gebhart/patrepeval huggingface dataset:
Bordetella adenylate cyclase: host toxicity and diagnostic utility. (1985)

Two toxins from Bordetella pertussis, pertussis toxin and Bordetella adenylate cyclase, cause profound disruptions of cAMP metabolism in mammalian cells. While the role of each toxin in the whooping cough syndrome is unknown, it is highly likely that together they confer on the organism an important proliferative advantage. Intact B. pertussis cells express large amounts of adenylate cyclase activity on their exterior surface. In a presently unknown fashion, this enzyme can enter human phagocytes, elevate cellular cAMP and impair host defense. We reasoned that this unusual enzyme might serve to signal the presence of B. pertussis in nasopharyngeal swabs from infected persons. Here we report a series of in vitro experiments which confirm the feasibility of such an approach. We find that calcium alginate swabs containing as few as 100 B. pertussis organisms produce readily detectable amounts of cAMP in our assay. Nasopharyngeal secretions swabbed from healthy volunteers, however produced no detectable cAMP alone and did not affect the production of cAMP by B. pertussis. We have also tested pure cultures of four common bacterial pathogens (Haemophilus influenzae, Streptococcus pyogenes, Staphylococcus aureus, and Escherichia coli) which may be co-isolated in clinical whooping cough and find that none interferes with the detection of B. pertussis. We conclude that the unique adenylate cyclase of B. pertussis might be a valuable diagnostic device.
A model based excursion protection algorithm for loudspeakers (2012)

Loudspeakers in portable consumer electronic devices are frequently small in size. Due to the low sensitivity of their drive units, they are pushed to their power handling and mechanical limits by powerful amplifiers in an attempt to reach high volumes. To protect against excessive diaphragm excursions, a model based algorithm is proposed which regulates the voltage input signal to the loudspeaker while minimizing unnecessary system interventions.
New 120 K Tl-Ca-Ba-Cu-O superconductor (1988)

Electronic and magnetic properties of the new 120 K Tl-Ca-Ba-Cu-O superconductor are presented. Resistance-temperature variations, ac susceptibility, and the (low) magnetic field dependence of the critical current density are reported. The new superconductor can be prepared in a molten state, which should allow processing leading to high critical current density. Preliminary x-ray diffraction data are also presented.
Automated Purification of Radiometals Produced by Liquid Targets (2018)

An automated process for the production and purification of radiometals produced by irradiating liquid targets in a medical cyclotron, using a commercially available module, has been developed. The method is suitable for the production and purification of radiometals such as 68Ga, 64Cu and 61Cu through irradiation of liquid targets and is important for producing high specific activity radioisotopes with a substantial reduction in processing time and cost when compared with the solid target approach. The “liquid target” process also eliminates the need for pre- and post-irradiation target preparation and simplifies the transfer of irradiated material from target to hotcell. A 68GaCl3 solution can be obtained in about 35 min with an average yield of 73.9 ± 6.7% in less than 10 mL of volume. 64CuCl2 solutions can be obtained with an average yield of 81.2 ± 7.8% in about 1 h of processing time. A dedicated single-use disposable kit is used on a commercial IBA Synthera® extension module.
Hierarchically Porous Graphene as a Lithium–Air Battery Electrode (2011)

The lithium-air battery is one of the most promising technologies among various electrochemical energy storage systems. We demonstrate that a novel air electrode consisting of an unusual hierarchical arrangement of functionalized graphene sheets (with no catalyst) delivers an exceptionally high capacity of 15000 mAh/g in lithium-O(2) batteries which is the highest value ever reported in this field. This excellent performance is attributed to the unique bimodal porous structure of the electrode which consists of microporous channels facilitating rapid O(2) diffusion while the highly connected nanoscale pores provide a high density of reactive sites for Li-O(2) reactions. Further, we show that the defects and functional groups on graphene favor the formation of isolated nanosized Li(2)O(2) particles and help prevent air blocking in the air electrode. The hierarchically ordered porous structure in bulk graphene enables its practical applications by promoting accessibility to most graphene sheets in this structure.
Towards Transactional PervasiveWorkflows (2006)

