gebhart/patrepeval huggingface dataset:
Performance Antipatterns: Detection and Evaluation of Their Effects in the Cloud (2014)

The way an application is designed and certain patterns thereof, play a significant role and might have a positive or a negative effect on the performance of the application. Some design patterns that have a negative effect on performance, also called performance antipatterns, may become important when evaluating migrating the application to the Cloud. Although there has been work done in the past related to defining performance antipatterns, there has been none that highlights the importance and effects of these performance antipatterns when an application is migrated to Cloud. In this work we present an approach to automatically detect important performance antipatterns in an application, by leveraging static code analysis and information about prospective deployment of the application components on the Cloud. We also experimentally show that these antipatterns may become prominent and pull down the application's performance if the application is migrated to the Cloud. Our results show that the performance of the parts of the application with such antipatterns suffer significantly and hence, the detection of these antipatterns has an overarching significance in the domain of software development for the Cloud. The approach we present here has also been implemented in a prototype cloud migration assessment tool.
Beyond Expectation: Deep Joint Mean and Quantile Regression for Spatiotemporal Problems (2020)

Spatiotemporal problems are ubiquitous and of vital importance in many research fields. Despite the potential already demonstrated by deep learning methods in modeling spatiotemporal data, typical approaches tend to focus solely on conditional expectations of the output variables being modeled. In this article, we propose a multioutput multiquantile deep learning approach for jointly modeling several conditional quantiles together with the conditional expectation as a way to provide a more complete "picture" of the predictive density in spatiotemporal problems. Using two large-scale data sets from the transportation domain, we empirically demonstrate that, by approaching the quantile regression problem from a multitask learning perspective, it is possible to solve the embarrassing quantile crossings problem while simultaneously significantly outperforming state-of-the-art quantile regression methods. Moreover, we show that jointly modeling the mean and several conditional quantiles not only provides a rich description about the predictive density that can capture heteroscedastic properties at a neglectable computational overhead but also leads to improved predictions of the conditional expectation due to the extra information and the regularization effect induced by the added quantiles.
Anaerobic Expression of<i>Escherichia coli</i>Succinate Dehydrogenase: Functional Replacement of Fumarate Reductase in the Respiratory Chain during Anaerobic Growth (1998)

Succinate-ubiquinone oxidoreductase (SQR) from Escherichia coli is expressed maximally during aerobic growth, when it catalyzes the oxidation of succinate to fumarate in the tricarboxylic acid cycle and reduces ubiquinone in the membrane. The enzyme is similar in structure and function to fumarate reductase (menaquinol-fumarate oxidoreductase [QFR]), which participates in anaerobic respiration by E. coli. Fumarate reductase, which is proficient in succinate oxidation, is able to functionally replace SQR in aerobic respiration when conditions are used to allow the expression of the frdABCD operon aerobically. SQR has not previously been shown to be capable of supporting anaerobic growth of E. coli because expression of the enzyme complex is largely repressed by anaerobic conditions. In order to obtain expression of SQR anaerobically, plasmids which utilize the PFRD promoter of the frdABCD operon fused to the sdhCDAB genes to drive expression were constructed. It was found that, under anaerobic growth conditions where fumarate is utilized as the terminal electron acceptor, SQR would function to support anaerobic growth of E. coli. The levels of amplification of SQR and QFR were similar under anaerobic growth conditions. The catalytic properties of SQR isolated from anaerobically grown cells were measured and found to be identical to those of enzyme produced aerobically. The anaerobic expression of SQR gave a greater yield of enzyme complex than was found in the membrane from aerobically grown cells under the conditions tested. In addition, it was found that anaerobic expression of SQR could saturate the capacity of the membrane for incorporation of enzyme complex. As has been seen with the amplified QFR complex, E. coli accommodates the excess SQR produced by increasing the amount of membrane. The excess membrane was found in tubular structures that could be seen in thin-section electron micrographs.
Phonons in One-Dimensional Quasi-Lattices (1986)

Vibrational properties in one-dimensional quasi-lattices constructed by the Fibonacci substitution rule are studied numerically within a harmonic approximation. Examining the generation dependence of the substitution, we find that the gross spectrum structure is generation-independent and self-similar, and that the ratio of the numbers of the eigenfrequencies contained in each band tends to the golden mean with the generation. The localization property of the eigenfunctions and other class of the quasi-lattice are discussed.
The Role of Prostate Specific Antigen in the Baseline Assessment of Patients undergoing Hormone Therapy for Advanced Prostate Cancer (1987)

