gebhart/patrepeval huggingface dataset:
Mechanism of Human Group V Phospholipase A2(PLA2)-induced Leukotriene Biosynthesis in Human Neutrophils (2001)

Human group V phospholipase A(2) (hVPLA(2)) has been shown to have high activity to elicit leukotriene production in human neutrophils (Han, S. K., Kim, K. P., Koduri, R., Bittova, L., Munoz, N. M., Leff, A. R., Wilton, D. C., Gelb, M. H., and Cho, W. (1999) J. Biol. Chem. 274, 11881-11888). To determine the mechanism by which hVPLA(2) interacts with cell membranes to induce leukotriene formation, we mutated surface cationic residues and a catalytic residue of hVPLA(2) and measured the interactions of mutants with model membranes, immobilized heparin, and human neutrophils. These studies showed that cationic residues, Lys(7), Lys(11), and Arg(34), constitute a part of the interfacial binding surface of hVPLA(2), which accounts for its moderate preference for anionic membranes. Additionally, hVPLA(2) binds heparin with high affinity and has a well defined heparin-binding site. The site is composed of Arg(100), Lys(101), Lys(107), Arg(108), and Arg(111), and is spatially distinct from its interfacial binding surface. Importantly, the activities of the mutants to hydrolyze cell membrane phospholipids and induce leukotriene biosynthesis, when enzymes were added exogenously to neutrophils, correlated with their activities on phosphatidylcholine membranes but not with their affinities for anionic membranes and heparin. These results indicate that hVPLA(2) acts directly on the outer plasma membranes of neutrophils to release fatty acids and lysophospholipids. Further studies suggest that products of hVPLA(2) hydrolysis trigger the cellular leukotriene production by activating cellular enzymes involved in leukotriene formation. Finally, the temporal and spatial resolution of exogenously added hVPLA(2) and mutants suggests that binding to cell surface heparan sulfate proteoglycans is important for the internalization and clearance of cell surface-bound hVPLA(2).
Diurnal variation in the stable isotope composition of water and dry matter in fruiting <i>Lupinus angustifolius</i> under field conditions (2002)

Abstract In this paper, we present an integrated account of the diurnal variation in the stable isotopes of water ( δ D and δ 18 O) and dry matter ( δ 15 N, δ 13 C, and δ 18 O) in the long‐distance transport fluids (xylem sap and phloem sap), leaves, pod walls, and seeds of Lupinus angustifolius under field conditions in Western Australia. The δ D and δ 18 O of leaf water showed a pronounced diurnal variation, ranging from early morning minima near 0‰ for both δ D and δ 18 O to early afternoon maxima of 62 and 23‰, respectively. Xylem sap water showed no diurnal variation in isotopic composition and had mean values of −13·2 and −2·3‰ for δ D and δ 18 O. Phloem sap water collected from pod tips was intermediate in isotopic composition between xylem sap and leaf water and exhibited only a moderate diurnal fluctuation. Isotopic compositions of pod wall and seed water were intermediate between those of phloem and xylem sap water. A model of average leaf water enrichment in the steady state (Craig & Gordon, pp. 9–130 in Proceedings of a Conference on Stable Isotopes in Oceanographic Studies and Palaeotemperatures , Lischi and Figli, Pisa, Italy, 1965; Dongmann et al ., Radiation and Environmental Biophysics 11, 41–52, 1974; Farquhar & Lloyd, pp. 47–70 in Stable Isotopes and Plant Carbon–Water Relations , Academic Press, San Diego, CA, USA, 1993) agreed closely with observed leaf water enrichment in the morning and early afternoon, but poorly during the night. A modified model taking into account non‐steady‐state effects (Farquhar and Cernusak, unpublished) gave better predictions of observed leaf water enrichments over a full diurnal cycle. The δ 15 N, δ 13 C, and δ 18 O of dry matter varied appreciably among components. Dry matter δ 15 N was highest in xylem sap and lowest in leaves, whereas dry matter δ 13 C was lowest in leaves and highest in phloem sap and seeds, and dry matter δ 18 O was lowest in leaves and highest in pod walls. Phloem sap, leaf, and fruit dry matter δ 18 O varied diurnally, as did phloem sap dry matter δ 13 C. These results demonstrate the importance of considering the non‐steady‐state when modelling biological fractionation of stable isotopes in the natural environment.
Particle Filtering-Based Indoor Positioning System for Beacon Tag Tracking (2020)

