gebhart/patrepeval huggingface dataset:
Proceedings of the ACM SIGPLAN 2003 conference on Programming language design and implementation (2003)

The PLDI conference is one of the premier forums for the presentation of new and exciting research in the areas of programming language design and implementation. The conference attracts a wide audience including researchers, practitioners, and educators. The program committee is pleased to present this proceedings of the 2003 ACM SIGPLAN Conference on Programming Language Design and Implementation which contains a collection of 28 technical papers covering a wide range of exciting topics.This year a total of 131 manuscripts were received from 20 countries. We received 96 submissions from North America, 17 submissions from Europe, 16 submissions from Asia, and 2 submissions from Australia. A total of 36 papers had at least one author from industry. From the 131 submissions, the program committee selected 28 submissions for inclusion in the program.The submission and review process worked as follows. Each submission was assigned to three program committee members for review. In addition, one external review was solicited for each paper. For papers with conflicting reviews email discussions preceded the program committee meeting. For papers with low confidence reviews additional reviews were sought from experts before the program committee meeting. The program committee meeting was held in New Orleans on January 19 and 20. Early in the meeting, the 131 papers were narrowed down to 75 papers whose discussion occupied the rest of the meeting.
Selection of full‐length IgGs by tandem display on filamentous phage particles and Escherichia coli fluorescence‐activated cell sorting screening (2010)

Phage display of antibody libraries is a powerful tool for antibody discovery and evolution. Recombinant antibodies have been displayed on phage particles as scFvs or Fabs, and more recently as bivalent F(ab')(2). We recently developed a technology (E-clonal) for screening of combinatorial IgG libraries using bacterial periplasmic display and selection by fluorescence-activated cell sorting (FACS) [Mazor Y et al. (2007) Nat Biotechnol 25, 563-565]. Although, as a single-cell analysis technique, FACS is very powerful, especially for the isolation of high-affinity binders, even with state of the art instrumentation the screening of libraries with diversity > 10(8) is technically challenging. We report here a system that takes advantage of display of full-length IgGs on filamentous phage particles as a prescreening step to reduce library size and enable subsequent rounds of FACS screening in Escherichia coli. For the establishment of an IgG phage display system, we utilized phagemid-encoded IgG with the fUSE5-ZZ phage as a helper phage. These phage particles display the Fc-binding ZZ protein on all copies of the phage p3 coat protein, and are exploited as both helper phages and anchoring surfaces for the soluble IgG. We demonstrate that tandem phage selection followed by FACS allows the selection of a highly diversified profile of binders from antibody libraries without undersampling, and at the same time capitalizes on the advantages of FACS for real-time monitoring and optimization of the screening process.
An approach to regulating Dual Series Static Compensator (DSSC) (2012)

For power flow control with specific attention to renewable energy resources based transmission in a meshed network, less complex coordinated control can be obtained with the proposed convertible static transmission controller (CSTC) concept which is connected across the substation power transformer and can be reconfigured to the required modes of operation. Dual Series Static Compensator (DSSC) mode or series-series mode available in the CSTC provides superior performance in terms of operating characteristics compared to conventional power flow controllers. In this paper, detailed steady-state and dynamic performance of DSSC will be investigated, and the control structure of DSSC will be proposed to control active and reactive power independently. This paper specifically explores the challenges of the proposed control method. In particular, the proposed control structure is based on line current PLL. The dynamic performance of DSSC is further investigated in PSCAD/EMTDC environment.
Nutritional Composition of Infant Cereal Prototypes Can Precisely Predict Their Glycemic Index (2022)

Designing cereal-based products with appropriate metabolic responses is of high interest to the food industry in view of the potential health impact of the product. The objective of this study was to test whether a model that used the nutrient composition of breakfast cereals to predict their glycemic index (GI) and glycemic load (GL) could also accurately predict the GI and GL for complete (containing protein, reconstituted in water) infant cereal prototypes. Four independent studies measured the postprandial glucose response of 20 complete infant cereal prototypes (51−76 g/100 g glycemic carbohydrates) in healthy adults. The predictions were strongly correlated with the measured values for both the GI (r = 0.93, p-value < 0.01) and GL (r = 0.98, p-value < 0.01). The in vivo incremental area under the curve (iAUC) for glucose showed a strong linear relationship with the predicted GL (r = 0.99, p < 0.01). In summary, the model previously developed to predict the GI and GL of breakfast cereals was both accurate and precise for infant cereals and could be considered a simple tool to support nutritionally responsible product development.
A high efficiency indirect matrix converter utifizing RB-IGBTs (2006)

