gebhart/patrepeval huggingface dataset:
Three-dimensional seismic monitoring of an enhanced oil recovery process (1987)

Abstract Seismic reflection data were used to monitor the progress of an in-situ combustion, enhanced oil recovery process. Three sets of three-dimensional (3-D) data were collected during a one-year period in order to map the extent and directions of propagation in time. Acquisition and processing parameters were identical for each survey so that direct one-to-one comparison of traces could be made. Seismic attributes were calculated for each common-depth-point data set, and in a unique application of seismic reflection data, the preburn attributes were subtracted from the midburn and postburn attributes. The resulting "difference volumes" of 3-D seismic data showed anomalies which were the basis for the interpretation shown in this case study. Profiles and horizon slices from the data sets clearly show the initiation and development of a bright spot in the reflection from the top of the reservoir and a dim spot in the reflection from a limestone below it. Interpretation of these anomalies is supported by information from postburn coring. The bright spot was caused by increased gas saturation along the top-of-reservoir boundary. From postburn core data, a map of burn volume distribution was made. In comparison, the bright spot covered a greater area, and it was concluded that combustion and injection gases had propagated ahead of the actual combustion zone. The dim spot anomaly shows good correlation with the burn volume in distribution and direction. Evidence from postburn logs supports the conclusion that the burn substantially decreased seismic velocity and increased seismic attenuation in the reservoir. Net burn thicknesses measured in the cores were used to calibrate the dim-spot amplitude. With this calibration, the dim-spot amplitude at each common depth point was inverted to net burn thickness and a map of estimated burn thickness was made from the seismic data.
LigandScout:  3-D Pharmacophores Derived from Protein-Bound Ligands and Their Use as Virtual Screening Filters (2004)

From the historically grown archive of protein-ligand complexes in the Protein Data Bank small organic ligands are extracted and interpreted in terms of their chemical characteristics and features. Subsequently, pharmacophores representing ligand-receptor interaction are derived from each of these small molecules and its surrounding amino acids. Based on a defined set of only six types of chemical features and volume constraints, three-dimensional pharmacophore models are constructed, which are sufficiently selective to identify the described binding mode and are thus a useful tool for in-silico screening of large compound databases. The algorithms for ligand extraction and interpretation as well as the pharmacophore creation technique from the automatically interpreted data are presented and applied to a rhinovirus capsid complex as application example.
Optimization of Advanced Flash Stripper for CO2 Capture using Piperazine (2014)

CO2 capture from coal-fired power plants using amine scrubbing typically incurs a 20–30% energy penalty. The major energy requirements are the reboiler duty for solvent regeneration and the compression work for CO2 sequestration. The advanced flash stripper using 8 m PZ was proposed, which recovers the stripping steam heat by employing cold and warm rich bypasses. The objective of this work is to quantify the benefits of the advanced regeneration system as energy and capital cost. The advanced flash stripper saves 10% total equivalent work that includes heat duty work, compression work, and pumping work compared to the simple stripper. From the economic analysis, it was found that the compressor and the cross exchangers are the two major capital costs of the regeneration system. By considering the cost of the main heat exchangers, the temperature approaches and pressure drops of the cross exchanger and the steam heater were optimized. The optimum LMTD of the cross exchanger is around 10 K, which saves 8% regeneration cost compared to the base case with 5 K. The annualized regeneration cost of the advanced flash stripper is $31/tonne CO2 at the optimum lean loading 0.20, providing 15% cost savings compared to the base case simple stripper (5 K cross exchanger LMTD).
Lung to blood passage of different-sized molecules during lung inflammation in the rat (1991)

