gebhart/patrepeval huggingface dataset:
PuDianNao (2015)

Machine Learning (ML) techniques are pervasive tools in various emerging commercial applications, but have to be accommodated by powerful computer systems to process very large data. Although general-purpose CPUs and GPUs have provided straightforward solutions, their energy-efficiencies are limited due to their excessive supports for flexibility. Hardware accelerators may achieve better energy-efficiencies, but each accelerator often accommodates only a single ML technique (family). According to the famous No-Free-Lunch theorem in the ML domain, however, an ML technique performs well on a dataset may perform poorly on another dataset, which implies that such accelerator may sometimes lead to poor learning accuracy. Even if regardless of the learning accuracy, such accelerator can still become inapplicable simply because the concrete ML task is altered, or the user chooses another ML technique.
Sensitivity Analysis for Predictive Uncertainty in Bayesian Neural Networks (2017)

We derive a novel sensitivity analysis of input variables for predictive epistemic and aleatoric uncertainty. We use Bayesian neural networks with latent variables as a model class and illustrate the usefulness of our sensitivity analysis on real-world datasets. Our method increases the interpretability of complex black-box probabilistic models.
Cellular interactions of CRKL, and SH2-SH3 adaptor protein. (1994)

Chronic myelogenous leukemia is characterized by a specific chromosomal translocation, t(9;22), in which the ABL protooncogene and the BCR gene become juxtaposed. The chimeric BCR/ABL gene produces a P210 fusion protein with deregulated tyrosine kinase activity. We have recently isolated a complementary DNA, CRKL, which could code for an adaptor protein consisting of one SH2 and two SH3 domains and lacking any catalytic domain. In the current study, we show that CRKL is highly phosphorylated in the chronic myelogenous leukemia cell line K562 and that it is a substrate for the p210 BCR/ABL and p145 ABL kinases. BCR/ABL and ABL are coimmunoprecipitated with CRKL in vivo, demonstrating that relatively stable complexes are formed. In addition, the nucleotide exchange factor mSOS1 was found to be coimmunoprecipitated with CRKL. These findings establish a putative signal transduction pathway way through which BCR/ABL mediates its oncogenic activity.
A Tutorial on Energy-Based Learning (2006)

Energy-Based Models (EBMs) capture dependencies between variables by associating a scalar energy to each configuration of the variables. Inference consists in clamping the value of observed variables and finding configurations of the remaining variables that minimize the energy. Learning consists in finding an energy function in which observed configurations of the variables are given lower energies than unobserved ones. The EBM approach provides a common theoretical framework for many learning models, including traditional discriminative and generative approaches, as well as graph-transformer networks, conditional random fields, maximum margin Markov networks, and several manifold learning methods. Probabilistic models must be properly normalized, which sometimes requires evaluating intractable integrals over the space of all possible variable configurations. Since EBMs have no requirement for proper normalization, this problem is naturally circumvented. EBMs can be viewed as a form of non-probabilistic factor graphs, and they provide considerably more flexibility in the design of architectures and training criteria than probabilistic approaches. 1
Gemfibrozil enhances the listeriacidal effects of fluoroquinolone antibiotics in J774 macrophages. (1992)

