gebhart/patrepeval huggingface dataset:
Defining the Difference Between Laboratory and Field-Generated Foamed Cement (2017)

Foamed cement has been used extensively across a variety of applications for oil and gas well cementing, including deepwater riserless cementing, low fracture gradient cementing, horizontal well cementing, steam injection well cementing, and high-pressure/high-temperature (HP/HT) cementing. When using foamed cement, laboratory testing is used to estimate the performance characteristics of foamed cement slurries that are designed for well applications. It is well known that significant differences exist between the methods used to generate foamed cement in the laboratory and those used to generate foamed cement for field applications. The implications of these differences on foamed slurry characteristics (e.g., bubble size distribution) and performance properties (e.g., stability, permeability, mechanical properties) has not been well analyzed or well understood. This paper documents a project that was undertaken through a joint effort between API Sub-Committee 10 and the National Energy Technology Laboratory (NETL) to examine the differences between foamed slurries generated with laboratory equipment and field foamed cementing equipment. Methods for generating and capturing foamed cement samples using field equipment are discussed, as well as analytical methods for evaluating the characteristics of foamed cements. References to the resulting data are provided. Finally, conclusions and recommendations are presented that were developed during the course of the project.
Faculty Opinions recommendation of Antibody epitopes in vaccine-induced immune thrombotic thrombocytopaenia. (2021)

Vaccine-induced immune thrombotic thrombocytopaenia (VITT) is a rare adverse effect of COVID-19 adenoviral vector vaccines1-3. VITT resembles heparin-induced thrombocytopaenia (HIT) in that it is associated with platelet-activating antibodies against platelet factor 4 (PF4)4; however, patients with VITT develop thrombocytopaenia and thrombosis without exposure to heparin. Here we sought to determine the binding site on PF4 of antibodies from patients with VITT. Using alanine-scanning mutagenesis5, we found that the binding of anti-PF4 antibodies from patients with VITT (n = 5) was restricted to eight surface amino acids on PF4, all of which were located within the heparin-binding site, and that the binding was inhibited by heparin. By contrast, antibodies from patients with HIT (n = 10) bound to amino acids that corresponded to two different sites on PF4. Biolayer interferometry experiments also revealed that VITT anti-PF4 antibodies had a stronger binding response to PF4 and PF4-heparin complexes than did HIT anti-PF4 antibodies, albeit with similar dissociation rates. Our data indicate that VITT antibodies can mimic the effect of heparin by binding to a similar site on PF4; this allows PF4 tetramers to cluster and form immune complexes, which in turn causes Fcγ receptor IIa (FcγRIIa; also known as CD32a)-dependent platelet activation. These results provide an explanation for VITT-antibody-induced platelet activation that could contribute to thrombosis.© 2021. The Author(s), under exclusive licence to Springer Nature Limited. PMID: 34233346
Cramer-Rao Bound For Finite Streams Of An Arbitrary Number Of Pulses (2014)

Publication in the conference proceedings of EUSIPCO, Lisbon, Portugal, 2014
Description of Meloidogyne fallax n. sp. (Nematoda : Heteroderidae), a root-knot nematode from The Netherlands. (1996)

Development of a sustainable bioeconomy requires valorization of renewable resources, such as wood hemicelluloses. The intra- and inter-molecular association of hemicelluloses within themselves or with other wood components can result in complex macromolecular features. These features exhibit functionality as hydrocolloids, however macromolecular characterization of these heterogeneous materials are challenging using conventional techniques such as size-exclusion chromatography. We studied galactoglucomannans (GGM) -rich softwood extracts at two grades of purity-as crude extract and after ethanol-precipitation. Asymmetrical flow field-flow fractionation (AF4) was optimized and utilized to fractionate size classes in GGM extracts, and subsequent characterization was performed with light scattering and microscopy techniques. Both GGM extracts contained polysaccharides of around 10,000 g/mol molar mass, and colloidal assemblies and/or particles in sub-micron size range. The optimized AF4 method facilitates the characterization of complex biomass-derived carbohydrates without pre-fractionation, and provides valuable understanding of their unique macromolecular features for their future application in food, pharmaceuticals, and cosmetics.
SHEP1 partners with CasL to promote marginal zone B-cell maturation (2010)

