gebhart/patrepeval huggingface dataset:
ParaLite: Supporting Collective Queries in Database System to Parallelize User-Defined Executable (2012)

This paper proposes extensions to parallel database systems called collective queries and User-Defined eXecutables (UDX). A collective query is an SQL query whose results are distributed to multiple clients and then processed by them in parallel, using arbitrary external programs (user-defined executables). The intended applications are data intensive work-flows, typically built out of various independently developed executables and scripts. Collective queries facilitate description of such workflows by making data parallel execution of external programs on big data easy and streamlined. It also provides the workflow developers with a familiar and powerful language SQL, for flexible data filtering and stereotypical data processing tasks. We implement this concept in a system "ParaLite", a parallel database system based on a popular lightweight database SQ Lite. It equips with data transfer optimization algorithms that distribute query results to multiple clients, taking both communication cost and compute loads into account. We verified the correctness and performance of Para Lite and the experimental results show that Para Lite has good performance on SQL processing and achieves good scalability for the parallelization of UDX.
ECG arrhythmia classification based on logistic model tree (2009)

This paper presents a diagnostic system for classification of cardiac arrhythmia from ECG data, using Logistic Model Tree (LMT) classifier. Clinically useful information in the ECG is found in the intervals and amplitudes of the characteristic waves. Any abnormality in the wave shape and duration of the wave features of the ECG is considered as arrhythmia. The ampli-tude and duration of the characteristic waves of the ECG can be more accurately obtained using Discrete Wavelet Transform (DWT) analysis. Further, the non-linear behavior of the cardiac system is well characterized by Heart Rate Variability (HRV). Hence, DWT and HRV techniques have been employed to extract a set of linear (time and frequency domain) and non-linear characteristic features from the ECG signals. These features are used as input to the LMT classifier to classify 11 different arrhyth-mias. The results obtained indicate an impressive prediction accuracy of 98%, validating the choice and combined use of the current popular techniques (DWT and HRV) for cardiac arrhythmia classification. The system can be de-ployed for practical use after validation by experts.
Cost‐effective fabrication of a phase mask by direct etching of the laser‐interference grating on fused silica substrate (2003)

Abstract A simple and cost‐effective method to manufacture a phase mask with high diffraction efficiency for deep UV application is proposed. The deep rectangular grating fabricated by using laser interference is etched directly into a fused silica substrate, instead of the dielectric coating on a substrate (done in a previous method). Using the metal layer on a dielectric layer for masking in the deep, dry etching process is also unnecessary in our technique. A fabricated rectangular grating with high diffraction efficiency is presented in this paper. We also demonstrate the fabrication processes and show the optimum parameters for our proposed technology. © 2003 Wiley Periodicals, Inc. Microwave Opt Technol Lett 38: 362–365, 2003; Published online in Wiley InterScience (www.interscience.wiley.com). DOI 10.1002/mop.11061
FORMATION OF RU-SUBCARBONYLS IN HIGH ELECTRIC FIELD (1989)

A microscopic theory of field adsorption is used to investigate the formation of Ru-subcarbonyls in high electric field. Due to the repulsion between the COs adsorbed on the same top Ru atom, the COs displace as far as possible from each other, weakening the interaction between the Ru(CO)n species and the external electric field with rising index n. In strong external electric field, the net charge on the O atoms changes from negative to positive, so that the Ru-C bonds and, especially the C-O bonds tend to rotate towards the direction of the electric field, resulting in an increase of the repulsion between the COs, especially for the Ru-subcarbonyls with high index. In summary, increasing the field strength is disadvantageous to the formation of Ru-subcarbonyls with high index, a conclusion in good agreement with experiment.
Predicting Remaining Useful Life using Time Series Embeddings based on Recurrent Neural Networks (2020)

We consider the problem of estimating the remaining useful life (RUL) of a system or a machine from sensor data. Many approaches for RUL estimation based on sensor data make assumptions about how machines degrade. Additionally, sensor data from machines is noisy and often suffers from missing values in many practical settings. We propose Embed-RUL: a novel approach for RUL estimation from sensor data that does not rely on any degradation-trend assumptions, is robust to noise, and handles missing values. Embed-RUL utilizes a sequence-to-sequence model based on Recurrent Neural Networks (RNNs) to generate embeddings for multivariate time series subsequences. The embeddings for normal and degraded machines tend to be different, and are therefore found to be useful for RUL estimation. We show that the embeddings capture the overall pattern in the time series while filtering out the noise, so that the embeddings of two machines with similar operational behavior are close to each other, even when their sensor readings have significant and varying levels of noise content. We perform experiments on publicly available turbofan engine dataset and a proprietary real-world dataset, and demonstrate that Embed-RUL outperforms the previously reported state-of-the-art (Malhotra, TV, et al., 2016) on several metrics.
Plastics, Additives (2000)