J774 macrophage-like cells express organic anion transporters that promote the efflux of fluoroquinolone antibiotics such as norfloxacin (NFX) from these cells. Gemfibrozil (GFZ) blocks organic anion transport in J774 cells, thereby facilitating the intracellular accumulation of NFX (Cao, C., H.C. Neu, and S.C. Silverstein. 1991. J. Cell Biol. 115:467a [Abstr.]). To determine whether GFZ enhances the efficacy of fluoroquinolone antibiotics against intracellular bacterial pathogens, J774 cells were infected with Listeria monocytogenes and incubated in medium containing a fluoroquinolone antibiotic in the presence or absence of GFZ. Intracellular growth of L. monocytogenes was evaluated by lysing J774 cells and assaying for colony-forming units of Listeria. GFZ intensified the bacteriostatic effect of 4 micrograms/ml NFX and rendered 8 micrograms/ml bactericidal for L. monocytogenes. GFZ had a similar potentiating effect when used in combination with 2 micrograms/ml ciprofloxacin (CFX). CFX plus GFZ was bactericidal for intracellular L. monocytogenes. Treatment of J774 cells with NFX plus GFZ markedly reduced the cytotoxic effect of the bacteria on these cells. Over 55% of cells treated with 8 micrograms/ml NFX alone were dead 16 h after infection, whereas only 5% of cells treated with 8 micrograms/ml NFX plus GFZ were dead at 16 h. Similarly, GFZ potentiated the ability of 2 micrograms/ml to protect J774 cells against the cytocidal effect of Listeria. NFX in combination with GFZ limited cell-to-cell spread of L. monocytogenes. In antibiotic-free medium, > 99% of J774 cells contained intracellular L. monocytogenes at 14 h after infection. NFX alone in the medium did not change this outcome. However, 4 micrograms/ml NFX plus GFZ decreased bacterial spread by approximately 40% at 24 h postinfection, and 8 micrograms/ml NFX plus GFZ prevented all spread beyond the initially infected cell population. These results suggest that GFZ could be used clinically to enhance the efficacy of fluoroquinolone and of other anionic antibiotics against bacteria that grow and/or reside within macrophages and/or other cells.
REVEALING GENETIC MARKERS IN <i>GELIDIUM VAGUM</i> (RHODOPHYTA) THROUGH THE RANDOM AMPLIFIED POLYMORPHIC DNA (RAPD) TECHNIQUE<sup>1</sup> (1993)

ABSTRACT The recently developed random amplified polymorphic DNA technique was evaluated as a method for characterizing isolates of the agarophyte Gelidium vagum Okamura. Reaction conditions for single primer polymerase chain reaction were optimized to obtain a high degree of reproducibility of the amplified bands generated from purified G. vagum DNA. A total of 165 primers, including both (A + T)‐ and (G + C)‐rich sequences, was screened for DNA amplification using template DNA from a single Gelidium isolate. None of the 45 (A + T)‐rich primers was positive (i.e. band‐producing). Of the (G + C)‐rich primers, 47 were positive, generating a total of 322 prominent amplification products for DNA from 13 different G. vagum isolates. Polymorphic DNA loci were detected by 37 of the primers. Unweighted pair‐group arithmetic average cluster analysis (UPGMA) of these loci was used to group the G. vagum isolates and thereby determine which were most similar. G. latifolium , used as an out‐group for the UPGMA analysis, showed a high degree of dissimilarity.
Efficient multiple hyperparameter learning for log-linear models (2007)

In problems where input features have varying amounts of noise, using distinct regularization hyperparameters for different features provides an effective means of managing model complexity. While regularizers for neural networks and support vector machines often rely on multiple hyperparameters, regularizers for structured prediction models (used in tasks such as sequence labeling or parsing) typically rely only on a single shared hyperparameter for all features. In this paper, we consider the problem of choosing regularization hyperparameters for log-linear models, a class of structured prediction probabilistic models which includes conditional random fields (CRFs). Using an implicit differentiation trick, we derive an efficient gradient-based method for learning Gaussian regularization priors with multiple hyperparameters. In both simulations and the real-world task of computational RNA secondary structure prediction, we find that multiple hyperparameter learning can provide a significant boost in accuracy compared to using only a single regularization hyperparameter.
Synchronization of codes by means of Kautz's Fibonacci encoding (1972)

It is shown how to detect or correct synchronization slippage in cyclic codes by using a prefix that incorporates the Fibonacci encoding technique developed by Kautz. Comparison with other methods shows that in many cases it seems to be more efficient. Implementation is simple. It is also shown how a similar technique can be used in comma-free codes. The resulting codes can be constructed algorithmic, ally from arbitrary information digits, that is, no table lookup is necessary. These codes seem to be the most efficient among those that require no code table.
A Reliable 2T2MTJ Nonvolatile Static Gain Cell STT-MRAM With Self-Referencing Sensing Circuits for Embedded Memory Application (2015)