Workflow technologies are becoming pervasive in that they enable the execution of business processes in distributed and ubiquitous computing environments. The execution of pervasive workflows raises transactional requirements due to their dynamicity and the need for relaxed atomicity. In this paper, we propose an adaptive transactional protocol for the pervasive workflow model developed in a previous work. The execution of this protocol takes place in two phases. First devices are assigned to tasks using an algorithm whereby workflow partners are selected based on functional and transactional requirements. The workflow execution further proceeds through a hierarchical coordination protocol managed by the workflow initiator and controlled based on a decision table computed as an outcome of the device assignment procedure. The resulting workflow execution is compliant with the defined consistency requirements and the coordination decisions depend on the transactional characteristics of the devices assigned to each task
InGaN self-assembled quantum dots grown by metalorganic chemical-vapor deposition with indium as the antisurfactant (2002)

Nanometer-scale InGaN self-assembled quantum dots have been formed in an InGaN single-quantum-well structure on a (0001) sapphire substrate with In as the antisurfactant using low-pressure metalorganic chemical-vapor deposition. High-resolution transmission electron microscopy reveals that the average dimensions of InGaN nanometer-scale structures are as small as 4 nm wide and 1.5 nm high. Strong photoluminescence emission of the InGaN quantum dots was observed at room temperature with an emission peak of about 2.56 eV (485 nm) and a full width at half maximum of about 150 meV (30 nm). The choice of In as the antisurfactant also avoids the incorporation of foreign atoms in the active layers.
Li<sub>3</sub>Y(PS<sub>4</sub>)<sub>2</sub> and Li<sub>5</sub>PS<sub>4</sub>Cl<sub>2</sub>: New Lithium Superionic Conductors Predicted from Silver Thiophosphates using Efficiently Tiered Ab Initio Molecular Dynamics Simulations (2016)

We report two novel, earth-abundant lithium superionic conductors, Li3Y(PS4)2 and Li5PS4Cl2, that are predicted to satisfy the necessary combination of good phase stability, high Li+ conductivity, wide band gap and good electrochemical stability for solid electrolyte applications in all-solid-state rechargeable lithium-ion batteries. These candidates were identified from a high-throughput first-principles screening of the Li–P–S ternary and Li–M–P–S (where M is a non-redox-active element) quaternary chemical spaces, including candidates obtained by replacing Ag with Li in the Ag–P–S and Ag–M–P–S chemical spaces. An efficient tiered screening strategy was developed that combines topological analysis with ab initio molecular dynamics simulations to exclude rapidly candidates unlikely to satisfy the stringent conductivity requirements of lithium superionic conductors. In particular, we find Li3Y(PS4)2 to be an extremely promising candidate exhibiting a room-temperature Li+ conductivity of 2.16 mS/cm, which can be increased multifold to 7.14 and 5.25 mS/cm via aliovalent doping with Ca2+ and Zr4+, respectively. More critically, we show that the phase and electrochemical stability of Li3Y(PS4)2 is expected to be better than current state-of-the-art lithium superionic conductors.
Performance analysis of distributed applications using automatic classification of communication inefficiencies (2000)

We present a technique for performance analysis that helps users understand the communication behavior of their message passing applications. Our method automatically classifies individual communication operations and it reveals the cause of communication inefficiencies in the application. This classification allows the developer to focus quickly on the culprits of truly inefficient behavior, rather than manually foraging through massive amounts of performance data. Specifically, we trace the message operations of MPI applications and then classify each individual communication event using decision tree classification, a supervised learning technique. We train our decision tree using microbenchmarks that demonstrate both efficient and inefficient communication. Since our technique adapts to the target system's configuration through these microbenchmarks, we can simultaneously automate the performance analysis process and improve classification accuracy. Our experiments on four applications demonstrate that our technique can improve the accuracy of performance analysis, and dramatically reduce the amount of data that users must encounter
Dissection of Chromosome 16p12 Linkage Peak Suggests a Possible Role for<i>CACNG3</i>Variants in Age-Related Macular Degeneration Susceptibility (2010)

