gebhart/patrepeval huggingface dataset:
Baseband amplifiers in transferred-substrate HBT technology (2002)

Baseband amplifiers have been fabricated in the transferred-substrate HBT process. A Darlington amplifier achieved a DC gain of 15.6 dB with >50 GHz bandwidth. A mirror doubler amplifier achieved a DC gain of 6.8 dB with 86 GHz bandwidth. These amplifiers will be useful for future work in ADCs, DACs, and fiber-optic receivers, and serve to benchmark the transferred-substrate technology.
Benchmark health considered harmful (2001)

In the past couple of years, a number of software and architectural techniques have been proposed for improving the performance of linked data structrues. These research ideas are often evaluated using the Olden benchmark suite [1]. Frequently, in such experients, the largest speed-up is attained for the benchmark called health . This article demonstrates that this benchmark is a micro-benchmark for enormous linked lists traversals, and not a good one at that. Given that linked lists of such size are not an efficient data structure, it is unlikely that this benchmark corresponds to any real program. Hence the benchmark should not be used. To demonstrate the inherent inefficiency in its use of linked data structures, the health program was modified algorithmically to generate the same output, while improving the execution time by over a factor of 200 on a 500Mhz Pentium II Xeon.
Generalizing the Dempster-Schafer theory to fuzzy sets (1990)

A generalization of the Dempster-Schafer (D-S) theory to deal with fuzzy sets is described in which the belief and plausibility functions are treated as lower and upper probabilities. It is shown that computing the degree of belief in a hypothesis in the D-S theory can be formulated as an optimization problem. The extended belief function is thus obtained by generalizing the objective function and the constraints of the optimization problem. To combine bodies of evidence that may contain vague information, Dempster's rule (1967) is extended by (1) combining generalized compatibility relations based on the possibility theory, and (2) normalizing combination results to account for partially conflicting evidence. The generalization not only extends the application of the D-S theory but also illustrates a way that probability theory and fuzzy set theory can be integrated in a sound manner in order to deal with different kinds of uncertain information in intelligent systems.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">></ETX>
Reaction-diffusion CNN chip. I. IC implementation (2002)

Many works have proved the capability of CNN architecture to reproduce complex phenomena described through partial differential equations (PDEs). This array of simple nonlinear systems called cells, for their analog and spatiotemporal distributed method of processing signals, are considered a powerful tool to generate real-time solutions of nonlinear PDEs. A two-layer 2D CNN is able to solve particular PDEs, so called Reaction-Diffusion Equations. This particular topology of CNN has been called RD-CNN. A silicon implementation of this architecture is presented.
Multi form pluggable 8-channel Tx/Rx module for OC-3/OC-12 (2004)

An 8-channel optical transmitter (Tx)/Receiver (Rx) pair using a 1310 nm edge emitting LD array and a PD array has been newly developed for OC-3 (STM-1) and OC-12 (STM-4) intermediate reach (IR-1) applications. These modules, Multi Form Pluggable (MFP) modules can reduce package size and power consumption drastically for virtually the same cost compared to the use of conventional single-channel 8 Small Form Pluggable (SFP) modules.
Biocompatibility and internalization of molecularly imprinted nanoparticles (2016)

Molecularly imprinted polymers (MIP) are receiving increasing attention thanks to their robustness, stability, and inexpensive manufacture compared with their bio-analogues such as antibodies. The molecular imprinting process can be defined as the generation of molecular recognition sites in a synthetic polymer. The template-derived sites created within a polymeric matrix allow MIPs (often referred as plastic antibodies) to selectively recognize and bind to the target molecule. Therefore, MIPs can be used in sensors and in separation and diagnostics. Owing to their size and functional properties, MIP nanoparticles (NPs) can potentially be used in biomedicine, but comprehensive analysis of their interaction with cells and in vitro toxicological tests must be performed first. Herein, we report the synthesis of bare and core–shell imprinted NPs using an innovative solid-phase approach and the toxicological evaluation of such NPs in different cell lines (HaCaT, MEFs, HT1080, and macrophages). We also evaluated the influence of the protein corona on particle stability, the internalization of NPs in cells, and the influence of various surface coatings. Studies on the metabolic effects of imprinted NPs on fibroblasts showed that bare MIPs do not alter cell metabolism, whereas some issues arise when specific particle coatings are used. Furthermore, in vitro cytokine release studies revealed that macrophages were not activated in the presence of the MIPs evaluated in this study. The results suggest that MIP NPs are biocompatible, paving the way for their in vivo application.
Legal Principles of Non-Socialist Economic Integration as Exemplified by the European Economic Community (1980)