This paper presents a reliable nonvolatile static gain cell made of two transistors and two magneto-tunneling junctions (MTJs) for cache memory application. The wide distribution in the resistance of MTJs in parallel and anti-parallel states and the variations in the threshold voltage of gain cells are overcome by connecting two complementary MTJs and self-reference sensing circuits, respectively. An enhanced sensing margin and immunity to read disturbance are achieved by applying high voltage across the stacked complementary MTJs. The sensing margin of $8\sigma $ is assured after the Monte Carlo simulation using the measured parameters of the MTJ, including a tunneling magneto-resistance of 200%, a 5% distribution of resistance, and a 5% distribution of threshold voltage in the 65 nm standard CMOS process.
Analysis and reduction of acoustic noise from a brushless DC drive (2000)

It has been found that stator excitation in brushless DC motor drives can excite mechanical resonances in the motor and, thus, produce acoustic noise in a similar way to switched reluctance drives. A technique has been developed to alter the commutation pattern of a brushless DC motor to avoid exciting and reinforcing these mechanical resonances producing a significant reduction in pure tone acoustic noise which is emitted during mechanical resonance. The origin of the vibration and acoustic noise is explained and the theory of discrete frequency noise reduction described in this paper. The method proposed for quieter control of the brushless DC motor could be achieved at a very low cost.
A sequential sampling algorithm for a general class of utility criteria (2000)

S.330-334
Study of Fuel Dilution in Direct-Injection and Multipoint Injection Gasoline Engines (2002)

<div class="htmlview paragraph">Fuel dilution is one of the phenomena requiring attention in direct-injection engines. This study examined the factors contributing to increased fuel dilution in direct-injection and conventional multipoint injection gasoline engines, focusing in particular on fuel dilution in the oil pan. The results showed that fuel dilution is affected by fuel consumption, fuel properties and oil/cooling water temperatures in multipoint injection engines. In addition to these factors, fuel injection timing is another factor that increases fuel dilution in direct-injection engines.</div>
Idiotypic regulation of autoantibody production. (1986)

The manuscript will deal with various aspects of the origin of autoantibody formation in relationship with idiotypy. The proposed analysis will cover three major aspects: (1) overview of the published data on idiotypic characterization of autoantibodies in various systems by conventional serologic investigation; (2) presentation of the structural and genetic data available for autoantibodies; and (3) description of the most significant experiment of in vivo manipulation of autoantibody production using idiotypy as the central element for immune regulation. The manuscript will also discuss some theoretical aspects of regulation by idiotype and its possible relevance to improve our understanding of autoreactivity as well as the pathogenesis of certain autoimmune diseases.
Avoiding the Rocket Scientist Syndrome: STEM Programs Are Not Only for the Best and the Brightest (2015)

Emphasis on science, technology, engineering, and mathematics (STEM) has permeated discussions of American at nearly every level. Our nation's ability to compete in global marketplace depends on our ability to properly engage, encourage, and equip our students in STEM. As we strive to address this issue in schools across country, however, we must include all students. A common misconception is that STEM programs should be reserved for best and brightest students--what I refer to as rocket scientist syndrome. We tend to direct students identified as having a positive disposition toward STEM subjects and careers into STEM programs of study, upper-level coursework, and college preparatory programs. These students often succeed in handling rigorous STEM coursework, but STEM refers to more than just content knowledge and understanding. STEM also involves a process of teaching and learning in which students develop skills in critical thinking, problem-solving, working cooperatively in groups, using technology effectively, and communicating orally and in writing. These STEM competencies are critical for success in any postsecondary setting or work-related field, and all students must work toward mastery in each of them to compete in everchanging workplace. A 2011 report indicated that jobs in STEM will grow from 6.8 million to 8 million 2018, and that 92% of STEM jobs will require some form of postsecondary and training (Carnevale, Smith, and Melton 2011). The report also stated that the demand for STEM-capable workers has increased even in traditionally non-STEM fields due to diffusion of technology across industries and occupations. This means that nearly every sector of employment our students can hope to attain will require STEM competencies demonstrated at postsecondary level. A Frameworkfor K-12 Science Education (NRC 2011), precursor to Next Generation Science Standards (NGSS Lead States 2013), states that by end of 12th grade, students should have gained sufficient knowledge of practices, crosscutting concepts, and core ideas of science and engineering to engage in public discussions on science-related issues, to be critical consumers of scientific information related to their everyday lives, and to continue to learn about science throughout their lives. [These] goals are for all students, not just those who pursue careers in science, engineering, or technology or those who continue on to higher education (NRC 2011, p. …
Photochemical Eliminations Involving Zwitterionic Intermediates Generated via Electrocyclic Ring Closure of Benzothiophene Carboxanilides (2011)

