gebhart/patrepeval huggingface dataset:
Characterization of Neutralizing Monoclonal Antibodies Directed Against <i>Staphylococcus aureus</i> Alpha-Toxin (1994)

A panel of neutralizing murine monoclonal antibodies (MAbs) against Staphylococcus aureus alpha-toxin has been established, using formaline-inactivated alpha-toxin as an immunogen. Five independent groups of neutralizing epitopes have been identified representing five functionally important structures in the toxin molecule. Because none of the antibodies binds to overlapping decapeptides representing the toxin sequence or to bromocyanogen cleavage products of alpha-toxin, they may all bind to conformational epitopes. Nevertheless, they all bind to monomeric alpha-toxin in a Western blot. Three of the antibodies bind to the toxin monomer in an enzyme-linked immunosorbent assay (ELISA) in the presence, but not in the absence, of detergent. These epitopes are not accessible in hexameric toxin; two of them may represent the contact sites of the toxin monomers upon hexamerization and one is related to a structurally important glycine-rich central hinge region. Two different antibodies bind to monomeric toxin in an ELISA in the presence and absence of detergent and their epitopes are present more than once on oligomeric toxin; they bind strongly to hexameric toxin in a Western blot. The binding properties of the antibodies to alpha-toxin in different assay systems are summarized in an epitope model, which describes the presence of neutralizing domains in the different conformational steps required for pore formation.
Palladium−Duphos Structural and Enantioselective Hydroarylation Chemistry (2002)

A series of Pd(II) complexes of 1,2-bis((2R,5R)-2,5-dimethylphospholano)benzene (MeDuphos; 1) have been prepared, and the solid-state structures for five of these, PdBr(p-CN-C6H4)(1), PdX(C6F5)(1) (X = Br, I), Pd(OAc)2(1), and [Pd(CH3CN)2(1)](PF6), have been determined by X-ray diffraction. Several of these complexes are catalyst precursors for the enantioselective hydroarylation of norbornene with PhX (X = Br, I, OTf). The maximum ee, 75%, is higher than the corresponding values previously reported for bidentate phosphine auxiliaries. NOESY NMR results show how complexed 1 interacts with the aryl ligand in PdBr(p-CN-C6H4)(1).
Species Identification of Mycobacteria by PCR-Restriction Fragment Length Polymorphism of the <i>rpoB</i> Gene (2000)

ABSTRACT PCR-restriction fragment length polymorphism analysis (PRA) using the novel region of the rpoB gene was developed for rapid and precise identification of mycobacteria to the species level. A total of 50 mycobacterial reference strains and 3 related bacterial strains were used to amplify the 360-bp region of rpoB , and the amplified DNAs were subsequently digested with restriction enzymes such as Msp I and Hae III. The results from this study clearly show that most of the mycobacterial species were easily differentiated at the species level by this PRA method. In addition, species with several subtypes, such as Mycobacterium gordonae , M. kansasii , M. celatum , and M. fortuitum , were also differentiated by this PRA method. Subsequently, an algorithm was constructed based on the results, and a blinded test was carried out with more than 260 clinical isolates that had been identified on the basis of conventional tests. Comparison of these two sets of results clearly indicates that this new PRA method based on the rpoB gene is more simple, more rapid, and more accurate than conventional procedures for differentiating mycobacterial species.
Statistical Analyses of Historical Pipeline Incident Data with Application to the Risk Assessment of Onshore Natural Gas Transmission Pipelines (2015)