Indoor positioning technology is one of the cornerstones for many services in Internet-of-Things (IoT) systems. However, the existing indoor positioning systems are still suffering from several issues, such as unstable positioning accuracy, a high system complexity, and a high deployment cost. To tackle these issues, this article presents a Particle Filter-based Indoor Positioning System (PFIPS) that can localize and track a tag that broadcasts Bluetooth Low Energy (BLE) beacon messages to BLE receivers. The proposed PFIPS uses a Kalman Filter to preprocess collected Received Signal Strength Indication (RSSI) information in order to smooth the fluctuated RSSI data. It also designs an effective Particle Filter (PF) to approximate the location of a tag, which gradually reduces the location uncertainties in a Gaussian belief space. To show the applicability of our PFIPS, we have developed PFIPS in a testbed based on commercial off-the-shelf (COTS) devices. Through intensive simulations and experiments, our experiment results show that our PFIPS outperforms the legacy indoor positioning systems in terms of location accuracy by 24.1% and achieves median accuracy of 1.16 m.
Investigation of Zr(<scp>iv</scp>) and <sup>89</sup>Zr(<scp>iv</scp>) complexation with hydroxamates: progress towards designing a better chelator than desferrioxamine B for immuno-PET imaging (2012)

Single crystal X-ray diffraction shows that Zr(iv) forms an octa-coordinated complex with 4 bidentate hydroxamates whose solution structures were investigated by utilizing density functional theory at the level of B3LYP/DGDZVP. Stability constants obtained by potentiometry were in accordance with the tendency observed when radiolabeling with (89)Zr.
A Perspective on Tailored Pulse Loading: A New Approach to Oil and Gas Well Stimulation (1985)

ABSTRACT Tailored pulse loading is a descriptor for intermediate strain rate rock fracturing processes. These processes are capable of generating multiple fractures in the reservoir rock when the proper energy-time profile is applied to the wellbore. Such multiple fracture networks have a high probability of intersecting natural fractures; hence initial applications have focused on low permeability, naturally fractured formations. Tailored Pulse Fracturing, a tailored pulse loading process, has undergone developmental testing in the San Andres formation in the Permian Basin. These tests have provided insights into the fracture characteristics and the production effects of multiple fracture networks. Concurrently, mathematical models have been developed to predict the performance of Tailored Pulse Fracturing. Discussed in the context of explosive and hydraulic fracturing, predicted fracture lengths and widths are presented as a function of applied energy and formation properties. Productivity indices are proposed based on multiple fractures affecting changes either in effective reservoir permeability or effective wellbore radius. Enhanced production results indicate either natural fracture intersection or a synergistic blend of production mechanisms. Field tests in the San Andres are discussed and production data are analyzed. The data is interpreted as indicating long fractures (&gt;100 feet) can be created and that long term conductivity is maintained.
Oxygen Requirement for the Biosynthesis of theS-2-Hydroxymyristate Moiety in Salmonella typhimurium Lipid A (2000)