Leaving groups such as carboxylate, thiolate, and phenolate are expelled via zwitterionic intermediates produced upon photochemical electrocyclic ring closure of benzothiophene carboxanilides in the triplet excited state. Chemical yields generally exceed 90%, while quantum yields vary with basicity of the released leaving group.
Data telemetry for ocean bottom instrumentation (2002)

A data delivery system was developed for the Northern Gulf of Mexico Littoral Initiative that allows access to data from bottom mounted instrumentation. The system consists of two parts, a trawl resistant sub-surface component and a separate surface buoy. The sub-surface component employs a trawl resistant bottom mount containing an acoustic Doppler current profiler equipped with a Micro-Modem (/spl mu/Modem). The surface expression consists of a buoy equipped with an acoustic receiver (Utility Acoustic Modem, or UAM), a system controller and an Argos transmitter (PTT). The /spl mu/Modem acoustically telemeters data from the ADCP on an hourly schedule to the UAM on the nearby (/spl sim/500 m) surface buoy. Data from the acoustic receiver are forwarded via the controller to the Argos transmitter. To maximize data throughput of the Argos link, the controller loads a circular buffer containing the most recent eight hours of data into the PTT each hour. These data are continuously transmitted until the next hourly update. The controller also performs resynchronization of the acoustic system in the event acoustic communications are lost. One particular benefit of this system is the ability to perform measurements in high traffic locations while maintaining the surface buoy at a safe distance from navigation aids. One system is currently deployed in a high traffic area, in Horn Island Pass, due south of Pascagoula, Mississippi. This paper describes the overall system and presents data from initial deployments.
Fast Compact City Modeling for Navigation Pre-Visualization (2006)

Nowadays, GPS-based car navigation systems mainly use speech and aerial views of simplified road maps to guide drivers to their destination. However, drivers often experience difficulties in linking the simple 2D aerial map with the visual impression that they get from the real environment, which is inherently ground-level based. Therefore, supplying realistically textured 3D city models at ground-level proves very useful for pre-visualizing an upcoming traffic situation. Because this pre-visualization can be rendered from the expected future viewpoints of the driver, the latter will more easily understand the required maneuver. 3D city models can be reconstructed from the imagery recorded by surveying vehicles. The vastness of image material gathered by these vehicles, however, puts extreme demands on vision algorithms to ensure their practical usability. Algorithms need to be as fast as possible and should result in compact, memory efficient 3D city models for future ease of distribution and visualization. For the considered application, these are not contradictory demands. Simplified geometry assumptions can speed up vision algorithms while automatically guaranteeing compact geometry models. We present a novel city modeling framework which builds upon this philosophy to create 3D content at high speed which could allow for pre-visualization of any conceivable traffic situation by car navigation modules.
Influence of Residual Monomer on Cracking in Ceramics Fabricated by Stereolithography (2010)

The conventional build methods for polymeric stereolithography intentionally leave small regions of uncured monomer. We show that for ceramic stereolithography, these regions of uncured monomer are associated with macrocracking during heating. The cracking is caused by strains arising from the thermal polymerization of residual monomer while heating. Cracking can be avoided by changing the build style to eliminate the residual monomer.
Knottin cyclization: impact on structure and dynamics (2008)