One hundred and thirty-nine patients with advanced prostate cancer were entered into a randomised trial to test the efficacy and tolerance of goserelin 3.6 mg depot (Zoladex) versus stilboestrol 3 mg/day. As well as the usual clinical and radiological assessments of extent of disease, we used an immunoradiometric assay of prostate specific antigen (PSA) (Hybritech Europe) and normal laboratory enzymatic assays of acid phosphatase (AP) and alkaline phosphatase (ALKP) for biochemical assessment. The upper limit of normal for PSA was taken as 10 micrograms/l. The range of PSA was wide and differed significantly from that of AP and to a lesser extent ALKP in metastatic cases. PSA outperformed both AP and ALKP in both the local and advanced groups in terms of sensitivity. There was no correlation, however, between histological grade and level of PSA, AP or ALKP (the latter in cases with bone disease). In patients with metastatic disease diagnosed by bone scan, nine patients had one abnormal site/one "hot spot", and all of these had a PSA greater than twice the normal upper limit. Early death due to prostate cancer was noted in four patients with levels of PSA greater than 2500 micrograms/l. PSA is more sensitive than either enzymatic AP or ALKP in both locally advanced and metastatic prostate cancer and is useful in identifying those advanced cases who have single lesions on bone scan. In this series PSA gave an overall sensitivity of 89%, compared with 63% for AP and 64% for ALKP in patients with metastatic disease.
Biological treatment in acute myelogenous leukaemia: how should T-cell targeting immunotherapy be combined with intensive chemotherapy? (2001)

T-cell targeting immunotherapy is now considered as a possible strategy in the treatment of acute myelogenous leukaemia (AML). Clinical importance of antileukaemic T-cell reactivity after allogeneic stem cell transplantation (SCT) is well established and the early experience from IL-2 therapy suggests that even autologous T-cells can mediate antileukaemic reactivity. The clinical experience also indicates that immunotherapy should begin when the leukaemia cell burden is minimal, and the detection of an operative cellular immune system, even in patients with chemotherapy-induced cytopenia, further suggests that it is possible to begin T-cell targeting therapy early after chemotherapy while patients are still cytopenic. However, adult patients in particular have a T-cell defect after chemotherapy that may last for several months. For this reason immunotherapy should probably be continued or repeated until a maximal effect is achieved when the patients no longer have a T-cell defect. This treatment approach may also be considered in combination with autologous SCT. T-cell targeting regimens should include, if possible, several therapeutic components. Firstly, native AML blasts can function as accessory cells during T-cell activation and in vivo therapy with T-cell growth factors (e.g., IL-2, IL-15) may then enhance antileukaemic reactivity or non-specific cytotoxicity against the AML cells; and secondly, a further enhancement of AML-specific reactivity may be achieved by vaccination with AML-specific peptides, immunisation with AML-blasts expressing a dendritic cell phenotype, or exposure to normal antigen-presenting cells (APC) pulsed with or expressing AML-specific peptide sequences.
Studies in spiroheterocycles, Part <b>XV</b>. Investigation of the reaction of 3‐(2‐oxocycloalkylidene)‐indol‐2‐ones with thiourea and urea derivatives (1989)

Abstract The reaction of 3‐(2‐oxocycloalkylidene)indol‐2‐one 1 with thiourea and urea derivatives has been investigated. Reaction of 1 with thiourea and urea in ethanolic potassium hydroxide media leads to the formation of spiro‐2‐indolinones 2a‐f in 40–50% yield and a novel tetracyclic ring system 4,5‐cycloalkyl‐1,3‐diazepino‐[4,5‐ b ]indole‐2‐thione/one 3a‐f in 30–35% yield. 3‐(2‐Oxocyclopentylidene)indol‐2‐one afforded 5′,6′‐cyclopenta‐2′‐thioxo/ oxospiro[3 H ‐indole‐3,4′(3′ H )pyrimidin]‐2(1 H )‐ones 2a,b and 3‐(2‐oxocyclohexylidene)indol‐2‐one gave 2′,4′a,5′,6′,7′,8′‐ hexahydro‐2′‐thioxo/oxospiro[3 H ‐indole‐3,4′ (3′ H )‐quinazolin]‐2(1 H )‐ones 2c‐f . Under exactly similar conditions, reaction of 1 with fluorinated phenylthiourea/cyclohexylthiourea/phenylurea gave exclusively spiro products 2g‐1 in 60–75% yield. The products have been characterized by elemental analyses, ir pmr. 19 F nmr and mass spectral studies.
Atypical teratoid/rhabdoid tumors—current concepts, advances in biology, and potential future therapies (2016)