Abstract The article contains sections titled: 1. Introduction 2. Antioxidants 2.1. Purpose and Requirements 2.2. Chemical Classes 2.3. Mechanism of Action 2.4. Test Methods 2.5. Uses 2.6. Legal Aspects 2.7. Economic Aspects 3. Light Stabilizers 3.1. Purpose and Requirements 3.2. Chemical Classes 3.3. Mechanism of Action 3.4. Test Methods 3.5. Uses 3.6. Economic Aspects 4. Heat Stabilizers for Poly(Vinyl Chloride) 4.1. Purpose and Requirements 4.2. Chemical Classes 4.2.1. Metal‐Containing Stabilizers 4.2.2. Metal‐Free Stabilizers 4.3. Mechanism of Action 4.4. Test Methods 4.5. Uses 4.6. Economic Aspects 5. Lubricants, Slip, Antiblocking, and Mold‐Release Agents 5.1. Purpose and Requirements 5.2. Chemical Classes 5.3. Mechanism of Action 5.4. Test Methods 5.5. Uses 5.6. Economic Aspects 6. Flame Retardants 6.1. Purpose and Requirements 6.2. Chemical Classes 6.3. Mechanism of Action 6.4. Test Methods and Standards 6.5. Uses 6.6. Toxicology 6.7. Economic Aspects 7. Fillers and Coupling Agents 7.1. Purpose and Requirements 7.2. Forms and Chemical Structures 7.3. Mechanism of Action 7.4. Test Methods 7.5. Uses 7.6. Economic Aspects 8. Dyes and Pigments 8.1. Requirements 8.2. Pigments 8.2.1. Inorganic Pigments 8.2.2. Organic Pigments 8.2.3. Dyes 9. Miscellaneous Additives 9.1. Nucleating Agents 9.2. Antistatic Agents 9.3. Impact Modifiers 9.4. Chemical Blowing Agents 9.5. Optical Brighteners
Development of separation technology for the removal of radium-223 from targeted thorium conjugate formulations. (2016)

New methods for radiochemical purification and preparation of a group of novel targeted radioactive cancer therapeutics have been developed and tested. Focus has been given to user-friendliness and minimization of the number of operational steps. Studies of the influence of product composition and process variables reveal the potential for development of easy to operate methods which give both a pure and potent product.\nConventional cancer drug treatments such as chemotherapy are often ineffective. The targeted cancer radiotherapy under development in Bayer AS which utilizes the radioactive element thorium-227, may give hope to cancer patients through a localized and efficient therapy within a number of cancer types. The first clinical candidate reached a phase I clinical trial in 2015.\nThorium emits a very high energy radiation over a short distance. This means that the cell killing of the tumor can be localized, leaving healthy tissue unharmed. By attaching thorium to immune system derived proteins called antibodies, the radiation may be carried to the tumor cells in the patient’s body. The antibodies are highly specific and capable of recognizing and binding to structures on the surface of various cancer cells.\nThe radioactive drugs are prepared directly in a radiopharmacy by simple complexation of thorium to an antibody conjugated with a chelator. When thorium emits radiation another radioactive element is formed; radium-223. Radium will not be attached to the antibodies and will thus have different tumor targeting abilities. It is therefore desirable to have a controlled amount of radium in the drug at the time of patient dose administration. Methods for purification of thorium at the radiopharmacy which remove radium with a high selectivity and efficiency while giving a high throughput of thorium have been the subject of this thesis.\nThe work has been carried out as a collaboration between the School of Pharmacy and Bayer AS through an industrial Ph.D. grant from the Research Council of Norway. The research has resulted in three patent applications.
Cyclization cascade of the C33-bisnorheptaprenoid catalyzed by recombinant squalene cyclase (2009)