Statistical analyses of the pipe-related incident data for onshore gas transmission pipelines between 2002 and 2013 collected by the Pipeline and Hazardous Material Safety Administration (PHMSA) of the United States Department of Transportation (DOT) are conducted. It is found that the total length of the onshore gas transmission pipelines in the US is approximately 480,000 km as of 2013. The third-party interference, external corrosion, material failure and internal corrosion are the leading causes for the pipe-related incidents, responsible for over 75% of the total incidents between 2002 and 2013. Based on the pipeline mileage and incident data, the average rate of rupture incidents over the 12-year period between 2002 and 2013 is calculated to be 3.1 × 10-5 per km per year. Furthermore, external corrosion is found to be the leading cause for rupture incidents, with a corresponding rupture rate of 1.0 × 10-5 per km per year\nA log-logistic model is developed to evaluate the probability of ignition (POI) given a rupture of an onshore gas transmission pipeline using the maximum likelihood method based on a total of 188 rupture incidents between 2002 and 2014 collected from the PHMSA pipeline incident database. The product of the pipeline internal pressure at the time of incident and outside diameter squared is observed to be strongly correlated to POI while the location class of the pipeline is not, and thus the former is adopted as the sole predictor in the model. The 95% confidence interval is evaluated, and for practical engineering use, the 95% upper confidence bound is tabulated in a look-up table. The proposed model is further validated using an independent dataset reported in the literature.\nThe quantitative risk assessment of a hypothetical onshore gas transmission pipelines is illustrated by incorporating the statistics of the pipeline rupture incidents and POI model obtained in the present study. The thermal radiation hazards resulting from an ignited rupture of the pipeline are quantified using the well-known C-FER model. The heat intensity thresholds leading to fatality and injury for both the outdoor and indoor exposure conditions are selected from the literature. The societal risk is then evaluated in terms of the expected number of casualties and F-N curve for the population located in the vicinity of the pipeline, whereas the individual risk is calculated as the annual probability of casualty of a specific individual located in the vicinity of the pipeline. The F-N curve is evaluated for each one kilometer section of the pipeline such that the section corresponding to the most critical F-N curve is identified.
Modulation of alpha7 nicotinic receptor-mediated calcium influx by nicotinic agonists. (1997)

Our previous work had demonstrated stable expression of rat alpha7 alpha-bungarotoxin (alpha-BGT) binding sites by GH4C1 rat pituitary cells, a clonal line that does not endogenously express nicotinic receptors. The stably expressed alpha7 sites had similar binding affinities, pharmacological profiles, kinetic properties, and molecular size as rat brain alpha-BGT receptors, suggesting that they represent a good model system for studying receptor function. The present data show that nicotinic receptor agonists increase intracellular calcium levels ([Ca2+]i), as assessed using Fura-2, in alpha7/GH4C1 cells in a dose-dependent manner with EC50 values that correlate well with the affinity of these ligands for alpha7/GH4C, alpha-BGT receptors. Nicotinic receptor antagonists inhibited agonist-induced increases in [Ca2+]i, with IC50 values in the nanomolar to micromolar range. The nicotinic agonist-induced increase in [Ca2+]i required extracellular calcium and did not occur in the presence of CdCl2, suggesting that agonist-induced increases in [Ca2+]i are due to an influx of extracellular calcium through voltage-gated calcium channels. Preexposure of the alpha7/GH4C1 cells to 8-bromo cAMP resulted in an enhanced [Ca2+]i in response to agonist, suggesting that phosphorylation by adenylate cyclase may regulate receptor responsiveness. Interestingly, short-term preexposure (40-60 sec) of the cells to subthreshold concentrations of nicotinic agonist-enhanced receptor-stimulated calcium influx (up to 55%) while activating agonist concentrations completely blocked receptor-mediated responses. Long-term exposure of alpha7/GH4C1 cells to K+ resulted in about a 2-fold increase in alpha-BGT receptors and in agonist-evoked calcium influx. The sensitivity of these up-regulated receptors were modulated by subthreshold and activating concentrations of agonist in a manner similar to control receptors. The present results, demonstrating a biphasic regulation of alpha7 receptor-mediated calcium influx by nicotinic agonists, suggest that these receptors may play an important role in neuronal function under control and depolarizing conditions.
Electrical Characteristics of p-Type Bulk Si Fin Field-Effect Transistor Using Solid-Source Doping With 1-nm Phosphosilicate Glass (2016)

