaction networks with the potential to influence various aspects of GBM heterogeneity including tumor neo-vascularization. We believe a better understanding of such mechanisms for regulation of GBM pathogenesis will be instrumental for future therapeutic options.
A slow cycling flux pump using digital control (1975)

A slow cycling flux pump has been constructed where operation is controlled by digital logic driving a high power operational amplifier. Hall sensors allow closed loop control of the secondary currents to enable switching the heater driven power cryotrons at the optimun time. Operating efficiency of 87% has been achieved.
Some problems in the use of the Coulter counter for erythrocyte total counts and volume distribution (1968)

Normal erythrocytes were subject to swelling and some haemolysis when suspended in a NaCl-formaldehyde-Na(2)EDTA diluent of pH 4.9 for routine blood-cell counting in the Coulter counter. A phosphate-buffered saline of pH 7.4 was substituted and has proven satisfactory for total erythrocyte counts. Polyvinyltoluene latex was unsuitable for volume calibration of the counter, because of aggregation of the particles in saline. Ragweed pollen grains gave a calibration factor that agreed well with that for fresh erythrocytes. Recent batches of Dade's Erythro-Trol (a suspension of fixed erythrocytes) were satisfactory for both total counts and volume calibration.
Micro- and Nanoscale Fluid Mechanics (2012)

This text focuses on the physics of fluid transport in micro- and nanofabricated liquid-phase systems, with consideration of gas bubbles, solid particles, and macromolecules. This text was designed with the goal of bringing together several areas that are often taught separately - namely, fluid mechanics, electrodynamics, and interfacial chemistry and electrochemistry - with a focused goal of preparing the modern microfluidics researcher to analyse and model continuum fluid mechanical systems encountered when working with micro- and nanofabricated devices. This text serves as a useful reference for practising researchers but is designed primarily for classroom instruction. Worked sample problems are included throughout to assist the student, and exercises at the end of each chapter help facilitate class learning.
Chain Breaking Antioxidant Activity of Heavy (S, Se, Te) Chalcogens Substituted Polyphenols (2019)

Polyphenols are probably the most important family of natural and synthetic chain-breaking antioxidants. Since long ago, chemists have studied how structural (bioinspired) modifications can improve the antioxidant activity of these compounds in terms of reaction rate with radical reactive oxygen species (ROS), catalytic character, multi-defence action, hydrophilicity/lipophilicity, biodistribution etc. In this framework, we will discuss the effect played on the overall antioxidant profile by the insertion of heavy chalcogens (S, Se and Te) in the phenolic skeleton.
Autonomous Power Control in a Reconfigurable 6.78-MHz Multiple-Receiver Wireless Charging System (2017)

This paper proposes and implements autonomous control of a multiple-receiver wireless charging system. The charging control problem is challenging due to the decentralized nature of the system, possible changing numbers and types of energy storage devices as loads of the receivers, and complexity in wireless power distribution mechanism. The game-theory-based control is developed that fully respects the unique characteristics of the transmitter (i.e., charger) and receivers. The preferences of the individual devices are first quantified using utility functions. Then, the charging control problem is formulated as a generalized Stackelberg game considering the leader-follower relationship between the transmitter and receivers, and the limited total charging power. At each control instant, the generalized Nash equilibrium among the receivers, i.e., charging power distribution here, is reached by searching the Lagrange multiplier while the total charging power from the transmitter is updated in a step-by-step manner. Both simulation and experimental results show that the proposed charging control autonomously manages and updates the power distribution in the cases where the receivers with different energy storage devices quit or join the wireless charging.
Über einige Aldol‐ und Kondensationsreaktionen des Phenylacetaldehyds (1952)

Abstract Die spontane und die alkalische Polymerisation des Phenylacetaldehyds sind Aldol‐Reaktionen, während Piperidinacetat eine Aldol‐Kondensation katalysiert. die saure Polymerisation führt zum Triphenyl‐paraldehyd.
Pen and voice interface for incremental design of graphic documents (1994)

The massive use of computer assistants stresses the need for user-friendliness in human-computer interaction. This question can be addressed at the level of the interaction, in order to provide better protocols or at the level of the application in order to provide an intelligent assistant. These two levels are strongly connected in the field of incremental design of graphical documents when the same medium, the pen, is used to produce the application data and the commands. An initial prototype (TAPAGE) has been developed for incrementally designing tables. >
Synthesis and Characterization of Prussian Blue Modified Magnetite Nanoparticles and Its Application to the Electrocatalytic Reduction of H<sub>2</sub>O<sub>2</sub> (2005)

Magnetite (Fe3O4) nanoparticles modified with electroactive Prussian Blue (PB) were first synthesized by a simple chemical method. Transmission electronic microscopy showed that the average size of the sample was about 12 nm, and X-ray powder diffraction, X-ray photoelectron spectroscopy, Fourier-transform IR, and UV−vis spectra showed the spinel structure for the nanoparticles and confirmed the existence of PB on the surface of Fe3O4. Magnetic properties of the sample were investigated by low-field alternating current susceptibility and superconducting quantum interference device measurement; the results indicated that the superparamagnetic properties remain for the sample with almost immeasurable remanence and coercivity at room temperature, while the value of saturation magnetization (Ms) reduces, and the blocking temperature (TB) of PB modified Fe3O4 is around 150 K, lower than that of the pure Fe3O4 nanoparticles, so the interaction between the particles is decreased. More interesting, when at 5 K, the Ms of PB-modified Fe3O4 is greatly larger than that at 300 K and shows ferromagnetic behavior. Furthermore, PB-modified Fe3O4 nanoparticles have been immobilized on the surface of glassy carbon electrode and applied to construct a sensor, it showed two well-defined pairs of redox peaks and a dramatic catalysis for the reduction of H2O2, which might be exploited to develop a new type of biosensor without any mediator.
Dynamic Generation of Dilemma-Based Interactive Narratives (2007)