Atypical teratoid/rhabdoid tumor (AT/RT) is the most common malignant CNS tumor of children below 6 months of age. The majority of AT/RTs demonstrate genomic alterations in SMARCB1 (INI1, SNF5, BAF47) or, to a lesser extent, SMARCA4 (BRG1) of the SWItch/sucrose nonfermentable chromatin remodeling complex. Recent transcription and methylation profiling studies suggest the existence of molecular subgroups. Thus, at the root of these seemingly enigmatic tumors lies a network of factors related to epigenetic regulation, which is not yet completely understood. While conventional-type chemotherapy may have significant survival benefit for certain patients, it remains to be determined which patients will eventually prove resistant to chemotherapy and thus need novel therapeutic strategies. Elucidation of the molecular consequences of a disturbed epigenome has led to the identification of a series of transduction cascades, which may be targeted for therapy. Among these are the pathways of cyclin D1/cyclin-dependent kinases 4 and 6, Hedgehog/GLI1, Wnt/ß-catenin, enhancer of zeste homolog 2, and aurora kinase A, among others. Compounds specifically targeting these pathways or agents that alter the epigenetic state of the cell are currently being evaluated in preclinical settings and in experimental clinical trials for AT/RT.
Monovalent Fab' immunoglobulin fragments from endemic pemphigus foliaceus autoantibodies reproduce the human disease in neonatal Balb/c mice. (1990)

Fogo selvagem (FS) is an autoimmune disease caused by IgG autoantibodies to desmoglein I (DG-I), a desmosomal glycoprotein. We have previously shown that the autoantibodies in these patients are pathogenic and restricted mainly to the IgG4 subclass. The purpose of this study was to determine if the Fc domain or the valence of FS autoantibodies were relevant in the induction of epidermal disease in neonatal mice. IgG4 was prepared from sera of FS patients by anion exchange chromatography, and digested with pepsin to yield F(ab')2 fragments. Monovalent FS Fab' were made by reduction and alkylation of FS F(ab')2. Intact FS IgG4, FS F(ab')2, and FS Fab' fragments were injected into neonatal mice. Intact FS IgG4 and both FS IgG fragments were pathogenic. The disease in the animals was dose dependent, and on the molar basis, FS Fab' fragments were more potent and efficient in producing disease than whole FS IgG. These results suggest: (a) simple binding of FS autoantibodies to DG-I may trigger keratinocyte detachment and epidermal disease; (b) DG-I may represent a keratinocyte cell adhesion molecule; and (c) complement activation and surface cross-linking may not be relevant in keratinocyte detachment.
Oral budesonide in the treatment of chronic refractory pouchitis (2007)

Eight-week treatment with oral budesonide appears effective in inducing remission in patients with active pouchitis refractory to antibiotic treatment in this open-label study.
Optimization-based placement algorithm for BiCMOS leaf cell generation (1994)

We present a transistor placement algorithm for the automatic layout synthesis of logic and interface cells comprised of a mixture of MOS and bipolar devices. Our algorithm is applicable to BiCMOS logic cells, ECL logic cells as well as TTL, CMOS and ECL compatible input/output (I/O) cells. The transistor placement problem is transformed into a layout floorplan design problem with a mixture of rigid and flexible modules. A constructive "branch-and-bound" algorithm is used to minimize the area of synthesized circuits subject to pre-placement constraints. Experimental results indicate that the algorithm can produce efficient placements under fixed-height constraints. The design space exploration mechanism can be controlled by the user so as to apportion computing resources judiciously.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">></ETX>
[Identification of Taenia saginata by mtCO I in four areas of Yunnan and Guizhou provinces]. (2003)