For scaling of bulk Si Fin field-effect transistor (FinFET), suppression of short-channel effects is required without ON-state current degradation. In this letter, solid-source doping for channel doping using 1-nm phosphosilicate glass was demonstrated on both p-type (100) Si substrate and p-type bulk Si FinFET. The profile of phosphorus in p-type (100) Si substrate was analyzed by secondary ion mass spectrometry and it was diffused deeper with higher thermal budget of anneal. Fabricated bulk Si FinFETs with using 1-nm phosphosilicate glass showed threshold voltage shift with several anneals at 1- <inline-formula xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink"> <tex-math notation="LaTeX">$\mu \text{m}$ </tex-math></inline-formula> and 70-nm gate lengths. Hole mobility at 1- <inline-formula xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink"> <tex-math notation="LaTeX">$\mu \text{m}$ </tex-math></inline-formula> gate length and transconductance at 70-nm gate length were also reduced due to increase in impurity concentration of phosphorus diffused by anneals into Fins. Phosphorus diffusion into Fins with using 1-nm phosphosilicate glass was investigated and phosphorus behavior after anneal was clarified by electrical data of p-type bulk Si FinFETs.
A Design of Fluorescent Probes for Superoxide Based on a Nonredox Mechanism (2004)

Fluorometric detection of O2-* is performed based on desulfonylation of 3 to the corresponding fluoresceins 4 through nucleophilic substitution, and this fluorescing process is quite specific toward O2-* over H2O2, t-BuOOH, NaOCl, 1O2, HO*, NO*, and ONOO-. Furthermore, effects of glutathione, cytochrome P450 reductase/NADPH, and diaphorase/NADH are relatively small on the fluorescing process of probe 3 with X = Y = F, which is useful to detect O2-* released from neutrophils stimulated by phorbol myristate acetate with satisfactory sensitivity.
Size, Staffing, and Psychiatric Hospital Effectiveness (1964)

There is general agreement among those who treat mental illness that psychiatric hospitals should be (a) small, and (b) highly staffed.<sup>3</sup>Two previous sources of data provide numerical support for the contention that smaller size and higher staffpatient ratio are related to higher rates of favorable outcome. The first previous set of data was computed by one of us (LU) from material presented by Bockoven<sup>1</sup>on "Moral Treatment in American Psychiatry." For data concerning operation of Worcester State Hospital over 12 consecutive decades, rankorder correlations were 0.76 (P<0.01) between per cent of admissions released and physicians per patient and –0.89 (P < 0.001) between per cent of admissions released and size of patient population. Jenkins,<sup>2</sup>using selected psychotic admissions at 12 hospitals, obtained a 0.64 correlation (P<0.05) between early release and per diem expense (reflecting overall staffing) and a
The Anguish of Angola: On Becoming Independent in the Last Quarter of the Twentieth Century (1975)

As the United States approaches its two-hundredth year of independence, Angola is entering upon its first. Fifteen years after most of Black Africa shed colonial rule, and fourteen after Angolan insurgents shattered the myth of multiracial harmony in Iusophone Africa, a total collapse of Portuguese authority has catapulted Angola to an uncertain nationhood born in chaos and civil war.
Perfusion and thermal field during hyperthermia. Experimental measurements and modelling in recurrent breast cancer (1998)