This paper presents a system which automatically generates interactive stories. These are focused on dilemmas in order to create dramatic tension. The system is provided with knowledge of generic story actions and dilemmas based on those cliches encountered in many of today&rsquo;s soap operas. The story designer is only required to provide genre specific storyworld knowledge, such as information on characters and their relations, locations and actions. These dilemmas and story actions are instantiated for the given storyworld and a story planner creates sequences of actions that each lead to a dilemma for a character (who can be the user). The user interacts with the story by making decisions on relevant dilemmas and by freely choosing their own actions. Using this input the system chooses and adapts future story lines according to the user's past behaviour.
Vaccinia Virus A25 and A26 Proteins Are Fusion Suppressors for Mature Virions and Determine Strain-Specific Virus Entry Pathways into HeLa, CHO-K1, and L Cells (2010)

Mature vaccinia virus enters cells through either fluid-phase endocytosis/macropinocytosis or plasma membrane fusion. This may explain the wide range of host cell susceptibilities to vaccinia virus entry; however, it is not known how vaccinia virus chooses between these two pathways and which viral envelope proteins determine such processes. By screening several recombinant viruses and different strains, we found that mature virions containing the vaccinia virus A25 and A26 proteins entered HeLa cells preferentially through a bafilomycin-sensitive entry pathway, whereas virions lacking these two proteins entered through a bafilomycin-resistant pathway. To investigate whether the A25 and A26 proteins contribute to entry pathway specificity, two mutant vaccinia viruses, WRDeltaA25L and WRDeltaA26L, were subsequently generated from the wild-type WR strain. In contrast to the WR strain, both the WRDeltaA25L and WRDeltaA26L viruses became resistant to bafilomycin, suggesting that the removal of the A25 and A26 proteins bypassed the low-pH endosomal requirement for mature virion entry. Indeed, WRDeltaA25L and WRDeltaA26L virus infections of HeLa, CHO-K1, and L cells immediately triggered cell-to-cell fusion at a neutral pH at 1 to 2 h postinfection (p.i.), providing direct evidence that viral fusion machinery is readily activated after the removal of the A25 and A26 proteins to allow virus entry through the plasma membrane. In summary, our data support a model that on vaccinia mature virions, the viral A25 and A26 proteins are low-pH-sensitive fusion suppressors whose inactivation during the endocytic route results in viral and cell membrane fusion. Our results also suggest that during virion morphogenesis, the incorporation of the A25 and A26 proteins into mature virions may help restrain viral fusion activity until the time of infections.
Interactions of transition-metal ions with photoexcited states of flavines. Fluorescence quenching studies (1972)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTInteractions of transition-metal ions with photoexcited states of flavines. Fluorescence quenching studiesArthur W. Varnes, R. Barry Dodson, and E. L. WehryCite this: J. Am. Chem. Soc. 1972, 94, 3, 946–950Publication Date (Print):February 1, 1972Publication History Published online1 May 2002Published inissue 1 February 1972https://pubs.acs.org/doi/10.1021/ja00758a037https://doi.org/10.1021/ja00758a037research-articleACS PublicationsRequest reuse permissionsArticle Views2579Altmetric-Citations498LEARN ABOUT THESE METRICSArticle Views are the COUNTER-compliant sum of full text article downloads since November 2008 (both PDF and HTML) across all institutions and individuals. These metrics are regularly updated to reflect usage leading up to the last few days.Citations are the number of other articles citing this article, calculated by Crossref and updated daily. Find more information about Crossref citation counts.The Altmetric Attention Score is a quantitative measure of the attention that a research article has received online. Clicking on the donut icon will load a page at altmetric.com with additional details about the score and the social media presence for the given article. Find more information on the Altmetric Attention Score and how the score is calculated. Share Add toView InAdd Full Text with ReferenceAdd Description ExportRISCitationCitation and abstractCitation and referencesMore Options Share onFacebookTwitterWechatLinked InRedditEmail Other access optionsGet e-Alertsclose Get e-Alerts
The elusive definition of pandemic influenza (2011)

There has been considerable controversy over the past year, particularly in Europe, over whether the World Health Organization (WHO) changed its definition of pandemic influenza in 2009, after novel H1N1 influenza was identified. Some have argued that not only was the definition changed, but that it was done to pave the way for declaring a pandemic. Others claim that the definition was never changed and that this allegation is completely unfounded. Such polarized views have hampered our ability to draw important conclusions. This impasse, combined with concerns over potential conflicts of interest and doubts about the proportionality of the response to the H1N1 influenza outbreak, has undermined the public trust in health officials and our collective capacity to effectively respond to future disease threats. WHO did not change its definition of pandemic influenza for the simple reason that it has never formally defined pandemic influenza. While WHO has put forth many descriptions of pandemic influenza, it has never established a formal definition and the criteria for declaring a pandemic caused by the H1N1 virus derived from "pandemic phase" definitions, not from a definition of "pandemic influenza". The fact that despite ten years of pandemic preparedness activities no formal definition of pandemic influenza has been formulated reveals important underlying assumptions about the nature of this infectious disease. In particular, the limitations of "virus-centric" approaches merit further attention and should inform ongoing efforts to "learn lessons" that will guide the response to future outbreaks of novel infectious diseases.