The marginal zone is a cellular niche bordering the marginal sinus of the spleen that contains specialized B-cell and macrophage subsets poised to capture bloodborne antigens. Marginal zone B cells are retained in this niche by integrin-mediated signaling induced by G protein-coupled receptors (GPCRs) and, likely, the B-cell receptor (BCR). Sphingosine-1-phosphate (S1P) signaling via the S1P family of GPCRs is known to be essential for B-cell localization in the marginal zone, but little is known about the downstream signaling events involved. Here, we demonstrate that the adaptor protein SHEP1 is required for marginal zone B-cell maturation. SHEP1 functions in concert with the scaffolding protein CasL, because we show that SHEP1 and CasL are constitutively associated in B cells. SHEP1 association is required for the BCR or S1P receptor(s) to induce the conversion of CasL into its serine/threonine hyperphosphorylated form, which is important for lymphocyte adhesion and motility. Thus, SHEP1 orchestrates marginal zone B-cell movement and retention as a key downstream effector of the BCR and S1P receptors.
Structure – Activity Relationships of PDE5 Inhibitors (Supporting Material) (2008)

cGMP has a short-term effect on smooth muscle tone and a longer-term effect on responses to chronic drug treatment or proliferative signals. cGMP-Phosphodiesterase type 5 (PDE5) hydrolizes cGMP, and the result is smooth muscle contraction. PDE5 is a relatively novel therapeutic target of various diseases, such as erectile dysfunction and pulmonary hypertension. The most intensively examined and marketed PDE5 inhibitor was sildenafil (Viagra) but recently vardenafil (Levitra) and tadalafil (Cialis) were launched with beneficial ADME parameters and PDE5 selectivity. The increasing interest in PDE5 inhibition made it reasonable to collect the available inhibitory data from the scientific literature and set up a structure-activity relationship study. Chemical structures of 438 compounds and their cGMP-PDE5 inhibitory data (IC50) were collected from recently published articles. In this paper physiology, regulation and inhibition of PDE5 (and briefly other PDE-s) are discussed and inhibitors are tabulated by the core structures. Finally, a general QSAR model built from these data is presented. All data used in the QSAR study were summarized in a Supplement (for description please see the online version of the article).
A Recombinant Chimeric La Crosse Virus Expressing the Surface Glycoproteins of Jamestown Canyon Virus Is Immunogenic and Protective against Challenge with either Parental Virus in Mice or Monkeys (2011)

La Crosse virus (LACV) and Jamestown Canyon virus (JCV), family Bunyaviridae, are mosquito-borne viruses that are endemic in North America and recognized as etiologic agents of encephalitis in humans. Both viruses belong to the California encephalitis virus serogroup, which causes 70 to 100 cases of encephalitis a year. As a first step in creating live attenuated viral vaccine candidates for this serogroup, we have generated a recombinant LACV expressing the attachment/fusion glycoproteins of JCV. The JCV/LACV chimeric virus contains full-length S and L segments derived from LACV. For the M segment, the open reading frame (ORF) of LACV is replaced with that derived from JCV and is flanked by the untranslated regions of LACV. The resulting chimeric virus retained the same robust growth kinetics in tissue culture as observed for either parent virus, and the virus remains highly infectious and immunogenic in mice. Although both LACV and JCV are highly neurovirulent in 21 day-old mice, with 50% lethal dose (LD₅₀) values of 0.1 and 0.5 log₁₀ PFU, respectively, chimeric JCV/LACV is highly attenuated and does not cause disease even after intracerebral inoculation of 10³ PFU. Parenteral vaccination of mice with 10¹ or 10³ PFU of JCV/LACV protected against lethal challenge with LACV, JCV, and Tahyna virus (TAHV). The chimeric virus was infectious and immunogenic in rhesus monkeys and induced neutralizing antibodies to JCV, LACV, and TAHV. When vaccinated monkeys were challenged with JCV, they were protected against the development of viremia. Generation of highly attenuated yet immunogenic chimeric bunyaviruses could be an efficient general method for development of vaccines effective against these pathogenic viruses.
Potential Regional Differences for the Tolerability Profiles of Fluoropyrimidines (2008)