Recurrences of malignant tumours in the chest wall are proposed as a valuable model of tissue mainly perfused by small size vessels (the so-called 'phase III' vessels). Invasive thermal measurements have been performed on two patients affected by cutaneous metastasis of malignant tumours during hyperthermic sessions. Thermal probes were inserted into catheters implanted into the tissue at different depths. In one of the catheters a probe connected with laser-Doppler equipment was inserted to assess blood perfusion in the tumour periphery. The perfusion was monitored throughout the sessions, and a noticeable temporal variability was observed. The effect of the perfusion on the thermal map in the tissue was evaluated locally and the 'effective conductivity' of the perfused tissue was estimated by means of the numerical integration of the 'bio-heat' equation. The tumour temperature, at the site where the perfusion probe is located, can be predicted by the numerical model provided two free parameters, alpha and beta, are evaluated with a fitting procedure. Alpha is related to the effective conductivity and beta to the SAR term of the bio-heat equation. The model aimed at estimating the 'effective conductivity' K(eff) of the perfused tissue, and average values of K(eff) of 0.27 +/- 0.03 W m(-1) degrees C(-1) in Patient 1 and of 0.665 +/- 0.005 W m(-1) degrees C(-1) in Patient 2 were obtained throughout the treatment. However, when the average temperature in a larger tumour volume is to be predicted but only a single, 'local' measurement of the perfusion is available and is assumed to be representative for the whole region, the model results are far less satisfactory. This is probably due to the fact that changes of blood perfusion throughout hyperthermic sessions occur to different extents within the tumour volume, and the differences in perfusion cannot be ignored. The above result suggests that, in addition to the 'temperature map', also a 'perfusion map' within the heated volume should be monitored routinely throughout hyperthermic sessions.
Phase-transfer free-radical reactions: the crown ether/potassium peroxydisulfate initiator system (1981)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTPhase-transfer free-radical reactions: the crown ether/potassium peroxydisulfate initiator systemJerald K. Rasmussen and Howell K. Smith IICite this: J. Am. Chem. Soc. 1981, 103, 3, 730–731Publication Date (Print):February 1, 1981Publication History Published online1 May 2002Published inissue 1 February 1981https://pubs.acs.org/doi/10.1021/ja00393a069https://doi.org/10.1021/ja00393a069research-articleACS PublicationsRequest reuse permissionsArticle Views283Altmetric-Citations46LEARN 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-Alertsclose Get e-Alerts
Inactivation of .gamma.-aminobutyric acid aminotransferase by (S,E)-4-amino-5-fluoropent-2-enoic acid and effect on the enzyme of (E)-3-(1-aminocyclopropyl)-2-propenoic acid (1986)

(S,E)-4-Amino-5-fluoropent-2-enoic acid (6) is synthesized in six steps starting from the known gamma-aminobutyric acid aminotransferase (gamma-Abu-T) inactivator, (S)-4-amino-5-fluoropentanoic acid (1). Compound 6 is a mechanism-based inactivator of gamma-Abu-T: time-dependent inactivation is saturatable and protected by substrate; thiols do not protect the enzyme from inactivation; no enzyme activity returns upon dialysis. This compound (6) binds 50 times more tightly to gamma-Abu-T than does the saturated analogue (1). No transamination of 6 occurs prior to inactivation. However, five molecules of 6 are required to inactivate the enzyme with concomitant release of five fluoride ions. Therefore, four molecules are being converted to product for each inactivation event. (E)-3-(1-Aminocyclopropyl)-2-propenoic acid is synthesized in seven steps from 1-aminocyclopropanecarboxylic acid. It is prepared as a cyclopropyl derivative of the proposed intermediate in the inactivation of gamma-Abu-T by 6. The cyclopropyl derivative, however, is a noncompetitive inhibitor and does not inactivate the enzyme. This study shows the usefulness and hazards of incorporation of a trans double bond into potential gamma-Abu-T inactivators.
Digital imaging in periodontal radiography (1988)

The development and the potential impact of digital imaging techniques for the analysis of dental radiographs are reviewed with emphasis on periodontal diagnosis. The introduction of video-based computer-assisted image analysis systems for the evaluation of standardized dental radiographs offered increased diagnostic accuracy in the detection of subtle density changes over interpretation of conventional radiographs. Digital subtraction images were interpreted qualitatively on a video monitor or quantitatively by applying programs which measure the density differences stored in digital format. Recently, these methods, which have been extensively tested in vitro, were applied to clinical trials for the assessment of alveolar bone density changes due to progression of disease or healing following therapy. The application of digital image analysis methods offers objective, quantitative and non-invasive ways to obtain additional diagnostic information from standardized radiographs in clinical trials.
Characterization of Channelized Reservoir Using Ensemble Kalman Filter with Clustered Covariance (2013)