Lipid A molecules of certain Gram-negative bacteria, including Salmonella typhimurium and Pseudomonas aeruginosa, may contain secondary S-2-hydroxyacyl chains. S. typhimurium has recently been shown to synthesize its S-2-hydroxymyristate-modified lipid A in a PhoP/PhoQ-dependent manner, suggesting a possible role for the 2-OH group in pathogenesis. We postulated that 2-hydroxylation might be catalyzed by a novel dioxygenase. Lipid A was extracted from a PhoP-constitutive mutant of S. typhimurium grown in the presence or absence of O(2). Under anaerobic conditions, no 2-hydroxymyristate-containing lipid A was formed. Matrix-assisted laser desorption/ionization time-of-flight mass spectrometry of lipid A from cells grown in the presence of (18)O(2) confirmed the direct incorporation of molecular oxygen into 2-hydroxyacyl-modified lipid A. Using several well characterized dioxygenase protein sequences as probes, tBLASTn searches revealed unassigned open reading frame(s) with similarity to mammalian aspartyl/asparaginyl beta-hydroxylases in bacteria known to make 2-hydroxyacylated lipid A molecules. The S. typhimurium aspartyl/asparaginyl beta-hydroxylase homologue (designated lpxO) was cloned into pBluescriptSK and expressed in Escherichia coli K-12, which does not contain lpxO. Analysis of the resulting construct revealed that lpxO expression is sufficient to induce O(2)-dependent formation of 2-hydroxymyristate-modified lipid A in E. coli. LpxO very likely is a novel Fe(2+)/alpha-ketoglutarate-dependent dioxygenase that catalyzes the hydroxylation of lipid A (or of a key precursor). The S. typhimurium lpxO gene encodes a polypeptide of 302 amino acids with predicted membrane-anchoring sequences at both ends. We hypothesize that 2-hydroxymyristate chains released from lipopolysaccharide inside infected macrophages might be converted to 2-hydroxymyristoyl coenzyme A, a well characterized, potent inhibitor of protein N-myristoyl transferase.
A model for adaptive multimodal mobile notification (2007)

Information is useless unless it is used whilst still applicable. Having a system that notifies the user of important messages using the most appropriate medium and device will benefit users that rely on time critical information. There are several existing systems and models for mobile notification as well as for adaptive mobile notification using context awareness. Current models and systems are typically designed for a specific set of mobile devices, modes and services. Communication however, can take place in many different modes, across many different devices and may originate from many different sources. The aim of this research was to develop a model for adaptive mobile notification using context awareness. An extensive literature study was performed into existing models for adaptive mobile notification systems using context awareness. The literature study identified several potential models but no way to evaluate and compare the models. A set of requirements to evaluate these models was developed and the models were evaluated against these criteria. The model satisfying the most requirements was adapted so as to satisfy the remaining criteria. The proposed model is extensible in terms of the modes, devices and notification sources supported. The proposed model determines the importance of a message, the appropriate device and mode (or modes) of communication based on the user‘s context, and alerts the user of the message using these modes. A prototype was developed as a proof-of-concept of the proposed model and evaluated by conducting an extensive field study. The field study highlighted the fact that most users did not choose the most suitable mode for the context during their initial subscription to the service. The field study also showed that more research needs to be done on an appropriate filtering mechanism for notifications. Users found that the notifications became intrusive and less useful the longer they used them.
Extracting Variability-Safe Feature Models from Source Code Dependencies in System Variants (2015)

To effectively cope with increasing customization demands, companies that have developed variants of software systems are faced with the challenge of consolidating all the variants into a Software Product Line, a proven development paradigm capable of handling such demands. A crucial step in this challenge is to reverse engineer feature models that capture all the required feature combinations of each system variant. Current research has explored this task using propositional logic, natural language, and search-based techniques. However, using knowledge from the implementation artifacts for the reverse engineering task has not been studied. We propose a multi-objective approach that not only uses standard precision and recall metrics for the combinations of features but that also considers variability-safety, i.e. the property that, based on structural dependencies among elements of implementation artifacts, asserts whether all feature combinations of a feature model are in fact well-formed software systems. We evaluate our approach with five case studies and highlight its benefits for the software engineer.
Phosphorus recovery from (1988)

A process for recovering phosphorus from phosphorus-containing pond sludge having a phosphorus concentration of from about 5% to about 70% by weight, the sludge being an emulsion of phosphorus in water, the process is described comprising the steps of: (a) mixing the pond sludge with additional water and heating the mixture in a vessel under mild agitation at a temperature of from about 165/sup 0/F to about 212/sup 0/F for at least about one-half hour to increase the phosphorus concentration in the sludge, the mild agitation being effective to prevent the formation of layers of different composition within the vessel, (b) allowing the concentrated sludge to settle to the bottom of the vessel; (c) introducing water at a temperature of from about 130/sup 0/F to about 150/sup 0/F into the vessel to wash the concentrated sludge, (d) repeating step (a) to further increase the phosphorus concentration in the sludge from step (c), and (e) recovering the sludge from step (d).
Co-occurrence Clusters of Aligned Pattern Clusters (2013)