This paper presents the design and construction of an Indirect Matrix Converter (IMC) utilizing newly available IGBTs with reverse voltage blocking capability (RB-IGBTs). The design process involves the characterization of the RB-IGBTs by measuring the on-state parameters and the switching behavior in the rectifier stage of an IMC topology. Based on analytical equations the semiconductor losses are calculated and are used to perform the thermal design and simulation of the cooling system. Experimental measurements demonstrate that the designed IMC is capable of generating sinusoidal input and output currents and that the RB-IGBTs ensure low rectifier stage conduction losses and/or high IMC power conversion efficiency.
Compact physical models for chip and package power and ground distribution networks for gigascale integration (GSI) (2008)

For the first time, compact physical models are derived in this work that enable quick package- and chip-scale calculations of the power supply noise and incorporate the distributed natures of on-chip power/ground grids and package-level power/ground planes. Designers can use these models to perform chip/package co-design for power distribution networks and tradeoff multiple design considerations such as metal resource allocation on chip and in package, decoupling capacitor insertion and I/O allocation. Such studies can be performed during early stages of design, even when detailed physical design information is not available. The models are used to model a ceramic package designed by IBM, and it is found that there is less than 10% difference between the model predictions and the commercial tool SPEED 2000 when predicting the peak noise value and time of occurrence. The models can have 10x speed-up compared to SPEED 2000.
ChemInform Abstract: L‐(+)‐Swainsonine and Other Pyrrolidine Inhibitors of Naringinase: Through an Enzymic Looking Glass from D‐Mannosidase to L‐Rhamnosidase? (1997)

Abstract ChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 100 leading journals. To access a ChemInform Abstract of an article which was published elsewhere, please select a “Full Text” option. The original article is trackable via the “References” option.
Monte Carlo analysis of an ODE Model of the Sea Urchin Endomesoderm Network (2009)

The method described in this paper enables an evaluation of network topologies of GRNs without requiring any parameter values. The benefit of this method is exemplified in the first mathematical analysis of the complete Endomesoderm Network Model. The predictions we provide deliver candidate nodes in the network that are likely to be erroneous or miss unknown connections, which may need additional experiments to improve the network topology. This mathematical model can serve as a scaffold for detailed and more realistic models. We propose that our method can be used to assess a completeness grade of any GRN. This could be especially useful for GRNs involved in human diseases, where often the amount of connectivity is unknown and/or many genes/interactions are missing.
Data from: Rapid conformational fluctuations in a model of methylcellulose (2015)

Methylcellulose is a thermoresponsive polymer that undergoes a morphological transition at elevated temperature, forming uniform diameter fibrils. However, the gelation mechanism is still unclear, in particular, at higher polymer concentrations. We use Langevin dynamics simulations to investigate a coarse-grained model for methylcellulose that produces collapsed ringlike structures in dilute solution with a radius close to the fibrils observed in experiments. We show that the competition between the dihedral potential and self-attraction causes these collapsed states to undergo a rapid conformational change, which helps the chain to avoid kinetic traps by permitting a transition between collapsed states. If the dihedral potential is removed, the chains do not escape from their collapsed configuration, whereas at high dihedral potentials, the chains cannot stabilize the collapsed state. We provide systematic data on the effect of the dihedral potential in a model of methylcellulose, and discuss the implication of these previously overlooked rapid conformational fluctuations on the spontaneous formation of high-aspect-ratio fibrils.
Nonvolatile Memristive Switching in Self-assembled Nanoparticle Dimers (2020)

The selective formation of heterogeneous nanoparticle (NP) agglomerates and their memristive switching properties are reported. Following surfactant-mediated self-assembly in suspension, agglomerates of silver nanocubes (AgNCs) and spherical silicon nanoparticles (SiNPs) are prepared in a bottom-up approach. Dimers comprising one AgNC and one SiNP are electrically contacted, and pronounced bipolar memristive switching is demonstrated. The formed nanoscale memristor junctions show in particular narrow distributions of the SET voltage, ON/OFF-resistance ratios in excess of three orders of magnitude, and good retention properties. Ex situ scanning electron microscopy studies directly support a switching model based on Ag-conductive filament formation in the polycrystalline SiNPs. We propose our self-assembled NP memristors as building blocks for the bottom-up construction of future 3D memristive networks.
Risk of Bacteremia in Patients with Hematological and other Malignancies after Initial Placement of a Central Venous Catheter (2007)