The passage of different-sized marker molecules over the lower respiratory tract into the blood circulation during pulmonary inflammation induced by dextran, endotoxin [i.e., lipopolysaccharide from Escherichia coli (LPS)], or ferritin was assessed in the rat. Bovine immunoglobulin G (BIgG, mol wt = 150,000 Da), bovine serum albumin (BSA, mol wt = 67,000 Da), and the nonapeptide 1-deaminocysteine-8-D-arginine vasopressin (dDAVP, mol wt = 1,067 Da) were used as permeability markers after intratracheal instillation. The pathophysiological indexes of a proceeding lung inflammation were increased total cell number, changed leukocyte proportions and increased total protein content obtained in bronchoalveolar lavage, and lung edema formation shown as an increased lung wet-dry weight difference. Intratracheal instillation of dextran induced a moderate neutrophil invasion into the lungs but had no effect on the passage of the different markers over the lungs (BIgG 1.8 +/- 0.6%, BSA 3.5 +/- 1.2%, dDAVP 26.1 +/- 20.7%) compared with control rats instilled with the markers alone (1.8 +/- 0.4%, 4.1 +/- 1.3%, 20.0 +/- 3.8%, respectively). Endotoxin administration resulted in markedly higher lavage cell counts and lung edema concomitantly with an increased lung passage of the markers (3.2 +/- 0.9%, 22.0 +/- 6.1%, 33.3 +/- 12.0%, respectively; P less than 0.01-P less than 0.001). The highest marker passage was obtained when the inflammation was most severe, i.e., after ferritin administration (17.6 +/- 2.3%, 60.0 +/- 6.7%, 41.6 +/- 6.9%, respectively; P less than 0.001), which resulted in markedly elevated lavage cell numbers and protein content as well as edema formation.(ABSTRACT TRUNCATED AT 250 WORDS)
Differences Between Polarized Light Dermoscopy and Immersion Contact Dermoscopy for the Evaluation of Skin Lesions (2007)

The capabilities of NPD, PCD, and PNCD are not equivalent, but complementary. Further studies are needed to evaluate the effect of these differences on clinical diagnosis.
Efficient searches for similar subsequences of different lengths in sequence databases (2002)

We propose an indexing technique for fast retrieval of similar subsequences using time warping distances. A time warping distance is a more suitable similarity measure than the Euclidean distance in many applications, where sequences may be of different lengths or different sampling rates. Our indexing technique uses a disk-based suffix tree as an index structure and employs lower-bound distance functions to filter out dissimilar subsequences without false dismissals. To make the index structure compact and thus accelerate the query processing, we convert sequences of continuous values to sequences of discrete values via a categorization method and store only a subset of suffixes whose first values are different from their preceding values. The experimental results reveal that our proposed technique can be a few orders of magnitude faster than sequential scanning.
Monolithic integration of Si nanowires with metallic electrodes: NEMS resonator and switch applications (2011)

The challenge of wafer-scale integration of silicon nanowires into microsystems is addressed by developing a fabrication approach that utilizes a combination of Bosch-process-based nanowire fabrication with surface micromachining and chemical-mechanical-polishing-based metal electrode/contact formation. Nanowires up to a length of 50 mu m are achieved while retaining submicron nanowire-to-electrode gaps. The scalability of the technique is demonstrated through using no patterning method other than optical lithography on conventional SOI substrates. Structural integrity of double-clamped nanowires is evaluated through a three-point bending test, where good clamping quality and fracture strengths approaching the theoretical strength of the material are observed. Resulting devices are characterized in resonator and switch applications-two areas of interest for CMOS-compatible solutions-with all-electrical actuation and readout schemes. Improvements and tuning of obtained performance parameters such as resonance frequency, quality factor and pull-in voltage are simply a question of conventional design and process adjustments. Implications of the proposed technique are far-reaching including system-level integration of either single-nanowire devices within thick Si layers or nanowire arrays perpendicular to the plane of the substrate.
Synthesis and photophysical characterization of a subphthalocyanine fused dimer–C<sub>60</sub>dyad (2005)

Photophysical studies of a newly synthesized fused subphthalocyanine dimer-C60 revealed a complex cascade of energy transfer events to succeed the initial SubPc dimer photoexcitation.
Mechanisms of Localized Vibration Control in Complex Structures (1996)