These results suggest that CACNG3 is the best candidate for an AMD risk gene within the 16p12 linkage peak. More studies are needed to confirm this association and clarify the role of the gene in AMD pathogenesis.
Rethinking custom ISE identification (2007)

The last decade has witnessed the emergence of the Application Specific Instruction-set Processor (ASIP) as a viable platform for embedded systems. Extensible ASIPs allow the user to augment a base processor with Instruction Set Extensions (ISEs) that execute on Application Specific Functional Units (AFUs)-dedicated hardware that executes the ISEs. Due to the limited number of read and write ports in the register file of the base processor, the size and complexity of AFUs are generally limited. Recent work has focused on overcoming these constraints by serialising access to the register file. Apart from these complications, the primary challenge in the identification and selection of the best AFU is the modelling of AFU performance in the context of different base processors: once the base processor changes, the ISE identification and AFU selection process must be re-done from scratch. Exhaustive ISE/AFU enumeration methods are not scalable and generally fail for larger applications. To address this concern, a new approach to ISE/AFU identification is proposed. In particular, we show that the speedup model of ISEs/AFUs is independent of the specific details of the base processor, under fairly reasonable assumptions. The approach presented here significantly prunes the list of best ISE/AFU candidates compared to previous approaches. Experimentally, we observe the new approach produces optimal results on larger applications where prior approaches either fail or produce inferior results.
Quantum rejection sampling (2012)

Rejection sampling is a well-known method to sample from a target distribution, given the ability to sample from a given distribution. The method has been first formalized by von Neumann (1951) and has many applications in classical computing. We define a quantum analogue of rejection sampling: given a black box producing a coherent superposition of (possibly unknown) quantum states with some amplitudes, the problem is to prepare a coherent superposition of the same states, albeit with different target amplitudes. The main result of this paper is a tight characterization of the query complexity of this quantum state generation problem. We exhibit an algorithm, which we call quantum rejection sampling, and analyze its cost using semidefinite programming. Our proof of a matching lower bound is based on the automorphism principle which allows to symmetrize any algorithm over the automorphism group of the problem. Our main technical innovation is an extension of the automorphism principle to continuous groups that arise for quantum state generation problems where the oracle encodes unknown quantum states, instead of just classical data. Furthermore, we illustrate how quantum rejection sampling may be used as a primitive in designing quantum algorithms, by providing three different applications. We first show that it was implicitly used in the quantum algorithm for linear systems of equations by Harrow, Hassidim and Lloyd. Secondly, we show that it can be used to speed up the main step in the quantum Metropolis sampling algorithm by Temme et al.. Finally, we derive a new quantum algorithm for the hidden shift problem of an arbitrary Boolean function and relate its query complexity to "water-filling" of the Fourier spectrum.
Cytidine methylation of regulatory sequences near the pi-class glutathione S-transferase gene accompanies human prostatic carcinogenesis. (1994)

Hypermethylation of regulatory sequences at the locus of the pi-class glutathione S-transferase gene GSTP1 was detected in 20 of 20 human prostatic carcinoma tissue specimens studied but not in normal tissues or prostatic tissues exhibiting benign hyperplasia. In addition, a striking decrease in GSTP1 expression was found to accompany human prostatic carcinogenesis. Immunohistochemical staining with anti-GSTP1 antibodies failed to detect the enzyme in 88 of 91 prostatic carcinomas analyzed. In vitro, GSTP1 expression was limited to human prostatic cancer cell lines containing GSTP1 alleles with hypomethylated promoter sequences; a human prostatic cancer cell line containing only hypermethylated GSTP1 promoter sequences did not express GSTP1 mRNA or polypeptides. Methylation of cytidine nucleotides in GSTP1 regulatory sequences constitutes the most common genomic alteration yet described for human prostate cancer.
Uncooled CMOS terahertz imager using a metamaterial absorber and pn diode (2016)