Background: Widespread use of central venous access devices has made catheter-related bacteremia an important concern. Therefore, we conducted a follow-up study on the risk of bacteremia in Danish patients with hematological or other malignancies after placement of their first central venous access devise. Patients and methods: At a Danish university hospital we identified 357 patients with hematological or other malignancies during a three-year period, 2000-2002. Data on catheter placement and bacteremias were obtained from hospital registries. Clinical data were abstracted from patients' charts. Results: 104 patients had a hematological malignancy (hem) and 253 patients had other malignancies (solid tumor). A total of 55 patients (34/21) developed bacteremia following catheter placement. After adjustment for age, sex, and comorbidity, the relative risk of bacteremia in the hem compared with the solid tumor group was 10.8 (95%; CI, 5.8−20.1). In both groups, the central venous catheter was the most frequent focus of infection with no major difference in proportion (50% and 33%, respectively); an unknown focus was also common (50% and 19%, respectively). Conclusion: Patients with hematological malignancies had a 10-fold increased risk of bacteremia compared with other cancer patients and the central venous catheter was not the only important focus.
Utilization of Active Surveillance as Initial Management of Newly Diagnosed Prostate Cancer: Data from the PURC (2019)

Purpose:We describe contemporary active surveillance utilization and variation in a regional prostate cancer collaborative. We identified demographic and disease specific factors associated with active surveillance in men with newly diagnosed prostate cancer.Materials and Methods:We analyzed data from the PURC (Pennsylvania Urologic Regional Collaborative), a cooperative effort of urology practices in southeastern Pennsylvania and New Jersey. We determined the rates of active surveillance among men with newly diagnosed NCCN (National Comprehensive Cancer Network®) very low, low or intermediate prostate cancer and compared the rates among participating practices and providers. Univariate and multivariable analyses were used to identify factors associated with active surveillance utilization.Results:A total of 1,880 men met inclusion criteria. Of the men with NCCN very low or low risk prostate cancer 57.4% underwent active surveillance as the initial management strategy. Increasing age was significantly ass...
Front Cover: Polymer‐Based Module for NAD+ Regeneration with Visible Light (ChemBioChem 20/2019) (2019)

Giant polymer vesicles carrying photocatalytic nanoparticles made out of a fully organic conjugated polymer were used to create a functional module able to artificially regenerate the oxidized form of the nicotinamide adenine nucleotide cofactor. The regeneration happens only under irradiation of visible light, with the catalytic process being efficiently shielded from external chemical stress due to the barrier offered by the membrane of the polymeric vesicles. More information can be found in the communication by K. A. I. Zhang, K. Landfester, et al. on page 2593 in Issue 20, 2019 (DOI: 10.1002/cbic.201900093).
Why Targeting PSMA Is a Game Changer in the Management of Prostate Cancer (2017)

Prostate-specific membrane antigen (PSMA) is a transmembrane glycoprotein that is highly expressed on prostate adenocarcinomas, exhibits only limited expression in benign and extraprostatic tissues, and thus represents an ideal target for the diagnosis and management of prostate cancer. Since its discovery over 30 y ago, significant effort has been made to develop clinical technology targeting PSMA. The last 5 y have seen an explosion of development of new agents targeting PSMA for diagnostic and therapeutic use. Imaging agents targeting PSMA have been developed for SPECT and PET platforms. PSMA PET imaging appears to outperform traditional imaging in the high-risk localized-disease state, in patients with biochemical recurrence after treatment, and in advanced disease. To date, most of the reported clinical studies of therapeutic agents have used PSMA-targeted radiometals to deliver β-radiation to metastatic disease sites, with <sup>177</sup>Lu being the most widely investigated therapeutic radioisotope. Studies of both antibodies and small-molecule agents have been published and have demonstrated encouraging results. Safety appears generally limited to mild transient bone marrow toxicity and xerostomia because of uptake of the small-molecule agents in the salivary glands. Radiologic responses can be dramatic, and decreases in pain have been observed. The effect on overall survival, however, has yet to be demonstrated.
Guided Sketching for Visual Search and Exploration in Large Scatter Plot Spaces (2014)

Recently, there has been an interest in methods for filtering large scatter plot spaces for interesting patterns. However, user interaction remains crucial in starting an explorative analysis in a large scatter plot space. We introduce an approach for explorative search and navigation in large sets of scatter plot diagrams. By means of a sketch-based query interface, users can start the exploration process by providing a visual example of the pattern they are interested in. A shadow-drawing approach provides suggestions for possibly relevant patterns while query drawing takes place, supporting the visual search process. We apply the approach on a large real-world data set, demonstrating the principal functionality and usefulness of our technique.
Synthesis of performance expression of bowed string instruments using “Expression Mark Functions” (2012)