In this work, we show that, in contrast to what could have been intuitively expected, cyclization of squash inhibitors does not provide clear stability or flexibility modification. Overall, our results suggest that, for squash inhibitors in standard conditions, the circularization impact might come from incorporation of an additional loop sequence, that can contribute to the miniprotein specificity and affinity, rather than from an increase in conformational rigidity or protein stability. Unfolding simulations showed however that cyclization is a stabilizing factor in strongly denaturing conditions. This information should be useful if one wants to use the squash inhibitor scaffold in drug design.
Jagged1-mediated Notch activation induces epithelial-to-mesenchymal transition through Slug-induced repression of E-cadherin (2007)

Aberrant expression of Jagged1 and Notch1 are associated with poor outcome in breast cancer. However, the reason that Jagged1 and/or Notch overexpression portends a poor prognosis is unknown. We identify Slug, a transcriptional repressor, as a novel Notch target and show that elevated levels of Slug correlate with increased expression of Jagged1 in various human cancers. Slug was essential for Notch-mediated repression of E-cadherin, which resulted in beta-catenin activation and resistance to anoikis. Inhibition of ligand-induced Notch signaling in xenografted Slug-positive/E-cadherin-negative breast tumors promoted apoptosis and inhibited tumor growth and metastasis. This response was associated with down-regulated Slug expression, reexpression of E-cadherin, and suppression of active beta-catenin. Our findings suggest that ligand-induced Notch activation, through the induction of Slug, promotes tumor growth and metastasis characterized by epithelial-to-mesenchymal transition and inhibition of anoikis.
Generation of Coherent Vacuum UV Radiation in Randomly Quasi-Phase-Matched Strontium Tetraborate (2015)

Tunable coherent radiation is generated in the VUV down to 121 nm using random quasi-phase-matching in strontium tetraborate, the shortest wavelength ever produced with a second-order nonlinear optical process in a solid-state material.
A fast algorithm for region-oriented texture coding (2002)

This paper addresses the framework of object-oriented image coding, describing a new algorithm, based on monodimensional Legendre polynomials, for texture approximation. Through the use of 1D orthogonal basis functions, the computational complexity which usually makes prohibitive most 2D region-oriented approaches is significantly reduced, while only a slight increment of distortion is introduced. With the aim of preserving the bidimensional intersample correlation of texture information as much as possible, suitable pseudo-bidimensional basis functions have been used, yielding significant improvements with respect to the straightforward 1D approach. The algorithm has been experimented with, for coding still images as well as motion compensated sequences, showing interesting possibilities of application for very low bit rate video coding.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">></ETX>
Temozolomide and Radiation in Low-Grade and Anaplastic Gliomas: Temoradiation (2007)

Recently completed trials suggest the addition of nitrosourea-based chemotherapy to radiotherapy increases the progression-free but not overall survival of grade II and III gliomas. Temozolomide has proven benefit in grade II/III gliomas progressive following standard therapy and when added to radiation for glioblastoma. Newly launched and planned phase III trials will explore whether the addition of temozolomide to radiotherapy improves overall survival in grade II/III as well as the prognostic and predictive value of 1p/19q analyses and MGMT promotor methylation status. Additionally, they will measure cognition and quality of life to determine if improvements in time to progression translate into better functional status and patient satisfaction.
HLA class I antigen expression in human solid tumors. (1996)

The expression of HLA class I antigens was studied by immunohistochemistry in various tumors in correlation with clinicopathologic characteristics. Reduced expression was observed in germ cell testicular cancer, kidney, prostate, gastric and colon cancer, and was associated with tumor aggressiveness, grade and penetration of the tumor through the organ wall. In bladder cancer reduced expression was associated with poor survival. Irradiation of brain tumors resulted in an increase in class I expression. Soluble class I levels were studied in breast and colon cancer patients and were found to be high in those with metastatic disease. The clinical relevance of reduced class I levels are discussed.