We demonstrate a low-cost uncooled terahertz (THz) imager fabricated in a standard 180 nm CMOS process. The imager is composed of a broadband THz metamaterial absorber coupled with a diode microbolometer sensor where the pn junction is used as a temperature sensitive device. The metamaterial absorber array is integrated in the top metallic layers of a six metal layer process allowing for complete monolithic integration of the metamaterial absorber and sensor. We demonstrate the capability of the detector for stand-off imaging applications by using it to form transmission and reflection images of a metallic object hidden in a manila envelope.
The closterovirus-derived gene expression and RNA interference vectors as tools for research and plant biotechnology (2013)

Important progress in understanding replication, interactions with host plants, and evolution of closteroviruses enabled engineering of several vectors for gene expression and virus-induced gene silencing (VIGS). Due to the broad host range of closteroviruses, these vectors expanded vector applicability to include important woody plants such as citrus and grapevine. Furthermore, large closterovirus genomes offer genetic capacity and stability unrivaled by other plant viral vectors. These features provided immense opportunities for using closterovirus vectors for the functional genomics studies and pathogen control in economically valuable crops. This review briefly summarizes advances in closterovirus research during the last decade, explores the relationships between virus biology and vector design, and outlines the most promising directions for future application of closterovirus vectors.
The surgical treatment of atrial fibrillation: The importance of tissue geometry and effective refractory period (2004)

Byrd, Gregory D. BS; Prasad, Sandip M. AB, MPhil; Schuessler, Richard B. PhD; Boineau, John P. MD; Damiano, Ralph J. Jr MD, FACS Author Information
Theoretical and Experimental Investigation of the Motion of Multiphase Fluids Containing Paramagnetic Nanoparticles in Porous Media (2010)

Abstract Paramagnetic nanoparticles are potentially useful for formation evaluation and reservoir monitoring, as they can be induced to move by an imposed magnetic field. Nanoparticles can be designed to have long-term dispersion stability in brine with minimal retention in reservoir rock and with preferential adsorption at oil-water interface. When exposed to magnetic field, they generate sufficient interfacial movements for external detection. When paramagnetic nanoparticles are either adsorbed at oil-water interface or dispersed in one of two fluid phases co-existing in reservoir rock pores, and exposed to external magnetic field, the resultant particle movements displace the interface. Interfacial tension acts as a restoring force, leading to interfacial fluctuation and a pressure (sound) wave. Our previous work (Prodanović et al, 2010) provided theoretical explanations for the motion of the interface between a suspension of paramagnetic nanorods and a non-magnetized fluid in a cylindrical dish, as measured by phase-sensitive optical coherence tomography (PS-OCT). Here we report on additional experiments carried out with a range of in-house synthesized and surface-modified iron-oxide nanoparticles. The numerical method was improved to be volume conserving for more quantitative matching. The measurements of interfacial motion by PS-OCT confirm theoretical predictions of the frequency doubling and the importance of material properties, such as magnetic susceptibility, for the interface displacement thus offering insights into behavior in real porous media. With the combined experimental and modeling work, strategies for improved nanoparticle design are developed so that the interfacial, thereby acoustic, response can be magnified. This laboratory and modeling study is an important step to develop a magnetic field-based method for an accurate, non-invasive determination of multiphase fluids distribution in reservoir rock.
Bilinear response in sub-100 psec InP:Fe optoelectronic switches (1982)