This paper will review three of the most important features of the European Community viewed as an exercise in integration: first, the effort to create supranational institutions; second, the creation of a distinct legal order; and third, the treaty-making power of the Community.
Tense in Ancient Greek Reports (2012)

Abstract This paper shows that tenses in Ancient Greek reports have both an anaphoric and a shifted-indexical component. It develops a new account of Ancient Greek tenses that deals with this combination of features. Following Klein's (1994) semantics of tense, I claim that tense indicates the relation between an anaphoric topic time and the moment of utterance, the now . As for Ancient Greek indirect discourse, I argue that the anaphoric component works exactly the same as in non-embedded discourse (contra von Stechow 1995). The indexical component, however, is di ferent in that the now is not provided by the actual context of utterance, but by the reported context. The DRT account developed models this combination of features, taking also into account the role of aspect.
Sub-pixel correction in comparison between in situ and satellite derived spectral reflectance (2003)

In comparison between in situ and satellite-derived spectral reflectance so as to validate a newly launched satellite sensor, the difficulty is that the ground measurement is generally carried out at a higher resolution than the satellite sensor, especially for moderate or high resolution sensors such as the Moderate Resolution Imaging Spectroradiometer (MODIS) or the Advanced Very High Resolution Radiometer (AVHRR) etc. To overcome this difficulty, we adopt sub-pixel correction method in a comparison study between in situ and MODIS-derived spectral reflectances of snow and sea ice in the Amundsen Sea, Antarctica. The position of the in situ measurement is accurately located within the imagery granule using the combination of small angle approximation and direct matching algorithms. Apparent reflectance retrieved from MODIS granule for the station pixel is atmospherically corrected. The corresponding spectral albedo and directional reflectance at the same viewing geometry as MODIS are derived from ground-based spectroradiometer measurements. The averaged spectral reflectance and albedo in the vicinity of each ice station are simulated for the corresponding MODIS pixel from ground spectral measurements by weighing over different surface types (various ice types and open water) so that reflectance difference at a sub-pixel level is appropriately corrected. Values of ground-based MODIS spectral simulation are compared with satellite-derived values so that the discrepancy is estimated.
Multiple tissue transcriptomic responses to<i>Piscirickettsia salmonis</i>in Atlantic salmon (<i>Salmo salar</i>) (2011)

The bacterium Piscirickettsia salmonis is the etiological agent of salmonid rickettsial septicemia (SRS), a severe disease that causes major economic losses to the Atlantic salmon aquaculture industry every year. Little is known about the infective strategy of P. salmonis, which is able to infect, survive within, and replicate inside salmonid macrophages as an intracellular parasite. Similarly there is little knowledge concerning the fish host's response to invasion by this pathogen. We have examined the transcriptional response of postsmolt Atlantic salmon (Salmo salar) to P. salmonis at 48 h following infection in three tissues, liver, head kidney, and muscle, using an Atlantic salmon oligonucleotide microarray (Salar_2, Agilent 4x44K). The infection led to a large alteration of transcriptional activity in all the tissues studied. In infected salmon 886, 207, and 153 transcripts were differentially expressed in liver, head kidney, and muscle, respectively. Assessment of enrichment for particular biological pathways by gene ontology analysis showed an upregulation of genes involved in oxidative and inflammatory responses in infected fish, indicative of the activation of the innate immune response. The downregulation of genes involved in the adaptive immune response, G protein signaling pathway, and apoptotic process in infected fish may be reflective of mechanisms used by P. salmonis to survive, replicate, and escape host defenses. There was also evidence of differential responses between studied tissues, with protein metabolism being decreased in muscle of infected fish and with a concomitant increase being shown in liver.
The Effect of Salt on the Water Structure at a Charged Solid Surface: Differentiating Second- and Third-order Nonlinear Contributions (2011)