Advances in bioinformatics have provided researchers with a large influx of novel sequences, thus making the analysis of the sequences for inherent biological knowledge crucial. Important protein segments can be represented by variable patterns, obtained as set of Aligned Pattern Clusters (APC) by using pattern discovery and pattern synthesis on protein family sequences. We develop a method for clustering APCs based on their co-occurrences on the same protein sequence. Their co-occurrence indicates how protein segments in a protein family interact with one another. The purpose of this paper is to provide a method that, given a list of discovered APCs from a family of a protein sequences, finds a set of interdependent APC clusters with high cooccurrence in sequences of a protein family. The significance of these co-occurrence clusters are verified by their corresponding three-dimensional structure and function of the protein. We applied our method to eight protein families obtained from pFam, including triosephosphate isomerase and ubiquitin. We found that the closely co-occurring clusters of APCs in each protein family are close in the three-dimensional protein structures, inferring interactions of the APC segments. In conclusion, we discover that there is a connection between high co-occurrence between APCs and three-dimensional closeness.
Enzymes in oligosaccharide synthesis: active-domain overproduction, specificity study, and synthetic use of an .alpha.-1,2-mannosyltransferase with regeneration of GDP-Man (1993)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTEnzymes in oligosaccharide synthesis: active-domain overproduction, specificity study, and synthetic use of an .alpha.-1,2-mannosyltransferase with regeneration of GDP-ManPeng Wang, Gwo Jenn Shen, Yi Fong Wang, Yoshitaka Ichikawa, and Chi Huey WongCite this: J. Org. Chem. 1993, 58, 15, 3985–3990Publication Date (Print):July 1, 1993Publication History Published online1 May 2002Published inissue 1 July 1993https://pubs.acs.org/doi/10.1021/jo00067a035https://doi.org/10.1021/jo00067a035research-articleACS PublicationsRequest reuse permissionsArticle Views1078Altmetric-Citations58LEARN ABOUT THESE METRICSArticle Views are the COUNTER-compliant sum of full text article downloads since November 2008 (both PDF and HTML) across all institutions and individuals. These metrics are regularly updated to reflect usage leading up to the last few days.Citations are the number of other articles citing this article, calculated by Crossref and updated daily. Find more information about Crossref citation counts.The Altmetric Attention Score is a quantitative measure of the attention that a research article has received online. Clicking on the donut icon will load a page at altmetric.com with additional details about the score and the social media presence for the given article. Find more information on the Altmetric Attention Score and how the score is calculated. Share Add toView InAdd Full Text with ReferenceAdd Description ExportRISCitationCitation and abstractCitation and referencesMore Options Share onFacebookTwitterWechatLinked InRedditEmail Other access optionsGet e-AlertscloseSupporting Info (1)»Supporting Information Supporting Information Get e-Alerts
Growth temperature and dopant species effects on deep levels in Si grown by low temperature molecular beam epitaxy (2003)

Deep-level transient spectroscopy measurements were performed in order to investigate the effects of substrate growth temperature and dopant species on deep levels in Si layers during low-temperature molecular beam epitaxial growth. The structures studied were n+-p junctions using B doping for the p layer and p+-n junctions using P doping for the n layer. While the density of hole traps H1 (0.38–0.41 eV) in the B-doped p layers showed a clear increase with decreasing growth temperature from 600 to 370 °C, the electron trap density was relatively constant. Interestingly, the minority carrier electron traps E1 (0.42–0.45 eV) and E2 (0.257 eV), found in the B-doped p layers, are similar to the majority carrier electron traps E11 (0.48 eV) and E22 (0.269 eV) observed in P-doped n layers grown at 600 °C. It is hypothesized that these dominating electron traps are associated with pure divacancy defects and are independent of the dopant species.
Bacterial Biofilm in Persistent Penile Prosthesis-Associated Infection (1986)