The Taenia prevalent in Lanping, Dali and Duyun is identified as T. saginata asiatica, while that isolated in Congjiang is the typical T. saginata.
Kinetics of acetaminophen absorption and gastric emptying in man (1978)

Eight healthy male volunteers ingested an aqueous solution containing acetaminophen (20 mg/kg) and a nonabsorbable isotopic marker. The concentrations of unconjugated acetaminophen in samples of blood plasma taken at frequent intervals were measured by gas-liquid chromatography. The data points followed a smooth curve in most cases and were fitted to the classical two-compartment pharmacokinetic model to obtain KA, the apparent first-order rate constant for absorption from the gastrointestinal tract. Gastric emptying was measured simultaneously from serial scintiscans of the subject's abdomen. The subjects were also studied after intramuscular injection of meperidine (150 mg) and pentazocine (60 mg) with and without naloxone (1.2 mg). The acetaminophen absorption curves and gastric emptying patterns were consistent with negligible absorption from the stomach. A new model is proposed in which the conventional single compartment used to represent the gastrointestinal tract is replaced by two compartments: one represents the stomach and the other the small intestine, from which absorption occurs rapidly. Pharmacokinetic analysis using this model showed good agreement in all cases, and provided an estimate of KA, the first-order rate constant for drug transfer from the intestinal lumen into the systemic circulation. The mean half-time for transfer was 6.8 +/- 0.9 min. As expected, KA was greater than KG (the first-order rate constant for gastric emptying), showing that gastric emptying was rate-limiting in the absorption of acetaminophen. The value of KA was greater than KA and the two were not related. The value of KA was not equal to KG in most studies because gastric emptying was not a single exponential process.
Genome-wide analysis of the UDP-glucose dehydrogenase gene family in Arabidopsis, a key enzyme for matrix polysaccharides in cell walls (2007)

Arabidopsis cell walls contain large amounts of pectins and hemicelluloses, which are predominantly synthesized via the common precursor UDP-glucuronic acid. The major enzyme for the formation of this nucleotide-sugar is UDP-glucose dehydrogenase, catalysing the irreversible oxidation of UDP-glucose into UDP-glucuronic acid. Four functional gene family members and one pseudogene are present in the Arabidopsis genome, and they show distinct tissue-specific expression patterns during plant development. The analyses of reporter gene lines indicate gene expression of UDP-glucose dehydrogenases in growing tissues. The biochemical characterization of the different isoforms shows equal affinities for the cofactor NAD(+) ( approximately 40 microM) but variable affinities for the substrate UDP-glucose (120-335 microM) and different catalytic constants, suggesting a regulatory role for the different isoforms in carbon partitioning between cell wall formation and sucrose synthesis as the second major UDP-glucose-consuming pathway. UDP-glucose dehydrogenase is feedback inhibited by UDP-xylose. The relatively (compared with a soybean UDP-glucose dehydrogenase) low affinity of the enzymes for the substrate UDP-glucose is paralleled by the weak inhibition of the enzymes by UDP-xylose. The four Arabidopsis UDP-glucose dehydrogenase isoforms oxidize only UDP-glucose as a substrate. Nucleotide-sugars, which are converted by similar enzymes in bacteria, are not accepted as substrates for the Arabidopsis enzymes.
11q23/MLL Acute Leukemia : Update of Clinical Aspects (2010)

Rearrangements of the MLL gene located at 11q23 are common chromosomal abnormalities associated with acute leukemia (AL), especially infant and secondary leukemia after previous treatment with DNA topoisomerase II inhibitors. 11q23/MLL abnormalities have been widely recognized as an important prognostic factor in AL. Over 70 chromosome partners of 11q23 have been identified to date, at least 50 of which have been cloned and characterized at the molecular level. Recent studies showed that the prognosis of 11q23/MLL AL varies widely according to the partner gene, the leukemia cell lineage, the age of the patient and the treatment administered. Special strategies are needed to treat 11q23/MLL AL, including allogeneic hematopoietic stem cell transplantation, according to the fusion partner. The development of novel methodologies, including new molecular therapeutic targets, is also needed to improve the prognosis of 11q23/MLL AL. The present article provides an update on the current status of prognosis and treatment of 11q23/MLL AL according to the fusion partner.
Diffraction separation based on the projected first Fresnel zone (2018)