We have used visible-infrared sum-frequency generation spectroscopy to reveal fundamental characteristics of water structure at the fused silica surface. By studying a wide range of ionic strengths, from 0.05 mM to 4 M, we are able to comment on the contributions of second- and third-order nonlinearities to the spectroscopic response. Spectra obtained from extremely dilute salt concentrations provide evidence of the previously sought increasing surface charge with ionic strength. This is followed by a screening regime where the extent to which the surface field penetrates into the bulk is limited by the electrolyte. Data from intermediate salt concentrations reveal a few strongly ordered layers of water immediately adjacent to the surface. At high concentrations, we observe a significant disruption of solvent ordering. Together, the observation of these four distinct regimes provides a unified understanding of interfacial water structure in the presence of salt that consolidates previous reports in the literature.
AlphaServer 4100 Performance Characterization (1996)

This paper characterizes the performance of the AlphaServer 4100 family, which consists of three models:
Glyceraldehyde‐3‐phosphate dehydrogenase from Ehrlich ascites carcinoma cells (1999)

Glyceraldehyde-3-phosphate dehydrogenase has been purified to apparent homogeneity from Ehrlich ascites carcinoma (EAC) cells. The enzyme is quite active over a pH range of 7.5-9.0 with an optimum pH of 8.4-8.7. The specific activity of the enzyme is much higher than that from other normal sources. In contrast to enzyme obtained from rabbit muscle, the EAC cell enzyme is not significantly inhibited by physiological concentrations of ATP at physiological pH. Kinetic studies using different substrates and inhibitors indicate that the properties of the EAC cell enzyme are significantly different from those of glyceraldehyde-3-phosphate dehydrogenase obtained from other normal sources. The striking dissimilarity of the malignant cell glyceraldehyde-3-phosphate dehydrogenase compared with this enzyme from other normal sources, particularly in respect to the interaction with ATP, may in part explain the high glycolysis of malignant cells.
Tooth Wear in Children with Down Syndrome (2002)

Given the potential consequences of high levels of tooth wear, associated with tooth grinding and an acidic oral environment in Down syndrome children, educational programmes aimed at increasing awareness of carers and health professionals are needed urgently.
Photon Dose Calculation Algorithms in the Presence of Low-Density Heterogeneity-a Mini Literature Review (2014)

Dose prediction accuracy in photon dose calculation algorithms is important to ensure accurate delivery of prescribed dose to the tumor during radiation therapy. The main objective of this article is to provide a brief review on most recent dose calculation algorithm called Acuros XB, which is used to calculate the cancer treatment plans in external beam radiation therapy.
Xeno-Free Culture of Human Pluripotent Stem Cells (2011)

Stem cell culture systems that rely on undefined animal-derived components introduce variability to the cultures and complicate their therapeutic use. The derivation of human embryonic stem cells and the development of methods to produce induced pluripotent stem cells combined with their potential to treat human diseases have accelerated the drive to develop xenogenic-free, chemically defined culture systems that support pluripotent self-renewal and directed differentiation. In this chapter, we describe four xeno-free culture systems that have been successful in supporting undifferentiated growth of hPSCs as well as methods for xeno-free subculture and cryopreservation of hPSCs. Each culture system consists of a xeno-free growth medium and xeno-free substratum: (1) TeSR2™ with human recombinant laminin (LN-511); (2) NutriStem™ with LN-511; (3) RegES™ with human foreskin fibroblasts (hFFs); (4) KO-SR Xeno-Free™/GF cocktail with CELLstart™ matrix.
Inhaled Microparticles Containing Clofazimine Are Efficacious in Treatment of Experimental Tuberculosis in Mice (2012)