This paper describes a numerical study of mechanisms for controlling all six degrees of freedom in localized areas of a complex structure. In localized vibration control, the controller attempts to stabilize one or more localized areas on the structure rather than attempting to stabilize the entire structure. The relative performance levels of different control strategies are evaluated by examining a frequency-dependent disturbance rejection property. A flat plate supported by two box girders is used as an example realistic structure. Plant dynamics from a finite-element model are used to draw general conclusions regarding the mechanisms by which localized vibration control is exerted.
Soluble Thy-1 reverses lung fibrosis via its integrin-binding motif (2019)

Loss of Thy-1 expression in fibroblasts correlates with lung fibrogenesis; however, the clinical relevance of therapeutic targeting of myofibroblasts via Thy-1-associated pathways remains to be explored. Using single (self-resolving) or repetitive (nonresolving) intratracheal administration of bleomycin in type 1 collagen-GFP reporter mice, we report that Thy-1 surface expression, but not mRNA, is reversibly diminished in activated fibroblasts and myofibroblasts in self-resolving fibrosis. However, Thy-1 mRNA expression is silenced in lung with nonresolving fibrosis following repetitive bleomycin administration, associated with persistent activation of αv integrin. Thy1-null mice showed progressive αv integrin activation and myofibroblast accumulation after a single dose of bleomycin. In vitro, targeting of αv integrin by soluble Thy-1-Fc (sThy-1), but not RLE-mutated Thy-1 or IgG, reversed TGF-β1-induced myofibroblast differentiation in a dose-dependent manner, suggesting that Thy-1's integrin-binding RGD motif is required for the reversibility of myofibroblast differentiation. In vivo, treatment of established fibrosis induced either by single-dose bleomycin in WT mice or by induction of active TGF-β1 by doxycycline in Cc10-rtTA-tTS-Tgfb1 mice with sThy-1 (1000 ng/kg, i.v.) promoted resolution of fibrosis. Collectively, these findings demonstrate that sThy-1 therapeutically inhibits the αv integrin-driven feedback loop that amplifies and sustains fibrosis.
Semi-supervised approach to rapid and reliable labeling of large data sets (2008)

In this paper, we propose a method, where the labeling of the data set is carried out in a semi-supervised manner with user-specified guarantees about the quality of the labeling. In our scheme, we assume that for each class, we have some heuristics available, each of which can identify instances of one particular class. The heuristics are assumed to have reasonable performance but they do not need to cover all instances of the class nor do they need to be perfectly reliable. We further assume that we have an infallible expert, who is willing to manually label a few instances. The aim of the algorithm is to exploit the cluster structure of the problem, the predictions by the imperfect heuristics and the limited perfect labels provided by the expert to classify (label) the instances of the data set with guaranteed precision (specificed by the user) with regards to each class. The specified precision is not always attainable, so the algorithm is allowed to classify some instances as dontknow. The algorithm is evaluated by the number of instances labeled by the expert, the number of dontknow instances (global coverage) and the achieved quality of the labeling. On the KDD Cup Network Intrusion data set containing 500,000 instances, we managed to label 96.6% of the instances while guaranteeing a nominal precision of 90% (with 95% confidence) by having the expert label 630 instances; and by having the expert label 1200 instances, we managed to guarantee 95% nominal precision while labeling 96.4% of the data. We also provide a case study of applying our scheme to label the network traffic collected at a large campus network.
An iterative approach for analysis of harmonic penetration in the power transmission networks (1991)

An iterative process of computing harmonic voltage profile on a power system transmission network is presented. A method based upon frequency domain analysis is utilized in conjunction with the fundamental load flow computations. The concepts of conventional reactive power and the distortion power incorporated to determine interaction between the power system and harmonic generating sources. The model of the transmission system considered lends itself to the determination of the standing wave pattern and can be used in identifying the points of maxima and minima on the transmission line as well as the two end points. A phase shifting model of the transformer is presented for the harmonic analysis. Three examples of power transmission systems are taken to illustrate use of the algorithm.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">></ETX>
Regulation of Fc fragment-induced murine spleen cell proliferation. (1980)