Recent work has shown that Fe-doped InP is an efficient photoconductive material with sub-100 psec response. 1 Optoelectronic switches fabricated from this material have potential applications in radiation detection, electronic gating, and high- voltage pulse generation. Many applications of the optoelectronic switch are possible because it is a simple photoconductor. Thus the important characteristics of a photoconductor are: (1) a response linear with applied voltage, (2) a response linear with excitation intensity, and (3) a speed of response independent of applied voltage. In this work we have investigated the transient response characteristics of InP:Fe optoelectronic switches to verify these basic properties. We have shown that these devices do in fact behave as photoconductors with the properties identified.
The feasibility of long-term fetal heart rate monitoring in the home environment using maternal abdominal electrodes (1995)

It is well established that fetal and maternal electrocardiograms (ECGs) can be obtained from the maternal abdomen using standard surface electrodes, although this cannot be guaranteed. The unobtrusive and non-invasive nature of such monitoring lends itself naturally to the long-term ambulatory collection of this data on cardiac activity. By employing suitable algorithms it would then be possible to extract records of both fetal and maternal heart rate. This article presents results of the collection of raw electrophysiological signals, containing both fetal and maternal ECGs from a single volunteer from the 20th week of gestation until term. The significance of the data is that they were recorded by the mother herself in her own environment. Previously written software was then used to extract fetal and maternal heart rate data. These results demonstrate the feasibility of using this method for the long-term recording of fetal and maternal heart rate in the mother's normal surroundings.
Finite Alphabet Iterative Decoders—Part II: Towards Guaranteed Error Correction of LDPC Codes via Iterative Decoder Diversity (2013)

Recently, we introduced a new class of finite alphabet iterative decoders (FAIDs) for low-density parity-check (LDPC) codes. These decoders are capable of surpassing belief propagation (BP) in the error floor region on the binary symmetric channel (BSC) with much lower complexity. In this paper, we introduce a novel scheme with the objective of guaranteeing the correction of a given and potentially large number of errors on column-weight-three LDPC codes. The proposed scheme uses a plurality of FAIDs which collectively correct more error patterns than a single FAID on a given code. The collection of FAIDs utilized by the scheme is judiciously chosen to ensure that individual decoders have different decoding dynamics and correct different error patterns. Consequently, they can collectively correct a diverse set of error patterns, which is referred to as decoder diversity. We provide a systematic method to generate the set of FAIDs for decoder diversity on a given code based on the knowledge of the most harmful trapping sets present in the code. Using the well-known column-weight-three (155,64) Tanner code with d <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">min</sub> = 20 as an example, we describe the method in detail and show, by means of exhaustive simulation, that the guaranteed error correction capability on short length LDPC codes can be significantly increased with decoder diversity.
Asphaltene Densities and Solubility Parameter Distributions: Impact on Asphaltene Gradients (2016)

Analysis of spatial gradients of the concentration of asphaltenes in reservoir crude oils has become an important tool for oilfield reservoir characterization. Modeling these gradients requires knowledge of asphaltene properties. For example, the commonly employed Flory–Huggins–Zuo (FHZ) equation requires the asphaltene particle size, solubility parameter, and density. Asphaltenes from various sources, particularly including sources beyond conventional crude oil, can have widely varying compositions such as the H/C ratio. Here, we measured the solubility parameters and densities of five asphaltenes that span a large range of H/C ratios, including asphaltenes from coal, petroleum, and shale, and then performed a sensitivity analysis to examine how that range of compositions impacts the magnitude of asphaltene gradients as predicted by the FHZ equation. Two case studies are included in the sensitivity analysis, one in which the asphaltene gradient is driven primarily by gravity, and another in which the asphaltene gradient is driven primarily by solubility. The results shows that the sensitivity of the modeled asphaltene gradients to the measured range of asphaltene solubility parameters and densities is low such that, for both case studies, varying these parameters across the entire measured range does not impact the assignment of the state of asphaltene aggregation determined by the fitted asphaltene particle size. These results suggest that asphaltene gradients can be modeled using the FHZ equation with default values for the asphaltene solubility parameter and density, and local calibration of those parameters will negligibly impact the analysis.