Regional differences exist in the tolerability profiles of fluoropyrimidines. More treatment-related toxicity was reported in the US compared with the rest of the world for bolus FU/LV and capecitabine in first-line MCRC and adjuvant colon cancer. In the adjuvant setting, a range of fluoropyrimidine tolerability was observed, with East Asian patients having the lowest, and US patients the highest, RR.
Enzymatic Breakage and Joining of Deoxyribonucleic Acid (1971)

Abstract Polynucleotide ligase of bacteriophage T4, in contrast to the DNA ligase of Escherichia coli, catalyzes the joining of oligomers of deoxyribonucleotides hydrogen-bonded to complementary strands of either polydeoxyribonucleotides or polyribonucleotides. Hybrid molecules in which oligomers of ribonucleotides are hydrogen-bonded to complementary strands of polydeoxyribonucleotides can also serve as substrates for the T4 enzyme. The rate of joining of oligomers in hybrid molecules of this type is only 1 to 2% of that observed when both strands are polydeoxyribonucleotides. No activity has been detected when both strands are polyribonucleotides. The products of these reactions have been characterized by sedimentation and end group analysis; in all cases joining occurs through phosphodiester bond formation. The activities toward hybrid molecules and toward DNA containing single strand breaks appear to be identical as indicated by: (a) identical ratio of the activities during a 1000-fold purification, (b) similar reaction requirements, and (c) identical thermosensitivity of both activities purified from cells infected with a mutant bacteriophage containing a temperature-sensitive ligase. It had been shown previously that the introduction of an rII mutation into phage T4 could suppress an amber mutation in the ligase gene. In these studies it is shown that the double mutant, T4rIIamH39X, carrying an amber mutation in the ligase gene, does not have detectable levels of T4 ligase in the nonpermissive host. Similarly, T4rIItsA80, carrying a temperature-sensitive mutation in the ligase gene, can grow at the nonpermissive temperature, despite retaining its temperature-sensitive ligase.
Preparation and properties of some tetrathiafulvalene donor-acceptor compounds with bis(dithiolene) metal complexes (1975)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTPreparation and properties of some tetrathiafulvalene donor-acceptor compounds with bis(dithiolene) metal complexesL. V. Interrante, K. W. Browall, H. R. Hart Jr., I. S. Jacobs, G. D. Watkins, and S. H. WeeCite this: J. Am. Chem. Soc. 1975, 97, 4, 889–890Publication Date (Print):February 1, 1975Publication History Published online1 May 2002Published inissue 1 February 1975https://doi.org/10.1021/ja00837a032RIGHTS & PERMISSIONSArticle Views159Altmetric-Citations43LEARN 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 InReddit PDF (291 KB) Get e-Alerts Get e-Alerts
Gain-of-Function RHOA Mutations Promote Focal Adhesion Kinase Activation and Dependency in Diffuse Gastric Cancer (2019)

Diffuse gastric cancer (DGC) is a lethal malignancy lacking effective systemic therapy. Among the most provocative recent results in DGC has been that of highly recurrent missense mutations in the GTPase RHOA. The function of these mutations has remained unresolved. We demonstrate that RHOA<sup>Y42C</sup>, the most common RHOA mutation in DGC, is a gain-of-function oncogenic mutant, and that expression of RHOA<sup>Y42C</sup> with inactivation of the canonical tumor suppressor <i>Cdh1</i> induces metastatic DGC in a mouse model. Biochemically, RHOA<sup>Y42C</sup> exhibits impaired GTP hydrolysis and enhances interaction with its effector ROCK. <i>RHOA</i> <sup>Y42C</sup> mutation and <i>Cdh1</i> loss induce actin/cytoskeletal rearrangements and activity of focal adhesion kinase (FAK), which activates YAP-TAZ, PI3K-AKT, and β-catenin. RHOA<sup>Y42C</sup> murine models were sensitive to FAK inhibition and to combined YAP and PI3K pathway blockade. These results, coupled with sensitivity to FAK inhibition in patient-derived DGC cell lines, nominate FAK as a novel target for these cancers. SIGNIFICANCE: The functional significance of recurrent RHOA mutations in DGC has remained unresolved. Through biochemical studies and mouse modeling of the hotspot RHOA<sup>Y42C</sup> mutation, we establish that these mutations are activating, detail their effects upon cell signaling, and define how RHOA-mediated FAK activation imparts sensitivity to pharmacologic FAK inhibitors.<i>See related commentary by Benton and Chernoff, p. 182</i>.<i>This article is highlighted in the In This Issue feature, p. 161</i>.
Neoplastic transformation of a human prostate epithelial cell line by the v‐Ki‐ras oncogene (1993)