Murine splenic lymphocytes proliferate in response to supernatant material derived from Fc fragment-pulsed splenic adherent cells. The stimulatory supernatant results from the interaction of Fc fragments with adherent cells or adherent cell supernate. Isolation of the stimulatory material in the supernate by Sephadex chromatography revealed that the mitogenic component was a cleavage product of Fc with a mol wt of approximately 14,000. The spleen cell type responsible for the generation of mitogenic Fc subfragments appears to be a macrophage. Unstimulated macrophages release an active supernate without being exposed to Fc fragments. The supernate of unstimulated macrophages apparently contain an enzyme which is capable of cleaving Fc fragments into the 14,000-mol wt mitogenic molecules. The spleen cell population induced to proliferate in response to the adherent cell supernate is present in T-cell depleted and Sephadex G-10 filtered cell preparations. Depletion of cells bearing immunoglobulin on their surfaces results in a reduced proliferative response to the mitogenic supernatant material indicating that it is probably a B cell.
Differential regulation of sphingosine kinases 1 and 2 in lung injury (2009)

Two mammalian sphingosine kinase (SphK) isoforms, SphK1 and SphK2, possess identical kinase domains but have distinct kinetic properties and subcellular localizations, suggesting each has one or more specific roles in sphingosine-1-phosphate (S1P) generation. Although both kinases use sphingosine as a substrate to generate S1P, the mechanisms controlling SphK activation and subsequent S1P generation during lung injury are not fully understood. In this study, we established a murine lung injury model to investigate LPS-induced lung injury in SphK1 knockout (SphK1(-/-)) and wild-type (WT) mice. We found that SphK1(-/-) mice were much more susceptible to LPS-induced lung injury compared with their WT counterparts, quantified by multiple parameters including cytokine induction. Intriguingly, overexpression of WT SphK1 delivered by adenoviral vector to the lungs protected SphK1(-/-) mice from lung injury and attenuated the severity of the response to LPS. However, adenoviral overexpression of a SphK1 kinase-dead mutant (SphKKD) in SphK1(-/-) mouse lungs further exacerbated the response to LPS as well as the extent of lung injury. WT SphK2 adenoviral overexpression also failed to provide protection and, in fact, augmented the degree of LPS-induced lung injury. This suggested that, in vascular injury, S1P generated by SphK2 activation plays a distinctly separate role compared with SphK1-dependent S1P generation and survival signaling. Microarray and real-time RT-PCR analysis of SphK1 and SphK2 expression levels during lung injury revealed that, in WT mice, LPS treatment caused significantly enhanced SphK1 expression ( approximately 5x) levels within 6 h, which declined back to baseline levels by 24 h posttreatment. In contrast, expression of SphK2 was gradually induced following LPS treatment and was elevated within 24 h. Collectively, our results for the first time demonstrate distinct functional roles of the two SphK isoforms in the regulation of LPS-induced lung injury.
Effects of Plasmid DNA Sizes and Several Other Factors on Transformation of<i>Bacillus subtilis</i>ISW1214 with Plasmid DNA by Electroporation (1995)

Plasmid DNAs in the range from 2.9 to 12.6 kbp were transferred into Bacillus subtilis ISW1214 intact cells by the use of electroporation. The transformation efficiency (transformants per microgram plasmid DNA) decreased with increases of size of the DNA. However that of 2.0 x 10(3) transformants per microgram of DNA were done routinely, by using a plasmid with a large molecular size of 12.6 kbp. The size of plasmid DNA in the range of 3.7 to 12.6 kbp did not affect the molecular efficiency (transformants per molecule input DNA). The transformation efficiency as high as 9.3 x 10(4) transformants per microgram of purified plasmid pUB110 was obtained, using a cell concentration of 7.6 x 10(10) cells/ml and DNA concentration of 4 micrograms/ml in buffer containing 0.3 M sucrose, 1 mM CaCl2, and 1 mM sodium citrate (pH 6.0) under optimal pulse conditions of an electric field strength of 7 kV/cm and a duration of 500 mus with a single squared pulse at 0 degrees C. The gene expression for antibiotic resistance after electroporation was completed within 1.5 h. The transformants were confirmed to harbor the same intact plasmid by agarose gel electrophoretic analysis.
Efficacy of the HSP90 inhibitor 17-AAG in human glioma cell lines and tumorigenic glioma stem cells (2008)