The ultrastructural microbiology of 2 cases of infection associated with rigid penile prostheses was studied. The persistence of these infections appeared to be related to the mode of growth of the bacteria in protected biofilms adherent to the inert surface of the prosthesis.
Statistically Based Decompression Tables. II. Equal Risk Air Diving Decompression Schedules. (1985)

Several sets of equal risk air decompression tables were calculated using a new methodology. Empirical decompression risk models were used to predict the probability of decompression sickness (DCS) for a given pressure exposure. These probabilistic models, earlier shown to have a considerable ability to separate tabulated experimental air dives according to DCS risk, were used to choose decompression schedules with an acceptable risk. The levels of risk used were 1% and 5% for standard air dives with an additional set of 0.5% no-decompression limits. As the new method calculates risk according to an integral over the dive and postdive period, many possible decompression schemes will have the same risk. The best schedules are defined as those requiring minimal total decompression time for the specified risk and subject to operational constraints. The constraints used here are decompression stops at even 10-ft intervals of depth for whole minutes. An algorithm was developed to obtain schedules in a partially optimal manner. The methodology can be used directly to produce tables for other operational constraints or risk levels. Because of the known limitations of source data and risk models, these tables represent considerable extrapolation from known procedures and should not be considered for use without testing.
A LARGE-SCALE GETTER PUMPING EXPERIMENT USING VAPOR DEPOSITED TITANIUM FILMS (1961)

BS> The use of titanium getter pumping for large vacuum systems is described. Techniques were developed which give sorption rates approaching the maximum theoretically possible for many of the chemically active gases. A simple method of determining sticking fractions is descrnkbed. Sticking fractions for hydrogen, deuterium, oxygen, nitrogen, carbon nknonoxnkde, carbon dioxide, and methane are given for various films. The capacity and sorption characteristics for these films are shown. Simple and reliable resistance-heated titanium evapdorators are described. lt was demonstrated that the pumping methods described provide outstanding performance and are both reliable and practical. (auth)
Structured Inference Networks for Nonlinear State Space Models (2017)

Gaussian state space models have been used for decades as generative models of sequential data. They admit an intuitive probabilistic interpretation, have a simple functional form, and enjoy widespread adoption. We introduce a unified algorithm to efficiently learn a broad class of linear and non-linear state space models, including variants where the emission and transition distributions are modeled by deep neural networks. Our learning algorithm simultaneously learns a compiled inference network and the generative model, leveraging a structured variational approximation parameterized by recurrent neural networks to mimic the posterior distribution. We apply the learning algorithm to both synthetic and real-world datasets, demonstrating its scalability and versatility. We find that using the structured approximation to the posterior results in models with significantly higher held-out likelihood.
A Ranking-based Approach for Multiple-document Information Extraction. (2010)

This paper presents a ranking-based approach used in a participating system for the TAC 2010 Information Extraction Task. We introduce a prioritization hierarchy consisting of four levels that are used to determine the most important sentences for extraction. The presence of named entities and the document date play major roles in our approach. 1
Sex Classification of Face Areas (1998)

Human subjects and an artificial neural network, composed of an autoassociative memory and a perceptron, gender classified the same 160 frontal face images (80 male and 80 female). All 160 face images were presented under three conditions (1) full face image with the hair cropped (2) top portion only of the Condition 1 image (3) bottom portion only of the Condition 1 image. Predictions from simulations using Condition 1 stimuli for training and testing novel stimuli in Conditions 1, 2, and 3, were compared to human subject performance. Although the network showed a fair ability to generalize learning to new stimuli under the three conditions, performing from 66 to 78% correctly on novel faces, and predicted main effects, a more detailed comparison with the human data was not as promising. As expected, human accuracy declined with decreased image area, but showed a surprising interaction between the sex of the face and the partial image conditions. The network failed to predict this interaction, or the likelihood of correct human classification for a particular face. This analysis on an item level raises concern about the psychological relevance of the model.