The enzymatic cyclization reaction of polyprenoid C(33) by squalene-hopene cyclase (SHC) was investigated with the intention of creating an unnatural hexacyclic compound. The enzymatic products consisted of mono-, bi-, tri-, tetra- and pentacyclic skeletons; however, hexacyclic products were not generated, contrary to our expectations. The absence of a hexacyclic skeleton indicated that the entire carbon chain of C(33) polyprene could not be included in the reaction cavity. Formation mechanisms of the products having mono- to pentacycles were discussed. Both chair/chair/boat conformation and chair/chair/chair conformations were formed for a tricycle, and both chair/chair/chair/boat conformation and chair/chair/chair/chair structures were constructed for a tetracycle. The pentacyclic product was created from the chair/chair/chair/chair/boat conformation. Squalene was folded in an all pre-chair conformation inside the reaction cavity to form the hopene skeleton. Therefore, the formation of a boat structure during the polycyclization reaction indicated that the molecule of polyprene C(33) was folded improperly due to incorrect arrangement/positioning in the reaction cavity. The creation of the hexacyclic core failed; however, it should be noted that SHC possessed great potential to tolerate the elongated squalene analog C(33), thus leading to the creation of novel compounds with C(33).
Domain-specific interface generation from dataflow specifications (1998)

In this paper, the problem of automatically mapping large-grain dataflow programs onto heterogeneous hardware/software architectures is treated. Starting with a given hardware/software partition, interfaces are automatically inserted into the specification to account for communication, in particular across hardware/software boundaries. Depending on the target architecture, the interfaces are refined according to given communication constraints (bus protocols, memory mapping, interrupts, DMA, etc.). An object-oriented approach is presented that enables an easy migration (retargeting) of typical communication primitives to other target architectures.
GaAs Substrate Recycling Using in-situ Deposited NaCl Layers via Molecular Beam Epitaxy (2020)

This work presents an alternative method to conventional III-V substrate recycling methods via growth of NaCl on nearly-lattice matched GaAs (001) substrates. Reflection high energy electron diffraction and transmission electron microscopy confirm an epitaxial relationship between the NaCl layers and the underlying GaAs. The NaCl fully desorbs from the surface if the sample is heated too much prior to GaAs deposition. The quality of the deposition of GaAs on NaCl ranges from amorphous at low temperature to polycrystalline at intermediate temperatures. Exposure to electron beams during growth results in larger and (001) textured grains. The substrate is separated from the GaAs film in seconds via submersion in water, revealing a substrate surface comparable to the original.
Draft Genome Sequencing of Giardia intestinalis Assemblage B Isolate GS: Is Human Giardiasis Caused by Two Different Species? (2009)

Giardia intestinalis is a major cause of diarrheal disease worldwide and two major Giardia genotypes, assemblages A and B, infect humans. The genome of assemblage A parasite WB was recently sequenced, and the structurally compact 11.7 Mbp genome contains simplified basic cellular machineries and metabolism. We here performed 454 sequencing to 16x coverage of the assemblage B isolate GS, the only Giardia isolate successfully used to experimentally infect animals and humans. The two genomes show 77% nucleotide and 78% amino-acid identity in protein coding regions. Comparative analysis identified 28 unique GS and 3 unique WB protein coding genes, and the variable surface protein (VSP) repertoires of the two isolates are completely different. The promoters of several enzymes involved in the synthesis of the cyst-wall lack binding sites for encystation-specific transcription factors in GS. Several synteny-breaks were detected and verified. The tetraploid GS genome shows higher levels of overall allelic sequence polymorphism (0.5 versus <0.01% in WB). The genomic differences between WB and GS may explain some of the observed biological and clinical differences between the two isolates, and it suggests that assemblage A and B Giardia can be two different species.
Excitation functions of nuclear reactions leading to the soft-radiation emitting radionuclides45Ca,49V and204Tl in beam collimator materials used in proton therapy (2010)