Glioblastoma multiforme (GBM) arises from genetic and signaling abnormalities in components of signal transduction pathways involved in proliferation, survival, and the cell cycle axis. Studies to date with single-agent targeted molecular therapy have revealed only modest effects in attenuating the growth of these tumors, suggesting that targeting multiple aberrant pathways may be more beneficial. Heat-shock protein 90 (HSP90) is a molecular chaperone that is involved in the conformational maturation of a defined group of client proteins, many of which are deregulated in GBM. 17-allylamino-17-demethoxygeldanamycin (17-AAG) is a well-characterized HSP90 inhibitor that should be able to target many of the aberrant signal transduction pathways in GBM. We assessed the ability of 17-AAG to inhibit the growth of glioma cell lines and glioma stem cells both in vitro and in vivo and assessed its ability to synergize with radiation and/or temozolomide, the standard therapies for GBM. Our results reveal that 17-AAG is able to inhibit the growth of both human glioma cell lines and glioma stem cells in vitro and is able to target the appropriate proteins within these cells. In addition, 17-AAG can inhibit the growth of intracranial tumors and can synergize with radiation both in tissue culture and in intracranial tumors. This compound was not found to synergize with temozolomide in any of our models of gliomas. Our results suggest that HSP90 inhibitors like 17-AAG may have therapeutic potential in GBM, either as a single agent or in combination with radiation.
Indexing techniques for file sharing in scalable peer-to-peer networks (2003)

File sharing is a very popular service provided by peer-to-peer (P2P) networks. In a P2P file-sharing network, users share files and issue queries to the network to find the locations of files residing at other peer nodes. Recently, proxy-enabled peers, or supernodes, have been incorporated to enhance scalability by providing indexing services to nodes on slower network connections. Typically, supernodes build a vector or multi-index of shared files stored on other (slower) peer nodes connected to them. We consider a new model whereby the index tables of individual nodes are merged into a single data structure stored by the supernode. We analyze this model in relation to the standard vectorized data structure. We compare the performance of these supernode indexing algorithms and provide a theoretical analysis that is asymptotic and probabilistic in nature. However, there are several significant constant factors that the theory does not account for, and which are important for designing an optimal system solution. We report on a series of simulation experiments which provide verification of the asymptotic analysis of the formal framework and tools to determine the magnitude of the constant factors. Our general conclusion is that when the query rate exceeds the rate of data updates, the new merged model is preferable to the vector model. However, the details of our analysis allow us to consider combinations of several parameters, and thereby enable the design of optimal indexing schemes via the incorporation of measurements of the parameters of particular applications.
Architectural Implications of Function-as-a-Service Computing (2019)

Serverless computing is a rapidly growing cloud application model, popularized by Amazon's Lambda platform. Serverless cloud services provide fine-grained provisioning of resources, which scale automatically with user demand. Function-as-a-Service (FaaS) applications follow this serverless model, with the developer providing their application as a set of functions which are executed in response to a user- or system-generated event. Functions are designed to be short-lived and execute inside containers or virtual machines, introducing a range of system-level overheads. This paper studies the architectural implications of this emerging paradigm. Using the commercial-grade Apache OpenWhisk FaaS platform on real servers, this work investigates and identifies the architectural implications of FaaS serverless computing. The workloads, along with the way that FaaS inherently interleaves short functions from many tenants frustrates many of the locality-preserving architectural structures common in modern processors. In particular, we find that: FaaS containerization brings up to 20x slowdown compared to native execution, cold-start can be over 10x a short function's execution time, branch mispredictions per kilo-instruction are 20x higher for short functions, memory bandwidth increases by 6x due to the invocation pattern, and IPC decreases by as much as 35% due to inter-function interference. We open-source FaaSProfiler, the FaaS testing and profiling platform that we developed for this work.