Investigations of mechanisms of human prostate carcinogenesis are limited by the unavailability of a suitable in vitro model system. We have demonstrated that an immortal, but nontumorigenic, human epithelial cell line (267B1) established from fetal prostate tissue can be malignantly transformed by a biological carcinogen, and can serve as a useful model for investigations of the progression steps of carcinogenesis. Activated Ki-ras was introduced into 267B1 cells by infection with the Kirsten murine sarcoma virus. Morphological alterations and anchorage-independent growth were observed; when cells were injected into nude mice, poorly differentiated adenocarcinomas developed. These findings represent the first evidence of malignant transformation of human prostate epithelial cells in culture, and support a role for Ki-ras activation in a multistep process for prostate neoplastic transformation.
Nanoscopic Electrolyte-Gated Vertical Organic Transistors with Low Operation Voltage and Five Orders of Magnitude Switching Range for Neuromorphic Systems (2022)

Electrolyte-gated organic transistors (EGOTs) are promising candidates as a new class of neuromorphic devices in hardware-based artificial neural networks that can outperform their complementary metal oxide semiconductor (CMOS) counterparts regarding processing speed and energy consumption. Several ways in which to implement such networks exist, two prominent methods of which can be implemented by nanoscopic vertical EGOTs, as we show here. First, nanoscopic vertical electrolyte-gated transistors with a donor-acceptor diketopyrrolopyrrole-terthiophene polymer as an active material can be used to reversibly switch the channel conductivity over five orders of magnitude (3.8 nS to 392 μS) and perform switching at low operation voltages down to -1 mV. Second, nanoscopic EGOTs can also mimic fundamental synaptic functions, and we show an interconnection of up to three transistors, highlighting the possibility to emulate biological nerve cells.
Nerve Growth Factor‐Induced Differentiation in Neuroblastoma Cells Expressing TrkA but Lacking p75NGFR (1994)

Nerve growth factor (NGF) binds to two distinct cell surface receptors, TrkA, which is a receptor tyrosine kinase, and p75NGFR, whose role in NGF-induced signal transduction remains unclear. We have found that human neuroblastoma IMR-32 cells express TrkA, but p75NGFR expression was not detectable in these cells by northern blot analysis, immunoblotting, or chemical crosslinking experiments. Despite the lack of p75NGFR expression, subnanomolar concentrations of recombinant human NGF induced neurite outgrowth, tyrosine phosphorylation, and immediate early gene expression in these cells. These results strongly suggest that NGF-induced neuronal differentiation in IMR-32 cells is initiated through TrkA in the absence of p75NGFR. Thus, IMR-32 cells may provide a model for studying neurotrophic effects of NGF on adult striatal cholinergic neurons, which also lack p75NGFR expression.
Electron and hole mobility in solution-processed small molecule-fullerene blend: Dependence on the fullerene content (2013)

We present a study of electron and hole mobility in blends of the solution-processed small molecule (DTS(PTTh2)2):fullerene as a function of the fullerene content. The mobilities are measured using the Field–Effect Transistor device configuration with the blend as the material in the channel. The hole mobility of the small molecule increases when about 10% of [6-6]-phenyl C71 butyric acid methyl ester (PC70BM) is added and then decreases at higher fullerene content. The electron mobility always increases as the fullerene content increases. Balanced charge transport occurred at 70:30 and 60:40 donor to acceptor ratios in the DTS(PTTh2)2:PC70BM system. The observation of balanced charge mobility agrees well with the reported solar cell performance.
Erratum: Correction: Quality of initial anticoagulant treatment and risk of CTEPH after acute pulmonary embolism (PloS one (2020) 15 4 (e0232354)) (2020)