Abstract Summary. Cross sections of nuclear reactions leading to the formation of the soft-radiation emitting radionuclides 45 Ca ( T 1/2 =163 d; β − =260 keV), 49 V ( T 1/2 =330 d; K α =4.51 keV) and 204 Tl ( T 1/2 =3.78 a; β − =763 keV) in proton induced reactions on titanium and lead, respectively, often used as collimators in proton therapy facilities, were measured for the first time over the energy range extending up to 200 MeV. Use was made of the stacked-foil technique. Elaborate radiochemical separations were performed and the radioactivity of the products was determined via anticoincidence beta counting, liquid scintillation counting or X-ray spectrometry. The experimental data were compared with the results of nuclear model calculations using the codes ALICE-IPPE and TALYS. In general good agreement was obtained. In the case of 204 Tl, however, the calculated values from ALICE-IPPE in the energy region above 80 MeV deviated considerably from the experimental data, possibly due to strong contributions of multiple particle emission reactions.
Real-Time Measurement of Diesel Particulate Emissions by the PAS Method Using a CO<sub>2</sub> Laser (1982)

&lt;div class="htmlview paragraph"&gt;This paper reports on real-time mass concentration measurements using the technique of photoacoustic spectroscopy. The measurements were made using a differential photoacoustic cell in which infrared absorption by diesel particulates at the 10.59 μm wavelength was measured with a 2.2 watt CO&lt;sub&gt;2&lt;/sub&gt; laser. Infrared absorption of the diesel particulates at 10.59 μm wavelength was treated as Rayieigh absorption since the mean mass diameter is around 0.1 μm and small enough to neglect the size effects. A dual cell method allows the separation of the particulate absorption signal from that of interfering gases present in diesel engine exhaust. In practice the sample gases from the dilution tunnel were introduced into two cells, one with and one without a particulate filter. The signals were calibrated by simultaneous measurement using the diesel particulate filter method of the U.S. EPA.&lt;/div&gt; &lt;div class="htmlview paragraph"&gt;The sensitivity of each PAS cell was found to depend upon the flow rate of the sample, the pressure in the cell, and the modulation frequency of the incoming light source. It was adjusted to be 2.0 mV/mWcm&lt;sup&gt;−1&lt;/sup&gt; at the longitudinally resonant frequency of 1.69 kHz where background acoustic noise is negligibly small. The results indicate that the PAS signal is linearly proportional to the mass concentration of the particulates in the range of 2.0 &lt;sup&gt;~&lt;/sup&gt; 140 mg/m&lt;sup&gt;3&lt;/sup&gt; within an accuracy of 15%. The response time of the measurement is less than 5 seconds.&lt;/div&gt;
Use of Force after 9/11 (2005)

The events of September 11, 2001, revealed to America and the world a new threat, qualitatively different than the dangers that have faced us in the past. This new threat has required us to adopt new policies to confront it. President Bush eloquently described the threat and the Administration's policy response in an address delivered at the National Defense University on February 11 of this year. He stated: In the Cold War, Americans lived under the threat of weapons of mass destruction but believed that deterrents made those weapons a last resort. What has changed in the 21st century is that in the hands of terrorists, weapons of mass destruction would be a first resort, the preferred means to further their ideology of suicide and random murder. These terrible weapons are becoming easier to acquire, build, hide, and transport. Armed with a single vial of a biological agent or a single nuclear weapon, small groups of fanatics or failing states could gain the power to threaten great nations, threaten the world peace. America and the entire civilized world will face this threat for decades to come. We must confront the danger with open eyes and unbending purpose. I have made clear to all the policy of this Nation: America will not permit terrorists and dangerous regimes to threaten us with the world's most deadly weapons.
An Unbiased Analysis Method to Quantify mRNA Localization Reveals Its Correlation with Cell Motility (2012)

Localization of mRNA is a critical mechanism used by a large fraction of transcripts to restrict its translation to specific cellular regions. Although current high-resolution imaging techniques provide ample information, the analysis methods for localization have either been qualitative or employed quantification in nonrandomly selected regions of interest. Here, we describe an analytical method for objective quantification of mRNA localization using a combination of two characteristics of its molecular distribution, polarization and dispersion. The validity of the method is demonstrated using single-molecule FISH images of budding yeast and fibroblasts. Live-cell analysis of endogenous β-actin mRNA in mouse fibroblasts reveals that mRNA polarization has a half-life of ~16 min and is cross-correlated with directed cell migration. This novel approach provides insights into the dynamic regulation of mRNA localization and its physiological roles.
Cytogenetic Studies of Allotetraploid Hybrids of Maize and Perennial Teosinte (1962)