Inhalable clofazimine-containing dry powder microparticles (CFM-DPI) and native clofazimine (CFM) were evaluated for activity against Mycobacterium tuberculosis in human monocyte-derived macrophage cultures and in mice infected with a low-dose aerosol. Both formulations resulted in 99% killing at 2.5 μg/ml in vitro. In mice, 480 μg and 720 μg CFM-DPI inhaled twice per week over 4 weeks reduced numbers of CFU in the lung by as much as log(10) 2.6; 500 μg oral CFM achieved a log(10) 0.7 reduction.
Facilitated isolation, purification, and analysis of glucuronoxylomannan of Cryptococcus neoformans (1991)

Cryptococcus neoformans was cultured in a chemically defined medium. The culture was adjusted to 0.25% formaldehyde or autoclaved after 5 days of growth at 35 degrees C, and a cell-free supernatant was obtained by centrifugation. Solid calcium acetate was added to the supernatant to give a 5% solution, and the pH was adjusted to approximately 5 with glacial acetic acid. The polysaccharide (PS) was precipitated by the addition of 3 volumes of 95% ethanol. The PS was dissolved in 0.2 M NaCl, and insoluble calcium salts were solubilized by the addition of several drops of glacial acetic acid. The PS solution was treated by ultrasonic irradiation for 15 min. This concurrently decreased the molecular weight of the PS and reduced the viscosity of the solution. The ultrasonically irradiated PS was precipitated by differential complexation with hexadecyltrimethylammonium bromide at 23 degrees C, the complex was dissolved in 1 M NaCl, and the glucuronoxylomannan was precipitated by adding 3 volumes of ethanol. The glucuronoxylomannan was dissolved in 1 M NaCl and then ultrasonically irradiated for 2 h to reduce the molecular mass to a limiting value of approximately 100 kDa (GXMS). The purified GXMS was centrifuged, dialyzed, and finally recovered by lyophilization. GXMS was chromatographed on DEAE-cellulose at reasonable concentrations without the complication of high solution viscosity. The sugar composition and structure of GXMS were determined by gas-liquid chromatography, permethylation gas-liquid chromatography-mass spectrometry, and 13C nuclear magnetic resonance spectroscopy. The improved solution characteristics of GXMS were ideal for the determination of its chemical and serological properties.
Chlorite Dismutation to Chlorine Dioxide Catalyzed by a Water‐Soluble Manganese Porphyrin (2010)

Chloride oxyanions are of interest because of their use as disinfectants and concerns over their accumulation in the environment. A water-soluble manganese porphyrin catalyzes the dismutation of chlorite (ClO2−) to chlorine dioxide (ClO2) through a series of electron- and atom-transfer reactions. A high-valent manganese(IV) oxo species is observed and the ClO2 product inhibits the reaction.
Topoisomerase II Inhibitors Induce DNA Damage-Dependent Interferon Responses Circumventing Ebola Virus Immune Evasion (2017)

Ebola virus (EBOV) protein VP35 inhibits production of interferon alpha/beta (IFN) by blocking RIG-I-like receptor signaling pathways, thereby promoting virus replication and pathogenesis. A high-throughput screening assay, developed to identify compounds that either inhibit or bypass VP35 IFN-antagonist function, identified five DNA intercalators as reproducible hits from a library of bioactive compounds. Four, including doxorubicin and daunorubicin, are anthracycline antibiotics that inhibit topoisomerase II and are used clinically as chemotherapeutic drugs. These compounds were demonstrated to induce IFN responses in an ATM kinase-dependent manner and to also trigger the DNA-sensing cGAS-STING pathway of IFN induction. These compounds also suppress EBOV replication <i>in vitro</i> and induce IFN in the presence of IFN-antagonist proteins from multiple negative-sense RNA viruses. These findings provide new insights into signaling pathways activated by important chemotherapy drugs and identify a novel therapeutic approach for IFN induction that may be exploited to inhibit RNA virus replication.<b>IMPORTANCE</b> Ebola virus and other emerging RNA viruses are significant but unpredictable public health threats. Therapeutic approaches with broad-spectrum activity could provide an attractive response to such infections. We describe a novel assay that can identify small molecules that overcome Ebola virus-encoded innate immune evasion mechanisms. This assay identified as hits cancer chemotherapeutic drugs, including doxorubicin. Follow-up studies provide new insight into how doxorubicin induces interferon (IFN) responses, revealing activation of both the DNA damage response kinase ATM and the DNA sensor cGAS and its partner signaling protein STING. The studies further demonstrate that the ATM and cGAS-STING pathways of IFN induction are a point of vulnerability not only for Ebola virus but for other RNA viruses as well, because viral innate immune antagonists consistently fail to block these signals. These studies thereby define a novel avenue for therapeutic intervention against emerging RNA viruses.
Spectrum analysis—A modern perspective (1981)