The second author's initials and the seventh author's initials are indexed incorrectly in PubMed. The correct initials for the second author are: van Rein N. The correct initials for the seventh author are: van der Meer FJM. The second author's initials also appear incorrectly in the citation. The correct citation is: Boon GJAM, van Rein N, Bogaard HJ, Ende-Verhaar YM, Huisman MV, Kroft LJM, et al. (2020) Quality of initial anticoagulant treatment and risk of CTEPH after acute pulmonary embolism. PLoS ONE 15(4): e0232354. https://doi.org/10.1371/journal.pone.0232354.
Dielectric properties of diblock copolymers (2003)

Dielectric spectroscopy was used to probe a series of diblock copolymers which have widely different degrees of order. The 1,2-polybutadiene/1,4-polybutadiene diblock copolymer system was chosen because both ordered and disordered morphologies can be obtained near room temperature. It is observed that the local motions of the high-temperature component are greatly enhanced in the block copolymer over the homopolymer. Als found is evidence of local concentration fluctuations of the low-temperature component which are large enough to exhibit a glass transition, even in samples that appear to be completely disordered on the length scales probed by SANS and rheological measurements.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
A Framework for Efficient Class-Based Scheduling (2009)

With an increasing requirement for network monitoring tools to classify traffic and track security threats, newer and efficient ways are needed for collecting traffic statistics and monitoring of network flows. However, traditional solutions based on random packet sampling treat all flows as equal and therefore, do not provide the flexibility required for these applications. In this paper, we propose a novel architecture called CLAMP that provides an efficient framework to implement size-based sampling. At the heart of CLAMP is a novel data structure called composite bloom filter (CBF) that consists of a set of bloom filters that work together to encapsulate various class definitions. In comparison to previous approaches that implement simple size-based sampling, our architecture requires substantially lower memory (upto 80x) and results in higher flow coverage (upto 8x more flows) under specific configurations.
Minimum Required Sensing Range for UAS Sense and Avoid Systems (2016)

Development of effective sense and avoid systems is a critical challenge for operation of unmanned aircraft systems (UAS) in the National Airspace. A key issue is achieving detection of potential targets at sufficient range to achieve a low probability of collision with lightweight, low cost sensors suitable for UAS. We present a closed form analytical approach to designing the minimum required sensing range based on worst-case collision encounter geometries. Using a minimum safe distance of 500 ft and known velocities for several different aircraft, this minimum required sensing range is found to be approximately 1.861 km using slack parameter of δr = 0.0354. We demonstrate that this is a feasible result by describing a radar sensor prototype that achieves the required minimum sensing range.
Phosphorylation of the Immunomodulatory Drug FTY720 by Sphingosine Kinases (2003)

The immunomodulatory drug FTY720 is phosphorylated in vivo, and the resulting FTY720 phosphate as a ligand for sphingosine-1-phosphate receptors is responsible for the unique biological effects of the compound. So far, phosphorylation of FTY720 by murine sphingosine kinase (SPHK) 1a had been documented. We found that, while FTY720 is also phosphorylated by human SPHK1, the human type 2 isoform phosphorylates the drug 30-fold more efficiently, because of a lower Km of FTY720 for SPHK2. Similarly, murine SPHK2 was more efficient than SPHK1a. Among splice variants of the human SPHKs, an N-terminally extended SPHK2 isoform was even more active than SPHK2 itself. Further SPHK superfamily members, namely ceramide kinase and a "SPHK-like" protein, failed to phosphorylate sphingosine and FTY720. Thus, only SPHK1 and 2 appear to be capable of phosphorylating FTY720. Using selective assay conditions, SPHK1 and 2 activities in murine tissues were measured. While activity of SPHK2 toward sphingosine was generally lower than of SPHK1, FTY720 phosphorylation was higher under conditions favoring SPHK2. In human endothelial cells, while activity of SPHK1 toward sphingosine was 2-fold higher than of SPHK2, FTY720 phosphorylation was 7-fold faster under SPHK2 assay conditions. Finally, FTY720 was poorly phosphorylated in human blood as compared with rodent blood, in line with the low activity of SPHK1 and in particular of SPHK2 in human blood. To conclude, both SPHK1 and 2 are capable of phosphorylating FTY720, but SPHK2 is quantitatively more important than SPHK1.