The importance of seismic diffractions has been recognized in subsurface imaging. Diffractions might contain useful information about small-scale geological structures and heterogeneities, e.g. faults, pinch-outs, thin lenses, fractures etc and can be very helpful for prospecting and development of fractured reservoirs. One of the most challenging task in diffraction imaging is the separation of diffractions from reflections. In this work, we present a new diffraction filter based on the projected (first) Fresnel zone (PFZ) to enhance diffraction separation and imaging. We found that the difference in the width of the PFZ appears to be a very consistent parameter for diffraction separation and thus, can be used as a robust diffraction filter. We derived the width of the PFZ from wavefront attributes, which are determined using the common-reflection-surface method. Applications to a simple gradient model as well as a complex synthetic data set validate our approach.
EMISSIONS OF NITROUS OXIDE (N2O) FROM FLUIDIZED BED BOILERS (1989)

ABSTRACT Measurements of emissions of nitrous oxide (N20) have been carried out on two kind of fluidized bed boilers. One of them, a circulating fluidized bed boiler has been run with three kind of fuels at different operating conditions. The results of the measurements show that the emission of N20 depends on bed temperature and fuel. The temperature dependence is explained by the strong influence of temperature on the rate of destruction of nitrous oxide by radicals in the gas phase.
Real Time Simulation Using Non-causal Physical Models (2009)

<div class="htmlview paragraph">As automotive electronics become more complex and more distributed, hardware in-the-loop simulation is now a widely adopted technique for performing controller software/hardware integration testing as well as controller/controller integration testing. Having real-time capable models that are correlated to physical hardware being controlled is key to successful implementation of hardware in-the-loop testing. Because models for hardware in-the-loop must be developed in a short amount of time and then stay in sync with the design through design changes, a best practice is to obtain such models from the system-level model used for requirements analysis and design trade offs. This way, one model can address the need of both requirements analysis and integration testing, reducing redevelopment of models and ensuring consistency between two process steps. While there has been significant progress made in recent years on real-time simulator technologies, including I/O accuracy, use of off-the-shelf hardware, acceleration using parallel processing, the process by which a system level simulation model is to be reused for hardware in-the-loop testing is not very well understood. This paper starts by examining options for developing a system level simulation model. When limited to causal modeling techniques, the process of creating models is often cumbersome and time-consuming. Many engineers find non-causal (or acausal) modeling methods to be much more intuitive. However, getting acausal models to run in real-time requires careful upfront planning and, when required, methodical reduction. The remaining sections of the paper deal with effective techniques for physical model development and reduction.</div>
Stereospecific Synthesis and Characterization of Oligodeoxyribonucleotides Containing an <i>N</i><sup>2</sup>-(1-Carboxyethyl)-2‘-deoxyguanosine (2007)

Methylglyoxal is a highly reactive alpha-ketoaldehyde that is produced endogenously and present in the environment and foods. It can modify DNA and proteins to form advanced glycation end products (AGEs). Emerging evidence has shown that N2-(1-carboxyethyl)-2'-deoxyguanosine (N2-CEdG) is a major marker for AGE-linked DNA adducts. Here, we report, for the first time, the preparation of oligodeoxyribonucleotides (ODNs) containing individual diastereomers of N2-CEdG via a postoligomerization synthesis method, which provided authentic substrates for examining the replication and repair of this lesion. In addition, thermodynamic parameters derived from melting temperature data revealed that the two diastereomers of N2-CEdG destabilized significantly the double helix as represented by a 4 kcal/mol increase in Gibbs free energy for duplex formation at 25 degrees C. Primer extension assay results demonstrated that both diastereomers of N2-CEdG could block considerably the replication synthesis mediated by the exonuclease-free Klenow fragment of Escherichia coli DNA polymerase I. Strikingly, the polymerase incorporated incorrect nucleotides, dGMP and dAMP, opposite the lesion more preferentially than the correct nucleotide, dCMP.
Application of data mining techniques in pharmacovigilance (2003)

In view of the importance of ADEs and the development of massive data storage systems and powerful computer systems, the use of data mining techniques in knowledge discovery in medical databases is likely to be of increasing importance in the process of pharmacovigilance as they are likely to be able to detect signals earlier than using current methods.