A summary of many of the new techniques developed in the last two decades for spectrum analysis of discrete time series is presented in this tutorial. An examination of the underlying time series model assumed by each technique serves as the common basis for understanding the differences among the various spectrum analysis approaches. Techniques discussed include the classical periodogram, classical Blackman-Tukey, autoregressive (maximum entropy), moving average, autotegressive-moving average, maximum likelihood, Prony, and Pisarenko methods. A summary table in the text provides a concise overview for all methods, including key references and appropriate equations for computation of each spectral estimate.
Saline Agriculture in the 21st Century: Using Salt Contaminated Resources to Cope Food Requirements (2012)

With the continue increase of the world population the requirements for food, freshwater, and fuel are bigger every day. This way an urgent necessity to develop, create, and practice a new type of agriculture, which has to be environmentally sustainable and adequate to the soils, is arising. Among the stresses in plant agriculture worldwide, the increase of soil salinity is considered the major stress. This is particularly emerging in developing countries that present the highest population growth rates, and often the high rates of soil degradation. Therefore, salt-tolerant plants provide a sensible alternative for many developing countries. These plants have the capacity to grow using land and water unsuitable for conventional crops producing food, fuel, fodder, fibber, resin, essential oils, and pharmaceutical products. In addition to their production capabilities they can be used simultaneously for landscape reintegration and soil rehabilitation. This review will cover important subjects concerning saline agriculture and the crop potential of halophytes to use salt-contaminated resources to manage food requirements.
Adjunctive Therapy for Percutaneous Revascularization in Acute Myocardial Infarction (2004)

Primary PCI is an effective reperfusion strategy for acute MI patients, which has evolved significantly in the last decade. While many adjunctive therapies have contributed to its success, substantial obstacles remain before optimal reperfusion can be achieved. Anti-platelet therapy with aspirin, clopidogrel and GP IIb/IIIa inhibitors reduces early ischemic complications, improves microvascular function and, potentially, affects the inflammatory response to ischemic injury. Current anti-thrombin therapy with UFH can be improved with LMWH, and, possibly with direct thrombin inhibitors. A number of important aspects of this strategy, though, need still to be elucidated. We need to optimize microvascular protection before and during PCI in order to capitalize on the myocardial sparing effects of reperfusion therapy. This will be probably achieved with a combination of pharmacological interventions and mechanical emboli protection devices. Improved and more targeted anti-inflammatory therapy should decrease the effects of neutrophil-related reperfusion injury, while a variety of metabolic interventions might preserve myocardial function during ischemia and after reperfusion.
Deep Learning for Case-Based Reasoning Through Prototypes: A Neural Network That Explains Its Predictions (2018)

Deep neural networks are widely used for classification. These deep models often suffer from a lack of interpretability---they are particularly difficult to understand because of their non-linear nature. As a result, neural networks are often treated as "black box" models, and in the past, have been trained purely to optimize the accuracy of predictions. In this work, we create a novel network architecture for deep learning that naturally explains its own reasoning for each prediction. This architecture contains an autoencoder and a special prototype layer, where each unit of that layer stores a weight vector that resembles an encoded training input. The encoder of the autoencoder allows us to do comparisons within the latent space, while the decoder allows us to visualize the learned prototypes. The training objective has four terms: an accuracy term, a term that encourages every prototype to be similar to at least one encoded input, a term that encourages every encoded input to be close to at least one prototype, and a term that encourages faithful reconstruction by the autoencoder. The distances computed in the prototype layer are used as part of the classification process. Since the prototypes are learned during training, the learned network naturally comes with explanations for each prediction, and the explanations are loyal to what the network actually computes.