Ensemble Kalman filter (EnKF) has the limitation of applications for multi-point geostatistics because it assumes Gaussian random field. It also uses all ensembles to get covariance matrix, even though they have different permeability field each other, resulting in filter divergence. The proposed method suggests the concept of clustered covariance by grouping initial ensembles using a distance-based method. Hausdorff distance is used for calculating similarity between permeability fields and they are separated by k-means clustering. When EnKF is applied to a 2D channel field, it shows overshooting problem and mismatches the true production data. The proposed method gives better history matching and future performance prediction without overshooting problems. Furthermore, it shows stable results for sensitivity analyses over the number of total ensembles. The more accurate covariance is calculated by clustering, the better results are obtained.
Interconnecting ISP networks (2001)

The Internet is rife with paradox. For example, new optical switches capable of forwarding terabits of data (in photonic format) must work with a decades-old protocol suite first developed for software-controlled electronic packet switches. Another example is that while IP multicast offers by far the most efficient delivery vehicle for large-scale multiparty communications, few service providers deploy it, choosing instead to consume bandwidth and host resources with multiple point-to-point connections. One of the most interesting Internet-related paradoxes is the relationship between Internet service providers. While competing very publicly for customers using price, value-add services, and performance as leverage, they must privately cooperate among themselves to provide global connectivity. Indeed, without this cooperation each ISP network might devolve into its own separate world with few or none of the global Internet's benefits. Fortunately, this is not the case; in fact, the Internet is a network of networks-a mesh of separately controlled, interconnected networks that form one large, global entity.
Biological recognition of phosphate and sulfate (1991)

The biological recognition of trigonal pyramids has been studied in a statistical analysis of the Cambridge Structural Data Base. The preferential stereochemistry of pyramidal anion-Lewis acid interactions is easily described for the phosphonyl dianion (R-PO3(2-), as found in the phosphate group) and the sulfonyl monoanion (R-SO3-, as found in the sulfate group) by trans/gauche conformational terminology. Interactions between these pyramidal anions and metals generally prefer gauche geometry (as defined by the R-X = O-Mn+ torsion angle, X = P or S). Interactions between phosphonyls and hydrogen bond donors likewise display a preference for gauche orientation. Interactions between sulfonyls and hydrogen bond donors exhibit a preference for gauche stereochemistry and also cluster in eclipsed regions. These hydrogen bond motifs provide a greater understanding of the function of pyramidal anions in biological structure and function. For example, interactions of the sulfate monoanion are important for the binding of heparin, a sulfated glycosaminoglycan, to antithrombin III.
P300 and Recall in an Incidental Memory Paradigm (1986)

ABSTRACT In previous research Karis, Fabiani, and Donchin (1984) found a relationship between the amplitude of the P300s elicited by words and subsequent recall performance. Words later recalled elicited larger P300s than words later not recalled. However, this relationship was dependent on the mnemonic strategies used by the subjects. There was a strong relationship between P300 amplitude and recall when rote rehearsal strategies were used, but when subjects used elaborative strategies the relationship between P300 amplitude and recall was not evident. In the present experiment we employed an incidental memory paradigm to reduce the use of rehearsal strategies. An “oddball’ task consisting of a series of names was presented, and subjects were required to count either the male or the female names. Event‐related brain potentials were recorded to the presentation of each name. Following the oddball task, subjects were asked, unexpectedly, to recall as many names as possible. The names that were recalled had elicited, on their initial presentation, larger P300s than names not recalled. Thus, these results confirm our hypothesis: when elaborative rehearsal strategies are not used, the relationship between P300 and memory emerges more consistently. Our data provide support for a “context updating’ hypothesis of the functional significance of the P300.
Breaking the barriers to successful refactoring (2008)

Refactoring is the process of changing the structure of code without changing its behavior. Refactoring can be semi-automated with tools, which should make it easier for programmers to refactor quickly and correctly. However, we have observed that many tools do a poor job of communicating errors triggered by the refactoring process and that programmers using them sometimes refactor slowly, conservatively, and incorrectly. In this paper we characterize problems with current refactoring tools, demonstrate three new tools to assist in refactoring, and report on a user study that compares these new tools against existing tools. The results of the study show that speed, accuracy, and user satisfaction can be significantly increased. From the new tools we induce a set of usability recommendations that we hope will help inspire a new generation of programmer-friendly refactoring tools.