This paper proposes a method for synthesis of performance expression of bowed string instruments. In order to reflect a creator's intention on a synthetic sound, physical model is efficient because the sound can be synthesized by the performance imagination. The physics of the bowed string instruments are still some issues remain unresolved, bowed string sound synthesis using only the physical model is difficult. In this paper, a method using a transfer function for expression mark is proposed. “Expression mark functions” is estimated from recorded performance sounds, using spectrum of string motion and inverse filter of resonant properties of the instruments. Bowed String motion is a triangular wave called the Helmholtz wave, and it can be determined from bowed string position. Changes of waveform from expression performance were estimated by non-negative matrix factorization. Resonant properties of an instrument were measured as TSP response using a “direct conduction speaker”. The expression mark functions of the performance is extracted by decomposing the actual performance. For evaluation of the quality of the synthesized sound, the scale by ten kinds of expression marks was synthesized using expression mark functions, and the questionnaire estimated the degree of agreement in five steps.
Rational Development of New Cooling Water Chemical Treatment Programs for Scale and Microbial Control (2005)

Crystal growth is part of a more extensive problem in supersaturated cooling waters known as scale formation. Scale usually refers to an intimate mixture of a multitude of sparingly soluble mineral salts. Depending on the pH, temperature and water chemistry, these salts include but are not limited to calcium carbonate, calcium phosphate, silica, silicate salts, calcium sulfate, corrosion products (iron (hydr)oxides) etc. Calcium carbonate is the predominant component of the hard and tenacious scale deposited from natural waters, especially in processes involving heat transfer. The main focus of this paper is on two major system stresses, high Ca2+ and oxidizing biocides, and under conditions common in Heating, Ventilation and Air Conditioning (HVAC) systems. The chief factor that promotes calcium carbonate scale formation is concentration of dissolved solids by repeated partial evaporation of the water.1,2 Therefore, a certain water that has no scale tendency will eventually become scale-forming when concentrated n times, where n = 2, 3, 4 and even higher. The number n is defined as cycles of concentration (COC's). Economic considerations to minimize water use require low blowdown and increased COC's. The severity of the scaling tendency of a certain water is related to the saturation index (SI), defined as follows: [Ca2+].[Ca32-] SI = (1) KspCaCO3
Oxidation and Reduction (2007)

This chapter contains sections titled: Oxidation by Metal Ions and Related Species Oxidation by Compounds of Non-metallic Elements Miscellaneous Oxidations Ozonolysis and Ozonation Peracids, Peroxides, and Superoxide Atomic Oxygen and Singlet Oxygen Other Reactions of Oxygen, including Autoxidation Reduction by Complex Metal Hydrides Reduction by Metals, Metal Ions, and Metal Complexes Miscellaneous Reductions Hydrogenation Reductions and Oxidations of Biological Interest
A Novel Approach to Estimate Freeway Traffic State: Parallel Computing and Improved Kalman Filter (2018)

This paper presents a novel approach for freeway traffic state estimation. Although there is currently a wide variety of estimation methods, new designs and technologies can still be created and implemented to improve the accuracy and time efficiency. In this study, a parallel computing framework is developed. The parallel computing framework uses a genetic algorithm process to calibrate the parameters of the traffic model based on the freeway traffic data once an hour. Meanwhile, the framework uses a Kalman filter algorithm process to optimize the traffic model results with the real-time freeway traffic data. Under the framework, the operations of the two processes will not interfere with each other, thus reducing the time it takes to estimate, increasing the efficiency. Furthermore, an improved Kalman filter algorithm is proposed. The algorithm optimizes the traffic model results by balancing the ratio of detector measurements to model results based on their variances, instead of using the Taylor series expansion. Therefore, time efficiency and accuracy of the Kalman filter algorithm are improved. The effectiveness of the approach is evaluated using real field data. Experiments have shown that this approach has high real-time tracking accuracy, and is faster and more accurate than the extended Kalman filter. Results also indicated that the estimation accuracy can be enhanced by accessing additional data sources.
The remarkable pliability and promiscuity of specialized metabolism (2013)

Metabolic pathways are often considered “perfected” or at least predictable as substrates efficiently rearrange into products through the intervention of a catalytically and/or metabolically optimized enzyme. Moreover, these individual steps link up forming a myriad of metabolic circuits that are often modeled with a high degree of certainty. However, upon closer examination, most enzymes are not precise with respect to their activity, using not just one substrate but often a variety, and producing not just one product but a diversity. Hence, the metabolic systems assembled from enzymes possessing varying degrees of what can be termed catalytic promiscuity are not clear‐cut and restrictive; rather, they may at times operate somewhat stochastically in the intracellular milieu. This “messiness” complicates our understanding of normal and aberrant cellular behavior while paradoxically sowing the seeds for future advantageous metabolic adaptations for the host organisms.