Shaver, Donald L. (Brookhaven Natl. Lab., Upton, New York.) Cytogenetic studies of allotetraploid hybrids of maize and perennial teosinte. Amer. Jour. Bot. 49(4): 348–354. Illus. 1962.—Euchlaena perennis (4n), “perennial teosinte,” was less fertile when pollinated with 4n Zea mays than when selfed. Cross fertility between the 2 genera was influenced by the particular maize stock involved. Chromosome numbers varied from 36 to 43 in a population of 4n maize maintained by interpollination without regard to chromosome number. In the 4n intergeneric hybrid, nearly every chromosome number from 29 to 44 was found. The expression of the perennial growth habit varied with the proportion of perennial teosinte germ plasm present. Triploid hybrids with 2 perennial teosinte genomes and 1 maize genome were usually perennial. Tetraploid hybrids having 2 genomes of each parent were usually not fully perennial. Tetraploid hybrids with only 1 perennial teosinte genome had no perennial tendency but had a strong tendency to tiller. As compared with autotetraploids of maize having the same genetic markers, intergeneric hybrids showed a highly significant degree of preferential segregation for each of the 12 marker genes studied. In the opinion of the author, these data may represent the best available measure of the relationship of maize to teosinte, and are considered to support the proposal of Reeves and Mangelsdorf that maize and teosinte are congeneric.
Lösliche TNFa-Rezeptor p55 als prognostischer Marker bei der Leberzirrhose mit portaler Hypertonie und TIPS (2010)

Hintergrund: Proinflammatorische TNFa-Spiegel sind auch ohne nachweisbare Infektion bei der Leberzirrhose erhöht. Dies wird u.a. mit einer kontinuierlichen Endotoxineinschwemmung ins Portalblut erklärt. Bei der kurzen Halbwertzeit des TNFa sind lösliche TNFa- Rezeptoren (p55, p75) geeigneter, um die TNFa-Freisetzung zu erfassen. p75 Spiegel korrelieren mit der Mortalität in der Leberzirrhose. Hier untersuchten wir die p55- und p75-Spiegel bei Patienten, die einen TIPS erhielten. Methoden: Bei 41 Patienten mit Leberzirrhose (12 virus-bedingt, 29 alkohol-toxisch) wurde eine TIPS-Anlage durchgeführt. Bei der Anlage und bei der invasiven Kontrolle zwei Wochen später wurden in portalem und zentralvenösem Blut die Spiegel von p55 und p75 mittels ELISA gemessen. Ergebnisse: Wir fanden keinen signifikanten Unterschied zwischen den p55- und p75- Spiegel im portalen und zentralvenösem Blut. Sowohl p55- und p75-Spiegel korrelierten direkt mit dem MELD-Score (p=0,001) und Kreatinin (p=0,0001), sowie invers mit Albumin (p=0,02) und Cholinesterase (p=0,01). Der invasiv gemessene Pfortaderdruck (TIPS) korrelierte nicht mit den p55- und p75- Spiegeln, dagegen zeigten der Pfortaderdruck nach TIPS-Anlage eine direkte Korrelation und der systolischer Blutdruck eine inverse Korrelation mit dem zentralvenösen p55-Spiegel. Das Überleben (mittlere Nachbeobachtung 150±25 Monaten) war invers mit den zentralvenösen p55-Spiegel korreliert (p=0,007). Diskussion: Diese Studie zeigt, dass höhere zentralvenöse p55 Spiegel sowohl mit einer hyperdynamen Zirkulationsstörung als auch mit einem schlechteren Überleben bei TIPS-Patienten einhergehen. Diese könnten daher als prognostischer Marker für Patienten vor TIPS-Anlage herangezogen werden.
Base-Calling in DNA Pyrosequencing with Reconfigurable Bayesian Network (2009)

A reconfigurable computing method based on dynamic Bayesian learning network is proposed for base-calling in pyrosequencing from microarray gene expression data. Due to long memory and stochastic non-idealities in the pyrosequencing process, exact inference on the proposed dynamic Bayesian learning network is computationally prohibitive in both run-time and memory usage for reasonable problem sizes. To circumvent these issues, we design a reconfigurable Bayesian learning network, whereby processing nodes evaluate posterior probabilities of all states in parallel and crossbar switch realizes network topology that interconnects all processing nodes. The success of the proposed method is demonstrated by a prototype system implemented with Berkeley Emulation Engine 3 (BEE3) board, which achieves close to 2 times increase in read length and about 3 orders of reduction in run-time than previously reported for both experimental and simulated pyrosequencing data.